轮烷稳定构象与穿梭过程的理论模拟研究
|
摘要
轮烷是一类新兴的超分子复合物,具有多个稳定构象和一个穿梭过程,使其在制备分子器件方面有着巨大的应用价值。然而,轮烷分子体积小柔性大,很难通过实验方法研究轮烷的结构细节。结构细节的缺失极大的阻碍了对现有器件的认识和新型器件的设计。因此,本论文采用理论模拟方法从微观角度分别研究两种轮烷的稳定构象和穿梭过程,旨在为现有分子器件的工作机理提供理论解释,同时为新型分子器件的结构设计提供理论指导。主要内容如下：
(1)分子项链是一种[n]轮烷,由n-1个环糊精包结在一个二硝基苯封端的聚乙二醇链上所形成,在药物/基因载体领域内有潜在的应用价值。采用理论模拟方法探索了分子项链的稳定构象。首先,通过分子动力学模拟结合自由能计算方法研究了三种准[3]轮烷的形成过程及稳定构象；其次,通过格点链Monte Carlo方法将对稳定构象的研究从准[3]轮烷推广到准[n]轮烷；最后,得到分子项链的稳定构象、形成机理和关键作用,丰富了对分子项链的认识。为开发基于分子项链的药物/基因载体提供理论基础,同时为探索其它化学和生物体系的自组装现象提供了一种新的研究方法。
(2)轮烷是由一个环状分子包结在一个两端封端的线状分子上形成的超分子复合物。线状分子内有多个可以和环状分子特异性结合的位点。通过外界刺激,环状分子在结合位点间的转移便形成轮烷的穿梭。穿梭运动是轮烷诸多应用的基础。通过理论模拟的方法研究了一种轮烷的穿梭运动。首先,优化了体系中三个分子片段的缺失参数；其次,使用分子动力学模拟结合自由能计算方法得到轮烷穿梭的自由能曲线,得到了能垒高度及穿梭时间,解释了实验现象；最后,通过分解自由能曲线,得到了轮烷穿梭的机理及驱动力,扩展了对实验现象的认识,并为进一步研究溶剂驱动的穿梭运动奠定了良好基础。
(3)溶剂驱动穿梭的轮烷可用于制备药物载体。该类载体能有效提高药物分子的穿膜效率并显著降低肿瘤细胞的抗药性。通过分子动力学模拟结合自由能计算方法研究了一种溶剂和温度驱动穿梭的轮烷分子,研究轮烷分子在不同溶剂和温度下的穿梭过程,得到了表征轮烷穿梭的自由能曲线。随后,通过自由能曲线分解,得到溶剂和温度对轮烷穿梭的驱动机理,合理的解释了实验现象,扩展了对轮烷穿梭的认识,并为进一步研究基于轮烷的药物载体奠定了良好基础。
(4)自由能微扰方法(free energy perturbation, FEP)是一种广泛使用的自由能计算方法,可以直接计算某个反应初始态间的自由能差而不必知晓具体的反应过程。使用Tcl／Tk语言编写了第一种针对FEP计算的分析插件,parseFEP。该插件包含方差计算、熵焓计算、双向模拟整合等多项数据处理功能,可以简化对计算结果的分析。其包含的图形显示功能可以实现计算结果的可视化。通过对冠醚与钾离子结合以及乙醇分子、甲基咪唑水化的研究验证了该插件的实用性。可见,parseFEP为分析FEP的计算结果提供了一个强有力的工具,且为FEP方法的进一步推广奠定了良好基础。
Rotaxanes are mechanically interlocked molecular complexes. They have two or more stable conformations. The shuttling processes can transform from one conformation to another one. Those unique properties make rotaxanes promising candidates ranging from molecular devices to drug carriers. However, incomplete knowledge about those properties of rotaxanes blocks their further improvements. In this dissertation, stable conformations and shuttling processes of two rotaxanes were investigated with the aid of molecular dynamics simulations and free energy calculations to shed lights on key factors contributed to stable conformations and driving forces underlying shuttling processes. The main contents of the present dissertation include:
(1) Molecular necklaces are one kind of [n]rotaxanes, which are formed by n-1a-cyclodextrins (a-CDs) threaded onto one poly(ethylene glycol) chain. Those necklaces have been envisioned to hold great promise as drug carriers and gene vectors. Their function depends intimately on their stable conformations. Here, molecular dynamics simulations, free-energy calculations, and lattice chain Monte Carlo simulations have been applied to explore this CD-based rotaxane. Stable conformations have been obtained. The results are consistent with experiments. Meanwhile, the methods used in this chapter are expected to help investigate other one dimentional chemical or biological self-assembly processes.
(2) Rotaxanes are composed by a linear molecule with stoppers at both termini and a macrocycle, i.e.,α-CD, threaded onto the latter. This macrocycle can shuttle between two or more stations connected by linkers under external stimuli. Here, molecular dynamics simulations combined with free-energy calculations have been applied to investigate a CD-based rotaxane. The free-energy profile characterizing the shuttling process of the CD along the molecular thread was determined and partitioned into tcontributions of different nature. The underlying molecular mechanism of the shuttling process has been deciphered. The present results rationalize experimental observations, and provide the theoretical basis for the investigataion of solvent-driven shuttling processes.
(3) The shuttling process of rotaxanes driven by solvents can greatly facilitate translocation of drugs across the plasma membrane. Here, molecular dynamics simulations combined with free-energy calculations have been applied to investigate a rotaxane drivened by solvent and temperature. The free-energy profiles delineating the shuttling processes of this rotaxane in different environments have been drawn. The underlying shuttling mechanism and driving force were obtained. The results match well with experimental measures, and pave the way for further investigation aimed at understanding the working mechanism of rotaxane-based drug carriers.
(4) Free-energy perturbation (FEP) is one of the most commonly chosen approaches for tackling transformations of a chemical process between two or more thermodynamic states. To augment the accuracy, the precision, and, hence, the reliability of these calculations, a number of good practices have been established. Here, a plugin, coined ParseFEP, was proposed to follow these prescriptions in a user-friendly environment. Written as a Tcl plugin, it allows FEP calculations carried out using the popular molecular-dynamics package NAMD to be analyzed seamlessly within the visualization platform VMD. The potential of this plugin is probed through a number of illustrative examples, which demonstrate cogently how pathological cases, often related to convergence issues, can be detected and remedied by means of a pictorial approach.
(1)分子项链是一种[n]轮烷,由n-1个环糊精包结在一个二硝基苯封端的聚乙二醇链上所形成,在药物/基因载体领域内有潜在的应用价值。采用理论模拟方法探索了分子项链的稳定构象。首先,通过分子动力学模拟结合自由能计算方法研究了三种准[3]轮烷的形成过程及稳定构象；其次,通过格点链Monte Carlo方法将对稳定构象的研究从准[3]轮烷推广到准[n]轮烷；最后,得到分子项链的稳定构象、形成机理和关键作用,丰富了对分子项链的认识。为开发基于分子项链的药物/基因载体提供理论基础,同时为探索其它化学和生物体系的自组装现象提供了一种新的研究方法。
(2)轮烷是由一个环状分子包结在一个两端封端的线状分子上形成的超分子复合物。线状分子内有多个可以和环状分子特异性结合的位点。通过外界刺激,环状分子在结合位点间的转移便形成轮烷的穿梭。穿梭运动是轮烷诸多应用的基础。通过理论模拟的方法研究了一种轮烷的穿梭运动。首先,优化了体系中三个分子片段的缺失参数；其次,使用分子动力学模拟结合自由能计算方法得到轮烷穿梭的自由能曲线,得到了能垒高度及穿梭时间,解释了实验现象；最后,通过分解自由能曲线,得到了轮烷穿梭的机理及驱动力,扩展了对实验现象的认识,并为进一步研究溶剂驱动的穿梭运动奠定了良好基础。
(3)溶剂驱动穿梭的轮烷可用于制备药物载体。该类载体能有效提高药物分子的穿膜效率并显著降低肿瘤细胞的抗药性。通过分子动力学模拟结合自由能计算方法研究了一种溶剂和温度驱动穿梭的轮烷分子,研究轮烷分子在不同溶剂和温度下的穿梭过程,得到了表征轮烷穿梭的自由能曲线。随后,通过自由能曲线分解,得到溶剂和温度对轮烷穿梭的驱动机理,合理的解释了实验现象,扩展了对轮烷穿梭的认识,并为进一步研究基于轮烷的药物载体奠定了良好基础。
(4)自由能微扰方法(free energy perturbation, FEP)是一种广泛使用的自由能计算方法,可以直接计算某个反应初始态间的自由能差而不必知晓具体的反应过程。使用Tcl／Tk语言编写了第一种针对FEP计算的分析插件,parseFEP。该插件包含方差计算、熵焓计算、双向模拟整合等多项数据处理功能,可以简化对计算结果的分析。其包含的图形显示功能可以实现计算结果的可视化。通过对冠醚与钾离子结合以及乙醇分子、甲基咪唑水化的研究验证了该插件的实用性。可见,parseFEP为分析FEP的计算结果提供了一个强有力的工具,且为FEP方法的进一步推广奠定了良好基础。
Rotaxanes are mechanically interlocked molecular complexes. They have two or more stable conformations. The shuttling processes can transform from one conformation to another one. Those unique properties make rotaxanes promising candidates ranging from molecular devices to drug carriers. However, incomplete knowledge about those properties of rotaxanes blocks their further improvements. In this dissertation, stable conformations and shuttling processes of two rotaxanes were investigated with the aid of molecular dynamics simulations and free energy calculations to shed lights on key factors contributed to stable conformations and driving forces underlying shuttling processes. The main contents of the present dissertation include:
(1) Molecular necklaces are one kind of [n]rotaxanes, which are formed by n-1a-cyclodextrins (a-CDs) threaded onto one poly(ethylene glycol) chain. Those necklaces have been envisioned to hold great promise as drug carriers and gene vectors. Their function depends intimately on their stable conformations. Here, molecular dynamics simulations, free-energy calculations, and lattice chain Monte Carlo simulations have been applied to explore this CD-based rotaxane. Stable conformations have been obtained. The results are consistent with experiments. Meanwhile, the methods used in this chapter are expected to help investigate other one dimentional chemical or biological self-assembly processes.
(2) Rotaxanes are composed by a linear molecule with stoppers at both termini and a macrocycle, i.e.,α-CD, threaded onto the latter. This macrocycle can shuttle between two or more stations connected by linkers under external stimuli. Here, molecular dynamics simulations combined with free-energy calculations have been applied to investigate a CD-based rotaxane. The free-energy profile characterizing the shuttling process of the CD along the molecular thread was determined and partitioned into tcontributions of different nature. The underlying molecular mechanism of the shuttling process has been deciphered. The present results rationalize experimental observations, and provide the theoretical basis for the investigataion of solvent-driven shuttling processes.
(3) The shuttling process of rotaxanes driven by solvents can greatly facilitate translocation of drugs across the plasma membrane. Here, molecular dynamics simulations combined with free-energy calculations have been applied to investigate a rotaxane drivened by solvent and temperature. The free-energy profiles delineating the shuttling processes of this rotaxane in different environments have been drawn. The underlying shuttling mechanism and driving force were obtained. The results match well with experimental measures, and pave the way for further investigation aimed at understanding the working mechanism of rotaxane-based drug carriers.
(4) Free-energy perturbation (FEP) is one of the most commonly chosen approaches for tackling transformations of a chemical process between two or more thermodynamic states. To augment the accuracy, the precision, and, hence, the reliability of these calculations, a number of good practices have been established. Here, a plugin, coined ParseFEP, was proposed to follow these prescriptions in a user-friendly environment. Written as a Tcl plugin, it allows FEP calculations carried out using the popular molecular-dynamics package NAMD to be analyzed seamlessly within the visualization platform VMD. The potential of this plugin is probed through a number of illustrative examples, which demonstrate cogently how pathological cases, often related to convergence issues, can be detected and remedied by means of a pictorial approach.
引文
[1]Collier C P, Wong E W, Belohradsky M, et al. Electronically configurable molecular-based logic gates. Science,1999,285(5426):391-394
[2]Luo Y, Collier C P, Jeppesen J O, et al. Two-dimensional molecular electronics circuits. ChemPhysChem,2002,3(6):519-525
[3]Green J E, Wook Choi J, Boukai A, et al. A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre. Nature,2007,445(7126):414-417
[4]N(?)rgaard K, Jeppesen J O, Laursen B W, et al. Evidence of strong hydration and significant tilt of amphiphilic [2]rotaxane molecules in langmuir films studied by synchrotron X-ray reflectivity. J Phys Chem B,2004,109(3):1063-1066
[5]Moulin J-F, Kengne J C, Kshirsagar R, et al. Self-organization of rotaxane thin films into spatially correlated nanostructures:□morphological and structural aspects. J Am Chem Soc, 2005,128(2):526-532
[6]Nygaard S, Leung K C F, Aprahamian I, et al. Functionally rigid bistable [2]rotaxanes. J Am Chem Soc,2007,129(4):960-970
[7]Panman M R, Bodis P, Shaw D J, et al. Operation mechanism of a molecular machine revealed using time-resolved vibrational spectroscopy. Science,2010,328(5983): 1255-1258
[8]Rijs A M, Kay E R, Leigh D A, et al. IR spectroscopy on jet-cooled isolated two-station rotaxanes. J Phys Chem A,2011,115(34):9669-9675
[9]Panman M R, Bodis P, Shaw D J, et al. Time-resolved vibrational spectroscopy of a molecular shuttle. Phys Chem Chem Phys,2012,14(6):1865-1875
[10]Raymo F M, Stoddart J F. Interlocked macromolecules. Chem Rev,1999,99(7):1643-1664
[11]Fahrenbach A C, Bruns C J, Cao D, et al. Ground-state thermodynamics of bistable redox-active donor-acceptor mechanically interlocked molecules. Acc Chem Res,2012, 45(9):1581-1592
[12]Harada A. Cyclodextrin-based molecular machines. Acc Chem Res,2001,34(6):456-464
[13]Wenz G, Han B-H, Muller A. Cyclodextrin rotaxanes and polyrotaxanes. Chem Rev,2006, 106(3):782-817
[14]Guo X Q, Song L X, Dang Z, et al. A comparative study on the formation and spectral properties of the polypseudorotaxanes of beta-cyclodextrin and poly(propylene glycol) under different conditions. Bull Chem Soc Jpn,2009,82(9):1209-1213
[15]Wang Y-H, Zhang H-M, Liu L, et al. Photoinduced electron transfer in a supramolecular species building of mono-6-p-nitrobenzoyl-β-cyclodextrin with naphthalene derivatives. J Org Chem,2002,67(8):2429-2434
[16]Harada A, Hashidzume A, Yamaguchi H, et al. Polymeric rotaxanes. Chem Rev,2009, 109(11):5974-6023
[17]Lee J W, Samal S, Selvapalam N, et al. Cucurbituril homologues and derivatives:□new opportunities in supramolecular chemistry. Acc Chem Res,2003,36(8):621-630
[18]Rowan A E, Elemans J A A W, Nolte R J M. Molecular and supramolecular objects from glycoluril. Acc Chem Res,1999,32(12):995-1006
[19]Belowich M E, Valente C, Smaldone R A, et al. Positive cooperativity in the template-directed synthesis of monodisperse macromolecules. J Am Chem Soc,2012, 134(11):5243-5261
[20]Zhang M, Xu D, Yan X, et al. Self-healing supramolecular gels formed by crown ether based host-guest interactions. Angew Chem Int Edit,2012,51(28):7011-7015
[21]Xue M, Yang Y, Chi X, et al. Pillararenes, a new class of macrocycles for supramolecular chemistry. Acc Chem Res,2012,45(8):1294-1308
[22]Hu X-B, Chen L, Si W, et al. Pillar[5]arene decaamine:synthesis, encapsulation of very long linear diacids and formation of ion pair-stopped [2]rotaxanes. Chem Commun,2011,47(16): 4694-4696
[23]Yu G, Han C, Zhang Z, et al. Pillar[6]arene-based photoresponsive host-guest complexation. J Am Chem Soc,2012,134(20):8711-8717
[24]Bodis P, Panman M R, Bakker B H, et al. Two-dimensional vibrational spectroscopy of rotaxane-based molecular machines. Acc Chem Res,2009,42(9):1462-1469
[25]Fuller A-M L, Leigh D A, Lusby P J. Sequence isomerism in [3]rotaxanes. J Am Chem Soc, 2010,132(13):4954-4959
[26]Wisner J A, Beer P D, Drew M G B, et al. Anion-templated rotaxane formation. J Am Chem Soc,2002,124(42):12469-12476
[27]Da Ros T, Guldi D M, Morales A F, et al. Hydrogen bond-assembled fullerene molecular shuttle. Org Lett,2003,5(5):689-691
[28]Movsisyan L D, Kondratuk D V, Franz M, et al. Synthesis of polyyne rotaxanes. Org Lett, 2012,14(13):3424-3426
[29]Goldup S M, Leigh D A, McGonigal P R, et al. Two axles threaded using a single template site:active metal template macrobicyclic [3]rotaxanes. J Am Chem Soc,2009,132(1): 315-320
[30]Crowley J D, Hanni K D, Lee A-L, et al. [2]Rotaxanes through palladium active-template dxidative heck cross-couplings. J Am Chem Soc,2007,129(40):12092-12093
[31]Crowley J D, Hanni K D, Leigh D A, et al. Diels-alder active-template synthesis of rotaxanes and metal-ion-switchable molecular shuttles. J Am Chem Soc,2010,132(14):5309-5314
[32]Pierro T, Gaeta C, Talotta C, et al. Fixed or invertible calixarene-based directional shuttles. Org Lett,2011,13(10):2650-2653
[33]Crowley J D, Leigh D A, Lusby P J, et al. A switchable palladium-complexed molecular shuttle and its metastable positional isomers. J Am Chem Soc,2007,129(48):15085-15090
[34]Li H, Fahrenbach A C, Coskun A, et al. A light-stimulated molecular switch driven by radical-radical interactions in water. Angew Chem Int Edit,2011,50(30):6782-6788
[35]Stoll R S, Friedman D C, Stoddart J F. Mechanically interlocked mechanophores by living-radical polymerization from rotaxane initiators. Org Lett,2011,13(10):2706-2709
[36]Chiu C-W, Lai C-C, Chiu S-H. "Threading-followed-by-swelling":□ a new protocol for rotaxane synthesis. J Am Chem Soc,2007,129(12):3500-3501
[37]Ooya T, Choi H S, Yamashita A, et al. Biocleavable polyrotaxane-plasmid DNA polyplex for enhanced gene delivery. J Am Chem Soc,2006,128(12):3852-3853
[38]Li J, Yang C, Li H, et al. Cationic supramolecules composed of multiple oligoethylenimine-grafted (3-cyclodextrins threaded on a polymer chain for efficient gene delivery. Adv Mater,2006,18(22):2969-2974
[39]Yang C, Wang X, Li H, et al. Cationic polyrotaxanes as gene carriers:physicochemical properties and real-time observation of DNA complexation, and gene transfection in cancer cells. J Phys Chem B,2009,113(22):7903-7911
[40]Balzani V, Gomez-Lopez M, Stoddart J F. Molecular machines. Acc Chem Res,1998,31(7): 405-414
[41]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2(10): 1353-1356
[42]Ye T, Kumar A S, Saha S, et al. Changing stations in single bistable rotaxane molecules under electrochemical control. ACS Nano,2010,4(7):3697-3701
[43]Balzani V, Clemente-Leon M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[44]Brouwer A M, Frochot C, Gatti F G, et al. Photoinduction of fast, reversible translational motion in a hydrogen-bonded molecular shuttle. Science,2001,291(5511):2124-2128
[45]Jacquot de Rouville H-P, Iehl J, Bruns C J, et al. A neutral naphthalene diimide [2]rotaxane. Org Lett,2012,14(20):5188-5191
[46]Zhang K-D, Zhao X, Wang G-T, et al. Foldamer-tuned switching kinetics and metastability of [2]rotaxanes. Angew Chem Int Edit,2011,50(42):9866-9870
[47]Ferrand Y, Gan Q, Kauffmann B, et al. Template-induced screw motions within an aromatic amide foldamer double helix. Angew Chem Int Edit,2011,50(33):7572-7575
[48]You Y-C, Tzeng M-C, Lai C-C, et al. Using oppositely charged ions to operate a three-station [2]rotaxane in two different switching modes. Org Lett,2012,14(4):1046-1049
[49]Barnes J C, Fahrenbach A C, Dyar S M, et al. Mechanically induced intramolecular electron transfer in a mixed-valence molecular shuttle. Proc. Natl. Acad. Sci. USA,2012,109(29): 11546-11551
[50]Li H, Zhu Z, Fahrenbach A C, et al. Mechanical bond-induced radical stabilization. J Am Chem Soc,2012,135(1):456-467
[51]Fahrenbach A C, Zhu Z, Cao D, et al. Radically enhanced molecular switches. J Am Chem Soc,2012,134(39):16275-16288
[52]Deng W-Q, Muller R P, Goddard W A. Mechanism of the Stoddart-Heath bistable rotaxane molecular switch. J Am Chem Soc,2004,126(42):13562-13563
[53]Dvornikovs V, House B E, Kaetzel M, et al. Host-[2]rotaxanes as cellular transport agents. J Am Chem Soc,2003,125(27):8290-8301
[54]Carlone A, Goldup S M, Lebrasseur N, et al. A three-compartment chemically-driven molecular information ratchet. J Am Chem Soc,2012,134(20):8321-8323
[55]Serreli V, Lee C-F, Kay E R, et al. A molecular information ratchet. Nature,2007,445(7127): 523-527
[56]Kay E R, Leigh D A, Zerbetto F. Synthetic molecular motors and mechanical machines. Angew Chem Int Edit,2007,46(1-2):72-191
[57]Zhao Y-L, Aprahamian I, Trabolsi A, et al. Organogel formation by a cholesterol-stoppered bistable [2]rotaxane and its dumbbell precursor. J Am Chem Soc,2008,130(20):6348-6350
[58]Pease A R, Jeppesen J O, Stoddart J F, et al. Switching devices based on interlocked molecules. Acc Chem Res,2001,34(6):433-444
[59]Berna J, Leigh D A, Lubomska M, et al. Macroscopic transport by synthetic molecular machines. Nat Mater,2005,4(9):704-710
[60]Wan P, Jiang Y, Wang Y, et al. Tuning surface wettability through photocontrolled reversible molecular shuttle. Chem Commun,2008,0(44):5710-5712
[61]Baumes J M, Murgu I, Oliver A, et al. Using the rotaxane mechanical bond to enhance chemical reactivity. Org Lett,2010,12(21):4980-4983
[62]Thordarson P, Bijsterveld E J A, Rowan A E, et al. Epoxidation of polybutadiene by a topologically linked catalyst. Nature,2003,424(6951):915-918
[63]Zhang H, Hu J, Qu D-H. Dual-mode control of PET process in a ferrocene-functionalized [2]rotaxane with high-contrast fluorescence output. Org Lett,2012,14(9):2334-2337
[64]Alvarez-Perez M, Goldup S M, Leigh D A, et al. A chemically-driven molecular information ratchet. J Am Chem Soc,2008,130(6):1836-1838
[65]Danquah M K, Zhang X A, Mahato R I. Extravasation of polymeric nanomedicines across tumor vasculature. Adv Drug Deliv Rev,2011,63(8):623-639
[66]Chen T. Overcoming drug resistance by regulating nuclear receptors. Adv Drug Deliv Rev, 2010,62(13):1257-1264
[67]Torchilin V P. Tat peptide-mediated intracellular delivery of pharmaceutical nanocarriers. Adv Drug Deliv Rev,2008,60(4-5):548-558
[68]Guo D-S, Wang K, Wang Y-X, et al. Cholinesterase-responsive supramolecular vesicle. J Am Chem Soc,2012,134(24):10244-10250
[69]Torney F, Trewyn B G, Lin V S Y, et al. Mesoporous silica nanoparticles deliver DNA and chemicals into plants. Nat Nano,2007,2(5):295-300
[70]Trewyn B G, Slowing I I, Giri S, et al. Synthesis and functionalization of a mesoporous silica nanoparticle based on the sol-gel process and applications in controlled release. Acc Chem Res,2007,40(9):846-853
[71]Angelos S, Johansson E, Stoddart J F, et al. Mesostructured silica supports for functional materials and molecular machines. Adv Funct Mater,2007,17(14):2261-2271
[72]Yang Y-W. Towards biocompatible nanovalves based on mesoporous silica nanoparticles. MedChemComm,2011,2(11):1033-1049
[73]Hernandez R, Tseng H-R, Wong J W, et al. An operational supramolecular nanovalve. J Am Chem Soc,2004,126(11):3370-3371
[74]Zhu Z, Fahrenbach A C, Li H, et al. Controlling switching in bistable [2]catenanes by combining donor-acceptor and radical-radical Interactions. J Am Chem Soc,2012,134(28): 11709-11720
[75]Ferris D P, Zhao Y-L, Khashab N M, et al. Light-operated mechanized nanoparticles. J Am Chem Soc,2009,131(5):1686-1688
[76]Sun Y-L, Yang B-J, Zhang S X-A, et al. Cucurbit[7]uril pseudorotaxane-based photoresponsive supramolecular nanovalve. Chem Eur J,2012,18(30):9212-9216
[77]Marquez C, Nau W M. Two mechanisms of slow host-guest complexation between cucurbit[6]uril and cyclohexylmethylamine:pH-responsive supramolecular kinetics. Angew Chem Int Edit,2001,40(17):3155-3160
[78]Marquez C, Hudgins R R, Nau W M. Mechanism of host-guest complexation by cucurbituril. J Am Chem Soc,2004,126(18):5806-5816
[79]Ling X, Samuel E L, Patchell D L, et al. Cucurbituril slippage:translation is a complex motion. Org Lett,2010,12(12):2730-2733
[80]Angelos S, Khashab N M, Yang Y-W, et al. pH clock-operated mechanized nanoparticles. J Am Chem Soc,2009,131(36):12912-12914
[81]Nguyen T D, Leung K C F, Liong M, et al. Construction of a pH-driven supramolecular nanovalve. Org Lett,2006,8(15):3363-3366
[82]Patel K, Angelos S, Dichtel W R, et al. Enzyme-responsive snap-top covered silica nanocontainers. J Am Chem Soc,2008,130(8):2382-2383
[83]Meng H, Xue M, Xia T, et al. Autonomous in vitro anticancer drug release from mesoporous silica nanoparticles by pH-sensitive nanovalves. J Am Chem Soc,2010,132(36): 12690-12697
[84]Zhao Y-L, Li Z, Kabehie S, et al. pH-operated nanopistons on the surfaces of mesoporous silica nanoparticles. J Am Chem Soc,2010,132(37):13016-13025
[85]Vassal G, Koscielny S, Challine D, et al. Busulfan disposition and hepatic veno-occlusive disease in children undergoing bone marrow transplantation. Cancer Chemoth Pharm,1995, 37(3):247-253
[86]Menuel S, Joly J-P, Courcot B, et al. Synthesis and inclusion ability of a bis-β-cyclodextrin pseudo-cryptand towards Busulfan anticancer agent. Tetrahedron,2007,63(7):1706-1714
[87]Porwanski S, Dumarcay-Charbonnier F, Menuel S, et al. Bis-β-cyclodextrinyl- and bis-cellobiosyl-diazacrowns:synthesis and molecular complexation behaviors toward Busulfan anticancer agent and two basic aminoacids. Tetrahedron,2009,65(31):6196-6203
[88]Zehnder D W, Smithrud D B. Facile synthesis of rotaxanes through condensation reactions of DCC-[2]rotaxanes. Org Lett,2001,3(16):2485-2487
[89]Smukste I, House B E, Smithrud D B. Host-[2]rotaxane:□ advantage of converging functional groups for guest recognition. J Org Chem,2003,68(7):2559-2571
[90]Bao X, Isaacsohn I, Drew A F, et al. Determining the intracellular transport mechanism of a cleft-[2]rotaxane. J Am Chem Soc,2006,128(37):12229-12238
[91]Wang X, Smithrud D B. Pt-rotaxanes as cytotoxic agents. Bioorg Med Chem Lett,2011, 21(22):6880-6883
[92]Zhu J, McFarland-Mancini M, Drew A F, et al. Host-rotaxanes with oligomeric axles are intracellular transport agents. Bioorg Med Chem Lett,2009,19(2):520-523
[93]Bao X, Isaacsohn I, Drew A F, et al. Determining the binding and intracellular transporting abilities of a host-[3]rotaxane. J Org Chem,2007,72(11):3988-4000
[94]Rouget J-B, Aksel T, Roche J, et al. Size and sequence and the volume change of protein folding. J Am Chem Soc,2011,133(15):6020-6027
[95]Ghosh K, Dill K A. Theory for protein folding cooperativity:helix bundles. J Am Chem Soc, 2009,131(6):2306-2312
[96]Metropolis N, Rosenbluth A W, Rosenbluth M N, et al. Equation of state calculations by fast computing machines. J Chem Phys,1953,21(6):1087-1092
[97]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[98]Yang L, Tan C-h, Hsieh M-J, et al. New-generation amber united-atom force field. J Phys Chem B,2006,110(26):13166-13176
[99]Oostenbrink C, Soares T, Vegt N A, et al. Validation of the 53A6 GROMOS force field. Eur Biophys J,2005,34(4):273-284
[100]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys,1992,97(3):1990-2001
[101]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[102]Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:New York,2007.
[103]Kollman P. Free energy calculations:applications to chemical and biochemical phenomena. Chem Rev,1993,93(7):2395-2417
[104]Simonson T, Archontis G, Karplus M. Free energy simulations come of age:□ protein-ligand recognition. Acc Chem Res,2002,35(6):430-437
[105]Landau L D. Statistical physics. The Clarendon Press, Oxford, U. K.,1938
[106]Zwanzig R W. High-temperature equation of state by a perturbation method. Ⅰ. Nonpolar gases. J Chem Phys,1954,22(8):1420-1426
[107]Kirkwood J G Statistical mechanics of fluid mixtures. J Chem Phys,1935,3(5):300-313
[108]H6nin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[109]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906
[110]Darve E, Rodriguez-G6mez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[111]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[112]Bennett C H. Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys,1976,22(2):245-268
[113]Ferrenberg A M, Swendsen R H. New Monte Carlo technique for studying phase transitions. Phys Rev Lett,1988,61(23):2635-2638
[114]Jarzynski C. Equilibrium free-energy differences from nonequilibrium measurements:a master-equation approach. Phys Rev Lett.,1997,56(5):5018-5035
[115]Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett,1997, 78(14):2690-2693
[116]Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B,2010,114(32):10235-10253
[117]Valleau J P, Torrie G M A. Guide to Monte Carlo for statistical mechanics:byways. In Modern theoretical chemistry; Berne B J, Ed.; Plenum:New York,1977; pp 169-194.
[118]McDonald I R, Singer K. Machine calculation of thermodynamic properties of a simple fluid at supercritical temperatures. J Chem Phys,1967,47(11):4766-4772
[119]Straatsma T P, Berendsen H J C, Postma J P M. Free energy of hydrophobic hydration:a molecular dynamics study of noble gases in water. J Chem Phys,1986,85(11):6720-6727
[120]McDonald I R, Singer K. Calculation of thermodynamic properties of liquid argon from Lennard-Jones parameters by a Monte Carlo method. Discuss Faraday Soc,1967,43:40-49
[121]Lu N, Kofke D A, Woolf T B. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J Comput Chem,2004,25(1): 28-40
[122]Lelievre T, Stoltz G, Rousset M. Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[123]Gumbart J C, Roux B, Chipot C. Standard binding free energies from computer simulations: what is the best strategy? J Chem Theory Comput,2012,9(1):794-802
[124]Chipot C. Milestones in the activation of a G protein-coupled receptor. Insights from molecular-dynamics simulations into the human cholecystokinin receptor-1. J Chem Theory Comput,2008,4(12):2150-2159
[125]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[126]Pan A C, Sezer D, Roux B. Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[127]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[128]Jang S S, Jang Y H, Kim Y-H, et al. Molecular dynamics simulation of amphiphilic bistable [2]rotaxane langmuir monolayers at the air/water interface. J Am Chem Soc,2005,127(42): 14804-14816
[129]Jang Y H, Jang S S, Goddard W A. Molecular dynamics simulation study on a monolayer of half [2]Rotaxane self-assembled on Au(111). J Am Chem Soc,2005,127(13):4959-4964
[130]Jang S S, Jang Y H, Kim Y-H, et al. Structures and properties of self-assembled monolayers of bistable [2]rotaxanes on Au (111) surfaces from molecular dynamics simulations validated with experiment. J Am Chem Soc,2005,127(5):1563-1575
[131]Carter E A, Ciccotti G, Hynes J T, et al. Constrained reaction coordinate dynamics for the simulation of rare events. Chem Phys Lett,1989,156(5):472-477
[132]Sprik M, Ciccotti G. Free energy from constrained molecular dynamics. J Chem Phys,1998, 109(18):7737-7744
[133]Kim H, Goddard W A, Jang S S, et al. Free energy barrier for molecular motions in bistable [2]rotaxane molecular electronic devices. J Phys Chem A,2009,113(10):2136-2143
[134]Raiteri P, Bussi G, Cucinotta C S, et al. Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. Angew Chem Int Edit,2008,47(19): 3536-3539
[135]Torrie G M, Valleau J P. Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid. Chem Phys Lett,1974,28(4):578-581
[136]Still W C, Tempczyk A, Hawley R C, et al. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc,1990,112(16):6127-6129
[137]Zhao Y-L, Dichtel W R, Trabolsi A, et al. A redox-switchable α-cyclodextrin-based [2]rotaxane. J Am Chem Soc,2008,130(34):11294-11296
[138]Zhang Q, Tu Y, Tian H, et al. Working mechanism for a redox switchable molecular machine based on cyclodextrin:a free energy profile approach. J Phys Chem B,2010,114(19): 6561-6566
[1]Galatsis K, Kang W, Botros Y, et al. Emerging memory devices:nontraditional possibilities based on nanomaterials and nanostructures. IEEE Circuits Device Maga,2006,22(3):12-21
[2]Collier C P, Wong E W, Belohradsky M, et al. Electronically configurable molecular-based logic gates. Science,1999,285(5426):391-394
[3]Balzani V, Gomez-Lopez M, Stoddart J F. Molecular machines. Ace Chem Res,1998,31 (7): 405-414
[4]Pease A R, Jeppesen J O, Stoddart J F, et al. Switching devices based on interlocked molecules. Acc Chem Res,2001,34(6):433-444
[5]Harada A, Kamachi M. Complex formation between poly(ethylene glycol) and a-cyclodextrin. Macromolecules,1990,23(10):2821-2823
[6]Harada A, Li J, Kamachi M. The molecular necklace:a rotaxane containing many threaded a-cyclodextrins. Nature,1992,356(6367):325-327
[7]Wu Y-L, Li J. Synthesis of supramolecular nanocapsules based on threading of multiple cyclodextrins over polymers on gold nanoparticles. Angew Chem Int Ed,2009,48(21): 3842-3845
[8]Ooya T, Choi H S, Yamashita A, et al. Biocleavable polyrotaxane-plasmid DNA polyplex for enhanced gene delivery. J Am Chem Soc,2006,128(12):3852-3853
[9]Harada A, Li J, Kamachi M. Preparation and characterization of a polyrotaxane consisting of monodisperse poly(ethylene glycol) and a-cyclodextrins. J Am Chem Soc,1994,116(8): 3192-3196
[10]Miyake K, Yasuda S, Harada A, et al. Formation process of cyclodextrin necklace-analysis of hydrogen bonding on a molecular level. J Am Chem Soc,2003,125(17):5080-5085
[11]Shigekawa H, Miyake K, Sumaoka J, et al. The molecular abacus:STM manipulation of cyclodextrin necklace. J Am Chem Soc,2000,122(22):5411-5412
[12]Bonnet P, Jaime C, Morin-Allory L. α-,β-, and y-Cyclodextrin dimers. Molecular modeling studies by molecular mechanics and molecular dynamics simulations. J Org Chem,2001, 66(3):689-692
[13]Bonnet P, Jaime C, Morin-Allory L. Structure and thermodynamics of α-, β-, and y-cyclodextrin dimers. molecular dynamics studies of the solvent effect and free binding energies. J Org Chem,2002,67(24):8602-8609
[14]Nascimento C S, Anconi C P A, Dos Santos H F, et al. Theoretical study of the a-cyclodextrin dimer. J Phys Chem A,2005,109(14):3209-3219
[15]Yu Y, Cai W, Chipot C, et al. Spatial arrangement of a-cyclodextrins in a rotaxane. Insights from free-energy calculations. J Phys Chem B,2008,112(17):5268-5271
[16]Tallury S S, Smyth M B, Cakmak E, et al. Molecular dynamics simulations of interactions between polyanilines in their inclusion complexes with β-cyclodextrins. J Phys Chem B, 2012,116(7):2023-2030
[17]Chipot C, Pohorille A. Calculating free energy differences using perturbation theory. In Free energy calculations; Chipot C, Pohorille A, Eds.; Springer Berlin Heidelberg,2007; Vol.86; pp 33-75.
[18]Lelievre T, Rousset M, Stoltz G. Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[19]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906-6
[20]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[21]Henin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[22]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[23]Brush S G. History of the Lenz-Ising model. Rev Mod Phys,1967,39(4):883-893
[24]Ising E. Beitrag zur theorie des ferromagnetismus. Z Phys A:Hadrons Nucl,1925,31(1): 253-258
[25]Hingerty B, Saenger W. Topography of cyclodextrin inclusion complexes.8. Crystal and molecular structure of the.alpha.-cyclodextrin-methanol-pentahydrate complex. Disorder in ahydrophobic cage. J Am Chem Soc,1976,98(11):3357-3365
[26]Insight II User Guide. Accelrys Software Inc., San Diego, CA,2005
[27]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[28]Hatcher E R, Guvench O, MacKerell A D. CHARMM additive all-atom force field for acyclic polyalcohols, acyclic carbohydrates, and inositol. J Chem Theory Comput,2009,5(5): 1315-1327
[29]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[30]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[31]Jorgensen W L, Chandrasekhar J, Madura J D, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys,1983,79(2):926-935
[32]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[33]Miyamoto S, Kollman P A. Settle:an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem,1992,13(8):952-962
[34]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[35]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys,1992,97(3):1990-2001
[36]Darden T, York D, Pedersen L. Particle mesh Ewald:an N log(N) method for Ewald sums in large systems. J Chem Phys,1993,98(12):10089-10092
[37]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[38]Henin J, Fiorin G, Chipot C, et al. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput,2010,6(1):35-47
[39]Jonkheijm P, van der Schoot P, Schenning A P H J, et al. Probing the solvent-assisted nucleation pathway in chemical self-assembly. Science,2006,313(5783):80-83
[40]Tanaka S, Scheraga H A. Model of protein folding:incorporation of a one-dimensional short-range (Ising) model into a three-dimensional model. Proc Natl Acad Sci USA,1977, 74(4):1320-1323
[41]Metropolis N, Rosenbluth A W, Rosenbluth M N, et al. Equation of state calculations by fast computing machines. J Chem Phys,1953,21(6):1087-1092
[42]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[43]Bolhuis P G, Dellago C, Chandler D. Reaction coordinates of biomolecular isomerization. Proc Natl Acad Sci USA,2000,97(11):5877-5882
[44]Pan A C, Sezer D, Roux B. Finding transition pathway:using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[45]Liu P, Chipot C, Shao X, et al. Solvent-controlled shuttling in a molecular switch. J Phys Chem C,2012,116(7):4471-4476
[46]Shrake A, Rupley J A. Environment and exposure to solvent of protein atoms. Lysozyrne and insulin. J Mol Biol,1973,79(2):351-371
[1]Green J E, Wook Choi J, Boukai A, et al. A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre. Nature,2007,445(7126):414-417
[2]Harada A. Cyclodextrin-based molecular machines. Acc Chem Res,2001,34(6):456-464
[3]Raymo F M, Stoddart J F. Interlocked macromolecules. Chem Rev,1999,99(7):1643-1664
[4]Zhao Y-L, Dichtel W R, Trabolsi A, et al. A redox-switchable a-cyclodextrin-based [2]rotaxane. J Am Chem Soc,2008,130(34):11294-11296
[5]Bissell R A, Cordova E, Kaifer A E, et al. A chemically and electrochemically switchable molecular shuttle. Nature,1994,369:133-137
[6]Berna J, Goldup S M, Lee A-L, et al. Cadiot-chodkiewicz active template synthesis of rotaxanes and switchable molecular shuttles with weak intercomponent interactions. Angew Chem Int Ed,2008,47(23):4392-4396
[7]Coutrot F, Romuald C, Busseron E. A new pH-switchable dimannosyl[c2]daisy chain molecular machine. Org Lett,2008,10(17):3741-3744
[8]Coskun A, Friedman D C, Li H, et al. A light-gated STOP-GO molecular shuttle. J Am Chem Soc,2009,131(7):2493-2495
[9]Balzani V, Clemente-Le6n M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[10]Murakami H, Kawabuchi A, Matsumoto R, et al. A multi-mode-driven molecular shuttle:□photochemically and thermally reactive azobenzene rotaxanes. J Am Chem Soc, 2005,127(45):15891-15899
[11]Marlin D S, Gonzalez Cabrera D, Leigh D A, et al. Complexation-induced translational isomerism:shuttling through stepwise competitive binding. Angew Chem Int Ed,2006,45(1): 77-83
[12]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2(10): 1353-1356
[13]Brough B, Northrop B H, Schmidt J J, et al. Evaluation of synthetic linear motor-molecule actuation energetics. Proc Natl Acad Sci USA,2006,103(23):8583-8588
[14]Belohradsky M, Elizarov A M, Stoddart J F. Speed-controlled molecular shuttles. Collect Czech Chem Commun,2002,67(11):1719-1728
[15]Kim H, Goddard W A, Jang S S, et al. Free energy barrier for molecular motions in bistable [2]rotaxane molecular electronic devices. J Phys Chem A,2009,113(10):2136-2143
[16]Raiteri P, Bussi G, Cucinotta C S, et al. Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. Angew Chem Int Ed,2008,47(19): 3536-3539
[17]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[18]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[19]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[20]Henin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[21]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906-6
[22]Yu Y, Chipot C, Cai W, et al. Molecular dynamics study of the inclusion of cholesterol into cyclodextrins. J Phys Chem B,2006,110(12):6372-6378
[23]Yu Y, Cai W, Chipot C, et al. Spatial arrangement of a-cyclodextrins in a rotaxane. Insights from free-energy calculations. J Phys Chem B,2008,112(17):5268-5271
[24]Eyring H. The activated complex in chemical reactions. J Chem Phys,1935,3(2):107-115
[25]Insight Ⅱ User Guide. Accelrys Software Inc., San Diego, CA,2005
[26]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[27]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[28]Liu X, Zhang S, Zhou G, et al. New force field for molecular simulation of guanidinium-based ionic liquids. J Phys Chem B,2006,110(24):12062-12071
[29]Strader M L, Feller S E. A flexible all-atom model of dimethyl sulfoxide for molecular dynamics simulations. J Phys Chem A,2002,106(6):1074-1080
[30]Pavelites J J, Gao J, Bash P A, et al. A molecular mechanics force field for NAD+, NADH, and the pyrophosphate groups of nucleotides. J Comput Chem,1997,18(2):221-239
[31]Foloppe N, MacKerell J A D. All-atom empirical force field for nucleic acids:Ⅰ. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem,2000,21(2):86-104
[32]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[33]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[34]Darden T, York D, Pedersen L. Particle mesh Ewald:an N log(N) method for Ewald sums in large systems. J Chem Phys,1993,98(12):10089-10092
[35]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[36]Ryckaert J-P, Ciccotti G, Berendsen H J C. Numerical integration of the cartesian equations of motion of a system with constraints:molecular dynamics of n-alkanes. J Comput Phys,1977, 23(3):327-341
[37]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[38]Flyvbjerg H, Petersen H G. Error estimates on averages of correlated data. J Chem Phys,1989, 91(1):461-466
[39]Frisch M J, Trucks G W, Schlegel H B, et al. Gaussian 03, ReVision C.03. Gaussian, Inc., Wallingford,CT,2004
[40]Vaiana A C, Coumia Z, Costescu I B, et al. AFMM:a molecular mechanics force field vibrational parametrization program. Comput Phys Commun,2005,167(1):34-42
[41]Kim H-W, Zeroka D. Trans-ethylphosphine and selected deuterated isotopomers:prediction of infrared spectra and potential energy distribution determination. THEOCHEM,2005,715: 21-31
[42]Kim H-W, Chechla A A, Kim B. Potential energy distribution study of infrared frequencies of methylamine and methylphosphine. THEOCHEM,2007,802:105-110
[43]Pulay P, Fogarasi G, Pang F, et al. Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives. J Am Chem Soc,1979,101(10): 2550-2560
[44]Bergeron R J, Channing M A, Gibeily G J, et al. Disposition requirements for binding in aqueous solution of polar substrates in the cyclohexaamylose cavity. J Am Chem Soc,1977, 99(15):5146-5151
[45]Li J, Harada A, Kamachi M. Formation of inclusion complexes of oligoethylene and its derivatives with a-cyclodextrin. Bull Chem Soc Jpn,1994,67:2808-2818
[1]Balzani V, Clemente-Le6n M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[2]Bissell R A, C6rdova E, Kaifer A E, et al. A chemically and electrochemically switchable molecular shuttle. Nature,1994,369(6476):133-137
[3]Hernandez R, Tseng H-R, Wong J W, et al. An operational supramolecular nanovalve. J Am Chem Soc,2004,126(11):3370-3371
[4]Dvornikovs V, House B E, Kaetzel M, et al. Host-[2]rotaxanes as cellular transport agents. J Am Chem Soc,2003,125(27):8290-8301
[5]Leung K C-F, Chak C-P, Lo C-M, et al. pH-controllable supramolecular systems. Chem Asian J,2009,4(3):364-381
[6]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2:1353-1356
[7]Umehara T, Kawai H, Fujiwara K, et al. Entropy- and hydrolytic-driven positional switching of macrocycle between imine- and hydrogen-bonding stations in rotaxane-based molecular shuttles. J Am Chem Soc,2008,130(42):13981-13988
[8]Vassal G, Koscielny S, Challine D, et al. Busulfan disposition and hepatic veno-occlusive disease in children undergoing bone marrow transplantation. Cancer Chemoth Pharm,1995, 37(3):247-253
[9]Zehnder D W, Smithrud D B. Facile synthesis of rotaxanes through condensation reactions of DCC-[2]rotaxanes. Org Lett,2001,3(16):2485-2487
[10]Smukste I, House B E, Smithrud D B. Host-[2]rotaxane:□ advantage of converging functional groups for guest recognition. J Org Chem,2003,68(7):2559-2571
[11]Bao X, Isaacsohn I, Drew A F, et al. Determining the intracellular transport mechanism of a cleft-[2]rotaxane. J Am Chem Soc,2006,128(37):12229-12238
[12]Liu P, Cai W, Chipot C, et al. Thermodynamic insights into the dynamic switching of a cyclodextrin in a bistable molecular shuttle. J Phys Chem Lett,2010,1(12):1776-1780
[13]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[14]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[15]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[16]Jorgensen W L, Chandrasekhar J, Madura J D, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys,1983,79(2):926-935
[17]Strader M L, Feller S E. A flexible all-atom model of dimethyl sulfoxide for molecular dynamics simulations. J Phys Chem A,2002,106(6):1074-1080
[18]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[19]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys,1992,97(3):1990-2001
[20]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[21]Miyamoto S, Kollman P A. Settle:an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem,1992,13(8):952-962
[22]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[23]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[24]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[25]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[26]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906-6
[27]Henin J, Fiorin G, Chipot C, et al. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput,2010,6(1):35-47
[28]Flyvbjerg H, Petersen H G. Error-estimates on averages of correlated data. J Chem Phys, 1989,91(1):461-466
[29]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[30]Pan A C, Sezer D, Roux B. Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[1]Kollman P. Free energy calculations:applications to chemical and biochemical phenomena. Chem Rev,1993,93(7):2395-2417
[2]Simonson T, Archontis G, Karplus M. Free energy simulations come of age:protein-ligand recognition. Acc Chem Res,2002,35(6):430-437
[3]Chipot C, Pearlman D A. Free energy calculations. The long and winding gilded road. Mol Simulat,2002,28(1-2):1-12
[4]Simonson T. Free energy calculations. In Computational biochemistry and biophysics; Becker O M, MacKerell A D J, Roux B, Watanabe M, Eds.; Marcel Dekker Inc.:New York, 2001; pp 169-197
[5]Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:New York,2007
[6]Born M. Volumen und hydratationswarme der ionen. Z Physik,1920,1(1):45-48
[7]Landau L D. Statistical physics. The Clarendon Press, Oxford, U. K.,1938
[8]Zwanzig R W. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys,1954,22(8):1420-1426
[9]Kirkwood J G Statistical mechanics of fluid mixtures. J Chem Phys,1935,3(5):300-313
[10]Bennett C H. Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys,1976,22(2):245-268
[11]Ferrenberg A M, Swendsen R H. New Monte Carlo technique for studying phase transitions. Phys Rev Lett,1988,61(23):2635-2638
[12]Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett,1997, 78(14):2690-2693
[13]Jarzynski C. Equilibrium free-energy differences from nonequilibrium measurements:a master-equation approach. Phys Rev Lett,1997,56(5):5018-5035
[14]Jorgensen W L, Ravimohan C. Monte Carlo simulation of differences in free energies of hydration. J Chem Phys,1985,83(6):3050-3054
[15]Bash P A, Singh U C, Langridge R, et al. Free energy calculations by computer simulation. Science,1987,236(4801):564-568
[16]van Gunsteren W, Beutler T, Fraternali F, et al. Computation of free energy in practice:choice of approximations and accuracy limiting factors. In Computer simulation of biomolecular systems; van Gunsteren W, Weiner P, Wilkinson A, Eds.; Escom Science Publishers:Leiden, The Netherlands,1993; pp 315-348
[17]Chipot C, Millot C, Maigret B, et al. Molecular dynamics free energy perturbation calculations:influence of nonbonded parameters on the free energy of hydration of charged and neutral species. J Phys Chem,1994,98(44):11362-11372
[18]Ding Y, Bernardo D N, Krogh-Jespersen K, et al. Solvation free energies of small amides and amines from molecular dynamics/free energy perturbation simulations using pairwise additive and many-body polarizable potentials. J Phys Chem,1995,99(29):11575-11583
[19]Morgantini P-Y, Kollman P A. Solvation free energies of amides and amines:disagreement between free energy calculations and experiment. J Am Chem Soc,1995,117(22): 6057-6063
[20]Rick S W, Berne B J. Free energy of the hydrophobic interaction from molecular dynamics simulations:□the effects of solute and solvent polarizability. J Phys Chem B,1997,101(49): 10488-10493
[21]Ponder J W, Wu C, Ren P, et al. Current status of the AMOEBA polarizable force field. J Phys Chem B,2010,114(8):2549-2564
[22]Oostenbrink C, Villa A, Mark A E, et al. A biomolecular force field based on the free enthalpy of hydration and solvation:the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem,2004,25(13):1656-1676
[23]Shirts M R, Pitera J W, Swope W C, et al. Extremely precise free energy calculations of amino acid side chain analogs:comparison of common molecular mechanics force fields for proteins. J Chem Phys,2003,119(11):5740-5761
[24]Jorgensen W L, Buckner J K, Boudon S, et al. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water. J Chem Phys, 1988,89(6):3742-3746
[25]van Gunsteren W F. Methods for calculation of free energies and binding constants:successes and problems. In Computer simulation of biomolecular systems:theoretical and experimental applications; Van Gunsteren W F, Weiner P K, Eds.; Escom Science Publishers:Leiden, The Netherlands,1989; pp 27-59
[26]Miyamoto S, Kollman P A. What determines the strength of noncovalent association of ligands to proteins in aqueous solution? Proc Natl Acad Sci USA,1993,90(18):8402-8406
[27]Aqvist J. Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. J Comput Chem,1996,17(14):1587-1597
[28]Aqvist J, Luzhkov V B, Brandsdal B O. Ligand binding affinities from MD simulations. Acc Chem Res,2002,35(6):358-365
[29]Archontis G, Simonson T, Karplus M. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. J Mol Biol,2001,306(2):307-327
[30]Boresch S, Tettinger F, Leitgeb M, et al. Absolute binding free energies:□a quantitative approach for their calculation. J Phys Chem B,2003,107(35):9535-9551
[31]Oostenbrink C, van Gunsteren W F. Free energies of ligand binding for structurally diverse compounds. Proc Natl Acad Sci USA,2005,102(19):6750-6754
[32]Woo H-J, Roux B. Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci USA,2005,102(19):6825-6830
[33]Wang J, Deng Y, Roux B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J,2006,91(8):2798-2814
[34]Mobley D L, Graves A P, Chodera J D, et al. Predicting absolute ligand binding free energies to a simple nodel site. J Mol Biol,2007,371(4):1118-1134
[35]Deng Y, Roux B. Computations of standard binding free energies with molecular dynamics simulations. J Phys Chem B,2009,113(8):2234-2246
[36]Jiang W, Roux B. Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations. J Chem Theory Comput,2010,6(9):2559-2565
[37]Pearlman D A, Charifson P S. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system. J Med Chem,2001, 44(21):3417-3423
[38]Chipot C, Rozanska X, Dixit S. Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein. J Comput Aided Mol Des,2005,19(11):765-770
[39]Chodera J D, Mobley D L, Shirts M R, et al. Alchemical free energy methods for drug discovery:progress and challenges. Curr Opin Struct Biol,2011,21(2):150-160
[40]Lelievre T, Stoltz G, Rousset M. Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[41]Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B.2010,114(32):10235-10253
[42]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[43]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[44]McDonald I R, Singer K. Machine calculation of thermodynamic properties of a simple fluid at supercritical temperatures. J Chem Phys,1967,47(11):4766-4772
[45]McDonald I R, Singer K. Calculation of thermodynamic properties of liquid argon from Lennard-Jones parameters by a Monte Carlo method. Discuss Faraday Soc,1967,43:40-49
[46]Valleau J P, Torrie G M A. Guide to Monte Carlo for statistical mechanics:byways. In Modern theoretical chemistry; Berne B J, Ed.; Plenum:New York,1977; pp 169-194
[47]Straatsma T P, Berendsen H J C, Postma J P M. Free energy of hydrophobic hydration:a molecular dynamics study of noble gases in water. J Chem Phys,1986,85(11):6720-6727
[48]Lu N, Kofke D A, Woolf T B. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J Comput Chem,2004,25(1): 28-40
[49]Kofke D A, Cummings P T. Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation. Fluid Phase Equilib, 1998:41-49
[50]Hahn A M, Then H. Characteristic of Bennett's acceptance ratio method. Phys Rev Lett., 2009,80(3):031111
[51]Shirts M R, Bair E, Hooker G, et al. Equilibrium free energies from nonequilibrium measurements using Maximum-Likelihood methods. Phys Rev Lett,2003,91(14):140601
[52]Flyvbjerg H, Petersen H G Error estimates on averages of correlated data. J Chem Phys,1989, 91(1):461-466
[53]Lu N, Kofke D A. Accuracy of free-energy perturbation calculations in molecular simulation. Ⅰ. Modeling. J Chem Phys,2001,114(17):7303-7311
[54]Lu N, Woolf T B. Understanding and improving free energy calculations in molecular simulations:error analysis and reduction methods. In Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:Berlin, 2007
[55]Lu N, Kofke D A. Accuracy of free-energy perturbation calculations in molecular simulation. Ⅱ. Heuristics. J Chem Phys,2001,115(15):6866-6875
[56]Hunenberger P H, McCammon J A. Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction:a continuum electrostatics study. J Chem Phys,1999, 110(4):1856-1872
[57]Zuckerman D M, Woolf T B. Theory of a systematic computational error in free energy differences. Phys Rev Lett,2002,89(18):180602
[58]Zuckerman D M, Woolf T B. Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities. J Stat Phys,2004,114(5-6):1303-1323
[59]Wan S, Stote R H, Karplus M. Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes. J Chem Phys,2004,121(19):9539-9548
[60]Cramer H. Mathematical methods of statistics. Princeton University Press, Princeton, NJ, 1957
[61]Valleau J P, Card D N. Monte Carlo estimation of the free energy by multistage sampling. J Chem Phys,1972,57(12):5457-5462
[62]Wolfenden R, Andersson L, Cullis P M, et al. Affinities of amino acid side chains for solvent water. Biochemistry,1981,20(4):849-85
[63]Ben-Naim A, Marcus Y. Solvation thermodynamics of nonionic solutes. J Chem Phys,1984, 81(4):2016-2027
[64]Anisimov V M, Vorobyov I V, Roux B, et al. Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput, 2007,3(6):1927-1946
[65]Zhong Y, Patel S. Nonadditive empirical force fields for short-chain linear alcohols; methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models. J Phys Chem B,2010,114(34):11076-11092
[66]Chipot C. Rational determination of charge distributions for free energy calculations. J Comput Chem,2003,24(4):409-415
[67]Levy R M, Gallicchio E. Computer simulations with explicit solvent:recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annu Rev Phys Chem,1998,49(1):531-567
[68]Kubo M M, Gallicchio E, Levy R M. Thermodynamic decomposition of hydration free energies by computer simulation:□ application to amines, oxides, and sulfides. J Phys Chem B,1997,101(49):10527-10534
[69]Shirts M R, Chodera J D. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys,2008,129(12):124105-124110
[70]Pohorille A, Darve E. A bayesian approach to calculating free energies in chemical and biological systems. Bayesian inference and maximum entropy methods in science and engineering. AIP Conference Proceedings. Melville, NY,2006. AIP:23-30
[71]Blinnikov S, Moessner R. Expansions for nearly Gaussian distributions. Astron Astrophys Suppl Ser,1998,130(1):193-205
[1]Collier C P, Wong E W, Belohradsky M, et al. Electronically configurable molecular-based logic gates. Science,1999,285(5426):391-394
[2]Luo Y, Collier C P, Jeppesen J O, et al. Two-dimensional molecular electronics circuits. ChemPhysChem,2002,3(6):519-525
[3]Green J E, Wook Choi J, Boukai A, et al. A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre. Nature,2007,445(7126):414-417
[4]N(?)rgaard K, Jeppesen J O, Laursen B W, et al. Evidence of strong hydration and significant tilt of amphiphilic [2]rotaxane molecules in langmuir films studied by synchrotron X-ray reflectivity, J Phys Chem B,2004,109(3):1063-1066
[5]Moulin J-F, Kengne J C, Kshirsagar R, et al. Self-organization of rotaxane thin films into spatially correlated nanostructures:□morphological and structural aspects. J Am Chem Soc, 2005,128(2):526-532
[6]Nygaard S, Leung K C F, Aprahamian I, et al. Functionally rigid bistable [2]rotaxanes. J Am Chem Soc,2007,129(4):960-970
[7]Panman M R, Bodis P, Shaw D J, et al. Operation mechanism of a molecular machine revealed using time-resolved vibrational spectroscopy. Science,2010,328(5983): 1255-1258
[8]Rijs A M, Kay E R, Leigh D A, et al. IR spectroscopy on jet-cooled isolated two-station rotaxanes. J Phys Chem A,2011,115(34):9669-9675
[9]Panman M R, Bodis P, Shaw D J, et al. Time-resolved vibrational spectroscopy of a molecular shuttle. Phys Chem Chem Phys,2012,14(6):1865-1875
[10]Raymo F M, Stoddart J F, Interlocked macromolecules. Chem Rev,1999,99(7):1643-1664
[11]Fahrenbach A C, Bruns C J, Cao D, et al. Ground-state thermodynamics of bistable redox-active donor-acceptor mechanically interlocked molecules. Acc Chem Res,2012, 45(9):1581-1592
[12]Harada A. Cyclodextrin-based molecular machines. Acc Chem Res,2001,34(6):456-464
[13]Wenz G, Han B-H, Muller A. Cyclodextrin rotaxanes and polyrotaxanes. Chem Rev,2006, 106(3):782-817
[14]Guo X Q, Song L X, Dang Z, et al. A comparative study on the formation and spectral properties of the polypseudorotaxanes of beta-cyclodextrin and poly(propylene glycol) under different conditions. Bull Chem Soc Jpn,2009,82(9):1209-1213
[15]Wang Y-H, Zhang H-M, Liu L, et al. Photoinduced electron transfer in a supramolecular species building of mono-6-p-nitrobenzoyl-β-cyclodextrin with naphthalene derivatives. J Org Chem,2002,67(8):2429-2434
[16]Harada A, Hashidzume A, Yamaguchi H, et al. Polymeric rotaxanes. Chem Rev,2009, 109(11):5974-6023
[17]Lee J W, Samal S, Selvapalam N, et al. Cucurbituril homologues and derivatives:□ new opportunities in supramolecular chemistry. Acc Chem Res,2003,36(8):621-630
[18]Rowan A E, Elemans J A A W, Nolte R J M. Molecular and supramolecular objects from glycoluril. Acc Chem Res,1999,32(12):995-1006
[19]Belowich M E, Valente C, Smaldone R A, et al. Positive cooperativity in the template-directed synthesis of monodisperse macromolecules. J Am Chem Soc,2012, 134(11):5243-5261
[20]Zhang M, Xu D, Yan X, et al. Self-healing supramolecular gels formed by crown ether based host-guest interactions. Angew Chem Int Edit,2012,51(28):7011-7015
[21]Xue M, Yang Y, Chi X, et al. Pillararenes, a new class of macrocycles for supramolecular chemistry. Acc Chem Res,2012,45(8):1294-1308
[22]Hu X-B, Chen L, Si W, et al. Pillar[5]arene decaamine:synthesis, encapsulation of very long linear diacids and formation of ion pair-stopped [2]rotaxanes. Chem Commun,2011,47(16): 4694-4696
[23]Yu G, Han C, Zhang Z, et al. Pillar[6]arene-based photoresponsive host-guest complexation. J Am Chem Soc,2012,134(20):8711-8717
[24]Bodis P, Panman M R, Bakker B H, et al. Two-dimensional vibrational spectroscopy of rotaxane-based molecular machines. Acc Chem Res,2009,42(9):1462-1469
[25]Fuller A-M L, Leigh D A, Lusby P J. Sequence isomerism in [3]rotaxanes. J Am Chem Soc, 2010,132(13):4954-4959
[26]Wisner J A, Beer P D, Drew M G B, et al. Anion-templated rotaxane formation. J Am Chem Soc,2002,124(42):12469-12476
[27]Da Ros T, Guldi D M, Morales A F, et al. Hydrogen bond-assembled fullerene molecular shuttle. Org Lett,2003,5(5):689-691
[28]Movsisyan L D, Kondratuk D V, Franz M, et al. Synthesis of polyyne rotaxanes. Org Lett, 2012,14(13):3424-3426
[29]Goldup S M, Leigh D A, McGonigal P R, et al. Two axles threaded using a single template site:active metal template macrobicyclic [3]rotaxanes. J Am Chem Soc,2009,132(1): 315-320
[30]Crowley J D, Hanni K D, Lee A-L, et al. [2]Rotaxanes through palladium active-template dxidative heck cross-couplings. J Am Chem Soc,2007,129(40):12092-12093
[31]Crowley J D, Hanni K D, Leigh D A, et al. Diels-alder active-template synthesis of rotaxanes and metal-ion-switchable molecular shuttles. J Am Chem Soc,2010,132(14):5309-5314
[32]Pierro T, Gaeta C, Talotta C, et al. Fixed or invertible calixarene-based directional shuttles. Org Lett,2011,13(10):2650-2653
[33]Crowley J D, Leigh D A, Lusby P J, et al. A switchable palladium-complexed molecular shuttle and its metastable positional isomers. J Am Chem Soc,2007,129(48):15085-15090
[34]Li H, Fahrenbach A C, Coskun A, et al. A light-stimulated molecular switch driven by radical-radical interactions in water. Angew Chem Int Edit,2011,50(30):6782-6788
[35]Stoll R S, Friedman D C, Stoddart J F. Mechanically interlocked mechanophores by living-radical polymerization from rotaxane initiators. Org Lett,2011,13(10):2706-2709
[36]Chiu C-W, Lai C-C, Chiu S-H. "Threading-followed-by-swelling":□ a new protocol for rotaxane synthesis. J Am Chem Soc,2007,129(12):3500-3501
[37]Ooya T, Choi H S, Yamashita A, et al. Biocleavable polyrotaxane-plasmid DNA polyplex for enhanced gene delivery. J Am Chem Soc,2006,128(12):3852-3853
[38]Li J, Yang C, Li H, et al. Cationic supramolecules composed of multiple oligoethylenimine-grafted β-cyclodextrins threaded on a polymer chain for efficient gene delivery. Adv Mater,2006,18(22):2969-2974
[39]Yang C, Wang X, Li H, et al. Cationic polyrotaxanes as gene carriers:physicochemical properties and real-time observation of DNA complexation, and gene transfection in cancer cells. J Phys Chem B,2009,113(22):7903-7911
[40]Balzani V, Gomez-L6pez M, Stoddart J F. Molecular machines. Acc Chem Res,1998,31 (7): 405-414
[41]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2(10): 1353-1356
[42]Ye T, Kumar A S, Saha S, et al. Changing stations in single bistable rotaxane molecules under electrochemical control. ACS Nano,2010,4(7):3697-3701
[43]Balzani V, Clemente-Leon M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[44]Brouwer A M, Frochot C, Gatti F G, et al. Photoinduction of fast, reversible translational motion in a hydrogen-bonded molecular shuttle. Science,2001,291(5511):2124-2128
[45]Jacquot de Rouville H-P, Iehl J, Bruns C J, et al. A neutral naphthalene diimide [2]rotaxane. Org Lett,2012,14(20):5188-5191
[46]Zhang K-D, Zhao X, Wang G-T, et al. Foldamer-tuned switching kinetics and metastability of [2]rotaxanes. Angew Chem Int Edit,2011,50(42):9866-9870
[47]Ferrand Y, Gan Q, Kauffmann B, et al. Template-induced screw motions within an aromatic amide foldamer double helix. Angew Chem Int Edit,2011,50(33):7572-7575
[48]You Y-C, Tzeng M-C, Lai C-C, et al. Using oppositely charged ions to operate a three-station [2]rotaxane in two different switching modes. Org Lett,2012,14(4):1046-1049
[49]Barnes J C, Fahrenbach A C, Dyar S M, et al. Mechanically induced intramolecular electron transfer in a mixed-valence molecular shuttle. Proc. Natl. Acad. Sci. USA,2012,109(29): 11546-11551
[50]Li H, Zhu Z, Fahrenbach A C, et al. Mechanical bond-induced radical stabilization. J Am Chem Soc,2012,135(1):456-467
[51]Fahrenbach A C, Zhu Z, Cao D, et al. Radically enhanced molecular switches. J Am Chem Soc,2012,134(39):16275-16288
[52]Deng W-Q, Muller R P, Goddard W A. Mechanism of the Stoddart-Heath bistable rotaxane molecular switch. J Am Chem Soc,2004,126(42):13562-13563
[53]Dvornikovs V, House B E, Kaetzel M, et al. Host-[2]rotaxanes as cellular transport agents. J Am Chem Soc,2003,125(27):8290-8301
[54]Carlone A, Goldup S M, Lebrasseur N, et al. A three-compartment chemically-driven molecular information ratchet. J Am Chem Soc,2012,134(20):8321-8323
[55]Serreli V, Lee C-F, Kay E R, et al. A molecular information ratchet. Nature,2007,445(7127): 523-527
[56]Kay E R, Leigh D A, Zerbetto F. Synthetic molecular motors and mechanical machines. Angew Chem Int Edit,2007,46(1-2):72-191
[57]Zhao Y-L, Aprahamian I, Trabolsi A, et al. Organogel formation by a cholesterol-stoppered bistable [2]rotaxane and its dumbbell precursor. J Am Chem Soc,2008,130(20):6348-6350
[58]Pease A R, Jeppesen J O, Stoddart J F, et al. Switching devices based on interlocked molecules. Acc Chem Res,2001,34(6):433-444
[59]Bema J, Leigh D A, Lubomska M, et al. Macroscopic transport by synthetic molecular machines. Nat Mater,2005,4(9):704-710
[60]Wan P, Jiang Y, Wang Y, et al. Tuning surface wettability through photocontrolled reversible molecular shuttle. Chem Commun,2008,0(44):5710-5712
[61]Baumes J M, Murgu I, Oliver A, et al. Using the rotaxane mechanical bond to enhance chemical reactivity. Org Lett,2010,12(21):4980-4983
[62]Thordarson P, Bijsterveld E J A, Rowan A E, et al. Epoxidation of polybutadiene by a topologically linked catalyst. Nature,2003,424(6951):915-918
[63]Zhang H, Hu J, Qu D-H. Dual-mode control of PET process in a ferrocene-functionalized [2]rotaxane with high-contrast fluorescence output. Org Lett,2012,14(9):2334-2337
[64]Alvarez-Perez M, Goldup S M, Leigh D A, et al. A chemically-driven molecular information ratchet. J Am Chem Soc,2008,130(6):1836-1838
[65]Danquah M K, Zhang X A, Mahato R I. Extravasation of polymeric nanomedicines across tumor vasculature. Adv Drug Deliv Rev,2011,63(8):623-639
[66]Chen T. Overcoming drug resistance by regulating nuclear receptors. Adv Drug Deliv Rev, 2010,62(13):1257-1264
[67]Torchilin V P. Tat peptide-mediated intracellular delivery of pharmaceutical nanocarriers. Adv Drug Deliv Rev,2008,60(4-5):548-558
[68]Guo D-S, Wang K, Wang Y-X, et al. Cholinesterase-responsive supramolecular vesicle. J Am Chem Soc,2012,134(24):10244-10250
[69]Torney F, Trewyn B G, Lin V S Y, et al. Mesoporous silica nanoparticles deliver DNA and chemicals into plants. Nat Nano,2007,2(5):295-300
[70]Trewyn B G, Slowing I I, Giri S, et al. Synthesis and functionalization of a mesoporous silica nanoparticle based on the sol-gel process and applications in controlled release. Acc Chem Res,2007,40(9):846-853
[71]Angelos S, Johansson E, Stoddart J F, et al. Mesostructured silica supports for functional materials and molecular machines. Adv Funct Mater,2007,17(14):2261-2271
[72]Yang Y-W. Towards biocompatible nanovalves based on mesoporous silica nanoparticles. MedChemComm,2011,2(11):1033-1049
[73]Hernandez R, Tseng H-R, Wong J W, et al. An operational supramolecular nanovalve. J Am Chem Soc,2004,126(11):3370-3371
[74]Zhu Z, Fahrenbach A C, Li H, et al. Controlling switching in bistable [2]catenanes by combining donor-acceptor and radical-radical Interactions. J Am Chem Soc,2012,134(28): 11709-11720
[75]Ferris D P, Zhao Y-L, Khashab N M, et al. Light-operated mechanized nanoparticles. J Am Chem Soc,2009,131(5):1686-1688
[76]Sun Y-L, Yang B-J, Zhang S X-A, et al. Cucurbit[7]uril pseudorotaxane-based photoresponsive supramolecular nanovalve. Chem Eur J,2012,18(30):9212-9216
[77]Marquez C, Nau W M. Two mechanisms of slow host-guest complexation between cucurbit[6]uril and cyclohexylmethylamine:pH-responsive supramolecular kinetics. Angew Chem Int Edit,2001,40(17):3155-3160
[78]Marquez C, Hudgins R R, Nau W M. Mechanism of host-guest complexation by cucurbituril. J Am Chem Soc,2004,126(18):5806-5816
[79]Ling X, Samuel E L, Patchell D L, et al. Cucurbituril slippage:translation is a complex motion. Org Lett,2010,12(12):2730-2733
[80]Angelos S, Khashab N M, Yang Y-W, et al. pH clock-operated mechanized nanoparticles. J Am Chem Soc,2009,131(36):12912-12914
[81]Nguyen T D, Leung K C F, Liong M, et al. Construction of a pH-driven supramolecular nanovalve. Org Lett,2006,8(15):3363-3366
[82]Patel K, Angelos S, Dichtel W R, et al. Enzyme-responsive snap-top covered silica nanocontainers. J Am Chem Soc,2008,130(8):2382-2383
[83]Meng H, Xue M, Xia T, et al. Autonomous in vitro anticancer drug release from mesoporous silica nanoparticles by pH-sensitive nanovalves. J Am Chem Soc,2010,132(36): 12690-12697
[84]Zhao Y-L, Li Z, Kabehie S, et al. pH-operated nanopistons on the surfaces of mesoporous silica nanoparticles. J Am Chem Soc,2010,132(37):13016-13025
[85]Vassal G, Koscielny S, Challine D, et al. Busulfan disposition and hepatic veno-occlusive disease in children undergoing bone marrow transplantation. Cancer Chemoth Pharm,1995, 37(3):247-253
[86]Menuel S, Joly J-P, Courcot B, et al. Synthesis and inclusion ability of a bis-β-cyclodextrin pseudo-cryptand towards Busulfan anticancer agent. Tetrahedron,2007,63(7):1706-1714
[87]Porwanski S, Dumarcay-Charbonnier F, Menuel S, et al. Bis-p-cyclodextrinyl-and bis-cellobiosyl-diazacrowns:synthesis and molecular complexation behaviors toward Busulfan anticancer agent and two basic aminoacids. Tetrahedron,2009,65(31):6196-6203
[88]Zehnder D W, Smithrud D B. Facile synthesis of rotaxanes through condensation reactions of DCC-[2]rotaxanes. Org Lett,2001,3(16):2485-2487
[89]Smukste I, House B E, Smithrud D B. Host-[2]rotaxane:□ advantage of converging functional groups for guest recognition. J Org Chem,2003,68(7):2559-2571
[90]Bao X, Isaacsohn I, Drew A F, et al. Determining the intracellular transport mechanism of a cleft-[2]rotaxane. J Am Chem Soc,2006,128(37):12229-12238
[91]Wang X, Smithrud D B. Pt-rotaxanes as cytotoxic agents. Bioorg Med Chem Lett,2011, 21(22):6880-6883
[92]Zhu J, McFarland-Mancini M, Drew A F, et al. Host-rotaxanes with oligomeric axles are intracellular transport agents. Bioorg Med Chem Lett,2009,19(2):520-523
[93]Bao X, Isaacsohn I, Drew A F, et al. Determining the binding and intracellular transporting abilities of a host-[3]rotaxane. J Org Chem,2007,72(11):3988-4000
[94]Rouget J-B, Aksel T, Roche J, et al. Size and sequence and the volume change of protein folding. J Am Chem Soc,2011,133(15):6020-6027
[95]Ghosh K, Dill K A. Theory for protein folding cooperativity:helix bundles. J Am Chem Soc, 2009,131(6):2306-2312
[96]Metropolis N, Rosenbluth A W, Rosenbluth M N, et al. Equation of state calculations by fast computing machines. J Chem Phys,1953,21(6):1087-1092
[97]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[98]Yang L, Tan C-h, Hsieh M-J, et al. New-generation amber united-atom force field. J Phys Chem B,2006,110(26):13166-13176
[99]Oostenbrink C, Soares T, Vegt N A, et al. Validation of the 53A6 GROMOS force field. Eur Biophys J,2005,34(4):273-284
[100]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys,1992,97(3):1990-2001
[101]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[102]Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:New York,2007.
[103]Kollman P. Free energy calculations:applications to chemical and biochemical phenomena. Chem Rev,1993,93(7-):2395-2417
[104]Simonson T, Archontis G, Karplus M. Free energy simulations come of age:□ protein-ligand recognition. Acc Chem Res,2002,35(6):430-437
[105]Landau L D. Statistical physics. The Clarendon Press, Oxford, U. K.,1938
[106]Zwanzig R W. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys,1954,22(8):1420-1426
[107]Kirkwood J G Statistical mechanics of fluid mixtures. J Chem Phys,1935,3(5):300-313
[108]Henin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[109]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906
[110]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[111]Rodriguez-G6mez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[112]Bennett C H. Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys,1976,22(2):245-268
[113]Ferrenberg A M, Swendsen R H. New Monte Carlo technique for studying phase transitions. Phys Rev Lett,1988,61(23):2635-2638
[114]Jarzynski C. Equilibrium free-energy differences from nonequilibrium measurements:a master-equation approach. Phys Rev Lett.,1997,56(5):5018-5035
[115]Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett,1997, 78(14):2690-2693
[116]Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B.2010,114(32):10235-10253
[117]Valleau J P, Torrie G M A. Guide to Monte Carlo for statistical mechanics:byways. In Modem theoretical chemistry; Berne B J, Ed.; Plenum:New York,1977; pp 169-194.
[118]McDonald I R, Singer K. Machine calculation of thermodynamic properties of a simple fluid at supercritical temperatures. J Chem Phys,1967,47(11):4766-4772
[119]Straatsma T P, Berendsen H J C, Postma J P M. Free energy of hydrophobic hydration:a molecular dynamics study of noble gases in water. J Chem Phys,1986,85(11):6720-6727
[120]McDonald I R, Singer K. Calculation of thermodynamic properties of liquid argon from Lennard-Jones parameters by a Monte Carlo method. Discuss Faraday Soc,1967,43:40-49
[121]Lu N, Kofke D A, Woolf T B. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J Comput Chem,2004,25(1): 28-40
[122]Lelievre T, Stoltz G, Rousset M. Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[123]Gumbart J C, Roux B, Chipot C. Standard binding free energies from computer simulations: what is the best strategy? J Chem Theory Comput,2012,9(1):794-802
[124]Chipot C. Milestones in the activation of a G protein-coupled receptor. Insights from molecular-dynamics simulations into the human cholecystokinin receptor-1. J Chem Theory Comput,2008,4(12):2150-2159
[125]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[126]Pan A C, Sezer D, Roux B. Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[127]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[128]Jang S S, Jang Y H, Kim Y-H, et al. Molecular dynamics simulation of amphiphilic bistable [2]rotaxane langmuir monolayers at the air/water interface. J Am Chem Soc,2005,127(42): 14804-14816
[129]Jang Y H, Jang S S, Goddard W A. Molecular dynamics simulation study on a monolayer of half [2]Rotaxane self-assembled on Au(111). J Am Chem Soc,2005,127(13):4959-4964
[130]Jang S S, Jang Y H, Kim Y-H, et al. Structures and properties of self-assembled monolayers of bistable [2]rotaxanes on Au (111) surfaces from molecular dynamics simulations validated with experiment. J Am Chem Soc,2005,127(5):1563-1575
[131]Carter E A, Ciccotti G, Hynes J T, et al. Constrained reaction coordinate dynamics for the simulation of rare events. Chem Phys Lett,1989,156(5):472-477
[132]Sprik M, Ciccotti G Free energy from constrained molecular dynamics. J Chem Phys,1998, 109(18):7737-7744
[133]Kim H, Goddard W A, Jang S S, et al. Free energy barrier for molecular motions in bistable [2]rotaxane molecular electronic devices. J Phys Chem A,2009,113(10):2136-2143
[134]Raiteri P, Bussi G, Cucinotta C S, et al. Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. Angew Chem Int Edit,2008,47(19): 3536-3539
[135]Torrie G M, Valleau J P. Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid. Chem Phys Lett,1974,28(4):578-581
[136]Still W C, Tempczyk A, Hawley R C, et al. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc,1990,112(16):6127-6129
[137]Zhao Y-L, Dichtel W R, Trabolsi A, et al. A redox-switchable a-cyclodextrin-based [2]rotaxane. J Am Chem Soc,2008,130(34):11294-11296
[138]Zhang Q, Tu Y, Tian H, et al. Working mechanism for a redox switchable molecular machine based on cyclodextrin:a free energy profile approach. J Phys Chem B,2010,114(19): 6561-6566
[139]Galatsis K, Kang W, Botros Y, et al. Emerging memory devices:nontraditional possibilities based on nanomaterials and nanostructures. IEEE Circuits Device Maga,2006,22(3):12-21
[140]Collier C P, Wong E W, Belohradsky M, et al. Electronically configurable molecular-based logic gates. Science,1999,285(5426):391-394
[141]Balzani V, Gomez-Lopez M, Stoddart J F. Molecular machines. Acc Chem Res,1998,31(7): 405-414
[142]Pease A R, Jeppesen J O, Stoddart J F, et al. Switching devices based on interlocked molecules. Acc Chem Res,2001,34(6):433-444
[143]Harada A, Kamachi M. Complex formation between poly(ethylene glycol) and α-cyclodextrin. Macromolecules,1990,23(10):2821-2823
[144]Harada A, Li J, Kamachi M. The molecular necklace:a rotaxane containing many threaded a-cyclodextrins. Nature,1992,356(6367):325-327
[145]Wu Y-L, Li J. Synthesis of supramolecular nanocapsules based on threading of multiple cyclodextrins over polymers on gold nanoparticles. Angew Chem Int Ed,2009,48(21): 3842-3845
[146]Ooya T, Choi H S, Yamashita A, et al. Biocleavable polyrotaxane-plasmid DNA polyplex for enhanced gene delivery. J Am Chem Soc,2006,128(12):3852-3853
[147]Harada A, Li J, Kamachi M. Preparation and characterization of a polyrotaxane consisting of monodisperse poly(ethylene glycol) and a-cyclodextrins. J Am Chem Soc,1994,116(8): 3192-3196
[148]Miyake K, Yasuda S, Harada A, et al. Formation process of cyclodextrin necklace-analysis of hydrogen bonding on a molecular level. J Am Chem Soc,2003,125(17):5080-5085
[149]Shigekawa H, Miyake K, Sumaoka J, et al. The molecular abacus:STM manipulation of cyclodextrin necklace. J Am Chem Soc,2000,122(22):5411-5412
[150]Bonnet P, Jaime C, Morin-Allory L. α-,β-, and y-Cyclodextrin dimers. Molecular modeling studies by molecular mechanics and molecular dynamics simulations. J Org Chem,2001, 66(3):689-692
[151]Bonnet P, Jaime C, Morin-Allory L. Structure and thermodynamics of α-, β-, and y-cyclodextrin dimers. molecular dynamics studies of the solvent effect and free binding energies. J Org Chem,2002,67(24):8602-8609
[152]Nascimento C S, Anconi C P A, Dos Santos H F, et al. Theoretical study of the α-cyclodextrin dimer. J Phys Chem A,2005,109(14):3209-3219
[153]Yu Y, Cai W, Chipot C, et al. Spatial arrangement of a-cyclodextrins in a rotaxane. Insights from free-energy calculations. J Phys Chem B,2008,112(17):5268-5271
[154]Tallury S S, Smyth M B, Cakmak E, et al. Molecular dynamics simulations of interactions between polyanilines in their inclusion complexes with β-cyclodextrins. J Phys Chem B, 2012,116(7):2023-2030
[155]Chipot C, Pohorille A. Calculating free energy differences using perturbation theory. In Free energy calculations; Chipot C, Pohorille A, Eds.; Springer Berlin Heidelberg,2007; Vol.86; pp 33-75.
[156]Lelievre T, Rousset M, Stoltz G Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[157]Chipot C, H6nin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,'123(24):244906-6
[158]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[159]Henin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[160]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[161]Brush S G. History of the Lenz-Ising model. Rev Mod Phys,1967,39(4):883-893
[162]Ising E. Beitrag zur theorie des ferromagnetismus. Z Phys A:Hadrons Nucl,1925,31(1): 253-258
[163]Hingerty B, Saenger W. Topography of cyclodextrin inclusion complexes.8. Crystal and molecular structure of the.alpha.-cyclodextrin-methanol-pentahydrate complex. Disorder in a hydrophobic cage. J Am Chem Soc,1976,98(11):3357-3365
[164]Insight II User Guide. Accelrys Software Inc., San Diego, CA,2005
[165]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[166]Hatcher E R, Guvench O, MacKerell A D. CHARMM additive all-atom force field for acyclic polyalcohols, acyclic carbohydrates, and inositol. J Chem Theory Comput,2009,5(5): 1315-1327
[167]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[168]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[169]Jorgensen W L, Chandrasekhar J, Madura J D, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys,1983,79(2):926-935
[170]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[171]Miyamoto S, Kollman P A. Settle:an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem,1992,13(8):952-962
[172]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[172]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys,1992,97(3):1990-2001
[174]Darden T, York D, Pedersen L. Particle mesh Ewald:an N log(N) method for Ewald sums in large systems. J Chem Phys,1993,98(12):10089-10092
[175]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[176]Henin J, Fiorin G, Chipot C, et al. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput,2010,6(1):35-47
[177]Jonkheijm P, van der Schoot P, Schenning A P H J, et al. Probing the solvent-assisted nucleation pathway in chemical self-assembly. Science,2006,313(5783):80-83
[178]Tanaka S, Scheraga H A. Model of protein folding:incorporation of a one-dimensional short-range (Ising) model into a three-dimensional model. Proc Natl Acad Sci USA,1977, 74(4):1320-1323
[179]Metropolis N, Rosenbluth A W, Rosenbluth M N, et al. Equation of state calculations by fast computing machines. J Chem Phys,1953,21(6):1087-1092
[180]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[181]Bolhuis P G, Dellago C, Chandler D. Reaction coordinates of biomolecular isomerization. Proc Natl Acad Sci USA,2000,97(11):5877-5882
[182]Pan A C, Sezer D, Roux B. Finding transition pathway:using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[183]Liu P, Chipot C, Shao X, et al. Solvent-controlled shuttling in a molecular switch. J Phys Chem C,2012,116(7):4471-4476
[184]Shrake A, Rupley J A. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol,1973,79(2):351-371
[185]Green J E, Wook Choi J, Boukai A, et al. A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre. Nature,2007,445(7126):414-417
[186]Harada A. Cyclodextrin-based molecular machines. Acc Chem Res,2001,34(6):456-464
[187]Raymo F M, Stoddart J F. Interlocked macromolecules. Chem Rev,1999,99(7):1643-1664
[188]Zhao Y-L, Dichtel W R, Trabolsi A, et al. A redox-switchable α-cyclodextrin-based [2]rotaxane. J Am Chem Soc,2008,130(34):11294-11296
[189]Bissell R A, Cordova E, Kaifer A E, et al. A chemically and electrochemically switchable molecular shuttle. Nature,1994,369:133-137
[190]Berna J, Goldup S M, Lee A-L, et al. Cadiot-chodkiewicz active template synthesis of rotaxanes and switchable molecular shuttles with weak intercomponent interactions. Angew Chem Int Ed,2008,47(23):4392-4396
[191]Coutrot F, Romuald C, Busseron E. A new pH-switchable dimannosyl[c2]daisy chain molecular machine. Org Lett,2008,10(17):3741-3744
[192]Coskun A, Friedman D C, Li H, et al. A light-gated STOP-GO molecular shuttle. J Am Chem Soc,2009,131(7):2493-2495
[193]Balzani V, Clemente-Leon M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[194]Murakami H, Kawabuchi A, Matsumoto R, et al. A multi-mode-driven molecular shuttle:□photochemically and thermally reactive azobenzene rotaxanes. J Am Chem Soc, 2005,127(45):15891-15899
[195]Marlin D S, Gonzalez Cabrera D, Leigh D A, et al. Complexation-induced translational isomerism:shuttling through stepwise competitive binding. Angew Chem Int Ed,2006,45(1): 77-83
[196]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2(10): 1353-1356
[197]Brough B, Northrop B H, Schmidt J J, et al. Evaluation of synthetic linear motor-molecule actuation energetics. Proc Natl Acad Sci USA,2006,103(23):8583-8588
[198]Belohradsky M, Elizarov A M, Stoddart J F. Speed-controlled molecular shuttles. Collect Czech Chem Commun,2002,67(11):1719-1728
[199]Kim H, Goddard W A, Jang S S, et al. Free energy barrier for molecular motions in bistable [2]rotaxane molecular electronic devices. J Phys Chem A,2009,113(10):2136-2143
[200]Raiteri P, Bussi G, Cucinotta C S, et al. Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. Angew Chem Int Ed,2008,47(19): 3536-3539
[201]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[202]Rodriguez-G6mez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[203]Darve E, Rodriguez-G6mez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[204]Henin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[205]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906-6
[206]Yu Y, Chipot C, Cai W, et al. Molecular dynamics study of the inclusion of cholesterol into cyclodextrins. J Phys Chem B,2006,110(12):6372-6378
[207]Yu Y, Cai W, Chipot C, et al. Spatial arrangement of α-cyclodextrins in a rotaxane. Insights from free-energy calculations. J Phys Chem B,2008,112(17):5268-5271
[208]Eyring H. The activated complex in chemical reactions. J Chem Phys,1935,3(2):107-115
[209]Insight II User Guide. Accelrys Software Inc., San Diego, CA,2005
[210]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[211]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[212]Liu X, Zhang S, Zhou G, et al. New force field for molecular simulation of guanidinium-based ionic liquids. J Phys Chem B,2006,110(24):12062-12071
[213]Strader M L, Feller S E. A flexible all-atom model of dimethyl sulfoxide for molecular dynamics simulations. J Phys Chem A,2002,106(6):1074-1080
[214]Pavelites J J, Gao J, Bash P A, et al. A molecular mechanics force field for NAD+, NADH, and the pyrophosphate groups of nucleotides. J Comput Chem,1997,18(2):221-239
[215]Foloppe N, MacKerell J A D. All-atom empirical force field for nucleic acids:I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem,2000,21(2):86-104
[216]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[217]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[218]Darden T, York D, Pedersen L. Particle mesh Ewald:an N log(N) method for Ewald sums in large systems. J Chem Phys,1993,98(12):10089-10092
[219]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[220]Ryckaert J-P, Ciccotti G, Berendsen H J C. Numerical integration of the cartesian equations of motion of a system with constraints:molecular dynamics of n-alkanes. J Comput Phys,1977, 23(3):327-341
[221]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[222]Flyvbjerg H, Petersen H G Error estimates on averages of correlated data. J Chem Phys,1989, 91(1):461-466
[223]Frisch M J, Trucks G W, Schlegel H B, et al. Gaussian 03, Revision C.03. Gaussian, Inc. Wallingford, CT,2004
[224]Vaiana A C, Cournia Z, Costescu I B, et al. AFMM:a molecular mechanics force field vibrational parametrization program. Comput Phys Commun,2005,167(1):34-42
[225]Kim H-W, Zeroka D. Trans-ethylphosphine and selected deuterated isotopomers:prediction of infrared spectra and potential energy distribution determination. THEOCHEM,2005,715: 21-31
[226]Kim H-W, Chechla A A, Kim B. Potential energy distribution study of infrared frequencies of methylamine and methylphosphine. THEOCHEM,2007,802:105-110
[227]Pulay P, Fogarasi G, Pang F, et al. Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives. J Am Chem Soc,1979,101(10): 2550-2560
[228]Bergeron R J, Channing M A, Gibeily G J, et al. Disposition requirements for binding in aqueous solution of polar substrates in the cyclohexaamylose cavity. J Am Chem Soc,1977, 99(15):5146-5151
[229]Li J, Harada A, Kamachi M. Formation of inclusion complexes of oligoethylene and its derivatives with a-cyclodextrin. Bull Chem Soc Jpn,1994,67:2808-2818
[230]Balzani V, Clemente-Leon M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[231]Bissell R A, Cordova E, Kaifer A E, et al. A chemically and electrochemically switchable molecular shuttle. Nature,1994,369(6476):133-137
[232]Hernandez R, Tseng H-R, Wong J W, et al. An operational supramolecular nanovalve. J Am Chem Soc,2004,126(11):3370-3371
[233]Dvornikovs V, House B E, Kaetzel M, et al. Host-[2]rotaxanes as cellular transport agents. J Am Chem Soc,2003,125(27):8290-8301
[234]Leung K C-F, Chak C-P, Lo C-M, et al. pH-controllable supramolecular systems. Chem Asian J,2009,4(3):364-381
[235]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2:1353-1356
[236]Umehara T, Kawai H, Fujiwara K, et al. Entropy- and hydrolytic-driven positional switching of macrocycle between imine- and hydrogen-bonding stations in rotaxane-based molecular shuttles. J Am Chem Soc,2008,130(42):13981-13988
[237]Vassal G, Koscielny S, Challine D, et al. Busulfan disposition and hepatic veno-occlusive disease in children undergoing bone marrow transplantation. Cancer Chemoth Pharm,1995, 37(3):247-253
[238]Zehnder D W, Smithrud D B. Facile synthesis of rotaxanes through condensation reactions of DCC-[2]rotaxanes. Org Lett,2001,3(16):2485-2487
[239]Smukste I, House B E, Smithrud D B. Host-[2]rotaxane:D advantage of converging functional groups for guest recognition. J Org Chem,2003,68(7):2559-2571
[240]Bao X, Isaacsohn I, Drew A F, et al. Determining the intracellular transport mechanism of a cleft-[2]rotaxane. J Am Chem Soc,2006,128(37):12229-12238
[241]Liu P, Cai W, Chipot C, et al. Thermodynamic insights into the dynamic switching of a cyclodextrin in a bistable molecular shuttle. J Phys Chem Lett,2010,1(12):1776-1780
[242]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[243]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[244]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[245]Jorgensen W L, Chandrasekhar J, Madura J D, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys,1983,79(2):926-935
[246]Strader M L, Feller S E. A flexible all-atom model of dimethyl sulfoxide for molecular dynamics simulations. J Phys Chem A,2002,106(6):1074-1080
[247]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[248]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys; 1992,97(3):1990-2001
[249]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[250]Miyamoto S, Kollman P A. Settle:an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem,1992,13(8):952-962
[251]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[252]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[253]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[254]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[255]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906-6
[256]Henin J, Fiorin G, Chipot C, et al. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput,2010,6(1):35-47
[257]Flyvbjerg H, Petersen H G. Error-estimates on averages of correlated data. J Chem Phys, 1989,91(1):461-466
[258]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[259]Pan A C, Sezer D, Roux B. Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[260]Kollman P. Free energy calculations:applications to chemical and biochemical phenomena. Chem Rev,1993,93(7):2395-2417
[261]Simonson T, Archontis G, Karplus M. Free energy simulations come of age:protein-ligand recognition. Acc Chem Res,2002,35(6):430-437
[262]Chipot C, Pearlman D A. Free energy calculations. The long and winding gilded road. Mol Simulat,2002,28(1-2):1-12
[263]Simonson T. Free energy calculations. In Computational biochemistry and biophysics; Becker O M, MacKerell A D J, Roux B, Watanabe M, Eds.; Marcel Dekker Inc.:New York, 2001; pp 169-197
[264]Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:New York,2007
[265]Born M. Volumen und hydratationswarme der ionen. Z Physik,1920,1(1):45-48
[266]Landau L D. Statistical physics. The Clarendon Press, Oxford, U. K.,1938
[267]Zwanzig R W. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys,1954,22(8):1420-1426
[268]Kirkwood J G. Statistical mechanics of fluid mixtures. J Chem Phys,1935,3(5):300-313
[269]Bennett C H. Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys,1976,22(2):245-268
[270]Ferrenberg A M, Swendsen R H. New Monte Carlo technique for studying phase transitions. Phys Rev Lett,1988,61(23):2635-2638
[271]Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett,1997, 78(14):2690-2693
[272]Jarzynski C. Equilibrium free-energy differences from nonequilibrium measurements:a master-equation approach. Phys Rev Lett,1997,56(5):5018-5035
[273]Jorgensen W L, Ravimohan C. Monte Carlo simulation of differences in free energies of hydration. J Chem Phys,1985,83(6):3050-3054
[274]Bash P A, Singh U C, Langridge R, et al. Free energy calculations by computer simulation. Science,1987,236(4801):564-568
[275]van Gunsteren W, Beutler T, Fraternali F, et al. Computation of free energy in practice:choice of approximations and accuracy limiting factors. In Computer simulation of biomolecular systems; van Gunsteren W, Weiner P, Wilkinson A, Eds.; Escom Science Publishers:Leiden, The Netherlands,1993; pp 315-348
[276]Chipot C, Millot C, Maigret B, et al. Molecular dynamics free energy perturbation calculations:influence of nonbonded parameters on the free energy of hydration of charged and neutral species. J Phys Chem,1994,98(44):11362-11372
[277]Ding Y, Bernardo D N, Krogh-Jespersen K, et al. Solvation free energies of small amides and amines from molecular dynamics/free energy perturbation simulations using pairwise additive and many-body polarizable potentials. J Phys Chem,1995,99(29):11575-11583
[278]Morgantini P-Y, Kollman P A. Solvation free energies of amides and amines:disagreement between free energy calculations and experiment. J Am Chem Soc,1995,117(22): 6057-6063
[279]Rick S W, Berne B J. Free energy of the hydrophobic interaction from molecular dynamics simulations:□ the effects of solute and solvent polarizability. J Phys Chem B,1997,101(49): 10488-10493
[280]Ponder J W, Wu C, Ren P, et al. Current status of the AMOEBA polarizable force field. J Phys Chem B,2010,114(8):2549-2564
[281]Oostenbrink C, Villa A, Mark A E, et al. A biomolecular force field based on the free enthalpy of hydration and solvation:the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem,2004,25(13):1656-1676
[282]Shirts M R, Pitera J W, Swope W C, et al. Extremely precise free energy calculations of amino acid side chain analogs:comparison of common molecular mechanics force fields for proteins. J Chem Phys,2003,119(11):5740-5761
[283]Jorgensen W L, Buckner J K, Boudon S, et al. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water. J Chem Phys, 1988,89(6):3742-3746
[284]van Gunsteren W F. Methods for calculation of free energies and binding constants:successes and problems. In Computer simulation of biomolecular systems:theoretical and experimental applications; Van Gunsteren W F, Weiner P K, Eds.; Escom Science Publishers:Leiden, The Netherlands,1989; pp 27-59
[285]Miyamoto S, Kollman P A. What determines the strength of noncovalent association of ligands to proteins in aqueous solution? Proc Natl Acad Sci USA,1993,90(18):8402-8406
[286]Aqvist J. Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. J Comput Chem,1996,17(14):1587-1597
[287]Aqvist J, Luzhkov V B, Brandsdal B O. Ligand binding affinities from MD simulations. Acc Chem Res,2002,35(6):358-365
[288]Archontis G, Simonson T, Karplus M. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. J Mol Biol,2001,306(2):307-327
[289]Boresch S, Tettinger F, Leitgeb M, et al. Absolute binding free energies:□a quantitative approach for their calculation. J Phys Chem B,2003,107(35):9535-9551
[290]Oostenbrink C, van Gunsteren W F. Free energies of ligand binding for structurally diverse compounds. Proc Natl Acad Sci USA,2005,102(19):6750-6754
[291]Woo H-J, Roux B. Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci USA,2005,102(19):6825-6830
[292]Wang J, Deng Y, Roux B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J,2006,91(8):2798-2814
[293]Mobley D L, Graves A P, Chodera J D, et al. Predicting absolute ligand binding free energies to a simple nodel site. J Mol Biol,2007,371(4):1118-1134
[294]Deng Y, Roux B. Computations of standard binding free energies with molecular dynamics simulations. J Phys Chem B,2009,113(8):2234-2246
[295]Jiang W, Roux B. Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations. J Chem Theory Comput,2010,6(9):2559-2565
[296]Pearlman D A, Charifson P S. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system. J Med Chem,2001, 44(21):3417-3423
[297]Chipot C, Rozanska X, Dixit S. Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein. J Comput Aided Mol Des,2005,19(11):765-770
[298]Chodera J D, Mobley D L, Shirts M R, et al. Alchemical free energy methods for drug discovery:progress and challenges. Curr Opin Struct Biol,2011,21(2):150-160
[299]Lelievre T, Stoltz G, Rousset M. Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[300]Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B.2010,114(32):10235-10253
[301]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[302]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[303]McDonald I R, Singer K. Machine calculation of thermodynamic properties of a simple fluid at supercritical temperatures. J Chem Phys,1967,47(11):4766-4772
[304]McDonald I R, Singer K. Calculation of thermodynamic properties of liquid argon from Lennard-Jones parameters by a Monte Carlo method. Discuss Faraday Soc,1967,43:40-49
[305]Valleau J P, Torrie G M A. Guide to Monte Carlo for statistical mechanics:byways. In Modern theoretical chemistry; Berne B J, Ed.; Plenum:New York,1977; pp 169-194
[306]Straatsma T P, Berendsen H J C, Postma J P M. Free energy of hydrophobic hydration:a molecular dynamics study of noble gases in water. J Chem Phys,1986,85(11):6720-6727
[307]Lu N, Kofke D A, Woolf T B. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J Comput Chem,2004,25(1): 28-40
[308]Kofke D A, Cummings P T. Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation. Fluid Phase Equilib, 1998:41-49
[309]Hahn A M, Then H. Characteristic of Bennett's acceptance ratio method. Phys Rev Lett., 2009,80(3):031111
[310]Shirts M R, Bair E, Hooker G, et al. Equilibrium free energies from nonequilibrium measurements using Maximum-Likelihood methods. Phys Rev Lett,2003,91(14):140601
[311]Flyvbjerg H, Petersen H G Error estimates on averages of correlated data. J Chem Phys,1989, 91(1):461-466
[312]Lu N, Kofke D A. Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling. J Chem Phys,2001,114(17):7303-7311
[313]Lu N, Woolf T B. Understanding and improving free energy calculations in molecular simulations:error analysis and reduction methods. In Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:Berlin, 2007
[314]Lu N, Kofke D A. Accuracy of free-energy perturbation calculations in molecular simulation. II. Heuristics. J Chem Phys,2001,115(15):6866-6875
[315]Hunenberger P H, McCammon J A. Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction:a continuum electrostatics study. J Chem Phys,1999, 110(4):1856-1872
[316]Zuckerman D M, Woolf T B. Theory of a systematic computational error in free energy differences. Phys Rev Lett,2002,89(18):180602
[317]Zuckerman D M, Woolf T B. Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities. J Stat Phys,2004,114(5-6):1303-1323
[318]Wan S, Stote R H, Karplus M. Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes. J Chem Phys,2004,121(19):9539-9548
[319]Cramer H. Mathematical methods of statistics. Princeton University Press, Princeton, NJ, 1957
[320]Valleau J P, Card D N. Monte Carlo estimation of the free energy by multistage sampling. J Chem Phys,1972,57(12):5457-5462
[321]Wolfenden R, Andersson L, Cullis P M, et al. Affinities of amino acid side chains for solvent water. Biochemistry,1981,20(4):849-855
[322]Ben-Naim A, Marcus Y. Solvation thermodynamics of nonionic solutes. J Chem Phys,1984, 81(4):2016-2027
[323]Anisimov V M, Vorobyov I V, Roux B, et al. Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput, 2007,3(6):1927-1946
[324]Zhong Y, Patel S. Nonadditive empirical force fields for short-chain linear alcohols: methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models. J Phys Chem B,2010,114(34):11076-11092
[325]Chipot C. Rational determination of charge distributions for free energy calculations. J Comput Chem,2003,24(4):409-415
[326]Levy R M, Gallicchio E. Computer simulations with explicit solvent:recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annu Rev Phys Chem,1998,49(1):531-567
[327]Kubo M M, Gallicchio E, Levy R M. Thermodynamic decomposition of hydration free energies by computer simulation:□application to amines, oxides, and sulfides. J Phys Chem B,1997,101(49):10527-10534
[328]Shirts M R, Chodera J D. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys,2008,129(12):124105-124110
[329]Pohorille A, Darve E. A bayesian approach to calculating free energies in chemical and biological systems. Bayesian inference and maximum entropy methods in science and engineering. AIP Conference Proceedings. Melville, NY,2006. AIP:23-30
[330]Blinnikov S, Moessner R. Expansions for nearly Gaussian distributions. Astron Astrophys Suppl Ser,1998,130(1):193-205
[2]Luo Y, Collier C P, Jeppesen J O, et al. Two-dimensional molecular electronics circuits. ChemPhysChem,2002,3(6):519-525
[3]Green J E, Wook Choi J, Boukai A, et al. A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre. Nature,2007,445(7126):414-417
[4]N(?)rgaard K, Jeppesen J O, Laursen B W, et al. Evidence of strong hydration and significant tilt of amphiphilic [2]rotaxane molecules in langmuir films studied by synchrotron X-ray reflectivity. J Phys Chem B,2004,109(3):1063-1066
[5]Moulin J-F, Kengne J C, Kshirsagar R, et al. Self-organization of rotaxane thin films into spatially correlated nanostructures:□morphological and structural aspects. J Am Chem Soc, 2005,128(2):526-532
[6]Nygaard S, Leung K C F, Aprahamian I, et al. Functionally rigid bistable [2]rotaxanes. J Am Chem Soc,2007,129(4):960-970
[7]Panman M R, Bodis P, Shaw D J, et al. Operation mechanism of a molecular machine revealed using time-resolved vibrational spectroscopy. Science,2010,328(5983): 1255-1258
[8]Rijs A M, Kay E R, Leigh D A, et al. IR spectroscopy on jet-cooled isolated two-station rotaxanes. J Phys Chem A,2011,115(34):9669-9675
[9]Panman M R, Bodis P, Shaw D J, et al. Time-resolved vibrational spectroscopy of a molecular shuttle. Phys Chem Chem Phys,2012,14(6):1865-1875
[10]Raymo F M, Stoddart J F. Interlocked macromolecules. Chem Rev,1999,99(7):1643-1664
[11]Fahrenbach A C, Bruns C J, Cao D, et al. Ground-state thermodynamics of bistable redox-active donor-acceptor mechanically interlocked molecules. Acc Chem Res,2012, 45(9):1581-1592
[12]Harada A. Cyclodextrin-based molecular machines. Acc Chem Res,2001,34(6):456-464
[13]Wenz G, Han B-H, Muller A. Cyclodextrin rotaxanes and polyrotaxanes. Chem Rev,2006, 106(3):782-817
[14]Guo X Q, Song L X, Dang Z, et al. A comparative study on the formation and spectral properties of the polypseudorotaxanes of beta-cyclodextrin and poly(propylene glycol) under different conditions. Bull Chem Soc Jpn,2009,82(9):1209-1213
[15]Wang Y-H, Zhang H-M, Liu L, et al. Photoinduced electron transfer in a supramolecular species building of mono-6-p-nitrobenzoyl-β-cyclodextrin with naphthalene derivatives. J Org Chem,2002,67(8):2429-2434
[16]Harada A, Hashidzume A, Yamaguchi H, et al. Polymeric rotaxanes. Chem Rev,2009, 109(11):5974-6023
[17]Lee J W, Samal S, Selvapalam N, et al. Cucurbituril homologues and derivatives:□new opportunities in supramolecular chemistry. Acc Chem Res,2003,36(8):621-630
[18]Rowan A E, Elemans J A A W, Nolte R J M. Molecular and supramolecular objects from glycoluril. Acc Chem Res,1999,32(12):995-1006
[19]Belowich M E, Valente C, Smaldone R A, et al. Positive cooperativity in the template-directed synthesis of monodisperse macromolecules. J Am Chem Soc,2012, 134(11):5243-5261
[20]Zhang M, Xu D, Yan X, et al. Self-healing supramolecular gels formed by crown ether based host-guest interactions. Angew Chem Int Edit,2012,51(28):7011-7015
[21]Xue M, Yang Y, Chi X, et al. Pillararenes, a new class of macrocycles for supramolecular chemistry. Acc Chem Res,2012,45(8):1294-1308
[22]Hu X-B, Chen L, Si W, et al. Pillar[5]arene decaamine:synthesis, encapsulation of very long linear diacids and formation of ion pair-stopped [2]rotaxanes. Chem Commun,2011,47(16): 4694-4696
[23]Yu G, Han C, Zhang Z, et al. Pillar[6]arene-based photoresponsive host-guest complexation. J Am Chem Soc,2012,134(20):8711-8717
[24]Bodis P, Panman M R, Bakker B H, et al. Two-dimensional vibrational spectroscopy of rotaxane-based molecular machines. Acc Chem Res,2009,42(9):1462-1469
[25]Fuller A-M L, Leigh D A, Lusby P J. Sequence isomerism in [3]rotaxanes. J Am Chem Soc, 2010,132(13):4954-4959
[26]Wisner J A, Beer P D, Drew M G B, et al. Anion-templated rotaxane formation. J Am Chem Soc,2002,124(42):12469-12476
[27]Da Ros T, Guldi D M, Morales A F, et al. Hydrogen bond-assembled fullerene molecular shuttle. Org Lett,2003,5(5):689-691
[28]Movsisyan L D, Kondratuk D V, Franz M, et al. Synthesis of polyyne rotaxanes. Org Lett, 2012,14(13):3424-3426
[29]Goldup S M, Leigh D A, McGonigal P R, et al. Two axles threaded using a single template site:active metal template macrobicyclic [3]rotaxanes. J Am Chem Soc,2009,132(1): 315-320
[30]Crowley J D, Hanni K D, Lee A-L, et al. [2]Rotaxanes through palladium active-template dxidative heck cross-couplings. J Am Chem Soc,2007,129(40):12092-12093
[31]Crowley J D, Hanni K D, Leigh D A, et al. Diels-alder active-template synthesis of rotaxanes and metal-ion-switchable molecular shuttles. J Am Chem Soc,2010,132(14):5309-5314
[32]Pierro T, Gaeta C, Talotta C, et al. Fixed or invertible calixarene-based directional shuttles. Org Lett,2011,13(10):2650-2653
[33]Crowley J D, Leigh D A, Lusby P J, et al. A switchable palladium-complexed molecular shuttle and its metastable positional isomers. J Am Chem Soc,2007,129(48):15085-15090
[34]Li H, Fahrenbach A C, Coskun A, et al. A light-stimulated molecular switch driven by radical-radical interactions in water. Angew Chem Int Edit,2011,50(30):6782-6788
[35]Stoll R S, Friedman D C, Stoddart J F. Mechanically interlocked mechanophores by living-radical polymerization from rotaxane initiators. Org Lett,2011,13(10):2706-2709
[36]Chiu C-W, Lai C-C, Chiu S-H. "Threading-followed-by-swelling":□ a new protocol for rotaxane synthesis. J Am Chem Soc,2007,129(12):3500-3501
[37]Ooya T, Choi H S, Yamashita A, et al. Biocleavable polyrotaxane-plasmid DNA polyplex for enhanced gene delivery. J Am Chem Soc,2006,128(12):3852-3853
[38]Li J, Yang C, Li H, et al. Cationic supramolecules composed of multiple oligoethylenimine-grafted (3-cyclodextrins threaded on a polymer chain for efficient gene delivery. Adv Mater,2006,18(22):2969-2974
[39]Yang C, Wang X, Li H, et al. Cationic polyrotaxanes as gene carriers:physicochemical properties and real-time observation of DNA complexation, and gene transfection in cancer cells. J Phys Chem B,2009,113(22):7903-7911
[40]Balzani V, Gomez-Lopez M, Stoddart J F. Molecular machines. Acc Chem Res,1998,31(7): 405-414
[41]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2(10): 1353-1356
[42]Ye T, Kumar A S, Saha S, et al. Changing stations in single bistable rotaxane molecules under electrochemical control. ACS Nano,2010,4(7):3697-3701
[43]Balzani V, Clemente-Leon M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[44]Brouwer A M, Frochot C, Gatti F G, et al. Photoinduction of fast, reversible translational motion in a hydrogen-bonded molecular shuttle. Science,2001,291(5511):2124-2128
[45]Jacquot de Rouville H-P, Iehl J, Bruns C J, et al. A neutral naphthalene diimide [2]rotaxane. Org Lett,2012,14(20):5188-5191
[46]Zhang K-D, Zhao X, Wang G-T, et al. Foldamer-tuned switching kinetics and metastability of [2]rotaxanes. Angew Chem Int Edit,2011,50(42):9866-9870
[47]Ferrand Y, Gan Q, Kauffmann B, et al. Template-induced screw motions within an aromatic amide foldamer double helix. Angew Chem Int Edit,2011,50(33):7572-7575
[48]You Y-C, Tzeng M-C, Lai C-C, et al. Using oppositely charged ions to operate a three-station [2]rotaxane in two different switching modes. Org Lett,2012,14(4):1046-1049
[49]Barnes J C, Fahrenbach A C, Dyar S M, et al. Mechanically induced intramolecular electron transfer in a mixed-valence molecular shuttle. Proc. Natl. Acad. Sci. USA,2012,109(29): 11546-11551
[50]Li H, Zhu Z, Fahrenbach A C, et al. Mechanical bond-induced radical stabilization. J Am Chem Soc,2012,135(1):456-467
[51]Fahrenbach A C, Zhu Z, Cao D, et al. Radically enhanced molecular switches. J Am Chem Soc,2012,134(39):16275-16288
[52]Deng W-Q, Muller R P, Goddard W A. Mechanism of the Stoddart-Heath bistable rotaxane molecular switch. J Am Chem Soc,2004,126(42):13562-13563
[53]Dvornikovs V, House B E, Kaetzel M, et al. Host-[2]rotaxanes as cellular transport agents. J Am Chem Soc,2003,125(27):8290-8301
[54]Carlone A, Goldup S M, Lebrasseur N, et al. A three-compartment chemically-driven molecular information ratchet. J Am Chem Soc,2012,134(20):8321-8323
[55]Serreli V, Lee C-F, Kay E R, et al. A molecular information ratchet. Nature,2007,445(7127): 523-527
[56]Kay E R, Leigh D A, Zerbetto F. Synthetic molecular motors and mechanical machines. Angew Chem Int Edit,2007,46(1-2):72-191
[57]Zhao Y-L, Aprahamian I, Trabolsi A, et al. Organogel formation by a cholesterol-stoppered bistable [2]rotaxane and its dumbbell precursor. J Am Chem Soc,2008,130(20):6348-6350
[58]Pease A R, Jeppesen J O, Stoddart J F, et al. Switching devices based on interlocked molecules. Acc Chem Res,2001,34(6):433-444
[59]Berna J, Leigh D A, Lubomska M, et al. Macroscopic transport by synthetic molecular machines. Nat Mater,2005,4(9):704-710
[60]Wan P, Jiang Y, Wang Y, et al. Tuning surface wettability through photocontrolled reversible molecular shuttle. Chem Commun,2008,0(44):5710-5712
[61]Baumes J M, Murgu I, Oliver A, et al. Using the rotaxane mechanical bond to enhance chemical reactivity. Org Lett,2010,12(21):4980-4983
[62]Thordarson P, Bijsterveld E J A, Rowan A E, et al. Epoxidation of polybutadiene by a topologically linked catalyst. Nature,2003,424(6951):915-918
[63]Zhang H, Hu J, Qu D-H. Dual-mode control of PET process in a ferrocene-functionalized [2]rotaxane with high-contrast fluorescence output. Org Lett,2012,14(9):2334-2337
[64]Alvarez-Perez M, Goldup S M, Leigh D A, et al. A chemically-driven molecular information ratchet. J Am Chem Soc,2008,130(6):1836-1838
[65]Danquah M K, Zhang X A, Mahato R I. Extravasation of polymeric nanomedicines across tumor vasculature. Adv Drug Deliv Rev,2011,63(8):623-639
[66]Chen T. Overcoming drug resistance by regulating nuclear receptors. Adv Drug Deliv Rev, 2010,62(13):1257-1264
[67]Torchilin V P. Tat peptide-mediated intracellular delivery of pharmaceutical nanocarriers. Adv Drug Deliv Rev,2008,60(4-5):548-558
[68]Guo D-S, Wang K, Wang Y-X, et al. Cholinesterase-responsive supramolecular vesicle. J Am Chem Soc,2012,134(24):10244-10250
[69]Torney F, Trewyn B G, Lin V S Y, et al. Mesoporous silica nanoparticles deliver DNA and chemicals into plants. Nat Nano,2007,2(5):295-300
[70]Trewyn B G, Slowing I I, Giri S, et al. Synthesis and functionalization of a mesoporous silica nanoparticle based on the sol-gel process and applications in controlled release. Acc Chem Res,2007,40(9):846-853
[71]Angelos S, Johansson E, Stoddart J F, et al. Mesostructured silica supports for functional materials and molecular machines. Adv Funct Mater,2007,17(14):2261-2271
[72]Yang Y-W. Towards biocompatible nanovalves based on mesoporous silica nanoparticles. MedChemComm,2011,2(11):1033-1049
[73]Hernandez R, Tseng H-R, Wong J W, et al. An operational supramolecular nanovalve. J Am Chem Soc,2004,126(11):3370-3371
[74]Zhu Z, Fahrenbach A C, Li H, et al. Controlling switching in bistable [2]catenanes by combining donor-acceptor and radical-radical Interactions. J Am Chem Soc,2012,134(28): 11709-11720
[75]Ferris D P, Zhao Y-L, Khashab N M, et al. Light-operated mechanized nanoparticles. J Am Chem Soc,2009,131(5):1686-1688
[76]Sun Y-L, Yang B-J, Zhang S X-A, et al. Cucurbit[7]uril pseudorotaxane-based photoresponsive supramolecular nanovalve. Chem Eur J,2012,18(30):9212-9216
[77]Marquez C, Nau W M. Two mechanisms of slow host-guest complexation between cucurbit[6]uril and cyclohexylmethylamine:pH-responsive supramolecular kinetics. Angew Chem Int Edit,2001,40(17):3155-3160
[78]Marquez C, Hudgins R R, Nau W M. Mechanism of host-guest complexation by cucurbituril. J Am Chem Soc,2004,126(18):5806-5816
[79]Ling X, Samuel E L, Patchell D L, et al. Cucurbituril slippage:translation is a complex motion. Org Lett,2010,12(12):2730-2733
[80]Angelos S, Khashab N M, Yang Y-W, et al. pH clock-operated mechanized nanoparticles. J Am Chem Soc,2009,131(36):12912-12914
[81]Nguyen T D, Leung K C F, Liong M, et al. Construction of a pH-driven supramolecular nanovalve. Org Lett,2006,8(15):3363-3366
[82]Patel K, Angelos S, Dichtel W R, et al. Enzyme-responsive snap-top covered silica nanocontainers. J Am Chem Soc,2008,130(8):2382-2383
[83]Meng H, Xue M, Xia T, et al. Autonomous in vitro anticancer drug release from mesoporous silica nanoparticles by pH-sensitive nanovalves. J Am Chem Soc,2010,132(36): 12690-12697
[84]Zhao Y-L, Li Z, Kabehie S, et al. pH-operated nanopistons on the surfaces of mesoporous silica nanoparticles. J Am Chem Soc,2010,132(37):13016-13025
[85]Vassal G, Koscielny S, Challine D, et al. Busulfan disposition and hepatic veno-occlusive disease in children undergoing bone marrow transplantation. Cancer Chemoth Pharm,1995, 37(3):247-253
[86]Menuel S, Joly J-P, Courcot B, et al. Synthesis and inclusion ability of a bis-β-cyclodextrin pseudo-cryptand towards Busulfan anticancer agent. Tetrahedron,2007,63(7):1706-1714
[87]Porwanski S, Dumarcay-Charbonnier F, Menuel S, et al. Bis-β-cyclodextrinyl- and bis-cellobiosyl-diazacrowns:synthesis and molecular complexation behaviors toward Busulfan anticancer agent and two basic aminoacids. Tetrahedron,2009,65(31):6196-6203
[88]Zehnder D W, Smithrud D B. Facile synthesis of rotaxanes through condensation reactions of DCC-[2]rotaxanes. Org Lett,2001,3(16):2485-2487
[89]Smukste I, House B E, Smithrud D B. Host-[2]rotaxane:□ advantage of converging functional groups for guest recognition. J Org Chem,2003,68(7):2559-2571
[90]Bao X, Isaacsohn I, Drew A F, et al. Determining the intracellular transport mechanism of a cleft-[2]rotaxane. J Am Chem Soc,2006,128(37):12229-12238
[91]Wang X, Smithrud D B. Pt-rotaxanes as cytotoxic agents. Bioorg Med Chem Lett,2011, 21(22):6880-6883
[92]Zhu J, McFarland-Mancini M, Drew A F, et al. Host-rotaxanes with oligomeric axles are intracellular transport agents. Bioorg Med Chem Lett,2009,19(2):520-523
[93]Bao X, Isaacsohn I, Drew A F, et al. Determining the binding and intracellular transporting abilities of a host-[3]rotaxane. J Org Chem,2007,72(11):3988-4000
[94]Rouget J-B, Aksel T, Roche J, et al. Size and sequence and the volume change of protein folding. J Am Chem Soc,2011,133(15):6020-6027
[95]Ghosh K, Dill K A. Theory for protein folding cooperativity:helix bundles. J Am Chem Soc, 2009,131(6):2306-2312
[96]Metropolis N, Rosenbluth A W, Rosenbluth M N, et al. Equation of state calculations by fast computing machines. J Chem Phys,1953,21(6):1087-1092
[97]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[98]Yang L, Tan C-h, Hsieh M-J, et al. New-generation amber united-atom force field. J Phys Chem B,2006,110(26):13166-13176
[99]Oostenbrink C, Soares T, Vegt N A, et al. Validation of the 53A6 GROMOS force field. Eur Biophys J,2005,34(4):273-284
[100]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys,1992,97(3):1990-2001
[101]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[102]Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:New York,2007.
[103]Kollman P. Free energy calculations:applications to chemical and biochemical phenomena. Chem Rev,1993,93(7):2395-2417
[104]Simonson T, Archontis G, Karplus M. Free energy simulations come of age:□ protein-ligand recognition. Acc Chem Res,2002,35(6):430-437
[105]Landau L D. Statistical physics. The Clarendon Press, Oxford, U. K.,1938
[106]Zwanzig R W. High-temperature equation of state by a perturbation method. Ⅰ. Nonpolar gases. J Chem Phys,1954,22(8):1420-1426
[107]Kirkwood J G Statistical mechanics of fluid mixtures. J Chem Phys,1935,3(5):300-313
[108]H6nin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[109]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906
[110]Darve E, Rodriguez-G6mez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[111]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[112]Bennett C H. Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys,1976,22(2):245-268
[113]Ferrenberg A M, Swendsen R H. New Monte Carlo technique for studying phase transitions. Phys Rev Lett,1988,61(23):2635-2638
[114]Jarzynski C. Equilibrium free-energy differences from nonequilibrium measurements:a master-equation approach. Phys Rev Lett.,1997,56(5):5018-5035
[115]Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett,1997, 78(14):2690-2693
[116]Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B,2010,114(32):10235-10253
[117]Valleau J P, Torrie G M A. Guide to Monte Carlo for statistical mechanics:byways. In Modern theoretical chemistry; Berne B J, Ed.; Plenum:New York,1977; pp 169-194.
[118]McDonald I R, Singer K. Machine calculation of thermodynamic properties of a simple fluid at supercritical temperatures. J Chem Phys,1967,47(11):4766-4772
[119]Straatsma T P, Berendsen H J C, Postma J P M. Free energy of hydrophobic hydration:a molecular dynamics study of noble gases in water. J Chem Phys,1986,85(11):6720-6727
[120]McDonald I R, Singer K. Calculation of thermodynamic properties of liquid argon from Lennard-Jones parameters by a Monte Carlo method. Discuss Faraday Soc,1967,43:40-49
[121]Lu N, Kofke D A, Woolf T B. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J Comput Chem,2004,25(1): 28-40
[122]Lelievre T, Stoltz G, Rousset M. Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[123]Gumbart J C, Roux B, Chipot C. Standard binding free energies from computer simulations: what is the best strategy? J Chem Theory Comput,2012,9(1):794-802
[124]Chipot C. Milestones in the activation of a G protein-coupled receptor. Insights from molecular-dynamics simulations into the human cholecystokinin receptor-1. J Chem Theory Comput,2008,4(12):2150-2159
[125]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[126]Pan A C, Sezer D, Roux B. Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[127]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[128]Jang S S, Jang Y H, Kim Y-H, et al. Molecular dynamics simulation of amphiphilic bistable [2]rotaxane langmuir monolayers at the air/water interface. J Am Chem Soc,2005,127(42): 14804-14816
[129]Jang Y H, Jang S S, Goddard W A. Molecular dynamics simulation study on a monolayer of half [2]Rotaxane self-assembled on Au(111). J Am Chem Soc,2005,127(13):4959-4964
[130]Jang S S, Jang Y H, Kim Y-H, et al. Structures and properties of self-assembled monolayers of bistable [2]rotaxanes on Au (111) surfaces from molecular dynamics simulations validated with experiment. J Am Chem Soc,2005,127(5):1563-1575
[131]Carter E A, Ciccotti G, Hynes J T, et al. Constrained reaction coordinate dynamics for the simulation of rare events. Chem Phys Lett,1989,156(5):472-477
[132]Sprik M, Ciccotti G. Free energy from constrained molecular dynamics. J Chem Phys,1998, 109(18):7737-7744
[133]Kim H, Goddard W A, Jang S S, et al. Free energy barrier for molecular motions in bistable [2]rotaxane molecular electronic devices. J Phys Chem A,2009,113(10):2136-2143
[134]Raiteri P, Bussi G, Cucinotta C S, et al. Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. Angew Chem Int Edit,2008,47(19): 3536-3539
[135]Torrie G M, Valleau J P. Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid. Chem Phys Lett,1974,28(4):578-581
[136]Still W C, Tempczyk A, Hawley R C, et al. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc,1990,112(16):6127-6129
[137]Zhao Y-L, Dichtel W R, Trabolsi A, et al. A redox-switchable α-cyclodextrin-based [2]rotaxane. J Am Chem Soc,2008,130(34):11294-11296
[138]Zhang Q, Tu Y, Tian H, et al. Working mechanism for a redox switchable molecular machine based on cyclodextrin:a free energy profile approach. J Phys Chem B,2010,114(19): 6561-6566
[1]Galatsis K, Kang W, Botros Y, et al. Emerging memory devices:nontraditional possibilities based on nanomaterials and nanostructures. IEEE Circuits Device Maga,2006,22(3):12-21
[2]Collier C P, Wong E W, Belohradsky M, et al. Electronically configurable molecular-based logic gates. Science,1999,285(5426):391-394
[3]Balzani V, Gomez-Lopez M, Stoddart J F. Molecular machines. Ace Chem Res,1998,31 (7): 405-414
[4]Pease A R, Jeppesen J O, Stoddart J F, et al. Switching devices based on interlocked molecules. Acc Chem Res,2001,34(6):433-444
[5]Harada A, Kamachi M. Complex formation between poly(ethylene glycol) and a-cyclodextrin. Macromolecules,1990,23(10):2821-2823
[6]Harada A, Li J, Kamachi M. The molecular necklace:a rotaxane containing many threaded a-cyclodextrins. Nature,1992,356(6367):325-327
[7]Wu Y-L, Li J. Synthesis of supramolecular nanocapsules based on threading of multiple cyclodextrins over polymers on gold nanoparticles. Angew Chem Int Ed,2009,48(21): 3842-3845
[8]Ooya T, Choi H S, Yamashita A, et al. Biocleavable polyrotaxane-plasmid DNA polyplex for enhanced gene delivery. J Am Chem Soc,2006,128(12):3852-3853
[9]Harada A, Li J, Kamachi M. Preparation and characterization of a polyrotaxane consisting of monodisperse poly(ethylene glycol) and a-cyclodextrins. J Am Chem Soc,1994,116(8): 3192-3196
[10]Miyake K, Yasuda S, Harada A, et al. Formation process of cyclodextrin necklace-analysis of hydrogen bonding on a molecular level. J Am Chem Soc,2003,125(17):5080-5085
[11]Shigekawa H, Miyake K, Sumaoka J, et al. The molecular abacus:STM manipulation of cyclodextrin necklace. J Am Chem Soc,2000,122(22):5411-5412
[12]Bonnet P, Jaime C, Morin-Allory L. α-,β-, and y-Cyclodextrin dimers. Molecular modeling studies by molecular mechanics and molecular dynamics simulations. J Org Chem,2001, 66(3):689-692
[13]Bonnet P, Jaime C, Morin-Allory L. Structure and thermodynamics of α-, β-, and y-cyclodextrin dimers. molecular dynamics studies of the solvent effect and free binding energies. J Org Chem,2002,67(24):8602-8609
[14]Nascimento C S, Anconi C P A, Dos Santos H F, et al. Theoretical study of the a-cyclodextrin dimer. J Phys Chem A,2005,109(14):3209-3219
[15]Yu Y, Cai W, Chipot C, et al. Spatial arrangement of a-cyclodextrins in a rotaxane. Insights from free-energy calculations. J Phys Chem B,2008,112(17):5268-5271
[16]Tallury S S, Smyth M B, Cakmak E, et al. Molecular dynamics simulations of interactions between polyanilines in their inclusion complexes with β-cyclodextrins. J Phys Chem B, 2012,116(7):2023-2030
[17]Chipot C, Pohorille A. Calculating free energy differences using perturbation theory. In Free energy calculations; Chipot C, Pohorille A, Eds.; Springer Berlin Heidelberg,2007; Vol.86; pp 33-75.
[18]Lelievre T, Rousset M, Stoltz G. Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[19]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906-6
[20]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[21]Henin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[22]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[23]Brush S G. History of the Lenz-Ising model. Rev Mod Phys,1967,39(4):883-893
[24]Ising E. Beitrag zur theorie des ferromagnetismus. Z Phys A:Hadrons Nucl,1925,31(1): 253-258
[25]Hingerty B, Saenger W. Topography of cyclodextrin inclusion complexes.8. Crystal and molecular structure of the.alpha.-cyclodextrin-methanol-pentahydrate complex. Disorder in ahydrophobic cage. J Am Chem Soc,1976,98(11):3357-3365
[26]Insight II User Guide. Accelrys Software Inc., San Diego, CA,2005
[27]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[28]Hatcher E R, Guvench O, MacKerell A D. CHARMM additive all-atom force field for acyclic polyalcohols, acyclic carbohydrates, and inositol. J Chem Theory Comput,2009,5(5): 1315-1327
[29]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[30]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[31]Jorgensen W L, Chandrasekhar J, Madura J D, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys,1983,79(2):926-935
[32]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[33]Miyamoto S, Kollman P A. Settle:an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem,1992,13(8):952-962
[34]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[35]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys,1992,97(3):1990-2001
[36]Darden T, York D, Pedersen L. Particle mesh Ewald:an N log(N) method for Ewald sums in large systems. J Chem Phys,1993,98(12):10089-10092
[37]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[38]Henin J, Fiorin G, Chipot C, et al. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput,2010,6(1):35-47
[39]Jonkheijm P, van der Schoot P, Schenning A P H J, et al. Probing the solvent-assisted nucleation pathway in chemical self-assembly. Science,2006,313(5783):80-83
[40]Tanaka S, Scheraga H A. Model of protein folding:incorporation of a one-dimensional short-range (Ising) model into a three-dimensional model. Proc Natl Acad Sci USA,1977, 74(4):1320-1323
[41]Metropolis N, Rosenbluth A W, Rosenbluth M N, et al. Equation of state calculations by fast computing machines. J Chem Phys,1953,21(6):1087-1092
[42]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[43]Bolhuis P G, Dellago C, Chandler D. Reaction coordinates of biomolecular isomerization. Proc Natl Acad Sci USA,2000,97(11):5877-5882
[44]Pan A C, Sezer D, Roux B. Finding transition pathway:using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[45]Liu P, Chipot C, Shao X, et al. Solvent-controlled shuttling in a molecular switch. J Phys Chem C,2012,116(7):4471-4476
[46]Shrake A, Rupley J A. Environment and exposure to solvent of protein atoms. Lysozyrne and insulin. J Mol Biol,1973,79(2):351-371
[1]Green J E, Wook Choi J, Boukai A, et al. A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre. Nature,2007,445(7126):414-417
[2]Harada A. Cyclodextrin-based molecular machines. Acc Chem Res,2001,34(6):456-464
[3]Raymo F M, Stoddart J F. Interlocked macromolecules. Chem Rev,1999,99(7):1643-1664
[4]Zhao Y-L, Dichtel W R, Trabolsi A, et al. A redox-switchable a-cyclodextrin-based [2]rotaxane. J Am Chem Soc,2008,130(34):11294-11296
[5]Bissell R A, Cordova E, Kaifer A E, et al. A chemically and electrochemically switchable molecular shuttle. Nature,1994,369:133-137
[6]Berna J, Goldup S M, Lee A-L, et al. Cadiot-chodkiewicz active template synthesis of rotaxanes and switchable molecular shuttles with weak intercomponent interactions. Angew Chem Int Ed,2008,47(23):4392-4396
[7]Coutrot F, Romuald C, Busseron E. A new pH-switchable dimannosyl[c2]daisy chain molecular machine. Org Lett,2008,10(17):3741-3744
[8]Coskun A, Friedman D C, Li H, et al. A light-gated STOP-GO molecular shuttle. J Am Chem Soc,2009,131(7):2493-2495
[9]Balzani V, Clemente-Le6n M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[10]Murakami H, Kawabuchi A, Matsumoto R, et al. A multi-mode-driven molecular shuttle:□photochemically and thermally reactive azobenzene rotaxanes. J Am Chem Soc, 2005,127(45):15891-15899
[11]Marlin D S, Gonzalez Cabrera D, Leigh D A, et al. Complexation-induced translational isomerism:shuttling through stepwise competitive binding. Angew Chem Int Ed,2006,45(1): 77-83
[12]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2(10): 1353-1356
[13]Brough B, Northrop B H, Schmidt J J, et al. Evaluation of synthetic linear motor-molecule actuation energetics. Proc Natl Acad Sci USA,2006,103(23):8583-8588
[14]Belohradsky M, Elizarov A M, Stoddart J F. Speed-controlled molecular shuttles. Collect Czech Chem Commun,2002,67(11):1719-1728
[15]Kim H, Goddard W A, Jang S S, et al. Free energy barrier for molecular motions in bistable [2]rotaxane molecular electronic devices. J Phys Chem A,2009,113(10):2136-2143
[16]Raiteri P, Bussi G, Cucinotta C S, et al. Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. Angew Chem Int Ed,2008,47(19): 3536-3539
[17]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[18]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[19]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[20]Henin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[21]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906-6
[22]Yu Y, Chipot C, Cai W, et al. Molecular dynamics study of the inclusion of cholesterol into cyclodextrins. J Phys Chem B,2006,110(12):6372-6378
[23]Yu Y, Cai W, Chipot C, et al. Spatial arrangement of a-cyclodextrins in a rotaxane. Insights from free-energy calculations. J Phys Chem B,2008,112(17):5268-5271
[24]Eyring H. The activated complex in chemical reactions. J Chem Phys,1935,3(2):107-115
[25]Insight Ⅱ User Guide. Accelrys Software Inc., San Diego, CA,2005
[26]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[27]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[28]Liu X, Zhang S, Zhou G, et al. New force field for molecular simulation of guanidinium-based ionic liquids. J Phys Chem B,2006,110(24):12062-12071
[29]Strader M L, Feller S E. A flexible all-atom model of dimethyl sulfoxide for molecular dynamics simulations. J Phys Chem A,2002,106(6):1074-1080
[30]Pavelites J J, Gao J, Bash P A, et al. A molecular mechanics force field for NAD+, NADH, and the pyrophosphate groups of nucleotides. J Comput Chem,1997,18(2):221-239
[31]Foloppe N, MacKerell J A D. All-atom empirical force field for nucleic acids:Ⅰ. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem,2000,21(2):86-104
[32]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[33]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[34]Darden T, York D, Pedersen L. Particle mesh Ewald:an N log(N) method for Ewald sums in large systems. J Chem Phys,1993,98(12):10089-10092
[35]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[36]Ryckaert J-P, Ciccotti G, Berendsen H J C. Numerical integration of the cartesian equations of motion of a system with constraints:molecular dynamics of n-alkanes. J Comput Phys,1977, 23(3):327-341
[37]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[38]Flyvbjerg H, Petersen H G. Error estimates on averages of correlated data. J Chem Phys,1989, 91(1):461-466
[39]Frisch M J, Trucks G W, Schlegel H B, et al. Gaussian 03, ReVision C.03. Gaussian, Inc., Wallingford,CT,2004
[40]Vaiana A C, Coumia Z, Costescu I B, et al. AFMM:a molecular mechanics force field vibrational parametrization program. Comput Phys Commun,2005,167(1):34-42
[41]Kim H-W, Zeroka D. Trans-ethylphosphine and selected deuterated isotopomers:prediction of infrared spectra and potential energy distribution determination. THEOCHEM,2005,715: 21-31
[42]Kim H-W, Chechla A A, Kim B. Potential energy distribution study of infrared frequencies of methylamine and methylphosphine. THEOCHEM,2007,802:105-110
[43]Pulay P, Fogarasi G, Pang F, et al. Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives. J Am Chem Soc,1979,101(10): 2550-2560
[44]Bergeron R J, Channing M A, Gibeily G J, et al. Disposition requirements for binding in aqueous solution of polar substrates in the cyclohexaamylose cavity. J Am Chem Soc,1977, 99(15):5146-5151
[45]Li J, Harada A, Kamachi M. Formation of inclusion complexes of oligoethylene and its derivatives with a-cyclodextrin. Bull Chem Soc Jpn,1994,67:2808-2818
[1]Balzani V, Clemente-Le6n M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[2]Bissell R A, C6rdova E, Kaifer A E, et al. A chemically and electrochemically switchable molecular shuttle. Nature,1994,369(6476):133-137
[3]Hernandez R, Tseng H-R, Wong J W, et al. An operational supramolecular nanovalve. J Am Chem Soc,2004,126(11):3370-3371
[4]Dvornikovs V, House B E, Kaetzel M, et al. Host-[2]rotaxanes as cellular transport agents. J Am Chem Soc,2003,125(27):8290-8301
[5]Leung K C-F, Chak C-P, Lo C-M, et al. pH-controllable supramolecular systems. Chem Asian J,2009,4(3):364-381
[6]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2:1353-1356
[7]Umehara T, Kawai H, Fujiwara K, et al. Entropy- and hydrolytic-driven positional switching of macrocycle between imine- and hydrogen-bonding stations in rotaxane-based molecular shuttles. J Am Chem Soc,2008,130(42):13981-13988
[8]Vassal G, Koscielny S, Challine D, et al. Busulfan disposition and hepatic veno-occlusive disease in children undergoing bone marrow transplantation. Cancer Chemoth Pharm,1995, 37(3):247-253
[9]Zehnder D W, Smithrud D B. Facile synthesis of rotaxanes through condensation reactions of DCC-[2]rotaxanes. Org Lett,2001,3(16):2485-2487
[10]Smukste I, House B E, Smithrud D B. Host-[2]rotaxane:□ advantage of converging functional groups for guest recognition. J Org Chem,2003,68(7):2559-2571
[11]Bao X, Isaacsohn I, Drew A F, et al. Determining the intracellular transport mechanism of a cleft-[2]rotaxane. J Am Chem Soc,2006,128(37):12229-12238
[12]Liu P, Cai W, Chipot C, et al. Thermodynamic insights into the dynamic switching of a cyclodextrin in a bistable molecular shuttle. J Phys Chem Lett,2010,1(12):1776-1780
[13]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[14]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[15]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[16]Jorgensen W L, Chandrasekhar J, Madura J D, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys,1983,79(2):926-935
[17]Strader M L, Feller S E. A flexible all-atom model of dimethyl sulfoxide for molecular dynamics simulations. J Phys Chem A,2002,106(6):1074-1080
[18]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[19]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys,1992,97(3):1990-2001
[20]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[21]Miyamoto S, Kollman P A. Settle:an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem,1992,13(8):952-962
[22]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[23]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[24]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[25]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[26]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906-6
[27]Henin J, Fiorin G, Chipot C, et al. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput,2010,6(1):35-47
[28]Flyvbjerg H, Petersen H G. Error-estimates on averages of correlated data. J Chem Phys, 1989,91(1):461-466
[29]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[30]Pan A C, Sezer D, Roux B. Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[1]Kollman P. Free energy calculations:applications to chemical and biochemical phenomena. Chem Rev,1993,93(7):2395-2417
[2]Simonson T, Archontis G, Karplus M. Free energy simulations come of age:protein-ligand recognition. Acc Chem Res,2002,35(6):430-437
[3]Chipot C, Pearlman D A. Free energy calculations. The long and winding gilded road. Mol Simulat,2002,28(1-2):1-12
[4]Simonson T. Free energy calculations. In Computational biochemistry and biophysics; Becker O M, MacKerell A D J, Roux B, Watanabe M, Eds.; Marcel Dekker Inc.:New York, 2001; pp 169-197
[5]Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:New York,2007
[6]Born M. Volumen und hydratationswarme der ionen. Z Physik,1920,1(1):45-48
[7]Landau L D. Statistical physics. The Clarendon Press, Oxford, U. K.,1938
[8]Zwanzig R W. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys,1954,22(8):1420-1426
[9]Kirkwood J G Statistical mechanics of fluid mixtures. J Chem Phys,1935,3(5):300-313
[10]Bennett C H. Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys,1976,22(2):245-268
[11]Ferrenberg A M, Swendsen R H. New Monte Carlo technique for studying phase transitions. Phys Rev Lett,1988,61(23):2635-2638
[12]Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett,1997, 78(14):2690-2693
[13]Jarzynski C. Equilibrium free-energy differences from nonequilibrium measurements:a master-equation approach. Phys Rev Lett,1997,56(5):5018-5035
[14]Jorgensen W L, Ravimohan C. Monte Carlo simulation of differences in free energies of hydration. J Chem Phys,1985,83(6):3050-3054
[15]Bash P A, Singh U C, Langridge R, et al. Free energy calculations by computer simulation. Science,1987,236(4801):564-568
[16]van Gunsteren W, Beutler T, Fraternali F, et al. Computation of free energy in practice:choice of approximations and accuracy limiting factors. In Computer simulation of biomolecular systems; van Gunsteren W, Weiner P, Wilkinson A, Eds.; Escom Science Publishers:Leiden, The Netherlands,1993; pp 315-348
[17]Chipot C, Millot C, Maigret B, et al. Molecular dynamics free energy perturbation calculations:influence of nonbonded parameters on the free energy of hydration of charged and neutral species. J Phys Chem,1994,98(44):11362-11372
[18]Ding Y, Bernardo D N, Krogh-Jespersen K, et al. Solvation free energies of small amides and amines from molecular dynamics/free energy perturbation simulations using pairwise additive and many-body polarizable potentials. J Phys Chem,1995,99(29):11575-11583
[19]Morgantini P-Y, Kollman P A. Solvation free energies of amides and amines:disagreement between free energy calculations and experiment. J Am Chem Soc,1995,117(22): 6057-6063
[20]Rick S W, Berne B J. Free energy of the hydrophobic interaction from molecular dynamics simulations:□the effects of solute and solvent polarizability. J Phys Chem B,1997,101(49): 10488-10493
[21]Ponder J W, Wu C, Ren P, et al. Current status of the AMOEBA polarizable force field. J Phys Chem B,2010,114(8):2549-2564
[22]Oostenbrink C, Villa A, Mark A E, et al. A biomolecular force field based on the free enthalpy of hydration and solvation:the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem,2004,25(13):1656-1676
[23]Shirts M R, Pitera J W, Swope W C, et al. Extremely precise free energy calculations of amino acid side chain analogs:comparison of common molecular mechanics force fields for proteins. J Chem Phys,2003,119(11):5740-5761
[24]Jorgensen W L, Buckner J K, Boudon S, et al. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water. J Chem Phys, 1988,89(6):3742-3746
[25]van Gunsteren W F. Methods for calculation of free energies and binding constants:successes and problems. In Computer simulation of biomolecular systems:theoretical and experimental applications; Van Gunsteren W F, Weiner P K, Eds.; Escom Science Publishers:Leiden, The Netherlands,1989; pp 27-59
[26]Miyamoto S, Kollman P A. What determines the strength of noncovalent association of ligands to proteins in aqueous solution? Proc Natl Acad Sci USA,1993,90(18):8402-8406
[27]Aqvist J. Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. J Comput Chem,1996,17(14):1587-1597
[28]Aqvist J, Luzhkov V B, Brandsdal B O. Ligand binding affinities from MD simulations. Acc Chem Res,2002,35(6):358-365
[29]Archontis G, Simonson T, Karplus M. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. J Mol Biol,2001,306(2):307-327
[30]Boresch S, Tettinger F, Leitgeb M, et al. Absolute binding free energies:□a quantitative approach for their calculation. J Phys Chem B,2003,107(35):9535-9551
[31]Oostenbrink C, van Gunsteren W F. Free energies of ligand binding for structurally diverse compounds. Proc Natl Acad Sci USA,2005,102(19):6750-6754
[32]Woo H-J, Roux B. Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci USA,2005,102(19):6825-6830
[33]Wang J, Deng Y, Roux B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J,2006,91(8):2798-2814
[34]Mobley D L, Graves A P, Chodera J D, et al. Predicting absolute ligand binding free energies to a simple nodel site. J Mol Biol,2007,371(4):1118-1134
[35]Deng Y, Roux B. Computations of standard binding free energies with molecular dynamics simulations. J Phys Chem B,2009,113(8):2234-2246
[36]Jiang W, Roux B. Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations. J Chem Theory Comput,2010,6(9):2559-2565
[37]Pearlman D A, Charifson P S. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system. J Med Chem,2001, 44(21):3417-3423
[38]Chipot C, Rozanska X, Dixit S. Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein. J Comput Aided Mol Des,2005,19(11):765-770
[39]Chodera J D, Mobley D L, Shirts M R, et al. Alchemical free energy methods for drug discovery:progress and challenges. Curr Opin Struct Biol,2011,21(2):150-160
[40]Lelievre T, Stoltz G, Rousset M. Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[41]Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B.2010,114(32):10235-10253
[42]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[43]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[44]McDonald I R, Singer K. Machine calculation of thermodynamic properties of a simple fluid at supercritical temperatures. J Chem Phys,1967,47(11):4766-4772
[45]McDonald I R, Singer K. Calculation of thermodynamic properties of liquid argon from Lennard-Jones parameters by a Monte Carlo method. Discuss Faraday Soc,1967,43:40-49
[46]Valleau J P, Torrie G M A. Guide to Monte Carlo for statistical mechanics:byways. In Modern theoretical chemistry; Berne B J, Ed.; Plenum:New York,1977; pp 169-194
[47]Straatsma T P, Berendsen H J C, Postma J P M. Free energy of hydrophobic hydration:a molecular dynamics study of noble gases in water. J Chem Phys,1986,85(11):6720-6727
[48]Lu N, Kofke D A, Woolf T B. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J Comput Chem,2004,25(1): 28-40
[49]Kofke D A, Cummings P T. Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation. Fluid Phase Equilib, 1998:41-49
[50]Hahn A M, Then H. Characteristic of Bennett's acceptance ratio method. Phys Rev Lett., 2009,80(3):031111
[51]Shirts M R, Bair E, Hooker G, et al. Equilibrium free energies from nonequilibrium measurements using Maximum-Likelihood methods. Phys Rev Lett,2003,91(14):140601
[52]Flyvbjerg H, Petersen H G Error estimates on averages of correlated data. J Chem Phys,1989, 91(1):461-466
[53]Lu N, Kofke D A. Accuracy of free-energy perturbation calculations in molecular simulation. Ⅰ. Modeling. J Chem Phys,2001,114(17):7303-7311
[54]Lu N, Woolf T B. Understanding and improving free energy calculations in molecular simulations:error analysis and reduction methods. In Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:Berlin, 2007
[55]Lu N, Kofke D A. Accuracy of free-energy perturbation calculations in molecular simulation. Ⅱ. Heuristics. J Chem Phys,2001,115(15):6866-6875
[56]Hunenberger P H, McCammon J A. Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction:a continuum electrostatics study. J Chem Phys,1999, 110(4):1856-1872
[57]Zuckerman D M, Woolf T B. Theory of a systematic computational error in free energy differences. Phys Rev Lett,2002,89(18):180602
[58]Zuckerman D M, Woolf T B. Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities. J Stat Phys,2004,114(5-6):1303-1323
[59]Wan S, Stote R H, Karplus M. Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes. J Chem Phys,2004,121(19):9539-9548
[60]Cramer H. Mathematical methods of statistics. Princeton University Press, Princeton, NJ, 1957
[61]Valleau J P, Card D N. Monte Carlo estimation of the free energy by multistage sampling. J Chem Phys,1972,57(12):5457-5462
[62]Wolfenden R, Andersson L, Cullis P M, et al. Affinities of amino acid side chains for solvent water. Biochemistry,1981,20(4):849-85
[63]Ben-Naim A, Marcus Y. Solvation thermodynamics of nonionic solutes. J Chem Phys,1984, 81(4):2016-2027
[64]Anisimov V M, Vorobyov I V, Roux B, et al. Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput, 2007,3(6):1927-1946
[65]Zhong Y, Patel S. Nonadditive empirical force fields for short-chain linear alcohols; methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models. J Phys Chem B,2010,114(34):11076-11092
[66]Chipot C. Rational determination of charge distributions for free energy calculations. J Comput Chem,2003,24(4):409-415
[67]Levy R M, Gallicchio E. Computer simulations with explicit solvent:recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annu Rev Phys Chem,1998,49(1):531-567
[68]Kubo M M, Gallicchio E, Levy R M. Thermodynamic decomposition of hydration free energies by computer simulation:□ application to amines, oxides, and sulfides. J Phys Chem B,1997,101(49):10527-10534
[69]Shirts M R, Chodera J D. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys,2008,129(12):124105-124110
[70]Pohorille A, Darve E. A bayesian approach to calculating free energies in chemical and biological systems. Bayesian inference and maximum entropy methods in science and engineering. AIP Conference Proceedings. Melville, NY,2006. AIP:23-30
[71]Blinnikov S, Moessner R. Expansions for nearly Gaussian distributions. Astron Astrophys Suppl Ser,1998,130(1):193-205
[1]Collier C P, Wong E W, Belohradsky M, et al. Electronically configurable molecular-based logic gates. Science,1999,285(5426):391-394
[2]Luo Y, Collier C P, Jeppesen J O, et al. Two-dimensional molecular electronics circuits. ChemPhysChem,2002,3(6):519-525
[3]Green J E, Wook Choi J, Boukai A, et al. A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre. Nature,2007,445(7126):414-417
[4]N(?)rgaard K, Jeppesen J O, Laursen B W, et al. Evidence of strong hydration and significant tilt of amphiphilic [2]rotaxane molecules in langmuir films studied by synchrotron X-ray reflectivity, J Phys Chem B,2004,109(3):1063-1066
[5]Moulin J-F, Kengne J C, Kshirsagar R, et al. Self-organization of rotaxane thin films into spatially correlated nanostructures:□morphological and structural aspects. J Am Chem Soc, 2005,128(2):526-532
[6]Nygaard S, Leung K C F, Aprahamian I, et al. Functionally rigid bistable [2]rotaxanes. J Am Chem Soc,2007,129(4):960-970
[7]Panman M R, Bodis P, Shaw D J, et al. Operation mechanism of a molecular machine revealed using time-resolved vibrational spectroscopy. Science,2010,328(5983): 1255-1258
[8]Rijs A M, Kay E R, Leigh D A, et al. IR spectroscopy on jet-cooled isolated two-station rotaxanes. J Phys Chem A,2011,115(34):9669-9675
[9]Panman M R, Bodis P, Shaw D J, et al. Time-resolved vibrational spectroscopy of a molecular shuttle. Phys Chem Chem Phys,2012,14(6):1865-1875
[10]Raymo F M, Stoddart J F, Interlocked macromolecules. Chem Rev,1999,99(7):1643-1664
[11]Fahrenbach A C, Bruns C J, Cao D, et al. Ground-state thermodynamics of bistable redox-active donor-acceptor mechanically interlocked molecules. Acc Chem Res,2012, 45(9):1581-1592
[12]Harada A. Cyclodextrin-based molecular machines. Acc Chem Res,2001,34(6):456-464
[13]Wenz G, Han B-H, Muller A. Cyclodextrin rotaxanes and polyrotaxanes. Chem Rev,2006, 106(3):782-817
[14]Guo X Q, Song L X, Dang Z, et al. A comparative study on the formation and spectral properties of the polypseudorotaxanes of beta-cyclodextrin and poly(propylene glycol) under different conditions. Bull Chem Soc Jpn,2009,82(9):1209-1213
[15]Wang Y-H, Zhang H-M, Liu L, et al. Photoinduced electron transfer in a supramolecular species building of mono-6-p-nitrobenzoyl-β-cyclodextrin with naphthalene derivatives. J Org Chem,2002,67(8):2429-2434
[16]Harada A, Hashidzume A, Yamaguchi H, et al. Polymeric rotaxanes. Chem Rev,2009, 109(11):5974-6023
[17]Lee J W, Samal S, Selvapalam N, et al. Cucurbituril homologues and derivatives:□ new opportunities in supramolecular chemistry. Acc Chem Res,2003,36(8):621-630
[18]Rowan A E, Elemans J A A W, Nolte R J M. Molecular and supramolecular objects from glycoluril. Acc Chem Res,1999,32(12):995-1006
[19]Belowich M E, Valente C, Smaldone R A, et al. Positive cooperativity in the template-directed synthesis of monodisperse macromolecules. J Am Chem Soc,2012, 134(11):5243-5261
[20]Zhang M, Xu D, Yan X, et al. Self-healing supramolecular gels formed by crown ether based host-guest interactions. Angew Chem Int Edit,2012,51(28):7011-7015
[21]Xue M, Yang Y, Chi X, et al. Pillararenes, a new class of macrocycles for supramolecular chemistry. Acc Chem Res,2012,45(8):1294-1308
[22]Hu X-B, Chen L, Si W, et al. Pillar[5]arene decaamine:synthesis, encapsulation of very long linear diacids and formation of ion pair-stopped [2]rotaxanes. Chem Commun,2011,47(16): 4694-4696
[23]Yu G, Han C, Zhang Z, et al. Pillar[6]arene-based photoresponsive host-guest complexation. J Am Chem Soc,2012,134(20):8711-8717
[24]Bodis P, Panman M R, Bakker B H, et al. Two-dimensional vibrational spectroscopy of rotaxane-based molecular machines. Acc Chem Res,2009,42(9):1462-1469
[25]Fuller A-M L, Leigh D A, Lusby P J. Sequence isomerism in [3]rotaxanes. J Am Chem Soc, 2010,132(13):4954-4959
[26]Wisner J A, Beer P D, Drew M G B, et al. Anion-templated rotaxane formation. J Am Chem Soc,2002,124(42):12469-12476
[27]Da Ros T, Guldi D M, Morales A F, et al. Hydrogen bond-assembled fullerene molecular shuttle. Org Lett,2003,5(5):689-691
[28]Movsisyan L D, Kondratuk D V, Franz M, et al. Synthesis of polyyne rotaxanes. Org Lett, 2012,14(13):3424-3426
[29]Goldup S M, Leigh D A, McGonigal P R, et al. Two axles threaded using a single template site:active metal template macrobicyclic [3]rotaxanes. J Am Chem Soc,2009,132(1): 315-320
[30]Crowley J D, Hanni K D, Lee A-L, et al. [2]Rotaxanes through palladium active-template dxidative heck cross-couplings. J Am Chem Soc,2007,129(40):12092-12093
[31]Crowley J D, Hanni K D, Leigh D A, et al. Diels-alder active-template synthesis of rotaxanes and metal-ion-switchable molecular shuttles. J Am Chem Soc,2010,132(14):5309-5314
[32]Pierro T, Gaeta C, Talotta C, et al. Fixed or invertible calixarene-based directional shuttles. Org Lett,2011,13(10):2650-2653
[33]Crowley J D, Leigh D A, Lusby P J, et al. A switchable palladium-complexed molecular shuttle and its metastable positional isomers. J Am Chem Soc,2007,129(48):15085-15090
[34]Li H, Fahrenbach A C, Coskun A, et al. A light-stimulated molecular switch driven by radical-radical interactions in water. Angew Chem Int Edit,2011,50(30):6782-6788
[35]Stoll R S, Friedman D C, Stoddart J F. Mechanically interlocked mechanophores by living-radical polymerization from rotaxane initiators. Org Lett,2011,13(10):2706-2709
[36]Chiu C-W, Lai C-C, Chiu S-H. "Threading-followed-by-swelling":□ a new protocol for rotaxane synthesis. J Am Chem Soc,2007,129(12):3500-3501
[37]Ooya T, Choi H S, Yamashita A, et al. Biocleavable polyrotaxane-plasmid DNA polyplex for enhanced gene delivery. J Am Chem Soc,2006,128(12):3852-3853
[38]Li J, Yang C, Li H, et al. Cationic supramolecules composed of multiple oligoethylenimine-grafted β-cyclodextrins threaded on a polymer chain for efficient gene delivery. Adv Mater,2006,18(22):2969-2974
[39]Yang C, Wang X, Li H, et al. Cationic polyrotaxanes as gene carriers:physicochemical properties and real-time observation of DNA complexation, and gene transfection in cancer cells. J Phys Chem B,2009,113(22):7903-7911
[40]Balzani V, Gomez-L6pez M, Stoddart J F. Molecular machines. Acc Chem Res,1998,31 (7): 405-414
[41]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2(10): 1353-1356
[42]Ye T, Kumar A S, Saha S, et al. Changing stations in single bistable rotaxane molecules under electrochemical control. ACS Nano,2010,4(7):3697-3701
[43]Balzani V, Clemente-Leon M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[44]Brouwer A M, Frochot C, Gatti F G, et al. Photoinduction of fast, reversible translational motion in a hydrogen-bonded molecular shuttle. Science,2001,291(5511):2124-2128
[45]Jacquot de Rouville H-P, Iehl J, Bruns C J, et al. A neutral naphthalene diimide [2]rotaxane. Org Lett,2012,14(20):5188-5191
[46]Zhang K-D, Zhao X, Wang G-T, et al. Foldamer-tuned switching kinetics and metastability of [2]rotaxanes. Angew Chem Int Edit,2011,50(42):9866-9870
[47]Ferrand Y, Gan Q, Kauffmann B, et al. Template-induced screw motions within an aromatic amide foldamer double helix. Angew Chem Int Edit,2011,50(33):7572-7575
[48]You Y-C, Tzeng M-C, Lai C-C, et al. Using oppositely charged ions to operate a three-station [2]rotaxane in two different switching modes. Org Lett,2012,14(4):1046-1049
[49]Barnes J C, Fahrenbach A C, Dyar S M, et al. Mechanically induced intramolecular electron transfer in a mixed-valence molecular shuttle. Proc. Natl. Acad. Sci. USA,2012,109(29): 11546-11551
[50]Li H, Zhu Z, Fahrenbach A C, et al. Mechanical bond-induced radical stabilization. J Am Chem Soc,2012,135(1):456-467
[51]Fahrenbach A C, Zhu Z, Cao D, et al. Radically enhanced molecular switches. J Am Chem Soc,2012,134(39):16275-16288
[52]Deng W-Q, Muller R P, Goddard W A. Mechanism of the Stoddart-Heath bistable rotaxane molecular switch. J Am Chem Soc,2004,126(42):13562-13563
[53]Dvornikovs V, House B E, Kaetzel M, et al. Host-[2]rotaxanes as cellular transport agents. J Am Chem Soc,2003,125(27):8290-8301
[54]Carlone A, Goldup S M, Lebrasseur N, et al. A three-compartment chemically-driven molecular information ratchet. J Am Chem Soc,2012,134(20):8321-8323
[55]Serreli V, Lee C-F, Kay E R, et al. A molecular information ratchet. Nature,2007,445(7127): 523-527
[56]Kay E R, Leigh D A, Zerbetto F. Synthetic molecular motors and mechanical machines. Angew Chem Int Edit,2007,46(1-2):72-191
[57]Zhao Y-L, Aprahamian I, Trabolsi A, et al. Organogel formation by a cholesterol-stoppered bistable [2]rotaxane and its dumbbell precursor. J Am Chem Soc,2008,130(20):6348-6350
[58]Pease A R, Jeppesen J O, Stoddart J F, et al. Switching devices based on interlocked molecules. Acc Chem Res,2001,34(6):433-444
[59]Bema J, Leigh D A, Lubomska M, et al. Macroscopic transport by synthetic molecular machines. Nat Mater,2005,4(9):704-710
[60]Wan P, Jiang Y, Wang Y, et al. Tuning surface wettability through photocontrolled reversible molecular shuttle. Chem Commun,2008,0(44):5710-5712
[61]Baumes J M, Murgu I, Oliver A, et al. Using the rotaxane mechanical bond to enhance chemical reactivity. Org Lett,2010,12(21):4980-4983
[62]Thordarson P, Bijsterveld E J A, Rowan A E, et al. Epoxidation of polybutadiene by a topologically linked catalyst. Nature,2003,424(6951):915-918
[63]Zhang H, Hu J, Qu D-H. Dual-mode control of PET process in a ferrocene-functionalized [2]rotaxane with high-contrast fluorescence output. Org Lett,2012,14(9):2334-2337
[64]Alvarez-Perez M, Goldup S M, Leigh D A, et al. A chemically-driven molecular information ratchet. J Am Chem Soc,2008,130(6):1836-1838
[65]Danquah M K, Zhang X A, Mahato R I. Extravasation of polymeric nanomedicines across tumor vasculature. Adv Drug Deliv Rev,2011,63(8):623-639
[66]Chen T. Overcoming drug resistance by regulating nuclear receptors. Adv Drug Deliv Rev, 2010,62(13):1257-1264
[67]Torchilin V P. Tat peptide-mediated intracellular delivery of pharmaceutical nanocarriers. Adv Drug Deliv Rev,2008,60(4-5):548-558
[68]Guo D-S, Wang K, Wang Y-X, et al. Cholinesterase-responsive supramolecular vesicle. J Am Chem Soc,2012,134(24):10244-10250
[69]Torney F, Trewyn B G, Lin V S Y, et al. Mesoporous silica nanoparticles deliver DNA and chemicals into plants. Nat Nano,2007,2(5):295-300
[70]Trewyn B G, Slowing I I, Giri S, et al. Synthesis and functionalization of a mesoporous silica nanoparticle based on the sol-gel process and applications in controlled release. Acc Chem Res,2007,40(9):846-853
[71]Angelos S, Johansson E, Stoddart J F, et al. Mesostructured silica supports for functional materials and molecular machines. Adv Funct Mater,2007,17(14):2261-2271
[72]Yang Y-W. Towards biocompatible nanovalves based on mesoporous silica nanoparticles. MedChemComm,2011,2(11):1033-1049
[73]Hernandez R, Tseng H-R, Wong J W, et al. An operational supramolecular nanovalve. J Am Chem Soc,2004,126(11):3370-3371
[74]Zhu Z, Fahrenbach A C, Li H, et al. Controlling switching in bistable [2]catenanes by combining donor-acceptor and radical-radical Interactions. J Am Chem Soc,2012,134(28): 11709-11720
[75]Ferris D P, Zhao Y-L, Khashab N M, et al. Light-operated mechanized nanoparticles. J Am Chem Soc,2009,131(5):1686-1688
[76]Sun Y-L, Yang B-J, Zhang S X-A, et al. Cucurbit[7]uril pseudorotaxane-based photoresponsive supramolecular nanovalve. Chem Eur J,2012,18(30):9212-9216
[77]Marquez C, Nau W M. Two mechanisms of slow host-guest complexation between cucurbit[6]uril and cyclohexylmethylamine:pH-responsive supramolecular kinetics. Angew Chem Int Edit,2001,40(17):3155-3160
[78]Marquez C, Hudgins R R, Nau W M. Mechanism of host-guest complexation by cucurbituril. J Am Chem Soc,2004,126(18):5806-5816
[79]Ling X, Samuel E L, Patchell D L, et al. Cucurbituril slippage:translation is a complex motion. Org Lett,2010,12(12):2730-2733
[80]Angelos S, Khashab N M, Yang Y-W, et al. pH clock-operated mechanized nanoparticles. J Am Chem Soc,2009,131(36):12912-12914
[81]Nguyen T D, Leung K C F, Liong M, et al. Construction of a pH-driven supramolecular nanovalve. Org Lett,2006,8(15):3363-3366
[82]Patel K, Angelos S, Dichtel W R, et al. Enzyme-responsive snap-top covered silica nanocontainers. J Am Chem Soc,2008,130(8):2382-2383
[83]Meng H, Xue M, Xia T, et al. Autonomous in vitro anticancer drug release from mesoporous silica nanoparticles by pH-sensitive nanovalves. J Am Chem Soc,2010,132(36): 12690-12697
[84]Zhao Y-L, Li Z, Kabehie S, et al. pH-operated nanopistons on the surfaces of mesoporous silica nanoparticles. J Am Chem Soc,2010,132(37):13016-13025
[85]Vassal G, Koscielny S, Challine D, et al. Busulfan disposition and hepatic veno-occlusive disease in children undergoing bone marrow transplantation. Cancer Chemoth Pharm,1995, 37(3):247-253
[86]Menuel S, Joly J-P, Courcot B, et al. Synthesis and inclusion ability of a bis-β-cyclodextrin pseudo-cryptand towards Busulfan anticancer agent. Tetrahedron,2007,63(7):1706-1714
[87]Porwanski S, Dumarcay-Charbonnier F, Menuel S, et al. Bis-p-cyclodextrinyl-and bis-cellobiosyl-diazacrowns:synthesis and molecular complexation behaviors toward Busulfan anticancer agent and two basic aminoacids. Tetrahedron,2009,65(31):6196-6203
[88]Zehnder D W, Smithrud D B. Facile synthesis of rotaxanes through condensation reactions of DCC-[2]rotaxanes. Org Lett,2001,3(16):2485-2487
[89]Smukste I, House B E, Smithrud D B. Host-[2]rotaxane:□ advantage of converging functional groups for guest recognition. J Org Chem,2003,68(7):2559-2571
[90]Bao X, Isaacsohn I, Drew A F, et al. Determining the intracellular transport mechanism of a cleft-[2]rotaxane. J Am Chem Soc,2006,128(37):12229-12238
[91]Wang X, Smithrud D B. Pt-rotaxanes as cytotoxic agents. Bioorg Med Chem Lett,2011, 21(22):6880-6883
[92]Zhu J, McFarland-Mancini M, Drew A F, et al. Host-rotaxanes with oligomeric axles are intracellular transport agents. Bioorg Med Chem Lett,2009,19(2):520-523
[93]Bao X, Isaacsohn I, Drew A F, et al. Determining the binding and intracellular transporting abilities of a host-[3]rotaxane. J Org Chem,2007,72(11):3988-4000
[94]Rouget J-B, Aksel T, Roche J, et al. Size and sequence and the volume change of protein folding. J Am Chem Soc,2011,133(15):6020-6027
[95]Ghosh K, Dill K A. Theory for protein folding cooperativity:helix bundles. J Am Chem Soc, 2009,131(6):2306-2312
[96]Metropolis N, Rosenbluth A W, Rosenbluth M N, et al. Equation of state calculations by fast computing machines. J Chem Phys,1953,21(6):1087-1092
[97]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[98]Yang L, Tan C-h, Hsieh M-J, et al. New-generation amber united-atom force field. J Phys Chem B,2006,110(26):13166-13176
[99]Oostenbrink C, Soares T, Vegt N A, et al. Validation of the 53A6 GROMOS force field. Eur Biophys J,2005,34(4):273-284
[100]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys,1992,97(3):1990-2001
[101]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[102]Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:New York,2007.
[103]Kollman P. Free energy calculations:applications to chemical and biochemical phenomena. Chem Rev,1993,93(7-):2395-2417
[104]Simonson T, Archontis G, Karplus M. Free energy simulations come of age:□ protein-ligand recognition. Acc Chem Res,2002,35(6):430-437
[105]Landau L D. Statistical physics. The Clarendon Press, Oxford, U. K.,1938
[106]Zwanzig R W. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys,1954,22(8):1420-1426
[107]Kirkwood J G Statistical mechanics of fluid mixtures. J Chem Phys,1935,3(5):300-313
[108]Henin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[109]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906
[110]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[111]Rodriguez-G6mez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[112]Bennett C H. Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys,1976,22(2):245-268
[113]Ferrenberg A M, Swendsen R H. New Monte Carlo technique for studying phase transitions. Phys Rev Lett,1988,61(23):2635-2638
[114]Jarzynski C. Equilibrium free-energy differences from nonequilibrium measurements:a master-equation approach. Phys Rev Lett.,1997,56(5):5018-5035
[115]Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett,1997, 78(14):2690-2693
[116]Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B.2010,114(32):10235-10253
[117]Valleau J P, Torrie G M A. Guide to Monte Carlo for statistical mechanics:byways. In Modem theoretical chemistry; Berne B J, Ed.; Plenum:New York,1977; pp 169-194.
[118]McDonald I R, Singer K. Machine calculation of thermodynamic properties of a simple fluid at supercritical temperatures. J Chem Phys,1967,47(11):4766-4772
[119]Straatsma T P, Berendsen H J C, Postma J P M. Free energy of hydrophobic hydration:a molecular dynamics study of noble gases in water. J Chem Phys,1986,85(11):6720-6727
[120]McDonald I R, Singer K. Calculation of thermodynamic properties of liquid argon from Lennard-Jones parameters by a Monte Carlo method. Discuss Faraday Soc,1967,43:40-49
[121]Lu N, Kofke D A, Woolf T B. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J Comput Chem,2004,25(1): 28-40
[122]Lelievre T, Stoltz G, Rousset M. Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[123]Gumbart J C, Roux B, Chipot C. Standard binding free energies from computer simulations: what is the best strategy? J Chem Theory Comput,2012,9(1):794-802
[124]Chipot C. Milestones in the activation of a G protein-coupled receptor. Insights from molecular-dynamics simulations into the human cholecystokinin receptor-1. J Chem Theory Comput,2008,4(12):2150-2159
[125]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[126]Pan A C, Sezer D, Roux B. Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[127]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[128]Jang S S, Jang Y H, Kim Y-H, et al. Molecular dynamics simulation of amphiphilic bistable [2]rotaxane langmuir monolayers at the air/water interface. J Am Chem Soc,2005,127(42): 14804-14816
[129]Jang Y H, Jang S S, Goddard W A. Molecular dynamics simulation study on a monolayer of half [2]Rotaxane self-assembled on Au(111). J Am Chem Soc,2005,127(13):4959-4964
[130]Jang S S, Jang Y H, Kim Y-H, et al. Structures and properties of self-assembled monolayers of bistable [2]rotaxanes on Au (111) surfaces from molecular dynamics simulations validated with experiment. J Am Chem Soc,2005,127(5):1563-1575
[131]Carter E A, Ciccotti G, Hynes J T, et al. Constrained reaction coordinate dynamics for the simulation of rare events. Chem Phys Lett,1989,156(5):472-477
[132]Sprik M, Ciccotti G Free energy from constrained molecular dynamics. J Chem Phys,1998, 109(18):7737-7744
[133]Kim H, Goddard W A, Jang S S, et al. Free energy barrier for molecular motions in bistable [2]rotaxane molecular electronic devices. J Phys Chem A,2009,113(10):2136-2143
[134]Raiteri P, Bussi G, Cucinotta C S, et al. Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. Angew Chem Int Edit,2008,47(19): 3536-3539
[135]Torrie G M, Valleau J P. Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid. Chem Phys Lett,1974,28(4):578-581
[136]Still W C, Tempczyk A, Hawley R C, et al. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc,1990,112(16):6127-6129
[137]Zhao Y-L, Dichtel W R, Trabolsi A, et al. A redox-switchable a-cyclodextrin-based [2]rotaxane. J Am Chem Soc,2008,130(34):11294-11296
[138]Zhang Q, Tu Y, Tian H, et al. Working mechanism for a redox switchable molecular machine based on cyclodextrin:a free energy profile approach. J Phys Chem B,2010,114(19): 6561-6566
[139]Galatsis K, Kang W, Botros Y, et al. Emerging memory devices:nontraditional possibilities based on nanomaterials and nanostructures. IEEE Circuits Device Maga,2006,22(3):12-21
[140]Collier C P, Wong E W, Belohradsky M, et al. Electronically configurable molecular-based logic gates. Science,1999,285(5426):391-394
[141]Balzani V, Gomez-Lopez M, Stoddart J F. Molecular machines. Acc Chem Res,1998,31(7): 405-414
[142]Pease A R, Jeppesen J O, Stoddart J F, et al. Switching devices based on interlocked molecules. Acc Chem Res,2001,34(6):433-444
[143]Harada A, Kamachi M. Complex formation between poly(ethylene glycol) and α-cyclodextrin. Macromolecules,1990,23(10):2821-2823
[144]Harada A, Li J, Kamachi M. The molecular necklace:a rotaxane containing many threaded a-cyclodextrins. Nature,1992,356(6367):325-327
[145]Wu Y-L, Li J. Synthesis of supramolecular nanocapsules based on threading of multiple cyclodextrins over polymers on gold nanoparticles. Angew Chem Int Ed,2009,48(21): 3842-3845
[146]Ooya T, Choi H S, Yamashita A, et al. Biocleavable polyrotaxane-plasmid DNA polyplex for enhanced gene delivery. J Am Chem Soc,2006,128(12):3852-3853
[147]Harada A, Li J, Kamachi M. Preparation and characterization of a polyrotaxane consisting of monodisperse poly(ethylene glycol) and a-cyclodextrins. J Am Chem Soc,1994,116(8): 3192-3196
[148]Miyake K, Yasuda S, Harada A, et al. Formation process of cyclodextrin necklace-analysis of hydrogen bonding on a molecular level. J Am Chem Soc,2003,125(17):5080-5085
[149]Shigekawa H, Miyake K, Sumaoka J, et al. The molecular abacus:STM manipulation of cyclodextrin necklace. J Am Chem Soc,2000,122(22):5411-5412
[150]Bonnet P, Jaime C, Morin-Allory L. α-,β-, and y-Cyclodextrin dimers. Molecular modeling studies by molecular mechanics and molecular dynamics simulations. J Org Chem,2001, 66(3):689-692
[151]Bonnet P, Jaime C, Morin-Allory L. Structure and thermodynamics of α-, β-, and y-cyclodextrin dimers. molecular dynamics studies of the solvent effect and free binding energies. J Org Chem,2002,67(24):8602-8609
[152]Nascimento C S, Anconi C P A, Dos Santos H F, et al. Theoretical study of the α-cyclodextrin dimer. J Phys Chem A,2005,109(14):3209-3219
[153]Yu Y, Cai W, Chipot C, et al. Spatial arrangement of a-cyclodextrins in a rotaxane. Insights from free-energy calculations. J Phys Chem B,2008,112(17):5268-5271
[154]Tallury S S, Smyth M B, Cakmak E, et al. Molecular dynamics simulations of interactions between polyanilines in their inclusion complexes with β-cyclodextrins. J Phys Chem B, 2012,116(7):2023-2030
[155]Chipot C, Pohorille A. Calculating free energy differences using perturbation theory. In Free energy calculations; Chipot C, Pohorille A, Eds.; Springer Berlin Heidelberg,2007; Vol.86; pp 33-75.
[156]Lelievre T, Rousset M, Stoltz G Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[157]Chipot C, H6nin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,'123(24):244906-6
[158]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[159]Henin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[160]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[161]Brush S G. History of the Lenz-Ising model. Rev Mod Phys,1967,39(4):883-893
[162]Ising E. Beitrag zur theorie des ferromagnetismus. Z Phys A:Hadrons Nucl,1925,31(1): 253-258
[163]Hingerty B, Saenger W. Topography of cyclodextrin inclusion complexes.8. Crystal and molecular structure of the.alpha.-cyclodextrin-methanol-pentahydrate complex. Disorder in a hydrophobic cage. J Am Chem Soc,1976,98(11):3357-3365
[164]Insight II User Guide. Accelrys Software Inc., San Diego, CA,2005
[165]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[166]Hatcher E R, Guvench O, MacKerell A D. CHARMM additive all-atom force field for acyclic polyalcohols, acyclic carbohydrates, and inositol. J Chem Theory Comput,2009,5(5): 1315-1327
[167]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[168]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[169]Jorgensen W L, Chandrasekhar J, Madura J D, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys,1983,79(2):926-935
[170]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[171]Miyamoto S, Kollman P A. Settle:an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem,1992,13(8):952-962
[172]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[172]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys,1992,97(3):1990-2001
[174]Darden T, York D, Pedersen L. Particle mesh Ewald:an N log(N) method for Ewald sums in large systems. J Chem Phys,1993,98(12):10089-10092
[175]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[176]Henin J, Fiorin G, Chipot C, et al. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput,2010,6(1):35-47
[177]Jonkheijm P, van der Schoot P, Schenning A P H J, et al. Probing the solvent-assisted nucleation pathway in chemical self-assembly. Science,2006,313(5783):80-83
[178]Tanaka S, Scheraga H A. Model of protein folding:incorporation of a one-dimensional short-range (Ising) model into a three-dimensional model. Proc Natl Acad Sci USA,1977, 74(4):1320-1323
[179]Metropolis N, Rosenbluth A W, Rosenbluth M N, et al. Equation of state calculations by fast computing machines. J Chem Phys,1953,21(6):1087-1092
[180]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[181]Bolhuis P G, Dellago C, Chandler D. Reaction coordinates of biomolecular isomerization. Proc Natl Acad Sci USA,2000,97(11):5877-5882
[182]Pan A C, Sezer D, Roux B. Finding transition pathway:using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[183]Liu P, Chipot C, Shao X, et al. Solvent-controlled shuttling in a molecular switch. J Phys Chem C,2012,116(7):4471-4476
[184]Shrake A, Rupley J A. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol,1973,79(2):351-371
[185]Green J E, Wook Choi J, Boukai A, et al. A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre. Nature,2007,445(7126):414-417
[186]Harada A. Cyclodextrin-based molecular machines. Acc Chem Res,2001,34(6):456-464
[187]Raymo F M, Stoddart J F. Interlocked macromolecules. Chem Rev,1999,99(7):1643-1664
[188]Zhao Y-L, Dichtel W R, Trabolsi A, et al. A redox-switchable α-cyclodextrin-based [2]rotaxane. J Am Chem Soc,2008,130(34):11294-11296
[189]Bissell R A, Cordova E, Kaifer A E, et al. A chemically and electrochemically switchable molecular shuttle. Nature,1994,369:133-137
[190]Berna J, Goldup S M, Lee A-L, et al. Cadiot-chodkiewicz active template synthesis of rotaxanes and switchable molecular shuttles with weak intercomponent interactions. Angew Chem Int Ed,2008,47(23):4392-4396
[191]Coutrot F, Romuald C, Busseron E. A new pH-switchable dimannosyl[c2]daisy chain molecular machine. Org Lett,2008,10(17):3741-3744
[192]Coskun A, Friedman D C, Li H, et al. A light-gated STOP-GO molecular shuttle. J Am Chem Soc,2009,131(7):2493-2495
[193]Balzani V, Clemente-Leon M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[194]Murakami H, Kawabuchi A, Matsumoto R, et al. A multi-mode-driven molecular shuttle:□photochemically and thermally reactive azobenzene rotaxanes. J Am Chem Soc, 2005,127(45):15891-15899
[195]Marlin D S, Gonzalez Cabrera D, Leigh D A, et al. Complexation-induced translational isomerism:shuttling through stepwise competitive binding. Angew Chem Int Ed,2006,45(1): 77-83
[196]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2(10): 1353-1356
[197]Brough B, Northrop B H, Schmidt J J, et al. Evaluation of synthetic linear motor-molecule actuation energetics. Proc Natl Acad Sci USA,2006,103(23):8583-8588
[198]Belohradsky M, Elizarov A M, Stoddart J F. Speed-controlled molecular shuttles. Collect Czech Chem Commun,2002,67(11):1719-1728
[199]Kim H, Goddard W A, Jang S S, et al. Free energy barrier for molecular motions in bistable [2]rotaxane molecular electronic devices. J Phys Chem A,2009,113(10):2136-2143
[200]Raiteri P, Bussi G, Cucinotta C S, et al. Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. Angew Chem Int Ed,2008,47(19): 3536-3539
[201]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[202]Rodriguez-G6mez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[203]Darve E, Rodriguez-G6mez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[204]Henin J, Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J Chem Phys,2004,121(7):2904-2914
[205]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906-6
[206]Yu Y, Chipot C, Cai W, et al. Molecular dynamics study of the inclusion of cholesterol into cyclodextrins. J Phys Chem B,2006,110(12):6372-6378
[207]Yu Y, Cai W, Chipot C, et al. Spatial arrangement of α-cyclodextrins in a rotaxane. Insights from free-energy calculations. J Phys Chem B,2008,112(17):5268-5271
[208]Eyring H. The activated complex in chemical reactions. J Chem Phys,1935,3(2):107-115
[209]Insight II User Guide. Accelrys Software Inc., San Diego, CA,2005
[210]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[211]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[212]Liu X, Zhang S, Zhou G, et al. New force field for molecular simulation of guanidinium-based ionic liquids. J Phys Chem B,2006,110(24):12062-12071
[213]Strader M L, Feller S E. A flexible all-atom model of dimethyl sulfoxide for molecular dynamics simulations. J Phys Chem A,2002,106(6):1074-1080
[214]Pavelites J J, Gao J, Bash P A, et al. A molecular mechanics force field for NAD+, NADH, and the pyrophosphate groups of nucleotides. J Comput Chem,1997,18(2):221-239
[215]Foloppe N, MacKerell J A D. All-atom empirical force field for nucleic acids:I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem,2000,21(2):86-104
[216]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[217]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[218]Darden T, York D, Pedersen L. Particle mesh Ewald:an N log(N) method for Ewald sums in large systems. J Chem Phys,1993,98(12):10089-10092
[219]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[220]Ryckaert J-P, Ciccotti G, Berendsen H J C. Numerical integration of the cartesian equations of motion of a system with constraints:molecular dynamics of n-alkanes. J Comput Phys,1977, 23(3):327-341
[221]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[222]Flyvbjerg H, Petersen H G Error estimates on averages of correlated data. J Chem Phys,1989, 91(1):461-466
[223]Frisch M J, Trucks G W, Schlegel H B, et al. Gaussian 03, Revision C.03. Gaussian, Inc. Wallingford, CT,2004
[224]Vaiana A C, Cournia Z, Costescu I B, et al. AFMM:a molecular mechanics force field vibrational parametrization program. Comput Phys Commun,2005,167(1):34-42
[225]Kim H-W, Zeroka D. Trans-ethylphosphine and selected deuterated isotopomers:prediction of infrared spectra and potential energy distribution determination. THEOCHEM,2005,715: 21-31
[226]Kim H-W, Chechla A A, Kim B. Potential energy distribution study of infrared frequencies of methylamine and methylphosphine. THEOCHEM,2007,802:105-110
[227]Pulay P, Fogarasi G, Pang F, et al. Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives. J Am Chem Soc,1979,101(10): 2550-2560
[228]Bergeron R J, Channing M A, Gibeily G J, et al. Disposition requirements for binding in aqueous solution of polar substrates in the cyclohexaamylose cavity. J Am Chem Soc,1977, 99(15):5146-5151
[229]Li J, Harada A, Kamachi M. Formation of inclusion complexes of oligoethylene and its derivatives with a-cyclodextrin. Bull Chem Soc Jpn,1994,67:2808-2818
[230]Balzani V, Clemente-Leon M, Credi A, et al. Autonomous artificial nanomotor powered by sunlight. Proc Natl Acad Sci USA,2006,103(5):1178-1183
[231]Bissell R A, Cordova E, Kaifer A E, et al. A chemically and electrochemically switchable molecular shuttle. Nature,1994,369(6476):133-137
[232]Hernandez R, Tseng H-R, Wong J W, et al. An operational supramolecular nanovalve. J Am Chem Soc,2004,126(11):3370-3371
[233]Dvornikovs V, House B E, Kaetzel M, et al. Host-[2]rotaxanes as cellular transport agents. J Am Chem Soc,2003,125(27):8290-8301
[234]Leung K C-F, Chak C-P, Lo C-M, et al. pH-controllable supramolecular systems. Chem Asian J,2009,4(3):364-381
[235]Kawaguchi Y, Harada A. A cyclodextrin-based molecular shuttle containing energetically favored and disfavored portions in its dumbbell component. Org Lett,2000,2:1353-1356
[236]Umehara T, Kawai H, Fujiwara K, et al. Entropy- and hydrolytic-driven positional switching of macrocycle between imine- and hydrogen-bonding stations in rotaxane-based molecular shuttles. J Am Chem Soc,2008,130(42):13981-13988
[237]Vassal G, Koscielny S, Challine D, et al. Busulfan disposition and hepatic veno-occlusive disease in children undergoing bone marrow transplantation. Cancer Chemoth Pharm,1995, 37(3):247-253
[238]Zehnder D W, Smithrud D B. Facile synthesis of rotaxanes through condensation reactions of DCC-[2]rotaxanes. Org Lett,2001,3(16):2485-2487
[239]Smukste I, House B E, Smithrud D B. Host-[2]rotaxane:D advantage of converging functional groups for guest recognition. J Org Chem,2003,68(7):2559-2571
[240]Bao X, Isaacsohn I, Drew A F, et al. Determining the intracellular transport mechanism of a cleft-[2]rotaxane. J Am Chem Soc,2006,128(37):12229-12238
[241]Liu P, Cai W, Chipot C, et al. Thermodynamic insights into the dynamic switching of a cyclodextrin in a bistable molecular shuttle. J Phys Chem Lett,2010,1(12):1776-1780
[242]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[243]Kuttel M, Brady J W, Naidoo K J. Carbohydrate solution simulations:producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem,2002,23(13):1236-1243
[244]MacKerell A D, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B,1998,102(18):3586-3616
[245]Jorgensen W L, Chandrasekhar J, Madura J D, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys,1983,79(2):926-935
[246]Strader M L, Feller S E. A flexible all-atom model of dimethyl sulfoxide for molecular dynamics simulations. J Phys Chem A,2002,106(6):1074-1080
[247]Feller S E, Zhang Y, Pastor R W, et al. Constant pressure molecular dynamics simulation:the Langevin piston method. J Chem Phys,1995,103(11):4613-4621
[248]Tuckerman M, Berne B J, Martyna G J. Reversible multiple time scale molecular dynamics. J Chem Phys; 1992,97(3):1990-2001
[249]Andersen H C. Rattle:a "velocity" version of the shake algorithm for molecular dynamics calculations. J Comput Phys,1983,52(1):24-34
[250]Miyamoto S, Kollman P A. Settle:an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem,1992,13(8):952-962
[251]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[252]Darve E, Rodriguez-Gomez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys,2008,128(14):144120-13
[253]Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys,2004,120(8):3563-3578
[254]Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys,2001, 115(20):9169-9183
[255]Chipot C, Henin J. Exploring the free-energy landscape of a short peptide using an average force. J Chem Phys,2005,123(24):244906-6
[256]Henin J, Fiorin G, Chipot C, et al. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J Chem Theory Comput,2010,6(1):35-47
[257]Flyvbjerg H, Petersen H G. Error-estimates on averages of correlated data. J Chem Phys, 1989,91(1):461-466
[258]Bolhuis P G, Chandler D, Dellago C, et al. Transition path sampling:throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem,2002,53(1):291-318
[259]Pan A C, Sezer D, Roux B. Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B,2008,112(11):3432-3440
[260]Kollman P. Free energy calculations:applications to chemical and biochemical phenomena. Chem Rev,1993,93(7):2395-2417
[261]Simonson T, Archontis G, Karplus M. Free energy simulations come of age:protein-ligand recognition. Acc Chem Res,2002,35(6):430-437
[262]Chipot C, Pearlman D A. Free energy calculations. The long and winding gilded road. Mol Simulat,2002,28(1-2):1-12
[263]Simonson T. Free energy calculations. In Computational biochemistry and biophysics; Becker O M, MacKerell A D J, Roux B, Watanabe M, Eds.; Marcel Dekker Inc.:New York, 2001; pp 169-197
[264]Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:New York,2007
[265]Born M. Volumen und hydratationswarme der ionen. Z Physik,1920,1(1):45-48
[266]Landau L D. Statistical physics. The Clarendon Press, Oxford, U. K.,1938
[267]Zwanzig R W. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys,1954,22(8):1420-1426
[268]Kirkwood J G. Statistical mechanics of fluid mixtures. J Chem Phys,1935,3(5):300-313
[269]Bennett C H. Efficient estimation of free energy differences from Monte Carlo data. J Comput Phys,1976,22(2):245-268
[270]Ferrenberg A M, Swendsen R H. New Monte Carlo technique for studying phase transitions. Phys Rev Lett,1988,61(23):2635-2638
[271]Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett,1997, 78(14):2690-2693
[272]Jarzynski C. Equilibrium free-energy differences from nonequilibrium measurements:a master-equation approach. Phys Rev Lett,1997,56(5):5018-5035
[273]Jorgensen W L, Ravimohan C. Monte Carlo simulation of differences in free energies of hydration. J Chem Phys,1985,83(6):3050-3054
[274]Bash P A, Singh U C, Langridge R, et al. Free energy calculations by computer simulation. Science,1987,236(4801):564-568
[275]van Gunsteren W, Beutler T, Fraternali F, et al. Computation of free energy in practice:choice of approximations and accuracy limiting factors. In Computer simulation of biomolecular systems; van Gunsteren W, Weiner P, Wilkinson A, Eds.; Escom Science Publishers:Leiden, The Netherlands,1993; pp 315-348
[276]Chipot C, Millot C, Maigret B, et al. Molecular dynamics free energy perturbation calculations:influence of nonbonded parameters on the free energy of hydration of charged and neutral species. J Phys Chem,1994,98(44):11362-11372
[277]Ding Y, Bernardo D N, Krogh-Jespersen K, et al. Solvation free energies of small amides and amines from molecular dynamics/free energy perturbation simulations using pairwise additive and many-body polarizable potentials. J Phys Chem,1995,99(29):11575-11583
[278]Morgantini P-Y, Kollman P A. Solvation free energies of amides and amines:disagreement between free energy calculations and experiment. J Am Chem Soc,1995,117(22): 6057-6063
[279]Rick S W, Berne B J. Free energy of the hydrophobic interaction from molecular dynamics simulations:□ the effects of solute and solvent polarizability. J Phys Chem B,1997,101(49): 10488-10493
[280]Ponder J W, Wu C, Ren P, et al. Current status of the AMOEBA polarizable force field. J Phys Chem B,2010,114(8):2549-2564
[281]Oostenbrink C, Villa A, Mark A E, et al. A biomolecular force field based on the free enthalpy of hydration and solvation:the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem,2004,25(13):1656-1676
[282]Shirts M R, Pitera J W, Swope W C, et al. Extremely precise free energy calculations of amino acid side chain analogs:comparison of common molecular mechanics force fields for proteins. J Chem Phys,2003,119(11):5740-5761
[283]Jorgensen W L, Buckner J K, Boudon S, et al. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water. J Chem Phys, 1988,89(6):3742-3746
[284]van Gunsteren W F. Methods for calculation of free energies and binding constants:successes and problems. In Computer simulation of biomolecular systems:theoretical and experimental applications; Van Gunsteren W F, Weiner P K, Eds.; Escom Science Publishers:Leiden, The Netherlands,1989; pp 27-59
[285]Miyamoto S, Kollman P A. What determines the strength of noncovalent association of ligands to proteins in aqueous solution? Proc Natl Acad Sci USA,1993,90(18):8402-8406
[286]Aqvist J. Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. J Comput Chem,1996,17(14):1587-1597
[287]Aqvist J, Luzhkov V B, Brandsdal B O. Ligand binding affinities from MD simulations. Acc Chem Res,2002,35(6):358-365
[288]Archontis G, Simonson T, Karplus M. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. J Mol Biol,2001,306(2):307-327
[289]Boresch S, Tettinger F, Leitgeb M, et al. Absolute binding free energies:□a quantitative approach for their calculation. J Phys Chem B,2003,107(35):9535-9551
[290]Oostenbrink C, van Gunsteren W F. Free energies of ligand binding for structurally diverse compounds. Proc Natl Acad Sci USA,2005,102(19):6750-6754
[291]Woo H-J, Roux B. Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci USA,2005,102(19):6825-6830
[292]Wang J, Deng Y, Roux B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J,2006,91(8):2798-2814
[293]Mobley D L, Graves A P, Chodera J D, et al. Predicting absolute ligand binding free energies to a simple nodel site. J Mol Biol,2007,371(4):1118-1134
[294]Deng Y, Roux B. Computations of standard binding free energies with molecular dynamics simulations. J Phys Chem B,2009,113(8):2234-2246
[295]Jiang W, Roux B. Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations. J Chem Theory Comput,2010,6(9):2559-2565
[296]Pearlman D A, Charifson P S. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system. J Med Chem,2001, 44(21):3417-3423
[297]Chipot C, Rozanska X, Dixit S. Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein. J Comput Aided Mol Des,2005,19(11):765-770
[298]Chodera J D, Mobley D L, Shirts M R, et al. Alchemical free energy methods for drug discovery:progress and challenges. Curr Opin Struct Biol,2011,21(2):150-160
[299]Lelievre T, Stoltz G, Rousset M. Free energy computations:a mathematical perspective. Imperial College Press, London,2010
[300]Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B.2010,114(32):10235-10253
[301]Humphrey W, Dalke A, Schulten K. VMD:visual molecular dynamics. J Mol Graphics,1996, 14(1):33-38
[302]Phillips J C, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem,2005,26(16):1781-1802
[303]McDonald I R, Singer K. Machine calculation of thermodynamic properties of a simple fluid at supercritical temperatures. J Chem Phys,1967,47(11):4766-4772
[304]McDonald I R, Singer K. Calculation of thermodynamic properties of liquid argon from Lennard-Jones parameters by a Monte Carlo method. Discuss Faraday Soc,1967,43:40-49
[305]Valleau J P, Torrie G M A. Guide to Monte Carlo for statistical mechanics:byways. In Modern theoretical chemistry; Berne B J, Ed.; Plenum:New York,1977; pp 169-194
[306]Straatsma T P, Berendsen H J C, Postma J P M. Free energy of hydrophobic hydration:a molecular dynamics study of noble gases in water. J Chem Phys,1986,85(11):6720-6727
[307]Lu N, Kofke D A, Woolf T B. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. J Comput Chem,2004,25(1): 28-40
[308]Kofke D A, Cummings P T. Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation. Fluid Phase Equilib, 1998:41-49
[309]Hahn A M, Then H. Characteristic of Bennett's acceptance ratio method. Phys Rev Lett., 2009,80(3):031111
[310]Shirts M R, Bair E, Hooker G, et al. Equilibrium free energies from nonequilibrium measurements using Maximum-Likelihood methods. Phys Rev Lett,2003,91(14):140601
[311]Flyvbjerg H, Petersen H G Error estimates on averages of correlated data. J Chem Phys,1989, 91(1):461-466
[312]Lu N, Kofke D A. Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling. J Chem Phys,2001,114(17):7303-7311
[313]Lu N, Woolf T B. Understanding and improving free energy calculations in molecular simulations:error analysis and reduction methods. In Free energy calculations. Theory and applications in chemistry and biology; Chipot C, Pohorille A, Eds.; Springer Verlag:Berlin, 2007
[314]Lu N, Kofke D A. Accuracy of free-energy perturbation calculations in molecular simulation. II. Heuristics. J Chem Phys,2001,115(15):6866-6875
[315]Hunenberger P H, McCammon J A. Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction:a continuum electrostatics study. J Chem Phys,1999, 110(4):1856-1872
[316]Zuckerman D M, Woolf T B. Theory of a systematic computational error in free energy differences. Phys Rev Lett,2002,89(18):180602
[317]Zuckerman D M, Woolf T B. Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities. J Stat Phys,2004,114(5-6):1303-1323
[318]Wan S, Stote R H, Karplus M. Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes. J Chem Phys,2004,121(19):9539-9548
[319]Cramer H. Mathematical methods of statistics. Princeton University Press, Princeton, NJ, 1957
[320]Valleau J P, Card D N. Monte Carlo estimation of the free energy by multistage sampling. J Chem Phys,1972,57(12):5457-5462
[321]Wolfenden R, Andersson L, Cullis P M, et al. Affinities of amino acid side chains for solvent water. Biochemistry,1981,20(4):849-855
[322]Ben-Naim A, Marcus Y. Solvation thermodynamics of nonionic solutes. J Chem Phys,1984, 81(4):2016-2027
[323]Anisimov V M, Vorobyov I V, Roux B, et al. Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput, 2007,3(6):1927-1946
[324]Zhong Y, Patel S. Nonadditive empirical force fields for short-chain linear alcohols: methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models. J Phys Chem B,2010,114(34):11076-11092
[325]Chipot C. Rational determination of charge distributions for free energy calculations. J Comput Chem,2003,24(4):409-415
[326]Levy R M, Gallicchio E. Computer simulations with explicit solvent:recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annu Rev Phys Chem,1998,49(1):531-567
[327]Kubo M M, Gallicchio E, Levy R M. Thermodynamic decomposition of hydration free energies by computer simulation:□application to amines, oxides, and sulfides. J Phys Chem B,1997,101(49):10527-10534
[328]Shirts M R, Chodera J D. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys,2008,129(12):124105-124110
[329]Pohorille A, Darve E. A bayesian approach to calculating free energies in chemical and biological systems. Bayesian inference and maximum entropy methods in science and engineering. AIP Conference Proceedings. Melville, NY,2006. AIP:23-30
[330]Blinnikov S, Moessner R. Expansions for nearly Gaussian distributions. Astron Astrophys Suppl Ser,1998,130(1):193-205