应用ABEEMσπ模型快速计算分子静电势
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摘要
分子的许多物理、化学性质都与其静电势密切相关。分子静电势作为量子化学的理论指标,对于判断分子的某些性质,尤其是分子的反应活性都具有重要价值。分子的静电势已经广泛应用到与化学相关的研究领域。由于静电势由分子本身的性质决定,那么不同分子在其周围空间各点产生的静电势是不同的,因此可以采用静电势来描述分子本身的性质。借助于Fortran和Matlab计算机语言程序,本文建立了一种新的快速计算分子静电势的方法。应用此方法计算了HF、H2O、C2H2、NH3和CH4小分子的静电势,并对乙醇分子以及环戊二烯、呋喃、噁唑及异噁唑这几个五元环分子的静电势进行了计算,最后对水分子二聚体十种低能结构也进行了静电势值的计算。并且本文探讨了这十种低能结构的静电势分布特征。其中用到的电荷采用原子-键电负性均衡方法σπ模型(ABEEMσπ)计算的结果,结构由MP2／6-311++G(d,p)方法优化所得。
杨等人首先定义了分子中一个电子所受到的作用势,并利用电子运动的经典转折点,定义和发展了一种新的表征分子界面的方法,即分子内禀特征轮廓。随着此模型的不断发展,杨等人又提出了分子形貌理论,此理论将电子密度标志在三维空间的分子内禀特征轮廓上,同时表征了分子的形状以及前沿电子密度。本文基于杨等人建立的内禀特征轮廓理论以及分子形貌理论,编制了分子静电势分布的程序,同时展示了分子的形状和其静电势的分布特征。分子的静电势分布图提供了分子静电性质的准确、客观和直观的图像。将我们的方法与从头算方法进行了比较,发现本文结果与从头算符合得很好,这就为大分子静电势的计算打下了基础。
Many physical and chemical properties of molecule are closely related to its electrostatic potential. Molecular electrostatic potential, a theory character of quantum chemistry for studying, can be used to judge some molecular properties, especially the molecular reactive activity. Molecular electrostatic potential has been widely applied to chemistry-related research. As the molecular electrostatic potential is determined by its properties, the electrostatic potential generated by each point of different molecules in their surrounding space is different. Therefore, we can use electrostatic potential to describe the nature of the molecule. We have proposed a new method to rapidly calculate the molecular electrostatic potential, and taken HF、H2O、C2H2、NH3 and CH4 as model molecules to calculate their electrostatic potential, and calculated the molecular electrostatic potential of ethanol、cyclopentadience、funan、oxazole、isoxazole, finally dozens of low-energy dimer structure of water were also calculated. And we discussed their electrostatic potential distribution. Where charges are directly calculated by atom-bond electronegativity equalization method atσπlevel, and the structure are optimized by MP2/6-311++G(d,p) method.
The potential acting on an electron within a molecular has been recently defined by Yang and coworkers. Based on the PAEM, in terms of the classical turning points of electronic motion, a new method, molecular intrinsic characteristic contour, has been developed for describing molecular shape and face electron density. Along with development of our model, the electron density described by our model becomes more and more significant. Yang and coworkers have again proposed the molecular face theory. We have exhibited the graphics of their electrostatic potential distributions, which is based on the molecular intrinsic characteristic contour theory and the molecular face theory. The electrostatic potential distributions provides accurate, objective and visual images of molecular electrostatic properties. And the results have fairly consistency with the ab initio results. This lays the foundation for the electrostatic potential of the macromolecules.
杨等人首先定义了分子中一个电子所受到的作用势,并利用电子运动的经典转折点,定义和发展了一种新的表征分子界面的方法,即分子内禀特征轮廓。随着此模型的不断发展,杨等人又提出了分子形貌理论,此理论将电子密度标志在三维空间的分子内禀特征轮廓上,同时表征了分子的形状以及前沿电子密度。本文基于杨等人建立的内禀特征轮廓理论以及分子形貌理论,编制了分子静电势分布的程序,同时展示了分子的形状和其静电势的分布特征。分子的静电势分布图提供了分子静电性质的准确、客观和直观的图像。将我们的方法与从头算方法进行了比较,发现本文结果与从头算符合得很好,这就为大分子静电势的计算打下了基础。
Many physical and chemical properties of molecule are closely related to its electrostatic potential. Molecular electrostatic potential, a theory character of quantum chemistry for studying, can be used to judge some molecular properties, especially the molecular reactive activity. Molecular electrostatic potential has been widely applied to chemistry-related research. As the molecular electrostatic potential is determined by its properties, the electrostatic potential generated by each point of different molecules in their surrounding space is different. Therefore, we can use electrostatic potential to describe the nature of the molecule. We have proposed a new method to rapidly calculate the molecular electrostatic potential, and taken HF、H2O、C2H2、NH3 and CH4 as model molecules to calculate their electrostatic potential, and calculated the molecular electrostatic potential of ethanol、cyclopentadience、funan、oxazole、isoxazole, finally dozens of low-energy dimer structure of water were also calculated. And we discussed their electrostatic potential distribution. Where charges are directly calculated by atom-bond electronegativity equalization method atσπlevel, and the structure are optimized by MP2/6-311++G(d,p) method.
The potential acting on an electron within a molecular has been recently defined by Yang and coworkers. Based on the PAEM, in terms of the classical turning points of electronic motion, a new method, molecular intrinsic characteristic contour, has been developed for describing molecular shape and face electron density. Along with development of our model, the electron density described by our model becomes more and more significant. Yang and coworkers have again proposed the molecular face theory. We have exhibited the graphics of their electrostatic potential distributions, which is based on the molecular intrinsic characteristic contour theory and the molecular face theory. The electrostatic potential distributions provides accurate, objective and visual images of molecular electrostatic properties. And the results have fairly consistency with the ab initio results. This lays the foundation for the electrostatic potential of the macromolecules.
引文
[1]Parr R G, Yang W T. Density Functional Theory of Atoms and Molecules. New York:Oxford University,1989,7:104-142.
[2]Levy M, Perdew H. Density-Functional Method in Physics. Plenum, New York,1985.
[3]Hohenberg P, Kohn W. Inhomogeneous Electron Gas. Phys Rev B,1964,136:864.
[4]Bader R F W. Atoms in Molecules:A Quantum Theory. Clarendon, Oxford,1994.
[5]陆润民.计算机图形学教程.清华大学出版社,2003,3：1-3.
[6]飞思科技产品研发中心.MATLAB 7基础与提高.电子工业出版社,2005,4：1-2.
[7]Matlab R2006b. Natick MA:The Mathworks, Inc,2006.
[8]Yang Z Z, Shen E Z. Molecular Electronegativity in Density Functional Theory (Ⅱ) —Direct Calculation of Group Electronegativity and the Atomic Charges in a Group, Science in China (Ser. B),1996,39:20.
[9]Yang Z Z, Wang C S. Atom-Bond Electronegativity Equalization Method 1 Calculation of the Charge Distribution in Large Molecules. J Phys Chem A,1997,101:6315-6321.
[10]Yang Z Z, Wang C S, Tang A Q. Molecular Electronegativity in Density Functional Theory (Ⅵ)—Atom-Bond Electronegativity Equalization Model, Science in China (Ser. B),1998, 41:331.
[11]Yang Z Z, Wang C S. Atom-Bond Electronegativity Equalization Method and its Applications Based on Density Functional Theory. J Theor Comput Chem,2003,2: 273-299.
[12]Wu Y, Yang Z Z. Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics. Ⅱ. A Seven-Site Fluctuating Charge and Flexible Body Water Potential Function for Liquid Water. J Phys Chem A,2004,108:7563-7576.
[13]杨忠志,丛尧,王长生.原子—键电负性均衡方法中的σπ模型及其应用.高等学校化学化学学报,1999,20(11)：1781.
[14]杨忠志,叶元杰,唐敖庆.大分子体系的量子化学.吉林大学出版社,2005,1：124-155.
[15]Ghanty T k, Ghosh S K. Electornegativity and Covalent Binding in Homonuclear Diatomic Molecules. J Phys Chem,1991,95:6512-6514.
[16]Ghosh S K. Electronegativity, Hardness, and a Semiempirical Density Functional Theory of Chemical Binging. Int J Quant Chem,1994,49:239-251.
[17]Parr R G, Donnelly R A, Levy Met al. Electronegativity:The Density Functional Viewpoint. J Chem Phys,1978,68(8):3801.
[18]Yang Z Z, Wu Y, Zhao D X. Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics. Ⅰ. A Seven-Site Fluctuating Charge and Flexible Body Water Potential Function for Water Clusters. J Chem Phys,2004,120:2541-2557.
[19]Wu Y, Yang,Z Z. Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics. II. A Seven-Site Fluctuating Charge and Flexible Body Water Potential Function for Liquid Water. J Phys Chem A,2004,108:7563-7576.
[20]Mezey P G. Shape in chemistry[M]. New York:VCH,1993.
[21]Leach A R. Molecular Modeling Principles and Applications[M]. Harlow:Addison Wesley Longman,1996.
[22]Grant J A, Pickup B T. A Gaussian description of molecular shape[J]. J Phys Chem, 1995,99(11):3503-3510.
[23]Politzer P, Truhlar D G. Chemical Applications of Atomic and Molecular Electrostatic Potential[M]. New York:Plenum, 1981.
[24]Politzer P, Murray J S, Boyd D B. Reviews in Computational Chemistry[M], New York: VCH,1991.
[25]Reynolds C A, Essex J W, Richards W G. Atomic charges for variable molecular conformations[J]. J Am Chem Soc,1992,114(23):9075-9097.
[26]Badenhoop J K, Weinhold F. Natural stcric analysis:Ab initio van der Waals radii of atoms and ions[J]. J Chem Phys,1997,107(14):5422-5432.
[27]Bash P A, Pattabiraman N, Huang C et al. van der Waals surfaces in molecular modeling: implementation with real-time computer graphics[J]. Science,1983,222:1325-1327.
[28]赵东霞,宫利东,杨忠志.在分子中单电子受到的作用势的理论研究[J].高等学校化学学报,2001,22：1893-1895.
[29]赵东霞.HX((X=-F,-Cl,-Br)分子中一个电子所受到的作用势与分子内禀特征轮廓[J].高等学校化学学报(增刊).2002,23：45-50.
[30]宫利东,赵东霞.有机小分子中一个电子所受到的作用势[J].高等学校化学学报(增刊),2002,23：85-89.
[31]Politzer P, Truhlar D G. Chemical applications of atomic and molecular electrostatic potentials[M]. New York:Plenum,1984.
[32]Kohn W, Sham L J. Self-consistent equation including exchange and correlation effects[J]. Phys. Rev. A,1965,140:1133-1138.
[33]赵东霞,夏刚山.杂环化合物的分子形貌的研究.辽宁师范大学学报(自然科学版),2008,31：469-473.
[34]杨忠志,赵东霞.关于分子特征形状的理论—Ⅰ.一种定义分子特征形状的新方法[J].中国科学B辑,1999,29：289-296.
[35]邢其毅,徐瑞秋,周政等.基础有机化学(第二版)下册[M].
[36]Dougherty D A. Cation-π interactions in Chemistry and Biology:a new view of Benzene phe, tyr, and Trp[J]. Science,1996,271:163-166.
[37]于春阳.二聚体水分子的十种稳定结构的MP2方法研究.辽宁师范大学学报(自然科学版),2007,31：48-52.
[38]Fellers, R S, Leforestier, C, Braly, L. B., Spectroscopic Determination of the Water Pair Potential. Science,1999,284:945-948.
[39]Odutola J A, Dyke T R. Partially Deuterated Water Dimers:Microwave Spectra and Structure. J Chem Phys,1980,72:5062-5070.
[40]Xantheas S S, Dunning T H. Ab initio Studies of Cyclic Water Clusters (H2O), n= 1-6. Ⅰ. Optimal Structures and Vibrational Spectra. J Chem Phys,1993,99:8774-8792.
[41]Xantheas, S S. Ab initio Studies of Cyclic Water Clusters (H2O)n, n= 1-6. Ⅲ. Comparison of density functional with MP2 results. J Chem Phys,1995,102:4505.
[2]Levy M, Perdew H. Density-Functional Method in Physics. Plenum, New York,1985.
[3]Hohenberg P, Kohn W. Inhomogeneous Electron Gas. Phys Rev B,1964,136:864.
[4]Bader R F W. Atoms in Molecules:A Quantum Theory. Clarendon, Oxford,1994.
[5]陆润民.计算机图形学教程.清华大学出版社,2003,3：1-3.
[6]飞思科技产品研发中心.MATLAB 7基础与提高.电子工业出版社,2005,4：1-2.
[7]Matlab R2006b. Natick MA:The Mathworks, Inc,2006.
[8]Yang Z Z, Shen E Z. Molecular Electronegativity in Density Functional Theory (Ⅱ) —Direct Calculation of Group Electronegativity and the Atomic Charges in a Group, Science in China (Ser. B),1996,39:20.
[9]Yang Z Z, Wang C S. Atom-Bond Electronegativity Equalization Method 1 Calculation of the Charge Distribution in Large Molecules. J Phys Chem A,1997,101:6315-6321.
[10]Yang Z Z, Wang C S, Tang A Q. Molecular Electronegativity in Density Functional Theory (Ⅵ)—Atom-Bond Electronegativity Equalization Model, Science in China (Ser. B),1998, 41:331.
[11]Yang Z Z, Wang C S. Atom-Bond Electronegativity Equalization Method and its Applications Based on Density Functional Theory. J Theor Comput Chem,2003,2: 273-299.
[12]Wu Y, Yang Z Z. Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics. Ⅱ. A Seven-Site Fluctuating Charge and Flexible Body Water Potential Function for Liquid Water. J Phys Chem A,2004,108:7563-7576.
[13]杨忠志,丛尧,王长生.原子—键电负性均衡方法中的σπ模型及其应用.高等学校化学化学学报,1999,20(11)：1781.
[14]杨忠志,叶元杰,唐敖庆.大分子体系的量子化学.吉林大学出版社,2005,1：124-155.
[15]Ghanty T k, Ghosh S K. Electornegativity and Covalent Binding in Homonuclear Diatomic Molecules. J Phys Chem,1991,95:6512-6514.
[16]Ghosh S K. Electronegativity, Hardness, and a Semiempirical Density Functional Theory of Chemical Binging. Int J Quant Chem,1994,49:239-251.
[17]Parr R G, Donnelly R A, Levy Met al. Electronegativity:The Density Functional Viewpoint. J Chem Phys,1978,68(8):3801.
[18]Yang Z Z, Wu Y, Zhao D X. Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics. Ⅰ. A Seven-Site Fluctuating Charge and Flexible Body Water Potential Function for Water Clusters. J Chem Phys,2004,120:2541-2557.
[19]Wu Y, Yang,Z Z. Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics. II. A Seven-Site Fluctuating Charge and Flexible Body Water Potential Function for Liquid Water. J Phys Chem A,2004,108:7563-7576.
[20]Mezey P G. Shape in chemistry[M]. New York:VCH,1993.
[21]Leach A R. Molecular Modeling Principles and Applications[M]. Harlow:Addison Wesley Longman,1996.
[22]Grant J A, Pickup B T. A Gaussian description of molecular shape[J]. J Phys Chem, 1995,99(11):3503-3510.
[23]Politzer P, Truhlar D G. Chemical Applications of Atomic and Molecular Electrostatic Potential[M]. New York:Plenum, 1981.
[24]Politzer P, Murray J S, Boyd D B. Reviews in Computational Chemistry[M], New York: VCH,1991.
[25]Reynolds C A, Essex J W, Richards W G. Atomic charges for variable molecular conformations[J]. J Am Chem Soc,1992,114(23):9075-9097.
[26]Badenhoop J K, Weinhold F. Natural stcric analysis:Ab initio van der Waals radii of atoms and ions[J]. J Chem Phys,1997,107(14):5422-5432.
[27]Bash P A, Pattabiraman N, Huang C et al. van der Waals surfaces in molecular modeling: implementation with real-time computer graphics[J]. Science,1983,222:1325-1327.
[28]赵东霞,宫利东,杨忠志.在分子中单电子受到的作用势的理论研究[J].高等学校化学学报,2001,22：1893-1895.
[29]赵东霞.HX((X=-F,-Cl,-Br)分子中一个电子所受到的作用势与分子内禀特征轮廓[J].高等学校化学学报(增刊).2002,23：45-50.
[30]宫利东,赵东霞.有机小分子中一个电子所受到的作用势[J].高等学校化学学报(增刊),2002,23：85-89.
[31]Politzer P, Truhlar D G. Chemical applications of atomic and molecular electrostatic potentials[M]. New York:Plenum,1984.
[32]Kohn W, Sham L J. Self-consistent equation including exchange and correlation effects[J]. Phys. Rev. A,1965,140:1133-1138.
[33]赵东霞,夏刚山.杂环化合物的分子形貌的研究.辽宁师范大学学报(自然科学版),2008,31：469-473.
[34]杨忠志,赵东霞.关于分子特征形状的理论—Ⅰ.一种定义分子特征形状的新方法[J].中国科学B辑,1999,29：289-296.
[35]邢其毅,徐瑞秋,周政等.基础有机化学(第二版)下册[M].
[36]Dougherty D A. Cation-π interactions in Chemistry and Biology:a new view of Benzene phe, tyr, and Trp[J]. Science,1996,271:163-166.
[37]于春阳.二聚体水分子的十种稳定结构的MP2方法研究.辽宁师范大学学报(自然科学版),2007,31：48-52.
[38]Fellers, R S, Leforestier, C, Braly, L. B., Spectroscopic Determination of the Water Pair Potential. Science,1999,284:945-948.
[39]Odutola J A, Dyke T R. Partially Deuterated Water Dimers:Microwave Spectra and Structure. J Chem Phys,1980,72:5062-5070.
[40]Xantheas S S, Dunning T H. Ab initio Studies of Cyclic Water Clusters (H2O), n= 1-6. Ⅰ. Optimal Structures and Vibrational Spectra. J Chem Phys,1993,99:8774-8792.
[41]Xantheas, S S. Ab initio Studies of Cyclic Water Clusters (H2O)n, n= 1-6. Ⅲ. Comparison of density functional with MP2 results. J Chem Phys,1995,102:4505.