腺嘌呤的氨基修饰增强DNA导电性的理论研究
|
摘要
利用密度泛函理论并结合非平衡态格林函数方法,研究了腺嘌呤A的碳2位氨基修饰对DNA导电性的影响.结果表明,形成的双氨基嘌呤D可以与胸腺嘧啶T通过3个氢键进行配对,由于氨基修饰形成了新的氢键,使配对碱基D和T之间的结合比AT更紧密.修饰后体系的能隙和电离能大大降低,紫外吸收光谱在一定程度上会发生红移,并增加了一些电荷转移跃迁.计算的沿氢键方向的横向电荷输运和沿DNA链方向的纵向电荷输运性质,证明了氨基的取代修饰可以很好地提高DNA的电荷输运性质.揭示了DNA导电性增强是由于修饰调整了碱基对DT的最高占据轨道(HOMO)能级,使之较天然碱基对AT更靠近GC的HOMO,从而降低了空穴在DNA中迁移的势垒.
The effect of amino modification of adenine( A) on DNA conductivity was studied by density functional theory combined with non-equilibrium Green 's function. The results show that the formed diaminopurine( D) could pair with thymine( T) through three hydrogen bonds. Owing to the new formed hydrogen bond by amino modification,the binding between the paired bases D and T was tighter than that in AT. Energy gaps and ionization energies of the modified systems were greatly decreased. And the UV absorption spectra are red shifted with more charge-transfer transitions for DT. Properties of the transverse charge transport along hydrogen bonds and the longitudinal charge transport along DNA strand directly demonstrated that replacing A with D could largely increase the conductivity of DNA. More importantly,the mechanism of enhancement effect was indicated. The amino modification adjusted the HOMO( highest occupied molecular orbital) level of DT base pair closer to that of GC compared with AT,thus reducing the energy barrier of hole migration in DNA. This may shed some light on the design of novel DNA-based molecular devices.
The effect of amino modification of adenine( A) on DNA conductivity was studied by density functional theory combined with non-equilibrium Green 's function. The results show that the formed diaminopurine( D) could pair with thymine( T) through three hydrogen bonds. Owing to the new formed hydrogen bond by amino modification,the binding between the paired bases D and T was tighter than that in AT. Energy gaps and ionization energies of the modified systems were greatly decreased. And the UV absorption spectra are red shifted with more charge-transfer transitions for DT. Properties of the transverse charge transport along hydrogen bonds and the longitudinal charge transport along DNA strand directly demonstrated that replacing A with D could largely increase the conductivity of DNA. More importantly,the mechanism of enhancement effect was indicated. The amino modification adjusted the HOMO( highest occupied molecular orbital) level of DT base pair closer to that of GC compared with AT,thus reducing the energy barrier of hole migration in DNA. This may shed some light on the design of novel DNA-based molecular devices.
引文
[1] Guo C. L.,Wang K.,Zerah-Harush E.,Hamill J.,Wang B.,Dubi Y.,Xu B. Q.,Nat. Chem.,2016,8(5),484—490
[2] Xiang D.,Wang X. L.,Jia C. C.,Lee T.,Guo X. F.,Chem. Rev.,2016,116(7),4318—4440
[3] Wang L.,Li Z.,Shen X. Q.,Ma N.,Chem. J. Chinese Universities,2018,39(1),32—40(王莉,李智,沈晓琴,马楠.高等学校化学学报,2018,39(1),32—40)
[4] Behnia S.,Fathizadeh S.,Akhshani A.,J. Phys. Chem. C,2016,120(5),2973—2983
[5] Shipman S. L.,Nivala J.,Macklis J. D.,Church G. M.,Nature,2017,547(7663),345—349
[6] Lin M. H.,Wen Y. L.,Li L. Y.,Pei H.,Liu G.,Song H. Y.,Zuo X. L.,Fan C. H.,Huang Q.,Anal. Chem.,2014,86(5),2285—2288
[7] Li M.,Kong H. F.,Guo Z. H.,Chem. J. Chinese Universities,2016,37(7),1269—1275(李敏,孔慧芳,郭志慧.高等学校化学学报,2016,37(7),1269—1275)
[8] Kasumov A. Y.,Kociak M.,Guéron S.,Reulet B.,Volkov V. T.,Klinov D. V.,Bouchiat H.,Science,2001,291(5502),280—282
[9] Porath D.,Bezryadin A.,de Vries S.,Dekker C.,Nature,2000,403(6770),635—638
[10] De Pablo P. J.,Moreno-Herrero F.,Colchero J.,Gómez-Herrero J.,Herrero P.,BaróA. M.,Ordejón P.,Soler J. M.,Artacho E.,Phys.Rev. Lett.,2000,85(23),4992—4995
[11] Steinbrecher T.,Koslowski T.,Case D. A.,J. Phys. Chem. B,2008,112(51),16935—16944
[12] Kawai K.,Kodera H.,Osakada Y.,Majima T.,Nat. Chem.,2009,1(2),156—159
[13] Nakatani K.,Dohno C.,Saito I.,J. Am. Chem. Soc.,2000,122(24),5893—5894
[14] Lee A. H. F.,Kool E. T.,J. Am. Chem. Soc.,2006,128(28),9219—9230
[15] Hernández A. R.,Kool E. T.,Org. Lett.,2011,13(4),676—679
[16] Liu H. Y.,Li G. Q.,Zhao P.,Chen G.,Bu Y. X.,Int. J. Quantum Chem.,2014,114(14),911—919
[17] Brancolini G.,Felice R. D.,J. Phys. Chem. B,2008,112(45),14281—14290
[18] Liu H. Y.,Li G. Q.,Ai H. Q.,Li J. L.,Bu Y. X.,J. Phys. Chem. C,2011,115(45),22547—22556
[19] Kawai K.,Kodera H.,Majima T.,J. Am. Chem. Soc.,2010,132(2),627—630
[20] Brancolini G.,Migliore A.,Corni S.,Fuentes-Cabrera M.,Luque F. J.,Di Felice R.,ACS Nano,2013,7(10),9396—9406
[21] Becke A. D.,J. Chem. Phys.,1993,98(7),5648—5652
[22] Lee C.,Yang W.,Parr R. G.,Phys. Rev. B:Condens. Matter,1988,37(2),785—789
[23] Frisch M. J.,Pople J. A.,Binkley J. S.,J. Chem. Phys.,1984,80(7),3265—3269
[24] Frisch M. J.,Trucks G. W.,Schlegel H. B.,Scuseria G. E.,Robb M. A.,Cheeseman J. R.,Scalmani G.,Barone V.,Mennucci B.,Petersson G. A.,Nakatsuji H.,Caricato M.,Li X.,Hratchian H. P.,Izmaylov A. F.,Bloino J.,Zheng G.,Sonnenberg J. L.,Hada M.,Ehara M.,Toyota K.,Fukuda R.,Hasegawa J.,Ishida M.,Nakajima T.,Honda Y.,Kitao O.,Nakai H.,Vreven T.,Montgomery J. A.,Peralta J. E.,Ogliaro F.,Bearpark M.,Heyd J. J.,Brothers E.,Kudin K. N.,Staroverov V. N.,Kobayashi R.,Normand J.,Raghavachari K.,Rendell A.,Burant J. C.,Iyengar S. S.,Tomasi J.,Cossi M.,Rega N.,Millam J. M.,Klene M.,Knox J. E.,Cross J. B.,Bakken V.,Adamo C.,Jaramillo J.,Gomperts R.,Stratmann R. E.,Yazyev O.,Austin A. J.,Cammi R.,Pomelli C.,Ochterski J. W.,Martin R. L.,Morokuma K.,Zakrzewski V. G.,Voth G. A.,Salvador P.,Dannenberg J. J.,Dapprich S.,Daniels A. D.,Farkas O.,Foresman J. B.,Ortiz J. V.,Cioslowski J.,Fox D. J.,Gaussian 09,Revision A.02,Gaussian Inc.,Wallingford CT,2009
[25] RappéA. K.,Bernstein E. R.,J. Phys. Chem. A,2000,104(26),6117—6128
[26] Boys S. F.,Bernardi F.,Mol. Phys.,1970,19(4),553—566
[27] Wang M.,Wang J.,Bu Y. X.,Chem. J. Chinese Universities,2015,36(11),2271—2282(王梅,王军,步宇翔.高等学校化学学报,2015,36(11),2271—2282)
[28] Liu C.,Wang Y.,Zhao D.,Gong L. D.,Yang Z. Z.,J. Mol. Graph. Model.,2014,47,62—76
[29] Yang B.,Rodgers M. T.,J. Am. Chem. Soc.,2014,136(1),282—290
[30] Jissy A. K.,Datta A.,J. Phys. Chem. Lett.,2014,5(1),154—166
[31] Foresman J. B.,Head-Gordon M.,Pople J. A.,Frisch M. J.,J. Phys. Chem.,1992,96(1),135—149
[32] Dreuw A.,Head-Gordon M.,Chem. Rev.,2005,105(11),4009—4037
[33] Shukla M. K.,Leszczynski J.,J. Phys. Chem. B,2005,109(36),17333—17339
[34] Zhang L.,Bu Y.,J. Phys. Chem. B,2008,112(34),10723—10731
[35] Broo A.,Holmén A.,J. Phys. Chem. A,1997,101(19),3589—3600
[36] Holmén A.,Broo A.,Albinsson B.,Nordén B.,J. Am. Chem. Soc.,1997,119(50),12240—12250
[37] Gorelsky S. I.,SWizard Program,Revision 4. 4,Centre for Catalysis Research and Innovation,University of Ottawa,Ottawa,2010(http://www.sg-chem.net/swizard)
[38] Atomistix Tool Kit Version 2015.1,Quantum Wise A/S,De nmark,2015(http://www.quantumwise.com)
[39] Brandbyge M.,Mozos J. L.,Ordejón P.,Taylor J.,Stokbro K.,Phys. Rev. B,2002,65,165401
[40] Staykov A.,Tsuji Y.,Yoshizawa K.,J. Phys. Chem. C,2011,115(8),3481—3490
[41] Smeu M.,Wolkow R. A.,Guo H.,J. Am. Chem. Soc.,2009,131(31),11019—11026
[42] Jiang L. M.,Qiu W.,Al-Dirini F.,Hossain F. M.,Evans R.,Skafidas E.,Appl. Phys.,2016,120(2),025501
[43] Liu H. M.,Wang N.,Zhao J. W.,Guo Y.,Yin X.,Boey F. Y. C.,Zhang H.,Chem. Phys. Chem.,2008,9(10),1416—1424
[44] Cohen R.,Stokbro K.,Martin J. M. L.,Ratner M. A.,J. Phys. Chem. C,2007,111(40),14893—14902
[45] Tada T.,Kondo M.,Yoshizawa K.,Chem. Phys. Chem.,2003,4(11),1256—1260
[46] Lukas M.,Kelly R. E. A.,Kantorovich L. N.,Otero R.,Xu W.,Laegsgaard E.,Stensgaard I.,Besenbacher F.,J. Chem. Phys.,2009,130(2),024705
[47] Perdew J. P.,Burke K.,Ernzerhof M.,Phys. Rev. Lett.,1996,77(18),3865—3868
[48] Troullier N.,Martins J. L.,Phys. Rev. B,1991,43(3),1993—2006
[49] Soler J. M.,Artacho E.,Gale J. D.,Garcia A.,Junquera J.,Ordejon P.,Sanchez-Portal D.,Physics,2002,14(11),2745—2779
[50] Monkhorst H. J.,Pack J. D.,Phys. Rev. B,1976,13(12),5188—5192
[51] Grimme S.,Antony J.,Ehrlich S.,Krieg H.,J. Chem. Phys.,2010,132(15),154104
[52] Piccirilli J. A.,Krauch T.,Moroney S. E.,Benner S. A.,Nature,1990,343(6253),33—37
[53] Okamoto A.,Maeda Y.,Tsukamoto T.,Ishikawa Y.,Kurita N.,Comp. Mater. Sci.,2012,53(1),416—424
[54] Nakano S.,Sugimoto N.,Molecules,2014,19(8),11613—11627
[55] Gervasio F. L.,Boero M.,Parrinello M.,Angew. Chem. Int. Ed.,2006,45(34),5606—5609
[56] Reynisson J.,Steenken S.,Phys. Chem. Chem. Phys.,2002,4,5353—5358
[57] Zhao Y.,Truhlar D. G.,Acc. Chem. Res.,2008,41(2),157—167
[58] Zhao Y.,Truhlar D. G.,Theor. Chem. Acc.,2008,120(1—3),215—241
[2] Xiang D.,Wang X. L.,Jia C. C.,Lee T.,Guo X. F.,Chem. Rev.,2016,116(7),4318—4440
[3] Wang L.,Li Z.,Shen X. Q.,Ma N.,Chem. J. Chinese Universities,2018,39(1),32—40(王莉,李智,沈晓琴,马楠.高等学校化学学报,2018,39(1),32—40)
[4] Behnia S.,Fathizadeh S.,Akhshani A.,J. Phys. Chem. C,2016,120(5),2973—2983
[5] Shipman S. L.,Nivala J.,Macklis J. D.,Church G. M.,Nature,2017,547(7663),345—349
[6] Lin M. H.,Wen Y. L.,Li L. Y.,Pei H.,Liu G.,Song H. Y.,Zuo X. L.,Fan C. H.,Huang Q.,Anal. Chem.,2014,86(5),2285—2288
[7] Li M.,Kong H. F.,Guo Z. H.,Chem. J. Chinese Universities,2016,37(7),1269—1275(李敏,孔慧芳,郭志慧.高等学校化学学报,2016,37(7),1269—1275)
[8] Kasumov A. Y.,Kociak M.,Guéron S.,Reulet B.,Volkov V. T.,Klinov D. V.,Bouchiat H.,Science,2001,291(5502),280—282
[9] Porath D.,Bezryadin A.,de Vries S.,Dekker C.,Nature,2000,403(6770),635—638
[10] De Pablo P. J.,Moreno-Herrero F.,Colchero J.,Gómez-Herrero J.,Herrero P.,BaróA. M.,Ordejón P.,Soler J. M.,Artacho E.,Phys.Rev. Lett.,2000,85(23),4992—4995
[11] Steinbrecher T.,Koslowski T.,Case D. A.,J. Phys. Chem. B,2008,112(51),16935—16944
[12] Kawai K.,Kodera H.,Osakada Y.,Majima T.,Nat. Chem.,2009,1(2),156—159
[13] Nakatani K.,Dohno C.,Saito I.,J. Am. Chem. Soc.,2000,122(24),5893—5894
[14] Lee A. H. F.,Kool E. T.,J. Am. Chem. Soc.,2006,128(28),9219—9230
[15] Hernández A. R.,Kool E. T.,Org. Lett.,2011,13(4),676—679
[16] Liu H. Y.,Li G. Q.,Zhao P.,Chen G.,Bu Y. X.,Int. J. Quantum Chem.,2014,114(14),911—919
[17] Brancolini G.,Felice R. D.,J. Phys. Chem. B,2008,112(45),14281—14290
[18] Liu H. Y.,Li G. Q.,Ai H. Q.,Li J. L.,Bu Y. X.,J. Phys. Chem. C,2011,115(45),22547—22556
[19] Kawai K.,Kodera H.,Majima T.,J. Am. Chem. Soc.,2010,132(2),627—630
[20] Brancolini G.,Migliore A.,Corni S.,Fuentes-Cabrera M.,Luque F. J.,Di Felice R.,ACS Nano,2013,7(10),9396—9406
[21] Becke A. D.,J. Chem. Phys.,1993,98(7),5648—5652
[22] Lee C.,Yang W.,Parr R. G.,Phys. Rev. B:Condens. Matter,1988,37(2),785—789
[23] Frisch M. J.,Pople J. A.,Binkley J. S.,J. Chem. Phys.,1984,80(7),3265—3269
[24] Frisch M. J.,Trucks G. W.,Schlegel H. B.,Scuseria G. E.,Robb M. A.,Cheeseman J. R.,Scalmani G.,Barone V.,Mennucci B.,Petersson G. A.,Nakatsuji H.,Caricato M.,Li X.,Hratchian H. P.,Izmaylov A. F.,Bloino J.,Zheng G.,Sonnenberg J. L.,Hada M.,Ehara M.,Toyota K.,Fukuda R.,Hasegawa J.,Ishida M.,Nakajima T.,Honda Y.,Kitao O.,Nakai H.,Vreven T.,Montgomery J. A.,Peralta J. E.,Ogliaro F.,Bearpark M.,Heyd J. J.,Brothers E.,Kudin K. N.,Staroverov V. N.,Kobayashi R.,Normand J.,Raghavachari K.,Rendell A.,Burant J. C.,Iyengar S. S.,Tomasi J.,Cossi M.,Rega N.,Millam J. M.,Klene M.,Knox J. E.,Cross J. B.,Bakken V.,Adamo C.,Jaramillo J.,Gomperts R.,Stratmann R. E.,Yazyev O.,Austin A. J.,Cammi R.,Pomelli C.,Ochterski J. W.,Martin R. L.,Morokuma K.,Zakrzewski V. G.,Voth G. A.,Salvador P.,Dannenberg J. J.,Dapprich S.,Daniels A. D.,Farkas O.,Foresman J. B.,Ortiz J. V.,Cioslowski J.,Fox D. J.,Gaussian 09,Revision A.02,Gaussian Inc.,Wallingford CT,2009
[25] RappéA. K.,Bernstein E. R.,J. Phys. Chem. A,2000,104(26),6117—6128
[26] Boys S. F.,Bernardi F.,Mol. Phys.,1970,19(4),553—566
[27] Wang M.,Wang J.,Bu Y. X.,Chem. J. Chinese Universities,2015,36(11),2271—2282(王梅,王军,步宇翔.高等学校化学学报,2015,36(11),2271—2282)
[28] Liu C.,Wang Y.,Zhao D.,Gong L. D.,Yang Z. Z.,J. Mol. Graph. Model.,2014,47,62—76
[29] Yang B.,Rodgers M. T.,J. Am. Chem. Soc.,2014,136(1),282—290
[30] Jissy A. K.,Datta A.,J. Phys. Chem. Lett.,2014,5(1),154—166
[31] Foresman J. B.,Head-Gordon M.,Pople J. A.,Frisch M. J.,J. Phys. Chem.,1992,96(1),135—149
[32] Dreuw A.,Head-Gordon M.,Chem. Rev.,2005,105(11),4009—4037
[33] Shukla M. K.,Leszczynski J.,J. Phys. Chem. B,2005,109(36),17333—17339
[34] Zhang L.,Bu Y.,J. Phys. Chem. B,2008,112(34),10723—10731
[35] Broo A.,Holmén A.,J. Phys. Chem. A,1997,101(19),3589—3600
[36] Holmén A.,Broo A.,Albinsson B.,Nordén B.,J. Am. Chem. Soc.,1997,119(50),12240—12250
[37] Gorelsky S. I.,SWizard Program,Revision 4. 4,Centre for Catalysis Research and Innovation,University of Ottawa,Ottawa,2010(http://www.sg-chem.net/swizard)
[38] Atomistix Tool Kit Version 2015.1,Quantum Wise A/S,De nmark,2015(http://www.quantumwise.com)
[39] Brandbyge M.,Mozos J. L.,Ordejón P.,Taylor J.,Stokbro K.,Phys. Rev. B,2002,65,165401
[40] Staykov A.,Tsuji Y.,Yoshizawa K.,J. Phys. Chem. C,2011,115(8),3481—3490
[41] Smeu M.,Wolkow R. A.,Guo H.,J. Am. Chem. Soc.,2009,131(31),11019—11026
[42] Jiang L. M.,Qiu W.,Al-Dirini F.,Hossain F. M.,Evans R.,Skafidas E.,Appl. Phys.,2016,120(2),025501
[43] Liu H. M.,Wang N.,Zhao J. W.,Guo Y.,Yin X.,Boey F. Y. C.,Zhang H.,Chem. Phys. Chem.,2008,9(10),1416—1424
[44] Cohen R.,Stokbro K.,Martin J. M. L.,Ratner M. A.,J. Phys. Chem. C,2007,111(40),14893—14902
[45] Tada T.,Kondo M.,Yoshizawa K.,Chem. Phys. Chem.,2003,4(11),1256—1260
[46] Lukas M.,Kelly R. E. A.,Kantorovich L. N.,Otero R.,Xu W.,Laegsgaard E.,Stensgaard I.,Besenbacher F.,J. Chem. Phys.,2009,130(2),024705
[47] Perdew J. P.,Burke K.,Ernzerhof M.,Phys. Rev. Lett.,1996,77(18),3865—3868
[48] Troullier N.,Martins J. L.,Phys. Rev. B,1991,43(3),1993—2006
[49] Soler J. M.,Artacho E.,Gale J. D.,Garcia A.,Junquera J.,Ordejon P.,Sanchez-Portal D.,Physics,2002,14(11),2745—2779
[50] Monkhorst H. J.,Pack J. D.,Phys. Rev. B,1976,13(12),5188—5192
[51] Grimme S.,Antony J.,Ehrlich S.,Krieg H.,J. Chem. Phys.,2010,132(15),154104
[52] Piccirilli J. A.,Krauch T.,Moroney S. E.,Benner S. A.,Nature,1990,343(6253),33—37
[53] Okamoto A.,Maeda Y.,Tsukamoto T.,Ishikawa Y.,Kurita N.,Comp. Mater. Sci.,2012,53(1),416—424
[54] Nakano S.,Sugimoto N.,Molecules,2014,19(8),11613—11627
[55] Gervasio F. L.,Boero M.,Parrinello M.,Angew. Chem. Int. Ed.,2006,45(34),5606—5609
[56] Reynisson J.,Steenken S.,Phys. Chem. Chem. Phys.,2002,4,5353—5358
[57] Zhao Y.,Truhlar D. G.,Acc. Chem. Res.,2008,41(2),157—167
[58] Zhao Y.,Truhlar D. G.,Theor. Chem. Acc.,2008,120(1—3),215—241