The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine-thymine and guanine-cytosine base pairs

Journal of Computer-Aided Molecular Design

Volumn 24, Issue 5, 2010, Pages 409-416

  Ebrahimi, A ^a   Khorassani, S M Habibi ^a   Delarami, H ^a   Esmaeeli, H ^a  

^a UNIVERSITY OF SISTAN AND BALUCHESTAN   (Iran)

Author keywords

Adenine thymine; Base pair; Electron density; Guanine cytosine; Individual hydrogen bond

Indexed keywords

BINDING ENERGY; ELECTRON DENSITY MEASUREMENT; ELECTRONS; GEOMETRY; HYDROGEN BONDS; NITROGEN OXIDES; POSITIVE IONS; QUANTUM THEORY;

ADENINE-THYMINE; BASE PAIRS; ELECTRON-DONATING; ELECTRON-WITHDRAWING SUBSTITUENTS; GUANINE; GUANINE CYTOSINES; INDIVIDUAL HYDROGEN BOND; INDIVIDUAL HYDROGEN BOND ENERGIES; QUANTUM-MECHANICAL CALCULATION; SUBSTITUENT EFFECT;

CARRIER CONCENTRATION;

ADENINE; AMINO ACID; CYTOSINE; FLUORIDE; GUANINE; METHENE; NITRITE; THYMINE; UNCLASSIFIED DRUG; DNA;

AMINO ACID SUBSTITUTION; ARTICLE; ATOM; BASE PAIRING; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; CONTROLLED STUDY; GEOMETRY; HYDROGEN BOND; PRIORITY JOURNAL; QUANTUM MECHANICS; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; STATIC ELECTRICITY; THERMODYNAMICS;

BASE PAIRING; COMPUTER SIMULATION; DNA; HYDROGEN BONDING; MODELS, CHEMICAL; MOLECULAR STRUCTURE; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 77953326812     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-010-9348-2     Document Type: Article

References (43)

1. C Xue PLA Popelier 2008 Computational study of substituent effects on the interaction energies of hydrogen-bonded Watson-Crick cytosine-guanine base pairs J Phys Chem B 112 5257 5264 10.1021/jp7108913 1:CAS:528: DC%2BD1cXjvFejtb0%3D
2. JD Watson FHC Crick 1953 A structure for deoxyribose nucleic acid Nature 171 737 738 10.1038/171737a0 1:CAS:528:DyaG2cXivVGktA%3D%3D
3. S Brenner F Jacob M Meselson 1961 An unstable intermediate carrying information from genes to ribosomes for protein synthesis Nature 190 576 581 10.1038/190576a0 1:CAS:528:DyaF3MXhtlWktr8%3D
4. CF Guerra FM Bickelhaupt JG Snijders EJ Baerends 1999 The nature of the hydrogen bond in DNA base pairs: the role of charge transfer and resonance assistance Chem A Eur J 5 3581 3594 10.1002/(SICI)1521-3765(19991203)5: 12<3581::AID-CHEM3581>3.0.CO;2-Y 1:CAS:528:DyaK1MXnvFKmsrY%3D
5. P Hobza J Sponer 1999 Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations Chem Rev 99 3247 3276 10.1021/cr9800255 1:CAS:528:DyaK1MXmsFarurY%3D
6. P Hobza R Zahradnik K Mueller-Dethlefs 2006 The world of non-covalent interactions Chem Commun 71 443 531 1:CAS:528:DC%2BD28XkslCmtbo%3D
7. OV Shishkin J Sponer P Hobza 1999 Intramolecular flexibility of DNA bases in adenine-thymine and guanine-cytosine Watson-Crick base pairs J Mol Struct 477 15 21 10.1016/S0022-2860(98)00603-6 1:CAS:528:DyaK1MXht1Oku7w%3D (Pubitemid 29159722)
8. 2) on the A-T and G-C base pairs: a theoretical study Chem Phys Lett 373 72 78 10.1016/S0009-2614(03)00590-6 1:CAS:528:DC%2BD3sXjs1Cmu7Y%3D (Pubitemid 36567404)
9. SI Kawahara T Uchimaru K Taira M Sekine 2002 An ab initio study of the hydrogen bond energy of base pairs formed between substituted 9-methylguanine derivatives and 1-methylcytosine J Phys Chem A 106 3207 3212 10.1021/jp0139538 1:CAS:528:DC%2BD38XhsF2itrg%3D (Pubitemid 35264132)
10. SI Kawahara A Kobori M Sekine T Uchimaru 2001 Theoretical study of the hydrogen bond energy of base pairs formed between substituted 1-methylcytosine derivatives and 9-methylguanine J Phys Chem A 105 10596 10601 10.1021/jp0124645 1:CAS:528:DC%2BD3MXnvVWmsLk%3D (Pubitemid 35378442)
11. SI Kawahara T Wada S Kawauchi T Uchimaru M Sekine 1999 Ab initio and density functional studies of substituent effects of an A-U base pair on the stability of hydrogen bonding J Phys Chem A 103 8516 8523 10.1021/jp9914525 1:CAS:528:DyaK1MXmt12mtbY%3D
12. SI Kawahara T Uchimaru K Taira M Sekine 2001 Ab initio evaluation of the substitution effect of the hydrogen bond energy of the Watson-Crick type base pair between 1-methyluracil and substituted 9-methyladenine derivatives J Phys Chem A 105 3894 3898 10.1021/jp004117l 1:CAS:528:DC%2BD3MXitFeksr0%3D (Pubitemid 35377874)
13. CX Xue PLA Popelier 2009 Prediction of interaction energies of substituted hydrogen-bonded Watson-Crick cytosine-guanine (8X) base pairs J Phys Chem B 113 3245 3250 10.1021/jp8071926 1:CAS:528:DC%2BD1MXhvFymurs%3D
14. A Moser R Guza N Tretyakova 2009 Density functional study of the influence of C5 cytosine substitution in base pairs with guanine Theor Chem Account 122 179 188 10.1007/s00214-008-0497-5 1:CAS:528:DC%2BD1MXhvF2ms7o%3D
15. JV Burda J Sponer P Hobza 1996 Ab initio study of the interaction of guanine and adenine with various mono-and bivalent metal cations (Li+, Na+, K+, Cs+; Cu+, Ag+, Au+; Mg2+, Ca2+, Sr2+, Ba2+; Zn2+, Cd2+, and Hg2+) J Phys Chem 100 7250 7255 10.1021/jp952941h 1:CAS:528:DyaK28XitVaqu74%3D
16. C Fonseca Guerra FM Bickelhaupt JG Snijders EJ Baerends 2000 Hydrogen bonding in DNA base pairs: reconciliation of theory and experiment J Am Chem Soc 122 4117 4128 10.1021/ja993262d (Pubitemid 30304846)
17. N Russo M Toscano A Grand 2001 Bond energies and attachments sites of sodium and potassium cations to DNA and RNA nucleic acid bases in the gas phase J Am Chem Soc 123 10272 10279 10.1021/ja010660j 1:CAS:528:DC%2BD3MXnsFChs7Y%3D (Pubitemid 32979776)
18. AS Petrov G Lamm GR Pack 2002 Water-mediated magnesium-guanine interactions J Phys Chem B 106 3294 3300 10.1021/jp013941m 1:CAS:528: DC%2BD38XhsF2qtr8%3D (Pubitemid 35290282)
19. + binding to the DNA and RNA nucleobases bond energies and attachment sites from the dissociation of metal ion-bound heterodimers J Am Chem Soc 118 11884 11892 10.1021/ja9613421 1:CAS:528:DyaK28Xmslaqurw%3D (Pubitemid 26417478)
20. 2+ cation with bases, base pairs, and nucleotides electron topology, natural bond orbital, electrostatic, and vibrational study J Phys Chem B 105 6051 6060 10.1021/jp010486l 1:CAS:528:DC%2BD3MXktVCrsbo%3D (Pubitemid 35339120)
21. 2+ with guanine, adenine, and the guanine-cytosine and adenine-thymine base pairs structures and energies characterized by polarizable molecular mechanics and ab initio calculations J Phys Chem B 103 11415 11427 10.1021/jp9921351 1:CAS:528:DyaK1MXnslSktro%3D
22. J Sponer M Sabat L Gorb J Leszczynski B Lippert P Hobza 2000 The effect of metal binding to the N7 Site of purine nucleotides on their structure, energy, and involvement in base pairing J Phys Chem B 104 7535 7544 10.1021/jp001711m 1:CAS:528:DC%2BD3cXks1ehtbc%3D
23. SR Gadre SS Pundlik AC Limaye AP Rendell 1998 Electrostatic investigation of metal cation binding to DNA bases and base pairs Chem Commun 5 573 574 10.1039/a708372f
24. + cation coupling J Phys Chem B 109 593 600 10.1021/jp0459817 1:CAS:528:DC%2BD2cXhtVGktr3F (Pubitemid 40134464)
25. A Destexhe J Smets L Adamowicz G Maes 1994 Matrix isolation FT-IR studies and ab initio calculations of hydrogen-bonded complexes of molecules modeling cytosine or isocytosine tautomers. 1. pyridine and pyrimidine complexes with water in argon matrixes J Phys Chem 98 1506 1514 10.1021/j100056a023 1:CAS:528:DyaK2cXhtVSqtL4%3D
26. IR Gould PA Kollman 1994 Theoretical investigation of the hydrogen bond strengths in guanine-cytosine and adenine-thymine base pairs J Am Chem Soc 116 2493 2499 10.1021/ja00085a033 1:CAS:528:DyaK2cXhvVGmtrw%3D
27. P Hobza J Sponer M Polasek 1995 H-bonded and stacked DNA base pairs: cytosine dimer An ab initio second-order moller-plesset study J Am Chem Soc 117 792 798 10.1021/ja00107a023 1:CAS:528:DyaK2MXivFOqsbc%3D
28. J Sponer P Hobza 1996 Nonempirical ab initio calculations on DNA base pairs Chem Phys 204 365 372 10.1016/0301-0104(95)00311-8 1:CAS:528: DyaK28XitFCjurw%3D
29. J Sponer P Hobza 1996 Thermodynamic characteristics for the formation of H-bonded DNA base pairs Chem Phys Lett 261 379 384 10.1016/0009-2614(96)00954-2 (Pubitemid 126163434)
30. J Sponer J Leszczynski P Hobza 1996 Nature of nucleic acid-base stacking: nonempirical ab initio and empirical potential characterization of 10 stacked base dimers comparison of stacked and H-bonded base pairs J Phys Chem 100 5590 5596 10.1021/jp953306e 1:CAS:528:DyaK28XhsVGnsrs%3D
31. J Sponer P Hobza 2000 Interaction energies of hydrogen-bonded formamide dimer, formamidine dimer, and selected DNA base pairs obtained with large basis sets of atomic orbitals J Phys Chem A 104 4592 4597 10.1021/jp9943880 1:CAS:528:DC%2BD3cXisVKkurg%3D
32. A Asensio N Kobko JJ Dannenberg 2003 Cooperative hydrogen-bonding in adenine-thymine and guanine-cytosine base pairs density functional theory and moller-plesset molecular orbital study J Phys Chem A 107 6441 6443 10.1021/jp0344646 1:CAS:528:DC%2BD3sXlslKnu74%3D
33. J Grunenberg 2004 Direct assessment of interresidue forces in Watson-Crick base pairs using theoretical compliance constants J Am Chem Soc 126 16310 16311 10.1021/ja046282a 1:CAS:528:DC%2BD2cXhtVCisb7L (Pubitemid 40081915)
34. H Dong W Hua S Li 2007 Estimation on the individual hydrogen-bond strength in molecules with multiple hydrogen bonds J Phys Chem A 111 2941 2945 10.1021/jp0709860 1:CAS:528:DC%2BD2sXjsVGrt7o%3D (Pubitemid 46686281)
35. A Ebrahimi SM Habibi khorasani H Delarami 2009 Estimation of individual binding energies in some dimers involving multiple hydrogen bonds using topological properties of electron charge density Chem Phys 365 18 23 10.1016/j.chemphys.2009.09.013 1:CAS:528:DC%2BD1MXhtlOksL%2FK
36. +/GC base pair derivatives Chem Phys 308 117 123 10.1016/j.chemphys.2004.08.003 1:CAS:528:DC%2BD2cXpslOjs7Y%3D
37. Bader RFW (1990) Atoms in molecules: a quantum theory. Oxford University Press, Oxford
38. AD Backe 1993 Density-functional thermochemistry. III. The role of exact exchange J Chem Phys 98 5648 5652 10.1063/1.464913
39. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2003) Gaussian03 (Revision B03). Gaussian, Inc, Pitts burgh, PA
40. SB Boys F Bernardi 1970 The calculations of small molecular interaction by the difference of separate total energies some procedures with reduce error Mol Phys 19 553 566 10.1080/00268977000101561 1:CAS:528:DC%2BD2sXht1alt7fM
41. FW Biegler Konig J Schonbohm D Bayles 2001 Software news and updates AIM2000 J Comput Chem 22 545 559 10.1002/1096-987X(20010415)22:5<545::AID- JCC1027>3.0.CO;2-Y (Pubitemid 32291692)
42. AE Reed LA Curtiss F Weinhold 1988 Intramolecular interactions from a natural bond orbital, donor-acceptor viewpoint Chem Rev 88 899 936 10.1021/cr00088a005 1:CAS:528:DyaL1cXmtlOitbw%3D
43. Glendening D, Reed AE, Carpenter JE, Weinhold F, NBO version 3.1