Probing the nature of hydrogen bonds in DNA base pairs

Journal of Molecular Modeling

Volumn 12, Issue 5, 2006, Pages 665-672

  Mo, Yirong ^a  

^a WESTERN MICHIGAN UNIVERSITY   (United States)

Author keywords

Charge transfer; DNA base pair; Electrostatic interaction; Hydrogen bond; Resonance assisted hydrogen bonding (RAHB)

Indexed keywords

ADENINE; AMINE; CARBONYL DERIVATIVE; CYTOSINE; DNA BASE; GUANINE; HYDROGEN; THYMINE;

ANALYTIC METHOD; ARTICLE; BASE PAIRING; CALCULATION; CHEMICAL ANALYSIS; CONTROLLED STUDY; COVALENT BOND; DECOMPOSITION; DIPOLE; ELECTRICITY; ELECTRON TRANSPORT; ENERGY; EXPERIMENTAL STUDY; HYDROGEN BOND; MOLECULAR INTERACTION; MOLECULAR MODEL; MOLECULAR STABILITY; PRIORITY JOURNAL; THEORETICAL STUDY;

BASE PAIRING; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DNA; ELECTRONS; HYDROGEN BONDING; IMAGING, THREE-DIMENSIONAL; MODELS, MOLECULAR;

EID: 33746432117     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-005-0021-y     Document Type: Article

References (55)

1. Burkert U, Allinger NL (1982) Molecular mechanics. American Chemical Society, Washington DC
2. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comp Chem 4:187-217
3. Reindl B, Clark T, Schleyer PvR (1996) J Comp Chem 17:1406-1430
4. Kitaura K, Morokuma K (1976) Int J Quantum Chem 10:325-340
5. Stevens WJ, Fink WH (1987) Chem Phys Lett 139:15-22
6. Gutowski M, Piela L (1988) Mol Phys 64:337-355
7. Cybulski SM, Scheiner S (1990) Chem Phys Lett 166:57-64
8. Moszynski R, Heijmen TGA, Jeziorski B (1994) Mol Phys 88:741-758
9. Glendening ED, Streitwieser A (1994) J Chem Phys 100:2900-2909
10. van der Vaart A, Merz KM Jr (1999) J Phys Chem A 103:3321-3329
11. Mo Y, Gao J, Peyerimhoff SD (2000) J Chem Phys 112:5530-5538
12. Gentle IR, Ritchie GLD (1989) J Phys Chem 93:7740-7744
13. Craven IE, Hesling MR, Laver DR, Lukins PB, Ritchie GLD, Vrbancich J (1989) J Phys Chem 93:627-631
14. Dougherty DA (1996) Science 271:163-168
15. Mecozzi S, West AP, Dougherty DA (1996) J Am Chem Soc 118:2307-2308
16. Cubero E, Luque FJ, Orozco M (1998) Proc Natl Acad Sci USA 95:5976-5980
17. Caldwell JW, Kollman PA (1995) J Am Soc Chem 117:4177-4178
18. Mo Y, Subramanian G, Ferguson DM, Gao J (2002) J Am Chem Soc 124:4832-4837
19. Morokuma K (1977) Acc Chem Res 10:294-300
20. Jeffrey GA (1997) An introduction to hydrogen bonding. Oxford University Press, New York
21. Šponer J, Jurecka P, Hobza P (2004) J Am Chem Soc 126:10142-10151
22. Cheatham TE III, Kollman PA (2000) Ann Rev Phys Chem 51:435-471
23. Kratochvíl M, Šponer J, Hobza P (2000) J Am Chem Soc 122:3495-3499
24. Guerra CF, Bickelhaupt FM (1999) Angew Chem Int Ed 38:2942-2945
25. Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (1999) Chem Eur J 5:3581-3594
26. Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (2000) J Am Chem Soc 122:4117-4128
27. Mo Y, Peyerimhoff SD (1998) J Chem Phys 109:1687-1697
28. Cubero E, Luque FJ, Orozco M (2001) J Am Chem Soc 123:12018-12025
29. Boys SF, Bernardi F (1970) Mol Phys 19:553-566
30. Mo Y, Gao J (2001) J Phys Chem A 105:6530-6536
31. Mo Y, Song L, Wu W, Zhang Q (2004) J Am Chem Soc 126:3974-3982
32. Gianinetti E, Raimondi, Tornaghi E (1996) Int J Quantum Chem 60:157-166
33. Gianinetti E, Vandoni I, Famulari A, Raimondi M (1998) Adv Quantum Chem 31:251-266
34. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JJ, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA (1993) J Comput Chem 14:1347-1363
35. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JAJ, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian 98, Ed. A.9. Gaussian Inc, Pittsburgh PA
36. Bertran J, Oliva A, Rodríguez-Santiago L, Sodupe M (1998) J Am Chem Soc 120:8159-8167
37. Brameld K, Dasgupta S, Goddard WA III (1997) J Phys Chem B 101:4851-4859
38. Gilli G, Bellucci F, Ferretti V, Bertolasi V (1989) J Am Chem Soc 111:1023-1028
39. Bertolasi V, Gilli P, Ferretti V, Gilli G (1991) J Am Chem Soc 113:4917-4925
40. Steiner T (1998) Chem Commun 411-412
41. Gilli P, Bertolasi V, Ferretti V, Gilli G (2000) J Am Chem Soc 122:10405-10417
42. Munn RW, Eckhardt CJ (2001) J Phys Chem A 105:6938-6942
43. Gilli P, Bertolasi V, Pretto L, Ferretti V, Gilli G (2004) J Am Chem Soc 126:3845-3855
44. Fiacco DL, Mo Y, Hunt SW, Ott ME, Roberts A, Leopold KR (2000) J Phys Chem A 105:484-493
45. Sutor DJ (1962) Nature 195:68-69
46. Desiraju GR, Steiner T (2001) The weak hydrogen bond in structural chemistry and biology. Oxford University Press, New York
47. Meadows ES, De Wall SL, Barbour LJ, Fronczek FR, Kim M-S, Gokel GW (2000) J Am Chem Soc 122:3325-3335
48. Senes A, Ubarretxena-Belandia I, Engelman DM (2001) Proc Natl Acad Sci USA 98:9056-9061
49. Aravinda S, Shamala N, Bandyopadhyay A, Balaram P (2003) J Am Chem Soc 125:15065-15075
50. Manikandan K, Ramakumar S (2004) Proteins 56:768-781
51. Petrella RJ, Karplus M (2004). Proteins 54:716-726
52. Guo H, Beahm RF, Guo H (2004) J Phys Chem B 108:18065-18072
53. Šponer J, Leszczynski J, Hobza P (1996) J Phys Chem 100:1965-1974
54. Šponer J, Hobza P (1998) In: Schleyer PvR (ed) Encyclopedia of computational chemistry. Wiley, New York, pp 777-789
55. Saenger W (1984) Principles of nucleic acid structure (and references therein). Springer, Berlin Heidelberg New York, pp 123-124