Structural and electronic structure differences due to the O-H···O and O-H···S bond formation in selected benzamide derivatives: A first-principles molecular dynamics study

Theoretical Chemistry Accounts

Volumn 124, Issue 5-6, 2009, Pages 319-330

  Jezierska, Aneta ^a,b   Panek, Jarosław J ^b   Mazzarello, Riccardo ^c  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b UNIVERSITY OF WROC AW   (Poland)

^c ETH ZURICH   (Switzerland)

Author keywords

Atoms in molecules; Car Parrinello molecular dynamics (CPMD); Intramolecular hydrogen bond; Path integrals molecular dynamics (PIMD)

Indexed keywords

EID: 77949874764     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-009-0612-2     Document Type: Article

References (76)

1. Soldatos CR, Kales A, Bixler EO, Scharf MB, Kales JD (1978) Pharmacol 16: 193-198.
2. Kirk RE, Othmer DF (1997) Kirk-Othmer encyclopedia of chemical technology, vol 21, 4th edn. Wiley, New York, pp 601-626.
3. Way EL, Takemori AE, Smith GE Jr, Anderson HH, Brodie DC (1953) J Pharmacol Exp Ther 108: 450-460.
4. Fuente De La R, Sonawane ND, Arumainayagam D, Verkman AS (2006) Br J Pharmacol 149: 551-559.
5. Zhu X-F, Wang J-S, Cai L-L, Zeng Y-X, Yang D (2006) Cancer Sci 97: 84-89.
6. Agrawal VK, Sharma S (1984) Pharmazie 39: 373-378.
7. Brown ME, Fitzner JN, Stevens T, Chin W, Wright CD, Boyce JP (2008) Bioorg Med Chem 16: 8760-8764.
8. Wagner G, Singer D, Weuffen W (1966) Pharmazie 21: 161-166.
9. Weuffen W, Wagner G, Singer D, Hellmuth L (1966) Pharmazie 21: 477-482.
10. Sur K, Shome SC (1971) Anal Chim Acta 57: 201-208.
11. Sur K, Mazumdar M, Shome SC (1972) Anal Chim Acta 59: 306-310.
12. Banerjee K, Raychaudhury S (1982) Bull Chem Soc Jpn 55: 3621-3624.
13. Hay BP, Dixon DA, Vargas R, Garza J, Raymond KN (2001) Inorg Chem 40: 3922-3935.
14. Padwa A, Beall LS, Heidelbaugh TM, Liu B, Sheehan SM (2000) J Org Chem 65: 2684-2695.
15. Price SL (2009) Acc Chem Res 42: 117-126.
16. Jeffrey GA (1997) An introduction to hydrogen bonding. Oxford University Press, New York.
17. Grabowski S (2006) Hydrogen bonding-new insights. Challenges and advances in computational chemistry and physics 3. Springer, Dordrecht.
18. Hobza P, Havlas Z (2000) Chem Rev 100: 4253.
19. Saam J, Tajkhorshid E, Hayashi S, Schulten K (2002) Biophys J 83: 3097-3112.
20. Haas AH, Lancaster CRD (2004) Biophys J 87: 4298-4315.
21. Betzel C, Gourinath S, Kumar P, Kaur P, Perbandt M, Eschenburg S, Singh TP (2001) Biochemistry 40: 3080-3088.
22. Bertolasi V, Gilli P, Ferretti V, Gilli G (1996) Chem Eur J 2: 925-934.
23. Tour JM, Kozaki M, Seminario JM (1998) J Am Chem Soc 120: 8486-8493.
24. Alarcón SH, Olivieri AC, Sanz D, Claramunt RM, Elguero J (2004) J Mol Struct 705: 1-9.
25. Sobczyk L, Grabowski SJ, Krygowski TM (2005) Chem Rev 105: 3513-3560.
26. Hammes-Schiffer S (2001) Acc Chem Res 34: 273-281.
27. Peters KS (2009) Acc Chem Res 42: 89-96.
28. Iordanova N, Hammes-Schiffer S (2002) J Am Chem Soc 124: 4848-4856.
29. Szatyłowicz H, Krygowski TM, Hobza P (2007) J Phys Chem A 111: 170-175.
30. Szatyłowicz H, Krygowski TM, Zachara-Horeglad JE (2007) J Chem Inf Model 47: 875-886.
31. Szatyłowicz H (2008) J Phys Org Chem 21: 897-914.
32. Gilli G, Bellucci F, Ferretti V, Bertolasi V (1989) J Am Chem Soc 111: 1023-1028.
33. Gilli P, Bertolasi V, Ferretti V, Gilli G (1994) J Am Chem Soc 116: 909-915.
34. Jezierska A, Panek JJ (2009) J Comput Chem 30: 1241-1250.
35. Steiner T (1998) Chem Commun 411-412.
36. Pertlik F (1992) Z Kristallogr 202: 17-23.
37. Steinwender E, Mikenda W (1990) Monatsh Chem 121: 809-820.
38. Mikenda W, Pertlik F, Steinwender E (1993) Monatsh Chem 124: 867-875.
39. Mikenda W, Steinwender E, Mereiter K (1995) Monatsh Chem 126: 495-504.
40. Pertlik F (1990) Monatsh Chem 121: 129-139.
41. Jezierska A, Novič M, Panek JJ (2009) Pol J Chem 83: 799-819.
42. Jezierska A, Panek JJ, Koll A (2008) Chem Phys Chem 9: 839-846.
43. Hohenberg P, Kohn W (1964) Phys Rev 136: B864-B871.
44. Kohn W, Sham LJ (1965) Phys Rev 140: A1133-A1138.
45. Car R, Parrinello M (1985) Phys Rev Lett 55: 2471-2474.
46. Marx D, Parrinello M (1996) Science 271: 179-181.
47. Becke AD (1993) J Chem Phys 98: 5648-5652.
48. Lee C, Yang W, Parr RG (1988) Phys Rev B 37: 785-789.
49. Krishnan R, Binkley JS, Seeger R, Pople JA (1980) J Chem Phys 72: 650-654.
50. 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, Bakken V, 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 (2004) Gaussian 03, revision C. 02. Gaussian Inc., Wallingford, CT.
51. Bader RFW (1990) Atoms in molecules. A quantum theory. Clarendon Press, Oxford.
52. Bader RFW (1991) AIMPAC, suite of programs for the theory of atoms in molecules. McMaster University, Hamilton, ON.
53. Perdew JP, Burke K, Ernzerhof M (1996) Phys Rev Lett 77: 3865-3868.
54. Troullier N, Martins JL (1991) Phys Rev B 43: 1993-2006.
55. Schlegel HB (1984) Theor Chim Acta 66: 333-340.
56. Nosé S (1984) Mol Phys 52: 255-268.
57. Nosé S (1984) J Chem Phys 81: 511-519.
58. Hoover WG (1985) Phys Rev A 31: 1695-1697.
59. Monkhorst HJ, Pack JD (1976) Phys Rev B 13: 5188-5192.
60. Marx D, Parrinello M (1996) J Chem Phys 104: 4077-4082.
61. Tuckerman ME, Marx D, Klein ML, Parrinello M (1996) J Chem Phys 104: 5579-5588.
62. Tuckerman ME, Berne BJ, Martyna GJ, Klein ML (1993) J Chem Phys 99: 2796-2808.
63. CPMD Copyright IBM Corp. 1990-2004, Copyright MPI fuer Festkoerperforschung Stuttgart 1997-2001.
64. Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14: 33-38.
65. Gnuplot, Copyright (C) 1986-1993, 1998, 2004 Williams T, Kelley C, Copyright (C) 2004-2007 Broeker HB, Campbell J, Cunningham R, Denholm D, Elber G, Fearick R, Grammes C, Hart L, Hecking L, Koenig T, Kotz D, Kubaitis E, Lang R, Lehmann A, Mai A, Steger C, Tkacik T, van der Woude J, van Zandt JR, Woo A, Merritt E, Mikulík P, Zellner J.
66. Mennucci B, Tomasi J (1997) J Chem Phys 106: 5151-5158.
67. Koch U, Popelier PLA (1995) J Phys Chem 99: 9747-9754.
68. Biswal HS, Chakraborty S, Wategaonkar S (2008) J Chem Phys 129: 184311.
69. Desiraju GR (2002) Acc Chem Res 35: 565-573.
70. Goebel JR, Ault BS, Del Bene JE (2001) J Phys Chem A 105: 11365-11370.
71. Posokhov Y, Gorski A, Spanget-Larsen J, Duus F, Hansen PE, Waluk J (2001) Chem Phys Lett 350: 502-508.
72. Pauling LJ (1932) J Am Chem Soc 54: 3570-3582.
73. Tangney P, Scandolo S (2002) J Chem Phys 116: 14-24.
74. Wathelet V, Champagne B, Mosley DH, André J-M, Massidda S (1997) Chem Phys Lett 275: 506-512.
75. Gaigeot M-P, Sprik M (2003) J Phys Chem B 107: 10344-10358.
76. Benoit M, Marx D (2005) Chem Phys Chem 6: 1738-1741.