How are hydrogen bonds modified by metal binding?

Journal of Biological Inorganic Chemistry

Volumn 18, Issue 5, 2013, Pages 499-522

  Husberg, Charlotte ^a   Ryde, Ulf ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Density functional theory; Dispersion correction; Hydrogen bonds; Metalloproteins; Quantum mechanical calculations

Indexed keywords

ACETIC ACID; AZURIN; CARBOXYPEPTIDASE; COBALT; COPPER; CYTOCHROME; HEME; IMIDAZOLE; IRON; MANGANESE; METAL ION; METALLOPROTEIN; NICKEL; NITRITE REDUCTASE; PEROXIDASE; PROPIONIC ACID; SUPEROXIDE DISMUTASE; WATER; ZINC;

ARTICLE; COMPLEX FORMATION; DENSITY FUNCTIONAL THEORY; HYDROGEN BOND; METAL BINDING; PRIORITY JOURNAL; PROTON TRANSPORT; SOLVATION;

EID: 84962339309     PISSN: 09498257     EISSN: 14321327     Source Type: Journal    
DOI: 10.1007/s00775-013-0996-2     Document Type: Article

References (73)

1. Jeffrey GA (1997) An introduction to hydrogen bonding. Oxford University Press, New York
2. Zhen Y-J, Merz KM (1992) J Comput Chem 13:1151-1169
3. Habermann SM, Murphy KP (1996) Protein Sci 5:1229-1239
4. Pudzianowski AT (1996) J Phys Chem 100:4781-4789
5. Gordon MS, Jensen JH (1996) Acc Chem Res 29:536-543
6. Tsuzuki S, Uchimaru T, Matsumura K, Mikami M, Tanabe K (1999) J Chem Phys 110:11906-11910
7. Halkier A, Klopper W, Helgaker T, Jorgensen P, Taylor PR (1999) J Chem Phys 111:9157-9167
8. Rappé AK, Bernstein ER (2000) J Phys Chem A 104:6117-6128
9. Scheiner S, Kar T, Pattanayak J (2002) J Am Chem Soc 124:13257-13264
10. Jurecka P, Sponer J, Cerny J, Hobza P (2006) Phys Chem Chem Phys 8:1985-1993
11. Riley KE, Hobza P (2007) J Phys Chem A 111:8257-8263
12. Riley KE, Pitonak M, Jurecka P, Hobza P (2010) Chem Rev 110:5023-5063
13. Rezac J, Riley KE, Hobza P (2011) J Chem Theory Comput 7:2427-2438
14. Goerigk L, Kruse H, Grimme S (2011) Chem Phys Chem 12:3421-3433
15. Thanthiriwatte KS, Hohenstein EG, Burns LA, Sherrill CD (2011) J Chem Theory Comput 7:88-96
16. Baes CF, Mesmer RE (1976) The hydrolysis of cations. Wiley, New York
17. Holm RH, Kennepohl P, Solomon EI (1996) Chem Rev 96:2239-2314
18. Källrot N, Nilsson K, Rasmussen T, Ryde U (2005) Int J Quantum Chem 102:520-541
19. Ryde U (1996) Eur Biophys J 24:213-221
20. Poulos TL (1987) Adv Inorg Biochem 7:1-36
21. Kaim W, Schwederski B (1994) Bioinorganic chemistry: inorganic elements in the chemistry of life. Wiley, Chichester
22. Rydberg P, Sigfridsson E, Ryde U (2004) J Biol Inorg Chem 9:203-223
23. Epstein LM, Shubina ES (2002) Coord Chem Rev 231:165-181
24. Falvello LR (2010) Angew Chem Int Ed 49:10045-10047
25. Helm L, Merbach AE (1999) Coord Chem Rev 187:151-181
26. Kropman MF, Bakker HJ (2001) Science 291:2118-2120
27. Mancinell R, Botti A, Bruni F, Ricci MA, Soper AK (2007) Phys Chem Chem Phys 9:2959
28. Paschek D, Ludwig R (2011) Angew Chem Int Ed 50:352
29. Bustamante M, Vlencia I, Castro M (2011) J Phys Chem A 115:4115-4134
30. Prell JS, O'Brien JT, Williams ER (2011) J Am Chem Soc 133:4810-4818
31. Pavlov M, Siegbahn PEM, Sandström M (1998) J Phys Chem A 102:219-228
32. Rode BM, Schwenk CF, Hofer TS, Randolf BR (2005) Coord Chem Rev 249:2993-3006
33. Ryde U (1994) Int J Quantum Chem 52:1229-1243
34. Andric JM, Janjic GV, Ninkovic DB, Zaric SD (2012) Phys Chem Chem Phys 14:10896-10898
35. Schmiedekamp A, Nanda V (2009) J Inorg Biochem 103:1054-1060
36. Wirstam M, Lippard SJ, Friesner RA (2003) J Am Chem Soc 125:3980-3987
37. Sigfridsson E, Ryde U (1999) J Biol Inorg Chem 4:99-110
38. Ryde U, Olsson MHM, Roos BO, Pierloot K, De Kerpel JOA (2000) J Biol Inorg Chem 5:565-574
39. Ryde U (1999) Biophys J 77:2777-2787
40. Jensen KP, Ryde U (2003) Mol Phys 101:2003-2018
41. Nilsson K, Hersleth H-P, Rod TH, Andersson KK, Ryde U (2004) Biophys J 87:3437-3447
42. Heimdal J, Rydberg P, Ryde U (2008) J Phys Chem B 112:2501-2510
43. Sigfridsson E, Olsson MHM, Ryde U (2001) Inorg Chem 40:2509-2519
44. Sigfridsson E, Olsson MHM, Ryde U (2001) J Phys Chem B 105:5546-5552
45. Jensen KP, Ryde U (2003) ChemBioChem 4:413-424
46. Jensen KP, Ryde U (2005) J Porphyr Phthalocyanines 9:581-606
47. Rulíšek L, Jensen KP, Lundgren K, Ryde U (2006) J Comput Chem 27:1398-1414
48. Becke AD (1988) Phys Rev A 38:3098-3100
49. Perdew JP (1986) Phys Rev B 33:8822-8824
50. Schäfer A, Horn H, Alrichs R (1992) J Chem Phys 97:2571
51. Schäfer A, Huber C, Ahlrichs R (1994) J Chem Phys 100:5829
52. Hehre WJ, Radom L, Schleyer PvR, Pople JA (1986) Ab initio molecular orbital theory. Wiley-Interscience, New York
53. Eichkorn K, Treutler O, Öhm H, Häser M, Ahlrichs R (1995) Chem Phys Lett 240:283-290
54. Eichkorn K, Weigend F, Treutler O, Ahlrichs R (1997) Theor Chem Acc 97:119-126
55. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785
56. Becke AD (1993) J Chem Phys 98:5648
57. Klamt A, Schüürmann J (1993) J Chem Soc Perkin Trans 2 799-805
58. Schäfer A, Klamt A, Sattel D, Lohrenz JCW, Eckert F (2000) Phys Chem Chem Phys 2:2187-2193
59. Klamt A, Jonas V, Bürger T, Lohrenz JCWJ (1998) Phys Chem 102:5074-5085
60. Sharp KA (1990) Annu Rev Biophys Biophys Chem 19:301
61. Honig B (1995) Science 268:1144
62. Treutler O, Ahlrichs RJ (1995) Chem Phys 102:346-354
63. Grimme S, Antony J, Ehrlich S, Krieg H (2010) J Chem Phys 132:154104
64. http://toc.uni-muenster.de/DFTD3/getd3.html
65. Miertus S, Scrocco E, Tomasi J (1981) Chem Phys 55:117
66. Tomasi J, Mennucci B, Cammi R (2005) Chem Rev 105:2999-3093
67. 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 (2003) Gaussian 03, revision D.01. Gaussian, Wallingford
68. Ryde U, Mata RA, Grimme S (2011) Dalton Trans 40:11176-11183
69. Boys SF, Bernardi F (1970) Mol Phys 19:553-566
70. Green MT (2009) Curr Opin Chem Biol 13:84-88
71. Shaik S, Cohen S, Wang Y, Chen H, Kumar D, Thiel W (2010) Chem Rev 110:949-1017
72. Shepard WEB, Anderson BF, Lewandoski DA, Norris GE, Bake EN (1990) J Am Chem Soc 112:7817-7819
73. Baker EN (1988) J Mol Biol 203:1071-1095