Solvation of Hydrogen Bonded Systems: CH···O, OH···O, and Cooperativity

Challenges and Advances in Computational Chemistry and Physics

Volumn 6, Issue , 2008, Pages 407-432

  Scheiner, Steve ^a  

^a UTAH STATE UNIVERSITY   (United States)

Author keywords

Interaction energy; Negative cooperativity; Proton acceptor; Total interaction energy; Water dimer

Indexed keywords

EID: 84857102686     PISSN: 25424491     EISSN: 25424483     Source Type: Book Series    
DOI: 10.1007/978-1-4020-8270-2_15     Document Type: Chapter

References (88)

1. Onsager L (1936) Electric moments of molecules in liquids. J Am Chem Soc 58:1486–1493
2. Wong MW, Frisch MJ, Wiberg KB (1991a) Solvent effects. 1. The mediation of electrostatic effects by solvents. J Am Chem Soc 113:4776–4782
3. Wong MW, Wiberg KB, Frisch M (1991b) Hartree–Fock second derivatives and electric field properties in a solvent reaction field: Theory and application. J Chem Phys 95:8991–8998
4. Cramer CJ, Truhlar DG (1999) Implicit solvation models: Equilibria, structure, spectra, and dynamics. Chem Rev 99:2161–2200
5. Tomasi J, Cammi R, Mennucci B, Cappellia C, Corni S (2002) Molecular properties in solution described with a continuum solvation model. Phys Chem Chem Phys 4:5697–5712
6. Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999–3093
7. Koch A, Thomas S, Kleinpeter E (1997) Ab initio study, semiempirical calculation and NMR spectroscopy of keto-enol tautomerism of triazolopyrimidines. J Mol Struct (Theochem) 401:1–14
8. Rega N, Cossi M, Barone V (1997) Intrinsic and environmental effects in the structure and magnetic properties of glycine radical in aqueous solution. J Am Chem Soc 119:12962–12967
9. Improta R, Scalmani G, Barone V (2001) Quantum mechanical prediction of the magnetic titration curve of a nitroxide ‘spin probe’. Chem Phys Lett 336:349–356
10. Saracino GAA, Tedeschi A, D’Errico G, Improta R, Franco L, Ruzzi M, Corvaia C, Barone V (2002) Solvent polarity and pH effects on the magnetic properties of ionizable nitroxide radicals: A combined computational and experimental study of 2,2,5,5-tetramethyl-3-carboxypyrrolidine and 2,2,6,6-tetramethyl-4-carboxypiperidine nitroxides. J Phys Chem A 106:10700–10706
11. Improta R, Barone V (2004) Interplay of electronic, environmental, and vibrational effects in determining the hyperfine coupling constants of organic free radicals. Chem Rev 104:1231–1253
12. Komeiji Y, Ishida T, Fedorov DG, Kitaura K (2007) Change in a protein’s electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin. J Comput Chem 28:1750–1762
13. 4, and an O-H· · · O hydrogen bond. Can J Chem 62:606–609
14. 3 bond in a tricyclic orthoamide; Experimental and theoretical evidence for C-H· · · O hydrogen bonds. Angew Chem Int Ed Engl 26:1175–1177
15. Wiberg KB, Waldron RF, Schulte G, Saunders M (1991) Lactones. 1. X-ray crystallographic studies of nonanolactone and tridecanoloactone: Nature of CH· · · O nonbonded interactions. J Am Chem Soc 113:971–977
16. Feller D, Feyereisen MW (1993) Ab initio study of hydrogen bonding in the phenol–water system. J Comput Chem 14:1027–1035
17. Turi L, Dannenberg JJ (1993) Molecular orbital study of acetic acid aggregation. 1. Monomers and dimers. J Phys Chem 97:12197–12204
18. Koch U, Popelier PLA (1995) Characterization of C-H-O hydrogen bonds on the basis of the charge density. J Phys Chem 99:9747–9754
19. 3. J Phys Chem 99:6457–6460
20. Novoa JJ, Mota F (1997) Substituent effects in intermolecular C(sp3)-H· · · O(sp3) contacts: How strong can a C(sp3)-H· · · O(sp3) hydrogen bond be? Chem Phys Lett 266:23–30
21. Hobza P, Spirko V, Havlas Z, Buchhold K, Reimann B, Barth H-D, Brutschy B (1999) Anti-hydrogen bond between chloroform and fluorobenzene. Chem Phys Lett 299:180–186
22. Cubero E, Orozco M, Hobza P, Luque FJ (1999) Hydrogen bond versus anti-hydrogen bond: A comparative analysis based on the electron density topology. J Phys Chem A 103:6394–6401
23. α-H· · · O=C hydrogen bond? J Am Chem Soc 122:4750–4755
24. Alkorta I, Rozas I, Elguero J (2000) Effects of fluorine substitution on hydrogen bond interactions. J Fluor Chem 101:233–238
25. Hobza P, Havlas Z (2000) Blue-shifting hydrogen bonds. Chem Rev 100:4253–4264
26. Grabowski SJ (2001) A new measure of hydrogen bonding strength – ab initio and atoms in molecules studies. Chem Phys Lett 338:361–366
27. Wetmore SD, Schofield R, Smith DM, Radom L (2001) A theoretical investigation of the effects of electronegative substitution on the strength of C-H· · · N hydrogen bonds. J Phys Chem A 105: 8718–8726
28. van der Veken B, Herrebout WA, Szostak R, Shchepkin DN, Havlas Z, Hobza P (2001) The nature of improper, blue-shifting hydrogen bonding verified experimentally. J Am Chem Soc 123: 12290–12293
29. Saar BG, O’Donoghue GP, Steeves AH, John W Thoman J (2006) Evidence for a blue-shifting intramolecular hydrogen bond in the vibrational overtone spectrum of 1 H-nonafluorobutane. Chem Phys Lett 417:159–163
30. 3 CHO· · ·HNO complexes. Int J Quantum Chem 106:1199–1207
31. Spirko V, Hobza P (2006) Theoretical investigations into the blue-shifting hydrogen bond in benzene complexes. Chem Phys Chem 7:640–643
32. Shishkin OV, Palamarchuk GV, Gorb L, Leszczynski J (2006) Intramolecular hydrogen bonds in canonical 2’-deoxyribonucleotides: An atoms in molecules study. J Phys Chem B 110:4413–4422
33. – ) complexes predicted by a perturbative model. Chem Phys Lett 424:239–242
34. Karpfen A, Kryachko ES (2006) On blue shifts of C–H stretching modes of dimethyl ether in hydrogen-and halogen-bonded complexes. Chem Phys Lett 431:428–433
35. Kryachko ES, Karpfen A (2006) Theoretical force-field model for blue-shifted hydrogen bonds with fluoromethanes. Chem Phys 329:313–328
36. Tamasi G, Botta F, Cini R (2006) DFT-molecular modeling analysis of C–H· · · N and C–H· · · S hydrogen bond type interactions in selected platinum–purine/pyrimidine complexes. J Mol Struct (Theochem) 766:61–72
37. Quinn JR, Zimmerman SC, Del Bene JE, Shavitt I (2007) Does the A.T or G.C base-pair possess enhanced stability? Quantifying the effects of CH··O interactions and secondary interactions on base-pair stability using a phenomenological analysis and ab initio calculations. J Am Chem Soc 129: 934–941
38. Jablonski M, Sadlej AJ (2007) Blue-shifting intramolecular C-H···O interactions. J Phys Chem A 111:3423–3431
39. Vener MV, Egorova AN, Fomin DP, Tsirelson VG (2007) QTAIM study of the closed-shell interactions in peptide secondary structures: A cluster treatment of oligo-and polyalanines. Chem Phys Lett 440:279–285
40. Pluháková K, Hobza P (2007) On the nature of the surprisingly small (red) shift in the halothane· · · acetone complex. Chem Phys Chem 8:1352–1356
41. 3 in the gas phase. J Chem Phys 127:084306
42. Wang Z-X, Wu C, Lei H, Duan Y (2007) Accurate ab initio study on the hydrogen-bond pairs in protein secondary structures. J Chem Theory Comput 3:1527–1537
43. Gu Y, Kar T, Scheiner S (1999) Fundamental properties of the CH· · · O interaction: Is it a true hydrogen bond? J Am Chem Soc 121:9411–9422
44. Gu Y, Kar T, Scheiner S (2000a) Comparison of the CH· · · N and CH· · · O interactions involving substituted alkanes. J Mol Struct 552:17–31
45. Scheiner S, Grabowski SJ, Kar T (2001a) Influence of hybridization and substitution upon the properties of the CH··O hydrogen bond. J Phys Chem A 105:10607–10612
46. Scheiner S, Kar T (2002) Red versus blue-shifting hydrogen bonds: Are there fundamental distinctions? J Phys Chem A 106:1784–1789
47. Kryachko E, Scheiner S (2004) CH··F hydrogen bonds. Dimers of fluoromethanes. J Phys Chem A 108:2527–2535
48. Gu Y, Kar T, Scheiner S (2000b) Evaluation of the H-bonding properties of CH· · · O interactions based upon NMR spectra. J Mol Struct (Theochem) 500:441–452
49. Scheiner S (2006) Contributions of NH··O and CH··O H-bonds to the stability of β-sheets in proteins. J Phys Chem B 110:18670–18679
50. Kurnig IJ, Scheiner S (1987) Ab initio investigation of the structure of hydrogen halide – amine complexes in the gas phase and in a polarizable medium. Int J Quantum Chem QBS 14:47–56
51. Scheiner S, Duan X (1991) Effect of intermolecular orientation upon proton transfer within a polarizable medium. Biophys J 60:874–883
52. Scheiner S, Kar T (2005) Effect of solvent upon CH··O hydrogen bonds with implications for protein folding. J Phys Chem B 109:3681–3689
53. Miertus S, Scrocco E, Tomasi J (1981) Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chem Phys 55: 117–129
54. Miertus S, Tomasi J (1982) Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes. Chem Phys 65:239–245
55. Mennucci B, Tomasi J (1997) Continuum solvation models: A new approach to the problem of solute’s charge distribution and cavity boundaries. J Chem Phys 106:5151–5198
56. Cancès E, Menucci B, Tomasi J (1997) A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics. J Chem Phys 107:3032–3041
57. Cossi M, Barone V, Mennucci B, Tomasi J (1998) Ab initio study of ionic solutions by a polarizable continuum dielectric model. Chem Phys Lett 286:253–260
58. Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J Phys Chem A 102:1995–2001
59. Foresman JB, Keith TA, Wiberg KB, Snoonian J, Frisch MJ (1996) Solvent effects. 5. Influence of cavity shape, truncation of electrostatics, and electron correlation on ab initio reaction field calculations. J Phys Chem 100:16098–16104
60. Barone V, Cossi M, Tomasi J (1997) A new definition of cavities for the computation of solvation free energies by the polarizable continuum model. J Chem Phys 107:3210–3221
61. Rega N, Cossi M, Barone V (1998) Structure and magnetic properties of glycine radical in aqueous solution at different pH values. J Am Chem Soc 120:5723–5732
62. α H··O hydrogen bond of amino acid residues. J Biol Chem 276:9832–9837
63. Scheiner S (2005) Relative strengths of NH··O and CH··O hydrogen bonds between polypeptide chain segments. J Phys Chem B 109:16132–16141
64. Scheiner S, Kar T (2007) Underlying source of the relation between polypeptide conformation and strength of NH··O hydrogen bonds. J Mol Struct 844–845:166–172
65. Jeffrey GA (1997) An introduction to hydrogen bonding. In: Truhlar DG (ed) Topics in physical chemistry, Oxford University Press, New York, p 303
66. Scheiner S (1997) Hydrogen bonding: A theoretical perspective, Oxford University Press, New York, p 375
67. Kurnig IJ, Szczesniak MM, Scheiner S (1986) Ab initio study of structure and cooperativity in H3N· · · HF· · · HF and H3P· · · HF· · · HF. J Phys Chem 90:4253–4258
68. Latajka Z, Scheiner S (1988) Structure, energetics and vibrational spectra of H-bonded systems. Dimers and trimers of HF and HCl. Chem Phys 122:413–430
69. Chalasinski G, Cybulski SM, Szczesniak MM, Scheiner S (1989) Nonadditive effects in HF and HCl trimers. J Chem Phys 91:7048–7056
70. 2 O trimer. J Chem Phys 94:2873–2883
71. DuPré DB, Yappert MC (2002) Cooperative hydrogen-and πH-bonded interactions involving water and the ethylenic double bond. J Phys Chem A 106:567–574
72. Chen C, Liu M-H, Wu L-S (2003) Local analysis and comparative study of the hydrogen bonds in the linear (HCN)n and (HNC)n clusters. J Mol Struct (Theochem) 630:187–204
73. Suh SB, Kim JC, Choi YC, Yun S, Kim KS (2003) Nature of one-dimensional short hydrogen bonding: Bond distances, bond energies, and solvent effects. J Am Chem Soc 126:2186–2193
74. n systems. Tentative models for the liquid state and dilute aqueous solution. J Am Chem Soc 99: 349–353
75. Sheridan RP, Lee RH, Peters N, Allen LC (1979) Hydrogen-bond cooperativity in protein secondary structure. Biopolymers 18:2451–2458
76. Kobko N, Dannenberg JJ (2003b) Cooperativity in amide hydrogen bonding chains. Relation between energy, position, and H-bond chain length in peptide and protein folding models. J Phys Chem A 107:10389–10395
77. Ireta J, Neugebauer J, Scheffler M, Rojo A, Galvan M (2003) Density functional theory study of the cooperativity of hydrogen bonds in finite and infinite α-helices. J Phys Chem B 107:1432–1437
78. 10-helical peptides. A density functional theory study. J Am Chem Soc 125:14065–14071
79. Wieczorek R, Dannenberg JJ (2003a) H-bonding cooperativity and energetics of α-helix formation of five 17-amino acid peptides. J Am Chem Soc 125:8124–8129
80. Kobko N, Dannenberg JJ (2003a) Cooperativity in amide hydrogen bonding chains. A comparison between vibrational coupling through hydrogen bonds. Implications for peptide vibrational spectra. J Am Chem Soc 107:6688–6697
81. Masella M, Flament J-P (1999) A theoretical study of five water/ammonia/formaldehyde cyclic trimers: Influence of cooperative effects. J Chem Phys 110:7245–7255
82. Alkorta I, Elguero J (2003) Interaction of protein backbone with nucleic acid bases. J Phys Chem B 107:5306–5310
83. Parra RD, Bulusu S, Zeng XC (2003) Cooperative effects in one-dimensional chains of three-center hydrogen bonding interactions. J Chem Phys 118:3499–3509
84. Rivelino R, Chaudhuri P, Canuto S (2003) Quantifying multiple-body interaction terms in H-bonded HCN chains with many-body perturbation/coupled-cluster theories. J Chem Phys 118: 10593–10601
85. Kar T, Scheiner S (2004) Comparison of cooperativity in CH··O and OH··O hydrogen bonds. J Phys Chem A 108:9161–9168
86. Scheiner S, Nagle JF (1983) Ab initio molecular orbital estimates of charge partitioning between Bjerrum and ionic defects in ice. J Phys Chem 87:4267–4272
87. Scheiner S, Kar T, Pattanayak J (2002) Comparison of various types of hydrogen bonds involving aromatic amino acids. J Am Chem Soc 124:13257–13264
88. Kar T, Scheiner S (2006) Cooperativity of conventional and unconventional hydrogen bonds involving imidazole. Int J Quantum Chem 106:843–851