Hydrogen bonds in galactopyranoside and glucopyranoside: A density functional theory study

Journal of Molecular Modeling

Volumn 19, Issue 2, 2013, Pages 589-599

  Mosapour Kotena, Zahrabatoul ^a   Behjatmanesh Ardakani, Reza ^b   Hashim, Rauzah ^a   Manickam Achari, Vijayan ^a  

^a UNIVERSITY OF MALAYA   (Malaysia)

^b PAYAME NOOR UNIVERSITY   (Iran)

Author keywords

Atoms in molecules theory; Density functional theory; Glycolipids; Hydrogen bonding; Natural bond orbital analysis

Indexed keywords

GALACTOPYRANOSIDE; GLUCOPYRANOSIDE; GLYCOSIDE; HYDROGEN; HYDROXYL GROUP; PROTON; UNCLASSIFIED DRUG;

ARTICLE; DENSITY FUNCTIONAL THEORY; DIPOLE; ELECTRON; ELECTROPHILICITY; HYDROGEN BOND; IONIZATION; PRIORITY JOURNAL; PROTON MOTIVE FORCE; STEREOISOMERISM;

ANTIDESMA PLATYPHYLLUM;

EID: 84962426726     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-012-1576-z     Document Type: Article

References (69)

1. Dembitsky VM (2004) Chemistry and biodiversity of the biologically active natural glycosides. Chem Biodivers 1(5):673-781. doi: 10.1002/cbdv.200490060
2. Dembitsky VM (2004) Astonishing diversity of natural surfactants: 1. Glycosides of fatty acids and alcohols. Lipids 39(10):933-953. doi: 10.1007/s11745-004-1316-1
3. Brooks NJ, Hamid HAA, Hashim R, Heidelberg T, Seddon JM, Conn CE, Husseini SMM, Zahid NI, Hussen RSD (2011) Thermotropic and lyotropic liquid crystalline phases of Guerbet branched-chain-D-glucosides. Liq Cryst 38(11-12):1725-1734. doi: 10.1080/02678292.2011.625689
4. Vill V, Hashim R (2002) Carbohydrate liquid crystals: structure-property relationship of thermotropic and lyotropic glycolipids. Curr Opin Colloid 7(5-6):395-409. doi: 10.1016/s1359-0294(02)00091-2
5. Ahmad N, Ramsch R, Esquena J, Solans C, Tajuddin HA, Hashim R (2012) Physico-chemical charactrization of natural-like branched-chain glycosides towards formation of hexosomes and vesicles. Langmuir 28(5):2395-2403
6. Balzer D, Lüders H (2000) Nonionic surfactants: Alkyl polyglucosides. 91. CRC, Boca Raton
7. Holmberg K (2001) Natural surfactants. Curr Opin Colloid 6(2):148-159
8. Hill K, Rhode O (1999) Sugar-based surfactants for consumer products and technical applications. Fett-Lipid 101(1):25-33
9. Jackson ML, Schmidt CF, Lichtenberg D, Litman BJ, Albert AD (1982) Solubilization of phosphatidylcholine bilayers by octyl glucoside. Biochemistry 21(19):4576-4582. doi: 10.1021/bi00262a010
10. Wang J, Balazs YS, Thompson LK (1997) Solid-state REDOR NMR distance measurements at the ligand site of a bacterial chemotaxis membrane receptor†. Biochemistry 36(7):1699-1703. doi: 10.1021/bi962578k
11. Harding MM, Anderberg PI, Haymet ADJ (2003) 'Antifreeze' glycoproteins from polar fish. Eur J Bio Chem 270(7):1381-1392. doi: 10.1046/j.1432-1033.2003. 03488.x
12. Varki A (1993) Biological roles of oligosaccharides: all of the theories are correct. Glycobiology 3(2):97-130. doi: 10.1093/glycob/3.2.97
13. Israelachvili J (1994) The science and applications of emulsions - an overview. Colloid Surf A 91:1-8. doi: 10.1016/0927-7757(94)02743-9
14. Helm CA, Israelachvili JN, McGuiggan PM (1992) Role of hydrophobic forces in bilayer adhesion and fusion. Biochemistry 31(6):1794-1805. doi: 10.1021/bi00121a030
15. Emsley J (1980) Very strong hydrogen bonding. Chem Soc Rev 9(1):91-124. doi: 10.1039/CS9800900091
16. Claesson PM, Kjellin M, Rojas OJ, Stubenrauch C (2006) Short-range interactions between non-ionic surfactant layers. Phys Chem Chem Phys 8(47):5501-5514. doi: 10.1039/B610295F
17. Larson JW, McMahon TB (1984) Gas-phase bihalide and pseudobihalide ions. An ion cyclotron resonance determination of hydrogen bond energies in XHY- species (X, Y = F, Cl, Br, CN). Inorg Chem 23(14):2029-2033. doi: 10.1021/ic00182a010
18. Jeffrey GA, Saenger W (1994) Hydrogen bonding in biological structures. Springer, Berlin
19. French AD, Brady JW (1990) Computer modeling of carbohydrates. Am Chem Soc 430. doi: 10.1021/bk-1990-0430.ch001
20. Fringant C, Tvaroska I, Mazeau K, Rinaudo M, Desbrieres J (1995) Hydration of α-maltose and amylose: molecular modelling and thermodynamics study. Carbohyd Res 278(1):27-41. doi: 10.1016/0008-6215(95)00232-1
21. Brady JW, Schmidt RK (1993) The role of hydrogen bonding in carbohydrates: molecular dynamics simulations of maltose in aqueous solution. J Phys Chem 97(4):958-966. doi: 10.1021/j100106a024
22. Chong TT, Heidelberg T, Hashim R, Gary S (2007) Computer modelling and simulations of thermotropic and lyotropic alkyl glycoside bilayers. Liq Cryst 34(3):349-363. doi: 10.1080/02678290601111556
23. Arunan E, Desiraju G, Klein R, Sadlej J, Scheiner S, Alkorta I, Clary D, Crabtree R, Dannenberg J, Hobza P (2010) Definition of the Hydrogen Bond(IUPAC Recommendation). Pure Appl Chem 83(8):1637-1641. doi: 10.1351/PacRec-10-01-02
24. Bader RFW (1991) A quantum theory of molecular structure and its applications. Chem Rev 91(5):893-928. doi: 10.1021/cr00005a013
25. Bader R, Essen H (1984) The characterization of atomic interactions. J Chem Phys 80:1943-1960
26. Arnold WD, Oldfield E (2000) The chemical nature of hydrogen bonding in proteins via NMR: j-couplings, chemical shifts, and AIM theory. J Am Chem Soc 122(51):12835-12841. doi: 10.1021/ja0025705
27. Espinosa E, Molins E, Lecomte C (1998) Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities. Chem Phys Lett 285(3-4):170-173
28. Grabowski SJ (2001) A new measure of hydrogen bonding strength-ab initio and atoms in molecules studies. Chem Phys Lett 338(4-6):361-366. doi: 10.1016/S0009-2614(01)00265-2
29. Ikushima Y, Hatakeda K, Saito N, Arai M (1998) An in situ Raman spectroscopy study of subcritical and supercritical water: the peculiarity of hydrogen bonding near the critical point. J Chem Phys 108:5855-5860
30. Ionescu AR, Bérces A, Zgierski MZ, Whitfield DM, Nukada T (2005) Conformational pathways of saturated six-membered rings. A static and dynamical density functional study. J Phys Chem A 109(36):8096-8105. doi: 10.1021/jp052197t
31. Barnett CB, Naidoo KJ (2008) Stereoelectronic and solvation effects determine hydroxymethyl conformational preferences in monosaccharides. J Phys Chem B 112(48):15450-15459
32. Grabowski SJ (2001) Ab Initio calculations on conventional and unconventional hydrogen bondsstudy of the hydrogen bond strength. J Phys Chem A 105(47):10739-10746. doi: 10.1021/jp011819h
33. Gilli P, Bertolasi V, Ferretti V, Gilli G (1994) Covalent nature of the strong homonuclear hydrogen bond. Study of the OH - O system by crystal structure correlation methods. J Am Chem Soc 116(3):909-915
34. Mó O, Yáñez M, Elguero J (1992) Cooperative (nonpairwise) effects in water trimers: an ab initio molecular orbital study. J Chem Phys 97:6628-6638
35. Vill V (2006) The stereochemistry of glycolipids. A key for understanding membrane functions? Liq Cryst 33(11-12):1351-1352. doi: 10.1080/ 02678290601140571
36. Espinosa E, Souhassou M, Lachekar H, Lecomte C (1999) Topological analysis of the electron density in hydrogen bonds. Acta Crystallogr Sec B 55(4):563-572. doi: 10.1107/S0108768199002128
37. Weinhold F (1997) Nature of H-bonding in clusters, liquids, and enzymes: an ab initio, natural bond orbital perspective. J Mol Struct 398-399:181-197. doi: 10.1016/S0166-1280(96)04936-6
38. Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev 88(6):899-926. doi: 10.1021/cr00088a005
39. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98(7):5648-5652. doi: 10.1063/1.464913
40. Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37(2):785-789
41. Ditchfield R, Hehre W, Pople JA (1971) Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules. J Chem Phys 54:724
42. Francl MM, Pietro WJ, Hehre WJ, Binkley JS, Gordon MS, DeFrees DJ, Pople JA (1982) Self-consistent molecular orbital methods. XXIII. A polarization-type basis set for second-row elements. J Chem Phys 77(7):3654-3665. doi: 10.1063/1.444267
43. Miertus S, Scrocco E, Tomasi J (1981) Electrostatic interaction of a solute with a continuum. A direct utilizaion of ab initio molecular potentials for the prevision of solvent effects. Chem Phys 55(1):117-129
44. Frisch MJ, Trucks GW, Schlegel HB et al (2009) Gaussian 09, Revision A. 02. Wallingford CT
45. Dennington R, Keith T, Millam JGV (2008) Version 5.0. 8. Semichem Inc, Shawnee Mission, KS
46. Bader R (1995) Atoms in molecules. A quantum theory. Oxford University Press, Oxford
47. Popelier P (2000) Atoms in molecules. An introduction. Prentice Hall
48. Biegler-König F, Schönbohm J, Derdau R, Bayles D, Bader R (2002) AIM2000, version 2.0. University of Applied Sciences, Bielefeld
49. Glendening E, Reed A, Carpenter J, Weinhold F (2003) NBO 3.1
50. Schuster P, Zundel G, Sandorfy C (1976) Hydrogen bond; recent developments in theory and experiments. North-Holland, Amsterdam
51. Pimentel GC, McClellan AL (1960) The hydrogen bond. Freeman, San Francisco
52. Momany FA, Appell M, Willett JL, Schnupf U, Bosma WB (2006) DFT study of α- and β-d-galactopyranose at the B3LYP/6-311++G**level of theory. Carbohyd Res 341(4):525-537
53. Panico R, Powell WH, Richer JC (1993) A guide to IUPAC nomenclature of organic compounds: recommendations 1993. International Union of Pure Applied Chemistry. Commission on the Nomenclature of Organic Chemistry. Blackwell Scientific, Oxford
54. Momany FA, Appell M, Willett JL, Bosma WB (2005) B3LYP/6- 311++G**geometry-optimization study of pentahydrates of a- and b-D-glucopyranose. Carbohyd Res 340:1638-1655
55. Appell M, Willett JL, Momany FA (2005) DFT study of α- and β-d-mannopyranose at the B3LYP/6-311++G**level. Carbohyd Res 340(3):459-468
56. Silvestrelli PL, Parrinello M (1999) Water molecule dipole in the gas and in the liquid phase. Phys Rev Lett 82(16):3308-3311
57. Parr RG, Lv S, Liu S (1999) Electrophilicity index. J Am Chem Soc 121(9):1922-1924. doi: 10.1021/ja983494x
58. Ortiz EV, López MB (2007) Density Functional Theory (DFT) applied to the study of the reactivity of platinum surface modified by nickel nanoparticles. Mec Comp 26:1692
59. Pearson RG, Pearson R (1997) Chemical hardness: applications from molecules to solids. Wiley-VCH, Weinheim
60. Parr RG, Zhou Z (1993) Absolute hardness: unifying concept for identifying shells and subshells in nuclei, atoms, molecules, and metallic clusters. Acc Chem Res 26(5):256-258. doi: 10.1021/ar00029a005
61. Pearson RG (1988) Absolute electronegativity and hardness: application to inorganic chemistry. Inorg Chem 27(4):734-740. doi: 10.1021/ic00277a030
62. Pearson RG (1987) Recent advances in the concept of hard and soft acids and bases. J Chem Edu 64(7):doi:10.1021/ed064p561
63. Bader RFW (1990) Atoms in molecules-a quantum theory. Oxford University Press, New York
64. Popelier P, Bader R (1992) The existence of an intramolecular C-H. O hydrogen bond in creatine and carbamoyl sarcosine. Chem Phys Lett 189(6):542-548. doi: 10.1016/0009-2614(92)85247-8
65. Popelier PLA (1998) Characterization of a dihydrogen bond on the basis of the electron density. J Phys Chem A 102(10):1873-1878. doi: 10.1021/jp9805048
66. Nazari F, Doroodi Z (2010) The substitution effect on heavy versions of cyclobutadiene. Int J Quantum Chem 110(8):1514-1528. doi: 10.1002/qua.22271
67. Reed AE, Weinhold F (1985) Natural localized molecular orbitals. J Chem Phys 83(4):1736-1740
68. Henderson R (2007) Wavelength considerations. Instituts für Umform-und Hochleistungs. Archived from the original on:10-28
69. Amerov A, Chen J, Arnold M (2004) Molar absorptivities of glucose, water and other biological molecules over the first overtone and combination regions of the near infrared spectrum. Appl Spect J 58:1195-1204