A Computational Study of N–H…O Hydrogen Bonding to Investigate Cooperative Effects

Authors: Setareh Shekarsaraei, Marjan Moridi, Nasser L. Hadipour

Abstract:

In this study, nuclear magnetic resonance spectroscopy and nuclear quadrupole resonance spectroscopy parameters of 14N (Nitrogen in imidazole ring) in N–H…O hydrogen bonding for Histidine hydrochloride monohydrate were calculated via density functional theory. We considered a five-molecule model system of Histidine hydrochloride monohydrate. Also we examined the trends of environmental effect on hydrogen bonds as well as cooperativity. The functional used in this research is M06-2X which is a good functional and the obtained results has shown good agreement with experimental data. This functional was applied to calculate the NMR and NQR parameters. Some correlations among NBO parameters, NMR and NQR parameters have been studied which have shown the existence of strong correlations among them. Furthermore, the geometry optimization has been performed using M062X/6-31++G(d,p) method. In addition, in order to study cooperativity and changes in structural parameters, along with increase in cluster size, natural bond orbitals have been employed.

Keywords: Hydrogen bonding, Density Functional Theory (DFT), Natural bond Orbitals (NBO), cooperativity effects.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1107842

References:

[1] I. G. Kaplan, Intermolecular Interactions: Physical Picture, Computational Methods and Model John Wiley & Sons Ltd England, 2006.
[2] J. S. Murray, M. C. Concha, P. Lane, P. Hobza, P. Politzer, Blue shifts vs red shifts in σ-hole bonding. J. Mol. Model., 2008, 14: 699–704.
[3] S. Scheiner, Hydrogen bonding: a theoretical perspective. Oxford University Press New York, 1997.
[4] M. D. Esrafili, H. Behzadi, N. L. Hadipour, Density functional theory study of N–H⋯O, O–H⋯O and C–H⋯O hydrogenbonding effects on the 14N and 2H nuclear quadrupole coupling tensors of N-acetyl-valine., Biophys. Chem., 2008, 133: 11–18.
[5] H. Behzadi, M. D. Esrafili, N. L. Hadipour, A theoretical study of 17O, 14N and 2H nuclear quadrupole coupling tensors in the real crystalline structure of acetaminophen., 2007, Chem. Phys. 333: 97–104.
[6] S. J. Grabowski, W. A. Sokalski, E. Dyguda, J. Leszczyńki, Quantitative classification of covalent and noncovalent H-bonds. Phys. Chem. B, 2006, 110, 6444–6446.
[7] S. J. Grabowski, What is the covalency of hydrogen bonding? Chem Rev., 2011, 111:2597–2625.
[8] M. D. Esrafili, A theoretical investigation of the characteristics of hydrogen/halogen bonding interactions in dibromo-nitroaniline., J Mol Model, 2013, 19:1417–1427.
[9] M. D. Esrafili, H. Behzadi, N. L. Hadipour, 14N and 17O electric field gradient tensors in benzamide clusters: theoretical evidence for cooperative and electronic delocalization effects in N–H···O hydrogen bonding., 2008, Chem Phys 348:175–180.
[10] M. D. Esrafili, Investigation of H-bonding and halogen-bonding effects in dichloroacetic acid: DFT calculations of NQR parameters and QTAIM analysis, 2012, J Mol Model 18:5005–5016.
[11] J. D. Watson, F. H. Crick General implications of the structure of Deoxyribonucleic acid Nature, 1953, 171:737.
[12] A. V. D. Vaart, K. M. Merz, Charge transfer in small hydrogen bonded clusters, 2002, J. Chem. Phys. 116:7380- 7388.
[13] N. V. Sidwich, The Electronic Theory of Valency Clarendon Oxford, 1972.
[14] W. B. Guggino, In Chloride Channels: Current Topics in Membranes, ed. Kleinzeller A and Fambrough DM Academic Press San Diego vol. 42, 1994.
[15] L. Goerigk, S. Grimme, A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions Phys. Chem. Chem. Phys., 2011, 13:6670- 88.
[16] S. Grimme, Semiempirical GGA-type density functional constructed with a long-range dispersion correction J. Comput. Chem., 2006, 27, 1787- 1799.
[17] E. A. C. Lucken, Nuclear Quadrupole Coupling Constants, Academic Press, London, 1969.
[18] A. Bax, Protein Sci., 2003, 12, 1-16.
[19] A. Bax, G. Kontaxis, N. Tjandra, Methods Enzymol., Part B, 2001, 339, 127-174.
[20] P. M. Hwang, L. E. Kay, Methods Enzymol., Part C, 2005, 394, 335- 350.
[21] L. E. Kay, J. Magn. Reson., 2005, 173, 193-207.
[22] K. Wu¨thrich, Angew. Chem., Int. Ed., 2003, 42, 3340-3363.
[23] D. Marulanda, M. L. Tasayco, A. McDermott, M. Cataldi, V. Arriaran, T. Polenova, J. Am. Chem. Soc., 2004, 126, 16608-16620.
[24] S. G. Zech, A. J. Wand, A. E. McDermott, J. Am. Chem. Soc., 2005, 127, 8618-8626.
[25] A. E. McDermott, Curr. Opin. Struct. Biol., 2004, 14, 554-561.
[26] E. K. Paulson, C. R. Morcombe, V. Gaponenko, B. Dancheck, R. A. Byrd, K. W. Zilm, J. Am. Chem. Soc., 2003, 125, 14222-14223.
[27] S. Luca, H. Heise, M. Baldus, Acc. Chem. Res., 2003, 36, 858-865.
[28] A. Lange, S. Becker, K. Seidel, K. Giller, O. Pongs, M. Baldus, Angew. Chem., Int. Ed., 2005, 44, 2089-2092.
[29] A. B. Siemer, C. Ritter, M. Ernst, R. Riek, B. H. Meier, Angew. Chem., Int. Ed., 2005, 44, 2441-2444.
[30] C. P. Jaroniec, C. E. MacPhee, V. S. Bajaj, M. T. McMahon, C. M. Dobson, R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A., 2004, 101, 711- 716.
[31] W. T. Franks, D. H. Zhou, B. J. Wylie, B. G. Money, D. T. Graesser, H. L. Frericks, G. Sahota, C. M. Rienstra, J. Am. Chem. Soc., 2005, 127, 12291-12305.
[32] P. T. F. Williamson, B. H. Meier, A. Watts, Eur. Biophys. J., 2004, 33, 247-254.
[33] S. Sharpe, N. Kessler, J. A. Anglister, W. M. Yau, R. Tycko, J. Am.Chem. Soc., 2004, 126, 4979-4990.
[34] J. C. C. Chan, N. A. Oyler, W. M. Yau, R. Tycko, Biochemistry, 2005, 44, 10669-10680.
[35] Y. Zhao, D. G. Truhlar, Acc. Chem. Res. 2008, 41, 157.
[36] Y. Zhao, D. G. Truhlar DG, Theor. Chem. Acc. 2008 120: 215
[37] M. J. Duer, Solid State NMR Spectroscopy. Blackwell Science Ltd. London, 2002.
[38] M. W. Schmidt, K. K. Baldridge, J. A. Boatz, S. T. Elbert, M. S. Gordon, J. H. Jensen, S. Koseki, N. Matsunaga, K. A. Nguyen, S. J. Su, T. L. Windus, M. Dupuis, J. A. Montgomery, General Atomic and Molecular Electronic Structure System. J Comput Chem, 1993, 14:1347– 1363
[39] H. Fuess, D. Hohlwein, S. A. Mason, Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. 33: 654–659, 1977.
[40] M. D. Esrafili, M. Vakili, Halogen bonds enhanced by σ-hole and π-hole interactions: a comparative study on cooperativity and competition effects between X···N and S···N interactions in H3N···XCN···SF2 and H3N···XCN···SO2 complexes (X=F, Cl, Br and I). J Mol Model 20:2291, 2014.
[41] A.E. Reed, L.A. Curtiss, F. Weinhold, Chem.Rev. 1988, 88, 899-926.
[42] L. Sobczyk, S.J. Grabowski, T.M. Krygowski, Chem.Rev., 2005, 105, 3513-3560.
[43] S.J. Grabowski, Chem.Rev., 2011, 11, 2597-2625.
[44] M. J. Hunt, A. L. Mackay, D. T. Edmonds, Department of physics University of Oxford Oxford UK, 1975.