A Computational Study of N–H…O Hydrogen Bonding to Investigate Cooperative Effects
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.
[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.
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[21] L. E. Kay, J. Magn. Reson., 2005, 173, 193-207.
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[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.
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Byrd, K. W. Zilm, J. Am. Chem. Soc., 2003, 125, 14222-14223.
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Chem., Int. Ed., 2005, 44, 2089-2092.
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Int. Ed., 2005, 44, 2441-2444.
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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.
[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.
@article{"International Journal of Chemical, Materials and Biomolecular Sciences:70542", author = "Setareh Shekarsaraei and Marjan Moridi and Nasser L. Hadipour", title = "A Computational Study of N–H…O Hydrogen Bonding to Investigate Cooperative Effects", 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.", volume = "9", number = "3", pages = "505-4", }
