Volume 7, Issue 4, December 2019, Page: 80-94
Theoretical Investigations of Hydrogen Bonding Interactions of (E)-1-(1H-Benzo[d]imidazol-2-yl)-3-Phenylprop-2-en-1-one Momoners and Dimers: NBO, QTAIM and NCI Study
Adenidji Ganiyou, Training and Research Unit of Sciences of Structures, Matter and Technology (UFR SSMT), Laboratory of Organic Chemistry and Natural Substances, Félix Houphouët-Boigny University, Abidjan, Côte d'Ivoire
Kicho Denis Yapo, Training and Research Unit of Sciences of Structures, Matter and Technology (UFR SSMT), Laboratory of Organic Chemistry and Natural Substances, Félix Houphouët-Boigny University, Abidjan, Côte d'Ivoire
Doumadé Zon, Training and Research Unit of Sciences of Structures, Matter and Technology (UFR SSMT), Laboratory of Organic Chemistry and Natural Substances, Félix Houphouët-Boigny University, Abidjan, Côte d'Ivoire; Department of Biochemistry-Genetics, Training and Research Unit in Biological Science, Peleforo Gon Coulibaly University, Korhogo, Côte-d’Ivoire
Mamadou Guy-Richard Kone, Faculty of Fundamental and Applied Sciences (UFR SFA), Laboratory of Thermodynamics and Physico-Chemistry of the Middle, Nangui Abrogoua University, Abidjan, Côte d'Ivoire
Received: Aug. 19, 2019;       Accepted: Sep. 16, 2019;       Published: Oct. 9, 2019
DOI: 10.11648/j.mc.20190704.11      View  83      Downloads  16
Hydrogen bonding is an essential interaction in nature and plays a crucial role in many formations of materials and biological processes, requiring a deeper understanding of its formation. Benzimidazole is an important structural unit found in a large number of natural and pharmacologically active molecules. In the present work, the electronic structures and properties and relatives stabilities of a series of (E)-1-(1H-benzo[d]imidazol-2-yl)-3-phenylprop-2-en-1-one monomers and dimers have been studied by density functional theory using B3LYP 6-31+G (d, p) calculation level. the strengths of the noncovalent interactions have been analyzed in terms of the QTAIM analysis, NCI analysis and natural bond orbital approaches. It was found that the dimers are formed by double N-H⋯O hydrogen bond. QTAIM analysis proved the presence of intramolecular hydrogen bond in monomers and coexistence of intramolecular and intermolecular hydrogen bond in dimers. Frequency analysis show that intermolecular N-H⋯O interactions are proper hydrogen bond while intramolecular C-H⋯N, C-H⋯O, C-H⋯H-C interactions are improper hydrogen bond. NBO and NCI analyses confirm the existence of hydrogen bonds in the studied monomers and dimers. The presence of weakly electron acceptor group on benzene ring favor the total interaction energy of dimerization.
NBO, QTAIM, NCI, Benzimidazole, Electron Density, Hydrogen Bond
To cite this article
Adenidji Ganiyou, Kicho Denis Yapo, Doumadé Zon, Mamadou Guy-Richard Kone, Theoretical Investigations of Hydrogen Bonding Interactions of (E)-1-(1H-Benzo[d]imidazol-2-yl)-3-Phenylprop-2-en-1-one Momoners and Dimers: NBO, QTAIM and NCI Study, Modern Chemistry. Vol. 7, No. 4, 2019, pp. 80-94. doi: 10.11648/j.mc.20190704.11
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Y. Wang, S. Xue, R. Li et al., “Synthesis and biological evaluation of novel synthetic chalcone derivatives as anti-tumor agents targeting Cat L and Cat K,” Bioorganic & medicinal chemistry, vol. 26, no. 1, pp. 8–16, 2018.
Z. M. Nofal, E. A. Soliman, S. S. Abd El-Karim et al., “Synthesis of Some New Benzimidazole-Thiazole Derivatives as Anticancer Agents,” Journal of Heterocyclic Chemistry, vol. 51, no. 6, pp. 1797–1806, 2014.
L.-t. Wu, Z. Jiang, J.-j. Shen et al., “Design, synthesis and biological evaluation of novel benzimidazole-2-substituted phenyl or pyridine propyl ketene derivatives as antitumour agents,” European journal of medicinal chemistry, vol. 114, pp. 328–336, 2016.
Ş. Demirayak, U. Abu Mohsen, and A. Çağri Karaburun, “Synthesis and anticancer and anti-HIV testing of some pyrazino[1,2-a]benzimidazole derivatives,” European journal of medicinal chemistry, vol. 37, no. 3, pp. 255–260, 2002.
Ş. Demirayak and L. Yurttaş, “Synthesis and anticancer activity of some 1,2,3-trisubstituted pyrazinobenzimidazole derivatives,” Journal of enzyme inhibition and medicinal chemistry, vol. 29, no. 6, pp. 811–822, 2014.
H. Göker, C. Kuş, D. W. Boykin et al., “Synthesis of some new 2-substituted-phenyl-1H-benzimidazole-5-carbonitriles and their potent activity against candida species,” Bioorganic & medicinal chemistry, vol. 10, no. 8, pp. 2589–2596, 2002.
H. Göker, S. Ozden, S. Yildiz et al., “Synthesis and potent antibacterial activity against MRSA of some novel 1,2-disubstituted-1H-benzimidazole-N-alkylated-5-carboxamidines,” European journal of medicinal chemistry, vol. 40, no. 10, pp. 1062–1069, 2005.
T. Pan, X. He, B. Chen et al., “Development of benzimidazole derivatives to inhibit HIV-1 replication through protecting APOBEC3G protein,” European journal of medicinal chemistry, vol. 95, pp. 500–513, 2015.
A. K. Tewari and A. Mishra, “Synthesis and Antiviral Activities of N-Substituted-2-substituted-benzimidazole Derivatives,” ChemInform, vol. 37, no. 23, p. 489, 2006.
H. A. BARKER, R. D. SMYTH, H. WEISSBACH et al., “Isolation and properties of crystalline cobamide coenzymes containing benzimidazole or 5, 6-dimethylbenzimidazole,” The Journal of biological chemistry, vol. 235, pp. 480–488, 1960.
Y. Yao, Y. Che, and J. Zheng, “The Coordination Chemistry of Benzimidazole-5,6-dicarboxylic Acid with Mn(II), Ni(II), and Ln(III) Complexes (Ln = Tb, Ho, Er, Lu),” Crystal Growth & Design, vol. 8, no. 7, pp. 2299–2306, 2008.
D. Olea-Román, A. Solano-Peralta, G. Pistolis et al., “Lanthanide coordination compounds with benzimidazole-based ligands. luminescence and EPR,” Journal of Molecular Structure, vol. 1163, pp. 252–261, 2018.
N. Şırecı, Ü. Yilmaz, H. Küçükbay et al., “Synthesis of 1-substituted benzimidazole metal complexes and structural characterization of dichlorobis(1-phenyl-1 H -benzimidazole- κN3)cobalt(II) and dichlorobis (1-phenyl-1 H -benzimidazole- κN3)zinc(II),” Journal of Coordination Chemistry, vol. 64, no. 11, pp. 1894–1902, 2011.
J. Kulhánek and F. Bureš, “Imidazole as a parent π-conjugated backbone in charge-transfer chromophores,” Beilstein journal of organic chemistry, vol. 8, pp. 25–49, 2012.
F. Saczewski, E. Dziemidowicz-Borys, P. J. Bednarski et al., “Synthesis, crystal structure and biological activities of copper(II) complexes with chelating bidentate 2-substituted benzimidazole ligands,” Journal of inorganic biochemistry, vol. 100, no. 8, pp. 1389–1398, 2006.
P. Gilli, V. Bertolasi, V. Ferretti et al., “Evidence for resonance-assisted hydrogen bonding. 4. Covalent nature of the strong homonuclear hydrogen bond. Study of the O-H--O system by crystal structure correlation methods,” Journal of the American Chemical Society, vol. 116, no. 3, pp. 909–915, 1994.
P. Gilli, V. Bertolasi, L. Pretto et al., “Covalent versus electrostatic nature of the strong hydrogen bond: Discrimination among single, double, and asymmetric single-well hydrogen bonds by variable-temperature X-ray crystallographic methods in beta-diketone enol RAHB systems,” Journal of the American Chemical Society, vol. 126, no. 12, pp. 3845–3855, 2004.
S. Scheiner, Hydrogen bonding: A theoretical perspective, Oxford University Press, New York, 1997.
P. Gilli, V. Bertolasi, V. Ferretti et al., “Evidence for Intramolecular N−H···O Resonance-Assisted Hydrogen Bonding in β-Enaminones and Related Heterodienes. A Combined Crystal-Structural, IR and NMR Spectroscopic, and Quantum-Mechanical Investigation,” Journal of the American Chemical Society, vol. 122, no. 42, pp. 10405–10417, 2000.
F. Cipcigan, V. Sokhan, G. Martyna et al., “Structure and hydrogen bonding at the limits of liquid water stability,” Scientific reports, vol. 8, no. 1, p. 1718, 2018.
J. Liu, X. He, J. Z. H. Zhang et al., “Hydrogen-bond structure dynamics in bulk water: Insights from ab initio simulations with coupled cluster theory,” Chemical science, vol. 9, no. 8, pp. 2065–2073, 2018.
C. Fonseca Guerra, F. M. Bickelhaupt, J. G. Snijders et al., “The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance,” Chemistry - A European Journal, vol. 5, no. 12, pp. 3581–3594, 1999.
S. J. Grabowski, “What is the covalency of hydrogen bonding?,” Chemical reviews, vol. 111, no. 4, pp. 2597–2625, 2011.
I. V. Alabugin, Stereoelectronic effects: A bridge between structure and reactivity, Wiley, Chichester, West Sussex, UK, Hoboken, NJ, USA, 2016.
A. S. Hansen, L. Du, and H. G. Kjaergaard, “The effect of fluorine substitution in alcohol-amine complexes,” Physical chemistry chemical physics: PCCP, vol. 16, no. 41, pp. 22882–22891, 2014.
P. Hobza and Z. Havlas, “Blue-Shifting Hydrogen Bonds,” Chemical Reviews, vol. 100, no. 11, pp. 4253–4264, 2000.
I. V. Alabugin, M. Manoharan, S. Peabody et al., “Electronic basis of improper hydrogen bonding: A subtle balance of hyperconjugation and rehybridization,” Journal of the American Chemical Society, vol. 125, no. 19, pp. 5973–5987, 2003.
R. G. Parr, “Density Functional Theory of Atoms and Molecules,” in Horizons of Quantum Chemistry: Proceedings of the Third International Congress of Quantum Chemistry Held at Kyoto, Japan, October 29 - November 3, 1979, K. Fukui and B. Pullman, Eds., pp. 5–15, Springer Netherlands, Dordrecht, 1980.
J. K. Labanowski and J. Andzelm, Density functional methods in chemistry, Springer New York, New York, N. Y., 1991.
Gaussian 09, Revision D.01 M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2013.
AIMAll (Version 10.05.04), Todd A. Keith, 2010 (aim.tkgristmill.com).
Glendening, A. E. Reed, J. E. Carpenter et al., “NBO Version 3.1,” NBO Version 3.1.
T. Lu and F. Chen, “Multiwfn: a multifunctional wavefunction analyzer,” Journal of computational chemistry, vol. 33, no. 5, pp. 580–592, 2012.
chemcraft, Zhurko, G. A. and Zhurko, D. A. Chemcraft. Version 1.8 (Build 523a).
S. F. Boys and F. Bernardi, “The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors,” Molecular Physics, vol. 19, no. 4, pp. 553–566, 1970.
F. Weinhold and C. R. Landis, “Natural Bond Orbitals and extensions of localized bonding concepts,” Chem. Educ. Res. Pract., vol. 2, no. 2, pp. 91–104, 2001.
R. F. W. Bader, Atoms in molecules: A quantum theory, Clarendon Press; Oxford University Press, Oxford England, New York, 1994.
I. Rozas, I. Alkorta, and J. Elguero, “Behavior of Ylides Containing N, O, and C Atoms as Hydrogen Bond Acceptors,” Journal of the American Chemical Society, vol. 122, no. 45, pp. 11154–11161, 2000.
Y.-Z. Yang, X.-F. Liu, R.-B. Zhang et al., “Joint experimental and theoretical studies of the surprising stability of the aryl pentazole upon noncovalent binding to β-cyclodextrin,” Physical chemistry chemical physics: PCCP, vol. 19, no. 46, pp. 31236–31244, 2017.
T. S. Koritsanszky, “Topology of X-Ray Charge Density of Hydrogen Bonds,” in Hydrogen bonding-new insights, S. J. Grabowski, Ed., pp. 441–470, Springer, Dordrecht, 2006.
R. Bianchi, G. Gervasio, and D. Marabello, “Experimental Electron Density Analysis of Mn 2 (CO) 10: Metal−Metal and Metal−Ligand Bond Characterization,” Inorganic Chemistry, vol. 39, no. 11, pp. 2360–2366, 2000.
E. Espinosa, E. Molins, and C. Lecomte, “Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities,” Chemical Physics Letters, vol. 285, 3-4, pp. 170–173, 1998.
B. Vijaya Pandiyan, P. Deepa, and P. Kolandaivel, “Do resonance-assisted intramolecular halogen bonds exist without a charge transfer and a σ-hole?,” Physical chemistry chemical physics: PCCP, vol. 17, no. 41, pp. 27496–27508, 2015.
E. R. Johnson, S. Keinan, P. Mori-Sánchez et al., “Revealing noncovalent interactions,” Journal of the American Chemical Society, vol. 132, no. 18, pp. 6498–6506, 2010.
J. Contreras-García, E. R. Johnson, S. Keinan et al., “NCIPLOT: a program for plotting non-covalent interaction regions,” Journal of chemical theory and computation, vol. 7, no. 3, pp. 625–632, 2011.
A. J. Cohen, P. Mori-Sánchez, and W. Yang, “Insights into current limitations of density functional theory,” Science (New York, N. Y.), vol. 321, no. 5890, pp. 792–794, 2008.
G. Saleh, C. Gatti, L. Lo Presti et al., “Revealing non-covalent interactions in molecular crystals through their experimental electron densities,” Chemistry (Weinheim an der Bergstrasse, Germany), vol. 18, no. 48, pp. 15523–15536, 2012.
D. N. Lande, S. A. Bhadane, and S. P. Gejji, “Noncovalent Interactions Accompanying Encapsulation of Resorcinol within Azacalix4pyridine Macrocycle,” The journal of physical chemistry. A, vol. 121, no. 8, pp. 1814–1824, 2017.
T. Steiner, “The Hydrogen Bond in the Solid State,” Angewandte Chemie International Edition, vol. 41, no. 1, pp. 48–76, 2002.
G. R. Desiraju and T. Steiner, The weak hydrogen bond: In structural chemistry and biology, Oxford University Press, Oxford etc., 1999.
U. Koch and P. L. A. Popelier, “Characterization of C-H-O Hydrogen Bonds on the Basis of the Charge Density,” The Journal of Physical Chemistry, vol. 99, no. 24, pp. 9747–9754, 1995.
P. L. A. Popelier, Atoms in molecules: An introduction, Prentice Hall, Harlow, 2000.
C. F. Matta, “Hydrogen–Hydrogen Bonding: The Non-Electrostatic Limit of Closed-Shell Interaction Between Two Hydro,” in Hydrogen bonding-new insights, S. J. Grabowski, Ed., pp. 337–375, Springer, Dordrecht, 2006.
C. F. Matta and R. J. Boyd, The Quantum Theory of Atoms in Molecules, Wiley, 2007.
P. Hobza and Z. Havlas, “Improper, blue-shifting hydrogen bond,” Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol. 108, no. 6, pp. 325–334, 2002.
F. Weinhold and C. R. Landis, “Supramolecular bonding,” in Valency and Bonding: A Natural Bond Orbital Donor-Acceptor Perspective, F. WEINHOLD and C. R. LANDIS, Eds., pp. 579–709, Cambridge University Press, Cambridge, 2005.
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