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Original Articles

A new insight for chalcogen bonding based on Point-of-Charge approach

ORCID Icon &
Pages 444-454 | Received 18 Jun 2018, Accepted 21 Sep 2018, Published online: 28 Dec 2018

References

  • Politzer, P.; Murray, J. S.; Clark, T. Halogen bonding and other σ-hole interactions: A perspective. Phys. Chem. Chem. Phys. 2013, 15, 11178–11189. DOI:10.1039/c3cp00054k.
  • Clark, T.; Hennemann, M.; Murray, J. S.; Politzer; P. Halogen bonding: The σ-hole. J. Mol. Model. 2007, 13, 291–296. DOI:10.1007/s00894-006-0130-2.
  • Ibrahim, M. A. A. Molecular mechanical perspective on halogen bonding. J. Mol. Model. 2012, 18, 4625–4638. DOI:10.1007/s00894-012-1454-8.
  • Langton, M. J.; Robinson, S. W.; Marques, I.; Félix, V.; Beer, P. D. Halogen bonding in water results in enhanced anion recognition in acyclic and rotaxane hosts. Nat. Chem. 2014, 6, 1039–1043. DOI:10.1038/nchem.2111.
  • Scholfield, M. R.; Zanden, C. M. V.; Carter, M.; Ho, P. S. Halogen bonding (X-bonding): A biological perspective. Protein Sci. 2013, 22, 139–152. DOI:10.1002/pro.2201.
  • Auffinger, P.; Hays, F. A.; Westhof, E.; Ho, P. S. Halogen bonds in biological molecules. Proc. Natl. Acad. Sci. USA 2004, 101, 16789–16794. DOI: 10.1073/pnas.0407607101.
  • Fang, Y.; Li, A. Y.; Ma, F. Y. A comparative study of the chalcogen bond, halogen bond and hydrogen bond S···O/Cl/H formed between SHX and HOCl. J. Mol. Model. 2015, 21, 61–70. DOI:10.1007/s00894-015-2612-6.
  • Rosenfield, R. E.; Parthasarathy, R.; Dunitz, J. D. Directional preferences of nonbonded atomic contacts with divalent sulfur .1. Electrophiles and nucleophiles. J. Am. Chem. Soc. 1977, 99, 4860–4862. DOI:10.1021/ja00456a072.
  • Wang, W. Z.; Ji, B. M.; Zhang, Y. Chalcogen bond: A sister noncovalent bond to halogen bond. J. Phys. Chem. A 2009, 113, 8132–8135. DOI:10.1021/jp904128b.
  • Scheiner, S. A new noncovalent force: Comparison of P···N interaction with hydrogen and halogen bonds. J. Chem. Phys. 2011, 134, 094315–094323. DOI:09431510.1063/1.3562209.
  • Alkorta, I.; Elguero, J.; Del Bene, J. E. Pnicogen bonded complexes of PO2X (X = F, Cl) with nitrogen bases. J. Phys. Chem. A 2013, 117, 10497–10503. DOI:10.1021/jp407097e.
  • Alkorta, I.; Rozas, I.; Elguero, J. Molecular complexes between silicon derivatives and electron-rich groups. J. Phys. Chem. A 2001, 105, 743–749. DOI:10.1021/jp002808b.
  • Bauza, A.; Mooibroek, T. J.; Frontera, A. Tetrel-Bonding Interaction: Rediscovered Supramolecular Force? Angew. Chem.-Int. Edit. 2013, 52, 12317–12321. DOI:10.1002/anie.201306501.
  • Grabowski, S. J. Tetrel bond–σ-hole bond as a preliminary stage of the SN2 reaction. Phys. Chem. Chem. Phys. 2014, 16, 1824–1834. DOI:10.1039/c3cp53369g.
  • Bundhun, A.; Ramasami, P.; Murray, J. S.; Politzer, P. Trends in σ-hole strengths and interactions of F3MX molecules (M = C, Si, Ge and X = F, Cl, Br, I). J. Mol. Model. 2013, 19, 2739–2746. DOI:10.1007/s00894-012-1571-4.
  • Iwaoka, M.; Isozumi, N. Hypervalent nonbonded interactions of a divalent sulfur atom. Implications in protein architecture and the functions. Molecules 2012, 17, 7266–7283. DOI:10.3390/molecules17067266.
  • Thomas, S. P.; Jayatilaka, D.; Guru Row; T. N. S···O chalcogen bonding in sulfa drugs: Insights from multipole charge density and X-ray wavefunction of acetazolamide. Phys. Chem. Chem. Phys. 2015, 17, 25411–25420. DOI:10.1039/c5cp04412j.
  • Patra, A.; Wijsboom, Y. H.; Leitus, G.; Bendikov, M. Synthesis, Structure, and Electropolymerization of 3, 4-Dimethoxytellurophene: Comparison with Selenium Analogue. Org. Lett. 2009, 11, 1487–1490. DOI:10.1021/ol9000608.
  • Rolf, G.; Werz, D. B. Elastic cycles as flexible hosts: How tubes built by cyclic chalcogenaalkynes individually host their guests. Chem. Lett. 2005, 34, 126–131. doi:10.1246/cl.2005.126.
  • Werz, D. B.; Staeb, T. H.; Benisch, C.; Rausch, B. J.; Rominger, F.; Gleiter, R. Self-organization of chalcogen-containing cyclic alkynes and alkenes to yield columnar structures. Org. Lett. 2002, 4, 339–342. DOI:10.1021/ol016953z.
  • Ho, P. C.; Szydlowski, P.; Sinclair, J.; Elder, P. J. W.; Kübel, J.; Gendy, C.; Lee, L. M.; Jenkins, H.; Britten, J. F.; Morim, D. R.; Vargas-Baca, I. Supramolecular macrocycles reversibly assembled by Te···O chalcogen bonding. Nat. Commun. 2016, 7, 11299–11308. DOI:10.1038/ncomms11299.
  • Bleiholder, C.; Werz, D. B.; Koppel, H.; Gleiter, R. Theoretical investigations on chalcogen-chalcogen interactions: What makes these nonbonded interactions bonding? J. Am. Chem. Soc. 2006, 128, 2666–2674. DOI:10.1021/ja056827g.
  • IUPAC: Categorizing chalcogen, pnictogen, and tetrel bonds, and other interactions involving groups 14-16 elements, Project No.:2016-001-2-300. https://iupac.org/projects/project-details/?project_nr=2016-001-2-300.
  • Ibrahim, M. A. A.; Moussa, N. A. M.; Safy, M. E. A. Quantum-mechanical investigation of tetrel bond characteristics based on the point-of-charge (PoC) approach. J. Mol. Model. 2018, 24, 219. DOI:10.1007/s00894-018-3752-2.
  • Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; J. A. Montgomery, J.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, Revision E.01, 2009, Gaussian, Inc., Wallingford CT, USA.
  • Møller, C.; Plesset, M. S. Note on an Approximation Treatment for Many-Electron Systems. Phys. Rev. 1934, 46, 618–622. DOI:10.1103/PhysRev.46.618.
  • Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. J. Chem. Phys. 1980, 72, 650–654. DOI:10.1063/1.438955.
  • Becke, A. D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 1988, 38, 3098–3100. DOI:10.1103/PhysRevA.38.3098.
  • Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 1988, 37, 785–789. DOI: 10.1103/PhysRevB.37.785.
  • Woon, D. E.; Dunning, Jr., T. H. Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties. J. Chem. Phys. 1994, 100, 2975–2988. DOI:10.1063/1.466439.
  • Woon, D. E.; Dunning, T. H. Gaussian basis sets for use in correlated molecular calculations. III. The atoms aluminum through argon. J. Chem. Phys. 1993, 98, 1358–1371. DOI:10.1063/1.464303.
  • Boys, S. F.; Bernardi, F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol. Phys. 1970, 19, 553–566. DOI:10.1080/00268977000101561.
  • Politzer, P.; Laurence, P. R.; Jayasuriya, K. Molecular electrostatic potentials: an effective tool for the elucidation of biochemical phenomena. Environ. Health Perspect. 1985, 61, 191–202.
  • Politzer, P.; Daiker, K. C.; Donnelly, R. A. Molecular electrostatic potentials: A new approach to the study of the metabolic and carcinogenic activities of hydrocarbons. Cancer Lett. 1976, 2, 17–23. DOI:https://doi.org/10.1016/S0304-3835(76)80005-5.
  • Orozco, M.; Luque, F. J. Generalization of the Molecular Electrostatic Potential for the Study of Noncovalent interactions. Theoretical and Computational Chemistry, Murray, J. S.; Sen, K., Eds.; Elsevier: Amsterdam, Netherlands, 1996; pp. 181–218. DOI:10.1016/S1380-7323(96)80044-6.
  • Ibrahim, M. A. A.; Hasb, A. A. M.; Mekhemer, G. A. H. Role and nature of halogen bonding in inhibitor…receptor complexes for drug discovery: casein kinase-2 (CK2) inhibition as a case study. Theor. Chem. Acc. 2018, 137, 38–47. DOI:10.1007/s00214-018-2207-2.
  • Wang, C. W.; Guan, L. Y.; Danovich, D.; Shaik, S.; Mo, Y. R. The origins of the directionality of noncovalent intermolecular interactions. J. Comput. Chem. 2016, 37, 34–45. DOI:10.1002/jcc.23946.
  • Reed, A. E.; Curtiss, L. A.; Weinhold, F. Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem. Rev. 1988, 88, 899–926. DOI:10.1021/cr00088a005.
  • Grabowski, S. J. Non-covalent interactions – QTAIM and NBO analysis. J. Mol. Model. 2013, 19, 4713–4721. DOI:10.1007/s00894-012-1463-7.

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