Molecular mechanical perspective on halogen bonding

Journal of Molecular Modeling

Volumn 18, Issue 10, 2012, Pages 4625-4638

  Ibrahim, Mahmoud A A ^a,b  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b Minia University ^*  (Egypt)

Author keywords

Hole; APCtMI approach; Halogen bond; Noncovalent interaction; PEP approach

Indexed keywords

AMMONIA; BROMOBENZENE; CHLOROBENZENE; FORMALDEHYDE; HALOGEN; IODINE; IODOBENZENE; LEWIS BASE; METHYL CHLORIDE;

ATOM; CHEMICAL BINDING; CHEMICAL BOND; COMPLEX FORMATION; CONTROLLED STUDY; MOLECULAR INTERACTION; MOLECULAR MECHANICS; PRIORITY JOURNAL; QUANTUM MECHANICS; REVIEW; STATIC ELECTRICITY;

BENZENE; FORMALDEHYDE; HALOGENS; MECHANICAL PHENOMENA; METHYL CHLORIDE; MODELS, MOLECULAR; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 84870547591     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-012-1454-8     Document Type: Review

References (32)

1. Politzer P, Murray JS, Clark T (2010) Halogen bonding: an electrostatically-driven highly directional noncovalent interaction. Phys Chem Chem Phys 12:7748-7757.
2. Politzer P, Lane P, Concha M, Ma Y, Murray J (2007) An overview of halogen bonding. J Mol Model 13:305-311.
3. Brammer L, Bruton EA, Sherwood P (2001) Understanding the behavior of halogens as hydrogen bond acceptors. Cryst Growth Des 1:277-290.
4. Kovács A, Varga Z (2006) Halogen acceptors in hydrogen bonding. Coord Chem Rev 250:710-727.
5. Auffinger P, Hays FA, Westhof E, Ho PS (2004) Halogen bonds in biological molecules. Proc Natl Acad Sci USA 101:16789-16794.
6. Clark T, Hennemann M, Murray J, Politzer P (2007) Halogen bonding: the σ-hole. J Mol Model 13:291-296.
7. Politzer P, Murray J, Concha M (2008) σ-Hole bonding between like atoms; a fallacy of atomic charges. J Mol Model 14:659-665.
8. Riley KE, Merz KM (2007) Insights into the strength and origin of halogen bonding: the halobenzene-formaldehyde dimer. J Phys Chem A 111:1688-1694.
9. Palusiak M (2010) On the nature of halogen bond: the Kohn-Sham molecular orbital approach. J Mol Struct (THEOCHEM) 945:89-92.
10. Metrangolo P, Murray JS, Pilati T, Politzer P, Resnati G, Terraneo G (2011) Fluorine-centered halogen bonding: a factor in recognition phenomena and reactivity. Cryst Growth Des 11:4238-4246.
11. Metrangolo P, Murray JS, Pilati T, Politzer P, Resnati G, Terraneo G (2011) The fluorine atom as a halogen bond donor, viz. a positive site. CrystEngComm 13:6593-6596.
12. Lu Y-X, Zou J-W, Wang Y-H, Jiang Y-J, Yu Q-S (2007) Ab initio investigation of the complexes between bromobenzene and several electron donors: some insights into the magnitude and nature of halogen bonding interactions. J Phys Chem A 111:10781-10788.
13. Lu Y-X, Zou J-W, Wang Y-H, Yu Q-S (2006) Ab initio and atoms in molecules analyses of halogen bonding with a continuum of strength. J Mol Struct (THEOCHEM) 776:83-87.
14. Riley KE, Hobza P (2008) Investigations into the nature of halogen bonding including symmetry adapted perturbation theory analyses. J Chem Theory Comput 4:232-242.
15. Lu Y, Shi T, Wang Y, Yang H, Yan X, Luo X, Jiang H, Zhu W (2009) Halogen bonding: a novel interaction for rational drug design? J Med Chem 52:2854-2862.
16. Ibrahim MAA (2011) Molecular mechanical study of halogen bonding in drug discovery. J Comput Chem 32:2564-2574.
17. Ibrahim MAA (2012) AMBER empirical potential describes the geometry and energy of noncovalent halogen interactions better than advanced semiempirical quantum mechanical method PM6- DH2X. J Phys Chem B 116:3659-3669.
18. Ibrahim MAA (2011) Performance assessment of semiempirical molecular orbital methods in describing halogen bonding: quantum mechanical and quantum mechanical/molecular mechanical- molecular dynamics study. J Chem Inf Model 51:2549-2559.
19. Møller C, Plesset MS (1934) Note on an approximation treatment for many-electron systems. Phys Rev 46:618-622.
20. Dunning JTH (1989) Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J Chem Phys 90:1007-1023.
21. Woon DE, Dunning JTH (1993) Gaussian basis sets for use in correlated molecular calculations. III. The atoms aluminum through argon. J Chem Phys 98:1358-1371.
22. Boys SF, Bernardi F (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19:553-566.
23. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA TV Jr, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, AustinAJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03. Gaussian Inc., Wallingford.
24. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09. Gaussian, Inc., Wallingford.
25. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157-1174.
26. Bayly CI, Cieplak P, Cornell W, Kollman PA (1993) A wellbehaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 97:10269-10280.
27. Bulat F, Toro-Labbé A, Brinck T, Murray J, Politzer P (2010) Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies. J Mol Model 16:1679-1691.
28. Bader RFW, Carroll MT, Cheeseman JR, Chang C (1987) Properties of atoms in molecules: atomic volumes. J Am Chem Soc 109:7968-7979.
29. Jurecka P, Sponer J, Cerny J, Hobza P (2006) Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Phys Chem Chem Phys 8:1985-1993.
30. Cybulski SM, Lytle ML (2007) The origin of deficiency of the supermolecule second-order Møller-Plesset approach for evaluating interaction energies. J Chem Phys 127:141102-141105.
31. Richard WD, Peter AK (1997) Advancing beyond the atomcentered model in additive and nonadditive molecular mechanics. J Comput Chem 18:1632-1646.
32. Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev 88:899-926.