Dimers and trimers of formamidine and its mono-halogenated analogues HNCHNHX, (X=H, Cl, Br, or I): A comparative study of resonance-assisted hydrogen and halogen bonds

Computational and Theoretical Chemistry

Volumn 998, Issue , 2012, Pages 183-192

  Parra, Ruben D ^a  

^a DEPAUL UNIVERSITY   (United States)

Author keywords

Ab initio; Density functional theory; Formamidine; Halogen bonding; Hydrogen bonding

Indexed keywords

EID: 84867139904     PISSN: 2210271X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comptc.2012.07.032     Document Type: Article

References (72)

1. Johnson E.R., Keinan S., Mori-Sanchez P., Contreras-Garcia J., Cohen A.J., Yang W. Revealing noncovalent interactions. J. Am. Chem. Soc. 2010, 6498:132.
2. P. Hobza, K. Müller-Dethlefs, Non-covalent Interactions: Theory and Experiment. RSC Theoretical and Computational Chemistry Series No. 2, 2009.
3. Müller-Dethlefs K., Hobza P. Non-covalent interactions: a challenge for experiment and theory. Chem. Rev. 2000, 143:100.
4. Steed J.W., Atwood J.L. Supramolecular Chemistry 2009, Wiley. second ed.
5. Latimer W.M., Rodebush W.H. Polarity and ionization from the standpoint of the Lewis theory of valence. J. Am. Chem. Soc. 1920, 1419:42.
6. Gilli P., Gilli G. The Nature of the Hydrogen Bond 2009, Oxford University Press, Oxford.
7. Hydrogen Bonding: New Insights 2006, Springer, Dordrecht. S.J. Grabowski (Ed.).
8. Desiraju G.R., Steiner T. The Weak Hydrogen Bond 1999, Oxford University Press, Oxford.
9. Scheiner S. Hydrogen Bonding: A Theoretical Perspective 1997, Oxford University Press, Oxford.
10. Jeffrey G.A. An Introduction to Hydrogen Bonding 1997, Oxford University Press, Oxford.
11. Bolen D.W., Rose G.D. Structure and energetics of the hydrogen-bonded backbone in protein folding. Annu. Rev. Biochem. 2008, 77:339.
12. Steiner T. The whole palette of hydrogen bonds. Angew. Chem. Int. Ed. 2002, 48:41.
13. Aakeroy C.B., Beatty A.M. Solid state, crystal engineering and hydrogen bonds. ChemInform 2004, 679:35.
14. Meot-Ner M. The ionic hydrogen bond. Chem. Rev. 2005, 213:105.
15. Hobza P., Havlas Z. Blue-shifting hydrogen bonds. Chem. Rev. 2000, 4253:100.
16. Barnes A. Blue-shifting hydrogen bonds? Are they improper or proper?. J. Mol. Struct. 2004, 3:704.
17. Akorta I., Rozas I., Elguero J. Non-conventional hydrogen bonds. Chem. Soc. Rev. 1998, 163:27.
18. Takahashi O., Kohno Y., Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab Initio MO calculations. Chem. Rev. 2010, 6049:110.
19. Grabowski S.J. What is the covalency of hydrogen bonding?. Chem. Rev. 2011, 2597:111.
20. Arunan E., Desiraju G.R., Klein R.A., Sadlej J., Scheiner S., Alkorta I., Clary D.C., Crabtree R.H., Dannenberg J.J., Hobza P., Kjaergaard H.G., Legon A.C., Mennucci B., Nesbitt D.J. Defining the hydrogen bond: an account. Pure Appl. Chem. 2011, 1619:83.
21. Arunan E., Desiraju G.R., Klein R.A., Sadlej J., Scheiner S., Alkorta I., Clary D.C., Crabtree R.H., Dannenberg J.J., Hobza P., Kjaergaard H.G., Legon A.C., Mennucci B., Nesbitt D.J. Definition of the hydrogen bond. Pure Appl. Chem. 2011, 1637:83.
22. Sánchez-Sanz G., Trujillo C., Alkorta I., Elguero J. Electron density shift description of non-bonding intramolecular interactions. COMPTC 2012, 991:124.
23. Y. Mo, Can QTAIM topological parameters be a measure of hydrogen bonding strength? J. Phys. Chem. A, DOI: 10.1021/jp3029769.
24. Hassel O. Science 1970, 497:170.
25. Legon A.C. The halogen bond: an interim perspective. Phys. Chem. Chem. Phys. 2010, 7736:12.
26. Metrangolo P., Meyer F., Pilati T., Resnati G., Terraneo G. Halogen bonding in supramolecular chemistry. Angew. Chem. Int. Ed. 2008, 6114:47.
27. Politzer P., Lane P., Concha M.C., Ma Y., Murray J.S. An overview of halogen bonding. J. Mol. Model. 2007, 305:13.
28. Clark T., Hennemann M., Murray J.S., Politzer P. Halogen bonding: the σ-hole. J. Mol. Model. 2007, 291:13.
29. Politzer P., Murray J.S., Lane P. σ-Hole bonding and hydrogen bonding: competitive interactions. Int. J. Quantum Chem. 2007, 3046:107.
30. Dikundwar A.G., Guru Row T.N. Evidence for the " Amphoteric" nature of fluorine in halogen bonds: an instance of Cl···F contact. Cryst. Growth Des. 2012, 1713:12.
31. Politzer P., Murray J.S., Clark T. Halogen bonding: an electrostatically-driven highly directional noncovalent interaction. Phys. Chem. Chem. Phys. 2010, 7748:12.
32. Cavallo G., Metrangolo P., Pilati T., Resnati G., Sansotera M., Terraneo G. Halogen bonding: a general route in anion recognition and coordination. Chem. Soc. Rev. 2010, 3772:39.
33. Auffinger P., Hays F.A., Westhof E., Shing Ho P. Halogen bonding in biological molecules. Proc. Natl. Acad. Sci. USA 2004, 16789:101.
34. Bertani R., Sgarbossa P., Venzo A., Lelj F., Amatic M., Resnatid G., Pilati T., Metrangolo P., Terraneo G. Halogen bonding in metal-organic-supramolecular networks. Coord. Chem. Rev. 2010, 677:254.
35. Parisini E., Metrangolo P., Pilati T., Resnati G., Terraneo G. Halogen bonding in halocarbon-protein complexes: a structural survey. Chem. Soc. Rev. 2011, 2267:40.
36. Halogen Bonding: Fundamentals and Applications 2008, Springer, Berlin. P. Metrangolo, G. Resnati (Eds.).
37. Metrangolo P., Neukirch H., Pilati T., Resnati G. Halogen bonding based recognition processes: a world parallel to hydrogen bonding. Acc. Chem. Res. 2005, 386:38.
38. Corradi E., Meille S.V., Messina M.T., Metrangolo P., Resnati G. Halogen bonding versus hydrogen bonding in driving self-assembly processes. Angew. Chem. Int. Ed. 2000, 1782:39.
39. Metrangolo P., Resnati G. Halogens versus hydrogen. Science 2008, 918:321.
40. Voth A.R., Hays F.A., Shing Ho P. Directing macromolecular conformation through halogen bonds. Proc Natl Acad Sci USA 2007, 6188:104.
41. Wang W., Zhang Y., Ji B. On the difference of the properties between the blue-shifting halogen bond and the blue-shifting hydrogen bond. J. Phys. Chem. A 2010, 7257:114.
42. Esrafili M.D., Hadipour N.L. Characteristics and nature of halogen bonds in linear clusters of NCX (X=Cl and Br): an ab initio, NBO, and QTAIM study. Mol. Phys. 2011, 2451:109.
43. Alkorta I., Blanco F., Elguero J. A computational study of the cooperativity in clusters of interhalogen derivatives. Struct. Chem. 2009, 63:20.
44. n complexes. Chem. Phys. Lett. 2006, 427:51.
45. Bilewicz E., Rybarczyk-Pirek A.J., Dubis A.T., Grabowski S.J. Halogen bonding in crystal structure of 1-methylpyrrol-2-yl trichloromethyl ketone. J. Mol. Struct. 2007, 829:208.
46. Lankau T.M., Wu Y.C., Zou J.W., Yu C.H. J. Theoret. Comput. Chem. 2008, 7:13.
47. Yunxiang L., Jianwei Z., Hongqing W., Qingsen Y., Huaxin Z., Yongjun J. Triangular halogen trimers. A DFT study of the structure, cooperativity, and vibrational properties. J. Phys. Chem. A 2005, 11956:109.
48. Alkorta I., Blanco F., Deya P.M., Elguero J., Estarellas C., Frontera A., Quinorero D. Cooperativity in multiple unusual weak bonds. Theor. Chem. Acc. 2010, 1:126.
49. 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, 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, D.J. Fox, Gaussian 09, Revision A.02, Gaussian, Inc., Wallingford, CT, 2009.
50. Dunning T.H. A road map for the calculation of molecular binding energies. J. Phys. Chem. A 2000, 9062:104.
51. Dunning T.H. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Phys. Chem. A 1989, 1007:90.
52. Peterson K.A., Figgen D., Dolg M., Stoll H. Energy-consistent relativistic pseudopotentials and correlation consistent basis sets for the 4d elements Y-Pd. J. Chem. Phys. 2007, 124101:126.
53. Becke A.D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 1988, 3098:38.
54. Becke A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 9(8):5648.
55. 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.
56. Stephens P.J., Devlin F.J., Chabalowski C.F., Frish M.J. Ab Initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem. 1994, 11623:98.
57. Zhao Y., Schultz N.E., Truhlar D.G. Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions. J. Chem. Theory Comput. 2006, 364:2.
58. Zhao Y., Truhlar D.G. Density functionals with broad applicability in chemistry. Acc. Chem. Res. 2008, 157:41.
59. Wang W., Zhang Y., Ji B., Tian A. On the correlation between bond-length change and vibrational frequency shift in halogen-bonded complexes. J. Chem. Phys. 2011, 224303:134.
60. Boys S.F., Bernardi F. Calculation of small molecular interactions by differences of separate total energies - some procedures with reduced errors. Mol. Phys. 1970, 553:19.
61. Bader R.F.W. Atoms in Molecules: A Quantum Theory 1990, Oxford University Press, Oxford, UK.
62. Biegler-König F., Schönbohm J., Bayles D. AIM2000 - a program to analyze and visualize atoms in molecules. J. Comput. Chem. 2001, 545:22.
63. A.E. Reed, J.E. Carpenter, F. Weinhold, NBO Version 3.1, E.D. Glendening.
64. Reed A.E., Weinhold F.J. Natural localized molecular-orbitals. J. Chem. Phys. 1985, 1736:83.
65. Reed A.E., Curtiss L.A., Weinhold F. Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem. Rev. 1988, 899:88.
66. Carlsson A.-C.C., Gräfenstein J., Laurilla J.L., Bergquist J., Erdélyi M. Symmetry of [NXN]+ halogen bonds in solution. Chem. Commun. 2012, 1458:48.
67. Carlsson A-C.C., Gräfenstein J., Budnjo A., Laurilla J.L., Bergquist J., Karim A., Kleinmaier R., Brath U., Erdélyi M. Symmetric halogen bonding is preferred in solution. J. Am. Chem. Soc. 2012, 5706:134.
68. Šponer J., Hobza P. Interaction energies of hydrogen-bonded formamide dimer, formamidine dimer, and selected DNA base pairs obtained with large basis sets of atomic orbitals. J. Phys. Chem. A 2000, 4592:104.
69. Grabowski S.J. QTAIM characteristics of halogen bond and related interactions. J. Phys. Chem. A 2012, 1838:116.
70. Lu Y., Zou J., Wang Y., Jiang Y., Yu Q. 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 2007, 10781:111.
71. Zou J.-W., Lu Y.-X., Yu Q.-S., Zhang H.-X., Jiang Y.-J. Halogen bonding: an AIM analysis of the weak interactions. Chin. J. Chem. 2006, 1709:24.
72. 3_nCBr (n=0, 1, 2, 3) and HMgH. J. Mol. Struct: THEOCHEM 2010, 145:942.