Electron density shift description of non-bonding intramolecular interactions

Computational and Theoretical Chemistry

Volumn 991, Issue , 2012, Pages 124-133

  Sánchez Sanz, Goar ^a   Trujillo, Cristina ^a,b   Alkorta, Ibon ^a   Elguero, José ^a  

^a INSTITUTO DE QUÍMICA MÉDICA   (Spain)

^b UNIVERSIDAD CARLOS III DE MADRID   (Spain)

Author keywords

Electron density shift; Intramolecular interactions; Molecular tailoring; MP2

Indexed keywords

EID: 84861705840     PISSN: 2210271X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comptc.2012.04.007     Document Type: Article

References (66)

1. Maréchan Y. The Hydrogen Bond and Water Molecule: The Physics and Chemistry of Water, Aqueous, and Bio-media 2007, Elsevier, Amsterdam.
2. Stiopkin I.V., Weeraman C., Pieniazek P.A., Shalhout F.Y., Skinner J.L., Benderskii A.V. Hydrogen bonding at the water surface revealed by isotopic dilution spectroscopy. Nature 2011, 474:192-195.
3. Nicodemus R.A., Corcelli S.A., Skinner J.L., Tokmakoff A. Collective hydrogen bond reorganization in water studied with temperature-dependent ultrafast infrared spectroscopy. J. Phys. Chem. B 2011, 115:5604-5616.
4. Zeidler A., Salmon P.S., Fischer H.E., Neuefeind J.C., Simonson J.M., Lemmel H., Rauch H., Markland T.E. Oxygen as a site specific probe of the structure of water and oxide materials. Phys. Rev. Lett. 2011, 107:145501.
5. Matta C.F., Castillo N., Boyd R.J. Extended weak bonding interactions in DNA: π-stacking (base-base), base-backbone, and backbone-backbone interactions. J. Phys. Chem. B 2005, 110:563-578.
6. Khesbak H., Savchuk O., Tsushima S., Fahmy K. The role of water H-bond imbalances in B-DNA substate transitions and peptide recognition revealed by time-resolved FTIR spectroscopy. J. Am. Chem. Soc. 2011, 133:5834-5842.
7. Yang E., Chen S.-Y., Liu Z.-S., Li J.-Q. Unprecedented pseudo water tapes stabilized by a one-dimensional Cu(II) coordination polymer. Chin. J. Struct. Chem. 2011, 30:101-104.
8. Scheiner S. Hydrogen Bonding. A Theoretical Perspective 1997, Oxford University Press, Oxford.
9. Desiraju G.R., Steiner T. The Weak Hydrogen Bond 1999, Oxford University Press, Oxford.
10. Grabowski S.J. Hydrogen bonding: new insights, in: Challenges and Advances in Computational Chemistry and Physics 2006, Oxford University Press, Oxford.
11. Metrangolo P., Resnati G. Halogen Bonding: Fundamentals and Applications 2008, Springer, Berlin.
12. Ali M.E., Oppeneer P.M. Influence of noncovalent cation/anion-π interactions on the magnetic exchange phenomenon. J. Phys. Chem. Lett. 2011, 2:939-943.
13. Blanco F., Kelly B., Alkorta I., Rozas I., Elguero J. Cation-π interactions: complexes of guanidinium and simple aromatic systems. Chem. Phys. Lett. 2011, 511:129-134.
14. Zahn S., Frank R., Hey-Hawkins E., Kirchner B. Pnicogen bonds: a new molecular linker?. Chem. Eur. J. 2011, 17:6034-6038.
15. Del Bene J.E., Alkorta I., Sanchez-Sanz G., Elguero J. 31P-31P spin-spin coupling constants for pnicogen homodimers. Chem. Phys. Lett. 2011, 512:184-187.
16. Sanz P., Yáñez M., Mó O. Resonance-assisted intramolecular chalcogen-chalcogen interactions?. Chem. Eur. J. 2003, 9:4548-4555.
17. Sánchez-Sanz G., Alkorta I., Elguero J. A theoretical study of the conformation of 2,2'-bifuran, 2,2'-bithiophene, 2,2'-bitellurophene and mixed derivatives: chalcogen-chalcogen interactions or dipole-dipole effects?. Comput. Theor. Chem. 2011, 974:37-42.
18. Bloom J.W.G., Wheeler S.E. Taking the aromaticity out of aromatic interactions. Angew. Chem. Int. Ed. 2011, 50:7847-7849.
19. Wheeler S.E. Local nature of substituent effects in stacking interactions. J. Am. Chem. Soc. 2011, 133:10262-10274.
20. Jalilov A.S., Nelsen S.F., Guzei I.A., Wu Q. Intramolecular π-stacking interactions of bridged bis-p-phenylenediamine radical cations and diradical dications: charge-transfer versus spin-coupling. Angew. Chem. Int. Ed. 2011, 50:6860-6863.
21. Lehn J.-M. Toward complex matter: supramolecular chemistry and self-organization. Proc. Natl. Acad. Sci. 2002, 99:4763-4768.
22. Desiraju G.R. Supramolecular synthons in crystal engineering - a new organic synthesis. Angew. Chem. Int. Ed. 1995, 34:2311-2327.
23. Milet A., Korona T., Moszynski R., Kochanski E. Anisotropic intermolecular interactions in van der Waals and hydrogen-bonded complexes: what can we get from density functional calculations?. J. Chem. Phys. 1999, 111:7727-7735.
24. Williams H.L., Chabalowski C.F. Using Kohn-Sham orbitals in symmetry-adapted perturbation theory to investigate intermolecular interactions. J. Phys. Chem. A 2000, 105:646-659.
25. Johnson E.R., Keinan S., Mori-Sanchez P., Contreras-Garcia J., Cohen A.J., Yang W. Revealing noncovalent interactions. J. Am. Chem. Soc. 2010, 132:6498-6506.
26. Kuhn B., Mohr P., Stahl M. Intramolecular hydrogen bonding in medicinal chemistry. J. Med. Chem. 2010, 53:2601-2611.
27. Espinosa E., Alkorta I., Elguero J., Molins E. From weak to strong interactions: a comprehensive analysis of the topological and energetic properties of the electron density distribution involving X-H[centered ellipsis]F-Y systems. J. Chem. Phys. 2002, 117:5529-5542.
28. Mallinson P.R., Smith G.T., Wilson C.C., Grech E., Wozniak K. From weak interactions to covalent bonds: a continuum in the complexes of 1,8-bis(dimethylamino)naphthalene. J. Am. Chem. Soc. 2003, 125:4259-4270.
29. Deev V., Collins M.A. Approximate ab initio energies by systematic molecular fragmentation. J. Chem. Phys. 2005, 122:154102-154112.
30. Zhang D.W., Zhang J.Z.H. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy. J. Chem. Phys. 2003, 119:3599-3605.
31. Deshmukh M.M., Gadre S.R., Bartolotti L.J. Estimation of intramolecular hydrogen bond energy via molecular tailoring approach. J. Phys. Chem. A 2006, 110:12519-12523.
32. Deshmukh M.M., Gadre S.R., Bartolotti L.J. Estimation of intramolecular hydrogen bond energy via molecular tailoring approach. J. Phys. Chem. A 2007, 111:10885.
33. Deshmukh M.M., Gadre S.R. Estimation of N-H···OC intramolecular hydrogen bond energy in polypeptides. J. Phys. Chem. A 2009, 113:7927-7932.
34. Bader R.F.W. Atoms in Molecules: A Quantum Theory 1990, Clarendon Press, Oxford.
35. Silvi B., Savin A. Classification of chemical bonds based on topological analysis of electron localization functions. Nature 1994, 371:683-686.
36. Becke A.D., Edgecombe K.E. A simple measure of electron localization in atomic and molecular systems. J. Chem. Phys. 1990, 92:5397-5403.
37. Stalke D. Meaningful structural descriptors from charge density. Chem. Eur. J. 2011, 17:9264-9278.
38. Kolman V., Marek R., Strelcova Z., Kulhanek P., Necas M., Svec J., Sindelar V. Electron density shift in imidazolium derivatives upon complexation with cucurbit[6]uril. Chem. Eur. J. 2009, 15:6926-6931.
39. Solimannejad M., Shirazi S.G., Scheiner S. Analysis of complexes pairing hydroperoxyl radical with peroxyformic acid. J. Phys. Chem. A 2007, 111:10717-10721.
40. Alkorta I., Soteras I., Elguero J., Del Bene J.E. The boron-boron single bond in diborane(4) as a non-classical electron donor for hydrogen bonding. Phys. Chem. Chem. Phys. 2011, 13:14026-14032.
41. Del Bene J.E., Alkorta I., Elguero J. Ab initio study of ternary complexes X:(HCNH)+:Z with X, Z=NCH, CNH, FH, ClH, and FCl: diminutive cooperative effects on structures, binding energies, and spin-spin coupling constants across hydrogen bonds. J. Phys. Chem. A 2011, 115:12677-12687.
42. Del Bene J.E., Alkorta I., Sanchez-Sanz G., Elguero J. Structures, Energies, bonding, and NMR properties of pnicogen complexes H2XP:NXH2 (X=H, CH3, NH2, OH, F, Cl). J. Phys. Chem. A 2011, 115:13724-13731.
43. Dong X.-F., Ren F.-D., Cao D.-L., Wang W.-N., Zhang F.-Q. A MP2(full) theoretical investigation on the π-halogen interaction between OCBBCO and X1X2 (X1, X2=F, Cl, Br). J. Mol. Struct. THEOCHEM 2010, 961:73-82.
44. Solimannejad M., Malekani M., Alkorta I. Cooperative and diminutive unusual weak bonding in F3CX...HMgH...Y and F3CX...Y...HMgH Trimers (X=Cl, Br; Y=HCN, and HNC). J. Phys. Chem. A 2010, 114:12106-12111.
45. Scheiner S., Adhikari U. Abilities of different electron donors (D) to engage in a P...D noncovalent interaction. J. Phys. Chem. A 2011, 115:11101-11110.
46. Scheiner S. Effects of substituents upon the P...N noncovalent interaction: the limits of its strength. J. Phys. Chem. A 2011, 115:11202-11209.
47. Møller C., Plesset M.S. Note on an approximation treatment for many-electron systems. Phys. Rev. 1934, 46:618-622.
48. Woon D.E., Dunning T.H. Gaussian basis sets for use in correlated molecular calculations. V. Core-valence basis sets for boron through neon. J. Chem. Phys. 1995, 103:4572-4585.
49. Dunning T.H. Gaussian-Basis sets for use in correlated molecular calculations.1. The atoms boron through neon and hydrogen. J. Chem. Phys. 1989, 90:1007-1023.
50. 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. Montgomery, J. A., 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, N.J. 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, ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, D.J. Fox, Gaussian 09, Gaussian, Inc., Wallingford CT, 2009.
51. T.A. Keith, AIMAll, TK Gristmill Software (aim.tkgristmill.com), in, 2011, pp. TK Gristmill Software, (aim.tkgristmill.com).
52. Hodgkin E.E., Richards W.G. Molecular similarity based on electrostatic potential and electric field. Int. J. Quant. Chem. Quant. Biol. Symp. 1987, 14:105-110.
53. Jesus A.J.L., Rosado M.T.S., Reva I., Fausto R., Eusébio M.E.S., Redinha J.S. Structure of isolated 1,4-butanediol: combination of MP2 calculations, NBO analysis, and matrix-isolation infrared spectroscopy. J. Phys. Chem. A 2008, 112:4669-4678.
54. Koch U., Popelier P.L.A. Characterization of CHO hydrogen bonds on the basis of the charge density. J. Phys. Chem. 1995, 99:9747-9754.
55. Klein R.A. Electron density topological analysis of hydrogen bonding in glucopyranose and hydrated glucopyranose. J. Am. Chem. Soc. 2002, 124:13931-13937.
56. Portella G., Poater J., Bofill J.M., Alemany P., Solà M. Local aromaticity of [n]acenes, [n]phenacenes, and [n]helicenes (n=1-9). J. Org. Chem. 2005, 70:2509-2521.
57. Matta C.F., Castillo N., Boyd R.J. Characterization of a closed-shell fluorine-fluorine bonding interaction in aromatic compounds on the basis of the electron density. J. Phys. Chem. A 2005, 109:3669-3681.
58. Minyaev R.M., Minkin V.I. Theoretical study of O→X (S, Se, Te) coordination in organic compounds. Can. J. Chem. 1998, 76:776-788.
59. Parcell R.F., Sanchez J.P. Synthesis of ketamine metabolites I and II and some anomalous reactions of 6-bromoketamine. J. Org. Chem. 1981, 46:5055-5060.
60. Alkorta I., Elguero J., Grabowski S.J. How to determine whether intramolecular H...H interactions can be classified as dihydrogen bonds. J. Phys. Chem. A 2008, 112:2721-2727.
61. Mitzel N.W., Losehand U. β-donor bonds in compounds containing SiON fragments. Angew. Chem. Int. Ed. 1997, 36:2807-2809.
62. 2. J. Am. Chem. Soc. 1998, 120:7320-7327.
63. Mitzel N.W., Losehand U., Wu A., Cremer D., Rankin D.W.H. (N,N-dimethylaminoxy)trifluorosilane: strong, dipole moment driven changes in the molecular geometry studied by experiment and theory in solid, gas, and solution phases. J. Am. Chem. Soc. 2000, 122:4471-4482.
64. 2 a model for the α-effect in silicon chemistry. J. Am. Chem. Soc. 2005, 127:13705-13713.
65. Mitzel N.W., Blake A.J., Rankin D.W.H. β-donor bonds in SiON units: an inherent structure - determining property leading to (4+4)-coordination in tetrakis-(N,N-dimethylhydroxylamido)silane. J. Am. Chem. Soc. 1997, 119:4143-4148.
66. Murray J., Concha M., Politzer P. Molecular surface electrostatic potentials as guides to SiON angle contraction: tunable σ-holes. J. Mol. Model. 2011, 17:2151-2157.