Hydrogen-hydrogen bonds in highly branched alkanes and in alkane complexes: A DFT, ab initio, QTAIM, and ELF study

Journal of Physical Chemistry A

Volumn 118, Issue 9, 2014, Pages 1730-1740

  Monteiro, Norberto K V ^a   Firme, Caio L ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO NORTE   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

BRANCHED ALKANES; BRANCHED ISOMERS; ELECTRICAL NEUTRALITY; ELECTRON LOCALIZATION FUNCTION; HYDROGEN ATOMS; INTERMOLECULAR INTERACTIONS; MOLECULAR ENERGIES; QUANTUM THEORY OF ATOMS IN MOLECULES;

ATOMS; COMPLEXATION; HYDROGEN BONDS; ISOMERS; QUANTUM THEORY;

PARAFFINS;

ALKANE; HYDROGEN;

ARTICLE; CHEMISTRY; HYDROGEN BOND; QUANTUM THEORY;

ALKANES; HYDROGEN; HYDROGEN BONDING; QUANTUM THEORY;

EID: 84897678656     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp500131z     Document Type: Article

References (94)

1. Bader, R. F. W. Atoms in Molecules A Quantum Theory; Oxford University Press: New York, 1994; p 226.
2. Matta, C. F.; Boyd, R. J. The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design; Wiley-VCH: New York, 2007.
3. Bader, R. F. W. Bond Paths Are Not Chemical Bonds J. Phys. Chem. A 2009, 113, 10391-10396
4. Bader, R. F. W. A Bond Path: A Universal Indicator of Bonded Interactions J. Phys. Chem. A 1998, 5639, 7314-7323
5. Popelier, P. L. A. Characterization of a Dihydrogen Bond on the Basis of the Electron Density J. Phys. Chem. A 1998, 5639, 1873-1878
6. +⋯π Complex Hydrogen Bonded? J. Phys. Chem. A 2004, 108, 1806-1812
7. Alkorta, I.; Blanco, F.; Elguero, J. π-Systems as Simultaneous Hydride and Hydrogen Bond Acceptors J. Phys. Chem. A 2008, 112, 6753-6759
8. Rozas, I.; Alkorta, I.; Elguero, J. Inverse Hydrogen-Bonded Complexes J. Phys. Chem. A 1997, 101, 4236-4244
9. Matta, C. F.; Hernández-Trujillo, J.; Tang, T.-H.; Bader, R. F. W. Hydrogen-Hydrogen Bonding: A Stabilizing Interaction in Molecules and Crystals Chem.-Eur. J. 2003, 9, 1940-1951
10. Glukhov, I. V.; Lyssenko, K. A.; Korlyukov, A. A.; A. M., Y. Nature of Weak Inter- and Intramolecular Contacts in Crystals 2. Character of Electron Delocalization and the Nature of X-H⋯H-X (X = C, B) Contacts in the Crystal of 1-Phenyl- O -Carborane Russ. Chem. Bull. 2005, 54, 547-559
11. Wang, C.-C.; Tang, T.-H.; Wu, L.-C.; Wang, Y. Topological Analyses and Bond Characterization of 1,3,5,7-Tetra- tert -butyl- S -indacene: A Weak Csp3-H⋯H-Csp2-Type Dihydrogen Interaction Acta Crystallogr., Sect. A 2004, 60, 488-493
12. Grabowski, S. J.; Pfitzner, A.; Zabel, M.; Dubis, A. T. Intramolecular H⋯H Interactions for the Crystal Structures of [4-((E)-But-1-Enyl)-2,6- Dimethoxyphenyl]pyridine-3-Carboxylate and [4-((E)-Pent-1-Enyl)-2,6- Dimethoxyphenyl]pyridine-3-Carboxylate; DFT Calculations on Modeled Styrene Derivatives J. Phys. Chem. B 2004, 108, 1831-1837
13. 3CN)] {LOH = α-(4-Pyridyl)benzhydrol} Eur. J. Inorg. Chem. 2004, 2004, 1985-1991
14. Nemes, G. C.; Silaghi-Dumitrescu, L.; Silaghi-Dumitrescu, I.; Escudié, J.; Ranaivonjatovo, H.; Molloy, K. C.; Mahon, M. F.; Zukerman-Schpector, J. Difluorenylsilanes, -Germanes, and -Stannanes Exhibiting an Unprecedented Parallel Arrangement of the Fluorene Units Organometallics 2005, 24, 1134-1144
15. Damodharan, L.; Pattabhi, V. Weak Dihydrogen Bond Interactions in Organic Crystals Tetrahedron Lett. 2004, 45, 9427-9429
16. Freitas, R. F.; Galembeck, S. E. Computational Study of the Interaction between TIBO Inhibitors and Y181 (C181), K101, and Y188 Amino Acids J. Phys. Chem. B 2006, 110, 21287-21298
17. Rzepa, H. S. A Double-Twist Möbius-Aromatic Conformation of [14]Annulene Org. Lett. 2005, 7, 4637-4639
18. 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 2006, 110, 563-578
19. Poater, J.; Solà, M.; Bickelhaupt, F. M. Hydrogen-Hydrogen Bonding in Planar Biphenyl, Predicted by Atoms-in-Molecules Theory, Does Not Exist Chem.-Eur. J. 2006, 12, 2889-2895
20. Bader, R. F. W. Pauli Repulsions Exist Only in the Eye of the Beholder Chem.-Eur. J. 2006, 12, 2896-2901
21. Poater, J.; Solà, M.; Bickelhaupt, F. M. A Model of the Chemical Bond Must Be Rooted in Quantum Mechanics, Provide Insight, and Possess Predictive Power Chemistry 2006, 12, 2902-2905
22. Nascimento, M. A. C. The Nature of the Chemical Bond J. Braz. Chem. Soc. 2008, 19, 245-256
23. Chermahini, A. N.; Mahdavian, M.; Teimouri, A. Theoretical Studies of Hydrogen Bond Interactions in Fluoroacetic Acid Dimer Bull. Korean Chem. Soc. 2010, 31, 941-948
24. Fuster, F.; Grabowski, S. J. Intramolecular Hydrogen Bonds: The QTAIM and ELF Characteristics J. Phys. Chem. A 2011, 115, 10078-10086
25. Koch, U.; Popelier, P. L. a. Characterization of C-H-O Hydrogen Bonds on the Basis of the Charge Density J. Phys. Chem. 1995, 99, 9747-9754
26. Popelier, P. L. A. Characterization of a Dihydrogen Bond on the Basis of the Electron Density J. Phys. Chem. A 1998, 5639, 1873-1878
27. Oliveira, B.; Araújo, R.; Ramos, M. A Topologia Molecular Qtaim ea Descrição Mecaînico-Quaîntica de Ligações de Hidrogeînio e Ligações de Di-Hidrogeînio Quim. Nov. 2010, 33, 1155-1162
28. Fletcher, R. Practical Methods of Optimization: Unconstrained Optimization; J. Wiley: New York, 1980.
29. Chai, J.-D.; Head-Gordon, M. Systematic Optimization of Long-Range Corrected Hybrid Density Functionals J. Chem. Phys. 2008, 128, 84106-84115
30. Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. Gaussian-4 Theory J. Chem. Phys. 2007, 126, 084108
31. Raghavachari, K.; Trucks, G. W.; Pople, J. A.; Head-Gordon, M. A Fifth-Order Perturbation Comparison of Electron Correlation Theories Chem. Phys. Lett. 1989, 157, 479-483
32. Zhao, Y.; Truhlar, D. G. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals Theor. Chem. Acc. 2008, 120, 215-241
33. Becke, A. D. Density-functional Thermochemistry. III. The Role of Exact Exchange J. Chem. Phys. 1993, 98, 5
34. 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
35. 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.; Gaussian 09, revision B.01.; Gaussian, Inc.: Wallingford, CT, 2009.
36. Hernández-Trujillo, J.; Matta, C. F. Hydrogen-Hydrogen Bonding in Biphenyl Revisited Struct. Chem. 2007, 18, 849-857
37. Grimme, S. Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction J. Comput. Chem. 2006, 27, 1787-1799
38. Becke, A. D. Density-Functional Thermochemistry. V. Systematic Optimization of Exchange-Correlation Functionals J. Chem. Phys. 1997, 107, 8554-8560
39. Biegler-König, F.; Schönbohm, J.; Bayles, D. AIM2000-A Program to Analyze and Visualize Atoms in Molecules J. Comput. Chem. 2001, 22, 545-559
40. Biegler-König, F.; Schönbohm, J. Update of the AIM2000-Program for Atoms in Molecules J. Comput. Chem. 2002, 23, 1489-1494
41. Noury, S.; Krokidis, X.; Fuster, F.; Silvi, B. Computational Tools for the Electron Localization Function Topological Analysis Comput. Chem. 1999, 23, 597-604
42. Noury, S.; Krokidis, X.; Fuster, F.; Silvi, B. TopMoD Package; Universite Pierre et Marie Curie: Paris, 1997
43. Bader, R. F. W. Everyman's Derivation of the Theory of Atoms in Molecules J. Phys. Chem. A 2007, 111, 7966-7972
44. 3) Struct. Chem. 2009, 20, 663-670
45. Bader, R. F. W. Quantum Topology of Molecular Charge Distributions. III. The Mechanics of an Atom in a Molecule J. Chem. Phys. 1980, 73, 2871
46. Bader, R. F. W. The Quantum Mechanical Basis of Conceptual Chemistry Monatsh. Chem. 2005, 136, 819-854
47. Firme, C. L. Topological Study of the First Step of Nucleophilically Unassisted Solvolysis of Protonated 2-Endo/exo-Norbornanol and Protonated 2-Endo/exo-Oxabicycloheptanol J. Braz. Chem. Soc. 2012, 23, 513-521
48. Firme, C. L.; Pontes, D. de L.; Antunes, O. A. C. Topological Study of Bis(cyclopentadienyl) Titanium and Bent Titanocenes Chem. Phys. Lett. 2010, 499, 193-198
49. Bankiewicz, B.; Matczak, P.; Palusiak, M. Electron Density Characteristics in Bond Critical Point (QTAIM) versus Interaction Energy Components (SAPT): The Case of Charge-Assisted Hydrogen Bonding J. Phys. Chem. A 2012, 116, 452-459
50. Knop, O.; Boyd, R. J.; Choi, S. C. Sulfur-Sulfur Bond Lengths, or Can a Bond Length Be Estimated from a Single Parameter? J. Am. Chem. Soc. 1988, 110, 7299-7301
51. Bader, R. F. W.; Matta, C. F. Bonding to Titanium Inorg. Chem. 2001, 40, 5603-5611
52. 5-pyridine Complexes J. Organomet. Chem. 2007, 692, 3866-3873
53. Krygowski, T.; Palusiak, M. Relationship between Substituent Effect and Aromaticity-Part III: Naphthalene as a Transmitting Moiety for Substituent Effect J. Phys. Org. Chem. 2007, 20, 297-306
54. Urbaniak, K.; Mloston, G. Role of C-H⋯S and C-H⋯N Hydrogen Bonds in Organic Crystal Structures: The Crystal and Molecular Structure of 3-Methyl-2,4-diphenyl-(1,3)-thiazolidine-5-spiro-2′-adamantane and 3-Methyl-2,4,5,5-tetraphenyl-(1,3)-thiazolidine J. Phys. Chem. A 2003, 107, 2730-2736
55. 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⋯F-Y Systems J. Chem. Phys. 2002, 117, 5529
56. Alkorta, I.; Elguero, J.; Foces-Foces, C. Dihydrogen Bonds (A-HH-B) Chem. Commun. 1996, 1633-1634
57. 2 Complexes (n = 1 or 2) Struct. Chem. 2009, 20, 897-902
58. Matta, C. F.; Hernández-Trujillo, J.; Tang, T.-H.; Bader, R. F. W. Hydrogen-Hydrogen Bonding: A Stabilizing Interaction in Molecules and Crystals Chemistry 2003, 9, 1940-1951
59. Grabowski, S. J. Covalent Character of Hydrogen Bonds Enhanced by π-Electron Delocalization Croat. Chem. Acta 2009, 82, 185-192
60. Bone, R.; Bader, R. F. W. Identifying and Analyzing Intermolecular Bonding Interactions in van Der Waals Molecules J. Phys. Chem. 1996, 3654, 10892-10911
61. Knop, O.; Rankin, K. N.; Boyd, R. J. Coming to Grips with N-H⋯N Bonds. 2. Homocorrelations between Parameters Deriving from the Electron Density at the Bond Critical Point1 J. Phys. Chem. A 2002, 107, 272-284
62. Boyd, R. J.; Choi, S. C. Hydrogen Bonding between Nitriles and Hydrogen Halides and the Topological Properties of Molecular Charge Distributions Chem. Phys. Lett. 1986, 129, 62-65
63. Keith, T. A.; Bader, R. F. W.; Aray, Y. Structural Homeomorphism between the Electron Density and the Virial Field Int. J. Quantum Chem. 1996, 57, 183-198
64. Gatti, C. The Quantum Theory of Atoms in Molecules: Bond Paths, Chemical Bonds and Chemical Binding. Workshop on the XD2006 program package: Advanced methods in X-ray Charge Density Analysis: Extracting properties from a Multipole Refinement, Martina Franca, Italy September 3-6, 2006.
65. Bader, R. F. W. Bond Paths Are Not Chemical Bonds J. Phys. Chem. A 2009, 113, 10391-10396
66. Slater, J. C. The Virial and Molecular Structure J. Chem. Phys. 1933, 1, 687-691
67. Slater, J. C. Quantum Theory of Molecules and Solids: The Self-Consistent Field for Molecules and Solids; McGraw-Hill: New York, 1963.
68. Tsirelson, V. G.; Zhou, P. F.; Tang, T.-H.; Bader, R. F. W. Topological Definition of Crystal Structure: Determination of the Bonded Interactions in Solid Molecular Chlorine Acta Crystallogr., Sect. A 1995, 51, 143-153
69. Scherer, W.; Spiegler, M.; Pedersen, B.; Tafipolsky, M.; Hieringer, W.; Reinhard, B.; Downs, A. J.; McGrady, G. S. Molecular Recognition in the Solid State: Topology of Experimental and Theoretical Charge Densities for Tetrasulfur Tetranitride Chem. Commun. 2000, 0, 635-636
70. Gibbs, G. V; Wallace, A. F.; Cox, D. F.; Dove, P. M.; Downs, R. T.; Ross, N. L.; Rosso, K. M. Role of Directed van Der Waals Bonded Interactions in the Determination of the Structures of Molecular Arsenate Solids J. Phys. Chem. A 2009, 113, 736-749
71. Wolstenholme, D. J.; Cameron, T. S. Comparative Study of Weak Interactions in Molecular Crystals: H-H Bonds vs Hydrogen Bonds J. Phys. Chem. A 2006, 110, 8970-8978
72. Slater, J. C. Hellmann-Feynman and Virial Theorems in the X Alpha Method J. Chem. Phys. 1972, 57, 2389-2396
73. Bader, R. F. W.; Hernández-Trujillo, J.; Cortés- Guzmán, F. Chemical Bonding: From Lewis to Atoms in Molecules J. Comput. Chem. 2007, 28, 4-14
74. Feynman, R. P. Forces in Molecules Phys. Rev. 1939, 56, 340-343
75. Becke, A. D.; Edgecombe, K. E. A Simple Measure of Electron Localization in Atomic and Molecular Systems J. Chem. Phys. 1990, 92, 5397
76. Noury, S.; Krokidis, X.; Fuster, F.; Silvi, B. Computational Tools for the Electron Localization Function Topological Analysis Comput. Chem. 1999, 23, 597-604
77. Noury, S.; Colonna, F.; Savin, A.; Silvi, B. Analysis of the Delocalization in the Topological Theory of Chemical Bond J. Mol. Struct. 1998, 450, 59-68
78. Chevreau, H.; Moreira, I.; de, P. R.; Silvi, B.; Illas, F. Charge Density Analysis of Triplet and Broken Symmetry States Relevant to Magnetic Coupling in Systems with Localized Spin Moments J. Phys. Chem. A 2001, 105, 3570-3577
79. 2 Isomers: A Topographical Study Heteroat. Chem. 2002, 13, 53-62
80. Chevreau, H. Time Dependent Topological Analysis of the Electron Density in the Allyl Radical Chem. Phys. Lett. 2004, 400, 59-61
81. Rosdahl, J.; Fässler, T. F.; Kloo, L. On the Structure of Nonastannide Clusters in Liquid and Solid State Eur. J. Inorg. Chem. 2005, 2005, 2888-2894
82. Silvi, B.; Savin, A. Classification of Chemical Bonds Based on Topological Analysis of Electron Localization Functions Nature 1994, 371, 683-686
83. Häussermann, U.; Wengert, S.; Hofmann, P.; Savin, A.; Jepsen, O.; Nesper, R. Localization of Electrons in Intermetallic Phases Containing Aluminum Angew. Chem., Int. Ed. Engl. 1994, 33, 2069-2073
84. Silvi, B. The Synaptic Order: A Key Concept to Understand Multicenter Bonding J. Mol. Struct. 2002, 614, 3-10
85. 2 and Chem. Phys. Lett. 2005, 411, 117-120
86. Fuster, F.; Silvi, B. Determination of Protonation Sites in Bases from Topological Rules Chem. Phys. 2000, 252, 279-287
87. 2O)1, 2·HCl: Accurate Energetic and Frequency Shift of HCl Phys. Chem. Chem. Phys. 2003, 5, 2494-2498
88. Alikhani, M. E.; Fuster, F.; Silvi, B. What Can Tell the Topological Analysis of ELF on Hydrogen Bonding? Struct. Chem. 2005, 16, 203-210
89. Zipse, H. Book Review: Advanced Organic Chemistry, 4th ed. Edited by Francis A. Carey and Richard J. Sunberg Angew. Chemie Int. Ed. 2002, 41, 866-867
90. Minenkov, Y.; Singstad, A.; Occhipinti, G.; Jensen, V. R. The Accuracy of DFT-Optimized Geometries of Functional Transition Metal Compounds: A Validation Study of Catalysts for Olefin Metathesis and Other Reactions in the Homogeneous Phase Dalt. Trans. 2012, 41, 5526-5541
91. Gronert, S. An Alternative Interpretation of the C-H Bond Strengths of Alkanes J. Org. Chem. 2006, 71, 1209-1219
92. Wodrich, M. D.; Schleyer, P. v. R. New Additivity Schemes for Hydrocarbon Energies Org. Lett. 2006, 8, 2135-2138
93. Kemnitz, C. R.; Mackey, J. L.; Loewen, M. J.; Hargrove, J. L.; Lewis, J. L.; Hawkins, W. E.; Nielsen, A. F. Origin of Stability in Branched Alkanes Chemistry 2010, 16, 6942-6949
94. Needham, D. E.; Wei, I. C.; Seybold, P. G. Molecular Modeling of the Physical Properties of Alkanes J. Am. Chem. Soc. 1988, 110, 4186-4194