Cooperative effects and optimal halogen bonding motifs for self-assembling systems

Journal of Physical Chemistry A

Volumn 118, Issue 15, 2014, Pages 2820-2826

  Yan, Xin Cindy ^a   Schyman, Patric ^a   Jorgensen, William L ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; DIMERS; HALOGEN COMPOUNDS; OPTIMIZATION; STRENGTH OF MATERIALS;

CO-OPERATIVE EFFECTS; INTERACTION ENERGIES; SECONDARY INTERACTIONS; SELF-ASSEMBLING; SELF-ASSEMBLING ARCHITECTURES; SELF-ASSEMBLING MATERIALS; STRUCTURAL MOTIFS; SUPRAMOLECULAR STRUCTURE;

DESIGN FOR TESTABILITY;

HALOGEN; IMIDAZOLE; IMIDAZOLE DERIVATIVE; PYRIDINE; PYRIDINE DERIVATIVE;

CHEMICAL STRUCTURE; CHEMISTRY; DIMERIZATION; HALOGENATION; HYDROGEN BOND; QUANTUM THEORY; THERMODYNAMICS;

DIMERIZATION; HALOGENATION; HALOGENS; HYDROGEN BONDING; IMIDAZOLES; MODELS, MOLECULAR; PYRIDINES; QUANTUM THEORY; THERMODYNAMICS;

EID: 84899027785     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp501553j     Document Type: Article

References (50)

1. Meyer, F.; Dubois, P. Halogen Bonding at Work: Recent Applications in Synthetic Chemistry and Materials Science CrystEngComm 2013, 15, 3058-3071
2. Xu, J. W.; Liu, X. M.; Lin, T. T.; Huang, J. C.; He, C. B. Synthesis and Self-Assembly of Difunctional Halogen-Bonding Molecules: A New Family of Supramolecular Liquid-Crystalline Polymers Macromolecules 2005, 38, 3554-3557
3. Saccone, M.; Cavallo, G.; MetrangolFo, P.; Pace, A.; Pibiri, I.; Pilati, T.; Resnati, G.; Terraneo, G. Halogen Bond Directionality Translates Tecton Geometry into Self-Assembled Architecture Geometry CrystEngComm 2013, 15, 3102-3105
4. Voth, A. R.; Hays, F. A.; Ho, P. S. Directing Macromolecular Conformation through Halogen Bonds Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 6188-6193
5. Voth, A. R.; Khuu, P.; Oishi, K.; Ho, P. S. Halogen Bonds as Orthogonal Molecular Interactions to Hydrogen Bonds Nat. Chem. 2009, 1, 74-79
6. Lu, Y.; Shi, T.; Wang, Y.; Yang, H.; Yan, X.; Luo, X.; Jiang, H.; Zhu, W. Halogen Bonding: A Novel Interaction for Rational Drug Design? J. Med. Chem. 2009, 52, 2854-2862
7. Politzer, P.; Murray, J. S.; Clark, T. Halogen Bonding: An Electrostatically-Driven Highly Directional Noncovalent Interaction Phys. Chem. Chem. Phys. 2010, 12, 7748-7757
8. Clark, T.; Hennemann, M.; Murray, J. S.; Politzer, P. Halogen Bonding: the Sigma-Hole J. Mol. Model. 2007, 13, 291-296
9. Ramasubbu, N.; Parthasarathy, R.; Murrayrust, P. Angular Preferences of Intermolecular Forces around Halogen Centers-Preferred Directions of Approach of Electrophiles and Nucleophiles around the Carbon Halogen Bond J. Am. Chem. Soc. 1986, 108, 4308-4314
10. Lommerse, J. P. M.; Stone, A. J.; Taylor, R.; Allen, F. H. The Nature and Geometry of Intermolecular Interactions Between Halogens and Oxygen or Nitrogen J. Am. Chem. Soc. 1996, 118, 3108-3116
11. Metrangolo, P.; Meyer, F.; Pilati, T.; Resnati, G.; Terraneo, G. Halogen Bonding in Supramolecular Chemistry Angew. Chem., Int. Ed. 2008, 47, 6114-6127
12. Fontana, F.; Forni, A.; Metrangolo, P.; Panzeri, W.; Pilatti, T.; Resnati, G. Perfluorocarbon-Hydrocarbon Discrete Intermolecular Aggregates: An Exceptionally Short N⋯I Contact Supramol. Chem. 2002, 14, 47-55
13. Metrangolo, P.; Neukirch, H.; Pilati, T.; Resnati, G. Halogen Bonding Based Recognition Processes: A World Parallel to Hydrogen Bonding Acc. Chem. Res. 2005, 38, 386-395
14. Ercolani, G. Assessment of Cooperativity in Self-Assembly J. Am. Chem. Soc. 2003, 125, 16097-16103
15. Alkorta, I.; Blanco, F.; Deya, P. M.; Elguero, J.; Estarellas, C.; Frontera, A.; Quinonero, D. Cooperativity in Multiple Unusual Weak Bonds Theor. Chem. Acc. 2010, 126, 1-14
16. 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, 208-211
17. n Complexes Chem. Phys. Lett. 2006, 427, 51-55
18. Solimannejad, M.; Malekani, M.; Alkorta, I. Substituent Effects on the Cooperativity of Halogen Bonding J. Phys. Chem. A 2013, 117, 5551-5557
19. Alkorta, I.; Blanco, F.; Elguero, J. A Computational Study of the Cooperativity in Clusters of Interhalogen Derivatives Struct. Chem. 2009, 20, 63-71
20. 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, 109, 2451-2460
21. Reed, A. E.; Curtiss, L. A.; Weinhold, F. Intermolecular Interactions from A Natural Bond Orbital, Donor-Acceptor Viewpoint Chem. Rev. 1988, 88, 899-926
22. Jorgensen, W. L.; Schyman, P. Treatment of Halogen Bonding in the OPLS-AA Force Field: Application to Potent Anti-HIV Agents J. Chem. Theory Comput. 2012, 8, 3895-3901
23. Ibrahim, M. A. A. 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 2012, 116, 3659-3669
24. Carter, M.; Rappe, A. K.; Ho, P. S. Scalable Anisotropic Shape and Electrostatic Models for Biological Bromine Halogen Bonds J. Chem. Theory Comput. 2012, 8, 2461-2473
25. Chen, Y. F.; Dannenberg, J. J. Cooperative 4-Pyridone H-Bonds with Extraordinary Stability. A DFT Molecular Orbital Study J. Am. Chem. Soc. 2006, 128, 8100-8101
26. Alkorta, I.; Blanco, F.; Elguero, J. Dihydrogen Bond Cooperativity in Aza-borane Derivatives J. Phys. Chem. A 2010, 114, 8457-8462
27. Scheiner, S. Hydrogen Bonding: A Theoretical Perspective; Oxford University Press: New York, 1997.
28. Hankins, D.; Moskowitz, J. W.; Stillinger, F. H. Water Molecule Interactions J. Chem. Phys. 1970, 53, 4544-4554
29. Rivelino, R.; Chaudhuri, P.; Canuto, S. Quantifying Multiple-Body Interaction Terms in H-Bonded HCN Chains with Many-Body Perturbation/Coupled- Cluster Theories J. Chem. Phys. 2003, 118, 10593-10601
30. 3 Z. Kristallogr. 1936, 95, 471-471
31. Maginn, S. J.; Compton, R. G.; Harding, M. S.; Brennan, C. M.; Docherty, R. Evidence for Anisotropy in Chlorine Nitrogen Interactions in the Cyanuric Chloride Crystal Structure Tetrahedron Lett. 1993, 34, 4349-4352
32. Pascal, R. A.; Ho, D. M. Nitrogen-Chlorine Donor-Acceptor Interactions Dominate the Structrure of Crystalline Cyanuric Chloride Tetrahedron Lett. 1992, 33, 4707-4708
33. 3 mit Verwendung der diffusen Röntgenstreustrahlung zur Bestimmung der Molekülorientierungen Z. Kristallogr. 1957, 108, 321-327
34. Xu, K.; Ho, D. M.; Pascal, R. A. Azaaromatic Chlorides-A Prescription for Crystal-Structures with Extensive Nitrogen-Chlorine Donor-Acceptor Interactions J. Am. Chem. Soc. 1994, 116, 105-110
35. Jorgensen, W. L.; Pranata, J. Importance of Secondary Interactions in Triply Hydrogen Bonded Complexes: Guanine-Cytosine vs Uracil-2,6-diaminopyridine J. Am. Chem. Soc. 1990, 112, 2008-2010
36. Lu, Y. X.; Zou, J. W.; Wang, Y. H.; Yu, Q. S. Bifurcated Halogen Bonds: An ab Initio Study of the Three-Center Interactions J. Mol. Struct. (THEOCHEM) 2006, 767, 139-142
37. Ji, B. M.; Wang, W. Z.; Deng, D. S.; Zhang, Y. Symmetrical Bifurcated Halogen Bond: Design and Synthesis Cryst. Growth Des. 2011, 11, 3622-3628
38. Jorgensen, W. L.; Jensen, K. P.; Alexandrova, A. N. Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion J. Chem. Theory Comput. 2007, 3, 1987-1992
39. Schyman, P.; Jorgensen, W. L. Exploring Adsorption of Water and Ions on Carbon Surfaces Using a Polarizable Force Field J. Phys. Chem. Lett. 2013, 4, 468-474
40. Chai, J. D.; Head-Gordon, M. Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections Phys. Chem. Chem. Phys. 2008, 10, 6615-6620
41. Kozuch, S.; Martin, J. M. L. Halogen Bonds: Benchmarks and Theoretical Analysis J. Chem. Theory Comput. 2013, 9, 1918-1931
42. 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 C.01; Gaussian: Wallingford, CT, USA, 2010.
43. Check, C. E.; Faust, T. O.; Bailey, J. M.; Wright, B. J.; Gilbert, T. M.; Sunderlin, L. S. Addition of Polarization and Diffuse Functions to the LANL2DZ Basis Set for p-Block Elements J. Phys. Chem. A 2001, 105, 8111-8116
44. Zhao, Y.; Truhlar, D. G. A New Local Density Functional for Main-Group Thermochemistry, Transition Metal Bonding, Thermochemical Kinetics, and Noncovalent Interactions J. Chem. Phys. 2006, 125, 194101
45. 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
46. 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
47. Chudzinski, M. G.; Taylor, M. S. Correlations between Computation and Experimental Thermodynamics of Halogen Bonding J. Org. Chem. 2012, 77, 3483-3491
48. Glendening, E. D.; Reed, A. E.; Carpenter, J. E.; Weinhold, F. NBO, Version 3.1; University of Wisconsin: Madison, WI, USA, 1996.
49. Jorgensen, W. L.; Tirado-Rives, J. Molecular Modeling of Organic and Biomolecular Systems using BOSS and MCPRO J. Comput. Chem. 2005, 26, 1689-1700
50. Udier-Blagovic, M.; De Tirado, P. M.; Pearlman, S. A.; Jorgensen, W. L. Accuracy of Free Energies of Hydration Using CM1 and CM3 Atomic Charges J. Comput. Chem. 2004, 25, 1322-1332