Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field

Journal of Physical Chemistry B

Volumn 118, Issue 24, 2014, Pages 6456-6465

  Mu, Xiaojiao ^a   Wang, Qiantao ^a,b   Wang, Lee Ping ^c   Fried, Stephen D ^c   Piquemal, Jean Philip ^d   Dalby, Kevin N ^b   Ren, Pengyu ^a  

^a The University of Texas at Austin   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c STANFORD UNIVERSITY   (United States)

^d SORBONNE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; ELECTROSTATICS; VAN DER WAALS FORCES;

ELECTRON DONORS; ELECTROSTATIC MODELS; ELECTROSTATIC POTENTIALS; HEAT OF VAPORIZATION; HYDRATION FREE ENERGIES; INTERACTION ENERGIES; ORGANOCHLORINE COMPOUNDS; REACTION FIELDS;

CHLORINE COMPOUNDS;

CARBON TETRACHLORIDE; CHLORINATED HYDROCARBON; GAS; HALOGEN; METHYL CHLORIDE;

CHEMICAL STRUCTURE; CHEMISTRY; GAS; QUANTUM THEORY; STATIC ELECTRICITY; THERMODYNAMICS;

CARBON TETRACHLORIDE; GASES; HALOGENS; HYDROCARBONS, CHLORINATED; METHYL CHLORIDE; MODELS, MOLECULAR; QUANTUM THEORY; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 84902983756     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp411671a     Document Type: Article

References (83)

1. Wilcken, R.; Liu, X.; Zimmermann, M. O.; Rutherford, T. J.; Fersht, A. R.; Joerger, A. C.; Boeckler, F. M. Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant P53 J. Am. Chem. Soc. 2012, 134 (15) 6810-6818
2. Scholfield, M. R.; Zanden, C. M. V.; Carter, M.; Ho, P. S. Halogen Bonding (X-Bonding): A Biological Perspective Protein Sci. 2013, 22 (2) 139-152
3. Xu, Z.; Yang, Z.; Liu, Y.; Lu, Y.; Chen, K.; Zhu, W. Halogen Bond: Its Role Beyond Drug-Target Binding Affinity for Drug Discovery and Development J. Chem. Inf. Model. 2014, 54 (1) 69-78
4. Metrangolo, P.; Resnati, G. Halogen Versus Hydrogen Science 2008, 321 (5891) 918-919
5. Voth, A. R. Macromolecular Halogen Bonds; Ph.D. Dissertation, Oregon State University, 2007.
6. Du, L.; Gao, J.; Bi, F.; Wang, L.; Liu, C. A Polarizable Ellipsoidal Force Field for Halogen Bonds J. Comput. Chem. 2013, 34 (23) 2032-2040
7. Riley, K.; Murray, J.; Fanfrlík, J.; Řezáč, J.; Solá, R.; Concha, M.; Ramos, F.; Politzer, P. Halogen Bond Tunability I: The Effects of Aromatic Fluorine Substitution on the Strengths of Halogen-Bonding Interactions Involving Chlorine, Bromine, and Iodine J. Mol. Model. 2011, 17 (12) 3309-3318
8. Riley, K.; Murray, J.; Fanfrlík, J.; Řezáč, J.; Solá, R.; Concha, M.; Ramos, F.; Politzer, P. Halogen Bond Tunability Ii: The Varying Roles of Electrostatic and Dispersion Contributions to Attraction in Halogen Bonds J. Mol. Model. 2013, 19 (11) 4651-4659
9. Clark, T.; Hennemann, M.; Murray, J.; Politzer, P. Halogen Bonding: The Σ-Hole J. Mol. Model. 2007, 13 (2) 291-296
10. Politzer, P.; Murray, J. S.; Lane, P. Σ-Hole Bonding and Hydrogen Bonding: Competitive Interactions Int. J. Quantum Chem. 2007, 107 (15) 3046-3052
11. Metrangolo, P.; Murray, J. S.; Pilati, T.; Politzer, P.; Resnati, G.; Terraneo, G. The Fluorine Atom as a Halogen Bond Donor, viz. A Positive Site CrystEngComm 2011, 13 (22) 6593-6596
12. Metrangolo, P.; Murray, J. S.; Pilati, T.; Politzer, P.; Resnati, G.; Terraneo, G. Fluorine-Centered Halogen Bonding: A Factor in Recognition Phenomena and Reactivity Cryst. Growth Des. 2011, 11 (9) 4238-4246
13. Politzer, P.; Murray, J. S. Halogen Bonding: An Interim Discussion ChemPhysChem 2013, 14 (2) 278-294
14. Politzer, P.; Murray, J. S.; Clark, T. Halogen Bonding and Other σ-Hole Interactions: A Perspective Phys. Chem. Chem. Phys. 2013, 15 (27) 11178-11189
15. Politzer, P.; Murray, J. S. Enthalpy and Entropy Factors in Gas Phase Halogen Bonding: Compensation and Competition CrystEngComm 2013, 15 (16) 3145-3150
16. Politzer, P.; Murray, J. S.; Clark, T. Halogen Bonding: An Electrostatically-Driven Highly Directional Noncovalent Interaction Phys. Chem. Chem. Phys. 2010, 12 (28) 7748-7757
17. Imakubo, T.; Sawa, H.; Kato, R. Novel Radical Cation Salts of Organic Π-Donors Containing Iodine Atom(S): The First Application of Strong Intermolecular-I⋯X- (X = Cn, Halogen Atom) Interaction to Molecular Conductors Synth. Met. 1995, 73 (2) 117-122
18. Imakubo, T.; Miyake, A.; Sawa, H.; Kato, R. Synthesis and Physical Properties of (Diets)2[Au(Cn)4]: A New Θ-Salt with a Unique Donor⋯Anion Network Synth. Met. 2001, 120 (1-3) 927-928
19. Kato, R.; Imakubo, T.; Yamamoto, H.; Maeda, R.; Fujiwara, M.; Yamaura, J.-I.; Sawa, H. An Application of Supramolecular Chemistry to Molecular Conductors Mol. Cryst. Liq. Cryst. 2002, 380 (1) 61-68
20. Fanfrlík, J.; Kolář, M.; Kamlar, M.; Hurný, D.; Ruiz, F. X.; Cousido-Siah, A.; Mitschler, A.; Řezáč, J.; Munusamy, E.; Lepšík, M. Modulation of Aldose Reductase Inhibition by Halogen Bond Tuning ACS Chem. Biol. 2013, 8 (11) 2484-2492
21. Parisini, E.; Metrangolo, P.; Pilati, T.; Resnati, G.; Terraneo, G. Halogen Bonding in Halocarbon-Protein Complexes: A Structural Survey Chem. Soc. Rev. 2011, 40 (5) 2267-2278
22. Zhao, X. Z.; Maddali, K.; Christie Vu, B.; Marchand, C.; Hughes, S. H.; Pommier, Y.; Burke, T. R., Jr Examination of Halogen Substituent Effects on HIV-1 Integrase Inhibitors Derived from 2,3-Dihydro-6,7-dihydroxy-1 H -isoindol-1-ones and 4,5-Dihydroxy-1 H -isoindole-1,3(2 H)-diones Bioorg. Med. Chem. Lett. 2009, 19 (10) 2714-2717
23. Bollini, M.; Domaoal, R. A.; Thakur, V. V.; Gallardo-Macias, R.; Spasov, K. A.; Anderson, K. S.; Jorgensen, W. L. Computationally-Guided Optimization of a Docking Hit to Yield Catechol Diethers as Potent Anti-HIV Agents J. Med. Chem. 2011, 54 (24) 8582-8591
24. 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 (10) 3895-3901
25. Auffinger, P.; Hays, F. A.; Westhof, E.; Ho, P. S. Halogen Bonds in Biological Molecules Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (48) 16789-16794
26. Voth, A. R.; Hays, F. A.; Ho, P. S. Directing Macromolecular Conformation through Halogen Bonds Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (15) 6188-6193
27. Politzer, P.; Murray, J. S.; Concha, M. C. σ-Hole Bonding between Like Atoms; a Fallacy of Atomic Charges J. Mol. Model. 2008, 14 (8) 659-665
28. Hennemann, M.; Murray, J. S.; Politzer, P.; Riley, K. E.; Clark, T. Polarization-Induced Σ-Holes and Hydrogen Bonding J. Mol. Model. 2012, 18 (6) 2461-2469
29. a of Ethane J. Am. Chem. Soc. 1987, 109 (22) 6857-6858
30. Ibrahim, M. A. A. Molecular Mechanical Study of Halogen Bonding in Drug Discovery J. Comput. Chem. 2011, 32 (12) 2564-2574
31. Rendine, S.; Pieraccini, S.; Forni, A.; Sironi, M. Halogen Bonding in Ligand-Receptor Systems in the Framework of Classical Force Fields Phys. Chem. Chem. Phys. 2011, 13 (43) 19508-19516
32. Kolář, M.; Hobza, P. On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds J. Chem. Theory Comput. 2012, 8 (4) 1325-1333
33. Hage, K. E.; Piquemal, J.-P.; Hobaika, Z.; Maroun, R. G.; Gresh, N. Could an Anisotropic Molecular Mechanics/Dynamics Potential Account for σ Hole Effects in the Complexes of Halogenated Compounds? J. Comput. Chem. 2013, 34 (13) 1125-1135
34. Kolar, M.; Hobza, P.; Bronowska, A. K. Plugging the Explicit σ-Holes in Molecular Docking Chem. Commun. 2013, 49 (10) 981-983
35. Ren, P.; Ponder, J. W. Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation J. Phys. Chem. B 2003, 107 (24) 5933-5947
36. Wu, J.; Chattree, G.; Ren, P. Automation of AMOEBA Polarizable Force Field Parameterization for Small Molecules Theor. Chem. Acc. 2012, 131 (3) 1-11
37. Shi, Y.; Xia, Z.; Zhang, J.; Best, R.; Wu, C.; Ponder, J. W.; Ren, P. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins J. Chem. Theory Comput. 2013, 9 (9) 4046-4063
38. Ren, P.; Wu, C.; Ponder, J. W. Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules J. Chem. Theory Comput. 2011, 7 (10) 3143-3161
39. Stern, H. A.; Rittner, F.; Berne, B. J.; Friesner, R. A. Combined Fluctuating Charge and Polarizable Dipole Models: Application to a Five-Site Water Potential Function J. Chem. Phys. 2001, 115 (5) 2237-2251
40. Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A. Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from Ab Initio Quantum Chemistry J. Phys. Chem. A 2003, 108 (4) 621-627
41. Ren, P.; Chun, J.; Thomas, D. G.; Schnieders, M. J.; Marucho, M.; Zhang, J.; Baker, N. A. Biomolecular Electrostatics and Solvation: A Computational Perspective Q. Rev. Biophys. 2012, 45 (04) 427-491
42. Lopes, P. E. M.; Lamoureux, G.; Roux, B.; MacKerell, A. D. Polarizable Empirical Force Field for Aromatic Compounds Based on the Classical Drude Oscillator J. Phys. Chem. B 2007, 111 (11) 2873-2885
43. Shi, Y.; Wu, C.; Ponder, J. W.; Ren, P. Multipole Electrostatics in Hydration Free Energy Calculations J. Comput. Chem. 2011, 32 (5) 967-977
44. Zhang, J.; Yang, W.; Piquemal, J.-P.; Ren, P. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential J. Chem. Theory Comput. 2012, 8 (4) 1314-1324
45. Ren, P.; Ponder, J. W. Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations J. Comput. Chem. 2002, 23 (16) 1497-1506
46. Jiao, D.; Golubkov, P. A.; Darden, T. A.; Ren, P. Calculation of Protein-Ligand Binding Free Energy by Using a Polarizable Potential Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (17) 6290-6295
47. Jiao, D.; Zhang, J.; Duke, R. E.; Li, G.; Schnieders, M. J.; Ren, P. Trypsin-Ligand Binding Free Energies from Explicit and Implicit Solvent Simulations with Polarizable Potential J. Comput. Chem. 2009, 30 (11) 1701-1711
48. Shi, Y.; Zhu, C. Z.; Martin, S. F.; Ren, P. Probing the Effect of Conformational Constraint on Phosphorylated Ligand Binding to an SH2 Domain Using Polarizable Force Field Simulations J. Phys. Chem. B 2012, 116 (5) 1716-1727
49. Xia, Z.; Wang, Q.; Mu, X.; Ren, P. Development of AMOEBA Force Field with Advanced Electrostatics. In Methods and Applications in Quantitative Biology; Zhou, R., Ed.; Taylor & Francis: New York, NY 2014.
50. Wang, Q.; Bryce, R. A. Accounting for Non-Optimal Interactions in Molecular Recognition: A Study of Ion-π Complexes Using a QM/MM Model with a Dipole-Polarisable MM Region Phys. Chem. Chem. Phys. 2011, 13 (43) 19401-19408
51. Stone, A. J.; Alderton, M. Distributed Multipole Analysis Mol. Phys. 1985, 56 (5) 1047-1064
52. Wang, L.-P.; Chen, J.; Van Voorhis, T. Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data J. Chem. Theory Comput. 2012, 9 (1) 452-460
53. Ponder, J. W. Tinker Molecular Modeling Package. Washington University Medical School: St. Louis, MO.
54. 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; Gaussian, Inc.: Wallingford, CT, 2009.
55. Jurecka, P.; Sponer, J.; Cerny, J.; Hobza, P. 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. 2006, 8 (17) 1985-1993
56. Wang, L.-P.; Head-Gordon, T.; Ponder, J. W.; Ren, P.; Chodera, J. D.; Eastman, P. K.; Martinez, T. J.; Pande, V. S. Systematic Improvement of a Classical Molecular Model of Water J. Phys. Chem. B 2013, 117 (34) 9956-9972
57. Bennett, C. H. Efficient Estimation of Free-Energy Differences from Monte Carlo Data J. Comput. Phys. 1976, 22 (2) 245-268
58. Fried, S. D.; Wang, L.-P.; Boxer, S. G.; Ren, P.; Pande, V. S. Calculations of the Electric Fields in Liquid Solutions J. Phys. Chem. B 2013, 117 (50) 16236-16248
59. Boxer, S. G. Stark Realities J. Phys. Chem. B 2009, 113 (10) 2972-2983
60. Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A. Current Status of the AMOEBA Polarizable Force Field J. Phys. Chem. B 2010, 114 (8) 2549-2564
61. Mobley, D. L.; Dumont, é.; Chodera, J. D.; Dill, K. A. Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent J. Phys. Chem. B 2007, 111 (9) 2242-2254
62. Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models J. Phys. Chem. 1994, 98 (7) 1978-1988
63. Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations J. Chem. Theory Comput. 2009, 5 (2) 350-358
64. Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L. Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model J. Phys. Chem. 1994, 98 (49) 13077-13082
65. Jiang, H.; Jordan, K. D.; Taylor, C. E. Molecular Dynamics Simulations of Methane Hydrate Using Polarizable Force Fields J. Phys. Chem. B 2007, 111 (23) 6486-6492
66. Riddick, J. A.; Bunger, W. B.; Sakano, T. K., Organic Solvents: Physical Properties and Methods of Purification, 4 th ed.; Wiley-Interscience: New York, 1986; Vol. 2.
67. Dreisbach, R. R. Physical Properties of Chemical Compounds-III; American Chemical Society: Washington, DC, 1961; Vol. 29; p 500.
68. Lide, D. R. CRC Handbook of Chemistry and Physics, 76 th ed.; CRC Press: Boca Raton, FL, 1995.
69. Abraham, M. H.; Whiting, G. S.; Fuchs, R.; Chambers, E. J. Thermodynamics of Solute Transfer from Water to Hexadecane J. Chem. Soc., Perkin Trans. 2 1990, 2) 291-300
70. Rizzo, R. C.; Aynechi, T.; Case, D. A.; Kuntz, I. D. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions J. Chem. Theory Comput. 2005, 2 (1) 128-139
71. Majer, V.; Svoboda, V. Enthalpies of Vaporization of Organic Compounds: A Critical Review and Data Compilation; Blackwell Science Inc.: Oxford, 1986.
72. Choi, J.-H.; Cho, M. Vibrational Solvatochromism and Electrochromism of Infrared Probe Molecules Containing C≡O, C≡N, C=O, or C-F Vibrational Chromophore J. Chem. Phys. 2011, 134 (15) 1-12(154513)
73. Fried, S. D.; Bagchi, S.; Boxer, S. G. Measuring Electrostatic Fields in Both Hydrogen-Bonding and Non-Hydrogen-Bonding Environments Using Carbonyl Vibrational Probes J. Am. Chem. Soc. 2013, 135 (30) 11181-11192
74. Wu, J. C.; Piquemal, J. P.; Chaudret, R.; Reinhardt, P.; Ren, P. Y. Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field J. Chem. Theory Comput. 2010, 6 (7) 2059-2070; PMCID: PMC2992432.
75. Piquemal, J.-P.; Perera, L.; Cisneros, G. A.; Ren, P.; Pedersen, L. G.; Darden, T. A. Towards Accurate Solvation Dynamics of Divalent Cations in Water Using the Polarizable Amoeba Force Field: From Energetics to Structure J. Chem. Phys. 2006, 125 (5) 054511-054517
76. 2+ Solvation Using Polarizable Atomic Multipole Potential J. Phys. Chem. B 2006, 110 (37) 18553-18559
77. Grossfield, A.; Ren, P. Y.; Ponder, J. W. Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field J. Am. Chem. Soc. 2003, 125 (50) 15671-15682
78. Hagler, A. T.; Huler, E.; Lifson, S. Energy Functions for Peptides and Proteins. I. Derivation of a Consistent Force Field Including the Hydrogen Bond from Amide Crystals J. Am. Chem. Soc. 1974, 96 (17) 5319-5327
79. Waldman, M.; Hagler, A. T. New Combining Rules for Rare-Gas Van der Waals Parameters J. Comput. Chem. 1993, 14 (9) 1077-1084
80. Al-Matar, A. K.; Rockstraw, D. A. A Generating Equation for Mixing Rules and Two New Mixing Rules for Interatomic Potential Energy Parameters J. Comput. Chem. 2004, 25 (5) 660-668
81. Cisneros, G. A.; Tholander, S. N. I.; Parisel, O.; Darden, T. A.; Elking, D.; Perera, L.; Piquemal, J. P. Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding Int. J. Quantum Chem. 2008, 108 (11) 1905-1912
82. Tafipolsky, M.; Engels, B. Accurate Intermolecular Potentials with Physically Grounded Electrostatics J. Chem. Theory Comput. 2011, 7 (6) 1791-1803
83. Piquemal, J.-P.; Gresh, N.; Giessner-Prettre, C. Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution J. Phys. Chem. A 2003, 107 (48) 10353-10359