Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field
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Jean-Philip Piquemal | Kevin N. Dalby | Stephen D. Fried | Pengyu Ren | Lee-Ping Wang | Qiantao Wang | Pengyu Y. Ren | Lee‐Ping Wang | J. Piquemal | K. Dalby | S. Fried | Qiantaoa Wang | Xiaojiao Mu | Xiaojia Mu | Jean‐Philip Piquemal
[1] M. Alderton,et al. Distributed multipole analysis , 2006 .
[2] W. M. Haynes. CRC Handbook of Chemistry and Physics , 1990 .
[3] David L Mobley,et al. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. , 2009, Journal of chemical theory and computation.
[4] B. Berne,et al. Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function , 2001 .
[5] Alexander D. MacKerell,et al. Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. , 2007, The journal of physical chemistry. B.
[6] K. Jordan,et al. Molecular dynamics simulations of methane hydrate using polarizable force fields. , 2007, The journal of physical chemistry. B.
[7] Reizo Kato,et al. Synthesis and physical properties of (DIETS)2[Au(CN)4]: A new θ-salt with a unique donor⋯anion network , 2001 .
[8] Yue Shi,et al. Multipole electrostatics in hydration free energy calculations , 2011, J. Comput. Chem..
[9] Nohad Gresh,et al. Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution. , 2003, The journal of physical chemistry. A.
[10] H. Sawa,et al. 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 , 1995 .
[11] Charles H. Bennett,et al. Efficient estimation of free energy differences from Monte Carlo data , 1976 .
[12] Weiliang Zhu,et al. Halogen Bond: Its Role beyond Drug-Target Binding Affinity for Drug Discovery and Development , 2014, J. Chem. Inf. Model..
[13] J. Choi,et al. Vibrational solvatochromism and electrochromism of infrared probe molecules containing C≡O, C≡N, C=O, or C-F vibrational chromophore. , 2011, The Journal of chemical physics.
[14] Timothy Clark,et al. Halogen bonding and other σ-hole interactions: a perspective. , 2013, Physical chemistry chemical physics : PCCP.
[15] Hiroshi Yamamoto,et al. An application of supramolecular chemistry to molecular conductors , 2002 .
[16] A. Voth. Macromolecular halogen bonds , 2007 .
[17] Guohui Li,et al. Trypsin‐ligand binding free energies from explicit and implicit solvent simulations with polarizable potential , 2009, J. Comput. Chem..
[18] Jindřich Fanfrlík,et al. Halogen bond tunability II: the varying roles of electrostatic and dispersion contributions to attraction in halogen bonds , 2013, Journal of Molecular Modeling.
[19] Patric Schyman,et al. Treatment of Halogen Bonding in the OPLS-AA Force Field; Application to Potent Anti-HIV Agents. , 2012, Journal of chemical theory and computation.
[20] Pengyu Ren,et al. Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations. , 2012, The journal of physical chemistry. B.
[21] Pierangelo Metrangolo,et al. Halogen Bonding in Halocarbon—Protein Complexes: A Structural Survey , 2011 .
[22] Timothy Clark,et al. Halogen bonding: an electrostatically-driven highly directional noncovalent interaction. , 2010, Physical chemistry chemical physics : PCCP.
[23] Pierangelo Metrangolo,et al. Fluorine-Centered Halogen Bonding: A Factor in Recognition Phenomena and Reactivity , 2011 .
[24] Pengyu Y. Ren,et al. Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations , 2002, J. Comput. Chem..
[25] Nathan A. Baker,et al. Biomolecular electrostatics and solvation: a computational perspective , 2012, Quarterly Reviews of Biophysics.
[26] Martin Lepšík,et al. Modulation of aldose reductase inhibition by halogen bond tuning. , 2013, ACS chemical biology.
[27] Jean-Philip Piquemal,et al. Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field. , 2010, Journal of Chemical Theory and Computation.
[28] Pavel Hobza,et al. On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds. , 2012, Journal of chemical theory and computation.
[29] S. Lifson,et al. Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. , 1974, Journal of the American Chemical Society.
[30] Pengyu Ren,et al. Automation of AMOEBA polarizable force field parameterization for small molecules , 2012, Theoretical Chemistry Accounts.
[31] Alan Grossfield,et al. Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. , 2006, The journal of physical chemistry. B.
[32] Pierangelo Metrangolo,et al. The fluorine atom as a halogen bond donor, viz. a positive site , 2011 .
[33] Peter Politzer,et al. Halogen bonding: an interim discussion. , 2013, Chemphyschem : a European journal of chemical physics and physical chemistry.
[34] R. C. Weast. CRC Handbook of Chemistry and Physics , 1973 .
[35] George A. Kaminski,et al. Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry , 2004 .
[36] 宁北芳,et al. 疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .
[37] Pengyu Y. Ren,et al. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. , 2006, The Journal of chemical physics.
[38] K. Sharp,et al. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models , 1994 .
[39] Eric Westhof,et al. Halogen bonds in biological molecules. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[40] Pengyu Y. Ren,et al. Calculations of the electric fields in liquid solutions. , 2013, The journal of physical chemistry. B.
[41] Nohad Gresh,et al. Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds? , 2013, J. Comput. Chem..
[42] Jindřich Fanfrlík,et al. Halogen bond tunability I: the effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine, bromine, and iodine , 2011, Journal of molecular modeling.
[43] Stephen H Hughes,et al. Examination of halogen substituent effects on HIV-1 integrase inhibitors derived from 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-ones and 4,5-dihydroxy-1H-isoindole-1,3(2H)-diones. , 2009, Bioorganic & medicinal chemistry letters.
[44] Peter Politzer,et al. σ‐Hole bonding and hydrogen bonding: Competitive interactions , 2007 .
[45] Maurizio Sironi,et al. Halogen bonding in ligand-receptor systems in the framework of classical force fields. , 2011, Physical chemistry chemical physics : PCCP.
[46] Arnold T. Hagler,et al. New combining rules for rare gas van der waals parameters , 1993, J. Comput. Chem..
[47] William L. Jorgensen,et al. Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model , 1994 .
[48] Pengyu Y. Ren,et al. The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins. , 2013, Journal of chemical theory and computation.
[49] T. Windus,et al. O + C2H4 potential energy surface: lowest-lying singlet at the multireference level , 2012, Theoretical Chemistry Accounts.
[50] R. Bryce,et al. 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. , 2011, Physical chemistry chemical physics : PCCP.
[51] Wei Yang,et al. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. , 2012, Journal of chemical theory and computation.
[52] David A. Rockstraw,et al. A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters , 2004, J. Comput. Chem..
[53] Pengyu Y. Ren,et al. Calculation of protein–ligand binding free energy by using a polarizable potential , 2008, Proceedings of the National Academy of Sciences.
[54] R. Dreisbach. Physical Properties of Chemical Compounds , 1955 .
[55] Miss A.O. Penney. (b) , 1974, The New Yale Book of Quotations.
[56] Margaret E. Johnson,et al. Current status of the AMOEBA polarizable force field. , 2010, The journal of physical chemistry. B.
[57] Pengyu Y. Ren,et al. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. , 2011, Journal of chemical theory and computation.
[58] Timothy Clark,et al. Halogen bonding: the σ-hole , 2007 .
[59] Lili Wang,et al. A polarizable ellipsoidal force field for halogen bonds , 2013, J. Comput. Chem..
[60] Mahmoud A. A. Ibrahim,et al. Molecular mechanical study of halogen bonding in drug discovery , 2011, J. Comput. Chem..
[61] Michael H. Abraham,et al. Thermodynamics of solute transfer from water to hexadecane , 1990 .
[62] S. Boxer,et al. Measuring electrostatic fields in both hydrogen-bonding and non-hydrogen-bonding environments using carbonyl vibrational probes. , 2013, Journal of the American Chemical Society.
[63] P. Metrangolo,et al. Halogen Versus Hydrogen , 2008, Science.
[64] David L Mobley,et al. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. , 2007, The journal of physical chemistry. B.
[65] William L Jorgensen,et al. Computationally-guided optimization of a docking hit to yield catechol diethers as potent anti-HIV agents. , 2011, Journal of medicinal chemistry.
[66] Pavel Hobza,et al. Plugging the explicit σ-holes in molecular docking. , 2013, Chemical communications.
[67] Irwin D Kuntz,et al. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions , 2022 .
[68] W. L. Jorgensen,et al. A priori calculations of pKa's for organic compounds in water. The pKa of ethane , 1987 .
[69] Pengyu Y. Ren,et al. Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation , 2003 .
[70] H. V. Kehiaian,et al. Enthalpies of vaporization of organic compounds : a critical review and data compilation , 1985 .
[71] Bernd Engels,et al. Accurate Intermolecular Potentials with Physically Grounded Electrostatics. , 2011, Journal of chemical theory and computation.
[72] P Shing Ho,et al. Directing macromolecular conformation through halogen bonds , 2007, Proceedings of the National Academy of Sciences.
[73] Peter Politzer,et al. σ-hole bonding between like atoms; a fallacy of atomic charges , 2008, Journal of molecular modeling.
[74] T. Darden,et al. Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding. , 2008, International journal of quantum chemistry.
[75] Pengyu Y. Ren,et al. Systematic improvement of a classical molecular model of water. , 2013, The journal of physical chemistry. B.
[76] S. Boxer,et al. Stark realities. , 2009, The journal of physical chemistry. B.
[77] Timothy Clark,et al. Polarization-induced σ-holes and hydrogen bonding , 2012, Journal of Molecular Modeling.
[78] Pierangelo Metrangolo,et al. Halogen bonding in halocarbon-protein complexes: a structural survey. , 2011, Chemical Society reviews.
[79] Lee-Ping Wang,et al. Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data. , 2013, Journal of chemical theory and computation.
[80] F. Rossini. Physical Properties of Chemical Compounds III. Advances in Chemistry Series Number 29. , 1962 .
[81] Arnold Weissberger,et al. Organic solvents;: Physical properties and methods of purification , 1970 .
[82] M. Scholfield,et al. Halogen bonding (X‐bonding): A biological perspective , 2013, Protein science : a publication of the Protein Society.
[83] Pengyu Y. Ren,et al. Ion solvation thermodynamics from simulation with a polarizable force field. , 2003, Journal of the American Chemical Society.
[84] Jirí Cerný,et al. 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. , 2006, Physical chemistry chemical physics : PCCP.
[85] J. Murray,et al. Enthalpy and entropy factors in gas phase halogen bonding: compensation and competition , 2013 .
[86] Markus O. Zimmermann,et al. Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant p53 , 2012, Journal of the American Chemical Society.