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Lambros E, Paesani F. How good are polarizable and flexible models for water: Insights from a many-body perspective. J Chem Phys 2020; 153:060901. [DOI: 10.1063/5.0017590] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
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Cisneros G, Wikfeldt KT, Ojamäe L, Lu J, Xu Y, Torabifard H, Bartók AP, Csányi G, Molinero V, Paesani F. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions. Chem Rev 2016; 116:7501-28. [PMID: 27186804 PMCID: PMC5450669 DOI: 10.1021/acs.chemrev.5b00644] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Indexed: 12/17/2022]
Abstract
Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.
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Affiliation(s)
| | - Kjartan Thor Wikfeldt
- Science
Institute, University of Iceland, VR-III, 107, Reykjavik, Iceland
- Department
of Physics, Albanova, Stockholm University, S-106 91 Stockholm, Sweden
| | - Lars Ojamäe
- Department
of Chemistry, Linköping University, SE-581 83 Linköping, Sweden
| | - Jibao Lu
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Yao Xu
- Lehrstuhl
Physikalische Chemie II, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Hedieh Torabifard
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Albert P. Bartók
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Gábor Csányi
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Valeria Molinero
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Francesco Paesani
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
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Shi Y, Ren P, Schnieders M, Piquemal JP. Polarizable Force Fields for Biomolecular Modeling. REVIEWS IN COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1002/9781118889886.ch2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys 2012; 45:427-91. [PMID: 23217364 PMCID: PMC3533255 DOI: 10.1017/s003358351200011x] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.
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Affiliation(s)
- Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin
| | | | | | | | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio
| | - Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Nathan A. Baker
- To whom correspondence should be addressed. Pacific Northwest National Laboratory, PO Box 999, MSID K7-29, Richland, WA 99352. Phone: +1-509-375-3997,
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de Courcy B, Piquemal JP, Gresh N. Energy Analysis of Zn Polycoordination in a Metalloprotein Environment and of the Role of a Neighboring Aromatic Residue. What Is the Impact of Polarization? J Chem Theory Comput 2008; 4:1659-68. [DOI: 10.1021/ct800200j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Benoit de Courcy
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris, France UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris, France UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris, France UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
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Tan YH, Tan C, Wang J, Luo R. Continuum polarizable force field within the Poisson-Boltzmann framework. J Phys Chem B 2008; 112:7675-88. [PMID: 18507452 DOI: 10.1021/jp7110988] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed and tested a complete set of nonbonded parameters for a continuum polarizable force field. Our analysis shows that the new continuum polarizable model is consistent with B3LYP/cc-pVTZ in modeling electronic response upon variation of dielectric environment. Comparison with experiment also shows that the new continuum polarizable model is reasonable, with accuracy similar to that of B3LYP/cc-pVTZ in reproduction of dipole moments of selected organic molecules in the gas phase. We have further tested the validity to interchange the Amber van der Waals parameters between the explicit and continuum polarizable force fields with a series of dimers. It can be found that the continuum polarizable model agrees well with MP2/cc-pVTZ, with deviations in dimer binding energies less than 0.9 kcal/mol in the aqueous dielectric environment. Finally, we have optimized atomic cavity radii with respect to experimental solvation free energies of 177 training molecules. To validate the optimized cavity radii, we have tested these parameters against 176 test molecules. It is found that the optimized Poisson-Boltzmann atomic cavity radii transfer well from the training set to the test set, with an overall root-mean-square deviation of 1.30 kcal/mol, an unsigned average error of 1.07 kcal/mol, and a correlation coefficient of 92% for all 353 molecules in both the training and test sets. Given the development documented here, the next natural step is the construction of a full protein/nucleic acid force field within the new continuum polarization framework.
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Affiliation(s)
- Yu-Hong Tan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA
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Gresh N, Cisneros GA, Darden TA, Piquemal JP. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J Chem Theory Comput 2007; 3:1960-1986. [PMID: 18978934 PMCID: PMC2367138 DOI: 10.1021/ct700134r] [Citation(s) in RCA: 276] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We present an overview of the SIBFA polarizable molecular mechanics procedure, which is formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical effects such as electrostatic penetration, exchange-polarization, and charge transfer. We address the issues of anisotropy, nonadditivity, and transferability by performing parallel QC computations on multimolecular complexes. These encompass multiply H-bonded complexes and polycoordinated complexes of divalent cations. Recent applications to the docking of inhibitors to Zn-metalloproteins are presented next, namely metallo-beta-lactamase, phosphomannoisomerase, and the nucleocapsid of the HIV-1 retrovirus. Finally, toward third-generation intermolecular potentials based on density fitting, we present the development of a novel methodology, the Gaussian electrostatic model (GEM), which relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. As GEM offers the possibility of a continuous electrostatic model going from distributed multipoles to densities, it allows an inclusion of short-range quantum effects in the molecular mechanics energies. The perspectives of an integrated SIBFA/GEM/QM procedure are discussed.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université René-Descartes, 45, rue des Saints-Pères, 75006 Paris, France, Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, and Laboratoire de Chimie Théorique, Université Pierre-et-Marie-Curie, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, 75252 Paris, France
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Khaliullin RZ, Cobar EA, Lochan RC, Bell AT, Head-Gordon M. Unravelling the Origin of Intermolecular Interactions Using Absolutely Localized Molecular Orbitals. J Phys Chem A 2007; 111:8753-65. [PMID: 17655284 DOI: 10.1021/jp073685z] [Citation(s) in RCA: 439] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing EDA methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed EDA method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.
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Affiliation(s)
- Rustam Z Khaliullin
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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Jensen JH, Li H, Robertson AD, Molina PA. Prediction and rationalization of protein pKa values using QM and QM/MM methods. J Phys Chem A 2007; 109:6634-43. [PMID: 16834015 DOI: 10.1021/jp051922x] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe the development and application of a computational method for the prediction and rationalization of pKa values of ionizable residues in proteins, based on ab initio quantum mechanics (QM) and the effective fragment potential (EFPs) method (a hybrid QM/MM method). The theoretical developments include (1) a covalent boundary method based on frozen localized orbitals, (2) divide-and-conquer methods for the ab initio computation of protein EFPs consisting of multipoles up to octupoles and dipole polarizability tensors, (3) a method for computing vibrational free energies for a localized molecular region, and (4) solutions of the polarized continuum model of bulk solvation equations for protein-sized systems. The QM-based pKa prediction method is one of the most accurate methods currently available and can be used in cases where other pKa prediction methods fail. Preliminary analysis of the computed results indicate that many pKa values (1) are primarily determined by hydrogen bonds rather than long-range charge-charge interactions and (2) are relatively insensitive to large-scale dynamical fluctuations of the protein structure.
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Affiliation(s)
- Jan H Jensen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA.
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11
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Piquemal JP, Marquez A, Parisel O, Giessner-Prettre C. A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contribution. J Comput Chem 2005; 26:1052-62. [PMID: 15898112 DOI: 10.1002/jcc.20242] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Intermolecular interaction energy decompositions using the Constrained Space Orbital Variation (CSOV) method are carried out at the Hartree-Fock level on the one hand and using DFT with usual GGA functionals on the other for a number of model complexes to analyze the role of electron correlation in the intermolecular stabilization energy. In addition to the overall stabilization, the results provide information on the variation, with respect to the computational level, of the different contributions to the interaction energy. The complexes studied are the water linear dimer, the N-methylformamide dimer, the nucleic acid base pairs, the benzene-methane and benzene-N2 van der Waals complexes, [Cu+ -(ImH)3]2, where "ImH" stands for the Imidazole ligand, and ImH-Zn++. The variation of the frozen core energy (the sum of the intermolecular electrostatic energy and the Pauli repulsion energy) calculated from the unperturbed orbitals of the interacting entities indicates that the intramolecular correlation contributions can be stabilizing as well as destabilizing, and that general trends can be derived from the results obtained using usual density functionals. The most important difference between the values obtained from HF and DFT computations concerns the charge transfer contribution, which, in most cases, undergoes the largest increase. The physical meaning of these results is discussed. The present work gives reference calculations that might be used to parametrize new correlated molecular mechanics potentials.
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Affiliation(s)
- Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR 7616-CNRS/UPMC, Université P. & M. Curie, Case courrier 137, 4 place Jussieu, F. 75252 Paris Cedex 05, France
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Molina PA, Li H, Jensen JH. Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations. J Comput Chem 2003; 24:1971-9. [PMID: 14531051 DOI: 10.1002/jcc.10333] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Two divide-and-conquer (DAQ) approaches for building multipole-based molecular electrostatic potentials of proteins are presented and evaluated for use in QM/MM calculations. One approach is a further development of the neutralization method of Bellido and Rullmann (J Comput Chem 1989, 10, 479-487) while the other is based on removing part of the electron density before performing the multipole expansion. Both methods create systems with integer charges without using charge renormalization. To determine their performance in terms of location of cuts and distance to QM region, the new DAQ approaches are tested in calculations of the proton affinity of N(zeta) of Lys55 in the inhibitor turkey ovomucoid third domain. Finally, the two methods are used to build a variety of MM regions, applied to calculations of the pK(a) of Lys55, and compared to other computational methodologies in which force field charges are employed.
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Affiliation(s)
- Pablo A Molina
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
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Affiliation(s)
- Jay W Ponder
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Antony J, Gresh N, Olsen L, Hemmingsen L, Schofield CJ, Bauer R. Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2002; 23:1281-96. [PMID: 12210153 DOI: 10.1002/jcc.10111] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The bacterial Zn2+ metallo-beta-lactamase from B. fragilis is a zinc-enzyme with two potential metal ion binding sites. It cleaves the lactam ring of antibiotics, thus contributing to the acquired resistance of bacteria against antibiotics. The present study bears on the binuclear form of the enzyme. We compare several possible binding modes of captopril, a mercaptocarboxamide inhibitor of several zinc-metalloenzymes. Two diastereoisomers of captopril were considered, with either a D- or an L-proline residue. We have used the polarizable molecular mechanics procedure SIBFA (Sum of Interactions Between Fragments ab initio computed). Two beta-lactamase models were considered, encompassing 104 and 188 residues, respectively. The energy balances included the inter and intramolecular interaction energies as well as the contribution from solvation computed using a continuum reaction field procedure. The thiolate ion of the inhibitor is binding to both metal ions, expelling the bridging solvent molecule from the uncomplexed enzyme. Different competing binding modes of captopril were considered, either where the inhibitor binds in a monodentate mode to the zinc cations only with its thiolate ion, or in bidentate modes involving additional zinc binding by its carboxylate or ketone carbonyl groups. The additional coordination by the inhibitor's carboxylate or carbonyl group always occurs at the zinc ion, which is bound by a histidine, a cysteine, and an aspartate side chain. For both diastereomers, the energy balances favor monodentate binding of captopril via S-. The preference over bidentate binding is small. The interaction energies were recomputed in model sites restricted to captopril, the Zn2+ cations, and their coordinating end side chains from beta-lactamase (98 atoms). The interaction energies and their ranking among competing arrangements were consistent with those computed by ab initio HF and DFT procedures.
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Affiliation(s)
- Jens Antony
- Department of Mathematics and Physics, The Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark
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Gresh N, Policar C, Giessner-Prettre C. Modeling Copper(I) Complexes: SIBFA Molecular Mechanics versus ab Initio Energetics and Geometrical Arrangements. J Phys Chem A 2002. [DOI: 10.1021/jp0106146] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Gresh
- Equipe de Pharmacochimie Moléculaire et Cellulaire, UMR 8638, Université René Descartes, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France, Laboratoire de Chimie Bioorganique et Bioinorganique, FRE 2127, Bâtiment 420, Université de Paris Sud, 91405 Orsay, Cedex, France, and Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France
| | - C. Policar
- Equipe de Pharmacochimie Moléculaire et Cellulaire, UMR 8638, Université René Descartes, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France, Laboratoire de Chimie Bioorganique et Bioinorganique, FRE 2127, Bâtiment 420, Université de Paris Sud, 91405 Orsay, Cedex, France, and Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France
| | - C. Giessner-Prettre
- Equipe de Pharmacochimie Moléculaire et Cellulaire, UMR 8638, Université René Descartes, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France, Laboratoire de Chimie Bioorganique et Bioinorganique, FRE 2127, Bâtiment 420, Université de Paris Sud, 91405 Orsay, Cedex, France, and Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France
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Krauss M, Gilson HSR, Gresh N. Structure of the First-Shell Active Site in Metallolactamase: Effect of Water Ligands. J Phys Chem B 2001. [DOI: 10.1021/jp012099h] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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van der Vaart A, Bursulaya BD, Brooks CL, Merz KM. Are Many-Body Effects Important in Protein Folding? J Phys Chem B 2000. [DOI: 10.1021/jp001193f] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Guo H, Gresh N, Roques BP, Salahub DR. Many-Body Effects in Systems of Peptide Hydrogen-Bonded Networks and Their Contributions to Ligand Binding: A Comparison of the Performances of DFT and Polarizable Molecular Mechanics. J Phys Chem B 2000. [DOI: 10.1021/jp0012247] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hong Guo
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Nohad Gresh
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Bernard P. Roques
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Dennis R. Salahub
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
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Foloppe N, MacKerell, Jr. AD. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 2000. [DOI: 10.1002/(sici)1096-987x(20000130)21:2<86::aid-jcc2>3.0.co;2-g] [Citation(s) in RCA: 1273] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Foloppe N, MacKerell, Jr. AD. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 2000. [DOI: 10.1002/(sici)1096-987x(20000130)21:2%3c86::aid-jcc2%3e3.0.co;2-g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Tiraboschi G, Gresh N, Giessner-Prettre C, Pedersen LG, Deerfield DW. Parallelab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: Variations of binding energy and of its components with number and charges of ligands. J Comput Chem 2000. [DOI: 10.1002/1096-987x(200009)21:12<1011::aid-jcc1>3.0.co;2-b] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gresh N, Šponer J. Complexes of Pentahydrated Zn2+ with Guanine, Adenine, and the Guanine−Cytosine and Adenine−Thymine Base Pairs. Structures and Energies Characterized by Polarizable Molecular Mechanics and ab Initio Calculations. J Phys Chem B 1999. [DOI: 10.1021/jp9921351] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nohad Gresh
- Unité de Pharmacochimie Moléculaire et Structurale, U266 INSERM, UMR 8600 CNRS, U.F.R. des Sciences Pharmaceutiques et Biologiques, 4, avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Jırí Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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Tiraboschi G, Roques BP, Gresh N. Joint quantum chemical and polarizable molecular mechanics investigation of formate complexes with penta- and hexahydrated Zn2+: Comparison between energetics of model bidentate, monodentate, and through-water Zn2+ binding modes and evaluation of nonadditivity effects. J Comput Chem 1999. [DOI: 10.1002/(sici)1096-987x(199910)20:13<1379::aid-jcc5>3.0.co;2-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Gresh N, Guo H, Salahub DR, Roques BP, Kafafi SA. Critical Role of Anisotropy for the Dimerization Energies of Two Protein−Protein Recognition Motifs: cis-N-Methylacetamide versus a β-Sheet Conformer of Alanine Dipeptide. A Joint ab Initio, Density Functional Theory, and Molecular Mechanics Investigation. J Am Chem Soc 1999. [DOI: 10.1021/ja9742489] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nohad Gresh
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Hong Guo
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Dennis R. Salahub
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Bernard P. Roques
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Sherif A. Kafafi
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
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Dumas F, Fressigné C, Langlet J, Giessner-Prettre C. Theoretical Investigations of the Influence of Pressure on the Selectivity of the Michael Addition of Diphenylmethaneamine to Stereogenic Crotonates. J Org Chem 1999; 64:4725-4732. [PMID: 11674545 DOI: 10.1021/jo9825308] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
SIBFA (sum of interactions between fragments ab initio computed) molecular mechanics systematics has been modified to take into account the effect of pressure on intra- and intermolecular energies. The van der Waals radii are related to the pressure, using Bridgman results on the variation of crystal volume, on one hand, and the relation between the volume of an atom and its van der Waals radius on the other. This procedure produces a decrease of the volume of the systems considered. The modified systematics is used for the study of the conformation at 1 atm and 15 kbar of two stereogenic crotonates and of the complexes formed by these two molecules with the diphenylmethaneamine and the three solvent molecules present in the experiment. The results obtained show that in the case of NMECC 1a the diastereoselectivity induced by high pressure and by the presence of methanol proceeds from an important stabilization of the pro-R reactive complex in which the crotonate has a stacked-transoid conformation. This stabilization is mainly due to intermolecular interactions. In the case of the second crotonate considered, NMCC 1b, our results indicate that pressure induces a stabilization of the pro-R and pro-S complexes having the axial conformation for which the reaction exhibits little diastereoselectivity in qualitative agreement with experimental data. This study tends to show that it is possible to account theoretically for the influence of pressure on molecular conformation and/or complex structure, using a molecular mechanics method that is able to take into account the variation of volumes of the different entities present in the system studied.
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Affiliation(s)
- F. Dumas
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Université P. & M. Curie, Case Courrier 137, 4, place Jussieu, 75252 Paris Cedex 05, France, and Centre Régional Universitaire de Spectroscopie UPRESA 6014 CNRS, IRCOF, Université de Rouen, 76821 Mont St Aignan Cedex, France
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Gresh N, Tiraboschi G, Salahub DR. Conformational properties of a model alanyl dipeptide and of alanine-derived oligopeptides: Effects of solvation in water and in organic solvents—A combined SIBFA/continuum reaction field, ab initio self-consistent field, and density functional theory investigation. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199805)45:6<405::aid-bip1>3.0.co;2-t] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gresh N, Parisel O, Giessner-Prettre C. Electronic distribution influence on molecular mechanics results. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(98)00346-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Gresh N. Model, Multiply Hydrogen-Bonded Water Oligomers (N = 3−20). How Closely Can a Separable, ab Initio-Grounded Molecular Mechanics Procedure Reproduce the Results of Supermolecule Quantum Chemical Computations? J Phys Chem A 1997. [DOI: 10.1021/jp9713423] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nohad Gresh
- Département de Pharmacochimie Moléculaire et Structurale, URA D1500 CNRS, U266 INSERM, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France
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