1
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Pederson JP, McDaniel JG. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics. J Chem Phys 2024; 161:034103. [PMID: 39007371 DOI: 10.1063/5.0219851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.
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Affiliation(s)
- John P Pederson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Jesse G McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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2
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Ghahremanpour MM, Saar A, Tirado-Rives J, Jorgensen WL. Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease. J Chem Inf Model 2023; 63:5309-5318. [PMID: 37561001 DOI: 10.1021/acs.jcim.3c00874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Accurate, routine calculation of absolute binding free energies (ABFEs) for protein-ligand complexes remains a key goal of computer-aided drug design since it can enable screening and optimization of drug candidates. For development and testing of related methods, it is important to have high-quality datasets. To this end, from our own experimental studies, we have selected a set of 16 inhibitors of the SARS-CoV-2 main protease (Mpro) with structural diversity and well-distributed BFEs covering a 5 kcal/mol range. There is also minimal structural uncertainty since X-ray crystal structures have been deposited for 12 of the compounds. For methods testing, we report ABFE results from 2 μs molecular dynamics (MD) simulations using free energy perturbation (FEP) theory. The correlation of experimental and computed results is encouraging, with a Pearson's r2 of 0.58 and a Kendall τ of 0.24. The results indicate that current FEP-based ABFE calculations can be used for identification of active compounds (hits). While their accuracy for lead optimization is not yet sufficient, this activity remains addressable in separate lead series by relative BFE calculations.
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Affiliation(s)
| | - Anastasia Saar
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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3
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Yang L, Liu X, Zhang Y, Yang Y, Xue Y. Influence of water content on the [2σ+2σ+2π] cycloaddition of dimethyl azodicarboxylate with quadricyclane in mixed methanol-water solvents from QM/MM Monte Carlo simulations. Phys Chem Chem Phys 2021; 23:20524-20532. [PMID: 34505591 DOI: 10.1039/d1cp01973b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mixed quantum mechanics/molecular mechanics Monte Carlo (QM/MM/MC) simulations combined with the free energy perturbation (FEP) theory have been performed to investigate the mechanism and solvent effect of the [2σ+2σ+2π] cycloaddition reaction between dimethyl azodicarboxylate and quadricyclanes in the binary mixture solvents of methanol and water by varying the water content from 0 to 100 vol%. The two-dimensional potentials of mean force (2D PMF) calculations demonstrated that the mechanism of the reaction is a collaborative asynchronous procedure. The transition structures do not show large variation among different solvents. The calculated free energies of activation indicated that the QM/MM/MC method reproduced well the tendency of rate enhancement from pure methanol to methanol-water mixtures to "on water" with the water content increasing obtained in the experimental observation. The analyses of the energy pair distribution and radial distribution functions illustrated that hydrogen bonding plays an indispensable role in the stabilization of the transition structures. According to the results in methanol-water mixtures at different volume ratios, it is clear that the site-specific hydrogen bond effects are the central reason which leads to fast rate increases in progressing from a methanol-water volume ratio of 3 : 1 to 1 : 1. This work provides a new insight into the solvent effect for the [2σ+2σ+2π] cycloaddition reaction.
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Affiliation(s)
- Lian Yang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China.
| | - Xudong Liu
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China.
| | - Yan Zhang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China.
| | - Yongsheng Yang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China.
| | - Ying Xue
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China.
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4
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Chen W, Deng Y, Russell E, Wu Y, Abel R, Wang L. Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges. J Chem Theory Comput 2018; 14:6346-6358. [PMID: 30375870 DOI: 10.1021/acs.jctc.8b00825] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Wei Chen
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Yuqing Deng
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ellery Russell
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Yujie Wu
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Robert Abel
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
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5
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Zhao J, He F, Zhang F, Yang X, Tian Z, Xue Y. The Role of Water in the Catalyst-Free Aldol Reaction of Water-Insoluble N-Methyl-2,4-thiazolidinedione with N-Methylisatin from QM/MM Monte Carlo Simulations. Chemphyschem 2017; 18:2123-2131. [PMID: 28544113 DOI: 10.1002/cphc.201700423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/22/2017] [Indexed: 11/08/2022]
Abstract
The role of water in the uncatalyzed aldol reaction of N-methyl-2,4-thiazolidinedione with N-methylisatin is investigated through Monte Carlo statistical mechanics simulations that utilize free energy perturbation theory and the mixed quantum mechanics and molecular mechanics (QM/MM) model with PDDG/PM3 for the QM method in "on-water" and DMSO environments. There are several conceivable orientations between thiazolidinedione and isatin in the process of C-C bond formation. However, the formation of the C-C bond takes place between the re face of isatin and the si face of (E)-enol of the thiazolidinedione to form the preferred anti-type product, which results from enhanced hydrogen-bonding interactions between water molecules and the oxygen atoms undergoing bond breakage and bond formation during the reaction. Novel insights into the effect of water on the aldol reaction are presented herein.
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Affiliation(s)
- Jianming Zhao
- College of Chemistry, Key Lab of Green Chemistry, and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, P.R. China
| | - Fen He
- College of Chemistry, Key Lab of Green Chemistry, and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, P.R. China
| | - Fan Zhang
- College of Chemistry, Key Lab of Green Chemistry, and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, P.R. China
| | - Xin Yang
- College of Chemistry, Key Lab of Green Chemistry, and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, P.R. China
| | - Zhiyue Tian
- College of Chemistry, Key Lab of Green Chemistry, and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, P.R. China
| | - Ying Xue
- College of Chemistry, Key Lab of Green Chemistry, and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, P.R. China
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6
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Beckett D, Krukau A, Raghavachari K. Charge redistribution in QM:QM ONIOM model systems: a constrained density functional theory approach. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1333643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Daniel Beckett
- Department of Chemistry, Indiana University, Bloomington, IN, USA
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7
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Ganguly A, Boulanger E, Thiel W. Importance of MM Polarization in QM/MM Studies of Enzymatic Reactions: Assessment of the QM/MM Drude Oscillator Model. J Chem Theory Comput 2017; 13:2954-2961. [DOI: 10.1021/acs.jctc.7b00016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Abir Ganguly
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Eliot Boulanger
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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8
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Yan XC, Tirado-Rives J, Jorgensen WL. Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water. J Phys Chem B 2016; 120:8102-14. [PMID: 26901452 DOI: 10.1021/acs.jpcb.6b00399] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to the importance of water in chemical and biological systems, a coarse-grained representation of the solvent can greatly simplify the description of the system while retaining key thermodynamic properties of the medium. A multiscale solvation model that couples all-atom solutes and polarizable Martini coarse-grained water (AAX/CGS) is developed to reproduce free energies of hydration of organic solutes. Using Monte Carlo/free energy perturbation (MC/FEP) calculations, results from multiscale and all-atom simulations are compared. Improved accuracy is obtained with the AAX/CGS approach for hydrophobic and sulfur- or halogen-containing solutes, but larger deviations are found for polar solute molecules where hydrogen bonding is featured. Furthermore, solvent effects on conformational and tautomeric equilibria of AA solutes were investigated using AA, CG, and GB/SA solvent models. It is found that the CG solvent model can reproduce well the medium effects from experiment and AA simulations; however, the GB/SA solvent model fails in some cases. A 7-30-fold reduction in computational cost is found for the present AAX/CGS multiscale simulations compared to the AA alternative.
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Affiliation(s)
- Xin Cindy Yan
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
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9
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Benighaus T, Thiel W. A General Boundary Potential for Hybrid QM/MM Simulations of Solvated Biomolecular Systems. J Chem Theory Comput 2015; 5:3114-28. [PMID: 26609991 DOI: 10.1021/ct900437b] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a general boundary potential for the efficient and accurate evaluation of electrostatic interactions in hybrid quantum mechanical/molecular mechanical (QM/MM) approaches called solvated macromolecule boundary potential (SMBP), which is designed for QM/MM calculations with any kind of QM method. The SMBP targets QM/MM single-point energy calculations and geometry optimizations. In the SMBP scheme, the outer solvent and macromolecule region is described by a boundary potential obtained with the use of Poisson-Boltzmann calculations (treating the bulk solvent as a dielectric continuum). In the QM calculations, the SMBP is represented by virtual point charges on a surface enclosing the explicitly treated inner region. These charges and their interactions with the QM density are determined through a self-consistent reaction field procedure. The accuracy of the SMBP is evaluated on three diverse test systems: the intramolecular proton transfer of glycine in water, the hydroxylation reaction in p-hydroxybenzoate hydroxylase, and the spin state energy splittings in the pentacoordinated ferric complex of cytochrome P450cam. In the case of solvated glycine, application of the SMBP turns out to be problematic since analogous QM/MM/SMBP and full QM/MM geometry optimizations lead to different close-lying local minima. In both enzymes, the SMBP performs very well and closely reproduces the results from full QM/MM optimizations of these more rigid test systems. Starting from optimized QM/MM/SMBP structures along a reaction path, one can apply the previously implemented generalized solvent boundary potential (GSBP) to sample over MM phase space in QM/MM free energy calculations within the framework of free energy perturbation theory. This reduces the overall computational costs of sampling by 1 order of magnitude while maintaining good accuracy. The combined use of SMBP and GSBP thus allows for efficient QM/MM free energy studies of enzymes.
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Affiliation(s)
- Tobias Benighaus
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1 45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1 45470, Mülheim an der Ruhr, Germany
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10
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Manna RN, Zinovjev K, Tuñón I, Dybala-Defratyka A. Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study. J Phys Chem B 2015; 119:15100-9. [DOI: 10.1021/acs.jpcb.5b07538] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rabindra Nath Manna
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
| | - Kirill Zinovjev
- Departament
de Química Física, Universitat de Valéncia, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat de Valéncia, 46100 Burjassot, Spain
| | - Agnieszka Dybala-Defratyka
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
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11
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Vilseck JZ, Kostal J, Tirado-Rives J, Jorgensen WL. Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions. J Comput Chem 2015; 36:2064-74. [PMID: 26311531 PMCID: PMC4575649 DOI: 10.1002/jcc.24045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 01/06/2023]
Abstract
Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods.
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Affiliation(s)
- Jonah Z. Vilseck
- Department of Chemistry, Yale University, New Haven, CT 06520-8107USA
| | - Jakub Kostal
- Department of Chemistry, Yale University, New Haven, CT 06520-8107USA
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12
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Dodda LS, Vilseck JZ, Cutrona KJ, Jorgensen WL. Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling. J Chem Theory Comput 2015; 11:4273-82. [PMID: 26575922 PMCID: PMC4857764 DOI: 10.1021/acs.jctc.5b00414] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Partial atomic charges for neutral molecules from quantum mechanical calculations are typically scaled for use in molecular modeling of liquid-phase systems. Optimal scale factors of 1.14 for CM1A and 1.27 for CM5 charges were previously determined for minimizing errors in free energies of hydration. The adequacy of the 1.14*CM1A and 1.27*CM5 models are evaluated here in pure liquid simulations in combination with the OPLS-AA force field. For 22 organic liquids, the 1.14*CM1A and 1.27*CM5 models yield mean unsigned errors (MUEs) of ca. 1.40 kcal/mol for heats of vaporization. Not surprisingly, this reflects overpolarization with the scale factors derived for aqueous media. Prediction of pure liquid properties using CM5 charges is optimized using a scale factor of 1.14, which reduces the MUE for heats of vaporization to 0.89 kcal/mol. However, due to the impracticality of using different scale factors in different explicit-solvent condensed-phase simulations, a universal scale factor of 1.20 emerged for CM5 charges. This provides a balance between errors in computed pure liquid properties and free energies of hydration. Computation of free energies of hydration by the GB/SA method further found that 1.20 is equally suited for use in explicit or implicit treatments of aqueous solvation. With 1.20*CM5 charges, a variety of condensed-phase simulations can be pursued while maintaining average errors of 1.0 kcal/mol in key thermodynamic properties.
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Affiliation(s)
- Leela S. Dodda
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Jonah Z. Vilseck
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Kara J. Cutrona
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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13
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Vilseck JZ, Tirado-Rives J, Jorgensen WL. Determination of partial molar volumes from free energy perturbation theory. Phys Chem Chem Phys 2015; 17:8407-15. [PMID: 25589343 PMCID: PMC4872387 DOI: 10.1039/c4cp05304d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.
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Affiliation(s)
- Jonah Z Vilseck
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA.
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14
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Jorgensen WL. Autobiography of William L. Jorgensen: Scientific History and Recollections. J Phys Chem B 2015; 119:624-32. [DOI: 10.1021/jp510442j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Rivail JL, Monari A, Assfeld X. The Non Empirical Local Self Consistent Field Method: Application to Quantum Mechanics/Molecular Mechanics (QM/MM) Modeling of Large Biomolecular Systems. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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16
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Lundborg M, Lindahl E. Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations. J Phys Chem B 2014; 119:810-23. [PMID: 25343332 DOI: 10.1021/jp505332p] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.
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Affiliation(s)
- Magnus Lundborg
- Department of Theoretical Physics and Swedish e-Science Research Center, Science for Life Laboratory, Royal Institute of Technology , SE-171 21 Solna, Sweden
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17
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A computational study of the dechlorination of β-hexachlorocyclohexane (β-HCH) catalyzed by the haloalkane dehalogenase LinB. Arch Biochem Biophys 2014; 562:43-50. [DOI: 10.1016/j.abb.2014.07.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 11/24/2022]
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18
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Vilseck J, Tirado-Rives J, Jorgensen WL. Evaluation of CM5 Charges for Condensed-Phase Modeling. J Chem Theory Comput 2014; 10:2802-2812. [PMID: 25061445 PMCID: PMC4095915 DOI: 10.1021/ct500016d] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Indexed: 11/30/2022]
Abstract
The recently developed Charge Model 5 (CM5) is tested for its utility in condensed-phase simulations. The CM5 approach, which derives partial atomic charges from Hirshfeld population analyses, provides excellent results for gas-phase dipole moments and is applicable to all elements of the periodic table. Herein, the adequacy of scaled CM5 charges for use in modeling aqueous solutions has been evaluated by computing free energies of hydration (ΔGhyd) for 42 neutral organic molecules via Monte Carlo statistical mechanics. An optimal scaling factor for the CM5 charges was determined to be 1.27, resulting in a mean unsigned error (MUE) of 1.1 kcal/mol for the free energies of hydration. Testing for an additional 20 molecules gave an MUE of 1.3 kcal/mol. The high precision of the results is confirmed by free energy calculations using both sequential perturbations and complete molecular annihilation. Performance for specific functional groups is discussed; sulfur-containing molecules yield the largest errors. In addition, the scaling factor of 1.27 is shown to be appropriate for CM5 charges derived from a variety of density functional methods and basis sets. Though the average errors from the 1.27*CM5 results are only slightly lower than those using 1.14*CM1A charges, the broader applicability and easier access to CM5 charges via the Gaussian program are additional attractive features. The 1.27*CM5 charge model can be used for an enormous variety of applications in conjunction with many fixed-charge force fields and molecular modeling programs.
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Affiliation(s)
- Jonah
Z. Vilseck
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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19
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Yang X, Xue Y. Medium Effects on the 1,3-Dipolar Cycloaddition of Pyridazinium Dicyanomethanide with Ethyl Vinyl Ketone in Pure and Mixed Solvents from QM/MM Simulations. J Org Chem 2014; 79:4863-70. [DOI: 10.1021/jo500184f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xin Yang
- College of Chemistry, Key
Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Ying Xue
- College of Chemistry, Key
Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People’s Republic of China
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Gao JY, Xue Y, Kim CK. Mechanism for the decomposition of 5-aza-2′-deoxycytidine: a theoretical study using Monte Carlo simulation plus local microhydration model. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1462-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Boulanger E, Thiel W. Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field. J Chem Theory Comput 2014; 10:1795-809. [DOI: 10.1021/ct401095k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eliot Boulanger
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
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22
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Acevedo O, Jorgensen WL. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014; 4:422-435. [PMID: 25431625 DOI: 10.1002/wcms.1180] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A recent review (Acc. Chem. Res. 2010, 43:142-151) examined our use and development of a combined quantum and molecular mechanical (QM/MM) technique for modelling organic and enzymatic reactions. Advances included the PDDG/PM3 semiempirical QM (SQM) method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo simulations, and a polynomial quadrature method for rapidly treating proton-transfer reactions. The current article serves as a follow up on our progress. Highlights include new reactions, alternative SQM methods, a polarizable OPLS force field, and novel solvent environments, e.g., "on water" and room temperature ionic liquids. The methodology is strikingly accurate across a wide range of condensed-phase and antibody-catalyzed reactions including substitution, decarboxylation, elimination, isomerization, and pericyclic classes. Comparisons are made to systems treated with continuum-based solvents and ab initio or density functional theory (DFT) methods. Overall, the QM/MM methodology provides detailed characterization of reaction paths, proper configurational sampling, several advantages over implicit solvent models, and a reasonable computational cost.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Wiliiam L Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
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23
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Kozlowski D, Pilmé J, Fleurat-Lessard P. Using the unusual weak N…CO bond as a solvation probe. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.842995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- David Kozlowski
- Laboratoire de Chimie, UMR CNRS 5182, École Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon Cedex 7, France
| | - Julien Pilmé
- Laboratoire de Chimie Théorique, UPMC Univ Paris 06 and CNRS, UMR 7616, F-75005, Paris, France
| | - Paul Fleurat-Lessard
- Laboratoire de Chimie, UMR CNRS 5182, École Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon Cedex 7, France
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24
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Yang X, Xue Y. QM/MM investigation on 1,3-dipolar cycloadditions of the phthalazinium dicyanomethanide with three different dipolarophiles on water and in solution. Phys Chem Chem Phys 2013; 15:11846-55. [PMID: 23760163 DOI: 10.1039/c3cp51048d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
An "on water" environment, describing the reactions with insoluble reactants in water, has been reported to give high yields of products compared to organic solvents. The 1,3-dipolar cycloadditions of phthalazinium dicyanomethanide 1 with three different dipolarophiles, methyl vinyl ketone (MVK), methyl acrylate (MAC), and styrene (STY), have been investigated using QM/MM calculations in water, acetonitrile, and acetonitrile-water solvent mixtures, as well as at the vacuum-water interface. Monte Carlo statistical mechanics simulations utilizing the free-energy perturbation theory and PDDG/PM3 for the QM method have been used. The transition structures for all three reactions do not show large variations among different solvents. However, the calculated free energies of activation at the interface are found to be higher than those calculated in bulk water. Computed energy pair distributions and radial distribution functions reveal a uniform loss of hydrogen bonds for the reactants and transitions states in progressing from bulk water to the vacuum-water interface. The hydrophobic effects in the reactions of 1 with MVK and MAC are similar for both, and weaker than the effect in the reaction with STY. According to the results in water-acetonitrile mixtures at different molar ratios, it is clear that the special hydrogen bonding effects are the main reason which leads to the rapid rate enhancement in progressing from a water-acetonitrile molar ratio of 0.9 : 0.1 to pure water. New insights into solvent effects for 1,3-dipolar cycloadditions are presented herein.
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Affiliation(s)
- Xin Yang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China
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25
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Nawaz H, Pires PAR, El Seoud OA. Kinetics and mechanism of imidazole-catalyzed acylation of cellulose in LiCl/N,N-dimethylacetamide. Carbohydr Polym 2013; 92:997-1005. [DOI: 10.1016/j.carbpol.2012.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 10/02/2012] [Accepted: 10/04/2012] [Indexed: 11/15/2022]
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26
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Sparta M, Shirvanyants D, Ding F, Dokholyan NV, Alexandrova AN. Hybrid dynamics simulation engine for metalloproteins. Biophys J 2013; 103:767-76. [PMID: 22947938 DOI: 10.1016/j.bpj.2012.06.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 06/08/2012] [Accepted: 06/18/2012] [Indexed: 11/15/2022] Open
Abstract
Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins' structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca(2+) form of the enzyme catechol O-methyl transferase, which, unlike the native Mg(2+) form, is catalytically inactive. The Mg(2+) site is ochtahedral, but the Ca(2+) is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight.
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Affiliation(s)
- Manuel Sparta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
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27
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Allen C, Sambasivarao SV, Acevedo O. An ionic liquid dependent mechanism for base catalyzed β-elimination reactions from QM/MM simulations. J Am Chem Soc 2013; 135:1065-72. [PMID: 23273322 DOI: 10.1021/ja3098614] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ionic liquids have been proposed to induce a mechanistic change in the reaction pathway for the fundamentally important base-induced β-elimination class compared to conventional solvents. The role of the reaction medium in the elimination of 1,1,1-tribromo-2,2-bis(3,4-dimethoxyphenyl)ethane via two bases, piperidine and pyrrolidine, has been computationally investigated using methanol and the ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate and hexafluorophosphate [BMIM][BF(4)] and [BMIM][PF(6)], respectively. QM/MM Monte Carlo simulations utilizing free-energy perturbation theory found the ionic liquids did produce a reaction pathway change from an E1cB-like mechanism in methanol to a pure E2 route that is consistent with experimental observations. The origin of the ionic liquid effect has been found as: (1) a combination of favorable electrostatic interactions, for example, bromine-imidazolium ion, and (2) π-π interactions that enhance the coplanarity between aromatic rings maximizing the electronic effects exerted on the reaction route. Solute-solvent interaction energies have been analyzed and show that liquid clathrate solvation of the transition state is primarily responsible for the observed mechanistic changes. This work provides the first theoretical evidence of an ionic liquid dependent mechanism and elucidates the interplay between sterics and electrostatics crucial to understanding the effect of these unique solvents upon chemical reactions.
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Affiliation(s)
- Caley Allen
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
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28
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Kaweetirawatt T, Yamaguchi T, Higashiyama T, Sumimoto M, Hori K. Theoretical study of keto-enol tautomerism by quantum mechanical calculations (the QM/MC/FEP method). J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.2944] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Thanayuth Kaweetirawatt
- Ube Technical Center (Asia) Co., Ltd; 140/8 Moo4, Tambol Tapong Muang Rayong Rayong 21000 Thailand
- Graduate School of Science and Engineering; Yamaguchi University; 2-16-1 Tokiwadai Ube Yamaguchi 755-8611 Japan
| | - Toru Yamaguchi
- Graduate School of Science and Engineering; Yamaguchi University; 2-16-1 Tokiwadai Ube Yamaguchi 755-8611 Japan
| | - Tsutomu Higashiyama
- Nissan Chemical Industries Ltd; 722-1 Tsuboi Cho Funabashi Shi Chiba 274-8507 Japan
| | - Michinori Sumimoto
- Graduate School of Science and Engineering; Yamaguchi University; 2-16-1 Tokiwadai Ube Yamaguchi 755-8611 Japan
| | - Kenji Hori
- Graduate School of Science and Engineering; Yamaguchi University; 2-16-1 Tokiwadai Ube Yamaguchi 755-8611 Japan
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29
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Theoretical study of the hydrolysis of ethyl benzoate in acidic aqueous solution using the QM/MC/FEP method. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Theoretical studies on the chemical decomposition of 5-aza-2′-deoxycytidine: DFT study and Monte Carlo simulation. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1108-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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31
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Caleman C, van Maaren PJ, Hong M, Hub JS, Costa LT, van der Spoel D. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant. J Chem Theory Comput 2012; 8:61-74. [PMID: 22241968 PMCID: PMC3254193 DOI: 10.1021/ct200731v] [Citation(s) in RCA: 463] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Indexed: 12/15/2022]
Abstract
The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.
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Affiliation(s)
- Carl Caleman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron Notkestraße 85, DE-22607 Hamburg, Germany
| | - Paul J. van Maaren
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Minyan Hong
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Jochen S. Hub
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Luciano T. Costa
- Departamento de Ciências Exatas, Federal University of Alfenas—MG Rua Gabriel Monteiro da Silva, 700 Alfenas—MG CEP:37130-000, Brazil
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
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32
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Vilseck JZ, Sambasivarao SV, Acevedo O. Optimal scaling factors for CM1 and CM3 atomic charges in RM1‐based aqueous simulations. J Comput Chem 2011; 32:2836-42. [DOI: 10.1002/jcc.21863] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 05/04/2011] [Accepted: 05/15/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Jonah Z. Vilseck
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | | | - Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
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33
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Chen ZQ, Zhang CH, Kim CK, Xue Y. Quantum mechanics study and Monte Carlo simulation on the hydrolytic deamination of 5-methylcytosine glycol. Phys Chem Chem Phys 2011; 13:6471-83. [PMID: 21380473 DOI: 10.1039/c0cp02783a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The efficient formation of 5-methylcytosine glycol (mCg) and its facile deamination to thymine glycol (Tg) may account for the prevalent C → T transition mutation found at methylated CpG site (mCpG) in human p53 gene, a hallmark for many types of human tumors. In this work, the hydrolytic deamination of mCg was investigated at the MP2 and B3LYP levels of theory using the 6-311G(d,p) basis set. In the gas phase, three pathways were explored, paths A-C, and it indicates that the direct deamination of mCg with H(2)O by either pathway is unlikely because of the high activation free energies involved in the rate-determining steps, the formation of the tetrahedral intermediate for paths A and B as well as the formation of the Tg tautomer for path C. In aqueous solution, the role of the water molecules in the deamination of mCg with H(2)O was analyzed in two separate parts: the direct participation of one water molecule in the reaction pathway, called the water-assisted mechanism; and the complementary participation of the aqueous solvation. The water-assisted mechanism was carried out for mCg and the cluster of two water molecules by quantum mechanical calculations in the gas phase. This indicates that the presence of the auxiliary water molecule significantly contributes to decreasing all the activation free energies. The bulk solution effect on the water-assisted mechanism was included by free energy perturbation implemented on Monte Carlo simulations, which is found to be substantial and decisive in the deamination mechanism of mCg. In this case, the water-assisted path A is the most plausible mechanism reported for the deamination of mCg, where the calculated activation free energy (22.6 kcal mol(-1) at B3LYP level of theory) agrees well with the experimentally determined activation free energy (24.8 kcal mol(-1)). The main striking results of the present DFT computational study which is in agreement with previous experimental data is the higher rate of deamination displayed by mCg residues with respect to 5-methylcytosine (mC) bases, which supports that the deamination of mCg contributes significantly to the C → T transition mutation at mCpG dinucleotide site.
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Affiliation(s)
- Ze Qin Chen
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China
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34
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Hori K, Yamaguchi T, Uezu K, Sumimoto M. A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent-dependent reactions. J Comput Chem 2010; 32:778-86. [DOI: 10.1002/jcc.21653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 07/28/2010] [Accepted: 07/30/2010] [Indexed: 11/09/2022]
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35
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Kostal J, Jorgensen WL. Thorpe-Ingold acceleration of oxirane formation is mostly a solvent effect. J Am Chem Soc 2010; 132:8766-73. [PMID: 20524660 PMCID: PMC2892976 DOI: 10.1021/ja1023755] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Thorpe-Ingold hypothesis for the gem-dimethyl effect in the cyclization reactions of 2-chloroethoxide derivatives has been investigated computationally in the gas phase and in aqueous solution. Ab initio MP2/6-311+G(d,p) and CBS-Q calculations reveal little intrinsic difference in reactivity with increasing alpha-methylation for the series of reactants 1-3. However, inclusion of continuum hydration or of explicit hydration through mixed quantum and statistical mechanics (MC/FEP) simulations does reproduce the substantial, experimentally observed rate increases with increasing alpha-methylation. Analysis of the MC/FEP results provides clear evidence that the rate increases stem primarily from increased steric hindrance to hydration of the nucleophilic oxygen atom with increasing alpha-methylation. Thus, the gem-dimethyl acceleration of oxirane formation for 1-3 is found to be predominantly a solvent effect.
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Affiliation(s)
- Jakub Kostal
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520-8107
| | - William L. Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520-8107
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36
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Acevedo O, Jorgensen WL. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Acc Chem Res 2010; 43:142-51. [PMID: 19728702 DOI: 10.1021/ar900171c] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Application of combined quantum and molecular mechanical (QM/MM) methods focuses on predicting activation barriers and the structures of stationary points for organic and enzymatic reactions. Characterization of the factors that stabilize transition structures in solution and in enzyme active sites provides a basis for design and optimization of catalysts. Continued technological advances allowed for expansion from prototypical cases to mechanistic studies featuring detailed enzyme and condensed-phase environments with full integration of the QM calculations and configurational sampling. This required improved algorithms featuring fast QM methods, advances in computing changes in free energies including free-energy perturbation (FEP) calculations, and enhanced configurational sampling. In particular, the present Account highlights development of the PDDG/PM3 semi-empirical QM method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo (MC) simulations, and a polynomial quadrature method for efficient modeling of proton-transfer reactions. The utility of this QM/MM/MC/FEP methodology is illustrated for a variety of organic reactions including substitution, decarboxylation, elimination, and pericyclic reactions. A comparison to experimental kinetic results on medium effects has verified the accuracy of the QM/MM approach in the full range of solvents from hydrocarbons to water to ionic liquids. Corresponding results from ab initio and density functional theory (DFT) methods with continuum-based treatments of solvation reveal deficiencies, particularly for protic solvents. Also summarized in this Account are three specific QM/MM applications to biomolecular systems: (1) a recent study that clarified the mechanism for the reaction of 2-pyrone derivatives catalyzed by macrophomate synthase as a tandem Michael-aldol sequence rather than a Diels-Alder reaction, (2) elucidation of the mechanism of action of fatty acid amide hydrolase (FAAH), an unusual Ser-Ser-Lys proteolytic enzyme, and (3) the construction of enzymes for Kemp elimination of 5-nitrobenzisoxazole that highlights the utility of QM/MM in the design of artificial enzymes.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - William L. Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
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37
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Rane SS, Anderson BD. Molecular dynamics simulations of functional group effects on solvation thermodynamics of model solutes in decane and tricaprylin. Mol Pharm 2009; 5:1023-36. [PMID: 19434921 DOI: 10.1021/mp8000606] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Triglycerides and related fatty acid esters constitute a large percentage of the lipid excipients employed in the development of lipid-based drug formulations. Computer simulations can provide useful information on the structural, dynamic, and thermodynamic properties of these systems and may ultimately be valuable in predicting relative drug solubilities in lipid vehicles. This study utilized all-atom molecular dynamics simulations to explore the solvation of several model solutes in lipid vehicles. First, a combined thermodynamic perturbation and integration approach was employed to calculate functional group contributions to the free energy of transfer from n-decane to tricaprylin for a set of polar substituents attached to the 9-position of anthracene. A scaling factor of 0.79 for all atomic charges in the dry lipid (where the unscaled charges were obtained at the level of the HF/6-31G* basis set) was necessary in order to match the calculated group contributions to the free energies of transfer with their experimental values at 37 degrees C. A second set of simulations was performed in water-saturated tricaprylin containing a single molecule of benzamide to explore the state of organization of solvent molecules, the distribution of water molecules, and the local environment surrounding the solute. Radial distribution functions revealed evidence of local structure in the liquid triglyceride. The dissolved water was found to exist approximately 50% as monomers and 50% as self-associated species. Substantial hydrogen-bonding of benzamide with ester carbonyl oxygen atoms was observed.
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Affiliation(s)
- Sagar S Rane
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
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Sheppard AN, Acevedo O. Multidimensional Exploration of Valley−Ridge Inflection Points on Potential-Energy Surfaces. J Am Chem Soc 2009; 131:2530-40. [DOI: 10.1021/ja803879k] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- April N. Sheppard
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
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Wallin G, Nervall M, Carlsson J, Åqvist J. Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method. J Chem Theory Comput 2009; 5:380-95. [DOI: 10.1021/ct800404f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Göran Wallin
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Martin Nervall
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Jens Carlsson
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
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40
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Benighaus T, Thiel W. Efficiency and Accuracy of the Generalized Solvent Boundary Potential for Hybrid QM/MM Simulations: Implementation for Semiempirical Hamiltonians. J Chem Theory Comput 2008; 4:1600-9. [DOI: 10.1021/ct800193a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tobias Benighaus
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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41
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Woods CJ, Manby FR, Mulholland AJ. An efficient method for the calculation of quantum mechanics/molecular mechanics free energies. J Chem Phys 2008; 128:014109. [DOI: 10.1063/1.2805379] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Lodola A, Woods CJ, Mulholland AJ. Applications and Advances of QM/MM Methods in Computational Enzymology. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2008. [DOI: 10.1016/s1574-1400(08)00009-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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43
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Acevedo O, Squillacote ME. A New Solvent-Dependent Mechanism for a Triazolinedione Ene Reaction. J Org Chem 2007; 73:912-22. [DOI: 10.1021/jo7022153] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
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44
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Chuev GN, Fedorov MV, Crain J. Improved estimates for hydration free energy obtained by the reference interaction site model. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.10.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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45
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Li QS, Fang WH, Yu JG. Theoretical studies of proton-transfer reactions of 2-hydroxypyridine--(H2O)n (n = 0-2) in the ground and excited states. J Phys Chem A 2007; 109:3983-90. [PMID: 16833720 DOI: 10.1021/jp044498t] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The potential energy profiles for proton-transfer reactions of 2-hydroxypyridine and its complexes with water were determined by MP2, CASSCF and MR-CI calculations with the 6-31G** basis set. The tautomerization reaction between 2-hydroxypyridine (2HP) and 2-pyridone (2PY) does not take place at room temperature because of a barrier of approximately 35 kcal/mol for the ground-state pathway. The water-catalyzed enol-keto tautomerization reactions in the ground state proceed easily through the concerted proton transfer, especially for the two-water complex. The S1 tautomerization between the 2HP and 2PY monomers has a barrier of 18.4 kcal/mol, which is reduced to 5.6 kcal/mol for the one-water complex and 6.4 kcal/mol for the two-water complex. The results reported here predict that the photoinduced tautomerization reaction between the enol and keto forms involves a cyclic transition state having one or two water molecules as a bridge.
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Affiliation(s)
- Quan-Song Li
- Department of Chemistry, Beijing Normal University, Beijing 100875, PR China
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46
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Acevedo O, Jorgensen WL. Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations. J Org Chem 2007; 71:4896-902. [PMID: 16776519 DOI: 10.1021/jo060533b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The decarboxylation of imidazolidin-2-one-1-carboxylate anion 2 has been investigated via combined quantum and statistical mechanics methodology. Monte Carlo statistical mechanics simulations utilizing free-energy perturbation theory and PDDG/PM3 for the QM method yielded free-energy profiles for the reaction in water, methanol, acetonitrile, and mixed solvents. The results for free energies of activation are uniformly in close accord with experimental data and reflect large rate accelerations in progressing from protic to dipolar aprotic media. Structural and energetic analyses confirm that the rate retardation in protic solvents comes from loss of hydrogen bonding in progressing from the carboxylate anion 2 to the more charge-delocalized transition state (TS). The structure of the TS is found to be significantly affected by the reaction medium; it occurs at a 0.2-A shorter C-N separation in protic solvents than in acetonitrile. Characterization of the hydrogen bonding for 2 and the TS also provided insights for design of decarboxylase catalysts, namely, it is desirable to have three hydrogen-bond donating groups positioned to interact with the ureido oxygen along with two hydrogen-bond donors positioned to interact with the ureido nitrogen of the breaking C-N bond.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, USA
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Acevedo O, Jorgensen WL. Understanding Rate Accelerations for Diels−Alder Reactions in Solution Using Enhanced QM/MM Methodology. J Chem Theory Comput 2007; 3:1412-9. [DOI: 10.1021/ct700078b] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, and Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
| | - William L. Jorgensen
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, and Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
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48
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Zhang Y, Lin H, Truhlar DG. Self-Consistent Polarization of the Boundary in the Redistributed Charge and Dipole Scheme for Combined Quantum-Mechanical and Molecular-Mechanical Calculations. J Chem Theory Comput 2007; 3:1378-98. [DOI: 10.1021/ct7000107] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan Zhang
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Hai Lin
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Chemistry Department, University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80217-3364, and Chemistry Department and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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49
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Nagy PI, Alagona G, Ghio C. Theoretical Investigation of Tautomeric Equilibria for Isonicotinic Acid, 4-Pyridone, and Acetylacetone in Vacuo and in Solution. J Chem Theory Comput 2007; 3:1249-66. [DOI: 10.1021/ct6002252] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter I. Nagy
- Department of Medicinal and Biological Chemistry and Center for Drug Design and Development, The University of Toledo, Toledo, Ohio 43606-3390, and CNR-IPCF, Institute for Physico-Chemical Processes, Molecular Modeling Lab, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Giuliano Alagona
- Department of Medicinal and Biological Chemistry and Center for Drug Design and Development, The University of Toledo, Toledo, Ohio 43606-3390, and CNR-IPCF, Institute for Physico-Chemical Processes, Molecular Modeling Lab, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Caterina Ghio
- Department of Medicinal and Biological Chemistry and Center for Drug Design and Development, The University of Toledo, Toledo, Ohio 43606-3390, and CNR-IPCF, Institute for Physico-Chemical Processes, Molecular Modeling Lab, Via Moruzzi 1, I-56124 Pisa, Italy
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50
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Wu Y, Xue Y, Xie DQ, Kim CK, Yan GS. Theoretical Studies on the Hydrolysis Mechanism of N-(2-oxo-1,2-dihydro-pyrimidinyl) Formamide. J Phys Chem B 2007; 111:2357-64. [PMID: 17295531 DOI: 10.1021/jp064510c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Density functional theory (B3LYP) and ab initio (MP2) methods with the 6-31G(d,p) basis set are used to study the mechanisms for the hydrolysis of N-(2-oxo-1,2-dihydro-pyrimidinyl) formamide (PFA) in the gas phase. The direct and the water-assisted hydrolysis processes are considered, involving one and two water molecules, respectively. Three different pathways are explored in each case. In the first pathway, the O atom of water first attacks at the C atom of amide while one H atom of water transfers toward the oxygen of amide, leading to an intermediate of tetrahedral coordinated carbon with two OH groups. In the subsequent step, the hydroxyl H atom transfers to the N atom of pyrimidine ring and the C-N covalent bond of amide dissociates simultaneously. In the second path, the O and one H of water attack at the C of amide and the N of pyrimidine ring, respectively, while the C-N bond of amide dissociates. In the third path, three processes occur simultaneously: the O of water attacks at the C of amide, one H atom attacks at the N of amide, and the C-N bond of amide is broken. It is shown that the second pathway is favored for the direct hydrolysis while the first pathway is favored for the water-assisted hydrolysis. It is also shown that the water-assisted hydrolysis is slightly more favorable than the direct hydrolysis. Moreover, solvent effects on five pathways are evaluated with Monte Carlo simulation (MC) and free energy perturbation methods. It is shown that the solvent water slightly reduces the energy barrier in each pathway. The first pathway in the water-assisted hydrolysis remains the most favorable when the solvent effects of bulk water are taken into account.
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Affiliation(s)
- Yong Wu
- College of Chemistry, Key Lab of Green Chemistry and Technology, Sichuan University, Chengdu 610064, People's Republic of China
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