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Semelak JA, Zeida A, Foglia NO, Estrin DA. Minimum Free Energy Pathways of Reactive Processes with Nudged Elastic Bands. J Chem Theory Comput 2023; 19:6273-6293. [PMID: 37647166 DOI: 10.1021/acs.jctc.3c00366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The determination of minimum free energy pathways (MFEP) is one of the most widely used strategies to study reactive processes. For chemical reactions in complex environments, the combination of quantum mechanics (QM) with a molecular mechanics (MM) representation is usually necessary in a hybrid QM/MM framework. However, even within the QM/MM approximation, the affordable sampling of the phase space is, in general, quite restricted. To reduce drastically the computational cost of the simulations, several methods such as umbrella sampling require performing a priori a selection of a reaction coordinate. The quality of the computed results, in an affordable computational time, is intimately related to the reaction coordinate election which is, in general, a nontrivial task. In this work, we provide an approach to model reactive processes in complex environments that does not require the a priori selection of a reaction coordinate. The proposed methodology combines QM/MM simulations with an extrapolation of the nudged elastic bands (NEB) method to the free energy surface (FENEB). We present and apply our own FENEB scheme to optimize MFEP in different reactive processes, using QM/MM frameworks at semiempirical and density functional theory levels. Our implementation is based on performing the FENEB optimization by uncoupling the optimization of the band in a perpendicular and tangential direction. In each step, a full optimization with the spring force is performed, which guarantees that the images remain evenly distributed. The robustness of the method and the influence of sampling on the quality of the optimized MFEP and its associated free energy barrier are studied. We show that the FENEB method provides a good estimation of the reaction barrier even with relatively short simulation times, supporting that its combination with QM/MM frameworks provides an adequate tool to study chemical processes in complex environments.
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Affiliation(s)
- Jonathan A Semelak
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Nicolás O Foglia
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
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2
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Daniyan MO, Ojo OT. In silico identification and evaluation of potential interaction of Azadirachta indica phytochemicals with Plasmodium falciparum heat shock protein 90. J Mol Graph Model 2019; 87:144-164. [DOI: 10.1016/j.jmgm.2018.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/31/2018] [Accepted: 11/30/2018] [Indexed: 01/13/2023]
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3
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Marion A, Gokcan H, Monard G. Semi-Empirical Born-Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package. J Chem Inf Model 2019; 59:206-214. [PMID: 30433776 DOI: 10.1021/acs.jcim.8b00605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Semi-empirical quantum methods from the neglect of differential diatomic overlap (NDDO) family such as MNDO, AM1, or PM3 are fast albeit approximate quantum methods. By combining them with linear scaling methods like the divide & conquer (D&C) method, it is possible to quickly evaluate the energy of systems containing hundreds to thousands of atoms. We here present our implementation in the Amber biomolecular package of a SEBOMD module that provides a way to run semi-empirical Born-Oppenheimer molecular dynamics. At each step of a SEBOMD, a fully converged self-consistent field (SCF) calculation is performed to obtain the semiempirical quantum potential energy of a molecular system encaged or not in periodic boundary conditions. We describe the implementation and the features of our SEBOMD implementation. We show the requirements to conserve the total energy in NVE simulations, and how to accelerate SCF convergence through density matrix extrapolation. Specific ways of handling periodic boundary conditions using mechanical embedding or electrostatic embedding through a tailored quantum Ewald summation is developed. The parallel performance of SEBOMD simulations using the D&C scheme are presented for liquid water systems of various sizes, and a comparison between the traditional full diagonalization scheme and the D&C approach for the reproduction of the structure of liquid water illustrates the potentiality of SEBOMD to simulate molecular systems containing several hundreds of atoms for hundreds of picoseconds with a quantum mechanical potential in a reasonable amount of CPU time.
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Affiliation(s)
- Antoine Marion
- Université de Lorraine, CNRS, LPCT , F-54000 Nancy , France.,Department of Chemistry , Middle East Technical University , 06800 , Ankara , Turkey
| | - Hatice Gokcan
- Université de Lorraine, CNRS, LPCT , F-54000 Nancy , France.,Department of Chemistry , University of North Texas , Denton , Texas 76201 , United States
| | - Gerald Monard
- Université de Lorraine, CNRS, LPCT , F-54000 Nancy , France
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Bai X, Yan L, Ji C, Zhang Q, Dong X, Chen A, Zhao M. A combination of ternary classification models and reporter gene assays for the comprehensive thyroid hormone disruption profiles of 209 polychlorinated biphenyls. CHEMOSPHERE 2018; 210:312-319. [PMID: 30005353 DOI: 10.1016/j.chemosphere.2018.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/24/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
Computational toxicology is widely applied to screen tens and thousands of potential environmental endocrine disruptors (EDCs) for its great efficiency and rapid evaluation in recent years. Polychlorinated biphenyls (PCBs) with 209 congeners have not been comprehensively tested for their ability to interact with the thyroid receptor (TR), which is one of the most extensively studied targets related to the effects of EDCs. In this study, we aimed to determine the thyroid-disrupting mechanisms of 209 PCBs through the combination of a novel computational ternary classification model and luciferase reporter gene assay. The reporter gene assay was performed to examine the hormone activities of 22 PCBs via TR to classify their profiles as agonistic, antagonistic or inactive. Thus, six agonists, eleven antagonists and seven inactive chemicals against TR were identified in in vitro assays. Then, six relevant variables, including molecular structural descriptors and molecular docking scores, were selected for describing compounds. Machine learning methods (i.e., linear discriminant analysis (LDA) and support vector machines (SVM)) were used to build classification models. The optimal model was obtained by using SVM, with an accuracy of 88.24% in the training set, 80.0% in the test set and 75.0% in 10-fold cross-validation. The remaining 187 PCB congeners' hormone activities were predicted using the obtained models. Out of these PCBs, the SVM model predicted 38 agonists and 81 antagonists. The findings revealed that higher chlorinated PCBs tended to have TR-antagonistic activities, whereas lower chlorinated PCBs were agonists. This study provided a reference for further exploring PCBs' thyroid effect.
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Affiliation(s)
- Xiaoxia Bai
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
| | - Lu Yan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310032, China
| | - Chenyang Ji
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310032, China
| | - Quan Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310032, China
| | - Xiaowu Dong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - An Chen
- College of Information Engineering, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Meirong Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310032, China.
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Šebesta F, Brela MZ, Diaz S, Miranda S, Murray JS, Gutiérrez-Oliva S, Toro-Labbé A, Michalak A, Burda JV. The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study. J Comput Chem 2017; 38:2680-2692. [PMID: 28925001 DOI: 10.1002/jcc.24911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/09/2017] [Accepted: 07/18/2017] [Indexed: 11/11/2022]
Abstract
This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+ , Zn2+ , and Hg2+ . Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 112 16, Czech Republic
| | - Mateusz Z Brela
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Silvia Diaz
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Sebastian Miranda
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, 70148
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Artur Michalak
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 112 16, Czech Republic
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Martins-Costa MTC, Ruiz-López MF. Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling. J Comput Chem 2017; 38:659-668. [PMID: 28093779 DOI: 10.1002/jcc.24723] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/14/2016] [Accepted: 12/19/2016] [Indexed: 12/27/2022]
Abstract
We report an enhanced sampling technique that allows to reach the multi-nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid-vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall-clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Marilia T C Martins-Costa
- SRSMC, Faculté des Sciences et Technologies, University of Lorraine, CNRS, BP 70236, 54506 Vandoeuvre-lès-Nancy, France
| | - Manuel F Ruiz-López
- SRSMC, Faculté des Sciences et Technologies, University of Lorraine, CNRS, BP 70236, 54506 Vandoeuvre-lès-Nancy, France
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7
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Schwörer M, Wichmann C, Tavan P. A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water. J Chem Phys 2016; 144:114504. [PMID: 27004884 DOI: 10.1063/1.4943972] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.
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Affiliation(s)
- Magnus Schwörer
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Christoph Wichmann
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Paul Tavan
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
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8
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Zheng M, Waller MP. Adaptive quantum mechanics/molecular mechanics methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1255] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Min Zheng
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation; Westfälische Wilhelms-Universität Münster; 48149 Münster, Germany
| | - Mark P. Waller
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation; Westfälische Wilhelms-Universität Münster; 48149 Münster, Germany
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9
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Structure of hydrogen tetroxide in gas phase and in aqueous environments: relationship to the hydroperoxyl radical self-reaction. Struct Chem 2015. [DOI: 10.1007/s11224-015-0717-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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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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Marion A, Monard G, Ruiz-López MF, Ingrosso F. Water interactions with hydrophobic groups: assessment and recalibration of semiempirical molecular orbital methods. J Chem Phys 2015; 141:034106. [PMID: 25053300 DOI: 10.1063/1.4886655] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.
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Affiliation(s)
- Antoine Marion
- Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
| | - Gérald Monard
- Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
| | | | - Francesca Ingrosso
- Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
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Free Energy Gradient Method and Its Recent Related Developments: Free Energy Optimization and Vibrational Frequency Analysis in Solution. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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König G, Hudson PS, Boresch S, Woodcock HL. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes. J Chem Theory Comput 2014; 10:1406-1419. [PMID: 24803863 PMCID: PMC3985817 DOI: 10.1021/ct401118k] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Indexed: 11/28/2022]
Abstract
![]()
The reliability of free energy simulations
(FES) is limited by
two factors: (a) the need for correct sampling and (b) the accuracy
of the computational method employed. Classical methods (e.g., force
fields) are typically used for FES and present a myriad of challenges,
with parametrization being a principle one. On the other hand, parameter-free
quantum mechanical (QM) methods tend to be too computationally expensive
for adequate sampling. One widely used approach is a combination of
methods, where the free energy difference between the two end states
is computed by, e.g., molecular mechanics (MM), and the end states
are corrected by more accurate methods, such as QM or hybrid QM/MM
techniques. Here we report two new approaches that significantly improve
the aforementioned scheme; with a focus on how to compute corrections
between, e.g., the MM and the more accurate QM calculations. First,
a molecular dynamics trajectory that properly samples relevant conformational
degrees of freedom is generated. Next, potential energies of each
trajectory frame are generated with a QM or QM/MM Hamiltonian. Free
energy differences are then calculated based on the QM or QM/MM energies
using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann
free energy perturbation (NB-FEP). Both approaches are applied to
calculate relative and absolute solvation free energies in explicit
and implicit solvent environments. Solvation free energy differences
(relative and absolute) between ethane and methanol in explicit solvent
are used as the initial test case for QM-NBB. Next, implicit solvent
methods are employed in conjunction with both QM-NBB and NB-FEP to
compute absolute solvation free energies for 21 compounds. These compounds
range from small molecules such as ethane and methanol to fairly large,
flexible solutes, such as triacetyl glycerol. Several technical aspects
were investigated. Ultimately some best practices are suggested for
improving methods that seek to connect MM to QM (or QM/MM) levels
of theory in FES.
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Affiliation(s)
- Gerhard König
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Phillip S Hudson
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - Stefan Boresch
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna , Währingerstraße 17, A-1090 Vienna, Austria
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
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Lonsdale R, Harvey JN, Mulholland AJ. Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions. J Chem Theory Comput 2012; 8:4637-45. [PMID: 26605619 DOI: 10.1021/ct300329h] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory (DFT) based quantum mechanical/molecular mechanical (QM/MM) calculations have provided valuable insight into the reactivity of the cytochrome P450 family of enzymes (P450s). A failure of commonly used DFT methods, such as B3LYP, is the neglect of dispersion interactions. An empirical dispersion correction has been shown to improve the accuracy of gas phase DFT calculations of P450s. The current work examines the effect of the dispersion correction in QM/MM calculations on P450s. The hydrogen abstraction from camphor, and hydrogen abstraction and C-O addition of cyclohexene and propene by P450cam have been modeled, along with the addition of benzene to Compound I in CYP2C9, at the B3LYP-D2/CHARMM27 level of theory. Single point energy calculations were also performed at the B3LYP-D3//B3LYP-D2/CHARMM27 level. The dispersion corrections lower activation energy barriers significantly (by ∼5 kcal/mol), as seen for gas phase calculations, but has a small effect on optimized geometries.These effects are likely to be important in modeling reactions catalyzed by other enzymes also. Given the low computational cost of including such dispersion corrections, we recommend doing so in all B3LYP based QM/MM calculations.
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Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Jeremy N Harvey
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
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Takenaka N, Kitamura Y, Koyano Y, Nagaoka M. An improvement in quantum mechanical description of solute-solvent interactions in condensed systems via the number-adaptive multiscale quantum mechanical/molecular mechanical-molecular dynamics method: Application to zwitterionic glycine in aqueous solution. J Chem Phys 2012; 137:024501. [DOI: 10.1063/1.4732307] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Takenaka N, Kitamura Y, Koyano Y, Nagaoka M. The number-adaptive multiscale QM/MM molecular dynamics simulation: Application to liquid water. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.12.053] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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17
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Koyano Y, Takenaka N, Nakagawa Y, Nagaoka M. An optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework. J Comput Chem 2010; 31:2628-41. [DOI: 10.1002/jcc.21558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Koyano Y, Takenaka N, Nakagawa Y, Nagaoka M. On the Importance of Lennard–Jones Parameter Calibration in QM/MM Framework: Reaction Path Tracing via Free Energy Gradient Method for Ammonia Ionization Process in Aqueous Solution. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20090296] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Poully JC, Grégoire G, Schermann JP. Evaluation of the ONIOM Method for Interpretation of Infrared Spectra of Gas-Phase Molecules of Biological Interest. J Phys Chem A 2009; 113:8020-6. [DOI: 10.1021/jp901696d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jean-Christophe Poully
- Laboratoire de Physique des Lasers, UMR 7538 CNRS, Université Paris 13, 93430 Villetaneuse, France
| | - Gilles Grégoire
- Laboratoire de Physique des Lasers, UMR 7538 CNRS, Université Paris 13, 93430 Villetaneuse, France
| | - Jean-Pierre Schermann
- Laboratoire de Physique des Lasers, UMR 7538 CNRS, Université Paris 13, 93430 Villetaneuse, France
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20
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Senthilkumar K, Mujika JI, Ranaghan KE, Manby FR, Mulholland AJ, Harvey JN. Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds. J R Soc Interface 2009; 5 Suppl 3:S207-16. [PMID: 18782723 DOI: 10.1098/rsif.2008.0243.focus] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly important for the study of chemical reactions and systems in condensed phases. Here, we have tested the accuracy of a density functional theory-based QM/MM implementation (B3LYP/6-311+G(d,p)/CHARMM27) on a set of biologically relevant interactions by comparison with full QM calculations. Intermolecular charge transfer due to hydrogen bond formation is studied to assess the severity of spurious polarization of QM atoms by MM point charges close to the QM/MM boundary. The changes in total electron density and natural bond orbital atomic charges due to hydrogen bond formation in selected complexes obtained at the QM/MM level are compared with full QM results. It is found that charge leakage from the QM atoms to MM atomic point charges close to the QM/MM boundary is not a serious problem, at least with limited basis sets. The results are encouraging in showing that important properties of key biomolecular interactions can be treated well at the QM/MM level employing good-quality levels of QM theory.
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Affiliation(s)
- Kittusamy Senthilkumar
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, UK
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21
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Pentikäinen U, Shaw KE, Senthilkumar K, Woods CJ, Mulholland AJ. Lennard−Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid Bases. J Chem Theory Comput 2009; 5:396-410. [DOI: 10.1021/ct800135k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ulla Pentikäinen
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Katherine E. Shaw
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Kittusamy Senthilkumar
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Christopher J. Woods
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock‘s Close, Bristol BS8 1TS, United Kingdom, and Department of Biological and Environmental Science and NanoScience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
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22
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Forti F, Barril X, Luque FJ, Orozco M. Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian. J Comput Chem 2008; 29:578-87. [PMID: 17705247 DOI: 10.1002/jcc.20814] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The need to simulate large-sized molecules or to deal with large series of compounds is a challenging topic in computational chemistry, which has stimulated the development of accurate semiempirical methods, such as the recently reported Recife Model 1 (RM1; J Comput Chem 2006, 27, 1101). Even though RM1 may prove to be of value simply due to the enhanced quantitative accuracy in gas phase, it is unclear how the new parameters optimized for RM1 affect the suitability of this semiempirical Hamiltonian to study chemical processes in condensed phases. To address this question, we report the parametrization of the MST/RM1 continuum model for neutral solutes in water, octanol, chloroform and carbon tetrachloride, and for ions in water. The results are used to discuss the transferability of the solvation parameters implemented in previous MST/AM1 and MST/PM3 models.
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Affiliation(s)
- Flavio Forti
- Facultat de Farmàcia, Departament de Fisicoquímica and Institut de Biomedicina, Universitat de Barcelona, Av. Diagonal 643, E-08028, Barcelona, Spain
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23
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Giese TJ, York DM. Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations. J Chem Phys 2008; 127:194101. [PMID: 18035873 DOI: 10.1063/1.2778428] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This work explores a new charge-dependent energy model consisting of van der Waals and polarization interactions between the quantum mechanical (QM) and molecular mechanical (MM) regions in a combined QMMM calculation. van der Waals interactions are commonly treated using empirical Lennard-Jones potentials, whose parameters are often chosen based on the QM atom type (e.g., based on hybridization or specific covalent bonding environment). This strategy for determination of QMMM nonbonding interactions becomes tedious to parametrize and lacks robust transferability. Problems occur in the study of chemical reactions where the "atom type" is a complex function of the reaction coordinate. This is particularly problematic for reactions, where atoms or localized functional groups undergo changes in charge state and hybridization. In the present work we propose a new model for nonelectrostatic nonbonded interactions in QMMM calculations that overcomes many of these problems. The model is based on a scaled overlap model for repulsive exchange and attractive dispersion interactions that is a function of atomic charge. The model is chemically significant since it properly correlates atomic size, softness, polarizability, and dispersion terms with minimal one-body parameters that are functions of the atomic charge. Tests of the model are examined for rare-gas interactions with neutral and charged atoms in order to demonstrate improved transferability. The present work provides a new framework for modeling QMMM interactions with improved accuracy and transferability.
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Affiliation(s)
- Timothy J Giese
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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24
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Tuttle T, Thiel W. OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application. Phys Chem Chem Phys 2008; 10:2159-66. [DOI: 10.1039/b718795e] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Geerke DP, Thiel S, Thiel W, van Gunsteren WF. QM–MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians. Phys Chem Chem Phys 2008; 10:297-302. [DOI: 10.1039/b713197f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Woodcock HL, Hodošček M, Gilbert ATB, Gill PMW, Schaefer HF, Brooks BR. Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. J Comput Chem 2007; 28:1485-1502. [PMID: 17334987 DOI: 10.1002/jcc.20587] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (i.e., parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster. To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments. For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O...H2O, H2O...Na+, and H2O...Cl- complexes have been explored. Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations. We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies. Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory.
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Affiliation(s)
- H Lee Woodcock
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Milan Hodošček
- Center for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Andrew T B Gilbert
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia
| | - Peter M W Gill
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia
| | - Henry F Schaefer
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-2556
| | - Bernard R Brooks
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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27
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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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28
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Nagaoka M, Nagae Y, Koyano Y, Oishi Y. Transition-State Characterization of the Ammonia Ionization Process in Aqueous Solution via the Free-Energy Gradient Method. J Phys Chem A 2006; 110:4555-63. [PMID: 16571063 DOI: 10.1021/jp056115c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For the ionization process of ammonia in aqueous solution, the transition-state (TS) structure was fully optimized for the first time on the free-energy surface (FES) by applying the free-energy gradient (FEG) method combined with a hybrid quantum mechanical and molecular mechanical molecular dynamics (QM/MM-MD) method. In aqueous solution, the ionization process was found to proceed by way of a clear TS (R(N1-H5) = 1.512 A), which does not exist in the gas phase. The free-energy (FE) of activation for ionization obtained was 14.7 kcal/mol, within the classical approximation, via the QM/MM-MD FEG method, and is found to be in good agreement with 9.57 kcal/mol estimated from the TS theory using the experimental value of the rate constant. Apart from the dynamic correction, it is indicated that the theoretical value would be improved to be 10.28 kcal/mol if the electronic-state calculation could be executed at the B3LYP/6-31G(d) level of theory.
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Affiliation(s)
- Masataka Nagaoka
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
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29
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Villar R, Gil MJ, García JI, Martínez-Merino V. Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs? J Comput Chem 2005; 26:1347-58. [PMID: 16021597 DOI: 10.1002/jcc.20276] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have examined the performance of semiempirical quantum mechanical methods in solving the problem of accurately predicting protein-ligand binding energies and geometries. Firstly, AM1 and PM3 geometries and binding enthalpies between small molecules that simulate typical ligand-protein interactions were compared with high level quantum mechanical techniques that include electronic correlation (e.g., MP2 or B3LYP). Species studied include alkanes, aromatic systems, molecules including groups with hypervalent sulfur or with donor or acceptor hydrogen bonding capability, as well as ammonium or carboxylate ions. B3LYP/6-311+G(2d,p) binding energies correlated very well with the BSSE corrected MP2/6-31G(d) values. AM1 binding enthalpies also showed good correlation with MP2 values, and their systematic deviation is acceptable when enthalpies are used for the comparison of interaction energies between ligands and a target. PM3 otherwise gave erratic energy differences in comparison to the B3LYP or MP2 approaches. As one would expect, the geometries of the binding complexes showed the known limitations of the semiempirical and DFT methods. AM1 calculations were subsequently applied to a test set consisting of "real" protein active site-ligand complexes. Preliminary results indicate that AM1 could be a valuable tool for the design of new drugs using proteins as templates. This approach also has a reasonable computational cost. The ligand-protein X-ray structures were reasonably reproduced by AM1 calculations and the corresponding AM1 binding enthalpies are in agreement with the results from the "small molecules" test set.
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Affiliation(s)
- R Villar
- Dep. Química Aplicada, Universidad Pública de Navarra, Campus Arrosadía, E-31006 Pamplona, Spain
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30
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Freindorf M, Shao Y, Furlani TR, Kong J. Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential. J Comput Chem 2005; 26:1270-8. [PMID: 15965971 DOI: 10.1002/jcc.20264] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechanical (MM) part of the system, described by the AMBER force field. The Lennard-Jones parameters for this potential are obtained by calculating hydrogen bond energies and hydrogen bond geometries for a large set of bimolecular systems, in which one hydrogen bond monomer is described quantum mechanically and the other is treated molecular mechanically. We have investigated more than 100 different bimolecular systems, finding very good agreement between hydrogen bond energies and geometries obtained from the combined QM/MM calculations and results obtained at the QM level of theory, especially with respect to geometry. Therefore, based on the Lennard-Jones parameters obtained in our study, we anticipate that the B3LYP/6-31+G*/AMBER potential will be a precise tool to explore intermolecular interactions inside a protein environment.
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Affiliation(s)
- Marek Freindorf
- Center for Computational Research, The State University of New York at Buffalo, Buffalo, NY 14260, USA.
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31
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Sagarik K, Chaiyapongs S. Structures and stability of salt-bridge in aqueous solution. Biophys Chem 2005; 117:119-40. [PMID: 15935545 DOI: 10.1016/j.bpc.2005.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2005] [Revised: 04/22/2005] [Accepted: 04/21/2005] [Indexed: 11/29/2022]
Abstract
Structures and stability of salt-bridges in aqueous solutions were investigated using a complex formed from the guanidinium (Gdm+) and formate (FmO-) ions as a model system. The Test-particle model (T-model) potentials to describe the interactions in the Gdm+-H2O, FmO(-)-H2O and Gdm+-FmO- complexes were constructed, tested and applied in molecular dynamics (MD) simulations of the aqueous solutions at 298 K. The three-dimensional structures and energetic of the hydrogen bond (H-bond) networks of water in the first hydration shells of the Gdm+ and FmO- ions, as well as the Gdm+-FmO- complex, were visualized and analyzed using various probability distribution (PD) maps. The structures of the average potential energy landscapes at the H-bond networks were employed to characterize the stability and dynamic behavior of water molecules in the first hydration shells of the solutes. It was observed that water molecules in the first hydration shell of the close-contact Gdm+-FmO- complex form associated H-bond networks, which introduce a net stabilization effect to the ion-pair, whereas those in the interstitial H-bond network destabilize and break the solvent-separated Gdm+-FmO- complex. The present results showed that, in order to provide complete insights into the structures and stability of ion-pairs in aqueous solutions, explicit water molecules have to be included in the model calculations.
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Affiliation(s)
- Kritsana Sagarik
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
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32
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Range K, Riccardi D, Cui Q, Elstner M, York DM. Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer. Phys Chem Chem Phys 2005; 7:3070-9. [PMID: 16186912 DOI: 10.1039/b504941e] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Benchmark calculations of proton affinities and gas-phase basicities of molecules most relevant to biological phosphoryl transfer reactions are presented and compared with available experimental results. The accuracy of proton affinity and gas-phase basicity results obtained from several multi-level model chemistries (CBS-QB3, G3B3, and G3MP2B3) and density-functional quantum models (PBE0, B1B95, and B3LYP) are assessed and compared. From these data, a set of empirical bond enthalpy, entropy, and free energy corrections are introduced that considerably improve the accuracy and predictive capability of the methods. These corrections are applied to the prediction of proton affinity and gas-phase basicity values of important biological phosphates and phosphoranes for which experimental data does not currently exist. Comparison is made with results from semiempirical quantum models that are commonly employed in hybrid quantum mechanical/molecular mechanical simulations. Data suggest that the design of improved semiempirical quantum models with increased accuracy for relative proton affinity values is necessary to obtain quantitative accuracy for phosphoryl transfer reactions in solution, enzymes, and ribozymes.
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Affiliation(s)
- Kevin Range
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455-0431, USA
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33
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Cummins PL, Gready JE. Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation. J Comput Chem 2005; 26:561-8. [PMID: 15726569 DOI: 10.1002/jcc.20192] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We describe a coupling parameter, that is, perturbation, approach to effectively create and annihilate atoms in the quantum mechanical Hamiltonian within the closed shell restricted Hartree-Fock formalism. This perturbed quantum mechanical atom (PQA) method is combined with molecular mechanics (MM) methods (PQA/MM) within a molecular dynamics simulation, to model the protein environment (MM region) effects that also make a contribution to the overall free energy change. Using the semiempirical PM3 method to model the QM region, the application of this PQA/MM method is illustrated by calculation of the relative protonation free energy of the conserved OD2 (Asp27) and the N5 (dihydrofolate) proton acceptor sites in the active site of Escherichia coli dihydrofolate reductase (DHFR) with the bound nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. For a number of choices for the QM region, the relative protonation free energy was calculated as the sum of contributions from the QM region and the interaction between the QM and MM regions via the thermodynamic integration (TI) method. The results demonstrate the importance of including the whole substrate molecule in the QM region, and the overall protein (MM) environment in determining the relative stabilities of protonation sites in the enzyme active site. The PQA/MM free energies obtained by TI were also compared with those estimated by a less computationally demanding nonperturbative method based on the linear response approximation (LRA). For some choices of QM region, the total free energies calculated using the LRA method were in very close agreement with the PQA/MM values. However, the QM and QM/MM component free energies were found to differ significantly between the two methods.
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Affiliation(s)
- Peter L Cummins
- Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
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34
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Tubert-Brohman I, Guimarães CRW, Repasky MP, Jorgensen WL. Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens. J Comput Chem 2004; 25:138-50. [PMID: 14635001 DOI: 10.1002/jcc.10356] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The new semiempirical methods, PDDG/PM3 and PDDG/MNDO, have been parameterized for halogens. For comparison, the original MNDO and PM3 were also reoptimized for the halogens using the same training set; these modified methods are referred to as MNDO' and PM3'. For 442 halogen-containing molecules, the smallest mean absolute error (MAE) in heats of formation is obtained with PDDG/PM3 (5.6 kcal/mol), followed by PM3' (6.1 kcal/mol), PDDG/MNDO (6.6 kcal/mol), PM3 (8.1 kcal/mol), MNDO' (8.5 kcal/mol), AM1 (11.1 kcal/mol), and MNDO (14.0 kcal/mol). For normal-valent halogen-containing molecules, the PDDG methods also provide improved heats of formation over MNDO/d. Hypervalent compounds were not included in the training set and improvements over the standard NDDO methods with sp basis sets were not obtained. For small haloalkanes, the PDDG methods yield more accurate heats of formation than are obtained from density functional theory (DFT) with the B3LYP and B3PW91 functionals using large basis sets. PDDG/PM3 and PM3' also give improved binding energies over the standard NDDO methods for complexes involving halide anions, and they are competitive with B3LYP/6-311++G(d,p) results including thermal corrections. Among the semiempirical methods studied, PDDG/PM3 also generates the best agreement with high-level ab initio G2 and CCSD(T) intrinsic activation energies for S(N)2 reactions involving methyl halides and halide anions. Finally, the MAEs in ionization potentials, dipole moments, and molecular geometries show that the parameter sets for the PDDG and reoptimized NDDO methods reduce the MAEs in heats of formation without compromising the other important QM observables.
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Affiliation(s)
- Ivan Tubert-Brohman
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520, USA
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35
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Loferer MJ, Loeffler HH, Liedl KR. A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems. J Comput Chem 2003; 24:1240-9. [PMID: 12820132 DOI: 10.1002/jcc.10283] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.
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Affiliation(s)
- Markus J Loferer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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36
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Balcells D, Drudis-Solé G, Besora M, Dölker N, Ujaque G, Maseras F, Lledós A. Some critical issues in the application of quantum mechanics/molecular mechanics methods to the study of transition metal complexes. Faraday Discuss 2003; 124:429-41; discussion 443-55. [PMID: 14527230 DOI: 10.1039/b211473a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of quantum mechanics/molecular mechanics (QM/MM) methods in transition metal chemistry is growing steadily. It becomes therefore appropriate to assess the importance of a number of technical issues associated to their implementation. This work presents the discussion of several of these issues, including the eventual need for conformational searches, the choice of the MM force field and the possibility of its tuning. The examples presented here prove that a proper handling of these technical aspects can lead to an improvement in the efficiency and quality of QM/MM calculations.
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Affiliation(s)
- David Balcells
- Unitat de Química Física, Edifici Cn, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
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Titmuss SJ, Cummins PL, Rendell AP, Bliznyuk AA, Gready JE. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis. J Comput Chem 2002; 23:1314-22. [PMID: 12214314 DOI: 10.1002/jcc.10122] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.
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Affiliation(s)
- Stephen J Titmuss
- Computational Proteomics and Therapy Design Group, Division of Biochemistry and Molecular Biology, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra, ACT 2601, Australia
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An iterative procedure to determine Lennard-Jones parameters for their use in quantum mechanics/molecular mechanics liquid state simulations. Chem Phys 2002. [DOI: 10.1016/s0301-0104(02)00785-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Cummins PL, Greatbanks SP, Rendell AP, Gready JE. Computational Methods for the Study of Enzymic Reaction Mechanisms. 1. Application to the Hydride Transfer Step in the Catalysis of Dihydrofolate Reductase. J Phys Chem B 2002. [DOI: 10.1021/jp021070q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter L. Cummins
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Stephen P. Greatbanks
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Alistair P. Rendell
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
| | - Jill E. Gready
- Computational Proteomics and Therapy Design Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia, and Department of Computer Science, Faculty of Engineering and Information Technology, Australian National University, P.O. Box 334, Canberra ACT 2601, Australia
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Laio A, VandeVondele J, Rothlisberger U. A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations. J Chem Phys 2002. [DOI: 10.1063/1.1462041] [Citation(s) in RCA: 521] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hirao H, Nagae Y, Nagaoka M. Transition-state optimization by the free energy gradient method: Application to aqueous-phase Menshutkin reaction between ammonia and methyl chloride. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)01131-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Gogonea V, Suárez D, van der Vaart A, Merz KM. New developments in applying quantum mechanics to proteins. Curr Opin Struct Biol 2001; 11:217-23. [PMID: 11297931 DOI: 10.1016/s0959-440x(00)00193-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Algorithmic improvements of quantum mechanical methodologies have increased our ability to study the electronic structure of fragments of a biomolecule (e.g. an enzyme active site) or entire biomolecules. Three main strategies have emerged as ways in which quantum mechanics can be applied to biomolecules. The supermolecule approach continues to be utilized, but it is slowly being replaced by the so-called coupled quantum mechanical/molecular mechanical methodologies. An exciting new direction is the continued development and application of linear-scaling quantum mechanical approaches to biomolecular systems.
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Affiliation(s)
- V Gogonea
- Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
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