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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Matsuoka W, Harabuchi Y, Maeda S. Virtual Ligand-Assisted Screening Strategy to Discover Enabling Ligands for Transition Metal Catalysis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wataru Matsuoka
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido 001-0021, Japan
- ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0044, Japan
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3
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Gallmetzer HG, Hofer TS. Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches. J Comput Chem 2022; 43:746-756. [PMID: 35239208 PMCID: PMC9314059 DOI: 10.1002/jcc.26830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/21/2022]
Abstract
Optimized link bond parameters for the Cα—Cβ bond of 22 different capped amino acid model systems have been determined at SCC DFTB/mio (self‐consistent charge density functional tight‐binding), SCC DFTB/3ob and GFNn‐xTB (n = 0, 1, and 2) level in conjunction with the AMBER 99SB, 14SB, and 19B force fields. The resulting parameter sets have been compared to newly calculated reference data obtained via resolution‐of‐identity 2nd order Møller–Plesset perturbation theory. The data collected in this work suggests that the optimized values in this study provide a more suitable setup of the QM/MM link bonds compared to the use of a single global setting applied to every amino acid fragmented by the QM/MM interface. The results also imply that a transfer of the ideal link bond settings between different levels of theory is not advised. In contrast, virtually identical parameters were obtained in calculations employing different variants of the AMBER force field. Considering the increasing success of tight binding based approaches being inter alia a results of their exceptional accuracy/effort ratio the provided collection of link atoms parameters provides a valuable resource for QM/MM studies of biomacromolecular systems as demonstrated in an exemplary QM/MM MD simulation of the β‐amyloid/Zn2+ complex.
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Affiliation(s)
- Hans Georg Gallmetzer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innsbruck, Austria
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innsbruck, Austria
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Treß RS, Hättig C, Höfener S. Employing Pseudopotentials to Tackle Excited-State Electron Spill-Out in Frozen Density Embedding Calculations. J Chem Theory Comput 2022; 18:1737-1747. [PMID: 35107998 DOI: 10.1021/acs.jctc.1c00732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In frozen density embedding (FDE), the properties of a target molecule are computed in the presence of an effective embedding potential, which accounts for the attractive and repulsive contributions of the environment. The formally exact embedding potential, however, is in practice calculated using explicit kinetic-energy functionals for which the resulting potentials are in many cases not repulsive enough to account fully for Pauli repulsion by the electrons of the environment and to compensate thereby the strong electron-nuclear attraction. For the excited states on the target molecule, this leads to charge spill-out when diffuse basis functions are included, which allow that valence electrons are excited to those regions of the environment where the strong nuclear attraction is not sufficiently compensated by repulsive contributions. To reduce this insufficiency, we propose in the present work the inclusion of atomic all-electron pseudopotentials for all environment atoms on top of the conventional embedding potential. In the current work, the pseudopotentials are applied for computing vertical excitation energies of local excited states in complex systems employing the second-order algebraic diagrammatic construction (ADC(2)) scheme. The proposed approach leads to significantly reduced charge spill-out and an improved agreement of FDE and supermolecular calculations in the frozen solvent approximation. In particular, when diffuse functions are employed, the mean absolute deviation (MAD) is reduced from 0.27 to 0.05 eV for the investigated cases.
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Affiliation(s)
- Robert S Treß
- Department of Theoretical Chemistry, Ruhr University Bochum, Bochum 44801, Germany
| | - Christof Hättig
- Department of Theoretical Chemistry, Ruhr University Bochum, Bochum 44801, Germany
| | - Sebastian Höfener
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
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5
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Grabarek D, Andruniów T. Removing artifacts in polarizable embedding calculations of one- and two-photon absorption spectra of fluorescent proteins. J Chem Phys 2021; 153:215102. [PMID: 33291919 DOI: 10.1063/5.0023434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The multiscale calculations involving excited states may suffer from the electron spill-out (ESO) problem. This seems to be especially the case when the environment of the core region, described with the electronic structure method, is approximated by a polarizable force field. The ESO effect often leads to incorrect physical character of electronic excitations, spreading outside the quantum region, which, in turn, results in erroneous absorption spectra. In this work, we investigate means to remove the artifacts in one-photon absorption (OPA) and two-photon absorption (TPA) spectra of green and yellow fluorescent protein representatives. This includes (i) using different basis sets, (ii) extending the core subsystem beyond the chromophore, (iii) modification of polarization interaction between the core region and its environment, and (iv) including the Pauli repulsion through effective core potentials (ECPs). Our results clearly show that ESO is observed when diffuse functions are used to assemble the multielectron wave function regardless of the exchange-correlation functional used. Furthermore, extending the core region, thus accounting for exchange interactions between the chromophore and its environment, leads to even more spurious excited states. Also, damping the interactions between the core subsystem and the polarizable force field is hardly helpful. In contrast, placing ECPs in the position of sites creating the embedding potential leads to the removal of artificious excited states that presumably should not be observed in the OPA and TPA spectra. We prove that it is a reliable and cost-effective approach for systems where the covalent bond(s) between the core region and its environment must be cut.
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Affiliation(s)
- Dawid Grabarek
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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6
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Mehmood R, Kulik HJ. Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase. J Chem Theory Comput 2020; 16:3121-3134. [PMID: 32243149 DOI: 10.1021/acs.jctc.0c00153] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Quantum-mechanical/molecular-mechanical (QM/MM) methods are essential to the study of metalloproteins, but the relative importance of sampling and degree of QM treatment in achieving quantitative predictions is poorly understood. We study the relative magnitude of configurational and QM-region sensitivity of energetic and electronic properties in a representative Zn2+ metal binding site of a DNA methyltransferase. To quantify property variations, we analyze snapshots extracted from 250 ns of molecular dynamics simulation. To understand the degree of QM-region sensitivity, we perform analysis using QM regions ranging from a minimal 49-atom region consisting only of the Zn2+ metal and its four coordinating Cys residues up to a 628-atom QM region that includes residues within 12 Å of the metal center. Over the configurations sampled, we observe that illustrative properties (e.g., rigid Zn2+ removal energy) exhibit large fluctuations that are well captured with even minimal QM regions. Nevertheless, for both energetic and electronic properties, we observe a slow approach to asymptotic limits with similarly large changes in absolute values that converge only with larger (ca. 300-atom) QM region sizes. For the smaller QM regions, the electronic description of Zn2+ binding is incomplete: the metal binds too tightly and is too stabilized by the strong electrostatic potential of MM point charges, and the Zn-S bond covalency is overestimated. Overall, this work suggests that efficient sampling with QM/MM in small QM regions is an effective method to explore the influence of enzyme structure on target properties. At the same time, accurate descriptions of electronic and energetic properties require a larger QM region than the minimal metal-coordinating residues in order to converge treatment of both metal-local bonding and the overall electrostatic environment.
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Affiliation(s)
- Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Marefat Khah A, Reinholdt P, Olsen JMH, Kongsted J, Hättig C. Avoiding Electron Spill-Out in QM/MM Calculations on Excited States with Simple Pseudopotentials. J Chem Theory Comput 2020; 16:1373-1381. [PMID: 32031806 DOI: 10.1021/acs.jctc.9b01162] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
QM/MM calculations of electronic excitations with diffuse basis sets often have large errors due to spill-out of electrons from the quantum subsystem. The Pauli repulsion of the electrons by the environment has to be included to avoid this. We propose transferable atomic all-electron pseudopotentials that can readily be combined with most MM force fields to avoid electron spill-out. QM/MM excitation energies computed with time-dependent Hartree-Fock and the algebraic diagrammatic construction through second-order are benchmarked against supermolecular calculations to validate these new pseudopotentials. The QM/MM calculations with pseudopotentials give accurate results that are stable with augmentation of the basis set with diffuse functions. We show that the largest contribution to residual deviations from full QM calculations is caused by the missing London dispersion interaction.
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Affiliation(s)
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Christof Hättig
- Quantum Chemistry Group, Ruhr University of Bochum, D-44801 Bochum, Germany
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8
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Yang Z, Mehmood R, Wang M, Qi HW, Steeves AH, Kulik HJ. Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation. REACT CHEM ENG 2019; 4:298-315. [PMID: 31572618 PMCID: PMC6768422 DOI: 10.1039/c8re00213d] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mengyi Wang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Helena W. Qi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Adam H. Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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9
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Kulik HJ. Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer. Phys Chem Chem Phys 2018; 20:20650-20660. [PMID: 30059109 PMCID: PMC6085747 DOI: 10.1039/c8cp03871f] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations provide key insights into enzyme structure-function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temperature properties with electrostatic embedding QM/MM. However, it is not well known if ab initio QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estimations that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-separated hybrid density functional theory free energy simulations in a representative methyltransferase. By studying 200 ps of ab initio QM/MM dynamics for each of five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify critical differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that important aspects of enzymatic rate enhancement in methyltransferases are identified with large-scale electronic structure.
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Affiliation(s)
- Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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10
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Karelina M, Kulik HJ. Systematic Quantum Mechanical Region Determination in QM/MM Simulation. J Chem Theory Comput 2017; 13:563-576. [DOI: 10.1021/acs.jctc.6b01049] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maria Karelina
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Kulik H, Zhang J, Klinman J, Martínez TJ. How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase. J Phys Chem B 2016; 120:11381-11394. [PMID: 27704827 PMCID: PMC5108028 DOI: 10.1021/acs.jpcb.6b07814] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/09/2016] [Indexed: 01/29/2023]
Abstract
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in studies of enzymatic catalysis. Until recently, it has been cost prohibitive to determine the asymptotic limit of key energetic and structural properties with respect to increasingly large QM regions. Leveraging recent advances in electronic structure efficiency and accuracy, we investigate catalytic properties in catechol O-methyltransferase, a prototypical methyltransferase critical to human health. Using QM regions ranging in size from reactants-only (64 atoms) to nearly one-third of the entire protein (940 atoms), we show that properties such as the activation energy approach within chemical accuracy of the large-QM asymptotic limits rather slowly, requiring approximately 500-600 atoms if the QM residues are chosen simply by distance from the substrate. This slow approach to asymptotic limit is due to charge transfer from protein residues to the reacting substrates. Our large QM/MM calculations enable identification of charge separation for fragments in the transition state as a key component of enzymatic methyl transfer rate enhancement. We introduce charge shift analysis that reveals the minimum number of protein residues (approximately 11-16 residues or 200-300 atoms for COMT) needed for quantitative agreement with large-QM simulations. The identified residues are not those that would be typically selected using criteria such as chemical intuition or proximity. These results provide a recipe for a more careful determination of QM region sizes in future QM/MM studies of enzymes.
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Affiliation(s)
- Heather
J. Kulik
- Department
of Chemistry and PULSE Institute, Stanford
University, Stanford, California 94305, United States
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jianyu Zhang
- Departments
of Chemistry and of Molecular and Cell Biology, and California Institute
for Quantitative Biosciences, University
of California, Berkeley, California 94720, United States
| | - Judith
P. Klinman
- Departments
of Chemistry and of Molecular and Cell Biology, and California Institute
for Quantitative Biosciences, University
of California, Berkeley, California 94720, United States
| | - Todd J. Martínez
- Department
of Chemistry and PULSE Institute, Stanford
University, Stanford, California 94305, United States
- SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
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12
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Affiliation(s)
- Xiaolei Zhu
- Department of Chemistry, Johns Hopkins University Baltimore, MD, USA
| | - David R. Yarkony
- Department of Chemistry, Johns Hopkins University Baltimore, MD, USA
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13
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Kratz EG, Walker AR, Lagardère L, Lipparini F, Piquemal JP, Cisneros GA. LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. J Comput Chem 2016; 37:1019-29. [PMID: 26781073 PMCID: PMC4808410 DOI: 10.1002/jcc.24295] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/21/2015] [Accepted: 12/17/2015] [Indexed: 12/23/2022]
Abstract
We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.
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14
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Liu L, Cui G, Fang WH. Excited States and Photochemistry of Chromophores in the Photoactive Proteins Explored by the Combined Quantum Mechanical and Molecular Mechanical Calculations. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 100:255-84. [PMID: 26415847 DOI: 10.1016/bs.apcsb.2015.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A photoactive protein usually contains a unique chromophore that is responsible for the initial photoresponse and functions of the photoactive protein are determined by the interaction between the chromophore and its protein surroundings. The combined quantum mechanical and molecular mechanical (QM/MM) approach is demonstrated to be a very useful tool for exploring structures and functions of a photoactive protein with the chromophore and its protein surroundings treated by the QM and MM methods, respectively. In this review, we summarize the basic formulas of the QM/MM approach and emphasize its applications to excited states and photoreactions of chromophores in rhodopsin protein, photoactive yellow protein, and green fluorescent protein.
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Affiliation(s)
- Lihong Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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15
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Song C, Wang LP, Sachse T, Preiß J, Presselt M, Martínez TJ. Efficient implementation of effective core potential integrals and gradients on graphical processing units. J Chem Phys 2015; 143:014114. [DOI: 10.1063/1.4922844] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chenchen Song
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Lee-Ping Wang
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Torsten Sachse
- Institute for Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Julia Preiß
- Institute for Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Martin Presselt
- Institute for Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
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16
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 743] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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17
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Zhang Z, Xu L, Wang G, Shao C, Jiang L. The development and validation of a pseudoatoms approach for combined quantum mechanics and molecular mechanics calculations of polypeptide. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Steric and electrostatic effects on photoisomerization dynamics using QM/MM ab initio multiple spawning. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1506-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Pezeshki S, Lin H. Recent developments in QM/MM methods towards open-boundary multi-scale simulations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.911870] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Chaudret R, Parks JM, Yang W. Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs. J Chem Phys 2013; 138:045102. [PMID: 23387624 DOI: 10.1063/1.4772182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In biological systems involving nucleosides, nucleotides, or their respective analogs, the ribose sugar moiety is the most common reaction site, for example, during DNA replication and repair. However, nucleic bases, which comprise a sizable portion of nucleotide molecules, are usually unreactive during such processes. In quantum mechanical∕molecular simulations of nucleic acid reactivity, it may therefore be advantageous to describe specific ribosyl or ribosyl phosphate groups quantum mechanically and their respective nucleic bases with a molecular mechanics potential function. Here, we have extended the pseudobond approach to enable quantum mechanical∕molecular mechanical simulations involving nucleotides, nucleosides, and their analogs in which the interface between the two subsystems is located between the sugar and the base, namely, the C(sp(3))-N(sp(2)) bond. The pseudobond parameters were optimized on a training set of 10 molecules representing several nucleotide and nucleoside bases and analogs, and they were then tested on a larger test set of 20 diverse molecules. Particular emphasis was placed on providing accurate geometries and electrostatic properties, including electrostatic potential, natural bond orbital (NBO) and atoms in molecules (AIM) charges and AIM first moments. We also tested the optimized parameters on five nucleotide and nucleoside analogues of pharmaceutical relevance and a small polypeptide (triglycine). Accuracy was maintained for these systems, which highlights the generality and transferability of the pseudobond approach.
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Affiliation(s)
- Robin Chaudret
- Department of Chemistry, Duke University, 124 Science Drive, 5301 French Science Center, Durham, North Carolina 27708-0346, USA
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21
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Knizia G, Chan GKL. Density Matrix Embedding: A Strong-Coupling Quantum Embedding Theory. J Chem Theory Comput 2013; 9:1428-32. [DOI: 10.1021/ct301044e] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gerald Knizia
- Department of Chemistry, Princeton University, Princeton,
New Jersey 08544, United States
| | - Garnet Kin-Lic Chan
- Department of Chemistry, Princeton University, Princeton,
New Jersey 08544, United States
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22
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Drujon J, Carissan Y. Pseudopotentials for hybridized carbon atoms. J Comput Chem 2013; 34:49-59. [DOI: 10.1002/jcc.23104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 08/10/2012] [Accepted: 08/13/2012] [Indexed: 11/09/2022]
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23
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Plasser F, Aquino AJA, Hase WL, Lischka H. UV Absorption Spectrum of Alternating DNA Duplexes. Analysis of Excitonic and Charge Transfer Interactions. J Phys Chem A 2012; 116:11151-60. [DOI: 10.1021/jp304725r] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Felix Plasser
- Institute of Theoretical
Chemistry, University of Vienna, Währingerstrasse
17, A-1090,
Vienna, Austria
| | - Adelia J. A. Aquino
- Institute
of Soil Research, University of Natural Resources and Life Sciences,
Peter-Jordan-Strasse 82, A-1190, Vienna, Austria
- Department of Chemistry
and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - William L. Hase
- Department of Chemistry
and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Hans Lischka
- Institute of Theoretical
Chemistry, University of Vienna, Währingerstrasse
17, A-1090,
Vienna, Austria
- Department of Chemistry
and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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24
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Affiliation(s)
- David R. Yarkony
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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25
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Svoboda O, Ončák M, Slavíček P. Simulations of light induced processes in water based on ab initio path integrals molecular dynamics. I. Photoabsorption. J Chem Phys 2011; 135:154301. [DOI: 10.1063/1.3649942] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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27
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Dynamic QM/MM: A Hybrid Approach to Simulating Gas-Liquid Interactions. MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY 2011; 307:43-67. [DOI: 10.1007/128_2011_130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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28
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Caricato M, Vreven T, Trucks GW, Frisch MJ. Link atom bond length effect in ONIOM excited state calculations. J Chem Phys 2010; 133:054104. [DOI: 10.1063/1.3474570] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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29
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Maurer P, Iftimie R. Combining ab initio quantum mechanics with a dipole-field model to describe acid dissociation reactions in water: First-principles free energy and entropy calculations. J Chem Phys 2010; 132:074112. [DOI: 10.1063/1.3317398] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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30
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Tu Y, Laaksonen A. Implementing Quantum Mechanics into Molecular Mechanics—Combined QM/MM Modeling Methods. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59001-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Raynaud C, del Rosal I, Jolibois F, Maron L, Poteau R. Multicentered effective group potentials: ligand-field effects in organometallic clusters and dynamical study of chemical reactivity. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0615-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Komin S, Sebastiani D. Optimization of Capping Potentials for Spectroscopic Parameters in Hybrid Quantum Mechanical/Mechanical Modeling Calculations. J Chem Theory Comput 2009; 5:1490-8. [DOI: 10.1021/ct800525u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sittipong Komin
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Sebastiani
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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33
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He J, Di Paola C, Kantorovich L. Partitioning scheme for density functional calculations of extended systems. J Chem Phys 2009; 130:144104. [DOI: 10.1063/1.3106661] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Abstract
Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
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Affiliation(s)
- Hans Martin Senn
- Department of Chemistry, WestCHEM and University of Glasgow, Glasgow G12 8QQ, UK.
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35
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Hu H, Yang W. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. ACTA ACUST UNITED AC 2009; 898:17-30. [PMID: 24146439 DOI: 10.1016/j.theochem.2008.12.025] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes.
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Affiliation(s)
- Hao Hu
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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36
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37
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Virshup AM, Punwong C, Pogorelov TV, Lindquist BA, Ko C, Martínez TJ. Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics. J Phys Chem B 2008; 113:3280-91. [DOI: 10.1021/jp8073464] [Citation(s) in RCA: 247] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aaron M. Virshup
- Center for Biophysics and Computational Biology, Department of Chemistry, and Department of Physics, University of Illinois, Urbana, Illinois, 61801
| | - Chutintorn Punwong
- Center for Biophysics and Computational Biology, Department of Chemistry, and Department of Physics, University of Illinois, Urbana, Illinois, 61801
| | - Taras V. Pogorelov
- Center for Biophysics and Computational Biology, Department of Chemistry, and Department of Physics, University of Illinois, Urbana, Illinois, 61801
| | - Beth A. Lindquist
- Center for Biophysics and Computational Biology, Department of Chemistry, and Department of Physics, University of Illinois, Urbana, Illinois, 61801
| | - Chaehyuk Ko
- Center for Biophysics and Computational Biology, Department of Chemistry, and Department of Physics, University of Illinois, Urbana, Illinois, 61801
| | - Todd J. Martínez
- Center for Biophysics and Computational Biology, Department of Chemistry, and Department of Physics, University of Illinois, Urbana, Illinois, 61801
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38
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Sumner I, Iyengar SS. Combining quantum wavepacketab initiomolecular dynamics with QM/MM and QM/QM techniques: Implementation blendingONIOMand empirical valence bond theory. J Chem Phys 2008; 129:054109. [DOI: 10.1063/1.2956496] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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39
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Huang P, Carter EA. Advances in correlated electronic structure methods for solids, surfaces, and nanostructures. Annu Rev Phys Chem 2008; 59:261-90. [PMID: 18031211 DOI: 10.1146/annurev.physchem.59.032607.093528] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Calculations of the electronic structure of solids began decades ago, but only recently have solid-state quantum techniques become sufficiently reliable that their application is nearly as routine as quantum chemistry is for molecules. We aim to introduce chemists to the pros and cons of first-principles methods that can provide atomic-scale insight into the properties and chemistry of bulk materials, interfaces, and nanostructures. The techniques we review include the ubiquitous density functional theory (DFT), which is often sufficient, especially for metals; extensions such as DFT + U and hybrid DFT, which incorporate exact exchange to rid DFT of its spurious self-interactions (critical for some semiconductors and strongly correlated materials); many-body Green's function (GW and Bethe-Salpeter) methods for excited states; quantum Monte Carlo, in principle an exact theory but for which forces (hence structure optimization and dynamics) are problematic; and embedding theories that locally refine the quantum treatment to improve accuracy.
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Affiliation(s)
- Patrick Huang
- Department of Mechanical and Aerospace Engineering and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544-5263, USA
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40
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Ohnishi YY, Nakao Y, Sato H, Sakaki S. Frontier Orbital Consistent Quantum Capping Potential (FOC-QCP) for Bulky Ligand of Transition Metal Complexes. J Phys Chem A 2008; 112:1946-55. [DOI: 10.1021/jp710310s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-ya Ohnishi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan, and ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraki-cho, Takano, Sakyo-ku, Kyoto 606-8103, Japan
| | - Yoshihide Nakao
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan, and ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraki-cho, Takano, Sakyo-ku, Kyoto 606-8103, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan, and ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraki-cho, Takano, Sakyo-ku, Kyoto 606-8103, Japan
| | - Shigeyoshi Sakaki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan, and ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraki-cho, Takano, Sakyo-ku, Kyoto 606-8103, Japan
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41
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Hu H, Yang W. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu Rev Phys Chem 2008; 59:573-601. [PMID: 18393679 PMCID: PMC3727228 DOI: 10.1146/annurev.physchem.59.032607.093618] [Citation(s) in RCA: 349] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications.
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Affiliation(s)
- Hao Hu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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42
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Xiao C, Zhang Y. Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons. J Chem Phys 2007; 127:124102. [PMID: 17902888 PMCID: PMC2773247 DOI: 10.1063/1.2774980] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A critical issue underlying the accuracy and applicability of the combined quantum mechanical/molecular mechanical (QM/MM) methods is how to describe the QM/MM boundary across covalent bonds. Inspired by the ab initio pseudopotential theory, here we introduce a novel design atom approach for a more fundamental and transparent treatment of this QM/MM covalent boundary problem. The main idea is to replace the boundary atom of the active part with a design atom, which has a different number of valence electrons but very similar atomic properties. By modifying the Troullier-Martins scheme, which has been widely employed to construct norm-conserving pseudopotentials for density functional calculations, we have successfully developed a design-carbon atom with five valence electrons. Tests on a series of molecules yield very good structural and energetic results and indicate its transferability in describing a variety of chemical bonds, including double and triple bonds.
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Affiliation(s)
- Chuanyun Xiao
- Department of Chemistry, New York University, New York, New York 10003, USA
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43
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Poterya V, Profant V, Fárník M, Slavícek P, Buck U. Experimental and theoretical study of the pyrrole cluster photochemistry: Closing the πσ* dissociation pathway by complexation. J Chem Phys 2007; 127:064307. [PMID: 17705596 DOI: 10.1063/1.2754687] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photolysis of size selected pyrrole clusters has been investigated and compared to the photolysis of an isolated pyrrole molecule. Experimentally, size distributions of different mean cluster sizes (n=3 and n>>5) have been prepared in supersonic expansions and the clusters were photolyzed at 243 and 193 nm. The kinetic energy distributions of the H photofragments have been measured. The distributions exhibit a bimodal character with fast and slow H-fragment peaks similar to the spectra of the bare molecule. However, with increasing cluster size the slow component gains intensity with respect to the fast one. A similar effect is observed with increasing the excitation energy from 243 to 193 nm. Theoretical calculations at the CASSCF/CASPT2 level have been performed for bare and complexed pyrroles (pyrrole is complexed with an argon atom and with another pyrrole unit). Combination of theoretical and experimental approaches leads to the conclusion that the direct dissociative pathway along the pisigma* potential energy surface in the N-H stretch coordinate is closed by the presence of the solvent molecule. This pathway is an important channel leading to the fast H atoms in the dissociation of the bare molecule. The solvent molecule influences significantly the electronic structure in the Rydberg-type pisigma* state while it has little influence on the valence states. The slow channel is mostly populated by the out-of-plane deformation mode which is also not influenced by solvation. We have also studied other possible reaction channels in pyrrole clusters (hydrogen transfer, dimerization). The present study shows that more insight into the bulk behavior of biologically relevant molecules can be gained from cluster studies.
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Affiliation(s)
- Viktoriya Poterya
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
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44
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Shao Y, Kong J. YinYang Atom: A Simple Combined ab Initio Quantum Mechanical Molecular Mechanical Model. J Phys Chem A 2007; 111:3661-71. [PMID: 17429951 DOI: 10.1021/jp067307q] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A simple interface is proposed for combined quantum mechanical (QM) molecular mechanical (MM) calculations for the systems where the QM and MM regions are connected through covalent bonds. Within this model, the atom that connects the two regions, called YinYang atom here, serves as an ordinary MM atom to other MM atoms and as a hydrogen-like atom to other QM atoms. Only one new empirical parameter is introduced to adjust the length of the connecting bond and is calibrated with the molecule propanol. This model is tested with the computation of equilibrium geometries and protonation energies for dozens of molecules. Special attention is paid on the influence of MM point charges on optimized geometry and protonation energy, and it is found that it is important to maintain local charge-neutrality in the MM region in order for the accurate calculation of the protonation and deprotonation energies. Overall the simple YinYang atom model yields comparable results to some other QM/MM models.
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Affiliation(s)
- Yihan Shao
- Q-Chem Inc., 5001 Baum Boulevard, Pittsburgh, PA 15213, USA
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