1
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Fedorov DG. Partition analysis of dipole moments in solution applied to functional groups in polypeptide motifs. Phys Chem Chem Phys 2024; 26:18614-18628. [PMID: 38919134 DOI: 10.1039/d4cp01654h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
A partition analysis based on segments is developed for density functional theory defining solute dipole moments of functional groups, and the corresponding induced solvent dipoles representing solvent screening. The accuracy of dipoles from the fragment molecular orbital method is evaluated in comparison to unfragmented values. The analysis is applied to evaluate dipole moments of side chains, amino and carbonyl groups in common polypeptide motifs, α-helixes, β-turns, and random coils in solution. The membrane domain of the ATP synthase (1B9U) is analyzed, revealing the effect of the bend splitting of the α-helix into two pieces.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan.
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2
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Seeber P, Seidenath S, Steinmetzer J, Gräfe S. Growing Spicy
ONIOMs
: Extending and generalizing concepts of
ONIOM
and many body expansions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Phillip Seeber
- Institute of Physical Chemistry Friedrich Schiller University Jena Jena Germany
| | - Sebastian Seidenath
- Institute of Physical Chemistry Friedrich Schiller University Jena Jena Germany
| | | | - Stefanie Gräfe
- Institute of Physical Chemistry Friedrich Schiller University Jena Jena Germany
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3
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Hayakawa D, Terauchi N, Iwasaki A, Watanabe Y, Gouda H. Systematic preparation method of a molecular model explicitly describing electron distributions for halogen bonds. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Hayakawa D, Watanabe Y, Gouda H. Unpolarizable molecular model describing electron distribution for treating halogen bonds. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Devereux M, Pezzella M, Raghunathan S, Meuwly M. Polarizable Multipolar Molecular Dynamics Using Distributed Point Charges. J Chem Theory Comput 2020; 16:7267-7280. [PMID: 33245239 DOI: 10.1021/acs.jctc.0c00883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic integration. Minimal DCM is further developed in a systematic fashion to reduce fitting errors in the electrostatic interaction energy, and a new fragment-based approach offers considerable speedup of the MDCM fitting process for larger molecules with increased numbers of off-centered charged sites. Finally, polarizable (M)DCM is also introduced in the present work. The developments are used in condensed-phase simulations of popular force fields with commonly applied simulation conditions. (M)DCM equivalents for a range of widely used water force fields and for fluorobenzene (PhF) are developed and applied along with the original models to evaluate the impact of reformulating the electrostatic term. Comparisons of the molecular electrostatic potential (MEP), electrostatic interaction energies, and bulk properties from molecular dynamics simulations for a range of models from simple TIPnP (n = 3-5) to the polarizable, multipolar iAMOEBA models for water and an existing quadrupolar model for PhF confirm that DCMs retain the accuracy of the original models, providing a homogeneous, efficient, and generic point charge alternative to a multipolar electrostatic model for force field development and multilevel simulations.
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Affiliation(s)
- Mike Devereux
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Marco Pezzella
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Shampa Raghunathan
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.,Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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6
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Unke OT, Devereux M, Meuwly M. Minimal distributed charges: Multipolar quality at the cost of point charge electrostatics. J Chem Phys 2018; 147:161712. [PMID: 29096479 DOI: 10.1063/1.4993424] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Most empirical force fields use atom-centered point charges (PCs) to represent the electrostatic potential (ESP) around molecules. While such PC models are computationally efficient, they are unable to capture anisotropic electronic features, such as σ holes or lone pairs. These features are better described using atomic multipole (MTP) moments, which significantly improve the quality of the resulting ESP. However, the improvement comes at the expense of a considerably increased computational complexity and cost for calculating the interaction energies and forces. In the present work, a novel minimal distributed charge model (MDCM) based on off-centered point charges is presented and the quality of the resulting ESP is compared to the performance of MTPs and atom-centered PC models for several test molecules. All three models are fitted using the same algorithm based on differential evolution, which is available as a Fortran90 program from the authors upon request. We show that the MDCM is capable of approximating the reference ab initio ESP with an accuracy as good as, or better than, MTPs without the need for computationally expensive higher order multipoles. Further it is demonstrated that the MDCM is numerically stable in molecular dynamics simulations and is able to reproduce electrostatic interaction energies and thermodynamic quantities with the same accuracy as MTPs at reduced computational cost.
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Affiliation(s)
- Oliver T Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Mike Devereux
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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7
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Duan JX, Zhou Y, Xie ZZ, Sun TL, Cao J. Incorporating spin–orbit effects into surface hopping dynamics using the diagonal representation: a linear-response time-dependent density functional theory implementation with applications to 2-thiouracil. Phys Chem Chem Phys 2018; 20:15445-15454. [DOI: 10.1039/c8cp01852a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Evaluation of SOC values employs Casida's wave functions and the Breit–Pauli spin–orbit Hamiltonian with effective charge approximation.
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Affiliation(s)
- Jun-Xin Duan
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan
- P. R. China
| | - Yun Zhou
- Guizhou Provincial Key Laboratory of Computational Nano-material Science
- Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology
- Guizhou Normal College
- Guiyang
- China
| | - Zhi-Zhong Xie
- Department of Chemistry
- School of Chemistry
- Chemical Engineering and Life Sciences
- Wuhan University of Technology
- Wuhan 430070
| | - Tao-Lei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan
- P. R. China
| | - Jun Cao
- Guizhou Provincial Key Laboratory of Computational Nano-material Science
- Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology
- Guizhou Normal College
- Guiyang
- China
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8
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Wu X, Teuler JM, Cailliez F, Clavaguéra C, Salahub DR, de la Lande A. Simulating Electron Dynamics in Polarizable Environments. J Chem Theory Comput 2017; 13:3985-4002. [DOI: 10.1021/acs.jctc.7b00251] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaojing Wu
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Jean-Marie Teuler
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Fabien Cailliez
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Carine Clavaguéra
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Dennis R. Salahub
- Department
of Chemistry, Centre for Molecular Simulation, Institute for Quantum
Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
- College
of Chemistry and Chemical Engineering, Henan University of Technology, No. 100, Lian Hua Street, High-Tech Development Zone, Zhengzhou 450001, P. R. China
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
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9
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Kratz EG, Duke RE, Cisneros GA. Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations. Theor Chem Acc 2016; 135:166. [PMID: 28367078 PMCID: PMC5373107 DOI: 10.1007/s00214-016-1923-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022]
Abstract
Taking long-range electrostatic effects into account in classical and hybrid quantum mechanics-molecular mechanics (QM/MM) simulations is necessary for an accurate description of the system under study. We have recently developed a method, termed long-range electrostatic corrections (LREC), for monopolar QM/MM calculations. Here, we present an extension of LREC for multipolar/polarizable QM/MM simulations within the LICHEM software package. Reaction barriers and QM-MM interaction energies converge with a LREC cutoff between 20 and 25 Å, in agreement with our previous results. Additionally, the LREC approach for the QM-MM interactions can be smoothly combined with standard shifting or Ewald summation methods in the MM calculations. We recommend the use of QM(LREC)/MM(PME), where the QM region is treated with LREC and the MM region is treated with particle mesh Ewald (PME) summation. This combination is an excellent compromise between simplicity, speed, and accuracy for large QM/MM simulations.
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Affiliation(s)
- Eric G Kratz
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Robert E Duke
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - G Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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10
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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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11
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Hartman JD, Monaco S, Schatschneider B, Beran GJO. Fragment-based (13)C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods. J Chem Phys 2015; 143:102809. [PMID: 26374002 DOI: 10.1063/1.4922649] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We assess the quality of fragment-based ab initio isotropic (13)C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic (13)C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Stephen Monaco
- The Pennsylvania State University, The Eberly Campus, 2201 University Dr, Lemont Furnace, Pennsylvania 15456, USA
| | - Bohdan Schatschneider
- The Pennsylvania State University, The Eberly Campus, 2201 University Dr, Lemont Furnace, Pennsylvania 15456, USA
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
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12
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Ivanov MV, Talipov MR, Timerghazin QK. Electrostatic point charge fitting as an inverse problem: Revealing the underlying ill-conditioning. J Chem Phys 2015; 143:134102. [DOI: 10.1063/1.4932105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Maxim V. Ivanov
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881, USA
| | - Marat R. Talipov
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881, USA
| | - Qadir K. Timerghazin
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881, USA
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13
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Hartman JD, Neubauer TJ, Caulkins BG, Mueller LJ, Beran GJO. Converging nuclear magnetic shielding calculations with respect to basis and system size in protein systems. JOURNAL OF BIOMOLECULAR NMR 2015; 62:327-40. [PMID: 25993979 PMCID: PMC4512207 DOI: 10.1007/s10858-015-9947-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/12/2015] [Indexed: 05/25/2023]
Abstract
Ab initio chemical shielding calculations greatly facilitate the interpretation of nuclear magnetic resonance (NMR) chemical shifts in biological systems, but the large sizes of these systems requires approximations in the chemical models used to represent them. Achieving good convergence in the predicted chemical shieldings is necessary before one can unravel how other complex structural and dynamical factors affect the NMR measurements. Here, we investigate how to balance trade-offs between using a better basis set or a larger cluster model for predicting the chemical shieldings of the substrates in two representative examples of protein-substrate systems involving different domains in tryptophan synthase: the N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F9) ligand which binds in the α active site, and the 2-aminophenol quinonoid intermediate formed in the β active site. We first demonstrate that a chemically intuitive three-layer, locally dense basis model that uses a large basis on the substrate, a medium triple-zeta basis to describe its hydrogen-bonding partners and/or surrounding van der Waals cavity, and a crude basis set for more distant atoms provides chemical shieldings in good agreement with much more expensive large basis calculations. Second, long-range quantum mechanical interactions are important, and one can accurately estimate them as a small-basis correction to larger-basis calculations on a smaller cluster. The combination of these approaches enables one to perform density functional theory NMR chemical shift calculations in protein systems that are well-converged with respect to both basis set and cluster size.
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Affiliation(s)
- Joshua D. Hartman
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, Tel.: +1-951-827-7869
| | - Thomas J. Neubauer
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, Tel.: +1-951-827-7869
| | - Bethany G. Caulkins
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, Tel.: +1-951-827-7869
| | - Leonard J. Mueller
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, Tel.: +1-951-827-7869
| | - Gregory J. O. Beran
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, Tel.: +1-951-827-7869
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14
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Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys Chem Chem Phys 2015; 16:10310-44. [PMID: 24740821 DOI: 10.1039/c4cp00316k] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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15
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Affiliation(s)
- Michael A Collins
- †Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Ryan P A Bettens
- ‡Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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16
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Simoncini D, Nakata H, Ogata K, Nakamura S, Zhang KY. Quality Assessment of Predicted Protein Models Using Energies Calculated by the Fragment Molecular Orbital Method. Mol Inform 2015; 34:97-104. [PMID: 27490032 DOI: 10.1002/minf.201400108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/13/2014] [Indexed: 12/12/2022]
Abstract
Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.
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Affiliation(s)
- David Simoncini
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan phone: +81(0)45-503-9560/fax: +81(0)45-503-9559.,Present address: Mathématiques et Informatique Appliquées de Toulouse, Unité de Recherche 875, Institut National de la Recherche Agronomique, F-31320 Castanet-Tolosan, France
| | - Hiroya Nakata
- RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan phone/fax: +81(0)48-467-9477/+81(0)48-467-8503.,Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Koji Ogata
- RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan phone/fax: +81(0)48-467-9477/+81(0)48-467-8503
| | - Shinichiro Nakamura
- RIKEN Research Cluster for Innovation, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan phone/fax: +81(0)48-467-9477/+81(0)48-467-8503.
| | - Kam Yj Zhang
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan phone: +81(0)45-503-9560/fax: +81(0)45-503-9559.
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17
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Reid DM, Collins MA. Calculating nuclear magnetic resonance shieldings using systematic molecular fragmentation by annihilation. Phys Chem Chem Phys 2015; 17:5314-20. [DOI: 10.1039/c4cp05116e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Systematic fragmentation accurately predicts theoretical chemical shieldings.
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Affiliation(s)
- David M. Reid
- Research School of Chemistry
- The Australian National University
- ACT
- Australia
| | - Michael A. Collins
- Research School of Chemistry
- The Australian National University
- ACT
- Australia
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18
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Devereux M, Raghunathan S, Fedorov DG, Meuwly M. A Novel, Computationally Efficient Multipolar Model Employing Distributed Charges for Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:4229-41. [PMID: 26588121 DOI: 10.1021/ct500511t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A truncated multipole expansion can be re-expressed exactly using an appropriate arrangement of point charges. This means that groups of point charges that are shifted away from nuclear coordinates can be used to achieve accurate electrostatics for molecular systems. We introduce a multipolar electrostatic model formulated in this way for use in computationally efficient multipolar molecular dynamics simulations with well-defined forces and energy conservation in NVE (constant number-volume-energy) simulations. A framework is introduced to distribute torques arising from multipole moments throughout a molecule, and a refined fitting approach is suggested to obtain atomic multipole moments that are optimized for accuracy and numerical stability in a force field context. The formulation of the charge model is outlined as it has been implemented into CHARMM, with application to test systems involving H2O and chlorobenzene. As well as ease of implementation and computational efficiency, the approach can be used to provide snapshots for multipolar QM/MM calculations in QM/MM-MD studies and easily combined with a standard point-charge force field to allow mixed multipolar/point charge simulations of large systems.
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Affiliation(s)
- Mike Devereux
- Universität Basel , Departement Chemie, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Shampa Raghunathan
- Universität Basel , Departement Chemie, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Dmitri G Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Markus Meuwly
- Universität Basel , Departement Chemie, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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