1
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Popelier PLA. Non-covalent interactions from a Quantum Chemical Topology perspective. J Mol Model 2022; 28:276. [PMID: 36006513 PMCID: PMC9411098 DOI: 10.1007/s00894-022-05188-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/07/2022] [Indexed: 11/12/2022]
Abstract
About half a century after its little-known beginnings, the quantum topological approach called QTAIM has grown into a widespread, but still not mainstream, methodology of interpretational quantum chemistry. Although often confused in textbooks with yet another population analysis, be it perhaps an elegant but somewhat esoteric one, QTAIM has been enriched with about a dozen other research areas sharing its main mathematical language, such as Interacting Quantum Atoms (IQA) or Electron Localisation Function (ELF), to form an overarching approach called Quantum Chemical Topology (QCT). Instead of reviewing the latter's role in understanding non-covalent interactions, we propose a number of ideas emerging from the full consequences of the space-filling nature of topological atoms, and discuss how they (will) impact on interatomic interactions, including non-covalent ones. The architecture of a force field called FFLUX, which is based on these ideas, is outlined. A new method called Relative Energy Gradient (REG) is put forward, which is able, by computation, to detect which fragments of a given molecular assembly govern the energetic behaviour of this whole assembly. This method can offer insight into the typical balance of competing atomic energies both in covalent and non-covalent case studies. A brief discussion on so-called bond critical points is given, highlighting concerns about their meaning, mainly in the arena of non-covalent interactions.
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Affiliation(s)
- Paul L A Popelier
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain, UK.
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2
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Yuan Y, Fu S, Huo D, Su W, Zhang R, Wei J. Multipolar electrostatics for hairpin and pseudoknots in RNA: Improving the accuracy of force field potential energy function. J Comput Chem 2021; 42:771-786. [PMID: 33586809 DOI: 10.1002/jcc.26497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/17/2021] [Accepted: 01/24/2021] [Indexed: 12/19/2022]
Abstract
Molecular dynamics (MD) simulations that rely on force field methods has been widely used to explore the structure and function of RNAs. However, the current commonly used force fields are limited by the electrostatic description offered by atomic charge, dipole and at most quadrupole moments, failing to capture the anisotropic picture of electronic features. Actually, the distribution of electrons around atomic nuclei is not spherically symmetric but is geometry dependent. A multipolar electrostatic model based on high rank multipole moments is described in this work, which allows us to combine polarizability and anisotropy of electron density. RNA secondary structure was taken as a research system, and its substructures including stem, loops (hairpin loop, bulge loop, internal loop, and multi-branch loop), and pseudoknots (H-type and K-type) were investigated, respectively, as well as the hairpin. First, the atom-atom electrostatic properties derived from one chain of a duplex RNA 2MVY in our previous work (Ref. 58) were measured by the pilot RNA systems of hairpin, hairpin loop, stem, and H-type pseudoknot, respectively. The prediction results were not satisfactory. Consequently, to obtain a general set of electrostatic parameters for RNA force fields, the convergence behavior of the atom-atom electrostatic interactions in the pilot RNA systems was explored using high rank atomic multipole moments. The pilot RNA systems were cut into four types of different-sized molecular fragments, and the single nucleotide fragment and nucleotide-paired fragment proved to be the most reasonable systems for base-unpairing regions and base-pairing regions to investigate the convergence behavior of all types of atom-atom electrostatic interactions, respectively. Transferability of the electrostatic properties drawn from the pilot RNA systems to the corresponding test systems was also investigated. Furthermore, the convergence behavior of atomic electrostatic interactions in other substructures including bulge loop, internal loop, multi-branch loop, and K-type pseudoknot was expected to be modeled via the hairpin.
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Affiliation(s)
- Yongna Yuan
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Shaowei Fu
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Dongxu Huo
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Wei Su
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Ruisheng Zhang
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Jiaxuan Wei
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
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3
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Yuan Y, Ma Y, Huo D, Mills MJL, Wei J, Su W, Zhang R. Multipolar Description of Atom-Atom Electrostatic Interaction Energies in Single/Double-Stranded DNAs. J Phys Chem B 2020; 124:10089-10103. [PMID: 33138384 DOI: 10.1021/acs.jpcb.0c06757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular force field simulation is an effective method to explore the properties of DNA molecules in depth. Almost all current popular force fields calculate atom-atom electrostatic interaction energies for DNAs based on the atomic charge and dipole or quadrupole moments, without considering high-rank atomic multipole moments for more accurate electrostatics. Actually, the distribution of electrons around atomic nuclei is not spherically symmetric but is geometry dependent. In this work, a multipole expansion method that allows us to combine polarizability and anisotropy was applied. One single-stranded DNA and one double-stranded DNA were selected as pilot systems. Deoxynucleotides were cut out from pilot systems and capped by mimicking the original DNA environment. Atomic multipole moments were integrated instead of fixed-point charges to calculate atom-atom electrostatic energies to improve the accuracy of force fields for DNA simulations. Also, the applicability of modeling the behavior of both single-stranded and double-stranded DNAs was investigated. The calculation results indicated that the models can be transferred from pilot systems to test systems, which is of great significance for the development of future DNA force fields.
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Affiliation(s)
- Yongna Yuan
- School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China
| | - Yan Ma
- School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China
| | - Dongxu Huo
- School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China
| | - Matthew J L Mills
- 3M Corporate Research Analytical Laboratory, Saint Paul, Minnesota 55114, United States
| | - Jiaxuan Wei
- School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China
| | - Wei Su
- School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China
| | - Ruisheng Zhang
- School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China
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4
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Liem SY, Popelier PLA. The influence of water potential in simulation: a catabolite activator protein case study. J Mol Model 2019; 25:216. [PMID: 31292786 PMCID: PMC7406532 DOI: 10.1007/s00894-019-4095-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/13/2019] [Indexed: 10/27/2022]
Abstract
We present a rare comparison of structures of the same protein but generated by different potentials. We used four popular water potentials (SPC, TIP3P, TIP4P, TIP5P) in conjunction with the equally popular ff99SB. However, the ff12SB protein potential was used with TI3P only. Simulations (60 ns) were run on the catabolite activator protein (CAP), which is a textbook case of allosteric interaction. Overall, all potentials generated largely similar structures but failed to reproduce a crucial structural feature determined by NMR experiment. This example shows the need to develop next-generation potentials. Graphical abstract Catabolite activator protein.
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Affiliation(s)
- Steven Y Liem
- Manchester Institute of Biotechnology (MIB), University of Manchester, 131 Princess Street, Manchester, M1 7DN, Great Britain.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), University of Manchester, 131 Princess Street, Manchester, M1 7DN, Great Britain. .,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain.
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5
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Xu X, Ren J, Ma Y, Liu H, Rong Q, Feng Y, Wang Y, Cheng Y, Ge R, Li Z, Bian J. Discovery of cyanopyridine scaffold as novel indoleamine-2,3-dioxygenase 1 (IDO1) inhibitors through virtual screening and preliminary hit optimisation. J Enzyme Inhib Med Chem 2019; 34:250-263. [PMID: 30734612 PMCID: PMC6327983 DOI: 10.1080/14756366.2018.1480614] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
With the aim of discovering novel IDO1 inhibitors, a combined similarity search and molecular docking approach was employed to the discovery of 32 hit compounds. Testing the screened hit compounds has led to several novel submicromolar inhibitors. Especially for compounds LVS-019 with cyanopyridine scaffold, showed good IDO1 inhibitory activity. To discover more compounds with similar structures to LVS-019, a shape-based model was then generated on the basis of it and the second-round virtual screening was carried out leading to 23 derivatives. Molecular docking studies suggested a possible binding mode of LVS-019, which provides a good starting point for the development of cyanopyridine scaffold compounds as potent IDO1 inhibitor. To improve potency of these hits, we further designed and synthesised another 14 derivatives of LVS-019. Among these compounds, LBJ-10 showed improved potency compared to the hits and displayed comparable potency to the control GDC-0919 analogue. LBJ-10 can serve as ideal leads for further modifications as IDO1 inhibitors for cancer treatment.
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Affiliation(s)
- Xi Xu
- a State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization , China Pharmaceutical University , Nanjing , People's Republic of China.,b Department of Medicinal Chemistry, School of Pharmacy , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Jie Ren
- a State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization , China Pharmaceutical University , Nanjing , People's Republic of China.,b Department of Medicinal Chemistry, School of Pharmacy , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Yinghe Ma
- a State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization , China Pharmaceutical University , Nanjing , People's Republic of China.,b Department of Medicinal Chemistry, School of Pharmacy , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Hongting Liu
- a State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Quanjin Rong
- a State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Yifan Feng
- a State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Yameng Wang
- a State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Yu Cheng
- a State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Ruijia Ge
- c The Madeira School , McLean , VA , USA
| | - Zhiyu Li
- a State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization , China Pharmaceutical University , Nanjing , People's Republic of China.,b Department of Medicinal Chemistry, School of Pharmacy , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Jinlei Bian
- a State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization , China Pharmaceutical University , Nanjing , People's Republic of China.,b Department of Medicinal Chemistry, School of Pharmacy , China Pharmaceutical University , Nanjing , People's Republic of China
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6
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Pendrill R, Mutter ST, Mensch C, Barron LD, Blanch EW, Popelier PLA, Widmalm G, Johannessen C. Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity. Chemphyschem 2019; 20:695-705. [PMID: 30688397 DOI: 10.1002/cphc.201801172] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/25/2019] [Indexed: 01/31/2023]
Abstract
Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.
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Affiliation(s)
- Robert Pendrill
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
| | - Shaun T Mutter
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Natural Sciences, Middlesex University, NW4 4BT, London, UK
| | - Carl Mensch
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171, 2020, Antwerp, Belgium.,Ghent Quantum Chemistry Group Department of Chemistry, University of Ghent, Krijgslaan 281, 9000, Ghent, Belgium
| | - Laurence D Barron
- School of Chemistry, University of Glasgow Joseph Black Building, Glasgow, G12 8QQ, UK
| | - Ewan W Blanch
- School of Science, RMIT University GPO Box 2476, Melbourne, VIC 3001, Australia
| | - Paul L A Popelier
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
| | - Christian Johannessen
- Department of Chemistry, University of Antwerp Groenenborgerlaan 171, 2020, Antwerp, Belgium
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7
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Yuan Y, Zhang Z, Mills MJL, Hu R, Zhang R. Assessing Force Field Potential Energy Function Accuracy via a Multipolar Description of Atomic Electrostatic Interactions in RNA. J Chem Inf Model 2018; 58:2239-2254. [PMID: 30362754 DOI: 10.1021/acs.jcim.8b00328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Computational investigations of RNA properties often rely on a molecular mechanical approach to define molecular potential energy. Force fields for RNA typically employ a point charge model of electrostatics, which does not provide a realistic quantum-mechanical picture. In reality, electron distributions around nuclei are not spherically symmetric and are geometry dependent. A multipole expansion method which allows for incorporation of polarizability and anisotropy in a force field is described, and its applicability to modeling the behavior of RNA molecules is investigated. Transferability of the model, critical for force field development, is also investigated.
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Affiliation(s)
- Yongna Yuan
- School of Information Science & Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Zhuangzhuang Zhang
- School of Information Science & Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | | | - Rongjing Hu
- School of Information Science & Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Ruisheng Zhang
- School of Information Science & Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
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8
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Simmonett AC, Pickard FC, Shao Y, Cheatham TE, Brooks BR. Efficient treatment of induced dipoles. J Chem Phys 2016; 143:074115. [PMID: 26298123 DOI: 10.1063/1.4928530] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most existing treatments of induced dipoles in polarizable molecular mechanics force field calculations use either the self-consistent variational method, which is solved iteratively, or the "direct" approximation that is non-iterative as a result of neglecting coupling between induced dipoles. The variational method is usually implemented using assumptions that are only strictly valid under tight convergence of the induced dipoles, which can be computationally demanding to enforce. In this work, we discuss the nature of the errors that result from insufficient convergence and suggest a strategy that avoids such problems. Using perturbation theory to reintroduce the mutual coupling into the direct algorithm, we present a computationally efficient method that combines the precision of the direct approach with the accuracy of the variational approach. By analyzing the convergence of this perturbation series, we derive a simple extrapolation formula that delivers a very accurate approximation to the infinite order solution at the cost of only a few iterations. We refer to the new method as extrapolated perturbation theory. Finally, we draw connections to our previously published permanent multipole algorithm to develop an efficient implementation of the electric field and Thole terms and also derive some necessary, but not sufficient, criteria that force field parameters must obey.
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Affiliation(s)
- Andrew C Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yihan Shao
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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9
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Skyner RE, McDonagh JL, Groom CR, van Mourik T, Mitchell JBO. A review of methods for the calculation of solution free energies and the modelling of systems in solution. Phys Chem Chem Phys 2016; 17:6174-91. [PMID: 25660403 DOI: 10.1039/c5cp00288e] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the past decade, pharmaceutical companies have seen a decline in the number of drug candidates successfully passing through clinical trials, though billions are still spent on drug development. Poor aqueous solubility leads to low bio-availability, reducing pharmaceutical effectiveness. The human cost of inefficient drug candidate testing is of great medical concern, with fewer drugs making it to the production line, slowing the development of new treatments. In biochemistry and biophysics, water mediated reactions and interactions within active sites and protein pockets are an active area of research, in which methods for modelling solvated systems are continually pushed to their limits. Here, we discuss a multitude of methods aimed towards solvent modelling and solubility prediction, aiming to inform the reader of the options available, and outlining the various advantages and disadvantages of each approach.
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Affiliation(s)
- R E Skyner
- School of Chemistry, University of St Andrews, Purdie Building, North Haugh, St Andrews, Fife KY16 9ST, UK.
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10
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Transferable kriging machine learning models for the multipolar electrostatics of helical deca-alanine. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1739-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Simmonett AC, Pickard FC, Schaefer HF, Brooks BR. An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald. J Chem Phys 2015; 140:184101. [PMID: 24832247 DOI: 10.1063/1.4873920] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Next-generation molecular force fields deliver accurate descriptions of non-covalent interactions by employing more elaborate functional forms than their predecessors. Much work has been dedicated to improving the description of the electrostatic potential (ESP) generated by these force fields. A common approach to improving the ESP is by augmenting the point charges on each center with higher-order multipole moments. The resulting anisotropy greatly improves the directionality of the non-covalent bonding, with a concomitant increase in computational cost. In this work, we develop an efficient strategy for enumerating multipole interactions, by casting an efficient spherical harmonic based approach within a particle mesh Ewald (PME) framework. Although the derivation involves lengthy algebra, the final expressions are relatively compact, yielding an approach that can efficiently handle both finite and periodic systems without imposing any approximations beyond PME. Forces and torques are readily obtained, making our method well suited to modern molecular dynamics simulations.
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Affiliation(s)
- Andrew C Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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12
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Mutter ST, Zielinski F, Popelier PLA, Blanch EW. Calculation of Raman optical activity spectra for vibrational analysis. Analyst 2015; 140:2944-56. [DOI: 10.1039/c4an02357a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review provides the necessary knowledge to accurately model ROA spectra of solvated systems and interpret their vibrational characteristics.
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Affiliation(s)
- Shaun T. Mutter
- Manchester Institute of Biotechnology and Faculty of Life Sciences
- University of Manchester
- Manchester
- UK
| | - François Zielinski
- Manchester Institute of Biotechnology and School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology and School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Ewan W. Blanch
- Manchester Institute of Biotechnology and Faculty of Life Sciences
- University of Manchester
- Manchester
- UK
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13
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Mills MJL, Popelier PLA. Electrostatic Forces: Formulas for the First Derivatives of a Polarizable, Anisotropic Electrostatic Potential Energy Function Based on Machine Learning. J Chem Theory Comput 2014; 10:3840-56. [DOI: 10.1021/ct500565g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Matthew J. L. Mills
- Manchester
Institute of Biotechnology (MIB), University of Manchester, 131 Princess
Street, Manchester M1 7DN, Great Britain
| | - Paul L. A. Popelier
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
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14
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Fletcher TL, Kandathil SM, Popelier PLA. The prediction of atomic kinetic energies from coordinates of surrounding atoms using kriging machine learning. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1499-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Cisneros GA, Karttunen M, Ren P, Sagui C. Correction to Classical Electrostatics for Biomolecular Simulations. Chem Rev 2014. [DOI: 10.1021/cr500124k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Multipolar electrostatics based on the Kriging machine learning method: an application to serine. J Mol Model 2014; 20:2172. [DOI: 10.1007/s00894-014-2172-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 02/07/2014] [Indexed: 10/25/2022]
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17
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