1
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Ramasami P, Murray JS. Radial Behavior of Electrostatic Potentials of Atoms and Ions Revisited: Isotropy and Anisotropy. Chemphyschem 2024; 25:e202400450. [PMID: 38775267 DOI: 10.1002/cphc.202400450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/17/2024] [Indexed: 07/12/2024]
Abstract
In this paper we revisit earlier work relating to monoatomic atoms and ions published by pioneers in the area of electrostatic potentials. We include plots of the radial distributions of the electrostatic potentials for spherically symmetric atoms and cations, and for singly, doubly and triply negative anions. For atoms with anisotropy in their densities and electrostatic potentials, such as the halonium cations, it is shown how the molecular surface approach for plotting electrostatic potentials complements that achieved by directional radial distributions.
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Affiliation(s)
- Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry Faculty of Science, University of Mauritius, Reduit, 80837, Mauritius
- Centre of Natural Product Research, Department of Chemical Sciences University of Johannesburg, Doornfontein Campus, Johannesburg, 2028, South Africa
| | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA
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2
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Brinck T, Borrfors AN. The Importance of Electrostatics and Polarization for Noncovalent Interactions: Ionic Hydrogen Bonds vs Ionic Halogen Bonds. J Mol Model 2022; 28:275. [PMID: 36006525 PMCID: PMC9411100 DOI: 10.1007/s00894-022-05189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/19/2022] [Indexed: 11/05/2022]
Abstract
A series of 26 hydrogen-bonded complexes between Br- and halogen, oxygen and sulfur hydrogen-bond (HB) donors is investigated at the M06-2X/6-311 + G(2df,2p) level of theory. Analysis using a model in which Br- is replaced by a point charge shows that the interaction energy ([Formula: see text]) of the complexes is accurately reproduced by the scaled interaction energy with the point charge ([Formula: see text]).This is demonstrated by [Formula: see text] with a correlation coefficient, R2 =0.999. The only outlier is (Br-H-Br)-, which generally is classified as a strong charge-transfer complex with covalent character rather than a HB complex. [Formula: see text] can be divided rigorously into an electrostatic contribution ([Formula: see text]) and a polarization contribution ([Formula: see text]).Within the set of HB complexes investigated, the former varies between -7.2 and -32.7 kcal mol-1, whereas the latter varies between -1.6 and -11.5 kcal mol-1. Compared to our previous study of halogen-bonded (XB) complexes between Br- and C-Br XB donors, the electrostatic contribution is generally stronger and the polarization contribution is generally weaker in the HB complexes. However, for both types of bonding, the variation in interaction strength can be reproduced accurately without invoking a charge-transfer term. For the Br-···HF complex, the importance of charge penetration on the variation of the interaction energy with intermolecular distance is investigated. It is shown that the repulsive character of [Formula: see text] at short distances in this complex to a large extent can be attributed to charge penetration.
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Affiliation(s)
- Tore Brinck
- Applied Physical Chemistry, Department of Chemistry, CBH, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden.
| | - André Nyberg Borrfors
- Applied Physical Chemistry, Department of Chemistry, CBH, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
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3
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Barcza B, Szirmai ÁB, Szántó KJ, Tajti A, Szalay PG. Comparison of approximate intermolecular potentials for ab initio fragment calculations on medium sized N-heterocycles. J Comput Chem 2022; 43:1079-1093. [PMID: 35478353 PMCID: PMC9321956 DOI: 10.1002/jcc.26866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/26/2022] [Accepted: 03/29/2022] [Indexed: 01/15/2023]
Abstract
The ground state intermolecular potential of bimolecular complexes of N-heterocycles is analyzed for the impact of individual terms in the interaction energy as provided by various, conceptually different theories. Novel combinations with several formulations of the electrostatic, Pauli repulsion, and dispersion contributions are tested at both short- and long-distance sides of the potential energy surface, for various alignments of the pyrrole dimer as well as the cytosine-uracil complex. The integration of a DFT/CCSD density embedding scheme, with dispersion terms from the effective fragment potential (EFP) method is found to provide good agreement with a reference CCSD(T) potential overall; simultaneously, a quantum mechanics/molecular mechanics approach using CHELPG atomic point charges for the electrostatic interaction, augmented by EFP dispersion and Pauli repulsion, comes also close to the reference result. Both schemes have the advantage of not relying on predefined force fields; rather, the interaction parameters can be determined for the system under study, thus being excellent candidates for ab initio modeling.
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Affiliation(s)
- Bónis Barcza
- Institute of Chemistry, Laboratory of Theoretical ChemistryELTE Eötvös Loránd UniversityBudapestHungary
| | - Ádám B. Szirmai
- Institute of Chemistry, Laboratory of Theoretical ChemistryELTE Eötvös Loránd UniversityBudapestHungary
| | - Katalin J. Szántó
- Institute of Chemistry, Laboratory of Theoretical ChemistryELTE Eötvös Loránd UniversityBudapestHungary
| | - Attila Tajti
- Institute of Chemistry, Laboratory of Theoretical ChemistryELTE Eötvös Loránd UniversityBudapestHungary
| | - Péter G. Szalay
- Institute of Chemistry, Laboratory of Theoretical ChemistryELTE Eötvös Loránd UniversityBudapestHungary
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4
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Das AK, Liu M, Head-Gordon T. Development of a Many-Body Force Field for Aqueous Alkali Metal and Halogen Ions: An Energy Decomposition Analysis Guided Approach. J Chem Theory Comput 2022; 18:953-967. [DOI: 10.1021/acs.jctc.1c00537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akshaya Kumar Das
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Meili Liu
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
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5
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Fan D, Chen L, Wang C, Yin S, Mo Y. Inter-anion chalcogen bonds: Are they anti-electrostatic in nature? J Chem Phys 2021; 155:234302. [PMID: 34937369 DOI: 10.1063/5.0076872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Inter-anion hydrogen and halogen bonds have emerged as counterintuitive linkers and inspired us to expand the range of this unconventional bonding pattern. Here, the inter-anion chalcogen bond (IAChB) was proposed and theoretically analyzed in a series of complexes formed by negatively charged bidentate chalcogen bond donors with chloride anions. The kinetic stability of IAChB was evidenced by the minima on binding energy profiles and further supported by ab initio molecular dynamic simulations. The block-localized wave function (BLW) method and its subsequent energy decomposition (BLW-ED) approach were employed to elucidate the physical origin of IAChB. While all other energy components vary monotonically as anions get together, the electrostatic interaction behaves exceptionally as it experiences a Coulombic repulsion barrier. Before reaching the barrier, the electrostatic repulsion increases with the shortening Ch⋯Cl- distance as expected from classical electrostatics. However, after passing the barrier, the electrostatic repulsion decreases with the Ch⋯Cl- distance shortening and subsequently turns into the most favorable trend among all energy terms at short ranges, representing a dominating force for the kinetic stability of inter-anions. For comparison, all energy components exhibit the same trends and vary monotonically in the conventional counterparts where donors are neutral. By comparing inter-anions and their conventional counterparts, we found that only the electrostatic energy term is affected by the extra negative charge. Remarkably, the distinctive (nonmonotonic) electrostatic energy profiles were reproduced using quantum mechanical-based atomic multipoles, suggesting that the crucial electrostatic interaction in IAChB can be rationalized within the classical electrostatic theory just like conventional non-covalent interactions.
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Affiliation(s)
- Dan Fan
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Li Chen
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Shiwei Yin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, USA
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6
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Rackers JA, Silva RR, Wang Z, Ponder JW. Polarizable Water Potential Derived from a Model Electron Density. J Chem Theory Comput 2021; 17:7056-7084. [PMID: 34699197 DOI: 10.1021/acs.jctc.1c00628] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States.,Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87123, United States
| | - Roseane R Silva
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States.,Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
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7
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Jiménez-Grávalos F, Suárez D. A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy. J Chem Theory Comput 2021; 17:4981-4995. [PMID: 34279923 PMCID: PMC8901103 DOI: 10.1021/acs.jctc.1c00263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Based on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the noncovalent complexes in the S66 database, the fragment-based and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. It also provides energetic descriptors at varying distance that directly address the atomic and molecular electrostatic interactions as described by point-charge or multipole-based potentials. Additionally, we propose a consistent definition of the charge penetration energy within quantum chemical topology, which is mainly characterized in terms of the intramolecular electrostatic energy. Finally, we discuss some practical implications of our results for the design and validation of electrostatic potentials.
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Affiliation(s)
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, E-33006 Oviedo, Spain
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8
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Peels M, Knizia G. Fast Evaluation of Two-Center Integrals over Gaussian Charge Distributions and Gaussian Orbitals with General Interaction Kernels. J Chem Theory Comput 2020; 16:2570-2583. [PMID: 32040326 DOI: 10.1021/acs.jctc.9b01296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present efficient algorithms for computing two-center integrals and integral derivatives, with general interaction kernels K(r12), over Gaussian charge distributions of general angular momenta l. While formulated in terms of traditional ab initio integration techniques, full derivations and required secondary information, as well as a reference implementation, are provided to make the content accessible to other fields. Concretely, the presented algorithms are based on an adaption of the McMurchie-Davidson Recurrence Relation (MDRR) combined with analytical properties of the solid harmonic transformation; this obviates all intermediate recurrences except the adapted MDRR itself, and allows it to be applied to fully contracted auxiliary kernel integrals. The technique is particularly well-suited for semiempirical molecular orbital methods, where it can serve as a more general and efficient replacement of Slater-Koster tables, and for first-principles quantum chemistry methods employing density fitting. But the formalism's high efficiency and ability of handling general interaction kernels K(r12) and multipolar Gaussian charge distributions may also be of interest for modeling electrostatic interactions and short-range exchange and charge penetration effects in classical force fields and model potentials. With the presented technique, a 4894 × 4894 univ-JKFIT Coulomb matrix JAB = (A|1/r12|B) (183 MiB) can be computed in 50 ms on a Q2'2018 notebook CPU, without any screening or approximations.
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Affiliation(s)
- Mieke Peels
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Gerald Knizia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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9
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Narsaria AK, Poater J, Fonseca Guerra C, Ehlers AW, Hamlin TA, Lammertsma K, Bickelhaupt FM. Distortion-Controlled Redshift of Organic Dye Molecules. Chemistry 2020; 26:2080-2093. [PMID: 31815315 PMCID: PMC7027851 DOI: 10.1002/chem.201905355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Indexed: 12/31/2022]
Abstract
It is shown, quantum chemically, how structural distortion of an aromatic dye molecule can be leveraged to rationally tune its optoelectronic properties. By using a quantitative Kohn-Sham molecular orbital (KS-MO) approach, in combination with time-dependent DFT (TD-DFT), the influence of various structural and electronic tuning parameters on the HOMO-LUMO gap of a benzenoid model dye have been investigated. These parameters include 1) out-of-plane bending of the aromatic core, 2) bending of the bridge with respect to the core, 3) the nature of the bridge itself, and 4) π-π stacking. The study reveals the coupling of multiple structural distortions as a function of bridge length and number of bridges in benzene to be chiefly responsible for a decreased HOMO-LUMO gap, and consequently, red-shifting of the absorption wavelength associated with the lowest singlet excitation (λ≈560 nm) in the model cyclophane systems. These physical insights together with a rational approach for tuning the oscillator strength were leveraged for the proof-of-concept design of an intense near-infrared (NIR) absorbing cyclophane dye at λ=785 nm. This design may contribute to a new class of distortion-controlled NIR absorbing organic dye molecules.
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Affiliation(s)
- Ayush K. Narsaria
- Department of Theoretical Chemistry and Amsterdam Center for, Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Jordi Poater
- ICREAPg. Lluís Companys 2308010BarcelonaSpain
- Departament de Química Inorgànica i Orgànica & IQTCUBUniversitat de BarcelonaMartí i Franquès 1-1108028BarcelonaSpain
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for, Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Gorlaeus LaboratoriesLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Andreas W. Ehlers
- van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
- Department of ChemistryUniversity of JohannesburgAuckland ParkJohannesburg2006South Africa
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry and Amsterdam Center for, Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Koop Lammertsma
- Department of Theoretical Chemistry and Amsterdam Center for, Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Department of ChemistryUniversity of JohannesburgAuckland ParkJohannesburg2006South Africa
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for, Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institute of Molecules and Materials (IMM)Radboud University NijmegenHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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10
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Chen T, Manz TA. A collection of forcefield precursors for metal-organic frameworks. RSC Adv 2019; 9:36492-36507. [PMID: 35539031 PMCID: PMC9075174 DOI: 10.1039/c9ra07327b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/25/2019] [Indexed: 12/14/2022] Open
Abstract
A host of important performance properties for metal-organic frameworks (MOFs) and other complex materials can be calculated by modeling statistical ensembles. The principle challenge is to develop accurate and computationally efficient interaction models for these simulations. Two major approaches are (i) ab initio molecular dynamics in which the interaction model is provided by an exchange-correlation theory (e.g., DFT + dispersion functional) and (ii) molecular mechanics in which the interaction model is a parameterized classical force field. The first approach requires further development to improve computational speed. The second approach requires further development to automate accurate forcefield parameterization. Because of the extreme chemical diversity across thousands of MOF structures, this problem is still mostly unsolved today. For example, here we show structures in the 2014 CoRE MOF database contain more than 8 thousand different atom types based on first and second neighbors. Our results showed that atom types based on both first and second neighbors adequately capture the chemical environment, but atom types based on only first neighbors do not. For 3056 MOFs, we used density functional theory (DFT) followed by DDEC6 atomic population analysis to extract a host of important forcefield precursors: partial atomic charges; atom-in-material (AIM) C6, C8, and C10 dispersion coefficients; AIM dipole and quadrupole moments; various AIM polarizabilities; quantum Drude oscillator parameters; AIM electron cloud parameters; etc. Electrostatic parameters were validated through comparisons to the DFT-computed electrostatic potential. These forcefield precursors should find widespread applications to developing MOF force fields.
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Affiliation(s)
- Taoyi Chen
- Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA
| | - Thomas A Manz
- Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA
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11
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Duke RE, Cisneros GA. Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM. J Mol Model 2019; 25:307. [PMID: 31501946 PMCID: PMC6741781 DOI: 10.1007/s00894-019-4194-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/28/2019] [Indexed: 10/26/2022]
Abstract
The development of accurate potentials for computational simulations has been an active area of research. Our group has been involved in the development of the Gaussian electrostatic model (GEM), a force field based on molecular densities. The philosophy of GEM is based on the pioneering work of N. Gresh and co-workers of the reproduction of individual inter-molecular interaction components obtained from quantum mechanical (QM) energy decomposition analysis (EDA). The molecular densities used in GEM are represented by fitting accurate QM molecular densities using auxiliary basis sets (comprised of Hermite Gaussians). The use of these molecular densities results in the need to evaluate a large number of Gaussian integrals. We have previously shown that the particle-mesh Ewald (PME), and fast Fourier Poisson (FFP) methods can be used for efficiently evaluating these types of integrals. Here, we present the latest parameterization of GEM* and its application for an extensive study of PME and FFP for molecular dynamics (MD) simulations using a hybrid version of our potential, GEM*. The temperature dependence of various bulk properties is presented and discussed, as well as the effect of various parameters affecting the performance/accuracy of both methods.
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Affiliation(s)
- Robert E Duke
- Department of Chemistry, University of North Texas, Denton, TX, 76202, USA
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX, 76202, USA.
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12
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Das AK, Urban L, Leven I, Loipersberger M, Aldossary A, Head-Gordon M, Head-Gordon T. Development of an Advanced Force Field for Water Using Variational Energy Decomposition Analysis. J Chem Theory Comput 2019; 15:5001-5013. [DOI: 10.1021/acs.jctc.9b00478] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Liu C, Piquemal JP, Ren P. AMOEBA+ Classical Potential for Modeling Molecular Interactions. J Chem Theory Comput 2019; 15:4122-4139. [PMID: 31136175 DOI: 10.1021/acs.jctc.9b00261] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration, and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model based on the AMOEBA+ framework captures various liquid-phase properties in molecular dynamics simulations while remaining consistent with SAPT energy decompositions, utilizing both ab initio data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.
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Affiliation(s)
- Chengwen Liu
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States.,Laboratoire de Chimie Théorique , Sorbonne Université, UMR7616 CNRS , Paris 75252 , France.,Institut Universitaire de France , Paris Cedex 05, 75005 , France
| | - Pengyu Ren
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
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14
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Brinck T, Borrfors AN. Electrostatics and polarization determine the strength of the halogen bond: a red card for charge transfer. J Mol Model 2019; 25:125. [DOI: 10.1007/s00894-019-4014-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022]
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15
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Vogiatzis KD, Polynski MV, Kirkland JK, Townsend J, Hashemi A, Liu C, Pidko EA. Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities. Chem Rev 2019; 119:2453-2523. [PMID: 30376310 PMCID: PMC6396130 DOI: 10.1021/acs.chemrev.8b00361] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 12/28/2022]
Abstract
Computational chemistry provides a versatile toolbox for studying mechanistic details of catalytic reactions and holds promise to deliver practical strategies to enable the rational in silico catalyst design. The versatile reactivity and nontrivial electronic structure effects, common for systems based on 3d transition metals, introduce additional complexity that may represent a particular challenge to the standard computational strategies. In this review, we discuss the challenges and capabilities of modern electronic structure methods for studying the reaction mechanisms promoted by 3d transition metal molecular catalysts. Particular focus will be placed on the ways of addressing the multiconfigurational problem in electronic structure calculations and the role of expert bias in the practical utilization of the available methods. The development of density functionals designed to address transition metals is also discussed. Special emphasis is placed on the methods that account for solvation effects and the multicomponent nature of practical catalytic systems. This is followed by an overview of recent computational studies addressing the mechanistic complexity of catalytic processes by molecular catalysts based on 3d metals. Cases that involve noninnocent ligands, multicomponent reaction systems, metal-ligand and metal-metal cooperativity, as well as modeling complex catalytic systems such as metal-organic frameworks are presented. Conventionally, computational studies on catalytic mechanisms are heavily dependent on the chemical intuition and expert input of the researcher. Recent developments in advanced automated methods for reaction path analysis hold promise for eliminating such human-bias from computational catalysis studies. A brief overview of these approaches is presented in the final section of the review. The paper is closed with general concluding remarks.
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Affiliation(s)
| | | | - Justin K. Kirkland
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jacob Townsend
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ali Hashemi
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Chong Liu
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Evgeny A. Pidko
- TheoMAT
group, ITMO University, Lomonosova 9, St. Petersburg 191002, Russia
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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16
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Ghahremanpour MM, van Maaren PJ, Caleman C, Hutchison GR, van der Spoel D. Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields. J Chem Theory Comput 2018; 14:5553-5566. [PMID: 30281307 DOI: 10.1021/acs.jctc.8b00430] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1 s-Gaussian or a ns-Slater ( n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library ( https://doi.org/10.5281/zenodo.1004711 ) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.
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Affiliation(s)
- Mohammad Mehdi Ghahremanpour
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology , Uppsala University , Husargatan 3 , Box 596, SE-75124 Uppsala , Sweden
| | - Paul J van Maaren
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology , Uppsala University , Husargatan 3 , Box 596, SE-75124 Uppsala , Sweden
| | - Carl Caleman
- Department of Physics and Astronomy , Uppsala University , Box 516, SE-75120 Uppsala , Sweden.,Center for Free-Electron Laser Science , Deutsches Elektronen-Synchrotron , DE-22607 Hamburg , Germany
| | - Geoffrey R Hutchison
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology , Uppsala University , Husargatan 3 , Box 596, SE-75124 Uppsala , Sweden
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17
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Yourdkhani S, Chojecki M, Korona T. Interaction of Non-polarizable Cations with Azaborine Isomers and Their Mono-Substituted Derivatives: Position, Induction, and Non-Classical Effects Matter. Chemphyschem 2018; 19:3092-3106. [DOI: 10.1002/cphc.201800691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Sirous Yourdkhani
- Department of Chemical Physics and Optics; Faculty of Mathematics and Physics; Charles University; Ke Karlovu 3, CZ- 12116 Prague 2 Czech Republic
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
| | - Michał Chojecki
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
| | - Tatiana Korona
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
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18
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Pan X, Rosta E, Shao Y. Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations. Molecules 2018; 23:E2500. [PMID: 30274290 PMCID: PMC6222767 DOI: 10.3390/molecules23102500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 11/16/2022] Open
Abstract
In QM/MM calculations, it is essential to handle electrostatic interactions between the QM and MM subsystems accurately and efficiently. To achieve maximal efficiency, it is convenient to adopt a hybrid scheme, where the QM electron density is used explicitly in the evaluation of short-range QM/MM electrostatic interactions, while a multipolar representation for the QM electron density is employed to account for the long-range QM/MM electrostatic interactions. In order to avoid energy discontinuity at the cutoffs, which separate the short- and long-range QM/MM electrostatic interactions, a switching function should be utilized to ensure a smooth potential energy surface. In this study, we benchmarked the accuracy of such hybrid embedding schemes for QM/MM electrostatic interactions using different multipolar representations, switching functions and cutoff distances. For test systems (neutral and anionic oxyluciferin in MM (aqueous and enzyme) environments), the best accuracy was acquired with a combination of QM electrostatic potential (ESP) charges and dipoles and two switching functions (long-range electrostatic corrections (LREC) and Switch) in the treatment of long-range QM/MM electrostatics. It allowed us to apply a 10Å distance cutoff and still obtain QM/MM electrostatics/polarization energies within 0.1 kcal/mol and time-dependent density functional theory (TDDFT)/MM vertical excitation energies within 10-3 eV from theoretical reference values.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019⁻5251, USA.
| | - Edina Rosta
- Department of Chemistry, King's College London, London SE1 1DB, UK.
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019⁻5251, USA.
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19
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Riquelme M, Lara A, Mobley DL, Verstraelen T, Matamala AR, Vöhringer-Martinez E. Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges. J Chem Inf Model 2018; 58:1779-1797. [PMID: 30125107 PMCID: PMC6195221 DOI: 10.1021/acs.jcim.8b00180] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computer simulations of biomolecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in biomolecular systems and are therein described by atomic point charges. In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model, and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the AM1-BCC and the MBIS atomic charge methods. The latter includes the solvent polarization and presents a root-mean-square error of 2.0 kcal mol-1 for the 613 organic molecules studied. The largest deviation was observed for phosphorus-containing molecules and the molecules with amide, ester and amine functional groups.
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Affiliation(s)
- Maximiliano Riquelme
- Departamento de Físico-Química, Facultad de Ciencias Químicas , Universidad de Concepción , 4070386 Concepción , Chile
| | - Alejandro Lara
- Departamento de Físico-Química, Facultad de Ciencias Químicas , Universidad de Concepción , 4070386 Concepción , Chile
| | - David L Mobley
- Departments of Pharmaceutical Sciences and Chemistry, 147 Bison Modular , University of California, Irvine , Irvine , California 92617 , United States
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM) , Ghent University , Technologiepark 903 , B-9052 Ghent , Belgium
| | - Adelio R Matamala
- Departamento de Físico-Química, Facultad de Ciencias Químicas , Universidad de Concepción , 4070386 Concepción , Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas , Universidad de Concepción , 4070386 Concepción , Chile
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20
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Bereau T, DiStasio RA, Tkatchenko A, von Lilienfeld OA. Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning. J Chem Phys 2018; 148:241706. [DOI: 10.1063/1.5009502] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg,
Luxembourg
| | - O. Anatole von Lilienfeld
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel,
Switzerland
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21
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Demerdash O, Mao Y, Liu T, Head-Gordon M, Head-Gordon T. Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations. J Chem Phys 2018; 147:161721. [PMID: 29096520 DOI: 10.1063/1.4999905] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we evaluate the accuracy of the classical AMOEBA model for representing many-body interactions, such as polarization, charge transfer, and Pauli repulsion and dispersion, through comparison against an energy decomposition method based on absolutely localized molecular orbitals (ALMO-EDA) for the water trimer and a variety of ion-water systems. When the 2- and 3-body contributions according to the many-body expansion are analyzed for the ion-water trimer systems examined here, the 3-body contributions to Pauli repulsion and dispersion are found to be negligible under ALMO-EDA, thereby supporting the validity of the pairwise-additive approximation in AMOEBA's 14-7 van der Waals term. However AMOEBA shows imperfect cancellation of errors for the missing effects of charge transfer and incorrectness in the distance dependence for polarization when compared with the corresponding ALMO-EDA terms. We trace the larger 2-body followed by 3-body polarization errors to the Thole damping scheme used in AMOEBA, and although the width parameter in Thole damping can be changed to improve agreement with the ALMO-EDA polarization for points about equilibrium, the correct profile of polarization as a function of intermolecular distance cannot be reproduced. The results suggest that there is a need for re-examining the damping and polarization model used in the AMOEBA force field and provide further insights into the formulations of polarizable force fields in general.
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Affiliation(s)
- Omar Demerdash
- Departments of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Departments of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tianyi Liu
- Departments of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Departments of Chemistry, University of California, Berkeley, California 94720, USA
| | - Teresa Head-Gordon
- Departments of Chemistry, University of California, Berkeley, California 94720, USA
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22
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Classical Polarizable Force Field to Study Hydrated Hectorite: Optimization on DFT Calculations and Validation against XRD Data. MINERALS 2018. [DOI: 10.3390/min8050205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Following our previous works on dioctahedral clays, we extend the classical Polarizable Ion Model (PIM) to trioctahedral clays, by considering dry Na-, Cs-, Ca- and Sr-hectorites as well as hydrated Na-hectorite. The parameters of the force field are determined by optimizing the atomic forces and dipoles on density functional theory calculations. The simulation results are validated by comparison with experimental X-ray diffraction (XRD) data. The XRD patterns calculated from classical molecular dynamics simulations performed with the PIM force field are in very good agreement with experimental results. In the bihydrated state, the less structured electronic density profile obtained with PIM compared to the one from the state-of-the-art non-polarizable force field clayFF explains the slightly better agreement between the PIM results and experiments.
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23
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Rackers JA, Wang Q, Liu C, Piquemal JP, Ren P, Ponder JW. An optimized charge penetration model for use with the AMOEBA force field. Phys Chem Chem Phys 2018; 19:276-291. [PMID: 27901142 DOI: 10.1039/c6cp06017j] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field. With a function derived from the charge distribution of a hydrogen-like atom and a limited number of parameters, our charge penetration model dramatically improves the description of electrostatics at short range. On a database of 101 biomolecular dimers, the charge penetration model brings the error in the electrostatic interaction energy relative to the ab initio SAPT electrostatic interaction energy from 13.4 kcal mol-1 to 1.3 kcal mol-1. The model is shown not only to be robust and transferable for the AMOEBA model, but also physically meaningful as it universally improves the description of the electrostatic potential around a given molecule.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational & Molecular Biophysics, Washington University, School of Medicine, Saint Louis, Missouri 63110, USA
| | - Qiantao Wang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA.
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24
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Abstract
Combining Hirshfeld surface analysis with single molecule electrostatic property calculations allows rationalizing crystalline packing motifs of organic semiconductors.
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Affiliation(s)
- M. Klues
- Fachbereich Physik
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - G. Witte
- Fachbereich Physik
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
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25
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Loboda O, Millot C. Geometry-dependent atomic multipole models for the water molecule. J Chem Phys 2017; 147:161718. [DOI: 10.1063/1.4995569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- O. Loboda
- Karl-Franzens Universität, Institut für Chemie, Heinrichstraße 28/IV, Graz A-8010, Austria
| | - C. Millot
- Université de Lorraine, CNRS, SRSMC UMR 7565, Faculté des Sciences et Technologies, Boulevard des Aiguillettes BP 70239, Vandoeuvre-lès-Nancy Cedex F-54506, France
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26
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Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. J Chem Theory Comput 2017; 13:1963-1979. [PMID: 28430427 DOI: 10.1021/acs.jctc.7b00089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH3, NH4+, CN-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.
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Affiliation(s)
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K.,Faculty of Applied Physics and Mathematics, Gdańsk University of Technology , Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | | | - Martin Head-Gordon
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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27
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Diller DJ. Development of a Simple Electron Transfer and Polarization Model and Its Application to Biological Systems. J Chem Theory Comput 2017; 13:329-339. [PMID: 27958737 DOI: 10.1021/acs.jctc.6b00852] [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
Here we present a new method for point charge calculation which we call QET (charges by electron transfer). The intent of this work is to develop a method that can be useful for studying charge transfer in large biological systems. It is based on the intuitive framework of the QEQ method with the key difference being that the QET method tracks all pairwise electron transfers by augmenting the QEQ pseudoenergy function with a distance dependent cost function for each electron transfer. This approach solves the key limitation of the QEQ method which is its handling of formally charged groups. First, we parametrize the QET method by fitting to electrostatic potentials calculated using ab initio quantum mechanics on over 11,000 small molecules. On an external test set of over 2500 small molecules the QET method achieves a mean absolute error of 1.37 kcal/mol/electron when compared to the ab initio electrostatic potentials. Second, we examine the conformational dependence of the charges on over 2700 tripeptides. With the tripeptide data set, we show that the conformational effects account for approximately 0.4 kcal/mol/electron on the electrostatic potentials. Third, we test the QET method for its ability to reproduce the effects of polarization and electron transfer on 1000 water clusters. For the water clusters, we show that the QET method captures about 50% of the polarization and electron transfer effects. Finally, we examine the effects of electron transfer and polarizability on the electrostatic interaction between p38 and 94 small molecule ligands. When used in conjunction with the Generalized-Born continuum solvent model, polarization and electron transfer with the QET model lead to an average change of 17 kcal/mol on the calculated electrostatic component of ΔG.
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Affiliation(s)
- David J Diller
- Data2Discovery Consulting, East Windsor, New Jersey 08520, United States
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28
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Gryn'ova G, Corminboeuf C. Implications of Charge Penetration for Heteroatom-Containing Organic Semiconductors. J Phys Chem Lett 2016; 7:5198-5204. [PMID: 27973870 DOI: 10.1021/acs.jpclett.6b02585] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The noncovalent interactions of neutral π-conjugated cores, pertinent to organic semiconductor materials, are intimately related to their charge transport properties and involve a subtle interplay of dispersion, Pauli repulsion, and electrostatic contributions. Realizing structural arrangements that are both energetically preferred and sufficiently conductive is a challenge. We tackle this problem by means of charge penetration contribution to the interaction energy, boosted in systems containing large heteroatoms (e.g., sulfur, selenium, phosphorus, silicon, and arsenic). We find that in both the model and "realistic" dimers of such heteroatom-containing cores dispersion is balanced out by the exchange and interaction energy is instead governed by substantial charge penetration. These systems also feature stronger electronic couplings compared to the dispersion-driven dimers of oligoacenes and/or the herringbone assemblies. Thus, charge penetration, enhanced in the π-conjugated cores comprising larger heteroatoms, arises as an attractive strategy toward potentially more stable and efficient organic electronic materials.
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Affiliation(s)
- Ganna Gryn'ova
- Institut des Sciences et Ingénierie Chimiques, École polytechnique fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Institut des Sciences et Ingénierie Chimiques, École polytechnique fédérale de Lausanne , CH-1015 Lausanne, Switzerland
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29
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Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK. TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field. J Chem Phys 2016; 145:124106. [DOI: 10.1063/1.4962909] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk, Poland
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Jay Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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30
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Öhrn A, Hermida-Ramon JM, Karlström G. Method for Slater-Type Density Fitting for Intermolecular Electrostatic Interactions with Charge Overlap. I. The Model. J Chem Theory Comput 2016; 12:2298-311. [DOI: 10.1021/acs.jctc.5b01155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anders Öhrn
- Department
of Theoretical Chemistry, Chemical Centre, P.O. Box 124, S-221 00 Lund, Sweden
| | - Jose M. Hermida-Ramon
- Departamento
de Química Física, Facultade de Química, Universidade de Vigo, 36310 Vigo, Spain
| | - Gunnar Karlström
- Department
of Theoretical Chemistry, Chemical Centre, P.O. Box 124, S-221 00 Lund, Sweden
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31
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Tafipolsky M, Ansorg K. Toward a Physically Motivated Force Field: Hydrogen Bond Directionality from a Symmetry-Adapted Perturbation Theory Perspective. J Chem Theory Comput 2016; 12:1267-79. [DOI: 10.1021/acs.jctc.5b01057] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maxim Tafipolsky
- Institut
für Physikalische
und Theoretische Chemie, Universität Würzburg, Campus
Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
| | - Kay Ansorg
- Institut
für Physikalische
und Theoretische Chemie, Universität Würzburg, Campus
Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
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32
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Manz TA, Limas NG. Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology. RSC Adv 2016. [DOI: 10.1039/c6ra04656h] [Citation(s) in RCA: 389] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We introduce a new atomic population analysis method that performs exceptionally well across an extremely broad range of periodic and non-periodic material types.
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Affiliation(s)
- Thomas A. Manz
- Department of Chemical & Materials Engineering
- New Mexico State University
- Las Cruces
- USA
| | - Nidia Gabaldon Limas
- Department of Chemical & Materials Engineering
- New Mexico State University
- Las Cruces
- USA
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33
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Wang B, Truhlar DG. Screened Electrostatic Interactions in Molecular Mechanics. J Chem Theory Comput 2015; 10:4480-7. [PMID: 26588144 DOI: 10.1021/ct5005142] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In a typical application of molecular mechanics (MM), the electrostatic interactions are calculated from parametrized partial atomic charges treated as point charges interacting by radial Coulomb potentials. This does not usually yield accurate electrostatic interactions at van der Waals distances, but this is compensated by additional parametrized terms, for example Lennard-Jones potentials. In the present work, we present a scheme involving radial screened Coulomb potentials that reproduces the accurate electrostatics much more accurately. The screening accounts for charge penetration of one subsystem's charge cloud into that of another subsystem, and it is incorporated into the interaction potential in a way similar to what we proposed in a previous article (J. Chem. Theory Comput. 2010, 6, 3330) for combined quantum mechanical and molecular mechanical (QM/MM) simulations, but the screening parameters are reoptimized for MM. The optimization is carried out with electrostatic-potential-fitted partial atomic charges, but the optimized parameters should be useful with any realistic charge model. In the model we employ, the charge density of an atom is approximated as the sum of a point charge representing the nucleus and inner electrons and a smeared charge representing the outermost electrons; in particular, for all atoms except hydrogens, the smeared charge represents the two outermost electrons in the present model. We find that the charge penetration effect can cause very significant deviations from the popular point-charge model, and by comparison to electrostatic interactions calculated by symmetry-adapted perturbation theory, we find that the present results are considerably more accurate than point-charge electrostatic interactions. The mean unsigned error in electrostatics for a large and diverse data set (192 interaction energies) decreases from 9.2 to 3.3 kcal/mol, and the error in the electrostatics for 10 water dimers decreases from 1.7 to 0.5 kcal/mol. We could have decreased the average errors further, but at the cost of sometimes significantly overestimating the screening; instead we chose a more conservative (safer) parametrization that systematically underestimates the screening (which by definition means it improves over point charges) and only occasionally overestimates it. Despite this conservative choice, we find that the screened MM method is even more accurate for the electrostatics than unscreened QM/MM calculations. This new method is easy to implement in any MM program, and it can be used to develop more physical force fields for molecular simulations.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
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Torabifard H, Starovoytov ON, Ren P, Cisneros GA. Development of an AMOEBA water model using GEM distributed multipoles. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1702-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Wang Q, Rackers JA, He C, Qi R, Narth C, Lagardere L, Gresh N, Ponder JW, Piquemal JP, Ren P. General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field. J Chem Theory Comput 2015; 11:2609-2618. [PMID: 26413036 PMCID: PMC4570253 DOI: 10.1021/acs.jctc.5b00267] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Indexed: 11/30/2022]
Abstract
Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge-charge function previously reported (Piquemal J.-P.; J. Phys. Chem. A2003, 107, 10353) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (Parker T. M.; J. Chem. Phys.2014, 140, 094106). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields.
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Affiliation(s)
- Qiantao Wang
- Department of Biomedical Engineering and Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States ; Department of Biomedical Engineering and Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Joshua A Rackers
- Computational and Molecular Biophysics Program, Division of Biology & Biomedical Sciences, Washington University in St. Louis , St. Louis, Missouri 63110, United States
| | - Chenfeng He
- Department of Biomedical Engineering and Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Rui Qi
- Department of Biomedical Engineering and Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Christophe Narth
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616 , Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France
| | - Louis Lagardere
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616 , Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616 , Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France
| | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616 , Case Courrier 137, 4 Place Jussieu, F-75005 Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering and Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Austin, Texas 78712, United States
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Goyal P, Qian HJ, Irle S, Lu X, Roston D, Mori T, Elstner M, Cui Q. Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B 2014; 118:11007-27. [PMID: 25166899 PMCID: PMC4174991 DOI: 10.1021/jp503372v] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We discuss the description of water and hydration effects that employs an approximate density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to explore, with the current formulation of DFTB3, the performance of this method for treating water in different chemical environments, the magnitude and nature of changes required to improve its performance, and factors that dictate its applicability to reactions in the condensed phase in a QM/MM framework. A relatively minor change (on the scale of kBT) in the O-H repulsive potential is observed to substantially improve the structural properties of bulk water under ambient conditions; modest improvements are also seen in dynamic properties of bulk water. This simple change also improves the description of protonated water clusters, a solvated proton, and to a more limited degree, a solvated hydroxide. By comparing results from DFTB3 models that differ in the description of water, we confirm that proton transfer energetics are adequately described by the standard DFTB3/3OB model for meaningful mechanistic analyses. For QM/MM applications, a robust parametrization of QM-MM interactions requires an explicit consideration of condensed phase properties, for which an efficient sampling technique was developed recently and is reviewed here. The discussions help make clear the value and limitations of DFTB3 based simulations, as well as the developments needed to further improve the accuracy and transferability of the methodology.
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Affiliation(s)
- Puja Goyal
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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Gao J, Truhlar DG, Wang Y, Mazack MJM, Löffler P, Provorse MR, Rehak P. Explicit polarization: a quantum mechanical framework for developing next generation force fields. Acc Chem Res 2014; 47:2837-45. [PMID: 25098651 PMCID: PMC4165456 DOI: 10.1021/ar5002186] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Molecular mechanical force fields have been successfully used to
model condensed-phase and biological systems for a half century. By
means of careful parametrization, such classical force fields can
be used to provide useful interpretations of experimental findings
and predictions of certain properties. Yet, there is a need to further
improve computational accuracy for the quantitative prediction of
biomolecular interactions and to model properties that depend on the
wave functions and not just the energy terms. A new strategy called
explicit polarization (X-Pol) has been developed to construct the
potential energy surface and wave functions for macromolecular and
liquid-phase simulations on the basis of quantum mechanics rather
than only using quantum mechanical results to fit analytic force fields.
In this spirit, this approach is called a quantum mechanical force
field (QMFF). X-Pol is a general fragment method for electronic
structure calculations
based on the partition of a condensed-phase or macromolecular system
into subsystems (“fragments”) to achieve computational
efficiency. Here, intrafragment energy and the mutual electronic polarization
of interfragment interactions are treated explicitly using quantum
mechanics. X-Pol can be used as a general, multilevel electronic structure
model for macromolecular systems, and it can also serve as a new-generation
force field. As a quantum chemical model, a variational many-body
(VMB) expansion approach is used to systematically improve interfragment
interactions, including exchange repulsion, charge delocalization,
dispersion, and other correlation energies. As a quantum mechanical
force field, these energy terms are approximated by empirical functions
in the spirit of conventional molecular mechanics. This Account first
reviews the formulation of X-Pol, in the full variationally correct
version, in the faster embedded version, and with systematic many-body
improvements. We discuss illustrative examples involving water clusters
(which show the power of two-body corrections), ethylmethylimidazolium
acetate ionic liquids (which reveal that the amount of charge transfer
between anion and cation is much smaller than what has been assumed
in some classical simulations), and a solvated protein in aqueous
solution (which shows that the average charge distribution of carbonyl
groups along the polypeptide chain depends strongly on their position
in the sequence, whereas they are fixed in most classical force fields).
The development of QMFFs also offers an opportunity to extend the
accuracy of biochemical simulations to areas where classical force
fields are often insufficient, especially in the areas of spectroscopy,
reactivity, and enzyme catalysis.
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Affiliation(s)
- Jiali Gao
- Theoretical
Chemistry Institute, State Key Laboratory of Theoretical and Computational
Chemistry, Jilin University, Changchun, Jilin Province 130028, People’s Republic of China
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Donald G. Truhlar
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yingjie Wang
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michael J. M. Mazack
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Patrick Löffler
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Makenzie R. Provorse
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Pavel Rehak
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
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Wang B, Yang KR, Xu X, Isegawa M, Leverentz HR, Truhlar DG. Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates. Acc Chem Res 2014; 47:2731-8. [PMID: 24841937 DOI: 10.1021/ar500068a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Ke R. Yang
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Xuefei Xu
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Miho Isegawa
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Hannah R. Leverentz
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
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Grimme S. A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations. J Chem Theory Comput 2014; 10:4497-514. [DOI: 10.1021/ct500573f] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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41
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Yang ZZ, Wang JJ, Zhao DX. Valence state parameters of all transition metal atoms in metalloproteins-development of ABEEMσπ fluctuating charge force field. J Comput Chem 2014; 35:1690-706. [DOI: 10.1002/jcc.23676] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/01/2014] [Accepted: 06/18/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Jian-Jiang Wang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
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42
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Zhou N, Lu Z, Wu Q, Zhang Y. Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis. J Chem Phys 2014; 140:214117. [PMID: 24908000 PMCID: PMC4048451 DOI: 10.1063/1.4881255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/21/2014] [Indexed: 11/14/2022] Open
Abstract
We examine interatomic interactions for rare gas dimers using the density-based energy decomposition analysis (DEDA) in conjunction with computational results from CCSD(T) at the complete basis set (CBS) limit. The unique DEDA capability of separating frozen density interactions from density relaxation contributions is employed to yield clean interaction components, and the results are found to be consistent with the typical physical picture that density relaxations play a very minimal role in rare gas interactions. Equipped with each interaction component as reference, we develop a new three-term molecular mechanical force field to describe rare gas dimers: a smeared charge multipole model for electrostatics with charge penetration effects, a B3LYP-D3 dispersion term for asymptotically correct long-range attractions that is screened at short-range, and a Born-Mayer exponential function for the repulsion. The resulted force field not only reproduces rare gas interaction energies calculated at the CCSD(T)/CBS level, but also yields each interaction component (electrostatic or van der Waals) which agrees very well with its corresponding reference value.
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Affiliation(s)
- Nengjie Zhou
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Zhenyu Lu
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Qin Wu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, USA
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43
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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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Duke RE, Starovoytov ON, Piquemal JP, Cisneros GA. GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:1361-5. [PMID: 26580355 PMCID: PMC5207213 DOI: 10.1021/ct500050p] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GEM*, a force field that combines Coulomb and Exchange terms calculated with Hermite Gaussians with the polarization, bonded, and modified van der Waals terms from AMOEBA is presented. GEM* is tested on an initial water model fitted at the same level as AMOEBA. The integrals required for the evaluation of the intermolecular Coulomb interactions are efficiently evaluated by means of reciprocal space methods. The GEM* water model is tested by comparing energies and forces for a series of water oligomers and MD simulations. Timings for GEM* compared to AMOEBA are presented and discussed.
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Affiliation(s)
- Robert E. Duke
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Oleg N. Starovoytov
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Jean-Philip Piquemal
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7616 Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu 75005, Paris, France
- CNRS, UMR 7616 Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu 75005, Paris, France
| | - G. Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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45
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Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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46
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Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
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Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
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Ansorg K, Tafipolsky M, Engels B. Cation−π Interactions: Accurate Intermolecular Potential from Symmetry-Adapted Perturbation Theory. J Phys Chem B 2013; 117:10093-102. [DOI: 10.1021/jp403578r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kay Ansorg
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Maxim Tafipolsky
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Bernd Engels
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
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48
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Lao KU, Herbert JM. An improved treatment of empirical dispersion and a many-body energy decomposition scheme for the explicit polarization plus symmetry-adapted perturbation theory (XSAPT) method. J Chem Phys 2013; 139:034107. [DOI: 10.1063/1.4813523] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Hou G, Cui Q. Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily. J Am Chem Soc 2013; 135:10457-69. [PMID: 23786365 PMCID: PMC3759165 DOI: 10.1021/ja403293d] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The first step for the hydrolysis of a phosphate monoester (pNPP(2-)) in enzymes of the alkaline phosphatase (AP) superfamily, R166S AP and wild-type NPP, is studied using QM/MM simulations based on an approximate density functional theory (SCC-DFTBPR) and a recently introduced QM/MM interaction Hamiltonian. The calculations suggest that similar loose transition states are involved in both enzymes, despite the fact that phosphate monoesters are the cognate substrates for AP but promiscuous substrates for NPP. The computed loose transition states are clearly different from the more synchronous ones previously calculated for diester reactions in the same AP enzymes. Therefore, our results explicitly support the proposal that AP enzymes are able to recognize and stabilize different types of transition states in a single active site. Analysis of the structural features of computed transition states indicates that the plastic nature of the bimetallic site plays a minor role in accommodating multiple types of transition states and that the high degree of solvent accessibility of the AP active site also contributes to its ability to stabilize diverse transition-state structures without the need of causing large structural distortions of the bimetallic motif. The binding mode of the leaving group in the transition state highlights that vanadate may not always be an ideal transition state analog for loose phosphoryl transfer transition states.
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Affiliation(s)
- Guanhua Hou
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
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50
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Du L, Gao J, Bi F, Wang L, Liu C. A polarizable ellipsoidal force field for halogen bonds. J Comput Chem 2013; 34:2032-40. [PMID: 23804187 DOI: 10.1002/jcc.23362] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/14/2013] [Accepted: 05/29/2013] [Indexed: 01/22/2023]
Abstract
The anisotropic effects and short-range quantum effects are essential characters in the formation of halogen bonds. Since there are an array of applications of halogen bonds and much difficulty in modeling them in classical force fields, the current research reports solely the polarizable ellipsoidal force field (PEff) for halogen bonds. The anisotropic charge distribution was represented with the combination of a negative charged sphere and a positively charged ellipsoid. The polarization energy was incorporated by the induced dipole model. The resulting force field is "physically motivated," which includes separate, explicit terms to account for the electrostatic, repulsion/dispersion, and polarization interaction. Furthermore, it is largely compatible with existing, standard simulation packages. The fitted parameters are transferable and compatible with the general AMBER force field. This PEff model could correctly reproduces the potential energy surface of halogen bonds at MP2 level. Finally, the prediction of the halogen bond properties of human Cathepsin L (hcatL) has been found to be in excellent qualitative agreement with the cocrystal structures.
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Affiliation(s)
- Likai Du
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, People's Republic China
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