1
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Juraskova V, Celerse F, Laplaza R, Corminboeuf C. Assessing the persistence of chalcogen bonds in solution with neural network potentials. J Chem Phys 2022; 156:154112. [DOI: 10.1063/5.0085153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environment effects, which promote competing interactions and alter their static gas-phase properties. Recently, neural network potentials (NNPs) trained on Density Functional Theory (DFT) data have become increasingly popular to simulate molecular phenomena in condensed phase with an accuracy comparable to ab initio methods. To date, most applications have centered on solid-state materials or fairly simple molecules made of a limited number of elements. Herein, we focus on the persistence and strength of chalcogen bonds involving a benzotelluradiazole in condensed phase. While the tellurium-containing heteroaromatic molecules are known to exhibit pronounced interactions with anions and lone pairs of different atoms, the relevance of competing intermolecular interactions, notably with the solvent, is complicated to monitor experimentally but also challenging to model at an accurate electronic structure level. Here, we train direct and baselined NNPs to reproduce hybrid DFT energies and forces in order to identify what are the most prevalent non-covalent interactions occurring in a solute-Cl$^-$-THF mixture. The simulations in explicit solvent highlight competition with chalcogen bonds formed with the solvent and the short-range directionality of the interaction with direct consequences for the molecular properties in the solution. The comparison with other potentials (e.g., AMOEBA, direct NNP and continuum solvent model) also demonstrates that baselined NNPs offer a reliable picture of the non-covalent interaction interplay occurring in solution.
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2
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Naseem-Khan S, Piquemal JP, Cisneros GA. Improvement of the Gaussian Electrostatic Model by separate fitting of Coulomb and exchange-repulsion densities and implementation of a new dispersion term. J Chem Phys 2021; 155:194103. [PMID: 34800949 PMCID: PMC8598263 DOI: 10.1063/5.0072380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/28/2021] [Indexed: 11/15/2022] Open
Abstract
The description of each separable contribution of the intermolecular interaction is a useful approach to develop polarizable force fields (polFFs). The Gaussian Electrostatic Model (GEM) is based on this approach, coupled with the use of density fitting techniques. In this work, we present the implementation and testing of two improvements of GEM: the Coulomb and exchange-repulsion energies are now computed with separate frozen molecular densities and a new dispersion formulation inspired by the Sum of Interactions Between Fragments Ab initio Computed polFF, which has been implemented to describe the dispersion and charge-transfer interactions. Thanks to the combination of GEM characteristics and these new features, we demonstrate a better agreement of the computed structural and condensed properties for water with experimental results, as well as binding energies in the gas phase with the ab initio reference compared with the previous GEM* potential. This work provides further improvements to GEM and the items that remain to be improved and the importance of the accurate reproduction for each separate contribution.
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Affiliation(s)
- Sehr Naseem-Khan
- Department of Chemistry, University of North Texas, Denton, Texas 76201, USA
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France
| | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, USA
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3
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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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4
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Zhang P, Han J, Cieplak P, Cheung MS. Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif. J Chem Phys 2021; 154:124104. [PMID: 33810667 DOI: 10.1063/5.0037517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding atoms required for stability. In this work, we observed a wide variation in Ca2+ binding loop conformations of the Ca2+-binding protein calmodulin, which adopts the most populated ternary structures determined from the molecular dynamics simulations, followed by ab initio quantum mechanical (QM) calculations on all 12 amino acids in the loop that coordinate Ca2+ in aqueous solution. Ca2+ charges were derived by fitting to the electrostatic potential in the context of a classical or polarizable force field (PFF). We discovered that the atomic radius of Ca2+ in conventional force fields is too large for the QM calculation to capture the variation in the coordination geometry of Ca2+ in its ionic form, leading to unphysical charges. Specifically, we found that the fitted atomic charges of Ca2+ in the context of PFF depend on the coordinating geometry of electronegative atoms from the amino acids in the loop. Although nearby water molecules do not influence the atomic charge of Ca2+, they are crucial for compensating for the coordination of Ca2+ due to the conformational flexibility in the EF-hand loop. Our method advances the development of force fields for metal ions and protein binding sites in dynamic environments.
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Affiliation(s)
- Pengzhi Zhang
- Department of Physics, University of Houston, Houston, Texas 77204, USA
| | - Jaebeom Han
- Department of Physics, University of Houston, Houston, Texas 77204, USA
| | - Piotr Cieplak
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, Texas 77204, USA
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5
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Lambros E, Paesani F. How good are polarizable and flexible models for water: Insights from a many-body perspective. J Chem Phys 2020; 153:060901. [DOI: 10.1063/5.0017590] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
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6
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Vázquez-Montelongo EA, Vázquez-Cervantes JE, Cisneros GA. Current Status of AMOEBA-IL: A Multipolar/Polarizable Force Field for Ionic Liquids. Int J Mol Sci 2020; 21:ijms21030697. [PMID: 31973103 PMCID: PMC7037047 DOI: 10.3390/ijms21030697] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/11/2020] [Accepted: 01/16/2020] [Indexed: 01/25/2023] Open
Abstract
Computational simulations of ionic liquid solutions have become a useful tool to investigate various physical, chemical and catalytic properties of systems involving these solvents. Classical molecular dynamics and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations of IL systems have provided significant insights at the atomic level. Here, we present a review of the development and application of the multipolar and polarizable force field AMOEBA for ionic liquid systems, termed AMOEBA–IL. The parametrization approach for AMOEBA–IL relies on the reproduction of total quantum mechanical (QM) intermolecular interaction energies and QM energy decomposition analysis. This approach has been used to develop parameters for imidazolium– and pyrrolidinium–based ILs coupled with various inorganic anions. AMOEBA–IL has been used to investigate and predict the properties of a variety of systems including neat ILs and IL mixtures, water exchange reactions on lanthanide ions in IL mixtures, IL–based liquid–liquid extraction, and effects of ILs on an aniline protection reaction.
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Affiliation(s)
| | | | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA; (E.A.V.-M.); (J.E.V.-C.)
- Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, TX 76201, USA
- Correspondence:
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7
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Vázquez-Montelongo EA, Cisneros GA, Flores-Ruiz HM. Multipolar/polarizable molecular dynamics simulations of Liquid–Liquid extraction of benzene from hydrocarbons using ionic liquids. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111846] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Bedrov D, Piquemal JP, Borodin O, MacKerell AD, Roux B, Schröder C. Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields. Chem Rev 2019; 119:7940-7995. [PMID: 31141351 PMCID: PMC6620131 DOI: 10.1021/acs.chemrev.8b00763] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Indexed: 11/30/2022]
Abstract
Many applications in chemistry, biology, and energy storage/conversion research rely on molecular simulations to provide fundamental insight into structural and transport properties of materials with high ionic concentrations. Whether the system is comprised entirely of ions, like ionic liquids, or is a mixture of a polar solvent with a salt, e.g., liquid electrolytes for battery applications, the presence of ions in these materials results in strong local electric fields polarizing solvent molecules and large ions. To predict properties of such systems from molecular simulations often requires either explicit or mean-field inclusion of the influence of polarization on electrostatic interactions. In this manuscript, we review the pros and cons of different treatments of polarization ranging from the mean-field approaches to the most popular explicit polarization models in molecular dynamics simulations of ionic materials. For each method, we discuss their advantages and disadvantages and emphasize key assumptions as well as their adjustable parameters. Strategies for the development of polarizable models are presented with a specific focus on extracting atomic polarizabilities. Finally, we compare simulations using polarizable and nonpolarizable models for several classes of ionic systems, discussing the underlying physics that each approach includes or ignores, implications for implementation and computational efficiency, and the accuracy of properties predicted by these methods compared to experiments.
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Affiliation(s)
- Dmitry Bedrov
- Department
of Materials Science & Engineering, University of Utah, 122 South Central Campus Drive, Room 304, Salt Lake City, Utah 84112, United States
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Université,
UMR 7616 CNRS, CC137, 4 Place Jussieu, Tour 12-13, 4ème étage, 75252 Paris Cedex 05, France
- Institut
Universitaire de France, 75005, Paris Cedex 05, France
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Oleg Borodin
- Electrochemistry
Branch, Sensors and Electron Devices Directorate, Army Research Laboratory, 2800 Powder Mill Road, Adelphi, Maryland 20703, United
States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, Gordon Center for Integrative
Science, University of Chicago, 929 57th Street, Chicago, Illinois 60637, United States
| | - Christian Schröder
- Department
of Computational Biological Chemistry, University
of Vienna, Währinger Strasse 17, A-1090 Vienna, Austria
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9
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Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Toward Learned Chemical Perception of Force Field Typing Rules. J Chem Theory Comput 2019; 15:402-423. [PMID: 30512951 PMCID: PMC6467725 DOI: 10.1021/acs.jctc.8b00821] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mechanics force fields define how the energy and forces in a molecular system are computed from its atomic positions, thus enabling the study of such systems through computational methods like molecular dynamics and Monte Carlo simulations. Despite progress toward automated force field parametrization, considerable human expertise is required to develop or extend force fields. In particular, human input has long been required to define atom types, which encode chemically unique environments that determine which parameters will be assigned. However, relying on humans to establish atom types is suboptimal. Human-created atom types are often developed without statistical justification, leading to over- or under-fitting of data. Human-created types are also difficult to extend in a systematic and consistent manner when new chemistries must be modeled or new data becomes available. Finally, human effort is not scalable when force fields must be generated for new (bio)polymers, compound classes, or materials. To remedy these deficiencies, our long-term goal is to replace human specification of atom types with an automated approach, based on rigorous statistics and driven by experimental and/or quantum chemical reference data. In this work, we describe novel methods that automate the discovery of appropriate chemical perception: SMARTY allows for the creation of atom types, while SMIRKY goes further by automating the creation of fragment (nonbonded, bonds, angles, and torsions) types. These approaches enable the creation of move sets in atom or fragment type space, which are used within a Monte Carlo optimization approach. We demonstrate the power of these new methods by automating the rediscovery of human defined atom types (SMARTY) or fragment types (SMIRKY) in existing small molecule force fields. We assess these approaches using several molecular data sets, including one which covers a diverse subset of the DrugBank database.
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Affiliation(s)
- Camila Zanette
- Department of Pharmaceutical Sciences, University of California, Irvine
| | | | | | - Josh Fass
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
| | - Michael R. Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - David L. Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine
- Department of Chemistry, University of California, Irvine
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10
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Vázquez-Montelongo EA, Vázquez-Cervantes JE, Cisneros GA. Polarizable ab initio QM/MM Study of the Reaction Mechanism of N- tert-Butyloxycarbonylation of Aniline in [EMIm][BF₄]. Molecules 2018; 23:E2830. [PMID: 30384470 PMCID: PMC6278528 DOI: 10.3390/molecules23112830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 12/25/2022] Open
Abstract
N-t e r t-butoxycarbonylation of amines in solution (water, organic solvents, or ionic liquids) is a common reaction for the preparation of drug molecules. To understand the reaction mechanism and the role of the solvent, quantum mechanical/molecular mechanical simulations using a polarizable multipolar force field with long⁻range electrostatic corrections were used to optimize the minimum energy paths (MEPs) associated with various possible reaction mechanisms employing the nudged elastic band (NEB) and the quadratic string method (QSM). The calculated reaction energies and energy barriers were compared with the corresponding gas-phase and dichloromethane results. Complementary Electron Localization Function (ELF)/NCI analyses provide insights on the critical structures along the MEP. The calculated results suggest the most likely path involves a sequential mechanism with the rate⁻limiting step corresponding to the nucleophilic attack of the aniline, followed by proton transfer and the release of CO 2 without the direct involvement of imidazolium cations as catalysts.
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Affiliation(s)
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA.
- The Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, TX 76201, USA.
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11
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Gökcan H, Kratz E, Darden TA, Piquemal JP, Cisneros GA. QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential. J Phys Chem Lett 2018; 9:3062-3067. [PMID: 29775314 PMCID: PMC6069983 DOI: 10.1021/acs.jpclett.8b01412] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The use of advanced polarizable potentials in quantum mechanical/molecular mechanical (QM/MM) simulations has been shown to improve the overall accuracy of the calculation. We have developed a density-based potential called the Gaussian electrostatic model (GEM), which has been shown to provide very accurate environments for QM wave functions in QM/MM. In this contribution we present a new implementation of QM/GEM that extends our implementation to include all components (Coulomb, exchange-repulsion, polarization, and dispersion) for the total intermolecular interaction energy in QM/MM calculations, except for the charge-transfer term. The accuracy of the method is tested using a subset of water dimers from the water dimer potential energy surface reported by Babin et al. ( J. Chem. Theory Comput. 2013 9, 5395-5403). Additionally, results of the new implementation are contrasted with results obtained with the classical AMOEBA potential. Our results indicate that GEM provides an accurate MM environment with average root-mean-square error <0.15 kcal/mol for every intermolecular interaction energy component compared with SAPT2+3/aug-cc-pVTZ reference calculations.
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Affiliation(s)
- Hatice Gökcan
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Eric Kratz
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Thomas A. Darden
- OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States
| | - Jean-Philip Piquemal
- Department of Chemistry, Sorbonne Université, Paris 75005, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Insitute Universitaire de France, Paris 75231, France
| | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
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12
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Blanco-Díaz EG, Vázquez-Montelongo EA, Cisneros GA, Castrejón-González EO. Computational investigation of non-covalent interactions in 1-butyl 3-methylimidazolium/bis(trifluoromethylsulfonyl)imide [bmim][Tf2N] in EMD and NEMD. J Chem Phys 2018; 148:054303. [DOI: 10.1063/1.5017987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Edgar G. Blanco-Díaz
- Departamento de Ingeniería Química, Tecnológico Nacional de México en Celaya, Celaya, Guanajuato 38010,
Mexico
| | | | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76206, USA
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13
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Torabifard H, Reed L, Berry MT, Hein JE, Menke E, Cisneros GA. Computational and experimental characterization of a pyrrolidinium-based ionic liquid for electrolyte applications. J Chem Phys 2017; 147:161731. [DOI: 10.1063/1.5004680] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hedieh Torabifard
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Luke Reed
- Department of Chemistry and Chemical Biology, University of California-Merced, Merced, California 95343, USA
| | - Matthew T. Berry
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Jason E. Hein
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Erik Menke
- Department of Chemistry and Chemical Biology, University of California-Merced, Merced, California 95343, USA
| | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76203, USA
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14
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Walker AR, Cisneros GA. Computational Simulations of DNA Polymerases: Detailed Insights on Structure/Function/Mechanism from Native Proteins to Cancer Variants. Chem Res Toxicol 2017; 30:1922-1935. [PMID: 28877429 PMCID: PMC5696005 DOI: 10.1021/acs.chemrestox.7b00161] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Genetic information is vital in the
cell cycle of DNA-based organisms.
DNA polymerases (DNA Pols) are crucial players in transactions dealing
with these processes. Therefore, the detailed understanding of the
structure, function, and mechanism of these proteins has been the
focus of significant effort. Computational simulations have been applied
to investigate various facets of DNA polymerase structure and function.
These simulations have provided significant insights over the years.
This perspective presents the results of various computational studies
that have been employed to research different aspects of DNA polymerases
including detailed reaction mechanism investigation, mutagenicity
of different metal cations, possible factors for fidelity synthesis,
and discovery/functional characterization of cancer-related mutations
on DNA polymerases.
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Affiliation(s)
- Alice R Walker
- Department of Chemistry, University of North Texas , 1155 Union Circle, Denton, Texas 76203, United States
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas , 1155 Union Circle, Denton, Texas 76203, United States
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15
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Torabifard H, Cisneros GA. Computational investigation of O 2 diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O 2 transport. Chem Sci 2017; 8:6230-6238. [PMID: 28989656 PMCID: PMC5628400 DOI: 10.1039/c7sc00997f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022] Open
Abstract
E. Coli AlkB catalyzes the direct dealkylation of various alkylated bases in damaged DNA. The diffusion of molecular oxygen to the active site in AlkB is an essential step for the oxidative dealkylation activity. Despite detailed studies on the stepwise oxidation mechanism of AlkB, there is no conclusive picture of how O2 molecules reach the active site of the protein. Yu et al. (Nature, 439, 879) proposed the existence of an intra-molecular tunnel based on their initial crystal structures of AlkB. We have employed computational simulations to investigate possible migration pathways inside AlkB for O2 molecules. Extensive molecular dynamics (MD) simulations, including explicit ligand sampling and potential of mean force (PMF) calculations, have been performed to provide a microscopic description of the O2 delivery pathway in AlkB. Analysis of intra-molecular tunnels using the CAVER software indicates two possible pathways for O2 to diffuse into the AlkB active site. Explicit ligand sampling simulations suggests that only one of these tunnels provides a viable route. The free energy path for an oxygen molecule to travel along each of these tunnels has been determined with AMBER and AMOEBA. Both PMFs indicate passive transport of O2 from the surface of the protein. However, the inclusion of explicit polarization shows a very large barrier for diffusion of the co-substrate out of the active site, compared with the non-polarizable potential. In addition, our results suggest that the mutation of a conserved residue along the tunnel, Y178, has dramatic effects on the dynamics of AlkB and on the transport of O2 along the tunnel.
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Affiliation(s)
- Hedieh Torabifard
- Department of Chemistry , Wayne State University , Detroit , MI 48202 , USA
| | - G Andrés Cisneros
- Department of Chemistry , University of North Texas , Denton , TX 76203 , USA .
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16
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Starovoytov ON, Zhang P, Cieplak P, Cheung MS. Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state. Phys Chem Chem Phys 2017; 19:22969-22980. [DOI: 10.1039/c7cp03177g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Free energy surface of the light-harvesting triad employing a non-polarizable force field (NFF) and a polarizable force field (PFF) shows that induced polarization limits the motion of rotation about chemical bonds as well as bending at the porphyrin, which are prominent using the NFF, thus limiting the conformational space of the triad.
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Affiliation(s)
| | - Pengzhi Zhang
- Department of Physics
- University of Houston
- Houston
- USA
| | - Piotr Cieplak
- Sanford Burnham Prebys Medical Discovery Institute
- La Jolla
- USA
| | - Margaret S. Cheung
- Department of Physics
- University of Houston
- Houston
- USA
- Center for Theoretical Biological Physics
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17
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Cisneros G, Wikfeldt KT, Ojamäe L, Lu J, Xu Y, Torabifard H, Bartók AP, Csányi G, Molinero V, Paesani F. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions. Chem Rev 2016; 116:7501-28. [PMID: 27186804 PMCID: PMC5450669 DOI: 10.1021/acs.chemrev.5b00644] [Citation(s) in RCA: 278] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Indexed: 12/17/2022]
Abstract
Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.
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Affiliation(s)
| | - Kjartan Thor Wikfeldt
- Science
Institute, University of Iceland, VR-III, 107, Reykjavik, Iceland
- Department
of Physics, Albanova, Stockholm University, S-106 91 Stockholm, Sweden
| | - Lars Ojamäe
- Department
of Chemistry, Linköping University, SE-581 83 Linköping, Sweden
| | - Jibao Lu
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Yao Xu
- Lehrstuhl
Physikalische Chemie II, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Hedieh Torabifard
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Albert P. Bartók
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Gábor Csányi
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Valeria Molinero
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Francesco Paesani
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
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