1
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Chatterjee S, Nochebuena J, Cisneros GA. Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity. J Am Chem Soc 2024; 146:13247-13257. [PMID: 38701006 DOI: 10.1021/jacs.4c01100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Horseradish peroxidase (HRP) is an enzyme that oxidizes pollutants from wastewater. A previous report indicated that peroxidases can have an enhancement in initial enzymatic activity in an aqueous solution of 0.26 M 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) at neutral pH. However, the atomistic details remain elusive. In the enzymatic landscape of HRP, compound II (Cpd II) plays a key role and involves a histidine (H42) residue. Cpd II exists as oxoferryl (2a) or hydroxoferryl (2b(FeIV)) forms, where 2a is the predominantly observed form in experimental studies. Intriguingly, the ferric 2b(FeIII) form seen in synthetic complexes has not been observed in HRP. Here, we have investigated the structure and dynamics of HRP in pure water and aqueous [EMIm][EtSO4] (0.26 M), as well as the reaction mechanism of 2a to 2b conversion using polarizable molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations. When HRP is solvated in aq [EMIm][EtSO4], the catalytic water displaces, and H42 directly orients over the ferryl moiety, allowing a direct proton transfer (PT) with a significant energy barrier reduction. Conversely, in neat water, the reaction of 2a to 2b follows the previously reported mechanism. We further investigated the deprotonated form of H42. Analysis of the electric fields at the active site indicates that the aq [EMIm][EtSO4] medium facilitates the reaction by providing a more favorable environment compared with the system solvated in neat water. Overall, the atomic level supports the previous experimental observations and underscores the importance of favorable electric fields in the active site to promote catalysis.
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Affiliation(s)
- Shubham Chatterjee
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
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2
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Solovyova IV, Yang S, Starovoytov ON. Molecular dynamics simulation studies of 1,3-dimethyl imidazolium nitrate ionic liquid with water. J Chem Phys 2023; 158:084505. [PMID: 36859108 DOI: 10.1063/5.0134465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The fundamental understanding of intermolecular interactions of ionic liquids (ILs) with water is essential in predicting IL-water thermodynamic properties. In this study, intermolecular or noncovalent interactions were studied for 1,3-dimethyl imidazolium [DMIM]+ cation and nitrate [NO3]- anion with water, employing quantum mechanics and molecular dynamics simulations. Molecular dynamics simulations were performed using a revised multipolar polarizable force field. The effect of water on ionic liquids was evaluated in terms of thermodynamic and dynamic properties. Thermodynamic properties included liquid densities ρ, excess molar volumes ΔVE, and liquid structures gr. Dynamic properties included self-diffusion coefficients D of mixture constituents as a function of water concentration. The density of ionic liquid-water mixtures monotonically decrease with increasing concentration of water. A negative excess volume was obtained for low and high water concentrations, demonstrating strong intermolecular interactions of water with ionic liquid components. Liquid structures of ionic liquid-water mixtures revealed a tendency for anions to interact with cations at shorter intermolecular distances when the water concentration is increased. Diffusion rates were found to increase for all mixture components with increase in the fraction of water. A significant change in the diffusion rate was found at ∼0.3 weight fraction of water. However, the water self-diffusion coefficient was dominant at all concentrations. The ratio of water/anion and anion/cation self-diffusion coefficients was found to decrease linearly with increasing concentration of water molecules.
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Affiliation(s)
- Iana V Solovyova
- Institute of Engineering Science, Ural Branch of the Russian Academy of Sciences, Yekaterinburg 620049, Russia
| | - Shizhong Yang
- Southern University and A&M College, Department of Computer Science, Baton Rouge, Louisiana 70807, USA
| | - Oleg N Starovoytov
- Southern University and A&M College, Department of Computer Science, Baton Rouge, Louisiana 70807, USA
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3
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Binninger T, Saraç D, Marsh L, Picard T, Doublet ML, Raynaud C. AMOEBA Polarizable Force Field for Molecular Dynamics Simulations of Glyme Solvents. J Chem Theory Comput 2023; 19:1023-1034. [PMID: 36692444 DOI: 10.1021/acs.jctc.2c00926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Classical molecular dynamics (MD) simulations of electrolyte systems are important to gain insight into the atom-scale properties that determine the battery-relevant performance. The recent Tinker-HP software release enables efficient and accurate MD simulations with the AMOEBA polarizable force field. In this work, we developed a procedure to construct a universal AMOEBA model for the solvent family of glymes (glycol methyl ethers), which involves a refinement scheme for valence parameters by fitting the AMOEBA-derived atomic forces to those computed at the DFT level. The refined AMOEBA model provides a good description of both local and nonlocal properties in terms of the spectroscopic response of glyme molecules, as well as the liquid glyme density and dielectric constant. In addition, the complexation energies of alkali and alkaline-earth metal cations with tetraglyme molecules obtained from AMOEBA calculations are in good agreement with DFT results, demonstrating the suitability of the developed AMOEBA model for an accurate simulation of glyme-based battery electrolytes. We also expect the procedure to be transferable to the development of AMOEBA models for other battery electrolyte systems.
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Affiliation(s)
- Tobias Binninger
- ICGM, Université de Montpellier, CNRS, ENSCM, 34095Montpellier, France
| | - Defne Saraç
- ICGM, Université de Montpellier, CNRS, ENSCM, 34095Montpellier, France.,Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS3459, Hub de l'Energie, 80039Amiens, France
| | - Liam Marsh
- ICGM, Université de Montpellier, CNRS, ENSCM, 34095Montpellier, France
| | - Tanguy Picard
- LEPMI, Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, Grenoble INP, 38000Grenoble, France
| | - Marie-Liesse Doublet
- ICGM, Université de Montpellier, CNRS, ENSCM, 34095Montpellier, France.,Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS3459, Hub de l'Energie, 80039Amiens, France
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4
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Chen S, Voth GA. How Does Electronic Polarizability or Scaled-Charge Affect the Interfacial Properties of Room Temperature Ionic Liquids? J Phys Chem B 2023; 127:1264-1275. [PMID: 36701801 PMCID: PMC9924258 DOI: 10.1021/acs.jpcb.2c07981] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/01/2023] [Indexed: 01/27/2023]
Abstract
The room temperature ionic liquid (RTIL) air-liquid interface plays an important role in many applications. Herein, we present molecular dynamics simulation results for the air-liquid interface of a common RTIL, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide, [C4mim][NTf2]. To elucidate the effects of electronic polarizability and scaled-charge ions on the properties of the RTIL air-liquid interface, we employ three different kinds of force fields: a nonpolarizable force field (FF) with united ion charges (FixQ), a nonpolarizable FF with scaled-charge by 0.8 (ScaleQ), and a polarizable FF (Drude). To identify whether the ions reside at the interface or not, the method of identification of the truly interfacial molecules is used. The structural and dynamical properties in the interfacial, subinterfacial, and central layers are evaluated. In general for bulk liquids, the FixQ model predicts too-ordered structures and too-sluggish dynamics, while the ScaleQ model can serve as a simple cure. However, the ScaleQ model cannot reproduce the results of the Drude model at the interface, due to an inappropriate scaled-down charge near the interface.
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Affiliation(s)
- Sijia Chen
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, The James Franck Institute,
and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois60637, United States
| | - Gregory A. Voth
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, The James Franck Institute,
and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois60637, United States
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5
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Szabadi A, Schröder C. Recent Developments in Polarizable Molecular Dynamics Simulations of Electrolyte Solutions. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2022. [DOI: 10.1142/s2737416521420035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Polarizable molecular dynamics simulations are a fast progressing field in the scientific research of ionic liquids. The fundamentals of polarizable simulations, as well as their application to ionic liquids, were summarized in a review [Bedrov, D.; Piquemal, J.-P.; Borodin, O.; MacKerell, Jr., A. D.; Roux, B.; Schröder, C. Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields. Chem. Rev. 2019, 119, 7940–7995] in 2019. Since then, new methods to treat intermolecular interaction of induced dipoles in these highly charged systems were developed. This concerns the damping of these interactions and additional charge transfer as well as the prediction of ionic materials with ultrahigh refractive indices. In addition to the progress of the polarizable force fields, also thermostats and barostats for polarizable simulations evolved recently.
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Affiliation(s)
- András Szabadi
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, A-1090 Vienna, Austria
| | - Christian Schröder
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, A-1090 Vienna, Austria
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6
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Maglia de Souza R, Karttunen M, Ribeiro MCC. Fine-Tuning the Polarizable CL&Pol Force Field for the Deep Eutectic Solvent Ethaline. J Chem Inf Model 2021; 61:5938-5947. [PMID: 34797679 DOI: 10.1021/acs.jcim.1c01181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polarizable force fields are gradually becoming a common choice for ionic soft matter, in particular, for molecular dynamics (MD) simulations of ionic liquids (ILs) and deep eutectic solvents (DESs). The CL&Pol force field introduced in 2019 is the first general, transferable, and polarizable force field for MD simulations of different types of DESs. The original formulation contains, however, some problems that appear in simulations of ethaline and may also have a broader impact. First, the originally proposed atomic diameter parameters are unbalanced, resulting in too weak interactions between the chlorides and the hydroxyl groups of the ethylene glycol molecules. This, in turn, causes an artificial phase separation in long simulations. Second, there is an overpolarization of chlorides due to strong induced dipoles that give rise to the presence of peaks and antipeaks at very low q-vector values (2.4 nm-1) in the partial components of the structure factors. In physical terms, this is equivalent to overestimated spatial nanoscale heterogeneity. To correct these problems, we adjusted the chloride-hydroxyl radial distribution functions against ab initio data and then extended the use of the Tang-Toennis damping function for the chlorides' induced dipoles. These adjustments correct the problems without losing the robustness of the CL&Pol force field. The results were also compared with the nonpolarizable version, the CL&P force field. We expect that the corrections will facilitate reliable use of the CL&Pol force field for other types of DESs.
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Affiliation(s)
- Rafael Maglia de Souza
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, São Paulo 05508-070, Brazil
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada.,Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect V.O. 31, St. Petersburg 199004, Russia
| | - Mauro Carlos Costa Ribeiro
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, São Paulo 05508-070, Brazil
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7
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Starovoytov ON. Development of a Polarizable Force Field for Molecular Dynamics Simulations of Lithium-Ion Battery Electrolytes: Sulfone-Based Solvents and Lithium Salts. J Phys Chem B 2021; 125:11242-11255. [PMID: 34586817 DOI: 10.1021/acs.jpcb.1c05744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A many-body polarizable force field (PFF) was developed for molecular dynamics (MD) simulations of sulfone-based solvents and lithium salts. Development of the polarizable force field included parameterization of atomic polarizabilities, electrostatic interactions, and van der Waals interactions of electrolyte components. 1λ6-thiolane-1,1-dione or sulfolane (SLF) compound was selected as one of the most appropriate solvents for high-voltage battery electrolytes. Atomic polarizabilities for the sulfolane solvent and lithium salts were obtained by means of a combination of quantum mechanics (QM) and molecular mechanics (MM) approaches using the isotropic atomic dipole polarizable (IADP) model. High-quality atomic polarizabilities were refined for 10 atomic types. Intermolecular interactions of Li+ ions with SLF were parameterized to reproduce the binding energies at the MP2/aug-cc-pvDZ level of theory in the gas phase. Intermolecular interactions of Li+ ions with polyatomic anions, such as nitrate [NO3]-, tetrafluoroborate [BF4]-, perchlorate [ClO4]-, hexafluorophosphate [PF6]-, bis(fluorosulfonyl)imide [FSI]-, and bis(trifluoromethylsulfonyl)imide [TFSI]-, were parameterized employing a similar methodology. A series of molecular dynamics simulations was performed for sulfolane-based electrolytes at several different lithium salt concentrations. Thermodynamic, structural, and transport properties were evaluated to validate the force field parameters against available simulation and experimental data. Transport properties of sulfolane were significantly improved as compared with those obtained from MD simulations using a nonpolarizable force field (NFF). A newly developed polarizable potential was shown to reproduce Li+ ion dynamics as a function of salt concentration. Faster diffusion of Li+ ions, among other electrolyte components, was obtained for high salt concentration electrolytes.
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Affiliation(s)
- Oleg N Starovoytov
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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8
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Klajmon M, Červinka C. Does Explicit Polarizability Improve Simulations of Phase Behavior of Ionic Liquids? J Chem Theory Comput 2021; 17:6225-6239. [PMID: 34520200 DOI: 10.1021/acs.jctc.1c00518] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics simulations are performed for a test set of 20 aprotic ionic liquids to investigate whether including an explicit polarizability model in the force field leads to higher accuracy and reliability of the calculated phase behavior properties, especially the enthalpy of fusion. A classical nonpolarizable all-atom optimized potentials for liquid simulations (OPLS) force-field model developed by Canongia Lopes and Pádua (CL&P) serves as a reference level of theory. Polarizability is included either in the form of Drude oscillators, resulting in the CL&P-D models, or in the framework of the atomic multipole optimized energetics for biomolecular application (AMOEBA) force field with polarizable atomic sites. Benchmarking of the calculated fusion enthalpy values against the experimental data reveals that overall the nonpolarizable CL&P model and polarizable CL&P-D models perform similarly with average deviations of about 30%. However, fusion enthalpies from the CL&P-D models exhibit a stronger correlation with their experimental counterparts. The least successful predictions are interestingly obtained from AMOEBA (deviation ca. 60%), which may indicate that a reparametrization of this force-field model is needed to achieve improved predictions of the fusion enthalpy. In general, all FF models tend to underestimate the fusion enthalpies. In addition, quantum chemical calculations are used to compute the electronic cohesive energies of the crystalline phases of the ionic liquids and of the interaction energies within the ion pair. Significant positive correlations are found between the fusion enthalpy and the cohesive energies. The character of the present anions predetermines the magnitude of individual mechanistic components of the interaction energy and related enthalpic and cohesive properties.
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Affiliation(s)
- Martin Klajmon
- Department of Physical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Ctirad Červinka
- Department of Physical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
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9
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Goloviznina K, Gong Z, Padua AAH. The
CL
&Pol polarizable force field for the simulation of ionic liquids and eutectic solvents. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1572] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
| | - Zheng Gong
- Laboratoire de Chimie École Normale Supérieure de Lyon & CNRS Lyon France
| | - Agilio A. H. Padua
- Laboratoire de Chimie École Normale Supérieure de Lyon & CNRS Lyon France
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10
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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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11
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Lu LN, Liu C, Yang ZZ. Systematic Parameterization and Simulation of Boronic Acid-β-Lactamase Aqueous Solution in Developing the ABEEMσπ Polarizable Force Field. J Phys Chem A 2020; 124:8614-8632. [PMID: 32910648 DOI: 10.1021/acs.jpca.0c06806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Boronic acid, an inhibitor of β-lactamase, has begun to be applied to the treatment of biological infections and tumors. Scientists are working to develop new and more effective boronic acid. Molecular dynamics (MD) simulation provides a powerful auxiliary tool for drug design. However, the current force fields have no boron-related parameters. In this work, an atom-bond electronegativity equalization method at the σπ level (ABEEMσπ) polarizable force field (ABEEMσπ PFF) of boronic acid and β-lactamase has been developed to determine the potential functions and parameters. The interaction between boron and serine in β-lactamase is regarded as a bonded mode. The interaction between them is simulated by the Morse potential energy function, which is close to the experimental change of the stretching potential energy in a large range. The potential energy surfaces of the bond length, bond angle, and dihedral angle of boronic acid-β-lactamase have the same stability point and change trend as M06-2X/6-311G**. For 47 boronic acid-β-lactamase training molecules, the linear correlation coefficient (R) of the charge distribution between the ABEEMσπ PFF and HF/STO-3G is greater than 0.96. Attributed to the fact that the charge distribution of the ABEEMσπ PFF can fluctuate with the change of geometry and environment, the polarization effect and charge-transfer effect are well reflected. The binding ability of different boronic acids with the same β-lactamase is different. A total of 10 boronic acid-β-lactamase model molecules and 10 boronic acid-β-lactamase and water complexes are simulated. The order of binding energy of five large model molecules calculated by the ABEEMσπ PFF is consistent with that of the MP2 method. The binding energies of boronic acid-β-lactamase and water complexes are close to those of the MP2 method. The results of MD simulation of five aqueous boronic acid-β-lactamase complexes in the NVT ensemble verify the rationality of boron-related parameters of the ABEEMσπ PFF, which have a good application prospect. This study lays a solid theoretical foundation for further study of the inhibition of boronic acid on β-lactamase.
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Affiliation(s)
- Li-Nan Lu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
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12
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Charge reduction in ions in the ionic liquid 1-ethy-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide on the Au(111) surface. Theor Chem Acc 2020. [DOI: 10.1007/s00214-019-2527-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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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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14
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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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15
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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: 278] [Impact Index Per Article: 55.6] [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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16
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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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17
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Tu YJ, Lin Z, Allen MJ, Cisneros GA. Molecular dynamics investigation of water-exchange reactions on lanthanide ions in water/1-ethyl-3-methylimidazolium trifluoromethylsufate ([EMIm][OTf]). J Chem Phys 2018; 148:024503. [PMID: 29331119 DOI: 10.1063/1.4997008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We report a kinetic study of the water exchange on lanthanide ions in water/[1-ethyl-3-methylimidazolium][trifluoromethylsufate] (water/[EMIm][OTf]). The results from 17O-NMR measurements show that the water-exchange rates in water/[EMIm][OTf] increase with decreasing size of the lanthanide ions. This trend for water-exchange is similar to the previously reported trend in water/1-ethyl-3-methylimidazolium ethyl sulfate (water/[EMIm][EtSO4]) but opposite to that in water. To gain atomic-level insight into these water-exchange reactions, molecular dynamics simulations for lanthanide ions in water/[EMIm][OTf] have been performed using the atomic-multipole-optimized-energetics-for-biomolecular-application polarizable force field. Our molecular dynamics simulations reproduce the experimental water-exchange rates in terms of the trend and provide possible explanations for the observed experimental behavior. The smaller lanthanide ions in water/[EMIm][OTf] undergo faster water exchange because the smaller lanthanide ions coordinate to the first shell [OTf]- anions more tightly, resulting in a stronger screening effect for the second-shell water. The screening effect weakens the interaction of the lanthanide ions with the second-shell water molecules, facilitating the dissociation of water from the second-shell and subsequent association of water molecules from the outer solvation shells.
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Affiliation(s)
- Yi-Jung Tu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Zhijin Lin
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Matthew J Allen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, USA
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18
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Lourenço TC, Zhang Y, Costa LT, Maginn EJ. A molecular dynamics study of lithium-containing aprotic heterocyclic ionic liquid electrolytes. J Chem Phys 2018; 148:193834. [DOI: 10.1063/1.5016276] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Tuanan C. Lourenço
- Instituto de Química, Universidade Federal Fluminense–Outeiro de São João Batista, s/n CEP:24020-141, Niterói, RJ, Brazil
| | - Yong Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Luciano T. Costa
- Instituto de Química, Universidade Federal Fluminense–Outeiro de São João Batista, s/n CEP:24020-141, Niterói, RJ, Brazil
| | - Edward J. Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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19
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McDaniel JG. Polarization Effects in Binary [BMIM+][BF4–]/1,2-Dichloroethane, Acetone, Acetonitrile, and Water Electrolytes. J Phys Chem B 2018; 122:4345-4355. [DOI: 10.1021/acs.jpcb.8b01714] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jesse G. McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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20
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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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21
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Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chem Sci 2018; 9:956-972. [PMID: 29732110 PMCID: PMC5909332 DOI: 10.1039/c7sc04531j] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/24/2017] [Indexed: 12/23/2022] Open
Abstract
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.
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Affiliation(s)
- Louis Lagardère
- Sorbonne Université , Institut des Sciences du Calcul et des Données , Paris , France
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Luc-Henri Jolly
- Sorbonne Université , Institut Parisien de Chimie Physique et Théorique , CNRS , FR 2622 , Paris , France
| | - Filippo Lipparini
- Universita di Pisa , Dipartimento di Chimica e Chimica Industriale , Pisa , Italy
| | - Félix Aviat
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Benjamin Stamm
- MATHCCES , Department of Mathematics , RWTH Aachen University , Aachen , Germany
| | - Zhifeng F Jing
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Matthew Harger
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Hedieh Torabifard
- Department of Chemistry , Wayne State University , Detroit , MI 48202 , USA
| | - G Andrés Cisneros
- Department of Chemistry , University of North Texas , Denton , TX 76202 , USA
| | - Michael J Schnieders
- The University of Iowa , Department of Biomedical Engineering , Iowa City , IA , USA
| | - Nohad Gresh
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
| | - Yvon Maday
- Sorbonne Université , Laboratoire Jacques-Louis Lions , UMR 7598 , CNRS , Paris , France
- Institut Universitaire de France , Paris , France
- Brown University , Division of Applied Maths , Providence , RI , USA
| | - Pengyu Y Ren
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
| | - Jay W Ponder
- Washington University in Saint Louis , Department of Chemistry , Saint Louis , MI , USA
| | - Jean-Philip Piquemal
- Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France .
- The University of Texas at Austin , Department of Biomedical Engineering , TX , USA
- Institut Universitaire de France , Paris , France
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22
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Uhlig F, Zeman J, Smiatek J, Holm C. First-Principles Parametrization of Polarizable Coarse-Grained Force Fields for Ionic Liquids. J Chem Theory Comput 2018; 14:1471-1486. [DOI: 10.1021/acs.jctc.7b00903] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frank Uhlig
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Johannes Zeman
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
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23
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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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24
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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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25
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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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26
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Shahini A, Jin H, Zhou Z, Zhao Y, Chen PY, Hua J, Cheng MMC. Toward individually tunable compound eyes with transparent graphene electrode. BIOINSPIRATION & BIOMIMETICS 2017; 12:046002. [PMID: 28463225 DOI: 10.1088/1748-3190/aa7084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present tunable compound eyes made of ionic liquid lenses, of which both curvatures (R 1 and R 2 in the lensmaker's equation) can be individually changed using electrowetting on dielectric (EWOD) and applied pressure. Flexible graphene is used as a transparent electrode and is integrated on a flexible polydimethylsiloxane (PDMS)/parylene hybrid substrate. Graphene electrodes allow a large lens aperture diameter of between 2.4 mm and 2.74 mm. Spherical aberration analysis is performed using COMSOL to investigate the optical property of the lens under applied voltage and pressure. The final lens system shows a resolution of 645.1 line pair per millimeter. A prototype of a tunable lens array is proposed for the application of a compound eye.
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Affiliation(s)
- Ali Shahini
- Department of Electrical and Computer Engineering, Wayne State University, Detroit, MI 48202, United States of America
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27
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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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28
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Aviat F, Levitt A, Stamm B, Maday Y, Ren P, Ponder JW, Lagardère L, Piquemal JP. Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations. J Chem Theory Comput 2016; 13:180-190. [PMID: 28068773 PMCID: PMC5228058 DOI: 10.1021/acs.jctc.6b00981] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We
introduce a new class of methods, denoted as Truncated Conjugate
Gradient(TCG), to solve the many-body polarization energy and its
associated forces in molecular simulations (i.e. molecular dynamics
(MD) and Monte Carlo). The method consists in a fixed number of Conjugate
Gradient (CG) iterations. TCG approaches provide a scalable solution
to the polarization problem at a user-chosen cost and a corresponding
optimal accuracy. The optimality of the CG-method guarantees that
the number of the required matrix-vector products are reduced to a
minimum compared to other iterative methods. This family of methods
is non-empirical, fully adaptive, and provides analytical gradients,
avoiding therefore any energy drift in MD as compared to popular iterative
solvers. Besides speed, one great advantage of this class of approximate
methods is that their accuracy is systematically improvable. Indeed,
as the CG-method is a Krylov subspace method, the associated error
is monotonically reduced at each iteration. On top of that, two improvements
can be proposed at virtually no cost: (i) the use of preconditioners
can be employed, which leads to the Truncated Preconditioned Conjugate
Gradient (TPCG); (ii) since the residual of the final step of the
CG-method is available, one additional Picard fixed point iteration
(“peek”), equivalent to one step of Jacobi Over Relaxation
(JOR) with relaxation parameter ω, can be made at almost no
cost. This method is denoted by TCG-n(ω). Black-box adaptive
methods to find good choices of ω are provided and discussed.
Results show that TPCG-3(ω) is converged to high accuracy (a
few kcal/mol) for various types of systems including proteins and
highly charged systems at the fixed cost of four matrix-vector products:
three CG iterations plus the initial CG descent direction. Alternatively,
T(P)CG-2(ω) provides robust results at a reduced cost (three
matrix-vector products) and offers new perspectives for long polarizable
MD as a production algorithm. The T(P)CG-1(ω) level provides
less accurate solutions for inhomogeneous systems, but its applicability
to well-conditioned problems such as water is remarkable, with only
two matrix-vector product evaluations.
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Affiliation(s)
- Félix Aviat
- Laboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France
| | - Antoine Levitt
- Inria Paris, F-75589 Paris Cedex 12, Université Paris-Est, CERMICS (ENPC) , Marne-la-Vallée, F-77455, France
| | - Benjamin Stamm
- MATHCCES, Department of Mathematics, RWTH Aachen University , Schinkelstraße 2, D-52062 Aachen, Germany.,Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , Jülich, 52425, Germany
| | - Yvon Maday
- Laboratoire Jacques-Louis Lions, UPMC Université Paris 06, UMR 7598 , F-75005, Paris, France.,Institut Universitaire de France , Paris Cedex 05, 75231, France.,Division of Applied Maths, Brown University , Providence, Rhode Island 02912, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis , Campus Box 1134, One Brookings Drive, Saint Louis, Missouri 63130, United States
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France.,Institut du Calcul et de la Simulation, UPMC Université Paris 06 , F-75005, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France.,Institut Universitaire de France , Paris Cedex 05, 75231, France
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29
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Qi R, Wang Q, Ren P. General van der Waals potential for common organic molecules. Bioorg Med Chem 2016; 24:4911-4919. [PMID: 27519463 DOI: 10.1016/j.bmc.2016.07.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 11/18/2022]
Abstract
This work presents a systematic development of a new van der Waals potential (vdW2016) for common organic molecules based on symmetry-adapted perturbation theory (SAPT) energy decomposition. The Buf-14-7 function, as well as Cubic-mean and Waldman-Hagler mixing rules were chosen given their best performance among other popular potentials. A database containing 39 organic molecules and 108 dimers was utilized to derive a general set of vdW parameters, which were further validated on nucleobase stacking systems and testing organic dimers. The vdW2016 potential is anticipated to significantly improve the accuracy and transferability of new generations of force fields for organic molecules.
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Affiliation(s)
- Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, United States
| | - Qiantao Wang
- West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, United States.
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30
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The effect of various quantum mechanically derived partial atomic charges on the bulk properties of chloride-based ionic liquids. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Tan SYS, Izgorodina EI. Comparison of the Effective Fragment Potential Method with Symmetry-Adapted Perturbation Theory in the Calculation of Intermolecular Energies for Ionic Liquids. J Chem Theory Comput 2016; 12:2553-68. [DOI: 10.1021/acs.jctc.6b00141] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samuel Y. S. Tan
- School of Chemistry, Monash University, 17 Rainforest
Walk, Clayton, Victoria 3800, Australia
| | - Ekaterina I. Izgorodina
- School of Chemistry, Monash University, 17 Rainforest
Walk, Clayton, Victoria 3800, Australia
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32
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Tu YJ, Allen MJ, Cisneros GA. Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water. Phys Chem Chem Phys 2016; 18:30323-30333. [DOI: 10.1039/c6cp04957e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Molecular dynamics simulations have been carried out to explain the water-exchange rates of lanthanide ions in water and water/[EMIm][EtSO4] observed from 17O-NMR experiments. Our simulations are in agreement with experimental results with respect to water-exchange trends.
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Affiliation(s)
- Yi-Jung Tu
- Department of Chemistry
- Wayne State University
- Detroit
- USA
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33
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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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34
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Keaveney ST, Harper JB, Croft AK. Computational approaches to understanding reaction outcomes of organic processes in ionic liquids. RSC Adv 2015. [DOI: 10.1039/c4ra14676j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The utility of using a combined experimental and computational approach for understanding ionic liquid media, and their effect on reaction outcome, is highlighted through a number of case studies.
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Affiliation(s)
| | - Jason B. Harper
- School of Chemistry
- University of New South Wales
- Sydney
- Australia
| | - Anna K. Croft
- Department of Chemical and Environmental Engineering
- University of Nottingham
- University Park
- Nottingham
- UK
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35
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Khrizman A, Cheng HY, Bottini G, Moyna G. Observation of aliphatic C–H⋯X hydrogen bonds in imidazolium ionic liquids. Chem Commun (Camb) 2015; 51:3193-5. [DOI: 10.1039/c4cc09783a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Measurement of H/D isotope effects on the19F resonances of sequentially deuterated 1-n-butyl-3-methylimidazolium hexafluorophosphate and tetrafluoroborate isotopologues reveals the formation of aliphatic C–H⋯X hydrogen bonds between the fluorinated anions and protons along theN-alkyl sidechains of the cations.
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Affiliation(s)
- Alexander Khrizman
- Department of Chemistry & Biochemistry
- University of the Sciences in Philadelphia
- Philadelphia
- USA
| | - Hiu Yan Cheng
- Department of Chemistry & Biochemistry
- University of the Sciences in Philadelphia
- Philadelphia
- USA
| | - Gualberto Bottini
- Departamento de Química del Litoral
- Centro Universitario Regional Litoral Norte
- Universidad de la República
- Paysandú 60000
- Uruguay
| | - Guillermo Moyna
- Department of Chemistry & Biochemistry
- University of the Sciences in Philadelphia
- Philadelphia
- USA
- Departamento de Química del Litoral
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36
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Salanne M. Simulations of room temperature ionic liquids: from polarizable to coarse-grained force fields. Phys Chem Chem Phys 2015; 17:14270-9. [DOI: 10.1039/c4cp05550k] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This perspective article summarizes the recent advances in the classical molecular modelling of room temperature ionic liquids.
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Affiliation(s)
- Mathieu Salanne
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR 8234
- PHENIX
- F-75005 Paris
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