1
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Schackert F, Biedermann J, Abdolvand S, Minniberger S, Song C, Plested AJR, Carloni P, Sun H. Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel. J Chem Inf Model 2023; 63:1293-1300. [PMID: 36758214 PMCID: PMC9976283 DOI: 10.1021/acs.jcim.2c01494] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are neurotransmitter-activated cation channels ubiquitously expressed in vertebrate brains. The regulation of calcium flux through the channel pore by RNA-editing is linked to synaptic plasticity while excessive calcium influx poses a risk for neurodegeneration. Unfortunately, the molecular mechanisms underlying this key process are mostly unknown. Here, we investigated calcium conduction in calcium-permeable AMPAR using Molecular Dynamics (MD) simulations with recently introduced multisite force-field parameters for Ca2+. Our calculations are consistent with experiment and explain the distinct calcium permeability in different RNA-edited forms of GluA2. For one of the identified metal binding sites, multiscale Quantum Mechanics/Molecular Mechanics (QM/MM) simulations further validated the results from MD and revealed small but reproducible charge transfer between the metal ion and its first solvation shell. In addition, the ion occupancy derived from MD simulations independently reproduced the Ca2+ binding profile in an X-ray structure of an NaK channel mimicking the AMPAR selectivity filter. This integrated study comprising X-ray crystallography, multisite MD, and multiscale QM/MM simulations provides unprecedented insights into Ca2+ permeation mechanisms in AMPARs, and paves the way for studying other biological processes in which Ca2+ plays a pivotal role.
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Affiliation(s)
- Florian
Karl Schackert
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany,Department
of Physics, RWTH Aachen University, 52062 Aachen, Germany
| | - Johann Biedermann
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Saeid Abdolvand
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Sonja Minniberger
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Chen Song
- Center
for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China,Peking-Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Andrew J. R. Plested
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Paolo Carloni
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany,Department
of Physics, RWTH Aachen University, 52062 Aachen, Germany,
| | - Han Sun
- Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany,Institute
of Chemistry, TU Berlin, Straße des 17 Juni 135, 10623 Berlin, Germany,
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2
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Berkowitz ML. Molecular Simulations of Aqueous Electrolytes: Role of Explicit Inclusion of Charge Transfer into Force Fields. J Phys Chem B 2021; 125:13069-13076. [PMID: 34807628 DOI: 10.1021/acs.jpcb.1c08383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe here simulations of aqueous salt solutions that are performed using an explicit charge transfer force field. The emphasis of the discussion is on the calculation of a dynamical property of the solutions: self-diffusion of water. While force fields that are based on pairwise additive potentials or on potentials with explicit inclusion of polarization or with scaled charges can provide at best a qualitative agreement with experiments, force fields with explicit inclusion of charge transfer can produce quantitative agreement with experiment for NaCl and KCl solutions. We argue that a force field with explicit charge transfer contains new physics absent in the previously used force fields described in recent reviews of molecular simulations of aqueous electrolytes.
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Affiliation(s)
- Max L Berkowitz
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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3
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Borah S. Hydration Properties of H nPO 4n-3 (n = 0-3) From Ab Initio Molecular Dynamics Simulations. J Phys Chem B 2020; 124:5454-5464. [PMID: 32484352 DOI: 10.1021/acs.jpcb.0c01769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For a comprehensive and detailed microscopic understanding of the hydration properties of primary aqueous phosphorus species of valence states V (viz., H3PO4, H2PO4-, HPO42-, and PO43-), a series of extensive ab initio molecular dynamics simulations is conducted at ambient temperature. In each of these cases, the spatially resolved, three-dimensional hydration shells are computed, allowing for a direct microscopic visual understanding of the hydration shells around the species. Since these species are excellent agents for the formation of hydrogen bonds (H-bonds) in water, which determine a wide range of their structural, dynamic, and spectroscopic features, a detailed analysis of the qualitative and quantitative aspects of the H-bonds, including their lifetime calculations, is performed. Vibrational density of states (VDOS) is calculated for each of the species in solute phases, resolved for each H-bonding site, and compared against the gas-phase normal modes of H3PO4 for the purpose of understanding the signatures of the peaks in VDOS plots and, in particular, the effects of solvation and H-bonding mechanisms. The results are well in line with available experimental data and other recent computer-aided studies in the literature.
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Affiliation(s)
- Sangkha Borah
- Okinawa Institute of Science and Technology Graduate University, 1919-1, Okinawa 904-0412, Japan.,Department of Physics, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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4
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Liu J, He X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids. Phys Chem Chem Phys 2020; 22:12341-12367. [PMID: 32459230 DOI: 10.1039/d0cp01095b] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To study large molecular systems beyond the system size that the current state-of-the-art ab initio electronic structure methods could handle, fragment-based quantum mechanical (QM) approaches have been developed over the past years, and proved to be efficient in dealing with large molecular systems at various ab initio levels. According to the fragmentation approach, a large molecular system can be divided into subsystems (fragments), and subsequently the property of the whole system can be approximately obtained by taking a proper combination of the corresponding terms of individual fragments. Therefore, the standard QM calculation of a large system could be circumvented by carrying out a series of calculations on small fragments, which significantly promotes computational efficiency. The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method is one of the fragment-based QM approaches which has been developed by our research group in recent years. This Perspective presents the theoretical framework of this fragmentation method and its applications in biomolecules, molecular clusters, molecular crystals and liquids, including total energy calculation, protein-ligand/protein binding affinity prediction, geometry optimization, vibrational spectrum simulation, ab initio molecular dynamics simulation, and prediction of excited-state properties.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
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5
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The Dependence of Implicit Solvent Model Parameters and Electronic Absorption Spectra and Photoinduced Charge Transfer. Sci Rep 2020; 10:3713. [PMID: 32111955 PMCID: PMC7048810 DOI: 10.1038/s41598-020-60757-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/17/2020] [Indexed: 11/20/2022] Open
Abstract
In this work, the relationship between multiple solvent parameters and charge transfer index was analyzed by multi-factor multi-variate partial least squares regression (PLSR). The charge transfer of the molecule is visualized by the analysis of the excited state wave function. Hydrogen bond basicity and surface tension can significantly affect charge transfer by studying the solvation model parameters and charge transfer index. Finally, a method in which a solvent regulates charge transfer strength and migration length is proposed.
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6
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Remsing RC, Klein ML. Lone Pair Rotational Dynamics in Solids. PHYSICAL REVIEW LETTERS 2020; 124:066001. [PMID: 32109086 DOI: 10.1103/physrevlett.124.066001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/20/2020] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
Traditional classifications of crystalline phases focus on nuclear degrees of freedom. Through the examination of both electronic and nuclear structure, we introduce the concept of an electronic plastic crystal. Such a material is classified by crystalline nuclear structure, while localized electronic degrees of freedom-here lone pairs-exhibit orientational motion at finite temperatures. This orientational motion is an emergent phenomenon arising from the coupling between electronic structure and polarization fluctuations generated by collective motions, such as phonons. Using ab initio molecular dynamics simulations, we predict the existence of electronic plastic crystal motion in halogen crystals and halide perovskites, and suggest that such motion may be found in a broad range of solids with lone pair electrons. Such fluctuations in the charge density should be observable, in principle, via synchrotron scattering.
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Affiliation(s)
- Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Michael L Klein
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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7
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Abstract
Coulomb interactions play a major role in determining the thermodynamics, structure, and dynamics of condensed-phase systems, but often present significant challenges. Computer simulations usually use periodic boundary conditions to minimize corrections from finite cell boundaries but the long range of the Coulomb interactions generates significant contributions from distant periodic images of the simulation cell, usually calculated by Ewald sum techniques. This can add significant overhead to computer simulations and hampers the development of intuitive local pictures and simple analytic theory. In this paper, we present a general framework based on local molecular field theory to accurately determine the contributions from long-ranged Coulomb interactions to the potential of mean force between ionic or apolar hydrophobic solutes in dilute aqueous solutions described by standard classical point charge water models. The simplest approximation leads to a short solvent (SS) model, with truncated solvent-solvent and solute-solvent Coulomb interactions and long-ranged but screened Coulomb interactions only between charged solutes. The SS model accurately describes the interplay between strong short-ranged solute core interactions, local hydrogen-bond configurations, and long-ranged dielectric screening of distant charges, competing effects that are difficult to capture in standard implicit solvent models.
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8
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Schröder C, Lyons A, Rick SW. Polarizable MD simulations of ionic liquids: How does additional charge transfer change the dynamics? Phys Chem Chem Phys 2020; 22:467-477. [DOI: 10.1039/c9cp05478b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new model for treating charge transfer in ionic liquids is developed and applied to 1-ethyl-3-methylimidazolium tetrafluoroborate. The model allows for us to examine the roles of charge transfer, polarizability, and charge scaling effects on the dynamics of ionic liquids.
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Affiliation(s)
- Christian Schröder
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Alex Lyons
- University of New Orleans
- Department of Chemistry
- New Orleans
- USA
| | - Steven W. Rick
- University of New Orleans
- Department of Chemistry
- New Orleans
- USA
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9
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Hofer TS, Kilchert FM, Tanjung BA. An effective partial charge model for bulk and surface properties of cubic ZrO 2, Y 2O 3 and yttrium-stabilised zirconia. Phys Chem Chem Phys 2019; 21:25635-25648. [PMID: 31720638 DOI: 10.1039/c9cp04307a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this work a newly parametrised Coulomb plus Buckingham potential formulation for cubic ZrO2, Y2O3 and yttrium-stabilised zirconia (YSZ) is presented. The density and pair distributions obtained for neat ZrO2 and Y2O3 under ambient conditions are in excellent agreement with experimental data, while the vibrational power spectra are highly similar compared to those obtained via ab initio molecular dynamics simulations at the PBEsol level. In addition, it is shown that the use of effective partial charges has several advantages compared to interaction potentials employing the oxidation states in the evaluation of the coulombic interactions: (i) the diffusion coefficient and the associated activation energy of oxygen ions evaluated for YSZn (n = 4 to 12) display the best agreement with experimental data; (ii) no unphysical reorganisation of the interface and the bulk are observed in simulations of the (110) and (111) surfaces of cubic ZrO2 and Y2O3, while due to the strong coulombic contributions in the case of the tested full-charge models a pronounced restructuring of the interface and the bulk is observed in the ZrO2 case, and (iii) the use of effective partial charges ensures compatibility with existing solvent models and force-fields for the treatment of molecular compounds.
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Affiliation(s)
- Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
| | - Franziska M Kilchert
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
| | - Bagas A Tanjung
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
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10
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Kariev AM, Green ME. Quantum Calculation of Proton and Other Charge Transfer Steps in Voltage Sensing in the Kv1.2 Channel. J Phys Chem B 2019; 123:7984-7998. [DOI: 10.1021/acs.jpcb.9b05448] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alisher M. Kariev
- Department of Chemistry and Biochemistry, City College of New York, New York, New York 10011, United States
| | - Michael E. Green
- Department of Chemistry and Biochemistry, City College of New York, New York, New York 10011, United States
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11
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Prasetyo N, Hünenberger PH, Hofer TS. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li + Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6443-6459. [PMID: 30284829 DOI: 10.1021/acs.jctc.8b00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δs GM+,wat◦ of the Li+ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li+ are also compared to those for Na+ and K+ from a previous study in terms of relative hydration free energies ΔΔs GM+,wat◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔs GM+,wat• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li+ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie , ETH Zürich, ETH-Hönggerberg , HCI Building , CH-8093 Zürich , Switzerland
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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12
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Kollar J, Frecer V. Diarylcyclopropane hydroxamic acid inhibitors of histone deacetylase 4 designed by combinatorial approach and QM/MM calculations. J Mol Graph Model 2018; 85:97-110. [PMID: 30145395 DOI: 10.1016/j.jmgm.2018.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/12/2018] [Accepted: 08/13/2018] [Indexed: 12/01/2022]
Abstract
Inhibitors of histone deacetylase superfamily (HDAC), which induce cell cycle arrest, trigger cell death and reduce angiogenesis appear as promising anti-cancer drugs targeting the epigenetic regulation of gene expression. Approved HDAC inhibitors were found effective against haematological and solid malignancies, other HDACIs are currently in clinical trials for the treatment of neurological diseases or immune disorders. Among those, diarylcyclopropane hydroxamic acids (DCHA) were found to be potent and selective inhibitors of the class IIa HDACs, specifically HDAC4, a pharmacological target for the treatment of Huntington's disease and muscular atrophy. Crystallographic analysis revealed that one of the aryl groups of the DCHA fills the lower specificity pocket of the HDAC4 catalytic site that is specific for the class IIa HDACs. We have used computer-assisted combinatorial chemistry, hybrid quantum mechanics/molecular mechanics (QM/MM) with implicit solvation and QSAR models to optimize DCHA inhibitors and propose more potent DCHA analogues. The QM/MM approach has been selected since the process of inhibitor binding to the catalytic zinc and polar amino acid residues of the deacetylase active site induces considerable rearrangement of electron density of the inhibitor. Virtual combinatorial library consisting of 12180 DCHA analogues was focused by means of structure-based evaluation to form a small combinatorial subset enriched in potentially interesting inhibitor candidates. Two validated QSAR models making use of computed relative binding affinities of the DCHA inhibitors to the HDAC4 (ΔΔGcomQM/MM) were utilized to estimate the inhibitory potencies of the new analogues. The predicted half-maximal inhibitory concentrations (IC50pre) of the designed analogues fall into the low nanomolar concentration range and their predicted ADME properties are also favourable. The best designed DCHA analogues contain indazole, phenylpiperidine, phenyloxazole or hydroxypyridine moieties and stabilize bound inhibitors by hydrogen bonds to the catalytic water molecule and backbone carbonyl groups of the deacetylase active site residues. This makes them more potent and more specific inhibitors towards the HDAC4 isoform than the known diarylcyclopropane hydroxamic acids. The analogues are recommended for synthesis and experimental verification of inhibitory potencies in medicinal chemistry laboratories.
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Affiliation(s)
- Jakub Kollar
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava SK-84215, Slovakia; Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava SK-83232, Slovakia
| | - Vladimir Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava SK-83232, Slovakia; International Centre for Applied Research and Sustainable Technology (ICARST n.o.), Bratislava SK-84104, Slovakia.
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13
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Torii H. Dynamical behavior of molecular partial charges implied by the far-infrared spectral profile of liquid water. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2017.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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14
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Nguyen M, Rick SW. The influence of polarizability and charge transfer on specific ion effects in the dynamics of aqueous salt solutions. J Chem Phys 2018; 148:222803. [PMID: 29907071 DOI: 10.1063/1.5012682] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The diffusion rates for water molecules in salt solutions depend on the identity of the ions, as well as their concentration. Among the alkali metal ions, cesium and potassium increase and sodium strongly decreases the diffusion constant of water. The origin of the difference can be understood by examining the simulation results using different potential models. In this work, aqueous solutions of salts are simulated with a variety of models. Commonly used non-polarizable models, which otherwise reproduce many experimental properties, do not capture the trend in the diffusion constant, while models which include polarization and/or charge transfer interactions do. For the non-polarizable models, the diffusion constant decreases too strongly with salt concentration. The changes in the water diffusion constant with increasing salt concentration match the diffusion constant of the ion. The ion diffusion constant is dependent on the residence time for water in the ion solvation shell. The non-polarizable models over-estimate the residence time, relative to the translational diffusion constant and so tend to under-estimate the ion and water diffusion constants.
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Affiliation(s)
- Mary Nguyen
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| | - Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
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15
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Ulman K, Busch S, Hassanali AA. Quantum mechanical effects in zwitterionic amino acids: The case of proline, hydroxyproline, and alanine in water. J Chem Phys 2018; 148:222826. [DOI: 10.1063/1.5008665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kanchan Ulman
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Geesthacht GmbH, Lichtenbergstr. 1, 85747 Garching bei München, Germany
| | - Ali A. Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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16
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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17
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Xu M, Zhu T, Zhang JZH. A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein. Front Chem 2018; 6:189. [PMID: 29900167 PMCID: PMC5989690 DOI: 10.3389/fchem.2018.00189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/09/2018] [Indexed: 12/28/2022] Open
Abstract
A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA)9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.
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Affiliation(s)
- Mingyuan Xu
- State Key Lab of Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Tong Zhu
- State Key Lab of Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.,NYU-ECNU Center for Computational Chemistry at New York University Shanghai, Shanghai, China
| | - John Z H Zhang
- State Key Lab of Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.,NYU-ECNU Center for Computational Chemistry at New York University Shanghai, Shanghai, China.,Department of Chemistry, New York University, New York, NY, United States.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
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18
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Mirkin NG, Krimm S. Milieu-Initiated Inversion of the Aqueous Polyproline II/β Propensity in the Alanine Tripeptide: Aggregation Origin of the Onset of Amyloid Formation. J Phys Chem B 2018; 122:4428-4432. [PMID: 29617133 DOI: 10.1021/acs.jpcb.8b00612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Extending our earlier analogous study of the alanine dipeptide (ADP), we have now analyzed the effect of the external environment on the polyproline II (P) and β relative energies, the P/β propensity, of the alanine tripeptide (ATP). Ab initio calculations of ATP(H2O)19 and ATP(H2O)19(HCl) exhibit the same propensity inversion as in ADP: in the pure water case the PP conformation is favored while the addition of the HCl molecule results in the ββ conformation being of lower energy. A comparison, following an intermediate insertion and departure of an HCl molecule, shows that the energy of a hydrogen-bonded (H2O)19βATP::βATP(H2O)19 structure is lower than that of the sum of two separate PP systems, i.e., that the aggregated state of the peptide is favored. This arises from the basic physical response to their total environmental influences. Questions about quantitative results from molecular dynamics simulations, obviously needed to analyze longer chains and other side chains, are addressed via rigid water calculations. The desirability of basing studies of amyloid formation on our proposed alternative milieu-folding paradigm is discussed.
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Affiliation(s)
- Noemi G Mirkin
- LSA Biophysics , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Samuel Krimm
- LSA Biophysics , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
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19
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Kollar J, Frecer V. How accurate is the description of ligand–protein interactions by a hybrid QM/MM approach? J Mol Model 2017; 24:11. [DOI: 10.1007/s00894-017-3537-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/15/2017] [Indexed: 11/28/2022]
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20
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Chen Y, Okur HI, Liang C, Roke S. Orientational ordering of water in extended hydration shells of cations is ion-specific and is correlated directly with viscosity and hydration free energy. Phys Chem Chem Phys 2017; 19:24678-24688. [DOI: 10.1039/c7cp03395h] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Specific ion effects in aqueous solutions are investigated at the molecular, nanoscopic and macroscopic levels.
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Affiliation(s)
- Yixing Chen
- Laboratory for fundamental BioPhotonics (LBP)
- Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX)
- School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS)
- École Polytechnique Fédérale de Lausanne (EPFL)
- Lausanne
| | - Halil I. Okur
- Laboratory for fundamental BioPhotonics (LBP)
- Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX)
- School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS)
- École Polytechnique Fédérale de Lausanne (EPFL)
- Lausanne
| | - Chungwen Liang
- Laboratory for fundamental BioPhotonics (LBP)
- Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX)
- School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS)
- École Polytechnique Fédérale de Lausanne (EPFL)
- Lausanne
| | - Sylvie Roke
- Laboratory for fundamental BioPhotonics (LBP)
- Institute of Bio-engineering (IBI), and Institute of Materials Science (IMX)
- School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS)
- École Polytechnique Fédérale de Lausanne (EPFL)
- Lausanne
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21
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Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method. J Mol Graph Model 2016; 69:144-53. [DOI: 10.1016/j.jmgm.2016.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/29/2016] [Accepted: 08/10/2016] [Indexed: 11/18/2022]
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22
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Toward a quantitative theory of Hofmeister phenomena: From quantum effects to thermodynamics. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.06.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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23
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Sumikama T. Origin of the Shape of Current-Voltage Curve through Nanopores: A Molecular Dynamics Study. Sci Rep 2016; 6:25750. [PMID: 27167118 PMCID: PMC4863172 DOI: 10.1038/srep25750] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/22/2016] [Indexed: 12/25/2022] Open
Abstract
Ion transports through ion channels, biological nanopores, are essential for life: Living cells generate electrical signals by utilizing ion permeation through channels. The measured current-voltage (i-V) relations through most ion channels are sublinear, however, its physical meaning is still elusive. Here we calculated the i-V curves through anion-doped carbon nanotubes, a model of an ion channel, using molecular dynamics simulation. It was found the i-V curve reflects the physical origin of the rate-determining step: the i-V curve is sublinear when the permeation is entropy bottlenecked, while it is superlinear in the case of the energy bottlenecked permeation. Based on this finding, we discuss the relation between the molecular mechanism of ion permeation through the biological K+ channels and the shape of the i-V curves through them. This work also provides a clue for a novel design of nanopores that show current rectification.
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24
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Liu J, Zhu T, Wang X, He X, Zhang JZH. Quantum Fragment Based ab Initio Molecular Dynamics for Proteins. J Chem Theory Comput 2015; 11:5897-905. [PMID: 26642993 DOI: 10.1021/acs.jctc.5b00558] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.
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Affiliation(s)
- Jinfeng Liu
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China
| | - Tong Zhu
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xianwei Wang
- Center for Optics & Optoelectronics Research, College of Science, Zhejiang University of Technology , Hangzhou, Zhejiang 310023, China
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Department of Chemistry, New York University , New York, New York 10003, United States
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25
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Soniat M, Kumar R, Rick SW. Hydrated proton and hydroxide charge transfer at the liquid/vapor interface of water. J Chem Phys 2015; 143:044702. [DOI: 10.1063/1.4926831] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marielle Soniat
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| | - Revati Kumar
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70808, USA
| | - Steven W. Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
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26
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Torii H. Electronic Structural Basis for the Atomic Partial Charges of Planar Molecular Systems Derived from Out-of-Plane Dipole Derivatives. J Phys Chem A 2015; 119:3277-84. [DOI: 10.1021/jp512884g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hajime Torii
- Department
of Chemistry,
Faculty of Education, and Department of Optoelectronics and Nanostructure
Science, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
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27
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Soniat M, Hartman L, Rick SW. Charge Transfer Models of Zinc and Magnesium in Water. J Chem Theory Comput 2015; 11:1658-67. [DOI: 10.1021/ct501173n] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Marielle Soniat
- Department
of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Lisa Hartman
- Benjamin Franklin High School, New Orleans, Louisiana 70122, United States
| | - Steven W. Rick
- Department
of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
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28
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Hammerich AD, Finlayson-Pitts BJ, Gerber RB. Mechanism for formation of atmospheric Cl atom precursors in the reaction of dinitrogen oxides with HCl/Cl− on aqueous films. Phys Chem Chem Phys 2015; 17:19360-70. [DOI: 10.1039/c5cp02664d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formation of atmospheric chlorine atom precursors ClNO2 and ClNO in the reaction of HCl with oxides of nitrogen on a water film: left – formation of N–Cl bond as N–O bond breaks; right – concurrent changes in Mulliken charges.
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Affiliation(s)
| | | | - R. Benny Gerber
- Department of Chemistry
- University of California Irvine
- Irvine
- USA
- Institute of Chemistry and the Fritz Haber Research Center
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29
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Yao Y, Kanai Y, Berkowitz ML. Role of Charge Transfer in Water Diffusivity in Aqueous Ionic Solutions. J Phys Chem Lett 2014; 5:2711-2716. [PMID: 26277968 DOI: 10.1021/jz501238v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We performed molecular dynamics simulations on four types of systems containing ion and solvating water. Two systems contained a cation (Na(+) or K(+)), and two other systems an anion (Cl(-) or I(-)). Classical molecular dynamics simulations were performed using three different force fields: a fixed charge force field, a polarizable force field that includes explicit polarization, and also a recently developed force field that includes polarization and charge transfer. These simulations were then compared to first-principles molecular dynamics simulations. While the first-principles simulations showed that the anions accelerated water translational diffusion, the cations slowed it down. In simulations with the classical force fields, only the force field that incorporates explicit charge transfer reproduced this ion-specific behavior. Additional simulations performed to understand the effect of charge transfer demonstrated that two competitive factors determine the behavior of water translational diffusion: the ions diminished charge accelerates water, while the net charge acquired by water either accelerates or slows down its dynamics. Our results show that charge transfer plays a crucial role in governing the water dynamics in aqueous ionic solutions.
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Affiliation(s)
- Yi Yao
- †Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yosuke Kanai
- †Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- ‡Condensed Matter and Materials Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Max L Berkowitz
- †Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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30
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Soniat M, Rick SW. Charge transfer effects of ions at the liquid water/vapor interface. J Chem Phys 2014; 140:184703. [DOI: 10.1063/1.4874256] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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31
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Torii H. Cooperative Contributions of the Intermolecular Charge Fluxes and Intramolecular Polarizations in the Far-Infrared Spectral Intensities of Liquid Water. J Chem Theory Comput 2014; 10:1219-27. [DOI: 10.1021/ct4011147] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hajime Torii
- Department
of Chemistry, School of Education, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
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32
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Mirkin NG, Krimm S. Note: Charge transfer in a hydrated peptide group is determined mainly by its intrinsic hydrogen-bond energetics. J Chem Phys 2014; 140:046101. [DOI: 10.1063/1.4862900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Torii H. Extended Nature of the Molecular Dipole of Hydrogen-Bonded Water. J Phys Chem A 2013; 117:2044-51. [DOI: 10.1021/jp4013015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hajime Torii
- Department of Chemistry, School
of Education, Shizuoka University, 836
Ohya, Shizuoka 422-8529, Japan
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34
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Komeiji Y, Fujiwara T, Okiyama Y, Mochizuki Y. Dynamic fragmentation with static fragments (DF/SF) algorithm designed for <i>ab initio</i> fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of polypeptides. CHEM-BIO INFORMATICS JOURNAL 2013. [DOI: 10.1273/cbij.13.45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | - Yoshio Okiyama
- Institute of Industrial Science, The University of Tokyo
| | - Yuji Mochizuki
- Institute of Industrial Science, The University of Tokyo
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University
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35
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Adriaanse C, Cheng J, Chau V, Sulpizi M, VandeVondele J, Sprik M. Aqueous Redox Chemistry and the Electronic Band Structure of Liquid Water. J Phys Chem Lett 2012; 3:3411-5. [PMID: 26290964 DOI: 10.1021/jz3015293] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The electronic states of aqueous species can mix with the extended states of the solvent if they are close in energy to the band edges of water. Using density functional theory-based molecular dynamics simulation, we show that this is the case for OH(-) and Cl(-). The effect is, however, badly exaggerated by the generalized gradient approximation leading to systematic underestimation of redox potentials and spurious nonlinearity in the solvent reorganization. Drawing a parallel to charged defects in wide gap solid oxides, we conclude that misalignment of the valence band of water is the main source of error turning the redox levels of OH(-) and Cl(-) in resonant impurity states. On the other hand, the accuracy of energies of levels corresponding to strongly negative redox potentials is acceptable. We therefore predict that mixing of the vertical attachment level of CO2 and the unoccupied states of water is a real effect.
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Affiliation(s)
- Christopher Adriaanse
- †Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jun Cheng
- †Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Vincent Chau
- †Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Marialore Sulpizi
- †Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Joost VandeVondele
- ‡Physical Chemistry Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Michiel Sprik
- †Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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36
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Kulik HJ, Luehr N, Ufimtsev IS, Martinez TJ. Ab Initio Quantum Chemistry for Protein Structures. J Phys Chem B 2012; 116:12501-9. [DOI: 10.1021/jp307741u] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Heather J. Kulik
- Department of Chemistry and
PULSE Institute, Stanford University, Stanford,
California, 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Nathan Luehr
- Department of Chemistry and
PULSE Institute, Stanford University, Stanford,
California, 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Ivan S. Ufimtsev
- Department of Chemistry and
PULSE Institute, Stanford University, Stanford,
California, 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Todd J. Martinez
- Department of Chemistry and
PULSE Institute, Stanford University, Stanford,
California, 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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37
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Soniat M, Rick SW. The effects of charge transfer on the aqueous solvation of ions. J Chem Phys 2012; 137:044511. [DOI: 10.1063/1.4736851] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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38
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Anisimov VM, Bliznyuk AA. Charge Transfer Effects in the GroEL–GroES Chaperonin Tetramer in Solution. J Phys Chem B 2012; 116:6261-8. [DOI: 10.1021/jp211385e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victor M. Anisimov
- National Center for Supercomputing
Applications, University of Illinois at Urbana—Champaign, 1205 West Clark Street, Urbana, Illinois 61801, United States
| | - Andrey A. Bliznyuk
- Australian National University, Supercomputer Facility, Leonard Huxley Bld.
(#56), Canberra, ACT 0200, Australia
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39
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Gao Y, Guo M, Mei Y, Zhang JZ. Protein–water hydrogen bonds are stabilized by electrostatic polarization. Mol Phys 2012. [DOI: 10.1080/00268976.2012.668965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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40
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Zhong Y, Bauer BA, Patel S. Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization. J Comput Chem 2011; 32:3339-53. [PMID: 21898464 PMCID: PMC3193586 DOI: 10.1002/jcc.21873] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 04/25/2011] [Accepted: 05/28/2011] [Indexed: 12/13/2022]
Abstract
N-Acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous nonpolarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas phase relative rotation energy of exocyclic hydroxymethyl side chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions (RDFs) and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.
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Affiliation(s)
- Yang Zhong
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Brad A. Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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41
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Lee AJ, Rick SW. The effects of charge transfer on the properties of liquid water. J Chem Phys 2011; 134:184507. [PMID: 21568521 DOI: 10.1063/1.3589419] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Alexis J Lee
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
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42
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Hassanali AA, Zhong D, Singer SJ. An AIMD study of CPD repair mechanism in water: role of solvent in ring splitting. J Phys Chem B 2011; 115:3860-71. [PMID: 21417372 DOI: 10.1021/jp107723w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this paper, we continue to explore the repair mechanisms of the cyclobutane pyrimidine dimer. We find that a full description of both C5-C5' and C6-C6' bond splitting requires a multidimensional treatment involving a solvent coordinate in addition to changes in internal dimer coordinates. Nonequilibrium effects are likely to be important as well, although the initial conditions following forward electron transfer to the dimer, beyond the scope of this study, will ultimately determine the importance of these effects. Throughout the splitting of C5-C5' and C6-C6' bonds, a significant amount of excess charge is delocalized onto the solvent. We have verified that this is not an artifact of the electronic density functional theory (DFT) method used for this anionic system with Schrödinger equation-based quantum chemical cluster calculations. The amount and variability of charge delocalization changes with the course of the reaction. The splitting of the C6-C6' bond is accompanied by both an increase in electron density on the C6 and C6' carbon atoms and an increase in the water density near those atoms. These features are observed both in our equilibrium umbrella sampling simulations and nonequilibrium trajectories.
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Affiliation(s)
- Ali A Hassanali
- Biophysics Program, Ohio State University, Columbus, Ohio 43210, USA.
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43
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Braunschweig B, Mukherjee P, Kutz RB, Wieckowski A, Dlott DD. Sum-frequency generation of acetate adsorption on Au and Pt surfaces: Molecular structure effects. J Chem Phys 2010; 133:234702. [DOI: 10.1063/1.3507257] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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44
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Yagasaki T, Saito S, Ohmine I. Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study. J Phys Chem A 2010; 114:12573-84. [PMID: 21077653 DOI: 10.1021/jp1084795] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.
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Affiliation(s)
- Takuma Yagasaki
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, and The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
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45
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Lupieri P, Ippoliti E, Altoè P, Garavelli M, Mwalaba M, Carloni P. Spectroscopic Properties of Formaldehyde in Aqueous Solution: Insights from Car−Parrinello and TDDFT/CASPT2 Calculations. J Chem Theory Comput 2010; 6:3403-9. [DOI: 10.1021/ct100384f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Paola Lupieri
- German Research School for Simulation Sciences GmbH, 52425 Jülich and RWTH Aachen, Germany, SISSA, via Bonomea 265, 34136 Trieste, Italy, Department of Chemistry “G. Ciamician”, University of Bologna, via Selmi 2, I-40126 Bologna, Italy, International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy, and Democritos Modeling Center for Research in Atomistic Simulation, via Bonomea 265, 34136 Trieste, Italy
| | - Emiliano Ippoliti
- German Research School for Simulation Sciences GmbH, 52425 Jülich and RWTH Aachen, Germany, SISSA, via Bonomea 265, 34136 Trieste, Italy, Department of Chemistry “G. Ciamician”, University of Bologna, via Selmi 2, I-40126 Bologna, Italy, International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy, and Democritos Modeling Center for Research in Atomistic Simulation, via Bonomea 265, 34136 Trieste, Italy
| | - Piero Altoè
- German Research School for Simulation Sciences GmbH, 52425 Jülich and RWTH Aachen, Germany, SISSA, via Bonomea 265, 34136 Trieste, Italy, Department of Chemistry “G. Ciamician”, University of Bologna, via Selmi 2, I-40126 Bologna, Italy, International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy, and Democritos Modeling Center for Research in Atomistic Simulation, via Bonomea 265, 34136 Trieste, Italy
| | - Marco Garavelli
- German Research School for Simulation Sciences GmbH, 52425 Jülich and RWTH Aachen, Germany, SISSA, via Bonomea 265, 34136 Trieste, Italy, Department of Chemistry “G. Ciamician”, University of Bologna, via Selmi 2, I-40126 Bologna, Italy, International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy, and Democritos Modeling Center for Research in Atomistic Simulation, via Bonomea 265, 34136 Trieste, Italy
| | - M. Mwalaba
- German Research School for Simulation Sciences GmbH, 52425 Jülich and RWTH Aachen, Germany, SISSA, via Bonomea 265, 34136 Trieste, Italy, Department of Chemistry “G. Ciamician”, University of Bologna, via Selmi 2, I-40126 Bologna, Italy, International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy, and Democritos Modeling Center for Research in Atomistic Simulation, via Bonomea 265, 34136 Trieste, Italy
| | - Paolo Carloni
- German Research School for Simulation Sciences GmbH, 52425 Jülich and RWTH Aachen, Germany, SISSA, via Bonomea 265, 34136 Trieste, Italy, Department of Chemistry “G. Ciamician”, University of Bologna, via Selmi 2, I-40126 Bologna, Italy, International Centre for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy, and Democritos Modeling Center for Research in Atomistic Simulation, via Bonomea 265, 34136 Trieste, Italy
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Hassanali AA, Zhang H, Knight C, Shin YK, Singer SJ. The Dissociated Amorphous Silica Surface: Model Development and Evaluation. J Chem Theory Comput 2010; 6:3456-71. [DOI: 10.1021/ct100260z] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ali A. Hassanali
- Biophysics Program, and Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Hui Zhang
- Biophysics Program, and Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Chris Knight
- Biophysics Program, and Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Yun Kyung Shin
- Biophysics Program, and Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Sherwin J. Singer
- Biophysics Program, and Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
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Marchese R, Grandori R, Carloni P, Raugei S. On the zwitterionic nature of gas-phase peptides and protein ions. PLoS Comput Biol 2010; 6:e1000775. [PMID: 20463874 PMCID: PMC2865515 DOI: 10.1371/journal.pcbi.1000775] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 03/31/2010] [Indexed: 11/18/2022] Open
Abstract
Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation.
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Affiliation(s)
- Roberto Marchese
- Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA-ISAS) and DEMOCRITOS, Trieste, Italy
| | - Rita Grandori
- Department of Bioscience and Biotechnology, Milano-Bicocca, Milano, Italy
- * E-mail: (RG); (SR)
| | - Paolo Carloni
- Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA-ISAS) and DEMOCRITOS, Trieste, Italy
- Italian Institute of Technology (IIT), Trieste, Italy
- Computational Biophysics sector, German Research School for Simulation Science, FZ-Juelich and RWTH, Juelich, Germany
| | - Simone Raugei
- Statistical and Biological Physics Sector, International School for Advanced Studies (SISSA-ISAS) and DEMOCRITOS, Trieste, Italy
- Center for Molecular Electrocatalysis, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail: (RG); (SR)
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49
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Rogers DM, Beck TL. Quasichemical and structural analysis of polarizable anion hydration. J Chem Phys 2010; 132:014505. [PMID: 20078170 DOI: 10.1063/1.3280816] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Quasichemical theory is utilized to analyze the relative roles of solute polarization and size in determining the structure and thermodynamics of bulk anion hydration for the Hofmeister series Cl(-), Br(-), and I(-). Excellent agreement with experiment is obtained for whole salt hydration free energies using the polarizable AMOEBA force field. The total hydration free energies display a stronger dependence on ion size than on polarizability. The quasichemical approach exactly partitions the solvation free energy into inner-shell, outer-shell packing, and outer-shell long-ranged contributions by means of a hard-sphere condition. The inner-shell contribution becomes slightly more favorable with increasing ion polarizability, indicating electrostriction of the nearby waters. Small conditioning radii, even well inside the first maximum of the ion-water(oxygen) radial distribution function, result in Gaussian behavior for the long-ranged contribution that dominates the ion hydration free energy. This in turn allows for a mean-field treatment of the long-ranged contribution, leading to a natural division into first-order electrostatic, induction, and van der Waals terms. The induction piece exhibits the strongest ion polarizability dependence, while the larger-magnitude first-order electrostatic piece yields an opposing but weaker polarizability dependence. The van der Waals piece is small and positive, and it displays a small ion specificity. The sum of the inner-shell, packing, and long-ranged van der Waals contributions exhibits little variation along the anion series for the chosen conditioning radii, targeting electrostatic effects (influenced by ion size) as the largest determinant of specificity. In addition, a structural analysis is performed to examine the solvation anisotropy around the anions. As opposed to the hydration free energies, the solvation anisotropy depends more on ion polarizability than on ion size: increased polarizability leads to increased anisotropy. The water dipole moments near the ion are similar in magnitude to bulk water, while the ion dipole moments are found to be significantly larger than those observed in quantum mechanical studies. Possible impacts of the observed over-polarization of the ions on simulated anion surface segregation are discussed.
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Affiliation(s)
- David M Rogers
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
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Zhao Z, Rogers DM, Beck TL. Polarization and charge transfer in the hydration of chloride ions. J Chem Phys 2010; 132:014502. [DOI: 10.1063/1.3283900] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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