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Newcomb K, Tiwari SP, Rai N, Maginn EJ. A molecular dynamics investigation of actinyl–ligand speciation in aqueous solution. Phys Chem Chem Phys 2018; 20:15753-15763. [DOI: 10.1039/c8cp01944d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Actinyl ions (AnO2n+), the form in which actinides are commonly found in aqueous solution, are important species in the nuclear fuel cycle.
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Affiliation(s)
- Ken Newcomb
- Department of Chemical and Biomolecular Engineering
- University of Notre Dame
- Notre Dame
- USA
| | - Surya Prakash Tiwari
- Department of Chemical and Biomolecular Engineering
- University of Notre Dame
- Notre Dame
- USA
| | - Neeraj Rai
- Dave C. Swalm School of Chemical Engineering
- Mississippi State University
- Mississippi State
- USA
| | - Edward J. Maginn
- Department of Chemical and Biomolecular Engineering
- University of Notre Dame
- Notre Dame
- USA
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2
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Alaghemandi M, Koller V, Green JR. Nonexponential kinetics of ion pair dissociation in electrofreezing water. Phys Chem Chem Phys 2017; 19:26396-26402. [PMID: 28944386 DOI: 10.1039/c7cp04572g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Temporally- or spatially-heterogeneous environments can participate in many kinetic processes, from chemical reactions and self-assembly to the forced dissociation of biomolecules. Here, we simulate the molecular dynamics of a model ion pair forced to dissociate in an explicit, aqueous solution. Triggering dissociation with an external electric field causes the surrounding water to electrofreeze and the ion pair population to decay nonexponentially. To further probe the role of the aqueous environment in the kinetics, we also simulate dissociation events under a purely mechanical force on the ion pair. In this case, regardless of whether the surrounding water is a liquid or already electrofrozen, the ion pair population decays exponentially with a well-defined rate constant that is specific to the medium and applied force. These simulation data, and the rate parameters we extract, suggest the disordered kinetics in an electrofreezing medium are a result of the comparable time scales of two concurrent processes, electrofreezing and dissociation.
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Affiliation(s)
- Mohammad Alaghemandi
- Department of Chemistry, University of Massachusetts Boston, Boston, MA 02125, USA.
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Shevkunov SV. Water vapor nucleation on ion pairs under the conditions of a planar nanopore. COLLOID JOURNAL 2016. [DOI: 10.1134/s1061933x16040177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Votapka LW, Amaro RE. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput Biol 2015; 11:e1004381. [PMID: 26505480 PMCID: PMC4624728 DOI: 10.1371/journal.pcbi.1004381] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/04/2015] [Indexed: 12/16/2022] Open
Abstract
The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations. The rate constants found using this method agreed well with experimentally and theoretically obtained values. We predicted the association rate of a small charged molecule toward both a charged and an uncharged spherical receptor and verified the estimated value with Smoluchowski theory. We also calculated the kon rate constant for superoxide dismutase with its natural substrate, O2-, in a validation of a previous experiment using similar methods but with a number of important improvements. We also calculated the kon for a new system: the N-terminal domain of Troponin C with its natural substrate Ca2+. The kon calculated for the latter two systems closely resemble experimentally obtained values. This novel multiscale approach is computationally cheaper and more parallelizable when compared to other methods of similar accuracy. We anticipate that this methodology will be useful for predicting kinetic rate constants and for understanding the process of binding between a small molecule and a protein receptor.
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Affiliation(s)
- Lane W. Votapka
- Department of Chemistry and Biochemistry and National Biomedical Computation Resource, University of California, San Diego, San Diego, California, United States of America
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry and National Biomedical Computation Resource, University of California, San Diego, San Diego, California, United States of America
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Yonetani Y. Distinct dissociation kinetics between ion pairs: Solvent-coordinate free-energy landscape analysis. J Chem Phys 2015; 143:044506. [DOI: 10.1063/1.4927093] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yoshiteru Yonetani
- Quantum Beam Science Center, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
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Peters B, Bolhuis PG, Mullen RG, Shea JE. Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency. J Chem Phys 2013; 138:054106. [PMID: 23406097 DOI: 10.1063/1.4775807] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We propose a method for identifying accurate reaction coordinates among a set of trial coordinates. The method applies to special cases where motion along the reaction coordinate follows a one-dimensional Smoluchowski equation. In these cases the reaction coordinate can predict its own short-time dynamical evolution, i.e., the dynamics projected from multiple dimensions onto the reaction coordinate depend only on the reaction coordinate itself. To test whether this property holds, we project an ensemble of short trajectory swarms onto trial coordinates and compare projections of individual swarms to projections of the ensemble of swarms. The comparison, quantified by the Kullback-Leibler divergence, is numerically performed for each isosurface of each trial coordinate. The ensemble of short dynamical trajectories is generated only once by sampling along an initial order parameter. The initial order parameter should separate the reactants and products with a free energy barrier, and distributions on isosurfaces of the initial parameter should be unimodal. The method is illustrated for three model free energy landscapes with anisotropic diffusion. Where exact coordinates can be obtained from Kramers-Langer-Berezhkovskii-Szabo theory, results from the new method agree with the exact results. We also examine characteristics of systems where the proposed method fails. We show how dynamical self-consistency is related (through the Chapman-Kolmogorov equation) to the earlier isocommittor criterion, which is based on longer paths.
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Affiliation(s)
- Baron Peters
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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Khavrutskii IV, Dzubiella J, McCammon JA. Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method. J Chem Phys 2008; 128:044106. [PMID: 18247929 DOI: 10.1063/1.2825620] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We establish the accuracy of the novel generalized gradient-augmented harmonic Fourier beads (ggaHFB) method in computing free-energy profiles or potentials of mean force (PMFs) through comparison with two independent conventional techniques. In particular, we employ umbrella sampling with one dimensional weighted histogram analysis method (WHAM) and free molecular dynamics simulation of radial distribution functions to compute the PMF for the Na(+)-Cl(-) ion-pair separation to 16 A in 1.0M NaCl solution in water. The corresponding ggaHFB free-energy profile in six dimensional Cartesian space is in excellent agreement with the conventional benchmarks. We then explore changes in the PMF in response to lowering the NaCl concentration to physiological 0.3 and 0.1M, and dilute 0.0M concentrations. Finally, to expand the scope of the ggaHFB method, we formally develop the free-energy gradient approximation in arbitrary nonlinear coordinates. This formal development underscores the importance of the logarithmic Jacobian correction to reconstruct true PMFs from umbrella sampling simulations with either WHAM or ggaHFB techniques when nonlinear coordinate restraints are used with Cartesian propagators. The ability to employ nonlinear coordinates and high accuracy of the computed free-energy profiles further advocate the use of the ggaHFB method in studies of rare events in complex systems.
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Affiliation(s)
- Ilja V Khavrutskii
- Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0365, USA.
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Loffler HH, Mohammed AM, Inada Y, Funahashi S. Water exchange dynamics of manganese(II), cobalt(II), and nickel(II) ions in aqueous solution. J Comput Chem 2006; 27:1944-9. [PMID: 17019720 DOI: 10.1002/jcc.20462] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The first row transition metal ions Mn(2+), Co(2+), and Ni(2+) have been studied by classical umbrella sampling molecular dynamics simulations. The water exchange mechanisms, estimates of reaction rates, as well as structural changes during the activation process are discussed. Mn(2+) was found to react via an I(A) mechanism, whereas Co(2+) and Ni(2+) both proceed via I(D). Reaction rate constants are generally higher than those obtained by experiment but the simply constructed metal(II) ion-water potential reproduces the relative order quite well.
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Affiliation(s)
- Hannes H Loffler
- Laboratory of Analytical Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
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11
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Masia M, Rey R. Reaction Rate Theory Approach to Thermodynamic State Dependence of Hydration Shell Exchange for Li+(Aq). J Phys Chem B 2003. [DOI: 10.1021/jp022271x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Marco Masia
- Departament de Fısica i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
| | - Rossend Rey
- Departament de Fısica i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
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Martí J. Transition Path Sampling Study of the Local Molecular Structure in the Aqueous Solvation of Sodium Chloride. MOLECULAR SIMULATION 2001. [DOI: 10.1080/08927020108023022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Koneshan S, Rasaiah JC. Computer simulation studies of aqueous sodium chloride solutions at 298 K and 683 K. J Chem Phys 2000. [DOI: 10.1063/1.1314341] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Dedonder-Lardeux C, Grégoire G, Jouvet C, Martrenchard S, Solgadi D. Charge Separation in Molecular Clusters: Dissolution of a Salt in a Salt-(Solvent)(n)() Cluster. Chem Rev 2000; 100:4023-38. [PMID: 11749338 DOI: 10.1021/cr990059s] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- C Dedonder-Lardeux
- Laboratoire de Photophysique Moléculaire du CNRS, Bât. 210, Université Paris-Sud, 91405 Orsay Cedex, France
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Martı́ J, Csajka FS, Chandler D. Stochastic transition pathways in the aqueous sodium chloride dissociation process. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00874-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Martı́ J, Csajka FS. The aqueous solvation of sodium chloride: A Monte Carlo transition path sampling study. J Chem Phys 2000. [DOI: 10.1063/1.481893] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Consta S, Kapral R. Ionization reactions of ion complexes in mesoscopic water clusters. J Chem Phys 1999. [DOI: 10.1063/1.480369] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Degrève L, da Silva FLB. Large ionic clusters in concentrated aqueous NaCl solution. J Chem Phys 1999. [DOI: 10.1063/1.479783] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Das AK, Tembe BL. Radial and orientational solvation structure of the sodium chloride ion pair in dimethyl sulfoxide. J Chem Phys 1998. [DOI: 10.1063/1.475680] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Das AK, Madhusoodanan M, Tembe BL. Dynamics of Na+−Cl-, Na+−Na+, and Cl-−Cl- Ion Pairs in Dimethyl Sulfoxide: Friction Kernels and Transmission Coefficients. J Phys Chem A 1997. [DOI: 10.1021/jp9614557] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ashok K. Das
- Department of Chemistry, Indian Institute of Technology, Bombay Powai, Mumbai, 400 076, India
| | - M. Madhusoodanan
- Department of Chemistry, Indian Institute of Technology, Bombay Powai, Mumbai, 400 076, India
| | - B. L. Tembe
- Department of Chemistry, Indian Institute of Technology, Bombay Powai, Mumbai, 400 076, India
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Gelabert H, Gauduel Y. Short-Time Electron Transfer Processes in Ionic Aqueous Solution: Counterion and H/D Isotope Effects on Electron−Atom Pairs Relaxation. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp960684q] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- H. Gelabert
- Laboratoire d'Optique Appliquée, CNRS URA 1406, INSERM U451, Ecole Polytechnique-ENS Techniques Avancées, 91125 Palaiseau cédex, France
| | - Y. Gauduel
- Laboratoire d'Optique Appliquée, CNRS URA 1406, INSERM U451, Ecole Polytechnique-ENS Techniques Avancées, 91125 Palaiseau cédex, France
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Rey R, Hynes JT. Hydration Shell Exchange Kinetics: An MD Study for Na+(aq). ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp953429z] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rossend Rey
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
| | - James T. Hynes
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
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Gauduel Y, Gelabert H, Ashokkumar M. Short-lived charge-transfer-to-solvent-states and multiple electronic relaxations following femtosecond excitation of aqueous chloride ion. Chem Phys 1995. [DOI: 10.1016/0301-0104(95)00143-c] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Gauduel Y, Gelabert H, Ashokkumar M. Ultrafast electronic relaxation dynamics: A comparison between water and ionic aqueous solutions. J Mol Liq 1995. [DOI: 10.1016/0167-7322(95)92821-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Smith DE, Dang LX. Computer simulations of NaCl association in polarizable water. J Chem Phys 1994. [DOI: 10.1063/1.466363] [Citation(s) in RCA: 924] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Schenter GK, Messina M, Garrett BC. Centroid‐density quantum rate theory: Dynamical treatment of classical recrossing. J Chem Phys 1993. [DOI: 10.1063/1.465284] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Rey R, Guàrdia E, Padró JA. Generalized Langevin dynamics simulation of activated processes in solution: Ion pair interconversion in water. J Chem Phys 1992. [DOI: 10.1063/1.463398] [Citation(s) in RCA: 9] [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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Rey R, Guàrdia E, Padró JA. Friction kernels for the relative dynamics of ion pairs in water. J Chem Phys 1992. [DOI: 10.1063/1.463261] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Ciccotti G, Ferrario M, Hynes JT, Kapral R. Dynamics of ion pair interconversion in a polar solvent. J Chem Phys 1990. [DOI: 10.1063/1.459437] [Citation(s) in RCA: 165] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Rasaiah JC. Theories of Electrolyte Solutions. THE LIQUID STATE AND ITS ELECTRICAL PROPERTIES 1988. [DOI: 10.1007/978-1-4684-8023-8_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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