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Keshri S, Tembe B. Ion association in binary mixtures of water-CO2 in supercritical conditions through classical molecular dynamics simulations. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.02.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2
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Remsing RC, Duignan TT, Baer MD, Schenter GK, Mundy CJ, Weeks JD. Water Lone Pair Delocalization in Classical and Quantum Descriptions of the Hydration of Model Ions. J Phys Chem B 2018; 122:3519-3527. [DOI: 10.1021/acs.jpcb.7b10722] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard C. Remsing
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Timothy T. Duignan
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Marcel D. Baer
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Gregory K. Schenter
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Christopher J. Mundy
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States
- Affiliate Professor, Department of Chemical Engineering, University of Washington, Seattle, Washington, United States
| | - John D. Weeks
- Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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Keshri S, Tembe BL. Structural and Dynamical Properties of Alkaline Earth Metal Halides in Supercritical Water: Effect of Ion Size and Concentration. J Phys Chem B 2017; 121:10543-10555. [DOI: 10.1021/acs.jpcb.7b07690] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sonanki Keshri
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - B. L. Tembe
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Nakano H, Sato H. Introducing the mean field approximation to CDFT/MMpol method: Statistically converged equilibrium and nonequilibrium free energy calculation for electron transfer reactions in condensed phases. J Chem Phys 2017; 146:154101. [DOI: 10.1063/1.4979895] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Hiroshi Nakano
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Japan
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Keshri S, Mandal R, Tembe B. Solvation structures and dynamics of alkaline earth metal halides in supercritical water: A molecular dynamics study. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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SARKAR ATANU, CHATTERJEE ANUPAM, TIWARI SC, TEMBE BL. Na+ Cl− ion pair association in water-DMSO mixtures: Effect of ion pair model potentials. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1093-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Keshri S, Sarkar A, Tembe B. Molecular dynamics simulations of Na+-Cl− ion-pair in supercritical methanol. J Supercrit Fluids 2015. [DOI: 10.1016/j.supflu.2015.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Pezeshki S, Lin H. Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems. J Comput Chem 2014; 35:1778-88. [DOI: 10.1002/jcc.23685] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/19/2014] [Accepted: 06/30/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Soroosh Pezeshki
- Chemistry Department; CB 194, University of Colorado Denver; PO Box 173364 Denver Colorado 80217
| | - Hai Lin
- Chemistry Department; CB 194, University of Colorado Denver; PO Box 173364 Denver Colorado 80217
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Basilevsky M, Odinokov A, Nikitina E, Petrov N. The dielectric continuum solvent model adapted for treating preferential solvation effects. J Electroanal Chem (Lausanne) 2011. [DOI: 10.1016/j.jelechem.2010.09.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Rogers DM, Rempe SB. Probing the thermodynamics of competitive ion binding using minimum energy structures. J Phys Chem B 2011; 115:9116-29. [PMID: 21721551 DOI: 10.1021/jp2012864] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ion binding is known to affect the properties of biomolecules and is directly involved in many biochemical pathways. Because of the highly polar environments where ions are found, a quantum-mechanical treatment is preferable for understanding the energetics of competitive ion binding. Due to computational cost, a quantum mechanical treatment may involve several approximations, however, whose validity can be difficult to determine. Using thermodynamic cycles, we show how intuitive models for complicated ion binding reactions can be built up from simplified, isolated ion-ligand binding site geometries suitable for quantum mechanical treatment. First, the ion binding free energies of individual, minimum energy structures determine their intrinsic ion selectivities. Next, the relative propensity for each minimum energy structure is determined locally from the balance of ion-ligand and ligand-ligand interaction energies. Finally, the environment external to the binding site exerts its influence both through long-ranged dispersive and electrostatic interactions with the binding site as well as indirectly through shifting the binding site compositional and structural preferences. The resulting picture unifies field-strength, topological control, and phase activation viewpoints into a single theory that explicitly indicates the important role of solute coordination state on overall reaction energetics. As an example, we show that the Na(+) → K(+) selectivities can be recovered by correctly considering the conformational contribution to the selectivity. This can be done even when constraining configuration space to the neighborhood around a single, arbitrarily chosen, minimum energy structure. Structural regions around minima for K(+)- and Na(+)-water clusters are exhibited that display both rigid/mechanical and disordered/entropic selectivity mechanisms for both Na(+) and K(+). Thermodynamic consequences of the theory are discussed with an emphasis on the role of coordination structure in determining experimental properties of ions in complex biological environments.
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Affiliation(s)
- David M Rogers
- Center for Biological and Materials Sciences, MS 0895, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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Wood RH, Dong H. Communication: Combining non-Boltzmann sampling with free energy perturbation to calculate free energies of hydration of quantum models from a simulation of an approximate model. J Chem Phys 2011; 134:101101. [DOI: 10.1063/1.3561685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Robert H. Wood
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Haitao Dong
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Odinokov A, Leontyev I, Basilevsky M, Petrov NC. Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations. Mol Phys 2011. [DOI: 10.1080/00268976.2010.515259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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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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Dong H, Liu W, Doren DJ, Wood RH. Structure of an Accurate ab Initio Model of the Aqueous Na+ Ion at High Temperatures. J Phys Chem B 2008; 112:13552-60. [DOI: 10.1021/jp8057405] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Haitao Dong
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Wenbin Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Douglas J. Doren
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Robert H. Wood
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
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Shevkunov SV. Charge separation in water molecule clusters under thermal fluctuations: 2. Ionization-recombination equilibrium. COLLOID JOURNAL 2008. [DOI: 10.1134/s1061933x08050153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Savelyev A, Papoian GA. Polyionic Charge Density Plays a Key Role in Differential Recognition of Mobile Ions by Biopolymers. J Phys Chem B 2008; 112:9135-45. [DOI: 10.1021/jp801448s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexey Savelyev
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290
| | - Garegin A. Papoian
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290
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Liu W, Wood RH, Doren DJ. Sodium Chloride in Supercritical Water as a Function of Density: Potentials of Mean Force and an Equation for the Dissociation Constant from 723 to 1073 K and from 0 to 0.9 g/cm3. J Phys Chem B 2008; 112:7289-97. [DOI: 10.1021/jp800686s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wenbin Liu
- Quest Pharmaceutical Services, Newark, DE 19711, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Robert H. Wood
- Quest Pharmaceutical Services, Newark, DE 19711, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Douglas J. Doren
- Quest Pharmaceutical Services, Newark, DE 19711, and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
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Dong H, Liu W, Doren D, Wood R. Structure of an accurate ab initio model of the aqueous Cl- ion at high temperatures. J Phys Chem B 2007; 110:18504-14. [PMID: 16970478 DOI: 10.1021/jp0628333] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The structure of an accurate ab initio model of aqueous chloride ion was calculated at two high-temperature state points (573 K, 0.725 g/cm(3) and 723 K, 0.0098 g/cm(3)) by a two-step procedure. First, the structure of an approximate model was calculated from a molecular dynamics simulation of the model. Then the difference between the structure of the ab initio model and the approximate model was calculated by non-Boltzmann weighting of a sample of configurations taken from the approximate model simulation. Radial distribution functions, average coordination numbers, the distribution of coordination numbers, an analysis of orientations of water in the first coordination shell, and the free energy of hydration of the chloride ion are reported for both state points. The most common water structure has one hydrogen close to the chloride ion and one pointing away (46% at 573 K and 57% at 723 K). Waters in the first coordination shell that are not strongly bound to the chloride ions are common. Several variations of the method were tested. Models in which the water-water interaction is calculated with ab initio methods predict only a slightly different structure than models in which water-water interactions are determined from the approximate models. Similarly, using the approximate model for solute-water interactions when the water is far from the chloride ion did not affect the results. Uncertainties due to the limited sample of configurations are estimated and found to be small. The results are in qualitative agreement with X-ray and neutron diffraction experiments and with simulations of approximate models.
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Affiliation(s)
- Haitao Dong
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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El-Dossoki FI, El-Seify FA. Spectrophotometric, pH-metric and Conductometric Studies on Some 3-Arylhydrazone Derivatives of (2-Thenoyl) Ethylpyruvate). JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2006. [DOI: 10.5012/jkcs.2006.50.2.099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Free energy perturbation and dynamical nucleation study of water dimer and trimer through TIP5P water model. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2005.09.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Asthagiri D, Pratt LR, Kress JD. Ab initio molecular dynamics and quasichemical study of H+(aq). Proc Natl Acad Sci U S A 2005; 102:6704-8. [PMID: 15831590 PMCID: PMC1100742 DOI: 10.1073/pnas.0408071102] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The excess proton in water, H(+)(aq), plays a fundamental role in aqueous solution chemistry. Its solution thermodynamic properties are essential to molecular descriptions of that chemistry and for validation of dynamical calculations. Within the quasichemical theory of solutions those thermodynamic properties are conditional on recognizing underlying solution structures. The quasichemical treatment identifies H(3)O(+) and H(2)O(5)(+) as natural inner-shell complexes, corresponding to the cases of n = 1, 2 water molecule ligands, respectively, of a distinguished H(+) ion. A quantum-mechanical treatment of the inner-shell complex with both a dielectric continuum and a classical molecular dynamics treatment of the outer-shell contribution identifies the latter case (the Zundel complex) as the more numerous species. Ab initio molecular dynamics simulations, with two different electron density functionals, suggest a preponderance of Zundel-like structures, but a symmetrical ideal Zundel cation is not observed.
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Affiliation(s)
- D Asthagiri
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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