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Li M, Lv L, Fang T, Hao L, Li S, Dong S, Wu Y, Dong X, Liu H. Self-Consistent Implementation of a Solvation Free Energy Framework to Predict the Salt Solubilities of Six Alkali Halides. J Chem Theory Comput 2023; 19:5586-5601. [PMID: 37471389 DOI: 10.1021/acs.jctc.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
To assess the salt solubilities of six alkali halides in aqueous systems, we proposed a thermodynamic cycle and an efficient molecular modeling methodology. The Gibbs free energy changes for vaporization, dissociation, and dissolution were calculated using the experimental data of ionic thermodynamic properties obtained from the NBS tables. Additionally, the Marcus' and Tissandier's solvation free energy data for Li+, Na+, K+, Cl-, and Br- ions were compared with the conventional solvation free energies by substituting into our self-consistent thermodynamic cycle. Furthermore, Tissandier's absolute solvation free energy data were used as the training set to refit the Lennard-Jones parameters of OPLS-AA force field for ions. To predict salt solubilities, an assumption of a pseudo-solvent was proposed to characterize the coupling work of a solute with its environment from infinitely diluted to saturated solutions, indicating that the Gibbs energy change of solvation process is a function of ionic strength. Following the self-consistency of the cycle, the newly derived formulas were used to determine the salt solubilities by interpolating the intersection of Gibbs free energy of dissolution and the zero free energy line. The refined ion parameters can also predict the structure and thermodynamic properties of aqueous electrolyte solutions, such as densities, pair correlation functions, hydration numbers, mean activity coefficients, vapor pressures, and the radial dependences of the net charge at 298.15 K and 1 bar. Our method can be used to characterize the solid-liquid equilibria of ions or charged particles in aqueous systems. Furthermore, for highly concentrated strong electrolyte systems, it is essential to introduce accurate water models and polarizable force fields.
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Affiliation(s)
- Miyi Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Liqiang Lv
- College of Chemical Engineering, Shijiazhuang University, Hebei, Shijiazhuang 050035, China
| | - Tao Fang
- Beijing Institute of Aerospace Testing Technology, Beijing 100074, China
| | - Long Hao
- Beijing Institute of Aerospace Testing Technology, Beijing 100074, China
| | - Shenhui Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Shoulong Dong
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Yufeng Wu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Xiao Dong
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
| | - Helei Liu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, China
- Key Laboratory of Low-Carbon Conversion Science & Engineering, Shanghai Advanced Research Institute, Chinese Academy of Sciences (Shanghai Advanced Research Institute, Chinese Academy of Sciences), Shanghai 201210, China
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2
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Otlyotov AA, Itkis D, Yashina LV, Cavallo L, Minenkov Y. Physical and numerical aspects of sodium ion solvation free energies via the cluster-continuum model. Phys Chem Chem Phys 2022; 24:29927-29939. [PMID: 36468644 DOI: 10.1039/d2cp03583a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Sodium cation solvation Gibbs free energies (ΔGsolv(Na+)) have been obtained in water, dimethylformamide, dimethyl sulfoxide, ethanol, acetone, acetonitrile, and methanol through the "monomer cycle" cluster-continuum approach where a solvent reference state is described by infinitely separated molecules. The following steps are vital for obtaining reliable ΔGsolv(Na+) values: (a) a meticulous conformational search involving dispersion corrected density functional theory (DFT-D) and the continuum solvation model (CSM); (b) gas-phase DFT-D geometry optimization followed by single-point (SP) domain-based local pair natural orbital coupled clusters including single, double, and partly triple excitation (DLPNO-CCSD(T)) calculations in conjunction with the complete basis set extrapolation; (c) advanced statistical thermodynamic treatment of the low harmonic frequencies (<100 cm-1) to obtain the robust gas-phase Gibbs free energy correction; (d) gas-phase and dielectric continuum SP with non-electrostatic contributions included in the CSM; (e) an evaluation of the relative thermodynamic stability of the Na+(S)n clusters to identify the number of explicit solvent molecules n to be considered. Our refined computational protocol is promising with a Pearson correlation coefficient between the predicted and experimental data, ρ, of 0.82, and the mean signed and mean unsigned errors of 0.3 and 1.4 kcal mol-1, respectively.
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Affiliation(s)
- Arseniy A Otlyotov
- N.N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russia.
| | - Daniil Itkis
- N.N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russia. .,Lomonosov Moscow State University, Leninskie Gory 1, Bld. 3, 119991 Moscow, Russia
| | - Lada V Yashina
- N.N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russia. .,Lomonosov Moscow State University, Leninskie Gory 1, Bld. 3, 119991 Moscow, Russia
| | - Luigi Cavallo
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology, Thuwal-23955-6900, Saudi Arabia.
| | - Yury Minenkov
- N.N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russia. .,Joint Institute for High Temperatures, Russian Academy of Sciences, 13-2 Izhorskaya Street, Moscow 125412, Russia
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3
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Otlyotov AA, Cavallo L, Minenkov Y. Cluster-Continuum Model as a Sanity Check of Sodium Ions’ Gibbs Free Energies of Transfer. Inorg Chem 2022; 61:18365-18379. [DOI: 10.1021/acs.inorgchem.2c02065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Arseniy A. Otlyotov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, Moscow 119991, Russian Federation
| | - Luigi Cavallo
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Yury Minenkov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, Moscow 119991, Russian Federation
- Joint Institute for High Temperatures, Russian Academy of Sciences, 13-2 Izhorskaya Street, Moscow 125412, Russian Federation
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4
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Delgado JA, Wineman-Fisher V, Pandit S, Varma S. Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions. J Chem Inf Model 2022; 62:4713-4726. [PMID: 36173398 DOI: 10.1021/acs.jcim.2c00758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The reliability of molecular mechanics simulations to predict effects of ion binding to proteins depends on their ability to simultaneously describe ion-protein, ion-water, and protein-water interactions. Force fields (FFs) to describe protein-water and ion-water interactions have been constructed carefully and have also been refined routinely to improve accuracy. Descriptions for ion-protein interactions have also been refined, although in an a posteriori manner through the use of "nonbonded-fix (NB-fix)" approaches in which parameters from default Lennard-Jones mixing rules are replaced with those optimized against some reference data. However, even after NB-fix corrections, there remains a significant need for improvement. This is also true for polarizable FFs that include self-consistent inducible moments. Our recent studies on the polarizable AMOEBA FF suggested that the problem associated with modeling ion-protein interactions could be alleviated by recalibrating polarization models of cation-coordinating functional groups so that they respond better to the high electric fields present near ions. Here, we present such a recalibration of carbonyls, carboxylates, and hydroxyls in the AMOEBA protein FF and report that it does improve predictions substantially─mean absolute errors in Na+-protein and K+-protein interaction energies decrease from 8.7 to 5.3 and 9.6 to 6.3 kcal/mol, respectively. Errors are computed with respect to estimates from van der Waals-inclusive density functional theory benchmarked against high-level quantum mechanical calculations and experiments. While recalibration does improve ion-protein interaction energies, they still remain underestimated, suggesting that further improvements can be made in a systematic manner through modifications in classical formalism. Nevertheless, we show that by applying our many-body NB-fix correction to Lennard-Jones components, these errors are further reduced to 2.7 and 2.6 kcal/mol, respectively, for Na+ and K+ ions. Finally, we show that the recalibrated AMOEBA protein FF retains its intrinsic reliability in predicting protein structure and dynamics in the condensed phase.
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Affiliation(s)
- Julián A Delgado
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Vered Wineman-Fisher
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Sagar Pandit
- Department of Physics, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Sameer Varma
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States.,Department of Physics, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
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5
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Radtke V, Gebel N, Priester D, Ermantraut A, Bäuerle M, Himmel D, Stroh R, Koslowski T, Leito I, Krossing I. Measurements and Utilization of Consistent Gibbs Energies of Transfer of Single Ions: Towards a Unified Redox Potential Scale for All Solvents. Chemistry 2022; 28:e202200509. [PMID: 35446995 PMCID: PMC9401597 DOI: 10.1002/chem.202200509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Indexed: 11/08/2022]
Abstract
Utilizing the “ideal” ionic liquid salt bridge to measure Gibbs energies of transfer of silver ions between the solvents water, acetonitrile, propylene carbonate and dimethylformamide results in a consistent data set with a precision of 0.6 kJ mol−1 over 87 measurements in 10 half‐cells. This forms the basis for a coherent experimental thermodynamic framework of ion solvation chemistry. In addition, we define the solvent independent peabsH2O
‐ and the EabsH2O
values that account for the electronating potential of any redox system similar to the pHabsH2O
value of a medium that accounts for its protonating potential. This EabsH2O
scale is thermodynamically well‐defined enabling a straightforward comparison of the redox potentials (reducities) of all media with respect to the aqueous redox potential scale, hence unifying all conventional solvents′ redox potential scales. Thus, using the Gibbs energy of transfer of the silver ion published herein, one can convert and unify all hitherto published redox potentials measured, for example, against ferrocene, to the EabsH2O
scale.
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Affiliation(s)
- Valentin Radtke
- Institut für Anorganische und Analytische Chemie Freiburger Materialforschungszentrum (FMF) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT) Albert-Ludwigs-Universität Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Niklas Gebel
- Institut für Anorganische und Analytische Chemie Freiburger Materialforschungszentrum (FMF) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT) Albert-Ludwigs-Universität Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Denis Priester
- Institut für Anorganische und Analytische Chemie Freiburger Materialforschungszentrum (FMF) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT) Albert-Ludwigs-Universität Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Andreas Ermantraut
- Institut für Anorganische und Analytische Chemie Freiburger Materialforschungszentrum (FMF) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT) Albert-Ludwigs-Universität Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Monika Bäuerle
- Institut für Anorganische und Analytische Chemie Freiburger Materialforschungszentrum (FMF) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT) Albert-Ludwigs-Universität Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Daniel Himmel
- Institut für Anorganische und Analytische Chemie Freiburger Materialforschungszentrum (FMF) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT) Albert-Ludwigs-Universität Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Regina Stroh
- Institut für Anorganische und Analytische Chemie Freiburger Materialforschungszentrum (FMF) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT) Albert-Ludwigs-Universität Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie Albert-Ludwigs-Universität Freiburg Albertstr. 23a 79104 Freiburg Germany
| | - Ivo Leito
- Institute of Chemistry University of Tartu Ravila 14a Str 50411 Tartu Estonia
| | - Ingo Krossing
- Institut für Anorganische und Analytische Chemie Freiburger Materialforschungszentrum (FMF) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT) Albert-Ludwigs-Universität Freiburg Albertstr. 21 79104 Freiburg Germany
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6
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Gentry BM, Choi TH, Belfield WS, Keith JA. Computational predictions of metal-macrocycle stability constants require accurate treatments of local solvent and pH effects. Phys Chem Chem Phys 2021; 23:9189-9197. [PMID: 33885118 DOI: 10.1039/d1cp00611h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rational design of molecular chelating agents requires a detailed understanding of physicochemical ligand-metal interactions in solvent phase. Computational quantum chemistry methods should be able to provide this, but computational reports have shown poor accuracy when determining absolute binding constants for many chelating molecules. To understand why, we compare and benchmark static- and dynamics-based computational procedures for a range of monovalent and divalent cations binding to a conventional cryptand molecule: 2.2.2-cryptand ([2.2.2]). The benchmarking comparison shows that dynamics simulations using standard OPLS-AA classical potentials can reasonably predict binding constants for monovalent cations, but these procedures fail for divalent cations. We also consider computationally efficient static procedure using Kohn-Sham density functional theory (DFT) and cluster-continuum modeling that accounts for local microsolvation and pH effects. This approach accurately predicts binding energies for monovalent and divalent cations with an average error of 3.2 kcal mol-1 compared to experiment. This static procedure thus should be useful for future molecular screening efforts, and high absolute errors in the literature may be due to inadequate modeling of local solvent and pH effects.
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Affiliation(s)
- Brian M Gentry
- Department of Chemical Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, PA 15261, USA.
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7
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Savastano M. Words in supramolecular chemistry: the ineffable advances of polyiodide chemistry. Dalton Trans 2021; 50:1142-1165. [PMID: 33496303 DOI: 10.1039/d0dt04091f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Polyiodide chemistry has a rich history deeply intertwined with the development of supramolecular chemistry. Technological and theoretical interest in polyiodides has not diminished in the last decade, quite the contrary; yet the advances this perspective intends to cover are muddled by the involution of supramolecular vocabulary, preventing their unbiased discussion. Herein we discuss the pressing necessity of ordering the current babel of novel - and less so - supramolecular terms. Shared decisions at the community level might be required to shape the field into a harmonious body of knowledge, dominated by concepts rather than words. Secondary, σ-hole and halogen bonding schools of thought are all addressed here, together with their respective impact on the field. Then, on the basis of a shared vocabulary, a discussion of polyiodide chemistry is presented, starting with a revisited view of triiodide. The contemporary fields of supramolecular caging and polyiodide networks are then discussed, with emphasis on how the terms we choose to use deeply affect scientific progress.
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Affiliation(s)
- Matteo Savastano
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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8
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Itkis D, Cavallo L, Yashina LV, Minenkov Y. Ambiguities in solvation free energies from cluster-continuum quasichemical theory: lithium cation in protic and aprotic solvents. Phys Chem Chem Phys 2021; 23:16077-16088. [PMID: 34291782 DOI: 10.1039/d1cp01454d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gibbs free energies for Li+ solvation in water, methanol, acetonitrile, DMSO, dimethylacetamide, dimethoxyethane, dimethylformamide, gamma-butyrolactone, pyridine, and sulfolane have been calculated using the cluster-continuum quasichemical theory. With n independent solvent molecules S initial state forming the "monomer" thermodynamic cycle, Li+ solvation free energies are found to be on average 14 kcal mol-1 more positive compared to those from the "cluster" thermodynamic cycle where the initial state is the cluster Sn. We ascribe the inconsistency between the "monomer" and "cluster" cycles mainly to the incorrectly predicted solvation free energies of solvent clusters Sn from the SMD and CPCM continuum solvation models, which is in line with the earlier study of Bryantsev et al., J. Phys. Chem. B, 2008, 112, 9709-9719. When experimental-based solvation free energies of individual solvent molecules and solvent clusters are employed, the "monomer" and "cluster" cycles result in identical numbers. The best overall agreement with experimental-based "bulk" scale lithium cation solvation free energies was obtained for the "monomer" scale, and we recommend this set of values. We expect that further progress in the field is possible if (i) consensus on the accuracy of experimental reference values is achieved; (ii) the most recent continuum solvation models are properly parameterized for all solute-solvent combinations and become widely accessible for testing.
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Affiliation(s)
- Daniil Itkis
- N.N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russia.
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9
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Absolute ion hydration free energy scale and the surface potential of water via quantum simulation. Proc Natl Acad Sci U S A 2020; 117:30151-30158. [PMID: 33203676 DOI: 10.1073/pnas.2017214117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
With a goal of determining an absolute free energy scale for ion hydration, quasi-chemical theory and ab initio quantum mechanical simulations are employed to obtain an accurate value for the bulk hydration free energy of the Na+ ion. The free energy is partitioned into three parts: 1) the inner-shell or chemical contribution that includes direct interactions of the ion with nearby waters, 2) the packing free energy that is the work to produce a cavity of size λ in water, and 3) the long-range contribution that involves all interactions outside the inner shell. The interfacial potential contribution to the free energy resides in the long-range term. By averaging cation and anion data for that contribution, cumulant terms of all odd orders in the electrostatic potential are removed. The computed total is then the bulk hydration free energy. Comparison with the experimentally derived real hydration free energy produces an effective surface potential of water in the range -0.4 to -0.5 V. The result is consistent with a variety of experiments concerning acid-base chemistry, ion distributions near hydrophobic interfaces, and electric fields near the surface of water droplets.
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10
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Cox SJ, Thorpe DG, Shaffer PR, Geissler PL. Assessing long-range contributions to the charge asymmetry of ion adsorption at the air-water interface. Chem Sci 2020; 11:11791-11800. [PMID: 34094413 PMCID: PMC8162909 DOI: 10.1039/d0sc01947j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Anions generally associate more favorably with the air–water interface than cations. In addition to solute size and polarizability, the intrinsic structure of the unperturbed interface has been discussed as an important contributor to this bias. Here we assess quantitatively the role that intrinsic charge asymmetry of water's surface plays in ion adsorption, using computer simulations to compare model solutes of various size and charge. In doing so, we also evaluate the degree to which linear response theory for solvent polarization is a reasonable approach for comparing the thermodynamics of bulk and interfacial ion solvation. Consistent with previous works on bulk ion solvation, we find that the average electrostatic potential at the center of a neutral, sub-nanometer solute at the air–water interface depends sensitively on its radius, and that this potential changes quite nonlinearly as the solute's charge is introduced. The nonlinear response closely resembles that of the bulk. As a result, the net nonlinearity of ion adsorption is weaker than in bulk, but still substantial, comparable to the apparent magnitude of macroscopically nonlocal contributions from the undisturbed interface. For the simple-point-charge model of water we study, these results argue distinctly against rationalizing ion adsorption in terms of surface potentials inherent to molecular structure of the liquid's boundary. Cations and anions have different affinities for the air-water interface. The intrinsic orientation of surface molecules suggests such an asymmetry, but the bias is dominated by solvent response that is spatially local and significantly nonlinear.![]()
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Affiliation(s)
- Stephen J Cox
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Dayton G Thorpe
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA.,Department of Physics, University of California Berkeley CA 94720 USA
| | - Patrick R Shaffer
- Department of Chemistry, University of California Berkeley CA 94720 USA
| | - Phillip L Geissler
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA.,Department of Chemistry, University of California Berkeley CA 94720 USA
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11
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Wineman-Fisher V, Delgado JM, Nagy PR, Jakobsson E, Pandit SA, Varma S. Transferable interactions of Li + and Mg 2+ ions in polarizable models. J Chem Phys 2020; 153:104113. [PMID: 32933310 DOI: 10.1063/5.0022060] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Therapeutic implications of Li+, in many cases, stem from its ability to inhibit certain Mg2+-dependent enzymes, where it interacts with or substitutes for Mg2+. The underlying details of its action are, however, unknown. Molecular simulations can provide insights, but their reliability depends on how well they describe relative interactions of Li+ and Mg2+ with water and other biochemical groups. Here, we explore, benchmark, and recommend improvements to two simulation approaches: the one that employs an all-atom polarizable molecular mechanics (MM) model and the other that uses a hybrid quantum and MM implementation of the quasi-chemical theory (QCT). The strength of the former is that it describes thermal motions explicitly and that of the latter is that it derives local contributions from electron densities. Reference data are taken from the experiment, and also obtained systematically from CCSD(T) theory, followed by a benchmarked vdW-inclusive density functional theory. We find that the QCT model predicts relative hydration energies and structures in agreement with the experiment and without the need for additional parameterization. This implies that accurate descriptions of local interactions are essential. Consistent with this observation, recalibration of local interactions in the MM model, which reduces errors from 10.0 kcal/mol to 1.4 kcal/mol, also fixes aqueous phase properties. Finally, we show that ion-ligand transferability errors in the MM model can be reduced significantly from 10.3 kcal/mol to 1.2 kcal/mol by correcting the ligand's polarization term and by introducing Lennard-Jones cross-terms. In general, this work sets up systematic approaches to evaluate and improve molecular models of ions binding to proteins.
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Affiliation(s)
- Vered Wineman-Fisher
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, USA
| | - Julián Meléndez Delgado
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, USA
| | - Péter R Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Eric Jakobsson
- National Center for Supercomputing Applications, Center for Biophysics and Computational Biology, Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Sagar A Pandit
- Department of Physics, University of South Florida, Tampa, Florida 33620, USA
| | - Sameer Varma
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, USA
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12
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Ahmed M, Inoue K, Nihonyanagi S, Tahara T. Hidden Isolated OH at the Charged Hydrophobic Interface Revealed by Two‐Dimensional Heterodyne‐Detected VSFG Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mohammed Ahmed
- Molecular Spectroscopy LaboratoryRIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Ultrafast Spectroscopy Research TeamRIKEN Center for Advanced Photonics (RAP), RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Ken‐ichi Inoue
- Molecular Spectroscopy LaboratoryRIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Present address: Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Satoshi Nihonyanagi
- Molecular Spectroscopy LaboratoryRIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Ultrafast Spectroscopy Research TeamRIKEN Center for Advanced Photonics (RAP), RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Tahei Tahara
- Molecular Spectroscopy LaboratoryRIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Ultrafast Spectroscopy Research TeamRIKEN Center for Advanced Photonics (RAP), RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
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13
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Ahmed M, Inoue KI, Nihonyanagi S, Tahara T. Hidden Isolated OH at the Charged Hydrophobic Interface Revealed by Two-Dimensional Heterodyne-Detected VSFG Spectroscopy. Angew Chem Int Ed Engl 2020; 59:9498-9505. [PMID: 32189396 DOI: 10.1002/anie.202002368] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Indexed: 02/04/2023]
Abstract
Water around hydrophobic groups mediates hydrophobic interactions that play key roles in many chemical and biological processes. Thus, the molecular-level elucidation of the properties of water in the vicinity of hydrophobic groups is important. We report on the structure and dynamics of water at two oppositely charged hydrophobic ion/water interfaces, that is, the tetraphenylborate-ion (TPB- )/water and tetraphenylarsonium-ion (TPA+ )/water interfaces, which are clarified by two-dimensional heterodyne-detected vibrational sum-frequency generation (2D HD-VSFG) spectroscopy. The obtained 2D HD-VSFG spectra of the anionic TPB- interface reveal the existence of distinct π-hydrogen bonded OH groups in addition to the usual hydrogen-bonded OH groups, which are hidden in the steady-state spectrum. In contrast, 2D HD-VSFG spectra of the cationic TPA+ interface only show the presence of usual hydrogen-bonded OH groups. The present study demonstrates that the sign of the interfacial charge governs the structure and dynamics of water molecules that face the hydrophobic region.
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Affiliation(s)
- Mohammed Ahmed
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Ken-Ichi Inoue
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Present address: Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Satoshi Nihonyanagi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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14
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Chaudhari MI, Vanegas JM, Pratt LR, Muralidharan A, Rempe SB. Hydration Mimicry by Membrane Ion Channels. Annu Rev Phys Chem 2020; 71:461-484. [PMID: 32155383 DOI: 10.1146/annurev-physchem-012320-015457] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if these protein channels provide environments similar to the aqueous solution hydration environment. Indeed, bulk aqueous solution is an important reference condition for the ion permeation process. Assessment of this hydration mimicry concept depends on understanding the hydration structure and free energies of metal ions in water in order to provide a comparison for the membrane channel environment. To refine these considerations, we review local hydration structures of ions in bulk water and the molecular quasi-chemical theory that provides hydration free energies. In doing so, we note some current views of ion binding to membrane channels and suggest new physical chemical calculations and experiments that might further clarify the hydration mimicry concept.
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Affiliation(s)
- Mangesh I Chaudhari
- Department of Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA;
| | - Juan M Vanegas
- Department of Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA; .,Current affiliation: Department of Physics, University of Vermont, Burlington, Vermont 05405, USA
| | - L R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA
| | - Ajay Muralidharan
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA.,Current affiliation: Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Susan B Rempe
- Department of Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA;
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15
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Duignan TT, Zhao XS. The Born model can accurately describe electrostatic ion solvation. Phys Chem Chem Phys 2020; 22:25126-25135. [DOI: 10.1039/d0cp04148c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solvation free energies of ions in water are consistent with the Born linear response model if the centre on which the ion–water repulsion force acts is moved from the oxygen atom towards the hydrogens.
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Affiliation(s)
- Timothy T. Duignan
- School of Chemical Engineering
- The University of Queensland
- St Lucia
- Australia
| | - X. S. Zhao
- School of Chemical Engineering
- The University of Queensland
- St Lucia
- Australia
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16
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Tomaník L, Muchová E, Slavíček P. Solvation energies of ions with ensemble cluster-continuum approach. Phys Chem Chem Phys 2020; 22:22357-22368. [DOI: 10.1039/d0cp02768e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
An alternative cluster-continuum approach for the calculation of solvation free energies of ions.
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Affiliation(s)
- Lukáš Tomaník
- Department of Physical Chemistry
- University of Chemistry and TechnologyTechnická 5
- 16628 Prague 6
- Czech Republic
| | - Eva Muchová
- Department of Physical Chemistry
- University of Chemistry and TechnologyTechnická 5
- 16628 Prague 6
- Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry
- University of Chemistry and TechnologyTechnická 5
- 16628 Prague 6
- Czech Republic
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17
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Basdogan Y, Groenenboom MC, Henderson E, De S, Rempe SB, Keith JA. Machine Learning-Guided Approach for Studying Solvation Environments. J Chem Theory Comput 2019; 16:633-642. [PMID: 31809056 DOI: 10.1021/acs.jctc.9b00605] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular-level understanding and characterization of solvation environments are often needed across chemistry, biology, and engineering. Toward practical modeling of local solvation effects of any solute in any solvent, we report a static and all-quantum mechanics-based cluster-continuum approach for calculating single-ion solvation free energies. This approach uses a global optimization procedure to identify low-energy molecular clusters with different numbers of explicit solvent molecules and then employs the smooth overlap for atomic positions learning kernel to quantify the similarity between different low-energy solute environments. From these data, we use sketch maps, a nonlinear dimensionality reduction algorithm, to obtain a two-dimensional visual representation of the similarity between solute environments in differently sized microsolvated clusters. After testing this approach on different ions having charges 2+, 1+, 1-, and 2-, we find that the solvation environment around each ion can be seen to usually become more similar in hand with its calculated single-ion solvation free energy. Without needing either dynamics simulations or an a priori knowledge of local solvation structure of the ions, this approach can be used to calculate solvation free energies within 5% of experimental measurements for most cases, and it should be transferable for the study of other systems where dynamics simulations are not easily carried out.
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Affiliation(s)
- Yasemin Basdogan
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
| | - Mitchell C Groenenboom
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
| | - Ethan Henderson
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
| | - Sandip De
- Laboratory of Computational Science and Modelling, Institute of Materials , École Polytechnique Fédérale de Lausanne , Lausanne 1015 , Switzerland
| | - Susan B Rempe
- Department of Nanobiology , Sandia National Laboratories , Albuquerque 87185 , New Mexico , United States
| | - John A Keith
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
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18
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Kepp KP. Free Energies of Hydration for Metal Ions from Heats of Vaporization. J Phys Chem A 2019; 123:6536-6546. [DOI: 10.1021/acs.jpca.9b05140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Kasper P. Kepp
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, DK, Denmark
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19
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Doyle CC, Shi Y, Beck TL. The Importance of the Water Molecular Quadrupole for Estimating Interfacial Potential Shifts Acting on Ions Near the Liquid–Vapor Interface. J Phys Chem B 2019; 123:3348-3358. [DOI: 10.1021/acs.jpcb.9b01289] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carrie C. Doyle
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Yu Shi
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Thomas L. Beck
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
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20
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Rokitskaya TI, Luzhkov VB, Korshunova GA, Tashlitsky VN, Antonenko YN. Effect of methyl and halogen substituents on the transmembrane movement of lipophilic ions. Phys Chem Chem Phys 2019; 21:23355-23363. [DOI: 10.1039/c9cp03460a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The introduction of a halogen or a methyl substituent changes the speed of the flip-flop of the penetrating cations and anions in the opposite way.
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Affiliation(s)
- Tatyana I. Rokitskaya
- Belozersky Institute of Physico-Chemical Biology
- Lomonosov Moscow State University
- Moscow 119991
- Russia
| | - Victor B. Luzhkov
- Department of Kinetics of Chemical and Biological Processes
- Institute of Problems of Chemical Physics
- Russian Academy of Sciences
- Moscow Region 142432
- Russia
| | - Galina A. Korshunova
- Belozersky Institute of Physico-Chemical Biology
- Lomonosov Moscow State University
- Moscow 119991
- Russia
| | | | - Yuri N. Antonenko
- Belozersky Institute of Physico-Chemical Biology
- Lomonosov Moscow State University
- Moscow 119991
- Russia
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