1
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Stevens MJ, Rempe SLB. Insight into the K channel's selectivity from binding of K +, Na + and water to N-methylacetamide. Faraday Discuss 2024; 249:195-209. [PMID: 37846738 DOI: 10.1039/d3fd00110e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
In potassium channels that conduct K+ selectively over Na+, which sites are occupied by K+ or water and the mechanism of selectivity are unresolved questions. The combination of the energetics and the constraints imposed by the protein structure yield the selective permeation and occupancy. To gain insight into the combination of structure and energetics, we performed density functional theory (DFT) calculations of multiple N-methyl acetamide (NMA) ligands binding to K+ and Na+, relative to hydrated K+ and Na+. NMA is an analogue of the amino acid backbone and provides the carbonyl binding to the ions that occurs in most binding sites of the K+ channel. Unconstrained optimal structures are obtained through geometry optimization calculations of the NMA ligand binding. The complexes formed by 8 NMA binding to the cations have the O atoms positioned in nearly identical locations as the O atoms in the selectivity filter. The transfer free energies between bulk water and K+ or Na+ bound to 8 NMA are almost identical, implying there is no selectivity by a single site. For water optimized with 8 NMA, binding is weak and O atoms are not positioned as in the K+ channel selectivity filter, suggesting that the ions are much more favored than water. Optimal structures of 8 NMA binding with two cations (K+ or Na+) are stable and have lower binding free energy than the optimal structures with just one cation. However, in the Na+ case, the optimal structure deforms and does not match the K+ channel; that is, two bound Na+ are destabilizing. In contrast, the two K+ structure is stabilized and the selectivity free energy favors K+. Overall, this study shows that binding site occupancy and the mechanism for K+ selectivity involves multiple K+ binding in multiple neighboring layers or sites of the K+ channel selectivity filter.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
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2
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Stevens MJ, Rempe SLB. Binding of carboxylate and water to monovalent cations. Phys Chem Chem Phys 2023; 25:29881-29893. [PMID: 37889481 DOI: 10.1039/d3cp04200f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The interactions of carboxylate anions with water and cations are important for a wide variety of systems, both biological and synthetic. To gain insight on properties of the local complexes, we apply density functional theory, to treat the complex electrostatic interactions, and investigate mixtures with varied numbers of carboxylate anions (acetate) and waters binding to monovalent cations, Li+, Na+ and K+. The optimal structure with overall lowest free energy contains two acetates and two waters such that the cation is four-fold coordinated, similar to structures found earlier for pure water or pure carboxylate ligands. More generally, the complexes with two acetates have the lowest free energy. In transitioning from the overall optimal state, exchanging an acetate for water has a lower free energy barrier than exchanging water for an acetate. In most cases, the carboxylates are monodentate and in the first solvation shell. As water is added to the system, hydrogen bonding between waters and carboxylate O atoms further stabilizes monodentate structures. These structures, which have strong electrostatic interactions that involve hydrogen bonds of varying strength, are significantly polarized, with ChelpG partial charges that vary substantially as the bonding geometry varies. Overall, these results emphasize the increasing importance of water as a component of binding sites as the number of ligands increases, thus affecting the preferential solvation of specific metal ions and clarifying Hofmeister effects. Finally, structural analysis correlated with free energy analysis supports the idea that binding to more than the preferred number of carboxylates under architectural constraints are a key to ion transport.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
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3
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Gomez DT, Pratt LR, Asthagiri DN, Rempe SB. Hydrated Anions: From Clusters to Bulk Solution with Quasi-Chemical Theory. Acc Chem Res 2022; 55:2201-2212. [PMID: 35829622 PMCID: PMC9386901 DOI: 10.1021/acs.accounts.2c00078] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The interactions of hydrated ions with molecular and macromolecular solution and interface partners are strong on a chemical energy scale. Here, we recount the foremost ab initio theory for the evaluation of the hydration free energies of ions, namely, quasi-chemical theory (QCT). We focus on anions, particularly halides but also the hydroxide anion, because they have been outstanding challenges for all theories. For example, this work supports understanding the high selectivity for F- over Cl- in fluoride-selective ion channels despite the identical charge and the size similarity of these ions. QCT is built by the identification of inner-shell clusters, separate treatment of those clusters, and then the integration of those results into the broader-scale solution environment. Recent work has focused on a close comparison with mass-spectrometric measurements of ion-hydration equilibria. We delineate how ab initio molecular dynamics (AIMD) calculations on ion-hydration clusters, elementary statistical thermodynamics, and electronic structure calculations on cluster structures sampled from the AIMD calculations obtain just the free energies extracted from the cluster experiments. That theory-experiment comparison has not been attempted before the work discussed here, but the agreement is excellent with moderate computational effort. This agreement reinforces both theory and experiment and provides a numerically accurate inner-shell contribution to QCT. The inner-shell complexes involving heavier halides display strikingly asymmetric hydration clusters. Asymmetric hydration structures can be problematic for the evaluation of the QCT outer-shell contribution with the polarizable continuum model (PCM). Nevertheless, QCT provides a favorable setting for the exploitation of PCM when the inner-shell material shields the ion from the outer solution environment. For the more asymmetrically hydrated, and thus less effectively shielded, heavier halide ions clustered with waters, the PCM is less satisfactory. We therefore investigate an inverse procedure in which the inner-shell structures are sampled from readily available AIMD calculations on the bulk solutions. This inverse procedure is a remarkable improvement; our final results are in close agreement with a standard tabulation of hydration free energies, and the final composite results are independent of the coordination number on the chemical energy scale of relevance, as they should be. Finally, a comparison of anion hydration structure in clusters and bulk solutions from AIMD simulations emphasize some differences: the asymmetries of bulk solution inner-shell structures are moderated compared with clusters but are still present, and inner hydration shells fill to slightly higher average coordination numbers in bulk solution than in clusters.
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Affiliation(s)
- Diego T. Gomez
- Department
of Chemical & Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States,
| | - Lawrence R. Pratt
- Department
of Chemical & Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States,
| | - Dilipkumar N. Asthagiri
- Department
of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States,
| | - Susan B. Rempe
- Center
for Integrated Nanotechnologies, Sandia
National Laboratories, Albuquerque, New Mexico 87185, United States,
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4
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Gomez DT, Pratt LR, Rogers DM, Rempe SB. Free Energies of Hydrated Halide Anions: High Through-Put Computations on Clusters to Treat Rough Energy-Landscapes. Molecules 2021; 26:molecules26113087. [PMID: 34064203 PMCID: PMC8196753 DOI: 10.3390/molecules26113087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022] Open
Abstract
With a longer-term goal of addressing the comparative behavior of the aqueous halides F−, Cl−, Br−, and I− on the basis of quasi-chemical theory (QCT), here we study structures and free energies of hydration clusters for those anions. We confirm that energetically optimal (H2O)nX clusters, with X = Cl−, Br−, and I−, exhibit surface hydration structures. Computed free energies, based on optimized surface hydration structures utilizing a harmonic approximation, typically (but not always) disagree with experimental free energies. To remedy the harmonic approximation, we utilize single-point electronic structure calculations on cluster geometries sampled from an AIMD (ab initio molecular dynamics) simulation stream. This rough-landscape procedure is broadly satisfactory and suggests unfavorable ligand crowding as the physical effect addressed. Nevertheless, this procedure can break down when n≳4, with the characteristic discrepancy resulting from a relaxed definition of clustering in the identification of (H2O)nX clusters, including ramified structures natural in physical cluster theories. With ramified structures, the central equation for the present rough-landscape approach can acquire some inconsistency. Extension of these physical cluster theories in the direction of QCT should remedy that issue, and should be the next step in this research direction.
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Affiliation(s)
- Diego T. Gomez
- Department of Chemical & Biomolecular Engineering, Tulane University, New Orleans, LA 70118, USA; (D.T.G.); (L.R.P.)
| | - Lawrence R. Pratt
- Department of Chemical & Biomolecular Engineering, Tulane University, New Orleans, LA 70118, USA; (D.T.G.); (L.R.P.)
| | - David M. Rogers
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA;
| | - Susan B. Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
- Correspondence: ; Tel.: +1-505-845-0253
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5
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Priest CW, Greathouse JA, Kinnan MK, Burton PD, Rempe SB. Ab initio and force field molecular dynamics study of bulk organophosphorus and organochlorine liquid structures. J Chem Phys 2021; 154:084503. [PMID: 33639727 DOI: 10.1063/5.0033426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We performed ab initio molecular dynamics (AIMD) simulations to benchmark bulk liquid structures and to evaluate results from all-atom force field molecular dynamics (FFMD) simulations with the generalized Amber force field (GAFF) for organophosphorus (OP) and organochlorine (OC) compounds. Our work also addresses the current and important topic of force field validation, applied here to a set of nonaqueous organic liquids. Our approach differs from standard treatments, which validate force fields based on thermodynamic data. Utilizing radial distribution functions (RDFs), our results show that GAFF reproduces the AIMD-predicted asymmetric liquid structures moderately well for OP compounds that contain bulky alkyl groups. Among the OCs, RDFs obtained from FFMD overlap well with AIMD results, with some offsets in position and peak structuring. However, re-parameterization of GAFF for some OCs is needed to reproduce fully the liquid structures predicted by AIMD. The offsets between AIMD and FFMD peak positions suggest inconsistencies in the developed force fields, but, in general, GAFF is able to capture short-ranged and long-ranged interactions of OPs and OCs observed in AIMD. Along with the local coordination structure, we also compared enthalpies of vaporization. Overall, calculated bulk properties from FFMD compared reasonably well with experimental values, suggesting that small improvements within the FF should focus on parameters that adjust the bulk liquid structures of these compounds.
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Affiliation(s)
- Chad W Priest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | | | - Mark K Kinnan
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Patrick D Burton
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Susan B Rempe
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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6
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Seethamraju S, Obrzut J, Douglas JF, Woodcock JW, Gilman JW. Quantifying Fluorogenic Dye Hydration in an Epoxy Resin by Noncontact Microwave Dielectric Spectroscopy. J Phys Chem B 2020; 124:2914-2919. [PMID: 32162926 DOI: 10.1021/acs.jpcb.9b11622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated a chemically modified rhodamine B dye as a sensor of local water content in dye-modified epoxy resins, where these measurements were combined with dielectric measurements to estimate the dye-water association ratio in the material. In particular, the water-sensitive fluorogenic dye was covalently attached to the epoxy resin backbone. This dye becomes fluorescent only upon photoactivation by ultraviolet light and its protonation in the presence of water. High-resolution noncontact microwave cavity dielectric measurements on these materials indicate a decrease of the dielectric permittivity upon photoactivation. We utilize this effect to determine the average extent of hydration of the activated dye molecules. Our results suggest that fluorogenic dyes are promising for the quantification of the local water content in polymer materials, such as the technologically important problem of interfacial water in epoxy materials.
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Affiliation(s)
- Sindhu Seethamraju
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8542, United States.,Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227, United States
| | - Jan Obrzut
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8542, United States
| | - Jack F Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8542, United States
| | - Jeremiah W Woodcock
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8542, United States
| | - Jeffrey W Gilman
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8542, United States
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7
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Maldonado AM, Basdogan Y, Berryman JT, Rempe SB, Keith JA. First-principles modeling of chemistry in mixed solvents: Where to go from here? J Chem Phys 2020; 152:130902. [PMID: 32268733 DOI: 10.1063/1.5143207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mixed solvents (i.e., binary or higher order mixtures of ionic or nonionic liquids) play crucial roles in chemical syntheses, separations, and electrochemical devices because they can be tuned for specific reactions and applications. Apart from fully explicit solvation treatments that can be difficult to parameterize or computationally expensive, there is currently no well-established first-principles regimen for reliably modeling atomic-scale chemistry in mixed solvent environments. We offer our perspective on how this process could be achieved in the near future as mixed solvent systems become more explored using theoretical and computational chemistry. We first outline what makes mixed solvent systems far more complex compared to single-component solvents. An overview of current and promising techniques for modeling mixed solvent environments is provided. We focus on so-called hybrid solvation treatments such as the conductor-like screening model for real solvents and the reference interaction site model, which are far less computationally demanding than explicit simulations. We also propose that cluster-continuum approaches rooted in physically rigorous quasi-chemical theory provide a robust, yet practical, route for studying chemical processes in mixed solvents.
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Affiliation(s)
- Alex M Maldonado
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yasemin Basdogan
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Joshua T Berryman
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Susan B Rempe
- Center for Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - John A Keith
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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8
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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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9
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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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10
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Muralidharan A, Pratt L, Chaudhari M, Rempe S. Quasi-chemical theory for anion hydration and specific ion effects: Cl-(aq) vs. F-(aq). ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cpletx.2019.100037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Baskin A, Prendergast D. "Ion Solvation Spectra": Free Energy Analysis of Solvation Structures of Multivalent Cations in Aprotic Solvents. J Phys Chem Lett 2019; 10:4920-4928. [PMID: 31322350 DOI: 10.1021/acs.jpclett.9b01569] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using advanced molecular dynamics free energy sampling techniques-both classical and ab initio-we analyze the solvation structures of multivalent cations in aprotic solvents. In contrast to previous studies of mono- and bivalent ions in organic solvents, mainly performed using hybrid cluster-continuum quantum chemistry calculations that rely on the assumption of uniqueness of ion solvation free energies, here we find that monatomic bivalent cations may have multiple well-defined minima, as previously reported only for water, or plateaus of free energy with respect to the ion-solvent coordination. These observations are generalized in the concept of the "ion solvation spectrum" to highlight the rich phenomenology related to ion solvation as opposed to the normally expected free energy profiles with a single coordination minimum. Specifically, we show that a single chemical species may exhibit a multiplicity of distinctly different electrochemical properties. Using one- and two-dimensional projections of the free energy landscape, we analyze the stability of ion solvation structures and reveal minimum free energy pathways for ion (de-)solvation with low-dimensional approximations to associated kinetic barriers. Unexpectedly, we show that in some cases the process of opening the first ion solvation shell, by removing a solvent molecule, may actually drive the ion into a free energy basin with a higher coordination number. Our study highlights some deficiencies of conventional methodologies for studying ion solvation as a path to determine redox potentials and provides experimentally testable predictions.
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Affiliation(s)
- Artem Baskin
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David Prendergast
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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12
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Friedman R. Simulations of Biomolecules in Electrolyte Solutions. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical SciencesLinnæus UniversityKalmar SE‐391 82 Sweden
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13
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Muralidharan A, Pratt LR, Chaudhari MI, Rempe SB. Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F -) Anion Hydration. J Phys Chem A 2018; 122:9806-9812. [PMID: 30475612 DOI: 10.1021/acs.jpca.8b08474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Accurate predictions of the hydration free energy for anions typically has been more challenging than that for cations. Hydrogen bond donation to the anion in hydrated clusters such as F(H2O) n - can lead to delicate structures. Consequently, the energy landscape contains many local minima, even for small clusters, and these minima present a challenge for computational optimization. Utilization of cluster experimental results for the free energies of gas-phase clusters shows that even though anharmonic effects are interesting they need not be of troublesome magnitudes for careful applications of quasi-chemical theory to ion hydration. Energy-optimized cluster structures for anions can leave the central ion highly exposed, and application of implicit solvation models to these structures can incur more serious errors than those for metal cations. Utilizing cluster structures sampled from ab initio molecular dynamics simulations substantially fixes those issues.
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Affiliation(s)
- A Muralidharan
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - L R Pratt
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - M I Chaudhari
- Center for Biological and Engineering Sciences , Sandia National Laboratories , Albuquerque , New Mexico 87185 , United States
| | - S B Rempe
- Center for Biological and Engineering Sciences , Sandia National Laboratories , Albuquerque , New Mexico 87185 , United States
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14
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Chaudhari MI, Rempe SB. Strontium and barium in aqueous solution and a potassium channel binding site. J Chem Phys 2018; 148:222831. [PMID: 29907035 DOI: 10.1063/1.5023130] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ion hydration structure and free energy establish criteria for understanding selective ion binding in potassium (K+) ion channels and may be significant to understanding blocking mechanisms as well. Recently, we investigated the hydration properties of Ba2+, the most potent blocker of K+ channels among the simple metal ions. Here, we use a similar method of combining ab initio molecular dynamics simulations, statistical mechanical theory, and electronic structure calculations to probe the fundamental hydration properties of Sr2+, which does not block bacterial K+ channels. The radial distribution of water around Sr2+ suggests a stable 8-fold geometry in the local hydration environment, similar to Ba2+. While the predicted hydration free energy of -331.8 kcal/mol is comparable with the experimental result of -334 kcal/mol, the value is significantly more favorable than the -305 kcal/mol hydration free energy of Ba2+. When placed in the innermost K+ channel blocking site, the solvation free energies and lowest energy structures of both Sr2+ and Ba2+ are nearly unchanged compared with their respective hydration properties. This result suggests that the block is not attributable to ion trapping due to +2 charge, and differences in blocking behavior arise due to free energies associated with the exchange of water ligands for channel ligands instead of free energies of transfer from water to the binding site.
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Affiliation(s)
- Mangesh I Chaudhari
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Susan B Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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15
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Chaudhari MI, Rempe SB, Pratt LR. Quasi-chemical theory of F -(aq): The "no split occupancies rule" revisited. J Chem Phys 2018; 147:161728. [PMID: 29096480 DOI: 10.1063/1.4986244] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We use ab initio molecular dynamics (AIMD) calculations and quasi-chemical theory (QCT) to study the inner-shell structure of F-(aq) and to evaluate that single-ion free energy under standard conditions. Following the "no split occupancies" rule, QCT calculations yield a free energy value of -101 kcal/mol under these conditions, in encouraging agreement with tabulated values (-111 kcal/mol). The AIMD calculations served only to guide the definition of an effective inner-shell constraint. QCT naturally includes quantum mechanical effects that can be concerning in more primitive calculations, including electronic polarizability and induction, electron density transfer, electron correlation, molecular/atomic cooperative interactions generally, molecular flexibility, and zero-point motion. No direct assessment of the contribution of dispersion contributions to the internal energies has been attempted here, however. We anticipate that other aqueous halide ions might be treated successfully with QCT, provided that the structure of the underlying statistical mechanical theory is absorbed, i.e., that the "no split occupancies" rule is recognized.
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Affiliation(s)
- Mangesh I Chaudhari
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Susan B Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA
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16
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Piquemal JP, Jordan KD. Preface: Special Topic: From Quantum Mechanics to Force Fields. J Chem Phys 2018; 147:161401. [PMID: 29096449 DOI: 10.1063/1.5008887] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.
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Affiliation(s)
- Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, UPMC, Sorbonne Universités, 75252 Paris Cedex 05, France
| | - Kenneth D Jordan
- Department of Chemistry, The University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
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17
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Duignan TT, Baer MD, Schenter GK, Mundy CJ. Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions. J Chem Phys 2017; 147:161716. [DOI: 10.1063/1.4994912] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Timothy T. Duignan
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Marcel D. Baer
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Gregory K. Schenter
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Chistopher J. Mundy
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98185, USA
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18
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Duignan TT, Baer MD, Schenter GK, Mundy CJ. Real single ion solvation free energies with quantum mechanical simulation. Chem Sci 2017; 8:6131-6140. [PMID: 28989643 PMCID: PMC5625628 DOI: 10.1039/c7sc02138k] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 05/26/2017] [Indexed: 01/11/2023] Open
Abstract
Single ion solvation free energies are one of the most important properties of electrolyte solutions and yet there is ongoing debate about what these values are. Only the values for neutral ion pairs are known. Here, we use DFT interaction potentials with molecular dynamics simulation (DFT-MD) combined with a modified version of the quasi-chemical theory (QCT) to calculate these energies for the lithium and fluoride ions. A method to correct for the error in the DFT functional is developed and very good agreement with the experimental value for the lithium fluoride pair is obtained. Moreover, this method partitions the energies into physically intuitive terms such as surface potential, cavity and charging energies which are amenable to descriptions with reduced models. Our research suggests that lithium's solvation free energy is dominated by the free energetics of a charged hard sphere, whereas fluoride exhibits significant quantum mechanical behavior that cannot be simply described with a reduced model.
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Affiliation(s)
- Timothy T Duignan
- Physical Science Division , Pacific Northwest National Laboratory , P.O. Box 999 , Richland , Washington 99352 , USA . ; Tel: +1 509 3756940
| | - Marcel D Baer
- Physical Science Division , Pacific Northwest National Laboratory , P.O. Box 999 , Richland , Washington 99352 , USA . ; Tel: +1 509 3756940
| | - Gregory K Schenter
- Physical Science Division , Pacific Northwest National Laboratory , P.O. Box 999 , Richland , Washington 99352 , USA . ; Tel: +1 509 3756940
| | - Christopher J Mundy
- Physical Science Division , Pacific Northwest National Laboratory , P.O. Box 999 , Richland , Washington 99352 , USA . ; Tel: +1 509 3756940
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19
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Chaudhari MI, Pratt LR, Rempe SB. Utility of chemical computations in predicting solution free energies of metal ions. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1342127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Mangesh I. Chaudhari
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, NM, USA
| | - Lawrence R. Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, USA
| | - Susan B. Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, NM, USA
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20
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Abstract
Specific ion binding by carboxylates (-COO-) is a broadly important topic because -COO- is one of the most common functional groups coordinated to metal ions in metalloproteins and synthetic polymers. We apply quantum chemical methods and the quasi-chemical free-energy theory to investigate how variations in the number of -COO- ligands in a binding site determine ion-binding preferences. We study a series of monovalent (Li+, Na+, K+, Cs+) and divalent (Zn2+, Ca2+) ions relevant to experimental work on ion channels and ionomers. Of two competing hypotheses, our results support the ligand field strength hypothesis and follow the reverse Hofmeister series for ion solvation and ion transfer from aqueous solution to binding sites with the preferred number of ligands. New insight arises from the finding that ion-binding sequences can be manipulated and even reversed just by constraining the number of carboxylate ligands in the binding sites. Our results help clarify the discrepancy in ion association between molecular ligands in aqueous solutions and ionomers, and their chemical analogues in ion-channel binding sites.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies and ‡Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies and ‡Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
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21
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Chaudhari MI, Nair JR, Pratt LR, Soto FA, Balbuena PB, Rempe SB. Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion. J Chem Theory Comput 2016; 12:5709-5718. [DOI: 10.1021/acs.jctc.6b00824] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mangesh I. Chaudhari
- Center
for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Jijeesh R. Nair
- Department
of Applied Science and Technology, Politecnico di Torino, Turin 10129, Italy
| | - Lawrence R. Pratt
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Fernando A. Soto
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Perla B. Balbuena
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Susan B. Rempe
- Center
for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
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22
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Soniat M, Rogers DM, Rempe SB. Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration. J Chem Theory Comput 2016; 11:2958-67. [PMID: 26575733 DOI: 10.1021/acs.jctc.5b00357] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment.
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Affiliation(s)
- Marielle Soniat
- Department of Chemistry, University of New Orleans , 2000 Lakeshore Drive, New Orleans, Louisiana 70148, United States
| | - David M Rogers
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87123, United States.,Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Susan B Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87123, United States
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23
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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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24
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Baer MD, Mundy CJ. Local Aqueous Solvation Structure Around Ca2+ During Ca2+···Cl– Pair Formation. J Phys Chem B 2016; 120:1885-93. [DOI: 10.1021/acs.jpcb.5b09579] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcel D. Baer
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher J. Mundy
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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25
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Chatterjee A, Higham J, Henchman RH. Instantaneous, parameter-free methods to define a solute’s hydration shell. J Chem Phys 2015; 143:234501. [DOI: 10.1063/1.4937376] [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
Affiliation(s)
- Anupam Chatterjee
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Jonathan Higham
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Richard H. Henchman
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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26
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Abstract
The hydration structure of Ba(2+) ion is important for understanding blocking mechanisms in potassium ion channels. Here, we combine statistical mechanical theory, ab initio molecular dynamics simulations, and electronic structure methods to calculate the hydration free energy and local hydration structure of Ba(2+)(aq). The predicted hydration free energy (-304 ± 1 kcal/mol) agrees with the experimental value (-303 kcal/mol) when a maximally occupied, unimodal inner solvation shell is treated. In the local environment defined by the first shell of hydrating waters, Ba(2+) is directly and stably coordinated by eight (8) waters. Octa-coordination resembles the crystal structure of Ba(2+) and K(+) bound in potassium ion channels, but differs from the local hydration structure of K(+)(aq) determined earlier.
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Affiliation(s)
- Mangesh I Chaudhari
- †Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Marielle Soniat
- ‡Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Susan B Rempe
- †Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
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27
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Mason PE, Ansell S, Neilson GW, Rempe SB. Neutron Scattering Studies of the Hydration Structure of Li+. J Phys Chem B 2015; 119:2003-9. [DOI: 10.1021/jp511508n] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- P. E. Mason
- Institute
of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - S. Ansell
- Rutherford Appleton Laboratories, Chilton, Oxfordshire OX11 0QX, United Kingdom
| | - G. W. Neilson
- Department Physics, University of Bristol, Tyndall Ave., Bristol BS8 1TL, United Kingdom
| | - S. B. Rempe
- Center for Biological and
Materials Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185-1315, United States
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28
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Chaudhari MI, Sabo D, Pratt LR, Rempe SB. Hydration of Kr(aq) in Dilute and Concentrated Solutions. J Phys Chem B 2014; 119:9098-102. [DOI: 10.1021/jp508866h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Mangesh I. Chaudhari
- Center
for Biological and
Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87123, United States
| | - Dubravko Sabo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Lawrence R. Pratt
- Department of Chemical
and
Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Susan B. Rempe
- Center for Biological and
Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
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29
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Zhang W, You X, Pratt LR. Multiscale Theory in the Molecular Simulation of Electrolyte Solutions. J Phys Chem B 2014; 118:7730-8. [DOI: 10.1021/jp410310m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- W. Zhang
- Department of Chemical and Biomolecular
Engineering, Tulane University, New Orleans, Lousiana 70118, United States
| | - X. You
- Department of Chemical and Biomolecular
Engineering, Tulane University, New Orleans, Lousiana 70118, United States
| | - L. R. Pratt
- Department of Chemical and Biomolecular
Engineering, Tulane University, New Orleans, Lousiana 70118, United States
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30
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Shiga M, Masia M. Boundary based on exchange symmetry theory for multilevel simulations. II. Multiple time scale approach. J Chem Phys 2013; 139:144103. [DOI: 10.1063/1.4823729] [Citation(s) in RCA: 7] [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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31
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Sepehr F, Paddison SJ. The solvation structure and thermodynamics of aqueous vanadium cations. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.08.089] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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