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Li M, Wang P, Yu X, Su Y, Zhao J. Impact of Nuclear Quantum Effects on the Structural Properties of Protonated Water Clusters. J Phys Chem A 2024; 128:5954-5962. [PMID: 39007820 DOI: 10.1021/acs.jpca.4c03340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Nuclear quantum effects (NQEs) play a crucial role in hydrogen-bonded systems due to quantum tunneling and proton fluctuation. Our understanding of how NQEs affect microstructures mainly focuses on bulk phases of liquids and solids but remains deficient for water clusters, including their hydrogen nuclei, hydrogen-bonded configurations, and temperature dependence. Here, we conducted ab initio molecular dynamics (MD) and path integral MD simulations to investigate the influence of NQEs on the structural properties of protonated water clusters H+(H2O)n (n = 3, 6, 9, 12). The results reveal that the NQEs become less evident as the cluster size increases due to the competition between NQEs and electrostatic interactions. Simulations of several H+(H2O)6 isomers at different temperatures indicate that the effect of elevated temperature on proton transfer is related to the initial structure. Interestingly, the process of proton transfer also involves the interconversion between Zundel-type and Eigen-type isomers. These findings significantly deepen our understanding of ion-water and water-water interactions, opening new avenues for the study of hydrated ion clusters and related systems.
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Affiliation(s)
- Mengxu Li
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, China
| | | | - Xueke Yu
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, China
| | - Yan Su
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, China
| | - Jijun Zhao
- Guangdong Basic Research Center of Excellence for Structure and Fundamental Interactions of Matter, Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics, South China Normal University, Guangzhou 510006, China
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2
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Tumakuru Nagarajappa L, Chikkappaiahnayaka S, Benedict Leoma M, Isamura BK, Venkatesh K, Singh KR, Sindogi K, Mandayam Anandalwar S, P Sadashiva M. Unraveling the crystal structure, stability and drug likeness of 1,3,4-oxadiazole derivatives against Myelofibrosis: a combined experimental and computational investigation. J Biomol Struct Dyn 2024:1-15. [PMID: 38555733 DOI: 10.1080/07391102.2024.2330013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/20/2024] [Indexed: 04/02/2024]
Abstract
Herein, we report the synthesis and characterization of novel 1,3,4-oxadiazole derivatives, 2-methoxybenzyl 5-(4-chlorophenyl)-1,3,4-oxadiazole-2-carboxylate (C1) 2-methoxybenzyl 5-(2-chlorophenyl)-1,3,4-oxadiazole-2-carboxylate (C2), and methoxybenzyl 5-(3-chlorophenyl)-1,3,4-oxadiazole-2-carboxylate (C3) obtained through desulfurative cyclization reaction. The compound C2 was crystallized, and its crystal structure was elucidated using single-crystal X-ray diffraction technique. The Hirshfeld surface analysis was carried out to analyze, visualize and globally appreciate the weak interactions involved in crystal packing. These analyses were complemented by Quantum Theory of Atoms In Molecules (QTAIM) and Reduced Density Gradient (RDG), which allowed us to decipher the nature and types of attractive forces that contribute to maintain the crystal structure of the titled compound. Moreover, the ADME profile of the compound was predicted to assess its drug likeness. Finally, in silico studies were performed to explore the binding affinity of the compounds (C1-3) against Myelofibrosis through molecular docking and molecular dynamic simulations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lohith Tumakuru Nagarajappa
- Department of Physics, The National Institute of Engineering, Mysuru, India
- Department of Studies in Physics, University of Mysore, Mysuru, Karnataka, India
| | | | | | | | - Karthik Venkatesh
- Department of Studies in Physics, University of Mysore, Mysuru, Karnataka, India
| | - Krishna Ravi Singh
- Department of Studies in Chemistry, University of Mysore, Mysuru, Karnataka, India
| | - Kishorkumar Sindogi
- Solid state and Structural Chemistry Unit (SSCU), Indian Institute of Science (IISc), Bangalore, India
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3
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Dempsey RL, Kaltsoyannis N. Computational study of the interactions of tetravalent actinides (An = Th-Pu) with the α-Fe 13 Keggin cluster. Dalton Trans 2024; 53:5947-5956. [PMID: 38456808 DOI: 10.1039/d3dt03761d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
In recent years, evidence has emerged that actinide (An) uptake at the enhanced actinide removal plant (EARP) at the UK's Sellafield nuclear site occurs via An interactions with an α-Fe13 Keggin molecular cluster during ferrihydrite formation. We here study theoretically the substitution of aquo complexes of the actinides Th-Pu onto a Na-decorated α-Fe13 Keggin cluster using DFT at the PBE0 level. The optimised Pu-O and Pu-Fe distances are in good agreement with experiment and Na/An substitutions are significantly favourable energetically, becoming more so across the early 5f series, with the smallest and largest ΔrG° being for Th and Pu at -335.7 kJ mol-1 and -396.0 kJ mol-1 respectively. There is strong correlation between the substitution reaction energy and the ionic radii of the actinides (Δrε0R2 = 0.97 and ΔrG° R2 = 0.91), suggesting that the principal An-Keggin binding mode is ionic. Notwithstanding this result, Mulliken and natural population analyses reveal that covalency increases from Th-Pu in these systems, supported by analysis of the occupied Kohn-Sham molecular orbitals where enhanced An(5f)-O(2p) overlap is observed in the Np and Pu systems. By contrast, quantum theory of atoms in molecules analysis shows that U-Keggin binding is the most covalent among the five actinides, in keeping with previous studies.
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Affiliation(s)
- Ryan L Dempsey
- Department of Chemistry, The University of Manchester, Manchester, M13 9PL, UK.
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4
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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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5
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Stevens MJ, Rempe SLB. Binding of Li + to Negatively Charged and Neutral Ligands in Polymer Electrolytes. J Phys Chem Lett 2023; 14:10200-10207. [PMID: 37930189 DOI: 10.1021/acs.jpclett.3c02565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Conceptually, single-ion polymer electrolytes (SIPE) with the anion bound to the polymer could solve major issues in Li-ion batteries, but their conductivity is too low. Experimentally, weakly interacting anionic groups have the best conductivity. To provide a theoretical basis for this result, density functional theory calculations of the optimized geometries and energies are performed for charged ligands used in SIPE. Comparison is made to neutral ligands found in dual-ion conductors, which demonstrate higher conductivity. The free energy differences between adding and subtracting a ligand are small enough for the neutral ligands to have the conductivity seen experimentally. However, charged ligands have large barriers, implying that lithium transport will coincide with the slow polymer diffusion, as observed in experiments. Overall, SIPE will require additional solvent to achieve a sufficiently high conductivity. Additionally, the binding of mono- and bidentate geometries varies, providing a simple and clear reason that polarizable force fields are required for detailed interactions.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
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6
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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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7
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Pederson MR, Withanage KPK, Hooshmand Z, Johnson AI, Baruah T, Yamamoto Y, Zope RR, Kao DY, Shukla PB, Johnson JK, Peralta JE, Jackson KA. Use of FLOSIC for understanding anion-solvent interactions. J Chem Phys 2023; 159:154112. [PMID: 37861122 DOI: 10.1063/5.0172300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023] Open
Abstract
An Achille's heel of lower-rung density-functional approximations is that the highest-occupied-molecular-orbital energy levels of anions, known to be stable or metastable in nature, are often found to be positive in the worst case or above the lowest-unoccupied-molecular-orbital levels on neighboring complexes that are not expected to accept charge. A trianionic example, [Cr(C2O4)3]3-, is of interest for constraining models linking Cr isotope ratios in rock samples to oxygen levels in Earth's atmosphere over geological timescales. Here we describe how crowd sourcing can be used to carry out self-consistent Fermi-Löwdin-Orbital-Self-Interaction corrected calculations (FLOSIC) on this trianion in solution. The calculations give a physically correct description of the electronic structure of the trianion and water. In contrast, uncorrected local density approximation (LDA) calculations result in approximately half of the anion charge being transferred to the water bath due to the effects of self-interaction error. Use of group-theory and the intrinsic sparsity of the theory enables calculations roughly 125 times faster than our initial implementation in the large N limit reached here. By integrating charge density densities and Coulomb potentials over regions of space and analyzing core-level shifts of the Cr and O atoms as a function of position and functional, we unambiguously show that FLOSIC, relative to LDA, reverses incorrect solute-solvent charge transfer in the trianion-water complex. In comparison to other functionals investigated herein, including Hartree-Fock and the local density approximation, the FLOSIC Cr 1s eigenvalues provide the best agreement with experimental core ionization energies.
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Affiliation(s)
- Mark R Pederson
- Physics Department, University of Texas at El Paso, El Paso, Texas 79968, USA
| | | | - Zahra Hooshmand
- Physics Department, University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Alex I Johnson
- Physics Department, University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Tunna Baruah
- Physics Department, University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Yoh Yamamoto
- Physics Department, University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Rajendra R Zope
- Physics Department, University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Der-You Kao
- NASA Postdoctoral Program, NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, USA
| | - Priyanka B Shukla
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - J Karl Johnson
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Juan E Peralta
- Physics Department, Central Michigan University, Mt. Pleasant, Michigan 48859, USA
| | - Koblar A Jackson
- Physics Department, Central Michigan University, Mt. Pleasant, Michigan 48859, USA
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8
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Benaïssa A, Bouhadiba A, Naili N, Chekkal F, Khelfaoui M, Bouras I, Madjram MS, Zouchoune B, Mogalli S, Malfi N, Nouar L, Madi F. Computational investigation of dimethoate and β-cyclodextrin inclusion complex: molecular structures, intermolecular interactions, and electronic analysis. Struct Chem 2023. [DOI: 10.1007/s11224-023-02162-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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9
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Theoretical insight into the acidity and cooperativity effect of the LLM-105∙(HNO3)2 system. J Mol Model 2022; 28:401. [DOI: 10.1007/s00894-022-05376-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/04/2022] [Indexed: 11/28/2022]
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10
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Stevens MJ, Rempe SLB. Carboxylate binding prefers two cations to one. Phys Chem Chem Phys 2022; 24:22198-22205. [PMID: 36093927 DOI: 10.1039/d2cp03561h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Almost all studies of specific ion binding by carboxylates (-COO-) have considered only a single cation, but clustering of ions and ligands is a common phenomenon. We apply density functional theory to investigate how variations in the number of acetate ligands in binding to two monovalent cations affects ion binding preferences. We study a series of monovalent (Li+, Na+, K+, Cs+) ions relevant to experimental work on many topics, including ion channels, battery storage, water purification and solar cells. We find that the preferred optimal structure has 3 acetates except for Cs+, which has 2 acetates. The optimal coordination of the cation by the carboxylate O atoms is 4 for both Na+ and K+, and 3 for Li+ and Cs+. There is a 4-fold coordination minimum just a few kcal mol-1 higher than the optimal 3-fold structure for Li+. For two cations, multiple minima occur in the vicinity of the lowest free energy state. We find that, for Li, Na and K, the preferred optimal structure with two cations is favored over a mixture of single cation complexes, providing a basis for understanding ionic cluster formation that is relevant for engineering proteins and other materials for rapid, selective 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. .,CBRN Defense and Energy Technologies, Sandia National Laboratories, Albuquerque, NM, 87185, USA.
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11
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Theoretical investigation into the solvent effect on the thermal decomposition of RDX in tetrahydrofuran, acetone, toluene, and benzene. J Mol Model 2021; 27:343. [PMID: 34739562 DOI: 10.1007/s00894-021-04966-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/22/2021] [Indexed: 10/19/2022]
Abstract
In order to clarify the solvent effect on the thermal decomposition of explosive, the N-NO2 trigger-bond strengths and ring strains of RDX (cyclotrimethylenetrinitramine) in its H-bonded complexes with solvent molecules (i.e., tetrahydrofuran, acetone, toluene, and benzene), and the activation energies of the intermolecular hydrogen exchanges between the solvent molecules and C3H8O2N4 or CH4O2N2, as the model molecule of RDX, were investigated by the BHandHLYP, B3LYP, MP2(full), and M06-2X methods with the 6-311 + + G(2df,2p) basis set, accompanied by a comparison with the calculations by the integral equation formalism polarized continuum model. The solvent effects ignore the ring strain while strengthening the N-NO2 bond, leading to a possible decreased sensitivity, as is opposite to the experimental results. However, the activation energies are in the order of C3H8O2N4/CH4O2N2∙∙∙acetone < C3H8O2N4/CH4O2N2∙∙∙THF < C3H8O2N4/CH4O2N2∙∙∙toluene < C3H8O2N4/CH4O2N2∙∙∙benzene < C3H8O2N4/CH4O2N2, suggesting that the order of the critical explosion temperatures might be RDX∙∙∙acetone < RDX∙∙∙THF < RDX∙∙∙toluene < RDX∙∙∙benzene < RDX, as is roughly consistent with the experimental results. Therefore, the intermolecular hydrogen exchange with the HONO elimination is a possible mechanism of the solvent effect on the initial thermal decomposition of RDX. The solvent effect on the sensitivity is analyzed by the surface electrostatic potentials.
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12
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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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13
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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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14
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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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Fabrizio A, Petraglia R, Corminboeuf C. Balancing Density Functional Theory Interaction Energies in Charged Dimers Precursors to Organic Semiconductors. J Chem Theory Comput 2020; 16:3530-3542. [DOI: 10.1021/acs.jctc.9b01193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Alberto Fabrizio
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Riccardo Petraglia
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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16
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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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17
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Duignan TT, Schenter GK, Fulton JL, Huthwelker T, Balasubramanian M, Galib M, Baer MD, Wilhelm J, Hutter J, Del Ben M, Zhao XS, Mundy CJ. Quantifying the hydration structure of sodium and potassium ions: taking additional steps on Jacob's Ladder. Phys Chem Chem Phys 2020; 22:10641-10652. [DOI: 10.1039/c9cp06161d] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability to reproduce the experimental structure of water around the sodium and potassium ions is a key test of the quality of interaction potentials due to the central importance of these ions in a wide range of important phenomena.
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Affiliation(s)
- Timothy T. Duignan
- Physical Science Division
- Pacific Northwest National Laboratory
- Richland
- USA
- School of Chemical Engineering
| | | | - John L. Fulton
- Physical Science Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Thomas Huthwelker
- Swiss Light Source
- Paul Scherrer Institut (PSI)
- 5232 Villigen
- Switzerland
| | | | - Mirza Galib
- Physical Science Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Marcel D. Baer
- Physical Science Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Jan Wilhelm
- Department of Chemistry
- University of Zurich
- CH-8057 Zürich
- Switzerland
- Institute of Theoretical Physics
| | - Jürg Hutter
- Department of Chemistry
- University of Zurich
- CH-8057 Zürich
- Switzerland
| | - Mauro Del Ben
- Computational Research Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - X. S. Zhao
- School of Chemical Engineering
- The University of Queensland
- Brisbane 4072
- Australia
| | - Christopher J. Mundy
- Physical Science Division
- Pacific Northwest National Laboratory
- Richland
- USA
- Department of Chemical Engineering
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18
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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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19
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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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20
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Wang P, Shi R, Su Y, Tang L, Huang X, Zhao J. Hydrated Sodium Ion Clusters [Na +(H 2O) n ( n = 1-6)]: An ab initio Study on Structures and Non-covalent Interaction. Front Chem 2019; 7:624. [PMID: 31572714 PMCID: PMC6751288 DOI: 10.3389/fchem.2019.00624] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/29/2019] [Indexed: 11/24/2022] Open
Abstract
Structural, thermodynamic, and vibrational characteristics of water clusters up to six water molecules incorporating a single sodium ion [Na+(H2O)n (n = 1–6)] are calculated using a comprehensive genetic algorithm combined with density functional theory on global search, followed by high-level ab initio calculation. For n ≥ 4, the coordinated water molecules number for the global minimum of clusters is 4 and the outer water molecules connecting with coordinated water molecules by hydrogen bonds. The charge analysis reveals the electron transfer between sodium ions and water molecules, providing an insight into the variations of properties of O–H bonds in clusters. Moreover, the simulated infrared (IR) spectra with anharmonic correction are in good agreement with the experimental results. The O–H stretching vibration frequencies show redshifts comparing with a free water molecule, which is attributed to the non-covalent interactions, including the ion–water interaction, and hydrogen bonds. Our results exhibit the comprehensive geometries, energies, charge, and anharmonic vibrational properties of Na+(H2O)n (n = 1–6), and reveal a deeper insight of non-covalent interactions.
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Affiliation(s)
- Pengju Wang
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian, China
| | - Ruili Shi
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian, China.,School of Mathematics and Physics, Hebei University of Engineering, Handan, China
| | - Yan Su
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian, China
| | - Lingli Tang
- College of Science, Dalian Nationalities University, Dalian, China
| | - Xiaoming Huang
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, China
| | - Jijun Zhao
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian, China
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21
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Theoretical explanation for the pharmaceutical incompatibility through the cooperativity effect of the drug-drug intermolecular interactions in the phenobarbital∙∙∙paracetamol∙∙∙H 2O complex. J Mol Model 2019; 25:181. [PMID: 31175465 DOI: 10.1007/s00894-019-4060-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 04/30/2019] [Indexed: 02/08/2023]
Abstract
In order to reveal the essence of the pharmaceutical incompatibility, the cooperativity effects of the drug-drug intermolecular π∙∙∙π and H∙∙∙O H-bonding interactions involving hydration were evaluated in the phenobarbital∙∙∙paracetamol∙∙∙H2O complex at the M06-2X/6-311++G** and MP2/6-311++G** levels. The thermodynamic cooperativity effects were also investigated by the statistical thermodynamic method. The results show that the π∙∙∙π stacking ternary complexes with the moderate anti-cooperativity effects are dominant in controling the aggregation process of phenobarbital, paracetamol, and H2O, as is confirmed by the atoms-in-molecules (AIM) and reduced density gradient (RDG) analyses. Therefore, it can be inferred that the anti-cooperativity effect plays an important role in forming the pharmaceutical incompatibility, and thus a deduction on the formation process of the pharmaceutical incompatibility between phenobarbital and paracetamol, with the hydration effect, is given. Several valuable models that relate the features of molecular surface electrostatic potentials or their statistical parameters, such as the surface areas, average values ([Formula: see text]), variances ([Formula: see text], [Formula: see text] and [Formula: see text]), and product of [Formula: see text] and electrostatic balance parameter (ν) ([Formula: see text]ν), to the values of the cooperativity effects were predicted. The formation of the pharmaceutical incompatibility is a thermodynamic cooperativity process driven by the enthalpy change. Graphical abstract Anti-cooperativity effect plays an important role in forming the pharmaceutical incompatibility.
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22
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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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23
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Prasetyo N, Hünenberger PH, Hofer TS. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li + Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6443-6459. [PMID: 30284829 DOI: 10.1021/acs.jctc.8b00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δs GM+,wat◦ of the Li+ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li+ are also compared to those for Na+ and K+ from a previous study in terms of relative hydration free energies ΔΔs GM+,wat◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔs GM+,wat• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li+ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie , ETH Zürich, ETH-Hönggerberg , HCI Building , CH-8093 Zürich , Switzerland
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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24
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Galib M, Schenter GK, Mundy CJ, Govind N, Fulton JL. Unraveling the spectral signatures of solvent ordering in K-edge XANES of aqueous Na+. J Chem Phys 2018; 149:124503. [DOI: 10.1063/1.5024568] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. Galib
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - G. K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - C. J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - N. Govind
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - J. L. Fulton
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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25
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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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26
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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27
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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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28
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Wonglakhon T, Surawatanawong P. Mechanistic insights into HCO2H dehydrogenation and CO2 hydrogenation catalyzed by Ir(Cp*) containing tetrahydroxy bipyrimidine ligand: the role of sodium and proton shuttle. Dalton Trans 2018; 47:17020-17031. [DOI: 10.1039/c8dt03283a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic HCO2H dehydrogenation by Ir(Cp*) tetrahydroxy bipyrimidine is influenced not only by the protonation states but also by the involvement of Na+ and the availability of HCO2H as a proton shuttle.
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Affiliation(s)
- Tanakorn Wonglakhon
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahidol University
- Bangkok 10400
- Thailand
| | - Panida Surawatanawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahidol University
- Bangkok 10400
- Thailand
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29
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Swift MW, Van de Walle CG, Fisher MPA. Posner molecules: from atomic structure to nuclear spins. Phys Chem Chem Phys 2018; 20:12373-12380. [DOI: 10.1039/c7cp07720c] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Posner molecule, Ca9(PO4)6, a possible intermediate step in bone growth, may also protect the constituent 31P spins from decoherence.
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30
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Theoretical insight into the solvent effect of H 2O and formamide on the cooperativity effect in HMX complex. J Mol Model 2017; 23:237. [PMID: 28735498 DOI: 10.1007/s00894-017-3397-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/25/2017] [Indexed: 01/28/2023]
Abstract
The cooperativity effects of the H-bonding interactions in HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane)∙∙∙HMX∙∙∙FA (formamide), HMX∙∙∙HMX∙∙∙H2O and HMX∙∙∙HMX∙∙∙HMX complexes involving the chair and chair-chair HMX are investigated by using the ONIOM2 (CAM-B3LYP/6-31++G(d,p):PM3) and ONIOM2 (M06-2X/6-31++G(d,p):PM3) methods. The solvent effect of FA or H2O on the cooperativity effect in HMX∙∙∙HMX∙∙∙HMX are evaluated by the integral equation formalism polarized continuum model. The results show that the cooperativity and anti-cooperativity effects are not notable in all the systems. Although the effect of solvation on the binding energy of ternary system HMX∙∙∙HMX∙∙∙HMX is not large, that on the cooperativity of H-bonds is notable, which leads to the mutually strengthened H-bonding interaction in solution. This is perhaps the reason for the formation of different conformation of HMX in different solvent. Surface electrostatic potential and reduced density gradient are used to reveal the nature of the solvent effect on cooperativity effect in HMX∙∙∙HMX∙∙∙HMX. Graphical abstract RDG isosurface and electrostatic potential surface of HMX∙∙∙HMX∙∙∙HMX.
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31
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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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32
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Deka BC, Bhattacharyya PK. DFT study on host-guest interaction in chitosan–amino acid complexes. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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33
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Wasserman A, Nafziger J, Jiang K, Kim MC, Sim E, Burke K. The Importance of Being Inconsistent. Annu Rev Phys Chem 2017; 68:555-581. [PMID: 28463652 DOI: 10.1146/annurev-physchem-052516-044957] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Adam Wasserman
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907
| | - Jonathan Nafziger
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Kaili Jiang
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907
| | - Min-Cheol Kim
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Eunji Sim
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Kieron Burke
- Department of Chemistry, University of California, Irvine, California 92697
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34
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Galib M, Baer MD, Skinner LB, Mundy CJ, Huthwelker T, Schenter GK, Benmore CJ, Govind N, Fulton JL. Revisiting the hydration structure of aqueous Na+. J Chem Phys 2017; 146:084504. [DOI: 10.1063/1.4975608] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- M. Galib
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - M. D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - L. B. Skinner
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - C. J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - T. Huthwelker
- Swiss Light Source, Paul Scherrer Institute (PSI), 5232, Villigen, Switzerland
| | - G. K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - C. J. Benmore
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - N. Govind
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - J. L. Fulton
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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35
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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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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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37
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Taimoory SM, Dudding T. An Evolving Insight into Chiral H-Bond Catalyzed Aza-Henry Reactions: A Cooperative Role for Noncovalent Attractive Interactions Unveiled by Density Functional Theory. J Org Chem 2016; 81:3286-95. [PMID: 27008440 DOI: 10.1021/acs.joc.6b00248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of cooperative effects arising from noncovalent attractive interactions as a vital factor governing stereoinduction in chiral H-bond catalyzed aza-Henry reactions is reported. Supporting this finding were density functional theory (DFT) calculations which revealed a shape and size dependency existed between the catalyst and substrates that when matched lead to high enantioselectivity, as reflected by favorable activation parameters. Associated with optimal catalyst and substrate pairing were a closed catalytic binding pocket and a synclinal orientation of the substrates that reinforced favorable stereoelectronic effects and dispersive type forces. Meanwhile, unfavorable steric interactions were found to be a dominant effect controlling diastereoselection.
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Affiliation(s)
| | - Travis Dudding
- Brock University , 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1 Canada
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DEKA BHABESHCHANDRA, BHATTACHARYYA PRADIPKR. Reactivity of chitosan derivatives and their interaction with guanine: A computational study. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1064-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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39
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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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40
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Anishkin A, Vanegas JM, Rogers DM, Lorenzi PL, Chan WK, Purwaha P, Weinstein JN, Sukharev S, Rempe SB. Catalytic Role of the Substrate Defines Specificity of Therapeutic l-Asparaginase. J Mol Biol 2015; 427:2867-85. [DOI: 10.1016/j.jmb.2015.06.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/20/2015] [Accepted: 06/26/2015] [Indexed: 12/23/2022]
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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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