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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Jafari M, Li Z, Song LF, Sagresti L, Brancato G, Merz KM. Thermodynamics of Metal-Acetate Interactions. J Phys Chem B 2024; 128:684-697. [PMID: 38226860 DOI: 10.1021/acs.jpcb.3c06567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Metal ions play crucial roles in protein- and ligand-mediated interactions. They not only act as catalysts to facilitate biological processes but are also important as protein structural elements. Accurately predicting metal ion interactions in computational studies has always been a challenge, and various methods have been suggested to improve these interactions. One such method is the 12-6-4 Lennard-Jones (LJ)-type nonbonded model. Using this model, it has been possible to successfully reproduce the experimental properties of metal ions in aqueous solution. The model includes induced dipole interactions typically ignored in the standard 12-6 LJ nonbonded model. In this we expand the applicability of this model to metal ion-carboxylate interactions. Using 12-6-4 parameters that reproduce the solvation free energies of the metal ions leads to an overestimation of metal ion-acetate interactions, thus, prompting us to fine-tune the model to specifically handle the latter. We also show that the standard 12-6 LJ model significantly falls short in reproducing the experimental binding free energy between acetate and 11 metal ions (Ni(II), Mg(II), Cu(II), Zn(II), Co(II), Cu(I), Fe(II), Mn(II), Cd(II), Ca(II), and Ag(I)). In this study, we describe optimized C4 parameters for the 12-6-4 LJ nonbonded model to be used with three widely employed water models (Transferable Intermolecular Potential with 3 Points (TIP3P), Simple Point Charge Extended (SPC/E), and Optimal Point Charge (OPC) water models). These parameters can accurately match the experimental binding free energy between 11 metal ions and acetate. These parameters can be applied to the study of metalloproteins and transition metal ion channels and transporters, as acetate serves as a representative of the negatively charged amino acid side chains from aspartate and glutamate.
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Affiliation(s)
- Majid Jafari
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lin Frank Song
- Biochemical and Biophysical Systems Group, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Luca Sagresti
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Kenneth M Merz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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3
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Yue S, Nandy A, Kulik HJ. Discovering Molecular Coordination Environment Trends for Selective Ion Binding to Molecular Complexes Using Machine Learning. J Phys Chem B 2023. [PMID: 38038675 DOI: 10.1021/acs.jpcb.3c06416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
The design of ion-selective materials with improved separation efficacy and efficiency is paramount, as current technologies fail to meet real-world deployment challenges. Selectivity in these materials can be informed by local ion binding in confined membrane ion channels. In this study, we utilize a data-driven approach to investigate design features in small molecular complexes coordinating ions as simplified models of ion channels. We curate a data set of 563 alkali metal coordinating molecular complexes (i.e., with Li+, Na+, or K+) from the Cambridge Structural Database and calculate differential ion binding energies using density functional theory. Using this information, we probe when and why structures favor exchange with alternate ions. Our analysis reveals that energetic preferences are related to ion size but are largely due to chemical interactions rather than structural reorganization. We identify unique trends in the selectivity for Li+ over other alkali ions, including the presence of N coordination atoms, planar coordination geometry, and small coordinating ring sizes. We use machine learning models to identify the key contributions of both geometric and electronic features in predicting selective ion binding. These physical insights offer preliminary guidance into the design of optimal membranes for ion selectivity.
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Affiliation(s)
- Shuwen Yue
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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4
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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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5
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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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6
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Wait EE, Gourary J, Liu C, Spoerke ED, Rempe SB, Ren P. Development of AMOEBA Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands. J Phys Chem B 2023; 127:1367-1375. [PMID: 36735638 PMCID: PMC9957963 DOI: 10.1021/acs.jpcb.2c07237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. Here, we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La3+) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La3+-ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion-water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion. This new model will allow investigation of fully solvated lanthanum ion-protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.
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Affiliation(s)
- Elizabeth E. Wait
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Justin Gourary
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Erik D. Spoerke
- Electronic, Optical, and Nano Materials Department, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Susan B. Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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7
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Metal-coordination and surface adhesion-assisted molding enabled strong, water-resistant carboxymethyl cellulose films. Carbohydr Polym 2022; 298:120084. [DOI: 10.1016/j.carbpol.2022.120084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 12/15/2022]
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8
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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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9
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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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10
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Vázquez-Durán A, Téllez-Isaías G, Hernández-Rodríguez M, Ruvalcaba RM, Martínez J, Nicolás-Vázquez MI, Aceves-Hernández JM, Méndez-Albores A. The Ability of Chlorophyll to Trap Carcinogen Aflatoxin B 1: A Theoretical Approach. Int J Mol Sci 2022; 23:6068. [PMID: 35682746 PMCID: PMC9181093 DOI: 10.3390/ijms23116068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 01/27/2023] Open
Abstract
The coordination of one and two aflatoxin B1 (AFB1, a potent carcinogen) molecules with chlorophyll a (chl a) was studied at a theoretical level. Calculations were performed using the M06-2X method in conjunction with the 6-311G(d,p) basis set, in both gas and water phases. The molecular electrostatic potential map shows the chemical activity of various sites of the AFB1 and chl a molecules. The energy difference between molecular orbitals of AFB1 and chl a allowed for the establishment of an intermolecular interaction. A charge transfer from AFB1 to the central cation of chl a was shown. The energies of the optimized structures for chl a show two configurations, unfolded and folded, with a difference of 15.41 kcal/mol. Chl a appeared axially coordinated to the plane (α-down or β-up) of the porphyrin moiety, either with the oxygen atom of the ketonic group, or with the oxygen atom of the lactone moiety of AFB1. The complexes of maximum stability were chl a 1-α-E-AFB1 and chl a 2-β-E-AFB1, at -36.4 and -39.2 kcal/mol, respectively. Additionally, with two AFB1 molecules were chl a 1-D-2AFB1 and chl a 2-E-2AFB1, at -60.0 and -64.8 kcal/mol, respectively. Finally, biosorbents containing chlorophyll could improve AFB1 adsorption.
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Affiliation(s)
- Alma Vázquez-Durán
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de Mexico 54714, Mexico; (A.V.-D.); (J.M.A.-H.); (A.M.-A.)
| | | | - Maricarmen Hernández-Rodríguez
- Laboratorio de Cultivo Celular, Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de Mexico 11340, Mexico;
| | - René Miranda Ruvalcaba
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de Mexico 54740, Mexico;
| | - Joel Martínez
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosi 78210, Mexico
| | - María Inés Nicolás-Vázquez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de Mexico 54740, Mexico;
| | - Juan Manuel Aceves-Hernández
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de Mexico 54714, Mexico; (A.V.-D.); (J.M.A.-H.); (A.M.-A.)
| | - Abraham Méndez-Albores
- Unidad de Investigación Multidisciplinaria L14 (Alimentos, Micotoxinas, y Micotoxicosis), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de Mexico 54714, Mexico; (A.V.-D.); (J.M.A.-H.); (A.M.-A.)
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11
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Larrue C, Bounor-Legaré V, Cassagnau P. Enhancement of EPDM Crosslinked Elastic Properties by Association of Both Covalent and Ionic Networks. Polymers (Basel) 2021; 13:polym13183161. [PMID: 34578061 PMCID: PMC8473281 DOI: 10.3390/polym13183161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 12/03/2022] Open
Abstract
The objective of this study was to replace elastomer crosslinking based on chemical covalent bonds by reversible systems under processing. One way is based on ionic bonds creation, which allows a physical crosslinking while keeping the process reversibility. However, due to the weak elasticity recovery of such a physical network after a long period of compression, the combination of both physical and chemical networks was studied. In that frame, an ethylene-propylene-diene terpolymer grafted with maleic anhydride (EPDM-g-MA) was crosslinked with metal salts and/or dicumyl peroxide (DCP). Thus, the influence of these two types of crosslinking networks and their combination were studied in detail in terms of compression set. The second part of this work was focused on the influence of different metallic salts (KOH, ZnAc2) and the sensitivity to the water of the physical crosslinking network. Finally, the combination of ionic and covalent network allowed combining the processability and better mechanical properties in terms of recovery elasticity. KAc proved to be the best ionic candidate to avoid water degradation of the ionic network and then to preserve the elasticity recovery properties under aging.
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12
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Li M, Ren G, Yang W, Wang F, Ma N, Fan X, Pan Q. Modulation of High-Spin Co(II) in Li/Co-MOFs as Efficient Fenton-like Catalysts. Inorg Chem 2021; 60:12405-12412. [PMID: 34296855 DOI: 10.1021/acs.inorgchem.1c01632] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Developing high-performance catalysts toward the Fenton reaction is important for environmental protection and sustainable development, yet it is still challenging. The high-spin states of first-row transition metal atoms with tetrahedral coordination provide a flexible electronic environment to activate the catalyst and elevate its catalytic activity. As a type of material with adjustable structures, metal-organic frameworks (MOFs) are excellent candidate catalysts as they can accurately regulate the coordination configurations of metal ions. In this paper, we investigate and summarize the direct formation of bimetallic carboxylate Li/Co-MOFs with tetrahedral coordination metal centers in a mixed H2O/polar organic solvent system. The induction of Li(I) ions is manifested in the generation of hydroxides during the dissociation of the Co(II) solvation structure to trigger the tetrahedral coordination behavior of Co(II). These Li/Co-MOFs containing high-spin Co(II) centers can serve as highly efficient Fenton-like catalysts for organics. This study provides a promising strategy for rational design of MOF-based catalysts with high-spin metal centers for application in environment governance.
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Affiliation(s)
- Meiling Li
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, College of Science, Hainan University, Haikou 570228, China
- School of Chemical Engineering and Technology, Hainan University, Haikou 570228, China
| | - Guojian Ren
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, College of Science, Hainan University, Haikou 570228, China
| | - Weiting Yang
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, College of Science, Hainan University, Haikou 570228, China
| | - Fuxiang Wang
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, College of Science, Hainan University, Haikou 570228, China
| | - Nana Ma
- College of Chemistry and Chemical Engineering, Henan Normal University, XinXiang 453007, China
| | - Xiaolei Fan
- Department of Chemical Engineering and Analytical Science, School of Engineering, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Qinhe Pan
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, College of Science, Hainan University, Haikou 570228, China
- School of Chemical Engineering and Technology, Hainan University, Haikou 570228, China
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13
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Percival SJ, Russo S, Priest C, Hill RC, Ohlhausen JA, Small LJ, Rempe SB, Spoerke ED. Bio-inspired incorporation of phenylalanine enhances ionic selectivity in layer-by-layer deposited polyelectrolyte films. SOFT MATTER 2021; 17:6315-6325. [PMID: 33982047 DOI: 10.1039/d1sm00134e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The addition of a common amino acid, phenylalanine, to a Layer-by-Layer (LbL) deposited polyelectrolyte (PE) film on a nanoporous membrane can increase its ionic selectivity over a PE film without the added amino acid. The addition of phenylalanine is inspired by detailed knowledge of the structure of the channelrhodopsins family of protein ion channels, where phenylalanine plays an instrumental role in facilitating sodium ion transport. The normally deposited and crosslinked PE films increase the cationic selectivity of a support membrane in a controllable manner where higher selectivity is achieved with thicker PE coatings, which in turn also increases the ionic resistance of the membrane. The increased ionic selectivity is desired while the increased resistance is not. We show that through incorporation of phenylalanine during the LbL deposition process, in solutions of NaCl with concentrations ranging from 0.1 to 100 mM, the ionic selectivity can be increased independently of the membrane resistance. Specifically, the addition is shown to increase the cationic transference of the PE films from 81.4% to 86.4%, an increase on par with PE films that are nearly triple the thickness while exhibiting much lower resistance compared to the thicker coatings, where the phenylalanine incorporated PE films display an area specific resistance of 1.81 Ω cm2 in 100 mM NaCl while much thicker PE membranes show a higher resistance of 2.75 Ω cm2 in the same 100 mM NaCl solution.
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Affiliation(s)
- Stephen J Percival
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Sara Russo
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Chad Priest
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Ryan C Hill
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - James A Ohlhausen
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Leo J Small
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Susan B Rempe
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Erik D Spoerke
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
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14
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Proteins maintain hydration at high [KCl] concentration regardless of content in acidic amino acids. Biophys J 2021; 120:2746-2762. [PMID: 34087206 PMCID: PMC8390907 DOI: 10.1016/j.bpj.2021.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/22/2021] [Accepted: 05/19/2021] [Indexed: 11/23/2022] Open
Abstract
Proteins of halophilic organisms, which accumulate molar concentrations of KCl in their cytoplasm, have a much higher content in acidic amino acids than proteins of mesophilic organisms. It has been proposed that this excess is necessary to maintain proteins hydrated in an environment with low water activity, either via direct interactions between water and the carboxylate groups of acidic amino acids or via cooperative interactions between acidic amino acids and hydrated cations. Our simulation study of five halophilic proteins and five mesophilic counterparts does not support either possibility. The simulations use the AMBER ff14SB force field with newly optimized Lennard-Jones parameters for the interactions between carboxylate groups and potassium ions. We find that proteins with a larger fraction of acidic amino acids indeed have higher hydration levels, as measured by the concentration of water in their hydration shell and the number of water/protein hydrogen bonds. However, the hydration level of each protein is identical at low (bKCl = 0.15 mol/kg) and high (bKCl = 2 mol/kg) KCl concentrations; excess acidic amino acids are clearly not necessary to maintain proteins hydrated at high salt concentration. It has also been proposed that cooperative interactions between acidic amino acids in halophilic proteins and hydrated cations stabilize the folded protein structure and would lead to slower dynamics of the solvation shell. We find that the translational dynamics of the solvation shell is barely distinguishable between halophilic and mesophilic proteins; if such a cooperative effect exists, it does not have that entropic signature.
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15
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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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16
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VanGordon MR, Prignano LA, Dempski RE, Rick SW, Rempe SB. Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate. Biophys J 2021; 120:1835-1845. [PMID: 33705762 PMCID: PMC8204341 DOI: 10.1016/j.bpj.2021.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/27/2022] Open
Abstract
Channelrhodopsins (ChR) are light-sensitive cation channels used in optogenetics, a technique that applies light to control cells (e.g., neurons) that have been modified genetically to express those channels. Although mutations are known to affect pore kinetics, little is known about how mutations induce changes at the molecular scale. To address this issue, we first measured channel opening and closing rates of a ChR chimera (C1C2) and selected variants (N297D, N297V, and V125L). Then, we used atomistic simulations to correlate those rates with changes in pore structure, hydration, and chemical interactions among key gating residues of C1C2 in both closed and open states. Overall, the experimental results show that C1C2 and its mutants do not behave like ChR2 or its analogous variants, except V125L, making C1C2 a unique channel. Our atomistic simulations confirmed that opening of the channel and initial hydration of the gating regions between helices I, II, III, and VII of the channel occurs with 1) the presence of 13-cis retinal; 2) deprotonation of a glutamic acid gating residue, E129; and 3) subsequent weakening of the central gate hydrogen bond between the same glutamic acid E129 and asparagine N297 in the central region of the pore. Also, an aspartate (D292) is the unambiguous primary proton acceptor for the retinal Schiff base in the hydrated channel.
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Affiliation(s)
- Monika R VanGordon
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana
| | - Lindsey A Prignano
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Robert E Dempski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana
| | - Susan B Rempe
- Sandia National Laboratories, Albuquerque, New Mexico.
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17
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Paren BA, Thurston BA, Neary WJ, Kendrick A, Kennemur JG, Stevens MJ, Frischknecht AL, Winey KI. Percolated Ionic Aggregate Morphologies and Decoupled Ion Transport in Precise Sulfonated Polymers Synthesized by Ring-Opening Metathesis Polymerization. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Benjamin A. Paren
- Dept. Of Materials Science & Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6272, United States
| | - Bryce A. Thurston
- Center for Integrated Nanotechnologies, Sandia National Labs, Albuquerque, New Mexico 87185-1411, United States
| | - William J. Neary
- Dept. Of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Aaron Kendrick
- Dept. Of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Justin G. Kennemur
- Dept. Of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Mark J. Stevens
- Center for Integrated Nanotechnologies, Sandia National Labs, Albuquerque, New Mexico 87185-1411, United States
| | - Amalie L. Frischknecht
- Center for Integrated Nanotechnologies, Sandia National Labs, Albuquerque, New Mexico 87185-1411, United States
| | - Karen I. Winey
- Dept. Of Materials Science & Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6272, United States
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18
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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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19
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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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20
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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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21
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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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22
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23
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Rank C, Häußler M, Rathenow P, King M, Globisch C, Peter C, Mecking S. Anisotropic Extended-Chain Polymer Nanocrystals. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00986] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Friedman R. Specific Ion and Concentration Effects in Acetate Solutions with Na + , K + and Cs .. Chemphyschem 2019; 20:1006-1010. [PMID: 30817057 DOI: 10.1002/cphc.201900163] [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: 02/18/2019] [Revised: 02/27/2019] [Indexed: 11/10/2022]
Abstract
How salt ions affect solutes and the water beyond the solvation shell is not well understood. Molecular dynamics simulations of alkali-acetate solutions were analysed here in order to examine if, and how, different cations and solute concentrations affect the water structure and the interactions between water and acetates. The results revealed that water structure is perturbed to more than 1 nm away from the acetates and that this effect is more pronounced in physiological than in molar electrolyte concentrations. Analysis of simulations of a soluble protein revealed that the water orientation is perturbed to at least 1.5 nm from the protein structure. Furthermore, modifications to the orientation of water around carboxylate side chains were shown to depend on the local environment on the protein surface, and could extend to well over 1 nm, which may have an effect on protein dynamics during MD simulations in small water boxes.
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Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, SE-391 82, Sweden
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25
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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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26
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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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27
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Schneeberger EM, Breuker K. Replacing H + by Na + or K + in phosphopeptide anions and cations prevents electron capture dissociation. Chem Sci 2018; 9:7338-7353. [PMID: 30542537 PMCID: PMC6237128 DOI: 10.1039/c8sc02470g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/07/2018] [Indexed: 01/29/2023] Open
Abstract
By successively replacing H+ by Na+ or K+ in phosphopeptide anions and cations, we show that the efficiency of fragmentation into c and z˙ or c˙ and z fragments from N-Cα backbone bond cleavage by negative ion electron capture dissociation (niECD) and electron capture dissociation (ECD) substantially decreases with increasing number of alkali ions attached. In proton-deficient phosphopeptide ions with a net charge of 2-, we observed an exponential decrease in electron capture efficiency with increasing number of Na+ or K+ ions attached, suggesting that electrons are preferentially captured at protonated sites. In proton-abundant phosphopeptide ions with a net charge of 3+, the electron capture efficiency was not affected by replacing up to four H+ ions with Na+ or K+ ions, but the yield of c, z˙ and c˙, z fragments from N-Cα backbone bond cleavage generally decreased next to Na+ or K+ binding sites. We interpret the site-specific decrease in fragmentation efficiency as Na+ or K+ binding to backbone amide oxygen in competition with interactions of protonated sites that would otherwise lead to backbone cleavage into c, z˙ or c˙, z fragments. Our findings seriously challenge the hypothesis that the positive charge responsible for ECD into c, z˙ or c˙, z fragments can generally be a sodium or other metal ion instead of a proton.
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Affiliation(s)
- Eva-Maria Schneeberger
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
| | - Kathrin Breuker
- Institute of Organic Chemistry , Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , Innrain 80/82 , 6020 Innsbruck , Austria . ; http://www.bioms-breuker.at/
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28
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Jing Z, Liu C, Qi R, Ren P. Many-body effect determines the selectivity for Ca 2+ and Mg 2+ in proteins. Proc Natl Acad Sci U S A 2018; 115:E7495-E7501. [PMID: 30038003 PMCID: PMC6094099 DOI: 10.1073/pnas.1805049115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Calcium ion is a versatile messenger in many cell-signaling processes. To achieve their functions, calcium-binding proteins selectively bind Ca2+ against a background of competing ions such as Mg2+ The high specificity of calcium-binding proteins has been intriguing since Mg2+ has a higher charge density than Ca2+ and is expected to bind more tightly to the carboxylate groups in calcium-binding pockets. Here, we showed that the specificity for Ca2+ is dictated by the many-body polarization effect, which is an energetic cost arising from the dense packing of multiple residues around the metal ion. Since polarization has stronger distance dependence compared with permanent electrostatics, the cost associated with the smaller Mg2+ is much higher than that with Ca2+ and outweighs the electrostatic attraction favorable for Mg2+ With the AMOEBA (atomic multipole optimized energetics for biomolecular simulation) polarizable force field, our simulations captured the relative binding free energy between Ca2+ and Mg2+ for proteins with various types of binding pockets and explained the nonmonotonic size dependence of the binding free energy in EF-hand proteins. Without electronic polarization, the smaller ions are always favored over larger ions and the relative binding free energy is roughly proportional to the net charge of the pocket. The many-body effect depends on both the number and the arrangement of charged residues. Fine-tuning of the ion selectivity could be achieved by combining the many-body effect and geometric constraint.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
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29
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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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30
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Jing Z, Qi R, Liu C, Ren P. Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field. J Chem Phys 2018; 147:161733. [PMID: 29096462 DOI: 10.1063/1.4985921] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The interactions between metal ions and proteins are ubiquitous in biology. The selective binding of metal ions has a variety of regulatory functions. Therefore, there is a need to understand the mechanism of protein-ion binding. The interactions involving metal ions are complicated in nature, where short-range charge-penetration, charge transfer, polarization, and many-body effects all contribute significantly, and a quantitative description of all these interactions is lacking. In addition, it is unclear how well current polarizable force fields can capture these energy terms and whether these polarization models are good enough to describe the many-body effects. In this work, two energy decomposition methods, absolutely localized molecular orbitals and symmetry-adapted perturbation theory, were utilized to study the interactions between Mg2+/Ca2+ and model compounds for amino acids. Comparison of individual interaction components revealed that while there are significant charge-penetration and charge-transfer effects in Ca complexes, these effects can be captured by the van der Waals (vdW) term in the AMOEBA force field. The electrostatic interaction in Mg complexes is well described by AMOEBA since the charge penetration is small, but the distance-dependent polarization energy is problematic. Many-body effects were shown to be important for protein-ion binding. In the absence of many-body effects, highly charged binding pockets will be over-stabilized, and the pockets will always favor Mg and thus lose selectivity. Therefore, many-body effects must be incorporated in the force field in order to predict the structure and energetics of metalloproteins. Also, the many-body effects of charge transfer in Ca complexes were found to be non-negligible. The absorption of charge-transfer energy into the additive vdW term was a main source of error for the AMOEBA many-body interaction energies.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
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31
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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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Chaudhari MI, Muralidharan A, Pratt LR, Rempe SB. Assessment of Simple Models for Molecular Simulation of Ethylene Carbonate and Propylene Carbonate as Solvents for Electrolyte Solutions. Top Curr Chem (Cham) 2018; 376:7. [PMID: 29435669 PMCID: PMC5809610 DOI: 10.1007/s41061-018-0187-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/23/2018] [Indexed: 01/13/2023]
Abstract
Progress in understanding liquid ethylene carbonate (EC) and propylene carbonate (PC) on the basis of molecular simulation, emphasizing simple models of interatomic forces, is reviewed. Results on the bulk liquids are examined from the perspective of anticipated applications to materials for electrical energy storage devices. Preliminary results on electrochemical double-layer capacitors based on carbon nanotube forests and on model solid-electrolyte interphase (SEI) layers of lithium ion batteries are considered as examples. The basic results discussed suggest that an empirically parameterized, non-polarizable force field can reproduce experimental structural, thermodynamic, and dielectric properties of EC and PC liquids with acceptable accuracy. More sophisticated force fields might include molecular polarizability and Buckingham-model description of inter-atomic overlap repulsions as extensions to Lennard-Jones models of van der Waals interactions. Simple approaches should be similarly successful also for applications to organic molecular ions in EC/PC solutions, but the important case of Li\documentclass[12pt]{minimal}
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\begin{document}$$^+$$\end{document}+ deserves special attention because of the particularly strong interactions of that small ion with neighboring solvent molecules. To treat the Li\documentclass[12pt]{minimal}
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\begin{document}$$^+$$\end{document}+ ions in liquid EC/PC solutions, we identify interaction models defined by empirically scaled partial charges for ion-solvent interactions. The empirical adjustments use more basic inputs, electronic structure calculations and ab initio molecular dynamics simulations, and also experimental results on Li\documentclass[12pt]{minimal}
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\begin{document}$$^+$$\end{document}+ thermodynamics and transport in EC/PC solutions. Application of such models to the mechanism of Li\documentclass[12pt]{minimal}
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\begin{document}$$^+$$\end{document}+ transport in glassy SEI models emphasizes the advantage of long time-scale molecular dynamics studies of these non-equilibrium materials.
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Affiliation(s)
- Mangesh I Chaudhari
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Ajay Muralidharan
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA 70118, USA
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA 70118, USA
| | - Susan B Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, NM 87185, USA.
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Kuwana R, Handa S, Futamata M. Elucidation of hydrated metal ions using flocculation-surface enhanced Raman scattering. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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A Systematic Analysis and Review of the Fundamental Acid-Base Properties of Biosorbents. ENVIRONMENTAL CHEMISTRY FOR A SUSTAINABLE WORLD 2018. [DOI: 10.1007/978-3-319-92111-2_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Hyde AM, Zultanski SL, Waldman JH, Zhong YL, Shevlin M, Peng F. General Principles and Strategies for Salting-Out Informed by the Hofmeister Series. Org Process Res Dev 2017. [DOI: 10.1021/acs.oprd.7b00197] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Alan M. Hyde
- Department of Process Chemistry, MRL, Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Susan L. Zultanski
- Department of Process Chemistry, MRL, Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Jacob H. Waldman
- Department of Process Chemistry, MRL, Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Yong-Li Zhong
- Department of Process Chemistry, MRL, Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Michael Shevlin
- Department of Process Chemistry, MRL, Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Feng Peng
- Department of Process Chemistry, MRL, Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
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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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