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Semrouni D, Wang HW, Clark SB, Pearce CI, Page K, Schenter G, Wesolowski DJ, Stack AG, Clark AE. Resolving local configurational contributions to X-ray and neutron radial distribution functions within solutions of concentrated electrolytes - a case study of concentrated NaOH. Phys Chem Chem Phys 2019; 21:6828-6838. [PMID: 30620014 DOI: 10.1039/c8cp06802j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Extreme conditions of complex materials often lead to a manifold of local environments that challenge characterization and require new advances at the intersection of modern experimental and theoretical techniques. In this contribution, highly caustic and viscous aqueous NaOD solutions were characterized with a combination of X-ray and neutron radial distribution function (RDF) analyses, molecular dynamics simulations and sub-ensemble analysis. While this system has been the topic of some study, the current work expands upon the state of knowledge regarding the extent to which water is perturbed within this chemically extreme solution. Further, we introduce analyses that goes beyond merely identifying the different local environments (ion solvation and coordination environments) that are present, but toward understanding their relative contributions to the ensemble solution RDF. This integrated approach yields unique insight into the experimental sensitivity of RDFs to changes in local geometries, the composition of solvation environments about ions, and the challenge of experimentally differentiating the ensemble of all superimposed local environments-a feature of increasing importance within the extreme condition of high ionic strength.
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Affiliation(s)
- David Semrouni
- Department of Chemistry and the Materials Science and Engineering Program, Washington State University, Pullman, WA 99164, USA.
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Graham TR, Semrouni D, Mamontov E, Ramirez-Cuesta AJ, Page K, Clark A, Schenter GK, Pearce CI, Stack AG, Wang HW. Coupled Multimodal Dynamics of Hydrogen-Containing Ion Networks in Water-Deficient, Sodium Hydroxide-Aluminate Solutions. J Phys Chem B 2018; 122:12097-12106. [DOI: 10.1021/acs.jpcb.8b09375] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Trent R. Graham
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David Semrouni
- Department of Chemistry and the Materials Science and Engineering Program, Washington State University, Pullman, Washington 99164, United States
| | | | | | | | - Aurora Clark
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Chemistry and the Materials Science and Engineering Program, Washington State University, Pullman, Washington 99164, United States
| | - Gregory K. Schenter
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Carolyn I. Pearce
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Mondloch JE, Katz MJ, Planas N, Semrouni D, Gagliardi L, Hupp JT, Farha OK. Are Zr6-based MOFs water stable? Linker hydrolysis vs. capillary-force-driven channel collapse. Chem Commun (Camb) 2014; 50:8944-6. [DOI: 10.1039/c4cc02401j] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Semrouni D, Sharma A, Dognon JP, Ohanessian G, Clavaguéra C. Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:3190-9. [DOI: 10.1021/ct5004065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- David Semrouni
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
| | - Ashwani Sharma
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
| | - Jean-Pierre Dognon
- CEA/Saclay, DSM/IRAMIS/NIMBE,
CNRS, Laboratoire de Chimie Moléculaire et de Catalyse pour
l’Energie, 91191 Gif-sur-Yvette, France
| | - Gilles Ohanessian
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
| | - Carine Clavaguéra
- Laboratoire de
Chimie Moléculaire, Ecole polytechnique, CNRS, 91128 Palaiseau Cedex, France, and
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Meng W, League AB, Ronson TK, Clegg JK, Isley WC, Semrouni D, Gagliardi L, Cramer CJ, Nitschke JR. Empirical and Theoretical Insights into the Structural Features and Host–Guest Chemistry of M8L4 Tube Architectures. J Am Chem Soc 2014; 136:3972-80. [DOI: 10.1021/ja412964r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Wenjing Meng
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Aaron B. League
- Department of Chemistry, Chemical Theory Center, and Supercomputer
Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Tanya K. Ronson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Jack K. Clegg
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - William C. Isley
- Department of Chemistry, Chemical Theory Center, and Supercomputer
Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - David Semrouni
- Department of Chemistry, Chemical Theory Center, and Supercomputer
Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Supercomputer
Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Christopher J. Cramer
- Department of Chemistry, Chemical Theory Center, and Supercomputer
Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Jonathan R. Nitschke
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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Semrouni D, Isley WC, Clavaguéra C, Dognon JP, Cramer CJ, Gagliardi L. Ab Initio Extension of the AMOEBA Polarizable Force Field to Fe2+. J Chem Theory Comput 2013; 9:3062-71. [DOI: 10.1021/ct400237r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- David Semrouni
- Department of Chemistry, Chemical
Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota
55455, United States
| | - William C. Isley
- Department of Chemistry, Chemical
Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota
55455, United States
| | - Carine Clavaguéra
- Laboratoire
des Mécanismes
Réactionnels, Département de Chimie, École Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Jean-Pierre Dognon
- CEA/Saclay, UMR 3299 CEA/CNRS SIS2M, Laboratoire de Chimie de Coordination
des Eléments f, F-91191 Gif-sur-Yvette, France
| | - Christopher J. Cramer
- Department of Chemistry, Chemical
Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota
55455, United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical
Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota
55455, United States
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Semrouni D, Clavaguéra C, Ohanessian G, Parks JH. Relationship between Conformational Dynamics and Electron Transfer in a Desolvated Peptide. Part I. Structures. J Phys Chem B 2013; 117:1746-55. [DOI: 10.1021/jp3078375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- David Semrouni
- Laboratoire des Mécanismes Réactionnels,
Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Carine Clavaguéra
- Laboratoire des Mécanismes Réactionnels,
Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Gilles Ohanessian
- Laboratoire des Mécanismes Réactionnels,
Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Joel H. Parks
- Rowland Institute at Harvard, 100 Edwin H. Land Boulevard, Cambridge,
Massachusetts 02142, United
States
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Parks JH, Semrouni D, Clavaguéra C, Ohanessian G. Relationship between Conformational Dynamics and Electron Transfer in a Desolvated Peptide. Part II. Temperature Dependence. J Phys Chem B 2013; 117:1756-69. [DOI: 10.1021/jp3078437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Joel H. Parks
- Rowland Institute at Harvard, 100 Edwin H. Land Boulevard, Cambridge,
Massachusetts 02142 United
States
| | - David Semrouni
- Laboratoire
des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Carine Clavaguéra
- Laboratoire
des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Gilles Ohanessian
- Laboratoire
des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
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Balaj OP, Semrouni D, Steinmetz V, Nicol E, Clavaguéra C, Ohanessian G. Structure of Sodiated Polyglycines. Chemistry 2012; 18:4583-92. [DOI: 10.1002/chem.201102812] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Indexed: 11/11/2022]
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Joshi K, Semrouni D, Ohanessian G, Clavaguéra C. Structures and IR Spectra of the Gramicidin S Peptide: Pushing the Quest for Low-Energy Conformations. J Phys Chem B 2011; 116:483-90. [DOI: 10.1021/jp207102v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kaustubh Joshi
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - David Semrouni
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Gilles Ohanessian
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
| | - Carine Clavaguéra
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
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Semrouni D, Balaj OP, Calvo F, Correia CF, Clavaguéra C, Ohanessian G. Structure of sodiated octa-glycine: IRMPD spectroscopy and molecular modeling. J Am Soc Mass Spectrom 2010; 21:728-38. [PMID: 20189824 DOI: 10.1016/j.jasms.2010.01.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 05/25/2023]
Abstract
The structure of the sodiated peptide GGGGGGGG-Na(+) or G(8)-Na(+) was investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD was carried out in both the fingerprint and N-H/O-H stretching regions. Modeling used the polarizable force field AMOEBA in conjunction with the replica-exchange molecular dynamics (REMD) method, allowing an efficient exploration of the potential energy surface. Geometries and energetics were further refined at B3LYP-D and MP2 quantum chemical levels. The IRMPD spectra indicate that there is no free C-terminus OH and that several N-Hs are free of hydrogen bonding, while several others are bound, however not very strongly. The structure must then be either of the charge solvation (CS) type with a hydrogen-bound acidic OH, or a salt bridge (SB). Extensive REMD searches generated several low-energy structures of both types. The most stable structures of each type are computed to be very close in energy. The computed energy barrier separating these structures is small enough that G(8)-Na(+) is likely fluxional with easy proton transfer between the two peptide termini. There is, however, good agreement between experiment and computations in the entire spectral range for the CS isomer only, which thus appears to be the most likely structure of G(8)-Na(+) at room temperature.
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Affiliation(s)
- David Semrouni
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique and CNRS, Palaiseau, France
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Semrouni D, Ohanessian G, Clavaguéra C. Structural, energetic and dynamical properties of sodiated oligoglycines: relevance of a polarizable force field. Phys Chem Chem Phys 2010; 12:3450-62. [DOI: 10.1039/b924317h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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