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Pérez-Conesa S, Torrico F, Martínez JM, Pappalardo RR, Marcos ES. A general study of actinyl hydration by molecular dynamics simulations usingab initioforce fields. J Chem Phys 2019; 150:104504. [DOI: 10.1063/1.5083216] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sergio Pérez-Conesa
- Departamento de Química Física, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Francisco Torrico
- Departamento de Química Física, Universidad de Sevilla, 41012 Sevilla, Spain
| | - José M. Martínez
- Departamento de Química Física, Universidad de Sevilla, 41012 Sevilla, Spain
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2
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Daub CD, Hänninen V, Halonen L. Ab Initio Molecular Dynamics Simulations of the Influence of Lithium Bromide on the Structure of the Aqueous Solution-Air Interface. J Phys Chem B 2019; 123:729-737. [PMID: 30605330 PMCID: PMC6727360 DOI: 10.1021/acs.jpcb.8b10552] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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We
present the results of ab initio molecular dynamics simulations
of the solution–air interface of aqueous lithium bromide (LiBr).
We find that, in agreement with the experimental data and previous
simulation results with empirical polarizable force field models,
Br– anions prefer to accumulate just below the first
molecular water layer near the interface, whereas Li+ cations
remain deeply buried several molecular layers from the interface,
even at very high concentration. The separation of ions has a profound
effect on the average orientation of water molecules in the vicinity
of the interface. We also find that the hydration number of Li+ cations in the center of the slab Nc,Li+–H2O ≈ 4.7 ±
0.3, regardless of the salt concentration. This estimate is consistent
with the recent experimental neutron scattering data, confirming that
results from nonpolarizable empirical models, which consistently predict
tetrahedral coordination of Li+ to four solvent molecules,
are incorrect. Consequently, disruption of the hydrogen bond network
caused by Li+ may be overestimated in nonpolarizable empirical
models. Overall, our results suggest that empirical models, in particular
nonpolarizable models, may not capture all of the properties of the
solution–air interface necessary to fully understand the interfacial
chemistry.
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Affiliation(s)
- Christopher D Daub
- Department of Chemistry , University of Helsinki , P.O. Box 55, Helsinki 00014 , Finland
| | - Vesa Hänninen
- Department of Chemistry , University of Helsinki , P.O. Box 55, Helsinki 00014 , Finland
| | - Lauri Halonen
- Department of Chemistry , University of Helsinki , P.O. Box 55, Helsinki 00014 , Finland
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3
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Caralampio DZ, Martínez JM, Pappalardo RR, Marcos ES. The hydration structure of the heavy-alkalines Rb+ and Cs+ through molecular dynamics and X-ray absorption spectroscopy: surface clusters and eccentricity. Phys Chem Chem Phys 2017; 19:28993-29004. [DOI: 10.1039/c7cp05346k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hydration shells around Rb+ and Cs+ are not symmetric; the cation and the 1st-shell water mass center are separated by ∼0.4 Å, and this is supported by agreement between the theoretical and experimental EXAFS spectrum.
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Affiliation(s)
| | - José M. Martínez
- Departmento de Quimica Fisica
- Universidad de Sevilla
- 41012-Seville
- Spain
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4
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Allen DT, Saaka Y, Pardo LC, Lawrence MJ, Lorenz CD. Specific effects of monovalent counterions on the structural and interfacial properties of dodecyl sulfate monolayers. Phys Chem Chem Phys 2016; 18:30394-30406. [DOI: 10.1039/c6cp05714d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Shows that NH4+ ions dehydrate the DS− headgroup by displacing hydrogen bonded waters from the interface.
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Affiliation(s)
- Daniel T. Allen
- Theory & Simulation of Condensed Matter Group
- Department of Physics
- Strand Campus
- King's College London
- London WC2R 2LS
| | - Yussif Saaka
- Pharmaceutical Biophysics Group
- Institute of Pharmaceutical Science
- King's College London
- London SE1 9NH
- UK
| | - Luis Carlos Pardo
- Departament de Fisica i Enginyeria Nuclear
- Escola Tècnica Superior d'Enginyeria Industrial de Barcelona (ETSEIB)
- Universitat Politecnica de Catalunya
- 08028 Barcelona
- Spain
| | - M. Jayne Lawrence
- Pharmaceutical Biophysics Group
- Institute of Pharmaceutical Science
- King's College London
- London SE1 9NH
- UK
| | - Christian D. Lorenz
- Theory & Simulation of Condensed Matter Group
- Department of Physics
- Strand Campus
- King's College London
- London WC2R 2LS
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5
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Ke H, van der Linde C, Lisy JM. Insights into the Structures of the Gas-Phase Hydrated Cations M+(H2O)nAr (M = Li, Na, K, Rb, and Cs; n = 3–5) Using Infrared Photodissociation Spectroscopy and Thermodynamic Analysis. J Phys Chem A 2015; 119:2037-51. [DOI: 10.1021/jp509694h] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Haochen Ke
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Christian van der Linde
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - James M. Lisy
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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6
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Pluhařová E, Mason PE, Jungwirth P. Ion Pairing in Aqueous Lithium Salt Solutions with Monovalent and Divalent Counter-Anions. J Phys Chem A 2013; 117:11766-73. [DOI: 10.1021/jp402532e] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Eva Pluhařová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Philip E. Mason
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
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7
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Hernández-Cobos J, Ramírez-Solís A, Maron L, Ortega-Blake I. Theoretical study of the aqueous solvation of HgCl2: Monte Carlo simulations using second-order Moller-Plesset-derived flexible polarizable interaction potentials. J Chem Phys 2012; 136:014502. [PMID: 22239784 DOI: 10.1063/1.3673780] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A study of the solvation of HgCl(2) including ab initio aggregates of up to 24 water molecules and the results of extensive Monte Carlo simulations for the liquid phase using MP2-derived interaction potentials is presented. The interaction potentials are flexible, polarizable, and include non-additive effects. We conclude that a cluster description of the solvation mechanism is limited when compared to the condensed phase. The molecular image derived from the MC simulations is peculiar. It resembles that of a hydrophobic solute, which explains the rather easy passage of this neutral molecule through the cell membrane; however, it also shows an intermittent binding of one, two, or three water molecules to HgCl(2) in the fashion of a hydrophilic solute.
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Affiliation(s)
- J Hernández-Cobos
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México.
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8
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9
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González-Espinoza A, Hernández-Cobos J, Ortega-Blake I. A refined potential for hydroxylamine clusters and the liquid phase. J Chem Phys 2011; 135:054502. [PMID: 21823707 DOI: 10.1063/1.3610344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A detailed study including ab initio calculations and classic Monte-Carlo simulations of hydroxylamine in the gas and liquid phases is presented. A classical interaction potential for hydroxylamine, which includes polarizability, many-body effects, and intramolecular relaxation, was constructed. The results of the simulation were compared to the available experimental data in order to validate the model. We conclude that liquid hydroxylamine has a multitude of hydrogen bonds leading to a large density where the existence of cis conformers and clusters of these conformers is possible. This explains the occurrence of the classical [R. Nast and I. Z. Foppl, Z. Anorg. Allg. Chem. 263, 310 (1950)] scheme for the molecule's decomposition at room temperature and its large exothermicity and instability.
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10
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Thomas AS, Elcock AH. Molecular Dynamics Simulations Predict a Favorable and Unique Mode of Interaction between Lithium (Li+) Ions and Hydrophobic Molecules in Aqueous Solution. J Chem Theory Comput 2011; 7:818-24. [DOI: 10.1021/ct100521v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew S. Thomas
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Adrian H. Elcock
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
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11
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Hernández-Cobos J, Vargas MC, Ramírez-Solís A, Ortega-Blake I. Aqueous solvation of As(OH)3: A Monte Carlo study with flexible polarizable classical interaction potentials. J Chem Phys 2010; 133:114501. [DOI: 10.1063/1.3483619] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Valente M, Sousa SF, Lopes Magalhães A, Freire C. Crown-Ether Type Podands as Alkali Metal Cation Extractants: Influence of the Number of Oxygens in the Chain. J SOLUTION CHEM 2010. [DOI: 10.1007/s10953-010-9579-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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A theoretical study of the hydration of Rb+ by Monte Carlo simulations with refined ab initio-based model potentials. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0644-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Villa A, Hess B, Saint-Martin H. Dynamics and Structure of Ln(III)−Aqua Ions: A Comparative Molecular Dynamics Study Using ab Initio Based Flexible and Polarizable Model Potentials. J Phys Chem B 2009; 113:7270-81. [DOI: 10.1021/jp8097445] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alessandra Villa
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, and Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apartado Postal 48-3, 62251 Cuernavaca, Morelos, México
| | - Berk Hess
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, and Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apartado Postal 48-3, 62251 Cuernavaca, Morelos, México
| | - Humberto Saint-Martin
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, and Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apartado Postal 48-3, 62251 Cuernavaca, Morelos, México
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15
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Petraglio G, Bartolini M, Branduardi D, Andrisano V, Recanatini M, Gervasio FL, Cavalli A, Parrinello M. The role of Li
+
, Na
+
, and K
+
in the ligand binding inside the human acetylcholinesterase gorge. Proteins 2008; 70:779-85. [PMID: 17729290 DOI: 10.1002/prot.21560] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Alkali cations can affect the catalytic efficiency of enzymes. This is particularly true when dealing with enzymes whose substrate bears a formal positive charge. Computational and biochemical approaches have been combined to shed light on the atomic aspects of the role of Li(+), Na(+), and K(+) on human acetylcholinesterase (hAChE) ligand binding. In this respect, molecular dynamics simulations and our recently developed metadynamics method were applied to study the entrance of the three cations in the gorge of hAChE, and their effect on the dynamical motion of a ligand (tetramethylammonium) from the bulk of the solvent into the deep narrow enzyme gorge. Furthermore, in order to support the theoretical results, K(M) and k(cat) for the acetylcholine hydrolysis in the presence of the three cations were evaluated by using an approach based on the Ellman's method. The combination of computational and biochemical experiments clearly showed that Li(+), Na(+), and K(+) may influence the ligand binding at the hAChE gorge.
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Affiliation(s)
- Gabriele Petraglio
- Computational Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, CH-6900 Lugano, Switzerland
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16
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Heyden A, Lin H, Truhlar DG. Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations. J Phys Chem B 2007; 111:2231-41. [PMID: 17288477 DOI: 10.1021/jp0673617] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In many applications of multilevel/multiscale methods, an active zone must be modeled by a high-level electronic structure method, while a larger environmental zone can be safely modeled by a lower-level electronic structure method, molecular mechanics, or an analytic potential energy function. In some cases though, the active zone must be redefined as a function of simulation time. Examples include a reactive moiety diffusing through a liquid or solid, a dislocation propagating through a material, or solvent molecules in a second coordination sphere (which is environmental) exchanging with solvent molecules in an active first coordination shell. In this article, we present a procedure for combining the levels smoothly and efficiently in such systems in which atoms or groups of atoms move between high-level and low-level zones. The method dynamically partitions the system into the high-level and low-level zones and, unlike previous algorithms, removes all discontinuities in the potential energy and force whenever atoms or groups of atoms cross boundaries and change zones. The new adaptive partitioning (AP) method is compared to Rode's "hot spot" method and Morokuma's "ONIOM-XS" method that were designed for multilevel molecular dynamics (MD) simulations. MD simulations in the microcanonical ensemble show that the AP method conserves both total energy and momentum, while the ONIOM-XS method fails to conserve total energy and the hot spot method fails to conserve both total energy and momentum. Two versions of the AP method are presented, one scaling as O(2N) and one with linear scaling in N, where N is the number of groups in a buffer zone separating the active high-level zone from the environmental low-level zone. The AP method is also extended to systems with multiple high-level zones to allow, for example, the study of ions and counterions in solution using the multilevel approach.
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Affiliation(s)
- Andreas Heyden
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA.
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17
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Carrillo-Tripp M, San-Román ML, Hernańdez-Cobos J, Saint-Martin H, Ortega-Blake I. Ion hydration in nanopores and the molecular basis of selectivity. Biophys Chem 2006; 124:243-50. [PMID: 16765508 DOI: 10.1016/j.bpc.2006.04.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 04/26/2006] [Accepted: 04/27/2006] [Indexed: 11/25/2022]
Abstract
Using a simple model, it is shown that the cost of constraining a hydrated potassium ion inside a narrow pore is smaller than the cost of constraining hydrated sodium or lithium ions in pores of radius around 1.5 A. The opposite is true for pores of radius around 2.5 A. The reason for the selectivity in the first region is that the potassium ion allows for a greater distortion of its hydration shell and can therefore maintain a better coordination, and the reason for the reverse selectivity in the second region is that the smaller ions retain their hydration shells in these pores. This is relevant to the molecular basis of ion selective channels, and since this mechanism does not depend on the molecular details of the pore, it could also operate in all sorts of nanotubes.
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