151
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Zen A, Luo Y, Mazzola G, Guidoni L, Sorella S. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo. J Chem Phys 2015; 142:144111. [PMID: 25877566 DOI: 10.1063/1.4917171] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
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Affiliation(s)
- Andrea Zen
- Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome, Italy
- London Centre for Nanotechnology, University College London, London WC1E 6BT, United Kingdom
| | - Ye Luo
- SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste, Italy
| | - Guglielmo Mazzola
- SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste, Italy
| | - Leonardo Guidoni
- Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’ Aquila, via Vetoio, 67100 L’ Aquila, Italy
| | - Sandro Sorella
- SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste, Italy
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152
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Callear SK, Johnston A, McLain SE, Imberti S. Conformation and interactions of dopamine hydrochloride in solution. J Chem Phys 2015; 142:014502. [DOI: 10.1063/1.4904291] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Samantha K. Callear
- ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Andrew Johnston
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Sylvia E. McLain
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Silvia Imberti
- ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, United Kingdom
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153
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Campetella M, De Santis S, Caminiti R, Ballirano P, Sadun C, Tanzi L, Gontrani L. Is a medium-range order pre-peak possible for ionic liquids without an aliphatic chain? RSC Adv 2015. [DOI: 10.1039/c5ra07567j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The pre-peak in the X-ray scattering patterns of ionic liquids is not always due to alkyl chains. In choline–proline (a bio-compatible ionic liquid), it is due to second-shell cation–cation distances.
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Affiliation(s)
- Marco Campetella
- Department of Chemistry
- University of Rome “La Sapienza”
- Roma
- Italy
| | - Serena De Santis
- Department of Chemistry
- University of Rome “La Sapienza”
- Roma
- Italy
| | - Ruggero Caminiti
- Department of Chemistry
- University of Rome “La Sapienza”
- Roma
- Italy
| | - Paolo Ballirano
- Department of Earth Sciences
- University of Rome “La Sapienza”
- Roma
- Italy
| | - Claudia Sadun
- Department of Chemistry
- University of Rome “La Sapienza”
- Roma
- Italy
| | - Luana Tanzi
- Department of Physical and Chemical Sciences
- University of L’Aquila
- 67100 Coppito
- Italy
| | - Lorenzo Gontrani
- Department of Chemistry
- University of Rome “La Sapienza”
- Roma
- Italy
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154
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Cipcigan FS, Sokhan VP, Jones AP, Crain J, Martyna GJ. Hydrogen bonding and molecular orientation at the liquid–vapour interface of water. Phys Chem Chem Phys 2015; 17:8660-9. [DOI: 10.1039/c4cp05506c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We discover two hydrogen bonding motifs in liquid water and a related asymmetry linked with molecular orientation at its liquid–vapour interface.
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Affiliation(s)
- Flaviu S. Cipcigan
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh EH9 3JZ
- UK
| | | | - Andrew P. Jones
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh EH9 3JZ
- UK
- National Physical Laboratory
| | - Jason Crain
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh EH9 3JZ
- UK
- National Physical Laboratory
| | - Glenn J. Martyna
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh EH9 3JZ
- UK
- IBM T. J. Watson Research Center
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155
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Chialvo AA, Vlcek L. NO3– Coordination in Aqueous Solutions by 15N/14N and 18O/natO Isotopic Substitution: What Can We Learn from Molecular Simulation? J Phys Chem B 2014; 119:519-31. [DOI: 10.1021/jp510355u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ariel A. Chialvo
- Chemical
Sciences Division, Geochemistry and Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, United States
| | - Lukas Vlcek
- Chemical
Sciences Division, Geochemistry and Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, United States
- Joint
Institute for Computational Sciences, Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831-6173, United States
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156
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Scoppola E, Sodo A, McLain SE, Ricci MA, Bruni F. Water-peptide site-specific interactions: a structural study on the hydration of glutathione. Biophys J 2014; 106:1701-9. [PMID: 24739169 DOI: 10.1016/j.bpj.2014.01.046] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/08/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022] Open
Abstract
Water-peptide interactions play an important role in determining peptide structure and function. Nevertheless, a microscopic description of these interactions is still incomplete. In this study we have investigated at the atomic scale length the interaction between water and the tripeptide glutathione. The rationale behind this work, based on the combination between a neutron diffraction experiment and a computer simulation, is twofold. It extends previous studies on amino acids, addressing issues such as the perturbation of the water network brought by a larger biomolecule in solution. In addition, and more importantly, it seeks a possible link between the atomic length scale description of the glutathione-water interaction with the specific biological functionality of glutathione, an important intracellular antioxidant. Results indicate a rather weak hydrogen bond between the thiol (-SH) group of cysteine and its first neighbor water molecule. This -SH group serves as a proton donor, is responsible for the biological activity of glutathione, and it is involved in the formation of glutathione disulfide, the oxidized form of glutathione. Moreover, the hydration shell of the chemically identical carboxylate group on the glutamic acid residue and on the glycine residue shows an intriguing different spatial location of water molecules and coordination numbers around the two CO2(-) groups.
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Affiliation(s)
- Ernesto Scoppola
- Dipartimento di Scienze, Università degli Studi di Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Armida Sodo
- Dipartimento di Scienze, Università degli Studi di Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Sylvia E McLain
- Department of Biochemistry, University of Oxford, South Park Road, Oxford, Oxfordshire OX1 3QU
| | - Maria Antonietta Ricci
- Dipartimento di Scienze, Università degli Studi di Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy
| | - Fabio Bruni
- Dipartimento di Scienze, Università degli Studi di Roma Tre, Via della Vasca Navale 84, 00146 Roma, Italy.
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157
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Busch S, Lorenz CD, Taylor J, Pardo LC, McLain SE. Short-Range Interactions of Concentrated Proline in Aqueous Solution. J Phys Chem B 2014; 118:14267-77. [DOI: 10.1021/jp508779d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sebastian Busch
- Department
of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | | | - Luis Carlos Pardo
- Departament
de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, 08028 Barcelona, Catalonia, Spain
| | - Sylvia E. McLain
- Department
of Biochemistry, University of Oxford, Oxford, United Kingdom
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158
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Farhi E, Ferran G, Haeck W, Pellegrini E, Calzavara Y. Light and heavy water dynamic structure factor for neutron transport codes. J NUCL SCI TECHNOL 2014. [DOI: 10.1080/00223131.2014.984002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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159
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Soper AK. Disordered Atom Molecular Potential for Water Parameterized against Neutron Diffraction Data. Application to the Structure of Ice Ih. J Phys Chem B 2014; 119:9244-53. [DOI: 10.1021/jp509909w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alan K. Soper
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K
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160
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Sun Q, Wang Q, Ding D. Hydrogen Bonded Networks in Supercritical Water. J Phys Chem B 2014; 118:11253-8. [DOI: 10.1021/jp503474s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qiang Sun
- Key Laboratory of Orogenic
Belts and Crustal Evolution, Ministry of Education, The School of
Earth and Planetary Sciences, Peking University, Beijing 100871, China
| | - Qianqian Wang
- Key Laboratory of Orogenic
Belts and Crustal Evolution, Ministry of Education, The School of
Earth and Planetary Sciences, Peking University, Beijing 100871, China
| | - Dongye Ding
- School of Resources and Environmental
Engineering, Shandong University of Technology, Zibo 255049, China
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161
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Clark II JK, Paddison SJ. Ab initio molecular dynamics simulations of water and an excess proton in water confined in carbon nanotubes. Phys Chem Chem Phys 2014; 16:17756-69. [DOI: 10.1039/c4cp00415a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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162
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Martiniano HFMC, Galamba N, Cabral BJC. Ab initio calculation of the electronic absorption spectrum of liquid water. J Chem Phys 2014; 140:164511. [PMID: 24784291 DOI: 10.1063/1.4871740] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O-H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.
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Affiliation(s)
- Hugo F M C Martiniano
- Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa, Portugal
| | - Nuno Galamba
- Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa, Portugal
| | - Benedito J Costa Cabral
- Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa, Portugal
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163
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Van Houteghem M, Ghysels A, Verstraelen T, Poelmans W, Waroquier M, Van Speybroeck V. Critical analysis of the accuracy of models predicting or extracting liquid structure information. J Phys Chem B 2014; 118:2451-70. [PMID: 24512612 DOI: 10.1021/jp411737s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work aims at a critical assessment of properties predicting or extracting information on the density and structure of liquids. State-of-the-art NVT and NpT molecular dynamics (MD) simulations have been performed on five liquids: methanol, chloroform, acetonitrile, tetrahydrofuran, and ethanol. These simulations allow the computation of properties based on first principles, including the equilibrium density and radial distribution functions (RDFs), characterizing the liquid structure. Refinements have been incorporated in the MD simulations by taking into account basis set superposition errors (BSSE). An extended BSSE model for an instantaneous evaluation of the BSSE corrections has been proposed, and their impact on the liquid properties has been assessed. If available, the theoretical RDFs have been compared with the experimentally derived RDFs. For some liquids, significant discrepancies have been observed, and a profound but critical investigation is presented to unravel the origin of these deficiencies. This discussion is focused on tetrahydrofuran where the experiment reveals some prominent peaks completely missing in any MD simulation. Experiments providing information on liquid structure consist mainly of neutron diffraction measurements offering total structure factors as the primary observables. The splitting of these factors in reciprocal space into intra- and intermolecular contributions is extensively discussed, together with their sensitivity in reproducing correct RDFs in coordinate space.
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Affiliation(s)
- Marc Van Houteghem
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University , Technologiepark 903, B-9052 Zwijnaarde, Belgium
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164
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Mancini G, Brancato G, Barone V. Combining the Fluctuating Charge Method, Non-Periodic Boundary Conditions and Meta-Dynamics: Aqua Ions as case studies. J Chem Theory Comput 2014; 10:1150-1163. [PMID: 26543440 DOI: 10.1021/ct400988e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We present the current status of development of our code for performing Molecular Dynamics (MD) simulations exploiting a polarizable force field based on the Fluctuating Charge (FQ) method and non-Periodic Boundary Conditions (NPBC). Continuing on the path set in a previous work, we increased the capabilities of the code by implementing a number of new features, including: a non-iterative algorithm for rigid trigonal molecule simulations; two additional temperature coupling schemes; a meta-dynamics based approach for effective free energy evaluations. Although these are well known algorithms, each present in one or more widely used MD packages, they have now been tested, for the first time, in the context of the FQ model coupled with NPBC. As case studies, we considered three aqueous ions of increasing charge, namely Na+, Ca2+ and La3+, at infinite dilution. In particular, by exploiting a computational approach recently proposed by our group and based on the metadynamics technique, we focused on the important role played by solvent polarization on ionic hydration structures, also investigating the free energy landscapes of ion coordination and the water exchange rates. Such an approach, previously tested with standard non-polarizable models, was applied here to evaluate the effects of explicit polarization on water exchange barriers between different solvent coordination structures. Moreover, we have analyzed and discussed in some detail non-linear electrostatic effects arising from solvent polarization while going from a mono- to a di- and trivalent ion.
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Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore, 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, Piazza dei Cavalieri 7, I-56126 Pisa, Italy ; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy ; Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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165
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Kühne TD, Khaliullin RZ. Nature of the asymmetry in the hydrogen-bond networks of hexagonal ice and liquid water. J Am Chem Soc 2014; 136:3395-9. [PMID: 24521433 DOI: 10.1021/ja411161a] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The interpretation of the X-ray spectra of water as evidence for its asymmetric structure has challenged the traditional nearly tetrahedral model and initiated an intense debate about the order and symmetry of the hydrogen-bond network in water. Here, we present new insights into the nature of local interactions in ice and liquid water obtained using a first-principle energy decomposition method. A comparative analysis shows that the majority of molecules in liquid water in our simulation exhibit hydrogen-bonding energy patterns similar to those in ice and retain the four-fold coordination with only moderately distorted tetrahedral configurations. Although this result indicates that the traditional description of liquid water is fundamentally correct, our study also demonstrates that for a significant fraction of molecules the hydrogen-bonding environments are highly asymmetric with extremely weak and distorted bonds.
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Affiliation(s)
- Thomas D Kühne
- Institute of Physical Chemistry and Center for Computational Sciences, Johannes Gutenberg University of Mainz , Staudinger Weg 7, 55128 Mainz, Germany
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166
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Kreck CA, Mancera RL. Characterization of the Glass Transition of Water Predicted by Molecular Dynamics Simulations Using Nonpolarizable Intermolecular Potentials. J Phys Chem B 2014; 118:1867-80. [DOI: 10.1021/jp411716y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Cara A. Kreck
- School of Biomedical Sciences,
CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
| | - Ricardo L. Mancera
- School of Biomedical Sciences,
CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, Western
Australia 6845, Australia
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167
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Soper AK. Radical re-appraisal of water structure in hydrophilic confinement. Chem Phys Lett 2013; 590:1-15. [PMID: 25843963 PMCID: PMC4376068 DOI: 10.1016/j.cplett.2013.10.075] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/22/2013] [Indexed: 11/29/2022]
Abstract
The structure of water confined in MCM41 silica cylindrical pores is studied to determine whether confined water is simply a version of the bulk liquid which can be substantially supercooled without crystallisation. A combination of total neutron scattering from the porous silica, both wet and dry, and computer simulation using a realistic model of the scattering substrate is used. The water in the pore is divided into three regions: core, interfacial and overlap. The average local densities of water in these simulations are found to be about 20% lower than bulk water density, while the density in the core region is below, but closer to, the bulk density. There is a decrease in both local and core densities when the temperature is lowered from 298 K to 210 K. The radical proposal is made here that water in hydrophilic confinement is under significant tension, around -100 MPa, inside the pore.
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168
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169
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Busch S, Pardo LC, O'Dell WB, Bruce CD, Lorenz CD, McLain SE. On the structure of water and chloride ion interactions with a peptide backbone in solution. Phys Chem Chem Phys 2013; 15:21023-33. [DOI: 10.1039/c3cp53831a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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