1
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Pruteanu CG, Naden Robinson V, Ansari N, Hassanali A, Scandolo S, Loveday JS. Squeezing Oil into Water under Pressure: Inverting the Hydrophobic Effect. J Phys Chem Lett 2020; 11:4826-4833. [PMID: 32496780 PMCID: PMC7467747 DOI: 10.1021/acs.jpclett.0c01410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
The molecular structure of dense homogeneous fluid water-methane mixtures has been determined for the first time using high-pressure neutron-scattering techniques at 1.7 and 2.2 GPa. A mixed state with a fully H-bonded water network is revealed. The hydration shell of the methane molecules is, however, revealed to be pressure-dependent with an increase in the water coordination between 1.7 and 2.2 GPa. In parallel, ab initio molecular dynamics simulations have been performed to provide insight into the microscopic mechanisms associated with the phenomenon of mixing. These calculations reproduce the observed phase change from phase separation to mixing with increasing pressure. The calculations also reproduce the experimentally observed structural properties. Unexpectedly, the simulations show mixing is accompanied by a subtle enhancement of the polarization of methane. Our results highlight the key role played by fine electronic effects on miscibility and the need to readjust our fundamental understanding of hydrophobicity to account for these.
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Affiliation(s)
- Ciprian G. Pruteanu
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, United Kingdom
| | - Victor Naden Robinson
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Narjes Ansari
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Ali Hassanali
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Sandro Scandolo
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - John S. Loveday
- SUPA,
School of Physics and Astronomy and Centre for Science at Extreme
Conditions, The University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
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2
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Melgar D, Ghaani MR, Lauricella M, O'Brien GS, English NJ. Acoustic-propagation properties of methane clathrate hydrates from non-equilibrium molecular dynamics. J Chem Phys 2019; 151:144505. [PMID: 31615221 DOI: 10.1063/1.5121712] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Given methane hydrates' importance in marine sediments, as well as the widespread use of seabed acoustic-signaling methods in oil and gas exploration, the elastic characterization of these materials is particularly relevant. A greater understanding of the properties governing phonon, sound, and acoustic propagation would help to better classify methane-hydrate deposits, aiding in their discovery. Recently, we have published a new nonequilibrium molecular-dynamics (NEMD) methodology to recreate longitudinal and transverse perturbations, observing their propagation through a crystalline lattice by various metrics, to study the underlying S- and P-wave velocities (achieving excellent agreement with experiment) [Melgar et al., J. Phys. Chem. 122(5), 3006-3013 (2018); ibid.150, 084101 (2019)]. Here, we apply these NEMD methods to methane-clathrate systems to study acoustic-propagation characteristics, as well as the lattice elastic behavior. In so doing, we determine S- and P-wave velocities in excellent accord with experiment; we also ascertain the allowable magnitude range of acoustic perturbation and establish a threshold for lattice breakup and hydrate decomposition. Interestingly, upon dissociation, we observe the formation of methane nanobubbles, which agrees with previous studies on the microscopic fundamentals of hydrate dissociation by various means.
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Affiliation(s)
- Dolores Melgar
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mohammad Reza Ghaani
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Marco Lauricella
- Instituto per le Applicazioni del Calcolo, Consiglio Nazionale delle Ricerche, Via dei Teurini 19, 00185 Rome, Italy
| | - Gareth S O'Brien
- Tullow Oil Limited, Number 1, Central Park, Leopardstown, Dublin 18, Ireland
| | - Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
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3
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Ghaani MR, English NJ. Hydrogen-/propane-hydrate decomposition: thermodynamic and kinetic analysis. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1567845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Mohammad Reza Ghaani
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Niall J. English
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
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4
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Ghaani MR, English NJ. Non-equilibrium molecular-dynamics study of electromagnetic-field-induced propane-hydrate dissociation. J Chem Phys 2018; 149:124702. [PMID: 30278679 DOI: 10.1063/1.5029457] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Non-equilibrium molecular-dynamics simulations have been performed for dissolution of planar propane-hydrate/water interfaces in externally-applied electromagnetic (e/m) fields in the microwave to far infrared range (∼2.45-200 GHz) at electric-field intensities up to 2.0 V/nm and at roughly 20 K over/under temperatures vis-à-vis the zero-field propane-hydrate melting point. Upon e/m-field application, there is a field-frequency threshold above which the dissociation rate drops significantly, with a plateau therein for larger-frequencies. It was found that higher intensity and lower frequency facilitates dissociation. Except in the presence of a thermal driving-force, the 10 GHz frequency shows more substantial rate-enhancement effect vis-à-vis static electric fields or, indeed, lower-frequency e/m fields.
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Affiliation(s)
- Mohammad Reza Ghaani
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
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5
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Ghaani MR, English NJ. Molecular-dynamics study of propane-hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis. J Chem Phys 2018; 148:114504. [PMID: 29566503 DOI: 10.1063/1.5018192] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Equilibrium and non-equilibrium molecular-dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar propane-hydrate interfaces in contact with liquid water over the 260-320 K range. Two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water, for comparison: a 001-direct surface cleavage and one with completed cages. Statistically significant differences in melting temperatures and initial break-up rates were observed between both interface types. Dissociation rates were observed to be strongly dependent on temperature, with higher rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model, developed previously, was applied to fit the observed dissociation profiles, and this helps us to identify clearly two distinct hydrate-decomposition régimes; following a highly temperature-dependent break-up phase, a second well-defined stage is essentially independent of temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. Further equilibrium MD-analysis of the two-phase systems at their melting point, with consideration of the relaxation times gleaned from the auto-correlation functions of fluctuations in a number of enclathrated guest molecules, led to statistically significant differences between the two surface-termination cases; a consistent correlation emerged in both cases between the underlying, non-equilibrium, thermal-driven dissociation rates sampled directly from melting with that from an equilibrium-MD fluctuation-dissipation approach.
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Affiliation(s)
- Mohammad Reza Ghaani
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
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6
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Akbarzadeh H, Abbaspour M, Salemi S, Nazarian A. Formation of methane clathrates in carbon nanotubes: a molecular dynamics study. NEW J CHEM 2018. [DOI: 10.1039/c8nj00618k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we investigated the possible formation of methane clathrates in CNTs with different sizes.
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Affiliation(s)
- Hamed Akbarzadeh
- Department of Chemistry
- Faculty of Basic Sciences
- Hakim Sabzevari University
- Sabzevar 96179-76487
- Iran
| | - Mohsen Abbaspour
- Department of Chemistry
- Faculty of Basic Sciences
- Hakim Sabzevari University
- Sabzevar 96179-76487
- Iran
| | - Sirous Salemi
- Department of Chemistry
- Faculty of Basic Sciences
- Hakim Sabzevari University
- Sabzevar 96179-76487
- Iran
| | - Ali Nazarian
- Department of Chemistry
- Faculty of Basic Sciences
- Hakim Sabzevari University
- Sabzevar 96179-76487
- Iran
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7
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Structure and energetic characteristics of methane hydrates. From single cage to triple cage: A DFT-D study. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Smirnov KS. A modeling study of methane hydrate decomposition in contact with the external surface of zeolites. Phys Chem Chem Phys 2017; 19:23095-23105. [DOI: 10.1039/c7cp01985h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methane hydrate dissociates on the external surface of siliceous zeolites with methane absorbed by the solid and water forming a liquid-like phase.
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Affiliation(s)
- Konstantin S. Smirnov
- Laboratoire de Spectrochimie Infrarouge et Raman
- UMR 8516 CNRS – Université de Lille
- Sciences et Technologies
- 59655 Villeneuve d'Ascq
- France
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9
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Costandy J, Michalis VK, Tsimpanogiannis IN, Stubos AK, Economou IG. Molecular dynamics simulations of pure methane and carbon dioxide hydrates: lattice constants and derivative properties. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1241442] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Joseph Costandy
- Chemical Engineering Program, Texas A&M University at Qatar, Doha, Qatar
| | | | - Ioannis N. Tsimpanogiannis
- Chemical Engineering Program, Texas A&M University at Qatar, Doha, Qatar
- Environmental Research Laboratory, National Center for Scientific Research (NCSR) “Demokritos”, Athens, Greece
| | - Athanassios K. Stubos
- Environmental Research Laboratory, National Center for Scientific Research (NCSR) “Demokritos”, Athens, Greece
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10
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Alavi S, Ohmura R. Understanding decomposition and encapsulation energies of structure I and II clathrate hydrates. J Chem Phys 2016; 145:154708. [DOI: 10.1063/1.4964673] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Misquitta AJ, Stone AJ. Ab Initio Atom–Atom Potentials Using CamCASP: Theory and Application to Many-Body Models for the Pyridine Dimer. J Chem Theory Comput 2016; 12:4184-208. [DOI: 10.1021/acs.jctc.5b01241] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alston J. Misquitta
- School
of Physics and Astronomy, Queen Mary, University of London, London E1 4NS, United Kingdom
| | - Anthony J. Stone
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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12
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Costandy J, Michalis VK, Tsimpanogiannis IN, Stubos AK, Economou IG. Lattice constants of pure methane and carbon dioxide hydrates at low temperatures. Implementing quantum corrections to classical molecular dynamics studies. J Chem Phys 2016; 144:124512. [DOI: 10.1063/1.4944325] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Joseph Costandy
- Chemical Engineering Program, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
| | - Vasileios K. Michalis
- Chemical Engineering Program, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
| | - Ioannis N. Tsimpanogiannis
- Chemical Engineering Program, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
- Environmental Research Laboratory, National Center for Scientific Research NCSR “Demokritos,” 15310 Aghia Paraskevi, Attikis, Greece
| | - Athanassios K. Stubos
- Environmental Research Laboratory, National Center for Scientific Research NCSR “Demokritos,” 15310 Aghia Paraskevi, Attikis, Greece
| | - Ioannis G. Economou
- Chemical Engineering Program, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
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13
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Burnham CJ, English NJ. Communication: Librational dynamics in water, sI and sII clathrate hydrates, and ice Ih: Molecular-dynamics insights. J Chem Phys 2016; 144:051101. [PMID: 26851900 DOI: 10.1063/1.4941330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Equilibrium molecular-dynamics simulations have been performed for liquid water, and on metastable sI and sII polymorphs of empty hydrate lattices, in addition to ice Ih, in order to study the dynamical properties of librational motion (rotation oscillation) depicted by protons in water molecules. In particular, hydrate lattices were found to display prominent "bifurcated" features, or peaks, at circa 70 and 80-95 meV (or ∼560 and 640-760 cm(-1), respectively), also displayed by ice, in essentially quantitative agreement with experimental neutron-scattering data. However, observed differences in dispersion between these librational modes between these two structures (both hydrate polymorphs vis-à-vis ice), owing primarily to density effects, have been decomposed into contributions arising from angular-velocity dynamics about axes in the local molecular frame of water molecules, with in-plane "wagging" and "twisting" rationalising one mode at ∼70 meV, and out-of-plane motion for the higher-frequency band. This was confirmed explicitly by a type of de facto normal-mode analysis, in which only immediate layers of water molecules about the one under consideration were allowed to move. In contrast, liquid water displayed no marked preference for such local in- or out-of-plane modes characterising librational motion, owing to the marked absence of rigid, pentamers or hexamers therein.
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Affiliation(s)
- Christian J Burnham
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
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14
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Yagasaki T, Matsumoto M, Tanaka H. Effects of thermodynamic inhibitors on the dissociation of methane hydrate: a molecular dynamics study. Phys Chem Chem Phys 2015; 17:32347-57. [PMID: 26587576 DOI: 10.1039/c5cp03008k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the effects of methanol and NaCl, which are known as thermodynamic hydrate inhibitors, on the dissociation kinetics of methane hydrate in aqueous solutions by using molecular dynamics simulations. It is shown that the dissociation rate is not constant but changes with time. The dissociation rate in the initial stage is increased by methanol whereas it is decreased by NaCl. This difference arises from the opposite effects of the two thermodynamic inhibitors on the hydration free energy of methane. The dissociation rate of methane hydrate is increased by the formation of methane bubbles in the aqueous phase because the bubbles absorb surrounding methane molecules. It is found that both methanol and NaCl facilitate the bubble formation. However, their mechanisms are completely different from each other. The presence of ions enhances the hydrophobic interactions between methane molecules. In addition, the ions in the solution cause a highly non-uniform distribution of dissolved methane molecules. These two effects result in the easy formation of bubbles in the NaCl solution. In contrast, methanol assists the bubble formation because of its amphiphilic character.
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Affiliation(s)
- Takuma Yagasaki
- Department of Chemistry, Faculty of Science, Okayama University, Okayama, 700-8530, Japan
| | - Masakazu Matsumoto
- Department of Chemistry, Faculty of Science, Okayama University, Okayama, 700-8530, Japan
| | - Hideki Tanaka
- Department of Chemistry, Faculty of Science, Okayama University, Okayama, 700-8530, Japan and Research Center of New Functional Materials for Energy Production, Storage and Transport, Okayama, 700-8530, Japan.
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15
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Gillan MJ, Alfè D, Manby FR. Energy benchmarks for methane-water systems from quantum Monte Carlo and second-order Møller-Plesset calculations. J Chem Phys 2015; 143:102812. [PMID: 26374005 DOI: 10.1063/1.4926444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quantum Monte Carlo (QMC) technique is used to generate accurate energy benchmarks for methane-water clusters containing a single methane monomer and up to 20 water monomers. The benchmarks for each type of cluster are computed for a set of geometries drawn from molecular dynamics simulations. The accuracy of QMC is expected to be comparable with that of coupled-cluster calculations, and this is confirmed by comparisons for the CH4-H2O dimer. The benchmarks are used to assess the accuracy of the second-order Møller-Plesset (MP2) approximation close to the complete basis-set limit. A recently developed embedded many-body technique is shown to give an efficient procedure for computing basis-set converged MP2 energies for the large clusters. It is found that MP2 values for the methane binding energies and the cohesive energies of the water clusters without methane are in close agreement with the QMC benchmarks, but the agreement is aided by partial cancelation between 2-body and beyond-2-body errors of MP2. The embedding approach allows MP2 to be applied without loss of accuracy to the methane hydrate crystal, and it is shown that the resulting methane binding energy and the cohesive energy of the water lattice agree almost exactly with recently reported QMC values.
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Affiliation(s)
- M J Gillan
- London Centre for Nanotechnology, University College London, Gordon St., London WC1H 0AH, United Kingdom
| | - D Alfè
- London Centre for Nanotechnology, University College London, Gordon St., London WC1H 0AH, United Kingdom
| | - F R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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16
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Karamertzanis PG, Raiteri P, Galindo A. The Use of Anisotropic Potentials in Modeling Water and Free Energies of Hydration. J Chem Theory Comput 2015; 6:1590-607. [PMID: 26615693 DOI: 10.1021/ct900693q] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We propose a novel, anisotropic rigid-body intermolecular potential model to predict the properties of water and the hydration free energies of neutral organic solutes. The electrostatic interactions of water and the solutes are modeled using atomic multipole moments up to hexadecapole; these are obtained from distributed multipole analysis of the quantum mechanically computed charge densities and include average polarization effects in solution. The repulsion-dispersion water-water interactions are modeled with a three-site, exp-6 model fitted to the experimental liquid water density and oxygen-oxygen radial distribution function at ambient conditions. The proposed water model reproduces well several water properties not used in its parametrization, including vapor-liquid coexistence densities, the maximum in liquid water density at atmospheric pressure, the structure of ordered ice polymorphs, and the liquid water heat capacity. The model is used to compute the hydration free energy of 10 neutral organic solutes using explicit-solvent free energy perturbation. The solute-solute repulsion-dispersion intermolecular potential is obtained from previous parametrizations on organic crystal structures. In order to calculate the free energies of hydration, water-solute repulsion-dispersion interactions are modeled using Lorenz-Berthelot combining rules. The root-mean-square error of the predicted hydration free energies is 1.5 kcal mol(-1), which is comparable to the error found using a continuum mean-field quantum mechanical approach parametrized using experimental free energy of hydration data. The results are also contrasted with explicit-solvent hydration free energies obtained with an atomic charge representation of the solute's charge density computed at the same level of theory used to compute the distributed multipoles. Replacing the multipole description of the solute's charge density with an atomic charge model changes the free energy of hydration by as much as 3 kcal mol(-1) and provides an estimate for the effect of the modeling quality of the intermolecular electrostatic forces in free energy of solvation calculations.
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Affiliation(s)
- Panagiotis G Karamertzanis
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom, and Department of Chemistry and Nanochemistry Research Institute, GPO Box U1987, 6845 Perth, Western Australia
| | - Paolo Raiteri
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom, and Department of Chemistry and Nanochemistry Research Institute, GPO Box U1987, 6845 Perth, Western Australia
| | - Amparo Galindo
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom, and Department of Chemistry and Nanochemistry Research Institute, GPO Box U1987, 6845 Perth, Western Australia
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17
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Zhang C, Lu C, Wang Q, Ponder JW, Ren P. Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate. J Chem Theory Comput 2015; 11:5326-39. [PMID: 26574325 PMCID: PMC4768686 DOI: 10.1021/acs.jctc.5b00562] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Phosphate groups are commonly observed
in biomolecules such as
nucleic acids and lipids. Due to their highly charged and polarizable
nature, modeling these compounds with classical force fields is challenging.
Using quantum mechanical studies and liquid-phase simulations, the
AMOEBA force field for dimethyl phosphate (DMP) ion and trimethyl
phosphate (TMP) has been developed. On the basis of ab initio calculations, it was found that ion binding and the solution environment
significantly impact both the molecular geometry and the energy differences
between conformations. Atomic multipole moments are derived from MP2/cc-pVQZ
calculations of methyl phosphates at several conformations with their
chemical environments taken into account. Many-body polarization is
handled via a Thole-style induction model using distributed atomic
polarizabilities. van der Waals parameters of phosphate and oxygen
atoms are determined by fitting to the quantum mechanical interaction
energy curves for water with DMP or TMP. Additional stretch-torsion
and angle-torsion coupling terms were introduced in order to capture
asymmetry in P–O bond lengths and angles due to the generalized
anomeric effect. The resulting force field for DMP and TMP is able
to accurately describe both the molecular structure and conformational
energy surface, including bond and angle variations with conformation,
as well as interaction of both species with water and metal ions.
The force field was further validated for TMP in the condensed phase
by computing hydration free energy, liquid density, and heat of vaporization.
The polarization behavior between liquid TMP and TMP in water is drastically
different.
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Affiliation(s)
- Changsheng Zhang
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Chao Lu
- Department of Chemistry, Washington University in Saint Louis , Saint Louis, Missouri 63130, United States
| | - Qiantao Wang
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis , Saint Louis, Missouri 63130, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
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18
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Cox SJ, Towler MD, Alfè D, Michaelides A. Benchmarking the performance of density functional theory and point charge force fields in their description of sI methane hydrate against diffusion Monte Carlo. J Chem Phys 2015; 140:174703. [PMID: 24811651 DOI: 10.1063/1.4871873] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
High quality reference data from diffusion Monte Carlo calculations are presented for bulk sI methane hydrate, a complex crystal exhibiting both hydrogen-bond and dispersion dominated interactions. The performance of some commonly used exchange-correlation functionals and all-atom point charge force fields is evaluated. Our results show that none of the exchange-correlation functionals tested are sufficient to describe both the energetics and the structure of methane hydrate accurately, while the point charge force fields perform badly in their description of the cohesive energy but fair well for the dissociation energetics. By comparing to ice Ih, we show that a good prediction of the volume and cohesive energies for the hydrate relies primarily on an accurate description of the hydrogen bonded water framework, but that to correctly predict stability of the hydrate with respect to dissociation to ice Ih and methane gas, accuracy in the water-methane interaction is also required. Our results highlight the difficulty that density functional theory faces in describing both the hydrogen bonded water framework and the dispersion bound methane.
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Affiliation(s)
- Stephen J Cox
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Michael D Towler
- Department of Earth Sciences, University College London Gower Street, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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19
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Perspectives on molecular simulation of clathrate hydrates: Progress, prospects and challenges. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2014.07.047] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Shultz MJ, Vu TH. Hydrogen Bonding between Water and Tetrahydrofuran Relevant to Clathrate Formation. J Phys Chem B 2014; 119:9167-72. [DOI: 10.1021/jp509343x] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mary Jane Shultz
- Laboratory
for Water and Surface Analysis, Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Tuan Hoang Vu
- Jet
Propulsion Laboratory, California Institute of Technology, 4800 Oak
Grove Drive, Pasadena, California 91109, United States
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21
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Mu X, Wang Q, Wang LP, Fried SD, Piquemal JP, Dalby KN, Ren P. Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. J Phys Chem B 2014; 118:6456-65. [PMID: 24484473 PMCID: PMC4065202 DOI: 10.1021/jp411671a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The charge distribution of halogen
atoms on organochlorine compounds
can be highly anisotropic and even display a so-called σ-hole,
which leads to strong halogen bonds with electron donors. In this
paper, we have systematically investigated a series of chloromethanes
with one to four chloro substituents using a polarizable multipole-based
molecular mechanics model. The atomic multipoles accurately reproduced
the ab initio electrostatic potential around chloromethanes, including
CCl4, which has a prominent σ-hole on the Cl atom.
The van der Waals parameters for Cl were fitted to the experimental
density and heat of vaporization. The calculated hydration free energy,
solvent reaction fields, and interaction energies of several homo-
and heterodimer of chloromethanes are in good agreement with experimental
and ab initio data. This study suggests that sophisticated electrostatic
models, such as polarizable atomic multipoles, are needed for accurate
description of electrostatics in organochlorine compounds and halogen
bonds, although further improvement is necessary for better transferability.
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Affiliation(s)
- Xiaojiao Mu
- Department of Biomedical Engineering, ‡Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Texas 78712, United States
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22
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Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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English NJ, Clarke ET. Molecular dynamics study of CO2 hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis. J Chem Phys 2013; 139:094701. [DOI: 10.1063/1.4819269] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Crystal structure, stability and spectroscopic properties of methane and CO2 hydrates. J Mol Graph Model 2013; 44:253-65. [DOI: 10.1016/j.jmgm.2013.06.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/11/2013] [Accepted: 06/26/2013] [Indexed: 11/18/2022]
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25
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Liu Y, Zhao J, Li F, Chen Z. Appropriate description of intermolecular interactions in the methane hydrates: An assessment of DFT methods. J Comput Chem 2012; 34:121-31. [DOI: 10.1002/jcc.23112] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/30/2012] [Accepted: 08/19/2012] [Indexed: 01/03/2023]
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26
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The Wolf method applied to the type I methane and carbon dioxide gas hydrates. J Mol Graph Model 2012; 38:455-64. [DOI: 10.1016/j.jmgm.2012.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/29/2012] [Accepted: 10/05/2012] [Indexed: 11/23/2022]
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27
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Chakraborty SN, Gelb LD. A Monte Carlo simulation study of methane clathrate hydrates confined in slit-shaped pores. J Phys Chem B 2012; 116:2183-97. [PMID: 22320214 DOI: 10.1021/jp205241n] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Monte Carlo simulations are used to study the structure, stability, and dissociation mechanisms of methane hydrate crystals inside carbon-like slit-shaped pores. The simulation conditions used mimic experimental studies of the dissociation of methane and propane hydrates in mesoporous silica gels (Handa, Y. P.; Stupin, D. J. Phys. Chem. 1992, 96, 8599). Simulations are performed under conditions of fixed methane pressure and fixed water loading, with the temperature increased in steps, with long equilibrations at each temperature. The initial structures of the confined hydrates are taken to be bulk-like, and pore widths chosen to accommodate integer or half-integer numbers of hydrate unit cells. Density profiles and orientational order parameter profiles are obtained and used to understand the structural changes associated with hydrate dissociation. Three different common water models, SPC/E, TIP4P, and TIP4P/2005, are used and the results compared. For water modeled using either the TIP4P or TIP4P/2005 potentials, dissociation temperatures are depressed proportionally to the inverse pore width, as predicted by the macroscopic Gibbs-Thomson equation. This behavior is observed for pores small enough that only half-cages of the clathrate structure are present. Experimental work has verified Gibbs-Thomson behavior for pores as small as 2 nm (Seshadri, K.; Wilder, J. W.; Smith, D. H. J. Phys. Chem. B 2001, 105, 2627); micropores of the size studied here have not yet been studied by experiment. Interestingly, the dissociation of hydrates modeled using the SPC/E water potential does not display the predicted pore-size dependence, and the dissociation mechanisms in this model seem to be quite different than those in the TIP4P-type models. In the SPC/E hydrates, with increasing temperature, cage dissocation occurs before methane desorption. In TIP4P-type hydrates, these processes occur either at the same temperature (to within the resolution of this study) or with dissociation occurring at higher temperatures than desorption. These simulations show that a variety of interesting clathrate structures and phase behaviors may be accessed in suitably designed microporous materials, with potentially useful applications in gas storage or separations.
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Affiliation(s)
- Somendra Nath Chakraborty
- Department of Materials Science and Engineering, University of Texas at Dallas, Richardson, Texas 75080, USA
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28
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Smirnov GS, Stegailov VV. Melting and superheating of sI methane hydrate: Molecular dynamics study. J Chem Phys 2012; 136:044523. [DOI: 10.1063/1.3679860] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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29
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Abstract
Crystal growth simulations of gas hydrates have suggested that hydrate cages may occasionally be occupied by H(2)O rather than guest molecules, leaving interstitial defects within the hydrate crystal. Further inspection of the behavior of these interstitial H(2)O molecules has revealed that they are relatively highly mobile entities within a gas hydrate. In this paper, we report these observations and examine the molecular mechanisms responsible for the transport of these interstitial molecules through hydrate crystals. Four distinct pathways for the H(2)O molecule transport between cages are found, each facilitated by the presence of empty cages. The relative richness of the observed behavior of interstitial defects suggests that interstitial diffusion could be an important mechanism for the mass transport of H(2)O molecules through gas hydrates.
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Affiliation(s)
- Shuai Liang
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada
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30
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Shi Y, Wu C, Ponder JW, Ren P. Multipole electrostatics in hydration free energy calculations. J Comput Chem 2010; 32:967-77. [PMID: 20925089 DOI: 10.1002/jcc.21681] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/20/2010] [Accepted: 08/22/2010] [Indexed: 11/06/2022]
Abstract
Hydration free energy (HFE) is generally used for evaluating molecular solubility, which is an important property for pharmaceutical and chemical engineering processes. Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here, we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio method. We have compared two approaches to derive the atomic multipoles from quantum mechanical calculations: one directly from the new distributed multipole analysis and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6-311G*, 6-311++G(2d,2p), cc-pVTZ, and aug-cc-pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug-cc-pVTZ). We conclude that aug-cc-pVTZ gives the best performance when used with AMOEBA, and 6-311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long-range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed-charge water in the HFE calculation.
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Affiliation(s)
- Yue Shi
- Department of Biomedical Engineering, The University of Texas, Austin, Texas 78712, USA
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31
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Cwiklik L, Devlin JP. Hindering of rotational motion of guest molecules in the Type I clathrate hydrate. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.06.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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32
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Vu TH, Dai Kälin S, Shultz MJ. Spectroscopic Identification of Water−Propane Interaction: Implications for Clathrate Nucleation. J Phys Chem A 2010; 114:6356-60. [DOI: 10.1021/jp101678z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tuan Hoang Vu
- Pearson Research Laboratory, Department of Chemistry, Tufts University, Medford, Massachusetts 02155, and AmniSure International LLC, 30 JFK Street, Cambridge, Massachusetts 02138
| | - Sarah Dai Kälin
- Pearson Research Laboratory, Department of Chemistry, Tufts University, Medford, Massachusetts 02155, and AmniSure International LLC, 30 JFK Street, Cambridge, Massachusetts 02138
| | - Mary Jane Shultz
- Pearson Research Laboratory, Department of Chemistry, Tufts University, Medford, Massachusetts 02155, and AmniSure International LLC, 30 JFK Street, Cambridge, Massachusetts 02138
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33
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Conde MM, Vega C, McBride C, Noya EG, Ramírez R, Sesé LM. Can gas hydrate structures be described using classical simulations? J Chem Phys 2010; 132:114503. [DOI: 10.1063/1.3353953] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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34
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Castillo-Borja F, Vázquez-Román R, Bravo-Sánchez U. Dynamic properties of methane, water and methane hydrates using computational simulations. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927020903196930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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35
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Matanović I, Xu M, Moskowitz JW, Eckert J, Bačić Z. Methane molecule confined in the small and large cages of structure I clathrate hydrate: Quantum six-dimensional calculations of the coupled translation-rotation eigenstates. J Chem Phys 2009; 131:224308. [DOI: 10.1063/1.3268623] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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36
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Elking DM, Cisneros GA, Piquemal JP, Darden TA, Pedersen LG. Gaussian Multipole Model (GMM). J Chem Theory Comput 2009; 6:190-202. [PMID: 20209077 DOI: 10.1021/ct900348b] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An electrostatic model based on charge density is proposed as a model for future force fields. The model is composed of a nucleus and a single Slater-type contracted Gaussian multipole charge density on each atom. The Gaussian multipoles are fit to the electrostatic potential (ESP) calculated at the B3LYP/6-31G* and HF/aug-cc-pVTZ levels of theory and tested by comparing electrostatic dimer energies, inter-molecular density overlap integrals, and permanent molecular multipole moments with their respective ab initio values. For the case of water, the atomic Gaussian multipole moments Q(lm) are shown to be a smooth function of internal geometry (bond length and bond angle), which can be approximated by a truncated linear Taylor series. In addition, results are given when the Gaussian multipole charge density is applied to a model for exchange-repulsion energy based on the inter-molecular density overlap.
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Affiliation(s)
- Dennis M Elking
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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37
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Buch V, Devlin JP, Monreal IA, Jagoda-Cwiklik B, Uras-Aytemiz N, Cwiklik L. Clathrate hydrates with hydrogen-bonding guests. Phys Chem Chem Phys 2009; 11:10245-65. [PMID: 19890506 DOI: 10.1039/b911600c] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Clathrate hydrates (CHs) are inclusion compounds in which "tetrahedrally" bonded H(2)O forms a crystalline host lattice composed of a periodic array of cages. The structure is stabilized by guest particles which occupy the cages and interact with cage walls via van der Waals interactions. A host of atoms or small molecules can act as guests; here the focus is on guests that are capable of strong to intermediate H-bonding to water (small ethers, H(2)S, etc.) but nevertheless "choose" this hydrate crystal form in which H-bonding is absent from the equilibrium crystal structure. These CHs can form by exposure of ice to guest molecules at temperatures as low as 100-150 K, at the (low) guest saturation pressure. This is in contrast to the "normal" CHs whose formation typically requires temperatures well above 200 K and at least moderate pressures. The experimental part of this study addresses formation kinetics of CHs with H-bonding guests, as well as transformation kinetics between different CH forms, studied by CH infrared spectroscopy. The accompanying computational study suggests that the unique properties of this family of CHs are due to exceptional richness of the host lattice in point defects, caused by defect stabilization by H-bonding of water to the guests.
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Affiliation(s)
- Victoria Buch
- The Fritz Haber Institute for Molecular Dynamics, The Hebrew University, Jerusalem, 91904, Israel
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38
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English NJ, Phelan GM. Molecular dynamics study of thermal-driven methane hydrate dissociation. J Chem Phys 2009; 131:074704. [DOI: 10.1063/1.3211089] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Walsh TR, Liang T. A multipole-based water potential with implicit polarization for biomolecular simulations. J Comput Chem 2009; 30:893-9. [PMID: 18785240 DOI: 10.1002/jcc.21111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A new water potential, DMIP (distributed multipoles, implicit polarization), is constructed using distributed multipoles to describe the electrostatic interactions, while accounting for polarization implicitly. In this procedure, small clusters are randomly sampled from atomistic simulations of bulk water using the AMOEBA (Ren and Ponder, J Comput Chem 2002, 23, 1497) potential. The multipole moments of the central water in each cluster are obtained from ab initio densities for each cluster, and the moments are then averaged over all clusters. Properties of bulk water calculated using DMIP compare favorably with existing data from AMOEBA simulations and experiment, with a conservative estimate of reduction in compute time of roughly 40%. The implicit force-field is also shown to work compatibly with existing polarizable multipole-based force-fields for biomolecules.
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Affiliation(s)
- T R Walsh
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom.
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40
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Schofield DP, Jordan KD. Molecular Dynamics Simulations of Bromine Clathrate Hydrates. J Phys Chem A 2009; 113:7431-8. [DOI: 10.1021/jp900237j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel P. Schofield
- Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Kenneth D. Jordan
- Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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41
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Myshakin EM, Jiang H, Warzinski RP, Jordan KD. Molecular Dynamics Simulations of Methane Hydrate Decomposition. J Phys Chem A 2009; 113:1913-21. [DOI: 10.1021/jp807208z] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Evgeniy M. Myshakin
- National Energy Technology Laboratory, U.S. Department of Energy, P.O. Box 10940, Pittsburgh, Pennsylvania 15236, Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Parsons, South Park, Pennsylvania 15129
| | - Hao Jiang
- National Energy Technology Laboratory, U.S. Department of Energy, P.O. Box 10940, Pittsburgh, Pennsylvania 15236, Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Parsons, South Park, Pennsylvania 15129
| | - Robert P. Warzinski
- National Energy Technology Laboratory, U.S. Department of Energy, P.O. Box 10940, Pittsburgh, Pennsylvania 15236, Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Parsons, South Park, Pennsylvania 15129
| | - Kenneth D. Jordan
- National Energy Technology Laboratory, U.S. Department of Energy, P.O. Box 10940, Pittsburgh, Pennsylvania 15236, Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Parsons, South Park, Pennsylvania 15129
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42
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Abascal JLF, Sanz E, Vega C. Triple points and coexistence properties of the dense phases of water calculated using computer simulation. Phys Chem Chem Phys 2009; 11:556-62. [DOI: 10.1039/b812832d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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43
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English NJ. Effect of electrostatics techniques on the estimation of thermal conductivity via equilibrium molecular dynamics simulation: application to methane hydrate. Mol Phys 2008. [DOI: 10.1080/00268970802360348] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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44
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Jiang H, Myshakin EM, Jordan KD, Warzinski RP. Molecular Dynamics Simulations of the Thermal Conductivity of Methane Hydrate. J Phys Chem B 2008; 112:10207-16. [DOI: 10.1021/jp802942v] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hao Jiang
- National Energy Technology Laboratory, U.S. Department of Energy, Post Office Box 10940, Pittsburgh, Pennsylvania 15236, Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Parsons Project Services, Inc., South Park, Pennsylvania 15129
| | - Evgeniy M. Myshakin
- National Energy Technology Laboratory, U.S. Department of Energy, Post Office Box 10940, Pittsburgh, Pennsylvania 15236, Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Parsons Project Services, Inc., South Park, Pennsylvania 15129
| | - Kenneth D. Jordan
- National Energy Technology Laboratory, U.S. Department of Energy, Post Office Box 10940, Pittsburgh, Pennsylvania 15236, Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Parsons Project Services, Inc., South Park, Pennsylvania 15129
| | - Robert P. Warzinski
- National Energy Technology Laboratory, U.S. Department of Energy, Post Office Box 10940, Pittsburgh, Pennsylvania 15236, Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Parsons Project Services, Inc., South Park, Pennsylvania 15129
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45
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Mastny EA, Miller CA, de Pablo JJ. The effect of the water/methane interface on methane hydrate cages: The potential of mean force and cage lifetimes. J Chem Phys 2008; 129:034701. [DOI: 10.1063/1.2925680] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Castillo-Borja F, Vázquez-Román R, Bravo-Sánchez U. The effect of flexibility on thermodynamic and structural properties in methane hydrates. MOLECULAR SIMULATION 2008. [DOI: 10.1080/08927020802036062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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47
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Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci U S A 2008; 105:6290-5. [PMID: 18427113 DOI: 10.1073/pnas.0711686105] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The binding of charged ligands benzamidine and diazamidine to trypsin was investigated by using a polarizable potential energy function and explicit-water molecular dynamics simulations. The binding free energies were computed from the difference between the free energies of decoupling the ligand from water and protein environments. Both the absolute and the relative free energies from the perturbation simulations agree with experimental measurements to within 0.5 kcal.mol(-1). Comparison of free-energy components sampled from different thermodynamic paths indicates that electrostatics is the main driving force behind benzamidine recognition of trypsin. The contribution of electronic polarization to binding appears to be crucial. By computing the free-energy contribution caused by the polarization between the ligand and its surroundings, we found that polarization has the opposite effect in dissimilar environments. Although polarization favors ligand solvation in water, it weakens the protein-ligand attraction by screening the electrostatic interaction between trypsin and benzamidine. We also examined the relative binding free energies of a benzamidine analog diazamidine to trypsin. The changes in free energy on benzamidine-diazamidine substitution were tens of kilocalories in both water and trypsin environments; however, the change in the total binding free energy is <2 kcal.mol(-1) because of cancellation, consistent with the experimental results. Overall, our results suggest that the use of a polarizable force field, given adequate sampling, is capable of achieving chemical accuracy in molecular simulations of protein-ligand recognition.
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48
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Vatamanu J, Kusalik PG. Heterogeneous crystal growth of methane hydrate on its sII [001] crystallographic face. J Phys Chem B 2008; 112:2399-404. [PMID: 18247598 DOI: 10.1021/jp077583k] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This paper presents a systematic molecular simulation study of the heterogeneous crystal growth of methane hydrate sII from supersaturated aqueous methane solutions. The growth of sII hydrate on the [001] crystallographic face is achieved through utilization of a recently proposed methodology, and rates of crystal growth of 1 A/ns were sustained for the molecular models and specific conditions employed in this work. Characteristics of the crystals grown as well as properties and structure of the interface are examined. Water cages with a 5(12)6(3) arrangement, which are improper to both sI and sII structures, are identified during the heterogeneous growth of sII methane hydrate. We show that the growth of a [001] face of sII hydrate can produce an sI crystalline structure, confirming that cross-nucleation of methane hydrate structures is possible. Defects consisting of two methane molecules trapped in large 5(12)6(4) cages and water molecules trapped in small and large cages are observed, where in one instance we have found a large 5(12)6(4) cage containing three water molecules.
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Affiliation(s)
- Jenel Vatamanu
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
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