1
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Clark JA, Douglas JF. Do Specific Ion Effects on Collective Relaxation Arise from Perturbation of Hydrogen-Bonding Network Structure? J Phys Chem B 2024; 128:6362-6375. [PMID: 38912895 PMCID: PMC11229691 DOI: 10.1021/acs.jpcb.4c02638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024]
Abstract
The change in the transport properties (i.e., water diffusivity, shear viscosity, etc.) when adding salts to water has been used to classify ions as either being chaotropic or kosmotropic, a terminology based on the presumption that this phenomenon arises from respective breakdown or enhancement of the hydrogen-bonding network structure. Recent quasi-elastic neutron scattering measurements of the collective structural relaxation time, τC, in aqueous salt solutions were interpreted as confirming this proposed origin of ion effects on the dynamics of water. However, we find similar changes in τC in the same salt solutions based on molecular dynamics (MD) simulations using a coarse-grained water model in which no hydrogen bonding exists, challenging this conventional interpretation of mobility change resulting from the addition of salts to water. A thorough understanding of specific ion effects should be useful in diverse material manufacturing and biomedical applications, where these effects are prevalent, but poorly understood.
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Affiliation(s)
- Jennifer A. Clark
- Materials Science and Engineering
Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Jack F. Douglas
- Materials Science and Engineering
Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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2
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Feigl E, Jedlovszky P, Sega M. Percolation transition and bimodal density distribution in hydrogen fluoride. J Chem Phys 2024; 160:204503. [PMID: 38785286 DOI: 10.1063/5.0207202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Hydrogen-bond networks in associating fluids can be extremely robust and characterize the topological properties of the liquid phase, as in the case of water, over its whole domain of stability and beyond. Here, we report on molecular dynamics simulations of hydrogen fluoride (HF), one of the strongest hydrogen-bonding molecules. HF has more limited connectivity than water but can still create long, dynamic chains, setting it apart from most other small molecular liquids. Our simulation results provide robust evidence of a second-order percolation transition of HF's hydrogen bond network occurring below the critical point. This behavior is remarkable as it underlines the presence of two different cohesive mechanisms in liquid HF, one at low temperatures characterized by a spanning network of long, entangled hydrogen-bonded polymers, as opposed to short oligomers bound by the dispersion interaction above the percolation threshold. This second-order phase transition underlines the presence of marked structural heterogeneity in the fluid, which we found in the form of two liquid populations with distinct local densities.
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Affiliation(s)
- Elija Feigl
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Wien A-1090, Austria
| | - Pál Jedlovszky
- Department of Chemistry, Eszterházy Károly Catholic University, Leányka utca 12, H-3300 Eger, Hungary
| | - Marcello Sega
- Department of Chemical Engineering, University College London, WC1E 7JE London, United Kingdom
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3
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Belleflamme F, Hehn AS, Iannuzzi M, Hutter J. A variational formulation of the Harris functional as a correction to approximate Kohn-Sham density functional theory. J Chem Phys 2023; 158:054111. [PMID: 36754794 DOI: 10.1063/5.0122671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Accurate descriptions of intermolecular interactions are of great importance in simulations of molecular liquids. We present an electronic structure method that combines the accuracy of the Harris functional approach with the computational efficiency of approximately linear-scaling density functional theory (DFT). The non-variational nature of the Harris functional has been addressed by constructing a Lagrangian energy functional, which restores the variational condition by imposing stationarity with respect to the reference density. The associated linear response equations may be treated with linear-scaling efficiency in an atomic orbital based scheme. Key ingredients to describe the structural and dynamical properties of molecular systems are the forces acting on the atoms and the stress tensor. These first-order derivatives of the Harris Lagrangian have been derived and implemented in consistence with the energy correction. The proposed method allows for simulations with accuracies close to the Kohn-Sham DFT reference. Embedded in the CP2K program package, the method is designed to enable ab initio molecular dynamics simulations of molecular solutions for system sizes of several thousand atoms. Available subsystem DFT methods may be used to provide the reference density required for the energy correction at near linear-scaling efficiency. As an example of production applications, we applied the method to molecular dynamics simulations of the binary mixtures cyclohexane-methanol and toluene-methanol, performed within the isobaric-isothermal ensemble, to investigate the hydrogen bonding network in these non-ideal mixtures.
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Affiliation(s)
- Fabian Belleflamme
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anna-Sophia Hehn
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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4
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Śmiechowski M. The influence of intermolecular correlations on the infrared spectrum of liquid dimethyl sulfoxide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119869. [PMID: 34015747 DOI: 10.1016/j.saa.2021.119869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/09/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Dimethyl sulfoxide (DMSO) is routinely applied as an excellent, water-miscible solvent and chemical reagent. Some of the most important data concerning its liquid structure were obtained using infrared (IR) spectroscopy. However, the actual extent of intermolecular correlations that connect the isolated monomer spectrum to the IR response of the bulk liquid is poorly studied thus far. Using ab initio molecular dynamics (AIMD) simulations, IR spectra of liquid DMSO are obtained here from first principles and further analyzed using an array of sophisticated spectral decomposition techniques. The calculated spectra when unfolded in space reveal non-trivial spatial correlations underlying the IR response of liquid DMSO. It is unequivocally demonstrated that some of the fundamental vibrations visible in the intramolecular limit are effectively suppressed by the solvation environment due to symmetry reasons and thus disappear in the bulk limit, escaping experimental detection. Overall, DMSO as an aprotic solvent with dominant dipole-dipole interactions displays strong intermolecular correlations that contribute significantly to the IR spectra, on par with the situation observed in strongly associated liquids, such as water.
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Affiliation(s)
- Maciej Śmiechowski
- Department of Physical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
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5
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Biswas A, Dasari S, Mallik BS. Cohesiveness and Nondiffusive Rotational Jump Dynamics of Protic Ionic Liquid from Dispersion-Corrected FPMD Simulations. J Phys Chem B 2020; 124:10752-10765. [DOI: 10.1021/acs.jpcb.0c05866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
| | - Sathish Dasari
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy 502285, Telangana, India
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6
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7
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Ojha D, Kühne TD. "On-The-Fly" Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface. Molecules 2020; 25:E3939. [PMID: 32872259 PMCID: PMC7504776 DOI: 10.3390/molecules25173939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/24/2022] Open
Abstract
In the present work, we provide an electronic structure based method for the "on-the-fly" determination of vibrational sum frequency generation (v-SFG) spectra. The predictive power of this scheme is demonstrated at the air-water interface. While the instantaneous fluctuations in dipole moment are obtained using the maximally localized Wannier functions, the fluctuations in polarizability are approximated to be proportional to the second moment of Wannier functions. The spectrum henceforth obtained captures the signatures of hydrogen bond stretching, bending, as well as low-frequency librational modes.
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Affiliation(s)
- Deepak Ojha
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Department of Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany;
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Department of Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany;
- Paderborn Center for Parallel Computing and Institute for Lightweight Design, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
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8
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Yadav S, Chandra A. Solvation Shell of the Nitrite Ion in Water: An Ab Initio Molecular Dynamics Study. J Phys Chem B 2020; 124:7194-7204. [PMID: 32706258 DOI: 10.1021/acs.jpcb.0c02221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We performed ab initio molecular dynamics simulation of a nitrite ion in water to investigate the structural and dynamical properties of its hydration shell. The nitrite ion is found to exhibit strong asymmetry toward hydrogen bonding due to its two different types of hydrogen bond acceptor sites. This difference is better captured through further partitioning of the hydration shell into its proximal and distal regions. The frequency shifts of the stretch modes of hydration shell water reveal that the nitrogen site forms a stronger hydrogen bond than its oxygen sites with the latter forming hydrogen bonds, which are similar in strength to that between a pair of water molecules. The escape dynamics of water from the hydration shell is found to be rather slow, which seems to classify the nitrite ion as a structure-maker. However, the dynamics of orientational and hydrogen bond relaxation reveal a faster mobility of water molecules in the hydration shell than bulk water in spite of strong ion-water interactions. It is found that the nitrite ion can hold water molecules in its solvation shell and still make them rotate fast in its vicinity through switching of their hydrogen bonds between its nitrogen and oxygen acceptor sites. The dipole moment of the solute in water is also calculated in the present study.
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Affiliation(s)
- Sushma Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016 Kanpur, India
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9
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Orabi EA, Faraldo-Gómez JD. New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology. J Chem Theory Comput 2020; 16:5105-5126. [PMID: 32615034 DOI: 10.1021/acs.jctc.0c00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)n clusters, for n = 3-7; various clusters of HF and H2O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H2O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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10
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Hsu PJ, Shinkai T, Tai PH, Fujii A, Kuo JL. Effects of mixing between short-chain and branched-chain alcohols in protonated clusters. Phys Chem Chem Phys 2020; 22:13223-13239. [PMID: 32500878 DOI: 10.1039/d0cp01116a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The previous analysis of the neat protonated branched-chain alcohol clusters revealed the impact of steric repulsion and dispersion of the bulky alkyl group on the hydrogen-bonded (H-bonded) structures and their temperature-dependence. To further understand the influence of the alkyl groups in H-bonded clusters, we studied the mixing of the two extremes of alcohols, methanol (MeOH) and tert-butyl alcohol (t-BuOH), with an excess proton. Infrared spectroscopy and a structural search of first principles calculations on the size-selected clusters H+(MeOH)m(t-BuOH)t (m + t = 4 and 5) were conducted. Temperature-dependence of the dominant H-bonded structures was explored by the Ar-tagging technique and quantum harmonic superposition approach. By introducing the dispersion-corrected density functional theory methods, it was shown that the effects of dispersion due to the bulky alkyl groups in the mixed clusters cannot be ignored for t≥ 2. The computational results qualitatively depicted the characteristics of the observed IR spectra, but overestimation of the temperature-dependence with dispersion correction was clearly seen due to the unbalanced correction between linear H-bonded structures and compact cyclic ones. These results demonstrate the importance of extensive investigation and benchmarks on different levels of theory, and that a properly sampled structure database is crucial to evaluate theoretical models.
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Affiliation(s)
- Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan.
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11
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Bakó I, Daru J, Pothoczki S, Pusztai L, Hermansson K. Effects of H-bond asymmetry on the electronic properties of liquid water – An AIMD analysis. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111579] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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12
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Dubbeldam D, Walton KS, Vlugt TJH, Calero S. Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900135] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- David Dubbeldam
- Van 't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 904 1098XH Amsterdam The Netherlands
| | - Krista S. Walton
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology311 Ferst Dr. NW Atlanta GA 30332‐0100 USA
| | - Thijs J. H. Vlugt
- Delft University of TechnologyProcess & Energy DepartmentLeeghwaterstraat 39 2628CB Delft The Netherlands
| | - Sofia Calero
- Department of PhysicalChemical and Natural SystemsUniversity Pablo de OlavideSevilla 41013 Spain
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13
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Choudhary A, Chandra A. An ab initio molecular dynamics study of benzene in water at supercritical conditions: Structure, dynamics, and polarity of hydration shell water and the solute. J Chem Phys 2019; 151:044508. [PMID: 31370512 DOI: 10.1063/1.5094570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Anisotropic structure and dynamics of the hydration shell of a benzene solute in supercritical water are investigated by means of ab initio molecular dynamics simulations. The polarity and structural distortion of the benzene solute in supercritical water are also investigated in this study. Calculations are done at 673 K for three different densities of the solvent. The simulations are carried out using the Becke-Lee-Yang-Parr (BLYP) and also the Becke-Lee-Yang-Parr functional including dispersion corrections of Grimme (BYLP-D). The structural anisotropy is found to exist even at supercritical conditions as elucidated by the radial distribution functions of different conical regions and also by angular and spatial distribution functions. The benzene-water πH-bond and also the water-water hydrogen bonds are found to exist even at the supercritical temperature of 673 K. However, the numbers of these hydrogen bonds are reduced substantially with a decrease in water density. The water molecules in the axial region of benzene are found to be preferably oriented with one OH vector pointing toward the benzene ring, whereas the water molecules located in the equatorial region are found to orient their dipoles mostly parallel to the ring plane. The orientational distributions, however, are found to be rather broad at the supercritical temperature due to thermal fluctuations. Although the water molecules have faster dynamics at these supercritical conditions, a slight difference is observed in the dynamics of the solvation shell and bulk molecules. The conformational flexibility of the ring is found to be enhanced which causes an increase in polarity of the benzene solute in water under supercritical conditions.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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14
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Lynes O, Austin J, Kerridge A. Ab initio molecular dynamics studies of hydroxide coordination of alkaline earth metals and uranyl. Phys Chem Chem Phys 2019; 21:13809-13820. [PMID: 31210212 DOI: 10.1039/c9cp00142e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ab initio molecular dynamics (AIMD) simulations of the Mg2+, Ca2+, Sr2+ and UO22+ ions in either a pure aqueous environment or an environment containing two hydroxide ions have been carried out at the density functional level of theory, employing the generalised gradient approximation via the PBE exchange-correlation functional. Calculated mean M-O bond lengths in the first solvation shell of the aquo systems compared very well to existing experimental and computational literature, with bond lengths well within values measured previously and coordination numbers in line with previously calculated values. When applied to systems containing additional hydroxide ions, the methodology revealed increased bond lengths in all systems. Proton transfer events (PTEs) were recorded and were found to be most prevalent in the strontium hydroxide systems, likely due to the low charge density of the ion and the consequent lack of hydroxide coordination. For all alkaline earths, intrashell PTEs which occurred outside of the first solvation shell were most prevalent. Only three PTEs were identified in the entire simulation data of the uranium dihydroxide system, indicating the clear impact of the increased charge density of the hexavalent uranium ion on the strength of metal-oxygen bonds in aqueous solution. Broadly, systems containing more charge dense ions were found to exhibit fewer PTEs than those containing ions of lower charge density.
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Affiliation(s)
- Olivia Lynes
- Department of Chemistry, Faraday Building, Lancaster University, Lancaster, LA1 4YB, UK.
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15
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Ojha D, Chandra A. Urea in Water: Structure, Dynamics, and Vibrational Echo Spectroscopy from First-Principles Simulations. J Phys Chem B 2019; 123:3325-3336. [DOI: 10.1021/acs.jpcb.9b01904] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Deepak Ojha
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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16
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Ojha D, Chandra A. Temperature dependence of the ultrafast vibrational echo spectroscopy of OD modes in liquid water from first principles simulations. Phys Chem Chem Phys 2019; 21:6485-6498. [DOI: 10.1039/c8cp07121g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The temperature dependence of the vibrational spectral diffusion of OD modes in liquid water is investigated through calculations of vibrational echo spectral observables from first principles molecular dynamics.
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Affiliation(s)
- Deepak Ojha
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India
| | - Amalendu Chandra
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India
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17
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Yadav S, Chandra A. Structural and Dynamical Nature of Hydration Shells of the Carbonate Ion in Water: An Ab Initio Molecular Dynamics Study. J Phys Chem B 2018; 122:1495-1504. [DOI: 10.1021/acs.jpcb.7b11636] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sushma Yadav
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
- Department
of Theoretical and Computational Molecular Science, Institute of Molecular Science, Myodaiji, Okazaki 444-8585, Aichi, Japan
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18
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Fetisov EO, Harwood DB, Kuo IFW, Warrag SEE, Kroon MC, Peters CJ, Siepmann JI. First-Principles Molecular Dynamics Study of a Deep Eutectic Solvent: Choline Chloride/Urea and Its Mixture with Water. J Phys Chem B 2018; 122:1245-1254. [DOI: 10.1021/acs.jpcb.7b10422] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evgenii O. Fetisov
- Department
of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - David B. Harwood
- Department
of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - I-Feng William Kuo
- Physical
and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Samah E. E. Warrag
- Department
of Chemical Engineering, The Petroleum Institute, Khalifa University of Science and Technology, P.O. Box 2533, Abu Dhabi, United Arab Emirates
| | - Maaike C. Kroon
- Department
of Chemical Engineering, The Petroleum Institute, Khalifa University of Science and Technology, P.O. Box 2533, Abu Dhabi, United Arab Emirates
| | - Cor J. Peters
- Department
of Chemical Engineering, The Petroleum Institute, Khalifa University of Science and Technology, P.O. Box 2533, Abu Dhabi, United Arab Emirates
| | - J. Ilja Siepmann
- Department
of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
- Department
of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455-0132, United States
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19
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Fujii A, Sugawara N, Hsu PJ, Shimamori T, Li YC, Hamashima T, Kuo JL. Hydrogen bond network structures of protonated short-chain alcohol clusters. Phys Chem Chem Phys 2018; 20:14971-14991. [DOI: 10.1039/c7cp08072g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protonated alcohol clusters enable extraction of the physical essence of the nature of hydrogen bond networks.
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Affiliation(s)
- Asuka Fujii
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Natsuko Sugawara
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Takuto Shimamori
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Ying-Cheng Li
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Toru Hamashima
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
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20
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Tang F, Ohto T, Hasegawa T, Xie WJ, Xu L, Bonn M, Nagata Y. Definition of Free O–H Groups of Water at the Air–Water Interface. J Chem Theory Comput 2017; 14:357-364. [DOI: 10.1021/acs.jctc.7b00566] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fujie Tang
- International
Center for Quantum Materials, School of Physics, Peking University, 5
Yiheyuan Road, Haidian, Beijing 100871, China
- Max Planck Institute
for Polymer Research, Ackermannweg
10, D-55128 Mainz, Germany
| | - Tatsuhiko Ohto
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Taisuke Hasegawa
- Max Planck Institute
for Polymer Research, Ackermannweg
10, D-55128 Mainz, Germany
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
| | - Wen Jun Xie
- Max Planck Institute
for Polymer Research, Ackermannweg
10, D-55128 Mainz, Germany
- College
of Chemistry and Molecular Engineering, Peking University, 5
Yiheyuan Road, Haidian, Beijing 100871, China
| | - Limei Xu
- International
Center for Quantum Materials, School of Physics, Peking University, 5
Yiheyuan Road, Haidian, Beijing 100871, China
- Collaborative Innovation
Center of Quantum Matter, Beijing 100871, China
| | - Mischa Bonn
- Max Planck Institute
for Polymer Research, Ackermannweg
10, D-55128 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute
for Polymer Research, Ackermannweg
10, D-55128 Mainz, Germany
- Institute for
Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
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21
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Yadav S, Choudhary A, Chandra A. A First-Principles Molecular Dynamics Study of the Solvation Shell Structure, Vibrational Spectra, Polarity, and Dynamics around a Nitrate Ion in Aqueous Solution. J Phys Chem B 2017; 121:9032-9044. [DOI: 10.1021/acs.jpcb.7b06809] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sushma Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India 208016
| | - Ashu Choudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India 208016
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22
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Galimberti DR, Milani A, Gaigeot MP, Radice S, Tonelli C, Picozzi R, Castiglioni C. Static vs dynamic DFT prediction of IR spectra of flexible molecules in the condensed phase: The (ClCF 2CF(CF 3)OCF 2CH 3) liquid as a test case. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:195-203. [PMID: 28448957 DOI: 10.1016/j.saa.2017.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 04/07/2017] [Accepted: 04/14/2017] [Indexed: 06/07/2023]
Abstract
First-principles molecular dynamics (FPMD) simulations in the framework of Density Functional Theory (DFT) are carried out for the prediction of the infrared spectrum of the fluorinated molecule ClCF2CF(CF3)OCF2CH3 in liquid and gas phase. This molecule is characterized by a flexible structure, allowing the co-existence of several stable conformers, that differ by values of the torsional angles. FPMD computed spectra are compared to the experimental ones, and to Boltzmann weighted IR spectra based on gas phase calculations.
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Affiliation(s)
- Daria Ruth Galimberti
- Politecnico di Milano - Dip. Chimica, Materiali, Ing. Chimica "G. Natta", Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Alberto Milani
- Politecnico di Milano - Dip. Chimica, Materiali, Ing. Chimica "G. Natta", Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry val d'Essonne, Boulevard F. Mitterrand, Bat Maupertuis, 91025 Evry, France
| | - Stefano Radice
- Solvay Specialty Polymers RD&T Center, Viale Lombardia 20, 20021 Bollate, MI, Italy
| | - Claudio Tonelli
- Solvay Specialty Polymers RD&T Center, Viale Lombardia 20, 20021 Bollate, MI, Italy
| | - Rosaldo Picozzi
- Solvay Specialty Polymers RD&T Center, Viale Lombardia 20, 20021 Bollate, MI, Italy
| | - Chiara Castiglioni
- Politecnico di Milano - Dip. Chimica, Materiali, Ing. Chimica "G. Natta", Piazza Leonardo da Vinci 32, 20133 Milan, Italy
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23
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Galib M, Duignan TT, Misteli Y, Baer MD, Schenter GK, Hutter J, Mundy CJ. Mass density fluctuations in quantum and classical descriptions of liquid water. J Chem Phys 2017; 146:244501. [DOI: 10.1063/1.4986284] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Mirza Galib
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Timothy T. Duignan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Yannick Misteli
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Marcel D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Gregory K. Schenter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Jürg Hutter
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Christopher J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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24
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Vibrational echo spectral observables and frequency fluctuations of hydration shell water around a fluoride ion from first principles simulations. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1313-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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White AD, Knight C, Hocky GM, Voth GA. Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data. J Chem Phys 2017; 146:041102. [DOI: 10.1063/1.4974837] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Andrew D. White
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, USA
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14627, USA
| | - Chris Knight
- Leadership Computing Facility, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Glen M. Hocky
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, USA
| | - Gregory A. Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, USA
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26
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Śmiechowski M, Krakowiak J, Bruździak P, Stangret J. Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent. Phys Chem Chem Phys 2017; 19:9270-9280. [DOI: 10.1039/c6cp08799j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Yoshida K, Yamaguchi T, Yokoo T, Itoh S. Collective dynamics measurement of liquid methanol by inelastic neutron scattering. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.07.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Gillan MJ, Alfè D, Michaelides A. Perspective: How good is DFT for water? J Chem Phys 2016; 144:130901. [DOI: 10.1063/1.4944633] [Citation(s) in RCA: 478] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Michael J. Gillan
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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29
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Choudhary A, Chandra A. Anisotropic structure and dynamics of the solvation shell of a benzene solute in liquid water from ab initio molecular dynamics simulations. Phys Chem Chem Phys 2016; 18:6132-45. [DOI: 10.1039/c5cp07352a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The anisotropic structure and dynamics of the hydration shell of a benzene solute in liquid water have been investigated by means of ab initio molecular dynamics simulations using the BLYP (Becke–Lee–Yang–Parr) and dispersion corrected BLYP-D functionals.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India 208016
| | - Amalendu Chandra
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India 208016
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30
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Biswas S, Mallik BS. Aqueous solvation of an amide molecule from first principles molecular simulations: Structure, hydrogen bond dynamics and spectral signature. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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31
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Ojha D, Chandra A. Ultrafast Vibrational Echo Spectroscopy of Liquid Water from First-Principles Simulations. J Phys Chem B 2015; 119:11215-28. [PMID: 26161933 DOI: 10.1021/acs.jpcb.5b03109] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vibrational echo spectroscopy has become a powerful technique to study vibrational spectral diffusion in water and aqueous solutions. The dynamics of vibrational spectral diffusion is intimately related to the hydrogen bond fluctuations in liquid water and other hydrogen bonded liquids. Earlier theoretical calculations of vibrational echo spectroscopy of aqueous systems were based on classical molecular dynamics simulations involving empirical force fields of water. In the current work, we have employed the method of ab initio molecular dynamics simulation to calculate the spectral observables of vibrational echo and two-dimensional infrared (2D-IR) spectroscopy of liquid water at room temperature under Condon and cumulant approximations. The time scales extracted from the temporal decay of the frequency-time correlation function (FTCF), short-time slope of three pulse photon echo (SP3E), dynamic line width (DLW), and the slope of nodal line of 2D-IR spectra are found to be in reasonably close agreement with each other which reinforces the assertion that signatures of FTCF can be captured using three pulse photon echo and 2D-IR spectroscopy.
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Affiliation(s)
- Deepak Ojha
- Department of Chemistry, Indian Institute of Technology , Kanpur, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology , Kanpur, India 208016
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32
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He J, Noto VD, Paddison SJ. The structure of water–methanol mixtures under an electric field: Ab initio molecular dynamics simulations. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Karmakar A, Chandra A. Water in Hydration Shell of an Iodide Ion: Structure and Dynamics of Solute-Water Hydrogen Bonds and Vibrational Spectral Diffusion from First-Principles Simulations. J Phys Chem B 2015; 119:8561-72. [DOI: 10.1021/jp510714e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Anwesa Karmakar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India 208016
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34
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Munaò G, Urbic T. Structure and thermodynamics of core-softened models for alcohols. J Chem Phys 2015; 142:214508. [DOI: 10.1063/1.4922164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Gianmarco Munaò
- Dipartimento di Fisica e di Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Tomaz Urbic
- Department of Chemistry and Chemical Technology, Chair of Physical Chemistry, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
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35
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Karmakar A, Chandra A. Ab initio molecular dynamics studies of hydrogen bonded structure, molecular motion, and frequency fluctuations of water in the vicinity of azide ions. J Chem Phys 2015; 142:164505. [DOI: 10.1063/1.4918579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Anwesa Karmakar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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36
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Mazack MJM, Gao J. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization. J Chem Phys 2015; 140:204501. [PMID: 24880295 DOI: 10.1063/1.4875922] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.
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Affiliation(s)
- Michael J M Mazack
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431, USA
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431, USA
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37
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Karmakar A, Chandra A. Effects of dispersion interaction on vibrational spectral diffusion in aqueous NaBr solutions: An ab initio molecular dynamics study. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2014.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Gillan MJ. Many-body exchange-overlap interactions in rare gases and water. J Chem Phys 2014; 141:224106. [DOI: 10.1063/1.4903240] [Citation(s) in RCA: 23] [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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39
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An ab initio molecular dynamics study of the hydrogen bonded structure, dynamics and vibrational spectral diffusion of water in the ion hydration shell of a superoxide ion. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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40
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Alfè D, Bartók AP, Csányi G, Gillan MJ. Analyzing the errors of DFT approximations for compressed water systems. J Chem Phys 2014; 141:014104. [DOI: 10.1063/1.4885440] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. Alfè
- Department of Earth Sciences, UCL, London WC1E 6BT, United Kingdom
- London Centre for Nanotechnology, UCL, London WC1H 0AH, United Kingdom
- Thomas Young Centre, UCL, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, UCL, London WC1E 6BT, United Kingdom
| | - A. P. Bartók
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - G. Csányi
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - M. J. Gillan
- London Centre for Nanotechnology, UCL, London WC1H 0AH, United Kingdom
- Thomas Young Centre, UCL, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, UCL, London WC1E 6BT, United Kingdom
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41
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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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42
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Gillan MJ, Alfè D, Bartók AP, Csányi G. First-principles energetics of water clusters and ice: A many-body analysis. J Chem Phys 2013; 139:244504. [DOI: 10.1063/1.4852182] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Gurina DL, Petrenko VE, Antipova ML. Calculating the radial distribution functions of supercritical methanol by means of Car-Parrinello and classical molecular dynamics. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2013. [DOI: 10.1134/s0036024413070121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Yadav VK, Chandra A. Dynamics of supercritical methanol of varying density from first principles simulations: Hydrogen bond fluctuations, vibrational spectral diffusion, and orientational relaxation. J Chem Phys 2013; 138:224501. [DOI: 10.1063/1.4808034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Frequency dependence of the reorientational motion of OD bonds of deuterated methanol in liquid phase: A first principles molecular dynamics study. J Mol Liq 2013. [DOI: 10.1016/j.molliq.2013.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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46
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Pressure effects on the dynamics of ions and solvent molecules in liquid methanol under ambient and cold conditions: Importance of solvent's H-bonding network. J Mol Liq 2013. [DOI: 10.1016/j.molliq.2013.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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47
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Kumar Yadav V, Chandra A. Dynamics of hydrogen bonds and vibrational spectral diffusion in liquid methanol from first principles simulations with dispersion corrected density functional. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.01.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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48
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Gómez-Álvarez P, Romaní L, González-Salgado D. Association effects in pure methanol via Monte Carlo simulations. I. Structure. J Chem Phys 2013; 138:044509. [DOI: 10.1063/1.4778596] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Miró P, Cramer CJ. Water clusters to nanodrops: a tight-binding density functional study. Phys Chem Chem Phys 2013; 15:1837-43. [DOI: 10.1039/c2cp43305b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Sieffert N, Bühl M, Gaigeot MP, Morrison CA. Liquid Methanol from DFT and DFT/MM Molecular Dynamics Simulations. J Chem Theory Comput 2012; 9:106-18. [DOI: 10.1021/ct300784x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nicolas Sieffert
- Université Joseph Fourier Grenoble I, CNRS UMR-5250 Département de Chimie Moléculaire, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
| | - Michael Bühl
- EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Marie-Pierre Gaigeot
- Université d’Evry val d’Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Blvd F. Mitterrand, Bat Maupertuis, 91025 Evry, France
- Institut Universitaire de France (IUF), 103 Blvd St Michel, 75005 Paris, France
| | - Carole A. Morrison
- EaStCHEM School of Chemistry, University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh, EH9 3JJ, United Kingdom
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