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Požar M, Lovrinčević B, Zoranić L, Mijaković M, Sokolić F, Perera A. A re-appraisal of the concept of ideal mixtures through a computer simulation study of the methanol-ethanol mixtures. J Chem Phys 2016. [DOI: 10.1063/1.4960435] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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Nishimoto Y, Nakata H, Fedorov DG, Irle S. Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method. J Phys Chem Lett 2015; 6:5034-9. [PMID: 26623658 DOI: 10.1021/acs.jpclett.5b02490] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with the fragment molecular orbital (FMO) method (FMO-DFTB). The response terms arising from the coupling of the electronic state to the embedding potential are derived, and the gradient accuracy is demonstrated on water clusters and a polypeptide. The radial distribution functions (RDFs) obtained with FMO-DFTB are found to be similar to those from conventional DFTB, while the computational cost is greatly reduced; for 256 water molecules one molecular dynamics (MD) step takes 73.26 and 0.68 s with full DFTB and FMO-DFTB, respectively, showing a speed-up factor of 108. FMO-DFTB/MD is applied to 100 ps MD simulations of liquid hydrogen halides and is found to reproduce experimental RDFs reasonably well.
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Affiliation(s)
- Yoshio Nishimoto
- Department of Chemistry, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University , 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan
| | - Hiroya Nakata
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , B-62 4259 Nagatsuta-cho, Midoriku, Yokohama 226-8501, Japan
- RIKEN, Research Cluster for Innovation , Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST) , 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Stephan Irle
- Department of Chemistry, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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JEDLOVSZKY BPAL, VALLAURI RENZO. Computer simulation study of liquid HF with a new effective pair potential model. Mol Phys 2010. [DOI: 10.1080/002689797170536] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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McLain SE, Soper AK, Watts A. Structural Studies on the Hydration of l-Glutamic Acid in Solution. J Phys Chem B 2006; 110:21251-8. [PMID: 17048953 DOI: 10.1021/jp062383e] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A combination of neutron diffraction augmented with isotopic substitution and computer modeling using empirical potential structure refinement has been used to extract detailed structural information for L-glutamic acid dissolved in 2 M NaOH solution. This work shows that the tetrahedral hydrogen bonding network in water is severely disrupted by the addition of glutamic acid and NaOH, with the number of water-water hydrogen bonds being reduced from 1.8 bonds per water molecule in pure water to 1.4 bonds per water molecule in the present solution. In the glutamic acid molecule, each carboxylate oxygen atom forms an average of three hydrogen bonds with the surrounding water solvent with one of these hydrogens being shared between the two oxygen atoms on each carboxylate group, while each amine hydrogen forms a single hydrogen bond with the surrounding water solvent. Additionally, the average conformation of the glutamic acid molecules in these solutions is extracted.
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Affiliation(s)
- Sylvia E McLain
- Rutherford Appleton Laboratory, ISIS Facility, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom.
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McLain SE, Soper AK, Luzar A. Orientational correlations in liquid acetone and dimethyl sulfoxide: A comparative study. J Chem Phys 2006; 124:74502. [PMID: 16497052 DOI: 10.1063/1.2170077] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The structure of acetone and dimethyl sulfoxide in the liquid state is investigated using a combination of neutron diffraction measurements and empirical potential structure refinement (EPSR) modeling. By extracting the orientational correlations from the EPSR model, the alignment of dipoles in both fluids is identified. At short distances the dipoles or neighboring molecules are found to be in antiparallel configurations, but further out the molecules tend to be aligned predominately as head to tail in the manner of dipolar ordering. The distribution of these orientations in space around a central molecule is strongly influenced by the underlying symmetry of the central molecule. In both liquids there is evidence for weak methyl hydrogen to oxygen intermolecular contacts, though these probably do not constitute hydrogen bonds as such.
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Affiliation(s)
- Sylvia E McLain
- ISIS Facility, Rutherford Appleton Laboratories, Chilton, Didcot, UK.
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Balucani U, Pasqualini D, Sutmann G, Vallauri R. The collective dynamical properties of HCl: The transverse current correlations. J Chem Phys 2001. [DOI: 10.1063/1.1352643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Londono JD, Annis BK, Habenschuss A, Borodin O, Smith GD, Turner JZ, Soper AK. Cation Environment in Molten Lithium Iodide Doped Poly(ethylene oxide). Macromolecules 1997. [DOI: 10.1021/ma9705681] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | - J. Z. Turner
- Crystallography Department, Birkbeck College, London WC1E 7HX, U.K
| | - A. K. Soper
- ISIS Science Division, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11-OQX, U.K
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Andreani C, Ricci MA, Nardone M, Ricci FP, Soper AK. Orientational correlations and hydrogen bonding in liquid hydrogen chloride. J Chem Phys 1997. [DOI: 10.1063/1.474368] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Anta JA, Lomba E, Alvarez M, Lombardero M, Martín C. Gas−Liquid Coexistence Properties from Reference Hypernetted Chain Theory for Linear Polar Solvents. J Phys Chem B 1997. [DOI: 10.1021/jp9629708] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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W. Neilson G, K. Adya A. Chapter 4. Neutron diffraction studies on liquids. ACTA ACUST UNITED AC 1997. [DOI: 10.1039/pc093101] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Affiliation(s)
- E. Y. Lau
- Contribution from the Department of Chemistry, University of California, Santa Barbara, Santa Barbara, California 93106
| | - J. T. Gerig
- Contribution from the Department of Chemistry, University of California, Santa Barbara, Santa Barbara, California 93106
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Alvarez M, Lomba E, Martín C, Lombardero M. Atom–atom structure factors of hydrogen halides: A molecular approach revisited. J Chem Phys 1995. [DOI: 10.1063/1.470044] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ricci MA, Nardone M, Ricci FP, Andreani C, Soper AK. Microscopic structure of low temperature liquid ammonia: A neutron diffraction experiment. J Chem Phys 1995. [DOI: 10.1063/1.469016] [Citation(s) in RCA: 69] [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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Londono JD, Annis BK, Turner JZ, Soper AK. The intermolecular hydrogen–hydrogen structure of chain–molecule liquids from neutron diffraction. J Chem Phys 1994. [DOI: 10.1063/1.468212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Andreani C, Menzinger F, Ricci MA, Soper AK, Dreyer J. Neutron diffraction from liquid hydrogen bromide: Study of the orientational correlations. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 49:3811-3820. [PMID: 10011273 DOI: 10.1103/physrevb.49.3811] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Soper AK, Andreani C, Nardone M. Reconstruction of the orientational pair-correlation function from neutron-diffraction data: The case of liquid hydrogen iodide. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1993; 47:2598-2605. [PMID: 9960291 DOI: 10.1103/physreve.47.2598] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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