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Donor-acceptor structure and dynamics: Molecular dynamics simulation study of TIP4P/2005 water model. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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2
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Jansen van Vuuren L, Visser HG, Schutte-Smith M. Crystal structure of 2-(methyl-amino)-tropone. Acta Crystallogr E Crystallogr Commun 2019; 75:1128-1132. [PMID: 31417778 PMCID: PMC6690460 DOI: 10.1107/s2056989019009502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/02/2019] [Indexed: 11/11/2022]
Abstract
The title compound, 2-(methyl-amino)-cyclo-hepta-2,4,6-trien-1-one, C8H9NO, crystallizes in the monoclinic space group P21/c, with three independent mol-ecules in the asymmetric unit. The planarity of the mol-ecules is indicated by planes fitted through the seven ring carbon atoms. Small deviations from the planes, with an extremal r.m.s. deviation of 0.0345 Å, are present. In complexes of transition metals with similar ligands, the large planar seven-membered aromatic rings have shown to improve the stability of the complex. Two types of hydrogen-bonding inter-actions, C-H⋯O and N-H⋯O, are observed, as well as bifurcation of these inter-actions. The N-H⋯O inter-actions link mol-ecules to form infinite chains. The packing of mol-ecules in the unit cell shows a pattern of overlapping aromatic rings, forming column-like formations. π-π inter-actions are observed between the overlapping aromatic rings at 3.4462 (19) Å from each other.
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Affiliation(s)
| | - Hendrik G. Visser
- Department of Chemistry, PO Box 339, University of the Free State, Bloemfontein, 9301, South Africa
| | - Marietjie Schutte-Smith
- Department of Chemistry, PO Box 339, University of the Free State, Bloemfontein, 9301, South Africa
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4
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Structural insights into two inorganic-organic hybrids based on chiral amino acids and polyoxomolybdates. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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Affiliation(s)
- Udo Kaatze
- Drittes Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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6
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Cheng D, Huang Z, Ye Z, Ren R, Wang J, Huang C. Study of the equilibrium swelling of poly(methyl methacrylate-co-n-butyl methacrylate) immersed in water via MD simulation. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2017.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Bakó I, Lábas A, Hermansson K, Bencsura Á, Oláh J. How can we detect hydrogen bond local cooperativity in liquid water: A simulation study. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.08.023] [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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8
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Henchman RH. Water's dual nature and its continuously changing hydrogen bonds. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:384001. [PMID: 27447299 DOI: 10.1088/0953-8984/28/38/384001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A model is proposed for liquid water that is a continuum between the ordered state with predominantly tetrahedral coordination, linear hydrogen bonds and activated dynamics and a disordered state with a continuous distribution of multiple coordinations, multiple types of hydrogen bond, and diffusive dynamics, similar to that of normal liquids. Central to water's heterogeneous structure is the ability of hydrogen to donate to either one acceptor in a conventional linear hydrogen bond or to multiple acceptors as a furcated hydrogen. Linear hydrogen bonds are marked by slow, activated kinetics for hydrogen-bond switching to more crowded acceptors and sharp first peaks in the hydrogen-oxygen radial distribution function. Furcated hydrogens, equivalent to free, broken, dangling or distorted hydrogens, have barrierless, rapid kinetics and poorly defined first peaks in their hydrogen-oxygen radial distribution function. They involve the weakest donor in a local excess of donors, such that barrierless whole-molecule vibration rapidly swaps them between the linear and furcated forms. Despite the low number of furcated hydrogens and their transient existence, they are readily created in a single hydrogen-bond switch and free up the dynamics of numerous surrounding molecules, bringing about the disordered state. Hydrogens in the ordered state switch with activated dynamics to make the non-tetrahedral coordinations of the disordered state, which can also combine to make the ordered state. Consequently, the ordered and disordered states are both connected by diffusive dynamics and differentiated by activated dynamics, bringing about water's continuous heterogeneity.
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Affiliation(s)
- Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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9
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Simulation of the effect of hydrogen bonds on water activity of glucose and dextran using the Veytsman model. Carbohydr Polym 2015; 117:236-246. [DOI: 10.1016/j.carbpol.2014.09.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/05/2014] [Accepted: 09/10/2014] [Indexed: 11/23/2022]
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10
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Zhu Z, Sheng N, Wan R, Fang H. Intrinsic Autocorrelation Time of Picoseconds for Thermal Noise in Water. J Phys Chem A 2014; 118:8936-41. [DOI: 10.1021/jp5009785] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhi Zhu
- Division of Interfacial
Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100080, China
| | - Nan Sheng
- Division of Interfacial
Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100080, China
| | - Rongzheng Wan
- Division of Interfacial
Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
| | - Haiping Fang
- Division of Interfacial
Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China
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11
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Choudhary M, Siwal S, Ul Islam R, Witcomb MJ, Mallick K. Polymer stabilized silver nanoparticle: An efficient catalyst for proton-coupled electron transfer reaction and the electrochemical recognition of biomolecule. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.101] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Enami S, Colussi AJ. Ion-Specific Long-Range Correlations on Interfacial Water Driven by Hydrogen Bond Fluctuations. J Phys Chem B 2014; 118:1861-6. [DOI: 10.1021/jp411385u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shinichi Enami
- The Hakubi
Center for Advanced Research, Kyoto University, Kyoto 606-8302, Japan
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Agustín J. Colussi
- Linde Center for Global Environmental
Science, California Institute of Technology, Pasadena, California 91125, United States
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Rajalakshmi P, Srinivasan N, Krishnakumar RV, Razak IA, Rosli MM. Supramolecular sheets in (4H-chromeno[4,3-c]isoxazol-3-yl)methanol and its hydrated 8-methyl-substituted analogue at 100 K. Acta Crystallogr C 2012; 68:o481-4. [PMID: 23124468 DOI: 10.1107/s0108270112043545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 10/20/2012] [Indexed: 11/10/2022] Open
Abstract
The title compounds, (4H-chromeno[4,3-c]isoxazol-3-yl)methanol, C(11)H(9)NO(3), (I), and (8-methyl-4H-chromeno[4,3-c]isoxazol-3-yl)methanol monohydrate, C(12)H(11)NO(3)·H(2)O, (II), crystallize in the monoclinic space groups P2(1)/c and C2/c, respectively. The simple addition of a methyl substituent in (II) results in a change in the structure type and substantially alters the intermolecular interaction patterns, while retaining the point-group symmetry 2/m. Compound (II) crystallizes as a hydrate and the resulting hydrogen-bonding interactions involving the water molecule are the cause of differences in the hydrogen-bonded supramolecular motifs present in (I) and (II). The water molecule in (II) is disordered over two positions having very similar orientations, with occupancies of 0.571 (18) and 0.429 (18), although the pattern of hydrogen-bonding interactions for the two disordered water molecules remains essentially the same. In both compounds, the primary donor hydroxy group adopts a trans conformation with respect to the isoxazole O atom, with a torsion angle of 170.65 (8)° for (I) and 179.56 (10)° for (II), the small difference being due to differences in the hydrogen-bonding environment of the hydroxy group. In (I), molecules are linked through two independent O-H···N and C-H···O hydrogen bonds and form sheets of centrosymmetric R(4)(4)(18) and R(4)(4)(14) rings extending parallel to the (100) plane. The supramolecular motifs in (II) generate two-dimensional sheets parallel to the (100) plane through a combination of O-H···X (X = N, O) and C-H···O hydrogen bonds, leading to water-assisted noncentrosymmetric R(2)(2)(8) and R(6)(6)(20) motifs. The present work is an example of how the simple replacement of a substituent in the main molecular scaffold may transform the structure type, paving the way for a variety of supramolecular motifs and consequently altering the complexity of the intermolecular interaction patterns.
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Affiliation(s)
- P Rajalakshmi
- Department of Physics, Thiagarajar College, Madurai 625 009, India
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Abstract
Water deviates from tetrahedral symmetry on different scales, creating "defects" that are important for its dynamics. In this Account, I trace the manifestations of these distortions from the isolated molecule through gas-phase clusters to the liquid phase. Unlike the common depiction, an isolated water molecule has a nonsymmetric charge distribution: although its positive charge is localized at the hydrogens, the negative charge is smeared between the lone-pair sites. This creates a "negativity track" along which a positive charge may slide. Consequently, the most facile motion within the water dimer is a reorientation of the hydrogen-bond (HB) accepting molecule (known as an "acceptor switch"), such that the donor hydrogen switches from one lone pair to the other. Liquid water exhibits asymmetry between donor and acceptor HBs. Molecular dynamics simulations show that the water oxygens accepting HBs from the central molecule are spatially localized, whereas water hydrogens donating HBs to it are distributed along the negativity track. This asymmetry is manifested in a wider acceptor- versus donor-HB distribution. There is a higher probability for a water molecule to accept one (trigonal symmetry) or three HBs than to donate one or three HBs. A simple model can explain semiquantitatively how these distributions evolve by distorting perfectly tetrahedral water. Just two reactions are required: the dissociation of a HB between a double-donor donating to a double-acceptor, D(2)···A(2), followed by a switching reaction in which a HB donor rotates its hydrogen between two double-acceptor molecules. The preponderance of D(2)···A(2) dissociation events is in line with HB "anticooperativity", whereas positive cooperativity is exhibited by conditional HB distributions: a molecule with more acceptor bonds tends to have more donor bonds and vice versa. Quantum mechanically, such an effect arises from intermolecular charge transfer, but it is observed even for fixed-charge water models. Possibly, in the liquid state this is partly a collective effect, for example, a more ordered hydration shell that enhances the probability for both acceptor and donor HBs. The activation energy for liquid water self-diffusion is considerably larger than its HB strength, pointing to the involvement of collective dynamics. The remarkable agreement between the temperature dependence of the water self-diffusion coefficient and its Debye relaxation time suggests that both share the same mechanism, likely consisting of coupled rotation and translation with collective rearrangement of the environment. The auto-correlation function of a hydrogen-bonded water molecule pair is depicted quantitatively by the solution of the diffusion equation for reversible geminate recombination, up to long times where the ubiquitous t(-3/2) power law prevails. From the model, one obtains the HB dissociation and formation rate coefficients and their temperature dependence. Both have a similar activation enthalpy, suggesting rapid formation of HBs with alternate partners, perhaps by the HB switching reaction involving the trigonal site. A detailed picture of how small fluctuations evolve into large-scale molecular motions in water remains elusive. Nonetheless, our results demonstrate how the plasticity of water can be traced to its asymmetric charge distribution, with duality between tetrahedral and trigonal ligation states.
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Affiliation(s)
- Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Presiado I, Gepshtein R, Erez Y, Huppert D. Excited-State Intermolecular Proton Transfer of Firefly Luciferin V. Direct Proton Transfer to Fluoride and Other Mild Bases. J Phys Chem A 2011; 115:7591-601. [DOI: 10.1021/jp203487j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Itay Presiado
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Rinat Gepshtein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yuval Erez
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dan Huppert
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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Henchman RH, Irudayam SJ. Topological hydrogen-bond definition to characterize the structure and dynamics of liquid water. J Phys Chem B 2010; 114:16792-810. [PMID: 21114302 DOI: 10.1021/jp105381s] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A definition that equates a hydrogen bond topologically with a local energy well in the potential energy surface is used to study the structure and dynamics of liquid water. We demonstrate the robustness of this hydrogen-bond definition versus the many other definitions which use fixed, arbitrary parameters, do not account for variable molecular environments, and cannot effectively resolve transition states. Our topology definition unambiguously shows that most water molecules are double acceptors but sizable proportions are single or triple acceptors. Almost all hydrogens are found to take part in hydrogen bonds. Broken hydrogen bonds only form when two molecules try to form two hydrogen bonds between them. The double acceptors have tetrahedral geometry, lower potential energy, entropy, and density, and slower dynamics. The single and triple acceptors have trigonal and trigonal bipyramidal geometry and when considered together have higher density, potential energy, and entropy, faster dynamics, and a tendency to cluster. These calculations use an extended theory for the entropy of liquid water that takes into account the variable number of hydrogen bonds. Hydrogen-bond switching is shown to depend explicitly on the variable number of hydrogen bonds accepted and the presence of interstitial water molecules. Transition state theory indicates that the switching of hydrogen bonds is a mildly activated process, requiring only a moderate distortion of hydrogen bonds. Three main types of switching events are observed depending on whether the donor and acceptor are already sharing a hydrogen bond. The switch may proceed with no intermediate or via a bifurcated-oxygen or cyclic dimer, both of which have a broken hydrogen bond and symmetric and asymmetric forms. Switching is found to be strongly coupled to whole-molecule vibration, particularly for the more mobile single and triple acceptors. Our analysis suggests that even though water is heterogeneous in terms of the number of hydrogen bonds, the coupling between neighbors on various length and time scales brings about greater continuity in its properties.
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Affiliation(s)
- Richard H Henchman
- Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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18
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Johnson Q, Doshi U, Shen T, Hamelberg D. Water’s Contribution to the Energetic Roughness from Peptide Dynamics. J Chem Theory Comput 2010; 6:2591-7. [DOI: 10.1021/ct100183s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Quentin Johnson
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
| | - Urmi Doshi
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
| | - Tongye Shen
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
| | - Donald Hamelberg
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
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Kuznetsov A, Ulstrup J. Proton and proton-coupled electron transfer with paradigms towards single-molecule systems. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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20
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Bizjak A, Urbic T, Vlachy V, Dill KA. Theory for the three-dimensional Mercedes-Benz model of water. J Chem Phys 2010; 131:194504. [PMID: 19929057 DOI: 10.1063/1.3259970] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The two-dimensional Mercedes-Benz (MB) model of water has been widely studied, both by Monte Carlo simulations and by integral equation methods. Here, we study the three-dimensional (3D) MB model. We treat water as spheres that interact through Lennard-Jones potentials and through a tetrahedral Gaussian hydrogen bonding function. As the "right answer," we perform isothermal-isobaric Monte Carlo simulations on the 3D MB model for different pressures and temperatures. The purpose of this work is to develop and test Wertheim's Ornstein-Zernike integral equation and thermodynamic perturbation theories. The two analytical approaches are orders of magnitude more efficient than the Monte Carlo simulations. The ultimate goal is to find statistical mechanical theories that can efficiently predict the properties of orientationally complex molecules, such as water. Also, here, the 3D MB model simply serves as a useful workbench for testing such analytical approaches. For hot water, the analytical theories give accurate agreement with the computer simulations. For cold water, the agreement is not as good. Nevertheless, these approaches are qualitatively consistent with energies, volumes, heat capacities, compressibilities, and thermal expansion coefficients versus temperature and pressure. Such analytical approaches offer a promising route to a better understanding of water and also the aqueous solvation.
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Affiliation(s)
- Alan Bizjak
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, 1000 Ljubljana, Slovenia
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21
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Lenz A, Ojamäe L. A theoretical study of water equilibria: The cluster distribution versus temperature and pressure for (H2O)n, n=1–60, and ice. J Chem Phys 2009; 131:134302. [DOI: 10.1063/1.3239474] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Florini N, Arnaud GF, Kónya B, Zucchi C, Pályi G. Synthesis of a water-soluble chiral NMR shift reagent: (S)-PDTA. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.02.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Brindza MR, Walker RA. Differentiating Solvation Mechanisms at Polar Solid/Liquid Interfaces. J Am Chem Soc 2009; 131:6207-14. [DOI: 10.1021/ja810117f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Michael R. Brindza
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Robert A. Walker
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
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Auer B, Skinner J. Water: Hydrogen bonding and vibrational spectroscopy, in the bulk liquid and at the liquid/vapor interface. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.01.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Markovitch O, Agmon N. Reversible geminate recombination of hydrogen-bonded water molecule pair. J Chem Phys 2009; 129:084505. [PMID: 19044833 DOI: 10.1063/1.2968608] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t(-3/2) asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.
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Affiliation(s)
- Omer Markovitch
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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