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Tainter CJ, Skinner JL. The water hexamer: three-body interactions, structures, energetics, and OH-stretch spectroscopy at finite temperature. J Chem Phys 2013; 137:104304. [PMID: 22979856 DOI: 10.1063/1.4746157] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using a newly developed and recently parameterized classical empirical simulation model for water that involves explicit three-body interactions, we determine the eleven most stable isomers of the water hexamer. We find that the lowest energy isomer is one of the cage structures, in agreement with far-IR and microwave experiments. The energy ordering for the binding energies is cage > glove > book > bag > chair > boat > chaise, and energies relative to the cage are in good agreement with CCSD(T) calculations. The three-body contributions to the cage, book, and chair are also in reasonable agreement with CCSD(T) results. The energy of each isomer results from a delicate balance involving the number of hydrogen bonds, the strain of these hydrogen bonds, and cooperative and anti-cooperative three-body interactions, whose contribution we can understand simply from the form of the three-body interactions in the simulation model. Oxygen-oxygen distances in the cage and book isomers are in good agreement with microwave experiments. Hydrogen-bond distances depend on both donor and acceptor, which can again be understood from the three-body model. Fully anharmonic OH-stretch spectra are calculated for these low-energy structures, and compared with shifted harmonic results from ab initio and density functional theory calculations. Replica-exchange molecular dynamics simulations were performed from 40 to 194 K, which show that the cage isomer has the lowest free energy from 0 to 70 K, and the book isomer has the lowest free energy from 70 to 194 K. OH-stretch spectra were calculated between 40 and 194 K, and results at 40, 63, and 79 K were compared to recent experiments, leading to re-assignment of the peaks in the experimental spectra. We calculate local OH-stretch cumulative spectral densities for different donor-acceptor types and compare to analogous results for liquid water.
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Affiliation(s)
- C J Tainter
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Yao L, Mebel AM, Lin SH. Dissociation Rate Constant of the Hydrogen Fluoride Dimer by the ab Initio Anharmonic RRKM Theory. J Phys Chem A 2009; 113:14664-9. [DOI: 10.1021/jp9044379] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- L. Yao
- Department of Physics, Dalian Maritime University, Dalian, China 116026
| | - A. M. Mebel
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199
| | - S. H. Lin
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei, Taiwan 10764 and Department of Applied Chemistry, National Chiao-Tung University, Hsin-chu, Taiwan
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Yao L, He R, Mebel A, Lin S. On the calculation of the dissociation rate constant of the water dimer by the ab initio anharmonic RRKM theory. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.01.074] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Takeuchi H. Development of an Efficient Geometry Optimization Method for Water Clusters. J Chem Inf Model 2008; 48:2226-33. [DOI: 10.1021/ci800238w] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Hiroshi Takeuchi
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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Douady J, Calvo F, Spiegelman F. Structure, stability, and infrared spectroscopy of (H2O)nNH4+ clusters: A theoretical study at zero and finite temperature. J Chem Phys 2008; 129:154305. [DOI: 10.1063/1.2987304] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Call ST, Zubarev DY, Boldyrev AI. Global minimum structure searches via particle swarm optimization. J Comput Chem 2007; 28:1177-86. [PMID: 17299774 DOI: 10.1002/jcc.20621] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Novel implementation of the evolutionary approach known as particle swarm optimization (PSO) capable of finding the global minimum of the potential energy surface of atomic assemblies is reported. This is the first time the PSO technique has been used to perform global optimization of minimum structure search for chemical systems. Significant improvements have been introduced to the original PSO algorithm to increase its efficiency and reliability and adapt it to chemical systems. The developed software has successfully found the lowest-energy structures of the LJ(26) Lennard-Jones cluster, anionic silicon hydride Si(2)H(5) (-), and triply hydrated hydroxide ion OH(-) (H(2)O)(3). It requires relatively small population sizes and demonstrates fast convergence. Efficiency of PSO has been compared with simulated annealing, and the gradient embedded genetic algorithm.
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Affiliation(s)
- Seth T Call
- Department of Computer Science, Utah State University, Logan, Utah 84322-0300, USA
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James T, Wales DJ, Hernández-Rojas J. Global minima for water clusters (H2O)n, n⩽21, described by a five-site empirical potential. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.09.019] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Buch * V, Sigurd B, Paul Devlin J, Buck U, Kazimirski JK. Solid water clusters in the size range of tens–thousands of H2O: a combined computational/spectroscopic outlook. INT REV PHYS CHEM 2004. [DOI: 10.1080/01442350412331316124] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kazimirski JK, Buch V. Search for Low Energy Structures of Water Clusters (H2O)n, n = 20−22, 48, 123, and 293. J Phys Chem A 2003. [DOI: 10.1021/jp0305436] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jan K. Kazimirski
- The Fritz Haber Institute for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel
| | - Victoria Buch
- The Fritz Haber Institute for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel
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Quack M, Stohner J, Suhm MA. Analytical three-body interaction potentials and hydrogen bond dynamics of hydrogen fluoride aggregates, (HF) n , n ≥3. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(01)00825-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Tissandier MD, Singer SJ, Coe JV. Enumeration and Evaluation of the Water Hexamer Cage Structure. J Phys Chem A 2000. [DOI: 10.1021/jp992711t] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael D. Tissandier
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210-1173
| | - Sherwin J. Singer
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210-1173
| | - James V. Coe
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210-1173
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Starikov EB, Lehrach H, Wanker EE. Folding of oligoglutamines: a theoretical approach based upon thermodynamics and molecular mechanics. J Biomol Struct Dyn 1999; 17:409-27. [PMID: 10636078 DOI: 10.1080/07391102.1999.10508374] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Folding of oligoglutamine chains of different lengths is of crucial interest for exploring the molecular mechanisms of Huntington's disease. A simple oligoglutamine model based upon the Flory-Huggins theory of polymer solutions demonstrates a random coil instability in chains containing more than 40 glutamine residues with respect to beta-sheet formation. This is in striking quantitative agreement with biochemical results on the chain length dependence of polyglutamine aggregation in vivo and in vitro, as well as with clinical data on the polyglutamine chain length dependence of the onset of Huntington's disease. Furthermore, a detailed molecular-mechanical investigation of a polypeptide chain carrying 40 glutamine residues was performed. Two possible folding modes of such an oligoglutamine chain were revealed: a) a beta-hairpin and b) a highly compact random coil entity stabilized by a wealth of H-bonds among the glutamine side chains. A possible role of these folding modes in polyglutamine aggregation, as well as in the onset of Huntington's disease, is discussed.
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Affiliation(s)
- E B Starikov
- Institute for Crystallography, Free University of Berlin, Germany.
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Abstract
Finding the optimal solution to a complex optimization problem is of great importance in many fields, ranging from protein structure prediction to the design of microprocessor circuitry. Some recent progress in finding the global minima of potential energy functions is described, focusing on applications of the simple "basin-hopping" approach to atomic and molecular clusters and more complicated hypersurface deformation techniques for crystals and biomolecules. These methods have produced promising results and should enable larger and more complex systems to be treated in the future.
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Affiliation(s)
- D J Wales
- University Chemical Laboratories, Lensfield Road, Cambridge, CB2 1EW, UK.
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Pappu RV, Hart RK, Ponder JW. Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization. J Phys Chem B 1998. [DOI: 10.1021/jp982255t] [Citation(s) in RCA: 218] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rohit V. Pappu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Reece K. Hart
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jay W. Ponder
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
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Li Z, Laidig KE, Daggett V. Conformational search using a molecular dynamics-minimization procedure: Applications to clusters of coulombic charges, Lennard-Jones particles, and waters. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(19980115)19:1<60::aid-jcc5>3.0.co;2-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Liu K, Brown MG, Saykally RJ. Terahertz Laser Vibration−Rotation Tunneling Spectroscopy and Dipole Moment of a Cage Form of the Water Hexamer. J Phys Chem A 1997. [DOI: 10.1021/jp9707807] [Citation(s) in RCA: 189] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. Liu
- Department of Chemistry, University of California, Berkeley, California 94720
| | - M. G. Brown
- Department of Chemistry, University of California, Berkeley, California 94720
| | - R. J. Saykally
- Department of Chemistry, University of California, Berkeley, California 94720
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Wales DJ, Doye JPK. Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms. J Phys Chem A 1997. [DOI: 10.1021/jp970984n] [Citation(s) in RCA: 2261] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David J. Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jonathan P. K. Doye
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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Amara P, Straub JE. Energy minimization using the classical density distribution: Application to sodium chloride clusters. PHYSICAL REVIEW. B, CONDENSED MATTER 1996; 53:13857-13863. [PMID: 9983141 DOI: 10.1103/physrevb.53.13857] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Field MJ. Global optimization usingab initioquantum mechanical potentials and simulated annealing of the classical Liouville equation. J Chem Phys 1995. [DOI: 10.1063/1.470064] [Citation(s) in RCA: 4] [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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Global geometry optimization of clusters using a growth strategy optimized by a genetic algorithm. Chem Phys Lett 1995. [DOI: 10.1016/0009-2614(95)00587-t] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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