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Proceedings of the 3rd International Conference on Molecular Simulation

Free energy surface for rotamers of cis-enol malonaldehyde in aqueous solution studied by molecular dynamics calculations

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Pages 850-856 | Received 30 Jan 2014, Accepted 08 Jul 2014, Published online: 16 Sep 2014

References

  • Rowe WF, Jr., Duerst RW, Wilson EB. The intramolecular hydrogen bond in malonaldehyde. J Am Chem Soc. 1976;98:4021–4023.
  • Firth DW, Beyer K, Dvorak MA, Reeve SW, Grushow A, Leopold KR. Tunable far-infrared spectroscopy of malonaldehyde. J Chem Phys. 1991;94:1812–1819.
  • Baba T, Tanaka T, Morino I, Yamada KMT, Tanaka K. Detection of the tunneling–rotation transitions of malonaldehyde in the submillimeter-wave region. J Chem Phys. 1999;110:4131–4133.
  • Schuster P. LCAO-MO-calculations on the enol form of acetylacetone and its metal complexes (LCAO-MO-studies on molecular structure III). Chem Phys Lett. 1969;3:433–436.
  • Isaacson AD, Morokuma K. Molecular orbital studies of hydrogen bonds. VIII. Malonaldehyde and symmetric hydrogen bonding in neutral species. J Am Chem Soc. 1975;97:4453–4457.
  • Kato S, Kato H, Fukui K, Theoretical A. Treatment on the behavior of the hydrogen-bonded proton in malonaldehyde. J Am Chem Soc. 1977;99:684–691.
  • Miller WH. Periodic orbit description of tunneling in symmetric and asymmetric double-well potentials. J Phys Chem. 1979;83:960–963.
  • Bicerano J, Schaefer HF III, Miller WH. Structure and tunneling dynamics of malonaldehyde. A theoretical study. J Am Chem Soc. 1983;105:2550–2553.
  • Carrington T, Jr., Miller WH. Reaction surface description of intramolecular hydrogen atom transfer in malonaldehyde. J Chem Phys. 1986;84:4364–4370.
  • Makri N, Miller WH. A semiclassical tunneling model for use in classical trajectory simulations. J Chem Phys. 1989;91:4026–4036.
  • Shida N, Almlof J, Barbara PF. Tunneling paths in intramolecular proton transfer. J Phys Chem. 1991;95:10457–10464.
  • Sewell TD, Guo Y, Thompson DL. Semiclassical calculations of tunneling splitting in malonaldehyde. J Chem Phys. 1995;103:8557–8565.
  • Yagi K, Taketsugu T, Hirao K. Generation of full-dimensional potential energy surface of intramolecular hydrogen atom transfer in malonaldehyde and tunneling dynamics. J Chem Phys. 2001;115:10647–10655.
  • Mil'nikov GV, Yagi K, Taketsugu T, Nakamura H, Hirao K. Simple and accurate method to evaluate tunneling splitting in polyatomic molecules. J Chem Phys. 2004;120:5036–5045.
  • Tautermann CS, Voegele AF, Loerting T, Liedl KR. The optimal tunneling path for the proton transfer in malonaldehyde. J Chem Phys. 2002;117:1962–1966.
  • Tew DP, Handy NC, Carter S. A reaction surface Hamiltonian study of malonaldehyde. J Chem Phys. 2006;125:084313-1–084313-15.
  • Wang Y, Braams BJ, Bowman JM, Carter S, Tew DP. Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface. J Chem Phys. 2008;128:224314-1–224314-9.
  • Coutinho-Neto MD, Viel A, Manthe U. The ground state tunneling splitting of malonaldehyde: accurate full dimensional quantum dynamics calculations. J Chem Phys. 2004;121:9207–9210.
  • Hammer T, Coutinho-Neto MD, Viel A, Manthe U. Multiconfigurational time-dependent Hartree calculations for tunneling splittings of vibrational states: theoretical considerations and application to malonaldehyde. J Chem Phys. 2009;131:224109-1–224109-13.
  • Wolf K, Mikenda W, Nusterer E, Schwarz K. Proton motion in malonaldehyde: an ab initio molecular dynamics study. J Mol Struct. 1998;448:201–207.
  • Yamada A, Okazaki S. A surface hopping method for chemical reaction dynamics in solution described by diabatic representation: an analysis of tunneling and thermal activation. J Chem Phys. 2006;124:094110-1–094110-11.
  • Yamada A, Okazaki S. A quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution based on the framework of mixed quantum-classical molecular dynamics. J Chem Phys. 2008;128:044507-1–044507-8.
  • Walewski L, Bala P, Elstner M, Frauenheim Th, Lesyng B. Fast QM/MM method and its application to molecular systems. Chem Phys Lett. 2004;397:451–458.
  • Garcia-Viloca M, Alhambra C, Truhlar DG, Gao J. Inclusion of quantum-mechanical vibrational energy in reactive potentials of mean force. J Chem Phys. 2001;114:9953–9958.
  • Walewski L, Krachtus D, Fischer S, Smith JC, Bala P, Lesyng B. SCC-DFTB energy barriers for single and double proton transfer processes in the model molecular systems malonaldehyde and porphycene. Int J Quantum Chem. 2006;106:636–640.
  • Aschi M, D'Abramo M, Ramondo F, Daidone I, D'Alessandro M, Di Nola A, Amadei A. Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde. J Phys Org Chem. 2006;19:518–530.
  • Bertz SH, Dabbagh G. Chemistry under physiological conditions. Part 8. NMR spectroscopy of malondialdehyde. J Org Chem. 1990;55:5161–5165.
  • Yamabe S, Tsuchida N, Miyajima K. Reaction paths of keto–enol tautomerization of β-diketones. J Phys Chem A. 2004;108:2750–2757.
  • Buemi G. Ab initio study of 2,4-dihalosubstituted malonaldehyde and 2-halo-phenols in gas phase and solution. Chem Phys. 2002;277:241–256.
  • Kurokawa Y, Kojima H, Yamada A, Okazaki S. An improved torsional force field for cis-enol malonaldehyde. Mol Simul. 2012;38:442–447.
  • Jorgensen WL, Tirado-Rives J. The OPLS potential functions for proteins. Energy minimization for crystals of cyclic peptides and crambin. J Am Chem Soc. 1988;110:1657–1666.
  • Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc. 1996;118:11225–11236.
  • McDonald NA, Jorgensen WL. Development of an all-atom force field for heterocycles. Properties of liquid pyrrole furan, diazoles, and oxazoles. J Phys Chem B. 1998;102:8049–8059.
  • Jorgensen WL, McDonald NA. Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes. J Mol Struct (Theochem). 1998;424:145–155.
  • Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926–935.
  • Frenkel D, Smit B. Understanding molecular simulation: from algorithms to applications. 2nd ed. New York: Academic Press; 2002.
  • Martyna GJ, Tuckerman ME, Tobias DJ, Klein ML. Explicit reversible integrators for extended systems dynamics. Mol Phys. 1996;87:1117–1157.
  • Martyna GJ, Tobias DJ, Klein ML. Constant pressure molecular dynamics algorithms. J Chem Phys. 1994;101:4177–4189.
  • Martyna GJ, Tuckerman ME, Tobias DJ, Klein ML. Explicit reversible integrators for extended systems dynamics. Mol Phys. 1996;87:1117–1157.
  • Mori Y, Okamoto Y. Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations. Phys Rev E. 2013;87:023301-1–023301-4.

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