Ab initio analysis of proton transfer dynamics in (H2O)3H+

Geissler, Phillip L.; Dellago, Christoph; Chandler, David; Hutter, Jürg; Parrinello, Michele

doi:10.1016/s0009-2614(00)00381-x

Cited by 56 publications

(37 citation statements)

References 15 publications

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“…Proton transfer in the protonated water trimer has been studied extensively with transition path sampling using empirical and ab initio models [10,15]. In these studies, shooting moves were implemented by using momentum displacements p only.…”

Section: Selecting Phase-space Displacementsmentioning

confidence: 99%

Transition Path Sampling

Dellago¹,

Bolhuis²,

Geissler³

2002

Advances in Chemical Physics

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499

834

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Often, the dynamics of complex condensed materials is characterized by the presence of a wide range of different time scales, complicating the study of such processes with computer simulations. Consider, for instance, dynamical processes occurring in liquid water. Here, the fastest molecular processes are intramolecular vibrations with periods in the 10-20 fs range. The translational and rotational motions of water molecules occur on a significantly longer time scale. Typically, the direction of translational motion of a molecule persist for about 500 fs, corresponding to 50 vibrational periods. Hydrogen bonds, responsible for many of the unique properties of liquid water, have an average lifetime of about 1 ps and the rotational motion of water molecules stays correlated for about 10 ps. Much longer time scales are typically involved if covalent bonds are broken and formed. For instance, the average lifetime of a water molecule in liquid water before it dissociates and forms hydroxide and hydronium ions is on the order of 10 hours. This enormous range of time scales, spanning nearly 20 orders of magnitude, is a challenge for the computer simulator who wants to study such processes.

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Section: Selecting Phase-space Displacementsmentioning

confidence: 99%

Transition Path Sampling

Dellago¹,

Bolhuis²,

Geissler³

2002

Advances in Chemical Physics

Self Cite

499

834

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“…Complementary to experimental work, theoretical and computational methods have been used to provide a more detailed understanding of PT processes (27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39). These methods are often based on empirical potentials (29 -32), Car-Parrinello, or related approaches (33)(34)(35)(36)(37)39).…”

mentioning

confidence: 99%

“…These methods are often based on empirical potentials (29 -32), Car-Parrinello, or related approaches (33)(34)(35)(36)(37)39). With standard force fields, it is not possible to examine in detail the dynamics of the proton transfer itself due to their inability to describe breaking and forming of chemical bonds.…”

mentioning

confidence: 99%

Water-assisted Proton Transfer in Ferredoxin I

Lütz

Tubert‐Brohman²,

Yang

et al. 2011

Journal of Biological Chemistry

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The role of water molecules in assisting proton transfer (PT) is investigated for the proton-pumping protein ferredoxin I (FdI) from Azotobacter vinelandii. , a larger barrier than for the forward reaction is correctly predicted, but it is quantitatively overestimated (23.1 kcal/mol from simulations versus 14.1 from experiment). Possible reasons for this discrepancy are discussed. Compared with the water-assisted process (⌬E ≈ 10 kcal/mol), water-unassisted proton transfer yields a considerably higher barrier of ⌬E ≈ 35 kcal/mol.

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“…88 These groups have formulated various recipes for determining the transition paths between reactants and products and have shown how to use this information to estimate the reaction rate. Chandler et al have applied their methods to reactions of biomolecular relevance using both ab initio QM and MM potentials, the former to a proton transfer in a water cluster 86 and the latter to the isomerization of the alanine dipeptide in solution. 87 …”

Section: Miscellaneous Developmentsmentioning

confidence: 99%

Simulating enzyme reactions: Challenges and perspectives

2001

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Elucidating how enzymes enhance the rates of the reactions that they catalyze is a major goal of contemporary biochemistry, and it is an area in which computational and theoretical techniques can make a major contribution. This article outlines some of the processes that need to be investigated if enzyme catalysis is to be understood, reviews the current state-of-the-art in enzyme simulation work, and highlights challenges for the future.

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Ab initio analysis of proton transfer dynamics in (H2O)3H+

Cited by 56 publications

References 15 publications

Transition Path Sampling

Transition Path Sampling

Water-assisted Proton Transfer in Ferredoxin I

Simulating enzyme reactions: Challenges and perspectives

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