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Development of a ReaxFF reactive force field for glycine and application to solvent effect and tautomerization.

ABSTRACT: Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process. In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure. To establish an accurate model that can be used for molecular dynamics simulations, a ReaxFF reactive force field has been developed for glycine. A training set for the ReaxFF hydrocarbon potential was augmented with several glycine conformers and glycine-water complexes. The force field parameters were optimized to reproduce the quantum mechanically derived energies of the species in the training set. The optimized potential could accurately describe the properties of gas-phase glycine. It was applied to investigate the effect of solvation on the conformational distribution of glycine. Molecular dynamics simulations indicated significant differences in the dominant conformers in the gas phase and in water. This suggests that the tautomerization of glycine occurs through a conformational isomerization followed by the proton transfer event. The direct reaction mechanism of the NF ? ZW proton transfer reaction in water, as well as mechanisms mediated by one or two water molecules, were investigated using molecular dynamics simulations. The results suggest that the proton transfer reaction is most likely mediated by a single water molecule. The ReaxFF potential developed in this work provides an accurate description of proton transfer in glycine and thus provides a useful methodology for simulating proton transfer reactions in organic molecules in the aqueous environment.

SUBMITTER: Rahaman O

PROVIDER: S-EPMC3042430 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

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Development of a ReaxFF reactive force field for glycine and application to solvent effect and tautomerization.

Rahaman Obaidur O van Duin Adri C T AC Goddard William A WA Doren Douglas J DJ

The journal of physical chemistry. B 20101217 2

Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process. In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure. To establish an accurate model that can be used fo ...[more]

PMID: 21166434

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Project description:Propane dehydrogenation (PDH) is an on-purpose catalytic technology to produce propylene from propane that operates at high temperatures, 773-973 K. Several key industry players have been active in developing new catalysts and processes with improved carbon footprint and economics, where Pt-based catalysts have played a central role. The optimization of these catalytic systems through computational and atomistic simulations requires large-scale models that account for their reactivity and dynamic properties. To address this challenge, we developed a new reactive ReaxFF force field (2023-Pt/C/H) that enables large-scale simulations of PDH reactions catalyzed on Pt surfaces. The optimization of force-field parameters relies on a large training set of density functional theory (DFT) calculations of Pt-catalyzed PDH mechanism, including geometries, adsorption and relative energies of reaction intermediates, and key C-H and C-C bond-breaking/forming reaction steps on the Pt(111) surface. The internal validation supports the accuracy of the developed 2023-Pt/C/H force-field parameters, resulting in mean absolute errors (MAE) against DFT data of 14 and 12 kJ mol-1 for relative energies of intermediates and energy barriers, respectively. We demonstrated the applicability of the 2023-Pt/C/H force field with reactive molecular dynamics simulations of propane on different Pt surface topologies and temperatures. The simulations successfully model the formation of propene in the gas phase as well as competitive, unproductive reactions such as deep dehydrogenation and C-C bond cleavage that produce H, C1 and C2 adsorbed species responsible of catalytic deactivation of Pt surface. Results show the following reactivity order: Pt(111) < Pt(100) < Pt(211), and that for the stepped Pt(211) surface, propane activation occurs on low-coordinated Pt atoms at the steps. The measured selectivity as a function of surface topology follows the same trend as activity, the Pt(211) facet being the most selective. The 2023-Pt/C/H reactive force field can also describe the increase of reactivity with the temperature. From these simulations, we were able to estimate the Arrhenius activation energy, 73 kJ mol-1, whose value is close to those reported experimentally for PDH catalyzed by large, supported Pt nanoparticles . The newly developed 2023-Pt/C/H reactive force field can be used in subsequent investigations of different Pt topologies and of collective effects such as temperature, propane pressure, or H surface coverage.

Dataset Information

Development of a ReaxFF reactive force field for glycine and application to solvent effect and tautomerization.

Publications

Development of a ReaxFF reactive force field for glycine and application to solvent effect and tautomerization.

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