Engineering Papers⌕ Search

Engineering topics

Voth, Gregory A.

Publications and source records attributed to Voth, Gregory A..

6 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package

Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system’s bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Molecular Tuning of Reactivity of Zeolite Protons in HZSM-5

In acidic HZSM-5 zeolite, the reactivity of a methanol molecule interacting with the zeolite proton is amenable to modification via coadsorbing a stochiometric amount of an electron density donor E to form the [(E)(CH 3 OH)(HZ)] complex. The rate of the methanol in this complex undergoing dehydration to dimethyl ether was determined for a series of E with proton affinity (PA) ranging from 659 kJ mol –1 for C 6 F 6 to 825 kJ mol –1 for C 4 H 8 O and was found to follow the expression: Ln(Rate) – Ln(Rate N 2 ) = β(PA – PA N 2 ) γ , where E = N 2 is the reference and β and γ are constants. This trend is probably due to the increased stability of the solvated proton in the [(E)(CH 3 OH)(HZ)] complex with increasing PA. Importantly, this is also observed in steady-state flow reactions when stoichiometric quantities of E are preadsorbed on the zeolite. As demonstrated with E being D 2 O, the effect on methanol reactivity diminishes when E is present in excess of the [(E)(CH 3 OH)(HZ)] complex. It is proposed that the methanol dehydration reaction involves [(E)(CH 3 OH)(CH 3 OH)(HZ)] as the transition state, which is supported by the isotopologue distribution of the initial dimethyl ether formed when a flow of CH 3 OH was passed over ZSM-5 containing one CD 3 OH per zeolite proton. Furthermore, the implication of this on the mechanism of catalytic methanol dehydration on HZSM-5 is discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Proton Dissociation and Delocalization under Stepwise Hydration of Zeolite HZSM-5

The protonation behavior of zeolite Brønsted acid sites (BAS) in the presence of water is important for the performance of these widely used catalysts. Despite extensive study, the number of water molecules necessary for deprotonation is not well understood, in large part because experiments have been unable to access this information. In this work, we report experimental evidence for full deprotonation of the BAS in the presence of two or more water molecules, with a deprotonation energy of 1.6 kcal/mol. Linear IR absorption and 2D IR spectra were measured over a wide range of controlled hydration levels from 0.5 to 8.0 equivalents of H 2 O/Al at a constant temperature. Distinct spectral signatures of the protonated BAS and excess proton are identified, and their hydration dependence is analyzed quantitatively. Using the experiment as a benchmark, ab initio molecular dynamics simulations are reported that reproduce the experimental trends in the protonation state and IR spectra. The proton charge position and delocalization are quantified in clusters of 1–8 H 2 O molecules using the recently developed rCEC method. This analysis provides insight into the proton structure in confined water clusters, showing that the excess charge remains relatively localized between two oxygen atoms across the hydration range.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Unveiling the catalytic mechanism of GTP hydrolysis in microtubules

Microtubules (MTs) are large cytoskeletal polymers, composed of αβ-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice versa. Depolymerization is coupled with hydrolysis of guanosine triphosphate (GTP) within β-tubulin. Hydrolysis is favored in the MT lattice compared to a free heterodimer with an experimentally observed rate increase of 500- to 700-fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated α-tubulin residues, α:E254 and α:D251, as catalytic residues completing the β-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP state and whether a “compacted” GDP-state lattice is required for hydrolysis. In this work, extensive quantum mechanics/molecular mechanics simulations with transition-tempered metadynamics free-energy sampling of compacted and expanded interdimer complexes, as well as a free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. α:E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice, disruption of a key salt bridge interaction renders α:E254 less effective. The simulations reveal a barrier decrease of 3.8 ± 0.5 kcal/mol for the compacted lattice compared to a free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 ± 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗