scholarly journals Achieving an Order of Magnitude Speedup in Hybrid-Functional- and Plane-Wave-Based Ab Initio Molecular Dynamics: Applications to Proton-Transfer Reactions in Enzymes and in Solution

2021 ◽  
Author(s):  
Sagarmoy Mandal ◽  
Vaishali Thakkur ◽  
Nisanth N. Nair
Keyword(s):  
Molecular Dynamics ◽  
Plane Wave ◽  
Proton Transfer ◽  
Ab Initio ◽  
Transfer Reactions ◽  
Ab Initio Molecular Dynamics ◽  
Hybrid Functional ◽  
Proton Transfer Reactions ◽  
Order Of Magnitude

Ab initio study of intramolecular proton transfer reactions in cytosine

1997 ◽  
Vol 280 (3-4) ◽  
pp. 233-238 ◽  
Author(s):  
Simone Morpurgo ◽  
Mario Bossa ◽  
Giorgio O. Morpurgo
Keyword(s):  
Proton Transfer ◽  
Ab Initio ◽  
Intramolecular Proton Transfer ◽  
Transfer Reactions ◽  
Ab Initio Study ◽  
Proton Transfer Reactions

scholarly journals Proton Transfer from a Photoacid to Water: First Principles Simulations and Fast Fluorescence Spectroscopy

2021 ◽  
Author(s):  
Alice R. Walker ◽  
Boning Wu ◽  
Jan Meisner ◽  
Michael D. Fayer ◽  
Todd J. Martinez
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Fluorescence Spectroscopy ◽  
Proton Transfer ◽  
Ab Initio ◽  
Time Constant ◽  
Emission Wavelength ◽  
Ab Initio Molecular Dynamics ◽  
Long Distance ◽  
Hydrogen Bonded

Proton transfer reactions are ubiquitous in chemistry, especially in aqueous solutions. We investigate photo-induced proton transfer between the photoacid 8-hydroxypyrene-1,3,6- trisulfonate (HPTS) and water using fast fluorescence spectroscopy and ab initio molecular dynamics simulations. Photo-excitation causes rapid proton release from the HPTS hydroxyl. Previous experiments on HPTS/water described the progress from photoexcitation to proton diffusion using kinetic equations with two time constants. The shortest time constant has been interpreted as protonated and photoexcited HPTS evolving into an “associated” state, where the proton is “shared” between the HPTS hydroxyl and an originally hydrogen bonded water. The longer time constant has been interpreted as indicating evolution to a “solvent separated” state where the shared proton undergoes long distance diffusion. In this work, we refine the previous experimental results using very pure HPTS. We then use excited state ab initio molecular dynamics to elucidate the detailed molecular mechanism of aqueous excited state proton transfer in HPTS. We find that the initial excitation results in rapid rearrangement of water, forming a strong hydrogen bonded network (a “water wire”) around HPTS. HPTS then deprotonates in ≤3 ps, resulting in a proton that migrates back and forth along the wire before localizing on a single water molecule. We find a near linear relationship between emission wavelength and proton-HPTS distance over the simulated time scale, suggesting that emission wavelength can be used as a ruler for proton distance. Our simulations reveal that the “associated” state corresponds to a water wire with a mobile proton and that the diffusion of the proton away from this water wire (to a generalized “solvent-separated” state) corresponds to the longest experimental time constant.

scholarly journals On the development of a gold-standard potential energy surface for the OH− + CH3I reaction

2020 ◽  
Vol 22 (7) ◽  
pp. 3775-3778 ◽  
Author(s):  
Domonkos A. Tasi ◽  
Tibor Győri ◽  
Gábor Czakó
Keyword(s):  
Potential Energy ◽  
Proton Transfer ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Gold Standard ◽  
Energy Surface ◽  
Transfer Reactions ◽  
Standard Potential ◽  
Proton Transfer Reactions

We develop the first accurate full-dimensional ab initio PES for the OH− + CH3I SN2 and proton-transfer reactions treating the failure of CCSD(T) at certain geometries.

Effect of anion reorientation on proton mobility in the solid acids family CsHyXO4 (X = S, P, Se, y = 1, 2) from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (19) ◽  
pp. 10738-10752 ◽  
Author(s):  
Christian Dreßler ◽  
Daniel Sebastiani
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Proton Transfer ◽  
Ab Initio ◽  
Solid Acids ◽  
Ab Initio Molecular Dynamics ◽  
Proton Mobility ◽  
Transfer Rates ◽  
High Proton ◽  
Dynamics Simulations

The high temperature phases of the solid acids CsHSeO4, CsHSO4 and CsH2PO4 show extraordinary high proton conductivities, which are enabled by the interplay of high proton transfer rates and frequent anion reorientation.

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