The Need for Enzymatic Steering in Abietic Acid Biosynthesis: Gas-Phase Chemical Dynamics Simulations of Carbocation Rearrangements on a Bifurcating Potential Energy Surface

2011 ◽  
Vol 133 (21) ◽  
pp. 8335-8343 ◽  
Author(s):  
Matthew R. Siebert ◽  
Jiaxu Zhang ◽  
Srirangam V. Addepalli ◽  
Dean J. Tantillo ◽  
William L. Hase
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Gas Phase ◽  
Abietic Acid ◽  
Energy Surface ◽  
Chemical Dynamics ◽  
Acid Biosynthesis ◽  
Dynamics Simulations ◽  
Phase Chemical

Gas-Phase Chemical Dynamics Simulations on the Bifurcating Pathway of the Pimaradienyl Cation Rearrangement: Role of Enzymatic Steering in Abietic Acid Biosynthesis

2012 ◽  
Vol 8 (4) ◽  
pp. 1212-1222 ◽  
Author(s):  
Matthew R. Siebert ◽  
Paranjothy Manikandan ◽  
Rui Sun ◽  
Dean J. Tantillo ◽  
William L. Hase
Keyword(s):  
Gas Phase ◽  
Abietic Acid ◽  
Chemical Dynamics ◽  
Acid Biosynthesis ◽  
Dynamics Simulations ◽  
Phase Chemical

Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires

2016 ◽  
Vol 195 ◽  
pp. 237-251 ◽  
Author(s):  
Rafał Szabla ◽  
Robert W. Góra ◽  
Mikołaj Janicki ◽  
Jiří Šponer
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Potential Energy ◽  
Proton Transfer ◽  
Potential Energy Surface ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Energy Surface ◽  
Water Molecules ◽  
Dynamics Simulations

Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N–H and O–H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation. Here, we present non-adiabatic molecular dynamics simulations and potential energy surface calculations of the photoexcited imidazole–(H2O)5 cluster using the algebraic diagrammatic construction method to the second-order [ADC(2)]. We show that electron driven proton transfer (EDPT) along a wire of at least two water molecules may lead to the formation of a πσ*/S0 state crossing, similarly to what we suggested for 2-aminooxazole. We expand on our previous findings by direct comparison of the imidazole–(H2O)5 cluster to non-adiabatic molecular dynamics simulations of imidazole in the gas phase, which reveal that the presence of water molecules extends the overall excited-state lifetime of the chromophore. To embed the results in a biological context, we provide calculations of potential energy surface cuts for the analogous photorelaxation mechanism present in adenine, which contains an imidazole ring in its structure.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

Kinetics and dynamics study of the OH + C2H6 → H2O + C2H5 reaction based on an analytical global potential energy surface

2020 ◽  
Vol 22 (26) ◽  
pp. 14796-14810 ◽  
Author(s):  
C. Rangel ◽  
M. Garcia-Chamorro ◽  
J. C. Corchado ◽  
J. Espinosa-Garcia
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Gas Phase ◽  
Energy Surface ◽  
Hydrogen Abstraction ◽  
Ethane Molecule ◽  
Abstraction Reaction ◽  
Kinetics And Dynamics ◽  
Oppenheimer Approximation ◽  
Hydrogen Abstraction Reaction

To describe the gas-phase hydrogen abstraction reaction between the hydroxyl radical and the ethane molecule, an analytical full-dimensional potential energy surface was developed within the Born–Oppenheimer approximation.

scholarly journals A [1 + 2] cycloaddition instead of usual [2 + 3] cycloaddition between the B12N12 cluster and methyl azide: Potential energy surface calculations and Born–Oppenheimer molecular dynamics simulations

2020 ◽  
Vol 45 ◽  
pp. 146867831990058
Author(s):  
Parvaneh Pakravan ◽  
Seyyed Amir Siadati
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Molecular Dynamics Simulations ◽  
Energy Surface ◽  
Cycloaddition Reaction ◽  
Reliable Data ◽  
Reaction Channel ◽  
Dynamics Simulations

We have examined here the possibility of functionalization of the B12N12 cluster by methyl azide by means of a [2 + 3] cycloaddition reaction in analogy with the spontaneous functionalization of C20 fullerene using the same reaction. To achieve more reliable data, all possible interactions at different positions and orientations were considered by reaction channel study and potential energy surface calculations. Also, Born–Oppenheimer molecular dynamics simulations were used to find probable species which could emerge during the reactions.

Full-dimensional analytical potential energy surface describing the gas-phase Cl + C2H6 reaction and kinetics study of rate constants and kinetic isotope effects

2018 ◽  
Vol 20 (6) ◽  
pp. 3925-3938 ◽  
Author(s):  
Cipriano Rangel ◽  
Joaquin Espinosa-Garcia
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Gas Phase ◽  
Energy Surface ◽  
Isotope Effects ◽  
Hydrogen Abstraction ◽  
System P ◽  
Abstraction Reaction ◽  
Analytical Potential ◽  
Oppenheimer Approximation

Within the Born–Oppenheimer approximation a full-dimensional analytical potential energy surface, PES-2017, was developed for the gas-phase hydrogen abstraction reaction between the chlorine atom and ethane, which is a nine body system.

Gas-Phase Interaction of H2S with O2:  A Kinetic and Quantum Chemistry Study of the Potential Energy Surface

2005 ◽  
Vol 109 (6) ◽  
pp. 1057-1062 ◽  
Author(s):  
Alejandro Montoya ◽  
Karina Sendt ◽  
Brian S. Haynes
Keyword(s):  
Potential Energy ◽  
Quantum Chemistry ◽  
Potential Energy Surface ◽  
Gas Phase ◽  
Energy Surface ◽  
Phase Interaction

Theoretical Studies of the Thermal Gas-Phase Decomposition of Vinyl Bromide on the Ground-State Potential-Energy Surface

1995 ◽  
Vol 99 (10) ◽  
pp. 2959-2977 ◽  
Author(s):  
Samuel A. Abrash ◽  
Robert W. Zehner ◽  
Gilbert J. Mains ◽  
Lionel M. Raff
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Gas Phase ◽  
Ground State ◽  
Energy Surface ◽  
Theoretical Studies ◽  
Phase Decomposition ◽  
Vinyl Bromide ◽  
State Potential

A GAUSSIAN-1 Type Ab Initio MO Study of the [CH2NO]+Potential Energy Surface. Theoretical Support for the Existence of Three Experimentally Distinguishable Isomers in the Gas Phase

1993 ◽  
Vol 33 (3) ◽  
pp. 277-286 ◽  
Author(s):  
Jan Hrušák ◽  
Max C. Holthausen ◽  
Norman Goldberg ◽  
Muhammad Iraqi ◽  
Wolfram Koch ◽  
...  
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Gas Phase ◽  
Energy Surface ◽  
Theoretical Support ◽  
Ab Initio Mo ◽  
Type Ab

Isomerization of AcetonitrileN-Methylide [CH3CNCH2]•+andN-Methylketenimine [CH3NCCH2]•+Radical Cations in the Gas Phase:  Theoretical Study of the [C3,H5,N]•+Potential Energy Surface

1999 ◽  
Vol 103 (7) ◽  
pp. 938-946 ◽  
Author(s):  
Jean-Yves Salpin ◽  
Minh Tho Nguyen ◽  
Guy Bouchoux ◽  
Pascal Gerbaux ◽  
Robert Flammang
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Gas Phase ◽  
Energy Surface ◽  
Theoretical Study ◽  
Radical Cations
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