Mechanism of Thiolate-Disulfide Exchange: Addition–Elimination or Effectively SN2? Effect of a Shallow Intermediate in Gas-Phase Direct Dynamics Simulations

2012 ◽  
Vol 116 (47) ◽  
pp. 11492-11499 ◽  
Author(s):  
Manikandan Paranjothy ◽  
Matthew R. Siebert ◽  
William L. Hase ◽  
Steven M. Bachrach
Keyword(s):  
Gas Phase ◽  
Disulfide Exchange ◽  
Direct Dynamics ◽  
Dynamics Simulations

Modeling the Effects of O-sulfonation on the CID of Serine

2020 ◽  
Author(s):  
Kenneth Lucas ◽  
George Barnes
Keyword(s):  
Sulfo Group ◽  
High Energy ◽  
Empirical Method ◽  
Side Chain ◽  
Energy Structure ◽  
Direct Dynamics ◽  
Theoretical Mass ◽  
Intermolecular Proton Transfer ◽  
Dynamics Simulations ◽  
Semi Empirical

We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of \textit{O}-sulfonation on the collision induced dissociation for serine. Towards this end, direct dynamics simulations of both serine and sulfoserine were performed at multiple collision energies and theoretical mass spectra obtained. Comparisons to experimental results are favorable for both systems. Peaks related to the sulfo group are identified and the reaction dynamics explored. In particular, three significant peaks (m\z 106, 88, and 81) seen in the theoretical mass spectrum directly related to the sulfo group are analyzed as well as major peaks shared by both systems. Our analysis shows that the m\z 106 peaks result from intramolecular rearrangements, intermolecular proton transfer among complexes composed of initial fragmentation products, and at high energy side-chain fragmentation. The \mz 88 peak was found to contain multiple constitutional isomers, including a previously unconsidered, low energy structure. It was also seen that the RM1 semi empirical method was not able to obtain all of the major peaks seen in experiment for sulfoserine. In contrast, PM6 did obtain all major experimental peaks.

scholarly journals Insights into the deactivation of 5-bromouracil after ultraviolet excitation

2017 ◽  
Vol 375 (2092) ◽  
pp. 20160202 ◽  
Author(s):  
Francesca Peccati ◽  
Sebastian Mai ◽  
Leticia González
Keyword(s):  
Gas Phase ◽  
Ground State ◽  
Surface Hopping ◽  
Ultraviolet Excitation ◽  
Quantum Chemistry Calculations ◽  
Electronic Structure Methods ◽  
Dna Strands ◽  
Potential Applications ◽  
Adiabatic Dynamics ◽  
Dynamics Simulations

5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ * state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C–Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1 n O π * and 3 ππ * states. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

scholarly journals Modelling Cysteine Disulfide Exchange Reactions by Molecular Dynamics Simulations

2016 ◽  
Vol 110 (3) ◽  
pp. 524a
Author(s):  
Katra Kolšek ◽  
Camilo Aponte-Santamaría ◽  
Frauke Gräter
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Exchange Reactions ◽  
Disulfide Exchange ◽  
Dynamics Simulations

The cubyl cation rearrangements

2016 ◽  
Vol 52 (16) ◽  
pp. 3403-3405 ◽  
Author(s):  
Said Jalife ◽  
Sukanta Mondal ◽  
Jose Luis Cabellos ◽  
Gerardo Martinez-Guajardo ◽  
Maria A. Fernandez-Herrera ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Dynamics Simulations ◽  
High Level

Born–Oppenheimer molecular dynamics simulations and high-level ab initio computations predict that the cage-opening rearrangement of the cubyl cation to the 7H+-pentalenyl cation is feasible in the gas phase.

Growth of Co isolated clusters in the gas phase: Experiment and molecular dynamics simulations

2008 ◽  
Vol 77 (8) ◽  
Author(s):  
Sébastien Rives ◽  
Alain Catherinot ◽  
Frédéric Dumas-Bouchiat ◽  
Corinne Champeaux ◽  
Arnaud Videcoq ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Dynamics Simulations

Chemical Dynamics Simulations in the Gas Phase and on Complex Surfaces A Tribute to William Hase

2006 ◽  
Vol 110 (4) ◽  
pp. 1201-1202
Author(s):  
Mary T. Rodgers ◽  
Gang-yu Liu
Keyword(s):  
Gas Phase ◽  
Chemical Dynamics ◽  
Complex Surfaces ◽  
Dynamics Simulations

Molecular dynamics simulations of energy dissipation and non-thermal diffusion on amorphous solid water

2018 ◽  
Vol 20 (8) ◽  
pp. 5569-5577 ◽  
Author(s):  
A. Fredon ◽  
H. M. Cuppen
Keyword(s):  
Molecular Dynamics ◽  
Energy Dissipation ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Thermal Diffusion ◽  
Amorphous Solid ◽  
Gas Phase Reactions ◽  
Amorphous Solid Water ◽  
Dynamics Simulations ◽  
Dust Grain

Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst.

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