Literature DB >> 25982874

An automated transition state search using classical trajectories initialized at multiple minima.

Emilio Martínez-Núñez1.   

Abstract

Very recently, we proposed an automated method for finding transition states of chemical reactions using dynamics simulations; the method has been termed Transition State Search using Chemical Dynamics Simulations (TSSCDS) (E. Martínez-Núñez, J. Comput. Chem., 2015, 36, 222-234). In the present work, an improved automated search procedure is developed, which consists of iteratively running different ensembles of trajectories initialized at different minima. The iterative TSSCDS method is applied to the complex C3H4O system, obtaining a total of 66 different minima and 276 transition states. With the obtained transition states and paths, statistical RRKM calculations and Kinetic Monte Carlo simulations are carried out to study the fragmentation dynamics of propenal, which is the global minimum of the system. The kinetic simulations provide a (three-body dissociation)/(CO elimination) ratio of 1.49 for an excitation energy of 148 kcal mol(-1), which agrees well with the corresponding value obtained in the photolysis of propenal at 193 nm (1.1), suggesting that at least these two channels: three-body dissociation (to give H2 + CO + C2H2) and CO elimination occur on the ground electronic state.

Entities:  

Year:  2015        PMID: 25982874     DOI: 10.1039/c5cp02175h

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  9 in total

1.  Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities.

Authors:  Konstantinos D Vogiatzis; Mikhail V Polynski; Justin K Kirkland; Jacob Townsend; Ali Hashemi; Chong Liu; Evgeny A Pidko
Journal:  Chem Rev       Date:  2018-10-30       Impact factor: 60.622

2.  Chemical reaction network knowledge graphs: the OntoRXN ontology.

Authors:  Diego Garay-Ruiz; Carles Bo
Journal:  J Cheminform       Date:  2022-05-30       Impact factor: 8.489

Review 3.  A Trajectory-Based Method to Explore Reaction Mechanisms.

Authors:  Saulo A Vázquez; Xose L Otero; Emilio Martinez-Nunez
Journal:  Molecules       Date:  2018-11-30       Impact factor: 4.411

4.  Editorial: Application of Optimization Algorithms in Chemistry.

Authors:  Jorge M C Marques; Emilio Martínez-Núñez; William L Hase
Journal:  Front Chem       Date:  2020-03-20       Impact factor: 5.221

5.  The PM6-FGC Method: Improved Corrections for Amines and Amides.

Authors:  Martiño Ríos-García; Berta Fernández; Jesús Rodríguez-Otero; Enrique M Cabaleiro-Lago; Saulo A Vázquez
Journal:  Molecules       Date:  2022-03-03       Impact factor: 4.411

Review 6.  Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations.

Authors:  Albert Rimola; Nadia Balucani; Cecilia Ceccarelli; Piero Ugliengo
Journal:  Int J Mol Sci       Date:  2022-04-12       Impact factor: 6.208

Review 7.  Graph-Driven Reaction Discovery: Progress, Challenges, and Future Opportunities.

Authors:  Idil Ismail; Raphael Chantreau Majerus; Scott Habershon
Journal:  J Phys Chem A       Date:  2022-10-03       Impact factor: 2.944

8.  An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis.

Authors:  J A Varela; S A Vázquez; E Martínez-Núñez
Journal:  Chem Sci       Date:  2017-03-07       Impact factor: 9.825

9.  Exploring the full catalytic cycle of rhodium(i)-BINAP-catalysed isomerisation of allylic amines: a graph theory approach for path optimisation.

Authors:  Takayoshi Yoshimura; Satoshi Maeda; Tetsuya Taketsugu; Masaya Sawamura; Keiji Morokuma; Seiji Mori
Journal:  Chem Sci       Date:  2017-05-03       Impact factor: 9.825

  9 in total

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