Literature DB >> 25581279

Single-ended transition state finding with the growing string method.

Paul M Zimmerman1.   

Abstract

Reaction path finding and transition state (TS) searching are important tasks in computational chemistry. Methods that seek to optimize an evenly distributed set of structures to represent a chemical reaction path are known as double-ended string methods. Such methods can be highly reliable because the endpoints of the string are fixed, which effectively lowers the dimensionality of the reaction path search. String methods, however, require that the reactant and product structures are known beforehand, which limits their ability for systematic exploration of reactive steps. In this article, a single-ended growing string method (GSM) is introduced which allows for reaction path searches starting from a single structure. The method works by sequentially adding nodes along coordinates that drive bonds, angles, and/or torsions to a desired reactive outcome. After the string is grown and an approximate reaction path through the TS is found, string optimization commences and the exact TS is located along with the reaction path. Fast convergence of the string is achieved through use of internal coordinates and eigenvector optimization schemes combined with Hessian estimates. Comparison to the double-ended GSM shows that single-ended method can be even more computationally efficient than the already rapid double-ended method. Examples, including transition metal reactivity and a systematic, automated search for unknown reactivity, demonstrate the efficacy of the new method. This automated reaction search is able to find 165 reaction paths from 333 searches for the reaction of NH3 BH3 and (LiH)4 , all without guidance from user intuition.
© 2015 Wiley Periodicals, Inc.

Entities:  

Keywords:  single-ended; string method; transition state

Year:  2015        PMID: 25581279     DOI: 10.1002/jcc.23833

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  23 in total

1.  Interrupted carbonyl-olefin metathesis via oxygen atom transfer.

Authors:  Jacob R Ludwig; Rebecca B Watson; Daniel J Nasrallah; Joseph B Gianino; Paul M Zimmerman; Ren A Wiscons; Corinna S Schindler
Journal:  Science       Date:  2018-09-28       Impact factor: 47.728

2.  Mechanistic Investigations of the Iron(III)-Catalyzed Carbonyl-Olefin Metathesis Reaction.

Authors:  Jacob R Ludwig; Susan Phan; Christopher C McAtee; Paul M Zimmerman; James J Devery; Corinna S Schindler
Journal:  J Am Chem Soc       Date:  2017-07-28       Impact factor: 15.419

3.  Nickel-Catalyzed Three-Component Cycloadditions of Enoates, Alkynes, and Aldehydes.

Authors:  Aireal D Jenkins; Michael T Robo; Paul M Zimmerman; John Montgomery
Journal:  J Org Chem       Date:  2020-02-14       Impact factor: 4.354

4.  Regiodivergent Glycosylations of 6-Deoxy-erythronolide B and Oleandomycin-Derived Macrolactones Enabled by Chiral Acid Catalysis.

Authors:  Jia-Hui Tay; Alonso J Argüelles; Matthew D DeMars; Paul M Zimmerman; David H Sherman; Pavel Nagorny
Journal:  J Am Chem Soc       Date:  2017-06-19       Impact factor: 15.419

5.  Lithium Diisopropylamide: Nonequilibrium Kinetics and Lessons Learned about Rate Limitation.

Authors:  Russell F Algera; Lekha Gupta; Alexander C Hoepker; Jun Liang; Yun Ma; Kanwal J Singh; David B Collum
Journal:  J Org Chem       Date:  2017-04-03       Impact factor: 4.354

6.  Discovery of conical intersection mediated photochemistry with growing string methods.

Authors:  Cody Aldaz; Joshua A Kammeraad; Paul M Zimmerman
Journal:  Phys Chem Chem Phys       Date:  2018-11-07       Impact factor: 3.676

7.  What Does the Machine Learn? Knowledge Representations of Chemical Reactivity.

Authors:  Joshua A Kammeraad; Jack Goetz; Eric A Walker; Ambuj Tewari; Paul M Zimmerman
Journal:  J Chem Inf Model       Date:  2020-03-03       Impact factor: 4.956

8.  Quantum Chemical Investigation of Dimerization in the Schlenk Equilibrium of Thiophene Grignard Reagents.

Authors:  Ethan R Curtis; Matthew D Hannigan; Andrew K Vitek; Paul M Zimmerman
Journal:  J Phys Chem A       Date:  2020-02-18       Impact factor: 2.781

9.  Fluoride Migration Catalysis Enables Simple, Stereoselective, and Iterative Glycosylation.

Authors:  Girish C Sati; Joshua L Martin; Yishu Xu; Tanmay Malakar; Paul M Zimmerman; John Montgomery
Journal:  J Am Chem Soc       Date:  2020-04-01       Impact factor: 15.419

10.  Catalytic Carbonyl-Olefin Metathesis of Aliphatic Ketones: Iron(III) Homo-Dimers as Lewis Acidic Superelectrophiles.

Authors:  Haley Albright; Paul S Riehl; Christopher C McAtee; Jolene P Reid; Jacob R Ludwig; Lindsey A Karp; Paul M Zimmerman; Matthew S Sigman; Corinna S Schindler
Journal:  J Am Chem Soc       Date:  2019-01-16       Impact factor: 15.419

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