Literature DB >> 27107577

Kudi: A free open-source python library for the analysis of properties along reaction paths.

Stefan Vogt-Geisse1,2.   

Abstract

With increasing computational capabilities, an ever growing amount of data is generated in computational chemistry that contains a vast amount of chemically relevant information. It is therefore imperative to create new computational tools in order to process and extract this data in a sensible way. Kudi is an open source library that aids in the extraction of chemical properties from reaction paths. The straightforward structure of Kudi makes it easy to use for users and allows for effortless implementation of new capabilities, and extension to any quantum chemistry package. A use case for Kudi is shown for the tautomerization reaction of formic acid. Kudi is available free of charge at www.github.com/stvogt/kudi.

Entities:  

Keywords:  Conceptual DFT; IRC; Python; Qunatum chemistry library; Reaction electronic flux; Reaction path following

Year:  2016        PMID: 27107577     DOI: 10.1007/s00894-016-2983-3

Source DB:  PubMed          Journal:  J Mol Model        ISSN: 0948-5023            Impact factor:   1.810


  22 in total

1.  Accurate reaction paths using a Hessian based predictor-corrector integrator.

Authors:  Hrant P Hratchian; H Bernhard Schlegel
Journal:  J Chem Phys       Date:  2004-06-01       Impact factor: 3.488

2.  Fine structure in the transition region: reaction force analyses of water-assisted proton transfers.

Authors:  Diana Yepes; Jane S Murray; Juan C Santos; Alejandro Toro-Labbé; Peter Politzer; Pablo Jaque
Journal:  J Mol Model       Date:  2012-06-26       Impact factor: 1.810

3.  The reaction force constant: an indicator of the synchronicity in double proton transfer reactions.

Authors:  Diana Yepes; Jane S Murray; Peter Politzer; Pablo Jaque
Journal:  Phys Chem Chem Phys       Date:  2012-07-10       Impact factor: 3.676

4.  Reaction Path Following with Sparse Interpolation.

Authors:  James Nance; Elena Jakubikova; C T Kelley
Journal:  J Chem Theory Comput       Date:  2014-08-12       Impact factor: 6.006

5.  The role of reaction force and chemical potential in characterizing the mechanism of double proton transfer in the adenine-uracil complex.

Authors:  Bárbara Herrera; Alejandro Toro-Labbé
Journal:  J Phys Chem A       Date:  2007-06-13       Impact factor: 2.781

6.  Reaction electronic flux: a new concept to get insights into reaction mechanisms. Study of model symmetric nucleophilic substitutions.

Authors:  Eleonora Echegaray; Alejandro Toro-Labbé
Journal:  J Phys Chem A       Date:  2008-10-23       Impact factor: 2.781

7.  Transition-path theory and path-finding algorithms for the study of rare events.

Authors:  Weinan E; Eric Vanden-Eijnden
Journal:  Annu Rev Phys Chem       Date:  2010       Impact factor: 12.703

8.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1988-01-15

9.  A fast tomographic method for searching the minimum free energy path.

Authors:  Changjun Chen; Yanzhao Huang; Xuewei Jiang; Yi Xiao
Journal:  J Chem Phys       Date:  2014-10-21       Impact factor: 3.488

10.  The reaction force constant as an indicator of synchronicity/nonsynchronicity in [4+2] cycloaddition processes.

Authors:  Diana Yepes; Oscar Donoso-Tauda; Patricia Pérez; Jane S Murray; Peter Politzer; Pablo Jaque
Journal:  Phys Chem Chem Phys       Date:  2013-05-21       Impact factor: 3.676

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