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Finding the transition state without initial guess: The growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine
Author(s) -
Quapp Wolfgang
Publication year - 2007
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20688
Subject(s) - isomerization , chemistry , transition state , dipeptide , maxima and minima , potential energy surface , helix (gastropod) , reaction coordinate , string (physics) , enantiomer , computational chemistry , curvilinear coordinates , state (computer science) , crystallography , stereochemistry , physics , mathematics , quantum mechanics , molecule , algorithm , mathematical analysis , catalysis , peptide , ecology , biochemistry , organic chemistry , snail , biology
We report a new, high‐dimensional application of a method for finding a transition state (TS) between a reactant and a product on the potential energy surface: the search of a growing string along a reaction path defined by any Newton trajectory in combination with the Berny method (Quapp, J Chem Phys (2005), 122, 174106; we have provided this algorithm on a web page). Two given minima are connected by a one‐dimensional, but usually curvilinear reaction coordinate. It leads to the TS region. The application of the method to alanine dipeptide finds the TS of the isomerisation C 7 ax → C 5 , some TSs of the enantiomerisation of C 7 ax from L ‐form to quasi‐ D ‐form, and it finds the TS region of a transition of a partly unfolded, bent structure which turns back into a mainly α‐helix in the Ac(Ala) 15 NHMe polyalanine (all at the quantum mechanical level B3LYP/6‐31G: the growing string calculation is interfaced with the Gaussian03 package). The formation or dissolvation of some α‐ or 3 10 ‐hydrogen bonds of the helix are discussed along the TS pathway, as well as the case of an enantiomer at the central residue of the helix. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007