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.
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 alpha-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 alpha- 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.
Quapp
Wolfgang
W
Mathematical Institute, University of Leipzig, Augustus-Platz, D-04109 Leipzig, Germany. quapp@rz.uni-leipzig.de
D004151:Dipeptides / Q000737:chemistry*; D007536:Isomerism; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D013237:Stereoisomerism
D004151:Dipeptides; D010455:Peptides; C019529:polyalanine