We report a new 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 (W.Quapp, J.Chem.Phys. 122 (2005) 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. An application of the method to alanine dipeptide finds the TS of the isomerisation C_{7ax} --> C_5, some TSs of the enantiomerization of C_{7ax} from L-form to D-form, and it finds a TS defile 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 is discussed along the TS pathway, as well as the case of an enantiomer at the central residue of the helix.
Figure: Approximation of NTs for alanine dipeptide between the
C_{7ax}-minima in L- and D-form,
and an intermediate minimum, for enantiomerization.
Method: modified CG+ optimization. 30 nodes are used for every of the two
parts, and thresholds $\epsilon$=0.009.
The chain of points approximating the reaction path (for molden- movie)
Alanine Dipeptide RP
Files for alanine dipeptide GS-NT Calculation.
Script : scriA22 Growing String
method for Newton Trajectories with modified CG+ in Cartesians,
for the alanine dipeptide molecular potential (22 atoms).
Use still #!/usr/local/bin/bash in the first line.
Gaussian03 call: CallGaussian03
Programs:
Fortran90 : Program1
Fortran90 : Program2
Fortran90 : Program3
Program 4 is the Gaussion03 PP
Fortran90 : Program5
Help-program: NumberCount in Corrector
Translate separately the parts with fort90 .
The point files are in xyz format: C7ax ,
Intermediate min
The point files are in zmat format: C7ax ,
Intermediate min
Note: here the numbering is different from that in Ref.21, G.A.Chass et al.
Output of the calculation: text
Figure: Poly(15)alanine in alpha-helix and bent structure
The chain of points approximating the reaction path (for molden- movie) Poly(15)Alanine RP
Files for alanine dipeptide GS-NT Calculation.
Script : scriStartPoly scriCorrPoly scriPredPoly Growing String method for Newton Trajectories with modified CG+,
under z-matirx coordinates, the interplay between Corrector (in Cartesians) and Predictor(in z-matrix coordinates) is done by Molden4.4
Use still #!/usr/local/bin/bash in the first line.
Fortran90 : Program1
Fortran90 : Program2
Fortran90 : Program3
Program 4 is the Gaussion03 PP
Fortran90 : Program5
Help-programs: NumberCount1 in Corrector NumberCount2 in Corrector
Translate separately the parts with fort90 .
The point files are in xyz format: bend , alpha-helix
The point files are in zmat format: bend , alpha-helix
Further Help-programs after use of Molden4.4 for conversion into Gaussian input:
CentreOfMass and SymbolsToNumber in xyz file
Last updated: 19. 10. 2006, W.Q.