[CPMD-list] transition state of a molecule

[Erik Emilio Santiso]

Dear Martin,

What I have done in similar cases (searching for TS in a rotational 
isomerization) is to change the torsion angle by hand to a value that 
would be close to the maximum (in this case probably 90 degrees), and run 
a geometry optimization with the torsion angle constrained to this value. 
Then run a vibrational analysis, check that there is an imaginary 
frequency (or at least that the softest mode corresponds to the torsion) 
and then run the PRFO re-using the Hessian from the vibrational analysis. 
This usually works well.

The only thing that worries me about your molecule is that it looks very 
similar to 2-butene (i.e., a double bond in the middle). When the molecule 
rotates you will break the double bond and end up with a diradical, which 
is tricky to model properly. I remember testing this with 2-butene a while 
ago, and what you get (even with LSD) is a much lower barrier than the 
real one. If anybody in the list has a suggestion on how to handle this 
particular problem, I'd like to hear about it too. Thanks!

Erik Santiso.

On Fri, 15 Jul 2005, Martin Konopka wrote:

> Dear CPMD community,
>
> I am trying to locate a transition state of the CH3-N-N-CH3 molecule
> using the P-RFO optimizer. However, I can not see any progress towards
> the expected TS. The molecule essentially remains in its starting
> structure. In more details, the molecule has two isomers,
>
>  the cis one:           the trans one:
>
>                                    C
>                                   /
>   N ------ N                     /
>    /      \             N ------ N
>   /        \             /
>  C          C           /
>                        C
>
> and a potential energy barrier between them. I am mostly starting from
> the slightly randomized cis structure and trying to locate the top
> of the barrier. I tried several choices for reaction core and mode to be
> followed. Regardless of setting the mode, the result remains the same and
> unsatisfactory. In some cases the atoms in the reaction core do not move
> at all (for example in a special case when I started from a
> hand-modified configuration presumably closer to the TS.)
>
> I would greatly appreciate some hint to this problem.
> Below is my input file and modes from vibrational analysis.
>
> I tried the 4th, 7th, 10th mode and also the 1st one, which is the
> default. I also have a question: If I use, for example
> PRFO MODE
> 10
> does it really mean that the mode corresponding to the 10th frequency of
> vibrational analysis is followed? If yes, then using PRFO MODE less than
> 7 (or 6 in special cases), which is the default, would have no sense since
> it corresponds to overall translations or rotations. Or do I
> misunderstand something?
>
>
> &CPMD
>  OPTIMIZE GEOMETRY XYZ
>  INITIALIZE WAVEFUNCTIONS ATOMS
>  RANDOMIZE COORDINATES
>   0.1D0
>  RESTFILE
>    4
>  STORE
>    100
>  LBFGS
>  PRFO MODE
>    10
>  PRFO CORE=4
>    1 2 9 10
>  CONVERGENCE
>    5.0D-7 5.0D-5
>  CONVERGENCE RELAX
>    15
>  SPLINE POINTS QFUNCTION
>    2001
>  ISOLATED MOLECULE
>  CENTER MOLECULE OFF
>  MEMORY BIG
>  LSD
> &END
>
> &DFT
>  FUNCTIONAL PBE
>  GC-CUTOFF
>    5.0D-5
> &END
>
> &SYSTEM
>  SYMMETRY
>    0
>  POISSON SOLVER TUCKERMAN
>  ANGSTROM
>  CELL
>    10.0D0  1.0D0  1.0D0  0.0D0  0.0D0  0.0D0
>  CUTOFF
>    25.0D0
>  MULTIPLICITY
>    1
> &END
>
> &ATOMS
> *N.uspp_ascii FORMATTED
>   LMAX=P
>    2
>     4.525338176055      4.920747785642      4.949904563339
>     5.765416638683      5.048851794396      5.079925564279
> *H.uspp_ascii FORMATTED
>   LMAX=S
>    6
>     4.265466440716      2.788011128505      4.858413782037
>     2.878604693260      3.791408955331      4.306112314885
>     4.333398001463      3.598265838244      3.267273093363
>     6.467823612522      3.016976904998      5.093103687689
>     6.554809448253      3.823511424486      3.501228774397
>     7.703325625270      4.291321957329      4.803526469019
> *C.uspp_ascii FORMATTED
>   LMAX=P
>    2
>     3.972567677301      3.700817361171      4.307476081948
>     6.672717274443      3.979768413937      4.589493362517
> &END
>
>
> vib. ana. for the optimized cis structure, after purification:
>
> HARMONIC FREQUENCIES [cm**-1]:
>
>          0.0000          0.0000          0.0000          0.0000
>          0.0000          0.0000         89.1253        160.4933
>        342.9720        461.3605        603.3003        854.8066
>        894.5454        918.9702       1033.3395       1041.1772
>       1122.1006       1310.9720       1322.4554       1397.1613
>       1406.4886       1414.6120       1437.0546       1535.1880
>       2896.9570       2900.3452       2961.5598       2972.3951
>       3036.4163       3036.7126
>
> (The 10th mode, 461.3605 cm^-1 is particularly interesting since it
> changes the dihedral angle of CNNC.)
> I also attach my output file for convenience.
>
> Thanks.
> Martin Konopka.
>