Subject: Re: CCL:Crystal structure vs geometry optimised structure

From: noel.oboyle2..at..mail.dcu.ie
Date: Tue, 29 Jul 2003 14:46:50 +0100

Hello,
Thanks to everybody who sent a reply to my query (see below) on whether
it is better to use crystal structures or DFT-optimised geometries for DFT
calculations (energy, orbitals, TD-DFT).

Overall, the general consensus seems to be that although it may be interesting
to calculate and compare the energies of the two structures, frequency calculations
may only be performed at a minimum (of the same level of theory).

One point which was not addressed was whether TD-DFT calculations must also
be performed at a minimum. Anybody care to comment?

Noel

Original Query:
**************

Hello CCLers,
I intend to carry out DFT calculations on inorganic complexes. In some cases
I have crystal structures available.

Is it better to use crystal structures as a starting point for energy and
frequency calculations, or to use DFT-optimised structures? (where the DFT-optimised
structure is in excellent agreement with the crystal structure)

Thanks,
Noel O'Boyle
Han Vos Research Group,
Dublin City University.
http://www.dcu.ie/~chemist/Staffpages/han_vos.htm

**************

Replies:
--------------

It depends on what kind of crystal structures you are using, if they 
are for proteins,
you will have to accept an experimental accuracy of 0.1-0.3 Angstroms; 
for smaller
inorganic complexes you might be better off with the accuracy.

If the complexes are not too big, I'd use both as starting point, see 
how much they are
alike, and calculate the freqs for both structures, and see which ones 
agree better with
experiment.

Marcel Swart <swart..at..chem.vu.nl>

--------------

If the minimized structure is indeed in "excellent" agreement with the
crystal structure, it is probably better to work from there. However, in
my
recent experience, you have to be very careful with the minimized
structures, as they may have lost some subtleties of the crystal structure.
You may want to do a test with the crystal structures you do have. Calculate
the molecular propertied you are interested in for the crystal and minimized
structures. If they are not terribly different than I would use the
minimized ones. If they are very different, than you have to give some
thought about why they are different and what that is telling you about
the
system.

Joslyn Kravitz
University of Michigan

"Joslyn Kravitz" <jyudenfr..at..umich.edu>

--------------

For doing frequency calculations, you will want to use the DFT
optimized structures, as the calculation won't be very meaningful
otherwise. You should only be calculating frequencies at a minimum.

If your DFT structures are in excellent agreement with your crystal
structures, you are probably better off using the DFT optimized
structures for energy comparisons as well. Of course, if in certain
cases your DFT optimized structures were fundamentally different from
the crystal structures, the DFT energy comparison might not make much
sense if you are trying to examine the energetic differences between
your (crystal) samples.

  Hope that helps - John

John Bushnell <bushnell..at..chem.ucsb.edu>

--------------

I have not worked with crystal structures of inorganic compounds but have
used crystal structures of organic compounds from the Cambridge
Crystallographic Database. The older structures often have to be treated
with caution. First, the coordinates of hydrogen atoms are missing. Many
modeling programs allow one to add the missing hydrogens. After that I
usually perform a geometry reoptimization. With organic compounds, I'll
stop at the HF level with a 3-21G* basis set and then perform single-point
calculations of the energy at higher levels of theory such as DFT.

Wayne E. Steinmetz
Coordinator of Molecular Biology
Carnegie Professor of Chemistry
Woodbadge Course Director
Chemistry Department
Pomona College
645 North College Avenue
Claremont, California 91711-6338
USA
phone: 1-909-621-8447
FAX: 1-909-707-7726
Email: wsteinmetz..at..pomona.edu
WWW: pages.pomona.edu/~wsteinmetz

--------------
Hello,

It is probably not a good idea to use experimental geometries for freq calc's,
because
freq calc's are strictly valid only at the geometry obtained by the same
method as the
freq calc. Thus a B3LYP/6-31G* freq calc should be done on a geometry obtained
by a
B3LYP/6-31G* optimization. Since your freq jobs are likely to be about as
long or longer
than any geom optimizations, you probably won't lose very much time by doing
the
optimizations first.
Another problem with crystal structures is that they may differ significantly
> from the
isolated molecule structures that I presume you will use for your freq jobs
(you won't
use a crystal lattice as input, I guess); but you took account of this by
saying "where
the DFT...is in excellent agreement..."
It would be interesting to do some freq calc's on both DFT-opt and experimental
structures and see how much they differ. But conventional wisdom is that
the DFT-opt
structures are the ones to use.

If you didn't want freqs, just relative energies of isomers, you could do
single-point
calculations (much faster than optimizations) on the experimental structures.
Again, it
might be interesting to compare relative energies based on the experimental
and the
DFT-opt structures.

E. Lewars

elewars <elewars..at..trentu.ca>

--------------

Hi Noel

Before carrying out a frequency calc it is essential that you have optimised
the geometry at the same level of theory. Therefore you can start with
either your crystal structure or your previously optimised structure.

Regards

Roma

"Roma Oakes" <r.e.oakes..at..btconnect.com>

--------------

Hai,
It is better to use x-ray straucture. Because, u need to compare the dft
results with experiments. In DFT, u need to chose a correct functional for
ur calculation. If u use the x-ray structure, u can validate the correct
functional by comparing with x-ray co-ordinates.
 
Cheers, Mahesh

Mahesh Sundararajan, 
C/O. Prof. Ian. H. Hillier
Ph.D Student, Theoretical & Computational Chemistry Group,
Department of chemistry, 
Oxford Road, The University of Manchester. 
Manchester - M13 9PL, UK 
07734321159, 0161 4480531

--------------

Hmm... I am not sure I understand you correctly....

You want to perform energy and frequency calculations only?

which structure (crystallographic or computational) is better for energy
calculations depends on your problem

but I do really not know how to use crystallographic geometry (without
geometry optimization???) in case of frequency calculations

Of course if you want to obtain only "real" frequencies

<zborowsk..at..chemia.uj.edu.pl>

--------------

Dear Noel

There have been some papers -- eg by Buntine at University of Adelaide
and one by my co-workers -- in which the difference between
the energies of the (optimised) gas-phase structures
and those of the crystal structures are interpreted as crystal
packing energy costs.

eg:
J. Beckmann, K. Jurkschat, M. Sch|rmann, D. Dakternieks, A. E. K. Lim 
and K. F. Lim, "Comparison of the flexibility of eight-membered 
tetrasiloxane and stannasiloxane rings: A crystallographic and 
computational study", Organometallics, 2001, 20 (24), 5125-5133 
<http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/om010620o> 
.

Kieran

------------------------------------------------------------
  Dr Kieran F Lim Biol. and Chemical Sciences
    (Lim Pak Kwan) Deakin University
  ph: + [61] (3) 5227-2146 Geelong VIC 3217
  fax: + [61] (3) 5227-1040 AUSTRALIA
  mobile phone: 0438 350 259 (within Australia)
  mailto:lim..at..deakin.edu.au http://www.deakin.edu.au/~lim
------------------------------------------------------------