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["Nuno A. G. Bandeira" <nuno.bandeira@ist.utl.pt>]

radu.baies@gmail.com wrote:
> Hi
> A new cooper acidic phospate was synthetized
> Its structure was solved ab-initio by x-ray powder diffraction
> All atoms was located except for hydrogen atoms
> Can I use abinit to find the positions for hydrogens?

Good crystallographers can already provide good guesses to where 
hydrogens should be even though you can't "see" them with xray 
diffractograms.

Do you actually know how many hydrogens you have in this compound ? 
Acidic phosphate can mean HPO4(2-) or H2PO4(-).

In principle to do what you ask all you need is to create a good model, 
optimise the structure and then calculate the frequency intensities to 
check if it's a true energy minimum (no negative or imaginary frequencies).

In practice it's not so easy to do this because you may have many 
conformational minima or transition states. Think of the ethane 
conformational barrier. Now if you do a conformational analysis of 
hexacoordinated metal complexes with hydrogenated ligands such as 
ammonia [M(NH3)6] or acetonitrile [M(NCCH3)6] then you're likely to run 
into several stationary points.
You can either perform molecular dynamics computations to find all the 
minima or, in your case, if you have experimental data you compare the 
final optimised structure with the xray structure and if it's a close 
match you got lucky. It helps that these conformational barriers are 
usually energetically very small (less than 10 kJ/mol) because the 
hydrogens are usually far apart from each other within the same molecule.


Regards,

--
Nuno A. G. Bandeira, AMRSC
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group,
Faculty of Science
University of Lisbon - C8 building, Campo Grande,
1749-016 Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html
Doctoral student @ IST,Lisbon
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