Re: [sdpd] General questions/stuck

[paula vera-cruz <pauveracruz...@gmail.com>]

Hi Phill,
I don't have any experience with FOX or JANA2006, but I can recommend
EXPO2009. I have used this programm to solve difficult structures and it is
very easy and straight forward. It lets you start from scratch, index the
pattern and then add the atoms in the unit cell to find space group and
atomic positions.
I have a few tutorials that could help you. If you decide to give it a try
write to me and I will send them to you.
Regarding the problem of two long lattice constants and one short one,
although it is a way to know that the cell is wrongly indexed, this is not
always the case. I work with MOFs and in these type of structures you often
get cells where one lattice constant is significantly shorter that the
others. So to know if the cell is right or wrong you need to look at similar
structures and see if this could be possible. See if you can explain the
short cell lattice, for example in my case I have an organic chain of 5A, so
a lattice of 5A is acceptable, but anything shorter is questionable.
I hope all this helps.
Regards
Paula

2010/8/5 phillenglish7 <phillenglish7...@yahoo.com.au>

>
>
> Dear SDPD group,
>
> I stumbled onto this group from the back of the SDPD book by David et al.
> and I was wondering if some of you might be able to help me some
> difficulties I've been having completing a structural determination. I'm
> going to try to give as much detailed info as possible to give some context
> to my question, so I hope you'll forgive me if I bang on a bit. Also, this
> is the first time for me posting to a mailing group, so I hope I get the
> protocol right!
>
> * I'm looking at the structure of TiOSO4.2H2O, the dihydrate in the series
> of TiOSO4 and TiOSO4.H2O whose structures have been well known for some time
> now. My supervisors and I are reasonably sure that the TiOSO4.2H2O will
> contain the same motifs of Ti-O octahedra shared with SO4 tetrahedra as seen
> in the rest of the series and in analogues of Zr and Hf (so that's our
> 'chemical information').
> * I've collected two sets of laboratory X-ray diffraction patterns (an old
> Siemens and a newer machine installed last year at my university), two sets
> of synchrotron X-ray diffraction (from the APS and the Australian
> Synchrotron) and a relatively poor, but still possibly useful neutron
> diffraction pattern (deuterated). We are very confident that we have
> single-phase diffraction patterns.
> * Following the general recipe/method for SDPD, I've obtained a unit cell
> that has been indexed using multiple programs and has been verified by the
> beamline scientists at the two synchrotron institutions.
> * Using the 'space group explorer' in the program FOX, I've generated a
> list of possible spacegroups.
> * In both the FOX and JANA2006 programs, I've used the Le Bail method to
> generate a list of integrated intensities to be used in the FOX, superflip
> and EXPO2004 routines.
>
> Now, at this stage I fall down a bit. Looking at other papers of
> (relatively) similar structures, such as those in
> http://scripts.iucr.org/cgi-bin/paper?la0055 and
> http://pubs.acs.org/doi/abs/10.1021/ic00268a025 it seems they generated a
> Patterson map in order to determine the positions of heavy atoms. Now, I'm a
> bit of a newbie and I cannot for the life of me figure out how they did
> this. So the most basic of my questions is: how can I generate a Patterson
> map in either FOX or JANA2006? JANA2006 has the option of producing a
> Fourier map, but in order to do so I need to add atoms, which seems
> counter-intuitive. Quite confused on this issue. :/
>
> Detouring from Patterson maps a bit, I've also tried invoking the FOX
> reverse Monte Carlo technique and the JANA2006 Superflip method, but I've
> received nothing but nonsense answers thus far from them. My first thought
> was that the unit cell might be incorrect, and so I checked into ways in
> which indexing from a synchrotron can go wrong, and noticed a quote in the
> David SDPD book about there being issues if two of the lattice constants are
> very long and one is short, and the peak that has been used to determine
> that short lattice constant is spurious. I have a similar situation with my
> indexed unit cell, (a ~ 18Ang, b~16Ang, c~5Ang) and so was wondering how I
> might check for this?
>
> If anyone is interested enough in this problem to want to lend a helping
> hand in a more direct way, feel free to contact me at
> phill.english...@gmail.com <phill.english%40gmail.com> and I can provide any
> data files/extra info you might need. I am entering the final stages of my
> Ph.D., and while I would love to have the time to puzzle all these problems
> out myself and learn from them, I'm spending more time banging my head
> against walls than is useful at this point. That said, I am well aware that
> all of you are professionals with your own challenges to overcome, and
> demands on your time.
>
> Thank you for your time and I hope to hear from some of you soon,
>
> Phillip English
>
>  
>


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