Structure Solution – Organics
Files needed: rod_solve_02.inp, d8_00796.RAW and those listed below.
Learning outcomes: Topas has lots of different methodologies built in for solving structures using simulated annealing. The approach used is to combine random movements of atoms/groups with rapid refinement of diffraction data. One can anneal coordinates of individual atoms or groups of atoms expressed as rigid bodies or using z-matrices. One can refine against powder or single crystal data. Powder data can be expressed as “pseudo single crystal data” by just considering peak intenisities in a number of ways.
Methodology: In this tutorial we’ll look at the rigid rod molecule that we used in an earlier example and some of the built in examples in topas. These can be found in the “TOPAS-Academic, INP format” menu under “Structure solution”. So that you don’t overwrite these/create any errors it’s probably safest to copy files to your area. They’re linked below.
1. Save the two files listed above to your area. These are on the same example as we looked at for restrained and rigid body refinements of a simple organic molecule. rod_solve_02.inp is set up to find the positions and angles of the rigid body using simulated annealing.
2. Save cime-decompose.inp and cime.xdd to your area. This example uses z-matrix formalism and attempts structure solution using a pattern which has been “decomposed” for speed.
3. Save cime-z-scr.inp and cime.scr to your area. This example uses a single crystal like pattern extracted by initial pawley fitting with the file cime_pawley.inp.
4. Save ae1-auto.inp. and ae1.hkl to your area. This example uses single crystal data to attempt to solve an organometallic species.