Morphology calculations![]() |
|||
![]() |
![]() |
![]() |
![]() |
Morphology and Powder Pattern calculationThe computational tools were developed by Dr David S Coombes funded by the E-Science project. The attachment energies and surface energies for the crystal structures
are calculated using the same repulsion-dispersion potential used in the
search (e.g. fit.pots, unless an anisotropic potential was used, in which
case a corresponding isotropic exp-6 potential must be used) and the potential
derived charges corresponding to the same wavefunction used for the DMA.
The calculated attachment energy morphologies are not very sensitive to
differences in the potential1 and hence this approximation, or ignoring
changes in the charges with minor changes in conformation is adequate
within the errors of the attachment energy model. The potential derived
charges in molecule.pdc have the format in this example 5azauracil.pdc The calculations uses the BDFH method (calculated by GDIS) to identify the most important faces, and then MARVIN2 to calculate the surface and attachment energies for these unrelaxed faces. By assuming that the proportionality between attachment energy and growth rate is the same for different crystals of the same molecule, a relative growth rate is also calculated by integration over the crystal volume3. (NB this assumes that there are no visible faces with AE’s of <-99.9 kJ/mol) Note that the quoted growth volumes are only relative, and scaled relative to a cube in which each face has an AE of 5 kJ/mol (i.e. volume is 1000 (kJ/mol)3 ) This information is stored in the structure.gv output file in a format that can be uploaded to the database and portal. The attachment energy model is based only on the crystallographic symmetry and the interactions between the molecules (i.e. absolutely no reference to solvent, and assumes a growth and spread mechanism below the roughening temperature) and so should be best at predicting the vapour grown morphology when the growth unit is the content of the asymmetric unit of the cell. Hence, comparing results between Z’=1 and other Z’ structures is not really valid and should be done with caution (and with an extended .pdc file). The growth volume and morphology data will therefore not usually be included in the database for symmetry reduced structures. The other input files are .res (Shelx files). The system can handle either the standard .res files (i.e. C1 type, though note that it currently needs chlorine as Cl etc) or the old style fort.16 outputs of CAR1 etc type. (The automatically discriminates between these file formats) The atomic types handled are C, H, N, O, S, F, Cl, Br and the program will identify HY, HP atomic types. The program will only deal with this set of atomic types. Note that the program uses the DMAREL system and needs to match the CAR3, HPD1 etc with those in the charges file in the same order, and have all the potentials defined as in DMAREL. The *.gin file reveals any problems with the identification of atomic types. The procedure also uses the input structure file to create a .spf file with the correct space group label, by using http://cci.lbl.gov/cctbx/shelx.html to convert the symmetry cards to the space group label. Since this step can only be performed through internet access, this step may need to be done separately from the bulk of the calculations. The powder pattern corresponding to a radiation of wavelength of 1.54056 Å, is also calculated using ObjCryst++, as part of the procedure. This result is tabulated in the structure.pp file, for upload to database and dataportal. Both the calculated morphologies and the powder patterns can be visualised, requiring the files structure.final.gmf for morphologies and .pdf or .svg for powder patterns. INSTRUCTIONS FOR PERFORMING MORPHOLOGY PROPERTIES CALCULATIONS
VISUALISATION for morphologies This can be done using the PC version of GDIS which can be downloaded
from ftp://ftp.seul.org/pub/gdis/ From Xenon Then type open and browse to find the .gmf file. STORAGE for DATABASE and DATAPORTAL For upload to database, need The Aspect Ratio is not yet programmed in, and there are still formatting problems with reading in the powder pattern. In addition, for upload to dataportal desire to keep all morphology &
powder pattern files together, hence Reference List 1. M. Brunsteiner and S. L. Price, Cryst. Growth Des., 2001, 1, 447-453. | |||
© UCL Chemistry Department 2022. This page was last updated on 17 August, 2022. If you have any problems with this page please email the WebMaster |