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Options There are a few options that could be applied in NEIGHBOURS. |
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Pasting
molecular structure in experimental crystal structure |
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Pasting is an option, where an ab intio molecular structure can be pasted into an experimental crystal structure in the same axis system. For example using experimental molecular structure and optimised it using an ab initio program such as CADPAC (or GAUSSIAN). The opposite could also be done, that is pasting in an experimental molecular structure into an ab initio optimised crystal structure. An example of this is when a blind prediction is needed, when the experimental structure is known, in order to check that the predicted structure is of reasonable quality, the experimental molecular structure can be pasted into the predicted structure for minimisation. The procedures
are as follow: 1. Run NEIGHBOURS
using the CSD
FDAT (or SHELX)
to get the molecular structure in the local axis system from the output
file fort.21. 3. Use the
ab initio molecular structure to calculate a new DMA punch file
in CADPAC
(or GAUSSIAN
with GDMA). 4. Run NEIGHBOURS
again (See below). The format of the paste input dataset is
I4,7X,A4,3F13.6 (5 Blank Lines) I4,7X,A4,3F13.6 NMOLECULES is the number of molecules in the unit cell. NATOMS are the corresponding number of atoms for each molecule. The
second set of labels and coordinates are for the inverted molecule for
which the z coordinate has the sign changed. The coordinates are input
in AU. Here
is an example running NEIGHBOURS to insert paste file: TYPE I FOR INTERACTIVE MODE i File name containing basis set ? file.fdat Filename differs from csd refcod, interactive mode
Input zero for no symmetry
subgroup or n to remove representation n
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Standardising
bond lengths |
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Standardising bond lengths is needed where the C-H bondlengths in the experimental crystal structure (all are 0.950 Å) must be corrected to the standard 1.08Å, as X-ray diffraction has reduced the C-H bondlengths. (See - F.H. Allen,
O. Kennard,
D. G. Watson, L. Brammer, A. G. R. Orpen, "Tables of bond lengths
determined by X-Ray and neutron diffractions. Part 1. Bond lengths in
organic compounds.", 1987, J. Chem. Soc. Perkin Trans., 2,
S1-S9.) Currently only C...H, N...H, O...H and water are recognised and set to a standard length, of 1.08 Å, 1.01 Å and 1.02 Å respectively.
Below is a list. |
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Atom
types |
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The following tables show the default atom types available. If additions need to be made, modifications can be done in the subroutine SETMAS.
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