Options

There are a few options that could be applied in NEIGHBOURS.

• Pasting molecular structure in experimental crystal structure
  
  
  
• Standardising bond lengths
  
  
  
• Atom types
  
  

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.

2. Optimise the molecular structure in CADPAC (or GAUSSIAN) to give an ab initio molecular structure.

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

TITLE
NMOLECULES NATOMS NATOMS
(5 Blank Lines)

I4,7X,A4,3F13.6
Index, Label, Coordinates

(5 Blank Lines)

I4,7X,A4,3F13.6
Index, Label, Coordinates

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.
example_paste_format

Here is an example running NEIGHBOURS to insert paste file:


prompt> neigh3.01

TYPE I FOR INTERACTIVE MODE

i

File name containing basis set ?

file.fdat

Filename differs from csd refcod, interactive mode

Used
cutoff
as file with standard bond lengths
Maximum required inter-molecular contact?
4.0
nbonds= 2
Do you want to standardise bond lengths to hydrogen?
n
Do you wish to insert any bond centre sites (Y/N) ?
n
CVECTOR
8.470000000000001

Input zero for no symmetry subgroup or n to remove representation n
0
Do you have a punch file yet (y/n)
y
File name for punch file
file.punch
Labelled basis to be written to
pyrene.dmain
This file will be overwritten
Do you have an axis definition file?
y
Enter filename for axis definition file.
axes
Do you want to paste coordinates?
y
Enter filename for coordinate pasting file.
paste_dataset
Do you have a potential input file?
y
Enter filename for potential input file.
potential.dat
Labelled nearest neighbour list to be written to file.nnl
This file will be overwritten
Labelled close contact list to be written to file.ccl
This file will be overwritten
MACROMODEL file to be written to file.mac
This file will be overwritten
NEMESIS file to be written to file.nem
This file will be overwritten

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.

Subroutine FUNGRP will recognise a number of additional functional groups, but no bond length is reset. Modifications can be made in the subroutine NORMBL for automatic normalising the bond lengths for the atom types below.

Below is a list.
101 H SP3 C
102 H SP1 C
103 H SP C
201 H N Ammonium NH4+ derivative
202 H N Ammonia NH3 derivative
301 H O SP3 C (alcohols etc)
302 H O Carboxylic acids
303 H O Other SP2 C (Phenols etc)
311 Water
401 Nitro group

The following tables show the default atom types available. If additions need to be made, modifications can be done in the subroutine SETMAS.