Urea geometry input

For molecular crystals special optional geometry keywords are available. As an example the urea crystalline structure will be used to illustrate such keywords.

The crystal structure of urea has a tetragonal cell with four molecules in the unit cell (see figure below, on the left). The molecules are linked to each other through hydrogen bonds, so as to form infinite planar tapes. The arrangement of tapes is depicted in the figure below on the right. They are mutually orthogonal, the cohesion among them is provided by hydrogen bonds. Hence, each oxygen is involved in four nearly equivalent hydrogen bonds, two within the tape and two with neighboring tapes. Notice that the molecules within adjoining tapes are oppositely oriented with respect to the crystallographic c axis; this provides a further source of tape binding through dipole-dipole forces.
 

From crystallographic data to the CRYSTAL geometry input

As for MgO, let us start from crystallographic data. Structural data on carbon-containing crystals can be find either on specific databases such as the Cambridge Structure Database (CSD) or directly from research articles and books. In the following, urea crystallographic data are reported from both of resources.

CSD entry:
#UREAXX1243850207       10  9  0  0  0  8  4  5  3  0  8132200000110000000000084
  5565  5565  4684    90    90    90333000 1 1 1 0 0 0  0  0113P-421m    240
R=0.0250
211 0121 0112 0101 0211 0110 0011 0101 0112 0121 0011 0110 0011 6121 6110 0
121 6211 6112 0211 6101 6110 0101 6011 6112 0
C  68H  23N  68O  68
C1         0  50000  32600 O1         0  50000  59530 N1     14590  64590  17660
H1     25750  75750  28270 H2     14410  64410  -3800 N1B   -14590  35410  17660
H1B   -25750  24250  28270 H2B   -14410  35590  -3800
 2 0 1 3 3 1 6 6

Crystal data from a resource book of crystal structure:

CSD crystal data corresponds to the urea structure determined at 12 K. As noticed in the discussion on the reliability of crystallographic structural data, structures which have been solved at low temperature are to be preferred over those determined at room temperature.
In the table above you can assess the dependence of the crystal data upon the temperature.
Hence, by using the structural data obtained at 12K the CRYSTAL geometry input for urea can be prepared:
 
UREA BULK
CRYSTAL
0 0 0
113
5.565  4.684
5
6  0.0000      0.5000      0.3260
8  0.0000      0.5000      0.5953
7  0.1459      0.6459      0.1766
1  0.2575      0.7575      0.2827
1  0.1441      0.6441     -0.0380
EN


The above material is extracted from the CRYSTAL TUTORIAL PROJECT: Geometry Input.

Index