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.
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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:
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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 |