5
$\begingroup$

I have been working on a CIF data file based on experimental data [1] (free full text isn't available, but the page 2 with the experiment details can be found in the free preview provided by Springer).

Unfortunately, I don't know an awful lot about crystallography parameters (although I have been consulting the CIF core dictionary). The CIF file I linked to was created using EnCIFer & VESTA (I mostly used VESTA to get a handle for the text formatting of CIF files). The non-coordinate data mentioned in this paper includes:

\begin{array}{ll} \hline Z & 4 \\ \text{Formula} & \ce{C9H7N7O2S} \\ M_r & 277.3 \\ \text{Coordinate system} & \text{monoclinic} \\ \beta & 105.99^\circ \\ a & \pu{4.488(2) Å} \\ b & \pu{31.886(4) Å} \\ c & \pu{8.067(2) Å} \\ V & \pu{1149.5 Å^3} \\ D_m & \pu{1.59 mg mm^{-3}}\\ D_c & \pu{1.60 mg mm^{-3}} \\ \lambda & \pu{0.7107 Å} \\ \text{Space group} & P2_1/c \\ \text{Crystal dimensions} & 0.7\times 0.1 \times 0.7\, \pu{mm} \\ \hline \end{array}

The problem is that Accelrys DS Visualizer so far renders my CIF file as:

enter image description here

Notice how some of the hydrogen atoms are disconnected from the main chunk of the azathioprine molecule.

  1. Acharya, K. R. Proc. Indian Acad. Sci. (Chem. Sci.) 1984, 93 (2), 183–187 DOI: 10.1007/BF02842141.
$\endgroup$
6
$\begingroup$

The coordinates of the hydrogen atoms of the methyl group in question are there (H16a, H16b, H16c).

The problem is a rendering problem of the Accelrys visualizer.

Other tools don't have a problem with this CIF file. The image below is a medium-quality PovRay rendering generated through PLATON. enter image description here

|improve this answer|||||
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.