Abstract
A general procedure of crystal packing reconstruction using a certain number of intermolecular interactions is introduced and demonstrated on the crystal structure of l-histidine·HCl·H2O. Geometric restrictions based on intermolecular interactions are used for formation of a molecular pair as a basic repetitive motif of the crystal packing. The geometric restrictions were applied gradually within a supervised procedure, narrowing the scope of possible arrangement of two adjacent molecules. Subsequently, a pair of histidine molecules was used for construction of a molecular chain. The chain formed contained translation information on histidine molecules in one dimension, which coincided with one of the cell parameters. Furthermore, the periodicity in the second and third dimensions can be accomplished by chain assembly into sheets (2D), and sheets can be arranged into the final 3D structure. For this purpose, the rest of the available intermolecular interactions could be used to control the mutual assembly of molecular chains and sheets. Complete molecular packing would enable derivation of standard crystallographic parameters that can be used for verification of the structural model obtained. However, the procedure described for construction of the whole 3D structure from molecular chains was not attempted, and is only briefly outlined here. The procedure described can be employed especially when standard crystallographic parameters are not available and traditional methods based on X-ray diffraction fail.
Highlights
X-ray structure analysis has an irreplaceable role in the determination of crystal structures of organic compounds, as supported by almost a million entries in the Cambridge Structure Database (CSD) [1]
When examining the data found in ref. [16] closely, the most information on involvement in intermolecular interactions was obtained for the imidazole moiety of the histidine molecule (Table 1)
The rest of the intermolecular interactions described belong to the interaction between the imidazole moiety and the CH2 group (H8···H3) and 3 interactions of histidine with water molecules trapped in the crystal lattice (H1···w, H5···w, H8···w)
Summary
X-ray structure analysis has an irreplaceable role in the determination of crystal structures of organic compounds, as supported by almost a million entries in the Cambridge Structure Database (CSD) [1]. Regarding single crystal X-ray analysis, the final structure is obtained in several steps performed in a specific order [2]. The chosen single crystal is mounted in a diffractometer, and within a few minutes, several diffraction frames are acquired. Based on the reflection positions, unit cell parameters are calculated, revealing the crystal system. The accuracy of the cell parameters rises with the number of acquired reflections. A particular space group of the system is proposed
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