Crystallography of vitamin B12 proteins

This review deals with results from crystallographic studies on proteins that interact with the essential micronutrient cobalamin (vitamin B12). Both B12-dependent enzymes and B12-transport proteins are described with an emphasis on structural aspects of cobalamin and its protein environment.     

Molecular Structure of trans-4-p-Tolylcyclophosphamide

The ‘trans’ assignment to the slower eluting diastereomer of 4-p-tolylcyclophosphamide is confirmed with a direct structure determination by X-ray crystallography. The compound crystallizes in the monoclinic space group P2,/c with Z=4 and cell dimensions a=11.636(4), b=12.394(5), c= 11.819(5)Å, β=93.9(3)°. Final R and R are 0.063 and 0.063, respectively.     

Vibrational spectra and crystal structure of the di‐amino acid peptide cyclo(L‐Met‐L‐Met): comparison of experimental data and DFT calculations

Experimental Raman and FT‐IR spectra of solid‐state non‐deuterated and N‐deuterated samples of cyclo(L ‐Met‐L ‐Met) are reported and discussed. The Raman and FT‐IR results show characteristic amide I vibrations (Raman: 1649 cm⁻¹, infrared: 1675 cm⁻¹) for molecules exhibiting a cis amide conformation. A Raman band, assigned to the cis amide II vibrational mode, is observed at ∼1493 cm⁻¹ but no IR band is observed in this region. Cyclo(L ‐Met‐L ‐Met) crystallises in the triclinic space group P1 with one molecule per unit cell. The overall shape of the diketopiperazine (DKP) ring displays a (slightly distorted) boat conformation. The crystal packing employs two strong hydrogen bonds, which traverse the entire crystal via translational repeats. B3‐LYP/cc‐pVDZ calculations of the structure of the molecule predict a boat conformation for the DKP ring, in agreement with the experimentally determined X‐ray structure. Copyright © 2009 John Wiley & Sons, Ltd.     

Symmetries in the representation of grain boundary-plane distributions

Symmetries play a crucial role in the theoretical analysis and visualization of the five macroscopic grain boundary parameters, including the misorientation (three parameters) and the orientation of the boundary-plane (two parameters). The symmetry aspects of the misorientation spaces are very well documented and in this article all possible boundary-plane symmetries are enumerated for the 32 crystallographic point groups. It is observed that the boundary-plane spaces exhibit a wide variety of point group symmetries, which depend both on the crystallographic point group and on the corresponding misorientation (i.e. location in the fundamental zone). The list of symmetries presented here should serve as a guide for graphical representations of not only the distributions of boundary-plane orientations but also for the representation of boundary-plane related properties such as energy, mobility etc.     

One-pot facile synthesis,crystal structure and antifungal activity of 1,2,3-triazoles bridged with amine-amide functionalities

A library of twenty five 1,2,3-triazoles bridged with amine-amide functionalities have been synthesized from reaction of N-substituted(prop-2-yn-1-yl)amines (2a–2e), 2-bromo-N-arylacetamides (4a–4e) and sodium azide through copper(I)-catalyzed alkyne-azide cycloaddition. The synthesized compounds were characterized by using FTIR, ¹H NMR, ¹³C NMR, and HRMS techniques. The structures of synthesized 5a (CCDC 1569245) and 5h (CCDC 1569249) were also confirmed by X-ray crystallography. Antifungal evaluation of newly synthesized triazoles was carried out against – Candida albicans and Aspergillus niger. Biological screening of synthesized 1,2,3-triazoles revealed moderate to good antifungal activity against tested strains.     

Total synthesis of diaportheone A

Diaportheone A (1), a chromone natural product was previously isolated from the endophytic fungi Diaporthe sp. P 133. Its structure was established by spectroscopic methods, however, its absolute configuration remained undefined. This study dealt on the total synthesis of diaportheone A (1) utilizing the cyclization and in situ thermal syn-elimination of a β-ketosulfoxide. The C-1R absolute configuration of the natural product was established by X-ray crystallography of the synthetic diaportheone A (1) (>99%?ee) and comparison with the optical rotation.     

Concomitant Polymorphism in an Organic Solid: Molecular and Crystal Structure and Intra- and Intermolecular Potential Contributions to tert-Butyl and Methyl Group Rotation

We investigate the relationship between structure (crystal and molecular) and tert-butyl and methyl group dynamics in 2-(tert-butyl)-9-(4-(tert-butyl)phenyl)anthracene. Powder and single-crystal X-ray diffraction, taken together, show that different polycrystalline samples recrystallized from different solvents have different amounts of at least four polymorphs (crystallites having different crystal structures), of which we have identified three by single crystal X-ray diffraction. The molecules in the asymmetric units of the different crystal structures differ by the dihedral angle the tert-butylphenyl group makes with the anthracene moiety. Ab initio electronic structure calculations on the isolated molecule show that very little intramolecular energy is required to change this angle over a range of about 60° which is probably the origin of the concomitant polymorphism (crystals of more than one polymorph in a polycrystalline sample). Solid state ¹H nuclear magnetic resonance (NMR) spin-lattice relaxation experiments support the powder and single-crystal X-ray results and provide average NMR activation energies (closely related to rotational barriers) for the rotation of the tert-butyl groups and their constituent methyl groups. These barriers have both an intramolecular and an intermolecular component. The latter is sensitive to the crystal structure. The intramolecular components of the rotational barriers of the two tert-butyl groups in the isolated molecule are investigated with ab initio electronic structure calculations.     

Powder diffraction from a continuous microjet of submicrometer protein crystals

Atomic‐resolution structures from small proteins have recently been determined from high‐quality powder diffraction patterns using a combination of stereochemical restraints and Rietveld refinement [Von Dreele (2007), J. Appl. Cryst. 40 , 133–143; Margiolaki et al. (2007), J. Am. Chem. Soc. 129 , 11865–11871]. While powder diffraction data have been obtained from batch samples of small crystal‐suspensions, which are exposed to X‐rays for long periods of time and undergo significant radiation damage, the proof‐of‐concept that protein powder diffraction data from nanocrystals of a membrane protein can be obtained using a continuous microjet is shown. This flow‐focusing aerojet has been developed to deliver a solution of hydrated protein nanocrystals to an X‐ray beam for diffraction analysis. This method requires neither the crushing of larger polycrystalline samples nor any techniques to avoid radiation damage such as cryocooling. Apparatus to record protein powder diffraction in this manner has been commissioned, and in this paper the first powder diffraction patterns from a membrane protein, photosystem I, with crystallite sizes of less than 500 nm are presented. These preliminary patterns show the lowest‐order reflections, which agree quantitatively with theoretical calculations of the powder profile. The results also serve to test our aerojet injector system, with future application to femtosecond diffraction in free‐electron X‐ray laser schemes, and for serial crystallography using a single‐file beam of aligned hydrated molecules.