Parthapratim Munshi

Estimated H-atom anisotropic displacement parameters: a comparison between different methods and with neutron diffraction results

Anisotropic displacement parameters (ADPs) are compared for H atoms estimated using three recently described procedures, both among themselves and with neutron diffraction results. The results convincingly demonstrate that all methods are capable of giving excellent results for several benchmark systems and identify systematic discrepancies for several atom types. A revised and extended library of internal H-atom mean-square displacements is presented for use with Madsens SHADE web server [J. Appl. Cryst. (2006), 39, 757-758; http://shade.ki.ku.dk], and the improvement over the original SHADE results is substantial, suggesting that this is now the most readily and widely applicable of the three approximate procedures. Using this new library--SHADE2--it is shown that, in line with expectations, a segmented rigid-body description of the heavy atoms yields only a small improvement in the agreement with neutron results. The SHADE2 library, now incorporated in the SHADE web server, is recommended as a routine procedure for deriving estimates of H-atom ADPs suitable for use in charge-density studies on molecular crystals, and its widespread use should reveal remaining deficiencies and perhaps overcome the inherent bias in the majority of such studies.

Evaluation of weak intermolecular interactions in molecular crystals via experimental and theoretical charge densities

Analysis of charge density distributions in molecular crystals has received considerable attention in the last decade both from high-resolution X-ray diffraction studies and from high-level theoretical calculations. An overview of the progress made in deriving one-electron properties, intermolecular interactions in terms of the Atoms in Molecule (AIM) approach (R.F.W. Bader. Atoms in Molecules-A Quantum Theory, Clarendon, Oxford (1990), R.F.W. Bader. J. Phys. Chem., A102, 7314 (1998)) is given with special emphasis on improvements in charge density models and development of both experimental and theoretical techniques to interpret and analyse the nature of weak intermolecular interactions. The significance of the derived results from the charge density of coumarin and its derivatives have been analysed to obtain insights into the nature of intermolecular C–H ··· O, C–H ··· π, π ··· π, C–H ··· S, and S ··· S contacts. The appearance of a ‘region of overlap’ to segregate hydrogen bonds from van der Waals interactions based on the criteria proposed by Koch and Popelier (U. Koch, P.L.A. Popelier. J. Phys. Chem., 99, 9747 (1995), P.L.A. Popelier. Atoms in Molecules. An Introduction, pp. 150–153, Prentice Hall, UK (2000)) and the identification of differences in energy surfaces in concomitant polymorphs of 3-acetylcoumarin are described.

Polymorphism in 3-methyl-4-methoxy-4′-nitrostilbene (MMONS), a highly active NLO material

During crystallization experiments two new polymorphs of the highly-active organic nonlinear optical (NLO) material 3-methyl-4-methoxy-4′-nitrostilbene (MMONS) have been discovered. Crystallization conditions of all three polymorphs and their characterization via crystal structure determination from single crystal X-ray diffraction data at 100 K have been discussed in detail. Two of the polymorphs exhibit different conformations, while a third polymorph incorporates both conformers as well as disorder. Comparisons between various types of intermolecular contacts in these three polymorphic forms have been quantified via Hirshfeld surface analysis.

Charge density based classification of intermolecular interactions in molecular crystals

Evaluation of intermolecular interactions in terms of both experimental and theoretical charge density analyses has produced a unified picture with which to classify strong and weak hydrogen bonds, along with van der Waals interactions, into three regions.

Refractive indices for molecular crystals from the response of X-ray constrained Hartree–Fock wavefunctions

Refractive indices for molecular crystals are obtained from Hartree-Fock wavefunctions constrained to reproduce a set of experimental X-ray structure factors. Coupled-perturbed Hartree-Fock theory is used to calculate the in-crystal effective polarizabilities from which the refractive indices are obtained, thus eliminating the need for the calibration procedure used in earlier work by Whitten et al. [J. Chem. Phys. 2006, 125, 174505]. The results clearly demonstrate that these X-ray constrained Hartree-Fock (XCHF) wavefunctions reflect genuine effects of intermolecular interactions in crystals. Molecular dipole moments are consistently in excellent agreement with ab initio MP2 estimates that incorporate the effects of the crystal field. Consistent agreement of the XCHF refractive indices with experimental measurements at optical frequencies confirms that this approach can provide both meaningful results and considerable insight into the relative importance of molecular properties and crystal field effects in determining the detailed nature of the refractivity tensor.

Redetermination, invariom-model and multipole refinement of L-ornithine hydrochloride

The structure of L-ornithine hydrochloride, C(5)H(13)N(2)O2+Cl(-), has been redetermined at 100 K by single-crystal X-ray diffraction within a project that aims to generate accurate bond-distance restraints for the invariom refinement of proteins. The high-resolution data were subject to an invariom and a multipole refinement, and the resulting electron densities on a grid were compared. Improvements in the conventional R factor obtained by multipole modelling were smaller than in other structures containing solely the elements CHNO owing to Cl core scattering. Cruickshanks diffraction-component precision index and Stevens & Coppens suitability factor are discussed.

Accessing Benzimidazoles via a Ring Distortion Strategy: An Oxone Mediated Tandem Reaction of 2-Aminobenzylamines

An exceptional oxone mediated tandem transformation of 2-aminobenzylamines to 2-substituted benzimidazoles is reported. It occurs at room temperature with aromatic, heteroaromatic, and aliphatic aldehydes. In this reaction initial condensation of 2-aminobenzylamine with appropriate aldehydes afforded a tetrahydroquinazoline intermediate which underwent oxone-mediated ring distortion to afford the desired compounds in moderate to excellent yields.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant.

Ketol-isomerases catalyze the reversible isomerization between aldoses and ketoses. D-Xylose isomerase carries out the first reaction in the catabolism of D-xylose, but is also able to convert D-glucose to D-fructose. The first step of the reaction is an enzyme-catalyzed ring opening of the cyclic substrate. The active-site amino-acid acid/base pair involved in ring opening has long been investigated and several models have been proposed. Here, the structure of the xylose isomerase E186Q mutant with cyclic glucose bound at the active site, refined against joint X-ray and neutron diffraction data, is reported. Detailed analysis of the hydrogen-bond networks at the active site of the enzyme suggests that His54, which is doubly protonated, is poised to protonate the glucose O5 position, while Lys289, which is neutral, promotes deprotonation of the glucose O1H hydroxyl group via an activated water molecule. The structure also reveals an extended hydrogen-bonding network that connects the conserved residues Lys289 and Lys183 through three structurally conserved water molecules and residue 186, which is a glutamic acid to glutamine mutation.

Isostructural polymorphs: qualitative insights from energy frameworks

Three isostructural polymorphs with two-dimensional and three-dimensional similarities are demonstrated quantitatively from similarity relationship analysis. The similarity dimensions are then visualized and correlated in a novel way via qualitative analysis using ‘energy frameworks’. Two of the three polymorphs with three-dimensional similarities exhibiting identical physical properties have almost equi-energetic crystal structures while the most stable third polymorph exhibits distinct properties. Thereby, structure–property correlations are derived, both quantitatively and qualitatively.