A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC).

Two conformational crystal polymorphs of 3-diethylamino-4-(4-methoxyphenyl)-1,1-dioxo-4H-1λ6,2-thiazete-4-carbonitrile (DTC) have been analyzed in the 100 K-room temperature range by single crystal X-ray diffraction and high quality DFT calculations. DTC has strongly polar as well as aliphatic substituents but no hydrogen bonding groups, and thus qualifies as a test molecule for the relative importance of electrostatic vs. dispersion-repulsion terms. The two polymorphs have the same P21/n space group and differ by a flipping of the -OCH3 group, the two conformations being almost equi-energetic and separated by a low barrier. The system is monotropic in the observed temperature range with nearly identical thermal expansion coefficients and energy-temperature slopes, one phase consistently predicted to be more stable in agreement with the relative ease of appearance. Energy decompositions show that the electrostatic term is dominant and stabilizes with decreasing temperature. Dispersion and repulsion show the expected behavior, the former becoming more stabilizing at lower temperature in contrast with increasing repulsion at higher density. Absolute values and trends are very similar in the two phases, explaining the small total energy difference. Geometrical analyses of intermolecular contacts using fingerprint plots, as well as the study of molecular dipole moments as a function of T in the framework of the Quantum Theory of Atoms in Molecules, reveal more details of phase stability.

Anharmonic motions versus dynamic disorder at the Mg ion from the charge densities in pyrope (Mg3Al2Si3O12) crystals at 30†K: six of one, half a dozen of the other.

The possible occurrence of static/dynamic disorder at the Mg site in pyrope (Mg3Al2Si3O12), with or without anharmonic contribution to the thermal vibrations even at low temperatures, has been largely debated but conclusions were contrasting. Here a report is given on the experimental charge density distribution, ρEXP, of synthetic pyrope at T = 30 K, built through a Stewart multipolar expansion up to l = 5 and based on a very precise and accurate set of in-home measured single-crystal X-ray diffraction amplitudes with a maximum resolution of 0.44 Å. Local and integral topological properties of ρEXP are in substantial agreement with those of ρTHEO, the corresponding DFT-grade quantum charge density of an ideal pyrope crystal, and those derived from synchrotron investigations of chemical bonding in olivines. Relevant thermal atomic displacements, probably anharmonic in nature, clearly affect the whole structure down to 30 K. No significant (> 2.5σ) residual Fourier peaks are detectable from the ρEXP distribution around Mg, after least-squares refinement of a multipole model with anharmonic thermal motion at the Mg site. Experimental findings were confirmed by a full analysis of normal vibration modes of the DFT-optimized structure of the perfect pyrope crystal. Mg undergoes wide displacements from its equilibrium position even at very low temperatures, as it is allocated in a ∼ 4.5 Šlarge dodecahedral cavity and involved in several soft phonon modes. Implications on the interplay among static/dynamic disorder of Mg and lattice vibrational degrees of freedom are discussed.

Detection and kinetics of the single-crystal to single-crystal complete transformation of a thiiranium ion into thietanium ion.

The conversion of a di-tert-butyl-methylthiiranium ion into thietanium ion, that is reported in the literature as taking place spontaneously at 25 degrees C in a CD(2)Cl(2) solution, has been discovered to occur quantitatively at room temperature (RT) also in the crystalline state. The ring enlargement reaction is accompanied, in the solid phase, by a modest deterioration of the quality of the sample under investigation, and all three specimens here studied by in situ crystallography maintained their single-crystal nature up to 100% conversion. The rearrangement reaction implies the breaking of a C-S bond and the formation of a new bond of the same type, together with the migration of a methyl group. The extent of the corresponding atomic displacements has been measured by comparing the initial and final crystal structures. Several intermediate stages of the process have been investigated and characterized by the site occupancy factor of the episulfonium ion. The RT temporal evolution of this factor and that of the unit-cell volume indicate multi-step kinetics, with processes of simple molecular reorientation or displacement before and after the main, central stage, where the conversion reaction takes place. The overall kinetics is well described by an Avrami-Erofeev equation, with exponent m = 1.75(3) and rate coefficient k = 10.4(3) x 10(-8) s(-1) at 25 degrees C. Ab initio calculations in the gas phase predict a three-step mechanism resulting in a slightly spontaneous reaction with an overall decrease of entropy.

On the role of data quality in experimental charge-density studies.

High-resolution X-ray diffraction data were collected at T = 19 K from two similar spherical crystals of the fungal metabolite citrinin, C(13)H(14)O(5). The two data sets were of markedly different quality, one data set (MQ, medium quality) comprising a single octant of the reciprocal lattice and including reflections with obviously peculiar intensity profiles while the second (HQ, high quality) comprised a hemisphere of reflections and showed no flawed profiles. Parallel multipolar refinements were carried out for both. While most of the resulting geometric parameters, including bond lengths and angles, were in close agreement (the standard uncertainties were approximately twice as large for the MQ data, reflecting the smaller number of observations), the agreement is noticeably worse for electronic properties such as electron densities and their Laplacians at the bond and ring critical points. These latter features are especially sensitive to the quality of the low-angle (and strong) intensities, which was not high for the MQ data. By contrast, the magnitudes of the molecular dipole moment from the two experiments are the same within 1 standard uncertainty, with an angle of about 13 degrees between the two vectors. It is concluded that only true high-quality data allow a fully significant and quantitative analysis of the details of the experimental electron density rho(exp), while high-resolution medium-quality data, measured at very low temperature and adequately processed, can still be used for a qualitative analysis, or for the derivation of overall electronic properties.