Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

The experimental electron density distribution (EDD) of 1-methyluracil (1-MUR) was obtained by single crystal X-ray diffraction (XRD) experiments at 23 K. Four different structural models fitting an extensive set of XRD data to a resolution of (sinθ/λ)max = 1.143 Å−1 are compared. Two of the models include anharmonic temperature factors, whose inclusion is supported by the Hamilton test at a 99.95% level of confidence. Positive Fourier residuals up to 0.5 eÅ–3 in magnitude were found close to the methyl group and in the region of hydrogen bonds. Residual density analysis (RDA) and molecular dynamics simulations in the solid-state demonstrate that these residuals can be likely attributed to unresolved disorder, possibly dynamical and long–range in nature. Atomic volumes and charges, molecular moments up to hexadecapoles, as well as maps of the molecular electrostatic potential were obtained from distributed multipole analysis of the EDD. The derived electrostatic properties neither depend on the details of the multipole model, nor are significantly affected by the explicit inclusion of anharmonicity in the least–squares model. The distribution of atomic charges in 1-MUR is not affected by the crystal environment in a significant way. The quality of experimental findings is discussed in light of in-crystal and gas-phase quantum simulations.

Experimental Charge Density Analysis and Electrostatic Properties of Crystalline 1,3-Bis(Dimethylamino)Squaraine and Its Dihydrate from Low Temperature (T = 18 and 20 K) XRD Data

Multipolar refinements of structural models fitting extensive sets of X-ray diffraction (XRD) data from single crystals of 1,3-bis(dimethylamino)squaraine [SQ, C8H12N2O2] and its dihydrate [SQDH, C8H12N2O2·2H2O], collected at very low T (18 ± 1 K for SQ, 20 ± 1 K for SQDH), led to an accurate description of their crystal electron density distributions. Atomic volumes and charges have been estimated from the experimental charge densities using the Quantum Theory of Atoms in Molecules (QTAIM) formalism. Our analysis confirms the common representation (in the literature and textbooks) of the squaraine central, four-membered squarylium ring as carrying two positive charges, a representation that has been recently questioned by some theoretical calculations: the integrated total charge on the C4 fragment is estimated as ca. +2.4e in SQ and +2.2e in SQDH. The topology of the experimental electron density for the SQ squaraine molecule is modified in the dihydrated crystal by interactions between the methyl groups and the H2O molecules in the crystal. Maps of the molecular electrostatic potential in the main molecular planes in both crystals clearly reveal the quadrupolar charge distribution of the squaraine molecules. Molecular quadrupole tensors, as calculated with the PAMoC package using both Stewart and QTAIM distributed multipole analysis (DMA), are the same within experimental error.

Ab initio prediction of the polymorphic structures of pyrazinamide: A validation study

A validation study to predict the possible stable polymorphs of Pyrazinamide within a low energy conformational region of the flexible torsion angle was made through a potential energy surface (PES) scan by gas phase optimisation using the MP2/6-31G(d,p) method. Hypothetical crystal structures with favourable packing density for each of the stable conformers generated from the PES scan were generated using a global search with a repulsion only potential field. The densest crystal structures with stable energy were analyzed with more accurate lattice energy minimisation via distributed multipole analysis using a repulsion-dispersion potential. The stability of the predicted crystal structures with similar close packing to the known experimental polymorphs of Pyrazinamide molecule was analyzed by inspecting their intermolecular short contacts. Studies to analyze the second derivative mechanical properties from the hessian matrix were carried out to emphasise the thermodynamic stability of predicted polymorphs of Pyrazinamide.