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

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.

Mining the Cambridge Database for theoretical chemistry. Mi-LJC: a new set of Lennard-Jones–Coulomb atom–atom potentials for the computer simulation of organic condensed matter

A novel, universal Lennard-Jones–Coulomb (LJC) atom–atom force field parametrization reproduces the experimental sublimation enthalpies of 377 molecular crystals drawn from the CSD.

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

The CLP-dyncry molecular dynamics (MD) program suite and force field environment is introduced and validated with its ad hoc features for the treatment of organic crystalline matter. The package, stemming from a preliminary implementation on organic liquids (Gavezzotti & Lo Presti, 2019), includes modules for the preliminary generation of molecular force field files from ab initio derived force constants, and for the preparation of crystalline simulation boxes from general crystallographic information, including Cambridge Structural Database CIFs. The intermolecular potential is the atom–atom Coulomb–London–Pauli force field, well tested as calibrated on sublimation enthalpies of organic crystals. These products are then submitted to a main MD module that drives the time integration and produces dynamic information in the form of coordinate and energy trajectories, which are in turn processed by several kinds of crystal-oriented analytic modules. The whole setup is tested on a variety of bulk crystals of rigid, non-rigid and hydrogen-bonded compounds for the reproduction of radial distribution functions and of crystal-specific collective orientational variables against X-ray data. In a series of parallel tests, some advantages of a dedicated program as opposed to software more oriented to biomolecular simulation (Gromacs) are highlighted. The different and improved view of crystal packing that results from joining static structural information from X-ray analysis with dynamic upgrades is also pointed out. The package is available for free distribution with I/O examples and Fortran source codes.

Solving the enigma of weak fluorine contacts in the solid state: a periodic DFT study of fluorinated organic crystals

The nature and strength of weak interactions with organic fluorine in the solid state are revealed by periodic density functional theory (periodic DFT) calculations coupled with experimental data on the structure and sublimation thermodynamics of crystalline organofluorine compounds. To minimize other intermolecular interactions, several sets of crystals of perfluorinated and partially fluorinated organic molecules are considered. This allows us to establish the theoretical levels providing an adequate description of the metric and electron-density parameters of the C–F⋯F–C interactions and the sublimation enthalpy of crystalline perfluorinated compounds. A detailed comparison of the C–F⋯F–C and C–H⋯F–C interactions is performed using the relaxed molecular geometry in the studied crystals. The change in the crystalline packing of aromatic compounds during their partial fluorination points to the structure-directing role of C–H⋯F–C interactions due to the dominant electrostatic contribution to these contacts. C–H⋯F–C and C–H⋯O interactions are found to be identical in nature and comparable in energy. The factors that determine the contribution of these interactions to the crystal packing are revealed. The reliability of the results is confirmed by considering the superposition of the electrostatic potential and electron density gradient fields in the area of the investigated intermolecular interactions.

The nature and strength of weak C–H⋯F–C and C–F⋯F–C interactions and their role in organofluorine molecular crystals were studied using periodic DFT coupled with CSD data mining and experimental sublimation enthalpies.