Preliminary studies on unusual polymorphs of thymine: Structural comparison with other nucleobases

NICE-FF: A non-empirical, intermolecular, consistent, and extensible force field for nucleic acids and beyond

A new non-empirical ab initio intermolecular force field (NICE-FF in buffered 14-7 potential form) has been developed for nucleic acids and beyond based on the dimer interaction energies (IEs) calculated at the spin component scaled-MI-second order Møller-Plesset perturbation theory. A fully automatic framework has been implemented for this purpose, capable of generating well-polished computational grids, performing the necessary ab initio calculations, conducting machine learning (ML) assisted force field (FF) parametrization, and extending existing FF parameters by incorporating new atom types. For the ML-assisted parametrization of NICE-FF, interaction energies of ∼18 000 dimer geometries (with IE < 0) were used, and the best fit gave a mean square deviation of about 0.46 kcal/mol. During this parametrization, atom types apparent in four deoxyribonucleic acid (DNA) bases have been first trained using the generated DNA base datasets. Both uracil and hypoxanthine, which contain the same atom types found in DNA bases, have been considered as test molecules. Three new atom types have been added to the DNA atom types by using IE datasets of both pyrazinamide and 9-methylhypoxanthine. Finally, the last test molecule, theophylline, has been selected, which contains already-fitted atom-type parameters. The performance of NICE-FF has been investigated on the S22 dataset, and it has been found that NICE-FF outperforms the well-known FFs by generating the most consistent IEs with the high-level ab initio ones. Moreover, NICE-FF has been integrated into our in-house developed crystal structure prediction (CSP) tool [called FFCASP (Fast and Flexible CrystAl Structure Predictor)], aiming to find the experimental crystal structures of all considered molecules. CSPs, which were performed up to 4 formula units (Z), resulted in NICE-FF being able to locate almost all the known experimental crystal structures with sufficiently low RMSD20 values to provide good starting points for density functional theory optimizations.

New Polymorphic Modifications of 6-Methyluracil: An Experimental and Quantum Chemical Study

Polymorphism of 6-methyluracil, which affects the regulation of lipid peroxidation and wound healing, has been studied by experimental and quantum chemical methods. Two known polymorphic modifications and two new crystalline forms were crystallized and characterized by single crystal and powder X-ray diffraction (XRD) methods as well as by the differential scanning calorimetry (DSC) method and infrared (IR) spectroscopy. The calculations of pairwise interaction energies between molecules and lattice energies in periodic boundary conditions have shown that the polymorphic form 6MU_I used in the pharmaceutical industry and two new forms 6MU_III and 6MU_IV, which can be formed due to temperature violations, may be considered as metastable. The centrosymmetric dimer bound by two N-H···O hydrogen bonds was recognized as a dimeric building unit in all of the polymorphic forms of 6-methyluracil. Four polymorphic forms have a layered structure from the viewpoint of interaction energies between dimeric building units. The layers parallel to the (100) crystallographic plane were recognized as a basic structural motif in the 6MU_I, 6MU_III, and 6MU_IV crystals. In the 6MU_II structure, a basic structural motif is a layer parallel to the (001) crystallographic plane. The ratio between the interaction energies within the basic structural motif and between neighboring layers correlates with the relative stability of the studied polymorphic forms. The most stable polymorphic form 6MU_II has the most anisotropic "energetic" structure, while the interaction energies in the least stable form 6MU_IV are very close in various directions. The modeling of shear deformations of layers in the metastable polymorphic structures has not revealed any possibility of these crystals to be deformed under external mechanical stress or pressure influence. These results allow the use of metastable polymorphic forms of 6-methyluracil in the pharmaceutical industry without any limitations.

Sublimation – a green route to new solid-state forms

Sublimation is an effective and ‘green’ method to prepare and identify new polymorphs, cocrystals, ionic cocrystals and molecular salts.

Characterization of thymine microcrystals by CARS and SHG microscopy

Identification of chemically homologous microcrystals in a polycrystal sample is a big challenge and requires developing specific highly sensitive tools. Second harmonic (SHG) and coherent anti-Stokes Raman scattering (CARS) spectroscopy can be used to reveal arrangement of thymine molecules, one of the DNA bases, in microcrystalline sample. Strong dependence of CARS and SHG intensity on the orientation of the linear polarization of the excitation light allows to obtain high resolution images of thymine microcrystals by additionally utilizing the scanning microscopy technique. Experimental findings and theoretical interpretation of the results are compared. Presented experimental data together with quantum chemistry-based theoretical interpretation allowed us to determine the most probable organization of the thymine molecules.