The first polymorph in the family of nucleobases: a second form of cytosine

Butterfly Effect in Cytarabine: Combined NMR-NQR Experiment, Solid-State Computational Modeling, Quantitative Structure-Property Relationships and Molecular Docking Study

Cytarabine (Ara-C) is a synthetic isomer of cytidine that differs from cytidine and deoxycytidine only in the sugar. The use of arabinose instead of deoxyribose hinders the formation of phosphodiester linkages between pentoses, preventing the DNA chain from elongation and interrupting the DNA synthesis. The minor structural alteration (the inversion of hydroxyl at the 2' positions of the sugar) leads to change of the biological activity from anti-depressant and DNA/RNA block builder to powerful anti-cancer. Our study aimed to determine the molecular nature of this phenomenon. Three 1H-14N NMR-NQR experimental techniques, followed by solid-state computational modelling (Quantum Theory of Atoms in Molecules, Reduced Density Gradient and 3D Hirshfeld surfaces), Quantitative Structure-Property Relationships, Spackman's Hirshfeld surfaces and Molecular Docking were used. Multifaceted analysis-combining experiments, computational modeling and molecular docking-provides deep insight into three-dimensional packing at the atomic and molecular levels, but is challenging. A spectrum with nine lines indicating the existence of three chemically inequivalent nitrogen sites in the Ara-C molecule was recorded, and the lines were assigned to them. The influence of the structural alteration on the NQR parameters was modeled in the solid (GGA/RPBE). For the comprehensive description of the nature of these interactions several factors were considered, including relative reactivity and the involvement of heavy atoms in various non-covalent interactions. The binding modes in the solid state and complex with dCK were investigated using the novel approaches: radial plots, heatmaps and root-mean-square deviation of the binding mode. We identified the intramolecular OH···O hydrogen bond as the key factor responsible for forcing the glycone conformation and strengthening NH···O bonds with Gln97, Asp133 and Ara128, and stacking with Phe137. The titular butterfly effect is associated with both the inversion and the presence of this intramolecular hydrogen bond. Our study elucidates the differences in the binding modes of Ara-C and cytidine, which should guide the design of more potent anti-cancer and anti-viral analogues.

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.

Electro-active properties of nanostructured films of cytosine and guanine nucleobases

The discovery of multifunctional properties related to electro-activity of organic systems of biomolecules is important for a variety of applications, especially for devices in the realm of biocompatible sensors and/or bioactuators. A further step towards such applications is to prepare thin films with the required properties. Here, the investigation is focused on the characterization of films of guanine and cytosine nucleobases, prepared by thermal evaporation-an industrial accessible deposition technique. The cytosine films have an orthorhombic non-centrosymmetric structure and grow in two interconnected nanostructured fractal patterns, of nearly equal proportion. Piezoresponse force microscopy images acquired at room temperature on the cytosine films display large zones with antiparallel alignment of the vertical components of the polarization vector. Guanine films have a dense nano-grained morphology. Our studies reveal electrical polarization switching effects which can be related to ferroelectricity in the films of guanine molecules. Characteristic ferroelectric polarization-electric-field hysteresis loops showing large electrical polarization are observed at low temperatures up to 200 K. Above this temperature, the guanine films have a preponderant paraelectric phase containing residual or locally induced nano-scopic ferroelectric domains, as observed by piezoresponse force microscopy at room temperature.

FFCASP: A Massively Parallel Crystal Structure Prediction Algorithm

A new algorithm called Fast and Flexible CrystAl Structure Predictor (FFCASP) was developed to predict the structure of covalent and molecular crystals. FFCASP is massively parallel and able to handle more than 200 atoms in the unit cell (in other terms, it allows global optimization around 100 individual parameters). It uses a global optimizer specialized for Crystal Structure Prediction (CSP) which combines particle swarm and simulated annealing optimizers. Three different molecular crystals, including diverse intermolecular interactions, namely, cytosine, coumarin, and pyrazinamide, have been selected to evaluate the performance of FFCASP. While cytosine polymorphs have been searched by employing two different force fields (a DFT-SAPT based intermolecular potential and generalized amber force field (GAFF)) up to Z = 16, only GAFF has been used both in coumarin and pyrazinamide polymorph searches up to Z = 4. For these three molecular crystals, FFCASP generated more than 20 000 crystal structures, and the unique ones have been further treated by DFT-D3. A combination of data mining and a machine learning approach was introduced to determine the unique structures and their distribution into different clusters, which ultimately gives an opportunity to retrieve the common features and relations between the resulting structures. There are two known experimental crystal structures of cytosine, and both were successfully located with FFCASP. Two of the reported crystal structures of coumarin have been reproduced. Similarly, in pyrazinamide, three known experimental structures have been rediscovered. In addition to finding the experimentally known structures, FFCASP also located other low-energy structures for each considered molecular crystals. These successes of FFCASP offer the possibility to discover the polymorphic nature of other important molecular crystals (e.g., drugs) as well.

Two novel polymorphic forms of iron-chelating agent deferiprone

Thalassemia is a genetic blood disorder requiring life-long blood transfusions. This process often results in iron overload and can be treated by an iron-chelating agent, like deferiprone (3-hydroxy-1,2-dimethylpyridin-4-one), C₇H₉NO₂, in an oral formulation. The first crystal structure of deferiprone, (Ia), was reported in 1988 [Nelson et al. (1988). Can. J. Chem. 66, 123-131]. In the present study, two novel polymorphic forms, (Ib) and (Ic), of deferiprone were identified concomitantly with polymorph (Ia) during the crystallization experiments. Polymorph (Ia) was redetermined at low temperature for comparison of the structural features and lattice energy values with polymorphs (Ib) and (Ic). Polymorph (Ia) crystallized in the orthorhombic space group Pbca, whereas both polymorphs (Ib) and (Ic) crystallized in the monoclinic space group P2₁/c. The asymmetric units of (Ia) and (Ib) contain one deferiprone molecule, while polymorph (Ic) has three crystallographically independent molecules (A, B and C). All three polymorphs have similar hydrogen-bonding features, such as an R₂²(10) dimer formed by O-H...O hydrogen bonds, an R₄³(20) tetramer formed by C-H...O hydrogen bonds and π-π interactions, but the polymorphs differ in their molecular arrangements in the solid state and are classified as packing polymorphs. O-H...O and C-H...O hydrogen bonds lead to the formation of two-dimensional hydrogen-bonded parallel sheets which are interlinked by π-π stacking interactions. In the three-dimensional crystal packing, the deferiprone molecules were aggregated as corrugated sheets in polymorphs (Ia) and (Ic), whereas in polymorph (Ib), they were aggregated as a square-grid network. The characteristic crystalline peaks of polymorphs (Ia), (Ib) and (Ic) were established through powder X-ray diffraction analysis. The Rietveld analysis was also performed to estimate the contribution of the polymorphs to the bulk material.

Dapsone Form V: A Late Appearing Thermodynamic Polymorph of a Pharmaceutical

Five anhydrate polymorphs (forms I-V) and the isomorphic dehydrate (Hy_dehy) of dapsone (4,4'-diaminodiphenyl sulfone or DDS) were prepared and characterized in an interdisciplinary experimental and computational study, elucidating the kinetic and thermodynamic stabilities, solid form interrelationships, and structural features of the known forms I-IV, the novel polymorph form V, and Hy_dehy. Calorimetric measurements, solubility experiments, and lattice energy calculations revealed that form V is the thermodynamically stable polymorph from absolute zero to at least 90 °C. At higher temperatures, form II, and then form I, becomes the most stable DDS solid form. The computed 0 K stability order (lattice energy calculations) was confirmed with calorimetric measurements as follows, V (most stable) > III > Hy_dehy > II > I > IV (least stable). The discovery of form V was complicated by the fact that the metastable but kinetically stabilized form III shows a higher nucleation and growth rate. By combining laboratory powder X-ray diffraction data and ab initio calculations, the crystal structure of form V ( P2₁/ c, Z' = 4) was solved, with a high energy DDS conformation allowing a denser packing and more stable intermolecular interactions, rationalizing the formation of a high Z' structure. The structures of the forms I and IV, only observed from the melt and showing distinct packing features compared to the forms II, III, and V, were derived from the computed crystal energy landscapes. Dehydration modeling of the DDS hydrate led to the Hy_dehy structure. This study expands our understanding about the complex crystallization behavior of pharmaceuticals and highlights the big challenge in solid form screening, especially that there is no clear end point.

Experimental and Computational Hydrate Screening: Cytosine, 5-Flucytosine and Their Solid Solution

The structural, temperature- and moisture dependent stability features of cytosine and 5-flucytosine monohydrates, two pharmaceutically important compounds, were rationalized using complementary experimental and computational approaches. Moisture sorption/desorption, water activity, thermal analysis and calorimetry were applied to determine the stability ranges of hydrate ↔ anhydrate systems, while X-ray diffraction, IR spectroscopy and crystal structure prediction provided the molecular level understanding. At 25 °C, the critical water activity for the cytosine hydrate ↔ anhydrate system is ~0.43 and for 5-flucytosine ~0.41. In 5-flucytosine the water molecules are arranged in open channels, therefore the kinetic desorption data, dehydration < 40% relative humidity (RH), conform with the thermodynamic data, whereas for the cytosine isolated site hydrate dehydration was observed at RH < 15%. Peritectic dissociation temperatures of the hydrates were measured to be 97 °C and 84.2 °C for cytosine and 5-flucytosine, respectively, and the monohydrate to anhydrate transition enthalpies to be around 10 kJ mol-1. Computed crystal energy landscapes not only revealed that the substitution of C5 (H or F) controls the packing and properties of cytosine/5-flucytosine solid forms, but also have enabled the finding of a monohydrate solid solution of the two substances which shows increased thermal- and moisture-dependent stability compared to 5-flucytosine monohydrate.

Prediction and experimental validation of solid solutions and isopolymorphs of cytosine/5-flucytosine

A computational search for polymorphs of cytosine, 5-flucytosine and a 1 : 1 mixture of the two substances not only rationalised the preferred packing arrangements but also enabled the finding and characterisation of cytosine/5-flucytosine solid solutions. The structures of the new solid forms were determined by combining laboratory powder X-ray diffraction data and computational modelling.