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

Water-mediated cytosine self-assembly in infrared perspective

Self-assembly plays a crucial role in the formation and allosteric processes of many biomolecules, water molecules can affect these processes. Cytosine (Cyt) has excellent self-assembly ability, forming a flat and ordered structure through hydrogen bonds (HBs) in the presence of water molecules. However, the vibration dynamics and interaction mechanism of water induced Cyt self-assembly are still unclear. In this work, infrared spectroscopy techniques, combined with density functional theory (DFT) theoretical calculations, were employed to investigate the vibrational characteristics and interactions of water molecule mediated self-assembly of Cyt and its reverse process. The results indicate that the induction of Cyt self-assembly by water molecules has differential effects on the various vibrational modes of the Cyt molecule. Multi-view infrared spectroscopy provides a powerful tool for the characterization of biomolecules in situ. This study will contribute to a deeper understanding and application of nucleic acid biological nanostructures.

Suppression of Disorder in Benzamide and Thiobenzamide Crystals by Fluorine Substitution

Disorder is a common feature of molecular crystals that complicates determination of structures and can potentially affect electric and mechanical properties. Suppression of disorder is observed in otherwise severely disordered benzamide and thiobenzamide crystals by substituting hydrogen with fluorine in the ortho-position of the phenyl ring. Fluorine occupancies of 20-30% are sufficient to suppress disorder without changing the packing motif. Crystal structure prediction calculations reveal a much denser lattice energy landscape for benzamide compared to 2-fluorobenzamide, suggesting that fluorine substitution makes disorder less likely.

Enhancement of Hydrate Stability through Substitutional Defects

Cytosine monohydrate (CM) and anhydrate crystal forms reversibly interconvert under high temperatures or high humidity conditions. Here, we demonstrate through defect engineering the ability to expand the thermal stability range of CM through the targeted creation of quantifiable defects in low-level concentrations. Twelve different molecular dyes with a variety of core structures and charges were screened as potential dopants in CM. CM-dye phases prepared with Congo red (CR), Evans blue (EB), and Azocarmine G (AG) exhibited the highest inclusion levels (up to 1.1 wt %). In these doped isomorphous materials, each dye is presumed to substitute for 4-7 cytosine molecules within the low-rugosity (102) planes of the CM matrixes, thereby creating a quantifiable substitutional defect and an impediment to the cooperative molecular motions which enable the transformation to the anhydrate. Dehydration of materials with these engineered defects requires significantly higher temperatures and proceeds with slower kinetics compared to pure CM. The CM-dye phases also exhibit a reduction in the thermal expansion along key crystallographic axes and yield dehydration products with altered particle morphologies.

Mechanisms of Crystal Plasticization by Lattice Water

PURPOSE

Water of crystallization has been observed to increase plasticity, decrease crystal hardness, and improve powder compressibility and tabletability of organic crystals. This work is aimed at gaining a molecular level insight into this observation.

METHOD

We systematically analyzed crystal structures of five stoichiometric hydrate systems, using several complementary techniques of analysis, including energy framework, water environment, overall packing change, hydrate stability, and slip plane identification.

RESULTS

The plasticizing effect by lattice water is always accompanied by an introduction of more facile slip planes, lower packing efficiency, and lower density in all hydrate systems examined in this work. Three distinct mechanisms include 1) changing the distribution of intermolecular interactions without significantly changing the packing of molecules to introduce more facile slip planes; 2) changing packing feature into a flat layered structure so that more facile slip planes are introduced; 3) reducing the interlayer interaction energies and increasing the anisotropy.

CONCLUSION

Although the specific mechanisms for these five systems differ, all five hydrates are featured with more facile slip planes, lower packing efficiency, and lower density.

Microcrystalline solid–solid transformations of conformationally-responsive solvates, desolvates and a salt of N,N′-(1,4-phenylene)dioxalamic acid: the energetics of hydrogen bonding and n/π → π* interactions

The supramolecular structures of H2pOx·2S (S = DMSO, DMF, ⅓(MeOH·2W), W) solvates were stablished. The energetics of amide N–H⋯O and n/π → π* interactions maintain the crystal network and the reversibility between polymorphs.

Polymorphs of phenazine hexacyanoferrate(II) hydrate: supramolecular isomerism in a 2D hydrogen-bonded network

The crystal structures of two polymorphs of a phenazine hexacyanoferrate(II) salt/cocrystal, with the formula (Hphen)₃[H₂Fe(CN)₆][H₃Fe(CN)₆]·2(phen)·2H₂O, are reported. The polymorphs are comprised of (Hphen)₂[H₂Fe(CN)₆] trimers and (Hphen)[(phen)₂(H₂O)₂][H₃Fe(CN)₆] hexamers connected into two-dimensional (2D) hydrogen-bonded networks through strong hydrogen bonds between the [H₂Fe(CN)₆]^2- and [H₃Fe(CN)₆]^- anions. The layers are further connected by hydrogen bonds, as well as through π-π stacking of phenazine moieties. Aside from the identical 2D hydrogen-bonded networks, the two polymorphs share phenazine stacks comprising both protonated and neutral phenazine molecules. On the other hand, the polymorphs differ in the conformation, placement and orientation of the hydrogen-bonded trimers and hexamers within the hydrogen-bonded networks, which leads to different packing of the hydrogen-bonded layers, as well as to different hydrogen bonding between the layers. Thus, aside from an exceptional number of symmetry-independent units (nine in total), these two polymorphs show how robust structural motifs, such as charge-assisted hydrogen bonding or π-stacking, allow for different arrangements of the supramolecular units, resulting in polymorphism.

Transformation of terahertz vibrational modes of cytosine under hydration

Cytosine and cytosine monohydrate are representative biomolecules for investigating the effect of hydrogen bonds in deoxyribonucleic acid. To better understand intermolecular interactions, such as hydrogen bonds, between nucleobases it is necessary to identify the low-frequency vibrational modes associated with intermolecular interactions and crystalline structures. In this study, we investigated the characteristic low-frequency vibrational modes of cytosine and cytosine monohydrate using terahertz time-domain spectroscopy (THz-TDS). The crystal geometry was obtained by the powder X-ray diffraction technique. The optimized atomic positions and the normal modes in the terahertz region were calculated using density functional theory (DFT), which agreed well with the experimental results. We found that overall terahertz absorption peaks of cytosine and cytosine monohydrate consist of collective vibrations mixed with intermolecular and intramolecular vibrations in mode character analysis, and that the most intense peaks of both samples involve remarkable intermolecular translational vibration. These results indicate that THz-TDS combined with DFT calculations including mode character analysis can be an effective method for understanding how water molecules contribute to the characteristics of the low-frequency vibrational modes by intermolecular vibrations with hydrogen bonding in biological and biomedical applications.

Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. II. Smoothed intramolecular potentials

The application of crystal structure prediction (CSP) to industrially relevant molecules requires the handling of increasingly large and flexible compounds. A revised model for the effect of molecular flexibility on the lattice energy that removes the discontinuities and non-differentiabilities present in earlier models (Sugden et al., 2016), with a view to improving the performance of CSP is presented. The approach is based on the concept of computing a weighted average of local models, and has been implemented within the CrystalPredictor code. Through the comparative investigation of several compounds studied in earlier literature, it is shown that this new model results in large reductions in computational effort (of up to 65%) and in significant increases in reliability. The approach is further applied to investigate, for the first time, the computational polymorphic landscape of flufenamic acid for Z' = 1 structures, resulting in the successful identification of all three experimentally resolved polymorphs within reasonable computational time.

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.