ζ-Glycine: insight into the mechanism of a polymorphic phase transition

Enhanced Sampling of Crystal Nucleation with Graph Representation Learnt Variables

In this study, we present a graph neural network (GNN)-based learning approach using an autoencoder setup to derive low-dimensional variables from features observed in experimental crystal structures. These variables are then biased in enhanced sampling to observe state-to-state transitions and reliable thermodynamic weights. In our approach, we used simple convolution and pooling methods. To verify the effectiveness of our protocol, we examined the nucleation of various allotropes and polymorphs of iron and glycine in their molten states. Our graph latent variables, when biased in well-tempered metadynamics, consistently show transitions between states and achieve accurate thermodynamic rankings in agreement with experiments, both of which are indicators of dependable sampling. This underscores the strength and promise of our GNN variables for improved sampling. The protocol shown here should be applicable for other systems and other sampling methods.

The Effect of High Pressure on Polymorphs of a Derivative of Blatter's Radical: Identification of the Structural Signatures of Subtle Phase Transitions

The effect of pressure on the α and β polymorphs of a derivative of Blatter's radical, 3-phenyl-1-(pyrid-2-yl)-1,4-dihydrobenzo[e][1,2,4]triazin-4-yl, has been investigated using single-crystal X-ray diffraction to maximum pressures of 5.76 and 7.42 GPa, respectively. The most compressible crystallographic direction in both structures lies parallel to π-stacking interactions, which semiempirical Pixel calculations indicate are also the strongest interactions present. The mechanism of compression in perpendicular directions is determined by void distributions. Discontinuities in the vibrational frequencies observed in Raman spectra measured between ambient pressure and ∼5.5 GPa show that both polymorphs undergo phase transitions, the α phase at 0.8 GPa and the β phase at 2.1 GPa. The structural signatures of the transitions, which signal the onset of compression of initially more rigid intermolecular contacts, were identified from the trends in the occupied and unoccupied volumes of the unit cell with pressure and in the case of the β phase by deviations from an ideal model of compression defined by Birch-Murnaghan equations of state.

Studying the impact of the pre-exponential factor on templated nucleation

Traditionally, the enhancement of nucleation rates in the presence of heterogeneous surfaces in crystallisation processes has been attributed to the modification of the interfacial energy of the system according to the classical nucleation theory. However, recent developments have shown that heterogeneous surfaces instead alter the pre-exponential factor of nucleation. In this work, the nucleation kinetics of glycine and diglycine in aqueous solutions have been explored in the presence and absence of a heterogeneous surface. Results from induction time experiments show that the presence of a heterogeneous surface increases the pre-exponential factor by 2-fold or more for both glycine and diglycine, while the interfacial energy remains unchanged for both species. This study suggests that the heterogeneous surface enhances the nucleation rate via hydrogen bond formation with both glycine and diglycine. This is verified by hydrogen bond propensity calculations, molecular functionality analysis, and calculation of the time taken for a solute molecule to attach to the growing nucleus, which is an order of magnitude shorter than the estimated lifetime of the hydrogen bond. The effect of the heterosurface is of greater magnitude for diglycine than for glycine, which may be due to the heightened molecular complementarity between the hydrogen bond donor and acceptor sites on diglycine and the heterosurface.

Polymorph evolution during crystal growth studied by 3D electron diffraction

3D electron diffraction (3DED) has been used to follow polymorph evolution in the crystallization of glycine from aqueous solution. The three polymorphs of glycine which exist under ambient conditions follow the stability order β < α < γ. The least stable β polymorph forms within the first 3 min, but this begins to yield the α-form after only 1 min more. Both structures could be determined from continuous rotation electron diffraction data collected in less than 20 s on crystals of thickness ∼100 nm. Even though the γ-form is thermodynamically the most stable polymorph, kinetics favour the α-form, which dominates after prolonged standing. In the same sample, some β and one crystallite of the γ polymorph were also observed.

Cohesive properties of the crystalline phases of twenty proteinogenic α-aminoacids from first-principles calculations

Cohesive properties (lattice and cohesive energy of the crystal and corresponding sublimation enthalpy) of the complete set of twenty enantiopure anhydrous proteinogenic amino acids are investigated using first-principles calculations. In contrast to neutral amino acid molecules in the vapor phase, all amino acids form crystals in their zwitterionic form. Therefore, reliable ab initio calculations of the proton transfer energy are an indispensable step of such calculations. Simplifying procedures, designed to rationalize the computational cost of the quasi-harmonic approximation, which proves too demanding if performed fully at the given quantum level of theory, are presented and tested. For this purpose, atomic multipoles (up to the quadrupoles) for the amoeba force field are parametrized for all amino acid zwitterions. While the calculated lattice energies of the amino acids range from 235-458 kJ mol-1 in absolute value, the proton transfer energies typically amount to 100-220 kJ mol-1, which translates to sublimation enthalpies ranging from 117-202 kJ mol-1, appreciably exceeding the sublimation enthalpy values common for nonionic molecular crystals. Critically assessed experimental data on sublimation enthalpies are used as a benchmark for comparison of the data calculated in this work. Cohesive properties of most amino acids calculated in this work, combining the PBE-D3(BJ)/PAW and CCSD(T)-F12/aug-cc-pVDZ levels of theory used for predictions of the lattice energies and of the proton transfer energies, respectively, exhibit a reasonable agreement with the experiment. At the same time, this work contains the first published data on cohesive properties for several enantiopure amino acids.

Intermolecular Interactions in Functional Crystalline Materials: From Data to Knowledge

Intermolecular interactions of organic, inorganic, and organometallic compounds are the key to many composition–structure and structure–property networks. In this review, some of these relations and the tools developed by the Cambridge Crystallographic Data Center (CCDC) to analyze them and design solid forms with desired properties are described. The potential of studies supported by the Cambridge Structural Database (CSD)-Materials tools for investigation of dynamic processes in crystals, for analysis of biologically active, high energy, optical, (electro)conductive, and other functional crystalline materials, and for the prediction of novel solid forms (polymorphs, co-crystals, solvates) are discussed. Besides, some unusual applications, the potential for further development and limitations of the CCDC software are reported.

Pressure-induced isosymmetric phase transition in biurea

An isosymmetric phase transition of biurea has been found in which the molecules appear to “snap” from one conformer to another upon compression.

Discovery and recovery of delta p-aminobenzoic acid

A new high-pressure recoverable form has been observed in the model system, p-aminobenzoic acid.

Structural investigation and compression of a co-crystal of indomethacin and saccharin

Indomethacin : saccharin cocrystal has been studied under high pressure conditions and the amide interactions compared with previous high pressure studies.

High-pressure polymorphism in l-threonine between ambient pressure and 22 GPa

The amino acid l-threonine undergoes three phase transitions between ambient pressure and 22.3 GPa which modify both hydrogen bonding and the molecular conformation.

Behavior of intermolecular interactions in α-glycine under high pressure

Pressure-response on the crystal structure of deuterated α-glycine was investigated at room temperature, using powder and single-crystal X-ray diffraction, and powder neutron diffraction measurements under high pressure. No phase change was observed up to 8.7 GPa, although anisotropy of the lattice compressibility was found. No significant changes in the compressibility and the intramolecular distance between non-deuterated α-glycine and deuterated α-glycine were observed. Neutron diffraction measurements indicated the distance of the intermolecular D⋯O bond along with the c-axis increased with compression up to 6.4 GPa. The distance of another D⋯O bond along with the a-axis decreased with increasing pressure and became the shortest intermolecular hydrogen bond above 3 GPa. In contrast, the lengths of the bifurcated N-D⋯O and C-D⋯O hydrogen bonds, which are formed between the layers of the α-glycine molecules along the b-axis, decreased significantly with increasing pressure. The decrease of the intermolecular distances resulted in the largest compressibility of the b-axis, compared to the other two axes. The Hirshfeld analysis suggested that the reduction of the void region size, rather than shrinkage of the strong N-D⋯O hydrogen bonds, occurred with compression.