An Isosymmetric High-Pressure Phase Transition in α-Glycylglycine: A Combined Experimental and Theoretical Study

Structural and vibrational analysis of glycyl-L-phenylalanine and phase transition under high-pressure

The structural and vibrational properties of the glycyl-L-phenylalanine dipeptide were investigated using vibrational spectroscopy (Raman and infrared) and first-principle calculations. Raman spectroscopy measurements were performed between 100 and 3200 cm-1 and infrared spectroscopy from 100 and 3200 cm-1 under ambient conditions. The conformational analysis of the zwitterionic form of the dipeptide was performed using the B3LYP functional, the 6-311++ base set and the Polarizable Continuum Model of solvation, determining the lowest energy conformation and assigning the vibrational modes. The effect of pressure on the glycyl-1-phenylalanine crystal was investigated using the Raman spectroscopy between 0.0 and -7.1 GPa in the spectral region of 100 - 3200 cm-1. As a result, conformational changes around 1.0 GPa were observed in the lattice modes and in some internal modes, showing a reorganization of the molecule in the crystal. In the decompression process, it was observed that the conformational change is reversible and the original Raman spectrum is recoverd.

Review of Applications of Density Functional Theory (DFT) Quantum Mechanical Calculations to Study the High-Pressure Polymorphs of Organic Crystalline Materials

Since its inception, chemistry has been predominated by the use of temperature to generate or change materials, but applications of pressure of more than a few tens of atmospheres for such purposes have been rarely observed. However, pressure is a very effective thermodynamic variable that is increasingly used to generate new materials or alter the properties of existing ones. As computational approaches designed to simulate the solid state are normally tuned using structural data at ambient pressure, applying them to high-pressure issues is a highly challenging test of their validity from a computational standpoint. However, the use of quantum chemical calculations, typically at the level of density functional theory (DFT), has repeatedly been shown to be a great tool that can be used to both predict properties that can be later confirmed by experimenters and to explain, at the molecular level, the observations of high-pressure experiments. This article's main goal is to compile, analyze, and synthesize the findings of works addressing the use of DFT in the context of molecular crystals subjected to high-pressure conditions in order to give a general overview of the possibilities offered by these state-of-the-art calculations.

Ab Initio Crystal Structure Prediction of the Energetic Materials LLM-105, RDX, and HMX

Crystal structure prediction (CSP) is performed for the energetic materials (EMs) LLM-105 and α-RDX, as well as the α and β conformational polymorphs of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX), using the genetic algorithm (GA) code, GAtor, and its associated random structure generator, Genarris. Genarris and GAtor successfully generate the experimental structures of all targets. GAtor's symmetric crossover scheme, where the space group symmetries of parent structures are treated as genes inherited by offspring, is found to be particularly effective. However, conducting several GA runs with different settings is still important for achieving diverse samplings of the potential energy surface. For LLM-105 and α-RDX, the experimental structure is ranked as the most stable, with all of the dispersion-inclusive density functional theory (DFT) methods used here. For HMX, the α form was persistently ranked as more stable than the β form, in contrast to experimental observations, even when correcting for vibrational contributions and thermal expansion. This may be attributed to insufficient accuracy of dispersion-inclusive DFT methods or to kinetic effects not considered here. In general, the ranking of some putative structures is found to be sensitive to the choice of the DFT functional and the dispersion method. For LLM-105, GAtor generates a putative structure with a layered packing motif, which is desirable thanks to its correlation with low sensitivity. Our results demonstrate that CSP is a useful tool for studying the ubiquitous polymorphism of EMs and shows promise of becoming an integral part of the EM development pipeline.

Kinetic Controlled Chirality Transfer and Induction in 2D Hydrogen-Bonding Assemblies of Glycylglycine on Au(111)

Chirality transfer is of vital importance that dominates the structure and functionality of biological systems and living matters. External physical stimulations, e.g. polarized light and mechanical forces, can trigger the chirality symmetry breaking, leading to the appearance of the enantiomeric entities created from a chiral self-assembly of achiral molecule. Here, several 2D assemblies with different chirality, synthesized on Au(111) surface by using achiral building blocks - glycylglycine (digly), the simplest polypeptide are reported. By delicately tuning the kinetic factors, i.e., one-step slow/rapid deposition, or stepwise slow deposition with mild annealing, achiral square hydrogen-bond organic frameworks (HOF), homochiral rhombic HOF and racemic rectangular assembly are achieved, respectively. Chirality induction and related symmetry broken in assemblies are introduced by the handedness (H-bond configurations in principle) of the assembled motifs and then amplified to the entire assemblies via the interaction between motifs. The results show that the chirality transfer and induction of biological assemblies can be tuned by altering the kinetic factors instead of applying external forces, which may offer an in-depth understanding and practical approach to peptide chiral assembly on the surfaces and can further facilitate the design of desired complex biomolecular superstructures.

Voronoi Tessellations and the Shannon Entropy of the Pentagonal Tilings

We used the complete set of convex pentagons to enable filing the plane without any overlaps or gaps (including the Marjorie Rice tiles) as generators of Voronoi tessellations. Shannon entropy of the tessellations was calculated. Some of the basic mosaics are flexible and give rise to a diversity of Voronoi tessellations. The Shannon entropy of these tessellations varied in a broad range. Voronoi tessellation, emerging from the basic pentagonal tiling built from hexagons only, was revealed (the Shannon entropy of this tiling is zero). Decagons and hendecagon did not appear in the studied Voronoi diagrams. The most abundant Voronoi tessellations are built from three different kinds of polygons. The most widespread is the combination of pentagons, hexagons, and heptagons. The most abundant polygons are pentagons and hexagons. No Voronoi tiling built only of pentagons was registered. Flexible basic pentagonal mosaics give rise to a diversity of Voronoi tessellations, which are characterized by the same symmetry group. However, the coordination number of the vertices is variable. These Voronoi tessellations may be useful for the interpretation of the iso-symmetrical phase transitions.

Dynamics and Rheology of Supramolecular Assemblies at Elevated Pressures

A methodology to investigate the linear viscoelastic properties of complex fluids at elevated pressures (up to 120 MPa) is presented. It is based on a dynamic light scattering (DLS) setup coupled with a stainless steel chamber, where the test sample is pressurized by means of an inert gas. The viscoelastic spectra are extracted through passive microrheology. We discuss an application to hydrogen-bonding motif 2,4-bis(2-ethylhexylureido)toluene (EHUT), which self-assembles into supramolecular structures (tubes and filaments) in apolar solvents dodecane and cyclohexane. High levels of pressure (roughly above 20 MPa) are found to slow down the terminal relaxation process; however, the increases in the entanglement plateau modulus and the associated persistence length are not significant. The concentration dependence of the plateau modulus, relaxation times (fast and slow), and correlation length is practically the same for all pressures and exhibits distinct power-law behavior in different regimes. Within the tube phase in dodecane, the relative viscosity increment is weakly enhanced with increasing pressure and reaches a plateau at about 60 MPa. In fact, depending on concentration, the application of pressure in the tube regime may lead to a transition from a viscous (unentangled) to a viscoelastic (partially entangled to well-entangled) solution. For well-entangled, long tubes, the extent of the plateau regime (ratio of high- to low-moduli crossover frequencies) increases with pressure. The collective information from these observations is summarized in a temperature-pressure state diagram. These findings provide ingredients for the formulation of a solid theoretical framework to better understand and exploit the role of pressure in the structure and dynamics of supramolecular polymers.

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.

Vibrational and conformational analysis of structural phase transition in Estradiol 17β valerate with temperature

Estradiol 17β valerate (E2V) is a hormonal medicine widely used in hormone replacement therapy. E2V undergoes a reversible isosymmetric structural phase transition at low temperature (̴ 250 K) which results from the reorientation of the valerate chain. The reversible isosymmetric structural phase transition follows Ehrenfest's classification when described as first-order and Buerger's classification when classified as order-disorder. The conformational difference also induces changes in molecular torsional angles and on the hydrogen bond pattern. In combination with density functional theory (DFT) calculations, vibrational spectroscopy has been used to correlate the valerate chain modes with the modifications of the dihedral angles on phase transition. We are expecting improvement in our understanding of the phase transition mechanism driven by the temperature. The Conformational analysis reveals the feasible structures corresponding to changes in the dihedral angles associated with the valerate chain. The infrared spectra of calculated conformers are in good agreement with the experimental spectra of E2V structure recorded at room temperature revealing that the changes in valerate chain modes at 1115 cm^-1, 1200 cm^-1and 1415 cm^-1 fingerprint the molecular conformation. An investigation made to determine the ligand-protein interaction of E2V through docking against estrogen receptor (ER) reveals the inhibitive and agonist nature of E2V.

Can We Predict the Isosymmetric Phase Transition? Application of DFT Calculations to Study the Pressure Induced Transformation of Chlorothiazide

Isosymmetric structural phase transition (IPT, type 0), in which there are no changes in the occupation of Wyckoff positions, the number of atoms in the unit cell, and the space group symmetry, is relatively uncommon. Chlorothiazide, a diuretic agent with a secondary function as an antihypertensive, has been proven to undergo pressure-induced IPT of Form I to Form II at 4.2 GPa. For that reason, it has been chosen as a model compound in this study to determine if IPT can be predicted in silico using periodic DFT calculations. The transformation of Form II into Form I, occurring under decompression, was observed in geometry optimization calculations. However, the reverse transition was not detected, although the calculated differences in the DFT energies and thermodynamic parameters indicated that Form II should be more stable at increased pressure. Finally, the IPT was successfully simulated using ab initio molecular dynamics calculations.

Can We Predict the Pressure Induced Phase Transition of Urea? Application of Quantum Molecular Dynamics

Crystalline urea undergoes polymorphic phase transition induced by high pressure. Form I, which is the most stable form at normal conditions and Form IV, which is the most stable form at 3.10 GPa, not only crystallize in various crystal systems but also differ significantly in the unit cell dimensions. The aim of this study was to determine if it is possible to predict polymorphic phase transitions by optimizing Form I at high pressure and Form IV at low pressure. To achieve this aim, a large number of periodic density functional theory (DFT) calculations were performed using CASTEP. After geometry optimization of Form IV at 0 GPa Form I was obtained, performing energy minimization of Form I at high pressure did not result in Form IV. However, employing quantum molecular isothermal–isobaric (NPT) dynamics calculations enabled to accurately predict this high-pressure transformation. This study shows the potential of different approaches in predicting the polymorphic phase transition and points to the key factors that are necessary to achieve the success.