Mechanically Responsive Crystals: Analysis of Macroscopic Strain Reveals "Hidden" Processes.

Mechanical response of single crystals to light, temperature, and/or force-an emerging platform for the development of new organic actuating materials for soft robotics-has recently been quantitatively described by a general and robust mathematical model ( Chem. Rev . 2015 , 115 , 12440 - 12490 ). The model can be used to extract accurate activation energies and kinetics of solid-state chemical reactions simply by tracking the time-dependent bending of the crystal. Here we illustrate that deviations of the macroscopic strain in the crystal from that predicted by the model reveal the existence of additional, "hidden" chemical or physical processes, such as sustained structural relaxation between the chemical transformation and the resulting macroscopic deformation of the crystal. This is illustrated with photobendable single crystals of 4-hydroxy-2-(2-pyridinylmethylene)hydrazide, a photochemical switch that undergoes E-to-Z isomerization. The irreversible isomerization in these crystals results in amorphization and plastic deformation that are observed as poor correlation between the transformation extent and the induced strains. The occurrence of these processes was independently confirmed by X-ray diffraction and differential scanning calorimetry. An extended mathematical model is proposed to account for this complex mechanical response.

Anisotropic lattice softening near the structural phase transition in the thermosalient crystal 1,2,4,5-tetrabromobenzene.

The thermosalient effect (crystal jumping on heating) attracts much attention as both an intriguing academic phenomenon and in relation to its potential for the development of molecular actuators but its mechanism remains unclear. 1,2,4,5-Tetrabromobenzene (TBB) is one of the most extensively studied thermosalient compounds that has been shown previously to undergo a phase transition on heating, accompanied by crystal jumping and cracking. The difference in the crystal structures and intermolecular interaction energies of the low- and high-temperature phases is, however, too small to account for the large stress that arises over the course of the transformation. The energy is released spontaneously, and crystals jump across distances that exceed the crystal size by orders of magnitude. In the present work, the anisotropy of lattice strain is followed across the phase transition by single-crystal X-ray diffraction, focusing on the structural evolution from 273 to 343 K. A pronounced lattice softening is observed close to the transition point, with the structure becoming more rigid immediately after the phase transition. The diffraction studies are further supported by theoretical analysis of pairwise intermolecular energies and zone-centre lattice vibrations. Only three modes are found to monotonically soften up to the phase transition, with complex behaviour exhibited by the remaining lattice modes. The thermosalient effect is delayed with respect to the structural transformation itself. This can originate from the martensitic mechanism of the transformation, and the accumulation of stress associated with vibrational switching across the phase transition. The finding of this study sheds more light on the nature of the thermosalient effect in 1,2,4,5-tetrabromobenzene and can be applicable also to other thermosalient compounds.

Pressure-driven phase transition mechanisms revealed by quantum chemistry: l-serine polymorphs.

The present study delivers a computational approach for the understanding of the mechanism of phase transitions between polymorphs of small organic molecules. By using state of the art periodic DFT calculations augmented with dispersion corrections and an external stress tensor together with gas-phase cluster calculations, we thoroughly explained the reversible phase transitions of three polymorphs of the model system, namely crystalline l-serine in the pressure range up to 8 GPa. This study has shown that at the macroscopic level the main driving force of the phase transitions is the decrease in the volume of the crystal unit cell, which contributes to the enthalpy difference between the two forms, but not to the difference in their internal crystal energies. At the microscopic level we suggest that hydrogen bond overstrain leads to a martensitic-like, cooperative, displacive phase transition with substantial experimental hysteresis, while no such overstrain was found for the "normal type", atom per atom, reconstructive phase transition. The predicted pressures for the phase transitions deducted by the minimum enthalpy criterion are in reasonable agreement with the observed ones. By delivering unambiguous explanations not provided by previous studies and probably not accessible to experiment, this work demonstrates the predictive and explanatory power of quantum chemistry, confirming its indispensable role in structural studies.

Hypervalency in Organic Crystals: A Case Study of the Oxicam Sulfonamide Group.

The theoretical charge density of the active pharmaceutical ingredient piroxicam (PXM) was evaluated through density functional theory with a localized basis set. To understand the electronic nature of the sulfur atom within the sulfonamide group, a highly ubiquitous functional group in pharmaceutical molecules, a theoretical charge density study was performed on PXM within the framework of Bader theory. Focus is on developing a topological description of the sulfur atom and its bonds within the sulfonamide group. It was found that sulfur d-orbitals do not participate in bonding. Instead, the existence of a strongly polarized ("ionic") bonding structure is found through a combined topological and natural bonding orbital analysis. This finding is in stark contrast to long-held theories of the bonding structure of organic sulfonamide and has important implications for the parametrization of calculations using classical approaches.

Isoenergetic Polymorphism: The Puzzle of Tolazamide as a Case Study.

In the present case study of tolazamide we illustrate how many seemingly contradictory results that have been obtained from experimental observations and theoretical calculations can finally start forming a consistent picture: a "puzzle put together". For many years, tolazamide was considered to have no polymorphs. This made this drug substance unique among the large family of sulfonylureas, which was known to be significantly more prone to polymorphism than many other organic compounds. The present work employs a broad and in-depth analysis that includes the use of optical microscopy, single-crystal and powder X-ray diffraction, IR and Raman spectroscopies, DSC, semiempirical PIXEL calculations and DFT of three polymorphs of tolazamide. This case study shows how the polymorphs of a molecular crystal can be overlooked even if discovered serendipitously on one of numerous crystallizations, and how very different molecular packings can be practically isoenergetic but still crystallize quite selectively and transform one into another irreversibly upon heating.

Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species.

BACKGROUND: The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures. RESULTS: The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified. CONCLUSIONS: The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.

Polymorphism of paracetamol: a new understanding of molecular flexibility through local methyl dynamics.

This study focuses on the interplay of molecular flexibility and hydrogen bonding manifested in the monoclinic (form I) and orthorhombic (form II) polymorphs of paracetamol. By means of incoherent inelastic neutron scattering and density functional theory calculations, the relaxation processes related to the methyl side-group reorientation were analyzed in detail. Our computational study demonstrates the importance of considering quantum effects to explain how methyl reorientations and subtle conformational changes of the molecule are intertwined. Indeed, by analyzing the quasi elastic signal of the neutron data, we were able to show a unique and complex motional flexibility in form II, reflected by a coupling between the methyl and the phenyl reorientation. This is associated with a higher energy barrier of the methyl rotation and a lower Gibbs free energy when compared to form I. We put forward the idea that correlating solubility and molecular flexibility, through the relation between pKa and methyl rotation activation energy, might bring new insights to understanding and predicting drug bioavailability.

Radiation damage as a source of information.

The structural strain induced by temperature (`phonon pressure') and radiation damage (`defect pressure') is not necessarily correlated because of different underlying structural mechanisms. Here synchrotron experiments may provide new and yet unexplored opportunities. A recent publication by McMonagle et al. [(2024), Acta Cryst. B80, 13-18] is an excellent illustration of this.

Elastic and piezoelectric properties of ß-glycine - a quantum crystallography view on intermolecular interactions and a high-pressure phase transition.

The effect of hydrostatic compression on the elastic and electronic properties of ß-glycine was studied using a quantum crystallography approach. The interrelations between the changes in the microscopic quantum pressure in the electronic continuum, macroscopic compressibility and piezoelectricity were considered. The geometries and energies of hydrogen bonds in the crystal structure of ß-glycine were considered as functions of pressure before and after a phase transition into the ß'-phase in relation to the mechanism of this phase transition.

Structural changes in Rochelle salt on phase transitions revisited in a multi-temperature single-crystal X-ray diffraction study.

Phase transitions in Rochelle salt [sodium potassium L(+)-tartrate tetrahydrate] are revisited in a single-crystal X-ray diffraction multi-temperature study on cooling from 308 to 100 K across the high-temperature paraelectric (PE) ↔ ferroelectric ↔ low-temperature PE phase transition points. The results of structure refinement using three different models (a harmonic with and without disorder, and an anharmonic) were compared. The temperature dependencies of anisotropic displacement parameters (ADPs) and Ueq, which can be calculated directly from ADPs, for the low-temperature PE phase indicate clearly the dynamic nature of disorder of the K1 atoms. The structures of the low-temperature and the high-temperature PE phases are compared for the first time at multiple temperatures for each phase based on diffraction data collected from the same single crystal. The data indicate that the high-temperature and the low-temperature paraelectric phases are probably not two different phases, as was assumed in earlier works, but are structurally the same phase at different temperatures.

A comparison of the isostructural [Co(NH3)5NO2]XNO3 and [Co(NH3)5ONO]XNO3, X = Cl- or Br- in relation to nitro-nitrito linkage isomerization and photomechanical effects.

A new photoactive cobalt coordination compound, [Co(NH3)5NO2]BrNO3 (I), was obtained. Its crystal structure was shown to be isostructural with previously known [Co(NH3)5NO2]ClNO3 (II) for which linkage isomerization accompanied with mechanical response of the crystal has been already reported. Single crystals of I are transformed into nitrito isomer [Co(NH3)5ONO]BrNO3 (III) on irradiation with blue light (λ = 465 nm) without being destroyed. The crystal structure of III was also solved using single-crystal X-ray diffraction and compared with previously known [Co(NH3)5ONO]ClNO3 (IV). A detailed comparison of the structures of I, II, III and IV, including unit-cell parameters, the distribution of free space (in particular, reaction cavities around the nitro ligand), the lengths of hydrogen bonds, coordination and Voronoi-Dirichlet polyhedra has been performed. Single-crystal X-ray diffraction data were complemented with IR spectra. The effect of the replacement of Cl- by Br- on the crystal structure and on the nitro-nitrito photoisomerization is discussed.

An interpretation of the "anomalous" changes in the low-wavenumber range of the Raman spectra of L-alanine crystals.

"Anomalous changes" in the temperature- and pressure- dependences of the intensities and wavenumbers of the two low-wavenumber modes in Raman spectra of single-crystals of L-alanine have been interpreted in terms of a change in relative contributions of stretching and deformational components into the intermolecular vibrational bands. The relative contributions of the two components into a lattice vibration result from a change of relative orientations of molecules linked by hydrogen bonds in a three-dimensional network on variations of temperature or pressure.

Dynamics and thermodynamics of crystalline polymorphs. 2. ß-Glycine, analysis of variable-temperature atomic displacement parameters.

The molecular dynamics in the crystal and the thermodynamic functions of the ß-polymorph of glycine have been determined from a combination of molecular translation-libration frequencies reflecting the temperature dependence of atomic displacement parameters (ADPs), with frequencies derived from ONIOM(DFT:PM3) calculations on a 15-molecule ß-glycine cluster. ADPs have been obtained from variable-temperature diffraction data to 0.5 Å resolution collected with X-ray synchrotron (10-300 K) and sealed tube radiation (50-298 K). At the higher temperatures, the ADPs of ß-glycine from synchrotron are larger than those from sealed tube probably due to different experimental conditions. The lattice vibration frequencies from normal-mode analysis of ADPs and the internal vibration frequencies from ONIOM(B3LYP/6-311+G(2d,p):PM3) calculations agree with those from spectroscopy. Estimation of thermodynamic functions using the vibrational frequencies, the Einstein and Debye models of heat capacity, and the room-temperature compressibility provides C(p), H(vib), and S(vib) that agree with those from calorimetry. The ß-phase with higher H and G is found to be less stable than the α-phase in the temperature range of the experiment.

A high-pressure polymorph of chlorpropamide formed on hydrostatic compression of the α-form in saturated ethanol solution.

The crystal structure of the high-pressure polymorph (α') of an antidiabetic drug, chlorpropamide [4-chloro-N-(propylaminocarbonyl)benzenesulfonamide, C(10)H(13)ClN(2)O(3)S], which is formed at ~2.8 GPa from the α-polymorph (P2(1)2(1)2(1)) on hydrostatic compression in saturated ethanol solution, has been determined. As a result of the phase transition, the a, c and α parameters change jumpwise, whereas the changes in b parameter are continuous through the phase transition point. The high-pressure form is monoclinic (P2(1)11) and has Z' equal to 2, the two independent molecules differing in their conformations. The hydrogen bonds expand slightly in the high-pressure polymorph after the transition, and this expansion is interrelated with the changes in molecular conformations enabling a denser packing. The transition is reversible, but the crystal quality deteriorates as a result of multiple compression-decompression cycles, and a pseudomerohedral twinning accompanies the transformation.

Semi-maleate salts of L- and DL-serinium: the first example of chiral and racemic serinium salts with the same composition and stoichiometry.

L-serinium semi-maleate, (I), and DL-serinium semi-maleate, (II), both C3H8NO3(+)·C4H3O4(-), provide the first example of chiral and racemic anhydrous serine salts with the same organic anion. A comparison of their crystal structures with each other, with the structures of the pure components (L-serine polymorphs, DL-serine and maleic acid) and with other amino acid maleates is important for understanding the formation of the crystal structures, their response to variations in temperature and pressure, and structure-property relationships. As in other known crystal structures of amino acid maleates, there are no direct links between the semi-maleate anions in the two new structures. The serinium cations have different conformations in (I) and (II). In (I), they are linked into infinite chains via hydrogen bonds between carboxylic acid and hydroxy groups. In (II), there are no such chains formed by the serinium cations. In both (I) and (II), there are C2(2)(12) chains consisting of alternating semi-maleate anions and serinium cations. Two types of such chains are present in (I) and (II), termed C2(2)(12) and C2(2)(12)'. In (I), these chains, lying in the same plane, are further linked to each other via hydrogen bonds, whereas in (II) they are not.

Betaine 0.77-perhydrate 0.23-hydrate and common structural motifs in crystals of amino acid perhydrates.

The title compound, betaine 0.77-perhydrate 0.23-hydrate, (CH3)3N(+)CH2COO(-)·0.77H2O2·0.23H2O, crystallizes in the orthorhombic noncentrosymmetric space group Pca2(1). Chiral molecules of hydrogen peroxide are positionally disordered with water molecules in a ratio of 0.77:0.23. Betaine, 2-(trimethylazaniumyl)acetate, preserves its zwitterionic state, with a positively charged ammonium group and a negatively charged carboxylate group. The molecular conformation of betaine here differs from the conformations of both anhydrous betaine and its hydrate, mainly in the orientation of the carboxylate group with respect to the C-C-N skeleton. Hydrogen peroxide is linked via two hydrogen bonds to carboxylate groups, forming infinite chains along the crystallographic a axis, which are very similar to those in the crystal structure of betaine hydrate. The present work contributes to the understanding of the structure-forming factors for amino acid perhydrates, which are presently attracting much attention. A correlation is suggested between the ratio of amino acid zwitterions and hydrogen peroxide in the unit cell and the structural motifs present in the crystal structures of all currently known amino acids perhydrates. This can help to classify the crystal structures of amino acid perhydrates and to design new crystal structures.

A new structure of a serotonin salt: comparison and conformational analysis of all known serotonin complexes.

Four serotonin salt structures (serotonin adipate, C10H13N2O(+)·C6H9O4(-), is a previously unknown structure) were analysed to understand the influence of the anion on serotonin conformation. Hydrogen bonding alone favours a flat conformation, whereas additional stacking interactions between ions may possibly account for the nonplanar conformation. Since molecular conformation, stability and biological activity are interrelated, one can consider influencing the chemical and biological properties of serotonin by selecting an appropriate counter-ion for salt formation.

Dynamic single crystals: kinematic analysis of photoinduced crystal jumping (the photosalient effect).

Crystals on the move: If they are subjected to a strong light stimulus, crystals of the cobalt coordination compound [Co(NH3)5(NO2)]Cl(NO3) undergo sudden jumps and leap over distances 10(2)-10(5) times their own size to release the strain that accumulates in their interior. The first quantitative kinematic analysis of this phenomenon is reported. The observed effect could be employed for actuation on the macroscopic scale.

A high-pressure single-crystal X-ray diffraction study of potassium guaninate hydrate, K+·C5H4N5O-·H2O.

The crystal structure of potassium guaninate hydrate, K+·C5H4N5O-·H2O, was studied in the pressure range of 1 atm to 7.3 GPa by single-crystal diffraction using synchrotron radiation and a laboratory X-ray diffraction source. Structural strain was compared to that of the same salt hydrate on cooling, and in 2Na+·C5H3N5O2-·7H2O under hydrostatic compression and on cooling. A polymorphic transition into a new, incommensurately modulated, phase was observed at ∼4-5 GPa. The transition was reversible with a hysteresis: the satellite reflections disappeared on decompression to ∼1.4 GPa.

Application of incoherent inelastic neutron scattering in pharmaceutical analysis: relaxation dynamics in phenacetin.

This study centers on the use of inelastic neutron scattering as an alternative tool for physical characterization of solid pharmaceutical drugs. On the basis of such approach, relaxation processes in the pharmaceutical compound phenacetin (p-ethoxyacetanilide, C(10)H(13)NO(2)) were evidenced on heating between 2 and 300 K. By evaluating the mean-square displacement obtained from the elastic fixed window approach, using the neutron backscattering technique, a crossover of the molecular fluctuations between harmonic and nonharmonic dynamical regimes around 75 K was observed. From the temperature dependence of the quasi-elastic line-width, summed over the total Q range explored by the time-of-flight technique, it was possible to attribute the onset of this anharmonicity to methyl group rotations. Finally, using density functional theory-based methods, we were able to calculate the lattice vibrations in the harmonic approximation. The overall spectral profile of the calculated partial contributions to the generalized density of states compares satisfactorily to the experimental spectra in the region of the lattice modes where the intermolecular interactions are expected to play an important role. This study contributes to understanding the relationships between intermolecular hydrogen bonds, intramolecular dynamics, and conformational flexibility in pharmaceuticals on a molecular level, which can help in evaluating phase stability with respect to temperature variations on processing or on storage, and is related to control of polymorphism and pseudopolymorphism.