Spiers Memorial Lecture: Mechanochemistry, tribochemistry, mechanical alloying - retrospect, achievements and challenges.

The paper presents a view on the achievements, challenges and prospects of mechanochemistry. The extensive reference list can serve as a good entry point to a plethora of mechanochemical literature.

Relating Excited States to the Dynamics of Macroscopic Strain in Photoresponsive Crystals.

Exposure of a photoreactive single crystal to light with a wavelength offset from its absorption maximum can have two distinct effects. The first is the "direct" effect, wherein the excited state generated in individual chemical species is influenced. The second is the "indirect" effect, which describes the penetration of light into the crystal and hence the spatial propagation and completeness of transformation. We illustrate using the nitro-nitrito isomerization of [Co(NH3)5NO2]Cl(NO3) as an example that the direct and indirect effects can be independently determined. This is achieved by comparing the dynamics of macroscopic crystal deformation (bending curvature and crystal elongation) induced by the photochemical reaction when irradiating a crystal at the absorption maximum and at different band edges (above or below the maximum) of the same band. Quantitative description of the macroscopic strain dynamics in comparison with experiments allowed us to suggest that irradiation at different tails of the same absorption band causes isomerization to proceed via different excited states and an additional photochemical reaction (presumably, reverse nitrito-nitro isomerization) can occur on irradiation at the ligand-field band edges.

Deletion Variants of Autotransporter from Psychrobacter cryohalolentis Increase Efficiency of 10FN3 Exposure on the Surface of Escherichia coli Cells.

The autotransporter AT877 from Psychrobacter cryohalolentis belongs to the family of outer membrane proteins containing N-terminal passenger and C-terminal translocator domains that form the basis for the design of display systems on the surface of bacterial cells. It was shown in our previous study that the passenger domain of AT877 can be replaced by the cold-active esterase EstPc or the tenth domain of fibronectin type III (10Fn3). In order to increase efficiency of the 10Fn3 surface display in Escherichia coli cells, four deletion variants of the Fn877 hybrid autotransporter were obtained. It was demonstrated that all variants are present in the membrane of bacterial cells and facilitate binding of the antibodies specific against 10Fn3 on the cell surface. The highest level of binding is provided by the variants Δ239 and Δ310, containing four and seven beta-strands out of twelve that comprise the structure of the translocator domain. Using electrophoresis under semi-native conditions, presence of heat modifiability in the full-size Fn877 and its deletion variants was demonstrated, which indicated preservation of beta structure in their molecules. The obtained results could be used to optimize the bacterial display systems of 10Fn3, as well as of other heterologous passenger domains.

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.

Mechanochemistry of inorganic and organic systems: what is similar, what is different?

Mechanochemistry of inorganic solids is a well-established field. In the last decade mechanical treatment has become increasingly popular as a method for achieving selective and "greener" syntheses also in organic systems. New groups and researchers enter the field of mechanochemistry, often re-discovering many of the previously known facts and effects, while at the same time neglecting other important concepts. The author of this contribution has long been involved in mechanochemical research in both inorganic and organic systems. The aim of this contribution is to provide an overview of the basic concepts of mechanochemistry in relation to inorganic and organic systems.

Relating solvatochromism and solvatomorphism in organic dyes using high pressure.

By using complementary experimental methods including in situ high-pressure single-crystal X-ray diffraction and UV-Vis spectroscopy, the intricate connection between solvatochromism and solvatomorphism has been elucidated in a recent publication [Sobczak & Katrusiak (2024). IUCrJ, 11, 528-537]. The connection was demonstrated for an important pigment - Reichardt's dye - with potential applications in nonlinear optoelectronics and molecular pressure sensor development.

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 comparative study of the effect of high-pressure and low temperature on the crystal structure of lithium xanthinate hydrate.

The crystal structure of lithium xanthinate hydrate was studied by single crystal X-ray diffraction and Raman spectroscopy on cooling to 100 K and under compression to 5.3 GPa. A phase transition at ∼4 GPa is observed. No phase transitions occur on cooling. Anisotropy of lattice strain and changes in intermolecular interactions are compared.

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.