CrystalClear: an open, modular protocol for predicting molecular crystal growth from solution

We present a new protocol for the prediction of free energies that determine the growth of sites in molecular crystals for subsequent use in Monte Carlo simulations using tools such as CrystalGrower [Hill et al., Chemical Science, 2021, 12, 1126-1146]. Key features of the proposed approach are that it requires minimal input, namely the crystal structure and solvent only, and provides automated, rapid generation of the interaction energies. The constituent components of this protocol, namely interactions between molecules (growth units) in the crystal, solvation contributions and treatment of long-range interactions are described in detail. The power of this method is shown via prediction of crystal shapes for ibuprofen grown from ethanol, ethyl acetate, toluene and acetonitrile, adipic acid grown from water, and five polymorphs (ON, OP, Y, YT04 and R) of ROY (5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile), with promising results. The predicted energies may be used directly or subsequently refined against experimental data, facilitating insight into the interactions governing crystal growth, while also providing a prediction of the solubility of the material. The protocol has been implemented in standalone, open-source software made available alongside this publication.

Tools shaping drug discovery and development

Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.

Mechanical Anisotropy and Tabletability of Famotidine Polymorphs

In the drug development process, early characterization of solid forms can help to envisage the bulk processability of a powder, which should assist in selecting an optimal solid form. In...

Crystal surface defects as possible origins of cocrystal dissociation

Atomic force microscopy is used as a characterisation tool to investigate cocrystal dissociation under high relative humidity. Caffeine–glutaric acid as a model system showed possible role of crystal surface defects in the process of cocrystal dissociation.

Use of Atomic Force Microscopy (AFM) to monitor surface crystallization in caffeine-oxalic acid (CAFOXA) cocrystal compacts

Our objective was to monitor the surface crystallization in disordered caffeine-oxalic acid (CAFOXA) cocrystals following exposure to elevated water vapor pressure. This was accomplished using atomic force microscopy (AFM). Disorder was induced in the cocrystal particles by the common pharmaceutical unit operations of milling and compaction. The 'activated' solid, upon exposure to elevated water vapor pressure, had a high propensity to sorb water. This led to a rise in molecular mobility and the surface underwent rapid crystallization to form needle shaped crystals of CAFOXA. Using AFM height and phase imaging, we were able to directly visualize phase transformations on the compact surface. The milled compacts exhibited higher processing induced disorder than the unmilled compacts, thereby accelerating the surface recrystallization.

Understanding stress-induced disorder and breakage in organic crystals: beyond crystal structure anisotropy

Crystal engineering has advanced the strategies for design and synthesis of organic solids with the main focus being on customising the properties of the materials. Research in this area has a significant impact on large-scale manufacturing, as industrial processes may lead to the deterioration of such properties due to stress-induced transformations and breakage. In this work, we investigate the mechanical properties of structurally related labile multicomponent solids of carbamazepine (CBZ), namely the dihydrate (CBZ·2H2O), a cocrystal of CBZ with 1,4-benzoquinone (2CBZ·BZQ) and the solvates with formamide and 1,4-dioxane (CBZ·FORM and 2CBZ·DIOX, respectively). The effect of factors that are external (e.g. impact stressing) and/or internal (e.g. phase transformations and thermal motion) to the crystals are evaluated. In comparison to the other CBZ multicomponent crystal forms, CBZ·2H2O crystals tolerate less stress and are more susceptible to breakage. It is shown that this poor resistance to fracture may be a consequence of the packing of CBZ molecules and the orientation of the principal molecular axes in the structure relative to the cleavage plane. It is concluded, however, that the CBZ lattice alone is not accountable for the formation of cracks in the crystals of CBZ·2H2O. The strength and the temperature-dependence of electrostatic interactions, such as hydrogen bonds between CBZ and coformer, appear to influence the levels of stress to which the crystals are subjected that lead to fracture. Our findings show that the appropriate selection of coformer in multicomponent crystal forms, targetting superior mechanical properties, needs to account for the intrinsic stress generated by molecular vibrations and not solely by crystal anisotropy. Structural defects within the crystal lattice, although highly influenced by the crystallisation conditions and which are especially difficult to control in organic solids, may also affect breakage.

Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior

Direct-acting antiviral regimens have transformed therapeutic management of hepatitis C across all prevalent genotypes. Most of the chemical matter in these regimens comprises molecules well outside the traditional drug development chemical space and presents significant challenges. Herein, the implications of high conformational flexibility and the presence of a 15-membered macrocyclic ring in paritaprevir are studied through a combination of advanced computational and experimental methods with focus on molecular chameleonicity and crystal form complexity. The ability of the molecule to toggle between high and low 3D polar surface area (PSA) conformations is underpinned by intramolecular hydrogen bonding (IMHB) interactions and intramolecular steric effects. Computational studies consequently show a very significant difference of over 75 Ų in 3D PSA between polar and apolar environments and provide the structural basis for the perplexingly favorable passive permeability of the molecule. Crystal packing and protein binding resulting in strong intermolecular interactions disrupt these intramolecular interactions. Crystalline Form I benefits from strong intermolecular interactions, whereas the weaker intermolecular interactions in Form II are partially compensated by the energetic advantage of an IMHB. Like Form I, no IMHB is observed within the receptor-bound conformation; instead, an intermolecular H-bond contributes to the potency of the molecule. The choice of metastable Form II is derisked through strategies accounting for crystal surface and packing features to manage higher form specific solid-state chemical reactivity and specific processing requirements. Overall, the results show an unambiguous link between structural features and derived properties from crystallization to dissolution, permeation, and docking into the protein pocket.

A combined approach to characterize ligand-induced solid-solid phase transitions in biomacromolecular crystals

Solid-solid phase transitions (SSPTs) are widespread naturally occurring phenomena. Understanding the molecular mechanisms and kinetics of SSPTs in various crystalline materials, however, has been challenging due to technical limitations. In particular, SSPTs in biomacromolecular crystals, which may involve large-scale changes and particularly complex sets of interactions, are largely unexplored, yet may have important implications for time-resolved crystallography and for developing synthetic biomaterials. The adenine riboswitch (riboA) is an RNA control element that uses ligand-induced conformational changes to regulate gene expression. Crystals of riboA, upon the addition of a ligand, undergo an SSPT from monoclinic to triclinic to orthorhombic. Here, solution atomic force microscopy (AFM) and polarized video microscopy (PVM) are used to characterize the multiple transition states throughout the SSPT in both the forward and the reverse directions. This contribution describes detailed protocols for growing crystals directly on mica or glass surfaces for AFM and PVM characterization, respectively, as well as methods for image processing and phase-transition kinetics analysis.

In situ nanoscale visualization of solvent effects on molecular crystal surfaces

Atomic force microscopy and molecular dynamics simulations probed the crystallinity and hydrophobicity of a paracetamol crystal surface in water–ethanol mixtures. We observe the formation of a dynamic heterogenous disordered surface (DHDS) layer.

Advances in Atomic Force Microscopy: Weakly Perturbative Imaging of the Interfacial Water

The structure and dynamics of interfacial water, determined by the water-interface interactions, are important for a wide range of applied fields and natural processes, such as water diffusion (Kim et al., 2013), electrochemistry (Markovic, 2013), heterogeneous catalysis (Over et al., 2000), and lubrication (Zilibotti et al., 2013). The precise understanding of water-interface interactions largely relies on the development of atomic-scale experimental techniques (Guo et al., 2014) and computational methods (Hapala et al., 2014b). Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields (Ichii et al., 2012; Shiotari and Sugimoto, 2017; Peng et al., 2018a). In this perspective, we review the recent progress in the noncontact atomic force microscopy (nc-AFM) imaging and AFM simulation techniques and discuss how the newly developed techniques are applied to study the properties of interfacial water. The nc-AFM with the quadrupole-like CO-terminated tip can achieve ultrahigh-resolution imaging of the interfacial water on different surfaces, trace the reconstruction of H-bonding network and determine the intrinsic structures of the weakly bonded water clusters and even their metastable states. In the end, we present an outlook on the directions of future AFM studies of interfacial water as well as the challenges faced by this field.

Implication of Differential Surface Anisotropy on Biopharmaceutical Performance of Polymorphic Forms of Ambrisentan

The aim of the present study was to compare the dissolution rate and in vivo biopharmaceutical performance of 2 polymorphic forms (form I and II) of ambrisentan and correlate with their surface molecular environment. Dominance of various functionalities on the surface of specific crystal facets of both forms was predicted by Bravais-Friedel-Donnay-Harker method. Hirshfeld surface analysis maps and 2D fingerprint plots indicate a difference in shape index, curvedness, and relative percentage contribution of various contacts in both forms. Pre- and post-intrinsic dissolution compact studied by atomic force microscopy showed a significant difference in surface roughness and defects formation in form II as compared to form I which is attributed to the presence of more hydrophilic surfaces. The hydrophilic molecular surface environment of form II is ascribed to its improved intrinsic dissolution rate than form I. Furthermore, in vivo pharmacokinetic study also showed significantly higher AUC_0-24 and C_max in form II compared to form I. Overall, this study demonstrates that form I and II of ambrisentan exhibited the differential surface anisotropy which has significant implications on their biopharmaceutical performance.

Mechanical behavior of crystalline ionic porphyrins

Mechanical properties of six different binary ionic porphyrin crystals with variable morphologies were measured and correlated with their structural properties. These solids were formed from stoichiometric combinations of negatively charged tectons, meso-tetra(4-sulfonatophenyl)porphyrin (TSPP), Cu(II) meso-tetra(4-sulfonatophenyl)porphyrin (CuTSPP), Ni(II) meso-tetra (4-sulfonatophenyl)porphyrin (NiTSPP), and four different cationic tectons, namely, meso-tetra (4-pyridyl)porphyrin (TPyP), tetra([Formula: see text]-methyl-4-pyridyl)porphyrin (TMPyP), Cu(II) meso-tetra([Formula: see text]-methyl-4-pyridyl)porphyrin (CuTMPyP), Ni(II) meso-tetra([Formula: see text]-methyl-4-pyridyl)porphyrin (NiTMPyP), and tetra(4-aminophenyl)porphyrin (TAPP). Crystal structures were determined from single crystal and powder X-ray diffraction patterns. Scanning electron and atomic force microscopes (SEM and AFM) provided topographical information. The common arrangement of the porphyrin tectons within the crystals is consistent with alternating face-to-face molecular arrangement forming coherent columns along the fast-growing long axis which are held together by electrostatic and [Formula: see text]–[Formula: see text] interactions as well as hydrogen bonding. In acquiring the indentation data of the porphyrin crystals using AFM, stress was applied perpendicular to the direction where ionic and [Formula: see text]–[Formula: see text] bonds dominate the packing. At indent loads [Formula: see text]50 nN/nm2, all the porphyrin structures deformed elastically. Young’s modulus ([Formula: see text] values for the different crystals range from 6 to 28 GPa. In a broader perspective, this study highlights the extraordinary mechanical behavior of porphyrin assemblies formed by ionic self-assembly. Judicious selection of charged porphyrin synthons can yield crystalline materials with mechanical properties that combine the elastic characteristics of ‘soft’ polymers with the stiffness of composite materials. Such high-performance materials are excellent candidates for deformable optoelectronic devices.

Combining two distinctive intermolecular forces in designing ternary co-crystals and molecular salts of 1,3,5-trinitrobenzene, 9-anthracenecarboxylic acid and ten substituted pyridines

Coloured three component complexes are made using both charge transfer and hydrogen bonding intermolecular interactions.

Dislocations in molecular crystals

Dislocations in molecular crystals remain terra incognita. Owing to the complexity of molecular structure, dislocations in molecular crystals can be difficult to understand using only the foundational concepts devised over decades for hard materials. Herein, we review the generation, structure, and physicochemical consequences of dislocations in molecular crystals. Unlike metals, ceramics, and semiconductors, molecular crystals are often characterized by flexible building units of low symmetry, thereby limiting analysis, complicating modeling, and prompting new approaches to elucidate their role in crystallography from growth to mechanics. Such considerations affect applications ranging from plastic electronics and mechanical actuators to the tableting of pharmaceuticals.

AFM Colloidal Probe Measurements Implicate Capillary Condensation in Punch-Particle Surface Interactions during Tableting

Adhesion of the powders to the punches is a common issue during tableting. This phenomenon is known as sticking and affects the quality of the manufactured tablets. Defective tablets increase the cost of the manufacturing process. Thus, the ability to predict the tableting performance of the formulation blend before the process is scaled-up is important. The adhesive propensity of the powder to the tableting tools is mostly governed by the surface-surface adhesive interactions. Atomic force microscopy (AFM) colloidal probe is a surface characterization technique that allows the measurement of the adhesive interactions between two materials of interest. In this study, AFM steel colloidal probe measurements were performed on ibuprofen, MCC (microcrystalline cellulose), α-lactose monohydrate, and spray-dried lactose particles as an approach to modeling the punch-particle surface interactions during tableting. The excipients (lactose and MCC) showed constant, small, attractive, and adhesive forces toward the steel surface after a repeated number of contacts. In comparison, ibuprofen displayed a much larger attractive and adhesive interaction increasing over time both in magnitude and in jump-in/jump-out separation distance. The type of interaction acting on the excipient-steel interface can be related to a van der Waals force, which is relatively weak and short-ranged. By contrast, the ibuprofen-steel interaction is described by a capillary force profile. Even though ibuprofen is not highly hydrophilic, the relatively smooth surfaces of the crystals allow "contact flooding" upon contact with the steel probe. Capillary forces increase because of the "harvesting" of moisture-due to the fast condensation kinetics-leaving a residual condensate that contributes to increase the interaction force after each consecutive contact. Local asperity contacts on the more hydrophilic surface of the excipients prevent the flooding of the contact zone, and there is no such adhesive effect under the same ambient conditions. The markedly different behavior detected by force measurements clearly shows the sticky and nonsticky propensity of the materials and allows a mechanistic description.

In situ nanoscale observations of gypsum dissolution by digital holographic microscopy

Recent topography measurements of gypsum dissolution have not reported the absolute dissolution rates, but instead focus on the rates of formation and growth of etch pits. In this study, the in situ absolute retreat rates of gypsum (010) cleavage surfaces at etch pits, at cleavage steps, and at apparently defect-free portions of the surface are measured in flowing water by reflection digital holographic microscopy. Observations made on randomly sampled fields of view on seven different cleavage surfaces reveal a range of local dissolution rates, the local rate being determined by the topographical features at which material is removed. Four characteristic types of topographical activity are observed: 1) smooth regions, free of etch pits or other noticeable defects, where dissolution rates are relatively low; 2) shallow, wide etch pits bounded by faceted walls which grow gradually at rates somewhat greater than in smooth regions; 3) narrow, deep etch pits which form and grow throughout the observation period at rates that exceed those at the shallow etch pits; and 4) relatively few, submicrometer cleavage steps which move in a wave-like manner and yield local dissolution fluxes that are about five times greater than at etch pits. Molar dissolution rates at all topographical features except submicrometer steps can be aggregated into a continuous, mildly bimodal distribution with a mean of 3.0 µmolm-2 s-1 and a standard deviation of 0.7 µmolm-2 s-1.

Synchrotron FTIR mapping of mineralization in a microfluidic device

Fourier transform infrared micro-spectroscopy provides an effective means of performing rapid, non-destructive, and label-free analysis of specimens according to their vibrational modes. However, as water absorbs very strongly in the infrared region, analysis of aqueous solutions in transmission mode can suffer from problems with signal saturation. We here describe the fabrication of a novel microfluidic device that overcomes this problem. Devices with channel depths of just 3 μm were constructed from calcium fluoride using photolithography and hot embossing bonding, where calcium fluoride was selected due to its transparency in the IR region. The utility of this device was then demonstrated by employing it to follow the precipitation pathways of calcium sulfate and calcium carbonate using synchrotron FTIR micro-spectroscopy. Importantly, due to the high brightness provided by synchrotron radiation, and the fact that the reacting ions (HCO₃^-, CO₃^2- and SO₄^2-) and the different mineral polymorphs all have finger print spectra in the measured IR range, this method can be used to acquire time-resolved, hyperspectral maps of the mineral particles formed within the sample cell, and then study the interaction and evolution of particles. The data provide new insight into the formation pathway of a population of crystals in confined volumes, and demonstrate that this in situ, real-time detection system provides a powerful tool for studying crystallization processes.

Exploring complex transitions between polymorphs on a small scale by coupling AFM, FTIR and DSC: the case of Irganox 1076® antioxidant

Thanks to adhesion force mapping by AFM, solid/solid transitions are distinguished from melting/recrystallization processes occurring in the same temperature range.

Insights into pharmaceutical nanocrystal dissolution: a molecular dynamics simulation study on aspirin

The presented molecular dynamics simulations are the first simulations to reveal dynamic dissolution of a pharmaceutical crystal in its experimentally determined shape. Continuous dissolution at constant undersaturation of the surrounding medium is ensured by introducing a plane of sticky dummy atoms into the water slab. These atoms have a strong interaction potential with dissolved aspirin molecules, but interactions with water are excluded from the calculations. Thus, the number of aspirin molecules diffusing freely in solution is kept at a low value and continuous dissolution of the aspirin crystal is monitored. Further insight into face-specific dissolution is drawn. The dissolution mechanism of receding edges is found for the (001) plane. These findings are in good agreement with experimental results. While the proposed dissolution mechanism for the (100) plane is terrace sinking on a rough surface, no pronounced dissolution of the perfectly flat face is seen in the present work. Molecular simulations of pharmaceuticals in their experimentally obtained structure therefore have shown to be especially suited for the investigation of dissolving faces, where the edges have a pronounced effect. In contrast to previous studies a propagation of the dissolution front into the crystal face is reported, and the crystal bulk is stable over the whole simulation time of 150 ns.

Use of in situ atomic force microscopy to follow phase changes at crystal surfaces in real time

AFM of cocrystals: Atomic force microscopy can be used to observe phase changes at crystal surfaces where the transformation is accompanied by a change in the spacing between layers of molecules. The conversion of a metastable polymorph of the caffeine-glutaric acid cocrystal into the thermodynamically stable form was analyzed continuously in situ using intermittent-contact-mode atomic force microscopy.

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.

Crystal engineering: from molecule to crystal

How do molecules aggregate in solution, and how do these aggregates consolidate themselves in crystals? What is the relationship between the structure of a molecule and the structure of the crystal it forms? Why do some molecules adopt more than one crystal structure? Why do some crystal structures contain solvent? How does one design a crystal structure with a specified topology of molecules, or a specified coordination of molecules and/or ions, or with a specified property? What are the relationships between crystal structures and properties for molecular crystals? These are some of the questions that are being addressed today by the crystal engineering community, a group that draws from the larger communities of organic, inorganic, and physical chemists, crystallographers, and solid state scientists. This Perspective provides a brief historical introduction to crystal engineering itself and an assessment of the importance and utility of the supramolecular synthon, which is one of the most important concepts in the practical use and implementation of crystal design. It also provides a look to the future from the viewpoint of the author, and indicates some directions in which this field might be moving.

Nanoindentation in crystal engineering: quantifying mechanical properties of molecular crystals

Nanoindentation is a technique for measuring the elastic modulus and hardness of small amounts of materials. This method, which has been used extensively for characterizing metallic and inorganic solids, is now being applied to organic and metal-organic crystals, and has also become relevant to the subject of crystal engineering, which is concerned with the design of molecular solids with desired properties and functions. Through nanoindentation it is possible to correlate molecular-level properties such as crystal packing, interaction characteristics, and the inherent anisotropy with micro/macroscopic events such as desolvation, domain coexistence, layer migration, polymorphism, and solid-state reactivity. Recent developments and exciting opportunities in this area are highlighted in this Minireview.