Polymorphism In Molecular Crystals Research Articles

The Origin of Delayed Polymorphism in Molecular Crystals Under Mechanochemical Conditions.

We show that mechanochemically driven polymorphic transformations can require extremely long induction periods, which can be tuned from hours to days by changing ball milling energy. The robust design and interpretation of ball milling experiments must account for this unexpected kinetics that arises from energetic phenomena unique to the solid state. Detailed thermal analysis, combined with DFT simulations, indicates that these marked induction periods are associated with processes of mechanical activation. Correspondingly, we show that the pre-activation of reagents can also lead to marked changes in the length of induction periods. Our findings demonstrate a new dimension for exerting control over polymorphic transformations in organic crystals. We expect mechanical activation to have a much broader implication across organic solid-state mechanochemistry.

Polymorphic Solid Solutions in Molecular Crystals: Tips, Tricks, and Switches.

Crystal polymorphism has been a topic of much interest for the past 20 years or so, especially since its scientific (and legal) importance to the pharmaceutical industry was realized. By contrast, the formation of solid solutions in molecular crystals has been overlooked despite its long-standing prevalence in the analogous field of inorganic crystals. Wilfully forgotten, crystalline molecular solid solutions may be very common in our world since molecular compounds are rarely produced with 100% purity, and impurities able to form solid solutions are difficult to reject via recrystallization. Given the importance of both polymorphism and solid solutions in molecular crystals, we share here some tips, tricks, and observations to aid in their understanding. First, we propose a nomenclature system fit for the description of molecular crystalline solid solutions capable of polymorphism (tips). Second, we highlight the challenges associated with their experimental and computational characterization (tricks). Third, we show that our recently reported observation that polymorph stabilities can change by virtue of solid solution formation is a general phenomenon, reporting it on a second system (switches). Our work focuses on the historically important compound benzamide forming solid solutions with nicotinamide and 3-fluorobenzamide.

Collective Variables for Conformational Polymorphism in Molecular Crystals.

Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long time scales (>1 μs). We present an efficient procedure for identifying collective variables that promote transitions between conformational polymorphs in molecular dynamics simulations. It involves applying a simple dimensionality reduction algorithm to data from short (∼ps) simulations of the isolated conformers that correspond to each polymorph. We demonstrate the utility of our method in the challenging case of the important energetic material, CL-20, which has three anhydrous conformational polymorphs at ambient pressure. Using these collective variables in Metadynamics simulations, we observe transitions between all solid polymorphs in the biased trajectories. We reconstruct the free energy surface and identify previously unknown defect and intermediate forms in the transition from one known polymorph to another. Our method provides insights into complex conformational polymorphic transitions of flexible molecular crystals.

A New Approach to Polymorphism in Molecular Crystals: Substrate‐Mediated Structures Revealed by Lattice Phonon Dynamics

AbstractThe issue of polymorphism in molecular crystals is discussed, taking into account the substrate‐mediated structures, that is, structures grown at the interface of different substrates. Bulk and thin films of a compound both share the potentiality to display different crystal forms. However, unlike bulk polymorphs, whose structures are determined by their different molecular packing, thin film structures depend very much on the molecular organization of the organic layers on the substrate, which may, or may not, lead to an ordered structure, depending on the nature of the interface and on the growth conditions. Based on large part in some of the authors’ recent works, these thin film structures are classified as distorted bulk, substrate‐selected and substrate‐stabilized polymorphs, with some subtle differences which may yield a polymorph to belong not exclusively to a single one of these categories. Some experiments are then focused upon, involving charge transport at the interface, as well as how far the effect of the surface goes. Furthermore, the authors comment on how the surface‐mediated structures evolve to the single crystal phase in the cases of pentacene and α‐sexithiophene. Finally, the transition from a 3‐ to a 2D regime of growth is shortly discussed in terms of low‐dimensional disorder.

Global analysis of the energy landscapes of molecular crystal structures by applying the threshold algorithm

Polymorphism in molecular crystals has important consequences for the control of materials properties and our understanding of crystallization. Computational methods, including crystal structure prediction, have provided important insight into polymorphism, but have usually been limited to assessing the relative energies of structures. We describe the implementation of the Monte Carlo threshold algorithm as a method to provide an estimate of the energy barriers separating crystal structures. By sampling the local energy minima accessible from multiple starting structures, the simulations yield a global picture of the crystal energy landscapes and provide valuable information on the depth of the energy minima associated with crystal structures. We present results from applying the threshold algorithm to four polymorphic organic molecular crystals, examine the influence of applying space group symmetry constraints during the simulations, and discuss the relationship between the structure of the energy landscape and the intermolecular interactions present in the crystals.

The interplay of intra- and intermolecular errors in modeling conformational polymorphs.

Conformational polymorphs of organic molecular crystals represent a challenging test for quantum chemistry because they require careful balancing of the intra- and intermolecular interactions. This study examines 54 molecular conformations from 20 sets of conformational polymorphs, along with the relative lattice energies and 173 dimer interactions taken from six of the polymorph sets. These systems are studied with a variety of van der Waals-inclusive density functionals theory models; dispersion-corrected spin-component-scaled second-order Møller-Plesset perturbation theory (SCS-MP2D); and domain local pair natural orbital coupled cluster singles, doubles, and perturbative triples [DLPNO-CCSD(T)]. We investigate how delocalization error in conventional density functionals impacts monomer conformational energies, systematic errors in the intermolecular interactions, and the nature of error cancellation that occurs in the overall crystal. The density functionals B86bPBE-XDM, PBE-D4, PBE-MBD, PBE0-D4, and PBE0-MBD are found to exhibit sizable one-body and two-body errors vs DLPNO-CCSD(T) benchmarks, and the level of success in predicting the relative polymorph energies relies heavily on error cancellation between different types of intermolecular interactions or between intra- and intermolecular interactions. The SCS-MP2D and, to a lesser extent, ωB97M-V models exhibit smaller errors and rely less on error cancellation. Implications for crystal structure prediction of flexible compounds are discussed. Finally, the one-body and two-body DLPNO-CCSD(T) energies taken from these conformational polymorphs establish the CP1b and CP2b benchmark datasets that could be useful for testing quantum chemistry models in challenging real-world systems with complex interplay between intra- and intermolecular interactions, a number of which are significantly impacted by delocalization error.

Low Temperature and High-Pressure Study of Bending L-Leucinium Hydrogen Maleate Crystals

The polymorphism of molecular crystals is a well-known phenomenon, resulting in modifications of physicochemical properties of solid phases. Low temperatures and high pressures are widely used to find phase transitions and quench new solid forms. In this study, L-Leucinium hydrogen maleate (LLHM), the first molecular crystal that preserves its anomalous plasticity at cryogenic temperatures, is studied at extreme conditions using Raman spectroscopy and optical microscopy. LLHM was cooled down to 11 K without any phase transition, while high pressure impact leads to perceptible changes in crystal structure in the interval of 0.0–1.35 GPa using pentane-isopentane media. Surprisingly, pressure transmitting media (PTM) play a significant role in the behavior of the LLHM system at extreme conditions—we did not find any phase change up to 3.05 GPa using paraffin as PTM. A phase transition of LLHM to amorphous form or solid–solid phase transition(s) that results in crystal fracture is reported at high pressures. LLHM stability at low temperatures suggests an alluring idea to prove LLHM preserves plasticity below 77 K.

Azobenzene crystal polymorphism enables tunable photoinduced deformations, mechanical behaviors and photoluminescence properties

Tuning polymorphism in azobenzene molecular crystals enables them to exhibit a remarkable difference in photomechanical deformations, mechanical behaviors and luminescence properties.

Prediction of lattice energy of benzene crystals: A robust theoretical approach.

We present an inexpensive and robust theoretical approach based on the fragment molecular orbital methodology and the spin-ratio scaled second-order Møller-Plesset perturbation theory to predict the lattice energy of benzene crystals within 2 kJ⋅mol-1 . Inspired by the Harrison method to estimate the Madelung constant, the proposed approach calculates the lattice energy as a sum of two- and three-body interaction energies between a reference molecule and the surrounding molecules arranged in a sphere. The lattice energy converges rapidly at a radius of 13 Å. Adding the corrections to account for a higher correlated level of theory and basis set superposition for the Hartree Fock (HF) level produced a lattice energy of -57.5 kJ⋅mol-1 for the benzene crystal structure at 138 K. This estimate is within 1.6 kJ⋅mol-1 off the best theoretical prediction of -55.9 kJ⋅mol-1 . We applied this approach to calculate lattice energies of the crystal structures of phase I and phase II-polymorphs of benzene-observed at a higher temperature of 295 K. The stability of these polymorphs was correctly predicted, with phase II being energetically preferred by 3.7 kJ⋅mol-1 over phase I. The proposed approach gives a tremendous potential to predict stability of other molecular crystal polymorphs.

Polymorphism and Morphology Folklore

Polymorphism of molecular crystals was Joel Bernstein’s (1941–2019) scientific focus. Polymorphism also has been the subject of lore: (1) McCrone made popular the belief that the longer you study a...

Understanding the Correlation between Electronic Coupling and Energetic Stability of Molecular Crystal Polymorphs: The Instructive Case of Quinacridone

A crucial factor determining charge transport in organic semiconductors is the electronic coupling between the molecular constituents, which is heavily influenced by the relative arrangement of the molecules. This renders quinacridone, with its multiple, structurally fundamentally different polymorphs and their diverse intermolecular interactions an ideal test case for analyzing the correlation between the electronic coupling in a specific configuration and the configuration's energetic stability. To provide an in-depth analysis of this correlation, starting from the $\alpha$-polymorph of quinacridone, we also construct a coplanar model crystal. This allows us to systematically compare the displacement-dependence of the electronic coupling with that of the total energy. In this way, we identify the combination of Pauli repulsion and orbital rehybridization as the driving force steering the system towards a structure in which the electronic coupling is minimal (especially for the valence band and at small displacements). The general nature of these observations is supported by equivalent trends for an analogous pentacene model system. This underlines that the design of high-performance materials cannot rely on the "natural" assembly of the $\pi$-conjugated backbones of organic semiconductors into their most stable configurations. Rather, it must include the incorporation of functional groups that steer crystal packing towards more favorable structures, where aiming for short-axis displacements or realizing comparably large long-axis displacements appear as strategies worthwhile exploring.

Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems

AbstractThis report advances the hypothesis that multifunctional systems may be associated with multifunnel potential and free energy landscapes, with particular focus on biomolecules. It compares systems that exhibit single, double, and multiple competing structures, and contrasts multifunnel landscapes associated with misfolded amyloidogenic oligomers, which presumably do not arise as an evolutionary target. In this context, intrinsically disordered proteins could be considered intrinsically multifunctional molecules, associated with multifunnel landscapes. Potential energy landscape theory enables biomolecules to be treated in a common framework together with self‐organizing and multifunctional systems based on inorganic materials, atomic and molecular clusters, crystal polymorphs, and soft matter.

Reliable and practical computational description of molecular crystal polymorphs.

Reliable prediction of the polymorphic energy landscape of a molecular crystal would yield profound insight into drug development in terms of the existence and likelihood of late-appearing polymorphs. However, the computational prediction of molecular crystal polymorphs is highly challenging due to the high dimensionality of conformational and crystallographic space accompanied by the need for relative free energies to within 1 kJ/mol per molecule. In this study, we combine the most successful crystal structure sampling strategy with the most successful first-principles energy ranking strategy of the latest blind test of organic crystal structure prediction methods. Specifically, we present a hierarchical energy ranking approach intended for the refinement of relative stabilities in the final stage of a crystal structure prediction procedure. Such a combined approach provides excellent stability rankings for all studied systems and can be applied to molecular crystals of pharmaceutical importance.

Predicting polymorphism in molecular crystals using orientational entropy

We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant polymorphs. This idea, however, conflicts with the fact that crystallization has a timescale much longer than that of molecular simulations. To bring the process within affordable simulation time, we enhance the fluctuations of a collective variable by constructing a bias potential with well-tempered metadynamics. We use as a collective variable an entropy surrogate based on an extended pair correlation function that includes the correlation between the orientations of pairs of molecules. We also propose a similarity metric between configurations based on the extended pair correlation function and a generalized Kullback-Leibler divergence. In this way, we automatically classify the configurations as belonging to a given polymorph, using our metric and a hierarchical clustering algorithm. We apply our method to urea and naphthalene. We find different polymorphs for both substances, and one of them is stabilized at finite temperature by entropic effects.

Revisiting polymorphism of molecular crystals from the melt

Revisiting polymorphism of molecular crystals from the melt

First-principles stability ranking of molecular crystal polymorphs with the DFT+MBD approach.

The ability to accurately calculate the relative stabilities of numerous polymorphs of a given molecular crystal is crucial for the success of any molecular crystal structure prediction (CSP) approach. We have recently presented a hierarchical CSP procedure based on van-der-Waals-inclusive density functional theory [Hoja et al., 2018, arXiv:1803.07503], which yields excellent stability rankings for molecular crystals involving rigid molecules, salts, co-crystals, and highly polymorphic drug-like molecules. This approach includes many-body dispersion effects, exact exchange, as well as vibrational free energies. Here, we discuss in detail the impact of these effects on the obtained stability rankings. In addition, we assess the impact of the approximations used in our hierarchical procedure. We show that our procedure is generally robust to 1-2 kJ mol-1 for the systems in the latest CSP blind test but vibrational free energies for crystals involving flexible molecules would benefit from directly including many-body dispersion interactions. In addition, we also discuss the effect of temperature on the structure of molecular crystals and a simple but effective method for estimating anharmonic effects.

Tuning crystal polymorphs of a π-extended tetrathiafulvalene-based cruciform molecule towards high-performance organic field-effect transistors

It is a common phenomenon for organic semiconductors to crystallize in two or more polymorphs, leading to various molecular packings and different charge transport properties. Therefore, it is a crucial issue of tuning molecular crystal polymorphs (i.e., adjusting the same molecule with different packing arrangements in solid state) towards efficient charge transport and high performance devices. Here, the choice of solvent had a marked effect on controlling the growth of α-phase ribbon and β-phase platelet during crystallization for an indenofluorene (IF) π-extended tetrathiafulvalene (TTF)-based cruciform molecule, named as IF-TTF. The charge carrier mobility of the α-phase IF-TTF crystals was more than one order of magnitude higher than that of β-phase crystals, suggesting the importance of reasonably tuning molecular packing in solid state for the improvement of charge transport in organic semiconductors.

ChemInform Abstract: Van der Waals Dispersion Interactions in Molecular Materials: Beyond Pairwise Additivity

AbstractReview: [115 refs.

Temperature-Mediated Polymorphism in Molecular Crystals: The Impact on Crystal Packing and Charge Transport

We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V–1 s–1, while the mobility of the 1D structure is significantly lower, at 0.028 ...

Imaging molecular crystal polymorphs and their polycrystalline microstructures in situ by ultralow-frequency Raman spectroscopy.

Ultralow-frequency Raman spectroscopy that can measure vibrational bands at as low as ±10 cm(-1) has enabled facile in situ imaging of polycrystalline microstructures such as grains and grain boundaries with high polymorph specificity. We demonstrate this method by investigating microcrystals of two distinct polymorphs of 1,1'-binaphthyl using a microscope.