The Crystal Polymorphism of Tetrolic Acid (CH3CCCOOH): A Molecular Dynamics Study of Precursors in Solution, and a Crystal Structure Generation

Biased Bowl-Direction of Monofluorosumanene in the Solid State

A new curved π-conjugated molecule 1-fluorosumanene (1) was designed and synthesized that possesses one fluorine atom on the benzylic carbon of sumanene. This compound can exhibit bowl inversion in solution, leading to the formation of two diastereomers, 1endo and 1exo, with different dipole moments. Experimental and theoretical investigation revealed an energetical relationship among 1exo, 1endo, and solvent to realize the various endo:exo ratios in the single crystals of 1 depending on the crystallization solvent. Significantly, the molecular dynamics (MD) simulations revealed that 1exo positively worked for the elongation of the stacking structure and the final endo:exo ratio was affected by the relative stability difference between 1endo and 1exo derived by solvation. Such an arrangeable endo:exo ratio of 1 realized the preparation of unique materials showing a different dielectric response from the same molecule 1 just by changing the crystallization solvent.

Unveiling the self-association and desolvation in crystal nucleation

As the first step in the crystallization process, nucleation has been studied by many researchers. In this work, phenacetin (PHEN) was selected as a model compound to investigate the relationship between the solvent and nucleation kinetics. Induction times at different supersaturation in six solvents were measured. FTIR and NMR spectroscopy were employed to explore the solvent-solute interactions and the self-association properties in solution. Density functional theory (DFT) was adopted to evaluate the strength of solute-solvent interactions and the molecular conformations in different solvents. Based on these spectroscopy data, molecular simulation and nucleation kinetic results, a comprehensive understanding of the relationship between molecular structure, crystal structure, solution chemistry and nucleation dynamics is discussed. Both the solute-solvent interaction strength and the supramolecular structure formed by the self-association of solute molecules affect the nucleation rate. The findings reported here shed new light on the molecular mechanism of nucleation in solution.

Overcoming the Solubility Barrier of Ibuprofen by the Rational Process Design of a Nanocrystal Formulation

Wet media milling, coupled with spay drying, is a commonly proposed formulation strategy for the production and solidification of nanosuspensions in order to overcome the solubility barrier of BCS Class II substances. However, the application of mechanically and thermally intensive processes is not straightforward in the cases of ductile and/or low melting point substances that may additionally be susceptible to eutectic formation. Using ibuprofen (IBU) as a model drug with non-favorable mechanical and melting properties, we attempt to rationalize nanocrystal formulation and manufacturing in an integrated approach by implementing Quality by Design (QbD) methodology, particle informatics techniques and computationally assisted process design. Wet media milling was performed in the presence of different stabilizers and co-milling agents, and the nanosuspensions were solidified by spray-drying. The effects of key process parameters (bead diameter, milling time and rotational speed) and formulation variables (stabilizer type and drug/stabilizer ratio) on the critical quality attributes (CQAs), i.e., Z-average size, polydispersity index (PDI), ζ-potential and redispersibility of spray-dried nanosuspensions were evaluated, while possible correlations between IBU free surface energy and stabilizer effectiveness were studied. The fracture mechanism and surface stabilization of IBU were investigated by computer simulation of the molecular interactions at the crystal lattice level. As a further step, process design accounting for mass-energy balances and predictive thermodynamic models were constructed to scale-up and optimize the design space. Contemplating several limitations, our multilevel approach offers insights on the mechanistic pathway applicable to the substances featuring thermosensitivity and eutectic tendency.

Insight into the role of pre-assembly and desolvation in crystal nucleation: a case of p-nitrobenzoic acid

As one of the most important phenomena in crystallization, the crystal nucleation process has always been the focus of research. In this work, influences of pre-assembly species and the desolvation process on the crystal nucleation process were studied. p-Nitrobenzoic acid (PNBA) was taken as a model compound to investigate the relationship between solution chemistry and nucleation kinetics in seven different solvents. One unsolvated form and four solvates of PNBA were obtained and one of the solvates was newly discovered. The nucleation behaviours and nucleation kinetics of PNBA in the seven solvents were studied and analyzed. Density functional theory (DFT) and solvation energy calculation were adopted to evaluate the strength of solute-solvent interactions. Vibrational spectroscopy combined with molecular simulation was applied to reveal the pre-assembly species in the solution. Based on these results, a comprehensive understanding of the relationship between molecular structure, crystal structure, solution chemistry and nucleation dynamics was proposed and discussed. It was found that the structural similarity between solution chemistry and crystal structure, the interaction between specific sites and the overall strength of solvation will jointly affect the nucleation process.

Evaluation of General and Tailor Made Force Fields via X-ray Thermal Diffuse Scattering Using Molecular Dynamics and Monte Carlo Simulations of Crystalline Aspirin

We have performed a comparison of the experimental thermal diffuse scattering (TDS) from crystalline Aspirin (form I) to that calculated from molecular dynamics (MD) simulations based on a variety of general force fields and a tailor-made force field (TMFF). A comparison is also made with Monte Carlo (MC) simulations which use a "harmonic network" approach to describe the intermolecular interactions. These comparisons were based on the hypothesis that TDS could be a useful experimental data in validation of such simulation parameter sets, especially when calculations of dynamical properties (e.g., thermodynamic free energies) from molecular crystals are concerned. Currently such a validation of force field parameters against experimental data is often limited to calculation of specific physical properties, e.g., absolute lattice energies usually at 0 K or heat capacity measurements. TDS harvested from in-house or synchrotron experiments comprises highly detailed structural information representative of the dynamical motions of the crystal lattice. Thus, TDS is a well-suited experimental data-driven means of cross validating theoretical approaches targeted at understanding dynamical properties of crystals. We found from the results of our investigation that the TMFF and COMPASS (from the commercial software "Materials Studio") parameter sets gave the best agreement with experiment. From our homologous MC simulation analysis we are able to show that force constants associated with the molecular torsion angles are likely to be a strong contributing factor for the apparent reason why these aforementioned force fields performed better.

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations

The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments.

Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation

Recent observations of prenucleation species and multi-stage crystal nucleation processes challenge the long-established view on the thermodynamics of crystal formation. Here, we review and generalize extensions to classical nucleation theory. Going beyond the conventional implementation as has been used for more than a century now, nucleation inhibitors, precursor clusters and non-classical nucleation processes are rationalized as well by analogous concepts based on competing interface and bulk energy terms. This is illustrated by recent examples of species formed prior to/instead of crystal nucleation and multi-step nucleation processes. Much of the discussed insights were obtained from molecular simulation using advanced sampling techniques, briefly summarized herein for both nucleation-controlled and diffusion-controlled aggregate formation.

Density functional theory study of the oligomerization of carboxylic acids

We present a density functional theory [M06-2X/6-31+G(d,p)] study of the structures and free energies of formation of oligomers of four carboxylic acids (formic acid, acetic acid, tetrolic acid, and benzoic acid) in water, chloroform, and carbon tetrachloride. Solvation effects were treated using the SMD continuum solvation model. The low-lying energy structures of molecular complexes were located by adopting an efficient search procedure to probe the potential energy surfaces of the oligomers of carboxylic acids (CA)n (n = 2-6). The free energies of the isomers of (CA)n in solution were determined as the sum of the electronic energy, vibrational-rotational-translational gas-phase contribution, and solvation free energy. The assessment of the computational protocol adopted in this study with respect to the dimerization of acetic acid, (AA)2, and formic acid, (FA)2, located new isomers of (AA)2 and (FA)2 and gave dimerization constants in good agreement with the experimental values. The calculation of the self-association of acetic acid, tetrolic acid, and benzoic acid shows the following: (i) Classic carboxylic dimers are the most stable isomer of (CA)2 in both the gas phase and solution. (ii) Trimers of carboxylic acid are stable in apolar aprotic solvents. (iii) Molecular clusters consisting of two interacting classic carboxylic dimers (CA)4,(D+D) are the most stable type of tetramers, but their formation from the self-association of classic carboxylic dimers is highly unfavorable. (iv) For acetic acid and tetrolic acid the reactions (CA)2 + 2CA → (CA)4,(D+D) and (CA)3 + CA → (CA)4,(D+D) are exoergonic, but these aggregation pathways go through unstable clusters that could hinder the formation of tetrameric species. (v) For tetrolic acid the prenucleation species that are more likely to form in solution are dimeric and trimeric structures that have encoded structural motifs resembling the α and β solid forms of tetrolic acid. (vi) Stable tetramers of benzoic acid could form in carbon tetrachloride from the aggregation of trimers and monomers. (vii) Higher order clusters such as acetic acid pentamers and tetrolic acid hexamers are highly unstable in all solvation environments.

Molecular simulation of AG nanoparticle nucleation from solution: redox-reactions direct the evolution of shape and structure

The association of Ag(+) ions and the early stage of Ag nanoparticle nucleation are investigated from molecular dynamics simulations. Combining special techniques for tackling crystal nucleation from solution with efficient approaches to model redox-reactions, we unravel the structural evolution of forming silver nanoparticles as a function of the redox-potential in the solution. Within a range of only 1 eV, the redox-potential is demonstrated to have a drastic effect on both the inner structure and the overall shape of the forming particles. On the basis of our simulations we identify surface charge and its distribution as an atomic scale mechanism that accounts for creating/avoiding 5-fold coordination polyhedra and thus the degree of (multiple)-twinning in silver nanoparticles.

Nucleation of organic crystals--a molecular perspective

The outcome of synthetic procedures for crystalline organic materials strongly depends on the first steps along the molecular self-assembly pathway, a process we know as crystal nucleation. New experimental techniques and computational methodologies have spurred significant interest in understanding the detailed molecular mechanisms by which nuclei form and develop into macroscopic crystals. Although classical nucleation theory (CNT) has served well in describing the kinetics of the processes involved, new proposed nucleation mechanisms are additionally concerned with the evolution of structure and the competing nature of crystallization in polymorphic systems. In this Review, we explore the extent to which CNT and nucleation rate measurements can yield molecular-scale information on this process and summarize current knowledge relating to molecular self-assembly in nucleating systems.

A tale of two polymorphic pharmaceuticals: pyrithyldione and propyphenazone and their 1937 co-crystal patent

A co-crystal of two polymorphic active pharmaceutical ingredients (APIs), first reported and patented in 1937, has been prepared and thoroughly characterised, including crystal structure analysis. The existence of four crystal forms of one of the APIs, the sedative and hypnotic active pharmaceutical ingredient 3,3-diethyl-2,4(1H,3H)-pyridinedione, pyrithyldione (PYR), and of three crystal forms of the co-crystal-forming second API, the non-steroidal anti-inflammatory drug 1,2-dihydro-1,5-dimethyl-4-(1-methylethyl)-2-phenyl-3H-pyrazol-3-one, propyphenazone (PROP), has been reported previously, but they have only been partly characterised. For both compounds, none of the metastable forms exist at room temperature. DSC, hot-stage microscopy, X-ray diffraction and powder synchrotron X-ray diffraction were employed to characterise the polymorphic forms and to determine the crystal structures of forms I-III of PYR and forms I and II of PROP.

Size-dependent phase stability of a molecular nanocrystal: a proxy for investigating the early stages of crystallization

We make the link between the size-dependent phase stability of a nanocrystal and the phase-transition behavior of emerging crystallites during the earliest stages of crystallization, by using the former as a proxy for the latter. We outline an extension of the classical nucleation theory to describe crystal nucleation and subsequent transformations of competing polymorphic phases that characterize Ostwald's rule of stages. The theoretical framework reveals that the relative stability of the competing phases is a function of cluster size, which in turn varies with time, and therefore explains the complex transformation behavior observed for some systems. We investigated the stability of a nanocrystal of dl-norleucine by means of molecular simulation as a proxy for post-nucleation phase-transformation behavior in emerging crystallites. The simulations reveal that, for nanocrystals, the surface energy of the transition state of a transformation can dominate the barrier to phase change, thus causing metastable phases to be stabilized, not because they are thermodynamically stable, but rather due to kinetic hindering. Therefore, in the context of the earliest stages of crystal growth, not only does phase stability vary as a function of cluster size, and hence time, but thermodynamically feasible transformations are also prone to kinetic hindering.

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials.

Kinetic Insights into the Role of the Solvent in the Polymorphism of 5-Fluorouracil from Molecular Dynamics Simulations

We investigate the fundamental factors controlling polymorphism in 5-fluorouracil by performing molecular dynamics simulations of solutions of the compound in water, nitromethane, and wet nitromethane. Analysis of the effect of solvent on the initial aggregation of 5-fluorouracil molecules shows that the strong binding of water to the 5-fluorouracil molecule hinders the formation of the doubly hydrogen-bonded dimer and, by default, promotes close hydrophobic F...F interactions that are a feature of the unusual (Z' = 4) structure of form I. In contrast, doubly hydrogen-bonded dimers are observed to form readily in solution in dry nitromethane, consistent with the crystallization of the doubly hydrogen-bonded ribbon structure of form II from this solvent. When nitromethane is doped with water, the water forms hydrogen bonds to the solute, interfering with the formation of the doubly hydrogen-bonded dimers, which is consistent with the crystallization of form I from this hygroscopic solvent when it is not dried. Overall, the molecular dynamics simulations provide an atomistic picture of how solvent-solute interactions can significantly affect the initial association of 5-fluorouracil molecules to the extent that they determine the polymorphic outcome of the crystallization.

Simulation of phase separation in alcohol/water mixtures using two-body force field and standard molecular dynamics

Standard molecular dynamics simulations have been carried out on pure alcohols and alcohol/water mixtures. A simple atom-atom force field consisting of Lennard-Jones potentials plus coulombic terms over atomic point charges, but without explicit polarization terms, has been specifically fitted to reproduce several experimental properties of the pure alcohols, and has been used for mixtures by developing combination rules with the TIP3P water model. Densities, enthalpies of vaporization, radial distribution functions, self-diffusion coefficients, and rotational correlation functions of the pure alcohols are well reproduced and compare favorably with those from more sophisticated force fields. Some key aspects of the phase behaviour are correctly reproduced by the molecular dynamics simulation, showing a distinct demixing process for the n-butanol/water mixture as opposed to the stability of the t-butanol/water mixtures. The results demonstrate the ability of a molecular dynamics simulation, even in its standard form and with easily accessible time ranges, but with a carefully optimized force field, to simulate and, to a certain extent, predict the properties of binary mixtures.

Linking solution chemistry to crystal nucleation: the case of tetrolic acid

The application of FTIR spectroscopy to concentrated solutions of tetrolic acid shows, for the first time, a direct relationship between molecular self association in solution and H-bonded motifs in the subsequently crystallised solid phases.

Ab initio crystal structure prediction?I. Rigid molecules

A new methodology for the prediction of molecular crystal structures using only the atomic connectivity of the molecule under consideration is presented. The approach is based on the global minimization of the lattice enthalpy of the crystal. The modeling of the electrostatic interactions is accomplished through a set of distributed charges that are optimally and automatically selected and positioned based on results of quantum mechanical calculations. A four-step global optimization algorithm is used for the identification of the local minima of the lattice enthalpy surface. A parallelized implementation of the algorithm permits a much more extensive search of the solution space than has hitherto been possible, allowing the identification of crystal structures in less frequently occurring space groups and with more than one molecule in the asymmetric unit. The algorithm has been applied successfully to the prediction of the crystal structures of 3-aza-bicyclo(3.3.1)nonane-2,4-dione (P2(1)/a, Z' = 1), allopurinol (P2(1)/c, Z' = 1), 1,3,4,6,7,9-hexa-azacycl(3.3.3)azine (Pbca, Z' = 2), and triethylenediamine (P6(3)/m, Z' = 1). In all cases, the experimentally known structure is among the most stable predicted structures, but not necessarily the global minimum.

The prediction, morphology, and mechanical properties of the polymorphs of paracetamol

The analgesic drug paracetamol (acetaminophen) has two reported metastable polymorphs, one with better tableting properties than the stable form, and another which remains uncharacterized. We have therefore performed a systematic crystal structure prediction search for minima in the lattice energy of crystalline paracetamol. The stable monoclinic form is found as the global lattice-energy minimum, but there are at least a dozen energetically feasible structures found, including the well-characterized metastable orthorhombic phase. Hence, we require additional criteria to reduce the number of hypothetical crystal structures that can be considered as potential polymorphs. For this purpose the elastic properties and vapor growth morphology of the known and predicted structures have been estimated using second-derivative analysis and the attachment-energy model. These inexpensive calculations give reasonable agreement with the available experimental data for the known polymorphs. Some of the hypothetical structures are predicted to have a low growth rate and plate-like morphology, and so are unlikely to be observed. Another is only marginally mechanically stable. Thus, this first consideration of such properties in a crystal-structure prediction study appears to reduce the number of predicted polymorphs while leaving a few candidates for the uncharacterized form.

Interanionic (-)O-H...O(-) interactions: a solid-state and computational study of the ring and chain motifs

The (-)O-H...O(-) interaction formed by the anions HCO3-, HCO4, HC4O4 and HC5O5- (HA-), obtained upon monodeprotonation of the corresponding carbonic, oxalic, squaric and croconic acids (H2A), has been investigated theoretically and experimentally. The ring (RING) and chain (CHAIN) hydrogen bond motifs established between these anions have been analysed in terms of geometry and energy and their occurrence in crystalline salts investigated by searching the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). It has been shown that hydrogen carbonates form RINGs, with the notable exception of NaHCO3, while only CHAINs are known for hydrogen oxalates. Hydrogen squarates and hydrogen croconates can form both RINGs and CHAINs. The structures of Rb- and Cs- hydrogen croconates, which present the two alternative motifs, have been discussed together with that of the hydrated salt NaHC5O5.H2O. The relationship between RING and CHAIN has been examined in the light of ab initio calculations. A rigorous quantum chemical study of the nature of the interanionic (-)O-H...O(-) interaction in both vacuum and condensed phase has shown that the interaction energy is dominated by the electrostatic component which becomes attractive at short O...O distances (less than 2.5 A) if the net ionic charge on the anion is delocalised away from the -OH group. It has been demonstrated that the RING motif is slightly metastable with respect to dissociation in the gas phase, but becomes stable in the crystal owing to the influence of the Madelung field. However, the CHAIN motif is unstable both in the gas phase and in the crystal. It is argued that interanionic (-)O-H...O(-) interactions ought to be regarded as stabilising bonding interactions rather than proper intermolecular hydrogen bonds because the RING and CHAIN aggregates are not energetically stable on an absolute scale of bonding energy (i.e., in the absence of counterions). The presence of very short non-hydrogen-bridged O...O contacts resulting from charge compression of polyatomic anions bridged by alkali cations is also discussed.

Examples of successful crystal structure prediction: polymorphs of primidone and progesterone

The field of crystal structure prediction and its potential value to the pharmaceutical industry is described. The process of structure prediction employed here is summarized and the results of its application to primidone and progesterone are reported. It is shown that the process successfully generates the known polymorphs of these molecules, starting from the molecular structure alone. Observations related to the application of the structure prediction process are reported.