Coformer Replacement as an Indicator for Thermodynamic Instability of Cocrystals: Competitive Transformation of Caffeine:Dicarboxylic Acid

yesThe thermodynamic stability of caffeine (CA) cocrystals with dicarboxylic acids (DAs) as coformers was investigated in the presence of a range of structurally related dicarboxylic acids (SRDs). Two experimental conditions (slurry and dry-grinding) were studied for mixing the cocrystal and the SRD additive. The additives oxalic, malonic and glutaric acid led to the replacement of the acid coformer for certain cocrystals. Interestingly, a change in stoichiometry was observed for the CA:maleic acid system. A stability order among the cocrystals was established depending on their tendency to replace the coformer. To understand the factors controlling the relative stabilities, lattice energies were calculated using dispersion corrected Density Functional Theory (DFT). Gibbs free energy changes were calculated from experimental solubilities. The observed stability order corroborated well with lattice energy and Gibbs free energy computations

Report on the sixth blind test of organic crystal-structure prediction methods

The sixth blind test of organic crystal-structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal, and a bulky flexible molecule. This blind test has seen substantial growth in the number of submissions, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and "best practices" for performing CSP calculations. All of the targets, apart from a single potentially disordered Z` = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms

Crystal Structure Prediction and Isostructurality of Three Small Molecule

NoA crystal structure prediction (CSP) study of three small, rigid and structurally related organic compounds (differing only in the position and number of methyl groups) is presented. A tailor-made force field (TMFF; a non-transferable force field specific for each molecule) was constructed with the aid of a dispersion-corrected density functional theory method (the hybrid method). Parameters for all energy terms in each TMFF were fitted to reference data generated by the hybrid method. Each force field was then employed during structure generation. The experimentally observed crystal structures of two of the three molecules were found as the most stable crystal packings in the lists of their force-field-optimised structures. A number of the most stable crystal structures were re-optimised with the hybrid method. One experimental crystal structure was still calculated to be the most stable structure, whereas for another compound the experimental structure became the third most stable structure according to the hybrid method. For the third molecule, the experimentally observed polymorph, which was found to be the fourth most stable form using its TMFF, became the second most stable form. Good geometrical agreements were observed between the experimental structures and those calculated by both methods. The average structural deviation achieved by the TMFFs was almost twice that obtained with the hybrid method. The TMFF approach was extended by exploring the accuracy of a more general TMFF (GTMFF), which involved fitting the force-field parameters to the reference data for all three molecules simultaneously. This GTMFF was slightly less accurate than the individual TMFFs but still of sufficient accuracy to be used in CSP. A study of the isostructural relationships between these molecules and their crystal lattices revealed a potential polymorph of one of the compounds that has not been observed experimentally and that may be accessible in a thorough polymorph screen, through seeding, or through the use of a suitable tailor-made additive

Rationalization of Racemate Resolution: Predicting Spontaneous Resolution through Crystal Structure Prediction.

NoCrystal structure prediction simulations are reported on 5-hydroxymethyl-2-oxazolidinone and 4-hydroxymethyl-2-oxazolidinone to establish the feasibility of predicting the spontaneous resolution of racemates of small organic molecules. It is assumed that spontaneous resolution occurs when the enantiomorph is more stable than the racemic solid. The starting point is a gas phase conformational search to locate all low-energy conformations. These conformations are used to predict the possible crystal structures of 5- and 4-hydroxymethyl-2-oxazolidinone. In both cases, the racemic crystal structure is predicted to have the lowest energy. The energy differences between the lowest-energy racemic solids and the lowest-energy enantiomorphs are 0.2 kcal mol-1 for 5-hydroxymethyl-2-oxazolidinone and 0.9 kcal mol-1 for 4-hydroxymethyl-2-oxazolidinone. In the case of 4-hydroxymethyl-2-oxazolidinone, where the racemic crystal is known to be more stable and the experimental crystal structures of both the racemate and the enantiomorph are available, the simulation results match the observed data. For 5-hydroxymethyl-2-oxazolidinone, where only enantiopure crystals are observed experimentally, the known experimental structure is found 1.6 kcal mol-1 above the lowest-energy predicted structure. This work shows that it is possible to predict whether the racemate of a small chiral molecule can be resolved spontaneously, although further advances in the accuracy of lattice energy calculations are required

A study of different approaches to the electrostatic interaction in force field methods for organic crystals

NoWe investigated five different methods for evaluating the electrostatic interaction between atoms in force field calculations on organic solids. Atomic charges and multipoles were obtained by fitting them to the molecular electrostatic potential, calculated in vacuum with an ab initio quantum mechanical method. Multipole moments were derived using three schemes, differing in the order in which the monopoles, dipoles and quadrupoles were fitted. For comparison, Gasteiger charges were also calculated. Using these electrostatic models, the lattice parameters and the molecular geometry of 48 organic crystals were optimised with the DREIDING force field. During the optimisation, the atomic multipoles were rotated with their local environment to account for molecular flexibility. For comparative reasons, rigid-body optimisations were performed on a subset of structures. The results were analysed in terms of structural parameters of the lattice and the molecules, and, for the ten polymorphic systems present in the test set, in terms of relative stability. On average, the multipole methods were not superior to the point charge methods for the full optimisation. For rigid molecules, however, the multipole models gave a substantial improvement in lattice parameters. No evidence was found that parameters for van der Waals energies need to be refitted for a specific electrostatic model. Energy differences between polymorphs were less than 5 kcal mol¿1 in eight out of ten cases, independent of the electrostatic model used. The results show that our use of distributed multipoles to describe the intra-molecular as well as inter-molecular electrostatic interactions does lead to an improvement in accuracy for rigid molecules, but not for flexible molecules. The investigation shows that accurate descriptions of the intra-molecular as well as the inter-molecular energies are crucial for the successful optimisation of crystal structures of organic solids

Progress in crystal structure prediction

The results of the application of a density functional theory method incorporating dispersive corrections in the 2010 crystal structure prediction blind test are reported. The method correctly predicted four out of the six experimental structures. Three of the four correct predictions were found to have the lowest lattice energy of any crystal structure for that molecule. The experimental crystal structures for all six compounds were found during the structure generation phase of the simulations, indicating that the tailor-made force fields used for screening structures were valid and that the structure generation engine, which combines a Monte Carlo parallel tempering algorithm with an efficient lattice energy minimiser, was working effectively. For the three compounds for which the experimental crystal structures did not correspond to the lowest energy structures found, the method for calculating the lattice energy needs to be further refined or there may be other polymorphs that have not yet been found experimentally

Experimental and theoretical investigations of the polymorphism of 5-chloroacetoxybenzoic acid (5-chloroaspirin)

From an initial crystallographic study of a large family of ring-substituted 2-acetoxybenzoic acids, only one member - the 5-chloro derivative - showed polymorphism, with two forms (alpha and beta) identified, the former having a marginally higher melting point. The two structures show a close 1-D similarity through a row of carboxylic dimers connected via Cl center dot center dot center dot O halogen bonds, which assemble to give an approximate 2-D similarity by the stacking of these rows in a second direction. However, the further packing arrangement of the resulting 2-D stacks is significantly different in the two forms, through different symmetry arrangements and subtle variations in C-H center dot center dot center dot O weak hydrogen bonds. A parallel crystal structure prediction (CSP) calculation identified the two experimental polymorphs in the correct stability order with effective energy rankings of 2 and 3 (lattice energy difference of 0.2 kcal mol(-1)). The lowest energy crystal structure found during the CSP, as yet not found experimentally, is more stable than the lowest energy observed polymorph by 0.08 kcal mol(-1). The predicted forms mostly comprise pairs of structures with nearly identical crystal structure arrangements, which differ only in the positioning of the carboxylate protons in the common carboxylate-carboxylate hydrogen-bonded dimers, relative to the positions of the neighboring acetyl substituents (syn or anti). The CSP calculations identify the correct isomer for each polymorph. One of the additional predicted forms is found to have 3-D packing similarity, and others partial similarities, with the crystal structures of particular members of the extended aspirin family

Modeling the interplay of inter- and intramolecular hydrogen bonding in conformational polymorphs.

noThe predicted stability differences of the conformational polymorphs of oxalyl dihydrazide and ortho-acetamidobenzamide are unrealistically large when the modeling of intermolecular energies is solely based on the isolated-molecule charge density, neglecting charge density polarization. Ab initio calculated crystal electron densities showed qualitative differences depending on the spatial arrangement of molecules in the lattice with the greatest variations observed for polymorphs that differ in the extent of inter- and intramolecular hydrogen bonding. We show that accounting for induction dramatically alters the calculated stability order of the polymorphs and reduces their predicted stability differences to be in better agreement with experiment. Given the challenges in modeling conformational polymorphs with marked differences in hydrogen bonding geometries, we performed an extensive periodic density functional study with a range of exchange-correlation functionals using both atomic and plane wave basis sets. Although such electronic structure methods model the electrostatic and polarization contributions well, the underestimation of dispersion interactions by current exchange-correlation functionals limits their applicability. The use of an empirical dispersion-corrected density functional method consistently reduces the structural deviations between the experimental and energy minimized crystal structures and achieves plausible stability differences. Thus, we have established which types of models may give worthwhile relative energies for crystal structures and other condensed phases of flexible molecules with intra- and intermolecular hydrogen bonding capabilities, advancing the possibility of simulation studies on polymorphic pharmaceuticals

Synthesis, Prediction, and Determination of Crystal Structures of (R/S)- and (S)-1,6-Dinitro-3,8-dioxa-1,6-diazaspiro[4.4]nonane-2,7-dione

Spiro-cyclic compounds frequently have screw-type symmetry (C-2) and are therefore optically active even though they do not contain an asymmetric carbon atom. (R/S)-1,6-Dinitro-3,8-dioxa-1,6-diazaspiro[4.4]nonane-2,7-dione is such a molecule. A blind crystal structure prediction study of structures containing one molecule in the asymmetric unit and considering all 230 space groups was undertaken using a dispersion-corrected density functional approach, which found a packing that matched the experimental structure of the (R/S) form as the lowest energy packing alternative. The densities of (R/S); and (S)- or (R)-1,6-dinitro-3,8-dioxa-1,6-diazaspiro[4.4]nonane-2,7-dione calculated for the Optimized experimental crystal structures confirmed that there is a small difference in the densities of the racemate and the optically active compound, with the optically active material being slightly more dense (1.875 versus 1.842 g/cm(3)). (R/S)-1,6-Dinitro-3,8-dioxa-1,6-diazaspiro[4.4]nonane-2,7-dione was synthesized as previously described Synthesis of the pure (S)-stereoisomer was accomplished by resolution of the racemic dithiourethane using a previously described method, followed by reaction of the pure enantiomer with acetyl nitrate. The absolute configuration of the l-3,8-dioxa-1,6-diazaspiro[4.4]nonane-2,7-dithione was established as (S)- by redetermining the crystal structure at 150 K. The racemate crystallizes in space group P2(1)/n with a density of 1.835 g/cm(3) (296 K). The (S)-compound crystallizes in space group P2(1)2(1)2(1) with a density of 1.854 g/cm(3) (296 K). This is the first demonstration of a difference in the density between the racemic mixture and the optically pure stereoisomer of an energetic material. It is also an apparent violation of Wallach\u27s rule, which states that racemic crystals tend to be denser than their optically active counterparts

Crystal Structure of a Rigid Ferrocence-based Macrocycle from High-Resolution X-ray Powder Diffraction.

NoA macrocycle, 6, has been synthesized in high yield from 2,5-di(pyrazol-1-yl)hydroquinone and 1,1`-fc[B(Me)NMe2]2 {fc = Fe(C5H4)2}. The molecule incorporates two redox-active 1,1`-ferrocenylene units in its backbone and contains four chiral boron centers, each of them possessing the same configuration. It is demonstrated that crystal structures of organometallics of moderate complexity can be solved from high-resolution X-ray powder diffraction patterns, once the connectivity between the functional groups is known