Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials.

Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the intermolecular forces involved in molecular recognition processes.

Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test.

We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their first ranked choice, albeit at a considerable computational expense. The results reflect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules.

Can the Formation of Pharmaceutical Cocrystals Be Computationally Predicted? 2. Crystal Structure Prediction.

We report a multistage lattice energy minimization methodology for generating stable packing arrangements of cocrystals containing flexible molecules. In the first approximation, the intermolecular electrostatic interactions are modeled with atomic charges and the molecular deformation energy is interpolated over a set of precomputed quantum mechanical values. At subsequent stages, the accuracy is improved by first using analytically rotated and then conformation-dependent multipole moments, computed from the isolated-molecule charge density, and "on-the-fly" quantum mechanical calculations to compute the intramolecular deformation energy. This multistage approach increases the efficiency of the search and establishes the molecule-dependent error due to the atomic charge representation of the charge density and the neglect of the conformational dependence of atomic multipole moments. The methodology is used to study the lattice energy landscapes of the cocrystals of 4-aminobenzoic acid with 2,2'-bipyridine and 4-nitrophenylacetic acid, as well as the single-component crystals. All single-component, experimentally determined crystal structures within the scope of the search were found at, or very close to, the global minimum. The experimental cocrystal with 2,2'-bipyridine is also predicted to be among the most stable packing arrangements. On the contrary, the lattice energy landscape of the cocrystal with 4-nitrophenylacetic acid contains several low energy structures that are more stable than the experimentally observed form and have different hydrogen bonding motifs. Overall, the methodology can provide worthwhile crystal energy landscapes for multicomponent organic solids and thereby contribute to understanding cocrystal formation.

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

The 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.

Is the Induction Energy Important for Modeling Organic Crystals?

We compare two methods for estimating the induction energy in organic molecular crystals by approximating the charge density polarization in the crystalline state. The first is a distributed atomic polarizability model combined with distributed multipole moments, derived from ab initio monomer properties. The second uses an ab initio calculation of the molecular charge density in a point-charge field. Various parameters of the models, such as the rank of polarizability model, effect of self-consistent iterations, and damping, are investigated. The methods are applied to a range of observed and predicted crystal structures of three particularly challenging molecules, namely oxalyl dihydrazide, 3-azabicyclo[3,3,1]nonane-2,4-dione, and carbamazepine, as well as demonstrating the importance of induction in the naphthalene crystal. The two models agree well considering the different approximations made, and it is shown that the induction energy can be an important discriminator in the relative lattice energies of structures with substantially different hydrogen-bonding motifs.

Search for a predicted hydrogen bonding motif--a multidisciplinary investigation into the polymorphism of 3-azabicyclo[3.3.1]nonane-2,4-dione.

The predictions of the crystal structure of 3-azabicyclo[3.3.1]nonane-2,4-dione submitted in the 2001 international blind test of crystal structure prediction (CSP2001) led to the conclusion that crystal structures containing an alternative hydrogen bonded dimer motif were energetically competitive with the known catemer-based structure. Here we report an extensive search for a dimer-based crystal structure. Using an automated polymorph screen a new catemer-based metastable polymorph (form 2) and two new catemer-based solvates were found, and concurrent thermal studies reproduced form 2 and identified a plastic phase (form 3), whose powder X-ray diffraction pattern was consistent with the cubic space group I23 (a = 7.5856(1) A). Computational studies on the monomer showed that the imide N-H was a weak hydrogen bond donor, rationalizing the occurrence of the plastic phase which involved the breaking of all hydrogen bonds, and modeling of small clusters showed that dimers could easily reorganize to give the catemer. FTIR spectra confirmed the weakness of the hydrogen bond, with the solute showing no self-assembly in solution. It is concluded that the weakness of the N-H donor, coupled with the globular shape of the molecule, allows unusually facile transformation between alternative hydrogen bonding motifs during aggregation and nucleation.