Stephan X. M. Boerrigter

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crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee.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.

Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

The results of the fifth blind test of crystal structure prediction, which show important success with more challenging large and flexible molecules, are presented and discussed.

Investigation of the Milling-Induced Thermal Behavior of Crystalline and Amorphous Griseofulvin

ABSTRACTPurposeTo gain a better understanding of the physical state and the unusual thermal behavior of milled griseofulvin.MethodsGriseofulvin crystals and amorphous melt quench samples were milled in a vibrating ball mill for different times and then analyzed using differential scanning calorimetry (DSC) and powder X-ray diffraction (PXRD). Modulated DSC (mDSC) and annealing studies were done for the milled amorphous samples to further probe the effects of milling.ResultsMilling of griseofulvin crystals results in decrease in crystallinity and amorphization of the compound. A double peak is seen for crystallization in the DSC, which is also seen for the milled melt quench sample. Both enthalpy and temperature of crystallization decrease for the milled melt quenched sample. Tg is visible under the first peak with the mDSC, and annealing shows that increasing milling time results in faster crystallization upon storage.ConclusionMilling of griseofulvin results in the formation of an amorphous form and not a mesophase. It increases the amount of surface created and the overall energy of the amorphous griseofulvin, which leads to a decreased temperature of crystallization. The two exotherms in the DSC are due to some particles having nuclei on the surface.

Investigating the effect of dehydration conditions on the compactability of glucose.

Hydrates are commonly found in pharmaceutical ingredients either in excipients or in the active pharmaceutical ingredient form. There is always the possibility that the processing involved in manufacturing can result in the dehydration of the hydrate components. It has been seen that different dehydration conditions can have an effect on the behavior of the final product; however this area has not been fully investigated. In this work, glucose monohydrate powder was dehydrated at four different conditions and then compressed to see the effect on the hardness of the compacts. Various analytical tools such as inverse gas chromatography, differential scanning calorimetry, X-ray powder diffractometry and scanning electron microscopy were used to determine any differences in the properties of the dehydrates and correlated with the obtained compact hardness. Annealing studies were performed to determine the effect of storage on the dehydrated materials both before and after compression. It was observed that while annealing of the powders did have an impact, annealing of the compacts did not influence the hardness. The results of the characterization and annealing studies showed that the difference in the behavior of glucose dehydrates were due to the presence of amorphous regions within the particulates.

Organic vapor sorption method of isostructural solvates and polymorph of tenofovir disoproxil fumarate

Tenofovir disoproxil fumarate (TDF) is a prodrug of tenofovir that belongs to a class of antiretroviral drugs, a nucleotide reverse transcriptase inhibitor. An acetonitrile solvate of TDF I, another new solvated form of TDF, was prepared and solid state characterization of its form was conducted using powder X-ray diffraction, FT-IR spectroscopy, and organic vapor sorption isotherm. During the characterization work, it was discovered that (1) TDF I can form solvates and polymorph with a wide variety of organic solvents as well as water and (2) to different extents, these solvates undergoes anisotropic lattice contraction/expansion during desolvation/solvation process suggesting the formation of isostructural solvates of TDF. Solvents used in this study include ethanol, isopropyl alcohol, acetonitrile, cyclohexane, toluene, and water. Four new solvates using ethanol, isopropyl alcohol, acetonitrile, and toluene vapor and one polymorph using water vapor were discovered. Their solid state characterizations were conducted using powder X-ray diffraction, differential scanning calorimetry, thermogravimetric analysis, and Fourier transform infrared spectroscopy. A variety of isostructural solvates and a polymorph of TDF was produced by an organic vapor sorption method, showing varying physicochemical properties. This study demonstrates an alternative crystallization method to obtain isostructural solvates.

Anisotropic crystal deformation measurements determined using powder X-ray diffraction and a new in situ compression stage.

This report addresses the development of experimental and computational estimations of the anisotropic elastic moduli (EM) of single crystals to aid in the a priori (i.e., starting with the crystal structure) prediction of the trend as a function of the direction of applied stress. Experimentally EM values in the normal direction to the X-, Y- and Z-planes of block shaped aspirin and acetaminophen crystals were determined using data generated by the newly designed compression stage housed in our powder X-ray diffractometer. Computational estimations of EM were made using the applicable modules in Material Studio 5.5. The measured EM values normal to the (100), (020) and (002) planes of aspirin, and (20-1), (020) and (001) planes of acetaminophen crystals by both methods succeeded in detected the anisotropic behavior. However, disparity in the relative values between measured EM values by different techniques was observed. This may be attributed to deformation sources other than lattice compression including inelastic processes such as local failure and plasticity as well as deformation at the crystal-probe interfaces due to crystal surface roughness (asperities). The trend of the ratio of the values from the respective methods showed reasonable agreement and promise for the technique. The present approach demonstrated the suitability of the compression stage to determine and predict anisotropic EM of subjected small molecular organic crystals.

Application of error‐ranked singular value decomposition for the determination of potential‐derived atomic‐centered point charges

The present work provides a detailed investigation on the use of singular value decomposition (SVD) to solve the linear least‐squares problem (LLS) for the purposes of obtaining potential‐derived atom‐centered point charges (PD charges) from the ab initio molecular electrostatic potential (VQM). Given the SVD of any PD charge calculation LLS problem, it was concluded that (1) all singular vectors are not necessary to obtain the optimal set of PD charges and (2) the most effective set of singular vectors do not necessarily correspond to those with the largest singular values. It is shown that the efficient use of singular vectors can provide statistically well‐defined PD charges when compared with conventional PD charge calculation methods without sacrificing the agreement with VQM. As can be expected, the methodology outlined here is independent of the algorithm for sampling VQM as well as the basis set used to calculate VQM. An algorithm is provided to select the best set of singular vectors used for optimal PD charge calculations. To minimize the subjective comparisons of different PD charge sets, we also provide an objective criterion for determining if two sets of PD charges are significantly different from one another.

Core–shell potential-derived point charges†

The present work details the development of a core‐shell model for the purposes of obtaining potential‐derived point charges from the ab initio molecular electrostatic potential. In contrast to atomic point charge models, the core‐shell model decomposes all atoms into a core with static charge located at a fixed atomic position and a shell with variable charge and position. The optimization of shell charges and positions is discussed. The core‐shell model was found to significantly improve description of the ab initio electrostatic potential when compared to potential‐derived net atomic point charge models as well as distributed multipoles with contributions up to atomic quadrupole moments. The core‐shell model was found to produce similar results as the Weller‐Williams lone‐pair model and differences in the implementation of the models are discussed.