Organic Crystal Structures Research Articles

Recent progress in predicting structural and electronic properties of organic solids with the van der Waals density functional

We review recent studies on electronic properties of the organic solids with the first-principles electronic structure methods, with the emphasis on the roles of the intermolecular van der Waals (vdW) interaction in electronic properties of the organic semiconductors. After a brief summary of the recent vdW inclusive first-principle theoretical methods, we discuss their performance in predicting cohesive properties of oligoacene crystals as examples of organic crystals. We show that a variant of the van der Waals density functional describes structure and energetics of organic crystals accurately. In addition, we review our recent study on the zinc phthalocyanine crystal and discuss the importance of the intermolecular distance and orientational angle in the band dispersion. Finally, we draw some general conclusions and the future perspectives.

Quantifying the symmetry preferences of intermolecular interactions in organic crystal structures

Many intermolecular interactions show preferences for particular crystallographic symmetries and the extent to which this is the case is quantifiable.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Impact of exact exchange in the description of the electronic structure of organic charge-transfer molecular crystals

We evaluate the impact that the amount of nonlocal Hartree-Fock (%HF) exchange included in a hybrid density functional has on the microscopic parameters (transfer integrals, band gaps, bandwidths, and effective masses) describing charge transport in high-mobility organic crystals. We consider both crystals based on a single molecule, such as pentacene, and crystals based on mixed-stack charge-transfer systems, such as dibenzo-TTF--TCNQ. In the pentacene crystal, the band gap decreases and the effective masses increase linearly with an increase in the amount of %HF exchange. In contrast, in the charge-transfer crystals, while the band gap increases linearly, the effective masses vary only slightly with an increase in %HF exchange. We show that the superexchange nature of the electronic couplings in charge-transfer systems is responsible for this peculiar evolution of the effective masses. We compare the density functional theory results with results obtained within the ${G}_{0}{W}_{0}$ approximation as a way of benchmarking the optimal amount of %HF exchange needed in a given functional.

Utilizing organic and organometallic structural data in powder diffraction

The Cambridge Structural Database (CSD) is a database of small molecule organic and organometallic crystal structures elucidated using X-Ray and neutron crystallography. The CSD is distributed alongside a system of software (the Cambridge Structural Database System) to academic and industrial users. The system contains a number of applications (in particular DASH, ConQuest, and Mogul) that can be used to aid crystallographers in the solution and refinement of crystal structures from powder diffraction data, and in the interpretation of crystal structure models (in particular, Mercury). This publication uses a racemic form of ornidazole (Z′ = 3) to illustrate the efficacy of DASH in the crystal structure solution from powder diffraction data. Furthermore, numerous features in Mogul and Mercury that aid crystal structure solution and interpretation of crystallographic data are revised. Finally, a review of a new method for using database-derived geometric information directly in structural solution is presented.

Using the Knowledge from Every Organic Crystal Structure Ever Published

The crystallographic community has done something remarkable and almost unique in science. It has operated in such a way that the data generated in virtually every experiment reported in a publication is available to all. This data, in the form of individual crystal structures, is valuable not just in itself, but as a collection. To fully exploit the results of a new structure determination, we never analyse a single structure, we analyse it in the context of every previous crystal structure. Our knowledge of molecular geometry and molecular interactions derived from these structural databases is put to routine use in almost every field of chemistry. This presentation will specifically highlight what we can learn from the world's database of small molecule crystal structures and demonstrate how we can apply that knowledge not just to increase our understanding in structural chemistry, but in structural biology too.

Theoretical Prediction of Crystal Polymorphs for Organic Molecules

Crystal structure prediction is one of the useful theoretical tools for designing and synthesizing new materials in pharmaceutical therapeutics and industrial electronics. Furthermore, the prediction can provide immense valuable scientific knowledge on a crystal growth, polymorphism and many properties of organic molecular crystals. Therefore, we have started the development of high-speed and high-accurate prediction method for organic molecular crystal structures [1,2]. In this work, we demonstrate the theoretical predictions of crystal structures of fourteen target molecules that were used in the international competitions known as CSP blind tests hosted by CCDC [3]. All strategies required for crystal lattice construction expanded to a given effective crystal radius, crystal energy calculation with the reliable molecular force field (MMFF94s) and exhaustive geometry search included a variety of crystal polymorphism are implemented into CONFLEX program [1]. As the results of the applications, we confirmed in all cases of target molecules that, at least, one calculated crystal structure in agreement with the corresponding observed ones can be found. Essential ability required for the prediction method to survive the CSP competitions is that the experimental crystal structure can computationally reproduce within top 3 of most stable structures in crystal energy evaluation. In these tests, only three applications to the target I (Orth. polymorph), II and VIII can successfully satisfy the demand. Details will be discussed in this conference.

ChemInform Abstract: Predicting Crystal Structures of Organic Compounds

AbstractReview: 53 refs.

Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB).

The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.

Real-time x-ray scattering study of the initial growth of organic crystals on polymer brushes

We studied the early-stage growth structures of pentacene organic crystals grown on polymer brushes using real-time x-ray scattering techniques. In situ x-ray reflectivity and atomic force microscopy analyses revealed that at temperatures close to the glass transition temperature of polymer brush, the pentacene overlayer on a polymer brush film showed incomplete condensation and 3D island structures from the first monolayer. A growth model based on these observations was used to quantitatively analyze the real-time anti-Bragg x-ray scattering intensities measured during pentacene growth to obtain the time-dependent layer coverage of the individual pentacene monolayers. The extracted total coverage confirmed significant desorption and incomplete condensation in the pentacene films deposited on the polymer brushes. These effects are ascribed to the change in the surface viscoelasticity of the polymer brushes around the glass transition temperature.

ChemInform Abstract: The Cambridge Structural Database in Retrospect and Prospect

AbstractReview: [52 refs.

Structure determination from powder data without prior indexing, using a similarity measure based on cross-correlation functions

A method to refine organic crystal structures from powder diffraction data with incorrect lattice parameters has been developed. The method is based on the similarity measure developed by de Gelder et al. [J. Comput. Chem. (2001), 22, 273-289], using the cross- and auto-correlation functions of a simulated and an experimental powder pattern. The lattice parameters, molecular position, molecular orientation and selected intramolecular degrees of freedom are optimized until the similarity measure reaches a maximum; subsequently, a Rietveld refinement is carried out. The program FIDEL (FIt with DEviating Lattice parameters) implements this method. The procedure is also suitable for unindexed powder data, powder diagrams of very low quality and powder diagrams of non-phase-pure samples. Various applications are shown, including structure determinations from powder data using crystal structure predictions by standard force-field methods. Other useful applications include the automatic structure determination from powder data starting from the crystal structures of isostructural compounds (e.g. a solvate, hydrate or chemical derivative), or from crystal data measured at a different temperature or pressure.

Comparison of the accuracy of powder and single-crystal X-ray diffraction techniques in determining organic crystal structure

This study demonstrates the accuracy of powder X-ray diffraction (PXRD) in determining the crystal structures of four organic molecules by comparing the structural information obtained from both single-crystal X-ray diffraction (SXRD) and PXRD techniques. Results showed that the PXRD technique had approximately the same precision as the SXRD technique. The majority of the relative deviations from PXRD-derived lattice parameters were within ±0.2 % of the correct values (average of the SXRD data), whereas the relative deviations in bond lengths and angles are within ±1.0 %. All of the relative deviations were subjected to normal statistical distributions (μ = 0) and coincided with the SXRD data. As an auxiliary implement of SXRD, PXRD is clearly an effective and powerful technique in establishing an accurate characterization of organic molecules.

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

The Cambridge Structural Database in Retrospect and Prospect

The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal-organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700,000 structures and is a comprehensive and fully retrospective historical archive of small-molecule crystallography. Nearly 40,000 new structures are added each year. As X-ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self-financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC's funding model in relation to open access and open data paradigms.

Halogen bonds in crystal TTF derivatives: an ab initio quantum mechanical study

The stabilisation energies of five ionic and neutral organic crystal structures containing various halogen bonds (I···I, Br···Br, I···Br, I···S and Br···S) were calculated using the DFT-D3 method (B97D/def2-QZVP). Besides them, the ionic I3(-)···I2 and neutral I2···I2, complexes (in the crystal geometries) were also studied. The nature of the bonds was deduced from the electrostatic potential evaluated for all subsystems. In almost all the cases, the σ-hole was positive; it was negative only for the ionic I3(-) system (although more positive than the respective belt value). The strongest halogen bonds were those that involved iodine as a halogen-bond donor and acceptor. Among ionic X···I3(-) and neutral X···I2 and X···Y dimers, the neutral X···I2 complexes were, surprisingly enough, the most stable; the highest stabilisation energy of 13.8 kcal mol(-1) was found for the I2···1,3-dithiole-2-thione-4-carboxylic acid complex. The stabilisation energies of the ionic I3(-)···I2 and neutral I2···1,3-dithiole-2-thione-4-carboxylic acid (20.2 and 20.42 kcal mol(-1), respectively) complexes are very high, which is explained by the favourable geometrical arrangement, allowing the formation of a strong halogen bond. An I···I halogen bond also exists in the neutral I2···I2 complex, having only moderate stabilisation energy (3.9 kcal mol(-1)). This stabilisation energy was, however, shown to be close to that in the optimal gas-phase L-shaped I2···I2 complex. In all the cases, the dispersion energy is important and comparable to electrostatic energy. Only in strong halogen bonds (e.g. I3(-)···I2), the electrostatic energy becomes dominant.

Predicting crystal structures of organic compounds

Currently, organic crystal structure prediction (CSP) methods are based on searching for the most thermodynamically stable crystal structure, making various approximations in evaluating the crystal energy. The most stable (global minimum) structure provides a prediction of an experimental crystal structure. However, depending on the specific molecule, there may be other structures which are very close in energy. In this case, the other structures on the crystal energy landscape may be polymorphs, components of static or dynamic disorder in observed structures, or there may be no route to nucleating and growing these structures. A major reason for performing CSP studies is as a complement to solid form screening to see which alternative packings to the known polymorphs are thermodynamically feasible.

Crystal structure versus charge transport in organic single crystals of [1]benzothieno[3,2-b][1]benzothiophene derivatives from a multiscale theoretical study

[1]Benzothieno[3,2-b][1]benzothiophene derivatives with high air stability have recently displayed excellent charge transport properties in field-effect devices. In particular, the average charge mobilities can reach as high as 16.4 ± 6.1 cm2 V−1 s−1 in devices with a high quality semiconductor/insulator interface, which is comparable to the performance for a rubrene single-crystal device. To better understand these excellent charge transport properties, a multiscale approach combining molecular dynamics and quantum-chemical calculations was used in this work to assess the structure–property relationship for three of the [1]benzothieno[3,2-b][1]benzothiophene derivatives with different alkyl side chains. It is indicated that the extremely large electronic couplings along the a-axis direction are responsible for the excellent charge transport properties in these systems. While the molecular packings are centrosymmetrical in the ab plane, the lattice vibrations were found to hamper the charge transport in optimized crystal structures at the COMPASS molecular mechanics level which is opposite to the recent findings that the lattice dynamics should have a negligible effect on the charge mobility in the centrosymmetrical plane. The reason for such behavior was analyzed and the predicted order of the overall charge mobilities for the studied systems was consistent with the experiments. Meanwhile, how well the force field reproduces the observed crystal structures and dimer intermolecular separations and orientations is discussed in this work. In addition, it is shown that the present charge transport model can not only predict the magnitude of the charge mobility but also the measured “band-like” charge transport in experiments, so the nuclear tunneling effect is very important for charge transport in organic semiconductors as was demonstrated in recent theoretical work.

Acidic Proton Modulation of a Stilbene-based Zwitterionic Sulfonic Acid in the Solid State: Mimicking a Biological Device

Abstract Acidic proton modulation of a stilbene-based zwitterionic sulfonic acid in the crystalline state was studied using three amines with different pKa values. The three organic crystal structures prepared from the intermolecular interactions of the acid with the amines and water were solved by single-crystal X-ray crystallography. These crystals included an ammonium salt and two hydrate crystals. Furthermore, the three generated crystals could mimic three distinct biological systems: a water/proton blockade, a protonated water array, and a one-dimensional water channel.

Deterioration of metal–organic framework crystal structure during fabrication of poly(l‐lactic acid) mixed‐matrix membranes

AbstractPoly(l‐lactic acid) (PLLA) and metal–organic framework (MOF) mixed‐matrix membranes were prepared by melt extrusion of PLLA with 5% (w/w) of either activated or water‐saturated Cu3(BTC)2 (Cu3(C9H3O6)2(H2O)3·xH2O, HKUST‐1). The morphology and the stability of injection‐molded samples were evaluated using thermogravimetric analysis, differential scanning calorimetry, gel permeation chromatography, X‐ray diffraction (XRD) and scanning electron microscopy (SEM). The presence of activated and saturated MOF crystals increased the cold crystallization onset temperature as compared to neat PLLA. This can be attributed to the MOF crystals incorporated in the PLLA matrix, which decreased the mobility of PLLA and thus impeded the crystallization process. According to the XRD results, the activated MOF crystals were successfully incorporated into the PLLA matrix without altering the crystal structure of the MOF. Moreover, the findings from permeability and tensile tests as well as SEM imaging indicated good interfacial interactions between PLLA and activated MOF. However, during melt extrusion of PLLA with saturated MOF, water molecules from the saturated MOF altered the MOF crystal structure and contributed to the degradation of the PLLA polymer by reducing its molecular weight by around 21%. © 2013 Society of Chemical Industry