Graeme Day obtained his PhD in computational and theoretical chemistry from University College London, after a BSc in Chemistry, Mathematics and Computing Science (Saint Mary's University) and an MSc in Theoretical Chemistry (Oxford University). In 2002, he joined the Pfizer Institute for Pharmaceutical Materials Science at the University of Cambridge and has held a Royal Society University Research Fellowship in Cambridge since 2005. His interests are in understanding and predicting the structure and properties of organic molecular materials, including the development of computational methods for predicting the structure and lattice dynamics in molecular crystals.
Abstract: The phonon modes of crystalline benzoic acid have been investigated using terahertz time-domain spectroscopy, rigid molecule atom-atom model potential and plane-wave density functional theory lattice dynamics calculations. The simulation results show good agreement with the measured 10 terahertz spectra and an assignment of the terahertz absorption features of benzoic acid is made with the help of both computational methods. Focussing on the strongest interactions in the crystal, we describe each vibration in terms of distortions of the benzoic acid hydrogen bonded dimers that are present in the crystal structure. The terahertz spectrum is also shown to be highly sensitive to the location of the carboxylic acid hydrogen atoms in the cyclic hydrogen-bonded dimers and we 15 have systematically explored the influence of the observed disorder in the hydrogen atom positions on the lattice dynamics.
Abstract: Predicting the ability of low molecular weight molecules to form hydrogels is difficult. Here, we have examined the self-assembly behavior of two chemically and structurally similar functionalized dipeptides, one of which is found to form a meta-stable hydrogel (1) and the other forming a crystalline solid (2). To investigate the reasons for these differences, we have employed computational methods to explore the crystal energy landscapes of the two molecules and examined differences in their preferred packing arrangements. We show that this method accurately predicts the packing for the crystalline solid, 2. Furthermore, the predictions for the gel-former 1 suggest that one-dimensional hydrogen-bonding arranged into tightly coiled molecular columns is a preferred mode of packing for this system, but is unfavorable for 2. The different tendencies of forming these columns could provide an explanation for the different behavior of the two molecules and demonstrate that this approach could be useful for the future predictable design of low molecular weight gelators.
Abstract: Crystal structure prediction calculations are performed for four hydrophobic amino acids (alanine, valine, leucine and isoleucine), to test the computational methods that have been developed for flexible organic molecules. Specific focus is placed on the final energy minimisation and optimisation of the molecular conformations in the computer-generated crystal structures. Overall, the results are very encouraging. The observed crystal structures are usually found as the lowest energy predicted structures, demonstrating that crystal packing is predictable by computational methods, even for fairly challenging systems. In addition to the assessment of the computational methods, comparison of the hypothetical with the observed crystal structures provides insight into the balance between hydrogen bonding and hydrophobic side-chain packing that determines the crystal structures of these biologically important molecules.
Abstract: A fast method for crystal structure determination Using crystal structure prediction and solid-state H-1 NMI is presented. This technique does not need any prior knowledge except the chemical formula; resonance assignment is not necessary. Starting from an ensemble of predicted crystal structures for powdered thymol, comparison between experimental and calculated H-1 solid-state isotropic NMR chemical shifts is sufficient to determine which predicted structure corresponds to the powder under study. The same approach using proton-proton spin-diffusion data is successful and can be used for cross-validation.
Abstract: 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 (Qat, 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 (at, 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 C15H12N2O, 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.
Abstract: We demonstrate that crystal structure prediction calculations can be used to predict both the stoichiometry and structure of multicomponent molecular crystals. The methods are used here to determine the structure of a recently discovered acetic acid solvate of theobromine.
Abstract: Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 1 complexes between hydrophobic L- and D-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.
Abstract: We have used well-established computational methods to generate and explore the crystal structure landscapes of four organic molecules of well-known inclusion behaviour. Using these methods, we are able to generate both close-packed crystal structures and high-energy open frameworks containing voids of molecular dimensions. Some of these high-energy open frameworks correspond to real structures observed experimentally when the appropriate guest molecules are present during crystallisation. We propose a combination of crystal structure prediction methodologies with structure rankings based on relative lattice energy and solvent-accessible volume as a way of selecting likely inclusion frameworks completely ab initio. This methodology can be used as part of a rational strategy in the design of inclusion compounds, and also for the anticipation of inclusion behaviour in organic molecules.
Abstract: 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.
Abstract: Terahertz time-domain-spectroscopy (THz-TDS) has emerged as a versatile spectroscopic technique, and an alternative to powder X-ray diffraction in the characterization of molecular crystals. We tested the ability of terahertz spectroscopy to distinguish between chiral and racemic hydrogen-bonded cocrystals that are similar in molecular and supramolecular structure. Terahertz spectroscopy readily distinguished between the isostructural cocrystals of theophylline with chiral and racemic forms of malic acid which are almost identical in molecular structure and supramolecular architecture. Similarly, the cocrystals of theophylline with chiral and racemic forms of tartaric acid, which are similar at the molecular level but dissimilar in crystal packing, were distinguished unequivocally. The investigation of the same cocrystals using X-ray powder diffraction and Raman spectroscopy suggested that THz-TDS is comparable in sensitivity to diffraction methods and more sensitive than Raman spectroscopy to changes in cocrystal architecture. The differences in spectra acquired by THz-TDS could be further enhanced by cooling the samples to 109 K.
Abstract: Recent theoretical studies suggest that the modulation of the electronic couplings (transfer integrals) between adjacent molecules by lattice vibrations, i.e., the so-called nonlocal electron-phonon coupling, plays a key role in the charge-transport properties of molecular organic semiconductors. However, a detailed understanding of this mechanism is still missing. Here, we combine density functional theory calculations and molecular mechanics simulations and use a chemistry-based insight to derive the nonlocal electron-phonon coupling constants due to the interaction of charge carriers with the optical lattice vibrations in the naphthalene crystal. The results point to a very strong coupling to both translational and librational intermolecular vibrational modes as well as to intramolecular modes. Along some crystal directions, the nonlocal interactions are found to be dominated by nontotally symmetric vibrational modes which lead to an alternation (Peierls-type dimerization) pattern. Importantly, we introduce two parameters that can be used: (i) to quantify the total strength of the nonlocal electron-vibration mechanism in the form of a reorganization energy term; and (ii) to define the extent of the thermal fluctuations of the electronic couplings. Interestingly, zero-point fluctuations are seen to be very significant.
Abstract: Poor mechanical properties of paracetamol are improved through the strategy of cocrystal formation. Mechanochemical screening by liquid-assisted grinding generated four cocrystals of paracetamol that readily form tablets by direct compression. Computational studies reveal the mechanical properties can be related to structural features, before all the formation of hydrogen-bonded layers.
Abstract: 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.
Abstract: The computer-generation of the crystal structures of the a-amino acid valine is used as a challenging test of lattice energy modeling methods for crystal structure prediction of flexible polar organic molecules and, specifically, to examine the importance of molecular polarization on calculated relative energies. Total calculated crystal energies, which combine atom-atom model potential calculations of intermolecular interactions with density functional theory intramolecular energies, do not effectively distinguish the real (known) crystal structures from the rest of the low energy computer-generated alternatives when the molecular electrostatic models are derived from isolated molecule calculations. However, we find that introducing a simple model for the bulk crystalline environment when calculating the molecular energy and electron density distribution leads to important changes in relative total crystal energies and correctly distinguishes the observed crystal structures from the set of computer-generated possibilities. This study highlights the importance of polarization of the molecular charge distribution in crystal structure prediction calculations, especially for polar flexible molecules, and suggests a computationally inexpensive approach to include its effect in lattice energy calculations.
Abstract: We report on the crystal structure of urea (U) with acetic acid (A), its physical stability and its predictability using computational methods. The crystal structure of urea:acetic acid (U:A) shows hydrogen-bond ribbons and a 1:2 stoichiometry. Crystal structure prediction calculations are presented for two sets of U:A stoichiometries: 1:1 and 1:2. A 1:3 stoichiome- try is also partially explored by means of a synthon approach. The calculated lattice energies, along with hydrogenbond patterns, of crystal structures predicted with the three stoichiometries are presented and analysed to provide a rationalisation for the stoichiometry observed. Exploring stoichiometric diversity using computational methods provides a tool for the rationalisation of stoichiometry preferences in crystalline multicomponent systems and a first step towards their prediction.
Notes: Rated a 'Very Important Paper' by the journal
Abstract: We report methods to predict the intrinsic aqueous solubility of crystalline organic molecules from two different thermodynamic cycles. We find that direct computation of solubility, via ab initio calculation of thermodynamic quantities at an affordable level of theory, cannot deliver the required accuracy. Therefore, we have turned to,a mixture of direct computation and informatics, using the calculated thermodynamic properties, along with a few other key descriptors, in regression models. The prediction of log intrinsic solubility (referred to mol/L) by a three-variable linear regression equation gave r(2) = 0.77 and RMSE = 0.71 for an external test set comprising drug molecules. The model includes a calculated crystal lattice energy which provides a computational method to account for the interactions in the solid state. We suggest that it is not necessary to know. the polymorphic form prior to prediction. Furthermore, the method developed here may be applicable to other solid-state systems such as salts or cocrystals.
Abstract: (S)-1-(Methylaminocarbonyl)-3-phenylpropanaminium chloride (S2 center dot HCl), C10H15N2O+center dot Cl-, crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a single formula unit per asymmetric unit. (5R/S)-5-Benzyl-2,2,3-trimethyl-4-oxoimidazolidin-1-ium chloride (R3 and S3), C13H19N2O+center dot Cl-, crystallize in the same space group as S2 center dot HCl but contain three symmetry-independent formula units. (R/S)-5-Benzyl-2,2,3-trimethyl-4-oxoimidazolidin-1-ium chloride monohydrate (R4 and S4), C13H19N2O+center dot Cl center dot H2O, crystallize in the space group P2(1) with a single formula unit per asymmetric unit. Calculations at the B3LYP/6-31G(d, p) and B3LYP/6-311G(d, p) levels of the conformational energies of the cation in R3, S3, R4 and S4 indicate that the ideal gas-phase global energy minimum conformation is not observed in the solid state. Rather, the effects of hydrogen- bonding and van der Waals interactions in the crystal structure cause the molecules to adopt higher-energy conformations, which correspond to local minima in the molecular potential energy surface.
Abstract: Carbamazepine, a first generation anticonvulsant, is known to crystallize in various polymorphic forms, all of which exhibit an anti-carboxamide hydrogen bond dimer motif. Furthermore, unless cocrystallized with carboxylic acids, these dimers are also present in most crystal structures of the known carbamazepine solvates. On the other hand, two derivatives of the drug (oxcarbazepine and 10,11-dihydrocarbamazepine) have been reported to adopt hydrogen bond chain motifs in their crystal structures, whereas the epoxy derivative (10,11-epoxycarbamazepine) shows a third mode of hydrogen bonding, syn-dimers. In order to rationalize the differences in hydrogen bonding caused by the small changes in molecular structure, computational searches for the low-energy crystal structures of these drugs were performed and hydrogen bond patterns in both the hypothetical and experimentally determined crystal structures were analyzed. In addition, interaction energies between pairs of molecules were calculated using the SCDS-PIXEL approach, which partitions the intermolecular interaction energy into its different contributions (Coulombic, polarization, dispersion, and repulsion). The importance of overall molecular shape and the influence that this has on the hydrogen bond arrangements in these structures is emphasized.
Abstract: The most populated space groups for a selection of solvates of chiral and achiral molecules with common solvents are presented to assist crystal structure prediction calculations on these complex systems.
Abstract: Crystal structure prediction calculations have been performed for the alpha-amino acid alanine with the intention of developing reliable computational methods for flexible molecules and, specifically, to study the crystal packing of the more flexible amino acids. For the alpha-amino acids, the density functional theory geometry optimised conformations of the isolated molecules are considerably different, in both geometry and form, to what is observed in the crystal structures. The molecules take the zwitterionic form in the observed crystals, but are nonionised for the isolated molecules. The quantum mechanically optimised structure of the isolated molecule is therefore a poor starting point for computationally generating putative crystal structures. We show that, by limiting the conformations of alanine to the torsion angle distributions in the observed crystal structures of similar molecules in the Cambridge Structural Database, sets of likely crystal structures can be generated, with the lowest energy racemic and enantiopure crystal structures corresponding to the experimentally observed crystal structures.
Abstract: A computational exploration of the low energy crystal structures of the pharmaceutical molecule phenobarbital is presented as a test of an approach for the crystal structure prediction of flexible molecules. Traditional transferable force field methods of modelling flexible molecules are unreliable for the level of accuracy required in crystal structure prediction and we outline a strategy for improving the evaluation of relative energies of large sets of crystal structures. The approach involves treating the molecule as a set of linked rigid units, whose conformational energy is expressed as a function of the relative orientations of the rigid groups. The conformational energy is calculated by electronic structure methods and the intermolecular interactions using an atomic multipole description of electrostatics. A key consideration in our approach is the scalability to more typical pharmaceutical molecules of higher molecular weight with many more atoms and degrees of flexibility. Based on our calculations, crystal structures are proposed for the as-yet uncharacterised forms IV and V, as well as further polymorphs of phenobarbital.
Abstract: Terahertz (THz) radiation probes intermolecular interactions through crystal lattice vibrations, allowing the characterization of solid materials(1,2). Thus, THz spectroscopy is a promising alternative to mainstream solid-state analytical tools such as X-ray diffraction or thermal analysis(3). The method provides the benefits of online measurement(4), remote sampling(5) and three-dimensional imaging(6), all of which are attractive for quality control and security applications. In the context of pharmaceutical solids, THz spectroscopy can differentiate and quantify different forms of active pharmaceutical ingredients(7,8). Here, we apply this technique to monitor a dynamic process involving two molecular crystals(9). In particular, we follow the mechanochemical construction of a two-component cocrystal(10-12) by grinding together phenazine (phen) and mesaconic acid (mes)(13). To rationalize the observed changes in the spectra, we conduct lattice dynamics calculations that lead to the tentative assignment of at least one feature in the cocrystal THz spectrum.
Abstract: We report on experimental and theoretical evidence for solvent inclusion in form II carbamazepine (R (3) over bar) and discuss the implications for the formation and stability of this form.
Abstract: The ability to identify the crystal structures of small molecules by visual inspection, given a list of computer-generated low-energy possibilities, has been tested in an experiment conducted at an international crystallographic conference. The surprising result of the test was that the experimentally observed crystal structures were the least popular of five choices for the two molecules included in the test, casting doubt on the reliability of crystallographic intuition as a complement to computational methods in crystal structure prediction.
Abstract: We report on the crystal structures of two polymorphs of scyllo-inositol. Crystallization of this inositol initially failed to yield a single crystal suitable for structure solution, so a computational prediction of the low-energy forms was performed in parallel with the crystallization experiments. When a single crystal was finally grown, its structure failed to explain the powder X-ray diffraction pattern of the bulk material, which seemed to show a mixture of polymorphs. With the aid of the lowest-energy predicted crystal structure from a lattice energy search and the DASH program for structure solution from powder data, we propose the structure of the second polymorph. The combined use of single-crystal structure solution, structure solution from powder diffraction data, and a lattice energy search for possible structures, which was necessary for the elucidation of the second polymorph of scylloinositol, demonstrates the synergy between experimental and computational studies of molecular organic materials.
Abstract: The unexpected appearance of a new polymorph of maleic acid is reported and a computational study addresses the predictability of this new polymorph and future potential polymorphism.
Abstract: Rigid molecule atomistic lattice dynamics calculations have been performed to predict the phonon spectra of the four polymorphs of carbamazepine, and these calculations predict that there should be differences in the spectra of all four forms. Terahertz spectra have been measured for forms I and III, and there are clearly different features between polymorphs' spectra, that are accentuated at low temperature. While carbamazepine adopts the same hydrogen bonded dimers in all of its known polymorphs, the calculations show that differences in packing arrangements of the dimers lead to changes in the frequency ranges for each type of hydrogen bond vibration, giving a physical explanation to the observed differences between the spectra. Although the agreement between calculated and observed spectra does not allow a definitive characterization of the spectra, it is possible to make tentative assignments of many of the observed features in the terahertz region for the simpler form III; we can only make some tentative assignments of specific modes in the more complex spectrum of form I. While harmonic rigid molecule lattice dynamics shows promise for understanding the differences in spectra between polymorphs of organic molecules, discrepancies between observed and calculated spectra suggest areas of improvement in the computational methods for more accurate modeling of the dynamics in molecular organic crystals.
Abstract: Carbamazepine is known to exist in various polymorphic forms. Here we report on crystal structure prediction calculations for carbamazepine in an attempt to examine the predictability and relative stability of the various polymorphs. Hypothetical crystal structures generated in 10 of the most common space groups were compared to the observed polymorphs. Particular attention has been given to the influence of amide pyramidalization on the relative energies of the predicted structures. While the actual generation of possible crystal structures was found to be independent of the degree of deformation of the amide group, their final ranking in energy was greatly affected by pyramidalization of the amide nitrogen. This effect was examined in detail through systematic variation of the NH2 geometry for each of the low-energy crystal structures; different amide geometries were favored in the various low-energy crystal structures. The results demonstrate that energetically feasible deformation of the amide group may occur in order to optimize hydrogen-bond interactions, and we conclude that neglect of amide pyramidalization introduces significant errors in crystal structure prediction for carbamazepine and similar molecules.
Abstract: The lattice energies of predicted and known crystal structures for 50 small organic molecules with constrained (rigid) geometries have been calculated with a model potential whose electrostatic component is described by atom-centered multipoles. In comparison to previous predictions using atomic point charge electrostatics, there are important improvements in the reliability of lattice energy minimization for the prediction of crystal structures. Half of the experimentally observed crystal structures are found either to be the global minimum energy structure or to have calculated lattice energies within 0.5 kJ/mol (0.1 kcal/mol) of the global minimum. Furthermore, in 69% of cases, there are five or fewer unobserved structures with lattice energies calculated to be lower than that of the observed structure. The results are promising for the advancement of global lattice energy minimization for the ab initio prediction of crystal structures and confirm the utility of representing electrostatic contributions to the energy with atom-centered multipoles.
Abstract: Following the interest generated by two previous blind tests of crystal structure prediction (CSP1999 and CSP2001), a third such collaborative project (CSP2004) was hosted by the Cambridge Crystallographic Data Centre. A range of methodologies used in searching for and ranking the likelihood of predicted crystal structures is represented amongst the 18 participating research groups, although most are based on the global minimization of the lattice energy. Initially the participants were given molecular diagrams of three molecules and asked to submit three predictions for the most likely crystal structure of each. Unlike earlier blind tests, no restriction was placed on the possible space group of the target crystal structures. Furthermore, Z' = 2 structures were allowed. Part-way through the test, a partial structure report was discovered for one of the molecules, which could no longer be considered a blind test. Hence, a second molecule from the same category (small, rigid with common atom types) was offered to the participants as a replacement. Success rates within the three submitted predictions were lower than in the previous tests - there was only one successful prediction for any of the three 'blind' molecules. For the 'simplest' rigid molecule, this lack of success is partly due to the observed structure crystallizing with two molecules in the asymmetric unit. As in the 2001 blind test, there was no success in predicting the structure of the flexible molecule. The results highlight the necessity for better energy models, capable of simultaneously describing conformational and packing energies with high accuracy. There is also a need for improvements in search procedures for crystals with more than one independent molecule, as well as for molecules with conformational flexibility. These are necessary requirements for the prediction of possible thermodynamically favoured polymorphs. Which of these are actually realised is also influenced by as yet insufficiently understood processes of nucleation and crystal growth.
Abstract: A crystal of 2-chlorophenol was grown from the liquid at ambient pressure by laser-assisted zone refinement; 4-fluorophenol was crystallized from ethanol. Different polymorphs were obtained at high pressure by compression of the liquids in a Merrill-Bassett diamond-anvil cell (crystallization pressures 0.12 and 0.28 GPa, respectively). The structures of all phases are characterized by OH---OH hydrogen-bond formation. In the ambient-pressure polymorph of 2-chlorophenol, a hydrogen-bonded chain is formed about a 32 screw-axis; the ambient-pressure phase of 4-fluorophenol contains hexameric rings located on 3 sites. In crystallizing in high-symmetry space groups, these two compounds conform to typical behavior for bulky monoalcohols. By contrast, at high-pressure both compounds form zigzag chains disposed about 21 screw-axes, behavior more characteristic of small monoalcohols. The halophenol moiety thus behaves as a bulky group at ambient pressure but a small group at high pressure. We show that Crystal Structure Prediction methodologies reproduce all four phases, even though the potentials used were developed using ambient-pressure data. This is especially encouraging as the ambient-pressure phase of 2-chlorophenol contains three molecules in the asymmetric unit, while the high-pressure phase of 4-fluorophenol is disordered.
Abstract: The growth morphology of paracetamol is known to show a strong supersaturation dependence. Most morphology prediction methods, like the attachment energy method, cannot include this dependence in their prediction. Monte Carlo simulations are able to use the supersaturation as an input parameter and can also include the growth mechanism. This makes the Monte Carlo technique a powerful tool to study the growth of organic crystals. Some studies in the literature show that the attachment energy method is only weakly influenced by the force field used to calculate the attachment energies. The present paper presents the sensitivity of the Monte Carlo simulation results to the force field and charge set using paracetamol as a case study. The force field and atomic point charges are found to influence the results to a large extent. This is due to subtle differences in step energies that determine the growth rates of the crystal faces.
Abstract: Lattice energy searches for theoretical low-energy crystal forms are presented for 50 small organic molecules, and we compare the experimentally observed crystal forms to these lists of hypothetical polymorphs. For each known crystal, the relative stability is calculated with respect to the global minimum energy structure, and we determine the number of unobserved structures lower in energy than the experimental form. The distributions of these relative energies and their rankings in the predicted lists are used to determine the efficacy of lattice energy minimization in crystal structure prediction. Although a simple form for the interaction energies has been used, the calculations produce almost a third of the known crystals as the global minimum in energy, and approximately a half of the known structures are within 1 kJ/mol of the global minimum. Molecules with no hydrogen-bonding capacity are most likely to be found close to the global minimum in lattice energy, while increasing the number of possible hydrogen-bond donor-acceptor combinations leads to less reliable predictions.
Abstract: Molecular dynamics simulations have been performed on crystalline imidazole at 100 K and 5-azauracil at 310 K with a model intermolecular potential that includes a distributed multipole representation of the molecular charge distribution using the program DL_MULTI. The anisotropic atom atom electrostatic model enabled the experimental crystal structures to be reproduced well in a constant pressure simulation and the simulations showed a physically reasonable thermal expansion relative to the minimum in the static lattice energy. The rigid-body molecular motions in a subsequent constant volume simulation were analysed to obtain the k = 0 frequencies corresponding to different symmetry representations, via the translational and rotational velocity autocorrelation functions. These frequencies were contrasted with the corresponding harmonic lattice modes calculated with the same molecular model and intermolecular potential. The agreement was good, with most, but not all, modes decreasing in frequency in the finite temperature simulation, by generally less than 5 cm(-1) in the case of imidazole (reducing the rms error in comparison with experimental frequencies to 18.8 cm(-1)) and by less than 20 cm(-1) for 5-azauracil. Quasi-harmonic calculations using experimental unit cell parameters and analyses of the modes in terms of the different hydrogen bonding motifs were unable to give any clear insight into the causes of the significant variations in the effects of temperature on the different motions.
Abstract: A computational search to predict the crystal structure of parabanic acid produced the known P21/c crystal structure as the global minimum in the lattice energy. However, there are many hypothetical structures only 2-6 kJ mol(-1) less stable than the known form, which are within the energy range of possible polymorphism and have reasonable mechanical properties and relative growth rates. The harmonic intermolecular frequencies and the attachment energy estimate of relative growth rates suggest that the known polymorph is thermodynamically and kinetically favoured, but the possibility of other polymorphs cannot be excluded. A simultaneous experimental search for new polymorphs found crystals with a new morphology and X-ray powder pattern when a solution of parabanic acid in methanol was left to evaporate. Eventually, the structure was shown by single crystal X-ray diffraction to be that of oxo-ureido-acetic acid methyl ester. Thus, under the conditions of recrystallisation from methanol, parabanic acid had undergone a previously unreported ring-opening reaction, and had not crystallised as a new polymorph as had seemed likely prior to single crystal characterisation. The combination of the experimental and theoretical studies indicates that new polymorphs of parabanic acid are unlikely to be found readily.
Abstract: Rigid-body, k = 0 phonon frequencies have been calculated within the crystal structure modeling program DMAREL, enabling the use of anisotropic atom-atom model potentials. Five organic crystals (hexamethylenetetramine, naphthalene, pyrazine, imidazole, and alpha-glycine) were chosen to sample a range of intermolecular interactions for determining the sensitivity of the calculated frequencies to changes in the empirical repulsion-dispersion parameters and the electrostatic model. A carefully parameterized simple exp-6 model can describe vibrations in simple van der Waals crystals and some hydrogen bonded crystals reasonably well. However, for weaker polar interactions, an accurate model of the electrostatics is needed. Bending of weak polar interactions and shearing of close contacts with delocalized pi-systems are particularly sensitive to the description of electrostatic interactions. Point charge models generally underestimate the resistance to deforming hydrogen bonds, and a distributed multipole model stabilizes these interactions. Because of their statistical nature, vibrational contributions to the energy can be estimated more accurately than the frequencies of individual modes, and the best models give good estimates of zero-point energies and the vibrational partition function, which should be useful in predicting the relative stability of polymorphs.
Abstract: A nearly nonempirical, transferable model potential is developed for the chlorobenzene molecules (C6ClnH6-n, n = 1 to 6) with anisotropy in the atom-atom form of both electrostatic and repulsion interactions. The potential is largely derived from the charge densities of the molecules, using a distributed multipole electrostatic model and a transferable dispersion model derived from the molecular polarizabilities. A nonempirical transferable repulsion model is obtained by analyzing the overlap of the charge densities in dinners as a function of orientation and separation and then calibrating this anisotropic atom-atom model against a limited number of intermolecular perturbation theory calculations of the short-range energies. The resulting model potential is a significant improvement over empirical model potentials in reproducing the twelve chlorobenzene crystal structures. Further validation calculations of the lattice energies and rigid-body k = 0 phonon frequencies provide satisfactory agreement with experiment, with the discrepancies being primarily due to approximations in the theoretical methods rather than the model intermolecular potential. The potential is able to give a good account of the three polymorphs of p-dichlorobenzene in a detailed crystal structure prediction study. Thus, by introducing repulsion anisotropy into a transferable potential scheme, it is possible to produce a set of potentials for the chlorobenzenes that can account for their crystal properties in an unprecedentedly realistic fashion.
Abstract: The oldest crystal structure of pyridine is unusually complex, with four molecules in the asymmetric unit cell of Pna2(1) symmetry. In an attempt to understand why pyridine crystallises with 16 molecules in the unit cell, we have considered its thermodynamic stability relative to hypothetical pyridine structures. These were generated by search for minima in the lattice energy of pyridine amongst the more common space groups, using the crystal structure prediction procedure MOLPAK followed by lattice energy minimisation using a distributed multipole-based intermolecular potential. We find over two dozen distinct crystal structures in the energy gap of less than 6 kJ mol(-1) between the corresponding models for the observed and most stable (hypothetical) structure. Adding harmonic phonon estimates of the intermolecular zero point energy and entropy at the melting point of pyridine slightly improves the relative stability of the observed Z = 16 structure. Several of these hypothetical structures can be eliminated as only just mechanically stable, or because the growth rate of the crystal is estimated to be very slow by the attachment energy model. Nevertheless, there are still over a dozen structures that appear competitive with the know structure as polymorphs of pyridine. Following these predictions, an intense experimental search has found a new polymorph of perdeutero-pyridine (form II), which was not found in the search. This structure is also predicted to be metastable with a similar energy to form I. Although there is some evidence for kinetic factors favouring the observed structures, the metastable Z = 16 structure and the new form II remain a challenge for our understanding of crystallisation.
Abstract: The analgesic drug paracetamol (acetaminophen) has two reported metastable polymorphs, one with better tabletting 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 platelike 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.
Abstract: Elastic constants of a set of molecular organic crystals have been calculated within the crystal modeling program DMAREL, which was developed to allow the use of highly accurate, anisotropic atom-atom potentials. A set of six molecular crystals (durene, m-dinitrobenzene, the beta form of resorcinol, pentaerythritol, urea, and hexamethylenetetramine) has been chosen to sample a range of intermolecular interactions and crystal symmetries. The sensitivity of such calculations to variations in empirical repulsion-dispersion parameters and the electrostatic model is determined and discussed relative to the other errors in the theoretical model and typical experimental uncertainties. We find that model potentials whose functional form has been simplified often reproduce crystal structures and lattice energies adequately but perform poorly when used to calculate elastic constants. This is because more theoretically justified potentials are required to satisfactorily model the curvature at the equilibrium geometries. The rigid-molecule approximation can result in exaggerated elastic constants, and the neglect of thermal effects also leads to significant overestimation of the stiffness constants.
Abstract: The electronic excitations of the low-valence bismuth cluster cations Bi-5(3+), Bi-8(2+), and Bi-9(5+) have been studied with experimental and theoretical techniques. The UV-visible spectra of the bismuth ions were measured in acidic chloroaluminate melts (mixture of 1-methyl-3-benzyl imidazolium chloride and AlCl3). The spectra of the Bi-5(3+) and Bi-8(2+) ions agree fairly well with previous reports but also revealed additional low-energy absorptions. Ab initio methods were employed to assign the experimentally observed electronic transitions of these homopolyatomic bismuth cations. Structures were optimized at the RHF, MP2, and B3LYP levels of theory by using split-valence LANL2DZ basis sets that were augmented with one and two sets of pure d functions The computed structures agree well with the results of neutron diffraction analyses of melts. Electronically excited states of the three clusters were treated by using the CI-Singles theory. The results of these calculations were used to explain the observed UV-visible spectra. The observed electronic excitations in the UV-visible range are ail found to result from transitions involving the molecular orbitals formed by 6p-atomic-orbital overlap. This leads to the necessity of using basis sets that include d-type functions, which allow for an adequate description of the bonding that results from such p-orbital overlap. Spin-orbit coupling becomes increasingly important with increasing atomic number and its consideration is necessary when describing the electronic transitions in clusters of heavy atoms. The calculations show that singlet-triplet transitions which are made accessible by strong spin-orbit coupling, are responsible for some of the observed absorptions.
Abstract: The azine of pentafluorobenzaldehyde had been previously prepared from pentafluorobenzaldehyde and hydrazine. However, the analogous reaction of 2,3,4,5,6-pentafluoroacetophenone 1 with hydrazine did not result in the formation of azine 3 but resulted instead in the formation of 3-methyl-4,5,6,7-tetrafluoro-1H-indazole, 4, via the hydrazone 2. The resulting indazole was characterized by high resolution mass spectroscopy and H-1-,C-13-, and F-19-NMR spectroscopy. The geometry and electrostatic properties of the parent indazole and its derivative, 4, were studied with db initio quantum theory and density functional methods. Our optimized structure of the parent indazole computed at the MP2(fc)/6-311G** level is presumably more accurate than the structure derived from microwave measurements. The preferred conformer of 4 was determined from RHF/6-31G* energies and full normal mode analyses were used to characterize both conformers. The minimum structure of 4 was refined at the MP2(fc)/6-311G** level of theory and compared to the unsubstituted structure. The electrostatic properties of the parent indazole and 4 are discussed and compared to those of benzene and hexafluorobenzene calculated at the same level. Natural bond order (NBO) calculations were performed to rationalize the difference in direction of the dipole moments of the parent indazole and 4. The gauge-invariant atomic orbital (GIAO) method was employed to calculate atomic shielding tensors of the indazoles using density functional theory at the B3LYP/6-311 + G(2d,p) level. The calculated chemical shifts were used to aid in assigning peaks in the NMR spectra.
