Applications Of Dl_poly And Dl_multi To Organic Molecular Crystals

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.

Crystal-energy landscapes of active pharmaceutical ingredients using composite approaches

Composite methods employing dispersion-corrected DFT consistently identify experimentally isolated polymorphs as the lowest-energy crystal structures of common APIs.

Assessing Force Field Potential Energy Function Accuracy via a Multipolar Description of Atomic Electrostatic Interactions in RNA

Computational investigations of RNA properties often rely on a molecular mechanical approach to define molecular potential energy. Force fields for RNA typically employ a point charge model of electrostatics, which does not provide a realistic quantum-mechanical picture. In reality, electron distributions around nuclei are not spherically symmetric and are geometry dependent. A multipole expansion method which allows for incorporation of polarizability and anisotropy in a force field is described, and its applicability to modeling the behavior of RNA molecules is investigated. Transferability of the model, critical for force field development, is also investigated.

Control and prediction of the organic solid state: a challenge to theory and experiment†

The ability of theoretical chemists to quantitatively model the weak forces between organic molecules is being exploited to predict their crystal structures and estimate their physical properties. Evolving crystal structure prediction methods are increasingly being used to aid the design of organic functional materials and provide information about thermodynamically plausible polymorphs of speciality organic materials to aid, for example, pharmaceutical development. However, the increasingly sophisticated experimental studies for detecting the range of organic solid-state behaviours provide many challenges for improving quantitative theories that form the basis for the computer modelling. It is challenging to calculate the relative thermodynamic stability of different organic crystal structures, let alone understand the kinetic effects that determine which polymorphs can be observed and are practically important. However, collaborations between experiment and theory are reaching the stage of devising experiments to target the first crystallization of new polymorphs or create novel organic molecular materials.

Evaluation of General and Tailor Made Force Fields via X-ray Thermal Diffuse Scattering Using Molecular Dynamics and Monte Carlo Simulations of Crystalline Aspirin

We have performed a comparison of the experimental thermal diffuse scattering (TDS) from crystalline Aspirin (form I) to that calculated from molecular dynamics (MD) simulations based on a variety of general force fields and a tailor-made force field (TMFF). A comparison is also made with Monte Carlo (MC) simulations which use a "harmonic network" approach to describe the intermolecular interactions. These comparisons were based on the hypothesis that TDS could be a useful experimental data in validation of such simulation parameter sets, especially when calculations of dynamical properties (e.g., thermodynamic free energies) from molecular crystals are concerned. Currently such a validation of force field parameters against experimental data is often limited to calculation of specific physical properties, e.g., absolute lattice energies usually at 0 K or heat capacity measurements. TDS harvested from in-house or synchrotron experiments comprises highly detailed structural information representative of the dynamical motions of the crystal lattice. Thus, TDS is a well-suited experimental data-driven means of cross validating theoretical approaches targeted at understanding dynamical properties of crystals. We found from the results of our investigation that the TMFF and COMPASS (from the commercial software "Materials Studio") parameter sets gave the best agreement with experiment. From our homologous MC simulation analysis we are able to show that force constants associated with the molecular torsion angles are likely to be a strong contributing factor for the apparent reason why these aforementioned force fields performed better.

Molecular dynamics simulations of aqueous glycine solutions

Pre-nucleation clusters of glycine are strongly hydrated dynamic solutes, which change size and shape within hundreds of picoseconds.

Analysis of the conformational profiles of fenamates shows route towards novel, higher accuracy, force-fields for pharmaceuticals

The conformational barriers of the fenamates which lead to conformational polymorphism can be represented by a novel, physically motivated, model intramolecular potential suitable for extension to other pharmaceuticals.

Salting out the polar polymorph: analysis by alchemical solvent transformation

We computationally examine how adding NaCl to an aqueous solution with α- and γ-glycine nuclei alters the structure and interfacial energy of the nuclei. The polar γ-glycine nucleus in pure aqueous solution develops a melted layer of amorphous glycine around the nucleus. When NaCl is added, a double layer is formed that stabilizes the polar glycine polymorph and eliminates the surface melted layer. In contrast, the non-polar α-glycine nucleus is largely unaffected by the addition of NaCl. To quantify the stabilizing effect of NaCl on γ-glycine nuclei, we alchemically transform the aqueous glycine solution into a brine solution of glycine. The alchemical transformation is performed both with and without a nucleus in solution and for nuclei of α-glycine and γ-glycine polymorphs. The calculations show that adding 80 mg/ml NaCl reduces the interfacial free energy of a γ-glycine nucleus by 7.7 mJ/m(2) and increases the interfacial free energy of an α-glycine nucleus by 3.1 mJ/m(2). Both results are consistent with experimental reports on nucleation rates which suggest: J(α, brine) < J(γ, brine) < J(α, water). For γ-glycine nuclei, Debye-Hückel theory qualitatively, but not quantitatively, captures the effect of salt addition. Only the alchemical solvent transformation approach can predict the results for both polar and non-polar polymorphs. The results suggest a general "salting out" strategy for obtaining polar polymorphs and also a general approach to computationally estimate the effects of solvent additives on interfacial free energies for nucleation.

Polymorph specific RMSD local order parameters for molecular crystals and nuclei: α-, β-, and γ-glycine

Crystal nucleation is important for many processes including pharmaceutical crystallization, biomineralization, and material synthesis. The progression of structural changes which occur during crystal nucleation are often described using order parameters. Polymorph specific order parameters have been developed for crystallization of spherically symmetric particles; however, polymorph specific order parameters for molecular crystals remain a challenge. We introduce template based polymorph specific order parameters for molecular crystals. For each molecule in a simulation, we compute the root mean squared deviation (RMSD) between the local environment around the molecule and a template of the perfect crystal structure for each polymorph. The RMSD order parameters can clearly distinguish the α-, β-, and γ-glycine polymorph crystal structures in the bulk crystal and also in solvated crystallites. Surface melting of glycine crystallites in supersaturated aqueous solution is explored using the newly developed order parameters. The solvated α-glycine crystallite has a thinner surface melted layer than the γ-glycine crystallite. α-glycine forms first out of aqueous solution, so surface melted layer thickness may provide insight into interfacial energy and polymorph selection.

A computational study of the mechanism of the selective crystallization of α- and β-glycine from water and methanol-water mixture

Understanding the control of polymorphism in organic crystals is of paramount importance to the pharmaceutical, chemical, and food industries. In this work, we investigated two mechanisms described in the literature about the selective crystallization of α- and β-glycine from water and from mixtures of water and methanol using molecular simulations. The link hypothesis (J. Phys. Chem. B 2008, 112, 7794; Cryst. Growth Des. 2006, 6, 1788; J. Inclusion Phenom. Mol. Recognit. Chem. 1990, 8, 395; J. Am. Chem. Soc. 1986, 108, 5871.), which tries to relate the structure of the polymorph obtained from crystallization to the structure of the prenucleation aggregates in the solutions, says the abundance of glycine cyclic dimers in aqueous solutions leads to the crystallization of α-glycine, the polymorph using cyclic dimers as the packing units. This hypothesis was studied first. We revisited the self-assembly of glycine molecules in solution using molecular dynamics to address the debate (Phys. Rev. Lett. 2007, 99, 115702; J. Phys. Chem. B 2008, 112, 7280; J. Am. Chem. Soc. 2008, 130, 13973.) about which is the dominating species in the glycine aqueous solutions and whether there is a link between the solution chemistry and the polymorphic outcome of crystallization. The structures of the glycine clusters were characterized using a structural parameter called cyclic dimer fraction. The glycine clusters in methanol-water mixtures have higher cyclic dimer compositions than those in the pure aqueous solutions. Moreover, the glycine open-chain dimer is more stable than the cyclic dimer regardless of the presence of methanol. All these suggest that the link hypothesis does not work for the polymorphic system of glycine, and the selective crystallization of α- and β-glycine from water and methanol-water mixture, respectively, is not due to the abundance of glycine aggregates in the solution phase with a similar structure to the crystallizing solid form. The hypothesis of the methanol inhibition on the growth of α-glycine {010} and {010} faces, proposed by Weissbuch (Angew. Chem., Int. Ed. 2005, 44, 3226.), was also studied. The interfaces between the {010} and {010} faces of both crystal forms (α and β) and both solvents (water and methanol-water 3:7 mixture) were studied using molecular simulation. No strong binding of methanol onto the {010} and {010} faces of both crystal forms was observed, and the addition of methanol dilutes the crystal-solvent interactions on all faces. Therefore, the selective crystallization of β and α-glycine with and without methanol does not follow either of the two mechanisms in the literature.