Precursor effects of the orthorhombic to monoclinic phase transition in benzocaine form (II) revealed by X-ray diffuse scattering

The Phase Diagram of the API Benzocaine and Its Highly Persistent, Metastable Crystalline Polymorphs

The availability of sufficient amounts of form I of benzocaine has led to the investigation of its phase relationships with the other two existing forms, II and III, using adiabatic calorimetry, powder X-ray diffraction, and high-pressure differential thermal analysis. The latter two forms were known to have an enantiotropic phase relationship in which form III is stable at low-temperatures and high-pressures, while form II is stable at room temperature with respect to form III. Using adiabatic calorimetry data, it can be concluded, that form I is the stable low-temperature, high-pressure form, which also happens to be the most stable form at room temperature; however, due to its persistence at room temperature, form II is still the most convenient polymorph to use in formulations. Form III presents a case of overall monotropy and does not possess any stability domain in the pressure-temperature phase diagram. Heat capacity data for benzocaine have been obtained by adiabatic calorimetry from 11 K to 369 K above its melting point, which can be used to compare to results from in silico crystal structure prediction.

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.

A method to perform modulated structure studies using the programZMC

The Monte Carlo simulation toolkitZMCprovides a general method for Monte Carlo simulation of disordered molecular displacements, orientations and site occupations. It is part of a suite of programs that allows convenient calculation of three-dimensional reciprocal space diffraction intensities. Such intensities are useful for extensive structure interpretations from diffraction experiments. Some physical properties can also be calculated from the simulation. This article reports the implementation of an integratedZMCmodule that facilitates the construction of modulated molecular crystals and allows the corresponding calculation of modulation satellites. Use of the module is explained and examples illustrated. The method is ideally suited for novice treatment of modulated structure features and also as a basic platform to explore complex structure/properties relationships using atomistic simulation techniques.

Temperature-induced reversible structural phase transition and X-ray diffuse scattering in 2-amino-3-nitropyridinium hydrogen sulfate

The novel polar material 2-amino-3-nitropyridinium hydrogen sulfate, C5H6N3O2(HSO4) (abbreviated as 2A3NP-HS), was obtained and structurally characterized by means of single-crystal X-ray diffraction. At room temperature, 2A3NP-HS crystallizes as a non-centrosymmetric disordered phase (I) in the orthorhombicPna21space group. On cooling below 298 K, 2A3NP-HS undergoes a reversible phase transition to phase (II) with the monoclinic non-centrosymmetricP21space group. This transition might be classified as an `order–disorder' type. The structural details in both phases are analysed. Additionally, for phase (I), in the 304–365 K temperature range, diffuse scattering was found to be present in the form of elongated streaks parallel to thea* direction. This can be unravelled when implementing a short-range order affecting anionic cationic ribbons occurring in the structure, with correlations acting both in thea-direction and in thebc-plane. The results of Monte Carlo simulations, adapting a two-dimensional Ising-type model, reveal the formation of domains, which areb-elongated and thin alonga. Locally, the stacking of the ribbons in the domains reflects the ordered arrangement observed in the low-temperature monoclinic phase (II).

Cytotoxic and Anti-inflammatory Sesquiterpenes from Ainsliaea henryi

Three new sesquiterpenoids, 4α-hydroxyeudesm-11(13)-en-12-yl 3-methylbutanoate (1), diaspanolide E (2), and (13α)-germacra-1(10),4-dien-12,8α-olid-15-oic acid (3), along with eight known sesquiterpenoids (4 - 11), were isolated from the aerial parts of Ainsliaea henryi. The chemical structures of compounds 1 - 3 were elucidated by spectroscopic analysis (1D-, 2D-NMR, MS and HR/MS). All isolates were evaluated for their inhibitory activities against nitric oxide (NO) production in lipopolysaccharide-induced RAW264.7 macrophage cells. Compound 10 exhibited significantly inhibition against NO release with an IC₅₀ value of 6.54 ± 0.16 μm. Also, all isolated compounds were tested for cytotoxicity against three human tumor cell lines A549, MGC803, and HCT116, among which compound 5 significantly inhibited the proliferation of MGC803 cell lines with an IC₅₀ value of 2.2 ± 0.2 μm.

An insight into real and average structure from diffuse X-ray scattering - a case study

Two-dimensional diffuse X-ray scattering from an organic salt [N-(3-(2,6-dimethylanilino)-1-methylbut-2-enylidene)-2,6-dimethylanilinium chloride, C21H27N2(+)Cl(-)] was interpreted with the help of an analytical model of diffuse scattering. An analysis of the relationship between symmetry and diffuse scattering for the studied system has been undertaken. The symmetry of the system explains the extinction pattern, taking the form of curves, on the diffuse scattering planes. We have also tested the relationship between the average structure model and scattering intensities. Two models, differing in their representation of overlapping atoms, were used. In the case of diffuse scattering the difference between resulting intensities is immense, while for the Bragg intensities it is much smaller. This sensitivity of diffuse scattering could potentially be used to improve the description of the average structure.

On the use of molecular dynamics simulation to calculate X-ray thermal diffuse scattering from molecular crystals

The use of molecular dynamics simulations to calculate the thermal diffuse scattering from X-ray diffraction experiments on molecular crystals is described, using the crystal structure of aspirin form I as an example system. Parameter settings that do not affect the actual simulation are varied in order to examine the effect on the final calculated diffraction pattern, and thus roughly determine a range for general settings that might be used in further experiments targeted at tailoring parameters associated with the functional forms for dispersion interaction terms commonly used in molecular simulation force fields. The proposed method is compared with that of the more widely accepted Monte Carlo technique, and possible advantages and drawbacks for the use of either method are discussed.

Diffuse scattering and partial disorder in complex structures

The study of single-crystal diffuse scattering (SCDS) goes back almost to the beginnings of X-ray crystallography. Because SCDS arises from two-body correlations, it contains information about local (short-range) ordering in the sample, information which is often crucial in the attempt to relate structure to function. This review discusses the state of the field, including detectors and data collection and the modelling of SCDS using Monte Carlo and ab initio techniques. High-quality, three-dimensional volumes of SCDS data can now be collected at synchrotron light sources, allowing ever more detailed and quantitative analyses to be undertaken, and opening the way to approaches such as three-dimensional pair distribution function studies (3D-PDF) and automated refinement of a disorder model, powerful techniques that require large volumes of low-noise data.

Understanding the structure details when drying hydrate crystals of pharmaceuticals – interpretations from diffuse scattering and inter-modulation satellites of a partially dehydrated crystal

Simplified models for the crystal lattice of the sesquihydrate form of the hemi-sulfate salt of (5S,6S,9R)-5-amino-6-(2,3-difluorophenyl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridin-9-yl 4-(2-oxo-2,3-dihydro-1H-imidazol[4,5b]pyridin-1-yl)-1-piperidine carboxylate (BMS-927711, C28H29F2N6O3+) are used to calculate diffuse diffraction features in order to develop a mechanistic understanding of the dehydration process with respect to disruption of the lattice, since a Bragg model cannot be established. The model demonstrates that what we observe when the water leaves the crystal is partial transformation from the parent form to a child form (a new form, less hydrated and structurally related to the parent). Yet this `dried' structure is not a pure phase. It consists of semi-random layers of both child, parent and an interfacial layer which has a modulated structure that represents a transitory phase. Understanding the fact that a single `dried' crystal can have the disordered layer structure described as well as understanding mechanistic relationships between the phases involved can have implications in understanding the effect of common large scale bulk drying procedures. During the development of BMS-927711, difficulties did arise during characterization of the dried bulk when using only routine solid-state analysis. The material is now better understood from this diffraction study. The diffraction experiments also reveal intermodulation satellites, which upon interpretation yield even more structural information about the crystal transformation. The model suggests the mechanism of transformation is laminar in which layers of the crystal are driven to approach a stableB-centered supercell phase of lower water content.

Nanoscale Order in Molecular Systems from Single Crystal Diffuse Scattering

Diffuse scattering – the coherently scattered intensity that is not localised on the reciprocal lattice – contains a wealth of information about the local order (order on the nanoscale) in crystalline materials. Since molecules and atoms will respond most strongly to their local chemical environments, it is a valuable tool in understanding how structure leads to properties. However, at present its collection and analysis are relatively specialised. Monte Carlo (MC) computer simulation of a model structure has become a powerful and well-accepted technique for aiding the interpretation and analysis of diffuse scattering patterns. Its great strength is its flexibility – as long as an MC energy can be defined, a model can be developed and tested. At one extreme a very simplified model may be useful in demonstrating particular qualitative effects, while at the other a quantitative and very detailed description of disordered structures can be obtained. Examples discussed include new results concerning p-chloro-N-(p-chloro-benzylidene)aniline, a molecule showing various degrees of molecular flexibility.

Study of the single-crystal X-ray diffuse scattering in paracetamol polymorphs

Single-crystal diffuse X-ray scattering from paracetamol polymorphs is successfully calculated with Monte Carlo (MC) models that are used to simulate the crystals. In order to obtain the correct model appropriate force constants are required that describe the interatomic potentials used in the MC algorithm. Coefficients for an empirical `Buckingham'-type formula are used to determine these force constants. These coefficients are subsequently refined using the least-squares method and are found to converge on similar values for both polymorphic forms. An investigation of the correlation space generated from each model provides what would be expected given that strong displacive correlations exist between the molecules comprising the densely hydrogen-bonded layers. More disordered motions between these layers are present in the model for form (II) as opposed to form (I). An investigation into the peculiarities of librational disorder was also conducted, however, correlation values turn out to be so small that any structural information concerning librational correlation is inconclusive. The purpose of this experiment was to identify if the diffuse scattering features could provide further insight into understanding the physical reasoning behind the metastability of form (II). The form (II) → (I) phase transition is also not currently well understood and usually phase transitional information can be obtained from pronounced diffuse scattering features. Since the diffuse scattering is modelled adequately using harmonic potentials it is our conjecture that the `diffuse' is essentially thermal in origin and does not afford any extra information about the form (II) → (I) phase transition.

Diffuse scattering study of aspirin forms (I) and (II)

Full three-dimensional diffuse scattering data have been recorded for both polymorphic forms [(I) and (II)] of aspirin and these data have been analysed using Monte Carlo computer modelling. The observed scattering in form (I) is well reproduced by a simple harmonic model of thermally induced displacements. The data for form (II) show, in addition to thermal diffuse scattering (TDS) similar to that in form (I), diffuse streaks originating from stacking fault-like defects as well as other effects that can be attributed to strain induced by these defects. The present study has provided strong evidence that the aspirin form (II) structure is a true polymorph with a structure quite distinct from that of form (I). The diffuse scattering evidence presented shows that crystals of form (II) are essentially composed of large single domains of the form (II) lattice with a relatively small volume fraction of intrinsic planar defects or faults comprising misoriented bilayers of molecular dimers. There is evidence of some local aggregation of these defect bilayers to form small included regions of the form (I) structure. Evidence is also presented that shows that the strain effects arise from the mismatch of molecular packing between the defect region and the surrounding form (II) lattice. This occurs at the edges of the planar defects in the b direction only.