From `crystallographic accuracy' to `thermodynamic accuracy': a redetermination of the crystal structure of calcium atorvastatin trihydrate (Lipitor).

With ever-improving quantum-mechanical computational methods, the accuracy requirements for experimental crystal structures increase. The crystal structure of calcium atorvastatin trihydrate, which has 56 degrees of freedom when determined with a real-space algorithm, was determined from powder diffraction data by Hodge et al. [Powder Diffr.

The seventh blind test of crystal structure prediction: structure generation methods.

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern.

Synthesis and Characterization of Two Novel Naphthalenediimide/Zinc Phosphonate Crystalline Materials Precipitated from Different Solvents.

Hybrid naphthalenediimide/zinc phosphonate materials (NDI/Zn) were prepared by mixing solutions of ,'-bis(2-phosphonoethyl)-1,4,5,8-naphthalenediimide (PNDI) and zinc nitrate, resulting in the precipitation of the desired compounds. Samples precipitated from water and ,-dimethylformamide (DMF) were produced. The obtained samples had the expected elemental composition, and the presence of naphthalenediimides (NDI) was ascertained by infrared and UV-visible spectroscopy.

Hydrogen bonding patterns and C-H...π interactions in the structure of the antiparkinsonian drug (R)-rasagiline mesylate determined using laboratory and synchrotron X-ray powder diffraction data.

The structure of (R)-rasagiline mesylate [(R)-RasH·Mes], an active pharmaceutical ingredient used to treat Parkinson's disease, is presented. The structure was determined from laboratory and synchrotron powder diffraction data, refined using the Rietveld method, and validated and optimized using dispersion-corrected DFT calculations. The unit-cell parameters obtained in both experiments are in good agreement and the refinement with both datasets converged to good agreement factors.

Crystal structure from X-ray powder diffraction data, DFT-D calculation, Hirshfeld surface analysis, and energy frameworks of ()-trichlorme-thia-zide.

The structure of racemic ()-trichlorme-thia-zide [systematic name: ()-6-chloro-3-(di-chloro-meth-yl)-1,1-dioxo-3,4-di-hydro-2-1λ,2,4-benzo-thia-di-azine-7-sulfonamide], CHClNOS (-TCMZ), a diuretic drug used in the treatment of oedema and hypertension, was determined from laboratory X-ray powder diffraction data using [David (2006 ▸). , 910-915.], refined by the Rietveld method with [Coelho (2018 ▸).

A jumping crystal predicted with molecular dynamics and analysed with TLS refinement against powder diffraction data.

By running a temperature series of molecular dynamics (MD) simulations starting from the known low-temperature phase, the experimentally observed phase transition in a 'jumping crystal' was captured, thereby providing a prediction of the unknown crystal structure of the high-temperature phase and clarifying the phase-transition mechanism. The phase transition is accompanied by a discontinuity in two of the unit-cell parameters. The structure of the high-temperature phase is very similar to that of the low-temperature phase.

Four interpenetrating hydrogen-bonded three-dimensional networks in divanillin.

The crystal structure of divainillin (systematic name: 6,6'-dihydroxy-5,5'-dimethoxy-[1,1'-biphenyl]-3,3'-dicarbaldehyde), CHO, was determined from laboratory powder X-ray diffraction data using the software EXPO2013 (direct methods) and WinPSSP (direct-space approach). Divanillin molecules crystallize in the orthorhombic space group Pba2 (No. 32), with two molecules per unit cell (Z' = 1/2).

How many ritonavir cases are there still out there?

Based on a thorough and critical analysis of the commercial crystal structure prediction studies of 41 pharmaceutical compounds, we conclude that for between 15 and 45% of all small-molecule drugs currently on the market the most stable experimentally observed polymorph is not the thermodynamically most stable crystal structure and that the appearance of the latter is kinetically hindered.

Crystal structure analysis of a star-shaped triazine compound: a combination of single-crystal three-dimensional electron diffraction and powder X-ray diffraction.

The solid-state structure of star-shaped 2,4,6-tris{(E)-2-[4-(dimethylamino)-phenyl]ethenyl}-1,3,5-triazine is determined from a powder sample by exploiting the respective strengths of single-crystal three-dimensional electron diffraction and powder X-ray diffraction data. The unit-cell parameters were determined from single crystal electron diffraction data. Using this information, the powder X-ray diffraction data were indexed, and the crystal structure was determined from the powder diffraction profile.

Validation of missed space-group symmetry in X-ray powder diffraction structures with dispersion-corrected density functional theory.

More than 600 molecular crystal structures with correct, incorrect and uncertain space-group symmetry were energy-minimized with dispersion-corrected density functional theory (DFT-D, PBE-D3). For the purpose of determining the correct space-group symmetry the required tolerance on the atomic coordinates of all non-H atoms is established to be 0.2 Å.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine.

Motional averaging has been proven to be significant in predicting the chemical shifts in solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example.

Crystallographic and Dynamic Aspects of Solid-State NMR Calibration Compounds: Towards ab Initio NMR Crystallography.

The excellent results of dispersion-corrected density functional theory (DFT-D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT-D calculations is a target, especially for the field of molecular NMR crystallography. Four (13) C ss-NMR calibration compounds are investigated by single-crystal X-ray diffraction, molecular dynamics and DFT-D calculations.

Local structure in the disordered solid solution of cis- and trans-perinones.

The cis- and trans-isomers of the polycyclic aromatic compound perinone, C26H12N4O2, form a solid solution (Vat Red 14). This solid solution is isotypic to the crystal structures of cis-perinone (Pigment Red 194) and trans-perinone (Pigment Orange 34) and exhibits a combined positional and orientational disorder: In the crystal, each molecular position is occupied by either a cis- or trans-perinone molecule, both of which have two possible molecular orientations. The structure of cis-perinone exhibits a twofold orientational disorder, whereas the structure of trans-perinone is ordered.

One hydrogen bond does not a separation make, or does it? Resolution of amines by diacetoneketogulonic acid.

Diacetoneketogulonic acid was used to separate primary amines from their racemic modifications and the selectivity of the acid was rationalized by lattice energy calculations and analyzing the weak interactions around the captured amines.

Structure of Pigment Yellow 181 dimethylsulfoxide N-methyl-2-pyrrolidone (1:1:1) solvate from XRPD + DFT-D.

With only a 2.6 Å resolution laboratory powder diffraction pattern of the θ phase of Pigment Yellow 181 (P.Y.

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.

Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-dihydro-1,3,4-thiadiazol-2-ylidene)-4-methylbenzenesulfonamide using DFT-D calculations and (13)C solid-state NMR.

The crystal structure of the title compound, C11H13N3O2S2, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated (13)C solid-state NMR spectra [Hangan et al. (2010). Acta Cryst.

On the correlation between hydrogen bonding and melting points in the inositols.

Inositol, 1,2,3,4,5,6-hexahydroxycyclohexane, exists in nine stereoisomers with different crystal structures and melting points. In a previous paper on the relationship between the melting points of the inositols and the hydrogen-bonding patterns in their crystal structures [Simperler et al. (2006 ▶).

Structures of cefradine dihydrate and cefaclor dihydrate from DFT-D calculations.

The crystal structure of cefradine dihydrate, C16H19N3O4S·2H2O, is considered in the pharmaceutical sciences to be the epitome of an isolated-site hydrate. The structure from single-crystal X-ray data was described in 1976, but atomic coordinates were not published. The atomic coordinates are determined here by combining the information available from the published single-crystal data with a dispersion-corrected density functional theory (DFT-D) method that has been validated to reproduce molecular crystal structures very accurately.

Reinterpretation of the monohydrate of clarithromycin from X-ray powder diffraction data as a trihydrate.

Noguchi, Fujiki, Iwao, Miura & Itai [Acta Cryst. (2012), E68, o667-o668] recently reported the crystal structure of clarithromycin monohydrate from synchrotron X-ray powder diffraction data. Voids in the crystal structure suggested the possible presence of two more water molecules.

Complementing high-throughput X-ray powder diffraction data with quantum-chemical calculations: Application to piroxicam form III.

High-throughput crystallisation and characterisation platforms provide an efficient means to carry out solid-form screening during the pre-formulation phase. To determine the crystal structures of identified new solid phases, however, usually requires independent crystallisation trials to produce single crystals or bulk samples of sufficient quantity to carry out high-quality X-ray diffraction measurements. This process could be made more efficient by a robust procedure for crystal structure determination directly from high-throughput X-ray powder diffraction (XRPD) data.