Analysing Friedel averages and differences

Chirality determination in crystals

This tutorial review article discusses chirality determination in the solid state, both in single crystals and in crystal assemblies, with an emphasis on X-ray diffraction. The main principles of using X-ray diffraction to reliably determine absolute structure are summarized, and the complexity which can be encountered in chiral structures-kryptoracemates, scalemates, and inversion twinning-is illustrated with examples from our laboratories and the literature. We then address the problem of the bulk crystallization and discuss different techniques to determine chirality in a large assembly of crystal structures, with a special prominence given to an X-ray natural circular dichroism mapping technique that we recently reported.

The Publications of Howard Flack (1943–2017)

Howard Flack was a driving force in the development of modern crystallography. Today “the Flack parameter” has entered into the common parlance of crystallography but his influence was far wider. This article provides an overview of his scientific output and a full bibliography.

Ethyl (3S)-3-[(3aR,5R,6S,6aR)-6-hydroxy-2,2-dimethyltetrahydrofuro[4,5-d][1,3]dioxol-5-yl]-3-{(3S)-3-[(3aR,5R,6S,6aR)-6-hydroxy-2,2-dimethyltetrahydrofuro[4,5-d][1,3]dioxol-5-yl]-5-oxoisoxazolidin-2-yl}propanoate chloroform monosolvate

The Flack and Watkin 2AD plot based on 1941 acentric Friedel pairs for the title chloro­form solvate shows that the observed intensity differences for Friedel opposites are dominated by random and systematic errors, erasing information about resonant scattering.

The title compound, C₂₂H₃₃NO₁₂·CHCl₃, was obtained as a product of a double aza-Michael addition of hydroxyl­amine on a Chiron with a known absolute configuration. The enanti­opure compound crystallized as a chloro­form solvate, in space group P1, and diffraction data were collected at room temperature with Ag Kα radiation. The Flack parameter refined to x = −0.01 (16); however, the Flack and Watkin 2AD plot clearly shows that differences between Friedel opposites (the D component of the plot) do not carry any reliable information about resonant scattering of Cl atoms, and are rather dominated by random and systematic errors. The R_D factor calculated using 1941 acentric Friedel pairs is R_D = 0.995. On the other hand, the 2A component of the plot, related to average intensities of Friedel pairs, shows that data are of good quality (R_A = 0.069). This example illustrates that while using Ag Kα radiation (λ = 0.56083 Å), scatterers heavier than Cl should be present in a chiral crystal in order to determine confidently the absolute structure of the crystal.

Monodentate phosphine substitution in [Pd(κ3-dppf)(PR3)][BF4]2 (dppf = 1,1′-bis(diphenylphosphino)ferrocene) compounds

The synthesis and dissociative monodentate phosphine substitution of [Pd(κ³-dppf)(P(p-C₆H₄R)₃)][BF₄]₂ compounds is presented. DFT calculations further examines the nature of the Fe–Pd interaction of the κ³-dppf ligand.

Why direct and post-refinement determinations of absolute structure may give different results

Direct determination of the Flack parameter as part of the structure refinement procedure usually gives different, though similar, values to post-refinement methods. The source of this discrepancy has been probed by analysing a range of data sets taken from the recent literature. Most significantly, it was observed that the directly refined Flack (x) parameter and its standard uncertainty are usually not much influenced by changes in the refinement weighting schemes, but if they are then there are probably problems with the data or model. Post-refinement analyses give Flack parameters strongly influenced by the choice of weights. Weights derived from those used in the main least squares lead to post-refinement estimates of the Flack parameters and their standard uncertainties very similar to those obtained by direct refinement. Weights derived from the variances of the observed structure amplitudes are more appropriate and often yield post-refinement Flack parameters similar to those from direct refinement, but always with lower standard uncertainties. Substantial disagreement between direct and post-refinement determinations are strongly indicative of problems with the data, which may be difficult to identify. Examples drawn from 28 structure determinations are provided showing a range of different underlying problems. It seems likely that post-refinement methods taking into account the slope of the normal probability plot are currently the most robust estimators of absolute structure and should be reported along with the directly refined values.

A study of the planarity of the pyrrolone fragment in 2-isopropyl-2,3-dihydro-1H-isoindol-1-one

Orthophthalaldehyde (o-phthalaldehyde, OPA) is an aromatic dialdehyde bearing two electron-withdrawing carbonyl groups. The reactions of OPA with primary amines are broadly applied for the synthesis of important heterocyclic compounds with biological relevance. A number of such reactions have been investigated recently and several structures of condensation products have been reported, however, the complex reaction mechanism is still not fully understood and comprises concurrent as well as consecutive reactions. The reaction products depend on the primary amine which reacts with OPA, the reaction environment (solvent) and the proportion of the reactants. The title molecule, C11H13NO, the product of the reaction of OPA with isopropylamine, contains a five-membered pyrrole C4N ring with a carbonyl substituent, which forms part of the isoindolinone unit. Though this pyrrole ring contains one C atom in the sp(3)-hybridized state, it is fairly planar. The title molecule has been compared with similar structures retrieved from the Cambridge Structural Database in order to study this phenomenon. The planarity of this fragment has been explained by the presence of partially delocalized C-C, C-N and C-O bonds, and by an inner angle in the planar pentagonal ring (∼108°), which is close to the ideal tetrahedral value for the sp(3)-hybridized state of the constituent C atom. Due to this propitious angle, this C atom can be present in states intermediate between sp(3)- and sp(2)-hybridized in different structures, while still maintaining the planarity of the ring. There are only weak intermolecular C-H...O hydrogen bonds and C-H...π-electron ring interactions in the structure. In particular, it is the pyrrole ring which is involved in these interactions.

Absolute structure determination using CRYSTALS

A study of post-refinement absolute structure determination using previously published data was carried out using the CRYSTALS software package. We show that absolute structure determination may be carried out optimally using the analyses available in CRYSTALS, and that it is not necessary to have the separate procedures absolute structure determination and no interest in absolute structure as proposed by Flack [Chimia (2014), 68, 26-30].

Lipase-Catalyzed Kinetic Resolution of Novel Antifungal N-Substituted Benzimidazole Derivatives

A series of new N-substituted benzimidazole derivatives was synthesized and their antifungal activity against Candida albicans was evaluated. The chemical step included synthesis of appropriate ketones containing benzimidazole ring, reduction of ketones to the racemic alcohols, and acetylation of alcohols to the esters. All benzimidazole derivatives were obtained with satisfactory yields and in relatively short times. All synthesized compounds exhibit significant antifungal activity against Candida albicans 900028 ATCC (% cell inhibition at 0.25 μg concentration > 98%). Additionally, racemic mixtures of alcohols were separated by lipase-catalyzed kinetic resolution. In the enzymatic step a transesterification reaction was applied and the influence of a lipase type and solvent on the enantioselectivity of the reaction was studied. The most selective enzymes were Novozyme SP 435 and lipase Amano AK from Pseudomonas fluorescens (E > 100).

Patterson functions

The paper deals with |F|2, A and D Patterson functions. The information available in the various volumes of International Tables for Crystallography is detailed. A and D are defined and the reason for their use is explained. The symmetry of these functions is explained. Calculation by symmetry-adapted Patterson functions and the Fast-Fourier algorithm are described. There are two examples. There is a very useful table presenting the relevant information.

Synthesis of novel 17-(5'-iodo)triazolyl-3-methoxyestrane epimers via Cu(I)-catalyzed azide-alkyne cycloadditon, and an evaluation of their cytotoxic activity in vitro

The regioselective Cu(I)-catalyzed 1,3-dipolar cycloaddition of 3-methoxyestrane 17α- and 17β-azide epimers (3 and 5) with different terminal alkynes afforded novel 1,4-substituted triazolyl derivatives (8a-f and 11a-f). If the Ph3P in the classical CuAAC process was replaced by Et3N, the formation of small quantities of 5-iodotriazoles (9a-f and 11a-f) was observed. For the preparation of 5-iodo-1,2,3-triazoles (9a-f and 11a-f), an improved method was developed, directly from steroidal azides and terminal alkynes, in reactions mediated by CuI and ICl as iodinating agents. The antiproliferative activities of the structurally related triazoles were determined in vitro with the microculture tetrazolium assay on six malignant human cell lines of gynecological origin (HeLa, A2780, MCF7, MDA-MB-231, MDA-MB-361 and T47D). X-ray analysis revealed the presence of the iodo substituent on the 1,2,3-triazole ring.

Synthesis and the absolute configuration of both enantiomers of 4,5-dihydroxy-3-(formyl)cyclopent-2-enone acetonide as a new chiral building block for prostanoid synthesis

The synthesis of both enantiomers of 4,5-dihydroxy-3-(formyl)cyclopent-2-enone acetonide (5) was accomplished in five steps starting from meso-tartaric acid (6). The key steps involved are preparation of the isopropylidene protected 3-[(dimethoxyphosphoryl)methyl]-4,5-dihydroxycyclopent-2-enone (9), resolution of the diastereoisomeric products 10 of the Horner reaction of racemic 9 with (R)-glyceraldehyde acetonide and the final regioselective ozonolysis of the exocyclic carbon–carbon double bond of the separated dienones 10 leading to both enantiomeric title compounds 5. The absolute configuration of both enantiomers was initially assigned based on the comparison of the chiroptical properties obtained from the DFT calculations with the experimental data and finally confirmed by X-ray analysis.

Tri-benzyl-ammonium chloride

Single crystals of the title salt, C21H21NH(+)·Cl(-), were isolated as a side product from the reaction involving [(C6H5CH2)3NH]2[HPO4] and Sn(CH3)3Cl in ethanol. Both the cation and the anion are situated on a threefold rotation axis. The central N atom in the cation has a slightly distorted tetra-hedral environment, with angles ranging from 107.7 to 111.16 (10)°. In the crystal, the tri-benzyl-ammonium cations and chloride anions are linked through N-H⋯Cl and C-H⋯Cl hydrogen bonds, leading to the formation of infinite chains along [001]. The crystal studied was a merohedral twin.

Absolute configuration of naturally occurring glabridin

The title compound {systematic name: 4-[(3R)-8,8-dimethyl-3,4-dihydro-2H-pyrano[2,3-f]chromen-3-yl]benzene-1,3-diol, commonly named glabridin}, C20H20O4, is a species-specific biomarker from the roots Glycyrrhiza glabra L. (European licorice, Fabaceae). In the present study, this prenylated isoflavan has been purified from an enriched CHCl3 fraction of the extract of the root, using three steps of medium-pressure liquid chromatography (MPLC) by employing HW-40F, Sephadex LH-20 and LiChroCN as adsorbents. Pure glabridin was crystallized from an MeOH-H2O mixture (95:5 v/v) to yield colorless crystals containing one molecule per asymmetric unit (Z' = 1) in the space group P212121. Although the crystal structure has been reported before, the determination of the absolute configuration remained uncertain. Stereochemical analysis, including circular dichroism, NMR data and an X-ray diffraction data set with Bijvoet differences, confirms that glabridin, purified from its natural source, is found only in a C3 R configuration. These results can therefore be used as a reference for the assignment of the configuration and enantiopurity of any isolated or synthetic glabridin sample.

TiGePt--a study of Friedel differences

The X-ray single-crystal diffraction intensities of the intermetallic compound TiGePt were analysed. These showed beyond doubt that the crystal structure is non-centrosymmetric. The analysis revolves around the resonant-scattering contribution to differences in intensity between Friedel opposites hkl and \bar h\bar k\bar l. The following techniques were used: R(merge) factors on the average (A) and difference (D) of Friedel opposites; statistical estimates of the resonant-scattering contribution to Friedel opposites; plots of 2A(obs) against 2A(model) and of D(obs) against D(model); the antisymmetric D-Patterson function. Moreover it was possible to show that a non-standard atomic model was unnecessary to describe TiGePt. Two data sets are compared. That measured with Ag Kα radiation at 295 K to a resolution of 1.25 Å(-1) is less conclusive than the one measured with Mo Kα radiation at 100 K to the lower resolution of 0.93 Å(-1). This result is probably due to the fact that the resonant scattering of Pt is larger for Mo Kα than for AgKα radiation.

Absolute-structure reports

All the 139 noncentrosymmetric crystal structures published inActa Crystallographica Section Cbetween January 2011 and November 2012 inclusive have been used as the basis of a detailed study of the reporting of absolute structure. These structure determinations cover a wide range of space groups, chemical composition and resonant-scattering contribution. DefiningAandDas the average and difference of the intensities of Friedel opposites, their level of fit has been examined using 2ADand selected-Dplots. It was found, regardless of the expected resonant-scattering contribution to Friedel opposites, that the Friedel-difference intensities are often dominated by random uncertainty and systematic error. An analysis of data collection strategy is provided. It is found that crystal-structure determinations resulting in a Flack parameter close to 0.5 may not necessarily be from crystals twinned by inversion. Friedifstatis shown to be a robust estimator of the resonant-scattering contribution to Friedel opposites, very little affected by the particular space group of a structure nor by the occupation of special positions. There is considerable confusion in the text of papers presenting achiral noncentrosymmetric crystal structures. Recommendations are provided for the optimal way of treating noncentrosymmetric crystal structures for which the experimenter has no interest in determining the absolute structure.<!?tpb=25.7pt>

Use of intensity quotients and differences in absolute structure refinement

Several methods for absolute structure refinement were tested using single-crystal X-ray diffraction data collected using Cu Kα radiation for 23 crystals with no element heavier than oxygen: conventional refinement using an inversion twin model, estimation using intensity quotients in SHELXL2012, estimation using Bayesian methods in PLATON, estimation using restraints consisting of numerical intensity differences in CRYSTALS and estimation using differences and quotients in TOPAS-Academic where both quantities were coded in terms of other structural parameters and implemented as restraints. The conventional refinement approach yielded accurate values of the Flack parameter, but with standard uncertainties ranging from 0.15 to 0.77. The other methods also yielded accurate values of the Flack parameter, but with much higher precision. Absolute structure was established in all cases, even for a hydrocarbon. The procedures in which restraints are coded explicitly in terms of other structural parameters enable the Flack parameter to correlate with these other parameters, so that it is determined along with those parameters during refinement.

Absolute structure of R-(-)-2-methylpiperazine and S-(+)-2-methylpiperazine

The absolute structures of R-(-)-2-methylpiperazine (rmpip), S-(+)-2-methylpiperazine (smpip), R-(-)-2-methylpiperazinediium dibromide (rmpipBr) and S-(+)-2-methylpiperazinediium dibromide (smpipBr) have been determined by anomalous dispersion employing the Parsons' Q and Hooft methods. The studies were undertaken to determine the limitations of the absolute structure determination of light element structures (C, H, N) employing routine single-crystal X-ray diffraction laboratory conditions. The structures of the neutral methylpiperazines were known from a priori non-crystallographic methods and were confirmed by the absolute structure determination of their dibromide salts. By employing the full data collection of Bijvoet pairs and minimizing systematic errors, the absolute structure parameters 0.09 (8) (Hooft) for R-(-)-2-methylpiperazine and 0.05 (8) (Hooft) for S-(+)-2-methylpiperazine were determined.