Absolute Crystal Structure Research Articles

Effect of Extra-Framework Anion Substitution on the Properties of a Chiral Crystalline Sponge.

Chiral metal-organic materials, CMOMs, are of interest as they can offer selective binding sites for chiral guests. Such binding sites can enable CMOMs to serve as chiral crystalline sponges (CCSs) to determine molecular structure and/or purify enantiomers. We recently reported on the chiral recognition properties of a homochiral cationic diamondoid, dia, network {[Ni(S-IDEC)(bipy)(H2O)][NO3]}n (S-IDEC = S-indoline-2-carboxylicate, bipy = 4,4'-bipyridine), CMOM-5[NO3]. The modularity of CMOM-5[NO3] means there are five feasible approaches to fine-tune structures and properties via substitution of one or more of the following components: metal cation (Ni2+); bridging ligand (S-IDEC); linker (bipy); extra-framework anion (NO3-); and terminal ligand (H2O). Herein, we report the effect of anion substitution on the CCS properties of CMOM-5[NO3] by preparing and characterizing {[Ni(S-IDEC)(bipy)(H2O)][BF4]}n, CMOM-5[BF4]. The chiral channels in CMOM-5[BF4] enabled it to function as a CCS for determination of the absolute crystal structures of both enantiomers of three chiral compounds: 1-phenyl-1-butanol (1P1B); methyl mandelate (MM); ethyl mandelate (EM). Chiral resolution experiments revealed CMOM-5[BF4] to be highly selective toward the S-isomers of MM and EM with enantiomeric excess, ee, values of 82.6 and 78.4%, respectively. The ee measured for S-EM surpasses the 64.3% exhibited by [DyNaL(H2O)4] 6H2O and far exceeds that of CMOM-5[NO3] (6.0%). Structural studies of the binding sites in CMOM-5[BF4] provide insight into their high enantioselectivity.

Making the Most of 3D Electron Diffraction: Best Practices to Handle a New Tool

Along with the adoption of three-dimensional electron diffraction (3D ED/MicroED) as a mainstream tool for structure determination from sub-micron single crystals, questions about best practices regarding each step along the workflow, from data collection to structure solutions, arise. In this paper, we discuss three particular aspects of a 3D ED/MicroED experiment which, after hundreds of structures solved in Rigaku’s laboratories, we have found to be important to consider carefully. First, for a representative model system of a hydrated compound (trehalose dihydrate), we show that cryo-transfer of the sample into the diffractometer is an effective means to prevent dehydration, while cooling of the sample without cryo-transfer yields a marginal improvement only. Next, we demonstrate for a small (tyrosine) and a large (clarithromycin) organic compound, how a simplified and fast workflow for dynamical diffraction calculations can determine absolute crystal structures with high confidence. Finally, we discuss considerations and trade-offs for choosing an optimal effective crystal-to-detector distance; while a long distance is mandatory for a protein (thaumatin) example, even a small molecule with difficult diffraction behavior (cystine) yields superior results at longer distances than the one used by default.

Crystallography without Crystals: A Structural Study of Fakein

AbstractSoftware from the MiCMoS Molecular Simulation platform (sites.unimi.it/xtal_chem_group/) and from the CryGen set of programs (www.angelogavezzotti.it) is used to prepare a molecular structure from a line formula for a non‐existent molecule, dubbed ‘fakein’. Possible crystal structures are generated in chiral space groups P21 and P212121, and for racemate in space groups P1− and P21/c. Lattice energies and crystal densities are in line with experimental values for organic molecules. Chiral crystals are less stable, and may not easily form hydrogen bonds, while bulk crystal stabilization is provided mostly by polarization‐dispersion. Hydrogen bonding and crystal packing are discussed in terms of molecular pairing modes. Links to possible experiments and to absolute crystal structure prediction are outlined, but the main aim here is to demonstrate that relevant solid‐state information can be derived if that goal is not achieved, actually even if the real substance is not available.

Synthesis, biological and theoretical properties of crystal zinc complex with thiosemicarbazone of glyoxylic acid

A new zinc complex with thiosemicarbazone of glyoxylic acid (1) was synthesized with zinc acetate dihydrate and thiosemicarbazone of glyoxylic acid and crystallized in water. The absolute crystal structure of the complex was defined using the single-crystal X-ray diffraction technique. It was seen in X-ray measurements that the complex crystallized in the triclinic system with the P-1 space group. The structure of 1 represents distorted octahedral geometry around the central zinc metal. Zn(II) complex with thiosemicarbazone of glyoxylic acid was an inhibitor of acetylcholinesterase (AChE), butyrylcholinesterase (BChE), human carbonic anhydrase I and II isoforms (hCA I and II) receptors and the inhibitor constant (Ki) values of the synthesized complex were 38.94 ± 8.2 μM for hCA I, 48.62 ± 11.3 μM for hCA II, 65.16 ± 11.4 μM for BChE and 82.04 ± 16.0 μM for AChE, respectively. The molecular docking method was used to show the complex-enzyme interactions. The pharmacokinetic properties of the complex were determined by ADME/Tox predictions and the results obtained showed that the complex could be a potential drug candidate.

Absolute structure and structure-function relationships of 4R,2′R and 4S,2′S Pidotimod®

Pidotimod® is a dipeptide with widely recognized immunomodulatory properties and with particularly beneficial effects for the treatment of acute respiratory and urinary tract infections. Pidotimod® presents two chiral centres which originate four stereoisomers. (4R,2′S, 4S,2′R, 4R,2′R and 4S,2′S). To date, only the 4R,2′S and 4S,2′R stereoisomers are reported in the literature. We report here the absolute crystal structure of the 4R,2′R and 4S,2′S diastereoisomers of Pidotimod®, obtained by crystals grown by slow evaporation of a mixture of water and ethanol. The analysis of the crystal structures revealed the key role of a solvent water molecule in the crystal packing engaged in an extended hydrogen bonds network. This water-assisted H-bond network explained the recalcitrance of 4R,2′R and 4S,2′S Pidotimod® to crystallize in pure ethanol, despite their high solubility, and the growth of well-diffracting crystals only in presence of water. Hence, Pidotimod®4R,2′R and 4S,2′S stereoisomers markedly differ from the 4R,2′S and 4S,2′R ones, which crystallize in absence of water.The molecular and crystal structures of the 4R,2′R and 4S,2′S Pidotimod® stereoisomers here presented gave some hints on the differences in bioactivity with respect to the 4R,2′S stereoisomer. In fact, beyond an expected different dispositions of hydrophilic ligands, 4R,2′R and 4S,2′S showed an incremented tendency to intermolecular H-bonds with water.

Structural and Magnetic Chirality of Cu2OSeO3

We determine the chirality of the magnetic and crystal structures, respectively, for the magnetoelectric insulator Cu2OSeO3using small-angle diffraction of polarized neutrons and resonant contribution to X-ray single crystal diffraction of synchrotron radiation. This compound crystallizes in the P213 space group similar to other chiral but metallic magnets, such as MnSi, MnGe, MnSi1+xGex, Fe1+xCoxSi, Mn1+xFexSi, Mn1+xCoxSi, FeGe, Mn1+xFexGe. It has recently been shown that the structural and magnetic chiralities for metallic helimagnets are linked to each other [1], also in the so-called skyrmion phase [2]. Here we measure the spin chirality by comparing neutron scattering maps from Cu2OSeO3with the reference MnSi, which has left-handed magnetic spiral and absolute crystal structure denoted as left-handed [1]. Similar to the reference MnSi system, the crystallographic chirality of Cu2OSeO3is fixed on the basis of absolute structure determination taking into account the refinement of the Flack parameter. We find that the crystal and magnetic structures of Cu2OSeO3have the same chirality. The similar relationship is found for MnSi, Mn1+xFexSi, MnGe, while FeGe and Fe1+xCoxSi always show the opposite chiral correlation between magnetic and crystal structures. Notably, the relationship between two chiralities for Cu2OSeO3found in the experiment is opposite to that proposed from recent theoretical calculations [3], thus calling for a revision of the theory of possible microscopic mechanisms contributing to the phenomenological antisymmetric magneto-lattice coupling.

The use of Mo Kα radiation in the assignment of the absolute configuration of light-atom molecules; the importance of high-resolution data.

Recent studies have confirmed the usefulness of the Hooft and Parsons methodologies for determination of the absolute crystal structures of enantiopure light-atom compounds using Cu Kα radiation. While many single-crystal diffractometers used for small-molecule structure determination are equipped with molybdenum anodes, use of data from such instruments for the absolute structure determination of light-atom crystal structures is rarely documented and has often been found to be unsuccessful. The Hooft and Parsons methodologies have been applied to 44 data sets obtained from single crystals containing light-atom molecules of known chirality using Mo Kα radiation. Several factors influencing the calculation of accurate and precise values for the Hooft and Parsons parameters obtained from these data sets have been identified, the inclusion of high-resolution diffraction data being particularly important. The correct absolute structure was obtained in all cases, with the standard uncertainties of the final absolute structure parameters below 0.1 for the great majority.

Crystal structure of the Ca3TaGa3Si2O14 compound

The absolute crystal structure of the Ca3TaGa3Si2O14 piezoelectric compound is refined using X-ray diffraction analysis. The unit cell parameters and final R factors are as follows: a = 8.112(1) A, c = 4.9862(6) A, space group P321, Z = 1, R = 0.98%, and R w = 1.42%. It is shown that the configuration of the absolute crystal structure inherited from the seed material determines the positive sense of the optical activity of the crystal under investigation. The structural and acoustical characteristics of the Ca3TaGa3Si2O14 crystals are compared with those of the La3Ga5SiO14 crystals.

Crystal Structures of Dihydro-α-ergokryptine and Dihydro-β-ergokryptine Mesylates

The absolute crystal structures of two related ergot alkaloids dihydro-α-ergokryptine mesylate (1) monohydrate ethanol solvate and dihydro-β-ergokryptine mesylate (2) monohydrate methanol solvate have been determined by X-ray diffraction and compared with the published structures of dihydroergocristine mesylate (3) monohydrate and dihydroergotamine mesylate (4) monohydrate.

Imino−Rhodium(III) and −Ruthenium(II) Compounds with Stereogenic Metal Centers

The synthesis and characterization of optically active imino complexes (RM or SM)-[(η5-C5Me5)RhCl(imine)][SbF6] (imine = Ln = N-(2-pyridylmethylene)-(R)-1-phenylethylamine (L1) (1a,a‘), N-(2-pyridylmethylene)-(R)-1-naphthylethylamine (L2) (2a,a‘), N-(2-pyridylmethylene)-(R)-1-cyclohexylethylamine (L3) (3a,a‘)) or [(η6-p-MeC6H4iPr)RuCl(imine)]A (A = SbF6, imine = L1 (4a,a‘), L2 (5a,a‘), L3 (6a,a‘), N-(2-pyridylmethylene)-(1R,2S,4R)-1-bornylamine) (L4) (7a,a‘); (A = BF4, imine = L1 (4b,b‘), L2 (5b,b‘), L3 (6b,b‘), L4 (7b,b‘)) is reported. The absolute crystal structures of the (RRh)-1a and (RRu)-7b epimers were determined by X-ray analysis. Both complexes possess a chiral metal center in a pseudo-octahedral environment, being bonded to an η5-C5Me5 group (1a) or to an (η6-p-MeC6H4iPr) ring (7b), a terminal chloride, and, in a chelating fashion, to the two nitrogen atoms of the imine ligand. At room temperature, in acetone or chloroform, the complexes are configurationally stable but in refluxing methanol epimerize at the metal center. Dichloromethane/acetone solutions of the solvate complexes [(ηn-ring)M(imine)S]2+ are active catalysts for the Diels−Alder reaction between methacrolein or acrolein and cyclopentadiene. The reaction occurs rapidly at room temperature and, in general, good exo/endo selectivities and moderate enantioselectivities are achieved.

Synthesis, Characterization, Properties, and Asymmetric Catalytic Diels−Alder Reactions of Chiral-at-Metal Imino−Iridium(III) Complexes

The synthesis and characterization of optically active imino complexes (RIr,RC)- and (SIr,RC)-[(η5-C5Me5)IrCl(imine)][SbF6] (imine = Ln = N-(2-pyridylmethylene)−(R)-1-phenylethylamine (L1; 1a,a‘), N-(2-pyridylmethylene)-(R)-1-naphthylethylamine (L2; 2a,a‘), N-(2-quinolylmethylene)−(R)-1-naphthylethylamine (L3; 3a,a‘), N-(6-methyl-2-pyridylmethylene)−(R)-1-naphthylethylamine (L4; 4a,a‘), N-(2-pyridylmethylene)−(R)-1-cyclohexylethylamine (L5; 5a,a‘), N-(2-pyridylmethylene)−(1R,2S,4R)-1-bornylamine) (L6; 6a,a‘)), (RIr,RC)- and (SIr,RC)-[(η5-C5Me5)IrCl(L2)][A] (A = Cl (7a,a‘), BF4 (8a,a‘), PF6 (9a,a‘), (1S)-camphor-10-sulfonate (R*SO3) (10a,a‘)) and (RIr,RC)- and (SIr,RC)-[(η5-C5Me5)(L6)(H2O)][SbF6]2 (11a,a‘)) are reported. The absolute crystal structures of (RIr,RC)-1a, (RIr,RC)-2a, and (RIr,RC)-3a were determined by X-ray analysis. All three complexes show the chiral metal center in a pseudo-octahedral environment, being bonded to an η5-C5Me5 ring, to a terminal chloride, and, in a chelate fashion, to the two nitrogen atoms of the imine ligands. For the chloride compounds 1−6, 1H NMR solution data reveal conformational differences between the crystal and solution structures. At room temperature, in acetone, complexes 1−11 are configurationally stable. At 62 °C, in methanol, the more labile chloro complex 5a epimerizes at Ir with a half-life of 68.0 min (activation parameters, ΔH⧧ = 97.7 ± 13.2 kJ mol-1 and ΔS⧧= −26.3 ± 6.2 J K-1mol-1; equilibrium constant, 5a‘/5a = 4.26 ± 1.65). Dichloromethane/acetone solutions of the solvate complexes [(η5-C5Me5)Ir(imine)S][SbF6]2, prepared in situ by treating complexes 1−6 with equimolar amounts of AgSbF6, are active catalysts for the Diels−Alder reaction between methacrolein and cyclopentadiene. The reaction occurs rapidly at room temperature with good exo:endo selectivity (84:16 to 95:5) and moderate enantioselectivities (up to 46%).

Alkaloids of Templetonia retusa. Chemistry, Structure and Absolute Configuration of (-)-Templetine

(-)-Cytisine, (+)-lupanine, (-)-anagyrine, (�)-piptanthine and (-)-templetine have been isolated from Templetonia retusa (Vent.) R.Br. The absolute crystal structures of the trihydrochloride dihydrate and the isomorphous trihydrobromide dihydrate of (-)- templetine have both been determined by single-crystal X-ray diffraction; diffractometer data at 295 K were refined by least-squares techniques to residuals of 0.045 and 0.031, respectively, for 2351 and 1948 'observed' reflections. Crystals of the trihydrochloride are orthorhombic P212121, a 8.830(4), b 14.201(6), c 19.122(12)Ǻ, Z 4. Crystals of the trihydrobromide are isomorphous, a 9.081(3), b 14.578(2), c 19.197(11)Ǻ, Z 4. The absolute structure (1) of (-)- templetine has led to the absolute structure of its dehydrogenation product (-)- dehydropiptanthine perchlorate (7) which, in turn, has allowed the absolute structures of (-)- ormosanine (6), (+)- piptanthine (4) and (-)- panamine (9) to be defined. (-)- Templetine (1) reacts with formaldehyde to form homotempletine (12) and with carbon disulfide to yield the thiourea (13). Treatment of either (12) or (13) with W-1 Raney nickel followed by perchloric acid has yielded the diperchlorate (15). The X-ray crystal structure of the diperchlorate (15) has also been determined: diffractometer data at 295 K were refined by least-squares techniques to a residual of 0.056 (1312 'observed' reflections). Crystals of the diperchlorate (15) are orthorhombic, P212121, a 18.636(5), b 12.569(6), c 10.403(4)Ǻ, Z 4.

X-Ray Crystal Structure Analysis of Ca2Pb(CH3CH2CO2)6in the Paraelectric and the Ferroelectric Phases

Absolute crystal structures of Ca 2 Pb(CH 3 CH 2 CO 2 ) 6 (DLP) were determined by X-ray diffraction from monodomain crystals at 70°C above T c and at 45°C and -80°C below T c . The space groups of dextrorotatory crystal are P4 3 2 1 2 and P4 3 above and below T c , respectively. Above T c , β-carbon atoms in three of the independent four propionate ions and α-carbon atom of one propionate ion are in the disordered state having two equilibrium positions with equal occupancy. At 45°C, these carbon atoms are in the partially disordered states. At -80°C, only one β-carbon remains in the partially disordered state, whereas all of the other α- and β-carbons are in the ordered state. The spontaneous polarization is well explained by displacements of Pb, Ca and O atoms along the c -axis.

Absolute crystal structure of C9H12O4 determined by three-beam scattering

C 9 H 12 O 4 cristallise dans P2 1 2 1 2 1 avec affinement jusqu'a 0,063. La structure absolue du compose est (1R,3S)

Crystal Structure of Deuterated Dicalcium Strontium Propionate, Ca2Sr(C2D5CO2)6in the Paraelectric and Ferroelectric Phases

The absolute crystal structure of the deuterated dicalcium strontium propionate (DDSP) has been determined by the X-ray diffraction with a four-circle automatic diffractometer at three temperatures in each of the paraelectric and ferroelectric phases. The space group is determined to be D 4 4 -P4 1 2 1 2 or D 4 8 -P4 3 2 1 2 in the paraelectric phase with the R -factors less than 3% and to be C 4 2 -P4 1 or C 4 4 -P4 3 in the ferroelectric phase with the R -factors less than 5%. The molecular structure of the deuterated propionates is also elucidated and compared with that of the nondeuterated one. The comparison confirms the structure quite similar to each other, indicating no isotope effect on the molecular structure. The disordered arrangement of the propionate molecules on (001) plane is observed in the ferroelectric phase similarly to the nondeuterated DSP.

X-ray studies of C25 terpenoids. IV. The crystal structure of retigeranic acid p-bromoanilide

The structure of retigeranic acid, C25H2802, a C25 terpenoid isolated from a lichen, has been determined by X-ray analysis of its p-bromoanilide. The crystal is monoclinic, space group P21 with a= 13142, b=937~, c= 1149a ~, fl= 10242 °, Z=2. The absolute crystal structure was determined from the phases calculated by the anomalous dispersion method for 409 Friedel pairs measured on a four-circle diffractometer with Mo Kct radiation. Refinement of the structure was carried out by the least-squares method for 1638 independent reflexions measured with Cu K~ radiation. The final R value is 0.09 without hydrogen atoms. The molecule has a unique pentacyclic structure consisting of four five-membered rings and one six-membered ring. The structure has no close correlation with the sesterterpenes known to date.

The absolute crystal structure of (−)-isolunine hydrobromide dihydrate at –150°C

Crystals of (-)-isolunine hydrobromide dihydrate, C16H17NO4.2H20.HBr, are monoclinic, space group P21, with a = 11.1 l, b = 7.24, c = 22-33/~, fl= 101 ° 11' at 150°C, Z = 4, the asymmetric unit consisting of two molecules. Application of image-seeking procedures revealed the main components of the structure, while electron density and difference syntheses led to a complete solution of the molecular skeleton. Differentiation of the nitrogen and oxygen atoms in the skeleton was assisted by a mass spectroscopic determination of the molecular weight. Refinement was by least-squares and the absolute chirality was defined by Bijvoet's technique. The crystal structure involves a short approach distance, 2.45/~, between the lactam oxygen atom and a water molecule, the grouping being stabilized by the interpolation of a proton, H +. The relation of isolunine to lunine is outlined.

The Crystal Structure of d-Tris-ethylenediamine-cobalt(III) Bromide Monohydrate, d-[Co en3]Br3·H2O, and the Absolute Configuration of the d-Tris-ethylenediamine-cobalt(III) Ion, d-[Co en3]3+

Abstract The absolute crystal structure of d- [Co en3]·Br3·H2O was determined by means of X-rays. The space group is P43212-D48, with four formula units in a cell of the dimensions a=9.95 and c=16.73Å. The complex ion takes the “lei” form designated by Corey and Bailar and is in the same configuration as had been determined previously. The structure can be most easily described as consisting of layers of complex ions, two types of bromine ions and water molecules perpendicular to the c-axis. The water molecules link the positive and negative ions to form a layer. A definition of “absolute structure” and “absolute configuration” was proposed. The absolute structure was determined by means of the X-ray absorption edge technique of Bijvoet. CuKa rays were used to observe visually the effect of the anomalous dispersion between the reflections (hkl) and (hk\barl), and quantitative measurements of the effect were attempted for some reflections. The absolute configuration of the complex ion deduced from the absolute structure of the crystal is in agreement with the one previously determined for the crystals d- and l-2[Co en3]Cl3·NaCl·6H2O.