Applications and properties of the Bijvoet intensity ratio.

An empirical relationship of use in prediction and evaluation is established between the standard uncertainty of the Flack parameter and the Bijvoet intensity ratio. The expected value of this ratio may be calculated from the chemical composition of the compound and the X-ray wavelength. Structure analyses published with intensity data have allowed various properties of the Bijvoet intensity ratio to be studied. It is found that, although the Bijvoet intensity ratio has a strong dependence on sin theta/lambda, extrapolation to sin theta/lambda = 0 of model intensity pairs leads to values satisfactorily close to those expected. Moreover, it is shown that there is no symmetry enhancement for general reflections of the Bijvoet ratio in agreement with theory. The behaviour of some special reflections is examined. Two methods of correcting the observed Bijvoet ratio for systematic and random effects have been tested and found to be unsatisfactory. Evidence is produced to show that standard uncertainties provided with intensities are unrealistic and that measurement protocols need improvement.

The use of X-ray crystallography to determine absolute configuration.

Essential background on the determination of absolute configuration by way of single-crystal X-ray diffraction (XRD) is presented. The use and limitations of an internal chiral reference are described. The physical model underlying the Flack parameter is explained. Absolute structure and absolute configuration are defined and their similarities and differences are highlighted. The necessary conditions on the Flack parameter for satisfactory absolute-structure determination are detailed. The symmetry and purity conditions for absolute-configuration determination are discussed. The physical basis of resonant scattering is briefly presented and the insights obtained from a complete derivation of a Bijvoet intensity ratio by way of the mean-square Friedel difference are exposed. The requirements on least-squares refinement are emphasized. The topics of right-handed axes, XRD intensity measurement, software, crystal-structure evaluation, errors in crystal structures, and compatibility of data in their relation to absolute-configuration determination are described. Characterization of the compounds and crystals by the physicochemical measurement of optical rotation, CD spectra, and enantioselective chromatography are presented. Some simple and some complex examples of absolute-configuration determination using combined XRD and CD measurements, using XRD and enantioselective chromatography, and in multiply-twinned crystals clarify the technique. The review concludes with comments on absolute-configuration determination from light-atom structures.

Centrosymmetric and pseudo-centrosymmetric structures refined as non-centrosymmetric.

The behaviour of the Flack parameter for centrosymmetric and pseudo-centrosymmetric crystal structures based on crystal structures published as being non-centrosymmetric is presented. It is confirmed for centrosymmetric structures that the value obtained for the Flack parameter is critically dependent on the Friedel coverage of the intensity data, approaching 0.5 for a coverage of 100% and sticking near the starting value for a coverage of 0%. For pseudo-centrosymmetric structures, even those very close to being centrosymmetric, it is found that it is often possible to obtain significant values of the Flack parameter. A theoretical basis for this surprising result is established. It has also been possible to establish an a priori estimate of the standard uncertainty of the Flack parameter based only on the chemical composition of the compound and the wavelength of the radiation. The paper concludes with preliminary presentations of bias in the Flack parameter and of inconsistent chemical and crystallographic data.

Understanding the formation of new clusters of alkali and alkaline Earth metals: a new synthetic approach, single-crystal structures, and theoretical calculations.

A new synthetic approach, reacting alkaline earth metal iodides with butyllithium, lithium hydroxide, and/or lithium butoxide under salt elimination, is presented, giving access to some interesting clusters of calcium, strontium, and barium, partially in combination with lithium. The so far largest calcium cluster Li[[Ca(7)(mu(3)-OH)(8)I(6)(thf)(12)](2)(mu(2)-I)].3THF, 4, and the new strontium compound [Sr(3)I(3)(OH)(2)(thf)(9)]I, 5, are shown to feature common building blocks of OH-capped M(3) triangles. On the basis of mainly electrostatic interactions, these clusters are not volatile. By introducing LiO(t)Bu, the two clusters [IM(O(t)Bu)(4)[Li(thf)](4)(OH)] (6, M = Sr; 7, M = Ba) are prepared, 7 exhibiting volatility as an important physical property, which makes it a potential precursor for chemical vapor deposition. The structural relationship between 4, 5, 6, and 7 and their respective starting materials is shown, and possible reaction mechanisms are proposed. Exhibiting surprising and new structural motifs, the bonding modes of these clusters are investigated by the electron localization function as well as by ab initio calculations.

New bromoterpenes from the red alga Laurencia luzonensis.

Extraction of a sample of Laurencia luzonensis collected off the coast of Kudaka Island, Okinawa, yielded the known sesquiterpenes palisol (1), palisadin B (2), palisadin A (3), pacifigorgiol (4), and aplysistatin (5), together with five new bromosesquiterpenes, isopalisol (6), luzonensol (7), luzonensol acetate (8), luzonensin (9), and (3Z,6E)-1-bromo-2-hydroxy-3,7,11-trimethyldodeca-3,6,10-triene (10). In addition, a new bromoditerpene of unusual structure, 3-bromobarekoxide (11), possessing a seven-membered ring fused to trans-decalin, was isolated.

Synthesis, enantiomeric conformations, and stereodynamics of aromatic ortho-substituted disulfones.

[structure in text] Aromatic ortho-disulfone derivatives are readily accessible from diiodide precursors by Cu(I)-mediated reactions with sodium sulfinate salts. The sulfone substituents adopt C(2)-symmetric enantiomeric conformations (lambda and delta) as evidenced by X-ray structural analysis and (1)H and (31)P NMR on chiral bis(sulfonyl)veratrol derivatives and hexacoordinated tris(benzenediolato)phosphate anions. Slow dynamic conformational isomerism (DeltaG(++) > or = 19.8 kcal mol(-1)) was detected in solution.

Molecular tricorns: self-assembly of trinuclear palladium(II) complexes.

Cyclometalation of the ligand 1,3-bis(1-alkylbenzimidazol-2-yl)benzene (1) with palladium carboxylates leads to a trimeric complex [Pd(3)(ligand)(3)(carboxylate)(3)] (3). Studies in solution show that the trinuclear core is stable but that the carboxylates are labile, undergoing intra- and intermolecular exchange on an NMR time scale. The structural analogue of 1, 2,6-bis(1-alkylbenzimidazol-2-yl)pyridine (4), gives only the mononuclear species [Pd(4)(carboxylate)(2)], characterized by X-ray diffraction. This complex forms a trimer if one carboxylate is labilized by the addition of strong acid; the resulting trinuclear species is readily cleaved by nucleophiles but can include weakly basic anions within its cavity.

Intramolecular Pd-catalyzed carbocyclization, Heck reactions, and aryl-radical cyclizations with planar chiral arene tricarbonyl chromium complexes.

(o-butenylhalobenzene)Cr(CO)(3) complexes were synthesized by diastereoselectve allylmetal additions to o-halo benzaldehyde complexes. The addition of allylZnBr proved particularly convenient and clean. The complexes undergo intramolecular Pd-catalyzed cyclizations (Heck reactions) without decomplexation and/or alkene isomerization. In complexes with a benzylic stereogenic center, the diastereoselectivity of the alkene carbopalladation is governed by the planar chirality of the complex rather than by the benzylic stereogenic center in the side chain. This reaction outcome can be rationalized by the geometry of the arene plane vs that of the Pd coordination plane in the transition step of the alkene carbopalladation step. An alternative cyclization procedure involves the generation of a Cr(CO)(3)-coordinated arene radical from the bromo and iodo complexes. Intramolecular aryl-radical cyclization affords indan complexes. The transition metal arene pi-bond remains intact during this process.

Predetermined chirality at metal centers of various coordination geometries: a chiral cleft ligand for tetrahedral (T-4), square-planar (SP-4), trigonal-bipyramidal (TB-5), square-pyramidal (SPY-5), and octahedral (OC-6) complexes

Two tetradentate bispinene-bipyridine type ligands, each with six stereogenic carbon centers, were synthesized from (-)-alpha-pinene. Their ability to predetermine chiral configurations at metal centers was studied. The two diastereoisomers, L1 and L2, differ in their absolute configuration at the bridgehead position. These ligands form metal complexes with Ag(I), Pd(II), Zn(II), Cu(II), and Cd(II), with coordination numbers four, five, and six and with complete control of chirality at the metal centers. Using L1 rather than L2 leads to complexes of inverted absolute configuration at the metal centers. These diastereomeric coordination species can be obtained either as separate compounds or, in some cases, as solids containing them in a 1:1 ratio. Ligands L1 and L2 thus show that the pinene-bipyridines are versatile molecules for the formation of metal complexes with predetermined chirality. In all cases, absolute configurations were determined in the solid state by X-ray diffraction methods and in solution by CD spectroscopy. The sign of exciton couplets from the pi-pi* transitions always agrees with the expectations for a given local configuration at the metal center. The five-coordinate, inherently chiral species of Zn(II) and Cu(II) described in this article are the first examples of trigonal-bipyramidal metal complexes with predetermined absolute configuration containing topologically linear ligands.

alpha-t-butyl- and alpha-i-propyl-ortho-hydroxybenzylamines: racemic synthesis/resolution and asymmetric synthesis.

Efficient routes to alpha-tert-butyl- and alpha-iso-propyl-ortho-hydroxybenzylamines 1a and 1b are described. Highly enantioenriched 1a and 1b were obtained by resolution of the methoxy derivatives 2 by recrystallization of the salts formed with mandelic acid followed by Lewis acid mediated demethylation. The chiral 1,3-amino alcohol 1a has also been obtained in an asymmetric synthesis with the key step a diastereoselective alkylation of the imine obtained by condensation of o-anisaldehyde with phenyl glycinol. The absolute stereochemistry of these 1,3-aminophenols was determined by CD spectroscopy of the salicylideneamines 12 and by an X-ray structure analysis of the salt formed between (R)-mandelic acid and (S)-alpha-tert-butyl-ortho-methoxybenzylamine ((S)-2a).

Configurational ordering of cationic chiral dyes using a novel C(2)-symmetric hexacoordinated phosphate anion

C(2)-Symmetry hexacoordinated phosphorus BINPHAT anion-of configuration controlled by a BINOL ligand-can be prepared readily in a one-pot process and behaves as an efficient NMR chiral shift agent and chiral inducer onto monomethinium dyes (CD, (1)H NMR).

Extended rodlike polyaromatic receptors with bent tridentate units complexed to lanthanide metal ions.

A synthetic strategy is developed to attach semirigid lipophilic sidearms to the 6-positions of bent aromatic tridentate 2,6-bis(benzimidazol-2-yl)pyridine cores to produce U-shaped ligands, L6,7. Differential scanning calorimetry (DSC) reveals that entropic contributions severely affect the isotropization processes of these flexible receptors, but no mesomorphism is detected. The attachment of oxygen linkers to the 5- or 6-positions of the benzimidazole sidearms lowers the ligand-centered 1 pi pi* and 3 pi pi* excited states, and the semiempirical ZINDO method assigns this effect to a destabilization of the HOMO orbitals resulting from pi-interactions. Reactions of L6 with Ln(NO3)3.xH2O provide the rodlike 1:1 complexes [Ln(L6)(NO3)3] (Ln = La-Lu), which are stable in the solid state but partially dissociate in acetonitrile. The crystal structure of [Lu(L6)(NO3)3].CH3CN (18a, LuC63H84N9O13, monoclinic, P2(1)/n, Z = 4) reveals an I-shaped arrangement of the ligand strand arising from the meridional complexation of the bent tridentate unit to nine-coordinate Lu(III). The replacement of nitrate anions with trifluoroacetate anions gives the centrosymmetric dimer [Lu(L6)(CF3CO2)3]2 (23, Lu2C134H162N10O20F18, triclinic, P1, Z = 1), in which the symmetry-related Lu atoms are connected by two bridging carboxylates, leading to an H-shaped dimetallic edifice. These complexes [Ln(L6)(NO3)3] and [Ln(L6)(CF3CO2)3]2 fulfill the geometrical criteria required by precursors of calamitic metallomesogens, but no mesomorphism can be detected, while photophysical studies indicate that the low energies of ligand-centered 3 pi pi* excited states drastically limit the luminescence of Eu(III) complexes. The relationships between structural and electronic properties resulting from 5- or 6-substitutions of the benzimidazole rings and the effects of these substitutions on photophysical and thermal properties are discussed.

Unusual electronic effects of electron-withdrawing sulfonamide groups in optically and magnetically active self-assembled noncovalent heterodimetallic d-f podates.

The segmental ligand 2-(6-(N,N-diethylcarbamoyl)pyridin-2-yl)-1,1'-dimethyl-2'-(5-(N,N-diethylsulfonamido)-pyridin-2-yl)-5,5'-methylenebis[1H-benzimidazole] (L3) is synthesized via a multistep strategy that allows the selective introduction of an electron-withdrawing sulfonamide group into the ligand backbone and its subsequent hydrolysis to the hydrophilic sulfonate group. Compared to that of the methylated analogue L1, the affinity of the bidentate binding unit of L3 for H+ and for trivalent lanthanide ions (LnIII) in [Ln(L3)3]3+ and [Ln2(L3)3]6+ is reduced because the electron-withdrawing sulfonamide substituent weakens sigma-bonding, but improved retro-pi-bonding between the bidentate binding units of L3 and soft 3d-block ions (M(II) = FeII, ZnII) overcomes this effect and leads to homometallic complexes [Mn(L(i))m]2n+ (i = 1, 3) displaying similar stabilities. Theoretical ab initio calculations associate this dual effect with a global decrease in energy of pi and sigma orbitals when the sulfonamide group replaces the methyl group, with an extra stabilization for the LUMO (pi). The reaction of L3 with a mixture of LnIII and M(II) (M = Fe, Ni, Zn) in acetonitrile gives the noncovalent podates [LnM(L3)3]5+ in which LnIII is nine-coordinated by the three wrapped tridentate segments, while the bidentate binding units provide a facial pseudooctahedral site around M(II). The X-ray structure of [EuZn(L3)3](ClO4)4(PF6)(CH3NO2)3(H2O) reveals that the bulky sulfonamide group at the 5-position of the pyridine ring only slightly increases the Zn-N bond distances as a result of sigma/pi compensation effects. The introduction of spectroscopically and magnetically active FeII and NiII into the pseudooctahedral site allows the detailed investigation of the electronic structure of the bidentate segment. Absorption spectra, combined with electrochemical data, experimentally demonstrate the dual effect associated with the attachment of the sulfonamide group (decrease of the sigma-donating ability of the pyridine lone pair and increase of the pi-accepting properties of the coordinated bidentate binding unit). The influences on the ligand field strength and on tunable room-temperature FeII spin-crossover processes occurring in [LnFe(L3)3]5+ are discussed, together with the origin of the entropic control of the critical temperature in these thermal switches.

Stereoselective Synthesis of Coordination Compounds: Self-Assembly of a Polymeric Double Helix with Controlled Chirality.

Its information content is infinitely smaller than that of DNA, but its structure (see picture) ressembles the double-stranded helix produced by nature. This self-assembled, configurationally predetermined coordination polymer is built up from enantiopure chiral bipyridine-type ligands and silver ions.

Absolute structure and absolute configuration.

Fundamental notions concerning absolute structure and absolute configuration, and their determination from single-crystal diffraction measurements, are presented and reviewed. A glossary of terms with definitions useful in this field is provided. For absolute structure and its determination, the separate but interacting influences of the structure and the inversion-distinguishing power of an X-ray diffraction experiment with dispersive scatterers are examined. Important experimental and algorithmic details of the current methods used for absolute-structure determination are provided. Characterization of crystals for absolute-structure determination and of molecules for absolute-configuration determination are treated. Attention is given to the analysis of absolute structure and absolute configuration in twinned crystals.

Structural investigations and modeling of cavities in clathrates.

A molecular-graphics study has been performed in order to build and visualize the shape of cavities within different clathrates from X-ray diffraction data [e.g. Dianin's compound, Werner complexes Ni(SCN)2(3-methylpyridine)4, Fe(acetylacetonate)3 and Ni(ethylxanthate)2(4,4'-dimethyl-2,2'-bipyridyl) complexes]. The algorithm of the solvent-accessible surfaces representation has been applied to a part of the whole crystal structure rather than to isolated host molecules, by using the MOLCAD molecular modeling package. This type of modelization has been found very efficient both to study the shape properties of the host cavities (cage or channel types) and to approach the structural features of the host/guest interactions.

Structures of 5-bromo-6-ethoxy-5,6-dihydrouridine and -thymidine derivatives, a class of potential antitumoral and antiviral N-nucleosides.

(I): (+)-(5R,6R)-5-Bromo-6-ethoxy-5,6-dihydro-2',3'-isopropylidene-beta-D- ribofuranosyl-uracil, C14H21BrN2O7, m.p. 408.7-409.6 K, [alpha]D23 degrees C = +31.1 degrees (c = 1.2% in MeOH), Mr = 409.2, monoclinic, P2(1), a = 9.218 (2), b = 9.6619(11) c = 10.4938 (14) A, beta = 99.305 (8) degrees, V = 922.4 (2) A3, Z = 2, Dx = 1.47 Mgm-3, lambda (Mo K alpha) = 0.71069 A, mu = 2.24 mm-1, F(000) = 420, room temperature, R (= wR) = 0.046 for 2595 observed reflections [(Fo)] greater than 4 sigma (Fo) and (Fo) greater than 8.0]. (II): (+)-(5R,6R)-5-Bromo-2'-deoxy-6-ethoxy-5,6-dihydro-beta-D-ribofuranosyl- thymine, C12H19BrN2O6, m.p. 376.1-376.5 K, [alpha]D 23 degrees C = + 58.8 degrees (c = 1.02% in MeOH), Mr = 367.2, monoclinic, clinic, P21, a = 6.0428 (9), b = 8.5270 (15), c = 14.589 (2) A, beta = 96.80 (1) degrees, V = 746.4 (1) A3, Z = 2, Dx = 1.63 Mg m-3, lambda(Mo K alpha) = 0.71069 A, mu = 2.75 mm-1, F(000) = 376, room temperature, R = 0.053 (wR = 0.040) for 1579 observed reflections [[F0[ less than 4 sigma(Fo)]. Both furanose rings adopt an envelope conformation with C(4')-exo and C(1')-exo for (I) and (II) respectively. The orientation of the dihydropyrimidine base relative to the sugar ring shows an unusual syn conformation [chi CN = 62.5 (6) degrees] for (I) whereas the glycosyl linkage of compound (II) shows an anti conformation [chi CN = -134.0 (8) degrees]. In both compounds the pyrimidine ring displays a half-chair form. The conformation of the hydroxymethyl group at C(4') is gauche-gauche for (I) [phi OO = -68.2 (7) degrees, phi OC = 50.1 (8) degrees] and trans-gauche for (II) [phi OO = 180 (1) degrees, phi OC = -61 (1) degrees]. The absolute configuration of (I) was confirmed by least-squares refinement of x [x = 0.008 (16)] [Bernardinelli & Flack (1985). Acta Cryst. A41, 500-511] and that of compound (II) deduced from the starting material. An intramolecular hydrogen bond occurs between the hydroxymethyl and the pyrimidine of (I). In both structures, the molecular packing is fixed by a network of hydrogen bonds.