Book Reviews

Structural Chemistry -     

Molecular structure and benzene ring deformation of three cyanobenzenes from gas-phase electron diffraction and quantum chemical calculations

The molecular structures of cyanobenzene, p-dicyanobenzene, and 1,2,4,5-tetracyanobenzene have been accurately determined by gas-phase electron diffraction and ab initio/DFT MO calculations. The equilibrium structures of these molecules are planar, but their average geometries in the gaseous phase are nonplanar because of large-amplitude vibrational motions of the substituents out of the plane of the benzene ring. The use of nonplanar models in electron diffraction analysis is necessary to yield ring angles consistent with the results of MO calculations. The angular deformation of the benzene ring in the three molecules is found to be much smaller than obtained from previous electron diffraction studies, as well as from microwave spectroscopy studies of cyanobenzene. While the deformation of the ring CC bonds and CCC angles in p-dicyanobenzene is well interpreted as arising from the superposition of independent effects from each substituent, considerable deviation from additivity occurs in 1,2,4,5-tetracyanobenzene. The changes in the ring geometry and C ipso-C cyano bond lengths in this molecule indicate an enhanced ability of the cyano group to withdraw pi-electrons from the benzene ring, compared with cyanobenzene and p-dicyanobenzene. In particular, gas-phase electron diffraction and MP2 or B3LYP calculations show a small but consistent increase in the mean length of the ring CC bonds for each cyano group and a further increase in 1,2,4,5-tetracyanobenzene. Comparison with accurate results from X-ray and neutron crystallography indicates that in p-dicyanobenzene the internal ring angle at the place of substitution opens slightly as the molecule is frozen in the crystal. The small geometrical change, about 0.6 degrees , is shown to be real and to originate from intermolecular C identical withN...HC interactions in the solid state.     

On the effect of 4f electrons on the structural characteristics of lanthanide trihalides: computational and electron diffraction study of dysprosium trichloride

The molecular and electronic structure of dysprosium trichloride, DyCl(3), was calculated by high-level quantum chemical methods in order to learn about the effect of the partially filled 4f subshell and of the possible spin-orbit coupling on them. High-temperature electron diffraction studies of DyCl(3) were also carried out so that we could compare the computed geometry with the experimental one, after thermal corrections on the latter. Dysprosium monochloride, DyCl, and the dimer of dysprosium trichloride, Dy(2)Cl(6), were also investigated by computation. We found that the electron configuration of the 4f subshell does not influence the geometry of the trichloride monomer molecule as the ground state and first excited state molecules have the same geometry. Nonetheless, taking the 4f electrons into account in the calculation, together with the 5s and 5p electrons, is important in order to get geometrical parameters consistent with the results from experiment. Based on electron diffraction and different levels of computation, the suggested equilibrium bond length (r(e)) of DyCl(3) is 2.443(14) A, while the thermal average distance (r(g)) from electron diffraction is 2.459(11) A. The molecule is trigonal planar in equilibrium. Although the ground electronic state splits due to spin-orbit coupling, the lowering of the total electronic energy is very small (about 0.025 hartree) and the geometrical parameters are not affected. In contrast with the monomeric trichloride molecule, the bond angles of the dimer seem to be different for different electronic states, indicating the influence of the 4f electronic configuration on their structure. We carried out an anharmonic analysis of the out-of-plane vibration of the trichloride monomer and found that the vibration is considerably anharmonic at 39.5 cm(-1), compared with the 30.5 cm(-1) harmonic value.     

Michael Polanyi—pupils and crossroads—on the 125th anniversary of his birth

Michael Polanyi (1891–1976) was a Hungarian-born British physician turned physical chemist turned philosopher. His milestone epistemological treatise Personal Knowledge followed his substantial discoveries in adsorption studies, X-ray crystallography, materials science, and the mechanism of chemical reactions. Michael Polanyi was one of the last polymaths and his teachings impacted the world views of other outstanding contributors to twentieth century science and culture.     

Molecular structure and conformation of nitrobenzene reinvestigated by combined analysis of gas-phase electron diffraction,rotational constants,and theoretical calculations

The molecular structure and conformation of nitrobenzene has been reinvestigated by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) spectroscopic data, and quantum chemical calculations. The equilibrium r _e structure of nitrobenzene was determined by a joint analysis of the GED data and rotational constants taken from the literature. The necessary anharmonic vibrational corrections to the internuclear distances (r _e ? r _a) and to rotational constants (B _e ⁽ⁱ⁾  ? B ₀ ⁽ⁱ⁾ ) were calculated from the B3LYP/cc-pVTZ quadratic and cubic force fields. A combined analysis of GED and MW data led to following structural parameters (r _e) of planar nitrobenzene (the total estimated uncertainties are in parentheses): r(C–C)_av = 1.391(3) Å, r(C–N) = 1.468(4) Å, r(N–O) = 1.223(2) Å, r(C–H)_av = 1.071(3) Å, \({\angle}\)C2–C1–C6 = 123.5(6)°, \({\angle}\)C1–C2–C3 = 117.8(3)°, \({\angle}\)C2–C3–C4 = 120.3(3)°, \({\angle}\)C3–C4–C5 = 120.5(6)°, \({\angle}\)C–C–N = 118.2(3)°, \({\angle}\)C–N–O = 117.9(2)°, \({\angle}\)O–N–O = 124.2(4)°, \({\angle}\)(C–C–H)_av = 120.6(20)°. These structural parameters reproduce the experimental B ₀ ⁽ⁱ⁾ values within 0.05 MHz. The experimental results are in good agreement with the theoretical calculations. The barrier height to internal rotation of nitro group, 4.1±1.0 kcal/mol, was estimated from the GED analysis using a dynamic model. The equilibrium structure was also calculated using the experimental rotational constants for nitrobenzene isotopomers and theoretical rotation–vibration interaction constants.     

Thio-click approach to the synthesis of stable glycomimetics

Carbon-sulfur-bridged glycomimetics were prepared by free radical hydrothiolation of the exocyclic double bond of unsaturated sugars. Reaction between benzoyl-substituted pyranoid-exoglycal and a range of thiols including peptide, 1-thioglycerol and 1-thiosugar derivatives gave β-D-configured carbon-sulfur-linked glycoconjugates with full stereoselectivity. Addition of a panel of thiols to a 3-exomethylene-glucofuranose derivative also proceeded in a stereoselective manner and afforded a series of D-allo-configured 3-deoxy-3-C-S-bridged glycoconjugates.     

Richard E. Dickerson,Present at the Flood: How structural molecular biology came about

Structural Chemistry -     

Direct photothermal techniques for rapid quantification of total anthocyanin content in sour cherry cultivars

The analytical performance of the newly proposed laser-based photoacoustic spectroscopy (PAS) and of optothermal window (OW) method for quantification of total anthocyanin concentration (TAC) in five sour cherry varieties is compared to that of the spectrophotometry (SP). High performance liquid chromatography (HPLC) was used to identify and quantify specific anthocyanins. Both, PAS and OW are direct methods that unlike SP and HPLC obviate the need for the extraction of analyte. The outcome of the study leads to the conclusion that PAS and OW are both suitable for quick screening of TAC in sour cherries. The correlation between the two methods and SP is linear with R² = 0.9887 for PAS and R² = 0.9918 for OW, respectively. Both methods are capable of the rapid determination of TAC in sour cherries without a need for a laborious sample pretreatment.     

Hydrophilic carotenoids: recent progress

Carotenoids are substantially hydrophobic antioxidants. Hydrophobicity is this context is rather a disadvantage, because their utilization in medicine as antioxidants or in food chemistry as colorants would require some water dispersibility for their effective uptake or use in many other ways. In the past 15 years several attempts were made to synthetize partially hydrophilic carotenoids. This review compiles the recently synthetized hydrophilic carotenoid derivatives.     

Molecular structure and vibrational spectra of mixed MDyX4 (M = Li, Na, K, Rb, Cs; X = F, Cl, Br, I) vapor complexes: a computational and matrix-isolation infrared spectroscopic study

The structures, energetic, and vibrational properties of MDyX(4) (M = Li, Na, K, Rb, Cs; X = F, Cl, Br, I) mixed alkali halide/dysprosium halide complexes have been investigated by a joint computational and experimental, matrix-isolation Fourier-transform infrared spectroscopic (MI-IR), study. According to our DFT computations for the complexes with heavier halides and alkali metals the ground-state structure is the tridentate isomer; while at high temperatures the bidentate structural isomer dominates. The survey of various dissociation processes revealed the preference of the dissociation to neutral MX and DyX(3) fragments over ionic and radical dissociation products. Cationic complexes are considerably less stable at 1000 K than the neutral complexes, and they prefer to dissociate to M(+) + DyX(4)(?) fragments. The vapor species of selected mixtures of NaBr and CsBr with DyBr(3) and of CsI with DyI(3) in the temperature range 900-1000 K have been isolated in krypton and xenon matrices and investigated by infrared spectroscopy. Besides the characteristic vibrational frequencies of the monomeric and dimeric alkali halide species and of the dysprosium trihalide molecules, certain signals indicated the formation of MDyX(4) (M = Na, Cs; X = Br, I) mixed complexes. Comparison with the computed vibrational and thermodynamic characteristics of the relevant species lead to the conclusion that these complexes appear in the vapor predominantly as the C(2v)-symmetry bidentate isomer. This is the first time that this structure was identified in an experimental vibrational spectroscopic study. The signals appearing upon performing a thermal anneal cycle were tentatively assigned to the double complex M(2)DyX(5) (M = Na, Cs; X = Br, I). A structure in which one alkali atom is bound to dysprosium by three and the other by two bridges is proposed for these double complexes.