The α-D-anomer of 2′-deoxycytidine: crystal structure, nucleoside conformation and Hirshfeld surface analysis

β-2′-Deoxyribonucleosides are the constituents of nucleic acids, whereas their anomeric α-analogues are rarely found in nature. Moreover, not much information is available on the structural and conformational parameters of α-2′-deoxyribonucleosides. This study reports on the single-crystal X-ray structure of α-2′-deoxycytidine, C9H13N3O4 (1), and the conformational parameters characterizing 1 were determined. The conformation at the glycosylic bond is anti, with χ = 173.4 (2)°, and the sugar residue adopts an almost symmetrical C2′-endo-C3′-exo twist (^2_3T; S-type), with P = 179.7°. Both values lie outside the conformational range usually preferred by α-nucleosides. In addition, the amino group at the nucleobase shows partial double-bond character. This is supported by two separated signals for the amino protons in the 1H NMR spectrum, indicating a hindered rotation around the C4—N4 bond and a relatively short C—N bond in the solid state. Crystal packing is controlled by N—H...O and O—H...O contacts between the nucleobase and sugar moieties. Moreover, two weak C—H...N contacts (C1′—H1′ and C3′—H3′A) are observed. A Hirshfeld surface analysis was carried out and the results support the intermolecular interactions observed by the X-ray analysis.

1,1′-Biisoquinolines—Neglected Ligands in the Heterocyclic Diimine Family That Provoke Stereochemical Reflections

1,1′-Biisoquinolines are a class of bidentate nitrogen donor ligands in the heterocyclic diimine family. This review briefly discusses their properties and the key synthetic pathways available and then concentrates upon their coordination behaviour. The ligands are of interest as they exhibit the phenomenon of atropisomerism (hindered rotation about the C1–C1′ bond). A notation for depicting the stereochemistry in coordination compounds containing multiple stereogenic centers is developed. The consequences of the chirality within the ligand on the coordination behaviour is discussed in detail.

Spectroscopic, X-ray Diffraction and Density Functional Theory Study of Intra- and Intermolecular Hydrogen Bonds in Ortho-(4-tolylsulfonamido)benzamides

The conformations of the title compounds were determined in solution (NMR and UV-Vis spectroscopy) and in the solid state (FT-IR and XRD), complemented with density functional theory (DFT) in the gas phase. The nonequivalence of the amide protons of these compounds due to the hindered rotation of the C(O)–NH2 single bond resulted in two distinct resonances of different chemical shift values in the aromatic region of their 1H-NMR spectra. Intramolecular hydrogen bonding interactions between the carbonyl oxygen and the sulfonamide hydrogen atom were observed in the solution phase and solid state. XRD confirmed the ability of the amide moiety of this class of compounds to function as a hydrogen bond acceptor to form a six-membered hydrogen bonded ring and a donor simultaneously to form intermolecular hydrogen bonded complexes of the type N–H···O=S. The distorted tetrahedral geometry of the sulfur atom resulted in a deviation of the sulfonamide moiety from co-planarity of the anthranilamide scaffold, and this geometry enabled oxygen atoms to form hydrogen bonds in higher dimensions.

Stereoselective [4+2] Cycloaddition of Singlet Oxygen to Naphthalenes Controlled by Carbohydrates

Stereoselective reactions of singlet oxygen are of current interest. Since enantioselective photooxygenations have not been realized efficiently, auxiliary control is an attractive alternative. However, the obtained peroxides are often too labile for isolation or further transformations into enantiomerically pure products. Herein, we describe the oxidation of naphthalenes by singlet oxygen, where the face selectivity is controlled by carbohydrates for the first time. The synthesis of the precursors is easily achieved starting from naphthoquinone and a protected glucose derivative in only two steps. Photooxygenations proceed smoothly at low temperature, and we detected the corresponding endoperoxides as sole products by NMR. They are labile and can thermally react back to the parent naphthalenes and singlet oxygen. However, we could isolate and characterize two enantiomerically pure peroxides, which are sufficiently stable at room temperature. An interesting influence of substituents on the stereoselectivities of the photooxygenations has been found, ranging from 51:49 to up to 91:9 dr (diastereomeric ratio). We explain this by a hindered rotation of the carbohydrate substituents, substantiated by a combination of NOESY measurements and theoretical calculations. Finally, we could transfer the chiral information from a pure endoperoxide to an epoxide, which was isolated after cleavage of the sugar chiral auxiliary in enantiomerically pure form.

Chiral bis(benzo[1,2-b:4,3-b']dithiophene) atropisomers: experimental and theoretical investigations of the stereochemical and chiroptical properties

Conformational chirality is a feature that may arise from the presence of a hindered rotation around a single bond that corresponds to a stereogenic axis. Atropisomers that feature such element...

Quantized Rotational Motion in a Plane

The angular momentum for the simplified case of a particle rotating in a fixed plane is treated. The ‘perimeter model’ is the analogue of the one-dimensional particle in a box (PiaB), with the particle moving on a circle with fixed radius. This requires cyclic – or periodic – boundary conditions. It is shown that the quantum perimeter model results can be obtained by re-interpreting the coordinate of the linear PiaB and by considering the periodic boundary conditions. The eigenvalue pattern leads to a 4n+2 Huckel rule. Next, the chapter discusses hindered rotations, such as the rotation of a methyl group around a C-C bond. The solutions to the hindered rotation problem combine features of the harmonic oscillator at low energies, with features of the perimeter model at high energies.

Perovskite Crystals: Unique Pseudo-Jahn–Teller Origin of Ferroelectricity, Multiferroicity, Permittivity, Flexoelectricity, and Polar Nanoregions

In a semi-review paper, we show that the local pseudo-Jahn–Teller effect (PJTE) in transition metal B ion center of ABO3 perovskite crystals, notably BaTiO3, is the basis of all their main properties. The vibronic coupling between the ground and excited electronic states of the local BO6 center results in dipolar distortions, leading to an eight-well adiabatic potential energy surface with local tunneling or over-the-barrier transitions between them. The intercenter interaction between these dipolar dynamic units results in the formation of the temperature-dependent three ferroelectric and one paraelectric phases with order–disorder phase transitions. The local PJTE dipolar distortion is subject to the presence of sufficiently close in energy local electronic states with opposite parity but the same spin multiplicity, thus limiting the electronic structure and spin of the B(dn) ions that can trigger ferroelectricity. This allowed us to formulate the necessary conditions for the transition metal perovskites to possess both ferroelectric and magnetic (multiferroic) properties simultaneously. It clarifies the role of spin in the spontaneous polarization. We also show that the interaction between the independently rotating dipoles in the paraelectric phase may lead to a self-assembly process resulting in polar nanoregions and relaxor properties. Exploring interactions of PJTE ferroelectrics with external perturbations, we revealed a completely novel property—orientational polarization in solids—a phenomenon first noticed by P. Debye in 1912 as a possibility, which was never found till now. The hindered rotation of the local dipole moments and their ordering along an external field is qualitatively similar to the behavior of polar molecules in liquids, thus adding a new dimension to the properties of solids—notably, the perovskite ferroelectrics. We estimated the contribution of the orientational polarization to the permittivity and flexoelectricity of perovskite crystals in different limiting conditions.

The Halogen-Bond Nature in Noble Gas–Dihalogen Complexes from Scattering Experiments and Ab Initio Calculations

In order to clarify the nature of the halogen bond (XB), we considered the prototype noble gas–dihalogen molecule (Ng–X2) systems, focusing on the nature, range, and strength of the interaction. We exploited data gained from molecular beam scattering experiments with the measure of interference effects to obtain a suitable formulation of the interaction potential, with the support of high-level ab initio calculations, and charge displacement analysis. The essential interaction components involved in the Ng–X2 adducts were characterized, pointing at their critical balance in the definition of the XB. Particular emphasis is devoted to the energy stability of the orientational Ng–X2 isomers, the barrier for the X2 hindered rotation, and the influence of the X2 electronic state. The present integrated study returns reliable force fields for molecular dynamic simulations in Ng–X2 complexes that can be extended to systems with increasing complexity and whose properties depend on the selective formation of XB.