Revisiting the bonding of the pentagonal-pyramidal C6H62+ and C6(CH3)62+ dications.

This work delves into the bonding nature of the pentagonal-pyramidal benzene and hexamethylbenzene dications, C6R62+ (R = H and CH3), which contain a hexacoordinate carbon. The study employs a range of methodologies to analyze a series of scalar fields, including electron density, electron localization function, local momentum representation, and the evaluation of the Coulomb hole through information theory-derived functions. The findings unveil that electron density undergoes transfer from the pentagonal ring to the apical group. As a result, the base of the complex accumulates the positive charge. Moreover, an extended electron density domain emerges between the carbon pentagon and the apical carbon atom. This phenomenon is related to the molecular orbitals with a dipolar character aligned with the principal axis of the molecule. The results also indicate an electron density polarization towards the apical carbon, coupled with an exclusion of electron density surrounding both the apical carbon and the lower portion of the pentagonal ring. These provide valuable insights into the complex bonding nature of hexacoordinate carbon and its implications for organic chemistry.

Exploring the Non-Covalent Bonding in Water Clusters.

QTAIM and source function analysis were used to explore the non-covalent bonding in twelve different water clusters (H2O)n obtained by considering n = 2-7 and various geometrical arrangements. A total of seventy-seven O-H⋯O hydrogen bonds (HBs) were identified in the systems under consideration, and the examination of the electron density at the bond critical point (BCP) of these HBs revealed the existence of a great diversity of O-H⋯O interactions. Furthermore, the analysis of quantities, such as |V(r)|/G(r) and H(r), allowed a further description of the nature of analogous O-H⋯O interactions within each cluster. In the case of 2-D cyclic clusters, the HBs are nearly equivalent between them. However, significant differences among the O-H⋯O interactions were observed in 3-D clusters. The assessment of the source function (SF) confirmed these findings. Finally, the ability of SF to decompose the electron density (ρ) into atomic contributions allowed the evaluation of the localized or delocalized character of these contributions to ρ at the BCP associated to the different HBs, revealing that weak O-H⋯O interactions have a significant spread of the atomic contributions, whereas strong interactions have more localized atomic contributions. These observations suggest that the nature of the O-H⋯O hydrogen bond in water clusters is determined by the inductive effects originated by the different spatial arrangements of the water molecules in the studied clusters.

A Theoretical Study of the C-X Bond Cleavage Mediated by Cob(II)Aloxime.

The C-X bond cleavage in different methyl halides (CH3X; X = Cl, Br, I) mediated by 5,6-dimethylbenzimidazole-bis(dimethylglyoximate)cobalt(II) (CoIICbx) was theoretically investigated in the present work. An SN2-like mechanism was considered to simulate the chemical process where the cobalt atom acts as the nucleophile and the halogen as the leaving group. The reaction path was computed by means of the intrinsic reaction coordinate method and analyzed in detail through the reaction force formalism, the quantum theory of atoms in molecules (QTAIM), and the calculation of one-electron density derived quantities, such as the source function (SF) and the spin density. A thorough comparison of the results with those obtained in the same reaction occurring in presence of 5,6-dimethylbenzimidazole-bis(dimethylglyoximate)cobalt(I) (CoICbx) was conducted to reveal the main differences between the two cases. The reactions mediated by CoIICbx were observed to be endothermic and possess higher activation energies in contrast to the reactions where the CoICbx complex is present. The latter was supported by the reaction force results, which suggest a relationship between the activation energy and the ionization potentials of the different nucleophiles present in the cleavage reaction. Moreover, the SF results indicates that the lower axial ligand (i.e., 5,6-dimethylbenzimidazole) exclusively participates on the first stage of the reaction mediated by the CoIICbx complex, while for the CoICbx case, it appears to have an important role along the whole process. Finally, the QTAIM charge analysis indicates that oxidation of the cobalt atom occurs in both cases; at the same time, it suggests the formation of an uncommon two-center one-electron bond in the CoIICbx case. The latter was confirmed by means of electron localization calculations, which resulted in a larger electron count at the Co-C interatomic region for the CoICbx case upon comparison with its CoIICbx counterpart.

Two conformational polymorphs of 4-methylhippuric acid.

4-Methylhippuric acid {systematic name: 2-[(4-methylbenzoyl)amino]ethanoic acid}, a p-xylene excreted metabolite with a backbone containing three rotatable bonds (R-bonds), is likely to produce more than one stable molecular structure in the solid state. In this work, we prepared polymorph I by slow solvent evaporation (plates with Z' = 1) and polymorph II by mechanical grinding (plates with Z' = 2). Potential energy surface (PES) analysis, rotating the molecule about the C-C-N-C torsion angle, shows four conformational energy basins. The second basin, with torsion angles near -73°, agree with the conformations adopted by polymorph I and molecules A of polymorph II, and the third basin at 57° matched molecules B of polymorph II. The energy barrier between these basins is 27.5 kJ mol-1. Superposition of the molecules of polymorphs I and II rendered a maximum r.m.s. deviation of 0.398 Å. Polymorphs I and II are therefore true conformational polymorphs. The crystal packing of polymorph I consists of C(5) chains linked by N-H...O interactions along the a axis and C(7) chains linked by O-H...O interactions along the b axis. In polymorph II, two molecules (A with A or B with B) are connected by two acid-amide O-H...O interactions rendering R22(14) centrosymmetric dimers. These dimers alternate to pile up along the b axis linked by N-H...O interactions. A Hirshfeld surface analysis localized weaker noncovalent interactions, C-H...O and C-H...π, with contact distances close to the sum of the van der Waals radii. Electron density at a local level using the Quantum Theory of Atoms in Molecules (QTAIM) and the Electron Localization Function (ELF), or a semi-local level using noncovalent interactions, was used to rank interactions. Strong closed shell interactions in classical O-H...O and N-H...O hydrogen bonds have electron density highly localized on bond critical points. Weaker delocalized electron density is seen around the p-methylphenyl rings associated with dispersive C-H...π and H...H interactions.

Non-covalent interactions in the multicomponent crystal of 1-aminocyclopentane carboxylic acid, oxalic acid and water: a crystallographic and a theoretical approach.

Single-crystal X-ray diffraction and quantum mechanical theories were used to examine in detail the subtle nature of non-covalent interactions in the [2:1:1] multicomponent crystal of 1,1-aminocyclopentanecarboxylic acid:oxalic acid:water. The crystal, which is a hydrate salt of the amino acid with the hydrogen-oxalate ion, also contains the zwitterion of the amino acid in equal proportions. It was found that a dimeric cation [Acc5(Z)...Acc5(C)]+ bonded by an O-H...O hydrogen bond exists due to a charge transfer between acid and carboxylate groups. The three-dimensional crystal is built by blocks stacked along the [101] direction by dispersion interactions, with each block growing along two directions: a hydrogen oxalate HOX-...HOX- catameric supramolecular structure along the [010] direction; and double ...HOX--W-[Acc5(Z)... Acc5(C)]+... chains related by inversion centers along the [1 0 {\bar 1}] direction. A PBE-DFT optimization, under periodic boundary conditions, was carried out. The fully optimized structure obtained was used to extract the coordinates to calculate the stabilization energy between the dimers under the crystal field, employing the M062X/aug-cc-pVTZ level of theory. The non-covalent index isosurfaces employed here allow the visualization of where the hydrogen bond and dispersion interactions contribute within the crystal. The crystal atomic arrangements are analyzed by employing the Atoms in Molecules and electron localization function theories. Within this context, the presence of density bond critical points is employed as a criterion for proving the existence of the hydrogen bond and it was found that these results agree with those rendered by the crystallographic geometrical analysis, with only three exceptions, for which bond critical points were not found.

Molecular and crystalline structures of three (S)-4-alkoxycarbonyl-2-azetidinones containing long alkyl side chains from synchrotron X-ray powder diffraction data.

The (S)-4-alkoxo-2-azetidinecarboxylic acids are optically active beta-lactam derivatives of aspartic acid, which are used as precursors of carbapenem-type antibiotics and poly-beta-aspartates. The crystal structures of three (S)-4-alkoxo-2-azetidinecarboxylic acids with alkyl chains with 10, 12 and 16 C atoms were solved using parallel tempering and refined against the X-ray powder diffraction data using the Rietveld method. The azetidinone rings in the three compounds display a pattern of asymmetrical bond distances and an almost planar conformation; these characteristics are compared with periodic solid-state, gas-phase density-functional theory (DFT) calculations and MOGUL average bond distances and angles from the CSD. The compounds pack along [001] as corrugated sheets separated by approximately 4.40 A and connected by hydrogen bonds of the type N-H...O.

Redetermination of 1-carboxy-cyclo-hexan-1-aminium chloride.

The crystal structure of the title compound, C(7)H(14)NO(2) (+)·Cl(-), was reported previously [Chacko, Srinivasan & Zand (1975 ▶). J. Cryst. Mol. Struct.5, 353-357] from Weissenberg photographic data with R = 0.113. It has now been redetermined, providing a significant increase in the precision of the derived geometric parameters, viz. mean σ(C-C) = 0.003 Šin the present work compared with 0.021 Šfor the previous work. The complete cation is generated by crystallographic mirrror symmetry, with three C atoms, two O atoms and the N atom lying on the reflecting plane; the chloride anion also has m site symmetry. The crystal structure is established by a two-dimensional network of O-H⋯Cl and N-H⋯Cl hydrogen bonds, generating C(1) (2)(4) and C(1) (2)(7) chains, and R(2) (4)(8) and R(2) (4)(14) rings.

(2S)-1-Carbamoylpyrrolidine-2-carboxylic acid.

In the title compound, also known as N-carbamoyl-L-proline, C(6)H(10)N(2)O(3), the pyrrolidine ring adopts a half-chair conformation, whereas the carboxyl group and the mean plane of the ureide group form an angle of 80.1 (2) degrees. Molecules are joined by N-H...O and O-H...O hydrogen bonds into cyclic structures with graph-set R(2)(2)(8), forming chains in the b-axis direction that are further connected via N-H...O hydrogen bonds into a three-dimensional network.