Noncovalent Interactions of Silatranes and Germatranes with the Surface of Stoichiometric and Hydroxylated 2D Silica.

Analysis of noncovalent interactions formed by the surface of a 2D silica bilayer and atrane molecules, as precursors of functional layers immobilized on a surface of silicatene, was performed. For this purpose, the systems of substituted silatranes and germatranes adsorbed on silicatene surfaces with different amounts of hydroxyl groups (0, 2, 4, and 30 per cell) were simulated by using quantum chemical modeling with periodic boundary conditions and full-electron basis sets. The observation results for interaction energy changes in the systems "atrane molecule-silicatene surface" with increasing silanol number of the silicatene surface can be used to predict the optimal degree of silicatene hydroxylation in order to control the effective progress of atrane deprotection on activated 2D silica materials. In addition to the typical hydrogen bonds, the ability of atranes to form noncovalent O···O and O···Hal interactions was discovered. In these bonds, the oxygen or halogen atoms of atranes act as electron-donor centers in relation to the silicatene oxygen atoms. The observed weakening of the Ge-O covalent bonds in germatranes, on which further deprotection reaction depends, is more manifested than for the Si-O bonds in adsorbed silatranes.

Electron delocalization in defect-containing graphene and its influence on tetrel bond formation.

Using the advanced analyses of electron density and fermionic potential, we show how electron delocalization influences the ability of defect-containing graphene to form tetrel bonds. The Cg atoms of a vacancy defect can produce one nonpolar interaction, alongside a peculiar polar Cg⋯Cg bond. The latter stems from the presence of a localized electron pair on a vacancy defect Cg atom and the local depletion of electron localization on another Cg atom. This interaction is an example of intralayer tetrel bond. In the presence of an absorbed molecule of bisphenol A diglycidyl ether (DGEBA), graphene is able to form incipient tetrel Cg⋯O bonds with an ether group oxygen. In contrast to an epoxy group oxygen, the disposition of the ether oxygen often causes the orientation of electron-rich π-domains of graphene carbon on the weakly expressed electrophilic region of the oxygen. In the case of graphene with a point Si defect, the Si atom can form quite strong Si⋯C interactions with the DGEBA aryl carbons. In contrast to other noncovalent bonds, this interaction significantly alters the electron (de)localization on the Si atom and in the aryl ring. The reliability of the obtained results is enhanced by the use of multiple 2D periodic models with defects located at different positions along the DGEBA skeleton.

Can We Merge the Weak and Strong Tetrel Bonds? Electronic Features of Tetrahedral Molecules Interacted with Halide Anions.

Using the orbital-free quantum crystallography approach, we have disclosed the quantitative trends in electronic features for bonds of different strengths formed by tetrel (Tt) atoms in stable molecular complexes consisting of electrically neutral tetrahedral molecules and halide anions. We have revealed the role of the electrostatic and exchange-correlation components of the total one-electron static potential that are determined by the equilibrium atomic structure and by kinetic Pauli potential, which reflects the spin-dependent electron motion features of the weak and strong bonds. The gap between the extreme positions in the electrostatic and total static potentials along the line linking the Tt atom and halide anion is wide for weak bonds and narrow for strong ones. It is in very good agreement with the number of minima in the Pauli potential between the bounded atoms. This gap exponentially correlates with the exchange-correlation potential in various series with a fixed nucleophilic fragment. A criterion for categorizing the noncovalent tetrel bonds (TtB) based on the potential features is suggested.

The Distance between Minima of Electron Density and Electrostatic Potential as a Measure of Halogen Bond Strength.

In this study, we present results of a detailed topological analysis of electron density (ED) of 145 halogen-bonded complexes formed by various fluorine-, chlorine-, bromine-, and iodine-containing compounds with trimethylphosphine oxide, Me3PO. To characterize the halogen bond (XB) strength, we used the complexation enthalpy, the interatomic distance between oxygen and halogen, as well as the typical set of electron density properties at the bond critical points calculated at B3LYP/jorge-ATZP level of theory. We show for the first time that it is possible to predict the XB strength based on the distance between the minima of ED and molecular electrostatic potential (ESP) along the XB path. The gap between ED and ESP minima exponentially depends on local electronic kinetic energy density at the bond critical point and tends to be a common limiting value for the strongest halogen bond.

Acylative kinetic resolution of racemic methyl-substituted cyclic alkylamines with 2,5-dioxopyrrolidin-1-yl (R)-2-phenoxypropanoate.

The diastereoselective acylation of a number of racemic methyl-substituted cyclic alkylamines with active esters of 2-phenoxypropanoic acid was studied in detail. The ester of (R)-2-phenoxypropanoic acid and N-hydroxysuccinimide was found to be the most selective agent. The highest stereoselectivity was observed in the kinetic resolution of racemic 2-methylpiperidine in toluene at -40 °C (selectivity factor s = 73) with the predominant formation of (R,R)-amide (93.7% de). To explain the observed stereoselectivity, DFT modelling of the transition states in the reactions of the title acylating agent with 2-methylpiperidine and 2-methylpyrrolidine was performed. The calculated values were in good agreement with experimental data. It has been demonstrated that the acylation proceeds via a concerted mechanism, in which the addition of an amine occurs simultaneously with the elimination of the hydroxysuccinimide fragment. The high stereoselectivity of the (R,R)-amide formation is largely ensured by the lower steric hindrances in the transition states as compared to the formation of (R,S)-amide.

Why are reactions of 2- and 8-thioquinoline derivatives with iodine different?

The crystal structures of 1,2-dihydro-1,1'-bi[thiazolo[3,2-a]quinoline]-10a,10a'-diium diiodide hemihydrate, C22H16N2S22+·2I-·0.5H2O, and 1,2-dihydro-1,1'-bi[thiazolo[3,2-a]quinoline]-10a,10a'-diium iodide triiodide, C22H16N2S22+·I-·I3-, obtained during the reaction of 1,4-bis(quinolin-2-ylsulfanyl)but-2-yne (2TQB) with iodine, have been determined at 120 K. The crystalline products contain the dication as a result of the reaction proceeding along the iodocyclization pathway. This is fundamentally different from the previously observed reaction of 1,4-bis(quinolin-8-ylsulfanyl)but-2-yne (8TQB) with iodine under similar conditions. A comparative analysis of the possible conformational states indicates differences in the relative stabilities and free rotation for the 2- and 8-thioquinoline derivatives which lead to a disparity in the convergence of the potential reaction centres for 2TQB and 8TQB.

An anatomy of intramolecular atomic interactions in halogen-substituted trinitromethanes.

The intramolecular interactions in substituted trinitromethanes, XC(NO2)3 (X = F, Cl, I, H) are studied and clarified by using a combination of the Quantum Theory of Atoms in Molecules (QTAIM), the non-covalent interaction analysis and the Interacting Quantum Atoms (IQA) methods. The stretching vibration modes are formed by the concerted displacements of atoms involved in the covalent bonds showing the significant multiatomic influence in substituted trinitromethanes. In agreement with that, the arrangement of the local reduced density gradient minima indicates that the electron density favors the non-covalent intramolecular interactions X···O and N···O. However, the corresponding QTAIM bond paths are not formed; instead, contacts, which we call uncompleted links in this context, are accompanied by "quasi-bonding channels" corresponding to the λ2() ≤ 0 regions on the sign[λ2(r)]ρ(r) contour maps. The intramolecular IQA energy contributions signal the appreciable electron exchange between the pairs of atoms associated with potential atomic interactions or the bond-path-free non-covalent links. The IQA analysis shows that the electrostatic term destabilizes FC(NO2)3 and distinctly stabilizes IC(NO2)3, whereas it is close to neutral in ClC(NO2)3. The exchange energy between the X atom and the NO2 groups, in contrast, stabilizes all the molecules.

Determination of covalent bond orders and atomic valence indices using topological features of the experimental electron density.

We present an approach for the determination of covalent bond orders from the experimental electron density and its derivatives at the bond critical points. An application of this method to a series of organic compounds has shown that it provides a bonding quantification that is in reasonable agreement with that obtained by orbital theory. The 'experimental' atomic valence indices are also defined and their significance for the characterization of chemical problems is discussed.

Atoms-in-molecules study of intra- and intermolecular bonding in the pentaerythritol tetranitrate crystal.

Chemical bonding in the pentaerythritol tetranitrate crystal based on the experimental electron density obtained from X-ray diffraction data at 100 K and theoretical calculations at the experimental molecular geometry have been analyzed in terms of the Quantum Theory of Atoms in Molecules. Features of the intra- and intermolecular bond critical points and the oxygen atom lone-pair locations are discussed. Numerous intermolecular bonding interactions, including O...H and O...O, have been found and characterized. Atomic charges and atomic energies were integrated and compared with those for similar compounds. The N-O topological bond orders have been calculated for the first time, and the PETN atomic valences have been estimated.