Analysis Of Electron Charge Density Research Articles

Systematic study of cooperative interplay between single-electron pnicogen bond and halogen bond in X3C···PH2Y···ClY (X=H, CH3; Y=CN, NC) complexes in two different minima configuration

UMP2 calculations with aug-cc-pVTZ basis set used to analyse intermolecular interactions in X3C···PH2Y···ClY (X = H, CH3; Y = CN, NC) complexes constructed via halogen bond and single-electron pnicogen bond in two discovered minima in the potential energy surface. The first minima presents short P−C distances and, in all cases, high interaction energies compared to the second one that shows long P−C distances with a typical weak pnicogen bond interaction. The impacts of the halogen bonds on the single-electron pnicogen interaction in each complex are systematically investigated by the means of cooperative effects. In all cases studied, a favorable cooperativity is observed but these values are much higher for first minima, which ranges from −19.73 to −36.82 kJ mol−1, than second minima with cooperative energy values between −0.75 and −4.69 kJ mol1. In order to unveil the mechanism of the cooperativity, these effects are analysed in terms of geometric, energetic, electrostatic potential analysis, electron charge density analysis performed using (QTAIM), many-body interaction analysis and electron density analysis.

Electron Density and Dielectric Properties of Highly Porous MOFs: Binding and Mobility of Guest Molecules in Cu3(BTC)2 and Zn3(BTC)2.

Two isostructural highly porous metal-organic frameworks, the well-known {Cu3(BTC)2} n (BTC = 1,3,5-benzenetricarboxylate), often appointed with the name HKUST-1, and {Zn3(BTC)2} n, have been investigated as models for the buildup of dielectric properties, differentiating the role of chemi- and physisorbed guest molecules and that of specific intraframework and framework-guest linkages. For this purpose, electron charge density analysis, impedance spectroscopy, density functional theory simulations, and atomic partitioning of the polarizabilities have been exploited. These analyses at different degrees of pores filling enabled one to observe structural and electronic changes induced by guest molecules, especially when chemisorbed. The electrostatic potential inside the pores allows one to describe the absorption mechanism and to estimate the polarization of guests induced by the framework. The dielectric constant shows very diverse frequency dependence and magnitude of real and imaginary components as a consequence of (I) capture of guest molecules in the pores during synthesis, (II) MOF activation, and (III) water absorption from the atmosphere after activation. Comparison with calculated static-dielectric constant and atomic polarizabilities of the material has allowed for evaluating building blocks' contribution to the overall property, paving the way for reverse crystal engineering of these species.

On the Importance of Noncovalent Carbon-Bonding Interactions in the Stabilization of a 1D Co(II) Polymeric Chain as a Precursor of a Novel 2D Coordination Polymer.

A new cobalt(II) coordination polymer 2 with μ1,5 dicyanamide (dca) and a bidentate ligand 3,5-dimethyl-1-(2'-pyridyl)pyrazole (pypz) is prepared in a stepwise manner using the newly synthesized one-dimensional linear Co(II) coordination polymer 1 as a precursor. The structural and thermal characterizations elucidate that the more stable complex 2 shows a two-dimensional layer structural feature. Here, Co(II) atoms with μ1,5 dicyanamido bridges are linked by the ligand pypz forming a macrocyclic chain that runs along the crystallographic 'c' axis having 'sql' (Shubnikov notation) net topology with a 4-connected uninodal node having point symbol {4(4).6(2)}. The remarkable noncovalent carbon-bonding contacts detected in the X-ray structure of compound 1 are analyzed and characterized by density functional theory calculations and the analysis of electron charge density (atoms in molecules).

Modeling of Structure and Nonlinear Optical Activity of Epoxy‐Based Oligomers with Dendritic Multichromophore Fragments

AbstractSummary: Epoxy‐based oligomers having length up to four units with dendritic chromophore‐containing fragments covalently attached through spacers to the bearing chain are studied. The structure of the oligomers was obtained in the course of conformational search by Monte‐Carlo method, the distribution of the torsion angles values in the dendritic fragment was examined by molecular dynamics. The nonlinear‐optical response of the studied oligomers and dendritic chromophore fragments was calculated by the TDHF method at AM1 level. Intradendron cross‐linking of chromophore groups is investigated, diphenylmethandiisocyanate used as hardening agent. Cross‐linking is shown to decrease the angles between the chromophores in the dendron, thus providing enhanced nonlinear‐optical characteristics of the oligomer. Stacking‐like arrangement of chromophore groups, observed in variety of oligomers, is investigated in the framework of topological analysis of electron charge density, and Van‐der‐Waals interactions are found to be responsible for the stacking effect.

Interaction between uracil nucleobase and phenylalanine amino acid: the role of sodium cation in stacking

The stacking interactions in the uracil:phenylalanine (U:PHE) and (U:PHE)···Na+ complexes have been studied at different levels of theory, in which the structures were optimized by both standard and gradient counterpoise corrected methods. The Na+ cation can interact with different sites of stacked U:PHE unit. The geometrical parameters of the optimized structures and the calculated binding energies reveal the influence of cation interaction on π–π stacking and vice versa. The interplay between π–π stacking and cation interaction has also been investigated by topological analysis of electron charge density using atoms in molecules (AIM) method. A good agreement between the results of AIM analysis and calculated binding energies has been observed in dimer and complexes.

The topological analysis of electronic charge densities: A reassessment of foundations

In this account the relationship between the topological analysis of electronic charge densities and the general theory of dynamical systems is considered in detail. It is shown that the main theorems of structural stability are best appreciated within the context of the general theory of dynamical systems. On the other hand, it is demonstrated that this theory may set the stage for a generalized topological analysis. This general framework could be applied easily to various scalar functions. In the end, it is emphasized that the very concepts of structure and structural stability are not intrinsically tied to the nuclear coordinates. Accordingly, by employing new variables like temperature or pressure it is possible to construct novel control spaces.

Structure and electron charge-density analysis of nano-sized BaTiO3 powder prepared by solvothermal method

Abstract The BaTiO3 powder with the average particle size of 20 nm were synthesized by a solvothermal method using Ba and Ti alkoxide solutions as precursors. The structural parameters of BaTiO3 powder were successfully determined by the Rietveld refinement based on the analysis of Raman spectra. The final weighted R-factor, Rwp, was 9.12% and the goodness-of-fit indicator, S (=Rwp/Re), was 1.28. The BaTiO3 powder consisted of cubic and tetragonal phases at room temperature. The weight fraction of cubic and tetragonal phases based on the refined scale factors was 83.2% and 16.8%, respectively. The lattice parameters for cubic and tetragonal phases were a (=b = c) = 4.0114(3) A, and a (=b) = 3.9954(2) A and c = 4.0327(2) A, respectively. According to the analysis of the electron charge-density distributions by maximum entropy method based on the observed structural factors to understand the chemical bonding nature of BaTiO3 powder, the ferroelectric phase was stabilized by ionic and weak covalent bonding.

Topological analysis of electronic charge densities as a tool to study protonation effects on thiocarbonyl compounds

AbstractThe substituent effects on the intrinsic basicity of a wide variety of thiocarbonyl compounds were investigated by means of a topological analysis of the electronic charge densities and their Laplacians for the neutral and the protonated species, and also by means of their harmonic vibrational frequencies. For the sake of comparison, a similar analysis was carried out for a reduced set of carbonyl compounds with similar substituents. The results show that the behaviour of the thiocarbonyl group with regard to the protonation process is similar to that predicted for the carbonyl group, in the sense that both groups are not much affected by protonation. The charge transferred to the proton results basically in a polarization and, in some cases, in a depopulation of the bonds in which the thiocarbonyl carbon atom participates. Accordingly, the intrinsic basicities of these kinds of compounds depend strongly on the ability of the substituents to be polarized. This conclusion seems to be ratified also by the shiftings undergone by the C=S stretching frequencies on protonation.