Anisotropy Of Electron Density Research Articles

On the Importance of Halogen Bonding Interactions in Two X-ray Structures Containing All Four (F, Cl, Br, I) Halogen Atoms

This manuscript reports the synthesis and X-ray characterization of two octahydro-1H-4,6-epoxycyclopenta[c]pyridin-1-one derivatives that contain the four most abundant halogen atoms (Ha) in the structure with the aim of studying the formation of Ha···Ha halogen bonding interactions. The anisotropy of electron density at the heavier halogen atoms provokes the formation of multiple Ha···Ha contacts in the solid state. That is, the heavier Ha-atoms exhibit a region of positive electrostatic potential (σ-hole) along the C–Ha bond and a belt of negative electrostatic potential (σ-lumps) around the atoms. The halogen bonding assemblies in both compounds were analyzed using density functional theory (DFT) calculations, molecular electrostatic potential (MEP) surfaces, the quantum theory of “atom-in-molecules” (QTAIM), the noncovalent interaction plot (NCIplot), and the electron localization function (ELF).

Multipolar electrostatics for hairpin and pseudoknots in RNA: Improving the accuracy of force field potential energy function.

Molecular dynamics (MD) simulations that rely on force field methods has been widely used to explore the structure and function of RNAs. However, the current commonly used force fields are limited by the electrostatic description offered by atomic charge, dipole and at most quadrupole moments, failing to capture the anisotropic picture of electronic features. Actually, the distribution of electrons around atomic nuclei is not spherically symmetric but is geometry dependent. A multipolar electrostatic model based on high rank multipole moments is described in this work, which allows us to combine polarizability and anisotropy of electron density. RNA secondary structure was taken as a research system, and its substructures including stem, loops (hairpin loop, bulge loop, internal loop, and multi-branch loop), and pseudoknots (H-type and K-type) were investigated, respectively, as well as the hairpin. First, the atom-atom electrostatic properties derived from one chain of a duplex RNA 2MVY in our previous work (Ref. 58) were measured by the pilot RNA systems of hairpin, hairpin loop, stem, and H-type pseudoknot, respectively. The prediction results were not satisfactory. Consequently, to obtain a general set of electrostatic parameters for RNA force fields, the convergence behavior of the atom-atom electrostatic interactions in the pilot RNA systems was explored using high rank atomic multipole moments. The pilot RNA systems were cut into four types of different-sized molecular fragments, and the single nucleotide fragment and nucleotide-paired fragment proved to be the most reasonable systems for base-unpairing regions and base-pairing regions to investigate the convergence behavior of all types of atom-atom electrostatic interactions, respectively. Transferability of the electrostatic properties drawn from the pilot RNA systems to the corresponding test systems was also investigated. Furthermore, the convergence behavior of atomic electrostatic interactions in other substructures including bulge loop, internal loop, multi-branch loop, and K-type pseudoknot was expected to be modeled via the hairpin.

Characterization of Local Aromaticity in Polycyclic Conjugated Hydrocarbons Based on Anisotropy of π‐Electron Density

AbstractIn recent contributions, it was demonstrated that the anisotropy of π‐electron density could be considered as a reliable descriptor to probe the aromaticity in a wide range of annulene and hetero‐monocyclic compounds. The electron density anisotropy on a plane can be simply measured by the ratio of two in‐plane Hessian eigenvalues associated with the eigenvectors lying in the plane. This descriptor is undirected and has a circular symmetry for aromatic rings, whereas it is directed and has an elliptical shape in antiaromatic cycles. This research takes a step forward towards the extension of this approach to polycyclic conjugated hydrocarbons. The obtained results show that the anisotropy of the π‐electron density works nicely for the assessment of local aromaticity in polycyclic compounds. This finding provides clear evidence to have a universally successful aromaticity descriptor based on the topological properties of one‐electron density distribution.

Description of heteroaromaticity on the basis of π-electron density anisotropy.

It is demonstrated that there is a direct connection between aromaticity and the anisotropy of the π-electron density on planes parallel to the molecular ring. The electron density anisotropy on the plane is measured through the ratio of the in-plane Hessian eigenvalues associated with the eigenvectors lying in the plane. Computations on a wide-ranging set of well-characterized monocyclic systems containing heteroatoms validate the correlation between this one-electron density-based descriptor and aromaticity; in aromatic compounds, the in-plane Hessian eigenvalues are degenerate (or near degenerate) and the anisotropy of the π-electron density is undirected, whereas the results for antiaromatic rings are reversed and the degeneracy of the eigenvalues completely disappears. This finding is in line with our very recent study on [n]annulenes and provides further evidence that the anisotropy of the π-electron density should be considered as a new manifestation of aromaticity.