In Silico Design and Characterization of a New Molecular Electride: Li@Calix[3]Pyrrole.

Electrides, in which anionic electrons are localized independently of the atoms in the compound, have shown promise, especially as catalysts and optoelectronic materials. Here, we present a new computationally designed molecular electride, Li@calix[3]pyrrole (Li@C3P). Electron density and electron localization function analyses unequivocally confirm the existence of localized electride electron density, outside the system, independent of any specific atoms. Non-covalent interaction plots further validate the character of the isolated localized electron, suggesting that the system can be accurately represented by Li+@calix[3]pyrrole ⋅ e-, denoting its distinct charge separation. The remarkable non-linear optical properties of Li@C3P, including average polarizability, α ‾ ${\bar{\alpha }}$ =412.4 au, first hyperpolarizability, ß=4.46×104 au, and second hyperpolarizability, γ ∥ ${{\gamma }_{\parallel }}$ =18.40×106 au, are unparalleled in the previously reported and similar Li@C4P molecular electride. Furthermore, energy decomposition analysis in combination with natural orbital for chemical valence theory sheds light on the mechanism of electron density transfer from Li to the C3P cage, yielding the charge-separated Li@C3P complex. In addition to the electron transfer, a key factor to its electride nature is the electronic structure of the CnP cage, which has its lowest unoccupied molecular orbital located in the void adjacent to the N-H groups at the back of the bowl-shaped CnP cage.

Electron Density Analysis of SARS-CoV-2 RNA-Dependent RNA Polymerase Complexes.

The work is devoted to the study of the complementarity of the electronic structures of the ligands and SARS-CoV-2 RNA-dependent RNA polymerase. The research methodology was based on determining of 3D maps of electron densities of complexes using an original quantum free-orbital AlteQ approach. We observed a positive relationship between the parameters of the electronic structure of the enzyme and ligands. A complementarity factor of the enzyme-ligand complexes has been proposed. The console applications of the AlteQ complementarity assessment for Windows and Linux (alteq_map_enzyme_ligand_4_win.exe and alteq_map_enzyme_ligand_4_linux) are available for free at the ChemoSophia webpage.

Electron density analysis of CDK complexes using the AlteQ method.

Background: A principle of complementarity is a well-established concept in chemistry and biology. This concept is based on the overlap of electron clouds of the molecules in question. Materials & methods: In this article, one such approach (an in-house developed quantum free-orbital AlteQ method) was used to evaluate the complementarity of 51 CDK-ligand complexes. Results: A significant universally applicable correlation (adjusted R2 = 0.9749; p < 2.2 × 10-16) relating the product of ligand and enzyme electron densities to the product of distances between the contacting atomic centers and the type of atoms involved in the interaction was found. Conclusion: The terms calculated in this article can provide a good basis for prognosis of bioactivity and scientifically based molecular docking.

Finding High-Quality Metal Ion-Centric Regions Across the Worldwide Protein Data Bank.

As the number of macromolecular structures in the worldwide Protein Data Bank (wwPDB) continues to grow rapidly, more attention is being paid to the quality of its data, especially for use in aggregated structural and dynamics analyses. In this study, we systematically analyzed 3.5 Å regions around all metal ions across all PDB entries with supporting electron density maps available from the PDB in Europe. All resulting metal ion-centric regions were evaluated with respect to four quality-control criteria involving electron density resolution, atom occupancy, symmetry atom exclusion, and regional electron density discrepancy. The resulting list of metal binding sites passing all four criteria possess high regional structural quality and should be beneficial to a wide variety of downstream analyses. This study demonstrates an approach for the pan-PDB evaluation of metal binding site structural quality with respect to underlying X-ray crystallographic experimental data represented in the available electron density maps of proteins. For non-crystallographers in particular, we hope to change the focus and discussion of structural quality from a global evaluation to a regional evaluation, since all structural entries in the wwPDB appear to have both regions of high and low structural quality.

Reversible electron transfer in organolanthanide chemistry.

This article relates the synthesis and characterization of novel heterobimetallic complexes containing a low-valent lanthanide, a tetradentate redox non-innocent ligand, viz. the 4,5,9,10-tetraazaphenanthrene, taphen ligand and transition metal fragments of PdMe2 and PtMe2. The experimental results are supported by a theoretical study. Investigation of their reduction properties allowed the formation of isostructural original heterotrimetallic complexes containing two Cp*2Yb fragments and the (taphen)MMe2 (M = Pd and Pt) motifs. These complexes are stable in non-coordinating solvent such as toluene but decompose in coordinating solvents such as thf. Investigation of the internal electron transfer shows that the taphen ligand behaves as a two-electrons reservoir but is capable of transferring back only one electron in thf. This reversible electron(s) transfer is rare in organolanthanide chemistry and show the potential interest of these complexes in reductive chemistry. Additionally, the trinuclear complexes feature odd X-ray crystal structures in which a deviation of symmetry is observed. The latter observation was studied in depth using quantum chemistry calculations highlighting the role of non-covalent weak interactions.

Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data.

Current software tools for the automated building of models for macromolecular X-ray crystal structures are capable of assembling high-quality models for ordered macromolecule and small-molecule scattering components with minimal or no user supervision. Many of these tools also incorporate robust functionality for modelling the ordered water molecules that are found in nearly all macromolecular crystal structures. However, no current tools focus on differentiating these ubiquitous water molecules from other frequently occurring multi-atom solvent species, such as sulfate, or the automated building of models for such species. PeakProbe has been developed specifically to address the need for such a tool. PeakProbe predicts likely solvent models for a given point (termed a `peak') in a structure based on analysis (`probing') of its local electron density and chemical environment. PeakProbe maps a total of 19 resolution-dependent features associated with electron density and two associated with the local chemical environment to a two-dimensional score space that is independent of resolution. Peaks are classified based on the relative frequencies with which four different classes of solvent (including water) are observed within a given region of this score space as determined by large-scale sampling of solvent models in the Protein Data Bank. Designed to classify peaks generated from difference density maxima, PeakProbe also incorporates functionality for identifying peaks associated with model errors or clusters of peaks likely to correspond to multi-atom solvent, and for the validation of existing solvent models using solvent-omit electron-density maps. When tasked with classifying peaks into one of four distinct solvent classes, PeakProbe achieves greater than 99% accuracy for both peaks derived directly from the atomic coordinates of existing solvent models and those based on difference density maxima. While the program is still under development, a fully functional version is publicly available. PeakProbe makes extensive use of cctbx libraries, and requires a PHENIX licence and an up-to-date phenix.python environment for execution.

Characterizing the sensitivity of bonds to the curvature of carbon nanotubes.

The way the bonding and reactivity of armchair carbon nanotubes depends on the curvature of the nanotube has been investigated using density functional theory. To understand the nature of the interaction between atoms in the nanotube, the Wiberg bond index, natural bond order analysis, and topological electron density analysis have been performed. All these tools confirm that the bonds in the hydrogen-capped carbon nanotubes considered here are primarily covalent. As the diameter of the nanotube decreases and its curvature increases, the covalency (bond order) decreases, a conclusion that is supported by the increase of the bond lengths and also the decrease of the electron density and the energy density along the bond paths as the curvature increases. To shed light on the orbital contribution in bond formation and the most effective interaction between donor bonding orbital and acceptor antibonding orbital, analysis of natural bond orbitals is carried out. We have observed that the higher the nanotube diameter is, the higher the energy gap.

Energetic Analysis of Conjugated Hydrocarbons Using the Interacting Quantum Atoms Method.

A number of aromatic, antiaromatic, and nonaromatic organic molecules was analyzed in terms of the contributions to the electronic energy defined in the quantum theory of atoms in molecules and the interacting quantum atoms method. Regularities were found in the exchange and electrostatic interatomic energies showing trends that are closely related to those of the delocalization indices defined in the theory. In particular, the CC interaction energies between bonded atoms allow to rationalize the energetic stabilization associated with the bond length alternation in conjugated polyenes. This approach also provides support to Clar's sextet rules devised for aromatic systems. In addition, the H⋯H bonding found in some of the aromatic molecules studied was of an attractive nature, according to the stabilizing exchange interaction between the bonded H atoms. © 2017 Wiley Periodicals, Inc.

The future of topological analysis in experimental charge-density research.

In a recent paper, Dittrich (2017) critically discussed the benefits of analysing experimental electron density within the framework of the quantum theory of atoms in molecules, often called simply the topological analysis of the charge density. The point he raised is important because it challenges the scientific production of a very active community. The question whether this kind of investigation is still sensible is intriguing and it fosters a multifaceted answer. Granted that none can predict the future of any field of science, but an alternative point of view emerges after answering three questions: Why should we investigate the electron charge (and spin) density? Is the interpretative scheme proposed by the quantum theory of atoms in molecules useful? Is an experimental charge density necessary?

Chemical bonding in excited states: Energy transfer and charge redistribution from a real space perspective.

This work provides a novel interpretation of elementary processes of photophysical relevance from the standpoint of the electron density using simple model reactions. These include excited states of H2 taken as a prototype for a covalent bond, excimer formation of He2 to analyze non-covalent interactions, charge transfer by an avoided crossing of electronic states in LiF and conical interesections involved in the intramolecular scrambling in C2 H4 . The changes of the atomic and interaction energy components along the potential energy profiles are described by the interacting quantum atoms approach and the quantum theory of atoms in molecules. Additionally, the topological analysis of one- and two-electron density functions is used to explore basic reaction mechanisms involving excited and degenerate states in connection with the virial theorem. This real space approach allows to describe these processes in a unified way, showing its versatility and utility in the study of chemical systems in excited states. © 2017 Wiley Periodicals, Inc.

Stability of noble-gas-bound SiH3⁺ clusters.

The stability of noble gas (Ng)-bound SiH3(+) clusters is explored by ab initio computations. Owing to a high positive charge (+1.53 e(-)), the Si center of SiH3(+) can bind two Ng atoms. However, the Si-Ng dissociation energy for the first Ng atom is considerably larger than that for the second one. As we go down group 18, the dissociation energy gradually increases, and the largest value is observed for the case of Rn. For NgSiH3(+) clusters, the Ar-Rn dissociation processes are endergonic at room temperature. For He and Ne, a much lower temperature is required for it to be viable. The formation of Ng2SiH3(+) clusters is also feasible, particularly for the heavier members and at low temperature. To shed light on the nature of Si-Ng bonding, natural population analysis, Wiberg bond indices computations, electron-density analysis, and energy-decomposition analysis were performed. Electron transfer from the Ng centers to the electropositive Si center occurs only to a small extent for the lighter Ng atoms and to a somewhat greater extent for the heavier analogues. The Si-Xe/Rn bonds can be termed covalent bonds, whereas the Si-He/Ne bonds are noncovalent. The Si-Ar/Kr bonds possess some degree of covalent character, as they are borderline cases. Contributions from polarization and charge transfer and exchange are key terms in forming Si-Ng bonds. We also studied the effect of substituting the H atoms of SiH3(+) by halide groups (-X) on the Ng binding ability. SiF3(+) showed enhanced Ng binding ability, whereas SiCl3(+) and SiBr3(+) showed a lower ability to bind Ng than SiH3(+). A compromise originates from the dual play of the inductive effect of the -X groups and X→Si π backbonding (p(z)-p(z) interaction).