The so-called "Lewis pair" is a ubiquitous phenomenon in chemistry and is often used as an intuitive construct to predict and rationalize chemical structure and behavior. Concepts from the very general Valence Shell Electron Pair Repulsion (VSEPR) model to the most esoteric reaction mechanism routinely rely on the notion that electrons tend to exist in pairs and that these pairs can be thought of as being localized to a particular region of space. It is precisely this localization that allows one to intuit how these pairs might behave, generally speaking, so that reasonable predictions may be made regarding molecular structure, intermolecular interactions, property trends, and reaction mechanisms, etc. Of course, it is rather unfortunate that the Lewis model is entirely qualitative and yields no information regarding how any specific electron pair is distributed. Here we demonstrate a novel electronic structure analysis technique that predicts and analyzes precise quantitative details about the relative and absolute distribution of individual electron pairs. This Single Electron Pair Distribution Analysis (SEPDA) reveals quantitative details about the distribution of the well-known Lewis pairs, such as how they are distributed in space and how their relative velocities change in various chemical contexts. We show that these distributions allow one to image the explicitly pairwise electronic behavior of bonds and lone pairs. We further demonstrate how this electronic behavior changes with several conditions to explore the nature of the covalent chemical bond, non-covalent interactions, bond formation, and exotic 3-center-2-electron species. It is shown that indications of the strength of bonded and non-bonded interactions may also be gleaned from such distributions and SEPDA can be used as a tool to differentiate between interaction types. We anticipate that SEPDA will be of broad utility in a wide variety of chemical contexts because it affords a very detailed, visual and intuitive analysis technique that is generally applicable.
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http://dx.doi.org/10.1021/jacs.7b08935 | DOI Listing |
Nat Commun
January 2025
State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
Planar cell polarity (PCP) is an evolutionarily conserved process for development and morphogenesis in metazoans. The well-organized polarity pattern in cells is established by the asymmetric distribution of two core protein complexes on opposite sides of the cell membrane. The Van Gogh-like (VANGL)-PRICKLE (PK) pair is one of these two key regulators; however, their structural information and detailed functions have been unclear.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Key Laboratory of Efficient Low-carbon Energy Conversion and Utilization of Jiangsu Provincial Higher Education Institutions, School of Physical Science and Technology, Suzhou University of Science and Technology, Suzhou 215009, China.
Despite the conventional view of liquid aluminum (l-Al) as a simple metal governed by the free-electron model, it exhibits unique bonding characteristics. This study uncovers a gradual transition from free electron to electride behavior in l-Al at high pressure and temperature, forming a type of two-component liquid where atomic and electride states coexist. The proportion of electride increases with pressure and temperature until reaching saturation, leading to notable changes in the pair-correlation function and coordination number of l-Al at saturation pressure.
View Article and Find Full Text PDFInorg Chem
January 2025
Department of Material and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden.
Zinc oxide (ZnO) is a semiconductor with a wide range of applications, and often the properties are modified by metal-ion doping. The distribution of dopant atoms within the ZnO crystal strongly affects the optical and magnetic properties, making it crucial to comprehend the structure down to the atomic level. Our study reveals the dopant structure and its contents in Eu-doped ZnO nanosponges with up to 20% Eu-O clusters.
View Article and Find Full Text PDFJ Phys Chem Lett
January 2025
Beijing National Laboratory for Molecular Science (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
ACS Omega
December 2024
State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry, Shaanxi University of Chinese Medicine, Xianyang 712083, China.
Due to the lower oxidation potential than natural nucleic acid bases, one-electron oxidation of DNA is usually funneled into the direction of intermediates for oxidized DNA damage like 8-oxo-7,8-dihydroadenine (8-oxoA) leading to a radical cation, which may undergo facile deprotonation. However, compared to the sophisticated studies devoted to natural bases, much less is known about the radical cation degradation behavior of an oxidized DNA base. Inspired by this, a comprehensive theoretical investigation is performed to illuminate the deprotonation of 8-oxoA radical cation (8-oxoA) in both free and encumbered context by calculating the p value and mapping the energy profiles.
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