scholarly journals Real-Space Interpretation of Interatomic Charge Transfer and Electron Exchange Effects by Combining Static and Kinetic Potentials and Associated Vector Fields

2022 ◽  
Author(s):  
Sergey A. Shteingolts ◽  
Adam I. Stash ◽  
Vladimir G. Tsirelson ◽  
Robert R. Fayzullin
Keyword(s):  
Charge Transfer ◽  
Electron Density ◽  
Vector Fields ◽  
Real Space ◽  
Electron Exchange ◽  
Gradient Force ◽  
Exchange Effect ◽  
Covalent Bonds ◽  
Lagrange Points ◽  
Ionic Bonds

Intricate behavior of one-electron potentials from the Euler equation for electron density and corresponding gradient force fields in crystals was studied. Bosonic and fermionic quantum potentials were utilized in bonding analysis as descriptors of the localization of electrons and electron pairs. Channels of locally enhanced kinetic potential and the corresponding saddle Lagrange points were found between chemically bonded atoms linked by the bond paths. Superposition of electrostatic φ_es (r) and kinetic φ_k (r) potentials and electron density ρ(r) allowed partitioning any molecules and crystals into atomic ρ- and potential-based φ-basins; the φ_k-basins explicitly account for electron exchange effect, which is missed for φ_es-ones. Phenomena of interatomic charge transfer and related electron exchange were explained in terms of space gaps between ρ- and φ-zero-flux surfaces. The gap between φ_es- and ρ-basins represents the charge transfer, while the gap between φ_k- and ρ-basins is proposed to be a real-space manifestation of sharing the transferred electrons. The position of φ_k-boundary between φ_es- and ρ-ones within an electron occupier atom determines the extent of electron sharing. The stronger an H‧‧‧O hydrogen bond is, the deeper hydrogen atom’s φ_k-basin penetrates oxygen atom’s ρ-basin. For covalent bonds, a φ_k-boundary closely approaches a φ_es-one indicating almost complete sharing the transferred electrons, while for ionic bonds, the same region corresponds to electron pairing within the ρ-basin of an electron occupier atom.

Charge Transfer via the Dative N−B Bond and Dihydrogen Contacts. Experimental and Theoretical Electron Density Studies of Four Deltahedral Boranes

2011 ◽  
Vol 115 (8) ◽  
pp. 1385-1395 ◽  
Author(s):  
Stefan Mebs ◽  
Roman Kalinowski ◽  
Simon Grabowsky ◽  
Diana Förster ◽  
Rainer Kickbusch ◽  
...  
Keyword(s):  
Charge Transfer ◽  
Electron Density

scholarly journals Rationalizing the diverse reactivity of [1.1.1]propellane through sigma-pi-delocalization

2020 ◽  
Author(s):  
Alistair Sterling ◽  
Alexander Durr ◽  
Russell C. Smith ◽  
Edward Anderson ◽  
Fernanda Duarte
Keyword(s):  
Charge Transfer ◽  
Electron Density ◽  
Computational Study ◽  
Unified Framework ◽  
Delocalized Electron ◽  
Materials Research ◽  
Pauli Repulsion ◽  
Opening Up

<p>[1.1.1]Propellane has gained increased attention due to its utility as a precursor to bicyclo[1.1.1]pentanes (BCPs) – motifs of high value in pharmaceutical and materials research – by addition of nucleophiles, radicals and electrophiles across its inter-bridgehead C–C bond. However, the origin of this broad reactivity profile is not well-understood. Here, we present a comprehensive computational study that attributes the omniphilicity of [1.1.1]propellane to a moldable, delocalized electron density, characterized by the mixing of the inter-bridgehead C–C bonding and antibonding orbitals. Reactions with anions and radicals are facilitated by stabilization of the adducts through sigma-pi-delocalization of electron density over the cage, while reactions with cations involve charge transfer that relieves Pauli repulsion inside the cage. These results provide a unified framework to rationalize propellane reactivity, opening up opportunities for the exploration of new chemistry of [1.1.1]propellane and related strained systems. </p>

On the transfer of theoretical multipole parameters for restoring static electron density and revealing and treating atomic anharmonic motion. Features of chemical bonding in crystals of an isocyanuric acid derivative

2021 ◽  
Vol 77 (6) ◽  
Author(s):  
Sergey A. Shteingolts ◽  
Julia K. Voronina ◽  
Liliya F. Saifina ◽  
Marina M. Shulaeva ◽  
Vyacheslav E. Semenov ◽  
...  
Keyword(s):  
Electron Density ◽  
Acid Derivative ◽  
Noncovalent Interactions ◽  
Initial Guess ◽  
Atomic Motion ◽  
Total Probability ◽  
Electronic Temperature ◽  
Covalent Bonds ◽  
Isocyanuric Acid ◽  
Static Electron

The crystal and electronic structure of an isocyanuric acid derivative was studied by high-resolution single-crystal X-ray diffraction within the Hansen–Coppens multipole formalism. The observed deformation electron density shows signs of thermal smearing. The experimental picture meaningfully assigned to the consequences of unmodelled anharmonic atomic motion. Straightforward simultaneous refinement of all parameters, including Gram–Charlier coefficients, resulted in more significant distortion of apparent static electron density, even though the residual density became significantly flatter and more featureless. Further, the method of transferring multipole parameters from the model refined against theoretical structure factors as an initial guess was employed, followed by the subsequent block refinement of Gram–Charlier coefficients and the other parameters. This procedure allowed us to appropriately distinguish static electron density from the contaminant smearing effects of insufficiently accounted atomic motion. In particular, some covalent bonds and the weak π...π interaction between isocyanurate moieties were studied via the mutual penetration of atomic-like kinetic and electrostatic potential φ-basins with complementary atomic ρ-basins. Further, local electronic temperature was applied as an advanced descriptor for both covalent bonds and noncovalent interactions. Total probability density function (PDF) of nuclear displacement showed virtually no negative regions close to and around the atomic nuclei. The distribution of anharmonic PDF to a certain extent matched the residual electron density from the multipole model before anharmonic refinement. No signs of disordering of the sulfonyl group hidden in the modelled anharmonic motion were found in the PDF.

First-Principles Study of Ag3Sn, AgZn3 and Ag5Zn8 Intermetallic Compounds

2021 ◽  
Vol 871 ◽  
pp. 254-263
Author(s):  
Zhan Cheng ◽  
Guan Xing Zhang ◽  
Wei Min Long ◽  
Svitlana Maksymova ◽  
Jian Xiu Liu
Keyword(s):  
First Principles ◽  
Density Functional ◽  
Elastic Anisotropy ◽  
Constant Density ◽  
Mulliken Population ◽  
Covalent Bonds ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Anisotropy Index ◽  
Ionic Bonds

The first-principles calculations by CASTEP program based on the density functional theory is applied to calculate the cohesive energy, enthalpy of formation, elastic constant, density of states and Mulliken population of Ag3Sn、AgZn3 and Ag5Zn8. Furthermore, the elastic properties, bonding characteristics, and intrinsic connections of different phases are investigated. The results show that Ag3Sn、AgZn3 and Ag5Zn8 have stability structural, plasticity characteristics and different degrees of elastic anisotropy; Ag3Sn is the most stable structural, has the strongest alloying ability and the best plasticity. AgZn3 is the most unstable structure, has the worst plasticity; The strength of Ag5Zn8 is strongest, AgZn3 has the weakest strength, the largest shear resistance, and the highest hardness. Ag5Zn8 has the maximum Anisotropy index and Ag3Sn has the minimum Anisotropy index. Ag3Sn、AgZn3 and Ag5Zn8 are all have covalent bonds and ionic bonds, the ionic bonds decrease in the order Ag3Sn>Ag5Zn8>AgZn3 and covalent bonds decreases in the order Ag5Zn8>Ag3Sn>AgZn3.

Charge Transfer Complexes of N-Arylcarbamates with π-Acceptors

1987 ◽  
Vol 42 (3) ◽  
pp. 284-288 ◽  
Author(s):  
Aboul-fetouh E. Mourad
Keyword(s):  
Charge Transfer ◽  
Electron Density ◽  
Nmr Spectra ◽  
Charge Transfer Complexes ◽  
H Nmr ◽  
Ct Complexes

The charge-transfer (CT) complexes of some N-arylcarbamates as donors with a number of π-acceptors have been studied spectrophotometrically. The Lewis basicities of the N-arylcarbamates as well as the types of interactions are discussed. The 1H-NMR spectra of some CT complexes with both 2,3-dichloro-5,6-dicyanobenzoquinone (DDQ) and 7,7,8,8 tetracyanoquinodimethane (TCNQ) indicate a decrease of the electron density on the donor part of the complex.

Structure and electron density of oxysulfide Sm2Ti2S2O4.9, a visible-light-responsive photocatalyst

2008 ◽  
Vol 64 (3) ◽  
pp. 291-298 ◽  
Author(s):  
Masatomo Yashima ◽  
Kiyonori Ogisu ◽  
Kazunari Domen
Keyword(s):  
Dft Calculations ◽  
Visible Light ◽  
Valence Band ◽  
Electron Density ◽  
Diffraction Data ◽  
Density Functional ◽  
Oxygen Deficiency ◽  
Covalent Bonds ◽  
Synchrotron Powder Diffraction ◽  
Visible Wavelengths

We report the crystal structure and electron density of samarium titanium oxysulfide, Sm2Ti2S2O4.9, photocatalyst obtained through the Rietveld analysis, maximum-entropy method (MEM) and MEM-based pattern fitting of the high-resolution synchrotron powder diffraction data taken at 298.7 K. The Sm2Ti2S2O4.9 has a tetragonal structure with the space group I4/mmm. Refined occupancy factors at the `equatorial' O1 and `apical' O2 sites were 0.994 (3) and 0.944 (12), respectively, which strongly suggest oxygen deficiency at the O2 site. Electron-density analyses based on the synchrotron diffraction data of Sm2Ti2S2O4.9 in combination with density-functional theory (DFT) calculations of stoichiometric Sm2Ti2S2O5 reveal covalent bonds between Ti and O atoms, while the Sm and S atoms are more ionic. The presence of S 3p and O 2p orbitals results in increased dispersion of the valence band, raising the top of the valence band and making the material active at visible wavelengths. The present DFT calculations of stoichiometric Sm2Ti2S2O5 indicate the possibility of overall splitting of water, although Sm2Ti2S2O4.9 works as a visible-light-responsive photocatalyst in aqueous solutions only in the presence of sacrificial electron donors or acceptors. The oxygen deficiency and cocatalyst seem to be factors affecting the catalytic activity.

scholarly journals How Far Can One Push the Noble Gases Towards Bonding?: A Personal Account

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2933 ◽  
Author(s):  
Ranajit Saha ◽  
Gourhari Jana ◽  
Sudip Pan ◽  
Gabriel Merino ◽  
Pratim Kumar Chattaraj
Keyword(s):  
Electron Density ◽  
High Pressures ◽  
Noble Gases ◽  
Activation Barrier ◽  
Covalent Bond ◽  
The Other ◽  
Personal Account ◽  
Covalent Bonds ◽  
Other Hand ◽  
Different Types

Noble gases (Ngs) are the least reactive elements in the periodic table towards chemical bond formation when compared with other elements because of their completely filled valence electronic configuration. Very often, extreme conditions like low temperatures, high pressures and very reactive reagents are required for them to form meaningful chemical bonds with other elements. In this personal account, we summarize our works to date on Ng complexes where we attempted to theoretically predict viable Ng complexes having strong bonding to synthesize them under close to ambient conditions. Our works cover three different types of Ng complexes, viz., non-insertion of NgXY type, insertion of XNgY type and Ng encapsulated cage complexes where X and Y can represent any atom or group of atoms. While the first category of Ng complexes can be thermochemically stable at a certain temperature depending on the strength of the Ng-X bond, the latter two categories are kinetically stable, and therefore, their viability and the corresponding conditions depend on the size of the activation barrier associated with the release of Ng atom(s). Our major focus was devoted to understand the bonding situation in these complexes by employing the available state-of-the-art theoretic tools like natural bond orbital, electron density, and energy decomposition analyses in combination with the natural orbital for chemical valence theory. Intriguingly, these three types of complexes represent three different types of bonding scenarios. In NgXY, the strength of the donor-acceptor Ng→XY interaction depends on the polarizing power of binding the X center to draw the rather rigid electron density of Ng towards itself, and sometimes involvement of such orbitals becomes large enough, particularly for heavier Ng elements, to consider them as covalent bonds. On the other hand, in most of the XNgY cases, Ng forms an electron-shared covalent bond with X while interacting electrostatically with Y representing itself as [XNg]+Y−. Nevertheless, in some of the rare cases like NCNgNSi, both the C-Ng and Ng-N bonds can be represented as electron-shared covalent bonds. On the other hand, a cage host is an excellent moiety to examine the limits that can be pushed to attain bonding between two Ng atoms (even for He) at high pressure. The confinement effect by a small cage-like B12N12 can even induce some covalent interaction within two He atoms in the He2@B12N12 complex.

scholarly journals A theoretical-electron-density databank using a model of real and virtual spherical atoms

2017 ◽  
Vol 73 (4) ◽  
pp. 610-625 ◽  
Author(s):  
Ayoub Nassour ◽  
Slawomir Domagala ◽  
Benoit Guillot ◽  
Theo Leduc ◽  
Claude Lecomte ◽  
...  
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Density Functional ◽  
Lone Pair ◽  
Density Functional Theory Calculations ◽  
Ligand Complex ◽  
Urea Molecule ◽  
Covalent Bonds ◽  
Similar Chemical ◽  
Chemical Groups

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

Validation of carbohydrate structures: not just nomenclature

2014 ◽  
Vol 70 (a1) ◽  
pp. C1481-C1481
Author(s):  
Jon Agirre ◽  
Kevin Cowtan
Keyword(s):  
Protein Data Bank ◽  
Correlation Coefficient ◽  
Electron Density ◽  
Systematic Study ◽  
Data Bank ◽  
Real Space ◽  
Space Correlation ◽  
Structure Factors ◽  
Ring Distortion ◽  
Experimental Electron Density

Despite the key implications carbohydrates have in a multitude of pathological processes, a large number of the sugar-containing structures deposited into the Protein Data Bank (PDB) show nomenclature errors [1] that persist even after the remediation of the PDB archive [2]. Here we present the results from a systematic study of the conformation and ring distortion of cyclic carbohydrate models for which structure factors have been deposited into the PDB. These models have also been scored using a real-space correlation coefficient calculated between model and experimental electron density. The results have enabled us to produce a database of well-refined carbohydrate structures for use in the framework of an automated sugar-detecting software, to be announced shortly.

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