The Molecular Electrostatic Potential: A Tool for Understanding and Predicting Molecular Interactions

1998 ◽  
Author(s):  
Jane S. Murray ◽  
Peter Politzer
Keyword(s):  
Physical Properties ◽  
Density Function ◽  
Molecular Interactions ◽  
Electrostatic Potential ◽  
Chemical Species ◽  
Quantitative Measure ◽  
Theoretical Chemistry ◽  
Electronic Density ◽  
Reactive Behavior ◽  
Improved Methods

The quest for improved methods for elucidating and predicting the reactive behavior of molecules and other chemical species is a continuing theme of theoretical chemistry. This has led to the introduction of a variety of indices of reactivity; some are rather arbitrary, while others are more or less directly related to real physical properties. They have been designed and are used to provide some quantitative measure of the chemical activities of various sites and/or regions of the molecule. In this chapter our focus is on one of these indices, the electrostatic potential V(r) that is created in the space around a molecule by its nuclei and electrons. V(r) can be computed rigorously, given the electronic density function ρ(r), by Eq. (3.1).

scholarly journals Current Research on Polyelectrolyte Nanostructures: From Molecular Interactions to Biomedical Applications

Macromol ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 155-172
Author(s):  
Aristeidis Papagiannopoulos
Keyword(s):  
Physical Properties ◽  
Molecular Interactions ◽  
Interdisciplinary Research ◽  
Biomedical Applications ◽  
Electrostatic Interactions ◽  
Soft Matter ◽  
Extracellular Polysaccharides ◽  
Polymer Science ◽  
Biological Matter ◽  
Biomedical Field

Polyelectrolytes have been at the center of interdisciplinary research for many decades. In the field of polymer science and soft matter, they have provided the dimensions of electrostatic interactions, which opens a vast variety of opportunities for new physical properties and applications. In biological matter, polyelectrolytes are present in many forms, from extracellular polysaccharides to complex DNA molecules and proteins. This review discusses the recent research on polyelectrolytes covering the fundamental level of their conformations and nanostructures, their molecular interactions with materials that have close relevance to bioapplications and their applications in the biomedical field. This approach is motivated by the fact that the polyelectrolyte research is constantly active in all the aforementioned levels and continually affects many critical scientific areas.

scholarly journals σ-Holes vs. Buildups of Electronic Density on the Extensions of Bonds to Halogen Atoms

Inorganics ◽  
2019 ◽  
Vol 7 (6) ◽  
pp. 71 ◽  
Author(s):  
Peter Politzer ◽  
Jane S. Murray
Keyword(s):  
Electrostatic Potential ◽  
Local Minimum ◽  
Halogen Atom ◽  
Local Maximum ◽  
Outer Side ◽  
Electronic Density ◽  
Halogen Atoms ◽  
Positive Electrostatic Potential

Our discussion focuses upon three possible features that a bonded halogen atom may exhibit on its outer side, on the extension of the bond. These are (1) a region of lower electronic density (a σ-hole) accompanied by a positive electrostatic potential with a local maximum, (2) a region of lower electronic density (a σ-hole) accompanied by a negative electrostatic potential that also has a local maximum, and (3) a buildup of electronic density accompanied by a negative electrostatic potential that has a local minimum. In the last case, there is no σ-hole. We show that for diatomic halides and halogen-substituted hydrides, the signs and magnitudes of these maxima and minima can be expressed quite well in terms of the differences in the electronegativities of the halogen atoms and their bonding partners, and the polarizabilities of both. We suggest that the buildup of electronic density and absence of a σ-hole on the extension of the bond to the halogen may be an operational indication of ionicity.

DEPPDB — DNA ELECTROSTATIC POTENTIAL PROPERTIES DATABASE: ELECTROSTATIC PROPERTIES OF GENOME DNA ELEMENTS

2012 ◽  
Vol 10 (02) ◽  
pp. 1241004 ◽  
Author(s):  
ALEXANDER A. OSYPOV ◽  
GLEB G. KRUTININ ◽  
EUGENIA A. KRUTININA ◽  
SVETLANA G. KAMZOLOVA
Keyword(s):  
Physical Properties ◽  
Electrostatic Potential ◽  
Binding Sites ◽  
Metabolic Switch ◽  
Electrostatic Properties ◽  
Protein Dna Interactions ◽  
Dna Elements ◽  
Ncbi Refseq ◽  
Analytical Tools ◽  
Eukaryotic Genomes

Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular, related to transcription. DEPPDB — DNA Electrostatic Potential (and other Physical) Properties Database — provides information on the electrostatic and other physical properties of genome DNA combined with its sequence and annotation of biological and structural properties of genomes and their elements. Genomes are organized on taxonomical basis, supporting comparative and evolutionary studies. Currently, DEPPDB contains all completely sequenced bacterial, viral, mitochondrial, and plastids genomes according to the NCBI RefSeq, and some model eukaryotic genomes. Data for promoters, regulation sites, binding proteins, etc., are incorporated from established DBs and literature. The database is complemented by analytical tools. User sequences calculations are available. Case studies discovered electrostatics complementing DNA bending in E.coli plasmid BNT2 promoter functioning, possibly affecting host-environment metabolic switch. Transcription factors binding sites gravitate to high potential regions, confirming the electrostatics universal importance in protein–DNA interactions beyond the classical promoter–RNA polymerase recognition and regulation. Other genome elements, such as terminators, also show electrostatic peculiarities. Most intriguing are gene starts, exhibiting taxonomic correlations. The necessity of the genome electrostatic properties studies is discussed.

scholarly journals Velocity profiles of [CII], [CI], CO, and [OI] and physical conditions in four star-forming regions in the Large Magellanic Cloud

2019 ◽  
Vol 621 ◽  
pp. A62 ◽  
Author(s):  
Yoko Okada ◽  
Rolf Güsten ◽  
Miguel Angel Requena-Torres ◽  
Markus Röllig ◽  
Jürgen Stutzki ◽  
...  
Keyword(s):  
Physical Properties ◽  
High Redshift ◽  
Line Emission ◽  
Chemical Species ◽  
Large Magellanic Cloud ◽  
Magellanic Cloud ◽  
Continuum Emission ◽  
Line Profiles ◽  
Star Forming ◽  
Star Forming Regions

Aims. The aim of our study is to investigate the physical properties of the star-forming interstellar medium (ISM) in the Large Magellanic Cloud (LMC) by separating the origin of the emission lines spatially and spectrally. The LMC provides a unique local template to bridge studies in the Galaxy and high redshift galaxies because of its low metallicity and proximity, enabling us to study the detailed physics of the ISM in spatially resolved individual star-forming regions. Following Okada et al. (Okada, Y., Requena-Torres, M. A., Güsten, R., et al. 2015, A&A, 580, A54), we investigate different phases of the ISM traced by carbon-bearing species in four star-forming regions in the LMC, and model the physical properties using the KOSMA-τ PDR model. Methods. We mapped 3–13 arcmin2 areas in 30 Dor, N158, N160, and N159 along the molecular ridge of the LMC in [C II] 158 μm with GREAT on board SOFIA. We also observed the same area with CO(2-1) to (6-5), 13CO(2-1) and (3-2), [C I] 3P1–3P0 and 3P2–3P1 with APEX. For selected positions in N159 and 30 Dor, we observed [O I] 145 μm and [O I] 63 μm with upGREAT. All spectra are velocity resolved. Results. In all four star-forming regions, the line profiles of CO, 13CO, and [C I] emission are similar, being reproduced by a combination of Gaussian profiles defined by CO(3-2), whereas [C II] typically shows wider line profiles or an additional velocity component. At several positions in N159 and 30 Dor, we observed the velocity-resolved [O I] 145 and 63 μm lines for the first time. At some positions, the [O I] line profiles match those of CO, at other positions they are more similar to the [C II] profiles. We interpret the different line profiles of CO, [C II] and [O I] as contributions from spatially separated clouds and/or clouds in different physical phases, which give different line ratios depending on their physical properties. We modeled the emission from the CO, [C I], [C II], and [O I] lines and the far-infrared continuum emission using the latest KOSMA-τ PDR model, which treats the dust-related physics consistently and computes the dust continuum SED together with the line emission of the chemical species. We find that the line and continuum emissions are not well-reproduced by a single clump ensemble. Toward the CO peak at N159 W, we propose a scenario that the CO, [C II], and [O I] 63 μm emission are weaker than expected because of mutual shielding among clumps.

scholarly journals The experimental and theoretical QTAIMC study of the atomic and molecular interactions in dinitrogen tetroxide

2009 ◽  
Vol 65 (5) ◽  
pp. 647-658 ◽  
Author(s):  
Vladimir G. Tsirelson ◽  
Anastasia V. Shishkina ◽  
Adam I. Stash ◽  
Simon Parsons
Keyword(s):  
Energy Density ◽  
Potential Energy ◽  
Electron Density ◽  
Molecular Interactions ◽  
Electrostatic Potential ◽  
Correlation Energy ◽  
Three Dimensional ◽  
Geometry Optimization ◽  
Intermolecular Bond ◽  
Experimental Electron Density

The atomic and molecular interactions in a crystal of dinitrogen tetraoxide, α-N2O4, have been studied in terms of the quantum topological theory of molecular structure using high-resolution, low-temperature X-ray diffraction data. The experimental electron density and electrostatic potential have been reconstructed with the Hansen–Coppens multipole model. In addition, the three-dimensional periodic electron density of crystalline α-N2O4 has been calculated at the B3LYP/cc-pVDZ level of theory with and without the geometry optimization. The application of the quantum theory of atoms in molecules and crystals (QTAIMC) recovered the two types of intermolecular bond paths between O atoms in crystalline α-N2O4, one measuring 3.094, the other 3.116 Å. The three-dimensional distribution of the Laplacian of the electron density around the O atoms showed that the lumps in the negative Laplacian fit the holes on the O atoms in the adjacent molecules, both atoms being linked by the intermolecular bond paths. This shows that the Lewis-type molecular complementarity contributes significantly to intermolecular bonding in crystalline N2O4. Partial overlap of atomic-like basins created by zero-flux surfaces in both the electron density and the electrostatic potential show that attractive electrostatic interaction exists between O atoms even though they carry the same net formal charge. The exchange and correlation contributions to the potential energy density were also computed by means of the model functionals, which use the experimental electron density and its derivatives. It was found that the intermolecular interactions in α-N2O4 are accompanied by the correlation energy-density `bridges' lowering the local potential energy along the intermolecular O...O bond paths in the electron density, while the exchange energy density governs the shape of bounded molecules.

scholarly journals Mixing in Turbulent Flows: An Overview of Physics and Modelling

Processes ◽  
2020 ◽  
Vol 8 (11) ◽  
pp. 1379
Author(s):  
Jacek Pozorski ◽  
Marta Wacławczyk
Keyword(s):  
Density Function ◽  
Turbulent Flows ◽  
Chemical Species ◽  
Scalar Fields ◽  
Industrial Applications ◽  
Mixing Models ◽  
Computing Technology ◽  
Filtered Density Function ◽  
Eddy Simulation ◽  
Large Eddy

Turbulent flows featuring additional scalar fields, such as chemical species or temperature, are common in environmental and industrial applications. Their physics is complex because of a broad range of scales involved; hence, efficient computational approaches remain a challenge. In this paper, we present an overview of such flows (with no particular emphasis on combustion, however) and we recall the major types of micro-mixing models developed within the statistical approaches to turbulence (the probability density function approach) as well as in the large-eddy simulation context (the filtered density function). We also report on some trends in algorithm development with respect to the recent progress in computing technology.

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