scholarly journals The Monomer Electron Density Force Field (MEDFF): A Physically Inspired Model for Noncovalent Interactions

2016 ◽  
Vol 13 (1) ◽  
pp. 161-179 ◽  
Author(s):  
Steven Vandenbrande ◽  
Michel Waroquier ◽  
Veronique Van Speybroeck ◽  
Toon Verstraelen
Keyword(s):  
Force Field ◽  
Electron Density ◽  
Noncovalent Interactions ◽  
Density Force

Unsupervised labelling of remote sensing images based on force field clustering

2021 ◽  
pp. 1-14
Author(s):  
Zhenggang Wang ◽  
Jin Jin
Keyword(s):  
Remote Sensing ◽  
Force Field ◽  
Image Data ◽  
Model Parameters ◽  
Remote Sensing Images ◽  
Initial Cluster ◽  
Data Points ◽  
Global Optimal ◽  
Density Force

Remote sensing image segmentation provides technical support for decision making in many areas of environmental resource management. But, the quality of the remote sensing images obtained from different channels can vary considerably, and manually labeling a mass amount of image data is too expensive and Inefficiently. In this paper, we propose a point density force field clustering (PDFC) process. According to the spectral information from different ground objects, remote sensing superpixel points are divided into core and edge data points. The differences in the densities of core data points are used to form the local peak. The center of the initial cluster can be determined by the weighted density and position of the local peak. An iterative nebular clustering process is used to obtain the result, and a proposed new objective function is used to optimize the model parameters automatically to obtain the global optimal clustering solution. The proposed algorithm can cluster the area of different ground objects in remote sensing images automatically, and these categories are then labeled by humans simply.

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.

scholarly journals Noncovalent Bonds, Spectral and Thermal Properties of Substituted Thiazolo[2,3-b][1,3]thiazinium Triiodides

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 506 ◽  
Author(s):  
Irina Yushina ◽  
Natalya Tarasova ◽  
Dmitry Kim ◽  
Vladimir Sharutin ◽  
Ekaterina Bartashevich
Keyword(s):  
Electron Density ◽  
Noncovalent Interactions ◽  
Material Design ◽  
Spectroscopic Properties ◽  
Structural Features ◽  
Halogen Bonds ◽  
X Ray Diffraction ◽  
Raman Spectroscopic ◽  
Pairwise Interactions ◽  
Noncovalent Bonds

The interrelation between noncovalent bonds and physicochemical properties is in the spotlight due to the practical aspects in the field of crystalline material design. Such study requires a number of similar substances in order to reveal the effect of structural features on observed properties. For this reason, we analyzed a series of three substituted thiazolo[2,3-b][1,3]thiazinium triiodides synthesized by an iodocyclization reaction. They have been characterized with the use of X-ray diffraction, Raman spectroscopy, and thermal analysis. Various types of noncovalent interactions have been considered, and an S…I chalcogen bond type has been confirmed using the electronic criterion based on the calculated electron density and electrostatic potential. The involvement of triiodide anions in the I…I halogen and S…I chalcogen bonding is reflected in the Raman spectroscopic properties of the I–I bonds: identical bond lengths demonstrate different wave numbers of symmetric triiodide vibration and different values of electron density at bond critical points. Chalcogen and halogen bonds formed by the terminal iodine atom of triiodide anion and numerous cation…cation pairwise interactions can serve as one of the reasons for increased thermal stability and retention of iodine in the melt under heating.

scholarly journals Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4′-Bipyridine Derivatives

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4409
Author(s):  
Carlo Gatti ◽  
Alessandro Dessì ◽  
Roberto Dallocchio ◽  
Victor Mamane ◽  
Sergio Cossu ◽  
...  
Keyword(s):  
Electron Density ◽  
Electrostatic Potential ◽  
Source Function ◽  
Noncovalent Interactions ◽  
Conformational Search ◽  
Atomic Group ◽  
Group Contributions ◽  
Conformational Freedom ◽  
Molecular Patterns ◽  
The Impact

Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader–Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4′-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C–Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (VS) and by comparing and dissecting in atomic/atomic group contributions the VS maxima (VS,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way.

scholarly journals Hydrogen vs. Halogen Bonds in 1-Halo-Closo-Carboranes

Materials ◽  
2020 ◽  
Vol 13 (9) ◽  
pp. 2163 ◽  
Author(s):  
Ibon Alkorta ◽  
Jose Elguero ◽  
Josep M. Oliva-Enrich
Keyword(s):  
Electron Density ◽  
Halogen Bond ◽  
Noncovalent Interactions ◽  
Decomposition Analysis ◽  
Binding Energies ◽  
Energy Decomposition Analysis ◽  
Bond Critical Point ◽  
Total Energy Density ◽  
Comparison Of The Results ◽  
Intermolecular Distances

A theoretical study of the hydrogen bond (HB) and halogen bond (XB) complexes between 1-halo-closo-carboranes and hydrogen cyanide (NCH) as HB and XB probe has been carried out at the MP2 computational level. The energy results show that the HB complexes are more stable than the XBs for the same system, with the exception of the isoenergetic iodine derivatives. The analysis of the electron density with the quantum theory of atoms in molecules (QTAIM) shows the presence of a unique intermolecular bond critical point with the typical features of weak noncovalent interactions (small values of the electron density and positive Laplacian and total energy density). The natural energy decomposition analysis (NEDA) of the complexes shows that the HB and XB complexes are dominated by the charge-transfer and polarization terms, respectively. The work has been complemented with a search in the CSD database of analogous complexes and the comparison of the results, with those of the 1-halobenzene:NCH complexes showing smaller binding energies and larger intermolecular distances as compared to the 1-halo-closo-carboranes:NCH complexes.

Anisotropic nonadditive ab initio force field for noncovalent interactions of H2

2007 ◽  
Vol 126 (17) ◽  
pp. 174307 ◽  
Author(s):  
A. G. Donchev ◽  
N. G. Galkin ◽  
V. I. Tarasov
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Noncovalent Interactions

scholarly journals 2019-nCoV vs. SARS-CoV: Which Truly Has a Higher ACE2 Affinity? A Quantum Chemical Perspective on Virus-Receptor Noncovalent Interactions

2020 ◽  
Author(s):  
Nitai Sylvetsky
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Force Field ◽  
Quantum Chemical ◽  
Noncovalent Interactions ◽  
Van Der Waals ◽  
Noncovalent Interaction ◽  
Van Der Waals Interactions ◽  
Virus Receptor ◽  
Electronic Structure Methods

Noncovalent interaction energetics associated with ACE2 affinity differences are investigated using electronic structure methods; Our results were found to challenge previous predictions – claiming a higher affinity for 2019-nCoV compared to SARS-CoV based merely on "chemical intuition". In addition, we demonstrate that a broadly-used classical molecular dynamics force field – MMFF94 – is clearly incapable of reproducing DFT-based noncovalent interaction energetics for the systems at hand (despite being specifically parameterized for van der Waals interactions).

scholarly journals Halogen Bonding: A Halogen-Centered Noncovalent Interaction Yet to Be Understood

Inorganics ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 40 ◽  
Author(s):  
Pradeep Varadwaj ◽  
Arpita Varadwaj ◽  
Helder Marques
Keyword(s):  
Electron Density ◽  
Weak Interactions ◽  
Early Recognition ◽  
Noncovalent Interactions ◽  
Covalent Bond ◽  
Halogen Bonding ◽  
Noncovalent Interaction ◽  
Type I ◽  
Type Ii ◽  
Halogen Bonds

In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.

scholarly journals Evaluation of Electron Density Shifts in Noncovalent Interactions

2021 ◽  
Author(s):  
Iñigo Iribarren ◽  
Goar Sánchez-Sanz ◽  
Ibon Alkorta ◽  
José Elguero ◽  
Cristina Trujillo
Keyword(s):  
Electron Density ◽  
Noncovalent Interactions ◽  
Electron Density Shifts
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