MANY-ATOM VAN DER WAALS INTERACTIONS LEAD TO DIRECTION-SENSITIVE INTERACTIONS OF COVALENT BONDS

2008 ◽  
Vol 06 (04) ◽  
pp. 693-707 ◽  
Author(s):  
ALEXEI V. FINKELSTEIN ◽  
MICHAEL Y. LOBANOV ◽  
NIKITA V. DOVIDCHENKO ◽  
NATALIA S. BOGATYREVA
Keyword(s):  
Physical Theory ◽  
Van Der Waals ◽  
Protein Structures ◽  
Covalent Bond ◽  
Covalent Bonding ◽  
Van Der Waals Interactions ◽  
Binding Affinities ◽  
Dispersion Interactions ◽  
Energy Effect ◽  
Covalent Bonds

Strict physical theory and numerical calculations show that a specific coupling of many-atom van der Waals interactions with covalent bonding can significantly (half as much) increase the strength of attractive dispersion interactions when the direction of interaction coincides with the direction of the covalent bond, and decrease this strength when the direction of interaction is perpendicular to the direction of the covalent bond. The energy effect is comparable to that caused by the replacement of atoms (e.g. N by C or O ) in conventional pairwise van der Waals interactions. Analysis of protein structures shows that they bear an imprint of this effect. This means that many-atom van der Waals interactions cannot be ignored in refinement of protein structures, in simulations of their folding, and in prediction of their binding affinities.

scholarly journals Theory and practice of modeling van der Waals interactions in electronic-structure calculations

2019 ◽  
Vol 48 (15) ◽  
pp. 4118-4154 ◽  
Author(s):  
Martin Stöhr ◽  
Troy Van Voorhis ◽  
Alexandre Tkatchenko
Keyword(s):  
Electronic Structure ◽  
Computational Modeling ◽  
State Of The Art ◽  
Van Der Waals ◽  
Electronic Structure Calculations ◽  
Black Box ◽  
Theory And Practice ◽  
Van Der Waals Interactions ◽  
Dispersion Interactions ◽  
Structure Calculations

Opening the black box of van der Waals-inclusive electronic structure calculations: a tutorial-style introduction to van der Waals dispersion interactions, state-of-the-art methods in computational modeling and complementary experimental techniques.

Photo-induced Contraction of Layered Materials

MRS Advances ◽  
2018 ◽  
Vol 3 (6-7) ◽  
pp. 333-338
Author(s):  
Hiroyuki Kumazoe ◽  
Aravind Krishnamoorthy ◽  
Lindsay Bassman ◽  
Fuyuki Shimojo ◽  
Rajiv K. Kalia ◽  
...  
Keyword(s):  
Van Der Waals ◽  
Optical Excitation ◽  
Layered Materials ◽  
Van Der Waals Interactions ◽  
Electronic Charge ◽  
Quantum Molecular Dynamics ◽  
Covalent Bonds ◽  
Coulombic Interactions ◽  
Hydrogen Bond Interactions ◽  
The Impact

ABSTRACTUltrafast atomic dynamics induced by electronic and optical excitation opens new possibilities for functionalization of two-dimensional and layered materials. Understanding the impact of perturbed valence band populations on both the strong covalent bonds and relatively weaker van der Waals interactions is important for these anisotropic systems. While the dynamics of strong covalent bonds has been explored both experimentally and theoretically, relatively fewer studies have focused on the impact of excitation on weak bonds like van der Waals and hydrogen-bond interactions. We perform non-adiabatic quantum molecular dynamics (NAQMD) simulations to study photo-induced dynamics in MoS2 bilayer. We observe photo-induced non-thermal contraction of the interlayer distance in the MoS2 bilayer within 100 femtoseconds after photoexcitation. We identify a large photo-induced redistribution of electronic charge density, whose Coulombic interactions could explain the observed inter-layer contraction.

A Comparative Study of Un-Modified and Modified Acrylate-SiO2 Nanocomposites

MRS Advances ◽  
2017 ◽  
Vol 2 (49) ◽  
pp. 2737-2743
Author(s):  
Mireya L. Hernández-Vargas ◽  
Rubén Castillo-Perez ◽  
Oscar Hernández-Guerrero ◽  
Bernardo F. Campillo-Illanes ◽  
Osvaldo Flores-Cedillo
Keyword(s):  
Physical Properties ◽  
Van Der Waals ◽  
Chemical Properties ◽  
Class Ii ◽  
Decomposition Temperature ◽  
Van Der Waals Interactions ◽  
Class I ◽  
Covalent Bonds ◽  
Neat Polymer ◽  
Hybrid Compounds

ABSTRACTBased on the nature of the links and interactions existing at the hybrid interface, hybrid materials can be broadly classified in two main designations: a) Hybrid compounds Class I, that include all systems with electrostatic forces, hydrogen bonding or Van der Waals interactions and b) Hybrid compounds Class II, showing that the inorganic and organic components are linked through strong covalent or ionic-covalent bonds. The physico–chemical properties of nanostructured copolymer acrylates based on butyl acrylate (BA), methyl methacrylate (MMA) and acrylic acid (AA) has been investigated employing un-modified SiO2 (Class I) and modified SiO2 particles (Class II) using 3-(trimethoxysilyl) propyl methacrylate (MPS) as compatibilizing agent. The synthesis was carried out using seeded batch emulsion polymerization system. Metastable nanostructured emulsions containing 1 wt% nanoparticles were obtained. Films casted from the in-situ nanostructured latex exhibited excellent optical transparency suggesting good nanoparticles dispersion. However, the mechanical properties showed by SiO2-MPS nanocomposite, are better than the Class I hybrid compounds. Therefore, SiO2-MPS surface treatment prior to polymerization enhances the physical properties of copolymer BA-MMA-AA film. The mass loss derivative traces for the polyacrylic nanocomposites and the neat polymer obtained by thermogravimetric analysis showed that the onset temperature for thermal decomposition was shifted towards a higher temperature than the neat polyacrylic, indicating the enhancement of thermal stability of the un-modified SiO2 nanocomposite. However, there is a decrease of 40°C in the decomposition temperature for the modified polyacrylic nanocomposite. The results obtained so far have shown that weak Van der Waals and H-bonding interactions may be sufficient to enable improvement of the physical properties of the acrylate nanocomposites.

scholarly journals Effect of van der Waals interactions on the adhesion strength at the interface of the hydroxyapatite–titanium biocomposite: a first-principles study

RSC Advances ◽  
2020 ◽  
Vol 10 (62) ◽  
pp. 37800-37805
Author(s):  
Irina Yu. Grubova ◽  
Maria A. Surmeneva ◽  
Roman A. Surmenev ◽  
Erik C. Neyts
Keyword(s):  
Adhesion Strength ◽  
Significant Role ◽  
First Principles ◽  
Bonding Strength ◽  
Van Der Waals ◽  
Molecular Simulations ◽  
Van Der Waals Interactions ◽  
Hydroxyapatite Coating ◽  
Dispersion Interactions ◽  
First Principles Study

Dispersion interactions play a significant role in altering the bonding strength of the hydroxyapatite coating to the substrate, and such interactions is critical in molecular simulations.

scholarly journals How anisotropic and isotropic atomic displacement parameters monitor protein covalent bonds rigidity: isotropic B-factors underestimate bond rigidity

Amino Acids ◽  
2021 ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Protein Structures ◽  
Covalent Bond ◽  
Atomic Displacement ◽  
High Quality ◽  
Covalent Bonds ◽  
The Mean ◽  
The Difference ◽  
Atomic Displacement Parameters ◽  
Protein Covalent ◽  
Better Than

AbstractUnder the assumption that covalent bonds are rigid, it is possible to compare the estimations of rigidity based on anisotropic and isotropic B-factors. This is done by computing the difference of the mean-square displacements (Delta-u) of atoms A and Z along the covalent bond A–Z, which must be close to zero for a rigid bond. The analysis of a high-quality set of protein structures, refined at a resolution better than (or equal to) 0.8 Angstroms, showed that Delta-u is significantly close to zero when anisotropic B-factors are used, with an average 60% Delta-u reduction. This reduction is larger for larger B-factors and this suggests that care should be taken in data-mining procedures that involve isotropic B-factors, especially at lower resolution, when anisotropic B-factors cannot be determined and when the average B-factor increases.

scholarly journals Covalent Inhibition of SARS-CoV-2 RBD-ACE2 Interaction by Aptamers with Multiple Sulfur(VI) Fluoride Exchange Modifications

2021 ◽  
Author(s):  
Zichen Qin ◽  
Yiying Zhu ◽  
Yu Xiang
Keyword(s):  
Human Serum ◽  
Covalent Bond ◽  
Covalent Bonding ◽  
Peptide Fragmentation ◽  
Host Cells ◽  
Great Promise ◽  
Enzyme Linked Immunosorbent Assay ◽  
Covalent Bonds ◽  
Target Proteins ◽  
Covalent Inhibitors

The SARS-CoV-2 spike protein uses its receptor-binding domain (RBD) to interact with the angiotensin-converting enzyme 2 (ACE2) receptor on host cells, establishing the first step of SARS-CoV-2 infection. Inhibitors of RBD-ACE2 interaction, therefore, have shown great promise in preventing SARS-CoV-2 infection. Currently known RBD-ACE2 inhibitors are all based on reversible binding and must compete with ACE2 or RBD at the equilibrium. On the other hand, covalent inhibitors, such as those based on sulfur(VI) fluoride exchange (SuFEx) chemistry, can form irreversible chemical bonds with target proteins and offer advantages including higher potency and longer duration of inhibition. Here, we report covalent aptamer inhibitors that can block RBD-ACE2 by forming covalent bonds with RBD. These covalent aptamer inhibitors were developed by equipping known RBD aptamers with multiple SuFEx (mSuFEx) modifications. The mSuFEx-aptamer 6C3-7SF underwent strong covalent bonding with RBD and some of its variants at fast rates (t1/2 = 20 ~ 29 min−1) and induced more efficient RBD-ACE2 inhibition (IC50 = 26 ~ 37 nM) than the original aptamer (IC50 > 200 nM) according to an in vitro enzyme-linked immunosorbent assay (ELISA). The covalent bond formation was highly selective to RBD over human serum albumin (HSA) and ACE2, and could occur efficiently in diluted human serum. Peptide fragmentation analyses of the RBD-6C3-7SF adducts revealed multiple sites of covalent bonding on RBD, including K378, R408, Y422, Y424, Y453, and K458. The surprising R408 suggests that context-specific non-N-terminal arginine could be a new type of targetable residue by SuFEx-based covalent inhibitors, which were never reported as reactive with any non-N-terminal arginine in target proteins. In addition, RBD R408 is responsible for binding with ACE2 N90 glycan, and this arginine is conserved in SARS-CoV-2 variants of concern or interest, suggesting that R408 could be the potential site of interest for developing SuFEx-based covalent inhibitors against threatening SARS-CoV-2 variants. Although the compatibility of mSuFEx-based covalent aptamers in cellular and in vivo systems should be further investigated, our study demonstrated the promise of mSuFEx chemistry in constructing potent covalent aptamers to inhibit important protein-protein interactions (PPIs).

Conceptual integration of covalent bond models by Algerian students

2014 ◽  
Vol 15 (4) ◽  
pp. 675-688 ◽  
Author(s):  
Hazzi Salah ◽  
Alain Dumon
Keyword(s):  
Covalent Bond ◽  
Covalent Bonding ◽  
Quantum Model ◽  
Covalent Bonds ◽  
Conceptual Integration ◽  
Knowledge Framework ◽  
Chemistry Learning ◽  
Valence Electrons ◽  
Lewis Structures ◽  
Hybrid Orbitals

The concept of covalent bonding is characterized by an interconnected knowledge framework based on Lewis and quantum models of atoms and molecules. Several research studies have shown that students at all levels of chemistry learning find the quantum model to be one of the most difficult subjects to understand. We have tried in this paper to analyze the extent to which Algerian students, at the end of their training, have integrated the covalent bonding theories based on the quantum model of atom theory and are able to interpret Lewis structures using the quantum model. The analysis of the responses to a written questionnaire showed that this integration was not achieved by our students and that they are not able to correctly describe covalent bonds in a Lewis structure using the concepts of the quantum model. They have a “quantum box” conception of atomic or hybrid orbitals. This conception acts as a “pedagogical learning impediment” to the integration of the geometrical representations of atomic and hybrid orbitals, the conditions of their overlapping to give bonds and consequently the description of covalent bonds using the quantum model. So, the students use an alternative conceptual framework based on the use of Lewis model paired valence electrons to form covalent bonds that we have named the: “electrons pair framework”. Furthermore, the students restricted the denomination of a covalent bond to the sharing of one electron (either s or p but not spn) from each atom to give one “electron pair σ”, and thought that σ bonds are only formed in single bonds.

scholarly journals Highly Stable Nanoparticle Supercrystals Formed by Aldol Reaction in Conjunction with Slow Solvent Evaporation

2020 ◽  
Author(s):  
Jiwhan Kim ◽  
Jahar Dey ◽  
Aminah Umar ◽  
Jae-Min Ha ◽  
Sang-Jo Lee ◽  
...  
Keyword(s):  
Structural Stability ◽  
Aldol Reaction ◽  
Three Dimensional ◽  
Covalent Bond ◽  
Intermolecular Forces ◽  
Particle Dispersion ◽  
Solvent Evaporation ◽  
Van Der Waals Interactions ◽  
Emergent Properties ◽  
Covalent Bonds

Abstract The nanoparticle supercrystals (NPSCs) have been of great interests for their collective emergent properties. While various NPSCs have been successfully fabricated using intermolecular forces, the limited structural stability of NPSCs due to the weak nature of the intermolecular forces still remains a major hurdle for practical applications. Herein, we report a new method to fabricate highly stable three-dimensional NPSCs by using aldol reaction, a model covalent bond forming reaction, in conjunction with slow solvent evaporation. Gold nanoparticles functionalized with thiol poly-ethylene glycol formyl are linked to each other by carbon-carbon covalent bonds formed by aldol reaction as the particle dispersion in aqueous NaOH solution is slowly evaporated, resulting in highly faceted three-dimensional NPSCs. As-synthesized NPSCs show excellent structural stability in solvents of different polartities as well as the dried condition and at temperature up to 160 °C, which is far superior to NPSCs stabilized by intermolecular forces such as hydrogen bonding and van der Waals interactions. The new covalent bonding appraoch opens up new opportunities in the synthesis of NPSCs and their applications.

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