scholarly journals Towards a Density-Based Description of Chemical Bonds and Noncovalent Interactions with Pauli Energy

2022 ◽  
Author(s):  
Shubin Liu ◽  
Shujing Zhong ◽  
Xin He ◽  
Siyuan Liu ◽  
Bin Wang ◽  
...  
Keyword(s):  
Strong Interaction ◽  
Theoretical Foundation ◽  
Noncovalent Interactions ◽  
Van Der Waals Forces ◽  
Noncovalent Interaction ◽  
Chemical Bonds ◽  
Interaction Index ◽  
Covalent Bonds ◽  
Covalent Interaction ◽  
Ionic Bonds

Chemical bonds and noncovalent interactions are extraordinarily important concepts in chemistry and beyond. Using density-based quantities to describe them has a long history in the literature, yet none can satisfactorily describe the entire spectrum of interactions from strong chemical bonds to weak van der Waals forces. In this work, employing Pauli energy as the theoretical foundation, we fill in that knowledge gap. Our results show that the newly established density-based index can describe single and multiple covalent bonds, ionic bonds, metallic bonds, and different kinds of noncovalent interactions, all with unique and readily identifiable signature shapes. Two new descriptors, NBI (nonbonding and bonding identification) index and USI (ultra-strong interaction) index, have been introduced in this work. Together with NCI (noncovalent interaction) and SCI (strong covalent interaction) indexes already available in the literature, a density-based description of both chemical bonds and noncovalent interactions is accomplished.

Towards a predictive model for polymer solubility using the noncovalent interaction index: polyethylene as a case study

2021 ◽  
Author(s):  
Mats Denayer ◽  
Jelle Vekeman ◽  
Frederik Tielens ◽  
Frank De Proft
Keyword(s):  
Predictive Model ◽  
Noncovalent Interaction ◽  
Intramolecular Interactions ◽  
Interaction Index ◽  
Covalent Interaction ◽  
Polymer Solubility

A novel solubility descriptor is presented based on the non-covalent interaction index, providing information on the solute’s inter- and intramolecular interactions, and its conformation. Polyethylene in (anti)solvent is used as a case-study.

scholarly journals First principle study of occupancy, bonding characteristics and alloying effect of Zr, Nb, V in bulk γ-Fe(C)

2020 ◽  
Vol 213 ◽  
pp. 01019
Author(s):  
Fei Liu ◽  
Shan Cong ◽  
Long Hao
Keyword(s):  
Solid Solution ◽  
Covalent Bond ◽  
Alloy Element ◽  
Chemical Bonds ◽  
Covalent Bonds ◽  
Binding Characteristics ◽  
Crystal Cell ◽  
Ionic Bonds ◽  
Crystal Cells ◽  
Bonding Characteristics

The total energy, binding characteristics, density of states, charge distribution and differential charge density of γ-Fe(C)-M crystal cells formed by solid solution of Zr, Nb and V in γ-Fe(C) were calculated by using the first-principles method. Thus, the mechanism of Zr, Nb, and V with γ-Fe(C) was investigated in this paper. The results show that Zr, Nb and V all preferentially replaced the Fe atoms which are at the top angle in γ-Fe(C). Crystal cell reaches its highest stability after V solid solution. Nb reaches after it, and Zr is relatively weak. In the γ-Fe(C)-Zr cell, Fe-Zr covalent bond and Zr-C ionic bond are the main chemical bonds. In the γ-Fe(C)-Nb and γ-Fe(C)-V cells, Fe-Nb and Fe-V covalent bonds are the main chemical bonds with a number of Nb-C and V-C ionic bonds. After solid solution, the electron cloud density around C atom changed little, while Fe atom changed obviously. The orbital electrons around Fe atoms in γFe(C)-V has maximal distribution, which means that the electrons delocalized most and most of the electrons are bonding. It is the main factor for the increase in the binding energy of crystal cell. The effects of Zr, Nb, V solution on austenitic stability are investigated by studying the influence of alloy element on γFe(C) electronic structure.

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.

scholarly journals Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 4979
Author(s):  
Marco Giampà ◽  
Elvira Sgobba
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Noncovalent Interactions ◽  
Conformational Dynamics ◽  
High Sensitivity ◽  
Maldi Mass Spectrometry ◽  
Noncovalent Interaction ◽  
Ionization Mass ◽  
Label Free

Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.

scholarly journals Automated Nano-Electrospray Mass Spectrometry for Protein-Ligand Screening by Noncovalent Interaction Applied to Human H-FABP and A-FABP

2003 ◽  
Vol 8 (3) ◽  
pp. 247-256 ◽  
Author(s):  
Kurt Benkestock ◽  
Colleen K. Van Pelt ◽  
Tomas Åkerud ◽  
Alistair Sterling ◽  
Per-Olof Edlund ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Fatty Acid Binding Protein ◽  
Noncovalent Interactions ◽  
Screening Method ◽  
Noncovalent Interaction ◽  
Ionization Mass ◽  
Fatty Acid Binding ◽  
Natural Ligand ◽  
Ligand Screening ◽  
High Throughput Screens

A method for ligand screening by automated nano-electrospray ionization mass spectrometry (nano-ESI/MS) is described. The core of the system consisted of a chip-based platform for automated sample delivery from a 96-well plate and subsequent analysis based on noncovalent interactions. Human fatty acid binding protein, H-FABP (heart) and A-FABP (adipose), with small potential ligands was analyzed. The technique has been compared with a previously reported method based on nuclear magnetic resonance (NMR), and excellent coorelation with the found hits was obtained. In the current MS screening method, the cycle time per sample was 1.1 min, which is approximately 50 times faster than NMR for single compounds and approximately 5 times faster for compound mixtures. High reproducibility was achieved, and the protein consumption was in the range of 88 to 100 picomoles per sample. Futhermore, a novel protocol for preparation of A-FABP without the natural ligand is presented. The described screening approach is suitable for ligand screening very early in the drug discovery process before conventional high-throughput screens (HTS) are developed and/or used as a secondary screening for ligands identified by HTS. ( Journal of Biomolecular Screening 2003:247-256)

Asymmetric Induction and Amplification in Stereodynamic Catalytic Systems by Noncovalent Interactions

Synlett ◽  
2020 ◽  
Author(s):  
Oliver Trapp ◽  
Jan Felix Scholtes
Keyword(s):  
Noncovalent Interactions ◽  
Noncovalent Interaction ◽  
Kinetic Properties ◽  
Catalytic Systems ◽  
Asymmetric Transformations ◽  
Chemical Systems ◽  
Chiral Induction ◽  
Chiral Amplification ◽  
Biochemical Systems ◽  
Local Transmission

AbstractThe local transmission of chiral information by noncovalent interactions is one of the most fundamental processes broadly found in nature, i.e. in complex biochemical systems. This review summarizes our accomplishments in investigating chiral induction in stereodynamic ligands and catalysts by weak intermolecular interactions. It includes our efforts to characterize numerous stereodynamic compounds in detail with respect to their thermodynamic and kinetic properties. Furthermore, many stereolabile ligands for enantioselective catalysis are described, where directed stereoinduction afforded highly enantio- or diastereoenriched catalysts for subsequent selective asymmetric transformations. Various approaches for the dynamic enrichment of one of the catalyst’s conformers are presented, such as noncovalent interaction of the ligand with a chiral environment or a chiral solute. Finally, successful chemical systems are presented in which a process of chiral induction can be coupled with an autoinductive mechanism triggered by the chirality of its own reaction product, realizing Nature-inspired feedback loops resulting in self-amplifying, enantioselective catalytic reactions.1 Introduction2 Mapping the Stereodynamic Landscape3 Chiral Induction by Noncovalent Interactions4 Autoinduction and Chiral Amplification5 Self-Alignment and Emergence of Chirality6 Conclusion

scholarly journals Pillararenes Trimer for Self-Assembly

Nanomaterials ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 651 ◽  
Author(s):  
Huacheng Zhang ◽  
Zhaona Liu ◽  
Hui Fu
Keyword(s):  
Self Assembly ◽  
Driving Forces ◽  
Click Reaction ◽  
Noncovalent Interactions ◽  
Coupling Reaction ◽  
Covalent Bonds ◽  
Guest Molecules ◽  
Palladium Catalyzed ◽  
Noncovalent Bonds ◽  
External Stimuli

Pillararenes trimer with particularly designed structural geometry and excellent capacity of recognizing guest molecules is a very efficient and attractive building block for the fabrication of advanced self-assembled materials. Pillararenes trimers could be prepared via both covalent and noncovalent bonds. The classic organic synthesis reactions such as click reaction, palladium-catalyzed coupling reaction, amidation, esterification, and aminolysis are employed to build covalent bonds and integrate three pieces of pillararenes subunits together into the “star-shaped” trimers and linear foldamers. Alternatively, pillararenes trimers could also be assembled in the form of host-guest inclusions and mechanically interlocked molecules via noncovalent interactions, and during those procedures, pillararenes units contribute the cavity for recognizing guest molecules and act as a “wheel” subunit, respectively. By fully utilizing the driving forces such as host-guest interactions, charge transfer, hydrophobic, hydrogen bonding, and C–H…π and π–π stacking interactions, pillararenes trimers-based supramolecular self-assemblies provide a possibility in the construction of multi-dimensional materials such as vesicular and tubular aggregates, layered networks, as well as frameworks. Interestingly, those assembled materials exhibit interesting external stimuli responsiveness to e.g., variable concentrations, changed pH values, different temperature, as well as the addition/removal of competition guests and ions. Thus, they could further be used for diverse applications such as detection, sorption, and separation of significant multi-analytes including metal cations, anions, and amino acids.

scholarly journals Route to high-$$T_{c}$$ superconductivity of $$\hbox {BC}_{{7}}$$ via strong bonding of boron–carbon compound at high pressure

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Prutthipong Tsuppayakorn-aek ◽  
Xiaoyong Yang ◽  
Prayoonsak Pluengphon ◽  
Wei Luo ◽  
Rajeev Ahuja ◽  
...  
Keyword(s):  
High Pressure ◽  
Surface Shape ◽  
First Principles Calculation ◽  
Chemical Bonds ◽  
Superconducting Transition ◽  
Covalent Bonds ◽  
Large Sheet ◽  
Very High ◽  
Carbon System ◽  
Boron Carbon

Abstract We have analyzed the compositions of boron–carbon system, in which the $$\hbox {BC}_{{7}}$$ BC 7 compound is identified as structural stability at high pressure. The first-principles calculation is used to identify the phase diagram, electronic structure, and superconductivity of $$\hbox {BC}_{{7}}$$ BC 7 . Our results have demonstrated that the $$\hbox {BC}_{{7}}$$ BC 7 is thermodynamically stable in the diamond-like $$P{\bar{4}}m2$$ P 4 ¯ m 2 structure at a pressure above 244 GPa, and under temperature also. Feature of chemical bonds between B and C atoms is presented using the electron localization function. The strong chemical bonds in diamond-like $$P{\bar{4}}m2$$ P 4 ¯ m 2 structure are covalent bonds, and it exhibits the s–p hybridization under the pressure compression. The Fermi surface shape displays the large sheet, indicating that the diamond-like $$P{\bar{4}}m2$$ P 4 ¯ m 2 phase can achieve a high superconducting transition temperature ($$\hbox {T}_{{c}}$$ T c ). The outstanding property of $$\hbox {BC}_{{7}}$$ BC 7 at 250 GPa has manifested very high-$$\hbox {T}_{{c}}$$ T c of superconductivity as 164 K, indicating that the carbon-rich system can induce the high-$$\hbox {T}_{{c}}$$ T c value as well.

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