covalent interactions
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2022 ◽  
Vol 0 (0) ◽  
Author(s):  
Peter Luger ◽  
Birger Dittrich

Abstract The electron density distribution (EDD) of a tetrasaccharide composed of four benzoylated fructopyranosyl units was obtained by refinement with scattering factors from the invariom library. X-ray diffraction data was downloaded from the Cambridge Structural Database (CSD). Bond topological and atomic properties were obtained by application of Bader’s QTAIM formalism. From a large number of 105 C–C bonds in the molecule average bond orders for 33 single and 72 aromatic bonds were calculated yielding values of 1.33 and 1.61. Molecular Hirshfeld and electrostatic potential (ESP) surfaces show that only weak non-covalent interactions exist. The phenyl rings of the benzoyl fragments in the outer regions of the molecule generate a positive ESP shell with repulsive properties between adjacent molecules. Weak surface interactions result in a rather unusual low density around 1.3 g cm−3, which is understandable when compared to other carbohydrates where strong O–H⋯O hydrogen bonds allow a 20% more dense packing with densities >1.5 g cm−3 as determined by single crystal X-ray diffraction.


2022 ◽  
Vol 9 ◽  
Author(s):  
Jingyi Zhao ◽  
Xiaoyan Zheng

Luminescent molecular aggregates have attracted worldwide attention because of their potential applications in many fields. The luminescent properties of organic aggregates are complicated and highly morphology-dependent, unraveling the intrinsic mechanism behind is urgent. This review summarizes recent works on investigating the structure–property relationships of organic molecular aggregates at different environments, including crystal, cocrystal, amorphous aggregate, and doped systems by multiscale modeling protocol. We aim to explore the influence of intermolecular non-covalent interactions on molecular packing and their photophysical properties and then pave the effective way to design, synthesize, and develop advanced organic luminescent materials.


2022 ◽  
Author(s):  
Jan Řezáč

The Non-Covalent Interactions Atlas (www.nciatlas.org) has been extended with two data sets of benchmark interaction energies in complexes dominated by London dispersion. The D1200 data set of equilibrium geometries provides a thorough sampling of an extended chemical space, while the D442×10 set features dissociation curves for selected complexes. In total, they provide 5,178 new CCSD(T)/CBS data points of the highest quality. The new data have been combined with previous NCIA data sets in a comprehensive test of dispersion-corrected DFT methods, identifying the ones that achieve high accuracy in all types of non-covalent interactions in a broad chemical space. Additional tests of dispersion-corrected MP2 and semiempirical QM methods are also reported.


2022 ◽  
Author(s):  
Guangyu Wang

The capsaicin receptor TRPV1 can be activated by heat and thus serves as a thermometer in a primary afferent sensory neuron for noxious heat detection. However, the underlying molecular mechanism is unclear. Here, a hairpin topological structural model, together with graph theory, was developed to examine a role of temperature-dependent hairpin melting in controlling non-covalent interactions along the heat-evoked gating pathway of TRPV1. The results showed that heat-dependent hairpin melting rearranges non-covalent interactions, releases the resident lipid, and induces TRPV1 gating. A larger hairpin in the outer pore initiates a temperature threshold as a heat starter for channel opening while some smaller hairpins in the S4-S5 linker and the outer pore stabilize the heat efficacy and avoid heat denaturation as a heat fuse. The heat-induced global gating rearrangement may be responsible for the high heat sensitivity. This hairpin model may provide a broad structural basis for the thermo-gated ion channels.


Synthesis ◽  
2022 ◽  
Author(s):  
Naba Abuhafez ◽  
Antoine Perennes ◽  
Rafael Gramage-Doria

The present review describes the most relevant advances dealing with supramolecular catalysis in which metalloporphyrins are employed as substrate-recognition sites in the second coordination sphere of the catalyst. The kinetically-labile interaction between metalloporphyrins (typically, those derived from zinc) and nitrogen- or oxygen-containing substrates is energetically comparable to those non-covalent interactions (i.e. hydrogen bonding) found in enzymes enabling substrate-preorganization. Much inspired from this host-guest phenomena, the catalytic systems described in this account display unique activities, selectivities and action modes difficult to reach applying purely covalent strategies.


2022 ◽  
Author(s):  
Patrick Schwarz ◽  
Marta Tena-Solsona ◽  
Kun Dai ◽  
Job Boekhoven

Using molecular self-assembly, supramolecular chemists can create Gigadalton-structures with angstrom precision held together by non-covalent interactions. However, despite relying on the same molecular toolbox for self-assembly, these synthetic structures lack...


2022 ◽  
Vol 9 (1) ◽  
Author(s):  
Dileep Kumar ◽  
K. M. Sachin ◽  
Naveen Kumari ◽  
Ajaya Bhattarai

In this study, kaempferol (0.2 m/mmol kg −1 ) dispersed cationic surfactant micelles were prepared as a function of alkyltrimethylammonium bromide (C n TAB) hydrophobicity (C = 12 to C = 16). The dispersion study of kaempferol in different C n TAB, i.e. dodecyltrimethylammonium bromide (C = 12), tetradecyltrimethylammonium bromide (C = 14) and hexadecyltrimethylammonium bromide (C = 16), was conducted with the physico-chemical properties of density, sound velocity, viscosity, surface tension, isentropic compressibility, acoustic impedance, surface excess concentration and area occupied per molecule and thermodynamic parameters Gibbs free energy, enthalpy and activation energy measured at 298.15 K. These properties were measured with varying concentration of C n TAB from 0.0260 to 0.0305 mol kg −1 in a 10% (w/w) aqueous dimethyl sulfoxide solvent system. The variations in these measured properties have been used to infer the kaempferol dispersion stability via hydrophobic–hydrophilic, hydrophilic–hydrophilic, van der Waals, hydrogen bonding and other non-covalent interactions.


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