scholarly journals Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition

2020 ◽  
Vol 76 (1) ◽  
pp. 122-136 ◽  
Author(s):  
Ivana S. Đorđević ◽  
Marko Popadić ◽  
Mirjana Sarvan ◽  
Marija Petković-Benazzouz ◽  
Goran V. Janjić
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Binding Sites ◽  
Quantum Chemical ◽  
Electrostatic Interactions ◽  
Docking Studies ◽  
Amino Acid Residues ◽  
Structural Database ◽  
Insight Into ◽  
Influence Of Substituents

Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C—H...Se and C—H...S interactions (∼80%), notably less numerous are structures with Se...Se and S...S interactions (∼5%), and Se...π and S...π interactions are the least numerous. The results of quantum-chemical calculations have indicated that C—H...Se (∼−0.8 kcal mol−1) and C—H...S interactions are weaker than the most stable parallel interaction (∼−3.3 kcal mol−1) and electrostatic interactions of σ/π type (∼−2.6 kcal mol−1). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O—H...Se (∼−4.4 kcal mol−1) and N—H...Se interactions (∼−2.2 kcal mol−1) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand.

Stacking interactions of resonance-assisted hydrogen-bridged rings and C6-aromatic rings

2020 ◽  
Vol 22 (24) ◽  
pp. 13721-13728 ◽  
Author(s):  
Jelena P. Blagojević Filipović ◽  
Michael B. Hall ◽  
Snežana D. Zarić
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Cambridge Structural Database ◽  
Stacking Interactions ◽  
Aromatic Rings ◽  
Structural Database

Stacking interactions between six-membered resonance-assisted hydrogen-bridged (RAHB) rings and C6-aromatic rings have been studied by analyzing crystal structures in the Cambridge Structural Database and performing quantum chemical calculations.

scholarly journals Geometrical and energetic characteristics of Se…Se interactions in crystal structures of organoselenium molecules

CrystEngComm ◽  
2021 ◽  
Author(s):  
Ivana S Veljković ◽  
Danijela S. Kretić ◽  
Dušan Ž Veljković
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Organic Molecules ◽  
Cambridge Structural Database ◽  
Structural Database ◽  
High Level

Non-covalent selenium-selenium interactions between selenium-containing organic molecules were studied in crystal structures from the Cambridge Structural Database and by high-level quantum chemical calculations. Se…Se contacts in crystal structures were analyzed...

scholarly journals Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations

2019 ◽  
Vol 75 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Ivana S. Antonijević ◽  
Dušan P. Malenov ◽  
Michael B. Hall ◽  
Snežana D. Zarić
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Energy Surface ◽  
Organic Conductors ◽  
Electron Donors ◽  
Cambridge Structural Database ◽  
Stacking Interactions ◽  
Structural Database ◽  
Calculated Potential Energy

Tetrathiafulvalene (TTF) and its derivatives are very well known as electron donors with widespread use in the field of organic conductors and superconductors. Stacking interactions between two neutral TTF fragments were studied by analysing data from Cambridge Structural Database crystal structures and by quantum chemical calculations. Analysis of the contacts found in crystal structures shows high occurrence of parallel displaced orientations of TTF molecules. In the majority of the contacts, two TTF molecules are displaced along their longer C 2 axis. The most frequent geometry has the strongest TTF–TTF stacking interaction, with CCSD(T)/CBS energy of −9.96 kcal mol−1. All the other frequent geometries in crystal structures are similar to geometries of the minima on the calculated potential energy surface.

Cyclisierung von Di(tert-butyl-methyl)ketazin zu 1,2-Diaza-3-bora- und 1,2-Diaza-3-sila-cyclopent-5-enen / Cyclization of Di(tert-butyl-methyl)ketazine to 1,2-Diaza-3-bora- and 1,2-Diaza-3-sila-cyclopent-5-enes

2006 ◽  
Vol 61 (10) ◽  
pp. 1261-1274 ◽  
Author(s):  
Florian Armbruster ◽  
Nina Armbruster ◽  
Uwe Klingebiel ◽  
Mathias Noltemeyer ◽  
Stefan Schmatz
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Chlorine Atom ◽  
Quantum Chemical ◽  
Membered Ring ◽  
Substitution Product ◽  
Tert Butyl ◽  
Isomeric Structures

The results of quantum chemical calculations on lithium ketazides suggest mainly four isomeric structures with different modes of lithium coordination (A-D). A monolithium ketazide thf-adduct (1) was isolated supporting the results of the quantum chemical calculations. In reactions of the lithiated di(tert-butyl-methyl)ketazine with BCl3 and Cl2BPh, 1,2-aza-azonia-3-borata-cyclopent-5-enes (2, 3) were isolated. Substitution of a chlorine atom of 2 and 3 with t-BuLi leads to the formation of derivatives 4 and 5. HCl elimination from 2 with Et3N gives - via a diazaboracyclopentene (6) - a bicyclus 7. In the reaction of the dilithiated ketazine with F2BN(SiMe3)2, the diaza-boracyclopentene 8 is obtained while with Cl4Si, F3SiN(SiMe3)2, and Cl2SiMe2 the diazasilacyclopentenes 9 - 11 are generated. SiF4 reacts with the dilithium ketazide to give a spirocyclus (12). The monolithium ketazide and Cl2SiMe2 react at 30 °C to give a four-membered ring isomer of the substitution product which is formed via a 1,3-chlorine shift from silicon to carbon (13). A tetrameric silanolate was isolated as a by-product in this reaction. It gives evidence for the structure of lithium ketazide A. Crystal structures of 5, 7, 10, and 14 are reported.

A density functional theory insight into the structure and reactivity of diphenyltin(IV) derivative of glycylphenylalanine

2016 ◽  
Vol 39 (3-4) ◽  
Author(s):  
Sandeep Pokharia ◽  
Rachana Joshi ◽  
Mamta Pokharia ◽  
Swatantra Kumar Yadav ◽  
Hirdyesh Mishra
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Functional Theory ◽  
Insight Into

AbstractThe quantum-chemical calculations based on density functional theory (DFT) have been performed on the diphenyltin(IV) derivative of glycyl-phenylalanine (H

scholarly journals What’s in an Atom? a Comparison of Carbon and Silicon-Centered Amidinium···carboxylate Frameworks

2020 ◽  
Author(s):  
Stephanie Boer ◽  
Li-Juan Yu ◽  
Tobias Genet ◽  
Kaycee Low ◽  
Duncan Cullen ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Building Blocks ◽  
Cambridge Structural Database ◽  
Bond Angles ◽  
Framework Materials ◽  
Carboxylate Anions ◽  
Tetrahedral Bond ◽  
Structural Database ◽  
Apparent Similarity

<div><div><div><p>Despite their apparent similarity, framework materials based on tetraphenylmethane and tetraphenylsilane building blocks often have quite different structures and topologies. Herein, we describe a new silicon tetraamidinium compound and use it to prepare crystalline hydrogen bonded frameworks with carboxylate anions in water. The silicon-containing frameworks are compared with those prepared from the analogous carbon tetraamidinium: when biphenyldicarboxylate or tetrakis(4-carboxyphenyl)methane anions were used similar channel-containing networks are observed for both the silicon and carbon tetraamidinium. When terephthalate or bicarbonate anions were used, different products form. Insights into possible reasons for the different products are provided by a survey of the Cambridge Structural Database and quantum chemical calculations, both of which indicate that, contrary to expectations, tetraphenylsilane derivatives have less geometrical flexibility than tetraphenylmethane derivatives, i.e. they are less able to distort away from ideal tetrahedral bond angles.</p></div></div></div>

Halogen bonds as a tool in the design of high energetic materials: evidence from crystal structures and quantum chemical calculations

CrystEngComm ◽  
2021 ◽  
Author(s):  
Aleksandra B. Đunović ◽  
Dušan Ž Veljković
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Electrostatic Potential ◽  
Energetic Materials ◽  
Quantum Chemical ◽  
Central Area ◽  
Molecular Surface ◽  
Halogen Bonds ◽  
Positive Electrostatic Potential

Positive electrostatic potential over the central area of the molecular surface is one of the main characteristics of high energetic materials (HEM) that determines their sensitivity towards detonation. The influence...

Crystal and electronic structure of the new ternary phosphide Ho5Pd19P12

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Olha Zhak ◽  
Oksana Karychort ◽  
Volodymyr Babizhetskyy ◽  
Chong Zheng
Keyword(s):  
Crystal Structure ◽  
Electronic Structure ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Structure Property ◽  
X Ray Diffraction ◽  
Structure Property Relationships ◽  
Metallic Bonding ◽  
Crystal And Electronic Structure ◽  
Insight Into

Abstract The title compound was prepared from the pure elements by sintering. The crystal structure was investigated by means of powder X-ray diffraction data. Ho5Pd19P12 exhibits the hexagonal Ho5Ni19P12-type structure with space group P 6 ‾ 2 m $P&#x203e;{6}2m$ , a = 13.1342(2), c = 3.9839(1) Å, R I = 0.060, R p = 0.080. The crystal structure can be described as a combination of two types of the structural units, [HoPd6P3] and [Ho3Pd10P6], respectively, mutually displaced by 1/2 along the crystallographic c axis. Quantum chemical calculations have been performed to analyze the electronic structure and provide deeper insight into the structure-property relationships. The results of the quantum chemical calculations indicate that the material features metallic bonding between Ho and Pd and covalent bonding between Pd and P.

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