scholarly journals IsoStar Program Suite for Studies of Noncovalent Interactions in Crystals of Chemical Compounds

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 162
Author(s):  
Alexander S. Novikov
Keyword(s):  
Molecular Modeling ◽  
Solid State ◽  
Web Application ◽  
Noncovalent Interactions ◽  
Chemical Compounds ◽  
Data Bank ◽  
Cambridge Crystallographic Data Centre ◽  
Data Centre ◽  
Knowledge Based ◽  
Biochemical Compounds

Both Cambridge Crystallographic Data Centre (CCDC) and Protein Data Bank (PDB) provide unique opportunities for finding information about the structures of chemical and biochemical compounds in the solid state. The IsoStar—a knowledge-based library of intermolecular interactions—is a very powerful tool for automatic analysis of a large amount of data from these databases. The IsoStar program suite could help chemists in understanding of probability of occurrence (frequencies) and spatial characteristics (directionalities) of noncovalent contacts (including hydrogen, halogen, and chalcogen bonds, as well as interactions involving π-systems) between pairs of chemical functional groups; this web application may also be useful for crystal engineers, crystallographers, medicinal chemists, and researchers in fields of computational chemistry and molecular modeling.

An insight to the noncovalent interactions in two triamine based mononuclear iron(III) Schiff base complexes with special emphasis on the formation of Br•••π halogen bonding

CrystEngComm ◽  
2021 ◽  
Author(s):  
Shouvik Chattopadhyay ◽  
Tanmoy Basak ◽  
Antonio Frontera
Keyword(s):  
Schiff Base ◽  
Solid State ◽  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Schiff Base Complexes ◽  
X Ray ◽  
Mononuclear Iron

Two mononuclear iron(III) complexes, [FeL1Cl]∙CH3CN (1) and [FeL2(N3)] (2) {H2L1= N,N′-bis(5-chlorosalicylidene)diethylenetriamine and H2L2= N,N′-bis(5-bromosalicylidene)diethylenetriamine}, have been synthesized and characterized by X-ray crystallographic studies. In the solid state, there are strong...

Palladium(II) complex with S-allyl-l-cysteine: New solid-state NMR spectroscopic measurements, molecular modeling and antibacterial assays

2011 ◽  
Vol 78 (1) ◽  
pp. 313-318 ◽  
Author(s):  
Marcelle B.M. Spera ◽  
Frederico A. Quintão ◽  
Diego K.D. Ferraresi ◽  
Wilton R. Lustri ◽  
Alviclér Magalhães ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Solid State ◽  
Solid State Nmr ◽  
Spectroscopic Measurements

scholarly journals Mercury 4.0: from visualization to analysis, design and prediction

2020 ◽  
Vol 53 (1) ◽  
pp. 226-235 ◽  
Author(s):  
Clare F. Macrae ◽  
Ioana Sovago ◽  
Simon J. Cottrell ◽  
Peter T. A. Galek ◽  
Patrick McCabe ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Engineering ◽  
Simple Structure ◽  
Visualization Tool ◽  
Cambridge Crystallographic Data Centre ◽  
Analysis Software ◽  
Scientific Communities ◽  
Data Centre ◽  
Chemical Crystallography ◽  
Analysis Design

The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.

scholarly journals The Importance of CH···X (X = O, π) Interaction of a New Mixed Ligand Cu(II) Coordination Polymer: Structure, Hirshfeld Surface and Theoretical Studies

Crystals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 455 ◽  
Author(s):  
Saikat Seth
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Noncovalent Interactions ◽  
Carbonyl Oxygen ◽  
Hirshfeld Surface ◽  
Mixed Ligand ◽  
Binding Energies ◽  
Zigzag Chain ◽  
X Ray ◽  
Π Interactions

In this study, a new equimolar (1:1:1) mixed ligand Cu(II) polymer, [Cu(IDA)(ImP)]n (1) with iminodiacetato (IDA) and imidazo[1,2-a]-pyridine (ImP) was synthesized and characterized by single crystal X-ray diffraction analysis. X-ray crystallography reveals that compound (1) consists of polymeric zigzag chain along [010] the carboxylate carbonyl oxygen atom by two-fold symmetry screw axis. The solid-state structure is stabilized through C–H···O hydrogen bonds and C–H···π interactions that lead the molecules to generate two-dimensional supramolecular assemblies. The intricate combinations of hydrogen bonds and C–H···π interactions are fully described along with computational studies. A thorough analysis of Hirshfeld surface and fingerprint plots elegantly quantify the interactions involved within the structure. The binding energies associated with the noncovalent interactions observed in the crystal structure and the interplay between them were calculated using theoretical DFT calculations. Weak noncovalent interactions were analyzed and characterized using Bader’s theory of ‘‘atoms-in-molecules’’ (AIM). Finally, the solid-state supramolecular assembly was characterized by the “Noncovalent Interaction” (NCI) plot index.

scholarly journals Symmetrical Noncovalent Interactions Br···Br Observed in Crystal Structure of Exotic Primary Peroxide

Symmetry ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 637 ◽  
Author(s):  
Dmitrii S. Bolotin ◽  
Mikhail V. Il’in ◽  
Vitalii V. Suslonov ◽  
Alexander S. Novikov
Keyword(s):  
Crystal Structure ◽  
Quantum Theory ◽  
Solid State ◽  
Single Crystal ◽  
Quantum Chemical ◽  
Driving Forces ◽  
Weak Interactions ◽  
Noncovalent Interactions ◽  
Type I ◽  
Single Crystal Xrd

4-Bromobenzamidrazone reacts with cyclopentanone giving 3-(4-bromophenyl)-5-(4-peroxobutyl)-1,2,4-triazole, which precipitated as pale-yellow crystals during the reaction. The intermolecular noncovalent interactions Br···Br in the single-crystal XRD structure of the peroxo compound were studied theoretically using quantum chemical calculations (ωB97XD/x2c-TZVPPall) and quantum theory of atoms in molecules (QTAIM) analysis. These attractive intermolecular noncovalent interactions Br···Br is type I halogen···halogen contacts and their estimated energy is 2.2–2.5 kcal/mol. These weak interactions are suggested to be one of the driving forces (albeit surely not the main one) for crystallization of the peroxo compound during the reaction and thus its stabilization in the solid state.

scholarly journals PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

2015 ◽  
Vol 43 (W1) ◽  
pp. W383-W388 ◽  
Author(s):  
David Sehnal ◽  
Lukáš Pravda ◽  
Radka Svobodová Vařeková ◽  
Crina-Maria Ionescu ◽  
Jaroslav Koča
Keyword(s):  
Protein Data Bank ◽  
Web Application ◽  
Data Bank ◽  
Structural Patterns ◽  
Fast Detection
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