scholarly journals Parallel interactions of aromatic and heteroaromatic molecules

2016 ◽  
Vol 70 (6) ◽  
pp. 649-659 ◽  
Author(s):  
Dusan Malenov ◽  
Snezana Zaric

Parallel interactions of aromatic and heteroaromatic molecules are very important in chemistry and biology. In this review, recent findings on preferred geometries and interaction energies of these molecules are presented. Benzene and pyridine were used as model systems for studying aromatic and heteroaromatic molecules, respectively. Searches of Cambridge Structural Database show that both aromatic and heteroaromatic molecules prefer interacting at large horizontal displacements, even though previous calculations showed that stacking interactions (with offsets of about 1.5 ?) are the strongest. Calculations of interaction energies at large horizontal displacements revealed that the large portion of interaction energy is preserved even when two molecules do not overlap. These substantial energies, as well as the possibility of forming larger supramolecular structures, make parallel interactions at large horizontal displacements more frequent in crystal structures than stacking interactions.

2020 ◽  
Vol 22 (24) ◽  
pp. 13721-13728 ◽  
Author(s):  
Jelena P. Blagojević Filipović ◽  
Michael B. Hall ◽  
Snežana D. Zarić

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.


CrystEngComm ◽  
2022 ◽  
Author(s):  
David Stephen Hughes ◽  
Ann L. Bingham ◽  
Andrew David Bond ◽  
M Hursthouse ◽  
Terence L. Threlfall

A set of 96 crystal structures containing sulfathiazole (SLFZ) is presented, comprising 52 new crystal structures and 39 structures retrieved from the Cambridge Structural Database. The set comprises five polymorphs,...


2016 ◽  
Vol 18 (37) ◽  
pp. 25791-25795 ◽  
Author(s):  
D. B. Ninković ◽  
D. Z. Vojislavljević-Vasilev ◽  
V. B. Medaković ◽  
M. B. Hall ◽  
E. N. Brothers ◽  
...  

Stacking interactions between cyclohexane and benzene were studied in crystal structures from the Cambridge Structural Database and by ab initio calculations.


Author(s):  
Lígia R. Gomes ◽  
John Nicolson Low ◽  
Diogo Magalhães e Silva ◽  
Fernando Cagide ◽  
Fernanda Borges

The crystal structures of five 6-mercaptopurine derivatives,viz.2-[(9-acetyl-9H-purin-6-yl)sulfanyl]-1-(3-methoxyphenyl)ethan-1-one (1), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfanyl]-1-(4-methoxyphenyl)ethan-1-one (2), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfanyl]-1-(4-chlorophenyl)ethan-1-one (3), C15H11ClN4O2S, 2-[(9-acetyl-9H-purin-6-yl)sulfanyl]-1-(4-bromophenyl)ethan-1-one (4), C15H11BrN4O2S, and 1-(3-methoxyphenyl)-2-[(9H-purin-6-yl)sulfanyl]ethan-1-one (5), C14H12N4O2S. Compounds (2), (3) and (4) are isomorphous and accordingly their molecular and supramolecular structures are similar. An analysis of the dihedral angles between the purine and exocyclic phenyl rings show that the molecules of (1) and (5) are essentially planar but that in the case of the three isomorphous compounds (2), (3) and (4), these rings are twisted by a dihedral angle of approximately 38°. With the exception of (1) all molecules are linked by weak C—H...O hydrogen bonds in their crystals. There is π–π stacking in all compounds. A Cambridge Structural Database search revealed the existence of 11 deposited compounds containing the 1-phenyl-2-sulfanylethanone scaffold; of these, only eight have a cyclic ring as substituent, the majority of these being heterocycles.


Author(s):  
Ivana S. Antonijević ◽  
Dušan P. Malenov ◽  
Michael B. Hall ◽  
Snežana D. Zarić

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.


2005 ◽  
Vol 38 (4) ◽  
pp. 694-696 ◽  
Author(s):  
Jacco van de Streek ◽  
Sam Motherwell

In order to establish the effect of exchanging one functional group by another on the crystal structure, one would like to be able to search the Cambridge Structural Database for all pairs of crystal structures where this substitution has been made. A program calledGRX(group exchange) was written for that purpose.


2020 ◽  
Vol 76 (6) ◽  
pp. 630-651
Author(s):  
Daniel Nguyen ◽  
Piero Macchi ◽  
Anatoliy Volkov

The previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170–175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536; Nguyen & Volkov (2019). Acta Cryst. A75, 448–464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, L-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283–4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10−5 kJ mol−1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28–64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.


2017 ◽  
Vol 73 (3) ◽  
pp. 240-245 ◽  
Author(s):  
Colin R. Groom ◽  
Jason C. Cole

Many ligand-discovery stories tell of the use of structures of protein–ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein–ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility.


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