dihedral angles
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Said Daoui ◽  
Israa Muwafaq ◽  
Emine Berrin Çınar ◽  
Abdulmalik Abudunia ◽  
Necmi Dege ◽  

The pyridazine ring in the title compound, C20H17ClN2O3, adopts a screw-boat conformation. The whole molecule is flattened, the dihedral angles subtended by the least-squares plane of the central aromatic ring with those of the terminal benzene and pyridazine rings being 15.18 (19) and 11.23 (19)°, respectively. In the crystal, the molecules are linked by pairs of N—H...O bonds into centrosymmetric dimers and by C—H...π contacts into columns. The results of the Hirshfeld surface analysis show that the most prominent interactions are H...H, accounting for 36.5% of overall crystal packing, and H...O/O...H (18.6% contribution) contacts.

Manzoor Ahmad Malla ◽  
Ravi Bansal ◽  
Ray J. Butcher ◽  
Sushil K. Gupta

The title compound, C70H70N8O4Se2, is a spiro bicyclic diselenide, made up of two [SeC6H4CH=N—N(CO)C6H4(C)C6H3NEt2(O)C6H3NEt2] units related by a twofold crystallographic symmetry element bisecting the diselenide bond. The compound crystallizes in a non-centrosymmetric polar space group (tetragonal, P\overline{4}b2) and the structure was refined as an inversion twin. The two diethyl amine groups and their attached phenyl groups of the xanthene ring are disordered over two orientations, with occupancies of 0.664 (19)/0.336 (19) and 0.665 (11)/0.335 (11), respectively. The dihedral angles between the mean planes of the central isoindoline and the phenyl rings are 26.8 (2) and 2.5 (4)°, respectively. The mean plane of the central xanthene ring forms dihedral angles of 2.0 (5), 8.8 (5), 1.7 (5) and 7.9 (6)° with the peripheral phenyl rings. The isoindoline and xanthene rings subtend a dihedral angle of 89.8 (2)°. The molecular conformation is stabilized by an intramolecular C—H...O hydrogen bond generating an S(6) ring motif. In the crystal, molecules are linked by C—H...O hydrogen bonds together with C—H...π (ring) interactions, forming a three-dimensional network. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H...H (68.1%), C...H/H...C (21.2%) and O...H/H...O (8.7%) contacts. The optimized structure calculated using density functional theory (DFT) at the B3LYP/6 – 31 G(d) level is compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO behaviour was used to determine the energy gap and the molecular electrostatic potential (MEP) of the compound was investigated.

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 67
Ramakotaiah Mulamreddy ◽  
William D. Lubell

The constrained dipeptide surrogates 5- and 7-hydroxy indolizidin-2-one N-(Boc)amino acids have been synthesized from L-serine as a chiral educt. A linear precursor ∆4-unsaturated (2S,8S)-2,8-bis[N-(Boc)amino]azelic acid was prepared in five steps from L-serine. Although epoxidation and dihydroxylation pathways gave mixtures of hydroxy indolizidin-2-one diastereomers, iodolactonization of the ∆4-azelate stereoselectively delivered a lactone iodide from which separable (5S)- and (7S)-hydroxy indolizidin-2-one N-(Boc)amino esters were synthesized by sequences featuring intramolecular iodide displacement and lactam formation. X-ray analysis of the (7S)-hydroxy indolizidin-2-one N-(Boc)amino ester indicated that the backbone dihedral angles embedded in the bicyclic ring system resembled those of the central residues of an ideal type II’ β-turn indicating the potential for peptide mimicry.

Nikolay Abrosimov ◽  
Bao Vuong

We consider a compact hyperbolic tetrahedron of a general type. It is a convex hull of four points called vertices in the hyperbolic space [Formula: see text]. It can be determined by the set of six edge lengths up to isometry. For further considerations, we use the notion of edge matrix of the tetrahedron formed by hyperbolic cosines of its edge lengths. We establish necessary and sufficient conditions for the existence of a tetrahedron in [Formula: see text]. Then we find relations between their dihedral angles and edge lengths in the form of a cosine rule. Finally, we obtain exact integral formula expressing the volume of a hyperbolic tetrahedron in terms of the edge lengths. The latter volume formula can be regarded as a new version of classical Sforza’s formula for the volume of a tetrahedron but in terms of the edge matrix instead of the Gram matrix.

Steven van Terwingen ◽  
Noah Nachtigall ◽  
Ulli Englert

Abstract The ligand 3-(4-(1,3,5-trimethyl-1H-pyrazol-4-yl)phenyl)acetylacetone (1) combines a Pearson hard O,O′ chelating acetylacetone donor with a softer pyrazole N donor bridged by a phenylene spacer. Deprotonation and coordination to CuII leads to a square planar bis-acetylacetonato complex; interpreting the close proximity of an adjacent complex’s pyrazole moiety as an η 2 ${{\eta}}^{2}$ coordination to the axial CuII position leads to a two dimensional extended structure. The N donor capabilities are proven by coordination to AgPF6 and AuCl; for AgI a cationic linear bis-pyrazole complex as a toluene solvate is obtained with toluene-pyrazole π-interactions and an essentially uncoordinated PF 6 - ${{\mathrm{PF}}_{6}}^{-}$ anion. In the case of AuCl a neutral linear coordination compound with one chlorido and one pyrazole ligand 1 is obtained. Comparing the dihedral angles with a closely related but shorter ligand reveals a larger rotational degree of freedom in 1, allowing for richer architectures in emerging coordination polymers.

2021 ◽  
Aayatti Mallick Gupta ◽  
Sasthi Charan Mandal ◽  
Jaydeb Chakrabarti ◽  
Sukhendu Mandal

SARS-CoV-2 has considerably higher mutation rate. SARS-CoV-2 possesses a RNA dependent RNA polymerase (RdRp) which helps to replicate its genome. The mutation P323L in RdRp is associated with the loss of a particular epitope (321-327) from this protein which may influence the pathogenesis of the concern SARS-CoV-2 through the development of antibody escape variants. We consider the effect of mutations in some of the epitope regions including the naturally occurring mutation P323L on the structure of the epitope and their interface with paratope using all-atom molecular dynamics (MD) simulation studies. P323L mutations cause conformational changes in the epitope region by opening up the region associated with increase in the radius of gyration and intramolecular hydrogen bonds, making the region less accessible. Moreover, the fluctuations in the dihedral angles in the epitope:paratope (IgG) interface increase which destabilize the interface. Such mutations may help in escaping antibody mediated immunity of the host.

IUCrData ◽  
2021 ◽  
Vol 6 (11) ◽  
C. Selva Meenatchi ◽  
S. Athimoolam ◽  
J. Suresh ◽  
S. Raja Rubina ◽  
R. Ranjith Kumar ◽  

In the title compound, C20H15ClN2O, the non-aromatic six-membered ring adopts a distorted envelope conformation with methylene-C atom nearest to the five-membered ring being the flap atom. The dihedral angle between the phenyl and chlorobenzene rings is 74.5 (1)°. The heterocyclic ring forms dihedral angles of 37.9 (1) and 64.3 (1)° with the phenyl and chlorobenzene rings, respectively. In the crystal, weak C—H...O interactions feature predominantly within the three-dimensional architecture. The intermolecular interactions are further analysed with the calculation of the Hirshfeld surfaces highlighting the prominent role of C—H...O interactions, along with H...H (36.8%) and C...H/H...C (26.5%) contacts.

2021 ◽  
Vol 44 (11) ◽  
Katarzyna Mądry ◽  
Waldemar Nowicki

Abstract The cellular model with periodic boundary conditions was proposed for the study of liquid–solid interface properties of solid surfaces decorated by a regular pattern. The solid surface was represented by a mosaic of truncated pyramids of two different slopes of side walls equivalent to a surface covered with triangular grooves of different dihedral angles. On the basis of the computations performed for a single elementary cell, the components of the interfacial energies and the apparent contact angles have been found for different Young contact angles and different tilting angles of the pyramid walls. It was found that at certain sets of angles, the wetting takes place with the partial coverage of the pyramid sidewalls—in between the Cassie–Baxter and Wenzel regimes. The influence of the line tension on the studied surface wettability was also examined. Graphic abstract

Nazariy T. Pokhodylo ◽  
Yurii Slyvka ◽  
Evgeny Goreshnik ◽  
Roman Lytvyn

The title compound, C17H7F8N3O, was obtained via the reaction of 1-azido-2,3,4,5,6-pentafluorobenzene with 4,4,4-trifluoro-1-(p-tolyl)butane-1,3-dione using triethylamine as a base catalyst and solvent. The dihedral angles between the pentafluorophenyl (A), triazole (B) and p-tolyl (C) rings are A/B = 62.3 (2), B/C = 43.9 (3) and A/C = 19.1 (3)°. In the crystal, the molecules are linked by C—H...F and C—H...O hydrogen bonds as well as by aromatic π–π stacking interactions into a three-dimensional network. To further analyse the intermolecular interactions, a Hirshfeld surface analysis was performed.

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