Water−Nucleobase “Stacking”:  H−π and Lone Pair−π Interactions in the Atomic Resolution Crystal Structure of an RNA Pseudoknot

2003 ◽  
Vol 125 (30) ◽  
pp. 8998-8999 ◽  
Author(s):  
Sanjay Sarkhel ◽  
Alexander Rich ◽  
Martin Egli
Keyword(s):  
Crystal Structure ◽  
Lone Pair ◽  
Atomic Resolution ◽  
Π Interactions ◽  
Rna Pseudoknot

scholarly journals Crystal structure of poly[[[μ4-5-(9H-carbazol-9-yl)isophthalato][μ3-5-(9H-carbazol-9-yl)isophthalato]bis(dimethylformamide)(methanol)dizinc] dimethylformamide monosolvate]

2015 ◽  
Vol 71 (8) ◽  
pp. m152-m153 ◽  
Author(s):  
Liubov M. Lifshits ◽  
Charles Campana ◽  
Jeremy K. Klosterman
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Title Compound ◽  
Solvent Molecule ◽  
Lone Pair ◽  
Π Interactions ◽  
Carboxylate Groups ◽  
Medium Strength ◽  
Secondary Building Units ◽  
Coordination Spheres

The structure of the polymeric title compound, {[Zn2(C20H11NO4)2(C3H7NO)2(CH3OH)]·C3H7NO}n, comprises carbazolylisophthalate moieties connecting dimetallic tetracarboxylate zinc secondary building units (SBUs) parallel to [100] and [010], leading to a layer-like arrangement parallel to (001). Each SBU consists of two Zn atoms in slightly distorted tetrahedral and octahedral coordination environments [Zn...Zn = 3.5953 (6) Å]. Three carboxylate groups bridge the two Zn atoms in a μ2-O:O′ mode, whereas the fourth coordinates through a single carboxylate O atom (μ1-O). The O atoms of two dimethylformamide (DMF) and one methanol molecule complete the Zn coordination spheres. The methanol ligand interacts with the noncoordinating DMF moleculeviaan O—H...O hydrogen bond of medium strength. Carbazoles between the layers interdigitate through weak C—H....π interactions to form a laminar solid stacked along [010]. Two kinds of C—H...π interactions are present, both with a distance of 2.64 Å, between the H atoms and the centroids, and a third C—H...π interaction, where the aromatic H atom is located above the carbazole N-atom lone pair (H...N = 2.89 Å). Several C—H...O interactions occur between the coordinating DMF molecule, the DMF solvent molecule, and ligating carboxylate O atoms.

scholarly journals Crystal Structure Evidence for the Directionality of Lone Pair−π interactions: Fact or Fiction?

2019 ◽  
Vol 19 (11) ◽  
pp. 6806-6821 ◽  
Author(s):  
Chuandong Jia ◽  
Haohao Miao ◽  
Benjamin P. Hay
Keyword(s):  
Crystal Structure ◽  
Lone Pair ◽  
Π Interactions

scholarly journals 2,17-Dichloro-8,9,10,11-tetrahydro-19H-dibenzo[k,n][1,10,4,7]dioxadiazacyclopentadecine-7,12(6H,13H)-dione

2012 ◽  
Vol 68 (6) ◽  
pp. o1698-o1699
Author(s):  
Michaela Pojarová ◽  
Michal Dušek ◽  
Zdeňka Sedláková ◽  
Emanuel Makrlík
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Lone Pair ◽  
Π Interactions ◽  
Compound C

In the crystal structure of the title compound, C19H18Cl2N2O4, N—H...O hydrogen bonds link the molecules into infinite chains along the b axis. The structure also features weak C—H...O and C—H...Cl hydrogen bonds and C—H...π and (lone pair)...π interactions [Cl...centroid = 3.5871 (7) Å]. An intramolecular N—H...O bond occurs.

The role of different nonspecific interactions and halogen contacts in the crystal structure organization of 5-chloroisatoic anhydride

2018 ◽  
Vol 74 (3) ◽  
pp. 372-380
Author(s):  
Dorota Pogoda ◽  
Agnieszka Matera-Witkiewicz ◽  
Marcin Listowski ◽  
Jan Janczak ◽  
Veneta Videnova-Adrabinska
Keyword(s):  
Crystal Structure ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Lone Pair ◽  
One Dimensional ◽  
Π Interactions ◽  
Dimensional Network ◽  
Nonspecific Interactions

The crystal structure of 6-chloro-2,4-dihydro-1H-3,1-benzoxazine-2,4-dione (5-chloroisatoic anhydride), C8H4ClNO3, has been determined and analysed in terms of connectivity and packing patterns. The compound crystallizes in the noncentrosymmetric space groupPna21with one molecule in the asymmetric unit. The role of different weak interactions is discussed with respect to three-dimensional network organization. Molecules are extended into one-dimensional helical arrangements, making use of N—H...O hydrogen bonds and π–π interactions. The helices are further organized into monolayersviaweak C—H...O and lone pair–π interactions, and the monolayers are packed into a noncentrosymmetric three-dimensional architecture by C—Cl...π interactions and C—H...Cl and Cl...Cl contacts. A Hirshfeld surface (HS) analysis was carried out and two-dimensional (2D) fingerprint plots were generated to visualize the intermolecular interactions and to provide quantitative data for their relative contributions. In addition, tests of the antimicrobial activity andin vitrocytotoxity effects against fitoblast L929 were performed and are discussed.

scholarly journals Crystal structure of bis[tris(1,10-phenanthroline-κ2N,N′)cobalt(II)] tetranitrateN,N′-(1,4-phenylenedicarbonyl)diglycine solvate octahydrate

2015 ◽  
Vol 71 (8) ◽  
pp. 910-914 ◽  
Author(s):  
Niels-Patrick Pook ◽  
Philipp Hentrich ◽  
Mimoza Gjikaj
Keyword(s):  
Crystal Structure ◽  
Title Compound ◽  
Complex Cation ◽  
Solvent Molecule ◽  
Three Dimensional ◽  
Lone Pair ◽  
Water Molecules ◽  
Supramolecular Network ◽  
Π Interactions ◽  
Distorted Octahedral

The complex cation of the title compound, [Co(C12H8N2)3]2(NO3)4·C12H12N2O6·8H2O, contains a CoIIatom with a distorted octahedral coordination environment defined by six N atoms from three bidentate 1,10-phenanthroline ligands. The asymmetric unit of the title compound is completed by one-half of theN,N′-(1,4-phenylenedicarbonyl)diglycine solvent molecule, which is located on a centre of inversion, by two nitrate counter-anions and four solvent water molecules. Two [Co(C12H8N2)3]2+cations are connected through C—H...O contacts and through lone-pair...π interactions involving the non-coordinatingN,N′-(1,4-phenylenedicarbonyl)diglycine and phenanthroline molecules. The different aromatic ring systems are involved in π–π stacking and C—H...π interactions, with centroid-to-centroid distances in the range 3.7094 (8)–3.9973 (9) Å. The crystal structure is stabilized by further anion...π interactions and C—H...O contacts, as well as O—H...O and N—H...O hydrogen bonds between water molecules, the non-coordinating nitrate anions,N,N′-(1,4-phenylenedicarbonyl)diglycine and phenanthroline molecules. These non-covalent interactions give rise to a three-dimensional supramolecular network.

Unusual π-π interactions directed by [{(C6H6)Ru}2W8O30(OH)2]6– hybrid anion

CrystEngComm ◽  
2021 ◽  
Author(s):  
Anna A Mukhacheva ◽  
Vladislav Komarov ◽  
Vasily Kokovkin ◽  
Alexander S. Novikov ◽  
Pavel A Abramov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Building Block ◽  
Π Interactions

The [{(C6H6)Ru}2W8O30(OH)2]6– hybrid (organometallic-POM) anion was used as a pH-tunable building block to create special conditions for realizing π-π interactions in the crystal structure. Changing pH of aqueous solution of...

scholarly journals Theoretical Study of the Structures of 4-(2,3,5,6-Tetrafluoropyridyl)Diphenylphosphine Oxide and Tris(Pentafluorophenyl)Phosphine Oxide: Why Does the Crystal Structure of (Tetrafluoropyridyl)Diphenylphosphine Oxide Have Two Different P=O Bond Lengths?

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2778
Author(s):  
Joseph R. Lane ◽  
Graham C. Saunders
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Phosphine Oxide ◽  
Density Functional ◽  
Lone Pair ◽  
Diphenylphosphine Oxide ◽  
Functional Theory ◽  
Weak Hydrogen Bonding ◽  
Independent Molecules ◽  
The Difference

The crystal structure of 4-(2,3,5,6-tetrafluoropyridyl)diphenylphosphine oxide (1) contains two independent molecules in the asymmetric unit. Although the molecules are virtually identical in all other aspects, the P=O bond distances differ by ca. 0.02 Å. In contrast, although tris(pentafluorophenyl)phosphine oxide (2) has a similar crystal structure, the P=O bond distances of the two independent molecules are identical. To investigate the reason for the difference, a density functional theory study was undertaken. Both structures comprise chains of molecules. The attraction between molecules of 1, which comprises lone pair–π, weak hydrogen bonding and C–H∙∙∙arene interactions, has energies of 70 and 71 kJ mol−1. The attraction between molecules of 2 comprises two lone pair–π interactions, and has energies of 99 and 100 kJ mol−1. There is weak hydrogen bonding between molecules of adjacent chains involving the oxygen atom of 1. For one molecule, this interaction is with a symmetry independent molecule, whereas for the other, it also occurs with a symmetry related molecule. This provides a reason for the difference in P=O distance. This interaction is not possible for 2, and so there is no difference between the P=O distances of 2.

(2RS,5SR,6SR)-Ethyl 2,6-bis(4-fluorophenyl)-4-hydroxy-5-phenylsulfanyl-1,2,5,6-tetrahydropyridine-3-carboxylate

2007 ◽  
Vol 63 (3) ◽  
pp. o1377-o1379 ◽  
Author(s):  
J. Suresh ◽  
R. Suresh Kumar ◽  
S. Perumal ◽  
S. Natarajan
Keyword(s):  
Crystal Structure ◽  
Title Compound ◽  
Chair Conformation ◽  
Π Interactions ◽  
Compound C ◽  
Graph Set

The title compound, C26H23F2NO3S, a polysubstituted piperidine enol, adopts a twisted half-chair conformation. The crystal structure is stabilized by N—H...F, C—H...O and weak C—H...π interactions. An intramolecular O—H...S interaction generates an S(5) graph-set motif.

scholarly journals Crystal structure of bis(azido-κN)bis[2,5-bis(pyridin-2-yl)-1,3,4-thiadiazole-κ2N2,N3]cobalt(II)

2015 ◽  
Vol 71 (5) ◽  
pp. 452-454 ◽  
Author(s):  
Abdelhakim Laachir ◽  
Fouad Bentiss ◽  
Salaheddine Guesmi ◽  
Mohamed Saadi ◽  
Lahcen El Ammari
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Title Complex ◽  
Octahedral Coordination ◽  
Maximum Deviation ◽  
Coordination Geometry ◽  
Acta Cryst ◽  
Π Interactions ◽  
The Mean

In the mononuclear title complex, [Co(N3)2(C12H8N4S)2], the cobalt(II) atom is located on an inversion centre and displays an axially weakly compressed octahedral coordination geometry. The equatorial positions are occupied by the N atoms of two 2,5-bis(pyridin-2-yl)-1,3,4-thiadiazole ligands, whereas the axial positions are occupied by N atoms of the azide anions. The thiadiazole and pyridine rings linked to the metal are almost coplanar, with a maximum deviation from the mean plane of 0.0273 (16) Å. The cohesion of the crystal is ensured by weak C—H...N hydrogen bonds and by π–π interactions between pyridine rings [intercentroid distance = 3.6356 (11) Å], forming a layered arrangement parallel to (001). The structure of the title compound is isotypic with that of the analogous nickel(II) complex [Laachiret al.(2013).Acta Cryst.E69, m351–m352].

Sign in / Sign up

Export Citation Format

Share Document