Two-dimensional condensation of nucleobases: A comparative study of halogen derivatives of cytosine

2009 ◽  
Vol 74 (11-12) ◽  
pp. 1611-1622 ◽  
Author(s):  
Lukáš Fojt ◽  
Vladimír Vetterl ◽  
Thomas Doneux
Keyword(s):  
Hydrogen Bonding ◽  
Intermolecular Interactions ◽  
Electrostatic Interactions ◽  
Dispersion Forces ◽  
Two Dimensional ◽  
Electrode Surfaces ◽  
Different Types ◽  
Self Association ◽  
Derivatives Of ◽  
Third Derivative

The high ability of self-association of nucleic acid components leads to a two-dimensional (2D) condensation at electrode surfaces. The driving force of the process resides in the intermolecular interactions, such as dispersion forces, hydrogen bonding or electrostatic interactions. In this study, the condensation of 5-halogen cytosine derivatives (5-fluorocytosine, 5-bromocytosine and 5-iodocytosine) at the hanging mercury drop electrode was investigated to evaluate the influence of the different types of intermolecular interactions in the phenomenon. All of these derivatives form 2D capacitance pits, but in distinct conditions of pH, concentrations and temperature. Dispersion forces are identified as the main contributor to the 2D condensation of 5-iodocytosine, while for 5-fluorocytosine this is hydrogen bonding in hemiprotonated dimers. The third derivative, 5-bromocytosine, is an intermediate case between the two formers.

Dissecting intermolecular interactions in the condensed phase of ibuprofen and related compounds: the specific role and quantification of hydrogen bonding and dispersion forces

2020 ◽  
Vol 22 (9) ◽  
pp. 4896-4904 ◽  
Author(s):  
V. N. Emel’yanenko ◽  
P. Stange ◽  
J. Feder-Kubis ◽  
S. P. Verevkin ◽  
R. Ludwig
Keyword(s):  
Hydrogen Bonding ◽  
Infrared Spectroscopy ◽  
Quantum Chemistry ◽  
Intermolecular Interactions ◽  
Condensed Phase ◽  
Specific Role ◽  
Dispersion Interaction ◽  
Dispersion Forces ◽  
Related Compounds

Hydrogen bonding and dispersion interaction in liquid ibuprofen is analyzed by thermodynamic methods, infrared spectroscopy and quantum chemistry.

scholarly journals 3-(3,5-Dichlorophenyl)benzene-1,2-diol

IUCrData ◽  
2019 ◽  
Vol 4 (9) ◽  
Author(s):  
Ram Dhakal ◽  
Sean Parkin ◽  
Hans-Joachim Lehmler
Keyword(s):  
Hydrogen Bonding ◽  
Dihedral Angle ◽  
Intermolecular Interactions ◽  
Two Dimensional ◽  
Dimensional Network ◽  
Benzene Rings

The title structure, C12H8Cl2O2, is a putative metabolite of 3,5-dichlorobiphenyl (PCB 14). The dihedral angle between the two benzene rings of the title compounds is 58.86 (4)°. In the crystal, it displays intra- and intermolecular O—H...O hydrogen bonding and intermolecular O—H...Cl hydrogen...chlorine interactions. The intermolecular interactions form a two-dimensional network parallel to (010).

scholarly journals Crystal structure of diethyl 3-(3-chlorophenyl)-2,2-dicyanocyclopropane-1,1-dicarboxylate

2016 ◽  
Vol 72 (2) ◽  
pp. 253-256
Author(s):  
Nóra Veronika May ◽  
Gyula Tamás Gál ◽  
Zsolt Rapi ◽  
Péter Bakó
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Layered Structure ◽  
Title Compound ◽  
Molecular Conformation ◽  
Two Dimensional ◽  
Free Molecule ◽  
Compound C

In the racemic title compound, C17H15ClN2O4, which has been synthesized and the crystal structure of the solvent-free molecule determined, the angle between the planes of the benzene and cyclopropane rings is 54.29 (10)°. The molecular conformation is stabilized by two weak intramolecular C—H...Ocarboxylinteractions. In the crystal, C—H...O hydrogen bonds form centrosymmetric cyclicR22(10) dimers which are linked into chain substructures extending alongc. Further C—H...Nnitrilehydrogen bonding, including a centrosymmetric cyclicR22(14) association, link the chain substructures, forming a two-dimensional layered structure extending across the approximateabplane. No significant π–π or halogen–halogen intermolecular interactions are present in the crystal.

scholarly journals The Effect of Deoxyfluorination on Intermolecular Interactions in the Crystal Structures of 1,6-Anhydro-2,3-epimino-hexopyranoses

Molecules ◽  
2022 ◽  
Vol 27 (1) ◽  
pp. 278
Author(s):  
Martin Jakubec ◽  
Ivana Císařová ◽  
Jindřich Karban ◽  
Jan Sýkora
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Hydroxy Group ◽  
Single Molecule ◽  
Electrostatic Interactions ◽  
Fluorine Atom ◽  
Weak Interactions ◽  
Qualitative Evaluation ◽  
Hydrogen Atoms

The effect of substitution on intermolecular interactions was investigated in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. The study focused on the qualitative evaluation of intermolecular interactions using DFT calculations and the comparison of molecular arrangements in the crystal lattice. Altogether, ten crystal structures were compared, including two structures of C4-deoxygenated, four C4-deoxyfluorinated and four parent epimino pyranoses. It was found that the substitution of the original hydroxy group by hydrogen or fluorine leads to a weakening of the intermolecular interaction by approximately 4 kcal/mol. The strength of the intermolecular interactions was found to be in the following descending order: hydrogen bonding of hydroxy groups, hydrogen bonding of the amino group, interactions with fluorine and weak electrostatic interactions. The intermolecular interactions that involved fluorine atom were rather weak; however, they were often supported by other weak interactions. The fluorine atom was not able to substitute the role of the hydroxy group in molecular packing and the fluorine atoms interacted only weakly with the hydrogen atoms located at electropositive regions of the carbohydrate molecules. However, the fluorine interaction was not restricted to a single molecule but was spread over at least three other molecules. This feature is a base for similar molecule arrangements in the structures of related compounds, as we found for the C4-Fax and C4-Feq epimines presented here.

Patterns of soft C—H...O hydrogen bonding in diaryl sulfones

2001 ◽  
Vol 57 (2) ◽  
pp. 190-200 ◽  
Author(s):  
Christopher Glidewell ◽  
William T. A. Harrison ◽  
John N. Low ◽  
Jamie G. Sime ◽  
James L. Wardell
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Cambridge Structural Database ◽  
Two Dimensional ◽  
One Dimensional ◽  
Different Types ◽  
Structural Database

In bis(4-tolyl) sulfone, C14H14O2S (1), 2,5,4′-trimethyldiphenyl sulfone, C15H16O2S (2), and 4-chlorodiphenyl sulfone, C12H9ClO2S (3), the molecules are linked by soft C—H...O hydrogen bonds into three different types of one-dimensional aggregate: simple chains in (1), molecular ladders in (2) and chains of fused rings in (3). In each of 3,4-dimethyl-4′-chlorodiphenyl sulfone, C14H13ClO2S (4), and 2,5-dimethyldiphenyl sulfone, C14H14O2S (5), the C—H...O hydrogen bonds link the molecules into two different types of two-dimensional sheet, based on a (4,4) net in (4) and a (3,6) net in (5). The patterns of soft C—H...O hydrogen bonds in (1)—(5) are compared with those in other diaryl sulfones, mainly retrieved from the Cambridge Structural Database, whose substitution patterns preclude the formation of hard hydrogen bonds. Observed aggregation modes range from the formation of no C—H...O hydrogen bonds at all, via finite (zero-dimensional) arrays through one-, two- and three-dimensional systems.

scholarly journals Determination of the dispersion forces in the gas phase structures of ionic liquids using exclusively thermodynamic methods

2021 ◽  
Author(s):  
Dzmitry H Zaitsau ◽  
Ralf Ludwig ◽  
Sergey P. Verevkin
Keyword(s):  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Thermodynamic Properties ◽  
Gas Phase ◽  
Coulomb Interaction ◽  
Dispersion Forces ◽  
Delicate Balance ◽  
Phase Structures ◽  
Different Types

Ionic liquids are described by a delicate balance of Coulomb interaction, hydrogen bonding and dispersion forces. Dissecting the different types of interaction from thermodynamic properties is still a challenge. Here,...

Template mediated crystal engineering

1994 ◽  
Vol 52 ◽  
pp. 480-481
Author(s):  
Brigid R. Heywood ◽  
S. Champ
Keyword(s):  
Crystal Engineering ◽  
Electrostatic Interactions ◽  
Alkyl Chain ◽  
Crystallographic Axis ◽  
Two Dimensional ◽  
Engineering Process ◽  
Solution Interface ◽  
Extensive Program ◽  
Geometric Homology ◽  
Long Alkyl Chain

Recent work on the crystallisation of inorganic crystals under compressed monomolecular surfactant films has shown that two dimensional templates can be used to promote the oriented nucleation of solids. When a suitable long alkyl chain surfactant is cast on the crystallisation media a monodispersied population of crystals forms exclusively at the monolayer/solution interface. Each crystal is aligned with a specific crystallographic axis perpendicular to the plane of the monolayer suggesting that nucleation is facilitated by recognition events between the nascent inorganic solid and the organic template.For example, monolayers of the long alkyl chain surfactant, stearic acid will promote the oriented nucleation of the calcium carbonate polymorph, calcite, on the (100) face, whereas compressed monolayers of n-eicosyl sulphate will induce calcite nucleation on the (001) face, (Figure 1 & 2). An extensive program of research has confirmed the general principle that molecular recognition events at the interface (including electrostatic interactions, geometric homology, stereochemical complementarity) can be used to promote the crystal engineering process.

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