Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Planar versus non-planar: The important role of weak C-H⋯O hydrogen bonds in the crystal structure of 5-methyl-salicyl-aldehyde.

ABSTRACT: The crystal structure of 5-methyl-salicyl-aldehyde (5-MSA; systematic name 2-hy-droxy-5-methyl-benzaldehyde), C₈H₈O₂, was discovered to be a textbook example of the drastic structural changes caused by just a few weak C-H⋯O inter-actions due to the additional methyl-ation of the aromatic ring compared to salicyl-aldehyde SA. This weak inter-molecular hydrogen bonding is observed between aromatic or methyl carbon donor atoms and hydroxyl or aldehyde acceptor oxygen atoms with d(D⋯A) = 3.4801 (18) and 3.499 (11) Å. The mol-ecule shows a distorted geometry of the aromatic ring with elongated bonds in the vicinity of substituted aldehyde and hydroxyl carbon atoms. The methyl hydrogen atoms are disordered over two sets of sites with occupancies of 0.69 (2) and 0.31 (2).

SUBMITTER: Baisch U

PROVIDER: S-EPMC5290555 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Planar versus non-planar: The important role of weak C-H⋯O hydrogen bonds in the crystal structure of 5-methyl-salicyl-aldehyde.

Baisch Ulrich U Scicluna Marie Christine MC Näther Christian C Vella-Zarb Liana L

Acta crystallographica. Section E, Crystallographic communications 20170113 Pt 2

The crystal structure of 5-methyl-salicyl-aldehyde (5-MSA; systematic name 2-hy-droxy-5-methyl-benzaldehyde), C8H8O2, was discovered to be a textbook example of the drastic structural changes caused by just a few weak C-H⋯O inter-actions due to the additional methyl-ation of the aromatic ring compared to salicyl-aldehyde SA. This weak inter-molecular hydrogen bonding is observed between aromatic or methyl carbon donor atoms and hydroxyl or aldehyde ...[more]

PMID: 28217332

Similar Datasets

Weak C-H···X (X = O, N) hydrogen bonds in the crystal structure of dihydroberberine.

Project description:Dihydroberberine (systematic name: 9,10-dimethoxy-6,8-dihydro-5H-1,3-dioxolo[4,5-g]isoquinolino[3,2-a]isoquinoline), C20H19NO4, a reduced form of pharmacologically important berberine, crystallizes from ethanol without interstitial solvent. The molecule shows a dihedral angle of 27.94 (5)° between the two arene rings at the ends of the molecule, owing to the partial saturation of the inner quinolizine ring system. Although lacking classical O-H or N-H donors, the packing in the crystalline state is clearly governed by C-H···N and C-H···O hydrogen bonds involving the two acetal-type C-H bonds of the 1,3-dioxole ring. Each dihydroberberine molecule is engaged in four hydrogen bonds with neighbouring molecules, twice as donor and twice as acceptor, thus forming a two-dimensional sheet network that lies parallel to the (100) plane.

| S-EPMC4165590 | biostudies-literature

4-(Diethyl-amino)-salicyl-aldehyde azine.

Project description:The title compound, C(22)H(30)N(4)O(2), has a crystallographic inversion center located at the mid-point of the N-N single bond. Apart from the four ethyl C atoms, the non-H atoms are nearly coplanar with a mean deviation of 0.0596 (2) Å. An intra-molecular O-H⋯N hydrogen bond occurs. In the crystal, weak inter-molecular C-H⋯O hydrogen bonds link the mol-ecules into layers parallel to (100).

| S-EPMC3089320 | biostudies-literature

Cooperative Effects in Weak Interactions: Enhancement of Tetrel Bonds by Intramolecular Hydrogen Bonds.

Project description:A series of silyl and germanium complexes containing halogen atoms (fluorine and chlorine atoms) and exhibiting tetrel bonds with Lewis bases were analyzed by means of Møller-Plesset computational theory. Binding energies of germanium derivatives were more negative than silicon ones. Amongst the different Lewis bases utilized, ammonia produced the strongest tetrel bonded complexes in both Ge and Si cases, and substitution of the F atom by Cl led to stronger complexes with an ethylene backbone. However, with phenyl backbones, the fluorosilyl complexes were shown to be less stable than the chlorosilyl ones, but the opposite occurred for halogermanium complexes. In all the cases studied, the presence of a hydroxyl group enhanced the tetrel bond. That effect becomes more remarkable when an intramolecular hydrogen bond between the halogen and the hydrogen atom of the hydroxyl group takes places.

| S-EPMC6359400 | biostudies-literature

Salicyl-aldehyde-4-(dimethyl-amino)-pyridine (1/1).

Project description:In the title compound, C(7)H(10)N(2)·C(7)H(6)O(2), the components are linked by an O-H⋯N hydrogen bond. The mean planes of two mol-ecules form a dihedral angle of 78.68 (5)°. The crystal packing exhibits weak non-classical C-H⋯O contacts.

| S-EPMC3008136 | biostudies-literature

Direct measurements of electric fields in weak OH···π hydrogen bonds.

Project description:Hydrogen bonds and aromatic interactions are of widespread importance in chemistry, biology, and materials science. Electrostatics play a fundamental role in these interactions, but the magnitude of the electric fields that support them has not been quantified experimentally. Phenol forms a weak hydrogen bond complex with the π-cloud of benzene, and we used this as a model system to study the role of electric fields in weak OH···π hydrogen bonds. The effects of complex formation on the vibrational frequency of the phenol OH or OD stretches were measured in a series of benzene-based aromatic solvents. Large shifts are observed and these can be converted into electric fields via the measured vibrational Stark effect. A comparison of the measured fields with quantum chemical calculations demonstrates that calculations performed in the gas phase are surprisingly effective at capturing the electrostatics observed in solution. The results provide quantitative measurements of the magnitude of electric fields and electrostatic binding energies in these interactions and suggest that electrostatics dominate them. The combination of vibrational Stark effect (VSE) measurements of electric fields and high-level quantum chemistry calculations is a general strategy for quantifying and characterizing the origins of intermolecular interactions.

| S-EPMC3202663 | biostudies-literature

Crystal structure, Hirshfeld surface analysis and computational study of a rhodamine B-salicyl-aldehyde Schiff base derivative.

Project description:The mol-ecular structure of the title compound {systematic name: 3',6'-bis(di-ethyl-amino)-2-[(2-hy-droxy-benzyl-idene)amino]-spiro-[isoindoline-1,9'-xan-then]-3-one}, C35H36N4O3 or RbSa, can be seen as being composed of two parts sharing a central quaternary carbon atom. Both the xanthene and iso-indole moieties are nearly planar: 14 atoms in the former moiety show an r.m.s. deviation of 0.0411 Å and eleven atoms in the latter moiety show an r.m.s. deviation of 0.0545 Å. These two planes are almost perpendicular to each other, the angle between the mean planes being 87.71 (2)°. The title compound appears to be in its enol form. The corresponding H atom was located and freely refined at a distance of 1.02 (3) Å from the O atom and 1.72 (2) Å from the N atom. The strong intra-molecular hydrogen bond O-H⋯N bridging the hydroxyl group and its neighboring nitro-gen atom forms an S(6) graph-set motif. Apart from the intra-molecular O-H⋯N hydrogen bond, C-H⋯O inter-actions are observed between two neighbouring RbSa mol-ecules related by an inversion center. The C-O donor-acceptor distance is 3.474 (2) Å. Moreover, C-H⋯π inter-actions are observed between the C-H bond of one of the ethyl groups and the centroid of the benzene ring of the iso-indole moiety. The C⋯centroid distance is 3.8191 (15) Å. No π-π inter-actions are observed in the crystal structure as the shortest distance between ring centroids is more than 4 Å. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H, C⋯H/H⋯C, O⋯H/H⋯O and N⋯H/H⋯N inter-actions. DFT calculations at the CAM-B3LYP/6-31 G(d) level were carried out to gain a better understanding of the relative energies and the tautomerization process between two possible conformers (keto and enol), as well as the transition state of the title compound.

| S-EPMC7336787 | biostudies-literature

Nature of Alkali- and Coinage-Metal Bonds versus Hydrogen Bonds.

Project description:We have quantum chemically studied the structure and nature of alkali- and coinage-metal bonds (M-bonds) versus that of hydrogen bonds between A-M and B- in archetypal [A-M⋅⋅⋅B]- model systems (A, B=F, Cl and M=H, Li, Na, Cu, Ag, Au), using relativistic density functional theory at ZORA-BP86-D3/TZ2P. We find that coinage-metal bonds are stronger than alkali-metal bonds which are stronger than the corresponding hydrogen bonds. Our main purpose is to understand how and why the structure, stability and nature of such bonds are affected if the monovalent central atom H of hydrogen bonds is replaced by an isoelectronic alkali- or coinage-metal atom. To this end, we have analyzed the bonds between A-M and B- using the activation strain model, quantitative Kohn-Sham molecular orbital (MO) theory, energy decomposition analysis (EDA), and Voronoi deformation density (VDD) analysis of the charge distribution.

| S-EPMC7898866 | biostudies-literature

Crystal structure of tris-(N-methyl-salicyl-aldiminato-κ(2) N,O)chromium(III).

Project description:The crystal structure of the title compound, [Cr(C8H8NO)3], is isotypic with the vanadium(III) analogue. The asymmetric unit consists of one Cr(3+) cation and three N-methyl-salicylaldiminate anions. The metal cation is octa-hedrally coordinated by three N,O-chelating N-methyl-salicylaldiminate ligands, leading to discrete and neutral complexes. In the crystal, neighbouring complexes are linked via C-H⋯O hydrogen-bonding inter-actions into chains propagating parallel to the c axis.

| S-EPMC4719857 | biostudies-literature

Synthesis and redetermination of the crystal structure of salicyl-aldehyde N(4)-morpholino-thio-semi-carbazone.

Project description:The structure of the title compound (systematic name: N-{[(2-hy-droxy-phen-yl)methyl-idene]amino}-morpholine-4-carbo-thio-amide), C12H15N3O2S, was prev-iously determined (Koo et al., 1977 ▸) using multiple-film equi-inclination Weissenberg data, but has been redetermined with higher precision to explore its conformation and the hydrogen-bonding patterns and supra-molecular inter-actions. The mol-ecular structure shows intra-molecular O-H⋯N and C-H⋯S inter-actions. The configuration of the C=N bond is E. The mol-ecule is slightly twisted about the central N-N bond. The best planes through the phenyl ring and the morpholino ring make an angle of 43.44 (17)°. In the crystal, the mol-ecules are connected into chains by N-H⋯O and C-H⋯O hydrogen bonds, which combine to generate sheets lying parallel to (002). The most prominent contribution to the surface contacts are H⋯H contacts (51.6%), as concluded from a Hirshfeld surface analysis.

| S-EPMC6727042 | biostudies-literature

Disulfonimides versus Phosphoric Acids in Bronsted Acid Catalysis: The Effect of Weak Hydrogen Bonds and Multiple Acceptors on Complex Structures and Reactivity.

Project description:In Brønsted acid catalysis, hydrogen bonds play a crucial role for reactivity and selectivity. However, the contribution of weak hydrogen bonds or multiple acceptors has been unclear so far since it is extremely difficult to collect experimental evidence for weak hydrogen bonds. Here, our hydrogen bond and structural access to Brønsted acid/imine complexes was used to analyze BINOL-derived chiral disulfonimide (DSI)/imine complexes. 1H and 15N chemical shifts as well as 1JNH coupling constants revealed for DSI/imine complexes ion pairs with very weak hydrogen bonds. The high acidity of the DSIs leads to a significant weakening of the hydrogen bond as structural anchor. In addition, the five hydrogen bond acceptors of DSI allow an enormous mobility of the imine in the binary DSI complexes. Theoretical calculations predict the hydrogen bonds to oxygen to be energetically less favored; however, their considerable population is corroborated experimentally by NOE and exchange data. Furthermore, an N-alkylimine, which shows excellent reactivity and selectivity in reactions with DSI, reveals an enlarged structural space in complexes with the chiral phosphoric acid TRIP as potential explanation of its reduced reactivity and selectivity. Thus, considering factors such as flexibility and possible hydrogen bond sites is essential for catalyst development in Brønsted acid catalysis.

| S-EPMC6863592 | biostudies-literature