Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Weak Intermolecular Interactions in a Series of Bioactive Oxazoles.

ABSTRACT: The intermolecular interactions in a series of nine similar 4,5-phenyl-oxazoles were studied on the basis of crystal structures determined by X-ray diffraction. The crystal architectures were analyzed for the importance and hierarchies of different, weak intermolecular interactions using three approaches: the geometrical characteristics, topological analysis (for the model based on the transfer of multipolar parameters), and energetics of the molecule-molecule interactions. The geometries of the molecules were quite similar and close to the typical values. The results of the analysis of the interactions suggest that the number of nonspecific interactions is more important than the apparent strength of the specific interactions. The interactions involving covalently bound bromine and divalent sulfur atoms were classified as secondary, they certainly did not define the crystal packing, and they played a minor role in the overall crystal cohesion energies. Incidentally, another method for confirming the degree of isostructurality, according to the topologies of the interactions, is described.

SUBMITTER: Grzeskiewicz AM

PROVIDER: S-EPMC8159086 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Weak interactions but potent effect: tunable mechanoluminescence by adjusting intermolecular C-H···? interactions.

Project description:A new mechanoluminescent material (4-(diphenylamino)phenyl)(4-(diphenylphosphanyl)phenyl)methanone (CDpP), which displays tunable mechanoluminescent emission colors, has been designed and successfully synthesized. CDpP shows two distinct mechanoluminescent colors (blue and green) in different crystalline states. Single-crystal analyses and femtosecond transient emission studies reveal that the striking tunable mechanoluminescence properties of CDpP mainly originate from the different C-H···? interactions in the crystal structures. CDpP crystals with more C-H···? interactions show blue mechanoluminescence (ML), and the emission is attributed to the locally excited (LE)-state because the twisting process for the excited state is restricted by C-H···? interactions. Conversely, CDpP crystals with fewer C-H···? interactions display green ML, in which the red-shifted emission band originates from the twisted intramolecular charge transfer (TICT) excited state because the diphenylamine moiety is relatively free to rotate. The manipulation of weak intermolecular interactions in the crystalline state is a useful and reliable strategy for the tuning of the ML emission wavelengths.

| S-EPMC6050600 | biostudies-literature

Intermolecular interactions in lipid/carotenoid monolayers.

Project description:The collapse pressure at the air-water interface of monomolecular films of 1,2-distearoyl derivatives of phosphatidylcholine and digalactosyldiacylglycerol containing various proportions of the carotenoid astaxanthin was related to the composition of the monolayer. The results were analysed by using a regular-association approximation by which it is assumed that there is a stepwise formation of ABi-type associations where A and B represent the diacyl lipid and astaxanthin respectively and 1 less than or equal to i less than or equal to 6. This treatment provides an adequate description of the experimental data and permits calculation of equilibrium constants for the steps in complex-formation; each step is said to have the same equilibrium constant. The value for the collapse-surface-pressure increment associated with formation of ABi complexes was also derived. Calculated values of equilibrium constants and collapse-surface-pressure increments are greater for phosphatidylcholine/astaxanthin mixed monolayers than for digalactosyldiacylglycerol/astaxanthin mixed monolayers. These differences are discussed in terms of intermolecular interactions between components in the two systems.

| S-EPMC1148631 | biostudies-other

Weak interactions in furan dimers.

Project description:Dimers of furan, 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran were investigated with the use of theoretical methods to determine the interactions that keep the molecules together. The QTAIM and NCI methods confirmed that for furan dimers the C-H⋯O hydrogen bond and stacking interactions can form the dimers with similar energy. For 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran, the decisive mechanism of dimer formation is the stacking interaction between the furan rings.

| S-EPMC6267657 | biostudies-literature

Weak Interactions and Instability Cascades.

Project description:Food web theory states that a weak interactor which is positioned in the food web such that it tends to deflect, or mute, energy away from a potentially oscillating consumer-resource interaction often enhances community persistence and stability. Here we examine how adding other weak interactions (predation/harvesting) on the stabilizing weak interactor alters the stability of food web using a set of well-established food web models/modules. We show that such "weak on weak" interaction chains drive an indirect dynamic cascade that can rapidly ignite a distant consumer-resource oscillator. Nonetheless, we also show that the "weak on weak" interactions are still more stable than the food web without them, and so weak interactions still generally act to stabilize food webs. Rather, these results are best interpreted to say that the degree of the stabilizing effect of a given important weak interaction can be severely compromised by other weak interactions (including weak harvesting).

| S-EPMC4518242 | biostudies-literature

Exploring weak intermolecular interactions in thiocyanate-bonded Zn(ii) and Cd(ii) complexes with methylimidazole: crystal structures, Hirshfeld surface analysis and luminescence properties.

Project description:Four new thiocyanate-Zn(ii) and -Cd(ii) complexes with 1-methylimidazole (1-MeIm) and 2-methylimidazole (2-MeIm), namely, Zn(1-MeIm)2(SCN)2 (1), Zn(2-MeIm)2(SCN)2 (2), Cd(1-MeIm)4(SCN)2 (3) and polymeric [Cd(2-MeIm)2(SCN)2] n (4), have been synthesized and characterized by IR, Raman and UV-Vis spectroscopy. The thermal behavior for all complexes was evaluated by thermo-gravimetric analysis and differential thermal analysis. The crystal structures of complexes 1-4 were solved by single-crystal X-ray diffraction methods. A study of intermolecular interactions in the solid state compounds revealed that molecules are linked by weak N-H⋯S and C-H⋯S hydrogen bonds and also by C-H⋯π interaction in the case of structures 2-4, which are responsible for the formation and stability of the molecular assemblies. Hirshfeld surfaces and 2D-fingerprint plots allowed us to visualize the intermolecular contacts and their relative contributions to the total surface for each compound. A comparative analysis against similar halogen-bonded complexes was carried out to investigate the tendency of inter-molecular interactions to form contacts in crystals by using the enrichment ratio descriptor. The emission spectra of the free imidazole derivatives and their Zn(ii) and Cd(ii) complexes were recorded in acetonitrile solutions. The emissions observed in the spectra of complexes were ascribed to the intra-ligand transitions and ligand-to-metal charge transfer and we have observed an interesting correlation between the fluorescence intensities and C-H⋯π interactions.

| S-EPMC9081733 | biostudies-literature

Intermolecular Interactions between Hsp90 and Hsp70.

Project description:Members of the Hsp90 and Hsp70 families of molecular chaperones are imp\ortant for the maintenance of protein homeostasis and cellular recovery following environmental stresses, such as heat and oxidative stress. Moreover, the two chaperones can collaborate in protein remodeling and activation. In higher eukaryotes, Hsp90 and Hsp70 form a functionally active complex with Hop (Hsp90-Hsp70 organizing protein) acting as a bridge between the two chaperones. In bacteria, which do not contain a Hop homolog, Hsp90 and Hsp70, DnaK, directly interact during protein remodeling. Although yeast possesses a Hop-like protein, Sti1, Hsp90, and Hsp70 can directly interact in yeast in the absence of Sti1. Previous studies showed that residues in the middle domain of Escherichia coli Hsp90 are important for interaction with the J-protein binding region of DnaK. The results did not distinguish between the possibility that (i) these sites were involved in direct interaction and (ii) the residues in these sites participate in conformational changes which are transduced to other sites on Hsp90 and DnaK that are involved in the direct interaction. Here we show by crosslinking experiments that the direct interaction is between a site in the middle domain of Hsp90 and the J-protein binding site of Hsp70 in both E. coli and yeast. Moreover, J-protein promotes the Hsp70-Hsp90 interaction in the presence of ATP, likely by converting Hsp70 into the ADP-bound conformation. The identification of the protein-protein interaction site is anticipated to lead to a better understanding of the collaboration between the two chaperones in protein remodeling.

| S-EPMC6599576 | biostudies-literature

Systematic Study of Solid-State Fluorescence and Molecular Packing of Methoxy-trans-Stilbene Derivatives, Exploration of Weak Intermolecular Interactions Based on Hirshfeld Surface Analysis

Project description:In recent years, fluorescent compounds that emit efficiently in the solid state have become particularly interesting, especially those that are easily prepared and inexpensive. Hence, exploring the photophysical properties of stilbene derivatives, supported by a detailed analysis of molecular packing obtained from single-crystal X-ray diffraction data, is a relevant area of research. A complete understanding of the interactions to determine the molecular packing in the crystal lattice and their effect on the material’s physicochemical properties is essential to tune various properties effectively. In the present study, we examined a series of methoxy-trans-stilbene analogs with substitution pattern-dependent fluorescence lifetimes between 0.82 and 3.46 ns and a moderate-to-high fluorescence quantum yield of 0.07–0.69. The relationships between the solid-state fluorescence properties and the structure of studied compounds based on X-ray analysis were investigated. As a result, the QSPR model was developed using PLSR (Partial Least Squares Regression). Decomposition of the Hirshfeld surfaces (calculated based on the arrangement of molecules in the crystal lattice) revealed the various types of weak intermolecular interactions that occurred in the crystal lattice. The obtained data, in combination with global reactivity descriptors calculated using HOMO and LUMO energy values, were used as explanatory variables. The developed model was characterized by good validation metrics (RMSECAL = 0.017, RMSECV = 0.029, R2CAL = 0.989, and R2CV = 0.968) and indicated that the solid-state fluorescence quantum yield of methoxy-trans-stilbene derivatives was mainly dependent on weak intermolecular C…C contacts corresponding to π-π stacking and C…O/O…C interactions. To a lesser extent and inversely proportional, the fluorescence quantum yield was affected by the interactions of the type O…H/H…O and H…H and the electrophilicity of the molecule.

| S-EPMC10139126 | biostudies-literature

An umpolung strategy for intermolecular [2 + 2 + 1] cycloaddition of aryl aldehydes and nitriles: a facile access to 2,4,5-trisubstituted oxazoles.

Project description:We have described the first example of an umpolung strategy for intermolecular [2 + 2 + 1] cycloaddition between two aryl aldehydes and a nitrile under the influence of TMSOTf that proceeds through the formation of N-C, O-C and C-C bonds providing a simple synthetic protocol for obtaining 2,4,5-trisubstituted oxazoles.

| S-EPMC9278343 | biostudies-literature

Intermolecular π-π Stacking Interactions Made Visible.

Project description:Mixing the liquids hexafluorobenzene (1) and 1,3,5-trimethylbenzene (mesitylene, 2) results in a crystalline solid with a melting point of 34 °C. The solid consists of alternating π-π stacked pillars of both aromatics. This simple experiment can be used to visually demonstrate the existence and the effect of noncovalent intermolecular π-π stacking interactions. Both benzene derivatives are relatively benign and widely available, and the experiment can be performed within minutes for less than $15 when done on a 22 mL scale (total volume). The demonstration is very robust, as 1:2 mixtures in volume ratios between 2/3 and 3/2 all give a visually similar result (molar ratios of 1.8-0.8). Substituting 2 with the liquid aromatics o-xylene, p-xylene, and aniline also resulted in the formation of a crystalline solid, while using many other liquid aromatics did not.

| S-EPMC7876799 | biostudies-literature

Intermolecular noncovalent interactions with carbon in solution.

Project description:One of the most familiar carbon-centered noncovalent interactions (NCIs) involving an antibonding π*-orbital situated at the Bürgi-Dunitz angle from the electron donor, mostly lone pairs of electrons, is known as n → π* interactions, and if it involves a σ* orbital in a linear fashion, then it is known as the carbon bond. These NCIs can be intra- or inter-molecular and are usually weak in strength but have a paramount effect on the structure and function of small-molecular crystals and proteins. Surprisingly, the experimental evidence of such interactions in the solution phase is scarce. It is even difficult to determine the interaction energy in the solution. Using NMR spectroscopy aided with molecular dynamics (MD) simulation and high-level quantum mechanical calculations, herein we provide the experimental evidence of intermolecular carbon-centered NCIs in solution. The challenge was to find appropriate heterodimers that could sustain room temperature thermal energy and collisions from the solvent molecules. However, after several trial model compounds, the pyridine-N-oxide:dimethyltetracyanocyclopropane (PNO-DMTCCP) complex was found to be a good candidate for the investigation. NBO analyses show that the PNO:DMTCCP complex is stabilized mainly by intermolecular n → π* interaction when a weaker carbon bond gives extra stability to the complex. From the NMR study, it is observed that the NCIs between DMTCCP and PNO are enthalpy driven with an enthalpy change of -28.12 kJ mol-1 and dimerization energy of ∼-38 kJ mol-1 is comparable to the binding energies of a conventional hydrogen-bonded dimer. This study opens up a new strategy to investigate weak intermolecular interactions such as n → π* interaction and carbon bonds in the solution phase.

| S-EPMC9749111 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data