Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Interactions in Model Ionic Dyads and Triads Containing Tetrel Atoms.

ABSTRACT: The interactions in model ionic YTX3···Z (Y = NC, F, Cl, Br; X = F, Cl, Br, Z = F-, Cl-, Br-, Li+) dyads containing the tetrel atoms, T = C, Si, Ge, were studied using ab initio computational methods, including an energy decomposition analysis, which found that the YTX3 molecules were stabilized by both anions (via tetrel bonding) and cations (via polarization). For the tetrel-bonded dyads, both the electrostatic and polarization forces make comparable contributions to the binding in the C-containing dyads, whereas, electrostatic forces are by far the largest contributor to the binding in the Si- and Ge-containing analogues. Model metastable Li+···NCTCl3···F- (T = C, Si, Ge) triads were found to be lower in energy than the combined energy of the Li+ + NCTCl3 + F- fragments. The pair energies and cooperative energies for these highly polar triads were also computed and discussed.

SUBMITTER: McDowell SAC

PROVIDER: S-EPMC7570900 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Interactions in Model Ionic Dyads and Triads Containing Tetrel Atoms.

McDowell Sean A C SAC Wang Ruijing R Li Qingzhong Q

Molecules (Basel, Switzerland) 20200914 18

The interactions in model ionic YTX3···Z (Y = NC, F, Cl, Br; X = F, Cl, Br, Z = F-, Cl-, Br-, Li+) dyads containing the tetrel atoms, T = C, Si, Ge, were studied using ab initio computational methods, including an energy decomposition analysis, which found that the YTX3 molecules were stabilized by both anions (via tetrel bonding) and cations (via polarization). For the tetrel-bonded dyads, both the electrostatic and polarization ...[more]

PMID: 32937741

Similar Datasets

BODIPY dyads and triads: synthesis, optical, electrochemical and transistor properties.

Project description:A series of D-A dyads and D-A-D triads molecular systems based on triphenylamine and 9-ethyl-carbarzole as donor (D) and BODIPY as acceptor (A) has been designed and synthesized. The optoelectronic properties including optical, electrochemical, and charge carrier mobility of these molecules have been investigated. We found that the D-A-D triads exhibited broader absorption, raising the HOMO energy levels and increase hole carrier mobilities. Analysis surface morphology revealed that BODIPY containing carbazole demonstrated smooth film and no macro phase aggregation was observed upon thermal annealing.

| S-EPMC5945575 | biostudies-literature

Association analysis of complex diseases using triads, parent-child dyads and singleton monads.

Project description:Triad families are routinely used to test association between genetic variants and complex diseases. Triad studies are important and popular since they are robust in terms of being less prone to false positives due to population structure. In practice, one may collect not only complete triads, but also incomplete families such as dyads (affected child with one parent) and singleton monads (affected child without parents). Since there is a lack of convenient algorithms and software to analyze the incomplete data, dyads and monads are usually discarded. This may lead to loss of power and insufficient utilization of genetic information in a study.We develop likelihood-based statistical models and likelihood ratio tests to test for association between complex diseases and genetic markers by using combinations of full triads, parent-child dyads, and affected singleton monads for a unified analysis. A likelihood is calculated directly to facilitate the data analysis without imputation and to avoid computational complexity. This makes it easy to implement the models and to explain the results.By simulation studies, we show that the proposed models and tests are very robust in terms of accurately controlling type I error evaluations, and are powerful by empirical power evaluations. The methods are applied to test for association between transforming growth factor alpha (TGFA) gene and cleft palate in an Irish study.

| S-EPMC3844511 | biostudies-literature

Kea, Nestor notabilis, achieve cooperation in dyads, triads, and tetrads when dominants show restraint.

Project description:Animal cooperation in the wild often involves multiple individuals that must tolerate each other in close proximity. However, most cooperation experiments in the lab are done with two animals, that are often also physically separated. Such experiments are useful for answering some pertinent questions, for example about the understanding of the role of the partner and strategies of partner control, but say little about factors determining successful cooperation with multiple partners in group settings. We explored the influence of dominance, rank distance, tolerance, affiliation, and coordination by testing kea parrots with a box requiring two, three, or four chains to be pulled simultaneously to access food rewards. The reward could be divided unevenly, but not monopolized completely. Eventually dyadic, triadic, and tetradic cooperation tasks were solved, showing that non-human animals are capable of tetradic cooperation in an experimental setup. Starting with two chains, we found that in a dyad monopolization of the box by the highest-ranking bird was the largest obstacle preventing successful cooperation. High-ranking birds learned to restrain themselves from monopolizing the box during a single session in which monopolization was hindered by the presence of a large number of birds. Thereafter, restraint by dominants remained the strongest factor determining success in the first trial in dyadic, triadic, and tetradic setups. The probability of success increased with the degree of restraint shown by all dominant subjects present. Previous experience with the task contributed to success in subsequent sessions, while increasing rank distance reduced success notably in the four-chain setup.

| S-EPMC7979628 | biostudies-literature

Engineering Crystals Using sp3 -C Centred Tetrel Bonding Interactions.

Project description:1,1,2,2-Tetracyanocyclopropane derivatives 1 and 2 were designed and synthesized to probe the utility of sp3 -C centred tetrel bonding interactions in crystal engineering. The crystal packing of 1 and 2 and their 1,4-dioxane cocrystals is dominated by sp3 -C(CN)2 ???O interactions, has significant C???O van der Waals overlap (?0.266?Å) and DFT calculations indicate interaction energies of up to -11.0?kcal?mol-1 . A cocrystal of 2 with 1,4-thioxane reveals that the cyclopropane synthon prefers interacting with O over S. Computational analyses revealed that the electropositive C2 (CN)4 pocket in 1 and 2 can be seen as a strongly directional 'tetrel-bond donor', similar to halogen bond or hydrogen bond donors. This disclosure is expected to have implications for the utility of such 'tetrel bond donors' in molecular disciplines such as crystal engineering, supramolecular chemistry, molecular recognition and medicinal chemistry.

| S-EPMC7496358 | biostudies-literature

Testing haplotype-environment interactions using case-parent triads.

Project description:ObjectiveJoint analysis of multiple SNP markers can be informative, but studying joint effects of haplotypes and environmental exposures is challenging. Population structure can involve both genes and exposures and a case-control study is susceptible to bias from either source of stratification. We propose a procedure that uses case-parent triad data and, though not fully robust, resists bias from population structure.MethodsOur procedure assumes that haplotypes under study have no influence on propensity to exposure. Then, under a no-interaction null hypothesis (multiplicative scale), transmission of a causative haplotype from parents to affected offspring might show distortion from Mendelian proportions but should be independent of exposure. We used this insight to develop a permutation test of no haplotype-by-exposure interaction.ResultsSimulations showed that our proposed test respects the nominal Type I error rate and provides good power under a variety of scenarios. We illustrate by examining whether SNP variants in GSTP1 modify the association between maternal smoking and oral clefting.ConclusionOur procedure offers desirable features: no need for haplotype estimation, validity under unspecified genetic main effects, tolerance to Hardy-Weinberg disequilibrium, ability to handle missing genotypes and a relatively large number of SNPs. Simulations suggest resistance to bias due to exposure-related population stratification.

| S-EPMC2912643 | biostudies-literature

Ionic scattering factors of atoms that compose biological molecules.

Project description:Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac-Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O-. Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and charged atoms in the spatial-resolution range explored in structural biology. The calculated X-ray and electron scattering factors have then been parameterized for the major scattering curve models used in X-ray and electron protein crystallography and single-particle cryo-EM. The X-ray and electron scattering factors and the fitting parameters are presented for future reference.

| S-EPMC5929380 | biostudies-literature

Comparison between Tetrel Bonded Complexes Stabilized by ? and ? Hole Interactions.

Project description:The ?-hole tetrel bonds formed by a tetravalent molecule are compared with those involving a ?-hole above the tetrel atom in a trivalent bonding situation. The former are modeled by TH?, TH?F, and TH?F? (T = Si, Ge, Sn) and the latter by TH?=CH?, THF=CH?, and TF?=CH?, all paired with NH? as Lewis base. The latter ?-bonded complexes are considerably more strongly bound, despite the near equivalence of the ? and ?-hole intensities. The larger binding energies of the ?-dimers are attributed to greater electrostatic attraction and orbital interaction. Each progressive replacement of H by F increases the strength of the tetrel bond, whether ? or ?. The magnitudes of the maxima of the molecular electrostatic potential in the two types of systems are not good indicators of either the interaction energy or even the full Coulombic energy. The geometry of the Lewis acid is significantly distorted by the formation of the dimer, more so in the case of the ?-bonded complexes, and this deformation intensifies the ? and ? holes.

| S-EPMC6100375 | biostudies-literature

Interactions of Biodegradable Ionic Liquids with a Model Naphthenic Acid.

Project description:Density functional theory models are used to examine five biodegradable ionic liquids (ILs) each one consisting of a substitutional group (-OH, -NH2, -COOH, -COOCH3, and -OCH3) incorporated into the cation of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]). The results reveal that hydrogen atoms in -NH2, -COOH, and -COOCH3 form intramolecular hydrogen bonds with fluorine atoms in [BF4]-, whereas hydrogen atoms in -OH and -OCH3 do not form hydrogen bonds with [BF4]-. Further analysis of electron density at bond critical points and noncovalent interactions suggest that [BMIM][BF4] with -COOH has stronger intramolecular hydrogen bonds than other ILs. The extraction mechanism for a model naphthenic acid is hydrogen bonding, with F···H being the strongest hydrogen bond and O···H ranking second. More intermolecular hydrogen bonds occur when model naphthenic acid is adsorbed by [BMIM][BF4] with -COOH and -COOCH3. The interaction energy between model naphthenic acid and ILs with -COOH and -COOCH3 is higher than that with -OH, -NH2, and -OCH3.

| S-EPMC5760565 | biostudies-literature

Design of activated serine-containing catalytic triads with atomic-level accuracy.

Project description:A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.

| S-EPMC4048123 | biostudies-literature

Multi-functional magnesium alloys containing interstitial oxygen atoms.

Project description:A new class of magnesium alloys has been developed by dissolving large amounts of oxygen atoms into a magnesium lattice (Mg-O alloys). The oxygen atoms are supplied by decomposing titanium dioxide nanoparticles in a magnesium melt at 720?°C; the titanium is then completely separated out from the magnesium melt after solidification. The dissolved oxygen atoms are located at the octahedral sites of magnesium, which expand the magnesium lattice. These alloys possess ionic and metallic bonding characteristics, providing outstanding mechanical and functional properties. A Mg-O-Al casting alloy made in this fashion shows superior mechanical performance, chemical resistance to corrosion, and thermal conductivity. Furthermore, a similar Mg-O-Zn wrought alloy shows high elongation to failure (>50%) at room temperature, because the alloy plastically deforms with only multiple slips in the sub-micrometer grains (<300 nm) surrounding the larger grains (~15 ?m). The metal/non-metal interstitial alloys are expected to open a new paradigm in commercial alloy design.

| S-EPMC4791639 | 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