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The Chemical Bond: When Atom Size Instead of Electronegativity Difference Determines Trend in Bond Strength.

ABSTRACT: We have quantum chemically analyzed element-element bonds of archetypal H_n X-YH_n molecules (X, Y=C, N, O, F, Si, P, S, Cl, Br, I), using density functional theory. One purpose is to obtain a set of consistent homolytic bond dissociation energies (BDE) for establishing accurate trends across the periodic table. The main objective is to elucidate the underlying physical factors behind these chemical bonding trends. On one hand, we confirm that, along a period (e. g., from C-C to C-F), bonds strengthen because the electronegativity difference across the bond increases. But, down a period, our findings constitute a paradigm shift. From C-F to C-I, for example, bonds do become weaker, however, not because of the decreasing electronegativity difference. Instead, we show that the effective atom size (via steric Pauli repulsion) is the causal factor behind bond weakening in this series, and behind the weakening in orbital interactions at the equilibrium distance. We discuss the actual bonding mechanism and the importance of analyzing this mechanism as a function of the bond distance.

SUBMITTER: Blokker E

PROVIDER: S-EPMC9298008 | biostudies-literature |

REPOSITORIES: biostudies-literature

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In-Situ Electronegativity and the Bridging of Chemical Bonding Concepts.

Project description:One challenge in chemistry is the plethora of often disparate models for rationalizing the electronic structure of molecules. Chemical concepts abound, but their connections are often frail. This work describes a quantum-mechanical framework that enables a combination of ideas from three approaches common for the analysis of chemical bonds: energy decomposition analysis (EDA), quantum chemical topology, and molecular orbital (MO) theory. The glue to our theory is the electron energy density, interpretable as one part electrons and one part electronegativity. We present a three-dimensional analysis of the electron energy density and use it to redefine what constitutes an atom in a molecule. Definitions of atomic partial charge and electronegativity follow in a way that connects these concepts to the total energy of a molecule. The formation of polar bonds is predicted to cause inversion of electronegativity, and a new perspective of bonding in diborane and guanine-cytosine base-pairing is presented. The electronegativity of atoms inside molecules is shown to be predictive of pKa .

| S-EPMC9299076 | biostudies-literature

Cell Size Determines the Strength of the Spindle Assembly Checkpoint during Embryonic Development.

Project description:The spindle assembly checkpoint (SAC) delays mitotic progression when chromosomes are not properly attached to microtubules of the mitotic spindle. Cells vary widely in the extent to which they delay mitotic progression upon SAC activation. To explore the mechanisms that determine checkpoint strength in different cells, we systematically measured the mitotic delay induced by microtubule disruption at different stages of embryogenesis in Caenorhabditis elegans. Strikingly, we observed a gradual increase in SAC strength after each round of division. Analysis of mutants that alter cell size or ploidy revealed that SAC strength is determined primarily by cell size and the number of kinetochores. These findings provide clear evidence in vivo that the kinetochore-to-cytoplasm ratio determines the strength of the SAC, providing new insights into why cells exhibit such large variations in their SAC responses.

| S-EPMC4748171 | biostudies-literature

Signaling strength determines proapoptotic functions of STING

Project description:T cells exhibit an intensified STING response, which leads to the expression of a distinct set of genes and results in the induction of apoptosis

2017-06-24 | GSE100411 | GEO

Strength of TRAF6 signalling determines osteoclastogenesis.

Project description:TRANCE/TRAF6 signalling governs osteoclastogenesis in vivo. Only the TRANCE receptor (TRANCE-R) has been shown to induce osteoclastogenesis, even though other immune receptors, including CD40 and IL-1R/Toll-like receptor, use TRAF6 to activate overlapping signalling cascades. These observations led us to question whether qualitative or quantitative differences exist between the TRAF6-mediated signals induced by TRANCE and by other ligand-receptor pairs. Here we show that stimulation by overexpressed wild-type CD40 can induce osteoclastogenesis. Stimulation through modified CD40 containing increased numbers of TRAF6-binding sites in the cytoplasmic tails showed a dose-dependent increase in the activation of p38 kinase and more pronounced osteoclastogenesis. Moreover, precursors overexpressing TRAF6 differentiate into osteoclasts in the absence of additional signals from TRANCE. Our results suggest that differences in the osteoclastogenesis-inducing capacity of TRANCE-R versus other TRAF6-associated receptors may in part stem from a quantitative difference in the TRAF6-mediated signals.

| S-EPMC1299255 | biostudies-literature

Difference between Metal-S and Metal-O Bond Orders: A Descriptor of Oxygen Evolution Activity for Isolated Metal Atom-Doped MoS2 Nanosheets.

Project description:Exploration of predictive descriptors for the performance of electrocatalytic oxygen evolution reaction (OER) is significant for material development in many energy conversion processes. In this work, we used high-throughput density functional theory (DFT) calculations to systematically investigate the OER performance of thirty kinds of isolated transition metal atoms-doped ultrathin MoS2 nanosheets (M-UMONs). The results showed that the OER activity could be a function of the decorated transition metal-sulfur (M-S) bond orders with a volcanic-shaped correlation, and a strong correlation could be found when the difference of the M-S bond orders and corresponding metal-oxygen (M-O) bond orders were taken into consideration, implying that the difference in M-S and M-O bond orders could be a predictive descriptor of OER activity for M-UMON system. This successful result also implies this calculation-based method for the exploring of descriptors would also provide a new promising avenue for the discovery of high-performance OER catalysts.

| S-EPMC6806669 | biostudies-other

Signalling strength determines proapoptotic functions of STING.

Project description:Mammalian cells use cytosolic nucleic acid receptors to detect pathogens and other stress signals. In innate immune cells the presence of cytosolic DNA is sensed by the cGAS-STING signalling pathway, which initiates a gene expression programme linked to cellular activation and cytokine production. Whether the outcome of the STING response varies between distinct cell types remains largely unknown. Here we show that T cells exhibit an intensified STING response, which leads to the expression of a distinct set of genes and results in the induction of apoptosis. Of note, this proapoptotic STING response is still functional in cancerous T cells and delivery of small molecule STING agonists prevents in vivo growth of T-cell-derived tumours independent of its adjuvant activity. Our results demonstrate how the magnitude of STING signalling can shape distinct effector responses, which may permit for cell type-adjusted behaviours towards endogenous or exogenous insults.The cGAS/STING signalling pathway is responsible for sensing intracellular DNA and activating downstream inflammatory genes. Here the authors show mouse primary T cells and T leukaemia are hyperresponsive to STING agonist, and this strong STING signalling is associated with apoptosis induction.

| S-EPMC5585373 | biostudies-literature

Metal-ligand bond strength determines the fate of organic ligands on the catalyst surface during the electrochemical CO<sub>2</sub> reduction reaction.

Project description:Colloidally synthesised nanocrystals (NCs) are increasingly utilised as catalysts to drive both thermal and electrocatalytic reactions. Their well-defined size and shape, controlled by organic ligands, are ideal to identify the parameters relevant to the activity, selectivity and stability in catalysis. However, the impact of the native surface ligands during catalysis still remains poorly understood, as does their fate. CuNCs are among the state-of-the-art catalysts for the electrochemical CO2 reduction reaction (CO2RR). In this work, we study CuNCs that are capped by different organic ligands to investigate their impact on the catalytic properties. We show that the latter desorb from the surface at a cathodic potential that depends on their binding strength with the metal surface, rather than their own electroreduction potentials. By monitoring the evolving surface chemistry in situ, we find that weakly bound ligands desorb very rapidly while strongly bound ligands impact the catalytic performance. This work provides a criterion to select labile ligands versus ligands that will persist on the surface, thus offering opportunity for interface design.

| S-EPMC8161676 | biostudies-literature

Modulating the Bond Strength of DNA-Nanoparticle Superlattices.

Project description:A method is introduced for modulating the bond strength in DNA-programmable nanoparticle (NP) superlattice crystals. This method utilizes noncovalent interactions between a family of [Ru(dipyrido[2,3-a:3',2'-c]phenazine)(N-N)2](2+)-based small molecule intercalators and DNA duplexes to postsynthetically modify DNA-NP superlattices. This dramatically increases the strength of the DNA bonds that hold the nanoparticles together, thereby making the superlattices more resistant to thermal degradation. In this work, we systematically investigate the relationship between the structure of the intercalator and its binding affinity for DNA duplexes and determine how this translates to the increased thermal stability of the intercalated superlattices. We find that intercalator charge and steric profile serve as handles that give us a wide range of tunability and control over DNA-NP bond strength, with the resulting crystal lattices retaining their structure at temperatures more than 50 °C above what nonintercalated structures can withstand. This allows us to subject DNA-NP superlattice crystals to conditions under which they would normally melt, enabling the construction of a core-shell (gold NP-quantum dot NP) superlattice crystal.

| S-EPMC8189661 | biostudies-literature

Intramolecular Hydrogen Bonds in Normal and Sterically Compressed o-Hydroxy Aromatic Aldehydes. Isotope Effects on Chemical Shifts and Hydrogen Bond Strength.

Project description:A number of o-hydroxy aromatic aldehydes have been synthesized to illustrate the effect of steric compression and O···O distances on the intramolecular hydrogen bond and the hydrogen bond energies. Hydrogen bond energies have been calculated using the 'hb and out' method using either the MP2 method or the B3LYP functional with the basis set 6-311++G(d,p). However, several compounds cannot be treated this way. Hydrogen bond energies are also determined using electron densities at bond critical points and these results are in good agreement with the results of the 'hb and out' model. Two-bond deuterium isotope effects on 13C chemical shifts are suggested as an experimental way to obtain information on hydrogen bond energies as they easily can be measured. Isotope effects on aldehyde proton chemical shifts have also been measured. The former show very good correlation with the hydrogen bond energies and the latter are related to short O···O distances. Short O···O distances can be obtained as the result of short C=C bond lengths, conjugative effects, and steric compression of the aldehyde group. Short O···O distances are in general related to high hydrogen bond energies in these intramolecularly hydrogen-bonded systems of resonance assisted hydrogen bond (RAHB) type.

| S-EPMC6943505 | biostudies-literature

All-Atom Simulations and Free-Energy Calculations of Antibodies Bound to the Spike Protein of SARS-CoV-2: The Binding Strength and Multivalent Hydrogen-Bond Interactions.

Project description:All-atom simulations of various antibodies bound to the receptor-binding domain (RBD) of the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are performed. Binding free energies calculated from umbrella sampling simulations show the strong binding between SARS-CoV-2 RBDs and antibodies, in agreement with recent experiments. Binding strengths of antibodies slightly differ, as further confirmed by calculating solvent accessible surface areas. Polar uncharged residues of RBD more predominantly bind to antibodies than do charged or hydrophobic residues of RBD. In particular, the binding between RBD and antibody is more significantly stabilized by multivalent hydrogen bonds of RBD residues (≈406th-505th) than by locally formed hydrogen bonds of only a few RBD residues (≈417th-487th or ≈487th-505th). Hydrogen-bond analyses reveal key residues of RBD for strong hydrogen-bond interactions between RBDs and antibodies, which help in the rational design of vaccine and drug molecules targeting the S protein of SARS-CoV-2.

| S-EPMC8250114 | biostudies-literature

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