Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hydrogen and proton exchange at carbon. Imbalanced transition state and mechanism crossover† † Electronic supplementary information (ESI) available: Methanol addition test to 1−−d1. Kinetics of the PTET reaction pathway. See DOI: 10.1039/c9sc05147c

ABSTRACT: A recent remarkable study of the C–H oxidation of substituted fluorenyl-benzoates together with the transfer of a proton to an internal receiving group by means of electron transfer outer-sphere oxidants, in the noteworthy absence of hydrogen-bonding interactions, is taken as an example to uncover the existence of a mechanism crossover, making the reaction pass from a CPET pathway to a PTET pathway as the driving force of the global reaction decreases. This was also the occasion to stress that considerations based on “imbalanced” or “asynchronous” transition states cannot replace activation/driving force models based on the quantum mechanical treatment of both electrons and transferring protons. Using the remarkable study of C–H oxidation of substituted fluorenyl-benzoates as an example, we have shown that a mechanism crossover takes place upon decreasing the driving force, from a CPET pathway to a PTET pathway.

SUBMITTER: Costentin C

PROVIDER: S-EPMC8146334 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Theoretical insights into excited-state hydrogen bonding effects and intramolecular proton transfer (ESIPT) mechanism for BTS system.

Project description:In this work, N,N'-bis(salicylidene)-(2-(3',4'-diaminophenyl)benzothiazole) (named as "BTS") system was studied about its excited-state intramolecular proton transfer (ESIPT) process. The analyses about reduced density gradient (RDG) reveal the formation of two intramolecular hydrogen bonds in BTS system. Bond lengths and angles, infrared (IR) vibrations as well as frontier molecular orbitals (MOs) using TDDFT method indicate that the strength of hydrogen bond should be enhanced in the S1 state. Particularly, hydrogen bond O1-H2···N3 undergoes larger variations compared with O4-H5···N6, which infers that hydrogen bond O1-H2···N3 may play a decisive role in the ESIPT process of BTS system. Given the two hydrogen bonds of BTS molecule, two types of potential energy curves have been constructed, which confirms that only single proton transfer process occurs due to lower energy barrier along with O1-H2···N3 rather than O4-H5···N6. This work not only presents a reasonable explanation for previous experiment, but also clarifies the specific ESIPT mechanism for BTS system.

| S-EPMC7083891 | biostudies-literature

Interplay between spin crossover and proton migration along short strong hydrogen bonds.

Project description:The iron(ii) salt [Fe(bpp)2](isonicNO)2·HisonicNO·5H2O (1) (bpp = 2,6-bis(pyrazol-3-yl)pyridine; isonicNO = isonicotinate N-oxide anion) undergoes a partial spin crossover (SCO) with symmetry breaking at T 1 = 167 K to a mixed-spin phase (50% high-spin (HS), 50% low-spin (LS)) that is metastable below T 2 = 116 K. Annealing the compound at lower temperatures results in a 100% LS phase that differs from the initial HS phase in the formation of a hydrogen bond (HB) between two water molecules (O4W and O5W) of crystallisation. Neutron crystallography experiments have also evidenced a proton displacement inside a short strong hydrogen bond (SSHB) between two isonicNO anions. Both phenomena can also be detected in the mixed-spin phase. 1 undergoes a light-induced excited-state spin trapping (LIESST) of the 100% HS phase, with breaking of the O4W⋯O5W HB and the onset of proton static disorder in the SSHB, indicating the presence of a light-induced activation energy barrier for proton motion. This excited state shows a stepped relaxation at T 1(LIESST) = 68 K and T 2(LIESST) = 76 K. Photocrystallography measurements after the first relaxation step reveal a single Fe site with an intermediate geometry, resulting from the random distribution of the HS and LS sites throughout the lattice.

| S-EPMC8179063 | biostudies-literature

Rechargeable proton exchange membrane fuel cell containing an intrinsic hydrogen storage polymer.

Project description:Proton exchange membrane fuel cells (PEMFCs) are promising clean energy conversion devices in residential, transportation, and portable applications. Currently, a high-pressure tank is the state-of-the-art mode of hydrogen storage; however, the energy cost, safety, and portability (or volumetric hydrogen storage capacity) presents a major barrier to the widespread dissemination of PEMFCs. Here we show an 'all-polymer type' rechargeable PEMFC (RCFC) that contains a hydrogen-storable polymer (HSP), which is a solid-state organic hydride, as the hydrogen storage media. Use of a gas impermeable SPP-QP (a polyphenylene-based PEM) enhances the operable time, reaching up to ca. 10.2 s mgHSP-1, which is more than a factor of two longer than that (3.90 s mgHSP-1) for a Nafion NRE-212 membrane cell. The RCFCs are cycleable, at least up to 50 cycles. The features of this RCFC system, including safety, ease of handling, and light weight, suggest applications in mobile, light-weight hydrogen-based energy devices.

| S-EPMC9814259 | biostudies-literature

Proton mediated spin state transition of cobalt heme analogs.

Project description:The spin state transition from low spin to high spin upon substrate addition is one of the key steps in cytochrome P450 catalysis. External perturbations such as pH and hydrogen bonding can also trigger the spin state transition of hemes through deprotonated histidine (e.g. Cytochrome c). In this work, we report the isolated 2-methylimidazole Cobalt(II) [Co(TPP)(2-MeHIm)] and [Co(TTP)(2-MeHIm)], and the corresponding 2-methylimidazolate derivatives where the N-H proton of axial 2-MeHIm is removed. Interestingly, various spectroscopies including EPR and XAFS determine a high-spin state (S = 3/2) for the imidazolate derivatives, in contrast to the low-spin state (S = 1/2) of all known imidazole analogs. DFT assisted stereoelectronic investigations are applied to understand the metal-ligand interactions, which suggest that the dramatically displaced metal center allowing a promotion eg(dπ) → b1g([Formula: see text]) is crucial for the occurrence of the spin state transition.

| S-EPMC6534676 | biostudies-literature

Amide proton solvent protection in amylin fibrils probed by quenched hydrogen exchange NMR.

Project description:Amylin is an endocrine hormone that accumulates in amyloid plaques in patients with advanced type 2 diabetes. The amyloid plaques have been implicated in the destruction of pancreatic ?-cells, which synthesize amylin and insulin. To better characterize the secondary structure of amylin in amyloid fibrils we assigned the NMR spectrum of the unfolded state in 95% DMSO and used a quenched hydrogen-deuterium exchange technique to look at amide proton solvent protection in the fibrils. In this technique, partially exchanged fibrils are dissolved in 95% DMSO and information about amide proton occupancy in the fibrils is determined from DMSO-denatured monomers. Hydrogen exchange lifetimes at pH 7.6 and 37°C vary between ?5 h for the unstructured N-terminus to 600 h for amide protons in the two ?-strands that form inter-molecular hydrogen bonds between amylin monomers along the length of the fibril. Based on the protection data we conclude that residues A8-H18 and I26-Y37 comprise the two ?-strands in amylin fibrils. There is variation in protection within the ?-strands, particularly for strand ?1 where only residues F15-H18 are strongly protected. Differences in protection appear to be due to restrictions on backbone dynamics imposed by the packing of two-layers of C2-symmetry-related ?-hairpins in the protofilament structure, with strand ?1 positioned on the surface and ?2 in the interior.

| S-EPMC3574092 | biostudies-literature

Molecular mechanism of proton transport in CLC Cl-/H+ exchange transporters.

Project description:CLC proteins underlie muscle, kidney, bone, and other organ system function by catalyzing the transport of Cl(-) ions across cell and organellar membranes. Some CLC proteins are ion channels while others are pumps that exchange Cl(-) for H(+). The pathway through which Cl(-) ions cross the membrane has been characterized, but the transport of H(+) and the principle by which their movement is coupled to Cl(-) movement is not well understood. Here we show that H(+) transport depends not only on the presence of a specific glutamate residue but also the presence of Cl(-) ions. H(+) transport, however, can be isolated and analyzed in the absence of Cl(-) by mutating the glutamate to alanine and adding carboxylate-containing molecules to solution, consistent with the notion that H(+) transfer is mediated through the entry of a carboxylate group into the anion pathway. Cl(-) ions and carboxylate interact with each other strongly. These data support a mechanism in which the glutamate carboxylate functions as a surrogate Cl(-) ion, but it can accept a H(+) and transfer it between the external solution and the central Cl(-) binding site, coupled to the movement of 2 Cl(-) ions.

| S-EPMC3406864 | biostudies-literature

Graphene-Derived Carbon Support Boosts Proton Exchange Membrane Fuel Cell Catalyst Stability.

Project description:The lack of efficient and durable proton exchange membrane fuel cell electrocatalysts for the oxygen reduction reaction is still restraining the present hydrogen technology. Graphene-based carbon materials have emerged as a potential solution to replace the existing carbon black (CB) supports; however, their potential was never fully exploited as a commercial solution because of their more demanding properties. Here, a unique and industrially scalable synthesis of platinum-based electrocatalysts on graphene derivative (GD) supports is presented. With an innovative approach, highly homogeneous as well as high metal loaded platinum-alloy (up to 60 wt %) intermetallic catalysts on GDs are achieved. Accelerated degradation tests show enhanced durability when compared to the CB-supported analogues including the commercial benchmark. Additionally, in combination with X-ray photoelectron spectroscopy Auger characterization and Raman spectroscopy, a clear connection between the sp 2 content and structural defects in carbon materials with the catalyst durability is observed. Advanced gas diffusion electrode results show that the GD-supported catalysts exhibit excellent mass activities and possess the properties necessary to reach high currents if utilized correctly. We show record-high peak power densities in comparison to the prior best literature on platinum-based GD-supported materials which is promising information for future application.

| S-EPMC9361283 | biostudies-literature

Transition-Metal-Free Carbon Isotope Exchange of Phenyl Acetic Acids.

Project description:A transition-metal-free carbon isotope exchange procedure on phenyl acetic acids is described. Utilizing the universal precursor CO2 , this protocol allows the carbon isotope to be inserted into the carboxylic acid position, with no need of precursor synthesis. This procedure enabled the labeling of 15 pharmaceuticals and was compatible with carbon isotopes [14 C] and [13 C]. A proof of concept with [11 C] was also obtained with low molar activity valuable for distribution studies.

| S-EPMC7496475 | biostudies-literature

Large transition state stabilization from a weak hydrogen bond.

Project description:A series of molecular rotors was designed to study and measure the rate accelerating effects of an intramolecular hydrogen bond. The rotors form a weak neutral O-H⋯O[double bond, length as m-dash]C hydrogen bond in the planar transition state (TS) of the bond rotation process. The rotational barrier of the hydrogen bonding rotors was dramatically lower (9.9 kcal mol-1) than control rotors which could not form hydrogen bonds. The magnitude of the stabilization was significantly larger than predicted based on the independently measured strength of a similar O-H⋯O[double bond, length as m-dash]C hydrogen bond (1.5 kcal mol-1). The origins of the large transition state stabilization were studied via experimental substituent effect and computational perturbation analyses. Energy decomposition analysis of the hydrogen bonding interaction revealed a significant reduction in the repulsive component of the hydrogen bonding interaction. The rigid framework of the molecular rotors positions and preorganizes the interacting groups in the transition state. This study demonstrates that with proper design a single hydrogen bond can lead to a TS stabilization that is greater than the intrinsic interaction energy, which has applications in catalyst design and in the study of enzyme mechanisms.

| S-EPMC8159443 | biostudies-literature

Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes.

Project description:Simulations based on perfectly funneled energy landscapes often capture many of the kinetic features of protein folding. We examined whether simulations based on funneled energy functions can also describe fluctuations in native-state protein ensembles. We quantitatively compared the site-specific local stability determined from structure-based folding simulations, with hydrogen exchange protection factors measured experimentally for ubiquitin, chymotrypsin inhibitor 2, and staphylococcal nuclease. Different structural definitions for the open and closed states based on the number of native contacts for each residue, as well as the hydrogen-bonding state, or a combination of both criteria were evaluated. The predicted exchange patterns agree with the experiments under native conditions, indicating that protein topology indeed has a dominant effect on the exchange kinetics. Insights into the simplest mechanistic interpretation of the amide exchange process were thus obtained.

| S-EPMC3203634 | 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