Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

?-Frontier molecular orbitals in S = 2 ferryl species and elucidation of their contributions to reactivity.

ABSTRACT: S = 2 Fe(IV) ? O species are key intermediates in the catalysis of most nonheme iron enzymes. This article presents detailed spectroscopic and high-level computational studies on a structurally-defined S = 2 Fe(IV) ? O species that define its frontier molecular orbitals, which allow its high reactivity. Importantly, there are both ?- and ?-channels for reaction, and both are highly reactive because they develop dominant oxyl character at the transition state. These ?- and ?-channels have different orientation dependences defining how the same substrate can undergo different reactions (H-atom abstraction vs. electrophilic aromatic attack) with Fe(IV) ? O sites in different enzymes, and how different substrates can undergo different reactions (hydroxylation vs. halogenation) with an Fe(IV) ? O species in the same enzyme.

SUBMITTER: Srnec M

PROVIDER: S-EPMC3437891 | biostudies-other | 2012 Sep

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

π-Frontier molecular orbitals in S = 2 ferryl species and elucidation of their contributions to reactivity.

Srnec Martin M Wong Shaun D SD England Jason J Que Lawrence L Solomon Edward I EI

Proceedings of the National Academy of Sciences of the United States of America 20120820 36

S = 2 Fe(IV) ═ O species are key intermediates in the catalysis of most nonheme iron enzymes. This article presents detailed spectroscopic and high-level computational studies on a structurally-defined S = 2 Fe(IV) ═ O species that define its frontier molecular orbitals, which allow its high reactivity. Importantly, there are both π- and σ-channels for reaction, and both are highly reactive because they develop dominant oxyl character at the transition state. These π- and σ-channels have differe ...[more]

PMID: 22908238

Similar Datasets

Describing Chemical Reactivity with Frontier Molecular Orbitalets.

Project description:Locality in physical space is critical in understanding chemical reactivity in the analysis of various phenomena and processes in chemistry, biology, and materials science, as exemplified in the concepts of reactive functional groups and active sites. Frontier molecular orbitals (FMOs) pinpoint the locality of chemical bonds that are chemically reactive because of the associated orbital energies and thus have achieved great success in describing chemical reactivity, mainly for small systems. For large systems, however, the delocalization nature of canonical molecular orbitals makes it difficult for FMOs to highlight the locality of the chemical reactivity. To obtain localized molecular orbitals that also reflect the frontier nature of the chemical processes, we develop the concept of frontier molecular orbitalets (FMOLs) for describing the reactivity of large systems. The concept of orbitalets was developed recently in the localized orbital scaling correction method, which aims for eliminating the delocalization error in common density functional approximations. Orbitalets are localized in both physical and energy spaces and thus contain both orbital locality and energy information. The FMOLs are thus the orbitalets with energies highest among occupied orbitalets and lowest among unoccupied ones. The applications of FMOLs to hexadeca-1,3,5,7,9,11,13,15-octaene in its equilibrium geometry, inter- and intra-molecular charge-transfer systems, and two transition states of a bifurcating reaction demonstrate that FMOLs can connect quantum mechanical treatments of chemical systems and chemical reactivities by locating the reactive region of large chemical systems. Therefore, FMOLs extend the role of FMOs for small systems and describe the chemical reactivity of large systems with energy and locality insight, with potentially broad applications.

| S-EPMC9241161 | biostudies-literature

Electronic Structure of the Ferryl Intermediate in the ?-Ketoglutarate Dependent Non-Heme Iron Halogenase SyrB2: Contributions to H Atom Abstraction Reactivity.

Project description:Low temperature magnetic circular dichroism (LT MCD) spectroscopy in combination with quantum-chemical calculations are used to define the electronic structure associated with the geometric structure of the Fe(IV)?O intermediate in SyrB2 that was previously determined by nuclear resonance vibrational spectroscopy. These studies elucidate key frontier molecular orbitals (FMOs) and their contribution to H atom abstraction reactivity. The VT MCD spectra of the enzymatic S = 2 Fe(IV)?O intermediate with Br(-) ligation contain information-rich features that largely parallel the corresponding spectra of the S = 2 model complex (TMG3tren)Fe(IV)?O (Srnec, M.; Wong, S. D.; England, J; Que, L; Solomon, E. I. Proc. Natl. Acad. Sci. USA 2012, 109, 14326-14331). However, quantitative differences are observed that correlate with ?-anisotropy and oxo donor strength that perturb FMOs and affect reactivity. Due to ?-anisotropy, the Fe(IV)?O active site exhibits enhanced reactivity in the direction of the substrate cavity that proceeds through a ?-channel that is controlled by perpendicular orientation of the substrate C-H bond relative to the halide-Fe(IV)?O plane. Also, the increased intrinsic reactivity of the SyrB2 intermediate relative to the ferryl model complex is correlated to a higher oxyl character of the Fe(IV)?O at the transition states resulting from the weaker ligand field of the halogenase.

| S-EPMC4927264 | biostudies-literature

Ferryl haem protonation gates peroxidatic reactivity in globins.

Project description:Ferryl (Fe(IV)=O) species are involved in key enzymatic processes with direct biomedical relevance; among others, the uncontrolled reactivities of ferryl Mb (myoglobin) and Hb (haemoglobin) have been reported to be central to the pathology of rhabdomyolysis and subarachnoid haemorrhage. Rapid-scan stopped-flow methods have been used to monitor the spectra of the ferryl species in Mb and Hb as a function of pH. The ferryl forms of both proteins display an optical transition with pK approximately 4.7, and this is assigned to protonation of the ferryl species itself. We also demonstrate for the first time a direct correlation between Hb/Mb ferryl reactivity and ferryl protonation status, simultaneously informing on chemical mechanism and toxicity and with broader biochemical implications.

| S-EPMC1876371 | biostudies-other

Contributions of distinct gold species to catalytic reactivity for carbon monoxide oxidation.

Project description:Small-size (<5 nm) gold nanostructures supported on reducible metal oxides have been widely investigated because of the unique catalytic properties they exhibit in diverse redox reactions. However, arguments about the nature of the gold active site have continued for two decades, due to the lack of comparable catalyst systems with specific gold species, as well as the scarcity of direct experimental evidence for the reaction mechanism under realistic working conditions. Here we report the determination of the contribution of single atoms, clusters and particles to the oxidation of carbon monoxide at room temperature, by the aid of in situ X-ray absorption fine structure analysis and in situ diffuse reflectance infrared Fourier transform spectroscopy. We find that the metallic gold component in clusters or particles plays a much more critical role as the active site than the cationic single-atom gold species for the room-temperature carbon monoxide oxidation reaction.

| S-EPMC5116099 | biostudies-literature

Frontier Molecular Orbital Contributions to Chlorination versus Hydroxylation Selectivity in the Non-Heme Iron Halogenase SyrB2.

Project description:The ability of an FeIV?O intermediate in SyrB2 to perform chlorination versus hydroxylation was computationally evaluated for different substrates that had been studied experimentally. The ?-trajectory for H atom abstraction (FeIV?O oriented perpendicular to the C-H bond of substrate) was found to lead to the S = 2 five-coordinate HO-FeIII-Cl complex with the C• of the substrate, ?-oriented relative to both the Cl- and the OH- ligands. From this ferric intermediate, hydroxylation is thermodynamically favored, but chlorination is intrinsically more reactive due to the energy splitting between two key redox-active d?* frontier molecular orbitals (FMOs). The splitting is determined by the differential ligand field effect of Cl- versus OH- on the Fe center. This makes chlorination effectively competitive with hydroxylation. Chlorination versus hydroxylation selectivity is then determined by the orientation of the substrate with respect to the HO-Fe-Cl plane that controls either the Cl- or the OH- to rebound depending on the relative ?-overlap with the substrate C radical. The differential contribution of the two FMOs to chlorination versus hydroxylation selectivity in SyrB2 is related to a reaction mechanism that involves two asynchronous transfers: electron transfer from the substrate radical to the iron center followed by late ligand (Cl- or OH-) transfer to the substrate.

| S-EPMC5310988 | biostudies-literature

A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase.

Project description:Nature employs high-energy metal-oxo intermediates embedded within enzyme active sites to perform challenging oxidative transformations with remarkable selectivity. Understanding how different local metal-oxo coordination environments control intermediate reactivity and catalytic function is a long-standing objective. However, conducting structure-activity relationships directly in active sites has proven challenging due to the limited range of amino acid substitutions achievable within the constraints of the genetic code. Here, we use an expanded genetic code to examine the impact of hydrogen bonding interactions on ferryl heme structure and reactivity, by replacing the N-H group of the active site Trp51 of cytochrome c peroxidase by an S atom. Removal of a single hydrogen bond stabilizes the porphyrin π-cation radical state of CcP W191F compound I. In contrast, this modification leads to more basic and reactive neutral ferryl heme states, as found in CcP W191F compound II and the wild-type ferryl heme-Trp191 radical pair of compound I. This increased reactivity manifests in a >60-fold activity increase toward phenolic substrates but remarkably has negligible effects on oxidation of the biological redox partner cytc. Our data highlight how Trp51 tunes the lifetimes of key ferryl intermediates and works in synergy with the redox active Trp191 and a well-defined substrate binding site to regulate catalytic function. More broadly, this work shows how noncanonical substitutions can advance our understanding of active site features governing metal-oxo structure and reactivity.

| S-EPMC8317151 | biostudies-literature

Herbaria are a major frontier for species discovery.

Project description:Despite the importance of species discovery, the processes including collecting, recognizing, and describing new species are poorly understood. Data are presented for flowering plants, measuring quantitatively the lag between the date a specimen of a new species was collected for the first time and when it was subsequently described and published. The data from our sample of new species published between 1970 and 2010 show that only 16% were described within five years of being collected for the first time. The description of the remaining 84% involved much older specimens, with nearly one-quarter of new species descriptions involving specimens >50 y old. Extrapolation of these results suggest that, of the estimated 70,000 species still to be described, more than half already have been collected and are stored in herbaria. Effort, funding, and research focus should, therefore, be directed as much to examining extant herbarium material as collecting new material in the field.

| S-EPMC3009773 | biostudies-literature

Elucidation of Cellular Contributions to Heparin-Induced Thrombocytopenia Using Omic Approaches.

Project description:Heparin-induced thrombocytopenia (HIT) is an unpredictable, complex, immune-mediated adverse drug reaction associated with a high mortality. Despite decades of research into HIT, fundamental knowledge gaps persist regarding HIT likely due to the complex and unusual nature of the HIT immune response. Such knowledge gaps include the identity of a HIT immunogen, the intrinsic roles of various cell types and their interactions, and the molecular basis that distinguishes pathogenic and non-pathogenic PF4/heparin antibodies. While a key feature of HIT, thrombocytopenia, implicates platelets as a seminal cell fragment in HIT pathogenesis, strong evidence exists for critical roles of multiple cell types. The rise in omic technologies over the last decade has resulted in a number of agnostic, whole system approaches for biological research that may be especially informative for complex phenotypes. Applying multi-omics techniques to HIT has the potential to bring new insights into HIT pathophysiology and identify biomarkers with clinical utility. In this review, we review the clinical, immunological, and molecular features of HIT with emphasis on key cell types and their roles. We then address the applicability of several omic techniques underutilized in HIT, which have the potential to fill knowledge gaps related to HIT biology.

| S-EPMC8814424 | biostudies-literature

Cerebral artery myogenic reactivity: The next frontier in developing effective interventions for subarachnoid hemorrhage.

Project description:Aneurysmal subarachnoid hemorrhage (SAH) is a devastating cerebral event that kills or debilitates the majority of those afflicted. The blood that spills into the subarachnoid space stimulates profound cerebral artery vasoconstriction and consequently, cerebral ischemia. Thus, once the initial bleeding in SAH is appropriately managed, the clinical focus shifts to maintaining/improving cerebral perfusion. However, current therapeutic interventions largely fail to improve clinical outcome, because they do not effectively restore normal cerebral artery function. This review discusses emerging evidence that perturbed cerebrovascular "myogenic reactivity," a crucial microvascular process that potently dictates cerebral perfusion, is the critical element underlying cerebral ischemia in SAH. In fact, the myogenic mechanism could be the reason why many therapeutic interventions, including "Triple H" therapy, fail to deliver benefit to patients. Understanding the molecular basis for myogenic reactivity changes in SAH holds the key to develop more effective therapeutic interventions; indeed, promising recent advancements fuel optimism that vascular dysfunction in SAH can be corrected to improve outcome.

| S-EPMC5757446 | biostudies-literature

Molecular characterization of a fungal cyclophilin allergen Rhi o 2 and elucidation of antigenic determinants responsible for IgE-cross-reactivity.

Project description:Cyclophilins are structurally conserved pan-allergens showing extensive cross-reactivity. So far, no precise information on cross-reactive IgE-epitopes of cyclophilins is available. Here, an 18-kDa IgE-reactive cyclophilin (Rhi o 2) was purified from Rhizopus oryzae, an indoor mold causing allergic sensitization. Based on LC-MS/MS-derived sequences of natural Rhi o 2, the full-length cDNA was cloned, and expressed as recombinant (r) allergen. Purified rRhi o 2 displayed IgE-reactivity and basophil degranulation with sera from all cyclophilin-positive patients. The melting curve of properly folded rRhi o 2 showed partial refolding after heat denaturation. The allergen displayed monomeric functional peptidyl-prolyl cis-trans isomerase (PPIase) activity. In IgE-inhibition assays, rRhi o 2 exhibited extensive cross-reactivity with various other cyclophilins reported as allergens from diverse sources including its homologous human autoantigen. By generating a series of deletion mutants, a conserved 69-residue (Asn81-Asn149) fragment at C terminus of Rhi o 2 was identified as crucial for IgE-recognition and cross-reactivity. Grafting of the Asn81-Asn149 fragment within the primary structure of yeast cyclophilin CPR1 by replacing its homologous sequence resulted in a hybrid molecule with structural folds similar to Rhi o 2. The IgE-reactivity and allergenic activity of the hybrid cyclophilin were greater than that of CPR1. Therefore, the Asn81-Asn149 fragment can be considered as the site of IgE recognition of Rhi o 2. Hence, Rhi o 2 serves as a candidate antigen for the molecular diagnosis of mold allergy, and determination of a major cross-reactive IgE-epitope has clinical potential for the design of next-generation immunotherapeutics against cyclophilin-induced allergies.

| S-EPMC7049968 | 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