Browse
Submit Data
Databases
API
Help

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Planar Iron Hydride Nanoclusters: Combined Spectroscopic and Theoretical Insights into Structures and Building Principles.

ABSTRACT: The controlled assembly of well-defined planar nanoclusters from molecular precursors is synthetically challenging and often plagued by the predominant formation of 3D-structures and nanoparticles. Herein, we report planar iron hydride nanoclusters from reactions of main group element hydrides with iron(II) bis(hexamethyldisilazide). The structures and properties of isolated Fe₄ , Fe₆ , and Fe₇ nanoplatelets and calculated intermediates enable an unprecedented insight into the underlying building principle and growth mechanism of iron clusters, metal monolayers, and nanoparticles.

SUBMITTER: Chakraborty U

PROVIDER: S-EPMC7919527 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Planar Iron Hydride Nanoclusters: Combined Spectroscopic and Theoretical Insights into Structures and Building Principles.

Chakraborty Uttam U Bügel Patrick P Fritsch Lorena L Weigend Florian F Bauer Matthias M Jacobi von Wangelin Axel A

ChemistryOpen 20210201 2

The controlled assembly of well-defined planar nanoclusters from molecular precursors is synthetically challenging and often plagued by the predominant formation of 3D-structures and nanoparticles. Herein, we report planar iron hydride nanoclusters from reactions of main group element hydrides with iron(II) bis(hexamethyldisilazide). The structures and properties of isolated Fe4 , Fe6 , and Fe7 nanoplatelets and calculated intermediates enable an unprecedented in ...[more]

PMID: 33646644

Similar Datasets

Structures and Spectroscopic Properties of Polysulfide Radical Anions: A Theoretical Perspective.

Project description:The potential involvement of polysulfide radical anions Sn•- is a recurring theme in discussions of the basic and applied chemistry of elemental sulfur. However, while the spectroscopic features for n = 2 and 3 are well-established, information on the structures and optical characteristics of the larger congeners (n = 4-8) is sparse. To aid identification of these ephemeral species we have performed PCM-corrected DFT calculations to establish the preferred geometries for Sn•- (n = 4-8) in the polar media in which they are typically generated. TD-DFT calculations were then used to determine the number, nature and energies of the electronic excitations possible for these species. Numerical reliability of the approach was tested by comparison of the predicted and experimental excitation energies found for S2•- and S3•-. The low-energy (near-IR) transitions found for the two acyclic isomers of S4•- (C2h and C2v symmetry) and for S5•- (Cs symmetry) can be understood by extension of the simple HMO π-only chain model that serves for S2•- and S3•-. By contrast, the excitations predicted for the quasi-cyclic structures Sn•- (n = 6-8) are better described in terms of σ → σ* processes within a localized 2c-3e manifold.

| S-EPMC10419630 | biostudies-literature

Multidimensional correlation spectroscopic imaging of exponential decays: From theoretical principles to in vivo human applications.

Project description:Multiexponential modeling of relaxation or diffusion MR signal decays is a popular approach for estimating and spatially mapping different microstructural tissue compartments. While this approach can be quite powerful, it is also limited by the fact that one-dimensional multiexponential modeling is an ill-posed inverse problem with substantial ambiguities. In this article, we present an overview of a recent multidimensional correlation spectroscopic imaging approach to this problem. This approach helps to alleviate ill-posedness by making advantageous use of multidimensional contrast encoding (e.g., 2D diffusion-relaxation encoding or 2D relaxation-relaxation encoding) combined with a regularized spatial-spectral estimation procedure. Theoretical calculations, simulations, and experimental results are used to illustrate the benefits of this approach relative to classical methods. In addition, we demonstrate an initial proof-of-principle application of this kind of approach to in vivo human MRI experiments.

| S-EPMC7338241 | biostudies-literature

Alkaline and Alkaline-earth Cyanoacetylides: A Combined Theoretical and Rotational Spectroscopic Investigation.

Project description:The metallic cyanoacetylides LiC3N, NaC3N, MgC3N and CaC3N have been investigated by combined spectroscopy measurements and theoretical calculations. The theoretical calculations predict for the four species that the linear isomer with formula MCCCN (M= Li, Na, Mg and Ca) is the most stable one. We used the laser ablation molecular beam Fourier transform microwave spectroscopy to synthesize these species by the reaction of metal vapors, produced by laser ablation, and the 3-bromo-2-propynenitrile (BrCCCN). The pure rotational spectra were observed by Fourier transform microwave spectroscopy in the 2-18 GHz frequency region only for LiCCCN and NaCCCN, while no spectral signatures for MgCCCN and CaCCCN could be detected. Finally, we have searched for LiCCCN and NaCCCN species towards the carbon-rich evolved star IRC + 10216 but only upper limits to their abundances have been obtained.

| S-EPMC6739221 | biostudies-literature

Bright Luminescence in Three Phases-A Combined Synthetic, Spectroscopic and Theoretical Approach.

Project description:Combining phase-dependent photoluminescence (PL) measurements and quantum chemical calculations is a powerful approach to help understand the influence of the molecular surroundings on the PL properties. Herein, a phosphine functionalized amidinate was used to synthesize a recently presented bimetallic gold complex, featuring an unusual charge separation. The latter was subsequently used as metalloligand to yield heterotetrametallic complexes with an Au-M-M-Au "molecular wire" arrangement (M=Cu, Ag, Au) featuring metallophilic interactions. All compounds show bright phosphorescence in the solid state, also at ambient temperature. The effect of the molecular environment on the PL was studied in detail for these tetrametallic complexes by comparative measurements in solution, in the solid state and in the gas phase and contrasted to time-dependent density functional theory computations.

| S-EPMC8597132 | biostudies-literature

Structures, Spectroscopic Properties, and Dioxygen Reactivity of 5- and 6-Coordinate Nonheme Iron(II) Complexes: A Combined Enzyme/Model Study of Thiol Dioxygenases.

Project description:The synthesis of four new FeII(N4S(thiolate)) complexes as models of the thiol dioxygenases are described. They are composed of derivatives of the neutral, tridentate ligand triazacyclononane (R3TACN; R = Me, iPr) and 2-aminobenzenethiolate (abtx; X = H, CF3), a non-native substrate for thiol dioxygenases. The coordination number of these complexes depends on the identity of the TACN derivative, giving 6-coordinate (6-coord) complexes for FeII(Me3TACN)(abtx)(OTf) (1: X = H; 2: X = CF3) and 5-coordinate (5-coord) complexes for [FeII(iPr3TACN)(abtx)](OTf) (3: X = H; 4: X = CF3). Complexes 1-4 were examined by UV-vis, 1H/19F NMR, and Mössbauer spectroscopies, and density functional theory (DFT) calculations were employed to support the data. Mössbauer spectroscopy reveals that the 6-coord 1-2 and 5-coord 3- 4 exhibit distinct spectra, and these data are compared with that for cysteine-bound CDO, helping to clarify the coordination environment of the cys-bound FeII active site. Reaction of 1 or 2 with O2 at -95 °C leads to S-oxygenation of the abt ligand, and in the case of 2, a rare di(sulfinato)-bridged complex, [Fe2III(?-O)((2-NH2) p-CF3C6H3SO2)2](OTf)2 ( 5), was obtained. Parallel enzymatic studies on the CDO variant C93G were carried out with the abt substrate and show that reaction with O2 leads to disulfide formation, as opposed to S-oxygenation. The combined model and enzyme studies show that the thiol dioxygenases can operate via a 6-coord FeII center, in contrast to the accepted mechanism for nonheme iron dioxygenases, and that proper substrate chelation to Fe appears to be critical for S-oxygenation.

| S-EPMC6596423 | biostudies-literature

First-principles calculated decomposition pathways for LiBH4 nanoclusters.

Project description:We analyze thermodynamic stability and decomposition pathways of LiBH4 nanoclusters using grand-canonical free-energy minimization based on total energies and vibrational frequencies obtained from density-functional theory (DFT) calculations. We consider (LiBH4)n nanoclusters with n?=?2 to 12 as reactants, while the possible products include (Li)n, (B)n, (LiB)n, (LiH)n, and Li2BnHn; off-stoichiometric LinBnHm (m???4n) clusters were considered for n?=?2, 3, and 6. Cluster ground-state configurations have been predicted using prototype electrostatic ground-state (PEGS) and genetic algorithm (GA) based structural optimizations. Free-energy calculations show hydrogen release pathways markedly differ from those in bulk LiBH4. While experiments have found that the bulk material decomposes into LiH and B, with Li2B12H12 as a kinetically inhibited intermediate phase, (LiBH4)n nanoclusters with n???12 are predicted to decompose into mixed LinBn clusters via a series of intermediate clusters of LinBnHm (m???4n). The calculated pressure-composition isotherms and temperature-pressure isobars exhibit sloping plateaus due to finite size effects on reaction thermodynamics. Generally, decomposition temperatures of free-standing clusters are found to increase with decreasing cluster size due to thermodynamic destabilization of reaction products.

| S-EPMC4870692 | biostudies-other

Combined Mossbauer spectroscopic, multi-edge X-ray absorption spectroscopic, and density functional theoretical study of the radical SAM enzyme spore photoproduct lyase.

Project description:Spore photoproduct lyase (SPL), a member of the radical S-adenosyl-L-methionine (SAM) superfamily, catalyzes the direct reversal of the spore photoproduct, a thymine dimer specific to bacterial spores, to two thymines. SPL requires SAM and a redox-active [4Fe-4S] cluster for catalysis. Mössbauer analysis of anaerobically purified SPL indicates the presence of a mixture of cluster states with the majority (40 %) as [2Fe-2S](2+) clusters and a smaller amount (15 %) as [4Fe-4S](2+) clusters. On reduction, the cluster content changes to primarily (60 %) [4Fe-4S](+). The speciation information from Mössbauer data allowed us to deconvolute iron and sulfur K-edge X-ray absorption spectra to uncover electronic (X-ray absorption near-edge structure, XANES) and geometric (extended X-ray absorption fine structure, EXAFS) structural features of the Fe-S clusters, and their interactions with SAM. The iron K-edge EXAFS data provide evidence for elongation of a [2Fe-2S] rhomb of the [4Fe-4S] cluster on binding SAM on the basis of an Fe···Fe scatterer at 3.0 Å. The XANES spectra of reduced SPL in the absence and presence of SAM overlay one another, indicating that SAM is not undergoing reductive cleavage. The X-ray absorption spectroscopy data for SPL samples and data for model complexes from the literature allowed the deconvolution of contributions from [2Fe-2S] and [4Fe-4S] clusters to the sulfur K-edge XANES spectra. The analysis of pre-edge features revealed electronic changes in the Fe-S clusters as a function of the presence of SAM. The spectroscopic findings were further corroborated by density functional theory calculations that provided insights into structural and electronic perturbations that can be correlated by considering the role of SAM as a catalyst or substrate.

| S-EPMC4089880 | biostudies-literature

Haem and non-haem iron sites in Escherichia coli bacterioferritin: spectroscopic and model building studies.

Project description:The bacterioferritin (BFR) of Escherichia coli is an iron-storage protein containing 24 identical subunits and between three and 11 protohaem IX groups per molecule. Titration with additional haem gave a maximum loading of 12-14 haems per molecule. The e.p.r. spectra and magnetic c.d. spectra of the protein-bound haem show it to be low-spin Fe(III), and coordinated by two methionine residues as previously reported for BFRs isolated from Pseudomonas aeruginosa and Azotobacter vinelandii [Cheesman, Thomson, Greenwood, Moore and Kadir, Nature (London) (1990) 346, 771-773]. A recent sequence alignment indicated that BFR may be structurally related to ferritin. The molecular model proposed for E. coli BFR has a four-alpha-helix-bundle subunit conformation and a quaternary structure similar to those of mammalian ferritins. In this model there are two types of hydrophobic pocket within which two methionine residues are correctly disposed to bind haem. The e.p.r. spectra also reveal a monomeric non-haem Fe(III) species with spin, S = 5/2. On the basis of sequence comparisons, a ferroxidase centre has recently been proposed to be present in BFR [Andrews, Smith, Yewdall, Guest and Harrison (1991) FEBS Lett. 293, 164-168] and the possibility that this Fe(III) ion may reside at or near the ferroxidase centre is discussed.

| S-EPMC1134267 | biostudies-other

Deamidation of Protonated Asparagine-Valine Investigated by a Combined Spectroscopic, Guided Ion Beam, and Theoretical Study.

Project description:Peptide deamidation of asparaginyl residues is a spontaneous post-translational modification that is believed to play a role in aging and several diseases. It is also a well-known small-molecule loss channel in the MS/MS spectra of protonated peptides. Here we investigate the deamidation reaction, as well as other decomposition pathways, of the protonated dipeptide asparagine-valine ([AsnVal + H]+) upon low-energy activation in a mass spectrometer. Using a combination of infrared ion spectroscopy, guided ion beam tandem mass spectrometry, and theoretical calculations, we have been able to identify product ion structures and determine the energetics and mechanisms for decomposition. Deamidation proceeds via ammonia loss from the asparagine side chain, initiated by a nucleophilic attack of the peptide bond oxygen on the ?-carbon of the Asn side chain. This leads to the formation of a furanone ring containing product ion characterized by a threshold energy of 129 ± 5 kJ/mol (15 kJ/mol higher in energy than dehydration of [AsnVal + H]+, the lowest energy dissociation channel available to the system). Competing formation of a succinimide ring containing product, as has been observed for protonated asparagine-glycine ([AsnGly + H]+) and asparagine-alanine ([AsnAla + H]+), was not observed here. Quantum-chemical modeling of the reaction pathways confirms these subtle differences in dissociation behavior. Measured reaction thresholds are in agreement with predicted theoretical reaction energies computed at several levels of theory.

| S-EPMC5846081 | biostudies-literature

Iron porphyrin carbenes as catalytic intermediates: structures, Mossbauer and NMR spectroscopic properties, and bonding.

Project description:Iron porphyrin carbenes (IPCs) are thought to be intermediates involved in the metabolism of various xenobiotics by cytochrome P450, as well as in chemical reactions catalyzed by metalloporphyrins and engineered?P450s. While early work proposed IPCs to contain Fe(II), more recent work invokes a double-bond description of the iron-carbon bond, similar to that found in Fe(IV) porphyrin oxenes. Reported herein is the first quantum chemical investigation of IPC Mössbauer and NMR spectroscopic properties, as well as their electronic structures, together with comparisons to ferrous heme proteins and an Fe(IV) oxene model. The results provide the first accurate predictions of the experimental spectroscopic observables as well as the first theoretical explanation of their electrophilic nature, as deduced from experiment. The preferred resonance structure is Fe(II)?{:C(X)Y}(0) and not Fe(IV)={C(X)Y}(2-), a result that will facilitate research on IPC reactivities in various chemical and biochemical systems.

| S-EPMC4124075 | 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