Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A density functional theory study of Fe(II)/Fe(III) distribution in single layer green rust: a cluster approach.

ABSTRACT: Green rust (GR) is a potentially important compound for the reduction of heavy metal and organic pollutants in subsurface environment because of its high Fe(II) content, but many details of the actual reaction mechanism are lacking. The reductive capacity distribution within GR is a key to understand how and where the redox reaction occurs and computational chemistry can provide more details about the electronic properties of green rust. We constructed three sizes of cluster models of single layer GR (i.e., without interlayer molecules or ions) and calculated the charge distribution of these structures using density functional theory. We found that the Fe(II) and Fe(III) are distributed unevenly in the single layer GR. Within a certain range of Fe(II)/Fe(III) ratios, the outer iron atoms behave more like Fe(III) and the inner iron atoms behave more like Fe(II). These findings indicate that the interior of GR is more reductive than the outer parts and will provide new information to understand the GR redox interactions.

SUBMITTER: Sun W

PROVIDER: S-EPMC8194116 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Thermal Treatment Effect on CO and NO Adsorption on Fe(II) and Fe(III) Species in Fe3O-Based MIL-Type Metal-Organic Frameworks: A Density Functional Theory Study.

Project description:The properties of metal-organic frameworks (MOFs) based on triiron oxo-centered (Fe3O) metal nodes are often related to the efficiency of the removal of the solvent molecules and the counteranion chemisorbed on the Fe3O unit by postsynthetic thermal treatment. Temperature, time, and the reaction environment play a significant role in modifying key features of the materials, that is, the number of open metal sites and the reduction of Fe(III) centers to Fe(II). IR spectroscopy allows the inspection of these postsynthetic modifications by using carbon monoxide (CO) and nitric oxide (NO) as probe molecules. However, the reference data sets are based on spectra recorded for iron zeolites and oxides, whose structures are different from the Fe3O one. We used density functional theory to study how the adsorption enthalpy and the vibrational bands of CO and NO are modified upon dehydration and reduction of Fe3O metal nodes. We obtained a set of theoretical spectra that can model the modification observed in previously reported experimental spectra. Several CO and NO bands were previously assigned to heterogeneous Fe(II) and Fe(III) sites, suggesting a large defectivity of the materials. On the basis of the calculations, we propose an alternative assignment of these bands by considering only crystallographic iron sites. These findings affect the common description of Fe3O-based MOFs as highly defective materials. We expect these results to be of interest to the large community of scientists working on Fe(II)- and Fe(III)-based MOFs and related materials.

| S-EPMC8371607 | biostudies-literature

Synthesis, Characterization, Antimicrobial, Density Functional Theory, and Molecular Docking Studies of Novel Mn(II), Fe(III), and Cr(III) Complexes Incorporating 4-(2-Hydroxyphenyl azo)-1-naphthol (Az).

Project description:This work synthesized three new CrAz2, MnAz2, and FeAz2 complexes and investigated them using IR, mass, UV spectroscopy, elemental analysis, conductivity and magnetic tests, and thermogravimetric analysis. The azo-ligand, 4-(2-hydroxyphenylAzo)-1-naphthol (Az), couples with metal ions via its nitrogen (in -N=N- bonds) and oxygen (in hydroxyl group) atoms, according to the IR spectra of these complexes. Through thermal examination (TG/TGA), the number and location of water in the complexes were also determined. Density functional theory (DFT) theory is applied to ameliorate the structures of the ligand (Az) and metal complexes and analyze the quantum chemical characteristics of these complexes. The antifungal and antibacterial activity of the ligand and its complexes opposed to several hazardous bacteria and fungi was investigated in vitro. Metal complexes were discovered to have a higher inhibitory impact on some organisms than the free ligand. The MnAz2 complex exhibited the best activity among the studied materials, whereas the CrAz2 complex had the lowest. The compounds' binding affinity to the E. coli (PDB ID: 1hnj) structure was predicted using molecular docking. Binding energies were calculated by analyzing protein-substrate interactions. These encouraging findings imply that these chemicals may have physiological effects and may be valuable for a variety of medical uses in the future.

| S-EPMC10373178 | biostudies-literature

Unsymmetrical bimetallic complexes with M(II)-(?-OH)-M(III) cores (M(II)M(III) = Fe(II)Fe(III), Mn(II)Fe(III), Mn(II)Mn(III)): structural, magnetic, and redox properties.

Project description:Heterobimetallic cores are important units within the active sites of metalloproteins but are often difficult to duplicate in synthetic systems. We have developed a synthetic approach for the preparation of a complex with a Mn(II)-(?-OH)-Fe(III) core, in which the metal centers have different coordination environments. Structural and physical data support the assignment of this complex as a heterobimetallic system. A comparison with analogous homobimetallic complexes, Mn(II)-(?-OH)-Mn(III) and Fe(II)-(?-OH)-Fe(III) cores, further supports this assignment.

| S-EPMC3826960 | biostudies-other

Abundance, distribution, and activity of Fe(II)-oxidizing and Fe(III)-reducing microorganisms in hypersaline sediments of Lake Kasin, southern Russia.

Project description:The extreme osmotic conditions prevailing in hypersaline environments result in decreasing metabolic diversity with increasing salinity. Various microbial metabolisms have been shown to occur even at high salinity, including photosynthesis as well as sulfate and nitrate reduction. However, information about anaerobic microbial iron metabolism in hypersaline environments is scarce. We studied the phylogenetic diversity, distribution, and metabolic activity of iron(II)-oxidizing and iron(III)-reducing Bacteria and Archaea in pH-neutral, iron-rich salt lake sediments (Lake Kasin, southern Russia; salinity, 348.6 g liter(-1)) using a combination of culture-dependent and -independent techniques. 16S rRNA gene clone libraries for Bacteria and Archaea revealed a microbial community composition typical for hypersaline sediments. Most-probable-number counts confirmed the presence of 4.26 × 10(2) to 8.32 × 10(3) iron(II)-oxidizing Bacteria and 4.16 × 10(2) to 2.13 × 10(3) iron(III)-reducing microorganisms per gram dry sediment. Microbial iron(III) reduction was detected in the presence of 5 M NaCl, extending the natural habitat boundaries for this important microbial process. Quantitative real-time PCR showed that 16S rRNA gene copy numbers of total Bacteria, total Archaea, and species dominating the iron(III)-reducing enrichment cultures (relatives of Halobaculum gomorrense, Desulfosporosinus lacus, and members of the Bacilli) were highest in an iron oxide-rich sediment layer. Combined with the presented geochemical and mineralogical data, our findings suggest the presence of an active microbial iron cycle at salt concentrations close to the solubility limit of NaCl.

| S-EPMC3370536 | biostudies-literature

Crystal structure of K0.75[Fe(II) 3.75Fe(III) 1.25(HPO3)6]·0.5H2O, an open-framework iron phosphite with mixed-valent Fe(II)/Fe(III) ions.

Project description:Single crystals of the title compound, potassium hexa-phosphito-penta-ferrate(II,III) hemihydrate, K0.75[Fe(II) 3.75Fe(III) 1.25(HPO3)6]·0.5H2O, were grown under mild hydro-thermal conditions. The crystal structure is isotypic with Li1.43[Fe(II) 4.43Fe(III) 0.57(HPO3)6]·1.5H2O and (NH4)2[Fe(II) 5(HPO3)6] and exhibits a [Fe(II) 3.75Fe(III) 1.25(HPO3)6](0.75-) open framework with disordered K(+) (occupancy 3/4) as counter-cations. The anionic framework is based on (001) sheets of two [FeO6] octa-hedra (one with point group symmetry 3.. and one with point group symmetry .2.) linked along [001] through [HPO3](2-) oxoanions. Each sheet is constructed from 12-membered rings of edge-sharing [FeO6] octa-hedra, giving rise to channels with a radius of ca 3.1 Å where the K(+) cations and likewise disordered water mol-ecules (occupancy 1/4) are located. O⋯O contacts between the water mol-ecule and framework O atoms of 2.864 (5) Å indicate hydrogen-bonding inter-actions of medium strength. The infrared spectrum of the compound shows vibrational bands typical for phosphite and water groups. The Mössbauer spectrum is in accordance with the presence of Fe(II) and Fe(III) ions.

| S-EPMC4704752 | biostudies-literature

Exome sequencing identifies NFS1 deficiency in a novel Fe-S cluster disease, infantile mitochondrial complex II/III deficiency.

Project description:Iron-sulfur (Fe-S) clusters are a class of highly conserved and ubiquitous prosthetic groups with unique chemical properties that allow the proteins that contain them, Fe-S proteins, to assist in various key biochemical pathways. Mutations in Fe-S proteins often disrupt Fe-S cluster assembly leading to a spectrum of severe disorders such as Friedreich's ataxia or iron-sulfur cluster assembly enzyme (ISCU) myopathy. Herein, we describe infantile mitochondrial complex II/III deficiency, a novel autosomal recessive mitochondrial disease characterized by lactic acidemia, hypotonia, respiratory chain complex II and III deficiency, multisystem organ failure and abnormal mitochondria. Through autozygosity mapping, exome sequencing, in silico analyses, population studies and functional tests, we identified c.215G>A, p.Arg72Gln in NFS1 as the likely causative mutation. We describe the first disease in man likely caused by deficiency in NFS1, a cysteine desulfurase that is implicated in respiratory chain function and iron maintenance by initiating Fe-S cluster biosynthesis. Our results further demonstrate the importance of sufficient NFS1 expression in human physiology.

| S-EPMC3907916 | biostudies-literature

Mossbauer, electron paramagnetic resonance, and density functional theory studies of synthetic S = 1/2 Fe(III)-O-Fe(IV)?O complexes. Superexchange-mediated spin transition at the Fe(IV)?O site.

Project description:Previously we have characterized two high-valent complexes [LFe(IV)(?-O)(2)Fe(III)L], 1, and [LFe(IV)(O)(?-O)(OH) Fe(IV)L], 4. Addition of hydroxide or fluoride to 1 produces two new complexes, 1-OH and 1-F. Electron paramagnetic resonance (EPR) and Mo?ssbauer studies show that both complexes have an S = 1/2 ground state which results from antiferromagnetic coupling of the spins of a high-spin (S(a) = 5/2) Fe(III) and a high-spin (S(b) = 2) Fe(IV) site. 1-OH can also be obtained by a 1-electron reduction of 4, which has been shown to have an Fe(IV)?O site. Radiolytic reduction of 4 at 77 K yields a Mo?ssbauer spectrum identical to that observed for 1-OH, showing that the latter contains an Fe(IV)?O. Interestingly, the Fe(IV)?O moiety has S(b) = 1 in 4 and S(b) = 2 in 1-OH and 1-F. From the temperature dependence of the S = 1/2 signal we have determined the exchange coupling constant J (? = JS(a)·S(b) convention) to be 90 ± 20 cm(-1) for both 1-OH and 1-F. Broken-symmetry density functional theory (DFT) calculations yield J = 135 cm(-1) for 1-OH and J = 104 cm(-1) for 1-F, in good agreement with the experiments. DFT analysis shows that the S(b) = 1 ? S(b) = 2 transition of the Fe(IV)?O site upon reduction of the Fe(IV)-OH site to high-spin Fe(III) is driven primarily by the strong antiferromagnetic exchange in the (S(a) = 5/2, S(b) = 2) couple.

| S-EPMC2957120 | biostudies-literature

Study of Complexes of Tannic Acid with Fe(III) and Fe(II).

Project description:UV-Vis absorption spectra of tannic acid were gained at pH 1.0?9.0. Due to the pH value dependence of complex, the stoichiometry of tannic acid with iron ions was tested in buffer solution by the mole ratio method. The result suggests that the complex ratio of tannic acid to Fe(III) is 1?:?1 and to Fe(II) 3?:?1 in the carbonate buffer solution, and the complex ratio of iron-tannic complexes is 1?:?1 at pH 2.2. Due to the different color changes of tannic acid with iron ions in the coordination reactions, a tannic acid test paper was designed. The concentrations of Fe(III) more than 5.000?×?10-6?mol/L and the concentrations of Fe(II) more than 1.000?×?10-5?mol/L in aqueous solution can be detected by this test paper.

| S-EPMC6378047 | biostudies-literature

Rational Design of a Confacial Pentaoctahedron: Anisotropic Exchange in a Linear ZnII FeIII FeIII FeIII ZnII Complex.

Project description:The first confacial pentaoctahedron comprised of transition metal ions namely ZnII FeIII A FeIII B FeIII A ZnII has been synthesized by using a dinucleating nonadentate ligand. The face-sharing bridging mode enforces short ZnII ⋅⋅⋅FeIII A and FeIII A ⋅⋅⋅FeIII B distances of 2.83 and 2.72 Å, respectively. Ab-initio CASSCF/NEVPT2 calculations provide significant negative zero-field splittings for FeIII A and FeIII B with |DA |>|DB | with the main component along the C3 axis. Hence, a spin-Hamiltonian comprised of anisotropic exchange, zero-field, and Zeeman term was employed. This allowed by following the boundary conditions from the theoretical results the simulation in a theory-guided parameter determination with Jxy =+0.37, Jz =-0.32, DA =-1.21, EA =-0.24, DB =-0.35, and EB =-0.01 cm-1 supported by simulations of high-field magnetic Mössbauer spectra recorded at 2 K. The weak but ferromagnetic FeIII A FeIII B interaction arises from the small bridging angle of 84.8° being at the switch from anti- to ferromagnetic for the face-sharing bridging mode.

| S-EPMC8596665 | biostudies-literature

Density Functional Theory Investigation of As(III) S-Adenosylmethionine Methyltransferase.

Project description:Arsenic is one of the most pervasive environmental toxins. It enters our water and food supply through many different routes, including the burning of fossil fuels, the application of arsenic-based herbicides, and natural sources. Using a density functional theory (DFT) cluster approach, the mechanism of arsenic (III) S-adenosylmethionine methyltransferases and various selenium-containing analogues was investigated. Notably, the methylation of arsenic by arsenic (III) S-adenosylmethionine is proposed to be a way to remove arsenic from contaminated water or soil. From the DFT cluster results, it was found that the selective substitution of the active-site Cys44, Cys72, and Cys174 residues with selenocysteines had a marginal effect on the barrier for CH3 transfer. Specifically, the average Gibbs activation energy was calculated to be only 4.2 kJ mol-1 lower than the Gibbs activation energy of 107.4 kJ mol-1 for the WT enzyme. However, importantly, it was found that with selective mutation, the methylation process becomes considerably more exergonic, where the methylation reaction can be made to be 26.4 kJ mol-1 more exergonic than the reaction catalyzed by the WT enzyme. Therefore, we propose that the selective substitution of the active-site Cys44, Cys72 and Cys174 residues with selenocysteines could make the process of methylation and volatilization more advantageous for bioremediation.

| S-EPMC7450623 | 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