Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Iron in Hydroxyapatite: Interstitial or Substitution Sites?

ABSTRACT: Iron-doped hydroxyapatite (Fe-HAp) is regarded as a promising magnetic material with innate biocompatibility. Despite the many studies reported in the literature, a detailed theoretical description of Fe inclusions is still missing. There is even no consensual view on what kind of Fe defects take place in Fe-HAp-iron interstitial or calcium substitutions? In order to address these questions, we employ modern first-principles methodologies, including hybrid density functional theory, to find the geometry, electronic, magnetic and thermodynamic properties of iron impurities in Fe-HAp. We consider a total of 26 defect configurations, including substitutional (phosphorus and calcium sites) and interstitial defects. Formation energies are estimated considering the boundaries of chemical potentials in stable hydroxyapatite. We show that the most probable defect configurations are: Fe3+ and Fe2+ substitutions of Ca(I) and Ca(II) sites under Ca-poor conditions. Conversely, Fe interstitials near the edge of the hydroxyl channel are favored in Ca-rich material. Substitutional Fe on the P site is also a probable defect, and unlike the other forms of Fe, it adopts a low-spin state. The analysis of Fe K-XANES spectra available in the literature shows that Fe-HAp usually contains iron in different configurations.

SUBMITTER: Avakyan L

PROVIDER: S-EPMC8625999 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Construction of New Active Sites: Cu Substitution Enabled Surface Frustrated Lewis Pairs over Calcium Hydroxyapatite for CO<sub>2</sub> Hydrogenation.

Project description:Calcium hydroxyphosphate, Ca10 (PO4 )6 (OH)2 , is commonly known as hydroxyapatite (HAP). The acidic calcium and basic phosphate/hydroxide sites in HAP can be modified via isomorphous substitution of calcium and/or hydroxide ions to enable a cornucopia of catalyzed reactions. Herein, isomorphic substitution of Ca2+ ions by Cu2+ ions especially at very low levels of exchange created new analogs of molecular surface frustrated Lewis pairs (SFLPs) in Cux Ca10- x (PO4 )6 (OH)2 , thereby boosting its performance metrics in heterogeneous CO2 photocatalytic hydrogenation. In situ Fourier transform infrared spectroscopy characterization and density functional theory calculations provided fundamental insights into the catalytically active SFLPs defined as proximal Lewis acidic Cu2+ and Lewis basic OH- . The photocatalytic pathway proceeds through a formate reaction intermediate, which is generated by the reaction of CO2 with heterolytically dissociated H2 on the SFLPs. Given the wealth of information thus uncovered, it is highly likely that this work will spur the further development of similar classes of materials, leading to the advancement and, ultimately, large-scale application of photocatalytic CO2 reduction technologies.

| S-EPMC8425883 | biostudies-literature

Mesoporous Iron(III)-Doped Hydroxyapatite Nanopowders Obtained via Iron Oxalate.

Project description:Mesoporous hydroxyapatite (HA) and iron(III)-doped HA (Fe-HA) are attractive materials for biomedical, catalytic, and environmental applications. In the present study, the nanopowders of HA and Fe-HA with a specific surface area up to 194.5 m2/g were synthesized by a simple precipitation route using iron oxalate as a source of Fe3+ cations. The influence of Fe3+ amount on the phase composition, powders morphology, Brunauer-Emmett-Teller (BET) specific surface area (S), and pore size distribution were investigated, as well as electron paramagnetic resonance and Mössbauer spectroscopy analysis were performed. According to obtained data, the Fe3+ ions were incorporated in the HA lattice, and also amorphous Fe oxides were formed contributed to the gradual increase in the S and pore volume of the powders. The Density Functional Theory calculations supported these findings and revealed Fe3+ inclusion in the crystalline region with the hybridization among Fe-3d and O-2p orbitals and a partly covalent bond formation, whilst the inclusion of Fe oxides assumed crystallinity damage and rather occurred in amorphous regions of HA nanomaterial. In vitro tests based on the MG-63 cell line demonstrated that the introduction of Fe3+ does not cause cytotoxicity and led to the enhanced cytocompatibility of HA.

| S-EPMC8005114 | biostudies-literature

Human telomeric proteins occupy selective interstitial sites.

Project description:Human telomeres are bound and protected by protein complexes assembled around the six core telomeric proteins RAP1, TRF1, TRF2, TIN2, TPP1, and POT1. The function of these proteins on telomeres has been studied extensively. Recently, increasing evidence has suggested possible roles for these proteins outside of telomeres. However, the non-canonical (extra-telomeric) function of human telomeric proteins remains poorly understood. To this end, we systematically investigated the binding sites of telomeric proteins along human chromosomes, by performing whole-genome chromatin immunoprecipitation (ChIP) for RAP1 and TRF2. ChIP sequencing (ChIP-seq) revealed that RAP1 and TRF2 could be found on a small number of interstitial sites, including regions that are proximal to genes. Some of these binding sites contain short telomere repeats, suggesting that telomeric proteins could directly bind to interstitial sites. Interestingly, only a small fraction of the available interstitial telomere repeat-containing regions were occupied by RAP1 and TRF2. Ectopically expressed TRF2 was able to occupy additional interstitial telomere repeat sites, suggesting that protein concentration may dictate the selective targeting of telomeric proteins to interstitial sites. Reducing RAP1 and TRF2 expression by RNA interference led to altered transcription of RAP1- and TRF2-targeted genes. Our results indicate that human telomeric proteins could occupy a limited number of interstitial sites and regulate gene transcription.

| S-EPMC3193500 | biostudies-literature

Hydroxyapatite Coated Iron Oxide Nanoparticles: A Promising Nanomaterial for Magnetic Hyperthermia Cancer Treatment.

Project description:Targeting cancer cells without injuring normal cells is the prime objective in treatment of cancer. In this present study, solvothermal and wet chemical precipitation techniques were employed to synthesize iron oxide (IO), hydroxyapatite (HAp), and hydroxyapatite coated iron oxide (IO-HAp) nanoparticles for magnetic hyperthermia mediated cancer therapy. The synthesized well dispersed spherical IO-HAp nanoparticles, magnetite, and apatite phases were confirmed by X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR) and Field emission transmission electron microscopy (FETEM) with Energy Dispersive X-ray spectroscopy (EDS). The non-toxic behavior of synthesized IO-HAp nanoparticles was confirmed by cytotoxicity assay (Trypan blue and MTT assay). The synthesized nanoparticles revealed a remarkable magnetic saturation of 83.2 emu/g for IO and 40.6 emu/g for IO-HAp nanoparticles in presence of 15,000 Oe (1.5 T) magnetic field at room temperature (300 K). The magnetic hyperthermia study that was performed with IO-HAp nanoparticles showed an excellent hyperthermia effect (SAR value 85 W/g) over MG-63 osteosarcoma cells. The in vitro hyperthermia temperature (~45 °C) was reached within 3 min, which shows a very high efficiency and kills nearly all of the experimental MG-63 osteosarcoma cells within 30 min exposure. These results could potentially open new perceptions for biomaterials that are aimed for anti-cancer therapies based on magnetic hyperthermia.

| S-EPMC5746916 | biostudies-literature

Effects of Substitution Ratios of Zinc-Substituted Hydroxyapatite on Adsorption and Desorption Behaviors of Bone Morphogenetic Protein-2.

Project description:Understanding interactions between bone morphogenetic proteins (BMPs) and biomaterials is of great significance in preserving the structure and bioactivity of BMPs when utilized in clinical applications. Currently, bone morphogenetic protein-2 (BMP-2) is one of the most important growth factors in bone tissue engineering; however, atomistic interactions between BMP-2 and zinc-substituted hydroxyapatite (Zn-HAP, commonly used in artificial bone implants) have not been well clarified until now. Thus, in this work, the interaction energies, binding/debinding states, and molecular structures of BMP-2 upon a series of Zn-HAP surfaces (Zn-HAPs, 1 at%, 2.5 at%, 5 at%, and 10 at% substitution) were investigated by hybrid molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. Meanwhile, cellular studies including alkaline phosphatase (ALP) activity and reverse transcription-polymerase chain reaction (RT-PCR) assay were performed to verify the theoretical modeling findings. It was found that, compared to pure HAP, Zn-HAPs exhibited a higher binding affinity of BMP-2 at the adsorption process; meanwhile, the detachment of BMP-2 upon Zn-HAPs was more difficult at the desorption process. In addition, molecular structures of BMP-2 could be well stabilized upon Zn-HAPs, especially for Zn10-HAP (with a 10 at% substitution), which showed both the higher stability of cystine-knots and less change in the secondary structures of BMP-2 than those upon HAP. Cellular studies confirmed that higher ALP activity and osteogenic marker gene expression were achieved upon BMP-2/Zn-HAPs than those upon BMP-2/HAP. These findings verified that Zn-HAPs favor the adsorption of BMP-2 and leverage the bioactivity of BMP-2. Together, this work clarified the interaction mechanisms between BMP-2 and Zn-HAPs at the atom level, which could provide new molecular-level insights into the design of BMP-2-loaded biomaterials for bone tissue engineering.

| S-EPMC9456158 | biostudies-literature

Magnetic Properties Controlled by Interstitial or Interlayer Cations in Iron Chalcogenides.

Project description:By applying density functional theory calculations to iron chalcogenides, we find that magnetic order in Fe1+yTe and magnetic instability at (?, ?) in KyFe2Se2 are controlled by interstitial and interlayer cations, respectively. While in Fe1+yTe, magnetic phase transitions occur among collinear, exotic bicollinear and plaquette-ordered antiferronmagnetic states when the height of interstitial irons measured from iron plane or the concentration of interstitial irons is varied, the magnetic instability at (?, ?) which is believed to be responsible for the Cooper pairing in iron pnictides is significantly enhanced when y is much smaller than 1 in KyFe2Se2. Our results indicate that, similar to iron pnictides, itinerant electrons play important roles in iron chalcogenides, even though the fluctuating local moments become larger.

| S-EPMC4705632 | biostudies-literature

Site occupancy of interstitial deuterium atoms in face-centred cubic iron.

Project description:Hydrogen composition and occupation state provide basic information for understanding various properties of the metal-hydrogen system, ranging from microscopic properties such as hydrogen diffusion to macroscopic properties such as phase stability. Here the deuterization process of face-centred cubic Fe to form solid-solution face-centred cubic FeDx is investigated using in situ neutron diffraction at high temperature and pressure. In a completely deuterized specimen at 988 K and 6.3 GPa, deuterium atoms occupy octahedral and tetrahedral interstitial sites with an occupancy of 0.532(9) and 0.056(5), respectively, giving a deuterium composition x of 0.64(1). During deuterization, the metal lattice expands approximately linearly with deuterium composition at a rate of 2.21 Å(3) per deuterium atom. The minor occupation of the tetrahedral site is thermally driven by the intersite movement of deuterium atoms along the ‹111› direction in the face-centred cubic metal lattice.

| S-EPMC4200519 | biostudies-literature

Mechanisms for <100> interstitial dislocation loops to diffuse in BCC iron.

Project description:The mobility of dislocation loops in materials is a principle factor in understanding the mechanical strength, and the evolution of microstructures due to deformation and radiation. In body-centered cubic (BCC) iron, the common belief is that <100> interstitial dislocation loops are immobile once formed. However, using self-adaptive accelerated molecular dynamics (SSAMD), a new diffusion mechanism has been discovered for <100> interstitial dislocation loops. The key aspect of the mechanism is the changing of the habit planes between the {100} plane and the {110} plane, which provides a path for the <100> loops to diffuse one-dimensionally. The migration behavior modeled with SSAMD is further confirmed by in-situ transmission electron microscopy (TEM) measurements, and represents a significant step for understanding the formation of <100> loop walls and the mechanical behavior of BCC Fe under irradiation.

| S-EPMC7801622 | biostudies-literature

Compensatory evolution in RNA secondary structures increases substitution rate variation among sites.

Project description:There is growing evidence that interactions between biological molecules (e.g., RNA-RNA, protein-protein, RNA-protein) place limits on the rate and trajectory of molecular evolution. Here, by extending Kimura's model of compensatory evolution at interacting sites, we show that the ratio of transition to transversion substitutions (kappa) at interacting sites should be equal to the square of the ratio at independent sites. Because transition mutations generally occur at a higher rate than transversions, the model predicts that kappa should be higher at interacting sites than at independent sites. We tested this prediction in 10 RNA secondary structures by comparing phylogenetically derived estimates of kappa in paired sites within stems (kappa(p)) and unpaired sites within loops (kappa(u)). Eight of the 10 structures showed an excellent match to the quantitative predictions of the model, and 9 of the 10 structures matched the qualitative prediction kappa(p) > kappa(u). Only the Rev response element from the human immunovirus (HIV) genome showed the reverse pattern, with kappa(p) < kappa(u). Although a variety of evolutionary forces could produce quantitative deviations from the model predictions, the reversal in magnitude of kappa(p) and kappa(u) could be achieved only by violating the model assumption that the underlying transition (or transversion) mutation rates were identical in paired and unpaired regions of the molecule. We explore the ability of the APOBEC3 enzymes, host defense mechanisms against retroviruses, which induce transition mutations preferentially in single-stranded regions of the HIV genome, to explain this exception to the rule. Taken as a whole, our findings suggest that kappa may have utility as a simple diagnostic to evaluate proposed secondary structures.

| S-EPMC2734131 | biostudies-literature

A Study of Vanadate Group Substitution into Nanosized Hydroxyapatite Doped with Eu3+ Ions as a Potential Tissue Replacement Material.

Project description:In this study, nanosized vanadate-substituted hydroxyapatites doped with 1 mol% and 2 mol% Eu3+ ions were obtained via the precipitation method. To evaluate the structure and morphology of the obtained compounds, the XRPD (X-ray powder diffraction) technique, Rietveld refinement, SEM-EDS (scanning electron microscopy-energy-dispersive spectrometry) and TEM (transmission electron microscopy) techniques as well as FTIR (Fourier transform infrared) spectroscopy were performed. Moreover, the chemical formula was confirmed using the ICP-OES (Inductively coupled plasma optical emission spectroscopy spectroscopy). The calculated average grain size for powders was in the range of 25 to 90 nm. The luminescence properties of vanadium-substituted hydroxyapatite were evaluated by recording emission spectra and excitation spectra as well as luminescence kinetics. The crucial step of this research was the evaluation of the biocompatibility of the synthesized nanomaterials. Therefore, the obtained compounds were tested toward sheep red blood cells and normal human dermal fibroblast to confirm the nontoxicity and biocompatibility of new nanosized Eu3+ ion-doped vanadate-hydroxyapatite. Moreover, the final step of the research allowed us to determine the time dependent ion release to the simulated body fluid environment. The study confirmed cytocompatibility of vanadium hydroxyapatite doped with Eu3+ ions.

| S-EPMC8746586 | 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