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Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations
(2023)
Radiation damage to DNA plays a central role in radiation therapy to cure cancer. The physico-chemical and biological processes involved encompass huge time and spatial scales. To obtain a comprehensive understanding on the nano and the macro scale is a very challenging tasks for experimental techniques alone. Therefore particle-scattering simulations are often applied to complement measurements and aide their interpretation, to help in the planning of experiments, to predict their outcome and to test damage models. In the last years, powerful multipurpose particle-scattering framework based on the Monte-Carlo simulation (MCS) method, such as Geant4 and Geant4-DNA, were extended by user friendly interfaces such as TOPAS and TOPAS-nBio. This shifts their applicability from the realm of dedicated specialists to a broader range of scientists. In the present review we aim to give an overview over MCS based approaches to understand radiation interaction on a broad scale, ranging from cancerous tissue, cells and their organelles including the nucleus, mitochondria and membranes, over radiosensitizer such as metallic nanoparticles, and water with additional radical scavenger, down to isolated biomolecules in the form of DNA, RNA, proteins and DNA-protein complexes. Hereby the degradation of biomolecules by direct damage from inelastic scattering processes during the physical stage, and the indirect damage caused by radicals during the chemical stage as well as some parts of the early biological response is covered. Due to their high abundance the action of hydroxyl radicals (•OH) and secondary low energy electrons (LEE) as well as prehydrated electrons are covered in additional detail. Applications in the prediction of DNA damage, DNA repair processes, cell survival and apoptosis, influence of radiosensitizer on the dose distribution within cells and their organelles, the study of linear energy transfer (LET), the relative biological effectiveness (RBE), ion beam cancer therapy, microbeam radiation therapy (MRT), the FLASH effect, and the radiation induced bystander effect are reviewed.
The ionic liquid 1,3-dimethyl-imidazolium-dimethylphosphate ([MMIM]+[DMP]−) was analyzed using (hard) x-ray photoelectron spectroscopy.
Here, XPS and HAXPES spectra are shown in comparison. For the acquisition of the XPS spectra, monochromatic Al Kα radiation at 1486.6 eV was used, while for the acquisition of the HAXPES spectra, monochromatic Cr Kα radiation at 5414.8 eV was applied. Here, survey scans and high-resolution spectra of P 2p, P 2s, C 1s, O 1s, and N 1s for both methods and P 1s, P KL2,3L2,3, and P KL1L2,3 for HAXPES are shown.
This work presents the determination of the corrosion characteristics of CrCoNi (medium entropy alloy) and CrMnFeCoNi (high entropy alloy) in 0.1 M NaCl and 0.1 M H2SO4. The morphology and chemical composition of the oxide layers formed on CrCoNi and CrMnFeCoNi were comparatively analyzed by scanning Kelvin probe microscopy (SKPFM) and scanning electron microscopy (SEM) and supported with chemical analysis by means of inductively coupled plasma mass spectrometry (ICP-MS) and X-Ray photoelectron spectroscopy (XPS). The analysis of the 3p core level peaks showed that the oxide layer (native and after anodic passivation) on CrCoNi consisted mainly of Cr oxides, while the oxide layer on CrMnFeCoNi was primarily composed of a mixture of Cr and Fe oxides. In addition, XPS was utilized to assess the oxide layer thicknesses. These results were compared to the thicknesses obtained by means of electrochemical impedance spectroscopy (EIS), with both approaches yielding values up to about 4 nm depending on the electrolyte and the alloy. Cyclic polarization measurements indicated superior corrosion resistance of CrCoNi in both aqueous environments compared to CrMnFeCoNi, as well as to AISI 304 stainless steel.
In order to bridge the gap between lab-scale and industrial-scale production of graphene it is necessary to develop processes, equipment and measurement procedures to control the material features. One of the crucial reasons of graphene’s limited commercialization is the lack of standard procedures to properly characterize and define the material chemical and structural properties down to the nanometer level. This leads to many issues regarding material synthesis repeatability, inappropriateness choice of measurands and measurement reproducibility which heavily affect the consistency of the material performance.
In our study, a comparative analysis is performed on two different series (G5 and G6) of industrial graphene powders, each series produced with four types of functionalization: raw graphene, oxygen-functionalized, nitrogen-functionalized and fluorine-functionalized. All the 8 sample variants were analyzed from a chemical and morphological point of view in the form of powders prepared as slightly pressed in metallic sample holders.
The results of the comparative chemical analyses XPS and EDS show a good agreement in the concentration values for all the elements present in the samples, despite the different analysis volumes addressed by the two techniques. For this reason, the samples can be considered homogeneous in both lateral and vertical direction.
A clear influence of the morphology on the composition is evident. Therefore, such correlative measurements of morphology and composition are necessary for a comprehensive characterization of industrial graphene flakes.
Nanosafety is becoming increasingly important as nanomaterials are widely used in industrial processes and consumer products. For nanotoxicity measurements prior sterilization of the samples is necessary, but as structure activity relationships are made with properties of pristine particles, the question arises, if the sterilization process has an impact on the physico-chemical properties of nanoparticles and thus on the biological behavior.
This question will be addressed in this talk. For this purpose, results from SEM and EDS measurements are combined with those of a novel lab-based HAXPES spectrometer in order to obtain a more complete picture. At the end, an influence of sterilization will be evident, which indicates a restructuring of the nanoparticles owing to sterilization.
The spatial distribution and concentration of lanthanide activator and sensitizer dopant ions are of key importance for the luminescence color and efficiency of upconverting nanoparticles (UCNPs). Quantifying dopant ion distributions and intermixing, and correlating them with synthesis methods require suitable analytical techniques. Here, X-ray photoelectron spectroscopy depth-profiling with tender X-rays (2000–6000 eV), providing probe depths ideally matched to UCNP sizes, is used to measure the depth-dependent concentration ratios of Er3+ to Yb3+, [Er3+]/[Yb3+], in three types of UCNPs prepared using different reagents and synthesis methods. This is combined with data simulations and inductively coupled plasma-optical emission spectroscopy (ICP-OES) measurements of the lanthanide ion concentrations to construct models of the UCNPs’ dopant ion distributions. The UCNP sizes and architectures are chosen to demonstrate the potential of this approach. Core-only UCNPs synthesized with XCl3·6H2O precursors (β-phase) exhibit a homogeneous distribution of lanthanide ions, but a slightly surface-enhanced [Er3+]/[Yb3+] is observed for UCNPs prepared with trifluroacetate precursors (α-phase). Examination of Yb-core@Er-shell UCNPs reveals a co-doped, intermixed region between the single-doped core and shell. The impact of these different dopant ion distributions on the UCNP's optical properties is discussed to highlight their importance for UCNP functionality and the design of efficient UCNPs.
Recent developments of X-ray photoelectron spectroscopy using excitation energies different from the usual lab-sources Mg Kα and Al Kα, thus covering larger and different kinetic energy ranges, require more flexible approaches for determining the transmission function than the well-established ones using reference spectra. Therefore, the approach using quantified peak areas (QPA) was refined allowing a more precise estimation of the transmission function. This refinement was tested by comparing the results obtained with the new version with former calculations. Furthermore, the obtained transmission function was validated by comparing the results with a transmission function using the reference spectrum of polyethylene. Additionally, an ionic liquid was used as reference for estimating the transmission function at the energy resolved HE-SGM beamline at BESSY II. Comparison between the measured and stoichiometric composition shows that a transmission function was determined, which allows a reasonable quantification.
Here, we present a study on agarose thin-film samples that represent a model system for the exopolysaccharide matrix of biofilms. Povidone-iodide (PVP-I) was selected as an antibacterial agent to evaluate our x-ray photoelectron spectroscopy (XPS)-based methodology to trace specific marker elements, here iodine, commonly found in organic matrices of antibiotics. The in-depth distribution of iodine was determined by XPS analyses with variable excitation energies and in combination with argon gas cluster ion beam sputter cycles. On mixed agarose/PVP-I nanometer-thin films, both methods were found to solve the analytical task and deliver independently comparable results. In the mixed agarose/PVP-I thin film, we found the outermost surface layer depleted in iodine, whereas the iodine is homogeneously distributed in the depth region between this outermost surface layer and the interface between the thin film and the substrate. Depletion of iodine from the uppermost surface in the thin-film samples is assumed to be caused by ultrahigh vacuum exposure resulting in a loss of molecular iodine (I2) as reported earlier for other iodine-doped polymers.
ISO Technical Report 23173 describes methods by which electron spectroscopies, including X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES) and synchrotron techniques, can be employed to calculate the Coating thicknesses and compositions of nanoparticles. The document has been developed to review and outline the current state-of-the-art for such measurements. Such analyses of core–shell nanoparticles are common within the literature, however the
methods employed are varied; the relative advantages and disadvantages of These methods, and the optimal usage of each may not be clear to the general analyst. ISO Technical Report 23173 aims to clarify the methods that are available, describe them in clear terms, exhibit examples of their use, and highlight potential issues users may face. The information provided should allow analysts of electron spectroscopy data to make clear choices regarding the appropriate analysis of electron spectroscopy data from coated nanoparticle systems and provide a basis for understanding and comparing results from different methods and systems.
Ionizing radiation damage to DNA plays a fundamental role in cancer therapy. X-ray photoelectron-spectroscopy (XPS) allows simultaneous irradiation and damage monitoring. Although water radiolysis is essential for radiation damage, all previous XPS studies were performed in vacuum. Here we present near-ambient-pressure XPS xperiments to directly measure DNA damage under water atmosphere. They permit in-situ monitoring of the effects of radicals on fully hydrated double-stranded DNA. The results allow us to distinguish direct damage, by photons and secondary low-energy electrons (LEE), from damage by hydroxyl radicals or hydration induced modifications of damage pathways. The exposure of dry DNA to x-rays leads to strand-breaks at the sugar-phosphate backbone, while deoxyribose and nucleobases are less affected. In contrast, a strong increase of DNA damage is observed in water, where OH-radicals are produced. In consequence, base damage and base release become predominant, even though the number of strand-breaks increases further.
Low-cost, high-efficient catalysts for water splitting can be potentially fulfilled by developing earthabundant metal oxides. In this work, surface galvanic formation of Co-OH on K0.45MnO2 (KMO) was achieved via the redox reaction of hydrated Co2+ with crystalline Mn4+. The synthesis method takes place at ambient temperature without using any surfactant agent or organic solvent, providing a clean, green route for the design of highly efficient catalysts. The redox reaction resulted in the formation of ultrathin Co-OH nanoflakes with high electrochemical surface area. X-ray absorption spectroscopy (XAS) and X-ray photoelectron spectroscopy (XPS) analysis confirmed the changes in the oxidation state of the bulk and
surface species on the Co-OH nanoflakes supported on the KMO. The effect of the anions, such as chloride, nitrate and sulfate, on the preparation of the catalyst was evaluated by electrochemical and spectrochemical means. XPS and Time of flight secondary ion mass spectrometry (ToF-SIMS) analysis demonstrated that the layer of CoOxHy deposited on the KMO and its electronic structure strongly depend on the anion of the precursor used during the synthesis of the catalyst. In particular, it was found that Cl- favors the formation of Co-OH, changing the rate-determining step of the reaction, which enhances the catalytic activity towards the OER, producing the most active OER catalyst in alkaline media.
Controlling thickness and tightness of surface passivation shells is crucial for many applications of core–shell nanoparticles (NP). Usually, to determine shell thickness, core and core/shell particle are measured individually requiring the availability of both nanoobjects. This is often not fulfilled for functional nanomaterials such as many photoluminescent semiconductor quantum dots (QD) used for bioimaging, solid state lighting, and display technologies as the core does not show the applicationrelevant functionality like a high photoluminescence (PL) quantum yield, calling for a whole nanoobject approach. By combining high-resolution transmission electron microscopy (HR-TEM) and X-ray photoelectron spectroscopy (XPS), a novel whole nanoobject approach is developed representatively for an ultrabright oleic acid-stabilized, thick shell CdSe/CdS QD with a PL quantum yield close to unity. The size of this spectroscopically assessed QD, is in the range of the information depth of usual laboratory XPS. Information on particle size and monodispersity were validated with dynamic light scattering (DLS) and small angle X-ray scattering (SAXS) and compared to data derived from optical measurements. In addition to demonstrating the potential of this novel whole nanoobject approach for determining architectures of small nanoparticles, the presented results also highlight challenges faced by different sizing and structural analysis methods and method-inherent uncertainties.
We studied the dissolution behavior of β NaYF4:Yb(20%), Er(2%) UCNP of two different sizes in biologically relevant media i.e., water (neutral pH), phosphate buffered saline (PBS), and Dulbecco’s modified Eagle medium (DMEM) at different temperatures and particle concentrations. Special emphasis was dedicated to assess the influence of different surface functionalizations, particularly the potential of mesoporous and microporous silica shells of different thicknesses for UCNP stabilization and protection. Dissolution was quantified electrochemically using a fluoride ion selective electrode (ISE) and by inductively coupled plasma optical emission spectrometry (ICP OES). In addition, dissolution was monitored fluorometrically. These experiments revealed that a thick microporous silica shell drastically decreased dissolution. Our results also underline the critical influence of the chemical composition of the aqueous environment on UCNP dissolution. In DMEM, we observed the formation of a layer of adsorbed molecules on the UCNP surface that protected the UCNP from dissolution and enhanced their fluorescence. Examination of this layer by X ray photoelectron spectroscopy (XPS) and mass spectrometry (MS) suggested that mainly phenylalanine, lysine, and glucose are adsorbed from DMEM. These findings should be considered in the future for cellular toxicity studies with UCNP and other nanoparticles and the design of new biocompatible surface coatings.
Implant-associated infections present severe and difficult-to-treat complications after surgery, related to implant biofilm colonization. Systemic administration of antibiotics cannot reach sufficient concentrations at the infected site and may be toxic. Here we describe how mussel-inspired dendritic material coated on a titanium surface can locally activate a prodrug of daptomycin (pro-dapto) to treat methicillin-resistant Staphylococcus aureus. The mechanism of the prodrug activation is based on bio-orthogonal click chemistry between a tetrazine (Tz) and trans-cyclooctene (TCO). The former is attached to the dendritic polymer, while the later converts daptomycin into a prodrug. Characterization of the material's properties revealed that it is hydrophobic, non-toxic, and stable for a prolonged period of time. We envision that the titanium coated dendritic material will be able to improve the treatment of implant-associated infections by concentrating systemically administered antibiotic prodrugs, thus converting them into active localized medicines.
Metal-Assisted and Solvent-Mediated Synthesis of Two-Dimensional Triazine Structures on Gram Scale
(2020)
Covalent triazine frameworks are an emerging material class that have shown promising performance for a range of applications. In this work, we report on a metal-assisted and solvent-mediated reaction between calcium carbide and cyanuric chloride, as cheap and commercially available precursors, to synthesize two-dimensional triazine structures (2DTSs). The reaction between the solvent, dimethylformamide, and cyanuric chloride was promoted by calcium carbide and resulted in dimethylamino-s-triazine intermediates, which in turn undergo nucleophilic substitutions. This reaction was directed into two dimensions by calcium ions derived from calcium carbide and induced the formation of 2DTSs. The role of calcium ions to direct the two-dimensionality of the final structure was simulated using DFT and further proven by synthesizing molecular intermediates. The water content of the reaction medium was found to be a crucial factor that affected the structure of the products dramatically. While 2DTSs were obtained under anhydrous conditions, a mixture of graphitic material/2DTSs or only graphitic material (GM) was obtained in aqueous solutions. Due to the straightforward and gram-scale synthesis of 2DTSs, as well as their photothermal and photodynamic properties, they are promising materials for a wide range of future applications, including bacteria and virus incapacitation.
What Does Ectoine Do to DNA? A Molecular-Scale Picture of Compatible Solute−Biopolymer Interactions
(2020)
Compatible solutes are accumulated in the cytoplasm of halophilic microorganisms. These molecules enable their survival in a high salinity environment. Ectoine is such a compatible solute. It is a zwitterionic molecule which strongly interacts with surrounding water molecules and changes the dynamics of the local hydration shell. Ectoine interacts with biomolecules such as lipids, proteins and DNA. The molecular interaction between ectoine and biomolecules in particular the interaction between ectoine and DNA is far from being understood.
In this paper we describe molecular aspects of the interaction between ectoine and double stranded DNA(dsDNA). Two 20 base pairs long dsDNA fragments were immobilized on a Gold surface via a thiol-tether. The interaction between the dsDNA monolayers with diluted and concentrated ectoine solutions was examined by means of X-ray photoelectron and polarization modulation infrared reflection absorption spectroscopies (PM IRRAS). Experimental results indicate that the ability of ectoine to bind water reduces the strength of hydrogen bonds formed to the ribose-phosphate backbone in the dsDNA. In diluted (0.1 M) ectoine solution, DNA interacts predominantly with water molecules. The sugar-phosphate backbone is involved in the formation of strong hydrogen bonds to water, which with elapsing time leads to a reorientation of the planes of nucleic acid bases. This reorientation destabilizes the hydrogen bonds strength between the bases and leads to a partial dehybridizaiton of the dsDNA. In concentrated ectoine solution (2.5 M), almost all water molecules interact with ectoine. Under this condition ectoine is able to interact directly with DNA. Density functional theory (DFT) calculations demonstrate that the direct interaction involves the nitrogen atoms in ectoine and phosphate groups in the DNA molecule. The results of the quantum chemical calculations Show that rearrangements in the ribose-phosphate backbone, caused by a direct interaction with ectoine, facilitates contacts between O atom in the phosphate group and H atoms in a nucleic acid base. In the PM IRRA spectra, an increase in the number of the IR absorption modes in the base pair frequency region proves that the hydrogen bonds between bases become weaker.
Thus, a sequence of reorientations caused by interaction with ectoine leads to a breakdown of hydrogen bonds between bases in the double helix.
Most real core-shell nanoparticle (CSNP) samples deviate from an ideal core-shell structure potentially having significant impact on the particle properties. An ideal structure displays a spherical core fully encapsulated by a shell of homogeneous thickness, and all particles in the sample exhibit the same shell thickness. Therefore,
analytical techniques are required that can identify and characterize such deviations.
This study demonstrates that by analysis of the inelastic background in X-ray photoelectron spectroscopy (XPS) survey spectra, the following types of deviations can be identified and quantified: the nonuniformity of the shell thickness within a nanoparticle sample and the incomplete encapsulation of the cores by the shell material. Furthermore, CSNP shell thicknesses and relative coverages can be obtained. These results allow for a quick and straightforward comparison between several batches of a specific CSNP, different coating approaches, and so forth. The presented XPS methodology requires a submonolayer distribution of CSNPs on a substrate.
Poly(tetrafluoroethylene)-poly(methyl methacrylate) and poly(tetrafluoroethylene)-polystyrene polymer CSNPs serve as model systems to demonstrate the applicability of the approach.
While noncovalent interactions at two-dimensional nanobiointerfaces are extensively investigated, less knowledge about covalent interactions at this interface is available. In this work, boronic acid-functionalized 2D MoS2 was synthesized and its covalent multivalent interactions with bacteria and nematodes were investigated. Polymerization of glycidol by freshly exfoliated MoS2 and condensation of 2,5-thiophenediylbisboronic acid on the produced platform resulted in boronic acid-functionalized 2D MoS2. The destructive interactions between 2D MoS2 and bacteria as well as nematodes were significantly amplified by boronic acid functional groups. Because of the high antibacterial and antinematodal activities of boronic acid-functionalized 2D MoS2, its therapeutic efficacy for diabetic wound healing was investigated. The infected diabetic wounds were completely healed 10 days after treatment with boronic acid-functionalized 2D MoS2, and a normal structure for recovered tissues including different layers of skin, collagen, and blood vessels was detected.
Low biodegradability of graphene derivatives and related health risks are the main limiting factors for their in vivo biomedical applications. Here, we present the synthesis of enzyme-functionalized graphene sheets with self-degrading properties under physiological conditions and their applications in Tumor therapy. The synergistic enzyme cascade glucose oxidase and myeloperoxidase are covalently conjugated to the surface of graphene sheets and two-dimensional (2D) platforms are obtained that can produce sodium hypochlorite from glucose. The enzyme-functionalized graphene sheets with up to 289 nm average size are degraded into small pieces (≤40 nm) by incubation under physiological conditions for 24 h. Biodegradable graphene sheets are further loaded with doxorubicin and their ability for Tumor therapy is evaluated in vitro and in vivo. The laser-triggered release of doxorubicin in combination with the enzymatic activity of the functionalized graphene sheets results in a synergistic antitumor activity.
Taking advantage of their neutrophil-like activity, fast biodegradability, high photo- and chemotherapeutic effects, the novel two-dimensional nanoplatforms can be used for tumor therapeutic applications.
Aiming at the overall negative surface charge of bacteria, a new strategy of antibacterial agents based on large polymer-modified graphene oxide (GO) sheets is assessed. The presented flexible, polycationic Sheets match the size and charge density of the Escherichia coli surface charge density (2 × 1014 cm−2). These matching parameters create an unspecific but very strong bacteria adsorber by multivalent, electrostatic attraction.
Their interaction with bacteria is visualized via atomic force and confocal microscopy and shows that they effectively bind and wrap around E. coli cells, and thereby immobilize them. The incubation of Gram-negative and -positive bacteria (E. coli and methicillin-resistant Staphylococcus aureus, MRSA) with these polycationic sheets leads to the inhibition of proliferation and a reduction of the colony forming bacteria over time.
This new type of antibacterial agent acts in a different mode of Action than classical biocides and could potentially be employed in medicinal, technical, or agriculture applications. The presented microsheets and their unspecific binding of cell interfaces could further be employed as adsorber material for bacterial filtration or immobilization for imaging, analysis, or sensor technologies.