Soft X-Ray-Induced Decomposition of Amino Acids: An XPS, Mass Spectrometry, and NEXAFS Study

Compelling DNA intercalation through 'anion-anion' anti-coulombic interactions: boron cluster self-vehicles as promising anticancer agents

Anticancer drugs inhibit DNA replication by intercalating between DNA base pairs, forming covalent bonds with nucleotide bases, or binding to the DNA groove. To develop safer drugs, novel molecular structures with alternative binding mechanisms are essential. Stable boron hydrides offer a promising alternative for cancer therapy, opening up additional options like boron neutron capture therapy based on 10B and thermal neutron beams or proton boron fusion therapy using 11B and proton beams. These therapies are more efficient when the boron compound is ideally located inside cancer cells, particularly in the nucleus. Current cancer treatments often utilize small, polycyclic, aromatic, planar molecules that intercalate between ds-DNA base pairs, requiring only a spacing of approximately 0.34 nm. In this paper, we demonstrate another type of intercalation. Notably, [3,3'-Fe(1,2-C2B9H11)2]-, ([o-FESAN]-), a compact 3D molecule measuring 1.1 nm × 0.6 nm, can as well intercalate by strong non-bonding interactions preferentially with guanine. Unlike known intercalators, which are positive or neutral, [o-FESAN]- is a negative species and when an [o-FESAN]- molecule approaches the negatively charged DNA phosphate chain an anion-anion interaction consistently anti-electrostatic via Ccluster-H⋯O-P bonds occurs. Then, when more molecules approach, an elongated outstandingly self-assembled structure of [o-FESAN]--[o-FESAN]- forms moving anions towards the interthread region to interact with base pairs and form aggregates of four [o-FESAN]- anions per base pair. These aggregates, in this environment, are generated by Ccluster-H⋯O-C, N-H⋯H-B and Ccluster-H⋯H-B interactions. The ferrabis(dicarbollide) boron-rich small molecules not only effectively penetrate the nucleus but also intercalate with ds-DNA, making them promising for cancer treatment. This amphiphilic anionic molecule, used as a carrier-free drug, can enhance radiotherapy in a multimodal perspective, providing healthcare professionals with improved tools for cancer treatment. This work demonstrates these findings with a plethora of techniques.

Energy Absorption and Beam Damage during Microfocus Synchrotron X-ray Diffraction

In this study, we combine in situ fast differential scanning calorimetry (FDSC) with synchrotron X-ray measurements to study simultaneously the structure and thermophysical properties of materials. Using the example of the organic compound BCH-52, we show that the X-ray beam can heat the sample and induce a shift of the heat-flow signal. The aim of this paper is to investigate the influence of radiation on sample behavior. The calorimetric data is used to quantify the absorbed beam energy and, together with the diffraction data, reveal an irreversible damage of the sample. The results are especially important for materials with high absorption coefficients and for high-energy X-ray and electron beams. Our findings illustrate that FDSC combined with X-ray diffraction is a suitable characterization method when beam damage must be minimized.

Near-edge x-ray absorption fine structure spectra and specific dissociation of small peptoid molecules

In this study, the total ion yield near-edge x-ray absorption fine structure spectra of four similar peptoid molecules, which differ in the numbers and positions of methyl groups, were investigated experimentally and theoretically. At each excitation energy, the intensity and branching ratio of each ionic product were measured. At a few resonant excitation energies, a specific dissociation of the C-CO bond at the nitrogen and oxygen K-edges and of the N-CO bond at the carbon K-edge was dominant, which correlated well with the predicted destination antibonding orbitals of the core electron excitation. These specific dissociation mechanisms of small peptoid molecules could provide insights into similar phenomena that occur in peptide molecules.

Amino acids modified nanoscale zero-valent iron: Density functional theory calculations, experimental synthesis and application in the Fenton-like degradation of organic solvents

To improve the adsorption and catalytic performance of heterogeneous Fenton-like catalysts for oil wastes, amino acids were used to modify nanoscale zero-valent iron (AA@Fe0), which were applied in the Fenton-like degradation of organic solvents (tributyl phosphate and n-dodecane, named TBP and DD). Twelve amino acids, i.e., glycine (Gly), alanine (Ala), leucine (Leu), proline (Pro), phenylalanine (Phe), methionine (Met), cysteine (Cys), asparagine (Asn), serine (Ser), glutamic acid (Glu), lysine (Lys) and arginine (Arg), were selected and calculated by density functional theory (DFT). The optimized structure, charge distribution, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), interaction region indicator (IRI) isosurface map and adsorption energy of AA@Fe0, AA@Fe0-TBP and AA@Fe0-DD were studied, which indicated that Fe is more likely to approach and charge transfer with -COO and -NH3 on the α-carbon of amino acids. There is strong attraction between Fe and -COO, and Van der Waals force between Fe and -NH3, respectively. In the interaction of AA@Fe0 with TBP and DD, Van der Waal force plays an important role. AA@Fe0 was synthesized in laboratory and characterized to investigate physicochemical properties. In Fenton-like degradation of organic solvents, the change of COD in water phase during the degradation process as well as the volume of the organic phase after the reaction were investigated. The results of calculations combined with experiments showed that Ser-modified Fe0 performed the best in these amino acids, with 98% removal of organic solvents. A possible catalytic mechanism was proposed in which amino acids acted a linking role between Fe and organic solvents, activating H2O2 to generate hydroxyl radicals for the degradation of organic solvents.

Resonant Inelastic Soft X-ray Scattering and X-ray Emission Spectroscopy of Solid Proline and Proline Solutions

The amino group of proline is part of a pyrrolidine ring, which makes it unique among the proteinogenic amino acids. To unravel its full electronic structure, proline in solid state and aqueous solution is investigated using X-ray emission spectroscopy and resonant inelastic soft X-ray scattering. By controlling the pH value of the solution, proline is studied in its cationic, zwitterionic, and anionic configurations. The spectra are analyzed within a "building-block principle" by comparing with suitable reference molecules, i.e., acetic acid, cysteine, and pyrrolidine, as well as with spectral calculations based on density functional theory. We find that the electronic structure of the carboxyl group of proline is very similar to that of other amino acids as well as acetic acid. In contrast, the electronic structure of the amino group is significantly different and strongly influenced by the ring structure of proline.

Adsorption and Mechanism of Glycine on the Anatase with Exposed (001) and (101) Facets

As a widely existing mineral types on Earth, semiconductor minerals play an important role in the origin of life and the material geochemical cycle. The first step of peptide formation is amino acid adsorption on the mineral surface, but the role and mechanism of different crystal facets of semiconductor minerals are not well understood. Anatase (TiO2) with exposed (001) facets was synthesized by a hydrothermal method, and then analyzed and compared with the purchased ordinary anatase (TiO2) for the adsorption of glycine, the simplest amino acid. XRD, SEM and TEM results show that the hydrothermally synthesized anatase (TiO2) has a good anatase crystal form, which is micro-nano-scale flake particles and mainly composed of (001) facets. The results of HPLC used in the adsorption experiment showed that under optimal conditions (pH 5 to 6, an adsorption time of 24 h, and an initial concentration of 0.09 mol/L), the adsorption quantity of glycine on anatase (TiO2) with exposed (001) facets may reach 10 mg/m2, which is larger than that for ordinary anatase (TiO2) with exposed (101) facets. Based on a combination of various characterizations and simulation calculations, the results proved that anatase can activate thermodynamically stable γ-glycine to β-glycine. The adsorption of glycine on anatase (TiO2) has two forms, one is the zwitterionic form in which the carboxyl group forms a bridge structure with two Ti atoms connected by surface bridging oxygen, and the dissociated form is in which the amino group forms a bond with the surface Ti atom. Among these, glycine is mainly adsorbed to anatase by dissociative molecules on the anatase (TiO2) with exposed (001) facets and by zwitterion adsorption on the anatase (TiO2) with exposed (101) facets. This research elucidates the conditions and mechanism of amino acid adsorption by semiconductor minerals in weak acidic environment, which is similar to the environmental pH that was beneficial to the formation of life on the early Earth. Therefore, these can provide a reference for the further study of the role of semiconductor minerals in the adsorption and polymerization of small biomolecules in the origin of life.

Low-Temperature Sintering of l-Alanine-Functionalized Metallic Copper Particles Affording Conductive Films with Excellent Oxidative Stability

Here, the alpha amino acid l-alanine is employed as both a capping and stabilizing agent in the aqueous synthesis of submicron-sized metallic copper particles under ambient atmospheric conditions. The reduction of the copper(II) precursor is achieved using l-ascorbic acid (vitamin C) as the reducing agent. The nature of the complex formed between l-alanine and the copper(II) precursor, pH of the medium, temperature, and the relative proportion of capping agent are found to play a significant role in determining the size, shape, and oxidative stability of the resulting particles. The adsorbed l-alanine is shown to act as a barrier imparting excellent thermal stability to capped copper particles, delaying the onset of temperature-induced aerial oxidation. The stability of the particles is complemented by highly favorable sintering conditions, rendering the formation of conductive copper films at significantly lower temperatures (T ≤ 120 °C) compared to alternative preparation methods. The resulting copper films are well-passivated by residual surface l-alanine molecules, promoting long-term stability without hindering the surface chemistry of the copper film as evidenced by the catalytic activity. Contrary to the popular belief that ligands with long carbon chains are best for providing stability, these findings demonstrate that very small ligands can provide highly effective stability to copper without significantly deteriorating its functionality while facilitating low-temperature sintering, which is a key requirement for emerging flexible electronic applications.

Mineralogical control on methylotrophic methanogenesis and implications for cryptic methane cycling in marine surface sediment

Minerals are widely proposed to protect organic carbon from degradation and thus promote the persistence of organic carbon in soils and sediments, yet a direct link between mineral adsorption and retardation of microbial remineralisation is often presumed and a mechanistic understanding of the protective preservation hypothesis is lacking. We find that methylamines, the major substrates for cryptic methane production in marine surface sediment, are strongly adsorbed by marine sediment clays, and that this adsorption significantly reduces their concentrations in the dissolved pool (up to 40.2 ± 0.2%). Moreover, the presence of clay minerals slows methane production and reduces final methane produced (up to 24.9 ± 0.3%) by a typical methylotrophic methanogen—Methanococcoides methylutens TMA-10. Near edge X-ray absorption fine structure spectroscopy shows that reversible adsorption and occlusive protection of methylamines in clay interlayers are responsible for the slow-down and reduction in methane production. Here we show that mineral-OC interactions strongly control methylotrophic methanogenesis and potentially cryptic methane cycling in marine surface sediments.

Adsorption of methylamines onto clay minerals provides a hitherto unrecognised control on methane production in marine surface sediment.

Impacts of solvation on photo-damage of polypeptides: Modulation and biological implications

We investigate the photon/matter interactions between soft X-rays and three selected polypeptides, poly-glycine (poly-Gly), poly-L-arginine (poly-Arg), and poly-l-lysine (poly-Lys), where the effects of molecular packing under the influence of solvent, e.g., water, substrates (Au foil or Si wafer) and X-ray irradiation under different durations were systematically investigated. Compared with negligible photo-damage on bare polypeptide powders, significantly enhanced degradation in pre-solvated polypeptides was observed likely because of the formation photo-generated radicals. X-ray photoemission spectroscopy (XPS) were employed as the analysis means to identify and quantify the chemical changes, especially the high-resolution photoemission spectra of C 1s, O 1s, N 1s and their evolution under continuous X-ray irradiation. The photo-degradation was found to preferentially occur on the CO entity in poly-Gly and the guanidinium group in poly-Arg. In poly-Arg, deprotonation occurs via the switch from zwittterionic to a neutral configuration, whereas poly-Lys deprotonates by directly losing the corresponding amine. The critical role of the interactions between amino acids, the building blocks of protein and almost all forms of biological activities, and the free-radical-generating living environment under irradiation was critically analyzed. The present study found that the preparation history of a sample, especially its inadvertent exposure to the sources of H₂O, O₂ and OH, could significantly alter the outcome of a radiation-related chemical process. Implications on the non-destructive probe of biologically important systems using physical methods involving X-rays were discussed as well.

Investigations into Spin- and Unpolarized Secondary Electron-Induced Reactions in Self-Assembled Monolayers of Cysteine

Cysteine is the simplest thiolated, chiral amino acid and is often used as the anchor for studies of self-assembled monolayers (SAMs) of complex biomolecules such as peptides. Understanding the interaction of SAMs of cysteine with low-energy secondary electrons (SEs) produced by X-rays can further our understanding of radiation damage in biomolecules. In particular, if the electrons are polarized, chiral-selective chemistry could have bearing on the origin of homochirality in nature. In the present paper, we use synchrotron radiation-based X-ray photoelectron spectroscopy to determine the changes that occur in the bonding of self-assembled layers of cysteine on gold as a result of soft X-ray irradiation. To investigate the possibility of chiral selectivity resulting from the interaction of low-energy, spin-polarized SEs (SPSEs), measurements were conducted on cysteine adsorbed on a 3 nm-thick gold layer deposited on a CoPt thin-film multilayer with perpendicular magnetic anisotropy. Time-dependent measurements of the C 1s, N 1s, O 1s, S 2p, and Au 4f core levels are used to follow the changes in surface chemistry and determine reaction cross-sections as a function of SE exposure. Analysis of the data results in cross-sections in the range of 5-7 Mb and suggests possible reaction pathways. Changing the magnetization direction of the CoPt multilayer produces SPSEs with opposite polarity. Some evidence of spin-dependent reactions is indicated but is inconclusive. Possible reasons for the discrepancy are posited.

Probing Structural Information of Gas-Phase Peptides by Near-Edge X-ray Absorption Mass Spectrometry

Near-edge X-ray absorption mass spectrometry (NEXAMS) is an action-spectroscopy technique of growing interest for investigations into the spatial and electronic structure of biomolecules. It has been used successfully to give insights into different aspects of the photodissociation of peptides and to probe the conformation of proteins. It is a current question whether the fragmentation pathways are sensitive toward effects of conformational isomerism, tautomerism, and intramolecular interactions in gas-phase peptides. To address this issue, we studied the cationic fragments of cryogenically cooled gas-phase leucine enkephalin ([LeuEnk+H]⁺) and methionine enkephalin ([MetEnk+H]⁺) produced upon soft X-ray photon absorption at the carbon, nitrogen, and oxygen K-edges. The interpretation of the experimental ion yield spectra was supported by density-functional theory and restricted-open-shell configuration interaction with singles (DFT/ROCIS) calculations. The analysis revealed several effects that could not be rationalized based on the peptide's amino acid sequences alone. Clear differences between the partial ion yields measured for both peptides upon C 1s → π*(C═C) excitations in the aromatic amino acid side chains give evidence for a sulfur-aromatic interaction between the methionine and phenylalanine side chain of [MetEnk+H]⁺. Furthermore, a peak associated with N 1s → π*(C═N) transitions, linked to a tautomeric keto-to-enol conversion of peptide bonds, was only present in the photon energy resolved ion yield spectra of [MetEnk+H]⁺.

Soft X-ray induced radiation damage in thin freeze-dried brain samples studied by FTIR microscopy

In order to push the spatial resolution limits to the nanoscale, synchrotron-based soft X-ray microscopy (XRM) experiments require higher radiation doses to be delivered to materials. Nevertheless, the associated radiation damage impacts on the integrity of delicate biological samples. Herein, the extent of soft X-ray radiation damage in popular thin freeze-dried brain tissue samples mounted onto Si₃N₄ membranes, as highlighted by Fourier transform infrared microscopy (FTIR), is reported. The freeze-dried tissue samples were found to be affected by general degradation of the vibrational architecture, though these effects were weaker than those observed in paraffin-embedded and hydrated systems reported in the literature. In addition, weak, reversible and specific features of the tissue-Si₃N₄ interaction could be identified for the first time upon routine soft X-ray exposures, further highlighting the complex interplay between the biological sample, its preparation protocol and X-ray probe.

Oxygen K-edge X-ray Absorption Spectra

We review oxygen K-edge X-ray absorption spectra of both molecules and solids. We start with an overview of the main experimental aspects of oxygen K-edge X-ray absorption measurements including X-ray sources, monochromators, and detection schemes. Many recent oxygen K-edge studies combine X-ray absorption with time and spatially resolved measurements and/or operando conditions. The main theoretical and conceptual approximations for the simulation of oxygen K-edges are discussed in the Theory section. We subsequently discuss oxygen atoms and ions, binary molecules, water, and larger molecules containing oxygen, including biomolecular systems. The largest part of the review deals with the experimental results for solid oxides, starting from s- and p-electron oxides. Examples of theoretical simulations for these oxides are introduced in order to show how accurate a DFT description can be in the case of s and p electron overlap. We discuss the general analysis of the 3d transition metal oxides including discussions of the crystal field effect and the effects and trends in oxidation state and covalency. In addition to the general concepts, we give a systematic overview of the oxygen K-edges element by element, for the s-, p-, d-, and f-electron systems.

Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine

The chemical and electronic structures of the 21st and 22nd proteinogenic amino acid selenocysteine (Sec), pyrrolysine (Pyl), and their derivatives (deprotonated and protonated ions) were extensively characterized for the first time. Through the fragment based step-by-step research on their potential energy surface (PES), electronic energies of the most stable conformers of Sec, Pyl and the related ions were finally determined at the advanced CBS-QB3 and DSD-PBEP86-D3(BJ)/aug-cc-pVTZ levels, respectively, with the identification of many new low-energy conformers. The infrared spectra (IR) at 298 K of the most abundant conformers in different forms were scaled by comparison with the anharmonic frequency calculations and analyzed comparing with the experimental spectra of similar molecules. The characteristic soft X-ray spectra (including X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine-structure spectra (NEXAFS)) of the most stable conformers at 498 K were also simulated. In particular, the two possible protonated configurations of Pyl can be clearly distinguished by their different spectral features. Furthermore, a small binding energy intersection appeared around 293 eV at the C 1s edge between the canonical and protonated Pyl conformers, which is different from all the previous studies. This work thus filled the gap in our knowledge by providing detailed information on the chemical and electronic structures of Sec and Pyl and will be a useful guidance for future experimental research.

DMSA-Functionalized Mesoporous Alumina with a High Capacity for Selective Isolation of Immunoglobulin G

A novel dimercaptosuccinic acid-functionalized mesoporous alumina (DMSA-MA) is synthesized by the dicarboxylic acid groups of dimercaptosuccinic acid molecules coordinating to the Al³⁺ ions located in the mesostructure. The as-prepared DMSA-MA composites possess a large surface area of 91.17 m²/g as well as a uniform pore size and a high pore volume of 17.22 nm and 0.23 cm³/g, respectively. DMSA coating of mesostructures significantly enhanced their selectivity for glycoprotein adsorption through a powerful hydrophilic binding force, and the maximum adsorption capacity of immunoglobulin G (IgG) can reach 2298.6 mg g^-1. The captured IgG could be lightly stripped from the DMSA-MA composites with an elution rate of 98.3% by using 0.5 wt % CTAB solution as the elution reagent. DMSA-MA is further employed as a sorbent for the enrichment of IgG heavy chain and light chain from human serum sample. SDS-PAGE assay results showed the obtained IgG with high purity compared to that of the standard solution of IgG.

Quantitative Characterization of a Desalination Membrane Model System by X-ray Photoelectron Spectroscopy

Aromatic polyamide films form the active layer in reverse osmosis desalination membranes. Despite widespread use of this technology, it suffers from low rejection rates for certain water contaminants and from membrane fouling. Through a better understanding of the fundamental surface chemical processes during reverse osmosis desalination, advances in membrane and material design are expected. The recent invention of a molecular layer-by-layer (mLbL) preparation technique [ Johnson , P. M. ; Molecular Layer-by-Layer Deposition of Highly Crosslinked Polyamide Films . J. Polym. Sci., Part B: Polym. Phys. 2012 , 50 ( 3 ), 168 - 173 ] yields films that are sufficiently smooth to warrant investigation with high-resolution microscopy and spectroscopy methods. We present high-resolution, quantitative X-ray photoelectron spectroscopy (XPS) data on the surface chemistry of ultrathin polyamide films that can serve as a model system for desalination membranes. We show that a quantitative analysis of the XPS spectra gives information about the functional groups of the film as well as other compounds present due to the synthesis under ambient conditions. Unpolymerized functional groups are identified and aid in understanding the degree of cross-linking. Investigation of polymers with synchrotron-based XPS requires taking beam-induced changes into account. We quantify X-ray beam damage and show that beam damage to the polyamide is limited, allowing long-term investigation of thin polyamide films. Characterizing mLbL-grown films via high-resolution XPS is the basis for a better understanding of the chemical interplay of polyamide surface functional groups with the major components of desalination systems.

Synchrotron X-radiolysis of l-cysteine at the sulfur K-edge: Sulfurous products, experimental surprises, and dioxygen as an oxidoreductant

In situ inventory of sulfurous products from the sulfur K-edge synchrotron X-radiolysis of l-cysteine in solid-phase and anaerobic (pH 5) and air-saturated (pH 5, 7, and 9) solutions without and with 40% glycerol is reported. Sequential K-edge X-ray Absorption Spectroscopic (XAS) spectra were acquired. l-cysteine degraded systematically in the X-ray beam. Radiolytic products were inventoried by fits using the XAS spectra of sulfur model compounds. Solid l-cysteine declined to 92% fraction after a single K-edge XAS scan. After six scans, 60% remained, accompanied by 14% cystine, 16% thioether, 5.4% elemental sulfur, and smaller fractions of more highly oxidized products. In air-saturated pH 5 solution, 73% of l-cysteine remained after ten scans, with 2% cystine and 19% elemental sulfur. Oxidation increased with 40% glycerol, yielding 67%, 5%, and 23% fractions, respectively, after ten scans. Higher pH solutions exhibited less radiolytic chemistry. All the reactivity followed first-order kinetics. The anaerobic experiment displayed two reaction phases, with sharp changes in kinetics and radiolytic chemistry. Unexpectedly, the radiolytic oxidation of l-cysteine was increased in anaerobic solution. After ten scans, only 60% of the l-cysteine remained, along with 17% cystine, 22% elemental sulfur, and traces of more highly oxidized products. A new aerobic reaction cycle is hypothesized, wherein dissolved dioxygen captures radiolytic H• or eaq -, enters HO2 •/O2 •-, reductively quenches cysteine thiyl radicals, and cycles back to O2. This cycle is suggested to suppress the radiolytic production of cystine in aerobic solution.

Electron beam damage of perfluorosulfonic acid studied by soft X-ray spectromicroscopy

Scanning transmission X-ray microscopy (STXM) was used to study chemical changes to perfluorosulfonic acid (PFSA) spun cast thin films as a function of dose imparted by exposure of a 200 kV electron beam in a Transmission Electron Microscope (TEM). The relationship between electron beam fluence and absorbed dose was calibrated using a modified version of a protocol based on the positive to negative lithography transition in PMMA [Leontowich et al, J. Synchrotron Rad. 19 (2012) 976]. STXM was used to characterize and quantify the chemical changes caused by electron irradiation of PFSA under several different conditions. The critical dose for CF₂-CF₂ amorphization was used to explore the effects of the sample environment on electron beam damage. Use of a silicon nitride substrate was found to increase the CF₂-CF₂ amorphization critical dose by ∼x2 from that for free-standing PFSA films. Freestanding PFSA and PMMA films were damaged by 200 kV electrons at ∼100 K and then the damage was measured by STXM at 300 K (RT). The lithography cross-over dose for PMMA was found to be ∼2x higher when the PMMA thin film was electron irradiated at 120 K rather than at 300 K. The critical dose for CF₂-CF₂ amorphization in PFSA irradiated at 120 K followed by warming and delayed measurement by STXM at 300 K was found to be ∼2x larger than at 300 K. To place these results in the context of the use of electron microscopy to study PFSA ionomer in fuel cell systems, an exposure of 300 e^-/nm² at 300 K (which corresponds to an absorbed dose of ∼20 MGy) amorphizes ∼10% of the CF₂-CF₂ bonds in PFSA. At this dose level, the spatial resolution for TEM imaging of PFSA is limited to 3.5 nm by radiation damage, if one is using a direct electron detector with DQE = 1. This work recommends caution about 2D and 3D morphological information of PFSA materials based on TEM studies which use fluences higher than 300 e^-/nm².

Kinetics and Mechanism of Aspartic Acid Adsorption and Its Explosive Decomposition on Cu(100)

The mechanism and kinetics of aspartic acid (Asp, HO₂CCH(NH₂)CH₂CO₂H) decomposition on Cu(100) have been studied using X-ray photoemission spectroscopy and temperature-programmed reaction spectroscopy. We investigate the Asp decomposition mechanism in detail using unlabeled d-Asp and isotopically labeled l-Asp-4-¹³C (HO₂CCH(NH₂)CH₂¹³CO₂H), l-Asp- d₇ (DO₂CCD(ND₂)CD₂CO₂D), l-Asp-2,3,3- d₃ (HO₂CCD(NH₂)CD₂CO₂H), and l-Asp-¹⁵N-2,3,3- d₃ (HO₂CCD(¹⁵NH₂)CD₂CO₂H). The monolayer of Asp adsorbed on the Cu(100) surface is in a doubly deprotonated bi-aspartate form (-O₂CCH(NH₂)CH₂CO₂-). During heating, Asp decomposes on Cu(100) with kinetics consistent with a vacancy-mediated explosion mechanism. The mechanistic steps yield CO₂ by sequential cleavage of the C3-C4 and C1-C2 bonds, and N≡CCH₃ and H₂ via decomposition of the remaining CH(NH₂)CH₂ intermediate. Deuterium labeling has been used to demonstrate that scrambling of H(D) occurs during the decomposition to acetonitrile of the CD(NH₂)CD₂ intermediate formed by decarboxylation of l-Asp-2,3,3- d₃ and l-Asp-¹⁵N-2,3,3- d₃.

A calibration procedure for a traceable contamination analysis on medical devices by combined X-ray spectrometry and ambient spectroscopic techniques

There is a strong need in the medical device industry to decrease failure rates of biomedical devices by reducing the incidence of defect structures and contaminants during the production process. The detection and identification of defect structures and contaminants is crucial for many industrial applications. The present study exploits reference-free X-ray fluorescence (XRF) analysis as an analytical tool for the traceable characterization of surface contaminants of medical devices, in particular N,N'-ethylene-bis (stearamide), an ubiquitous compound used in many industrial applications as a release agent or friction reduction additive. Reference-free XRF analysis as primary method has been proven to be capable of underpinning all other applied methods since it yields the absolute mass deposition of the selected N,N'-ethylene-bis (stearamide) contaminant whilst X-ray absorption fine structure analysis determines the chemical species. Ambient vibrational spectroscopy and mass spectroscopy methodologies such as Fourier transform infrared, Raman, and secondary ion mass spectroscopy have been used in this systematic procedure providing an extensive range of complementary analyses. The calibration procedure described in this paper was developed using specially designed and fabricated model systems varying in thickness and substrate material. Furthermore, typical real medical devices such as both a polyethylene hip liner and a silver-coated wound dressing have been contaminated and investigated by these diverse methods, enabling testing of this developed procedure. These well-characterized samples may be used as calibration standards for bench top instrumentation from the perspective of providing traceable analysis of biomaterials and surface treatments. These findings demonstrate the potential importance and usefulness of combining complementary methods for a better understanding of the relevant organic materials.

Impacts of hydrous manganese oxide on the retention and lability of dissolved organic matter

Minerals constitute a primary ecosystem control on organic C decomposition in soils, and therefore on greenhouse gas fluxes to the atmosphere. Secondary minerals, in particular, Fe and Al (oxyhydr)oxides-collectively referred to as "oxides" hereafter-are prominent protectors of organic C against microbial decomposition through sorption and complexation reactions. However, the impacts of Mn oxides on organic C retention and lability in soils are poorly understood. Here we show that hydrous Mn oxide (HMO), a poorly crystalline δ-MnO₂, has a greater maximum sorption capacity for dissolved organic matter (DOM) derived from a deciduous forest composite O_i, O_e, and O_a horizon leachate ("O horizon leachate" hereafter) than does goethite under acidic (pH 5) conditions. Nonetheless, goethite has a stronger sorption capacity for DOM at low initial C:(Mn or Fe) molar ratios compared to HMO, probably due to ligand exchange with carboxylate groups as revealed by attenuated total reflectance-Fourier transform infrared spectroscopy. X-ray photoelectron spectroscopy and scanning transmission X-ray microscopy-near-edge X-ray absorption fine structure spectroscopy coupled with Mn mass balance calculations reveal that DOM sorption onto HMO induces partial Mn reductive dissolution and Mn reduction of the residual HMO. X-ray photoelectron spectroscopy further shows increasing Mn(II) concentrations are correlated with increasing oxidized C (C=O) content (r = 0.78, P < 0.0006) on the DOM-HMO complexes. We posit that DOM is the more probable reductant of HMO, as Mn(II)-induced HMO dissolution does not alter the Mn speciation of the residual HMO at pH 5. At a lower C loading (2 × 10² μg C m^-2), DOM desorption-assessed by 0.1 M NaH₂PO₄ extraction-is lower for HMO than for goethite, whereas the extent of desorption is the same at a higher C loading (4 × 10² μg C m^-2). No significant differences are observed in the impacts of HMO and goethite on the biodegradability of the DOM remaining in solution after DOM sorption reaches steady state. Overall, HMO shows a relatively strong capacity to sorb DOM and resist phosphate-induced desorption, but DOM-HMO complexes may be more vulnerable to reductive dissolution than DOM-goethite complexes.

Experimental characterization and simulation of amino acid and peptide interactions with inorganic materials

Inspired by nature, many applications and new materials benefit from the interplay of inorganic materials and biomolecules. A fundamental understanding of complex organic-inorganic interactions would improve the controlled production of nanomaterials and biosensors to the development of biocompatible implants for the human body. Although widely exploited in applications, the interaction of amino acids and peptides with most inorganic surfaces is not fully understood. To date, precisely characterizing complex surfaces of inorganic materials and analyzing surface-biomolecule interactions remain challenging both experimentally and computationally. This article reviews several approaches to characterizing biomolecule-surface interactions and illustrates the advantages and disadvantages of the methods presented. First, we explain how the adsorption mechanism of amino acids/peptides to inorganic surfaces can be determined and how thermodynamic and kinetic process constants can be obtained. Second, we demonstrate how this data can be used to develop models for peptide-surface interactions. The understanding and simulation of such interactions constitute a basis for developing molecules with high affinity binding domains in proteins for bioprocess engineering and future biomedical technologies.

Radiation chemistry of molecular compounds and polymers by soft X-ray spectroscopy and microscopy

Soft X-ray-induced radiation chemistry in selected Fe molecular compounds and some aliphatic polymers was studied using soft X-ray absorption spectroscopy, and scanning transmission X-ray microscopy. X-ray absorption near-edge structure (XANES) spectroscopy was used to elucidate the radiation chemistry. The results show that damage to the Fe molecular complexes involves Fe-ligand bond breaking, ligand damage, and subsequent photoreduction of Fe(III) if it is not tightly bonded to oxygen. Upon radiation damage, polymer PAN primarily undergoes chemical structure changes without mass loss, PECA experiences chemical structure changes as well as small mass loss, while PPC and PEC suffer large mass loss with chemical structure changes. These studies are not only important to X-ray analysis of radiation sensitive materials but also are valuable to the applications of X-ray lithography and other types of nanofabrication involving photoresist.

Tautomerization of Thymine Using Ultraviolet Light

Ultraviolet-light-induced changes to the nucleobase thymine deposited onto a MoS₂ surface were studied using photoelectron spectroscopy and first-principles calculations. These measurements suggest changes in the molecular structure indicated by changes in core electron binding energies. The experimental work has been interpreted by means of ab initio calculations using coupled cluster singles and doubles (CCSD) linear response theory. Contrary to the expected behavior, i.e., the dimerization of two thymine molecules into a pyrimidine dimer, a shift between two tautomeric forms was observed upon UV-exposure. Exposure to ionizing radiation is known to induce damage in many biological molecules, and the present work gives additional insight into its effects on thymine, the interactions of the molecules, and finally how certain UV photoproducts may be avoided.

Use of a DNA film on a self-assembled monolayer for investigating the physical process of DNA damage induced by core electron ionization

PURPOSE

A novel two-layer sample composed of a deoxyribonucleic acid (DNA) film and self-assembled monolayer (SAM) was prepared on an inorganic surface to mimic the processes in which DNA is damaged by soft X-ray irradiation.

MATERIALS AND METHODS

A mercaptopropyltrimethoxysilane (MPTS) SAM was formed on a sapphire surface, then oligonucleotide (OGN) molecules were adsorbed on the MPTS-SAM. The thicknesses and chemical states of the layers were determined by X-ray photoelectron spectroscopy (XPS) and near-edge X-ray fine structure (NEXAFS) around the phosphorus (P) and sulfur (S) K-edges. To induce the damage to the OGN molecules, the sample was irradiated with synchrotron soft X-rays. The chemical state of the OGN molecules before and after irradiation was examined by NEXAFS around the nitrogen (N) K-edge region.

RESULTS

The thickness of the MPTS-OGN layer was approximately 7.7 nm. The S atom of the OGN molecules was located at the bottom of the OGN layer. The peak shape of the N K-edge NEXAFS spectra of the MPTS-OGN layers clearly changed following irradiation.

CONCLUSIONS

The MPTS-OGN layer formed on the sapphire surface. The chemical states and the structure of the interface were elucidated using synchrotron soft X-rays. The OGN molecules adsorbed on the MPTS films decomposed upon exposure to soft X-ray irradiation.

Band edge engineering of TiO2@DNA nanohybrids and implications for capacitive energy storage devices

Novel mesoporous TiO2@DNA nanohybrid electrodes, combining covalently encoded DNA with mesoporous TiO2 microbeads using dopamine as a linker, were prepared and characterised for application in supercapacitors. Detailed information about donor density, charge transfer resistance and chemical capacitance, which have an important role in the performance of an electrochemical device, were studied by electrochemical methods. The results indicated the improvement of electrochemical performance of the TiO2 nanohybrid electrode by DNA surface functionalisation. A supercapacitor was constructed from TiO2@DNA nanohybrids with PBS as the electrolyte. From the supercapacitor experiment, it was found that the addition of DNA played an important role in improving the specific capacitance (Cs) of the TiO2 supercapacitor. The highest Cs value of 8 F g(-1) was observed for TiO2@DNA nanohybrids. The nanohybrid electrodes were shown to be stable over long-term cycling, retaining 95% of their initial specific capacitance after 1500 cycles.

Shape-controllable and versatile synthesis of copper nanocrystals with amino acids as capping agents

Thanks to their outstanding properties and a wide range of promising applications, the development of a versatile and convenient preparation method for metallic copper nanocrystals with controllable shape is of primary significance. Different from the literature that utilized a capping agent bearing only one kind of Cu binding functionality, either an amino or a carboxylic unit, for their preparation and shape control, this contribution reports a convenient method to engage both amino and carboxylic binding units at the same time. In this method, natural amino acids have been chosen as capping agents and demonstrated their versatile capabilities for the preparation of both Cu nanoparticles and nanowires. Detailed X-ray photoelectron spectroscopy revealed that the binding mode between amino acids and the Cu surface is highly dependent on their chemical structures. Interestingly, the produced Cu nanocrystals, exhibited an extraordinarily excellent anti-oxidation power. Furthermore, it was found that the multiple functionalities of amino acids not only have a great impact on the properties of their capped nanocrystals, such as solvent dispersibility, but also provide a convenient route for their further modification and functionalization.

Soft X-Ray Microscopy Radiation Damage On Fixed Cells Investigated With Synchrotron Radiation FTIR Microscopy

Radiation damage of biological samples remains a limiting factor in high resolution X-ray microscopy (XRM). Several studies have attempted to evaluate the extent and the effects of radiation damage, proposing strategies to minimise or prevent it. The present work aims to assess the impact of soft X-rays on formalin fixed cells on a systematic manner. The novelty of this approach resides on investigating the radiation damage not only with XRM, as often reported in relevant literature on the topic, but by coupling it with two additional independent non-destructive microscopy methods: Atomic Force Microscopy (AFM) and FTIR Microscopy (FTIRM). Human Embryonic Kidney 293 cells were exposed to different radiation doses at 1 keV. In order to reveal possible morphological and biochemical changes, the irradiated cells were systematically analysed with AFM and FTIRM before and after. Results reveal that while cell morphology is not substantially affected, cellular biochemical profile changes significantly and progressively when increasing dose, resulting in a severe breakdown of the covalent bonding network. This information impacts most soft XRM studies on fixed cells and adds an in-depth understanding of the radiation damage for developing better prevention strategies.

Formation of bioinorganic complexes by the corrosive adsorption of (S)-proline on Ni/Au(111)

Nickel nanoparticles modified by the adsorption of chiral amino acids are known to be effective enantioselective heterogeneous catalysts. The leaching of nickel by amino acids has a number of potential effects including the induction of chirality in the nickel atoms left behind in the nanoparticle and the creation of catalytically active nickel complexes. The adsorption of (S)-proline onto Au(111) precovered by two-dimensional nickel nanoclusters was investigated by scanning tunneling microscopy, X-ray photoelectron spectroscopy, and high-resolution electron energy loss spectroscopy. Adsorption of (S)-proline at 300 K resulted in the corrosion of the nickel clusters, the oxidation of the leached nickel, and the on-surface formation of bioinorganic complexes, which are concluded to contain three prolinate species in an octahedral arrangement around the central Ni ion. Two distinguishable forms of nickel prolinate complexes were identified. One form self-assembles into 1-D chains, and the other form gives rise to porous 2-D islands. Octahedral complexes of the type M(AB)3 are intrinsically chiral, resulting in two pairs of enantiomers. The mirror symmetry of each pair of enantiomers is broken when, as in this study, the bidentate ligand itself possesses a chiral center. DFT calculations are used to examine the relative energies of each Ni(prolinate)3 complex as isolated gas phase species and isolated adsorbed species.

Physicochemical properties of surface charge-modified ZnO nanoparticles with different particle sizes

In this study, four types of standardized ZnO nanoparticles were prepared for assessment of their potential biological risk. Powder-phased ZnO nanoparticles with different particle sizes (20 nm and 100 nm) were coated with citrate or L-serine to induce a negative or positive surface charge, respectively. The four types of coated ZnO nanoparticles were subjected to physicochemical evaluation according to the guidelines published by the Organisation for Economic Cooperation and Development. All four samples had a well crystallized Wurtzite phase, with particle sizes of ∼30 nm and ∼70 nm after coating with organic molecules. The coating agents were determined to have attached to the ZnO surfaces through either electrostatic interaction or partial coordination bonding. Electrokinetic measurements showed that the surface charges of the ZnO nanoparticles were successfully modified to be negative (about −40 mV) or positive (about +25 mV). Although all the four types of ZnO nanoparticles showed some agglomeration when suspended in water according to dynamic light scattering analysis, they had clearly distinguishable particle size and surface charge parameters and well defined physicochemical properties.

Dissociation pathways in the cysteine dication after site-selective core ionization

A photoelectron-ion-ion coincidence experiment has been carried out on the amino acid molecule cysteine after core-ionization of the O 1s, N 1s, C 1s, and S 2p orbitals. A number of different dissociation channels have been identified. Some of them show strong site-selective dependence that can be attributed to a combination of nuclear motion in the core-ionized state and Auger processes that populate different final electronic states in the dication.

The relationship between interfacial bonding and radiation damage in adsorbed DNA

Illustration showing that secondary electrons have a higher damage probability for thiolated DNA as opposed to unthiolated DNA, due to the former's higher density of LUMO states, which leads to more efficient capture of the low energy electrons.

Formation of carboxy- and amide-terminated alkyl monolayers on Silicon(111) investigated by ATR-FTIR, XPS, and X-ray scattering: construction of photoswitchable surfaces

We have prepared high-quality, densely packed, self-assembled monolayers (SAMs) of carboxy-terminated alkyl chains on Si(111). The samples were made by thermal grafting of methyl undec-10-enoate under an inert atmosphere and subsequent cleavage of the ester functionality to disclose the carboxylic acid end-group. X-ray photoelectron spectroscopy (XPS) and grazing incidence X-ray diffraction (GIXD) indicate a surface coverage of about 50% of the initially H-terminated sites. In agreement, GIXD implies a rectangular unit mesh of 6.65 and 7.68 Å side lengths, containing two molecules in a regular zigzag-like substitution pattern for the ester- and carboxy-terminated monolayer. Hydrolysis of the remaining H-Si(111) bonds at the surface furnished HO-Si(111) groups according to XPS and attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) studies. The amide-terminated alkyl SAM on Si(111) assembled in a 2-(6-chloro-1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate (HCTU)-mediated one-pot coupling reaction under an inert atmosphere, whereby the active ester forms in situ prior to the reaction with an amino-functionalized photoswitchable fulgimide. ATR-FTIR and XPS studies of the fulgimide samples revealed closely covered amide-terminated SAMs. Reversible photoswitching of the headgroup was read out by applying XPS, ATR-FTIR, and difference absorption spectra in the mid-IR. In XPS, we observed a reversible breathing of the amide/imide C1s and N1s signals of the fulgimide. The results demonstrate the general suitability of HCTU as a reagent for amide couplings to carboxy-terminated alkyl SAMs and the on-chip functionalization toward photoswitchable Si(111) surfaces.