What Are the Key Factors for the Detection of Peptides Using Mass Spectrometry on Boron-Doped Diamond Surfaces?

We investigated the use of boron-doped diamond (BDD) with different surface morphologies for the enhanced detection of nine different peptides by matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS). For the first time, we compared three different nanostructured BDD film morphologies (Continuous, Nanograss, and Nanotips) with differently terminated surfaces (-H, -O, and -F) to commercially available Ground Steel plates. All these surfaces were evaluated for their effectiveness in detecting the nine different peptides by MALDI-MS. Our results demonstrated that certain nanostructured BDD surfaces exhibited superior performance for the detection of especially hydrophobic peptides (e.g., bradykinin 1-7, substance P, and the renin substrate), with a limit of detection of down to 2.3 pM. Further investigation showed that hydrophobic peptides (e.g., bradykinin 1-7, substance P, and the renin substrate) were effectively detected on hydrogen-terminated BDD surfaces. On the other hand, the highly acidic negatively charged peptide adrenocorticotropic hormone fragment 18-39 was effectively identified on oxygen-/fluorine-terminated BDD surfaces. Furthermore, BDD surfaces reduced sodium adduct contamination significantly.

Improved Gas Sensing Capabilities of MoS2/Diamond Heterostructures at Room Temperature.

Molybdenum disulfide (MoS2) and nanocrystalline diamond (NCD) have attracted considerable attention due to their unique electronic structure and extraordinary physical and chemical properties in many applications, including sensor devices in gas sensing applications. Combining MoS2 and H-terminated NCD (H-NCD) in a heterostructure design can improve the sensing performance due to their mutual advantages. In this study, the synthesis of MoS2 and H-NCD thin films using appropriate physical/chemical deposition methods and their analysis in terms of gas sensing properties in their individual and combined forms are demonstrated. The sensitivity and time domain characteristics of the sensors were investigated for three gases: oxidizing NO2, reducing NH3, and neutral synthetic air. It was observed that the MoS2/H-NCD heterostructure-based gas sensor exhibits improved sensitivity to oxidizing NO2 (0.157%·ppm-1) and reducing NH3 (0.188%·ppm-1) gases compared to pure active materials (pure MoS2 achieves responses of 0.018%·ppm-1 for NO2 and -0.0072%·ppm-1 for NH3, respectively, and almost no response for pure H-NCD at room temperature). Different gas interaction model pathways were developed to describe the current flow mechanism through the sensing area with/without the heterostructure. The gas interaction model independently considers the influence of each material (chemisorption for MoS2 and surface doping mechanism for H-NCD) as well as the current flow mechanism through the formed P-N heterojunction.

Light emission dynamics of silicon vacancy centers in a polycrystalline diamond thin film.

Diamond thin films can be, at a relatively low-cost, prepared with a high-density of light-emitting negatively charged silicon vacancy (SiV) centers, which opens up the possibility of their application in photonics or sensing. The films are composed of diamond grains with both the SiV centers and sp2-carbon phase, the ratio of these two components being dependent on the preparation conditions. The grain surface and the sp2-related defects might act as traps for the carriers excited within the SiV centers, consequently decreasing their internal photoluminescence (PL) quantum efficiency. Here, we show that in a 300 nm thick polycrystalline diamond film on a quartz substrate, the SiV centers in the diamond grains possess similar temperature-dependent (13-300 K) PL decay dynamics as the SiV centers in monocrystalline diamond, which suggests that most of the SiV centers are not directly interconnected with the defects of the diamond thin films, i.e. that the carriers excited within the centers do not leak into the defects of the film. The activation energy ΔE = 54 meV and the attempt frequency α = 2.6 were extracted from the measured data. These values corresponded very well with the published values for SiV centers in monocrystalline diamond. We support this claim by measuring the transient absorption via a pump and probe technique, where we separated the nanosecond recombination dynamics of carriers in SiV centers from the picosecond decay dynamics of polycrystalline diamond defects. Our results show that PL emission properties of SiV centers in polycrystalline diamond thin films prepared via chemical vapor deposition are very similar to those in monocrystalline diamond thereby opening the door for their application in diamond photonics and sensing.

Erbium ion implantation into LiNbO3, Al2O3, ZnO and diamond - measurement and modelling - an overview.

The presented overview deals with the study of the luminescence properties of lanthanide ions incorporated into different dielectric crystalline materials for use in photonics and optoelectronics. From the crystalline materials, non-centrosymmetric hexagonal crystals of LiNbO3, Al2O3 and ZnO, together with the centrosymmetric cubic crystal of diamond, were chosen. The above-mentioned materials represent a certain cross-section through various crystal structure geometries with different internal bonding of atoms which represent different crystal vicinity for the incorporated Er ions. During more than ten years of our research, each of the crystals was doped with erbium ions and the resulting structural and luminescence properties were studied in detail and compared between the mentioned crystalline materials to find similar behaviour for erbium ions in the different crystalline materials. To better understand the incorporation of erbium in the studied crystalline materials, theoretical simulations of different erbium-doped crystal models were carried out. In the calculations, cohesive energies of the structures and erbium defect-formation energies were compared in order to find the most favourable erbium positions in the crystals. Also, from the geometry optimization calculations, the optimal geometry arrangements in the vicinity of erbium ions in different crystals were studied and visualized. The results of the theoretical simulations confirmed the experimental results - i.e., from all the theoretical erbium-doped crystal models, the most stable structures contained erbium in the substitutional positions with octahedral oxygen coordination.

Optical Characterization of Few-Layer PtSe2 Nanosheet Films.

Thin films of transition-metal dichalcogenides are potential materials for optoelectronic applications. However, the application of these materials in practice requires knowledge of their fundamental optical properties. Many existing methods determine optical constants using predefined models. Here, a different approach was used. We determine the sheet conductance and absorption coefficient of few-layer PtSe2 in the infrared and UV-vis ranges without recourse to any particular model for the optical constants. PtSe2 samples with a thickness of about 3-4 layers were prepared by selenization of 0.5 nm thick platinum films on sapphire substrates at different temperatures. Differential reflectance was extracted from transmittance and reflectance measurements from the front and back of the sample. The film thickness, limited to a few atomic layers, allowed a thin-film approximation to calculate the optical conductance and absorption coefficient. The former has a very different energy dependence in the infrared, near-infrared, and visible ranges. The absorption coefficient exhibits a strong power-law dependence on energy with an exponent larger than three in the mid-infrared and near-infrared regions. We have not observed any evidence for a band gap in PtSe2 thin layers down to an energy of 0.4 eV from our optical measurements.

Photonic crystal cavity-enhanced emission from silicon vacancy centers in polycrystalline diamond achieved without postfabrication fine-tuning.

Diamond optical centers have recently emerged as promising single-photon sources for quantum photonics. Particularly, negatively charged silicon vacancy (SiV-) centers show great promise due to their narrow zero-phonon emission line present also at room temperature. However, due to fabrication tolerances it is challenging to prepare directly photonic structures with optical modes spectrally matching the emission of SiV- centers. To reach the spectral overlap, photonic structures must typically undergo complicated post-processing treatment. In this work, suspended photonic crystal cavities made of polycrystalline diamond are engineered and more than 2.5-fold enhancement of the SiV- center zero-phonon line intensity via coupling to the cavity photonic mode is demonstrated. The intrinsic non-homogeneous thickness of the diamond thin layer within the sample is taken as an advantage that enables reaching the spectral overlap between the emission from SiV- centers and the cavity modes without any post-processing. Even with lower optical quality compared to monocrystalline diamond, the fabricated photonic structures show comparable efficiency for intensity enhancement. Therefore, the results of this work may open up a promising route for the application of polycrystalline diamond in photonics.

Ni-mediated reactions in nanocrystalline diamond on Si substrates: the role of the oxide barrier.

Nanocrystalline diamond (NCD) films grown on Si substrates by microwave plasma enhanced chemical vapor deposition (MWPECVD) were subjected to Ni-mediated graphitization to cover them with a conductive layer. Results of transmission electron microscopy including electron energy-loss spectroscopy of cross-sectional samples demonstrate that the oxide layer on Si substrates (∼5 nm native SiO2) has been damaged by microwave plasma during the early stage of NCD growth. During the heat treatment for graphitizing the NCD layer, the permeability or absence of the oxide barrier allow Ni nanoparticles to diffuse into the Si substrate and cause additional solid-state reactions producing pyramidal crystals of NiSi2 and SiC nanocrystals. The latter are found impinged into the NiSi2 pyramids but only when the interfacial oxide layer is absent, replaced by amorphous SiC. The complex phase morphology of the samples is also reflected in the temperature dependence of electrical conductivity, where multiple pathways of the electronic transport dominate in different temperature regions. We present models explaining the observed cascade of solid-state reactions and resulting electronic transport properties of such heterostructures.

Great Variety of Man-Made Porous Diamond Structures: Pulsed Microwave Cold Plasma System with a Linear Antenna Arrangement.

Synthetic diamond films are routinely grown using chemical vapor deposition (CVD) techniques. Due to their extraordinary combination of intrinsic properties, they are used as the functional layers in various bio-optoelectronic devices. It is a challenge to grow the dimensional layers or porous structures that are required. This study reviews the fabrication of various porous diamond-based structures using linear antenna microwave plasma (LAMWP) chemical vapor deposition (CVD), a low-cost technology for growing diamond films over a large area (>1 m2) at low pressure (<100 Pa) and at low temperature (even at 350 °C). From a technological point of view, two different approaches, i.e., templated diamond growth using three different prestructured (macro-, micro-, and nanosized) porous substrates and direct bottom-up growth of ultra-nanoporous diamond (block-stone and dendritelike) films, are successfully employed to form diamond-based structures with controlled porosity and an enhanced surface area. As a bottom-up strategy, the LAMWP CVD system allows diamond growth at as high as 80% CO2 in the CH4/CO2/H2 gas mixture. In summary, the low-pressure and cold plasma conditions in the LAMWP system facilitate the growth on three-dimensionally prestructured substrates of various materials that naturally form porous self-standing diamond structures.

Lytic and genomic properties of spontaneous host-range Kayvirus mutants prove their suitability for upgrading phage therapeutics against staphylococci.

Lytic bacteriophages are valuable therapeutic agents against bacterial infections. There is continual effort to obtain new phages to increase the effectivity of phage preparations against emerging phage-resistant strains. Here we described the genomic diversity of spontaneous host-range mutants of kayvirus 812. Five mutant phages were isolated as rare plaques on phage-resistant Staphylococcus aureus strains. The host range of phage 812-derived mutants was 42% higher than the wild type, determined on a set of 186 methicillin-resistant S. aureus strains representing the globally circulating human and livestock-associated clones. Comparative genomics revealed that single-nucleotide polymorphisms from the parental phage 812 population were fixed in next-step mutants, mostly in genes for tail and baseplate components, and the acquired point mutations led to diverse receptor binding proteins in the phage mutants. Numerous genome changes associated with rearrangements between direct repeat motifs or intron loss were found. Alterations occurred in host-takeover and terminal genomic regions or the endolysin gene of mutants that exhibited the highest lytic activity, which implied various mechanisms of overcoming bacterial resistance. The genomic data revealed that Kayvirus spontaneous mutants are free from undesirable genes and their lytic properties proved their suitability for rapidly updating phage therapeutics.

Covalent Diamond-Graphite Bonding: Mechanism of Catalytic Transformation.

Aberration-corrected transmission electron microscopy of the atomic structure of diamond-graphite interface after Ni-induced catalytic transformation reveals graphitic planes bound covalently to the diamond in the upright orientation. The covalent attachment, together with a significant volume expansion of graphite transformed from diamond, gives rise to uniaxial stress that is released through plastic deformation. We propose a comprehensive model explaining the Ni-mediated transformation of diamond to graphite and covalent bonding at the interface as well as the mechanism of relaxation of uniaxial stress. We also explain the mechanism of electrical transport through the graphitized surface of diamond. The result may thus provide a foundation for the catalytically driven formation of graphene-diamond nanodevices.

Silicon-Vacancy Centers in Ultra-Thin Nanocrystalline Diamond Films.

Color centers in diamond have shown excellent potential for applications in quantum information processing, photonics, and biology. Here we report the optoelectronic investigation of shallow silicon vacancy (SiV) color centers in ultra-thin (7⁻40 nm) nanocrystalline diamond (NCD) films with variable surface chemistry. We show that hydrogenated ultra-thin NCD films exhibit no or lowered SiV photoluminescence (PL) and relatively high negative surface photovoltage (SPV) which is ascribed to non-radiative electron transitions from SiV to surface-related traps. Higher SiV PL and low positive SPV of oxidized ultra-thin NCD films indicate an efficient excitation-emission PL process without significant electron escape, yet with some hole trapping in diamond surface states. Decreasing SPV magnitude and increasing SiV PL intensity with thickness, in both cases, is attributed to resonant energy transfer between shallow and bulk SiV. We also demonstrate that thermal treatments (annealing in air or in hydrogen gas), commonly applied to modify the surface chemistry of nanodiamonds, are also applicable to ultra-thin NCD films in terms of tuning their SiV PL and surface chemistry.

Erbium Luminescence Centres in Single- and Nano-Crystalline Diamond-Effects of Ion Implantation Fluence and Thermal Annealing.

We present a fundamental study of the erbium luminescence centres in single- and nano-crystalline (NCD) diamonds. Both diamond forms were doped with Er using ion implantation with the energy of 190 keV at fluences up to 5 × 1015 ions·cm-2, followed by annealing at controllable temperature in Ar atmosphere or vacuum to enhance the near infrared photoluminescence. The Rutherford Backscattering Spectrometry showed that Er concentration maximum determined for NCD films is slightly shifted to the depth with respect to the Stopping and Range of Ions in Matter simulation. The number of the displaced atoms per depth slightly increased with the fluence, but in fact the maximum reached the fully disordered target even in the lowest ion fluence used. The post-implantation annealing at 800 °C in vacuum had a further beneficial effect on erbium luminescence intensity at around 1.5 µm, especially for the Er-doped NCD films, which contain a higher amount of grain boundaries than single-crystalline diamond.

Two-dimensional photonic crystals increasing vertical light emission from Si nanocrystal-rich thin layers.

We have fabricated two-dimensional photonic crystals (PhCs) on the surface of Si nanocrystal-rich SiO2 layers with the goal to maximize the photoluminescence extraction efficiency in the normal direction. The fabricated periodic structures consist of columns ordered into square and hexagonal pattern with lattice constants computed such that the red photoluminescence of Si nanocrystals (SiNCs) could couple to leaky modes of the PhCs and could be efficiently extracted to surrounding air. Samples having different lattice constants and heights of columns were investigated in order to find the configuration with the best performance. Spectral overlap of the leaky modes with the luminescence spectrum of SiNCs was verified experimentally by measuring photonic band diagrams of the leaky modes employing angle-resolved spectroscopy and also theoretically by computing the reflectance spectra. The extraction enhancement within different spatial angles was evaluated by means of micro-photoluminescence spectroscopy. More than 18-fold extraction enhancement was achieved for light propagating in the normal direction and up to 22% increase in overall intensity was obtained at the spatial collection angle of 14°.

Ultrathin Nanocrystalline Diamond Films with Silicon Vacancy Color Centers via Seeding by 2 nm Detonation Nanodiamonds.

Color centers in diamonds have shown excellent potential for applications in quantum information processing, photonics, and biology. Here we report chemical vapor deposition (CVD) growth of nanocrystalline diamond (NCD) films as thin as 5-6 nm with photoluminescence (PL) from silicon-vacancy (SiV) centers at 739 nm. Instead of conventional 4-6 nm detonation nanodiamonds (DNDs), we prepared and employed hydrogenated 2 nm DNDs (zeta potential = +36 mV) to form extremely dense (∼1.3 × 1013 cm-2), thin (2 ± 1 nm), and smooth (RMS roughness < 0.8 nm) nucleation layers on an Si/SiOx substrate, which enabled the CVD growth of such ultrathin NCD films in two different and complementary microwave (MW) CVD systems: (i) focused MW plasma with an ellipsoidal cavity resonator and (ii) pulsed MW plasma with a linear antenna arrangement. Analytical ultracentrifuge, infrared and Raman spectroscopies, atomic force microscopy, and scanning electron microscopy are used for detailed characterization of the 2 nm H-DNDs and the nucleation layer as well as the ultrathin NCD films. We also demonstrate on/off switching of the SiV center PL in the NCD films thinner than 10 nm, which is achieved by changing their surface chemistry.

Enhanced Extraction of Silicon-Vacancy Centers Light Emission Using Bottom-Up Engineered Polycrystalline Diamond Photonic Crystal Slabs.

Silicon vacancy (SiV) centers are optically active defects in diamond. The SiV centers, in contrast to nitrogen vacancy (NV) centers, possess narrow and efficient luminescence spectrum (centered at ≈738 nm) even at room temperature, which can be utilized for quantum photonics and sensing applications. However, most of light generated in diamond is trapped in the material due to the phenomenon of total internal reflection. In order to overcome this issue, we have prepared two-dimensional photonic crystal slabs from polycrystalline diamond thin layers with high density of SiV centers employing bottom-up growth on quartz templates. We have shown that the spectral overlap between the narrow light emission of the SiV centers and the leaky modes extracting the emission into almost vertical direction (where it can be easily detected) can be obtained by controlling the deposition time. More than 14-fold extraction enhancement of the SiV centers photoluminescence was achieved compared to an uncorrugated sample. Computer simulation confirmed that the extraction enhancement originates from the efficient light-matter interaction between light emitted from the SiV centers and the photonic crystal slab.

Erbium ion implantation into diamond - measurement and modelling of the crystal structure.

Diamond is proposed as an extraordinary material usable in interdisciplinary fields, especially in optics and photonics. In this contribution we focus on the doping of diamond with erbium as an optically active centre. In the theoretical part of the study based on DFT simulations we have developed two Er-doped diamond structural models with 0 to 4 carbon vacancies in the vicinity of the Er atom and performed geometry optimizations by the calculation of cohesive energies and defect formation energies. The theoretical results showed an excellent agreement between the calculated and experimental cohesive energies for the parent diamond. The highest values of cohesive energies and the lowest values of defect formation energies were obtained for models with erbium in the substitutional carbon position with 1 or 3 vacancies in the vicinity of the erbium atom. From the geometry optimization the structural model with 1 vacancy had an octahedral symmetry whereas the model with 3 vacancies had a coordination of 10 forming a trigonal structure with a hexagonal ring. In the experimental part, erbium doped diamond crystal samples were prepared by ion implantation of Er+ ions using ion implantation fluences ranging from 1 × 1014 ions per cm2 to 5 × 1015 ions per cm2. The experimental results revealed a high degree of diamond structural damage after the ion implantation process reaching up to 69% of disordered atoms in the samples. The prepared Er-doped diamond samples annealed at the temperatures of 400, 600 and 800 °C in a vacuum revealed clear luminescence, where the 〈110〉 cut sample has approximately 6-7 times higher luminescence intensity than the 〈001〉 cut sample with the same ion implantation fluence. The reported results are the first demonstration of the Er luminescence in the single crystal diamond structure for the near-infrared spectral region.

High-yield fabrication and properties of 1.4 nm nanodiamonds with narrow size distribution.

Detonation nanodiamonds (DNDs) with a typical size of 5 nm have attracted broad interest in science and technology. Further size reduction of DNDs would bring these nanoparticles to the molecular-size level and open new prospects for research and applications in various fields, ranging from quantum physics to biomedicine. Here we show a controllable size reduction of the DND mean size down to 1.4 nm without significant particle loss and with additional disintegration of DND core agglutinates by air annealing, leading to a significantly narrowed size distribution (±0.7 nm). This process is scalable to large quantities. Such molecular-sized DNDs keep their diamond structure and characteristic DND features as shown by Raman spectroscopy, infrared spectroscopy, STEM and EELS. The size of 1 nm is identified as a limit, below which the DNDs become amorphous.

Molecular characterization of a new efficiently transducing bacteriophage identified in meticillin-resistant Staphylococcus aureus.

In Staphylococcus aureus, generalized transduction mediated by temperate bacteriophages represents a highly efficient way of transferring antibiotic resistance genes between strains. In the present study, we identified and characterized in detail a new efficiently transducing bacteriophage of the family Siphoviridae, designated ϕJB, which resides as a prophage in the meticillin-resistant S. aureus (MRSA) strain Jevons B. Whole-genome sequencing followed by detailed in silico analysis uncovered a linear dsDNA genome consisting of 43 ,12 bp and comprising 70 ORFs, of which ∼40 encoded proteins with unknown function. A global genome alignment of ϕJB and other efficiently transducing phages ϕ11, ϕ53, ϕ80, ϕ80α and ϕNM4 showed a high degree of homology with ϕNM4 and substantial differences with regard to other phages. Using a model transduction system with a well-defined donor and recipient, ϕJB transferred the tetracycline resistance plasmid pT181 and a penicillinase plasmid with outstanding frequencies, beating most of the above-mentioned phages by an order of magnitude. Moreover, ϕJB demonstrated high frequencies of transferring antibiotic resistance plasmids even upon induction from a lysogenic donor strain. Considering such transducing potential, ϕJB and related bacteriophages may serve as a suitable tool for elucidating the nature of transduction and its contribution to the spread of antibiotic resistance genes in naturally occurring MRSA populations.

Size and Purity Control of HPHT Nanodiamonds down to 1 nm.

High-pressure high-temperature (HPHT) nanodiamonds originate from grinding of diamond microcrystals obtained by HPHT synthesis. Here we report on a simple two-step approach to obtain as small as 1.1 nm HPHT nanodiamonds of excellent purity and crystallinity, which are among the smallest artificially prepared nanodiamonds ever shown and characterized. Moreover we provide experimental evidence of diamond stability down to 1 nm. Controlled annealing at 450 °C in air leads to efficient purification from the nondiamond carbon (shells and dots), as evidenced by X-ray photoelectron spectroscopy, Raman spectroscopy, photoluminescence spectroscopy, and scanning transmission electron microscopy. Annealing at 500 °C promotes, besides of purification, also size reduction of nanodiamonds down to ∼1 nm. Comparably short (1 h) centrifugation of the nanodiamonds aqueous colloidal solution ensures separation of the sub-10 nm fraction. Calculations show that an asymmetry of Raman diamond peak of sub-10 nm HPHT nanodiamonds can be well explained by modified phonon confinement model when the actual particle size distribution is taken into account. In contrast, larger Raman peak asymmetry commonly observed in Raman spectra of detonation nanodiamonds is mainly attributed to defects rather than to the phonon confinement. Thus, the obtained characteristics reflect high material quality including nanoscale effects in sub-10 nm HPHT nanodiamonds prepared by the presented method.

Osteogenic cell differentiation on H-terminated and O-terminated nanocrystalline diamond films.

Nanocrystalline diamond (NCD) films are promising materials for bone implant coatings because of their biocompatibility, chemical resistance, and mechanical hardness. Moreover, NCD wettability can be tailored by grafting specific atoms. The NCD films used in this study were grown on silicon substrates by microwave plasma-enhanced chemical vapor deposition and grafted by hydrogen atoms (H-termination) or oxygen atoms (O-termination). Human osteoblast-like Saos-2 cells were used for biological studies on H-terminated and O-terminated NCD films. The adhesion, growth, and subsequent differentiation of the osteoblasts on NCD films were examined, and the extracellular matrix production and composition were quantified. The osteoblasts that had been cultivated on the O-terminated NCD films exhibited a higher growth rate than those grown on the H-terminated NCD films. The mature collagen fibers were detected in Saos-2 cells on both the H-terminated and O-terminated NCD films; however, the quantity of total collagen in the extracellular matrix was higher on the O-terminated NCD films, as were the amounts of calcium deposition and alkaline phosphatase activity. Nevertheless, the expression of genes for osteogenic markers - type I collagen, alkaline phosphatase, and osteocalcin - was either comparable on the H-terminated and O-terminated films or even lower on the O-terminated films. In conclusion, the higher wettability of the O-terminated NCD films is promising for adhesion and growth of osteoblasts. In addition, the O-terminated surface also seems to support the deposition of extracellular matrix proteins and extracellular matrix mineralization, and this is promising for better osteoconductivity of potential bone implant coatings.