Automotive braking is a source of highly charged aerosol particles.

Although the last several decades have seen a dramatic reduction in emissions from vehicular exhaust, nonexhaust emissions (e.g., brake and tire wear) represent an increasingly significant class of traffic-related particulate pollution. Aerosol particles emitted from the wear of automotive brake pads contribute roughly half of the particle mass attributed to nonexhaust sources, while their relative contribution to urban air pollution overall will almost certainly grow coinciding with vehicle fleet electrification and the transition to alternative fuels. To better understand the implications of this growing prominence, a more thorough understanding of the physicochemical properties of brake wear particles (BWPs) is needed. Here, we investigate the electrical properties of BWPs as emitted from ceramic and semi-metallic brake pads. We show that up to 80% of BWPs emitted are electrically charged and that this fraction is strongly dependent on the specific brake pad material used. A dependence of the number of charges per particle on charge polarity and particle size is also demonstrated. We find that brake wear produces both positive and negative charged particles that can hold in excess of 30 elementary charges and show evidence that more negative charges are produced than positive. Our results will provide insights into the currently limited understanding of BWPs and their charging mechanisms, which potentially have significant implications on their atmospheric lifetimes and thus their relevance to climate and air quality. In addition, our study will inform future efforts to remove BWP emissions before entering the atmosphere by taking advantage of their electric charge.

Comparison of N-Glycopeptide to Released N-Glycan Abundances and the Influence of Glycopeptide Mass and Charge States on N-Linked Glycosylation of IgG Antibodies.

We report the comparison of mass-spectral-based abundances of tryptic glycopeptides to fluorescence abundances of released labeled glycans and the effects of mass and charge state and in-source fragmentation on glycopeptide abundances. The primary glycoforms derived from Rituximab, NISTmAb, Evolocumab, and Infliximab were high-mannose and biantennary complex galactosylated and fucosylated N-glycans. Except for Evolocumab, in-source ions derived from the loss of HexNAc or HexNAc-Hex sugars are prominent for other therapeutic IgGs. After excluding in-source fragmentation of glycopeptide ions from the results, a linear correlation was observed between fluorescently labeled N-glycan and glycopeptide abundances over a dynamic range of 500. Different charge states of human IgG-derived glycopeptides containing a wider variety of abundant attached glycans were also investigated to examine the effects of the charge state on ion abundances. These revealed a linear dependence of glycopeptide abundance on the mass of the glycan with higher charge states favoring higher-mass glycans. Findings indicate that the mass spectrometry-based bottom-up approach can provide results as accurate as those of glycan release studies while revealing the origin of each attached glycan. These site-specific relative abundances are conveniently displayed and compared using previously described glycopeptide abundance distribution spectra "GADS" representations. Mass spectrometry data are available from the MAssIVE repository (MSV000093562).

Salt-coated air oxidation nanodiamond surface purification with a photoluminescence spectroscopy quality control.

Emerging fields of quantum technologies and biomedical applications demand pure nanodiamonds (NDs) with well-defined surface chemistry. Therefore, an inexpensive, scalable and eco-friendly ND surface purification technology is required. In this study, we report our method, salt-coated air oxidation (SCAO) thermal annealing, to achieve uniform purification of a ND surface without the loss of diamond material. A photoluminescence (PL) spectroscopy quality control method is proposed to evaluate the degree of purification. The presence of an isoemission point in the set of nitrogen vacancy (NV) center PL spectra, obtained through the photochromic effect, is examined as a surface purity indicator. The ratio of the NV centers in NDs after the SCAO treatment was determined by decomposing the PL spectra using the non-negative matrix factorization technique.

All-Optical Reconfigurable Excitonic Charge States in Monolayer MoS2.

Excitons are quasi-particles composed of electron-hole pairs through Coulomb interaction. Due to the atomic-thin thickness, they are tightly bound in monolayer transition metal dichalcogenides (TMDs) and dominate their optical properties. The capability to manipulate the excitonic behavior can significantly influence the photon emission or carrier transport performance of TMD-based devices. However, on-demand and region-selective manipulation of the excitonic states in a reversible manner remains challenging so far. Herein, harnessing the coordinated effect of femtosecond-laser-driven atomic defect generation, interfacial electron transfer, and surface molecular desorption/adsorption, we develop an all-optical approach to manipulate the charge states of excitons in monolayer molybdenum disulfide (MoS2). Through steering the laser beam, we demonstrate reconfigurable optical encoding of the excitonic charge states (between neutral and negative states) on a single MoS2 flake. Our technique can be extended to other TMDs materials, which will guide the design of all-optical and reconfigurable TMD-based optoelectronic and nanophotonic devices.

Uncovering the Contributions of Charge Regulation to the Stability of Single Alpha Helices.

The single alpha helix (SAH) is a recurring motif in biology. The consensus sequence has a di-block architecture that includes repeats of four consecutive glutamate residues followed by four consecutive lysine residues. Measurements show that the overall helicity of sequences with consensus E4 K4 repeats is insensitive to a wide range of pH values. Here, we use the recently introduced q-canonical ensemble, which allows us to decouple measurements of charge state and conformation, to explain the observed insensitivity of SAH helicity to pH. We couple the outputs from separate measurements of charge and conformation with atomistic simulations to derive residue-specific quantifications of preferences for being in an alpha helix and for the ionizable residues to be charged vs. uncharged. We find a clear preference for accommodating uncharged Glu residues within internal positions of SAH-forming sequences. The stabilities of alpha helical conformations increase with the number of E4 K4 repeats and so do the numbers of accessible charge states that are compatible with forming conformations of high helical content. There is conformational buffering whereby charge state heterogeneity buffers against large-scale conformational changes thus making the overall helicity insensitive to large changes in pH. Further, the results clearly argue against a single, rod-like alpha helical conformation being the only or even dominant conformation in the ensembles of so-called SAH sequences.

Tunable Single-Atomic Charges on a Cleaved Intercalated Transition Metal Dichalcogenide.

Control of a single ionic charge state by altering the number of bound electrons has been considered as an ultimate testbed for atomic charge-induced interactions and manipulations, and such subject has been studied in artificially deposited objects on thin insulating layers. We demonstrate that an entire layer of controllable atomic charges on a periodic lattice can be obtained by cleaving metallic Co1/3NbS2, an intercalated transition metal dichalcogenide. We identified a metastable charge state of Co with a different valence and manipulated atomic charges to form a linear chain of the metastable charge state. Density functional theory investigation reveals that the charge state is stable due to a modified crystal field at the surface despite the coupling between NbS2 and Co via a1g orbitals. The idea can be generalized to other combinations of intercalants and base matrices, suggesting that they can be a new platform to explore single-atom-operational 2D electronics/spintronics.

Investigation of the Influence of Charge State and Collision Energy on Oligonucleotide Fragmentation by Tandem Mass Spectrometry.

Due to the increasing pharmaceutical interest of oligonucleotides, for example in antisense therapy and vaccines, their analytical characterization is of fundamental importance due to their complex structure. For this purpose, mass spectrometry is a viable tool for structural studies of nucleic acids. Structural information regarding the primary sequence of a nucleic acid can reliably be gained via tandem mass spectrometry (MSMS) fragmentation. In this work, we present the characteristic fragmentation behavior of short-chain oligonucleotides (15-35 nucleotides) with respect to the collision-induced dissociation (CID) voltage used. The relationship and influence of the length of the oligonucleotide and its charge state is also discussed. The results presented here can be helpful for estimating the required fragmentation energies of short-chain oligonucleotides and their sequencing.

Enhancement of sensitivity and quantification quality in the LC-MS/MS measurement of large biomolecules with sum of MRM (SMRM).

Liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) provides a simple and efficient means for the measurement of analytes in biological matrices with high selectivity and specificity. LC-MS/MS plays an important role in the pharmaceutical industry and biomedical research, but it requires analytes to be in an ionized form in order to be detected. This can pose a challenge for large molecules such as proteins and peptides, because they can exist in multiple charged forms, and this will reduce the total analyte signal by distributing it into multiple ion peaks with a different number of charges in a mass spectrum. In conventional LC-MS/MS analysis of such macromolecules, one charged form is selected as the precursor ion which is then fragmented by collision-induced dissociation (CID) in MS/MS to generate product ions, a process referred to as multiple-reaction monitoring (MRM). The MRM method minimizes interference from endogenous molecules within biological matrices that share the same molecular weight of the precursor ion, but at the expense of signal intensity as compared to precursor ion intensity. We describe here an approach to boost detection sensitivity and expand dynamic range in the quantitation of large molecules while maintaining analytical specificity using summation of MRM (SMRM) transitions and LC separation technique. Protein image from PDB-101 (PDB101.rscb.org).

Relative Stability of Boron Planar Clusters in Diatomic Molecular Model.

In the recently introduced phenomenological diatomic molecular model imagining the clusters as certain constructions of pair interatomic chemical bonds, there are estimated specific (per atom) binding energies of small all-boron planar clusters Bn, n = 1-15, in neutral single-anionic and single-cationic charge states. The theoretically obtained hierarchy of their relative stability/formation probability correlates not only with results of previous calculations, but also with available experimental mass-spectra of boron planar clusters generated in process of evaporation/ablation of boron-rich materials. Some overestimation in binding energies that are characteristic of the diatomic approach could be related to differences in approximations made during previous calculations, as well as measurement errors of these energies. According to the diatomic molecular model, equilibrium binding energies per B atom and B-B bond lengths are expected within ranges 0.37-6.26 eV and 1.58-1.65 Å, respectively.

Multiple Ways Realizing Charge-State Transform in AuCu Bimetallic Nanoclusters with Atomic Precision.

Thiolate-protected nanoclusters with different charge states usually show similar structure frameworks but different electronic configurations, which are proved to dramatically affect their properties such as magnetism, photoluminescence, and catalytic activity. Until now, few nanoclusters with alterable charge states have been reported and only some of them are structurally solved, limiting the in-depth studies on their interesting properties. Here, a new AuCu alloy nanocluster [Au18 Cu32 (SPhCl)36 ]2- (HSPhCl = 4-chlorophenylthiophenol) is synthesized and structurally solved by X-ray crystallography. Interestingly, it is found that this nanocluster can be reduced to another nanocluster with a different charge state, that is, [Au18 Cu32 (SPhCl)36 ]3- . This change in charge states is clearly proved by X-ray crystallography, electrospray ionization mass spectrometry, thermogravimetric analysis, and electron paramagnetic resonance. Furthermore, several redox methods are carried out to realize the reversible interconversion between these two nanoclusters, including electrochemical redox, introduction of H2 O2 /NaBH4 , and oxidation with silica under air atmosphere. This work offers new insight into the transform progress of charge states with AuCu alloy nanoclusters which contributes to the understanding of the relationship between electronic structure and properties of nanoclusters and further development of AuCu nanoclusters with excellent performance.

Prediction of LC-MS/MS Properties of Peptides from Sequence by Deep Learning.

Deep learning models for prediction of three key LC-MS/MS properties from peptide sequences were developed. The LC-MS/MS properties or behaviors are indexed retention times (iRT), MS1 or survey scan charge state distributions, and sequence ion intensities of HCD spectra. A common core deep supervised learning architecture, bidirectional long-short term memory (LSTM) recurrent neural networks was used to construct the three prediction models. Two featurization schemes were proposed and demonstrated to allow for efficient encoding of modifications. The iRT and charge state distribution models were trained with on order of 105 data points each. An HCD sequence ion prediction model was trained with 2 × 106 experimental spectra. The iRT prediction model and HCD sequence ion prediction model provide improved accuracies over the start-of-the-art models available in literature. The MS1 charge state distribution prediction model offers excellent performance. The prediction models can be used to enhance peptide identification and quantification in data-dependent acquisition and data-independent acquisition (DIA) experiments as well as to assist MRM (multiple reaction monitoring) and PRM (parallel reaction monitoring) experiment design.

Atom Probe Tomography of a Cu-Doped TiNiSn Thermoelectric Material: Nanoscale Structure and Optimization of Analysis Conditions.

Cu-doping and crystallographic site occupations within the half-Heusler (HH) TiNiSn, a promising thermoelectric material, have been examined by atom probe tomography. In particular, this investigation aims to better understand the influence of atom probe analysis conditions on the measured chemical composition. Under a voltage-pulsing mode, atomic planes are clearly resolved and suggest an arrangement of elements in-line with the expected HH (F-43m space group) crystal structure. The Cu dopant is also distributed uniformly throughout the bulk material. For operation under laser-pulsed modes, the returned composition is highly dependent on the selected laser energy, with high energies resulting in the measurement of excessively high absolute Ti counts at the expense of Sn and in particular Ni. High laser energies also appear to be correlated with the detection of a high fraction of partial hits, indicating nonideal evaporation behavior. The possible mechanisms for these trends are discussed, along with suggestions for optimal analysis conditions for these and similar thermoelectric materials.

xcalib: a focal spot calibrator for intense X-ray free-electron laser pulses based on the charge state distributions of light atoms.

The xcalib toolkit has been developed to calibrate the beam profile of an X-ray free-electron laser (XFEL) at the focal spot based on the experimental charge state distributions (CSDs) of light atoms. Characterization of the fluence distribution at the focal spot is essential to perform the volume integrations of physical quantities for a quantitative comparison between theoretical and experimental results, especially for fluence-dependent quantities. The use of the CSDs of light atoms is advantageous because CSDs directly reflect experimental conditions at the focal spot, and the properties of light atoms have been well established in both theory and experiment. Theoretical CSDs are obtained using xatom, a toolkit to calculate atomic electronic structure and to simulate ionization dynamics of atoms exposed to intense XFEL pulses, which involves highly excited multiple core-hole states. Employing a simple function with a few parameters, the spatial profile of an XFEL beam is determined by minimizing the difference between theoretical and experimental results. The optimization procedure employing the reinforcement learning technique can automatize and organize calibration procedures which, before, had been performed manually. xcalib has high flexibility, simultaneously combining different optimization methods, sets of charge states, and a wide range of parameter space. Hence, in combination with xatom, xcalib serves as a comprehensive tool to calibrate the fluence profile of a tightly focused XFEL beam in the interaction region.

Two-dimensional decomposition of H-D exchange mass spectra of multicharged ions of biopolymers and their separation into components with independent H-D substitutions.

The work is aimed at developing a numerical method for analysing mass spectra of deutero-substituted multicharged ions of biopolymers to determine contributions of components presumably corresponding to different biomolecule conformations. The two-dimensional decomposition of the H-D exchange mass spectra of two, three and four charged apamin ions with their separation suggests that the reaction of apamin ions with ND3 molecules in the gas phase reveals hypothetically three different structural modifications of apamin ions. Usually for H-D exchange mass spectra, the presence of many resolvable protein structures was determined from measured distributions of peak intensities of ions with the same charge state. The method is new and has no published analogues. Graphical abstract.

Charge-State Field Evaporation Behavior in Cu(V) Nanocrystalline Alloys.

Atom probe tomography (APT) of a nanocrystalline Cu-7 at.% V thin film annealed at 400°C for 1 h revealed chemical partitioning in the form of solute segregation. The vanadium precipitated along high angle grain boundaries and at triple junctions, determined by cross-correlative precession electron diffraction of the APT specimen. Upon field evaporation, the V2+/(V1+ + VH1+) ratio from the decomposed ions was ~3 within the matrix grains and ~16 within the vanadium precipitates. It was found that the VH1+ complex was prevalent in the matrix, with its presence explained in terms of hydrogen's ability to assist in field evaporation. The change in the V2+/(V1+ + VH1+) charge-state ratio (CSR) was studied as a function of base temperature (25-90 K), laser pulse energy (50-200 pJ), and grain orientation. The strongest influence on changing the CSR was with the varied pulse laser, which made the CSR between the precipitates and the matrix equivalent at the higher laser pulse energies. However, at these conditions, the precipitates began to coarsen. The collective results of the CSRs are discussed in terms of field strengths related to the chemical coordination.

Optimizing charge state distribution is a prerequisite for accurate protein biomarker quantification with LC-MS/MS, as illustrated by hepcidin measurement.

BACKGROUND: Targeted quantification of protein biomarkers with liquid chromatography-tandem mass spectrometry (LC-MS/MS) has great potential, but is still in its infancy. Therefore, we elucidated the influence of charge state distribution and matrix effects on accurate quantification, illustrated by the peptide hormone hepcidin. METHODS: An LC-MS/MS assay for hepcidin, developed based on existing literature, was improved by using 5 mM ammonium formate buffer as mobile phase A and as an elution solution for solid phase extraction (SPE) to optimize the charge state distribution. After extensive analytical validation, focusing on interference and matrix effects, the clinical consequence of this method adjustment was studied by performing receiving operating characteristic (ROC)-curve analysis in patients with iron deficiency anemia (IDA, n=44), anemia of chronic disease (ACD, n=42) and non-anemic patients (n=93). RESULTS: By using a buffered solution during sample preparation and chromatography, the most abundant charge state was shifted from 4+ to 3+ and the charge state distribution was strongly stabilized. The matrix effects which occurred in the 4+ state were therefore avoided, eliminating bias in the low concentration range of hepcidin. Consequently, sensitivity, specificity and positive predictive value (PPV) for detection of IDA patients with the optimized assay (96%, 97%, 91%, respectively) were much better than for the original assay (73%, 70%, 44%, respectively). CONCLUSIONS: Fundamental improvements in LC-MS/MS assays greatly impact the accuracy of protein quantification. This is urgently required for improved diagnostic accuracy and clinical value, as illustrated by the validation of our hepcidin assay.

Protecting a Diamond Quantum Memory by Charge State Control.

In recent years, solid-state spin systems have emerged as promising candidates for quantum information processing. Prominent examples are the nitrogen-vacancy (NV) center in diamond, phosphorus dopants in silicon (Si:P), rare-earth ions in solids, and VSi-centers in silicon-carbide. The Si:P system has demonstrated that its nuclear spins can yield exceedingly long spin coherence times by eliminating the electron spin of the dopant. For NV centers, however, a proper charge state for storage of nuclear spin qubit coherence has not been identified yet. Here, we identify and characterize the positively charged NV center as an electron-spin-less and optically inactive state by utilizing the nuclear spin qubit as a probe. We control the electronic charge and spin utilizing nanometer scale gate electrodes. We achieve a lengthening of the nuclear spin coherence times by a factor of 4. Surprisingly, the new charge state allows switching of the optical response of single nodes facilitating full individual addressability.

Resolving the Spatial Structures of Bound Hole States in Black Phosphorus.

Understanding the local electronic properties of individual defects and dopants in black phosphorus (BP) is of great importance for both fundamental research and technological applications. Here, we employ low-temperature scanning tunnelling microscope (LT-STM) to probe the local electronic structures of single acceptors in BP. We demonstrate that the charge state of individual acceptors can be reversibly switched by controlling the tip-induced band bending. In addition, acceptor-related resonance features in the tunnelling spectra can be attributed to the formation of Rydberg-like bound hole states. The spatial mapping of the quantum bound states shows two distinct shapes evolving from an extended ellipse shape for the 1s ground state to a dumbbell shape for the 2px excited state. The wave functions of bound hole states can be well-described using the hydrogen-like model with anisotropic effective mass, corroborated by our theoretical calculations. Our findings not only provide new insight into the many-body interactions around single dopants in this anisotropic two-dimensional material but also pave the way to the design of novel quantum devices.

Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases.

BACKGROUND: (-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is a tumour promoter, PKC isozymes act as tumour promoters or suppressors, depending on the cancer type. In particular, PKCε is frequently implicated in cancer promotion, making it a potential target for anticancer drugs. To improve isozyme selectivity of balanol, exhaustive structural and activity relationship (SAR) studies have been performed in the last two decades, but with limited success. More recently, fluorination on balanol has shown improved selectivity for PKCε, although the fluorine effect is not yet clearly understood. Understanding the origin to this fluorine-based selectivity will be valuable for designing better balanol-based ATP mimicking inhibitors. Computational approaches such as molecular dynamics (MD) simulations can decipher the fluorine effect, provided that correct charges have been assigned to a ligand. Balanol analogues have multiple ionisable functional groups and the effect of fluorine substitutions on the exact charge state of each analogue bound to PKA and to PKCε needs to be thoroughly investigated in order to design highly selective inhibitors for therapeutic applications. RESULTS: We explored the charge states of novel fluorinated balanol analogues using MD simulations. For different potential charge states of these analogues, Molecular Mechanics Generalized Born Surface Area (MMGBSA) binding energy values were computed. This study suggests that balanol and the most potent fluorinated analogue (5S fluorine substitution on the azepane ring), have charges on the azepane ring (N1), and the phenolic (C6''OH) and the carboxylate (C15''O2H) groups on the benzophenone moiety, when bound to PKCε as well as PKA. CONCLUSIONS: To the best our knowledge, this is the first study showing that the phenolate group is charged in balanol and its analogues binding to the ATP site of PKCε. Correct charge assignments of ligands are important to obtain predicted binding energy values from MD simulations that reflect experimental values. Both fluorination and the local enzymatic environment of the ATP site can influence the exact charge states of balanol analogues. Overall, this study is highly valuable for further rational design of potent balanol analogues selective to PKCε.

Conformational effects in protein electrospray-ionization mass spectrometry.

Electrospray-ionization mass spectrometry (ESI-MS) is a key tool of structural biology, complementing the information delivered by conventional biochemical and biophysical methods. Yet, the mechanism behind the conformational effects in protein ESI-MS is an object of debate. Two parameters-solvent-accessible surface area (As) and apparent gas-phase basicity (GBapp)-are thought to play a role in controlling the extent of protein ionization during ESI-MS experiments. This review focuses on recent experimental and theoretical investigations concerning the influence of these parameters on ESI-MS results and the structural information that can be derived. The available evidence supports a unified model for the ionization mechanism of folded and unfolded proteins. These data indicate that charge-state distribution (CSD) analysis can provide valuable structural information on normally folded, as well as disordered structures.