Metal nanoclusters: from fundamental aspects to electronic properties and optical applications.

Monolayer-protected noble metal clusters, also called nanoclusters, can be produced with the atomic precision and in large-scale quantity and are playing an increasingly important role in the field of nanoscience. To outline the origin and the perspectives of this new field, we overview the main results obtained on free metal clusters produced in gas phase including mainly electronic properties, the giant atom concept, the optical properties, briefly the role of the metal atom (alkali, divalent, noble metal) and finally the atomic structure of clusters. We also discuss the limitations of the free clusters. Then, we describe the field of monolayer-protected metal clusters, the main results, the new offered perspectives, the added complexity, and the role of the ligand beyond the superatom concept.

High performance {Nb5TaX12}@PVP (X = Cl, Br) cluster-based nanocomposites coatings for solar glazing applications.

The development of highly ultraviolet (UV) and near-infrared (NIR) absorbent transparent coatings is an important enabling technology and area of research for environmental sustainability and energy conservation. Different amounts of K4[{Nb5TaXi 12}Xa 6] cluster compounds (X = Cl, Br) dispersed into polyvinylpyrrolidone matrices were prepared by a simple, nontoxic and low-cost wet chemical method. The resulting solutions were used to fabricate visibly transparent, highly UV and NIR absorbent coatings by drop casting. The properties of the solution and films were investigated by complementary techniques (optical absorption, electrospray ionization mass spectrometry and Raman spectroscopy). The UV and NIR absorption of such samples strongly depended on the concentration, dispersion and oxidation state of the [{Nb5TaXi 12}Xa 6] nanocluster-based units. By varying and controlling these parameters, a remarkable improvement of the figures of merit TL/TE and SNIR for solar-glazing applications was achieved compared to the previous results on nanocomposite coatings based on metal atom clusters.

Exploring Conformational Landscapes Using Trap and Release Tandem Ion Mobility Spectrometry.

The dynamics and thermodynamics of structural changes in isolated glu-fibrinopeptide B (GluFib) were investigated by tandem ion mobility spectrometry (IMS). Doubly protonated GluFib2+ ions were first selected by IMS and then stored for a controlled duration in a thermalized ion trap. Temperature-induced conformational changes were finally monitored by IMS as a function of trapping time. Based on this procedure, isomerization rates and equilibrium populations of the different conformers were determined as a function of temperature. We demonstrate that the measured thermodynamic quantities can be directly compared to simulated observables from ensemble molecular modeling based on appropriate order parameters. We obtained good qualitative agreement with replica-exchange molecular dynamics simulations based on the AMOEBA force field and processed using the weighted histogram analysis method. This suggests that the balance between Coulomb repulsion and optimal charge solvation is the main source of the observed conformational bistability. Our results emphasize the differences between the kinetically driven quasi-equilibrium distributions obtained after collisional activation and the thermodynamically driven distributions from the present equilibrium experiments due to entropic effects. As a consequence, our measurements not only allow straightforward determination of Arrhenius activation energies but also yield the relative enthalpy and entropy changes associated to a structural transition.

Photo-control of bimolecular reactions: reactivity of the long-lived Rhodamine 6G triplet excited state with ˙NO.

Photo-chemistry provides a non-intuitive but very powerful way to probe kinetically limited, sometimes thermodynamically non-favored reactions and, thus, access highly specific products. However, reactivity in the excited state is difficult to characterize directly, due to short lifetimes and challenges in controlling the reaction medium. Among photo-activatable reagents, rhodamine dyes find widespread uses due to a number of favorable properties including their high absorption coefficient. Their readily adaptable synthesis allows development of tailor-made dyes for specific applications. Remarkably, few studies have directly probed the chemical reactivity of their triplet excited state. Here we present a new conceptual approach to examine the specific chemistry of the triplet excited state. We have developed a pump (488 nm) - probe (600 nm) strategy to examine the gas-phase lifetime and reactivity of the triplet cation of Rhodamine 6G (3Rh6G+) in an ion trap mass spectrometer. The confounding effects of solvent, aggregation and formation of other reactive intermediates is thus avoided allowing fundamental reactivity to be explored. In the presence, in the ion trap, of helium seeded with 1% of nitric oxide (˙NO) (∼ 60 ion/˙NO collisions per second), the triplet lifetime is shortened from 1.9 s to 0.7 s. Simultaneously, the reaction products [Rh6G-H]˙+ and [Rh6G-H + NO]+ are observed. Reaction of 3Rh6G+ with ˙NO2 yields [Rh6G-H]˙+, [Rh6G-H + NO2]+ and [Rh6G-2H]+. None of these products are observed for the singlet, 1Rh6G+. DFT calculations suggest a stepwise mechanism only allowed from 3Rh6G+, in which H atom abstraction by ˙NOx (x = 1 or 2) yields [Rh6G-H]˙+ which, then, reacts with another ˙NOx molecule. This illustrates the power of light to initiate specific chemical reactions, and the relevance of gas-phase ion-molecule reaction approaches to understand stepwise reaction mechanism from specific excited states.

Phenyl argentate aggregates [AgnPhn+1]- (n = 2-8): Models for the self-assembly of atom-precise polynuclear organometallics.

Electrospray ionization of phenyl argentates formed by transmetalation reactions between phenyl lithium and silver cyanide provides access to the argentate aggregates, [AgnPhn+1]-, which were individually mass-selected for n = 2-8 in order to generate their gas-phase Ultraviolet Photodissociation (UVPD) "action" spectra over the range 304-399 nm. A strong bathochromic shift in optical spectra was observed with increasing size/n. Theoretical calculations allowed the assignment of the experimental UVPD spectra to specific isomer(s) and provided crucial insights into the transition from the 2D to 3D structure of the metallic component with the increasing size of the complex. The [AgnPhn+1]- aggregates contain neither pronounced metallic cluster properties nor ligated metallic cluster features and are thus not superatom complexes. They therefore represent novel organometallic characteristics built from Ag2Ph subunits.

Kinetic study of azobenzene E/Z isomerization using ion mobility-mass spectrometry and liquid chromatography-UV detection.

Z and E azobenzene isomers are molecular switches which can interconvert both photochemically and thermally. Presently, we studied a ketal-substituted bridged azobenzene in which two stable diastereomeric conformers (Z1 and Z2) photochemically interconvert through the transient E isomer. UV-VIS absorption spectroscopy is commonly used to study the relaxation kinetics of azobenzenes, but it does not allow direct quantitation of the process in this case. In the present paper, liquid chromatography coupled to UV detection (LC-UV) and ion mobility-mass spectrometry (IMS-MS) were combined to study the thermal back relaxation kinetics of the E isomer. LC separation of the three isomers was achieved in less than 10 minutes, allowing the characterization of the relatively slow thermal back relaxation kinetics at low temperature through UV detection. In addition, the faster E→Z thermal back relaxation at higher temperature was studied using IMS-MS, which allows shorter timescale separation than LC. Baseline separation of the two Z isomers was achieved in IMS-MS for [Z + Ag]+ ions, and their gas-phase conformations were determined by IRMPD experiments. Both IMS-MS and LC-UV methodologies succeeded to study the E→Z thermal back relaxation kinetics, and appeared to be complementary techniques. We show that the combination of the two techniques allows the characterization of the isomerization processes over a broad temperature range, and the determination of the associated thermodynamic observables.

Structure and Charge Heterogeneity in Isomeric Au25(MBA)18 Nanoclusters-Insights from Ion Mobility and Mass Spectrometry.

Atomically precise Au25(MBA)18 nanoclusters were investigated by mass spectrometry and ion mobility spectrometry. We show that clusters sharing the same chemical composition and bearing the same net charge may display different structures and different charge repartition patterns, namely, the number of charges corresponding to deprotonation of the ligand moieties through carboxyl groups is not the same for all detected species. Part of the observed heterogeneity is a consequence of spontaneous electron loss occurring in the gas phase, which modifies the net charge of the clusters while maintaining the initial (de)protonation state.

Direct Radiation Effects on the Structure and Stability of Collagen and Other Proteins.

In this review, recent progress in understanding the direct effects of radiation on the structure and stability of collagen, the most abundant protein in the human body, and other proteins is surveyed. Special emphasis is placed on the triple-helical structure of collagen, as studied by means of collagen mimetic peptides. The emerging patterns are the dose dependence of radiation processes and their abundance, the crucial role of radicals in covalent-bond formation (crosslinking) or cleavage, and the influence of the radiation energy and nature. Future research should allow fundamental questions, such as charge transfer and fragmentation dynamics triggered by ionization, to be answered, as well as developing applications such as protein-based biomaterials, notably with properties controlled by irradiation.

Ion mobility resolved photo-fragmentation to discriminate protomers.

RATIONALE: Among the sources of structural diversity in biomolecular ions, the co-existence of protomers is particularly difficult to take into account, which in turn complicates structural interpretation of gas-phase data. METHODS: We investigated the sensitivity of gas-phase photo-fragmentation measurements and ion mobility spectrometry (IMS) to the protonation state of a model peptide derivatized with chromophores. Accessible interconversion pathways between the different identified conformers were probed by tandem ion mobility measurement. Furthermore, the excitation coupling between the chromophores has been probed through photo-fragmentation measurements on mobility-selected ions. All results were interpreted based on molecular dynamics simulations. RESULTS: We show that protonation can significantly affect the photo-fragmentation yields. Especially, conformers with very close collision cross sections (CCSs) may display dramatically different photo-fragmentation yields in relation with different protonation patterns. CONCLUSIONS: We show that, even if precise structure assignment based on molecular modeling is in principle difficult for large biomolecular assemblies, the combination of photo-fragmentation and IMS can help to identify the signature of protomer co-existence for a population of biomolecular ions in the gas phase. Such spectroscopic data are particularly suitable to follow conformational changes.

Sub-100 nanometer silver doped gold-cysteine supramolecular assemblies with enhanced nonlinear optical properties.

The ability of gold(i) thiolates to self-assemble into supramolecular architectures opens the route for a new class of nanomaterials with a unique structure-optical property relationship. However, for a confirmed structure-optical property relationship, a control of the supramolecular architectures is required. In this work, we report a simple synthesis of sub-100 nanometer gold-cysteine and silver doped gold-cysteine supramolecular assemblies. We explore in particular silver-doping as a strategy to enhance the optical properties of these supramolecular assemblies. By an accurate characterization of as-synthesized supramolecular nanoparticles, we have been able to measure for the first time, their absolute two-photon absorption cross-section, two-photon excited fluorescence cross-section and first hyperpolarizabilities at different near-IR wavelengths. Huge values are obtained for silver doped gold-cysteine supramolecular assemblies, as compared to their corresponding undoped counterpart. In addition, we employ DFT and TD-DFT methods to study the geometric and electronic structures of model gold-cysteine and silver doped gold-cysteine compounds in order to address the structure-linear/nonlinear optical property relationship. The aim is to gain insights into the origin of the nonlinear optical enhancement of silver-doped gold supramolecular assemblies.

Data-Independent Acquisition Coupled to Visible Laser-Induced Dissociation at 473 nm (DIA-LID) for Peptide-Centric Specific Analysis of Cysteine-Containing Peptide Subset.

Thanks to comprehensive and unbiased sampling of all precursor ions, the interest to move toward bottom-up proteomic with data-independent acquisition (DIA) is continuously growing. DIA offers precision and reproducibility performances comparable to true targeted methods but has the advantage of enabling retrospective data testing with the hypothetical presence of new proteins of interest. Nonetheless, the chimeric nature of DIA MS/MS spectra inherent to concomitant transmission of a multiplicity of precursor ions makes the confident identification of peptides often challenging, even with spectral library-based extraction strategy. The introduction of specificity at the fragmentation step upon ultraviolet or visible laser-induced dissociation (LID) range targeting only the subset of cysteine-containing peptides (Cys-peptide) has been proposed as an option to streamline and reduce the search space. Here, we describe the first coupling between DIA and visible LID at 473 nm to test for the presence of Cys-peptides with a peptide-centric approach. As a test run, a spectral library was built for a pool of Cys-synthetic peptides used as surrogates of human kinases (1 peptide per protein). By extracting ion chromatograms of query standard and kinase peptides spiked at different concentration levels in an Escherichia coli proteome lysate, DIA-LID demonstrates a dynamic range of detection of at least 3 decades and coefficients of precision better than 20%. Finally, the spectral library was used to search for endogenous kinases in human cellular extract.

Characterization of foreign materials in paraffin-embedded pathological specimens using in situ multi-elemental imaging with laser spectroscopy.

Pathologists typically encounter many disparate exogenous materials in clinical specimens during their routine histopathological examinations, especially within the skin, lymph nodes, and lungs. These foreign substances may be free extracellular deposits or induce several clinical abnormalities or histopathological patterns. However, pathologists almost never investigate or report the chemical nature of exogenous metals in clinical specimens due to a lack of convenient and available technologies. In this paper, a novel strategy based on laser-induced breakdown spectroscopy (LIBS) technology is evaluated for in situ multi-elemental tissue imaging. The improved procedures allow visualization of the presence of chemical elements contained within paraffin-embedded specimens of medical interest with elemental images that are stackable with conventional histology images. We selected relevant medical situations for which the associated pathology reports were limited to the presence of lymphohistiocytic and inflammatory cells containing granules (a granuloma and a pseudolymphoma) or to lymph nodes or skin tissues containing pigments or foreign substances. Exogenous elements such as aluminum, titanium, copper, and tungsten were identified and localized within the tissues. The all-optical LIBS elemental imaging instrument that we developed is fully compatible with conventional optical microscopy used for pathology analysis. When combined with routine histopathological analysis, LIBS is a versatile technology that might help pathologists establish or confirm diagnoses for a wide range of medical applications, particularly when the nature of external agents present in tissues needs to be investigated.

Isolated Collagen Mimetic Peptide Assemblies Have Stable Triple-Helix Structures.

The origin of the triple-helix structure and high stability of collagen has been debated for many years. As models of the triple helix and building blocks for new biomaterials, collagen mimetic peptide (CMP) assemblies have been deeply studied in the condensed phase. In particular, it was found that hydroxylation of proline, an abundant post-translational modification in collagen, increases its stability. Two main hypotheses emerged to account for this behavior: 1) intra-helix stereoelectronic effects, and 2) the role of water molecules H-bound to hydroxyproline side-chains. However, in condensed-phase investigations, the influence of water cannot be fully removed. Therefore, we employed a combination of tandem ion mobility and mass spectrometries to assess the structure and stability of CMP assemblies in the gas phase. These results show a conservation of the structure and stability properties of triple helix models in the absence of solvent, supporting an important role of stereoelectronic effects. Moreover, evidence that small triple helix assemblies with controlled stoichiometry can be studied in the gas phase is given, which opens new perspectives in the understanding of the first steps of collagen fiber growth.

Bulky Counterions: Enhancing the Two-Photon Excited Fluorescence of Gold Nanoclusters.

Increasing fluorescence quantum yields of ligand-protected gold nanoclusters has attracted wide research interest. The strategy consisting in using bulky counterions has been found to dramatically enhance the fluorescence. In this Communication, we push forward this concept to the nonlinear optical regime. We show that by an appropriate choice of bulky counterions and of solvent, a 30-fold increase in two-photon excited fluorescence (TPEF) signal at ≈600 nm for gold nanoclusters can be obtained. This would correspond to a TPEF cross-section in the range of 0.1 to 1 GM.

Photo-induced linkage isomerization in the gas phase probed by tandem ion mobility and laser spectroscopy.

Ruthenium complexes involving sulfoxide ligands can undergo linkage isomerization upon light absorption, accompanied by dramatic changes in their optical properties. These remarkable photochromic properties are sensitive to the nature of the ligand as well as to that of the solvent. We used tandem ion mobility spectrometry coupled to mass spectrometry to gain direct experimental insight into the isomerization pathways connecting the different linkage isomers of an isolated ruthenium complex with two dimethyl-sulfoxide ligands. We find that the isomerization behavior of the solvent-free complex differs from that previously reported in the solution-phase, which is in line with recent theoretical predictions.

Infrared laser dissociation of single megadalton polymer ions in a gated electrostatic ion trap: the added value of statistical analysis of individual events.

In this study, we report the unimolecular dissociation mechanism of megadalton SO3-containing poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) polymer cations and anions with the aid of infrared multiphoton dissociation coupled to charge detection ion trap mass spectrometry. A gated electrostatic ion trap ("Benner trap") is used to store and detect single gaseous polymer ions generated by positive and negative polarity in an electrospray ionization source. The trapped ions are then fragmented due to the sequential absorption of multiple infrared photons produced from a continuous-wave CO2 laser. Several fragmentation pathways having distinct signatures are observed. Highly charged parent ions characteristically adopt a distinctive "stair-case" pattern (assigned to the "fission" process) whereas low charge species take on a "funnel like" shape (assigned to the "evaporation" process). Also, the log-log plot of the dissociation rate constants as a function of laser intensity between PAMPS positive and negative ions is significantly different.

Action-Self Quenching: Dimer-Induced Fluorescence Quenching of Chromophores as a Probe for Biomolecular Structure.

To obtain a more detailed understanding of how structure influences the function and interaction of biomolecules, it is important to develop structure sensitive techniques to probe these relationships. Alongside in vivo and in vitro techniques, it is instructive to consider in vacuo methodologies: for example native mass spectrometry, ion mobility mass spectrometry, and FRET. Here, we propose a novel technique for probing biomolecular structure based on the changes in photophysics of a chromophore upon dimer formation. Comparison of solution and gas phase measurements on a doubly tagged tripeptide shows that dimer-induced fluorescence quenching is accompanied by an increase in photofragmentation yield. The 12-28 fragment of amyloid beta was used to show that as the charge state was increased-previously shown to cause a conformational change from compact random coil to extended helical structure-the disappearance of a band at 495 nm could be correlated with the level of self-quenching. The presence of features in the action spectrum of the +3 charge state of both quenched and unquenched chromophores allowed inference of multiple conformations. Single wavelength measurements on doubly tagged ubiquitin cations were performed to show that the technique is feasible on a small protein. These results demonstrate that self-quenching is a sensitive and fast gas-phase probe of biomolecular structure that can be directly linked to solution phase measurements. Further, it is capable of probing very small changes in conformation, making it complementary to FRET based techniques, which are insensitive at very short chromophore separations.

Conformational Dynamics in Ion Mobility Data.

The shape of the spectral features in arrival time distributions (ATDs) recorded by ion mobility spectrometry (IMS) can often be interpreted in terms of the coexistence of different isomeric species. Interconversion between such species is also acknowledged to influence the shape of the ATD, even if no general quantitative description of this effect is available. We present an analytical model that allows simulating ATDs resulting from interconverting species. This model is used to reproduce experimental data obtained on a bistable system and to interpret discrepancies between measurements on different types of instruments. We show that the proposed model can be further exploited to extract kinetic and thermodynamic data from tandem-IMS measurements.

Fragmentation patterns of chromophore-tagged peptides in visible laser induced dissociation.

RATIONALE: Tandem mass spectrometry (MS/MS) is the pivotal tool for protein structural characterization and quantification. Identification relies on the fragmentation step of tryptic peptides in bottom-up strategy. Specificity of fragmentation can be obtained using laser-induced dissociation (LID) in the visible range, after tagging of the targeted peptides with an adequate chromophore. Backbone fragmentation is required to obtain specific fragments and confident identification. We present herein a study of fragmentation patterns of chromophore-tagged peptides in LID, showing the potential of LID methodology to provide the maximum number of fragments for further identification and quantification. METHODS: A total of 401 cysteine-containing tryptic peptides originating from the human proteome were derivatizated on the thiol group of cysteine with a Dabcyl maleimide chromophore, which has a high photo-absorption cross section at 473 nm. The derivatized peptides were then analyzed by LID at 473 nm on a Q Exactive instrument. RESULTS: LID spectra present a characteristic fragment at m/z 252.112 for all precursors. This product ion arises from the internal dissociation of the Dabcyl chromophore. Several peptide-backbone fragment ions are also detected. Results show the quasi absence of fragmentation at the cysteine site. This indicates that part of the energy must be redistributed across the entire system despite excitation initially localized at the chromophore. Indeed, the fragmentation mainly occurs at 3 to 5 amino acids from the derivatized cysteine residue. CONCLUSIONS: LID of derivatized cysteine-containing peptides displays the initial fragmentation of the chromophore. As energy is redistributed all along the peptide sequence, fragmentation of the peptide backbone is also observed. Thus, LID of chromophore-tagged peptides produces adequate fragment ions, allowing both good sequence coverage for a greater confidence of identification, and a large choice of transitions for specific quantification.

Dimerization and conformation-related free energy landscapes of dye-tagged amyloid-ß12-28 linked to FRET experiments.

We have investigated the free energy landscape of Aß-peptide dimer models in connection to gas-phase FRET experiments. We use a FRET-related distance coordinate and one conformation-related coordinate per monomer for accelerated structural exploration with well-tempered metadynamics in solvent and in vacuo. The free energy profiles indicate that FRET under equilibrium conditions should be significantly affected by the de-solvation upon the transfer of ions to the gas-phase. In contrast, a change in the protonation state is found to be less impacting once de-solvated. Comparing F19P and WT alloforms, for which we measure different FRET efficiencies in the gas-phase, we predict only the relevant structural differences in the solution populations, not under gas-phase equilibrium conditions. This finding supports the hypothesis that the gas-phase action-FRET measurement after ESI operates under non-equilibrium conditions, with a memory of the solution conditions - even for the dimer of this relatively short peptide. The structural differences in solution are rationalized in terms of conformational propensities around residue 19, which show a transition to a poly-proline type of pattern upon mutation to F19P - a difference that gets lost in the gas-phase.