Screening of Subnanoscale Metal Hydride Formation for Late Transition Metals Using Dimer Cations─Group IX Element.

The energetically stable structures of M2Hm+ (M = Co, Rh, Ir; m = 2, 4, 6, ...) were investigated using density functional theory calculations, and possible reaction pathways for the sequential adsorption of H2 molecules on M2+ were proposed. Based on the most stable structures, adsorption energies of H2 were calculated for each adsorption step, and the maximum numbers of adsorbed H atoms on Co2+, Rh2+, and Ir2+ were estimated to be 14, 16, and 16, respectively. Compared to group XI elements (M = Cu, Ag, and Au), which are conceivably inert to H2, more H atoms were bound to Co2+, Rh2+, and Ir2+. The adsorption of H2 on M2+ (M = Co, Rh, Ir, or Cu) in the gas phase was investigated experimentally at 300 K using mass spectrometry. Although Rh2+ and Ir2+ stored numerous H2 molecules as predicted by calculations, Co2+ was found to adsorb no H atoms. It was probably due to the insufficient adsorption energy of Co2+ and the kinetic effect in the H2 adsorption process. Thus, computational calculations can overestimate the number of adsorbed H atoms.

Hydrogen Storage Capacity of Cobalt Cluster Ions.

The adsorption of H2 on gas-phase Con± (n = 5-12) clusters at 300 K and the desorption of H2 from ConHm± upon heating were studied experimentally by combining thermal desorption spectrometry and mass spectrometry to elucidate the hydrogen storage property of the Co clusters. Hydrogen atoms adsorbed well on Con+ (n = 5, 10-12) and Con- (n = 5-12) at 300 K to form ConHm±. The atomic ratios, m/n, for ConHm- (0.9-1.4) were higher than those for ConHm+ (0.2-1.1). According to density functional theory (DFT) calculations, the first few H2 molecules had a tendency to dissociatively adsorb onto the Co clusters. Further, the bonding nature of the H atoms was ionic, similar to the H atoms in the metallic hydrides. In contrast, H2, adsorbed molecularly, was explained in terms of σ complex formation. H2 molecules were desorbed from the clusters upon heating. The temperature dependences showed that ConHm- released H2 at a higher temperature (700-800 K) than ConHm+ (600-700 K), suggesting that Con- should have a higher affinity to hydrogen than Con+. The desorption temperatures were lower than those of VnHm+, which was consistent with the fact that the adsorption energies of H2 were lower for the Co clusters than those for the V clusters. The low adsorption energies were ascribed to their large highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps in the Co clusters.

Size-dependent reactivity of Rh cationic clusters to reduce NO by CO in the gas phase at high temperatures.

The reactivity of the reduction of NO pre-adsorbed on Rh2-9+ clusters by CO was investigated using a combination of an alternate on-off gas injection method and thermal desorption spectrometry. The reduction of RhnNxOy+ clusters by CO was evaluated by varying the CO concentration at T = 903 K. Among the RhnNxOx+ clusters, the Rh3N2O2+ cluster exhibited the highest reduction activity, whereas the other clusters, Rh2,4-9NxOx+, showed lower reactivity. Density functional theory (DFT) calculations for Rh3+ and Rh6+ revealed that the rate-determining step for NO reduction in the presence of CO was NO bond dissociation through the kinetics analysis using the RRKM theory. The reduction of Rh3N2O2+ is kinetically preferable to that of Rh6N2O2+. The DFT results were in qualitative agreement with the experimental results.

Hydrogen Storage Mechanism by Gas-Phase Vanadium Cluster Cations Revealed by Thermal Desorption Spectrometry.

The adsorption of hydrogen on gas-phase vanadium cluster cations, Vn+ (n = 3-14), at 300 K and desorption of hydrogen from hydride clusters, VnHm+, upon heating were observed experimentally by combined thermal desorption spectrometry and mass spectrometry analyses. The ratio m/n was approximately 1.3 for all n values at 300 K, which was reduced to approximately zero at 1000 K. For n = 4, stable cluster geometries of V4Hm+ (m = 0, 2, 4, and 6) were investigated by DFT calculations, revealing that V4 adopted a trigonal pyramidal structure and the H atoms adsorbed mainly on the µ2 bridge sites. The adsorption reaction pathway of one H2 molecule on V4+ was also investigated. The experimentally estimated desorption energies of the H2 molecules were consistent with their calculated binding energies. Among the observed hydride clusters, V6H8+ was found to be significantly thermally durable, probably because of its close-packed octahedral V6 core structure, with H atoms occupying all hollow sites.

Hydrogen Storage Capacity of Single-Nb-Atom-Doped Al Clusters in the Gas Phase Revealed by Thermal Desorption Spectrometry.

Hydrogen is a promising energy resource as a substitute for fossil fuels, and metal alloy hydrides are considered to be good candidates as hydrogen storage materials. In the hydrogen storage processes, hydrogen desorption is as important as hydrogen adsorption. In order to understand the hydrogen desorption features of those clusters, here, single-Nb-atom-doped Al clusters were prepared in the gas phase and their reaction with hydrogen was investigated using thermal desorption spectrometry (TDS). On average, six to eight H atoms were adsorbed in AlnNb+ (n = 4-18) clusters, and most H atoms were released upon heating of the clusters to 800 K. Two types of desorption features of AlnNb+ clusters were found, which related to the flexibility of the clusters. This study demonstrated the potential of Nb-doped Al alloy as an efficient hydrogen storage material with high storage capacity, thermal stability at room temperature, and hydrogen desorption ability upon moderate heating.

Dissociative Adsorption of Water on CaMn4O5 Cationic Clusters.

Water splitting is catalyzed by photosystem II, which comprises an inorganic core (CaMn4O5) and protein ligands. To understand the evolution of CaMn4O5 after attaching water molecules, an isolated CaMn4O5+ cluster was investigated using vibrational spectroscopy and density functional theory calculations. Computational findings suggest that when a water molecule adsorbs on the Ca atom through the O atom of water, one of the OH bonds forms a hydrogen bond with a µ-oxo bridge, which dissociates into two OH groups. This is consistent with the fact that no isomers with molecularly adsorbed water were experimentally observed.

NO Bond Cleavage on Gas-Phase Irn+ Clusters Investigated by Infrared Multiple Photon Dissociation Spectroscopy.

The adsorption forms of NO on Irn+ (n = 3-6) clusters were investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations. Spectral features indicative both for molecular NO adsorption (the NO stretching vibration in the 1800-1900 cm-1 range) and for dissociative NO adsorption (the terminal Ir-O vibration around 940 cm-1) were observed, elucidating the co-existence of molecular and dissociative adsorption of NO. In all calculated structures for molecular adsorption, NO is adsorbed via the N atom on on-top sites. For dissociative adsorption, the O atom adsorbs exclusively on on-top sites (µ1) of the clusters, whereas the N atom is found on either a bridge (µ2) or a hollow (µ3) site. For Ir5+ and Ir6+, the N atom is also found on the on-top sites. The observed propensity for NO dissociation on Irn+ (n = 3-6) is higher than that for Rh6+, which can be explained by the higher metal-oxygen bond strengths for iridium.

Zooming in on the initial steps of catalytic NO reduction using metal clusters.

The study of reactions relevant to heterogeneous catalysis on the surface of well-defined metal clusters with full control over the number of consituent atoms and elemental composition can lead to a detailed insight into the interactions between metal and reactants. We here review experimental and theoretical studies involving the adsorption of NO molecules on mostly rhodium-based clusters under near-thermal conditions in a molecular beam. We show how IR spectrosopic characterization can give information on the binding nature of NO to the clusters for at least the first three NO molecules. The complementary technique of thermal desorption spectrometry reveals at what temperatures multiple NO molecules on the cluster surface desorb or combine to form rhodium oxides followed by N2 elimination. Variation of the cluster elemental composition can be a powerful method to identify how the propensity of the critical first step of NO dissociation can be increased. The testing of such concepts with atomic detail can be of great help in guiding the choices in rational catalyst design.

Adsorption Forms of NO on Iridium-Doped Rhodium Clusters in the Gas Phase Revealed by Infrared Multiple Photon Dissociation Spectroscopy.

The adsorption of an NO molecule on a cationic iridium-doped rhodium cluster, Rh5Ir+, was investigated by infrared multiple photon dissociation spectroscopy (IRMPD) of Rh5IrNO+·Arp complexes in the 300-2000 cm-1 spectral range, where the Ar atoms acted as a messenger signaling IR absorption. Complementary density functional theory (DFT) calculations predicted two near-isoenergetic structures as the putative global minimum: one with NO adsorbed in molecular form in the on-top configuration on the Ir atom in Rh5Ir+, and one where NO is dissociated with the O atom bound to the Ir atom in the on-top configuration and the N atom on a hollow site formed by three Rh atoms. A comparison between the experimental IRMPD spectrum of Rh5IrNO+ and calculated spectra indicated that NO mainly adsorbs molecularly on Rh5Ir+, but evidence was also found for structures with dissociatively adsorbed NO. The estimated fraction of Rh5IrNO+ structures with dissociatively adsorbed NO is approximately 10%, which was higher than that found for Rh6+, but lower than that for Ir6+. The DFT calculations indicated the existence of an energy barrier in the NO dissociation pathway that is exothermic with respect to the reactants, which was considered to prevent NO from dissociating readily on Rh5Ir+. The height of the barrier is lower than that for NO dissociation over Rh6+, which is attributed to the higher binding energy of atomic O to the Ir atom in Rh5Ir+ than to a Rh atom in Rh6+.

Decomposition of nitric oxide by rhodium cluster cations at high temperatures.

Decomposition reactions of NO molecules on gas-phase Rhn+ (n = 6-9) clusters were investigated by gas-phase thermal desorption spectrometry and density functional theory calculations. We found that NO adsorbs on the clusters, forming RhnNxOx+ at room temperature. Upon heating, NO desorption was observed below 800 K. Above 800 K, while for n = 7 and 8, each of Rh7N3O3+, Rh7N4O4+, and Rh8N3O3+ was found to release an N2 molecule, no N2 formation was clearly observed for Rh6,9NxOy+. We considered that both Rh7N3O3+ and Rh8N3O3+ have at least two dissociated NO molecules, while Rh6NxOx+ (x = 1-3) has one or less. Our computational results for Rh8N3O3+ suggested that the formation of an N-N bond in the Rh8N3O3+ structure must overcome an energy barrier of ∼2 eV, which is the highest among the suggested possible reaction pathways. These findings suggested that the size-dependent activity of NO decomposition is governed primarily by how NO molecules are adsorbed on Rhn+ clusters, i.e. whether two or more N atoms from dissociated NO molecules exist in the NO adsorbed clusters, and secondly, by the readiness of the N-N bond formation.

Structures of Nitrogen Oxides Attached to Anionic Gold Clusters Au4- Revealed by Infrared Multiple Photon Dissociation Spectroscopy.

The adsorption forms of NO and NO2 on anionic Au4- clusters were investigated by a combination of IR multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations. For all three species investigated (Au4NO-, Au4N2O2-, and Au4NO2-), the spectra were found to be consistent with a Y-shaped Au4- cluster with triangular Au3 and one Au atom sticking out, on which NO and NO2 molecules adsorb molecularly. These species are considered as intermediates of the Au4--mediated disproportionation reaction of NO, Au4(NO)3- → Au4(NO2)(N2O)-. We discuss the reaction path on the basis of the found geometries and energies and conclude that the disproportionation reaction of NO can occur catalytically on the Au4- cluster.

Substitution of O with a Single Au Atom as an Electron Acceptor in Al Oxide Clusters.

Al atoms generally adopt the +3 oxidation state and form stoichiometric oxides such as Al2O3 in the bulk phase. Among small cationic gas-phase clusters, near-stoichiometric clusters such as Al3O4+, Al3O5+, Al4O6+, Al4O7+, Al5O7+, and Al5O8+ have been readily generated in experimental studies. However, when a single Au atom was included in the clusters, oxygen-deficient clusters such as AuAl4O5+ were formed in high abundance; in these clusters, the Au atom accepted electron density from the Al atoms. The geometrical structures and atomic charges in the clusters suggest that a single Au atom can substitute for O atoms in Al oxide clusters. This propensity originates from the high electron and low oxygen affinities, which, together, constitute an unusual property of Au.

Oxophilicity as a Descriptor for NO Cleavage Efficiency over Group IX Metal Clusters.

Iridium and rhodium are group IX elements that can both catalytically reduce NO. To understand the difference in their reactivity toward NO, the adsorption forms of NO onto clusters of Ir and Rh are compared using vibrational spectra, recorded via infrared multiple-photon dissociation spectroscopy. The spectra give evidence for the existence of at least two specific adsorption forms. The main Ir6+NO isomer is one in which NO is dissociated, whereas one other is a local minimum structure in the reaction pathway leading to dissociative adsorption. In contrast to adsorption onto Rh6+, where less than 10% of the isomeric population was found in the global minimum associated with dissociative adsorption, a substantial fraction (about 50%) of NO dissociates on Ir6+. This higher efficiency is attributed to a considerably reduced activation barrier for dissociation on Ir6+. The key chemical property identified for dissociation efficiency is the cluster's affinity to atomic oxygen.

Microcanonical Nucleation Theory for Anisotropic Materials Validated on Alumina Clusters.

Nucleation kinetics in gas phase remains an open issue with no general model. The derivation of the reaction constants assuming a canonical ensemble fails to describe anisotropic materials such as oxides. We have developed a general and versatile model using activated complex kinetics with a microcanonical approach. This approach handles the kinetics issue in cluster growth when the transient nature of the processes hinders the use of the canonical ensemble. The model efficiently reproduces experimental size distributions of alumina clusters formed by laser ablation with different buffer gas densities, including magic numbers. We show that the thermodynamic equilibrium is not reached during the growth. The bounding energy measured is 10 times lower than the one deduced from DFT calculation, but also the one expected from the bulk cohesive energy.

Hydrophilicity and oxophilicity of the isolated CaMn4O5 cationic cluster modeling inorganic core of the oxygen-evolving complex.

Bond splitting and oxidation of water is known to be catalyzed in photosystem II, which consists of protein ligands and an inorganic core, CaMn4O5. In the present study, the redox properties of the isolated CaMn4Ok+ clusters and the effect of water on them were investigated by gas phase thermal desorption spectrometry and density functional theory (DFT) calculations.

Effect of atomicity on the oxidation of cationic copper clusters studied using thermal desorption spectrometry.

The resistivity to oxidation of small copper clusters, Cun+ (n ≤ 5), in the gas phase with a precise atomicity at the molecular level was investigated using a combination of thermal desorption spectrometry and mass spectrometry. Oxide clusters, CunOm+, with more O atoms than those present with a stoichiometry of n : m = 1 : 1 were produced at room temperature in the presence of O2, and the weakly bound excess oxygen atoms involved in the clusters were removed by post heating. Non-oxidized Cu2+ and Cu3+ clusters were formed in the range of 323-923 K, whereas partially oxidized clusters, Cu4O2+ and Cu5O2+, were generated for n = 4 and 5. Considering the fact that CunOm+ (m = n/2 + 1) tends to be generated for n ≥ 6, the small copper clusters were concluded to be resistive to oxidation. The possible reaction paths for the oxidation of Cu2+ and Cu4+ clusters were obtained by density functional calculations, which were consistent with the experimental findings. The oxidation states of the Cu atoms in the clusters were discussed based on the natural charges of the atoms.

Improvement of Production and Isolation of Human Neuraminidase-1 in Cellulo Crystals.

In cellulo crystallization is a developing technique to provide crystals for protein structure determination, particularly for proteins that are difficult to prepare by in vitro crystallization. This method has a key advantage: it requires neither a protein purification step nor a crystallization step. However, there is still no systematic strategy for improving the technique of in cellulo crystallization because the process occurs spontaneously. Here we report a protocol to produce and extract in cellulo crystals of human lysosomal neuraminidase-1 (NEU1) in human cultured cells. Overexpression of NEU1 protein by the retransfection of cells pretransfected with neu1-overexpressing plasmid improved the efficiency of NEU1 crystallization. Microscopic analysis revealed that NEU1 proteins were not crystallized in the lysosome but in the endoplasmic reticulum (ER). Screening of the buffer conditions used to extract crystals from cells further improved the crystal yield. The optimal pH was 7.0, which corresponds to the pH in the ER. Use of a high-yield flask with a large surface area also yielded more crystals. These optimizations enabled us to execute a serial femtosecond crystallography experiment with a sufficient number of crystals to generate a complete data set. Optimization of the in cellulo crystallization method was thus shown to be possible.

Thermal stability of iron-sulfur clusters.

The thermal decomposition of free cationic iron-sulfur clusters FexSy+ (x = 0-7, y = 0-9) is investigated by collisional post-heating in the temperature range between 300 and 1000 K. With increasing temperature the preferential formation of stoichiometric FexSy+ (y = x) or near stoichiometric FexSy+ (y = x ± 1) clusters is observed. In particular, Fe4S4+ represents the most abundant product up to 600 K, Fe3S3+ and Fe3S2+ are preferably formed between 600 K and 800 K, and Fe2S2+ clearly dominates the cluster distribution above 800 K. These temperature dependent fragment distributions suggest a sequential fragmentation mechanism, which involves the loss of sulfur and iron atoms as well as FeS units, and indicate the particular stability of Fe2S2+. The potential fragmentation pathways are discussed based on first principles calculations and a mechanism involving the isomerization of the cluster prior to fragmentation is proposed. The fragmentation behavior of the iron-sulfur clusters is in marked contrast to the previously reported thermal dissociation of analogous iron-oxide clusters, which resulted in the release of O2 molecules only, without loss of metal atoms and without any tendency to form particular prominent and stable FexOy+ clusters at high temperatures.

Nanosecond pump-probe device for time-resolved serial femtosecond crystallography developed at SACLA.

X-ray free-electron lasers (XFELs) have opened new opportunities for time-resolved X-ray crystallography. Here a nanosecond optical-pump XFEL-probe device developed for time-resolved serial femtosecond crystallography (TR-SFX) studies of photo-induced reactions in proteins at the SPring-8 Angstrom Compact free-electron LAser (SACLA) is reported. The optical-fiber-based system is a good choice for a quick setup in a limited beam time and allows pump illumination from two directions to achieve high excitation efficiency of protein microcrystals. Two types of injectors are used: one for extruding highly viscous samples such as lipidic cubic phase (LCP) and the other for pulsed liquid droplets. Under standard sample flow conditions from the viscous-sample injector, delay times from nanoseconds to tens of milliseconds are accessible, typical time scales required to study large protein conformational changes. A first demonstration of a TR-SFX experiment on bacteriorhodopsin in bicelle using a setup with a droplet-type injector is also presented.

Oxygen Release from Cationic Niobium-Vanadium Oxide Clusters, NbnVmOk+, Revealed by Gas Phase Thermal Desorption Spectrometry and Density Functional Theory Calculations.

Thermal dissociation of the cationic niobium-vanadium oxide clusters, NbnVmOk+ (n + m = 2-8), was investigated by gas phase thermal desorption spectrometry. The oxygen-rich NbnVmOk+ released O and O2 for odd and even values of n + m, respectively. Substitution of more than one Nb atom in NbnOk+ by V drastically lowered the desorption temperature of O2 for even values of n + m, whereas the substitution of more than two Nb atoms opened a new desorption path involving the release of O2 for odd values of n + m. The substitution effects can be explained by the fact that Nb atoms display the +5 state, whereas V atoms can exist in either the +4 or +5 states. The geometrical structures of selected NbnVmOk+ clusters were optimized and the energetics of the release of O/O2 from the clusters was discussed on the basis of the results of DFT calculations.