Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins

Vibrational spectroscopy combined with theoretical calculations is a powerful tool for analyzing the interaction and conformation of peptides at the atomistic level. Nonetheless, identifying the structure becomes increasingly difficult as the peptide size grows large. One example is acetyl-SIVSF-N-methylamide, a capped pentapeptide, whose atomistic structure has remained unknown since its first observation [T. Sekiguchi, M. Tamura, H. Oba, P. Çarçarbal, R. R. Lozada-Garcia, A. Zehnacker-Rentien, G. Grégoire, S. Ishiuchi and M. Fujii, Angew. Chem., Int. Ed., 2018, 57, 5626-5629]. Here, we propose a novel conformational search method, which exploits the structure-spectrum correlation using a similarity score that measures the agreement of theoretical and experimental spectra. Surprisingly, the two conformers have distinctly different energy and geometry. The second conformer is 25 kJ mol-1 higher in energy than the other, lowest-energy conformer. The result implies that there are multiple pathways in the early stage of the folding process: one to the global minimum and the other to a different basin. Once such a structure is established, the second conformer is unlikely to overcome the barrier to produce the most stable structure due to a vastly different hydrogen bond network of the backbone. Our proposed method can characterize the lowest-energy conformer and kinetically trapped, high-energy conformers of complex biomolecules.

Confining Bimetal Sites in Porous Metal Silicate Materials for Aerobic Oxidation of Phenols under Mild Conditions

Inspired by the unique catalytic properties of enzymes, numerous biomimetic catalysts have been developed with the intention to realize activation of unreactive reactants under mild conditions; however, the requirement of harsh activation conditions heavily deters their practical applications. We report herein a porous metal silicate (PMS) material PMS-12 that consists of redox-active copper and vanadium metal sites, which exhibits similar catalytic behaviors of enzymes by synergistically activating different reactant molecules and generating local redox potential to facilitate electron and charge transfer, demonstrating the highest catalytic efficiency for aerobic oxidation of phenols to produce highly value-added benzoquinones under mild conditions. Therefore, this work paves a practically applicable strategy for developing high-performance heterogeneous catalysts, which could activate unreactive reactant molecules to produce highly value-added chemicals under mild conditions.

Gas-Phase Mechanism of O.- /Ni2+ -Mediated Methane Conversion to Formaldehyde

The gas-phase reaction of NiAl₂ O₄ ⁺ with CH₄ is studied by mass spectrometry in combination with vibrational action spectroscopy and density functional theory (DFT). Two product ions, NiAl₂ O₄ H⁺ and NiAl₂ O₃ H₂ ⁺ , are identified in the mass spectra. The DFT calculations predict that the global minimum-energy isomer of NiAl₂ O₄ ⁺ contains Ni in the +II oxidation state and features a terminal Al-O^.- oxygen radical site. They show that methane can react along two competing pathways leading to formation of either a methyl radical (CH₃ ⋅) or formaldehyde (CH₂ O). Both reactions are initiated by hydrogen atom transfer from methane to the terminal O^.- site, followed by either CH₃ ⋅ loss or CH₃ ⋅ migration to an O^2- site next to the Ni²⁺ center. The CH₃ ⋅ attaches as CH₃ ⁺ to O^2- and its unpaired electron is transferred to the Ni-center reducing it to Ni⁺ . The proposed mechanism is experimentally confirmed by vibrational spectroscopy of the reactant and two different product ions.

Structural Characterization of Nickel-Doped Aluminum Oxide Cations by Cryogenic Ion Trap Vibrational Spectroscopy

Isolated nickel-doped aluminum oxide cations (NiO_m)(Al₂O₃)_n(AlO)⁺ with m = 1-2 and n = 1-3 are investigated by infrared photodissociation (IRPD) spectroscopy in combination with density functional theory and the single-component artificial force-induced reaction method. IRPD spectra of the corresponding He-tagged cations are reported in the 400-1200 cm^-1 spectral range and assigned based on a comparison to calculated harmonic IR spectra of low-energy isomers. Simulated spectra of the lowest energy structures generally match the experimental spectra, but multiple isomers may contribute to the spectra of the m = 2 series. The identified structures of the oxides (m = 1) correspond to inserting a Ni-O moiety into an Al-O bond of the corresponding (Al₂O₃)_1-3(AlO)⁺ cluster, yielding either a doubly or triply coordinated Ni²⁺ center. The m = 2 clusters prefer similar structures in which the additional O atom either is incorporated into a peroxide unit, leaving the oxidation state of the Ni²⁺ atom unchanged, or forms a biradical comprising a terminal oxygen radical anion Al-O^•- and a Ni³⁺ species. These clusters represent model systems for under-coordinated Ni sites in alumina-supported Ni catalysts and should prove helpful in disentangling the mechanism of selective oxidative dehydrogenation of alkanes by Ni-doped catalysts.

Transition Metal Chain Complexes Supported by Soft Donor Assembling Ligands

The chemistry of discrete molecular chains constituted by metals in low oxidation states, displaying metal-metal proximity and stabilized by suitable metal-bridging, assembling ligands comprising at least one soft donor atom is comprehensively reviewed; complexes with a single (hard or soft) bridging atom (e.g., μ-halide, μ-sulfide, or μ-PR₂ etc.) as well as "closed" metal arrays (that fall in the realm of cluster chemistry) are excluded. The focus is on transition metal-based systems, with few excursions to cases combining transition and post-transition elements. Most relevant supporting ligands have neutral C, P, O, or S donor (mainly, N-heterocyclic carbene, phosphine, ether, thioether) or anionic donor (mainly phenyl, ylide, silyl, phosphide, thiolate) groups. A supporting-ligand-based classification of the metal chains is introduced, using as the classifying parameter the number of "bites" (i.e., ligand bridges) subtending each intermetallic separation. The ligands are further grouped according to the number of donor atoms interacting with the metal chain (called denticity in the following) and the column of the Periodic Table to which the set of donor atoms belongs (in ascending order). A complementary metal-based compilation of the complexes discussed is also provided in a concise tabular form.

Gas-Phase Anionic Metal Clusters are Model Systems for Surface Oxidation: Kinetics of the Reactions of Mn- with O2 (M = V, Cr, Co, Ni; n = 1-15)

The reactions of anionic metal clusters M_n^- with O₂ (M = V (n = 1-15), Cr (n = 1-15), Co (n = 1-12), and Ni (n = 1-14)) are investigated from 300 to 600 K using a selected-ion flow tube. All rate constants show a positive temperature dependence, well described by an Arrhenius equation. Rate constants exceed (or are extrapolated to exceed at higher temperatures) the Langevin-Gioumousis-Stevenson capture rate constant. Application of a capture model accounting for the finite size of the clusters reproduces the size-dependent trends in reactivity. The assumption that reactivity is further controlled by an energetic barrier early in the reaction coordinate is consistent with the experimental observations. An observed correlation of the derived barrier heights on the electron binding energy of M_n^- suggests the barrier may be formed at an avoided crossing between electronic states correlating to M_n^- + O₂ and M_n + O₂^- reactants, analogous to that previously proposed for Al_n^- + O₂ systems. The mechanism is analogous to that for reactions of O₂ with neutral metal surfaces, indicating that gas-phase reactions of anionic metal clusters can be an appropriate model systems for surface oxidation.

Neutral noble-metal-free VCoO2 and CrCoO2 cluster catalysts for CO oxidation by O2

Neutral noble-metal-free metal oxide cluster catalysts (VCoO₂ and CrCoO₂) were developed for multiple CO oxidation reactions by O₂.

Direct Identification of Acetaldehyde Formation and Characterization of the Active Site in the [VPO4 ].+ /C2 H4 Couple by Gas-Phase Vibrational Spectroscopy

The gas‐phase reaction of the heteronuclear oxide cluster [VPO₄]^.+ with C₂H₄ is studied under multiple collision conditions at 150 K using cryogenic ion‐trap vibrational spectroscopy combined with electronic structure calculations. The exclusive formation of acetaldehyde is directly identified spectroscopically and discussed in the context of the underlying reaction mechanism. In line with computational predictions it is the terminal P=O and not the V=O unit that provides the oxygen atom in the barrier‐free thermal C₂H₄→CH₃CHO conversion. Interestingly, in the course of the reaction, the emerging CH₃CHO product undergoes a rather complex intramolecular migration, coordinating eventually to the vanadium center prior to its liberation. Moreover, the spectroscopic structural characterization of neutral C₂H₄O deserves special mentioning as in most, if not all, ion/molecule reactions, the neutral product is usually only indirectly identified.

Identification of Active Sites and Structural Characterization of Reactive Ionic Intermediates by Cryogenic Ion Trap Vibrational Spectroscopy

Cryogenic ion trap vibrational spectroscopy paired with quantum chemistry currently represents the most generally applicable approach for the structural investigation of gaseous cluster ions that are not amenable to direct absorption spectroscopy. Here, we give an overview of the most popular variants of infrared action spectroscopy and describe the advantages of using cryogenic ion traps in combination with messenger tagging and vibrational predissociation spectroscopy. We then highlight a few recent studies that apply this technique to identify highly reactive ionic intermediates and to characterize their reactive sites. We conclude by commenting on future challenges and potential developments in the field.