Heteronuclear Cluster Research Articles

A new active learning approach for global optimization of atomic clusters

In catalysis, an accurate structural elucidation of molecules, atomic clusters, nanoparticles and solid surfaces is required to understand chemical processes. Therefore, an efficient and automatic structure determination for these systems is of great benefit since it requires a global search within huge chemical spaces. In this work, we propose a new active learning (AL) method intended for atomic clusters that uses different supervised machine learning techniques and their uncertainties to decide the promising non-observed (virtual) structures to be evaluated from quantum calculations. The method was developed for structural elucidation of (I) clusters where all atomic coordinates are allowed to change in a continuous chemical space and (II) doped ones where the atoms exchange in a sufficiently rigid structure, thus, a discrete search space where all cluster descriptors are known. Particularly for case I, a genetic algorithm operator was used to create the unknown virtual structures (and then their descriptors) from the observed ones to improve the performance of the AL search. The proposed AL was applied to the global optimization of heteronuclear (Al4Si7 and 4Al@Si11) and homonuclear (Na20) clusters using self-consistent charge density-functional tight-binding (SCC-DFTB), where a new repulsion parameter was developed to reproduce isomers evaluated from high-level calculations. The performance of the Gaussian process and artificial neural network algorithms was evaluated together with several uncertainty quantification methods: from Gaussian process, K-fold cross-validation and nonparametric bootstrap (BS) resampling. The efficiency of the AL was compared to conventional global optimization methods, such as random search and a genetic algorithm. The results show that the AL can find efficiently the global minimum of atomic clusters.

Construction of Titanium-Based Metal-Organic Frameworks Based on the Ti/Cu Heteronuclear Cluster.

Presented here are two titanium-based metal-organic frameworks (Ti-MOFs) based on well-defined [Ti6Cu6(μ3-O)2(μ2-O)9(HSO4)2(SO4)6], which can be easily obtained from a cheap Ti source and CuSO4 and exhibited interesting magnetic properties. Furthermore, this clusters can be isolated in pure phase. Numerous uncoordinated sites of SO4 and labile ligands on the Ti and Cu centers of this cluster make it a good candidate as a secondary building unit to construct various Ti-MOFs in the future.

Catalytic CO Oxidation by O2 Mediated with Single Gold Atom Doped Titanium Oxide Cluster Anions AuTi2 O4-6.

Gas-phase studies on catalytic CO oxidation by O2 mediated with gold-containing heteronuclear metal oxide clusters are vital to obtain the structure-reactivity relationship of supported gold catalysts, while it is challenging to trigger the reactivity of clusters with closed-shell electronic structure in O2 activation. Herein, we identified that CO oxidation by O2 can be catalyzed by the AuTi2 O4-6- clusters, among which AuTi2 O4- with closed-shell electronic structure can effectively activate O2 . The reactions were characterized by mass spectrometry and quantum chemical calculations. Theoretical calculations showed that in the initial stage of O2 activation, the Ti2 O4 moiety in AuTi2 O4- contributes dominantly to activate O2 into superoxide (O2- ⋅) without participation of the Au atom. In subsequent steps, the intimate charge transfer interaction between Au and the Ti2 O4 moiety drives the direct dissociation of the O2- ⋅ unit.

Isomers in the phosphine-substituted heteronuclear cluster RuOs3(µ-H)2(CO)12(PPh3) – A re-examination

The solution-state isomers of the heteronuclear cluster RuOs3(µ-H)2(CO)12(PPh3) have been re-examined in the light of conflicting structural assignments for a closely-related analogue. The result is a reassignment of the structures and hence the exchange processes observed in the NMR spectra.

Thermodynamics of Al2M3 (M = 3d Element) Metal Clusters in the Frame of DFT Quantum-Chemical Modeling

The standard thermodynamic parameters of formation (ΔfH°(298 K), ΔfS°(298 K), and ΔfG°(298 K)) for p,d-metal clusters of Al2M3 (M = 3d) stoichiometry and the standard enthalpy, entropy, and Gibbs free energy of their formation reactions from monoatomic species in the gas phase were calculated by the hybrid density functional (DFT) method in OPBE/TZVP approximation and Gaussian09 software. Such reactions were found to be exothermic with an enthalpy factor, and the thus-formed heteronuclear metal clusters are distinguished by a high thermal stability. Both the individual thermodynamic characteristics of the considered metal clusters and the thermodynamic parameters of their formation reactions were found to have intricate variation dynamics depending on the nature of 3d element.

Mg2+ vs Ca2+ bound active site of group II intron– A MD study

Group II introns are enzymes which undergo self-splicing and remove itself from pre-messenger RNA. X-ray structures of group II intron of Oceanobacillus iheyensis at various stages of the self-splicing pathway (pre-hydrolytic, post-hydrolytic, and ligand-free state) revealed intricate atomic interaction network in the active site of the intron. It has been confirmed that a heteronuclear metal ion cluster consisting of four metal ions (K1, K2 sites with K+ and M1, M2 sites with Mg2+) are crucial for function. Substitution of Mg2+ by Ca2+ results in loss of enzymatic activity. The X-ray structures not only opens up the possibility of modelling Mg2+ and Ca2+ bound active site of group II intron and quantitatively estimate the energetics of Mg2+ vs Ca2+ preference but also explore the relative structural and dynamical differences in response to divalent metal ion substitution. Thus, using X-ray structures as a template we performed molecular dynamics simulations to compare structural and dynamical differences between Mg2+ and Ca2+ bound active site of group II intron at various stages of the splicing pathway (i.e., pre-hydrolytic, post-hydrolytic, and ligand-free state). Quantitative estimation of Mg2+ vs Ca2+ selectivity at the M1, M2 sites confirmed Mg2+ preference at intron active sites relative to Ca2+. Ca2+ is relatively more hydrated in the intron active site relative to Mg2+. The local environment (bound nucleophilic water, interaction with scissile phosphate) around M2 is strikingly different between Mg2+ and Ca2+ bound pre-hydrolytic state. In the post-hydrolytic state, the exon part of the hydrolysis product is involved in direct interaction with the M1, whereas the intron part is highly flexible in our MD trajectories. Solvent exposure of M1, M2 sites are least in the pre-hydrolytic state, highest in the ligand-free state, and intermediate in the post-hydrolytic state.

Infrared Photodissociation Spectroscopy of Heteronuclear Arsenic-Iron Carbonyl Cluster Anions.

Heteronuclear arsenic-iron carbonyl cluster anions AsmFe(CO)n- (m, n = 2, 3) have been generated in the gas phase and investigated by mass-selected infrared photodissociation spectroscopy and density functional theory calculations at the B3LYP/BP86/TPSS levels. All the AsmFe(CO)n- (m, n = 2, 3) cluster anions are determined to contain Fe(CO)n- fragments, which can be regarded as being formed by replacing one arsenic atom of the arsenic clusters Asm+1 with the Fe(CO)n- group. Bonding analyses indicated that each As2Fe(CO)n- (n = 2, 3) cluster anion involves two Fe-As single bonds and one As-As double bond. Each As3Fe(CO)n- (n = 2, 3) cluster anion has three Fe-As single bonds and three As-As single bonds. The Fe(CO)3- group with a 15-electron configuration is valence isoelectronic to the As atom and can serve as a building block for forming heteronuclear arsenic-iron carbonyl clusters.

Design of a graphene nitrene two-dimensional catalyst providing a well-defined site accommodating up to three metals, with application to N2 reduction electrocatalysis.

We consider here a novel two-dimensional catalyst M3-C2N that we apply to electrocatalytic N2 reduction. Using the PBE-D3 flavor of density functional theory (DFT), we studied 12 choices for the M3 metal clusters to find two cases: homonuclear Rh3-C2N and heteronuclear Co2Mo-C2N that are particularly promising for electrocatalytic reduction of N2.

An Eight-Atom Iridium-Aluminum Oxide Cluster IrAlO6+ Catalytically Oxidizes Six CO Molecules.

Fundamental understanding regarding oxygen storage capacity involving how and why an active site can buffer a large number of oxygen atoms in redox processes is vital to the design of advanced oxygen storage materials, while it is challenging because of the complexity of heterogeneous catalysis. Herein, we identified that an eight-atom iridium-aluminum oxide cluster IrAlO6+ can transfer all the oxygen atoms to catalytically oxidize six CO molecules. This finding represents a breakthrough in cluster catalysis where at most three oxygen atoms from a heteronuclear metal oxide cluster can be catalytically involved in CO oxidation. We found that oxygen prefers to be stored on aluminum to form an O3-• radical in the energetically unfavorable IrAlO6+ isomer and generate the low-coordinated iridium that is pivotal to capturing CO and triggering the catalysis. The powerful electron cycling capability of iridium and the cooperative iridium-aluminum interplay are emphasized to drive the oxygen atom-transfer behavior.

Energy transfer in heteronuclear rare gas clusters under multiphoton excitation and ionization

The ionization processes of the ArM, XeN and XeNArM clusters in a supersonic beam with multiphoton excitation were studied. The third 263 nm harmonics of a femtosecond Ti : sapphire laser were used for excitation and ionization. Kinetic energy spectra of photoelectrons has been recorded by a magnetic bottle time-of-flight electron spectrometer. Analysis of the electronic spectra of multiphoton ionization of clusters shows that, in heteronuclear clusters, the transfer of excitation energy between xenon and argon atoms plays a significant role in ionization.

Direct Identification of Acetaldehyde Formation and Characterization of the Active Site in the [VPO4].+/C2H4 Couple by Gas‐Phase Vibrational Spectroscopy

AbstractThe 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.

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.

Catalytic CO Oxidation by Gas-Phase Metal Oxide Clusters

Oxidation of CO into CO2 is a prototypical reaction in heterogeneous catalysis and is one of the extensively studied reactions in the gas phase to explore the underlying mechanisms of related catalysis. In this Feature Article, we present and discuss our recent advances in the fundamental understanding of catalytic CO oxidation by O2 mediated with heteronuclear metal oxide clusters (HMOCs) using state-of-the-art mass spectrometry and quantum chemistry calculations. The HMOCs can be considered as ideal models for active sites on mixed or oxide supported catalysts at a strictly molecular level. A concept of electronegativity-ladder effect was proposed to account for the enhanced reactivity of noble metal (NM) doped HMOCs, and then this effect was successfully extended in the design of NM-free HMOCs in catalytic CO oxidation by O2. The future directions and the challenges were also discussed.

Fully versus constrained statistical fragmentation of carbon clusters and their heteronuclear derivatives.

The Microcanonical Metropolis Monte Carlo (MMMC) method has been shown to describe reasonably well fragmentation of clusters composed of identical atomic species. However, this is not so clear in the case of heteronuclear clusters as some regions of phase space might be inaccessible due to the different mobility of the different atomic species, the existence of large isomerization barriers, or the quite different chemical nature of the possible intermediate species. In this paper, we introduce a constrained statistical model that extends the range of applicability of the MMMC method to such mixed clusters. The method is applied to describe fragmentation of isolated clusters with high, moderate, and no heteronuclear character, namely, CnHm, CnN, and Cn clusters for which experimental fragmentation branching ratios are available in the literature. We show that the constrained statistical model describes fairly well fragmentation of CnHm clusters in contrast with the poor description provided by the fully statistical model. The latter model, however, works pretty well for both Cn and CnN clusters, thus showing that the ultimate reason for this discrepancy is the inability of the MMMC method to selectively explore the whole phase space. This conclusion has driven us to predict the fragmentation patterns of the C4N cluster for which experiments are not yet available.

CO oxidation by neutral gold-vanadium oxide clusters

Oxidation of CO by gas-phase atomic clusters is being actively studied to understand the molecular-level mechanisms of heterogeneous CO oxidation over related catalytic surfaces. However, it is experimentally challenging to study CO oxidation by neutral heteronuclear metal oxide clusters because of the difficulty of cluster ionization and detection without fragmentation. Herein, the neutral AuVO2−4 clusters were experimentally generated and their reactions with CO and O2 were studied. The experimental results showed that CO adsorption is the dominant channel on the interactions of AuVO4 and AuVO3 with CO, and AuVO2 can pick up an O2 molecule to generate AuVO4. Theoretical studies indicated that the oxidation of the trapped CO in AuVO3,4CO into CO2 is exothermic while the reaction barriers have to be overcome at the elevated temperatures. A catalytic cycle for CO oxidation by AuVO2−4 is proposed.

Quantum-chemical calculation of molecular structures of Al2Mn3 and Al2Zn3 clusters by using DFT method

By using DFT method in the OPBE/TZVP level, key parameters of molecular structures of five-atomic heteronuclear clusters having Al2M3 composition where M = Mn or Zn (bond lengths, bond angles, and torsion (dihedral) angles) have been calculated. It has been found that the first of these clusters exist in 25 modifications different substantially in their total energy whereas the second, in 14 modifications. Also, it has been noted that the molecular structures of Al2Mn3 and Al2Zn3 differ very significantly between each other both in terms of geometric parameters and in external form; in addition, the most stable modifications of these metal clusters differ between them rather considerably in geometric form, too.

Neutral Au1-Doped Cluster Catalysts AuTi2O3-6 for CO Oxidation by O2.

Oxide supported gold catalysts (e.g., Au/TiO2) are of great significance in heterogeneous catalysis owing to their extraordinary catalytic activity. Study of heteronuclear metal oxide clusters (HMOCs, e.g., Au xTi yO z q) is an important way to uncover the molecular-level mechanisms of gold catalysis in the related heterogeneous catalytic systems. However, the current studies of HMOCs are focused on charged clusters with little attention paid to neutral species. The reactivity study of neutral HMOCs is vital to have a comprehensive understanding of heterogeneous catalysis, but it is experimentally challenging because of the difficulty of cluster ionization and detection without fragmentation. Herein, benefiting from a homemade time-of-flight mass spectrometer coupled with a vacuum ultraviolet laser system, the reactivity of neutral Au1-doped titanium oxide clusters AuTi2O3-6 in catalytic CO oxidation by O2 has been successfully identified. The mechanistic details of the catalysis have been elucidated by quantum chemistry calculations. The crucial roles of the mobile AuCO species that can facilitate not only the process of CO oxidation but also the process of O2 activation have been discovered in the cluster catalysis. The fascinating results are of substantial importance to understand the mechanisms of CO oxidation over Au/TiO2, one type of the best studied gold catalysts.

Stopping power of cluster ions in a free-electron gas from partial-wave analysis

A nonlinear model for the stopping power of cluster ions based on partial-wave analysis is developed through the generalization of the induced density approach (IDA) model for the interaction of homo- and heteronuclear molecular ions with a free-electron gas (IDAMol). We apply IDAMol to the energy loss of ${{\mathrm{H}}_{2}}^{+}$ dimers in ${\mathrm{SiO}}_{2}$ and ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$, where we find that the results are consistent with established linear (dielectric) models at higher speeds, as expected for small perturbations (small values of the projectile charge or high velocities). Specifically at low projectile energies, however, it is important that IDAMol goes beyond perturbation theory. This feature appears to be central for a good description of negative and positive vicinage effects, a measure of the deviation from the independent-atom model. The focus of this work, however, is the investigation of enhanced nonlinear effects. Here we present experimental results for a heteronuclear cluster ion namely ${\mathrm{HeH}}^{+}$ on ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$, in the energy range of few tens of keV/u using the medium energy ion scattering technique. The IDAMol results are corroborated by the experimental data and time-dependent density-functional calculations for this case. Strong nonlinearities are observed for the energy loss of the fragment ${\mathrm{H}}^{+}$ due to the higher charge of its He companion.

Crystal Structures, Magnetic Properties, and Theoretical Investigations of Three Linear Cluster Complexes with Pyridine-2-Amidoxime

Three novel trinuclear mixed-transition-metal complexes of Fe(III), Co(III, II), Ni(II) and Cr(III)), with pyridine-2-amidoxime (Hpa) ligand are synthesized, i.e. [FeNi2(pa)6]Cl·15H2O (1), [CrNi2(pa)6]OH·5H2O (2), and [CoCo2(pa)6]NO3 (3). These complexes are characterized by variable-temperature magnetic susceptibility, electrochemistry, and single crystal X-ray diffraction methods. 1 and 2 are heteronuclear metal clusters in the perfect linear arrangement, i.e. [NiII⋯FeIII⋯NiII and [NiII⋯CrIII⋯NiII] respectively, while 3 is linear [CoII⋯CoIII⋯CoII] trinuclear. Theoretical calculations are employed to successfully account for the experimental results of the variable temperature magnetic susceptibility.

Structure and Thermodynamic Stability of Rhenium and Ruthenium Oxoalkoxo Derivatives MxN4 – xO6(OMе)10 (M, N = Re, Ru; x = 4–0)

Quantum-chemical calculations of the structure and relative thermodynamic stability of tetranuclear clusters MxN4 – xO6(OMе)10 (M, N = Re, Ru; x = 4–0) including geometric isomers of bimetallic clusters are performed to establish the possibility of replacing Re atoms by Ru atoms while maintaining a cyclic tetranuclear structure. As the initial model, the structure of Re4O6(OPri)10 was chosen which is an almost regular rhombus. The values of the metal–metal and metal–oxygen interatomic distances are calculated, and features of their variation under the transition from mononuclear to heteronuclear clusters and from neutral clusters to anions are discussed. Differences between the relative thermodynamic stability of homometallic and heterometallic tetranuclear clusters, including the geometric isomers of the latter, are discussed.