Eight-atom Cluster Research Articles

Cluster Fragments in Amorphous Phosphorus and their Evolution under Pressure.

Amorphous phosphorus (a-P) has long attracted interest because of its complex atomic structure, and more recently as an anode material for batteries. However, accurately describing and understanding a-P at the atomistic level remains a challenge. Here, it is shown that large-scale molecular-dynamics simulations, enabled by a machine-learning (ML)-based interatomic potential for phosphorus, can give new insights into the atomic structure of a-P and how this structure changes under pressure. The structural model so obtained contains abundant five-membered rings, as well as more complex seven- and eight-atom clusters. Changes in the simulated first sharp diffraction peak during compression and decompression indicate a hysteresis in the recovery of medium-range order. An analysis of cluster fragments, large rings, and voids suggests that moderate pressure (up to about 5GPa) does not break the connectivity of clusters, but higher pressure does. The work provides a starting point for further computational studies of the structure and properties of a-P, and more generally it exemplifies how ML-driven modeling can accelerate the understanding of disordered functional materials.

Understanding the Effect of Single Cysteine Mutations on Gold Nanoclusters as Studied by Spectroscopy and Density Functional Theory Modeling.

Fluorescent metal nanoclusters have generated considerable excitement in nanobiotechnology, particularly in the applications of biolabeling, targeted delivery, and biological sensing. The present work is an experimental and computational study that aims to understand the effects of protein environment on the synthesis and electronic properties of gold nanoclusters. MPT63, a drug target of Mycobacterium tuberculosis, was used as the template protein to synthesize, for the first time, gold nanoclusters at a low micromolar concentration of the protein. Two single cysteine mutants of MPT63, namely, MPT63Gly20Cys (mutant I) and MPT63Gly40Cys (mutant II) were employed for this study. The experimental results show that cysteine residues positioned in two different regions of the protein induce varying electronic states of the nanoclusters depending on the surrounding amino acids. A mixture of five-atom and eight-atom clusters was generated for each mutant, and the former was found to be predominant in both cases. Computational studies, including density functional theory (DFT), frontier molecular orbital (FMO), and natural bond orbital (NBO) calculations, validated the experimental observations. The as-prepared protein-stabilized nanoclusters were found to have applications in the imaging of live cells.

Novel Approach to Multimetal Metallaborane Clusters. Synthesis of Hypoelectronicnido-Cp*3IrRu2B5H9from the Reaction ofarachno-Cp*IrB3H9withnido-(Cp*RuH)2B3H7

Two new mixed-metal metallaborane clusters, Cp*3Ru2IrB5H9 and Cp*3Ru2IrB5H5, were isolated from the reaction of an iridaborane with a ruthenaborane. The structures show the former to have an unusual nido eight-atom cluster shape with a low electron count and the latter to have the expected bicapped-octahedral geometry.

Nonicosahedral growth and magnetic behavior of rhodium clusters

Ab initio pseudopotential calculations of the atomic structures and magnetic behavior of ${\mathrm{Rh}}_{n}\phantom{\rule{0.2em}{0ex}}(n\ensuremath{\leqslant}15)$ clusters using the generalized gradient approximation for the exchange-correlation energy, reveal new lowest energy structures that are noncompact and have no atom at the center upto $n=13$, leading to a nonicosahedral growth. An eight-atom cluster has cubic structure and is magic. Some clusters beyond $13\phantom{\rule{0.3em}{0ex}}\text{atoms}$ also do not have close packed structures due to some covalent character in the bonding. The calculated magnetic moments are generally lower and in better agreement with experiments than obtained before. Further studies on ${\mathrm{Ru}}_{13}$ and ${\mathrm{Pd}}_{13}$ clusters show that the lowest energy isomers of these clusters are also nonicosahedral. These findings of the novel behavior of technologically important transition metal clusters provide new ground for a better understanding and design of new catalysts.

Theoretical and experimental study of NO/NO2 adsorption over Co-exchanged type-A zeolite

Abstract Adsorption of NO and NO2 on cobalt exchanged type-A (Co-A) zeolite, has been studied by combining experimental and theoretical techniques. Adsorption energies were determined from temperature programmed desorption (TPD) measurements and ab initio calculations at the B3LYP/6-31G(d) level of theory. TPD profiles suggest that NO is disproportionated upon desorption on Co-A while NO2 desorbs without transformation. An eight-atom cluster model of the transition metal and its closest environment in zeolite Co-A appears to qualitatively reproduce basic features of NOx adsorption. Results from geometrical optimizations confirm that nitrogen monoxide (NO) is preferentially adsorbed through its nitrogen atom, whereas the two oxygen atoms of nitrogen dioxide (NO2) appear to interact more favorably with Co-A. Upon NO adsorption on Co-A, a bent cobalt-mononitrosyl complex is formed. However, a negative charge is not developed on the nitrosyl and cobalt is not oxidized. Similarly, adsorption of nitrogen dioxide over Co-A does not change the oxidation state of cobalt. Theoretical calculations appear to reproduce the experimental adsorption energies within expected limits of error.

Cluster simulations of structural transformations in yellow arsenic

Yellow arsenic (y-As) consists of tetrahedral As 4 molecules that may be packed in some amorphous and crystalline structures. Like many other arsenic structures, y-As is metastable and undergoes irreversible transitions (polymerization) under irradiation. The process of y-As polymerization, which is observed experimentally, usually leads to the formation of amorphous arsenic (a-As) possessing a continuous random network structure. Our previous quantum chemical simulation for an eight-atom cluster model performed using semi-empirical CNDO/BW approach, combined with optimization technique of cyclic coordinate descent, have shown a formation of molecular dimers due to breaking of one bond in each tetrahedral As 4 molecule accompanied with bond switching over to chair-like structure. In that case a pair of approaching As 4 molecules is positioned in a staggered “face-to-face” configuration ( D 2 d symmetry), which may be considered as a conformation with a six-membered chair-shaped ring dominating in the structure of a polymerized a-As. Two energetically preferable configurations of an As 8 cluster have been found here after careful semi-empirical optimization of the face-to-face structure: they possess either cubane configuration ( O h symmetry) or eclipsed “edge-to-edge” configuration ( D 2 h symmetry). For the first time, a two-dimensional energy surface E( z, θ) has been calculated in order to analyze possible paths of structural transformations in y-As. Analogous qualitative results have been just obtained by us when using ab initio Hartree–Fock method combined with the electron correlation corrections for eight-atom cluster model of molecular arsenic. A comparison of both quantum chemical simulations, together with data from previous experimental studies allows us to describe a possible mechanism of the initial stage of the polymerization of y-As.

Prismane C8: A new form of carbon?

Our numerical calculations on small carbon clusters point to the existence of a metastable three-dimensional eight-atom cluster C$_8$ which has a shape of a six-atom triangular prism with two excess atoms above and below its bases. We gave this cluster the name "prismane". The binding energy of the prismane equals to 5.1 eV/atom, i.e., is 0.45 eV/atom lower than the binding energy of the stable one-dimensional eight-atom cluster and 2.3 eV/atom lower than the binding energy of the bulk graphite or diamond. Molecular dynamics simulations give evidence for a rather high stability of the prismane, the activation energy for a prismane decay being about 0.8 eV. The prismane lifetime increases rapidly as the temperature decreases indicating a possibility of experimental observation of this cluster.

Vibrational frequencies for NO chemisorbed on different sites: DFT calculations on Pd clusters

Density functional theory calculations within the adiabatic coupling method have been performed for NO bound to Pd clusters exhibiting the structure appropriate to Pd{110} in order to estimate the influence of adsorption site on the NO stretching frequency. Three cluster sizes were investigated, with four, five and eight Pd atoms. In each case the NO bond length is found to be stretched, by 0.01 to 0.05Å, and the NO stretching frequency is lowered by 186 cm−1 (atop), 233 cm−1 (bridged) and 449 cm−1 (hollow). The adsorption energy for the eight-atom cluster at the bridged site (160–185 kJ mol−1) is considerably higher than at the hollow (∼ 69kJ mol−1) and atop (∼ − 11–40kJ mol−1) sites. The calculations are in good agreement with experimental data for NO on Pd{110}. NEXAFS experimental data show that NO on Pd{110} occupies bridge sites, and RAIRS data provide a NO stretching frequency of 1644 cm−1 (in the low coverage limit), a decrease of 261 cm−1. It is, however, concluded that experimental NO stretching frequencies alone are not a clear indicator of adsorption site.

Electronic structure of small titanium clusters: Emergence and evolution of the 3d band.

The electronic structure of titanium clusters $({\mathrm{Ti}}_{n},n\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}3--65)$ is probed by size-selected anion photoelectron spectroscopy. It is observed that the 3d band emerges at the eight-atom cluster beyond which the d band broadens and evolves toward that of the bulk. The electronic structure of the titanium clusters is found to become bulklike at relatively small cluster sizes. This is discussed in terms of the delocalization of the titanium 3d orbitals and the implications for the cluster structures.

A self-consistent cluster theory of amorphous materials

A cluster method for the electronic structure of amorphous materials is presented with an application to amorphous diamond. Eight-atom cluster model gives a pseudogap in the density of states.