Density functional study on size-dependent structures, stabilities, electronic and magnetic properties of Au n M (M = Al and Si, n?=?1–9) clusters: comparison with pure gold clusters

The density functional theory (DFT) method has been employed to systematically investigate the geometrical structures, relative stabilities, and electronic and magnetic properties of Au(n)M (M = Al and Si, n = 1-9) clusters for clarifying the effect of Al(Si) modulation on the gold nanostructures. Of all the clusters studied, the most stable configurations adopt a three-dimensional structure for Au(n)Al at n = 4-8 and Au(n)Si at n = 3-9, while for pure gold systems, no three-dimensional lowest energy structures are obtained. Through a careful analysis of the fragmentation energy, second-order difference of energy, HOMO-LUMO energy gap, and magnetic moment as a function of cluster size, an odd-even alternative phenomenon has been observed. The results show that the clusters with even-number valence electrons have a higher relative stability, but lower magnetic moments. Furthermore, Al(Si) doping is found to enhance the stabilities of gold frameworks. In addition, the charge analysis has been given to understand the different effects of individual doped atom on electronic properties and compared further.     

Probing the structural, electronic and magnetic properties of multicenter Fe2S2 0/−, Fe3S4 0/− and Fe4S4 0/− clusters

The structural, electronic and magnetic properties of neutral and anion Fe₂S₂, Fe₃S₄ and Fe₄S₄ have been investigated with the aid of previous photoelectron spectroscopy and density functional theory calculations. Theoretical electron detachment energies (both vertical and adiabatic) of anion clusters for the lowest energy structure were computed and compared with the experimental results to verify the ground states. The optimized structures show that the ground state structures of Fe₂S₂ ^0/?, Fe₃S₄ ^0/? and Fe₄S₄ ^0/? favor high spin state and are similar to their structures in proteins. The electron delocalization pattern for all the clusters and the nature of bonding between Fe and S atoms were studied by analyzing molecular orbitals. Natural population analysis demonstrates that Fe atoms act as an electron donor in all clusters, and the electron density difference map clearly shows the direction of the electron flow over the whole complex. Furthermore, the investigated magnetism shows that the Fe atoms carried most of the magnetic moments, which is due mainly to the 3d state, while only very small magnetic moments are found on S atoms.     

Reexamination of structures,stabilities, and electronic properties of holmium-doped silicon clusters HoSi<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 12–20)

The total energies, growth patterns, equilibrium geometries, relative stabilities, hardnesses, intramolecular charge transfer, and magnetic moments of HoSi _n (n?=?12–20) clusters have been reexamined theoretically using two different density functional schemes in combination with relativistic small-core Stuttgart effective core potentials (ECP28MWB) for the Ho atoms. The results show that when n?=?12–15, the most stable structures are predicted to be exohedral frameworks with a quartet ground state, but when n?=?16–20, they are predicted to be endohedral frameworks with a sextuplet ground state. These trend in stability across the clusters (gauged from their dissociation energies) was found to be approximately the same regardless of the DFT scheme used in the calculations, with HoSi₁₃, HoSi₁₆, HoSi₁₈, and HoSi₂₀ calculated to be more stable than the other clusters. The results obtained for cluster hardness indicated that doping the Ho atom into Si₁₃ and Si₁₆ leads to the most stable HoSi _n clusters, while doping Ho into the other Si _n clusters increases the photochemical sensitivity of the cluster. Analyses of intracluster charge transfer and magnetic moments revealed that charge always shifts from the Ho atom to the Si _n cluster during the creation of exohedral HoSi _n (n?=?12–15) structures. However, the direction of charge transfer is reversed during the creation of endohedral HoSi _n (n?=?16–20) structures, which implies that Ho acts as an electron acceptor when it is encapsulated in the Si _n cage. Furthermore, when the most stable exohedral HoSi _n (n?=?12–15) structures are generated, the 4f electrons of Ho are virtually unchanged and barely participate in intracluster bonding. However, in the most stable endohedral HoSi _n (n?=?16–20) frameworks, a 4f electron does participate in bonding. It does this by transferring to the 5d orbital, which hybridizes with the 6s and 6p orbitals and then interacts with Si valence sp orbitals. Meanwhile, the total magnetic moments of the HoSi _n (n?=?16–20) clusters are considerably higher than those of HoSi _n (n?=?12–15). Interestingly, the endohedral HoSi₁₆ and HoSi₂₀ clusters can be viewed as the most suitable building blocks for novel high-density magnetic storage nanomaterials and for novel optical and optoelectronic photosensitive nanomaterials, respectively.     

Stability and electronic properties of praseodymium-doped silicon clusters PrSin (<Emphasis Type="Italic">n</Emphasis> = 12–21)

The neutral PrSi _n (n = 12–21) species considering various spin configurations were systematically studied using PBE0 and B3LYP schemes in combination with relativistic small-core potentials (ECP28MWB) for Pr atoms and cc-pVTZ basis set for Si atoms. The total energy, growth-pattern, equilibrium geometry, relative stability, hardness, charge transfer, and magnetic moments are calculated and discussed. The results reveal that when n < 20, the ground-state structure of PrSi _n evaluated to be prolate clusters. Starting from n = 20, the ground-state structures of PrSi _n are evaluated to be endohedral cagelike clusters. Although the relative stabilities based on various binding energies and different functional is different from each other, the consensus is that the PrSi₁₃, PrSi₁₆, PrSi₁₈, and PrSi₂₀ are more stable than the others, especially the PrSi₂₀. Analyses of hardness show that introducing Pr into Si _n (n = 12–21) elevates the photochemical sensitivity, especially for PrSi₂₀. Calculated result of magnetic moment and charge transfer shows that the 4f electrons of Pr in the clusters are changed, especially in endohedral structures such as PrSi₂₀, in which one electron transfers from 4f to 5d orbital. That is, the 4f electron of Pr in the clusters participates in bonding. The way to participate in bonding is that a 4f electron transfers to 5d orbital. Although the 4f electron of Pr atom participates in bonding, the total magnetic moment of PrSi _n is equal to that of isolated Pr atom. The charge always transfers from Pr atom to Si _n cluster for the ground state structures of PrSi_n (n = 12–19), but charge transfer is reverse for n ≥ 20. The largest charge transfer for endohedral structure reveals that the bonding between Pr and Si _n is ionic in nature and very strong. The fullerenelike structure of PrSi₂₀ is the most stable among all of these clusters and can act as the building blocks for novel functional nanotubes.     

Probing structure,thermochemistry, electron affinity,and magnetic moment of thulium-doped silicon clusters TmSi<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 3–10) and their anions with density functional theory

The most stable structures and electronic properties of TmSi _n (n?=?3–10) clusters and their anions have been probed by using the ABCluster global search technique combined with the PBE, TPSSh, and B3LYP density functional methods. The results revealed that the most stable structures of neutral TmSi _n and their anions can be regarded as substituting a Si atom of the ground state structure of Si _n?+?1 with a Tm atom. The reliable AEAs, VDEs and simulated PES of TmSi _n (n?=?3–10) are presented. Calculations of HOMO-LUMO gap revealed that introducing Tm atom to Si cluster can improve photochemical reactivity of the cluster. The NPA analyses indicated that the 4f electron of Tm atom in TmSi _n (n?=?3–10) and their anions do not participate in bonding. The total magnetic moments of TmSi _n are mainly provided by the 4f electrons of Tm atom. The dissociation energy of Tm atom from the most stable structure of TmSi _n and their anions has been calculated to examine relative stability.     

Modeling of Platinum Clusters in H-Mordenite

The size, location and structure of Pt clusters in H-mordenite have been investigated by molecular mechanics energy minimization and molecular dynamics simulation techniques using the Catalysis software of Molecular Simulations (MSI). Lattice energy minimizations are performed to study the effects of the specific framework aluminum positions on the location and stability of monoatomic Pt sites in H-mordenite. The lattice energies relative to the siliceous platinum-aluminosilicate structure reveal that the stability of a single Pt atom in H-mordenite is remarkably influenced by the specific location of the Al atoms in the lattice. At the studied Si/Al ratio of two Al ions per unit cell, a stabilization of the H-mordenite lattice upon Pt deposition is obtained. Moreover, lattice energy calculations on Pt/aluminosilicate mordenites of different metal contents per unit cell have been performed. An optimum size for the aggregate confined to the 12-ring main channel that is almost independent of the Pt content per mordenite unit cell has been found. The structural features of the resulting clusters at the end of molecular dynamics simulations on Pt/alumina-mordenites reflect a strong metal-zeolite interaction. The present results are consistent with a previous molecular dynamics simulation study on the structure of platinum deposited on SiO₂ surfaces.     

X-ray absorption analysis of the active site of Streptomyces antibioticus Tyrosinase upon binding of transition state analogue inhibitors

The key structural features that define the reaction mechanism of the binuclear copper enzyme Tyrosinase (Ty) from Streptomyces antibioticus were investigated by X-ray absorption spectroscopy. The data for the met form, the halide bound derivative and the adduct with the competitive inhibitor and transition state analogue Kojic acid were analysed using the recently developed MXAN package. This analysis permitted the definition of structural clusters that include all atoms within 5A from the metal ions of the active site. The data obtained for the different forms provide validation of the structural models previously proposed on the basis of the magnetic properties investigated by both pulsed EPR and paramagnetic NMR spectroscopies. The structural model of the reaction center obtained in this solution study is compared with the crystallographic structures recently proposed for several derivatives of bacterial Ty to suggest that only one of these structures is relevant to solution conditions.     

Stabilization of the cobalt coordination site in transmetalation processes on dinuclear salen derivatives

Two dinuclear cobalt/copper compounds have been isolated from the reaction between N,N′-ethylenebis(salicylideniminato)cobalt(II), [Co(salen)], and copper(II) chloride in different conditions. The first one is a dinuclear cobalt(III)/copper(II) derivative, [Co(salen)Cl₂Cu(EtOH)₂Cl], 1, that have the cobalt atom six-coordinated to the four donor atoms of the salen ligand and to two chlorine atoms in a slightly distorted octahedral environment and the copper atom five-coordinated to the two bridging oxygen atoms of the salen ligand, two ethanol molecules and one extra chlorine atom. This compound is the only reported example of a cobalt/copper derivative with the cobalt maintaining the salen coordinative site, since the usual reaction takes place by a transmetalation process. This reaction is observed in the second derivative, [Cu(salen)CoCl₂], 2, where the copper atom displaces the cobalt from the salen cavity. The copper atom adopts a square-planar coordinative environment, while the cobalt is tetrahedrically coordinated to the two bridging oxygen and two chlorine atoms. Both compounds present several intermolecular contacts that increase the dimensionality in the crystal and some of which can transmit magnetic interactions. The magnetic properties confirm the structural picture, with isolated copper(II) centres in 1, where the cobalt(III) is in the low spin form, and with antiferromagnetically coupled S = ¹/₂ and S = ³/₂ centres in 2.     

Bis(heptalene) “submarine” metal dimer sandwich compounds (C12H10)2M2 (M = Ti, V, Cr, Mn, Fe, Co, Ni)

The bis(heptalene)dimetal complexes (C₁₂H₁₀)₂M₂ of the first row transition metals from Ti to Ni are predicted by density functional theory to exhibit “submarine” sandwich structures with a pair of metal atoms sandwiched between the two heptalene rings. For the early transition metal derivatives (C₁₂H₁₀)₂M₂ (M = V, Cr) there are two types of such structures. In one structural type the metals are sandwiched between two heptahapto heptalene rings with metal-metal distances (3.5–3.8 Å) too long for direct metal-metal bonding. The other type of (C₁₂H₁₀)₂M₂ (M = V, Cr, Mn) structure has a pair of bonded metal atoms sandwiched between a fully bonded heptalene ligand and a heptalene ligand bonded to the metals only through an eight-carbon heptafulvene subunit, leaving an uncomplexed cis-1,3-diene unit. The formal metal-metal bond orders in these latter structures are 3, 2, and 1 for M = V, Cr, and Mn with predicted bond lengths of 2.5, 2.7, and 2.8 Å, respectively. For (C₁₂H₁₀)₂Fe₂ a singlet structure with each iron atom sandwiched between a hexahapto and a tetrahapto heptalene ring is energetically preferred over an alternate structure with ferrocene-like iron atoms sandwiched between two pentahapto heptalene rings. Partial bonding of each heptalene ring to the metal atoms occurs in the late transition metal derivatives (C₁₂H₁₀)₂M₂ (M = Co, Ni). This leads to an unsymmetrical structure for the cobalt derivative and a structure for the nickel derivative with each nickel atom sandwiched between a trihapto ligand and a tetrahapto ligand.

Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase

To understand the molecular mechanism underlying phosphoryl transfer of cAMP-dependent protein kinase, the structure of the catalytic subunit in complex with ADP, aluminum fluoride, Mg2+ ions and a substrate peptide was determined at 2.0 A resolution. Aluminum fluoride was modeled as AlF3 in a planar geometry; it is positioned 2.3 A from both the donor oxygen of ADP and the hydroxyl group of the recipient Ser residue. In this configuration, the aluminum atom forms a trigonal bipyramidal coordination with the oxygen atoms of the donor and recipient groups at the apical positions. This arrangement suggests that aluminum fluoride mimics the transition state and provides the first direct structural evidence for the in-line mechanism of phosphoryl transfer in a protein kinase.     

First-principle investigation on growth patterns and properties of cobalt-doped lithium nanoclusters

A systematic theoretical investigation on cobalt lithium clusters Li_nCo [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] was performed with a DFT approach. The location of global minima and structural evolution were carried out using the partical swarm optimization method. Li₆Co is the transition structure in going from low-coordinated structures to three-dimensional torispherical structures with a cobalt atom enclosed by lithium atoms. Maxima of ?₂ E and E _b for Li_nCo were found at n?=?3, 6, 8, 10, indicating that these clusters possess higher relative stability than their neighbors. In comparison with small clusters, n?=?1–6, the greater electron transfer from Li-2s to Co-3d within cage-like clusters Li_nCo (n?=?7–12) strengthens the bonding effect between Li_n and Co, which is reflected in the Wiberg bond index of Co and atomic binding energy analysis. AdNDP analysis verified the presence of both Lewis bonding elements (1c–2e objects) and delocalized bonding elements (6c–2e, 9c–2e and 10c–2e bonds). It is hoped that this theoretical work will provide favorable information to help understand the influence of dopant transition metal atoms on the properties of lithium-based materials.     

Structures, energies and bonding in neutral and charged Li microclusters

Structural and chemical properties of charged and neutral Lithium microclusters are investigated for [Formula: see text]. A total of 18 quantum conformational spaces are randomly walked to produce candidate structures for local minima. Very rich potential energy surfaces are produced, with the largest structural complexity predicted for anionic clusters. Analysis of the electron charge distributions using the quantum theory of atoms in molecules (QTAIM) predicts major stabilizing roles of Non-nuclear attractors (NNAs) via NNA···Li interactions with virtually no direct Li···Li interactions, except in the least stable configurations. A transition in behavior for clusters containing more than seven nuclei is observed by using the recently introduced quantum topology to determine in a quantum mechanically consistent fashion the number of spatial dimensions each cluster has. We experiment with a novel scheme for extracting persistent structural motifs with increase in cluster size. The new structural motifs correlate well with the energetic stability, particularly in highlighting the least stable structures. Quantifying the degree of covalent character in Lithium bonding independently agrees with the observation in the transition in cluster behavior for lithium clusters containing more than seven nuclei. Good correlation with available experimental data is obtained for all properties reported in this work.     

Transition from exo- to endo- Cu absorption in CuSi(n) clusters: A Genetic Algorithms Density Functional Theory (DFT) Study

The characterization and prediction of the structures of metal silicon clusters is important for nanotechnology research because these clusters can be used as building blocks for nano devices, integrated circuits and solar cells. Several authors have postulated that there is a transition between exo to endo absorption of Cu in Si(n) clusters and showed that for n larger than 9 it is possible to find endohedral clusters. Unfortunately, no global searchers have confirmed this observation, which is based on local optimizations of plausible structures. Here we use parallel Genetic Algorithms (GA), as implemented in our MGAC software, directly coupled with DFT energy calculations to show that the global search of CuSi(n) cluster structures does not find endohedral clusters for n < 8 but finds them for n ≥ 10.     

A first-principles study of Ni<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>Pd<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (n = 1 − 5) clusters

A first-principle investigation of structures and properties of Ni _n Pd _n (n=1-5) clusters is presented. For this study, the linear combination of Gaussian-type orbitals auxiliary density functional theory (LCGTO-ADFT) method has been employed. In order to determine the lowest energy structures, several isomers in different spin multiplicities were studied, for each cluster size. Initial structures, for which successive geometry optimization was computed without any constrain, were taken along Born–Oppenheimer molecular dynamics (BOMD) trajectories. To discriminate between minima and transition state structures, harmonic frequency analyses were performed at the optimized structures. Ground state structures, bond lengths, harmonic frequencies, dissociation energy, ionization potential, electron affinity and spin density plots are presented. This work demonstrates, that the Pd atoms prefer to allocate on the surface of the cluster structures whose core is formed by the 3d TM atoms type. Moreover, it has been observed that the ground-state structure spin multiplicity increases as the system size grows. The results of this study contribute to gain insight into how structures and energy properties change with cluster size in bimetallic Pd-based alloys.     

Molecular dynamics simulation of melting and crystallization processes of polyethylene clusters confined in armchair single-walled carbon nanotubes

The confined interaction is important to understand the melting and crystallization of polymers within single-wall carbon tube (SWNT). However, it is difficult for us to observe this interaction. In the current work, the structures and behaviors of melting and crystallization for polyethylene (PE) clusters confined in armchair single-walled carbon nanotubes ((n,n)-SWNTs) are investigated and examined based on molecular dynamics (MD) simulations. The nonbonded energies, structures, Lindemman indices, radial density distributions, and diffusion coefficients are used to demonstrate the features of melting phase transition for PE clusters confined in (n,n)-SWNTs. The chain end-to-end distance (R _n) and chain end-to-end distribution are used to examine the flexibility of the PE chain confined in SWNT. The global orientational order parameter (P₂) is employed to reveal the order degree of whole PE polymer. The effect of polymerization degree on melting temperature and the influence of SWNT chirality on structure of PE cluster are examined and discussed. Results demonstrate that within the confined environment of SWNT, PE clusters adopt novel co-axial crystalline layer structure, in which parallel chains of each layer are approximately vertical to tube axis. The disordered-ordered transformation of PE chains in each layer is an important structural feature for crystallization of confined PE clusters. SWNTs have a considerable effect on the structures and stabilities of the confined PE clusters.     

Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model

The src SH3 domain has been known to be a two-state folder near room temperature. However, in a previous study with an all-atom model simulation near room temperature, the transition state of this protein was not successfully detected on a free-energy profile using two axes: the radius of gyration (R(g)) and native contact reproduction ratio (Q value). In this study, we focused on an atom packing effect to characterize the transition state and tried another analysis to detect it. To explore the atom packing effect more efficiently, we introduced a charge-neutralized all-atom model, where all of the atoms in the protein and water molecules were treated explicitly, but their partial atomic charges were set to zero. Ten molecular dynamics simulations were performed starting from the native structure at 300 K, where the simulation length of each run was 90 ns, and the protein unfolded in all runs. The integrated trajectories (10 x 90 = 900 ns) were analyzed by a principal component analysis (PCA) and showed a clear free-energy barrier between folded- and unfolded-state conformational clusters in a conformational space generated by PCA. There were segments that largely deformed when the conformation passed through the free-energy barrier. These segments correlated well with the structural core regions characterized by large phi-values, and the atom-packing changes correlated with the conformational deformations. Interestingly, using the same simulation data, no significant barrier was found in a free-energy profile using the R(g) and Q values for the coordinate axes. These results suggest that the atom packing effect may be one of the most important determinants of the transition state.     

Structure and energetics of small iron clusters

Electronic properties of Fe(2-10) clusters and their ions are described by an all-electron ab initio density functional theory computational analysis using the Handy's OPTX exchange and the gradient-corrected correlation functional of Perdew, Burke and Ernzerhof with a triple-zeta valence basis set plus polarization functions. Ground state structures, magnetic moments, dissociation energies, binding energies, IR vibrational spectra, vertical and adiabatic ionization energies, and electron affinities are reported. Two possible states for Fe(2) which are separated by 81.54 meV are described as possible Fe(2), while the septet (ground state) yields an accurate bond distance (error of 0.02??); the nonet yields a precise vibrational frequency (error of 10.1?cm(-1)). Fe(2) binding energy (0.05 eV/atom error) more closely resembles experimental data than any other previously reported computational methods. In addition, the Fe(6) is found to be the most stable cluster within our set being analyzed.     

A consensus-binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine-containing complexes

Attempts to derive structural features of ligand-binding sites have traditionally involved seeking commonalities at the residue level. Recently, structural studies have turned to atomic interactions of small molecular fragments to extract common binding-site properties. Here, we explore the use of larger ligand elements to derive a consensus binding structure for the ligand as a whole. We superimposed multiple molecular structures from a nonredundant set of adenosine-5'-triphosphate (ATP) protein complexes, using the adenine moiety as template. Clustered binding-site atoms of compatible atomic classes forming attractive contacts with the adenine probe were extracted. A set of atomic clusters characterizing the adenine binding pocket was then derived. Among the clusters are three vertices representing the interactions of adenine atom N6 with its protein-binding niche. These vertices, together with atom C6 of the purine ring system, complete the set of four vertices for the pyramid-like structure of the N6 anchor atom. Also, the sequence relationship for the adenine-binding loop interacting with the C2-N6 end of the conjugated ring system is expanded to include a third hydrophilic cluster interacting with atom N1. A search procedure involving interatomic distances between cluster centers was formulated and applied to seek putative binding sites in test cases. The results show that a consensus network of clusters, based on an adenine probe and an ATP-complexed training set of proteins, is sufficient to recognize the experimental cavity for adenine in a wide spectrum of ligand-protein complexes.     

Application of electron energy loss spectroscopy and electron spectroscopic imaging to aluminum determination in biological tissue

Electron energy loss spectroscopy (EELS) is a high spatial resolution electron microscopic technique with the potential to quantify elements at the subcellular level. The presence of each element is demonstrated by the electron energy loss edge at the energy characteristic of that element. The area of the edge may indicate the quantity of element present. Electron spectroscopic imaging (ESI) is a similar technique generating graphic images of elemental localization in the specimens. An ESI of an aluminum (Al)-loaded rabbit hippocampus showed Al only in pyramidal cell lysosomes, but no EELS edge could be obtained. To determine the sensitivity of EELS for Al and to be able to adjust the instrument to optimal operating conditions, standards containing 50–5000 ppm Al were produced. An Al-chloride:dicyclohexano-18-crown-6 (Al:crown) complex was synthesized. The purity of the complex was confirmed by nuclear magnetic resonance (NMR) spectroscopy and the percentage of Al in the complex was determined by electrothermal atomic absorption spectroscopy (ETAAS). The complex was introduced into a biological tissue embedding resin (Spurr medium) and appeared to be compatible with the resin at Al concentrations ≤500 ppm. EELS signals from the Al K edge could be obtained at a spatial resolution of 3.3 nm in a 30-nm thick section from 2.78×10^?21 g of Al, representing a sample concentration of 1% Al.