Binding of gold clusters with DNA base pairs: a density functional study of neutral and anionic GC-Aun and AT-Aun (n = 4, 8) complexes

Binding of clusters of gold atoms (Au) with the guanine-cytosine (GC) and adenine-thymine (AT) Watson-Crick DNA base pairs was studied using the density functional theory (DFT). Geometries of the neutral GC-Au(n) and AT-Au(n) and the corresponding anionic (GC-Au(n))(-1) and (AT-Au(n))(-1) (n = 4, 8) complexes were fully optimized in different electronic states, that is, singlet and triplet states for the neutral complexes and doublet and quartet states for the anionic complexes, using the B3LYP density functional method. The 6-31+G basis set was used for all atoms except gold. For gold atoms, the Los Alamos effective core potential (ECP) basis set LanL2DZ was employed. Vibrational frequency calculations were performed to ensure that the optimized structures corresponded to potential energy surface minima. The gold clusters around the neutral GC and AT base pairs have a T-shaped structure, which satisfactorily resemble those observed experimentally and in other theoretical studies. However, in anionic GC and AT base pairs, the gold clusters have extended zigzag and T-shaped structures. We found that guanine and adenine have high affinity for Au clusters, with their N3 and N7 sites being preferentially involved in binding with the same. The calculated adiabatic electron affinities (AEAs) of the GC-Au(n)complexes (n = 4, 8) were found to be much larger than those of the isolated base pairs.     

A photoelectron spectroscopic and computational study of sodium auride clusters, NanAun- (n = 1-3)

Negatively charged sodium auride clusters, NanAun- (n = 1-3), have been investigated experimentally using photoelectron spectroscopy and ab initio calculations. Well-resolved electronic transitions were observed in the photoelectron spectra of NanAun- (n = 1-3) at several photon energies. Very large band gaps were observed in the photoelectron spectra of the anion clusters, indicating that the corresponding neutral clusters are stable closed-shell species. Calculations show that the global minimum of Na2Au2- is a quasi-linear species with Cs symmetry. A planar isomer of D2h symmetry is found to be 0.137 eV higher in energy. The two lowest energy isomers of Na3Au3- consist of three-dimensional structures of Cs symmetry. The global minimum of Na3Au3- has a bent-flake structure lying 0.077 eV below a more compact structure. The global minima of the sodium auride clusters are confirmed by the good agreement between the calculated electron detachment energies of the anions and the measured photoelectron spectra. The global minima of neutral Na2Au2 and Na3Au3 are found to possess higher symmetries with a planar four-membered ring (D2h) and a six-membered ring (D3h) structure, respectively. The chemical bonding in the sodium auride clusters is found to be highly ionic with Au acting as the electron acceptor.     

计算机模拟原子簇的稳定构型和能量性质

用密度泛函(DFT)方法研究了铜原子簇Cu~n(n=2,3,4,6)的稳定几何构型和电子结构。通过拟合从头算势能面构造铜原子簇势能函数的双体、三体及四体项,并利用该函数和全局优化“Basin-Hopping”算法得到较大铜原子簇(n=13～56)能量极小的结构,计算结果与实验及其它计算结果相一致。     

Structure evolution of gold cluster anions between the planar and cage structures by isoelectronic substitution: Au(n)- (n = 13-15) and MAu(n)- (n = 12-14; M = Ag, Cu)

The structural and electronic effects of isoelectronic substitution by Ag and Cu atoms on gold cluster anions in the size range between 13 and 15 atoms are studied using a combination of photoelectron spectroscopy and first-principles density functional calculations. The most stable structures of the doped clusters are compared with those of the undoped Au clusters in the same size range. The joint experimental and theoretical study reveals a new C(3v) symmetric isomer for Au(13)(-), which is present in the experiment, but has hitherto not been recognized. The global minima of Au(14)(-) and Au(15)(-) are resolved on the basis of comparison between experiment and newly computed photoelectron spectra that include spin-orbit effects. The coexistence of two isomers for Au(15)(-) is firmly established with convincing experimental evidence and theoretical calculations. The overall effect of the isoelectronic substitution is minor on the structures relative to those of the undoped clusters, except that the dopant atoms tend to lower the symmetries of the doped clusters.     

Structure, bonding, and linear optical properties of a series of silver and gold nanorod clusters: DFT/TDDFT studies

DFT/TDDFT calculations have been carried out for a series of silver and gold nanorod clusters (Ag(n), Au(n), n = 12-120) whose structures are of cigar-type. Pentagonal Ag(n) clusters with n = 49-121 and hexagonal Au(n) clusters with n = 14-74 were also calculated for comparison. Metal-metal distances, binding energies per atom, ionization potentials, and electron affinities were determined, and their trends with cluster size were examined. The TDDFT calculated excitation energies and oscillator strengths were fit by a Lorentz line shape modification, which gives rise to the simulated absorption spectra. The significant features of the experimental spectra for actual silver and gold nanorod particles are well reproduced by the calculations on the clusters. The calculated spectral patterns are also in agreement with previous theoretical results on different-type Ag(n) clusters. Many differences in the calculated properties are found between the Ag(n) and Au(n) clusters, which can be explained by relativistic effects.     

Enhanced stability by three-dimensional aromaticity of endohedrally doped clusters X(10)M(0/-) with X = Ge, Sn, Pb and M = Cu, Ag, Au

The group 14 clusters encapsulated by coinage metals in neutral and anionic states X(10)M(0/-) (X = Ge, Sn, Pb and M = Cu, Ag, Au) are investigated using quantum chemical calculations with the DFT/B3LYP functional and coupled-cluster CCSD(T) theory. Addition of transition metals into the empty cages forms high symmetry endohedral structures, except for Ge(10)Ag(0/-). In agreement with experiments available for X(10)Cu, the D(4d) global minima of the anions are calculated to be magic clusters with large frontier orbital gaps, high vertical and adiabatic detachment energies, and large embedding energies and binding energies as compared to those of the empty cages X(10)(2-). The enhanced stability of these magic clusters can be rationalized by the three-dimensional aromaticity.     

Surface bonding and dynamical behavior of the CH3SH molecule on Au(111)

The chemisorption of the undissociated CH3SH molecule on the Au(111) surface has been studied at 5 K using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The molecule was found to adsorb on atop Au sites on the defect-free surface. CH3SH undergoes hindered rotation about the Au-S bond on the defect-free surface which is seen in STM as a time-averaged 6-fold pattern. The pattern suggests that the potential minima directions occur for the rotating molecule at the six hollow sites surrounding the atop adsorption site. The barrier for rotation, obtained by DFT calculations, is approximately 0.1 kcal.mol(-1). At low coverages, preferential adsorption occurs at defect sites in the surface, namely, the herringbone "elbows" and random atomic step sites. Molecules adsorbed on these sites do not exhibit rotational freedom.     

Interaction between benzenedithiolate and gold: classical force field for chemical bonding

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.     

Adsorption energies of molecular oxygen on Au clusters

The adsorption properties of O(2) molecules on anionic, cationic, and neutral Au(n) clusters (n=1-6) are studied using the density functional theory (DFT) with the generalized gradient approximation (GGA), and with the hybrid functional. The results show that the GGA calculations with the PW91 functional systemically overestimate the adsorption energy by 0.2-0.4 eV than the DFT ones with the hybrid functional, resulting in the failure of GGA with the PW91 functional for predicting the adsorption behavior of molecular oxygen on Au clusters. Our DFT calculations with the hybrid functional give the same adsorption behavior of molecular oxygen on Au cluster anions and cations as the experimental measurements. For the neutral Au clusters, the hybrid DFT predicts that only Au(3) and Au(5) clusters can adsorb one O(2) molecule.     

Mechanistic Insights into the Formation of Lithium Fluoride Nanotubes

Born–Oppenheimer molecular dynamics (BOMD) and periodic density functional theory (DFT) calculations have been applied for describing the mechanism of formation of lithium fluoride (LiF) nanotubes with cubic, hexagonal, octagonal, decagonal, dodecagonal, and tetradecagonal cross-sections. It has been shown that high energy structures, such as nanowires, nanorings, nanosheets, and nanopolyhedra are transient species for the formation of stable nanotubes. Unprecedented (LiF)_n clusters (n≤12) were also identified, some of them lying less than 10 kcal mol^−[1] above their respective global minima. Such findings indicate that stochastic synthetic techniques, such as laser ablation and chemical vapor deposition, should be combined with a template-driven procedure in order to generate the nanotubes with adequate efficiency. Apart from the stepwise growth of LiF units, the formation of nanotubes was also studied by rolling up a planar square sheet monolayer, which could be hypothetically produced from the exfoliation of the FCC crystal structure. It was shown that both pathways could lead to the formation of alkali halide nanotubes, a still unprecedented set of one-dimensional materials.     

A DFT Investigation on the Electronic Structures and Au Adatom Assisted Hydrogenation of Graphene Nanoflake Array

Graphene nanoribbons with zigzag edges(ZGNRs) have attracted much attention for their spin-polarized edge states predicted more than 15 years ago. Since the ZGNRs are fabricated on metal substrates using molecular precursors, due to their strong coupling with metal substrates, experimental detection of the spin-polarized edge states is still difficult. Here, we design a partially hydrogenated graphene(PHGr), in which periodic hexagonal graphene nanoflakes(GNFs) with zigzag boundaries are embedded in a hydrogenated graphene layer. Using density functional theory(DFT) based first-principles calculations, we find that the hexagonal GNFs exhibit spin-polarized boundary states at their opposite zigzag boundaries, which is similar with the bow-tie-shaped GNFs and ZGNRs. DFT calculations demonstrate that the PHGr is a semiconductor with an antiferromagnetic ground state. Moreover, the antiferromagnetic boundary states and semiconduc-ting properties keep unchanged when the size of GNF varies from 1.4 nm to 2.3 nm. The robustness of the spin-polarized boundary states enables this PHGr as a robust material for detecting spin-polarized boundary states coming from zigzag boundaries. In addition, we find that single Au atoms selectively adsorbed on boundaries catalyze H₂ dissociation and therefore lower the barrier of graphene hydrogenation. Therefore, the PHGr can be used not only in carbon-based spintronic devices but also as a platform for single atom catalyst.     

Critical examination of the supermolecule density functional theory calculations of intermolecular interactions

The results of calculations employing twelve different combinations of exchange and correlation functionals are compared with results of ab initio calculations for two different configurations of the water dimer and three different configurations of the thymine-adenine complex. None of the density functional theory (DFT) treatments could properly reproduce the results of coupled-cluster calculations for all configurations examined. The DFT approaches perform well when the interaction energy is dominated by the electrostatic component and the dispersion energy is less important. Two mechanisms that compensate for the missing dispersion component were identified. The first one is the decrease of the magnitude of the intermolecular exchange-repulsion and the second one is the increase of the magnitude of the attractive deformation energy. For some functionals both effects are observed together, but for some other ones only the second effect occurs. The three correlation functionals that were examined were found to make only very small contributions to the deformation energy. The examination of angular and distance dependence of the interactions shows that the currently available DFT approaches are not suitable for developing intermolecular potential energy surfaces. They could however be used to find global minima on potential energy surfaces governed by intermolecular electrostatic interactions. Additional single point ab initio calculations are recommended as the means of validating optimized structures.     

Formation of Pd/Au nanostructures from Pd nanowires via galvanic replacement reaction

Bimetallic nanostructures with non-random metal atoms distribution are very important for various applications. To synthesize such structures via benign wet chemistry approach remains challenging. This paper reports a synthesis of a Au/Pd alloy nanostructure through the galvanic replacement reaction between Pd ultrathin nanowires (2.4 +/- 0.2 nm in width, over 30 nm in length) and AuCl3 in toluene. Both morphological and structural changes were monitored during the reaction up to 10 h. Continuous changes of chemical composition and crystalline structure from Pd nanowires to Pd68Au32 and Pd45Au55 alloys, and to Au nanoparticles were observed. More interestingly, by using combined techniques such as high-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), energy dispersive X-ray spectrometry (EDS), UV-vis absorption, and extended X-ray absorption fine structure (EXAFS) spectroscopy, we found the formation of Pd68Au32 non-random alloy with Au-rich core and Pd-rich shell, and random Pd45Au55 alloy with uniformly mixed Pd and Au atom inside the nanoparticles, respectively. Density functional theory (DFT) calculations indicated that alkylamine will strongly stabilize Pd to the surface, resulting in diffusion of Au atoms into the core region to form a non-random alloy. We believe such benign synthetic techniques can also enable the large scale preparation of various types of non-random alloys for several technically important catalysis applications.     

Global optimization and the energy landscapes of Dzugutov clusters

The global minima of clusters bound by a Dzugutov potential form non-compact polytetrahedral clusters mainly composed of interpenetrating and face-sharing 13-atom icosahedra. As the size increases, these icosahedral units first form linear arrays, then two-dimensional rings, then three-dimensional networks. Characterization of the energy landscapes of these clusters shows that they are particularly rough and generally exhibit a multiple-funnel topography. These results provide new insights into the structure and dynamics of bulk supercooled Dzugutov liquids and the form of the bulk phase diagram.     

Structures of mixed gold-silver cluster cations (Ag(m)Au(n)+, m+n<6): ion mobility measurements and density-functional calculations

The collision cross sections of Ag(m)Au(n)+ (m+n)<6 cluster ions were determined. For bimetallic clusters, we observe a significant intracluster charge transfer leaving most of the ions positive charge on the silver atoms. The mixed trimeric ions Ag2Au+ and AgAu2+ are triangular like the pure gold and silver trimers. Most of the tetrameric clusters are rhombus shaped, with the exception of Ag3Au+, which has a Y structure with the gold atom in the center. Among the pentamers we find distorted X structures for all systems. For Ag2Au3+ we find an additional isomer which is a trigonal bipyramid. These findings are in line with predictions based on density-functional theory calculations, i.e., all these structures either represent the global minima or are within less than 0.1 eV of the predicted global minimum.     

Geometry optimization of atomic clusters using a heuristic method with dynamic lattice searching

In this paper, a global optimization method is presented to determine the global-minimum structures of atomic clusters, where several already existing techniques are combined, such as the dynamic lattice searching method and two-phase local minimization method. The present method is applied to some selected large-sized Lennard-Jones (LJ) clusters and silver clusters described by the Gupta potential in the size range N = 13-140 and 300. Comparison with the results reported in the literature shows that the method is highly efficient and a lot of new global minima missed in previous papers are found for the silver clusters. The method may be a promising tool for the theoretical determination of ground-state structure of atomic clusters. Additionally, the stabilities of silver clusters are also analyzed and it is found that in the size range N = 13-140 there exist 12 particularly stable clusters.     

Challenges in the simulation of dye-sensitized ZnO solar cells: quantum confinement, alignment of energy levels and excited state nature at the dye/semiconductor interface

We report a first principles density functional theory/time-dependent density functional theory (DFT/TDDFT) computational investigation on a prototypical perylene dye anchored to realistic ZnO nanostructures, approaching the size of the ZnO nanowires used in dye-sensitized solar cells devices. DFT calculations were performed on (ZnO)(n) clusters of increasing size, with n up to 222, of 1.3 × 1.5 × 3.4 nm dimensions, and for the related dye-sensitized models. We show that quantum confinement in the ZnO nanostructures substantially affects the dye/semiconductor alignment of energy levels, with smaller ZnO models providing unfavourable electron injection. An increasing broadening of the dye LUMO is found moving to larger substrates, substantially contributing to the interfacial electronic coupling. TDDFT excited state calculations for the investigated dye@(ZnO)(222) system are fully consistent with experimental data, quantitatively reproducing the red-shift and broadening of the visible absorption spectrum observed for the ZnO-anchored dye compared to the dye in solution. TDDFT calculations on the fully interacting system also introduce a contribution to the dye/semiconductor admixture, due to configurational excited state mixing. Our results highlight the importance of quantum confinement in dye-sensitized ZnO interfaces, and provide the fundamental insight lying at the heart of the associated DSC devices.     

Molecular dynamics simulations of stretched gold nanowires: the relative utility of different semiempirical potentials

The mechanical elongation of a finite gold nanowire has been studied by molecular dynamics simulations using different semiempirical potentials for transition metals. These potentials have been widely used to study the mechanical properties of finite metal clusters. Combining with density functional theory calculations along several atomic-configuration trajectories predicted by different semiempirical potentials, the authors conclude that the second-moment approximation of the tight-binding scheme (TB-SMA) potential is the most suitable one to describe the energetics of finite Au clusters. They find that for the selected geometries of Au wires studied in this work, the ductile elongation of Au nanowires along the [001] direction predicted by the TB-SMA potential is largely independent of temperature in the range of 0.01-298 K. The elongation leads to the formation of monatomic chains, as has been observed experimentally. The calculated force-versus-elongation curve is remarkably consistent with available experimental results.     

Effect of adsorption site, size, and composition of Pt/Au bimetallic clusters on the CO frequency: a density functional theory study

Density functional theory (DFT) calculations were performed to investigate the C-O stretching frequency changes when a CO molecule was adsorbed to Pt/Au clusters of 2-4 atoms. Our calculations show that the adsorption site is the most sensitive quantity to the C-O stretching frequency shifts. All the bridge site adsorptions yield a CO frequency band of 1737-1927 cm-1 with the CO bond distance of 1.167-1.204 A regardless of cluster composition and size, and all the atop site adsorptions yield a CO frequency band of 2000-2091 cm-1 with the CO bond distance of 1.151-1.167 A. More detailed analysis of the two frequency bands shows that each band may consist of two emerging subbands with the lower frequencies corresponding to the CO adsorption to Pt atoms and the higher frequencies to the CO adsorption to Au atoms. The insensitivity of the CO frequency shift to the cluster size indicates that the trend discussed here for small clusters may be used to interpret the experimental observations for nanoparticles. Our results also illustrated that the Fourier transform infrared spectroscopy measurement may be used as a sensitive tool to identify adsorption sites of the Pt/Au nanoparticles using CO adsorption as the probe.