Rest Atoms Research Articles

Mechanistic Insights into Nonadiabatic Interband Transitions on a Semiconductor Surface Induced by Hydrogen Atom Collisions.

To understand the recently observed enigmatic nonadiabatic energy transfer for hyperthermal H atom scattering from a semiconductor surface, Ge(111)c(2 × 8), we present a mixed quantum-classical nonadiabatic molecular dynamics model based on the time-dependent evolution of Kohn-Sham orbitals and a classical path approximation. Our results suggest that facile nonadiabatic electronic transitions from the valence band to the conduction band occur selectively at the rest atom site, where surface states are doubly occupied, but not at the adatom site, where empty surface states are localized. This drastic site specificity can be attributed to the changes of the local band structure upon energetic H collisions at different surface sites, leading to transient near degeneracies and significant couplings between occupied and unoccupied orbitals at the rest atom but not at the adatom. These insights shed valuable light on the collision-induced nonadiabatic dynamics at semiconductor surfaces.

Clarification of Au dimer adsorption sites on Si (111)-7 × 7 surface by AFM/KPFM

Atomic-scale surface adsorption has been a significant research topic in recent years, with a particular emphasis on the adsorption properties of Au/Si(111)-7 × 7, which are vitally important for pioneering future novel semiconductor devices. Here, we investigated the adsorption of Au dimers on the Si(111)-7 × 7 surface with atomic resolution using non-contact atomic force microscopy and Kelvin probe force microscopy at room temperature. Our results show that the Au dimer adsorbs in the vicinity of the Si rest atoms, exhibiting a distinct localized electron distribution. In density functional theory calculations, three candidate Au dimer adsorption sites have been identified, and the most stable site of Au dimer adsorption aligns with experimental findings. Furthermore, the local electron transfer of Au dimer adsorption has been analyzed, confirming the distribution of electrons around the Au dimer adsorption site. This research reveals that the structure and charge transfer of adsorbed Au dimers on Si(111)-7 × 7 provide insight into the mechanism of the metal-semiconductor system.

New insight on the role of localisation in the electronic structure of the Si(111)(7\u2009\xd7\u20097) surfaces

New angle-resolved photoelectron spectroscopy (ARPES) data, recorded at several different photon energies from the Si(111)(7 × 7) surface, show that the well-known S1 and S2 surface states that lie in the bulk band gap are localised at specific (adatom and rest atom) sites on the reconstructed surface. The variations in the photoemission intensity from these states as a function of polar and azimuthal emission angle, and incident photon energy, are not consistent with Fermi surface mapping but are well-described by calculations of the multiple elastic scattering in the final state. This localisation of the most shallowly bound S1 state is consistent with the lack of significant dispersion, with no evidence of Fermi surface crossing, implying that the surface is not, as has been previously proposed, metallic in character. Our findings highlight the importance of final state scattering in interpreting ARPES data, an aspect that is routinely ignored and can lead to misleading conclusions.

Efficient Embedded Cluster Density Approximation Calculations with an Orbital-Free Treatment of Environments.

The computational cost of the Kohn-Sham density functional theory (KS-DFT), employing advanced orbital-based exchange-correlation (XC) functionals, increases quickly for large systems. To tackle this problem, we recently developed a local correlation method in the framework of KS-DFT: the embedded cluster density approximation (ECDA). The aim of ECDA is to obtain accurate electronic structures in an entire system. With ECDA, for each atom in a system, we define a cluster to enclose that atom, with the rest atoms treated as the environment. The system's electron density is then partitioned among the cluster and the environment. The cluster's XC energy density is then calculated based on its electron density using an advanced orbital-based XC functional. The system's XC energy is obtained by patching all clusters' XC energy densities in an atom-by-atom manner. In our previous formulation of ECDA, environments were treated by KS-DFT, which makes the following two tasks computationally expensive for large systems. The first task is to partition the system's electron density among a cluster and its environment. The second task is to solve the environments' Sternheimer equations for calculating the system's XC potential. In this work, we remove these two computational bottlenecks by treating the environments with the orbital-free (OF) DFT. The new method is called ECDA-envOF. The performance of ECDA-envOF is examined in two systems: ester and Cl-tetracene, for which the exact exchange (EXX) is used as the advanced XC functional. We show that ECDA-envOF gives results that are very close to the previous formulation in which the environments were treated by KS-DFT. Therefore, ECDA-envOF can be used for future large-scale simulations. Another focus of this work is to examine ECDA-envOF's performance on systems having different bond types. With ECDA-envOF, we calculate the energy curves for stretching/compressing some covalent, metallic, and ionic systems. ECDA-envOF's predictions agree well with the benchmarks by using reasonably large clusters. These examples demonstrate that ECDA-envOF is nearly a black-box local correlation method for investigating heterogeneous materials in which different bond types exist.

Adsorption of Acetonitrile on Si(111)-(7 × 7).

The adsorption of acetonitrile (CH3CN) on Si(111)-(7 × 7) at a room temperature has been investigated using scanning tunneling microscopy (STM) and first-principles calculations. The site-specific information on adsorption enables us to understand the site-by-site and step-by-step adsorption mechanism. From theoretical simulations, the most stable configuration of CH3CN on Si(111)-(7 × 7) is found to be a molecularly chemisorbed CH3CN with the carbon and nitrogen atoms of CN bonded to the rest atom and adatom on the Si surface, respectively. Some chemisorption-induced features in the STM topographic image are assigned based on the theoretical calculations.

Electronic Properties of Artificial Metal‐DNA Base Pair Complexes Formed from Hydroxypyridone Base

AbstractThe metal‐mediated hydroxypyridone base pairs containing Ni2+, Cu2+, Zn2+, Pd2+, Cd2+, Pt2+, and Hg2+ ions were designed theoretically using by density functional theory (DFT) method in Gaussian 09 program. The calculations which were performed in the gas phase, methanol, water, and formamide were done at B3LYP functional with LANL2DZ and 6–311++G (d, p) basis sets which were used metals and rest atoms, respectively. The Gibbs free energies of the complexes were calculated and their relative stabilities were determined in the mentioned fields. Furthermore, geometric parameters, HOMO, LUMO, energy gap energies of the compounds were computed in all media and effect on these parameters of solvents were determined. Based on these parameters, the relative conductivities of the investigated molecules were predicted. On the other hand, using Atomistix ToolKit (ATK‐VNL) 2016 program, nonequilibrium Green's function (NEGF) calculations based on the combination DFT of the mentioned complexes were carried out. The transport properties of the molecules were found in detailed via NEGF‐DFT method.

Hydrogen adsorption induced nanomagnetism at the Si(111)- (7×7) surface

The creation of magnetism on non-magnetic semiconductor surfaces is of importance for the realization of spintronics devices. Especially, the coupling of electron spins within quantum nanostructures can be utilized for nanomagnetism applications. Here, we demonstrate, based on first-principles density-functional theory calculations, that the adsorption of H atoms on the Si(111)-(7$\times$7) surface induces the spin polarization of surrounding Si dangling bonds (DBs) and their spin orderings. It is revealed that the H adsorption on a rest-atom site exhibits a Jahn-Teller-like distortion that accompanies a charge transfer from the rest atom to the nearest neighboring adatoms. This charge transfer increases the local density of states of such three adatoms at the Fermi level, thereby inducing a Stoner-type instability to produce a ferrimagnetic order of adatom DBs around the adsorbed H atom. Meanwhile, the H adsorption on an adatom site cannot induce spin polarization, but, as adsorbed H atoms increase, the ferrimagnetic order of rest-atom DBs emerges through the charge transfer from rest atoms to adatoms. Our findings provide a microscopic mechanism of the H-induced spin orderings of Si DBs at the atomic scale, which paves a novel way to the design of nanoscale magnetism in the representative semiconductor surface.

Investigations of structural, spectral, electronic and biological properties of N-heterocyclic carbene Ag(I) and Pd(II) complexes

Computational analyses of two Ag(I) and two Pd(II) complexes were done. Benchmark analyses were performed to obtain the most appropriate calculation level for studied complexes. HF, B3LYP and M062× method were selected as calculation method. As for the basis set, lanl2dz, 6-31G, 6-31G(d) and 6-31G(d,p) were selected. LANL2DZ was used for metal atoms and the others were for the rest atoms in related molecules. The most appropriate calculation level was determined as B3LYP/6-31G(d)(LANL2DZ). Structural and spectral analyses (IR, UV-VIS and NMR) were performed. Additionally, non-linear optical (NLO) properties and biological properties were investigated and examined in detail. According to calculation results, complex (4) was found as the best candidate for NLO applications. Additionally, complex (4) was found as the best candidate for lung cancer drug.

Energy dissipation unveils atomic displacement in the noncontact atomic force microscopy imaging ofSi(111)−(7×7)

The kinetic energy of the oscillating cantilever of noncontact atomic force microscopy (nc-AFM) at room temperature was considerably dissipated over regions between a Si adatom and its neighboring rest atom for $\text{Si}(111)\text{\ensuremath{-}}(7\ifmmode\times\else\texttimes\fi{}7)$ in close proximity to a Si tip on the cantilever. However, nc-AFM topographic images showed no atomic features over those regions, which were the hollow sites of the $(7\ifmmode\times\else\texttimes\fi{}7)$. This energy dissipation likely originated from displacement of Si adatoms with respect to the tip over the hollow sites, leading to a lateral shift of the adatoms toward the rest atom. This interaction led to hysteresis over each cantilever oscillation cycle; when the tip was retracted, the Si adatom likely returned to its original position. To confirm the atomic processes involved in the force interactions through Si dangling bonds, the $\text{Si}(111)\text{\ensuremath{-}}(7\ifmmode\times\else\texttimes\fi{}7)$ surface was partly terminated with atomic hydrogen (H) and examined by nc-AFM. When the Si adatoms and/or the rest atoms were terminated with H, the hollow sites were not bright (less dissipation) in images of the energy dissipation channels by nc-AFM. The hollow sites acted as metastable sites for Si adatoms in surface diffusion and atom manipulation; thus, the dissipation energy which is saturated on the tip likely corresponds to the difference in the potential energy between the hollow site and the Si adatom site. In this study, we demonstrated the ability of dissipation channels of nc-AFM to enable visualization of the dynamics of atoms and molecules on surfaces, which cannot be revealed by nc-AFM topographic images alone.

Construction, physical properties and applications of low-dimensional atomic/molecular crystals

In this article, we review the representative work that has been done by Hong-Jun Gao's group in the past two decades in Institute of Physics, Chinese Academy of Sciences. The work focuses on the construction, properties and applications of low-dimensional atomic/molecular crystals, covering the following 3 aspects. 1) Construction and growth mechanisms of low-dimensional quantum structures. Firstly, we demonstrate the fabrication and growth mechanism of a seahorse shaped fractal pattern in C60-TCNQ multilayer thin films by using the ionized-cluster-beam method. Secondly, by modifying the tip of the scanning tunneling microscope (STM), we clearly resolve the six rest atoms and twelve adatoms on a Si(111)-77 unit cell, showing the highest-resolution STM images of the Si(111)-77 surface. According to this work, we investigate the adsorption and bonding of Ge atoms on Si(111)-77 at low coverages. The configurations and growth behaviors of iron phthalocyanine molecules on Au(111) surface from sub-monolayer to bilayer are also reviewed. Furthermore, we demonstrate that organic molecules bond preferentially to different facets of the Ag(775) substrate under different deposition sequences, molecular lengths, terrace widths, and step heights. This can contribute to the design of non-templated selective functionalization of nanocrystals. 2) Reversible conductance transition and spin on-off in low-dimensional quantum structures and applications in ultrahigh-density information storage. Firstly, we implement reversible, erasable, and rewritable nano-recordings on molecular thin films as a result of conductance transition. Then we demonstrate that the Kondo resonance of iron phthalocyanine molecules on an Au(111) substrate depends strongly on adsorption configuration, and the Kondo resonance of manganese phthalocyanine molecules can reversibly switch ON and OFF via attachment and detachment of single hydrogen atom to the molecule. Moreover, we achieve the site-dependent g factor of a single magnetic molecule with sub-molecular resolution, which shows an inhomogeneous distribution of the g factor within a single molecule. These results open up new routes to realizing ultrahigh-density information storage and controlling local spin properties within a single molecule. 3) Construction, physical properties and applications of graphene and other two-dimensional atomic crystals. We start with the fabrication of a wafer-size, high-quality (almost defect free), single-crystalline graphene on Ru(0001). Then we demonstrate the structure of novel two-dimensional (2D) atomic crystals of mono-element, such as silicene,germanene, hafnene, and antimonene. Last but not least, we present the formation of intrinsically patterned bi-elements 2D materials, PtSe2 and CuSe, which can serve as templates for selective self-assembly of molecules and nanoclusters, as well as dual functionalization for catalysis or other applications. The series of work done in Hong-Jun Gao's group has laid a solid foundation in the research field of low-dimensional quantum structures and their applications.

Effect on frontier molecular orbitals of substituents in 5-position of uracil base pairs in vacuum and water

The most stable structure of 5-substituted uracil base pairs and metal-mediated-5-substituted uracil complexes are determined. Density functional theory (DFT) method is used in the calculations which are carried out both in vacuum and water. LANL2DZ and 6–311[Formula: see text]G(d,p) basis sets are used for metals and the rest atoms, respectively. Effects on frontier molecular orbitals and energy gaps of substituents in 5-position of uracil base pairs in vacuum and water are found. Conductivity of base pairs or complexes are investigated for single nanowires studied by band theory. It is expected that this study will be an example for future studies that require new nanotechnological applications.

Si(775)-Au atomic chains: Geometry, optical properties, and spin order

The geometry and electronic structure of self-assembled atomic scale Au wires on Si(775) are investigated within density functional theory. The calculated surface diagram indicates the existence of two stable configurations with Au coverages of 0.32 and 0.96 monolayers, respectively. The low-coverage structure is predicted to host an antiferromagnetic spin chain localized at the Si rest atom dangling bonds, while the high-coverage structure is characterized by a Au-induced $\ensuremath{\beta}\text{\ensuremath{-}}\sqrt{3}$-like structure on the terrace. These structural models are supported by the comparison of measured and calculated surface optical anisotropies.

Tuning the conductivity along atomic chains by selective chemisorption

Adsorption of Au on vicinal Si(111) surfaces results in growth of long-range ordered metallic quantum wires. In this paper, we utilized site-specific and selective adsorption of oxygen to modify chemically the transport via different channels in the systems Si(553)-Au and Si(557)-Au. They were analyzed by electron diffraction and four-tip STM-based transport experiments. Modeling of the adsorption process by density functional theory shows that the adatoms and rest atoms on Si(557)-Au provide energetically favored adsorption sites, which predominantly alter the transport along the wire direction. Since this structural motif is missing on Si(553)-Au, the transport channels remain almost unaffected by oxidation.

Comparative STM analysis of C60 and C70 fullerene adsorption sites on pristine and Al-modified Si(111)7 × 7 surfaces

Using scanning tunneling microscopy observations, preferable adsorption sites of C60 and C70 fullerenes on pristine Si(111)7 × 7 and Al-modified Si(111)α–7 × 7-Al surfaces at 300 and 450 K were determined. The C60 and C70 molecules display similar, albeit not identical, adsorption behavior while the most essential variance is related with the hosting surfaces, pristine 7×7 or α–7 × 7-Al. Both C60 and C70 prefer to occupy positions above the Si rest atoms upon adsorption onto Si(111)7 × 7 at 300 K and change their preferable sites for those located at the Si edge adatom at 450 K, that is plausibly accompanied by releasing the Si adatom. Upon C60 and C70 adsorption onto Si(111)α–7 × 7-Al surface at 300 K, the fullerenes prefer to occupy the asymmetric sites at the dimer rows. At 450 K, the C70 fullerenes preserve this location, while about half of the C60 fullerenes change it for that at the corner Si adatom position. The present experimental data set serves as a useful basis for theoretical analysis.

General Approach to Diffusion under a Stress in Metals and Interstitial Alloys

One of the main aims of our work is to obtain general equations for the diffusion fluxes under strain that give the possibility for using these equations at low temperatures, as in this case the strain influence on the diffusion fluxes is manifested in maximal degree. Our approach takes into consideration that the strains can alter the surrounding atom configuration near the jumping atom and consequently the local magnitude of the activation barrier and a rate of atom jumps. The approach is derived under assumptions that the total energy depends on the pair distances only and the attempt frequencies are the same for all jumps. The rates of atom jumps in different directions define the flux density of the defects. Now we take into account that the strain tensor is different at the saddle point and at the rest atom position, that differentiates our approach from previous ones. As a result, general equations for the vacancy fluxes and impurity fluxes are obtained for fcc and bcc metals. These equations differ significantly from those obtained earlier.

Atomic epn(ep) Spin Models and Spectral Lines

We confirmed that how many kinds of epn spins the atoms have by calculating heat capacity of metals according to energy levels in the previous reference. To know more the spin models of epn of hydrogen and helium are imagined and their line spectra are counted. And the explanation of interference is discussed. Gas atoms make line spectra by optical interference. Solid atoms make them by exciting the lowest epns of their cluster first. They all make s, p energy orbit. One axis is composed of two epns. 1s or 2s of atoms except for lithium generally makes the symmetric axis. When each energy level is filled up by epns, these are symmetrically paired first. The atoms which fit the number of line spectra correctly by optical interference are hydrogen and helium. By counting the number of alignments of epns spins within the cluster, the atoms which fit the number of line spectra correctly are lithium, beryllium and phosphorus. The number of line spectra of the rest atoms which we have counted approaches the experimented numbers approximately, not correctly.

Adsorption of formic acid on Si(111)7 × 7 at room temperature: a valence band photoemission and Si2p photodesorption study

Formic acid is the simplest of the carboxylic acids and a model adsorption system for several surfaces. In spite of the simple structure, formic acid reactivity and photoreactivitymay be quite complex. In this paper, a study is presented on the deuterated formic acid adsorption on Si(111)7× 7 at roomtemperature. The study is performed both by valence band photoemission and by photonstimulated desorption as a function of time and of photon energy in the 90–120 eV range. A primarily adsorption on rest atoms is found. This is verified by monitoring rest atoms and adatom intensity as a function of formic acid exposure. Further checks were made to control that surface adatoms were still free to react after the adsorption of formic acid. The photon stimulated desorption produces 5 single positively charged fragments: D+, O+, OD+ CO+ and CDO+. Possible fragmentation mechanisms are discussed.

Reaction Mechanism and Regioselectivity of Methyl Oxirane on Si(111)-(7 × 7)

The reaction mechanism and regioselectivity of methyl oxirane (C3H6O) adsorbed on Si(111)-(7 × 7) have been studied using high-resolution electron energy loss spectroscopy (HREELS), in situ scanning tunneling microscopy (STM), and density functional theory (DFT) calculations. The experimental results demonstrate that methyl oxirane chemically binds to Si(111)-(7 × 7) through both dative-bonded addition and ring-opening reaction via cleavage of C–C or one C–O bond within the epoxy group. The STM images also reveal that the adsorption is site-selective with a preference for center adatoms on the faulted half of the (7 × 7) unit cell. The DFT calculations further show that breaking the C(CH3)–O bond is most kinetically favorable with a relatively small barrier of ∼3 kcal/mol. The dative-bonded states are observable on the surface only after three adjacent adatom–rest atom pairs within one-half unit cell are fully reacted with the methyl oxirane molecules during the ring-opening reaction.

Band Jahn–Teller effects in Rh2TMSn full Heusler compounds

Electronic structures of Rh2TMSn (TM=Cr, Mn, Fe, Co, Ni and Cu) full Heusler compounds are calculated by the state-of-the-art electronic structure codes with the local density approximation aiming to understand the structure instability microscopically. The instability of the compounds can be explained by the band Jahn–Teller effect. The compounds can be categorized into two groups: In the first group, the density of states at the Fermi level are contributed mainly from Rh, while in the rest, both the Rh and TM atoms contribute. The high density of states at the Fermi level of the first group compounds may be smoothed and the highly symmetric phase is stable as found in experiments. The compounds in the second group tetragonally distort according to our calculation and was found in the experiments.

Electronic and atomic structure of Co/Ge nanoislands on the Ge(111) surface

We report on a detailed investigation of the electronic and atomic structure of nanometer-size Co/Ge islands obtained by solid-state reactive deposition of Co atoms on a $\mathrm{Ge}(111)c(2\ifmmode\times\else\texttimes\fi{}8)$ surface. Relying on scanning tunneling microscopy (STM) and spectroscopy (STS) measurements combined with density functional theory based calculations, the atomic structure of the Co/Ge(111)$\sqrt{13}\ifmmode\times\else\texttimes\fi{}\sqrt{13}\phantom{\rule{0.16em}{0ex}}R13.{9}^{\ensuremath{\circ}}$ surface reconstruction is determined. Real-space STM imaging combined with Fourier-transform analysis reveals the coexistence of two inequivalent phases of $\sqrt{13}\ifmmode\times\else\texttimes\fi{}\sqrt{13}\phantom{\rule{0.16em}{0ex}}R13.{9}^{\ensuremath{\circ}}$ reconstructed Co/Ge nanoislands that are rotated by $+13.{9}^{\ensuremath{\circ}}$ and $\ensuremath{-}13.{9}^{\ensuremath{\circ}}$ with respect to the $[2\overline{11}]$ direction. STS spectra probe a small band gap that varies within the $\sqrt{13}\ifmmode\times\else\texttimes\fi{}\sqrt{13}\phantom{\rule{0.16em}{0ex}}R13.{9}^{\ensuremath{\circ}}$ surface unit cell between 10 and $250\phantom{\rule{4pt}{0ex}}\mathrm{meV}$, suggesting local metallic behavior. According to the proposed atomic-structure model, each Co/Ge(111)$\sqrt{13}\ifmmode\times\else\texttimes\fi{}\sqrt{13}\phantom{\rule{0.16em}{0ex}}R13.{9}^{\ensuremath{\circ}}$ surface unit cell contains one Ge adatom and six Co atoms that are located at hollow sites below the top surface Ge layer and that are stacked in the form of an equilateral triangle. The Ge adatom is located asymmetrically with respect to the Co triangle and occupies two different, yet physically equivalent, positions, giving rise to two chiral phases of Co/Ge nanoislands. The Co/Ge valence band is dominated by Co atom derived 3$d$ states, while states in the conduction band stem from Ge adatom and Ge rest-atom derived states. Analysis of the bonding properties confirms the stability of the proposed Co/Ge atomic structure and reveals significant charge transfer from Co atoms to Ge rest atoms, suggesting ionic or metallic-covalent interaction.