Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method

A potential sensing mechanism for DNA nucleobases by optical properties of GO and MoS2 Nanopores

We propose a new DNA sensing mechanism based on optical properties of graphene oxide (GO) and molybdenum disulphide (MoS2) nanopores. In this method, GO and MoS2 is utilized as quantum dot (QD) nanopore and DNA molecule translocate through the nanopore. A recently-developed hybrid quantum/classical method (HQCM) is employed which uses time-dependent density functional theory and quasi-static finite difference time domain approach. Due to good biocompatibility, stability and excitation wavelength dependent emission behavior of GO and MoS2 we use them as nanopore materials. The absorption and emission peaks wavelengths of GO and MoS2 nanopores are investigated in the presence of DNA nucleobases. The maximum sensitivity of the proposed method to DNA is achieved for the 2-nm GO nanopore. Results show that insertion of DNA nucleobases in the nanopore shifts the wavelength of the emitted light from GO or MoS2 nanopore up to 130 nm. The maximum value of the relative shift between two different nucleobases is achieved by the shift between cytosine (C) and thymine (T) nucleobases, ~111 nm for 2-nm GO nanopore. Results show that the proposed mechanism has a superior capability to be used in future DNA sequencers.

Chiral Inversion of Thiolate-Protected Gold Nanoclusters via Core Reconstruction without Breaking a Au-S Bond

On the basis of density functional theory computations of the well-known chiral Au₃₈(SR)₂₄ nanocluster and its Pd- and Ag-doped derivatives, we propose here a mechanism for chiral inversion that does not require the breaking of a metal–sulfur bond at the metal–ligand interface but features a collective rotation of the gold core. The calculated energy barriers for this mechanism for Au₃₈ and Pd-doped Au₃₈ are in the range of 1–1.5 eV, significantly lower than barriers involving the breakage of Au–S bonds (2.5 eV). For Ag-doped Au₃₈, barriers for both mechanisms are similar (1.3–1.5 eV). Inversion barriers for a larger chiral Au₁₄₄(SR)₆₀ are much higher (2.5−2.8 eV). Our computed barriers are in good agreement with racemization barriers estimated from existing experiments for bare and doped Au₃₈. These results highlight the sensitivity of chiral inversion to the size, structure, and metal composition of the metal core and sensitivity to the detailed structure of the metal–thiolate interface. Our work also predicts that enantiopure Au₁₄₄(SR)₆₀ clusters would be promising materials for applications requiring high resistance to chiral inversion.

Plasmon-Induced Direct Hot-Carrier Transfer at Metal-Acceptor Interfaces

Plasmon-induced hot-carrier transfer from a metal nanostructure to an acceptor is known to occur via two key mechanisms: (i) indirect transfer, where the hot carriers are produced in the metal nanostructure and subsequently transferred to the acceptor, and (ii) direct transfer, where the plasmons decay by directly exciting carriers from the metal to the acceptor. Unfortunately, an atomic-level understanding of the direct-transfer process, especially with regard to its quantification, remains elusive even though it is estimated to be more efficient compared to the indirect-transfer process. This is due to experimental challenges in separating direct from indirect transfer as both processes occur simultaneously at femtosecond time scales. Here, we employ time-dependent density-functional theory simulations to isolate and study the direct-transfer process at a model metal-acceptor (Ag₁₄₇-Cd₃₃Se₃₃) interface. Our simulations show that, for a 10 fs Gaussian laser pulse tuned to the plasmon frequency, the plasmon formed in the Ag₁₄₇-Cd₃₃Se₃₃ system decays within 10 fs and induces the direct transfer with a probability of about 40%. We decompose the direct-transfer process further and demonstrate that the direct injection of both electrons and holes into the acceptor, termed direct hot-electron transfer (DHET) and direct hot-hole transfer (DHHT), takes place with similar probabilities of about 20% each. Finally, effective strategies to control and tune the probabilities of DHET and DHHT processes are proposed. We envision our work to provide guidelines toward the design of metal-acceptor interfaces that enable more efficient plasmonic hot-carrier devices.

Assessment of Initial Guesses for Self-Consistent Field Calculations. Superposition of Atomic Potentials: Simple yet Efficient

Electronic structure calculations, such as in the Hartree-Fock or Kohn-Sham density functional approach, require an initial guess for the molecular orbitals. The quality of the initial guess has a significant impact on the speed of convergence of the self-consistent field (SCF) procedure. Popular choices for the initial guess include the one-electron guess from the core Hamiltonian, the extended Hückel method, and the superposition of atomic densities (SAD). Here, we discuss alternative guesses obtained from the superposition of atomic potentials (SAP), which is easily implementable even in real-space calculations. We also discuss a variant of SAD which produces guess orbitals by purification of the density matrix that could also be used in real-space calculations, as well as a parameter-free variant of the extended Hückel method, which resembles the SAP method and is easy to implement on top of existing SAD infrastructure. The performance of the core Hamiltonian, the SAD, and the SAP guesses as well as the extended Hückel variant is assessed in nonrelativistic calculations on a data set of 259 molecules ranging from the first to the fourth periods by projecting the guess orbitals onto precomputed, converged SCF solutions in single- to triple-ζ basis sets. It is shown that the proposed SAP guess is the best guess on average. The extended Hückel guess offers a good alternative, with less scatter in accuracy.

Structural, electronic and magnetic properties of stoichiometric cobalt oxide clusters (CoO)nq (n=3−10,q=0,+1): A modified basin-hopping Monte Carlo algorithm with spin-polarized DFT

The structural, electronic and magnetic properties of the neutral and cationic cobalt oxide clusters (CoO)[Formula: see text] ([Formula: see text], [Formula: see text]) have been studied using a modified basin-hopping Monte Carlo (BHMC) algorithm refined by spin-polarized DFT. A systematic search of global minimum structures predicts new global minima of (CoO)[Formula: see text] and reproduced other minima that are in excellent agreement with previous works. For most low-spin and high-spin states, the structural transition from planar-like to compact structure occurs at (CoO)[Formula: see text], which is in contrast with the general notion that the structural changes at (CoO)[Formula: see text]. Supported by the results of the binding energy, second-order total energy difference, chemical hardness, chemical potential and HOMO-LUMO gap confirms the stability of (CoO)4. Results of the spin magnetic moments for the global minima show that (CoO)4 and (CoO)8 spin configurations exhibit a fully antiferromagnetic (AFM) ordering, while (CoO)9 spin displays the highest ferromagnetic (FM) ordering. Interestingly, elongation of Co–Co bond in (CoO)4 causes O being polarized by the neighboring Co atoms that accordingly follows the Goodenough-Kanamori-Anderson rule of FM super-exchange coupling for the Co-O-Co structural rearrangement to 90∘ ([Formula: see text] structure) in order to accommodate the spin magnetic ordering changes. This rearrangement is a result of the valence band being shifted away from the Fermi level to lower energy causing high population of the spin-up density of state and leading to the asymmetrical polarization of the whole (CoO)4 structure. As far as the dissociation energy surfaces are concerned, the first ever such surfaces are constructed corresponding to [Formula: see text], which identify a complete dissociation pathway linking the cationic and neutral clusters and finally confirm (CoO)[Formula: see text] as the most stable cluster compared to the rest.

Mechanistic Understanding of Cu-CHA Catalyst as Sensor for Direct NH3-SCR Monitoring: The Role of Cu Mobility

The concept to utilize a catalyst directly as a sensor is fundamentally and technically attractive for a number of catalytic applications, in particular, for the catalytic abatement of automotive emission. Here, we explore the potential of microporous copper-exchanged chabazite (Cu-CHA, including Cu-SSZ-13 and Cu-SAPO-34) zeolite catalysts, which are used commercially in the selective catalytic reduction of automotive nitrogen oxide emission by NH₃ (NH₃-SCR), as impedance sensor elements to monitor directly the NH₃-SCR process. The NH₃-SCR sensing behavior of commercial Cu-SSZ-13 and Cu-SAPO-34 catalysts at typical reaction temperatures (i.e., 200 and 350 °C) was evaluated according to the change of ionic conductivity and was mechanistically investigated by complex impedance-based in situ modulus spectroscopy. Short-range (local) movement of Cu ions within the zeolite structure was found to determine largely the NH₃-SCR sensing behavior of both catalysts. Formation of NH₃-solvated, highly mobile Cu^I species showed a predominant influence on the ionic conductivity of both catalysts and, consequently, hindered NH₃-SCR sensing at 200 °C. Density functional theory calculations over a model Cu-SAPO-34 system revealed that Cu^II reduction to Cu^I by coadsorbed NH₃ and NO weakened significantly the coordination of the Cu site to the CHA framework, enabling high mobility of Cu^I species that influences substantially the NH₃-SCR sensing. The in situ spectroscopic and theoretical investigations not only unveil the mechanisms of Cu-CHA catalyst as sensor elements for direct NH₃-SCR monitoring but also allow us to get insights into the speciation of active Cu sites in NH₃-SCR under different reaction conditions with varied temperatures and gas compositions.

Hydrogen interaction with graphene on Ir(1 1 1): a combined intercalation and functionalization study

We demonstrate a procedure for obtaining a H-intercalated graphene layer that is found to be chemically decoupled from the underlying metal substrate. Using high-resolution x-ray photoelectron spectroscopy and scanning tunneling microscopy techniques, we reveal that the hydrogen intercalated graphene is p-doped by about 0.28 eV, but also identify structures of interfacial hydrogen. Furthermore, we investigate the reactivity of the decoupled layer towards atomic hydrogen and vibrationally excited molecular hydrogen and compare these results to the case of non-intercalated graphene. We find distinct differences between the two. Finally, we discuss the possibility to form graphane clusters on an iridium substrate by combined intercalation and H atom exposure experiments.

Ultrafast X-Ray Scattering Measurements of Coherent Structural Dynamics on the Ground-State Potential Energy Surface of a Diplatinum Molecule

We report x-ray free electron laser experiments addressing ground-state structural dynamics of the diplatinum anion Pt_{2}POP_{4} following photoexcitation. The structural dynamics are tracked with <100  fs time resolution by x-ray scattering, utilizing the anisotropic component to suppress contributions from the bulk solvent. The x-ray data exhibit a strong oscillatory component with period 0.28 ps and decay time 2.2 ps, and structural analysis of the difference signal directly shows this as arising from ground-state dynamics along the PtPt coordinate. These results are compared with multiscale Born-Oppenheimer molecular dynamics simulations and demonstrate how off-resonance excitation can be used to prepare a vibrationally cold excited-state population complemented by a structure-dependent depletion of the ground-state population which subsequently evolves in time, allowing direct tracking of ground-state structural dynamics.

Space partitioning of exchange-correlation functionals with the projector augmented-wave method

We implement a Becke fuzzy cells type space partitioning scheme for the purposes of exchange-correlation within the GPAW projector augmented-wave method based density functional theory code. Space partitioning is needed in the situation where one needs to treat different parts of a combined system with different exchange-correlation functionals. For example, bulk and surface regions of a system could be treated with functionals that are specifically designed to capture the distinct physics of those regions. Here, we use the space partitioning scheme to implement the quasi-nonuniform exchange-correlation scheme, which is a useful practical approach for calculating metallic alloys on the generalized gradient approximation level. We also confirm the correctness of our implementation with a set of test calculations.

Grand-canonical approach to density functional theory of electrocatalytic systems: Thermodynamics of solid-liquid interfaces at constant ion and electrode potentials

Properties of solid-liquid interfaces are of immense importance for electrocatalytic and electrochemical systems, but modeling such interfaces at the atomic level presents a serious challenge and approaches beyond standard methodologies are needed. An atomistic computational scheme needs to treat at least part of the system quantum mechanically to describe adsorption and reactions, while the entire system is in thermal equilibrium. The experimentally relevant macroscopic control variables are temperature, electrode potential, and the choice of the solvent and ions, and these need to be explicitly included in the computational model as well; this calls for a thermodynamic ensemble with fixed ion and electrode potentials. In this work, a general framework within density functional theory (DFT) with fixed electron and ion chemical potentials in the grand canonical (GC) ensemble is established for modeling electrocatalytic and electrochemical interfaces. Starting from a fully quantum mechanical description of multi-component GC-DFT for nuclei and electrons, a systematic coarse-graining is employed to establish various computational schemes including (i) the combination of classical and electronic DFTs within the GC ensemble and (ii) on the simplest level a chemically and physically sound way to obtain various (modified) Poisson-Boltzmann (mPB) implicit solvent models. The detailed and rigorous derivation clearly establishes which approximations are needed for coarse-graining as well as highlights which details and interactions are omitted in vein of computational feasibility. The transparent approximations also allow removing some of the constraints and coarse-graining if needed. We implement various mPB models within a linear dielectric continuum in the GPAW code and test their capabilities to model capacitance of electrochemical interfaces as well as study different approaches for modeling partly periodic charged systems. Our rigorous and well-defined DFT coarse-graining scheme to continuum electrolytes highlights the inadequacy of current linear dielectric models for treating properties of the electrochemical interface.

Face-centered tetragonal (FCT) Fe and Co alloys of Pt as catalysts for the oxygen reduction reaction (ORR): A DFT study

Proton exchange membrane fuel cells (PEMFCs) are promising candidates for alternate energy conversion devices owing to their various advantages including high efficiency, reliability, and environmental friendliness. The performance of PEMFCs is fundamentally limited by the sluggish kinetics of the oxygen reduction reaction (ORR) at the cathode. Various studies have addressed myriads of Pt-based alloys as potential catalysts for ORR. However, most of these studies only focus on the cubic-structured Pt-based alloys which require further improvements especially in terms of stability and required loading. In this work, we perform first-principle density functional theory calculations to explore Fe and Co alloys of Pt in a different face centered tetragonal (L1₀) geometry as potential catalysts for ORR. The work focuses on understanding the reaction mechanism of ORR by both dissociative and associative mechanisms on L1₀-FePt/Pt(111) and L1₀-CoPt/Pt(111) surfaces. The binding pattern of each reaction intermediate is studied along with the complete reaction free energy landscape as a function of Pt overlayers. The L1₀-FePt/Pt(111) and L1₀-CoPt/Pt(111) surfaces show higher calculated surface activity for ORR as compared to the native fcc Pt(111) surface. The decrease in the required overpotential (η) for the alloys with respect to the unstrained Pt(111) surface is found to be in the range (0.04 V-0.25 V) assuming the dissociative mechanism and (0.02 V-0.10 V) assuming the associative mechanism, where the variation depends on the thickness of Pt overlayers. We further correlate the binding behavior of the reaction intermediates to the applied biaxial strain on the Pt(111) surface with the help of a mechanical eigenforce model. The eigenforce model gives a (semi-) quantitative prediction of the binding energies of the ORR intermediates under applied biaxial strain. The numerical values of the limiting potential (U_L) obtained from the eigenforce model are found to be very close to ones obtained from electronic structure calculations (less than 0.1 V difference). The eigenforce model is further used to predict the ideal equi-biaxial strain range required on Pt(111) surfaces for optimum ORR activity.

Study of Li Adsorption on Graphdiyne Using Hybrid DFT Calculations

Promising applications of graphdiyne have often been initiated by theoretical predictions especially using DFT known as the most powerful first-principles electronic structure calculation method. However, there is no systematic study on the reliability of DFT for the prediction of the electronic properties of the graphdiyne. Here, we performed a study of Li adsorption on the graphdiyne using hybrid DFT with LC-ωPBE and compared the results with those of PBE, because accurate prediction of the Li adsorption is important for performance as a Li storage that was first theoretically suggested and then experimentally realized. Our results show that PBE overestimates the adsorption energy inside a pore and the barrier height at the transition state of in-plane diffusion compared to the those of LC-ωPBE. In particular, LC-ωPBE predicted almost barrier-less in-plane diffusion of Li on the graphdiyne because of the presence of both in-plane and out-of-plane π orbitals. Also, LC-ωPBE favors a high spin state due to the exact exchange energy when several Li atoms are adsorbed on the graphdiyne, whereas PBE favors a low spin state. Thus, the use of the hybrid DFT is critical for reliable predictions on the electronic properties of the graphdiyne.

Electric-field control of spin orientation of manganocene: An insight into molecule-substrate interactions

The manipulation of spin orientations in molecular nanomagnets assembled on surfaces is essential for the development of memory devices. These properties are dominated by interactions with the substrate. Here, we show that individual manganocene molecules deposited on Cu(111) exhibit different easy magnetization directions in an applied electric-field due to different contact geometries. Using Hubbard-U corrected density-functional theory to describe strong correlation effects and a non-self-consistent diagonalization method to treat spin-orbit coupling, we demonstrate that the field-induced spin reorientation transition occurs in the standing-up molecule in both high-spin (HS) and low-spin states, while the transition only occurs in the HS state for the flat-lying molecule. We propose plausible mechanisms in terms of charge polarization at the interface as well as modifications of the electronic states near the Fermi level E _F. We show that the molecule largely preserves its arrangement of 3d orbitals in the standing configuration due to the "insulating layer" (bridging ligand), whereas direct contact of the Mn ion with the substrate in the lying configuration induces an orbital degeneracy around E _F, thus preventing the electrical modulation of magnetic anisotropies.

Atom-specific activation in CO oxidation

We report on atom-specific activation of CO oxidation on Ru(0001) via resonant X-ray excitation. We show that resonant 1s core-level excitation of atomically adsorbed oxygen in the co-adsorbed phase of CO and oxygen directly drives CO oxidation. We separate this direct resonant channel from indirectly driven oxidation via X-ray induced substrate heating. Based on density functional theory calculations, we identify the valence-excited state created by the Auger decay as the driving electronic state for direct CO oxidation. We utilized the fresh-slice multi-pulse mode at the Linac Coherent Light Source that provided time-overlapped and 30 fs delayed pairs of soft X-ray pulses and discuss the prospects of femtosecond X-ray pump X-ray spectroscopy probe, as well as X-ray two-pulse correlation measurements for fundamental investigations of chemical reactions via selective X-ray excitation.

Atom-by-Atom Construction of a Cyclic Artificial Molecule in Silicon

Hydrogen atoms on a silicon surface, H-Si (100), behave as a resist that can be patterned with perfect atomic precision using a scanning tunneling microscope. When a hydrogen atom is removed in this manner, the underlying silicon presents a chemically active site, commonly referred to as a dangling bond. It has been predicted that individual dangling bonds function as artificial atoms, which, if grouped together, can form designer molecules on the H-Si (100) surface. Here, we present an artificial ring structure molecule spanning three dimer rows, constructed from dangling bonds, and verified by spectroscopic measurement of its molecular orbitals. We found that removing 8 hydrogen atoms resulted in a molecular analog to 1,4-disilylene-hexasilabenzene (Si₈H₈). Scanning tunneling spectroscopic measurements reveal molecular π and π* orbitals that agree with those expected for the same molecule in a vacuum; this is validated by density functional theory calculations of the dangling bond system on a silicon slab that show direct links both to the experimental results and to calculations for the isolated molecule. We believe the unique electronic structure of artificial molecules constructed in this manner can be engineered to enable future molecule-based electronics, surface catalytic functionality, and templating for subsequent site-selective deposition.

The Influence of Tin(II) Incorporation on Visible Light Absorption and Photocatalytic Activity in Defect-Pyrochlores

The defect pyrochlore KTaWO₆ has been used to systematically investigate the effect of Sn^II incorporation conditions on the band structure and subsequent photocatalytic properties. Different tin precursors show varying influence on the resulting band gap. While the optimum conditions diminish the band gap by up to 1.4 eV, the increase in visible light absorption does not correlate with an increase of photocatalytic activity.

In Pursuit of 2D Materials for Maximum Optical Response

Despite being only a few atoms thick, single-layer two-dimensional (2D) materials display strong electron-photon interactions that could be utilized in efficient light modulators on extreme subwavelength scales. In various applications involving light modulation and manipulation, materials with strong optical response at different wavelengths are required. Using qualitative analytical modeling and first-principles calculations, we determine the theoretical limit of the maximum optical response such as absorbance ( A) and reflectance ( R) in 2D materials and also conduct a computational survey to seek out those with best A and R in various frequency ranges, from mid-infrared to deep-ultraviolet. We find that 2D boron has broadband reflectance R > 99% for >100 layers, surpassing conventional thin films of bulk metals such as silver. Moreover, we identify 2D monolayer semiconductors with maximum response, for which we obtain quantitative estimates by calculating quasiparticle energies and accounting for excitonic effects by solving the Bethe-Salpeter equation. We found several monolayer semiconductors with absorbances ≳30% in different optical ranges, which are more than half of the maximum possible value, A_lim = 1/2, for a freestanding 2D material. Our study predicts 2D materials which can potentially be used in ultrathin reflectors and absorbers for optoelectronic application in various frequency ranges.

Water Dissociation and Hydroxyl Ordering on Anatase TiO_{2}(001)-(1×4)

We studied the interaction of water with the anatase TiO_{2}(001) surface by means of scanning tunneling microscopy, x-ray photoelectron spectroscopy, and density functional theory calculations. Water adsorbs dissociatively on the ridges of a (1×4) reconstructed surface, resulting in a (3×4) periodic structure of hydroxyl pairs. We observed this process at 120 K, and the created hydroxyls desorb from the surface by recombination to water, which occurs below 300 K. Our calculations reveal the water dissociation mechanism and uncover a very pronounced dependence on the coverage. This strong coverage dependence is explained through water-induced reconstruction on anatase TiO_{2}(001)-(1×4). The high intrinsic reactivity of the anatase TiO_{2}(001) surface towards water observed here is fundamentally different from that seen on other surfaces of titania and may explain its high catalytic activity in heterogeneous catalysis and photocatalysis.

Dipole-Induced Transition Orbitals: A Novel Tool for Investigating Optical Transitions in Extended Systems

Optical absorption spectra for nanostructures and solids can be obtained from the macroscopic dielectric function within the random phase approximation. While experimental spectra can be reproduced with good accuracy, important properties, such as the charge-transfer character associated with a particular transition, are not retrievable. This contribution presents a computationally inexpensive method for the analysis of optical and excitonic properties for extended systems based on solely their electronic ground-state structure. We formulate a perturbative orbital transformation theory based on dipole-induced transition moments between orbitals, which yields correlated pairs of particle and hole functions. To demonstrate the potency of this new transformation formalism, we investigate the nature of excitations in inorganic molecular complexes and in extended systems. With our method, it is possible to extract mechanistic insights from the transitions observed in the optical spectrum, without requiring explicit calculation of the many-electron excited states.

Reactivity of Amorphous Carbon Surfaces: Rationalizing the Role of Structural Motifs in Functionalization Using Machine Learning

Systematic atomistic studies of surface reactivity for amorphous materials have not been possible in the past because of the complexity of these materials and the lack of the computer power necessary to draw representative statistics. With the emergence and popularization of machine learning (ML) approaches in materials science, systematic (and accurate) studies of the surface chemistry of disordered materials are now coming within reach. In this paper, we show how the reactivity of amorphous carbon (a-C) surfaces can be systematically quantified and understood by a combination of ML interatomic potentials, ML clustering techniques, and density functional theory calculations. This methodology allows us to process large amounts of atomic data to classify carbon atomic motifs on the basis of their geometry and quantify their reactivity toward hydrogen- and oxygen-containing functionalities. For instance, we identify subdivisions of sp and sp² motifs with markedly different reactivities. We therefore draw a comprehensive, both qualitative and quantitative, picture of the surface chemistry of a-C and its reactivity toward -H, -O, -OH, and -COOH. While this paper focuses on a-C surfaces, the presented methodology opens up a new systematic and general way to study the surface chemistry of amorphous and disordered materials.

Reactivity of Amorphous Carbon Surfaces: Rationalizing the Role of Structural Motifs in Functionalization Using Machine Learning

Systematic atomistic studies of surface reactivity for amorphous materials have not been possible in the past because of the complexity of these materials and the lack of the computer power necessary to draw representative statistics. With the emergence and popularization of machine learning (ML) approaches in materials science, systematic (and accurate) studies of the surface chemistry of disordered materials are now coming within reach. In this paper, we show how the reactivity of amorphous carbon (a-C) surfaces can be systematically quantified and understood by a combination of ML interatomic potentials, ML clustering techniques, and density functional theory calculations. This methodology allows us to process large amounts of atomic data to classify carbon atomic motifs on the basis of their geometry and quantify their reactivity toward hydrogen- and oxygen-containing functionalities. For instance, we identify subdivisions of sp and sp2 motifs with markedly different reactivities. We therefore draw a comprehensive, both qualitative and quantitative, picture of the surface chemistry of a-C and its reactivity toward -H, -O, -OH, and -COOH. While this paper focuses on a-C surfaces, the presented methodology opens up a new systematic and general way to study the surface chemistry of amorphous and disordered materials.

Point Group Symmetry Analysis of the Electronic Structure of Bare and Protected Metal Nanocrystals

The electronic structures of a variety of experimentally identified gold and silver nanoclusters from 20 to 246 atoms, either unprotected or protected by several types of ligands, are characterized by using point group specific symmetry analysis. The delocalized electron states around the HOMO–LUMO energy gap, originating from the metal s-electrons in the cluster core, show symmetry characteristics according to the point group that describes best the atomic arrangement of the core. This indicates strong effects of the lattice structure and overall shape of the metal core to the electronic structure, which cannot be captured by the conventional analysis based on identification of spherical angular momentum shells in the “superatom” model. The symmetry analysis discussed in this paper is free from any restrictions regarding shape or structure of the metal core, and is shown to be superior to the conventional spherical harmonics analysis for any symmetry that is lower than I_h. As an immediate application, we also demonstrate that it is possible to reach considerable savings in computational time by using the symmetry information inside a conventional linear-response calculation for the optical absorption spectrum of the Ag₅₅ cluster anion, without any loss in accuracy of the computed spectrum. Our work demonstrates an efficient way to analyze the electronic structure of nonspherical, but atomically ordered nanocrystals and ligand-protected clusters with nanocrystal metal cores, and it can be viewed as the generalization of the superatom model demonstrated for spherical shapes 10 years ago (Walter, M.; et al. Proc. Natl. Acad. Sci. U. S. A.2008, 105, 9157−916218599443).

3D Dirac Plasmons in the Type-II Dirac Semimetal PtTe_{2}

Transition-metal dichalcogenides showing type-II Dirac fermions are emerging as innovative materials for nanoelectronics. However, their excitation spectrum is mostly unexplored yet. By means of high-resolution electron energy loss spectroscopy and density functional theory, here, we identify the collective excitations of type-II Dirac fermions (3D Dirac plasmons) in PtTe_{2} single crystals. The observed plasmon energy in the long-wavelength limit is ∼0.5  eV, which makes PtTe_{2} suitable for near-infrared optoelectronic applications. We also demonstrate that interband transitions between the two Dirac bands in PtTe_{2} give rise to additional excitations at ∼1 and ∼1.4  eV. Our results are crucial to bringing to fruition type-II Dirac semimetals in optoelectronics.

Co-crystallization of atomically precise metal nanoparticles driven by magic atomic and electronic shells

This paper reports co-crystallization of two atomically precise, different-size ligand-stabilized nanoclusters, a spherical (AuAg)267(SR)80 and a smaller trigonal-prismatic (AuAg)45(SR)27(PPh3)6 in 1:1 ratio, characterized fully by X-ray crystallographic analysis (SR = 2,4-SPhMe2). The larger cluster has a four concentric-shell icosahedral structure of Ag@M12@M42@M92@Ag120(SR)80 (M = Au or Ag) with the inner-core M147 icosahedron observed here for metal nanoparticles. The cluster has an open electron shell of 187 delocalized electrons, fully metallic, plasmonic behavior, and a zero HOMO-LUMO energy gap. The smaller cluster has an 18-electron shell closing, a notable HOMO-LUMO energy gap and a molecule-like optical spectrum. This is the first direct demonstration of the simultaneous presence of competing effects (closing of atom vs. electron shells) in nanocluster synthesis and growth, working together to form a co-crystal of different-sized clusters. This observation suggests a strategy that may be helpful in the design of other nanocluster systems via co-crystallization.

Silver-Stabilized Guanine Duplex: Structural and Optical Properties

Recent experimental duplexes of DNA stabilized by Ag cations, pairing homostrands of guanine-guanine, cytosine-cytosine, adenine-thymine, and thymine-thymine, display much higher stability than the Watson-Crick paired DNA duplexes; these broaden the range of applications for DNA nanotechnology. Here we focus on silver-stabilized guanine duplexes in water. Using hybrid quantum mechanics/molecular mechanics simulations, we propose an atomic structure for the Ag⁺-mediated guanine duplex with two nucleobases per strand, G₂-Ag₂⁺-G₂. We then compare experimental and time-dependent density functional theory-simulated electronic circular dichroism (ECD) spectra to validate our results. Both experimental and simulated ECD share two negative peaks around 220 and 280 nm, with no positive signal in the measured wavelength range. We found that the left- or right-handed disposition of bases in the structure has a decisive effect on the signs of the ECD. We conclude that G₂-Ag₂⁺-G₂ is left-hand-oriented, and extrapolation of this orientation to longer strands gives rise to a left-hand-oriented parallel helix stabilized by interplanar H bonds.

Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory

We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag+-mediated DNA species.

Electron-Beam Manipulation of Silicon Dopants in Graphene

The direct manipulation of individual atoms in materials using scanning probe microscopy has been a seminal achievement of nanotechnology. Recent advances in imaging resolution and sample stability have made scanning transmission electron microscopy a promising alternative for single-atom manipulation of covalently bound materials. Pioneering experiments using an atomically focused electron beam have demonstrated the directed movement of silicon atoms over a handful of sites within the graphene lattice. Here, we achieve a much greater degree of control, allowing us to precisely move silicon impurities along an extended path, circulating a single hexagon, or back and forth between the two graphene sublattices. Even with manual operation, our manipulation rate is already comparable to the state-of-the-art in any atomically precise technique. We further explore the influence of electron energy on the manipulation rate, supported by improved theoretical modeling taking into account the vibrations of atoms near the impurities, and implement feedback to detect manipulation events in real time. In addition to atomic-level engineering of its structure and properties, graphene also provides an excellent platform for refining the accuracy of quantitative models and for the development of automated manipulation.

Thermodynamic and Kinetic Limitations for Peroxide and Superoxide Formation in Na-O2 Batteries

The Na-O₂ system holds great potential as a low-cost, high-energy-density battery, but under normal operating conditions, the discharge is limited to sodium superoxide (NaO₂), whereas the high-capacity peroxide state (Na₂O₂) remains elusive. Here, we apply density functional theory calculations with an improved error-correction scheme to determine equilibrium potentials and free energies as a function of temperature for the different phases of NaO₂ and Na₂O₂, identifying NaO₂ as the thermodynamically preferred discharge product up to ∼120 K, after which Na₂O₂ is thermodynamically preferred. We also investigate the reaction mechanisms and resulting electrochemical overpotentials on stepped surfaces of the NaO₂ and Na₂O₂ systems, showing low overpotentials for NaO₂ formation (η_dis = 0.14 V) and depletion (η_cha = 0.19 V), whereas the overpotentials for Na₂O₂ formation (η_dis = 0.69 V) and depletion (η_cha = 0.68 V) are found to be prohibitively high. These findings are in good agreement with experimental data on the thermodynamic properties of the Na _xO₂ species and provide a kinetic explanation for why NaO₂ is the main discharge product in Na-O₂ batteries under normal operating conditions.

Real-space imaging with pattern recognition of a ligand-protected Ag374 nanocluster at sub-molecular resolution

High-resolution real-space imaging of nanoparticle surfaces is desirable for better understanding of surface composition and morphology, molecular interactions at the surface, and nanoparticle chemical functionality in its environment. However, achieving molecular or sub-molecular resolution has proven to be very challenging, due to highly curved nanoparticle surfaces and often insufficient knowledge of the monolayer composition. Here, we demonstrate sub-molecular resolution in scanning tunneling microscopy imaging of thiol monolayer of a 5 nm nanoparticle Ag₃₇₄ protected by tert-butyl benzene thiol. The experimental data is confirmed by comparisons through a pattern recognition algorithm to simulated topography images from density functional theory using the known total structure of the Ag₃₇₄ nanocluster. Our work demonstrates a working methodology for investigations of structure and composition of organic monolayers on curved nanoparticle surfaces, which helps designing functionalities for nanoparticle-based applications.

Translating high-resolution imaging methods to the curved organic surface of a nanoparticle has been challenging. Here, the authors are able to spatially resolve the sub-molecular surface details of a silver nanocluster by comparing scanning tunneling microscopy images and simulated topography data through a pattern recognition algorithm.

Effects of the cooperative interaction on the diffusion of hydrogen on MgO(100)

Understanding hydrogen diffusion is important for applications such as hydrogen storage and spillover materials. On semiconductors, where paired electron acceptors and donors stabilize each other, the hydrogen diffusion depends on the number of adsorbed fragments. Using density functional theory, we investigate the effects of preadsorbed hydrogens on activation energy and reaction path for hydrogen diffusion on MgO(100): the presence of an unpaired hydrogen causes a diffusion, on O-sites, above the surface with a lower activation energy compared to the case of paired hydrogens where the diffusion distorts the surface. This effect is missing for diffusion on Mg-sites.

Topotactic Growth of Edge-Terminated MoS2 from MoO2 Nanocrystals

Layered transition metal dichalcogenides have distinct physicochemical properties at their edge-terminations. The production of an abundant density of edge structures is, however, impeded by the excess surface energy of edges compared to basal planes and would benefit from insight into the atomic growth mechanisms. Here, we show that edge-terminated MoS₂ nanostructures can form during sulfidation of MoO₂ nanocrystals by using in situ transmission electron microscopy (TEM). Time-resolved TEM image series reveal that the MoO₂ surface can sulfide by inward progression of MoO₂(202̅):MoS₂(002) interfaces, resulting in upright-oriented and edge-exposing MoS₂ sheets. This topotactic growth is rationalized in the interplay with density functional theory calculations by successive O-S exchange and Mo sublattice restructuring steps. The analysis shows that formation of edge-terminated MoS₂ is energetically favorable at MoO₂(110) surfaces and provides a necessary requirement for the propensity of a specific MoO₂ surface termination to form edge-terminated MoS₂. Thus, the present findings should benefit the rational development of transition metal dichalcogenide nanomaterials with abundant edge terminations.

Combined DFT and Differential Electrochemical Mass Spectrometry Investigation of the Effect of Dopants in Secondary Zinc-Air Batteries

Zinc-air batteries offer the potential of low-cost energy storage with high specific energy, but at present secondary Zn-air batteries suffer from poor cyclability. To develop economically viable secondary Zn-air batteries, several properties need to be improved: choking of the cathode, catalyzing the oxygen evolution and reduction reactions, limiting dendrite formation and suppressing the hydrogen evolution reaction (HER). Understanding and alleviating HER at the negative electrode in a secondary Zn-air battery is a substantial challenge, for which it is necessary to combine computational and experimental research. Here, we combine differential electrochemical mass spectrometry (DEMS) and density functional theory (DFT) calculations to investigate the fundamental role and stability when cycling in the presence of selected beneficial additives, that is, In and Bi, and Ag as a potentially unfavorable additive. We show that both In and Bi have the desired property for a secondary battery, that is, upon recharging they will remain on the surface, thereby retaining the beneficial effects on Zn dissolution and suppression of HER. This is confirmed by DEMS, where it is observed that In reduces HER and Bi affects the discharge potential beneficially compared to a battery without additives. Using a simple procedure based on adsorption energies calculated with DFT, it is found that Ag suppresses OH adsorption, but, unlike In and Bi, it does not hinder HER. Finally, it is shown that mixing In and Bi is beneficial compared to the additives by themselves as it improves the electrochemical performance and cyclic stability of the secondary Zn-air battery.

Driving spin transition at interface: Role of adsorption configurations

A clear insight into the electrical manipulation of molecular spins at interface is crucial to the design of molecule-based spintronic devices. Here we report on the electrically driven spin transition in manganocene physisorbed on a metallic surface in two different adsorption configurations predicted by ab initio techniques, including a Hubbard-U correction at the manganese site and accounting for the long-range van der Waals interactions. We show that the application of an electric field at the interface induces a high-spin to low-spin transition in the flat-lying manganocene, while it could hardly alter the high-spin ground state of the standing-up molecule. This phenomenon cannot be explained by either the molecule-metal charge transfer or the local electron correlation effects. We demonstrate a linear dependence of the intra-molecular spin-state splitting on the energy difference between crystal-field splitting and on-site Coulomb repulsion. After considering the molecule-surface binding energy shifts upon spin transition, we reproduce the obtained spin-state energetics. We find that the configuration-dependent responses of the spin-transition originate from the binding energy shifts instead of the variation of the local ligand field. Through these analyses, we obtain an intuitive understanding of the effects of molecule-surface contact on spin-crossover under electrical bias.