Bare Dimers Research Articles

Boosting Light–Matter Interaction in a Longitudinal Bonding Dipole Plasmon Hybrid Anapole System

Achieving strong electromagnetic enhancement is critical for realizing strong light–matter coupling at the nanoscale. In this study, we constructed a hybrid anapole system composed of a nanohole silicon disk and a longitudinal bonding dipole plasmon mode-supported plasmonic dimer. Compared with the bare dimer plasmon, the hybrid system shows strong plasmonic resonance tuning ability, and its resonance peak can be tuned to the near-infrared region only by adjusting the radius of the silicon disk. Meanwhile, the E-field enhancement in the gap region can exceed four orders of magnitude without sacrificing the quality factor of the system. Furthermore, it is demonstrated that the emitter’s radiative decay rate enhancement in the hybrid system is much higher than that of a similar LBDP mode-supported plasmonic dimer nanodisk and the reported plasmonic nanocavity. In summary, our hybrid anapole systems combine the advantages of metal plasmonic nanodimers and conventional anapole mode-supported systems and avoid their disadvantages. This study provides a useful reference for the further exploration of single-photon emission sources, light harvesting, and other quantum nanophotonic applications.

Stabilization of Zn group dimers: A theoretical study

AbstractQuantum chemical calculations have been carried out to investigate the possibility of Group 12 (Zn, Cd, Hg) dimer formation supported by the B3ring. All these complexes have significantly shorter M‐M (M = Zn, Cd, Hg) distances compared to their bare dimers, M2. The staggered and eclipsed forms of these complexes were found to be nearly degenerate. They have significant bond strengths as revealed from the significantly higher values of Wiberg bond indices as well as bond dissociation energies. The topological feature of electron density reveals significant covalency in the M‐M interaction which has also been confirmed from natural orbital for chemical valence analysis coupled with extended transition state (ETS‐NOCV) calculations.

Chemical Switching of the Magnetic Coupling in a MnPc Dimer by Means of Chemisorption and Axial Ligands

We present an ab initio density functional theory study of the magnetic properties of manganese phthalocyanine dimers, where we focus on the magnetic coupling between the Mn centers and on how it is affected by external factors like chemisorption or atomic axial ligands. We have studied several different configurations for the gas phase dimers, which resulted in ferromagnetic couplings of different magnitudes. For the bare dimer we find a significant ferromagnetic coupling between the Mn centers, which decreases by about 20% when a H atom is adsorbed on one of the Mn atoms and is reduced to about 7% when a Cl atom is adsorbed. The magnetic coupling is almost fully quenched when the dimer, bare or with the H ligand, is deposited on the ferromagnetic substrate Co(001). Our calculations indicate that the coupling between the two Mn atoms principally occurs via a superexchange interaction along two possible paths within a Mn–N–Mn–N four-atom loop. When these electrons get involved in chemical bonding outside the dimer itself, an appreciable alteration of the overlap between Mn and N molecular orbitals along the loop occurs, and consequently, the magnetic interaction between the Mn centers varies. We show that this is reflected by the electronic structure of the dimer in various configurations and is also visible in the structure of the atomic loop. The chemical tuning of the magnetic coupling is highly relevant for the design of nanodevices like molecular spin valves, where the molecules need to be anchored to a support.

Luminescence Spectroscopy of Rhodamine Homodimer Dications in Vacuo Reveals Strong Dye-Dye Interactions.

Being alone or together makes a difference for the photophysics of dyes but for ionic dyes it is difficult to quantify the interactions due to solvent screening and nearby counter ions. Gas-phase luminescence experiments are desirable and now possible based on recent developments in mass spectrometry. Here we present results on tailor-made rhodamine homodimers where two dye cations are separated by methylene linkers, (CH2 )n . In solution the fluorescence is almost identical to that from the monomer whereas the emission from bare cation dimers redshifts with decreasing n. In the absence of screening, the electric field from the charge on one dye is strong enough to polarize the other dye, both in the ground state and in the excited state. An electrostatic model based on symmetric dye responses (equal induced-dipole moments in ground state) captures the underlying physics and demonstrates interaction even at large distances. Our results have possible implications for gas-phase Förster Resonance Energy Transfer.

Sub-nanometer pore formation in single-molecule-thick polyurea molecular-sieving membrane: a computational study.

A polymeric network of 1-(4-tritylphenyl)urea (TPU) built via layer-by-layer cross-linking polymerization has been proposed to be an excellent mesh equipped with single-molecule-thick pores (i.e., cyclic poly-TPU rings), which can sieve glucose (∼0.7 nm) out of its mixture with urea for hemodialysis applications. Monte Carlo search for the lowest-energy conformation of various sizes of poly-TPU rings unravels the origin of narrow pore size distribution, which is around the sizes of dimer and trimer rings (0.3-0.8 nm). Flexible rings larger than the dimer and trimer rings, in particular tetramer rings, prefer a twisted conformation in the shape of the infinity symbol (∞, which looks like two dimer rings joined together) locked by a hydrogen bond between diphenylurea linker groups facing each other. Translocation energy profiles across these TPU rings reveal their urea-versus-glucose sieving mechanism: glucose is either too large (to enter dimers and twisted tetramers) or too perfectly fit (to exit trimers), leaving only a dimer-sized free space in the ring, whereas smaller-sized urea and water pass through these effective dimer-sized rings (bare dimers, twisted tetramers, and glucose-filled trimers) without encountering a substantial energy barrier or trap.

Structures of [M(Ura-H)(Ura)]+ and [M(Ura-H)(H2O)n]+ (M = Cu, Zn, Pb; n = 1–3) complexes in the gas phase by IRMPD spectroscopy in the fingerprint region and theoretical studies

The gas-phase structures of the bare dimers, [M(Ura-H)(Ura)]+, and hydrated monomers, [M(Ura-H)(H2O)n]+, were examined using infrared multiple photon dissociation spectroscopy in the fingerprint region (1000cm−1–1900cm−1) for M=Cu, Zn, and Pb and n=1–3. The experimental results were compared to those calculated using density functional methods The dimeric structures all show deprotonation of one uracil moiety at N3, and forms a tetracoordinate interaction with N3 and O4 of the deprotonated uracil, and N3 and O2 of the neutral uracil. The hydrated monomers, [M(Ura-H)(H2O)]+, all have rather different structures. Uracil is deprotonated at N3 for M=Zn and Pb, but for Cu, uracil is deprotonated at N1 and Cu2+ is bound to N1 and O2. Like the [M(Ura-H)(Ura)]+ complexes, in [Pb(Ura-H)(H2O)]+ the metal is bound to N3 and O4. The Zn2+ complex actually better resembles [M(Ura)(OH)]+ with a proton apparently transferred from water to O4 of uracil and the metal cation coordinated to O2. Unlike the singly hydrated complex, uracil is deprotonated at N3 in [Cu(Ura-H)(H2O)2]+. In all singly, doubly, and triply solvated complexes studied, water is found to be coordinated to the metal cation.

Structural, Vibrational, and Magnetic Properties of FeCoOn0/+ (n = 1–6) Bimetallic Oxide Clusters

FeCo nanostructures are very interesting for storage media, sensing, and biomedical applications. To learn how an oxidizing environment may affect the physical and chemical properties of FeCo nanoparticles in the molecular limit, we investigated, by means of density functional theoretic calculations, the structural, electronic, and magnetic properties of neutral and ionized oxides of the magnetic dimer FeCo as a function of the oxygen content (FeCoOn and FeCoOn+ with n = 1-6). Our aim was to rationalize the structural pattern, energetics, effects of oxidation on the local and total magnetic moments and magnetic couplings, and effect of the ionization on all those properties. The binding energy shows saturation for an oxygen content in the range of n = 4-6. The metal-metal bond weakens with increasing oxygen content. This is reflected in the metal-to-oxygen charge transfer although not systematically in the magnetic properties because the total spin moment oscillates as a function of n between high-spin states (characterized by parallel magnetic couplings) and low-spin states (characterized by antiparallel couplings). Oxide clusters in the high-spin state retain the same total moment as the bare FeCo dimer because of the direct contribution of the oxygen atoms. Upon ionization, the weakening of the metal-metal bond is less marked and the overall magnetic moment decreases because of the increasing tendency toward antiparallel couplings. We calculated the vibrational frequencies and IR intensities of certain isomers of different geometries and spin states, from which future IR spectroscopy experiments could confirm the structural pattern and, indirectly, the magnetic state.

Does the metal–metal sextuple bond exist in the bimetallic sandwich compounds Cr2(C6H6)2, Mo2(C6H6)2, and W2(C6H6)2?†

Although evanescent at best, the bare dimers of the elements Cr, Mo, and W have been identified as possible candidates for the sextuple metal–metal bond. The corresponding dibenzene sandwich compounds Cr2(C6H6)2, Mo2(C6H6)2, and W2(C6H6)2, satisfy the ‘18-Electron Rule’, and might achieve high-order metal–metal bonds and longer lifetimes at the same time. Twenty-two different DFT methods have been used to evaluate this possibility. Based on the present Wiberg bond index and molecular orbital analyses, however, only quadruple metal–metal bonds are predicted for the electronic ground states of Cr2(C6H6)2, Mo2(C6H6)2, and W2(C6H6)2, rather than the sextuple or even quintuple bonds, for both singlet and triplet electronic states. It is possible to force the hypothesised D 6h sextuple bond electron configuration, but the resulting energy is 39 kcal/mol above the D 2h quadruple bond structure for Cr2(C6H6)2. However, the constrained sextuple bond structure for Mo2(C6H6)2 lies 19 kcal/mol above the MoMo singlet. For W2(C6H6)2 the sextuple bond structure is predicted to lie only 3 kcal/mol above the WW structure. Thus the answer to the question raised in our title is ‘almost’ for the tungsten–sextuple bond.

Optical binding force of gold nanorod dimers coupled to a metallic slab

By full-wave 3D electromagnetic simulations and using the Maxwell's stress tensor integration technique, we calculate the optical forces on a gold nanorod dimer placed head-to-tail near a metallic slab. It is found that the plasmonic resonance wavelength λres of the system shifts obviously as the nanorod gap g and the dimer–slab spacing h are changed. Meanwhile, the optical forces under plane wave illumination crucially depend on the geometrical parameters and can be enhanced dramatically comparing to the bare dimer case. Moreover, numerical results show that when both g and h are far less than the resonant wavelength λres, the resonant binding force between the two nanorods decreases, while the force acting on each nanorod toward the slab increases, both monotonically as h is reduced. On the contrary, as the dimer–slab spacing h increases, there is a local maximum force at h≈λres/4 for various g. Both the strong near-field coupling and the standing wave formed by incident and reflected waves need to be accounted for the observed characteristics in the optical force spectra. Our results are useful for selective optical manipulation on particles over a substrate platform.

Initial oxidation structure of chlorinated Si(001)

The Cl-saturated Si(001) surface is investigated by employing density functional theory calculations. From the electronic density of states, the low- and the high-bias filled-state images and the empty-state images are found to originate from Cl(3p) states directed in-plane, in parallel with the Si dimer row, and perpendicular to the surface (z), respectively. The bright triplet, which is a characteristic scanning tunneling microscopy (STM) feature of an unchlorinated bare Si dimer, is attributed to an occupied dangling bond state of the bare Si dimer that is hybridized with the neighboring Cl(3pz) orbital. The previously observed split-dimer feature is confirmed to be the dimer-bond oxidized structure. Finally, we suggest that the initial back-bond oxidation does not occur on the chlorinated Si(001) surface because it is energetically not favored compared with dimer-bond oxidation and because its STM simulation does not match experimental images.

Aggregation of Kanamycin A: dimer formation with physiological cations

Global cluster geometry optimization has focused so far on clusters of atoms or of compact molecules. We are demonstrating here that present-day techniques also allow to globally optimize clusters of extended, flexible molecules, and that such studies have immediate relevance to experiment. For example, recent experimental findings point to production of larger clusters of an aminoglycoside closely related to Kanamycin A (KA), together with certain preferred physiological cations, by Pseudomonas aeruginosa. The present study provides first theoretical support for KA clustering, with a close examination of the monomer, the bare dimer, and dimers with sodium and potassium cations, employing global cluster structure optimization, in conjunction with force fields, semiempirical methods, DFT and ab-initio approaches. Interestingly, already at this stage the theoretical findings support the experimental observation that sodium cations are preferred over potassium cations in KA clusters, due to fundamentally different cationic embedding. Theoretically predicted NMR and IR spectra for these species indicate that it should be possible to experimentally detect the aggregation state and even the cationic embedding mode in such clusters.

Electronic properties of then-doped hydrogenated silicon (100) surface and dehydrogenated structures at 5 K

We present a comparative study of the electronic properties of the clean Si(100) and the hydrogenated Si(100):H surfaces performed with a low-temperature (5 K) scanning tunneling microscope. Various surface structures such as single silicon dangling bonds and bare silicon dimers created by local desorption of hydrogen atoms from the Si(100):H surface are also investigated. The experimental scanning tunneling spectroscopy (STS) curves acquired locally on each of these structures are compared with STS measurements performed on the Si(100) and Si(100):H surfaces. First principle density-functional theory calculations of the projected local density of states, taking into account the influence of the dopant atoms (As), enable to assign the observed STS spectra.

Atomic processes during Cl supersaturation etching ofSi(100)−(2×1)

Supersaturation etching starts with Cl insertion into Si-Si bonds of Si(100) and leads to the desorption of ${\text{SiCl}}_{2}$ pairs. During etching, insertion occurs through a ${\text{Cl}}_{2}$ dissociative chemisorption process mediated by single dangling bond sites created by phonon-activated electron-stimulated desorption of atomic Cl. Based on scanning tunneling microscopy results, we identify a surface species, describe its involvement in supersaturation etching, and explore the energetics that control this process. In doing so, we show that insertion occurs at room temperature and that paired dangling bonds of bare dimers also mediate this process.

Single hydrogen atoms on the Si(001) surface

Chemisorption of a single hydrogen atom on the $n$-type Si(001) surface is investigated by scanning tunneling microscopy (STM) and first-principles density functional theory (DFT) calculations. The STM experiments show that the formation of a hemihydride induces static buckling of the neighboring Si-Si dimers and suggest that different buckling configurations of these dimers are observed at negative and positive biases. They also show that the appearance of an isolated Si-Si-H hemihydride on Si(001) exhibits a complex voltage dependence with the brightness of the dangling bond of the hemihydride changing significantly at negative sample bias. DFT calculations predict two stable, ground state atomic configurations for the hemihydride on Si(001). These correspond to parallel and antiparallel configurations of the Si-Si-H hemihydride with respect to the neighboring bare Si-Si dimers. In order to understand the bias-dependent appearance in the STM images of the $n$-type Si(001) surface, we include the effect of hemihydride charging due to tip-induced band bending. In filled state, the STM images are shown to result from the electronic and structural features that originate from the charge-dependent parallel configuration. In empty state, the energetics and STM measurements support the charge independent antiparallel configuration, while either structure can produce simulated images consistent with experiment.

First-principles study of the tunnel current between a scanning tunneling microscopy tip and a hydrogen-adsorbedSi(001)surface

A scanning tunneling microscopy (STM) image of a hydrogen-adsorbed Si(001) surface is studied using first-principles electron-conduction calculation. The resultant STM image and scanning tunneling spectroscopy spectra are in agreement with experimental results. The contributions of the $\pi$ states of bare dimers to the tunnel current are markedly large, and the $\sigma$ states of the dimers rarely affect the STM images. The tunnel currents do not pass through the centers of the dimers but go through the edges of the dimers with local loop currents. In addition, when the tip exists above the hydrogen-adsorbed dimer, there are certain contributions from the $\pi$ state of the adjacing bare dimers to the tunnel current. This leads to the STM image in which the hydrogen-adsorbed dimers neighboring bare dimers look higher than those surrounded by hydrogen-adsorbed dimers. These results are consistent with the experimental images observed by STM.

First-Principles Calculation of Tunneling Current of H2- or NH3-Adsorbed Si(001) Surface in Scanning Tunneling Microscopy

The tunneling current flowing between molecule-adsorbed Si(001) surfaces and a tip in scanning tunneling microscopy (STM) is studied using the first-principles electron-transport calculations. The amount of the tunneling current evaluated in this study is consistent with the experimental results. The tunneling current with the tip above the molecule-adsorbed dimer is lower than that with the tip above the bare dimer, which is interpreted by the stabilization of the Si–Si π bonding states due to adsorption of the molecules. These results agree with the experimental results, where molecule-adsorbed dimers look geometrically lower than bare dimers.

First-Principles Study on the Scanning Tunneling Microscopy Image of H-Adsorbed Si(001)

The tunneling current flowing between the tip and H-adsorbed Si(001) surface in Scanning Tunneling Microscopy (STM) is investigated using the first-principles calculations based on the real-space finite-difference method. The resultant current map is consistent with the STM image in which H-adsorbed dimer looks geometrically lower than the bare dimer. Although the isosurface of the local density of states above the H-terminated Si dimer, which are mainly attributed by the Si-H σ bonding states, locate itself higher than that above the bare Si buckled dimer, these bonding states do not contribute to the tunneling current. On the other hand, many electrons tunnel from π bond of the unreacted dimer into the tip. Accordingly, the H-adsorbed dimer appears geometrically lower than the bare dimer in the STM, since the tip must approach closer to the sample surface in order to achieve the constant tunneling current.

Ultrafast nuclear dynamics induced by photodetachment of Ag2– and Ag2O2–: oxygen desorption from a molecular silver surface

Femtosecond nuclear dynamics of mass-selected neutral Ag2 and Ag2O2 clusters are investigated with the 'negative ion-to neutral-to positive ion'(NeNePo) technique. For the bare silver dimer, wave packet dynamics occurring in the neutral electronic ground state and in the first excited triplet state are observed after photodetachment from the anion with 3.05 eV photon energy. While the dynamics in the ground state lead to an oscillatory structure in the NeNePo-pump-probe spectra with a vibrational constant of 185 cm-1, the dynamics in the triplet state are assigned to a bound-free transition leading to dissociation. Photodetachment from the Ag2O2- complex results in the desorption of O2. The experimental data clearly show the influence of the desorbing oxygen ligand on the nuclear dynamics of the silver dimer inducing a red shift in the vibrational frequency and an intensity enhancement of the oscillatory signal.

Dimer-anticorrelation-induced stabilization of adsorbate clustering on the Si100-(2 x 1) surface.

It is well established that absorbate-absorbate interactions play a key role in determining the distribution of adsorbates on surfaces. In cases where these interactions are repulsive adsorbates frequently arrange so as to minimize these unfavorable interactions. This simple picture, however, neglects the influence of adsorption on the properties on the underlying substrate. Here, using STM, we show that on Si(100) many intrinsically repulsive adsorbates cluster to form surface patches even at low surface coverages. With the aid of density functional theory calculations and Monte Carlo simulations, we show that patch formation is an intrinsic property of the Si(100) surface that is driven by the energy lowering associated with the formation of extended regions of bare dimers. The enhanced attraction between anticorrelated tilted bare dimers is sufficient to offset the repulsions between adsorbates.

Dynamics of surface roughening of Cl-terminated Si(100)-(2×1) at 700 K

The dynamics of surface roughening and healing induced by Cl on Si(100)-(2\ifmmode\times\else\texttimes\fi{}1) were studied with variable-temperature scanning tunneling microscopy. Clean samples were exposed to ${\mathrm{Cl}}_{2}$ at room temperature, heated to as high as 700 K, and imaged for periods that exceeded 20 h. Chlorine caused surface roughening via a Cl recycling pathway that created pits and regrowth islands with minimal desorption of ${\mathrm{SiCl}}_{2}.$ This reaction pathway is accessible at $\ensuremath{\sim}675\mathrm{K}$ if the surface is not saturated with Cl. Images showed dimer vacancy creation and pit growth, together with vacancy capture by pits. They also showed dimer vacancy escape from pits and pit annihilation, which had not been reported previously. When the terrace coverage was 0.93 ML, the diffusivity of dimer vacancies along the dimer rows was $\ensuremath{\sim}0.7{\mathrm{\AA{}}}^{2}/\mathrm{sec},$ about three orders-of-magnitude lower than that on clean Si(100). Single Si adatoms were created on terraces and bonded to Si dimers that were Cl-free. They could form new regrowth dimers or they could be accommodated at the ends of existing islands. Adatoms could also be released from regrowth islands. Pairs of atom vacancy lines separated by one or two Si dimers were observed and the transition between those lines and dimer vacancy lines was recorded. Local areas with (3\ifmmode\times\else\texttimes\fi{}2) symmetry were created from the latter. These dynamic changes all require Cl-free Si dimers, and the rate of change of the surface morphology reflects the surface concentration. The rate of change increases with time as the density of bare dimers increases due to the creation of new sites for Cl on an increasingly rough surface and limited desorption.