Dimer Axis Research Articles

Surface-enhanced Raman scattering and gap-mode tip-enhanced Raman scattering investigations of phthalocyanine molecules on gold nanostructured substrates

This study reports the use of surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering (TERS), both independent and in combination, to investigate Raman enhancement of films under different confinement geometries. The experiments are performed on ultrathin cobalt phthalocyanine (CoPc) films deposited on specially designed SERS structures. The SERS structures are fabricated by electron-beam lithography and contain nanostructured gold films and gold dimer arrays with controlled size and internanocluster distance. Such structures allow investigation of the effects of nanocluster size and internanocluster distance, excitation wavelength, and polarization of light upon the electromagnetic SERS enhancement. Significant enhancement of the Raman scattering by CoPc is observed under 632.8 nm excitation because of the double resonance originating from the energy match between the laser excitation and the localized surface plasmon and electronic transitions in CoPc. The SERS signal of CoPc is further enhanced by decreasing the internanocluster distance. Maximum SERS enhancement occurs when the polarization of the incident light is perpendicular to the dimer axis. Under 514.5 nm excitation, nanostructured gold films give greater enhancement than any of the nanocluster arrays, with the highest enhancement realized using the so-called “gap-mode TERS” wherein the SERS structures are probed in the TERS condition. The TERS experiment is performed using a customized TERS setup and all-metal atomic force microscopy tips custom fabricated. In terms of obtaining the ultimate sensitivity in Raman spectroscopy, further enhancement is achieved by confining the electromagnetic field in a gap between two metallic nanostructures either by using SERS or by combining SERS and TERS.

Quasi-static potential created by an oscillating dipole in the vicinity of two nanospheres (dimer): inversion transformation method

We present a method based on the inversion transformation for obtaining the quasi-static potential created by an oscillating dipole in the vicinity of two dielectric nanospheres (dimer). In the inversion space, a Poisson equation for another potential must be solved in which the source is an effective charge density composed of a point dipole and a point charge; the charge of this point charge depends on the radial component of the dipole moment with respect to the inversion center. We particularly derive the solution of the potential when the dipole is on the dimer axis. Our formalism can provide an alternative physical insight for explaining the radiative properties of localized emitters (molecules) as well as intermolecular interactions mediated by electromagnetic fields. In addition, this method can yield to a less computational effort for calculating the electric field. To illustrate our method, the spatial distributions of the electric field created by a dipole for two particular setups are obtained.

Communication between the zinc and tetrahydrobiopterin binding sites in nitric oxide synthase (774.1)

The nitric oxide synthase (NOS) dimer is stabilized by a Zn2+ ion coordinated to symmetry related Cys residues exactly on the dimer axis. Each of the two essential tetrahydrobiopterin (H4B) molecules in the dimer interacts directly with the heme, and each H4B molecule is about 12 Å from the Zn2+. We have solved the crystal structures of the bovine endothelial NOS (eNOS) dimer oxygenase domain bound to three different pterin compounds and they reveal an intimate structural communication between the H4B and Zn2+ sites. The structure of one of these compounds, WSG1002, bound to eNOS with varying levels of Zn2+, showed that WSG1002 and Zn2+ cannot bind to eNOS simultaneously. WSG1002 both directly and indirectly disrupts hydrogen bonding between key residues in the zinc binding motif, resulting in destabilization of the dimer. Addition of excess Zn2+ stabilizes the Zn2+ site which decreases binding of WSG1002. These results have directed our attention to differences between eNOS and the other two mammalian NOS isoforms, neuronal NOS (nNOS) and inducible NOS (iNOS), that provide a structural basis for why the order of dimer stability is eNOS>nNOS>iNOS.Grant Funding Source: Supported by NIH

Magnetic anisotropy of heteronuclear dimers in the gas phase and supported on graphene: relativistic density-functional calculations

The structural and magnetic properties of mixed PtCo, PtFe, and IrCo dimers in the gas phase and supported on a free-standing graphene layer have been calculated using density-functional theory, both in the scalar-relativistic limit and self-consistently including spin–orbit coupling. The influence of the strong magnetic moments of the 3d atoms on the spin and orbital moments of the 5d atoms, and the influence of the strong spin–orbit coupling contributed by the 5d atom on the orbital moments of the 3d atoms have been studied in detail. The magnetic anisotropy energy is found to depend very sensitively on the nature of the eigenstates in the vicinity of the Fermi level, as determined by band filling, exchange splitting and spin–orbit coupling. The large magnetic anisotropy energy of free PtCo and IrCo dimers relative to the easy direction parallel to the dimer axis is coupled to a strong anisotropy of the orbital magnetic moments of the Co atom for both dimers, and also on the Ir atom in IrCo. In contrast the PtFe dimer shows a weak perpendicular anisotropy and only small spin and orbital anisotropies of opposite sign on the two atoms. For dimers supported on graphene, the strong binding within the dimer and the stronger interaction of the 3d atom with the substrate stabilizes an upright geometry. Spin and orbital moments on the 3d atom are strongly quenched, but due to the weaker binding within the dimer the properties of the 5d atom are more free-atom-like with increased spin and orbital moments. The changes in the magnetic moment are reflected in the structure of the electronic eigenstates near the Fermi level, for all three dimers the easy magnetic direction is now parallel to the dimer axis and perpendicular to the graphene layer. The already very large magnetic anisotropy energy (MAE) of IrCo is further enhanced by the interaction with the support, the MAE of PtFe changes sign, and that of the PtCo dimer is reduced. These changes are discussed in relation to the relativistic electronic structure of free and supported dimers and it is demonstrated that the existence of a partially occupied quasi-degenerate state at the Fermi level favors the formation of a large magnetic anisotropy.

Plasmon Mediated Multiphoton Photoemission Microscopy of Au Nanoholes and Nanohole Dimers

Multiphoton photoemission from “nanoholes” and “nanohole dimers” fabricated by nanosphere shadow lithography in a thin Au film are investigated by ultrafast scanning photoionization microscopy (SPIM), which provides detailed information on laser polarization and local electric field enhancement effects for novel 2D plasmonic architectures. The net photoemission signals (at 800 nm) from isotropic nanohole monomers both (i) below (d ≪ λ) and (ii) comparable to (d ≈ λ) the diffraction limit are insensitive to laser polarization, though SPIM images of the larger species clearly reveal strongly enhanced electron emission from nanohole tangent edges perpendicular to incident laser polarization. Fundamentally contrasting behavior is observed for intrinsically anisotropic plasmonic architectures such as nanohole dimers. Specifically, small nanohole dimers reveal enhanced electron emission for λ = 800 nm light polarized perpendicular to the dimer axis, whereas larger nanohole dimers produce optimum electron yields...

Interaction energy between dipole lines applied on symmetric (2 × 1) reconstructed Si(001)

To study Si(001) vicinals, a periodic array of lines of dipole forces f=(0, fy, fz) is applied on symmetric (2×1) reconstructed Si(001), the lines being directed towards x. The elastic relaxation at T=0K by using the MEAM potential gives surface deformations and line–line interaction energies. The results compared with the Marchenko–Parshin (MP) improved by adding an extra contraction contribution due to surface stress. Two cases are studied: f perpendicular to dimer axis and f parallel to dimer axis. Otherwise, f is either (0, fy, 0) or (0, 0, fz) for better identification. As predicted by the improved MP model with small λ, surface deformations vary as Λf(1−λf)/y2 where Λ is deduced from elastic constants, y is the surface position from the dipole line and λ, present only for f=fy, reflects the extra contraction of the terrace due to surface stress. For f perpendicular to dimer axis, Λ can be deduced from bulk elastic constants (Λb), i.e. equal to between 0.7 and 0.8Λb. λ (present only for f=(0, fy, 0)) is low and at least ten times smaller than this predicted by the improved MP model. This results from the reconstructed nature of Si(001). From surface deformations, this model correctly reproduces interaction energies between dipole lines. For f parallel to dimer axis, λ is non-existent, regardless of the direction of f. The constant Λ cannot be deduced from Λb. In respect to Λb and for (0, fy, 0) and (0, 0, fz), respectively, different Λ's are equal to 1.5 and 1.0 for surface deformations and 2.7 and 1.5 for line–line interaction energies.

Orientation dependence in multiple ionization ofHe2andNe2induced by fast, highly charged ions: Probing the impact-parameter-dependent ionization probability in 11.37-MeV/uS14+collisions with He and Ne

We investigate orientation effects in the fragmentation of He${}_{2}$ and ${\mathrm{Ne}}_{2}$ induced by ${S}^{14+}$ projectiles at an impact energy of 11.37 MeV/u. Multiple ionization shows a strong dependence on the orientation of the dimer axis with respect to the projectile beam axis. We attribute these effects to the impact-parameter-dependent ionization probability $P(b)$ for the atomic scattering process S${}^{14+}+\mathrm{He}$ and S${}^{14+}+\mathrm{Ne}$ and compare our data with a Monte Carlo simulation.

Single-Molecule and Single-Particle-Based Correlation Studies between Localized Surface Plasmons of Dimeric Nanostructures with ∼1 nm Gap and Surface-Enhanced Raman Scattering

Understanding the detailed electromagnetic field distribution inside a plasmonically coupled nanostructure, especially for structures with ~ 1 nm plasmonic gap, is the fundamental basis for the control and use of the strong optical properties of plasmonic nanostructures. Using a multistep AFM tip-matching strategy that enables us to gain the optical spectra with the optimal signal-to-noise ratio as well as high reliability in correlation measurement between localized surface plasmon (LSP) and surface-enhanced Raman scattering (SERS), the coupled longitudinal dipolar and high-order multipolar LSPs were detected within a dimeric structure, where a single Raman dye is located via a single-DNA hybridization between two differently sized Au-Ag core-shell particles. On the basis of the characterization of each LSP component, the distinct phase differences, attributed to different quantities of the excited quadrupolar LSPs, between the transverse and longitudinal regimes were observed for the first time. By assessing the relative ratio of dipolar and quadrupolar LSPs, we found that these LSPs of the dimer with ~ 1 nm gap were simultaneously excited, and large longitudinal bonding dipolar LSP/longitudinal bonding quadrupolar LSP value is required to generate high SERS signal intensity. Interestingly, a minor population of the examined dimers exhibited strong SERS intensities along not only the dimer axis but also the direction that arises from the interaction between the coupled transverse dipolar and longitudinal bonding quadrupolar LSPs. Overall, our high-precision correlation measurement strategy with a plasmonic heterodimer with ~ 1 nm gap allows for the observation of the characteristic spectral features with the optimal signal-to-noise ratio and the subpopulation of plasmonic dimers with a distinct SERS behavior, hidden by a majority of dimer population, and the method and results can be useful in understanding the whole distribution of SERS enhancement factor values and designing plasmonic nanoantenna structures.

Surface stresses on symmetric (2 × 1) reconstructed Si(001) calculated from surface energy variations

On Si(001) vicinals, the orientation of the dimers on the (2×1) reconstructed terrace is mutually perpendicular on either side of a monoatomic step. Understanding the surface stresses on (2×1) reconstructed Si(001) is crucial for the discussion of forces representing steps and possibly stability issues at vicinal surfaces. The surface stresses are calculated from the surface energy variations in function of the deformation parallel to the surface. For the deformation parallel to the dimer rows (x), the first monolayer stress is high as for unreconstructed surfaces. For the other direction (y) parallel to the dimer axis, the first monolayer is weakly stressed while the second monolayer stress is high due to the bond between dimer atoms. In the direction diagonal between x and y, the first monolayer stress is decreased at the expense of the other surface monolayers. The surface stresses are calculated by using the MEAM potential. This potential considers the second nearest neighbouring (2NN) bond between dimer atoms while the 2NN bonds are screened in bulk. This paper validates clearly the Shuttleworth formula.

Near‐field optical enhancement by lead‐sulfide quantum dots and metallic nanoparticles for SERS

There is a growing interest in using quantum dots (QDs) and metallic nanoparticles (NPs), both for luminescence enhancement and surface‐enhanced Raman scattering (SERS). Here, we study the electromagnetic‐field enhancement that can be generated by lead‐sulfide (PbS) QDs using three‐dimensional finite‐element simulations. We investigate the field enhancement associated with combinations of PbS QDs with metallic NPs and substrates. The results show that high field enhancement can be achieved by combining PbS QDs with metallic NPs of larger sizes. The ideal size for Ag NPs is 25 nm, providing a SERS enhancement factor of ~5*108 for light polarization parallel to the NP dimer axis and a gap of 0.6 nm. For Au NPs, the bigger the size, the higher is the field for the studied diameters, up to 50 nm. The near‐field values for PbS QDs above metallic substrates were found to be lower compared to the case of PbS QD‐metal NP dimers. This study provides the understanding for the design and application of QDs for the enhancement of near‐field phenomena. Copyright © 2013 John Wiley & Sons, Ltd.

Surface enhanced Raman scattering by organic and inorganic semiconductors formed on laterally ordered arrays of Au nanoclusters

This work is devoted to the investigation of surface-enhanced Raman scattering by vibrational modes of cobalt phthalocyanine ultrathin films and CuS nanocrystals prepared using by organic molecular beam vapor deposition and the Langmuir–Blodgett technique, respectively, on laterally ordered arrays of Au nanoclusters formed by electron beam lithography on Si and GaAs substrates.The surface-enhanced Raman scattering study of cobalt phthalocyanine films demonstrates the strong dependence of Raman intensity of vibrational modes in cobalt phthalocyanine on the laser excitation wavelength as well as on the size and period of Au nanoclusters. By tuning the optical resonance conditions a maximal enhancement factor of 2×104 is achieved. The investigation of surface-enhanced Raman scattering by cobalt phthalocyanine deposited on laterally ordered arrays of paired Au nanoclusters (dimers) reveals anisotropic enhancement with respect to polarization of the scattered light parallel or perpendicular to the dimer axis.

Reversal of optical binding force by Fano resonance in plasmonic nanorod heterodimer

We present calculations of the optical force on heterodimer of two gold nanorods aligned head-to-tail, under plane wave illumination that is polarized along the dimer axis. It is found that near the dipole-quadrupole Fano resonance, the optical binding force between the nanorods reverses, indicating an attractive to repulsive transition. This is in contrast to homodimer which in similar configuration shows no negative binding force. Moreover, the force spectrum features asymmetric line shape and shifts accordingly when the Fano resonance is tuned by varying the nanorods length or their gap. We show that the force reversal is associated with the strong phase variation between the hybridized dipole and quadrupole modes near the Fano dip. The numerical results may be demonstrated by a near-field optical tweezer and shall be useful for studying "optical matters" in plasmonics.

Giant circular dichroism of a molecule in a region of strong plasmon resonances between two neighboring gold nanocrystals

We report on giant circular dichroism (CD) of a molecule inserted into a plasmonic hot spot. Naturally occurring molecules and biomolecules typically have CD signals in the UV range, whereas plasmonic nanocrystals exhibit strong plasmon resonances in the visible spectral interval. Therefore, excitations of chiral molecules and plasmon resonances are typically off-resonant. Nevertheless, we demonstrate theoretically that it is possible to create strongly enhanced molecular CD utilizing the plasmons. This task is doubly challenging since it requires both creation and enhancement of the molecular CD in the visible region. We demonstrate this effect within the model which incorporates a chiral molecule and a plasmonic dimer. The associated mechanism of plasmonic CD comes from the Coulomb interaction, which is greatly amplified in a plasmonic hot spot. An important feature of the system is anisotropy that results in giant enhancement for the molecular dipoles parallel to the dimer axis. The proposed effect offers very interesting possibilities for enhanced sensing of chiral molecules using visible light.

Coinage metal exciplexes with helium atoms: a theoretical study of M*(2L)Hen (M = Cu, Ag, Au; L = P,D)

The structure and energetics of exciplexes M*((2)L)He(n) (M = Cu, Ag and Au; L = P and D) in their vibrational ground state are studied by employing diffusion Monte Carlo (DMC). Interaction potentials between the excited coinage metals and He atoms are built using the Diatomics-in-Molecule (DIM) approach and ab initio potential curves for the M((2)L)-He dimers. Extending our previous work [Cargnoni et al., J. Phys. Chem. A, 2011, 115, 7141], we computed the dimer potential for Au in the (2)P and (2)D states, as well for Cu and Ag in the (2)D state, employing basis set superposition error-corrected Configuration Interaction calculations. We found that the (2)Π potential correlating with the (2)P state of Au is substantially less binding than for Ag and Cu, a trend well supported by the M(+) ionic radiuses. Conversely, the interaction potentials between a (n - 1)d(9)ns(2 2)D metal and He present a very weak dependency on M itself or the projection of the angular momentum along the dimer axis. This is due to the screening exerted by the ns(2) electrons on the hole in the (n - 1)d shell. Including the spin-orbit coupling perturbatively in the DIM energy matrix has a major effect on the lowest potential energy surface of the (2)P manifold, the one for Cu allowing the formation of a "belt" of five He atoms while the one for Au being completely repulsive. Conversely, spin-orbit coupling has only a weak effect on the (2)D manifold due to the nearly degenerate nature of the diatomic potentials. Structural and energetic results from DMC have been used to support experimental indications for the formation of metastable exciplexes or the opening of non-radiative depopulation channels in bulk and cold gaseous He.

Structures of N2Ar, O2Ar, and O2Xe dimers studied by Coulomb explosion imaging

We use intense femtosecond laser pulses to multiply ionize and directly image the structures of N(2)Ar, O(2)Ar, and O(2)Xe dimers by coincidently measuring the momenta of the fragment ions. All these dimers are found to have an equilibrium T-shaped structure in which the bond of the diatomic molecule is perpendicular to the dimer axis. The equilibrium distance between the rare-gas atom and the center-of-mass of the diatomic molecule is estimated to be R(N2-Ar) ~ 3.86 Å, R(O2-Ar) ~ 3.65 Å, and R(O2-Xe) ~ 4.07 Å, respectively. For the T-shaped N(2)Ar dimer, both sequential and direct triple-ionization-induced three-body breakups are observed. In contrast to N(2)Ar dimer, other structures are found to coexist with the dominating T-shaped one for O(2)Ar and O(2)Xe.

Plasmon coupling in circular-hole dimers: From separation- to touching-coupling regimes

The optical properties of a metal film perforated with periodic circular-hole dimers have been studied and the role of plasmon coupling between the dimer holes has been analyzed. For light polarization perpendicular to the dimer axis, the resonance is sensitive to the hole distance, especially when the dimer holes are nearly touching. Depending on whether the holes are touching or not, two coupling regimes have been explored, where different coupling mechanisms and behaviors are involved. In the separation-coupling regime, the coupling of dimer holes is mainly mediated by the surrounding current or magnetic dipoles. Accordingly, the coupling mode blue-shifts with an increase of hole separation. In the touching-coupling regime, instead, the coupling is mainly governed by two apexes, which carry opposite surface charges and behave as electric dipoles. With the increase of hole distance or approaching of two apexes, the mode shifts drastically to the longer wavelength. The hole touching can also set a cutoff for the current near the apexes, thus, producing a strong circulating current (or magnetic field) around (or inside) the dimer holes. Such a strong magnetic field is not present for single circular holes. In addition, for light polarization parallel to the dimer axis, no obvious shifts of the plasmon mode can be observed. The structure may be employed to boost light-matter interactions via the enhanced electric or magnetic fields and filter light with the desired wavelength or polarization.

Unoccupied dimer-bond state at Si(001) surfaces

Two-photon photoemission is used to identify the unoccupied dimer-bond state on the Si(001) surface at an energy 2.83 eV above the valence-band maximum. A strong resonance enhancement is found for excitation from the occupied dangling-bond state. The azimuthal and polarization dependence proves the orientation of the observed state along the dimer axis. The dispersion is dominated by the occupied initial state described by $\ensuremath{-}0.50$ free-electron masses in one- and two-photon photoemission.

Plasmon Coupling in Silver Nanocube Dimers: Resonance Splitting Induced by Edge Rounding

Absolute extinction cross sections of individual silver nanocube dimers are measured using spatial modulation spectroscopy in correlation with their transmission electron microscopy images. For very small interparticle distances and an incident light polarized along the dimer axis, we give evidence for a clear splitting of the main dipolar surface plasmon resonance which is found to be essentially induced by cube edge rounding effects. Supported by discrete dipole approximation and finite element method calculations, this phenomenon highlights the high sensitivity of the plasmonic coupling to the exact shape of the effective capacitor formed by the facing surfaces of both particles, especially in the regime of very close proximity.

Near Field Enhancement in Ag Au Nanospheres Heterodimers

The near field enhancement in Ag Au nanospheres heterodimers excited at their respective resonance wavelengths is studied in detail using rigorous electrodynamics calculations based on the Generalized Multiparticle Mie theory. The effect of incident polarization, nanosphere radius, and interparticle separation on the distribution pattern and magnitude of the near field enhancement is analyzed. As in the homodimer case, the highest enhancement values are found for incident polarization parallel to the dimer axis. However, there are significant different enhancement patterns around the dimer according to the excitation wavelength. Analyzing the vector field plot of the enhancement, and comparing it with those corresponding to Ag and Au nanospheres homodimers, the differences observed are rationalized in terms of multipole excitations to explain the effect of breaking the symmetry of the plasmonic heterodimer. The results presented could be a useful tool for future design and engineering of plasmonic devices...

The Structure of the CRISPR-Associated Protein Csa3 Provides Insight into the Regulation of the CRISPR/Cas System

Adaptive immune systems have recently been recognized in prokaryotic organisms where, in response to viral infection, they incorporate short fragments of invader-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). In subsequent infections, the CRISPR loci are transcribed and processed into guide sequences for the neutralization of the invading RNA or DNA. The CRISPR-associated protein machinery (Cas) lies at the heart of this process, yet many of the molecular details of the CRISPR/Cas system remain to be elucidated. Here, we report the first structure of Csa3, a CRISPR-associated protein from Sulfolobus solfataricus (Sso1445), which reveals a dimeric two-domain protein. The N-terminal domain is a unique variation on the dinucleotide binding domain that orchestrates dimer formation. In addition, it utilizes two conserved sequence motifs [Thr-h-Gly-Phe-(Asn/Asp)-Glu-X4-Arg and Leu-X2-Gly-h-Arg] to construct a 2-fold symmetric pocket on the dimer axis. This pocket is likely to represent a regulatory ligand-binding site. The N-terminal domain is fused to a C-terminal MarR-like winged helix–turn–helix domain that is expected to be involved in DNA recognition. Overall, the unique domain architecture of Csa3 suggests a transcriptional regulator under allosteric control of the N-terminal domain. Alternatively, Csa3 may function in a larger complex, with the conserved cleft participating in protein–protein or protein–nucleic acid interactions. A similar N-terminal domain is also identified in Csx1, a second CRISPR-associated protein family of unknown function.