Simulating Surface-Enhanced Raman Optical Activity Using Atomistic Electrodynamics-Quantum Mechanical Models

The Amsterdam Modeling Suite

In this paper, we present the Amsterdam Modeling Suite (AMS), a comprehensive software platform designed to support advanced molecular and materials simulations across a wide range of chemical and physical systems. AMS integrates cutting-edge quantum chemical methods, including Density Functional Theory (DFT) and time-dependent DFT, with molecular mechanics, fluid thermodynamics, machine learning techniques, and more, to enable multi-scale modeling of complex chemical systems. Its design philosophy allows for seamless coupling between components, facilitating simulations that range from small molecules to complex biomolecular and solid-state systems, making it a versatile tool for tackling interdisciplinary challenges, both in industry and in academia. The suite also emphasizes user accessibility, with an intuitive graphical interface, extensive scripting capabilities, and compatibility with high-performance computing environments.

Bisignate Surface-Enhanced Raman Optical Activity with Analyte-Capped Colloids

Spectroscopic detection of chiral compounds is often hampered by a low sensitivity. For Raman optical activity (ROA), the signal can be dramatically increased in surface-enhanced experiments. So far, however, reproducible surface-enhanced ROA (SEROA) spectra were obtained for a reporter molecule only via induced chirality, and the intensities were just proportional to the Raman scattering. In the present study, we show that the signal can be substantially increased if colloidal silver nanoparticles are prepared already in the presence of a chiral analyte. In this case, both the analyte's and reporter's bands are visible. In addition, some experiments provided bisignate SEROA patterns, thus significantly enhancing information about the molecular structure provided by this spectroscopic method. Increased electronic circular dichroism (ECD) of the capped aggregated colloids suggests that ECD and polarized Raman scattering (ECD-Raman) contribute to the monosignate SEROA intensities, while well-dispersed nonaggregating colloids are important for observation of true (bisignate) molecular vibrational SEROA.

The near field response of molecules coupled with plasmons at atomistic resolution

The interaction between nanoparticles on mirror (NPoM) nanostructures and molecules is of great significance for the development of plasmon-enhanced spectroscopy (PES) techniques. However, the coupling mechanism between resonantly excited molecules and plasmonics has not been fully understood. In this work, we took viologen molecules within an Au plasmonic nanocavity (AuNC) as an example to illustrate how resonant molecules influence the near-field distributions. We found that the near-fields are highly enhanced and the near-field distributions are altered when the monocationic viologen (V+˙) is in resonance. In the AuNC, the near-field enhancement of a molecule is significantly enhanced by the adjacent molecules. However, the average near-field enhancements experienced by each molecule decrease with the increasing coverage of the molecular monolayer. Furthermore, the contributions of molecules to the near-field enhancement initially increase and then decrease as coverage increases. The interactions between the molecules and the nanocavity exhibit negative contributions to near-field enhancement. Overall, this work offers valuable insights into the impact of resonantly excited molecules on near-field enhancements in nanocavities and offers guidance for tuning excitation wavelength. We propose that the resonance state and coverage of molecules are critical to improving the sensitivity and specificity of PES techniques.

Development of discrete interaction models for ultra-fine nanoparticle plasmonics

Plasmonics serves as a most outstanding feature of nanoparticle technology and is nowadays used in numerous applications within imaging, sensing and energy harvesting, like plasmonically enhanced solar cells, nanoparticle bioimaging, plasmon-controlled fluorescence for molecular tracking in living cells, plasmon-controlled electronic molecular devices and surface enhanced Raman spectroscopy for single molecular detection. Although plasmonics has been utilized since ancient times, the understanding of its basic interactions has not been fully achieved even under the emergence of modern nanoscience. In particular, it has been difficult to address the "ultra-fine" 1-10 nm regime, important for applications especially in bioimaging and biomedical areas, where neither classical nor quantum based theoretical methods apply. Recently, new approaches have been put forward to bridge this size gap based on semi-empirical discrete interaction models where each atom makes a difference. A primary aim of this perspective article is to review some of the most salient features of these models, and in particular focus on a recent extension - the extended discrete interaction model (Ex-DIM), where the geometric and environmental features are extended - and highlight a set of benchmark studies using this model concerning size, shape, material, temperature dependence and other characteristics of ultra-fine plasmonic nanoparticles. We also analyze new possibilities offered by the model for designing ultra-fine plasmonic particles for applications in the areas of bioimaging, biosensing, photothermal therapy, infrared light harvesting and photodetection. We foresee that future modelling activities will be closely connected to collaborative experimental work including synthesis, device fabrication and measurements with feedback and validation in a systematic fashion. With this strategy we can expect that modelling of ultra-fine plasmonics particles can be integrated in the development of novel plasmonic systems with unprecedented performance and applicability.

Circular Polarization-Resolved Raman Optical Activity: A Perspective on Chiral Spectroscopies of Vibrational States

Circular polarization-resolved Raman scattering methods include Raman optical activity (ROA) and its derivative─surface-enhanced Raman optical activity (SEROA). These spectroscopic modalities are rapidly developing due to their high information content, stand-off capabilities, and rapid development of Raman-active chiral nanostructures. These methods enable a direct readout of the vibrational energy levels of chiral molecules, crystals, and nanostructured materials, making it possible to study complex interactions and the dynamic interfaces between them. They were shown to be particularly valuable for nano- and biotechnological fields encompassing complex particles with nanoscale chirality that combine strong scattering and intense polarization rotation. This perspective dives into recent advancements in ROA and SEROA, their distinction from surface-enhanced Raman scattering, and the potential of these information-rich label-free spectroscopies for the detection of chiral biomolecules.

Modeling the near-field effect on molecular excited states using the discrete interaction model/quantum mechanical method

Strong light-matter interactions significantly modify the optical properties of molecules in the vicinity of plasmonic metal nanoparticles. Since the dimension of the plasmonic cavity approaches that of the molecules, it is critical to explicitly describe the nanoparticle junctions. In this work, we use the discrete interaction model/quantum mechanical (DIM/QM) method to model the coupling between the plasmonic near-field and molecular excited states. DIM/QM is a combined electrodynamics/quantum mechanical model that uses an atomistic description of the nanoparticle. We extend the DIM/QM method to include the local field effects in the sum-over-state formalism of time-dependent density functional theory. As a test of the method, we study the interactions between small organic chromophores and metal nanoparticles. In particular, we examine how the inclusion of multiple electronic transitions and intermolecular interactions modify the coupling between molecules and nanoparticles. Using the sum-over-state formalism of DIM/QM, we show that two-state models break down when the plasmon excitation is detuned from the molecular excitations. To gain further insight, we compare the simple coupled-dipole model (CDM) with the DIM/QM model. We find that CDM works well for simple systems but fails when going beyond the single molecule or single nanoparticle cases. We also find that the coupling depends strongly on the site of the nanoparticle in which the chromophore couples to. Our work suggests the importance of explicitly describing the cavity to capture the atomistic level local field environment in which the molecule strongly couples to.

Local-Field Effects in Linear Response Properties within a Polarizable Frozen Density Embedding Method

In this work, we present a polarizable frozen density embedding (FDE) method for calculating polarizabilities of coupled subsystems. The method (FDE-pol) combines a FDE method with an explicit polarization model such that the expensive freeze/thaw cycles can be bypassed, and approximate nonadditive kinetic potentials are avoided by enforcing external orthogonality between the subsystems. To describe the polarization of the frozen environment, we introduce a Hirshfeld partition-based density-dependent method for calculating the atomic polarizabilities of atoms in molecules, which alleviates the need to fit the atomic parameters to a specific system of interest or to a larger general set of molecules. We show that the Hirshfeld partition-based method predicts molecular polarizabilities close to the basis set limit, and thus, a single basis set-dependent scaling parameter can be introduced to improve the agreement against the reference polarizability data. To test the model, we characterized the uncoupled and coupled response of small interacting molecular complexes. Here, the coupled response properties include the perturbation of the frozen system due to the external perturbation which is ignored in the uncoupled response. We show that FDE-pol can accurately reproduce both the exact uncoupled polarizability and the coupled polarizabilities of the supermolecular systems. Using damped response theory, we also demonstrate that the coupled frequency-dependent polarizability can be described by including local field effects. The results emphasize the necessity of including local-field effects for describing the response properties of coupled subsystems, as well as the importance of accurate atomic polarizability models.

Measurement and Theory of Resonance Raman Optical Activity for Gases, Liquids, and Aggregates. What It Tells about Molecules

Resonance Raman Optical Activity (RROA) appeared as a natural extension of the nonresonance branch. It combines the structural sensitivity of chiroptical spectroscopy with the signal enhancement coming from the resonance of molecular electronic transitions with the excitation laser light. However, the idea has been hampered by many technical and theoretical problems that are being clarified only in recent years. We provide the theoretical basis and several examples documenting the problems, achievements, and potential of RROA, in particular in biomolecular studies.

A discrete interaction model/quantum mechanical method for simulating surface-enhanced Raman spectroscopy in solution

Since surface-enhanced Raman scattering (SERS) is of considerable interest for sensing applications in aqueous solution, the role that solvent plays in the spectroscopy must be understood. However, these efforts are hindered due to a lack of simulation approaches for modeling solvent effects in SERS. In this work, we present an atomistic electrodynamics-quantum mechanical method to simulate SERS in aqueous solution based on the discrete interaction model/quantum mechanical method. This method combines an atomistic electrodynamics model of the nanoparticle with a time-dependent density functional theory description of the molecule and a polarizable embedding method for the solvent. The explicit treatment of solvent molecules and nanoparticles results in a large number of polarizable dipoles that need to be considered. To reduce the computational cost, a simple cut-off based approach has been implemented to limit the number of dipoles that need to be treated without sacrificing accuracy. As a test of this method, we have studied how solvent affects the SERS of pyridine in the junction between two nanoparticles in aqueous solution. We find that the solvent leads to an enhanced SERS due to an increased local field at the position of the pyridine. We further demonstrate the importance of both image field and local field effects in determining the enhancements and the spectral signatures. Our results show the importance of describing the local environment due to the solvent molecules when modeling SERS.

Mapping Molecular Adsorption Configurations with <5 nm Spatial Resolution through Ambient Tip-Enhanced Raman Imaging

We interrogate para-mercaptobenzoic acid (MBA) molecules chemisorbed onto plasmonic silver nanocubes through tip-enhanced Raman (TER) spectral nanoimaging. Through a detailed examination of the spectra, aided by correlation analysis and density functional theory calculations, we find that MBA chemisorbs onto the plasmonic particles with at least two distinct configurations: S- and CO₂-bound. High spatial resolution TER mapping allows us to distinguish between the distinct adsorption geometries with a pixel-limited (<5 nm) spatial resolution under ambient laboratory conditions.

A Discrete Interaction Model/Quantum Mechanical Method for Simulating Plasmon-Enhanced Two-Photon Absorption

In this work, we extend the discrete interaction model/quantum mechanical (DIM/QM) method to simulate plasmon-enhanced two-photon absorption (PETPA). The metal nanoparticle is treated atomistically by means of electrodynamics, while the molecule is described using damped cubic response theory within a time-dependent density functional theory framework. Using DIM/QM, we study the PETPA of para-nitroaniline ( p-NA) with a focus on the local and image field effects, the molecular orientation effects, and the molecule-nanoparticle distance effects. Our findings show that the enhancement is more complex than the simple | E|⁴ enhancement mechanism, where | E| is the local field at the position of the molecule. Because of specific interactions with the nanoparticle, we find that a TPA dark state of p-NA can be significantly enhanced through a coupling with the plasmon excitation. The results presented in this work illustrate that the coupling between molecular excitations and plasmons can give rise to unusual and complex behavior in nonlinear spectroscopy that cannot simply be understood by considering the optical properties of the individual molecules and nanoparticles separately. The method presented here provides detailed insights into the enhancement of nonlinear optical properties of molecules coupled to plasmonic nanoparticles.

Searching the Theoretical Ultimate Limits of Probing Surface-Enhanced Raman Optical Activity

The single-molecule Raman detection has been realized for a long time because of the enhancement effect of surface plasmons. However, the small cross section of Raman optical activity (ROA) makes it so hard to detect the ROA of even a few molecules; and a normal surface-enhanced ROA (SE-ROA) is also very time consumable even with strong laser power. Detecting ROA in an economic way is an important issue. In this paper, we discuss the ultimate limit of the SE-ROA and provide the enhancement factor formula for SE-ROA. Following the formula, we proposed a structure with both huge Raman enhancement and ROA enhancement, which is helpful for single-molecule ROA detection.

Raman optical activity (ROA) and surface-enhanced ROA (SE-ROA) of (+)-(R)-methyloxirane adsorbed on a Ag20cluster

Chirality is ubiquitous in nature and plays an important role in biochemistry because biological function is largely dependent on the handedness of chiral molecules.

Theory of Linear and Nonlinear Surface-Enhanced Vibrational Spectroscopies

The vibrational spectroscopy of molecules adsorbed on metal nanoparticles can be enhanced by many orders of magnitude so that the detection and identification of single molecules are possible. The enhancement of most linear and nonlinear vibrational spectroscopies has been demonstrated. In this review, we discuss theoretical approaches to understanding linear and nonlinear surface-enhanced vibrational spectroscopies. A unified description of enhancement mechanisms classified as either electromagnetic or chemical in nature is presented. Emphasis is placed on understanding the spectral changes necessary for interpretation of linear and nonlinear surface-enhanced vibrational spectroscopies.

Fano resonance assisting plasmonic circular dichroism from nanorice heterodimers for extrinsic chirality

In this work, the circular dichroisms (CD) of nanorice heterodimers consisting of two parallel arranged nanorices with the same size but different materials are investigated theoretically. Symmetry-breaking is introduced by using different materials and oblique incidence to achieve strong CD at the vicinity of Fano resonance peaks. We demonstrate that all Au-Ag heterodimers exhibit multipolar Fano resonances and strong CD effect. A simple quantitative analysis shows that the structure with larger Fano asymmetry factor has stronger CD. The intensity and peak positions of the CD effect can be flexibly tuned in a large range by changing particle size, shape, the inter-particle distance and surroundings. Furthermore, CD spectra exhibit high sensitivity to ambient medium in visible and near infrared regions. Our results here are beneficial for the design and application of high sensitive CD sensors and other related fields.

Plasmonic circular dichroism of 310- and α-helix using a discrete interaction model/quantum mechanics method

Plasmonic circular dichroism (CD) of chiral molecules in the near field of plasmonic nanoparticles (NPs) may be used to enhance molecular CD signatures or to induce a CD signal at the plasmon resonance. A recent few-states theory explored these effects for model systems and showed an orientation dependence of the sign of the induced CD signal for spherical NPs. Here, we use the discrete interaction model/quantum mechanical (DIM/QM) method to simulate the CD and plasmonic CD of the 310- and α-helix conformations of a short alanine peptide. We find that the interactions between the molecule and the plasmon lead to significant changes in the CD spectra. In the plasmon region, we find that the sign of the CD depends strongly on the orientation of the molecule as well as specific interactions with the NP through image dipole effects. A small enhancement of the CD is found in the molecular region of the spectrum, however, the molecular signatures may be significantly altered through interactions with the NP. We also show that the image dipole effect can result in induced plasmonic CD even for achiral molecules. Overall, we find that the specific interactions with the NP can lead to large changes to the CD spectrum that complicates the interpretation of the results.