Plasmon-enhanced stimulated Raman scattering microscopy with single-molecule detection sensitivity

Surface Enhanced Nonlinear Raman Processes for Advanced Vibrational Probing

Surface enhanced Raman scattering (SERS) is not restricted to the well-known one-photon excited spontaneous Raman process that gives information on molecular composition, structure, and interaction through vibrational probing with high sensitivity. The enhancement mainly originates in high local fields, specifically those provided by localized surface plasmon resonances of metal nanostructures. High local fields can particularly support nonlinear Raman scattering, as it depends on the fields to higher powers. By revealing plasmon-molecule interactions, nonlinear Raman processes provide a very sensitive access to the properties of metal nanomaterials and their interfaces with molecules and other materials. This Perspective discusses plasmon-enhanced spontaneous and coherent nonlinear Raman scattering with the aim of identifying advantages that lead to an advanced vibrational characterization of such systems. The discussion will highlight the aspects of vibrational information that can be gained based on specific advantages of different incoherent and coherent Raman scattering and their surface enhancement. While the incoherent process of surface enhanced hyper Raman scattering (SEHRS) gives highly selective and spectral information complementary to SERS, the incoherent process of surface enhanced pumped anti-Stokes Raman scattering (SEPARS) can help to infer effective nonresonant SERS cross sections and allows to see "hot" vibrational transitions. Surface enhanced coherent anti-Stokes Raman scattering (SECARS) and surface enhanced stimulated Raman scattering (SESRS) combine the advantages of high local fields and coherence, which gives rise to high detection sensitivity and offers possibilities to explore molecule-plasmon interactions for a comprehensive characterization of composite and hybrid structures in materials research, catalysis, and nanobiophotonics.

Time-dependent surface-enhanced Raman scattering: A theoretical approach

A new procedure for computing the time-dependent Raman scattering of molecules in the proximity of plasmonic nanoparticles (NPs) is proposed, drawing inspiration from the pioneering Lee and Heller's theory. This strategy is based on a preliminary simulation of the molecular vibronic wavefunction in the presence of a plasmonic nanostructure and an incident light pulse. Subsequently, the Raman signal is evaluated through an inverse Fourier Transform of the coefficients' dynamics. Employing a multiscale approach, the system is treated by coupling the quantum mechanical description of the molecule with the polarizable continuum model for the NP. This method offers a unique advantage by providing insights into the time evolution of the plasmon-enhanced Raman signal, tracking the dynamics of the incident electric field. It not only provides for the total Raman signal at the process's conclusion but also gives transient information. Importantly, the flexibility of this approach allows for the simulation of various incident electric field profiles, enabling a closer alignment with experimental setups. This adaptability ensures that the method is relevant and applicable to diverse real-world scenarios.

Viewing 3D spatial biology with highly-multiplexed Raman imaging: from spectroscopy to biotechnology

Understansding complex biological systems requires the simultaneous characterization of a large number of interacting components in their native 3D environment with high spatial resolution. Highly-multiplexed Raman imaging is an emerging general strategy for detecting biomarkers with scalable multiplexity and ultra-sensitivity based on a series of stimulated Raman scattering (SRS) techniques. Here we review recent advances in highly-multiplexed Raman imaging and how they contribute to the technological revolution in 3D spatial biology, focusing on the developmental pathway from spectroscopy study to biotechnology invention. We envision highly-multiplexed Raman imaging is taking off, which will greatly facilitate our understanding in biological and medical research fields.

Simultaneous Protein Colorful Imaging via Raman Signal Classification

Protein imaging aids diagnosis and drug development by revealing protein-drug interactions or protein levels. However, the challenges of imaging multiple proteins, reduced sensitivity, and high reliance on specific protein properties such as Raman peaks or refractive index hinder the understanding. Here, we introduce multiprotein colorful imaging through Raman signal classification. Our method utilized machine learning-assisted classification of Raman signals, which are the distinctive features of label-free proteins. As a result, three types of proteins could be imaged simultaneously. In addition, we could quantify individual proteins from a mixture of multiple proteins over a wide detection range (10 fg/mL-1 μg/mL). These results showed a 1000-fold improvement in sensitivity and a 30-fold increase in the upper limit of detection compared to existing methods. These advances will enhance our understanding of biology and facilitate the development of disease diagnoses and treatments.

Noise learning of instruments for high-contrast, high-resolution and fast hyperspectral microscopy and nanoscopy

The low scattering efficiency of Raman scattering makes it challenging to simultaneously achieve good signal-to-noise ratio (SNR), high imaging speed, and adequate spatial and spectral resolutions. Here, we report a noise learning (NL) approach that estimates the intrinsic noise distribution of each instrument by statistically learning the noise in the pixel-spatial frequency domain. The estimated noise is then removed from the noisy spectra. This enhances the SNR by ca. 10 folds, and suppresses the mean-square error by almost 150 folds. NL allows us to improve the positioning accuracy and spatial resolution and largely eliminates the impact of thermal drift on tip-enhanced Raman spectroscopic nanoimaging. NL is also applicable to enhance SNR in fluorescence and photoluminescence imaging. Our method manages the ground truth spectra and the instrumental noise simultaneously within the training dataset, which bypasses the tedious labelling of huge dataset required in conventional deep learning, potentially shifting deep learning from sample-dependent to instrument-dependent.

Hyper-Raman spectroscopy of biomolecules

The hyper-Raman scattering (HRS) spectra of biologically significant molecules (D-glucose, L-alanine, L-arabinose, L-tartaric acid) in aqueous solutions are reported. The HRS spectra were measured using a picosecond laser at 532 nm operating at a MHz repetition rate. High signal to noise spectra were collected with a commercial spectrometer and CCD without resonant, nanoparticle, or surface enhancement. The HRS peak frequencies, relative intensities, band assignments, and depolarization ratios are examined. By comparing HRS to Raman scattering (RS) and infrared absorption spectra we verify that the IR-active vibrational modes of the target molecules are observed in HRS spectra but come with substantially different peak intensities. The HRS of the biomolecules as well as water, dimethyl sulfoxide, methanol, and ethanol were deposited into a data repository to support the development of theoretical descriptions of HRS for these molecules. Depositing the spectra in a repository also supports future dual detection RS, HRS microscopes which permit simultaneous high-spatial-resolution vibrational spectroscopy of IR-active and Raman-active vibrational modes.

Raman spectroscopy and its plasmon-enhanced counterparts: A toolbox to probe protein dynamics and aggregation

Protein unfolding and aggregation are often correlated with numerous diseases such as Alzheimer's, Parkinson's, Huntington's, and other debilitating neurological disorders. Such adverse events consist of a plethora of competing mechanisms, particularly interactions that control the stability and cooperativity of the process. However, it remains challenging to probe the molecular mechanism of protein dynamics such as aggregation, and monitor them in real-time under physiological conditions. Recently, Raman spectroscopy and its plasmon-enhanced counterparts, such as surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS), have emerged as sensitive analytical tools that have the potential to perform molecular studies of functional groups and are showing significant promise in probing events related to protein aggregation. We summarize the fundamental working principles of Raman, SERS, and TERS as nondestructive, easy-to-perform, and fast tools for probing protein dynamics and aggregation. Finally, we highlight the utility of these techniques for the analysis of vibrational spectra of aggregation of proteins from various sources such as tissues, pathogens, food, biopharmaceuticals, and lastly, biological fouling to retrieve precise chemical information, which can be potentially translated to practical applications and point-of-care (PoC) devices. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Diagnostic Nanodevices Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Stimulated Raman photothermal microscopy toward ultrasensitive chemical imaging

Stimulated Raman scattering (SRS) microscopy has shown enormous potential in revealing molecular structures, dynamics, and couplings in complex systems. However, the sensitivity of SRS is fundamentally limited to the millimolar level due to shot noise and the small modulation depth. To overcome this barrier, we revisit SRS from the perspective of energy deposition. The SRS process pumps molecules to their vibrationally excited states. The subsequent relaxation heats up the surroundings and induces refractive index changes. By probing the refractive index changes with a laser beam, we introduce stimulated Raman photothermal (SRP) microscopy, where a >500-fold boost of modulation depth is achieved. The versatile applications of SRP microscopy on viral particles, cells, and tissues are demonstrated. SRP microscopy opens a way to perform vibrational spectroscopic imaging with ultrahigh sensitivity.

Plasmonic Nanostructure Biosensors: A Review

Plasmonic nanostructure biosensors based on metal are a powerful tool in the biosensing field. Surface plasmon resonance (SPR) can be classified into localized surface plasmon resonance (LSPR) and propagating surface plasmon polariton (PSPP), based on the transmission mode. Initially, the physical principles of LSPR and PSPP are elaborated. In what follows, the recent development of the biosensors related to SPR principle is summarized. For clarity, they are categorized into three groups according to the sensing principle: (i) inherent resonance-based biosensors, which are sensitive to the refractive index changes of the surroundings; (ii) plasmon nanoruler biosensors in which the distances of the nanostructure can be changed by biomolecules at the nanoscale; and (iii) surface-enhanced Raman scattering biosensors in which the nanostructure serves as an amplifier for Raman scattering signals. Moreover, the advanced application of single-molecule detection is discussed in terms of metal nanoparticle and nanopore structures. The review concludes by providing perspectives on the future development of plasmonic nanostructure biosensors.

Stimulated Raman Photothermal Microscopy towards Ultrasensitive Chemical Imaging

Stimulated Raman scattering (SRS) microscopy has shown enormous potential in revealing molecular structures, dynamics and coupling in a complex system. However, the bond-detection sensitivity of SRS microscopy is fundamentally limited to milli-molar level due to the shot noise and the small modulation depth in either pump or Stokes beam4. Here, to overcome this barrier, we revisit SRS from the perspective of energy deposition. The SRS process pumps molecules to their vibrational excited states. The thereafter relaxation heats up the surrounding and induces a change in refractive index. By probing the refractive index change with a continuous wave beam, we introduce stimulated Raman photothermal (SRP) microscopy, where a >500-fold boost of modulation depth is achieved on dimethyl sulfide with conserved average power. Versatile applications of SRP microscopy on viral particles, cells, and tissues are demonstrated. With much improved signal to noise ratio compared to SRS, SRP microscopy opens a new way to perform vibrational spectroscopic imaging with ultrahigh sensitivity and minimal water absorption.

Imaging and controlling coherent phonon wave packets in single graphene nanoribbons

The motion of atoms is at the heart of any chemical or structural transformation in molecules and materials. Upon activation of this motion by an external source, several (usually many) vibrational modes can be coherently coupled, thus facilitating the chemical or structural phase transformation. These coherent dynamics occur on the ultrafast timescale, as revealed, e.g., by nonlocal ultrafast vibrational spectroscopic measurements in bulk molecular ensembles and solids. Tracking and controlling vibrational coherences locally at the atomic and molecular scales is, however, much more challenging and in fact has remained elusive so far. Here, we demonstrate that the vibrational coherences induced by broadband laser pulses on a single graphene nanoribbon (GNR) can be probed by femtosecond coherent anti-Stokes Raman spectroscopy (CARS) when performed in a scanning tunnelling microscope (STM). In addition to determining dephasing (~440 fs) and population decay times (~1.8 ps) of the generated phonon wave packets, we are able to track and control the corresponding quantum coherences, which we show to evolve on time scales as short as ~70 fs. We demonstrate that a two-dimensional frequency correlation spectrum unequivocally reveals the quantum couplings between different phonon modes in the GNR.

Hybrid Plasmonic Nanostructures for Enhanced Single-Molecule Detection Sensitivity

Biosensing applications based on fluorescence detection often require single-molecule sensitivity in the presence of strong background signals. Plasmonic nanoantennas are particularly suitable for these tasks, as they can confine and enhance light in volumes far below the diffraction limit. The recently introduced antenna-in-box (AiB) platforms achieved high single-molecule detection sensitivity at high fluorophore concentrations by placing gold nanoantennas in a gold aperture. However, hybrid AiB platforms with alternative aperture materials such as aluminum promise superior performance by providing better background screening. Here, we report on the fabrication and optical characterization of hybrid AiBs made of gold and aluminum for enhanced single-molecule detection sensitivity. We computationally optimize the optical properties of AiBs by controlling their geometry and materials and find that hybrid nanostructures not only improve signal-to-background ratios but also provide additional excitation intensity and fluorescence enhancements. We further establish a two-step electron beam lithography process to fabricate hybrid material AiB arrays with high reproducibility and experimentally validate the higher excitation and emission enhancements of the hybrid nanostructures as compared to their gold counterpart. We foresee that biosensors based on hybrid AiBs will provide improved sensitivity beyond the capabilities of current nanophotonic sensors for a plethora of biosensing applications ranging from multicolor fluorescence detection to label-free vibrational spectroscopy.

Toward the Next Frontiers of Vibrational Bioimaging

Chemical imaging based on vibrational contrasts can extract molecular information entangled in complex biological systems. To this end, nonlinear Raman scattering microscopy, mid-infrared photothermal (MIP) microscopy, and atomic force microscopy (AFM)-based force-detected photothermal microscopies are emerging with better chemical sensitivity, molecular specificity, and spatial resolution than conventional vibrational methods. Their utilization in bioimaging applications has provided biological knowledge in unprecedented detail. This Perspective outlines key methodological developments, bioimaging applications, and recent technical innovations of the three techniques. Representative biological demonstrations are also highlighted to exemplify the unique advantages of obtaining vibrational contrasts. With years of effort, these three methods compose an expanding vibrational bioimaging toolbox to tackle specific bioimaging needs, benefiting many biological investigations with rich information in both label-free and labeling manners. Each technique will be discussed and compared in the outlook, leading to possible future directions to accommodate growing needs in vibrational bioimaging.

Label-free multiphoton imaging flow cytometry

Label-free imaging flow cytometry is a powerful tool for biological and medical research as it overcomes technical challenges in conventional fluorescence-based imaging flow cytometry that predominantly relies on fluorescent labeling. To date, two distinct types of label-free imaging flow cytometry have been developed, namely optofluidic time-stretch quantitative phase imaging flow cytometry and stimulated Raman scattering (SRS) imaging flow cytometry. Unfortunately, these two methods are incapable of probing some important molecules such as starch and collagen. Here, we present another type of label-free imaging flow cytometry, namely multiphoton imaging flow cytometry, for visualizing starch and collagen in live cells with high throughput. Our multiphoton imaging flow cytometer is based on nonlinear optical imaging whose image contrast is provided by two optical nonlinear effects: four-wave mixing (FWM) and second-harmonic generation (SHG). It is composed of a microfluidic chip with an acoustic focuser, a lab-made laser scanning SHG-FWM microscope, and a high-speed image acquisition circuit to simultaneously acquire FWM and SHG images of flowing cells. As a result, it acquires FWM and SHG images (100 × 100 pixels) with a spatial resolution of 500 nm and a field of view of 50 μm × 50 μm at a high event rate of four to five events per second, corresponding to a high throughput of 560-700 kb/s, where the event is defined by the passage of a cell or a cell-like particle. To show the utility of our multiphoton imaging flow cytometer, we used it to characterize Chromochloris zofingiensis (NIES-2175), a unicellular green alga that has recently attracted attention from the industrial sector for its ability to efficiently produce valuable materials for bioplastics, food, and biofuel. Our statistical image analysis found that starch was distributed at the center of the cells at the early cell cycle stage and became delocalized at the later stage. Multiphoton imaging flow cytometry is expected to be an effective tool for statistical high-content studies of biological functions and optimizing the evolution of highly productive cell strains.

Internal Standard Assisted Surface-Enhanced Raman Scattering Nanoprobe with 4-NTP as Recognition Unit for Ratiometric Imaging Hydrogen Sulfide in Living Cells

Hydrogen sulfide (H₂S), as the third endogenous gasotransmitter, is closely associated with various physiological and pathological processes, whereas many aspects of its functions remain unclear. Effective tools for the accurate detection of H₂S in living organisms are urgently needed. We herein reported an internal standard assisted surface-enhanced Raman scattering (SERS) nanoprobe for ratiometric detection of H₂S in vitro and in living cells based on the reduction of nitros with H₂S. This nanoprobe consists of an internal standard (4-mercaptobenzonitrile, MPBN) embedded core-molecule-shell Au nanoflower (Au@MPBN@Au) as the high plasmonic active SERS substrate and the 4-nitrothiophenol (4-NTP) molecule immobilized on the surface as the H₂S recognition unit. With the addition of H₂S, the nitros peak (1329 cm^-1) decreased. Meanwhile, three obvious new peaks appeared at 1139, 1387, and 1433 cm^-1, which were related to the vibration of the dimerized product 4,4'-dimercaptoazobisbenzene (DMAB) of 4-aminothiophenol (4-ATP). However, the peak intensity at 2223 cm^-1 derived from MPBN was not influenced by the outer environment. Thus, the H₂S level was able to be determined based on the ratio of two peak intensities (I₁₁₃₉/I₂₂₂₃) with a detection limit as low as 0.24 μM. Notably, we have proved that SERS nanoprobe Au@MPBN@Au@4-NTP could ratiometrically image both the endogenous and exogenous H₂S in living cells. We anticipate that Au@MPBN@Au@4-NTP could be applied for the study of H₂S-related physiological function in the future.

Trace Analysis of Gases and Liquids with Spontaneous Raman Scattering Based on the Integrating Sphere Principle

Spontaneous Raman scattering is an attractive optical technique for the analysis of gases and liquids; however, their low densities and notoriously weak scattering cross sections demand an enhancement of the spontaneous Raman scattering signal for detection. Here, we have developed a simple but highly effective and fast technique to enhance the signal of spontaneous Raman scattering from gases and liquids. The technique is developed based on the principle of an integrating sphere, which realizes the multiple pass actions of low-energy pump light and the collection of all Raman scattered light for a sample volume of 2 mL. By measuring the ambient air sample with an exposure time of 180 s, we found the experimental detection limit of our spontaneous Raman scattering setup can reach 3 ppm. CH₄ (<2 ppm) in air can be also examined by increasing the exposure time to 300 s. The performance of our setup used for the analysis of trace gases is further illustrated by characterizing ethane, propane, butane, and pentane in methane as well as isotopes of carbon dioxide. The results reveal that the detection limit of our setup for liquids can be improved by nearly 4 orders of magnitude compared to that of confocal Raman scattering spectroscopy with the same experimental conditions.

Plasmon resonance of gold and silver nanoparticle arrays in the Kretschmann (attenuated total reflectance) vs. direct incidence configuration

While the behaviour of plasmonic solid thin films in the Kretschmann (also known as Attenuated Total Reflection, ATR) configuration is well-understood, the use of discrete nanoparticle arrays in this optical configuration is not thoroughly explored. It is important to do so, since close packed plasmonic nanoparticle arrays exhibit exceptionally strong light-matter interactions by plasmonic coupling. The present work elucidates the optical properties of plasmonic Au and Ag nanoparticle arrays in both the direct normal incidence and Kretschmann configuration by numerical models, that are validated experimentally. First, hexagonal close packed Au and Ag nanoparticle films/arrays are obtained by air–liquid interfacial assembly. The numerical models for the rigorous solution of the Maxwell’s equations are validated using experimental optical spectra of these films before systematically investigating various parameters. The individual far-field/near-field optical properties, as well as the plasmon relaxation mechanism of the nanoparticles, vary strongly as the packing density of the array increases. In the Kretschmann configuration, the evanescent fields arising from p- and s-polarized (or TM and TE polarized) incidence have different directional components. The local evanescent field intensity and direction depends on the polarization, angle of incidence and the wavelength of incidence. These factors in the Kretschmann configuration give rise to interesting far-field as well as near-field optical properties. Overall, it is shown that plasmonic nanoparticle arrays in the Kretschmann configuration facilitate strong broadband absorptance without transmission losses, and strong near-field enhancement. The results reported herein elucidate the optical properties of self-assembled nanoparticle films, pinpointing the ideal conditions under which the normal and the Kretschmann configuration can be exploited in multiple light-driven applications.

Understanding the Excitation Wavelength Dependence and Thermal Stability of the SARS-CoV-2 Receptor-Binding Domain Using Surface-Enhanced Raman Scattering and Machine Learning

COVID-19 has cost millions of lives worldwide. The constant mutation of SARS-CoV-2 calls for thorough research to facilitate the development of variant surveillance. In this work, we studied the fundamental properties related to the optical identification of the receptor-binding domain (RBD) of SARS-CoV-2 spike protein, a key component of viral infection. The Raman modes of the SARS-CoV-2 RBD were captured by surface-enhanced Raman spectroscopy (SERS) using gold nanoparticles (AuNPs). The observed Raman enhancement strongly depends on the excitation wavelength as a result of the aggregation of AuNPs. The characteristic Raman spectra of RBDs from SARS-CoV-2 and MERS-CoV were analyzed by principal component analysis that reveals the role of secondary structures in the SERS process, which is corroborated with the thermal stability under laser heating. We can easily distinguish the Raman spectra of two RBDs using machine learning algorithms with accuracy, precision, recall, and F1 scores all over 95%. Our work provides an in-depth understanding of the SARS-CoV-2 RBD and paves the way toward rapid analysis and discrimination of complex proteins of infectious viruses and other biomolecules.

A Flexible Chamber for Time-Lapse Live-Cell Imaging with Stimulated Raman Scattering Microscopy

Stimulated Raman scattering (SRS) microscopy is a label-free chemical imaging technology. Live-cell imaging with SRS has been demonstrated for many biological and biomedical applications. However, long-term time-lapse SRS imaging of live cells has not been widely adopted. SRS microscopy often uses a high numerical aperture (NA) water-immersion objective and a high NA oil-immersion condenser to achieve high-resolution imaging. In this case, the gap between the objective and the condenser is only a few millimeters. Therefore, most commercial stage-top environmental chambers cannot be used for SRS imaging because of their large thickness with a rigid glass cover. This paper describes the design and fabrication of a flexible chamber that can be used for time-lapse live-cell imaging with transmitted SRS signal detection on an upright microscope frame. The flexibility of the chamber is achieved by using a soft material - a thin natural rubber film. The new enclosure and chamber design can be easily added to an existing SRS imaging setup. The testing and preliminary results demonstrate that the flexible chamber system enables stable, long-term, time-lapse SRS imaging of live cells, which can be used for various bioimaging applications in the future.

Enhancement of Molecular Coherent Anti-Stokes Raman Scattering with Silicon Nanoantennas

Surface-enhanced coherent anti-Stokes Raman scattering (SE-CARS) takes advantage of surface plasmon resonances supported on metallic nanostructures to amplify the coherent Raman response of target molecules. While these metallic antennas have found significant success in SE-CARS studies, photoinduced morphological changes to the nanoantenna under ultrafast excitation introduce significant hurdles in terms of stability and reproducilibty. These hurdles need to be overcome in order to establish SE-CARS as a reliable tool for rapid biomolecular sensing. Here, we address this challenge by performing molecular CARS measurements enhanced by nanoantennas made from high-index dielectric particles with more favorable thermal properties. We present the first experimental demonstration of enhanced molecular CARS signals observed at Si nanoantennas, which offer much improved thermal stability compared to their metallic counterparts.

Stimulated Raman scattering microscopy in chemistry and life science - Development, innovation, perspectives

In this review, we present a summary of the basics of the Stimulated Raman Scattering (SRS) phenomenon, methods of detecting the signal, and collection of the SRS images. We demonstrate the advantages of SRS imaging, and recent developments, but also the limitations, especially in image capture speeds and spatial resolution. We also compare the use of SRS microscopy in biological system studies with other techniques such as fluorescence microscopy, second-harmonic generation (SHG)-based microscopy, coherent anti-Stokes Raman scattering (CARS), and spontaneous Raman, and we show the compatibility of SRS-based systems with other discussed methods. The review is also focused on indicating innovations in SRS microscopy, on the background of which we present the layout and performance of our homemade setup built from commercially available elements enabling for imaging of the molecular structure of single cells over the spectral range of 800-3600 cm^-1. Methods of image analysis are discussed, including machine learning methods for obtaining images of the distribution of selected molecules and for the detection of pathological lesions in tissues or malignant cells in the context of clinical diagnosis of a wide range of diseases with the use of SRS microscopy. Finally, perspectives for the development of SRS microscopy are proposed.

Dimensional Design for Surface-Enhanced Raman Spectroscopy

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique that enables specific identification of target analytes with sensitivity down to the single-molecule level by harnessing metal nanoparticles and nanostructures. Excitation of localized surface plasmon resonance of a nanostructured surface and the associated huge local electric field enhancement lie at the heart of SERS, and things will become better if strong chemical enhancement is also available simultaneously. Thus, the precise control of surface characteristics of enhancing substrates plays a key role in broadening the scope of SERS for scientific purposes and developing SERS into a routine analytical tool. In this review, the development of SERS substrates is outlined with some milestones in the nearly half-century history of SERS. In particular, these substrates are classified into zero-dimensional, one-dimensional, two-dimensional, and three-dimensional substrates according to their geometric dimension. We show that, in each category of SERS substrates, design upon the geometric and composite configuration can be made to achieve an optimized enhancement factor for the Raman signal. We also show that the temporal dimension can be incorporated into SERS by applying femtosecond pulse laser technology, so that the SERS technique can be used not only to identify the chemical structure of molecules but also to uncover the ultrafast dynamics of molecular structural changes. By adopting SERS substrates with the power of four-dimensional spatiotemporal control and design, the ultimate goal of probing the single-molecule chemical structural changes in the femtosecond time scale, watching the chemical reactions in four dimensions, and visualizing the elementary reaction steps in chemistry might be realized in the near future.

Single molecule detection; from microscopy to sensors

Single molecule detection is necessary to find out physical, chemical properties and their mechanism involved in the normal functioning of body cells. In this way, they can provide a new direction to the healthcare system. Various techniques have been developed and employed for their successful detection. Herein, we have emphasized various traditional methods as well as biosensing technology which offer single molecule sensitivity. The various methods including plasmonic resonance, nanopores, whispering gallery mode, Simoa assay and recognition tunneling are discussed in the initial part which has been followed by a discussion about biosensor-based detection. Plasmonic, SERS, CRISPR/Cas, and other types of biosensors are focused in this review and found to be highly sensitive for single molecule detection. This review provides an overview of progression in different techniques employed for single molecule detection.

Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing

Sequence identification of peptides and proteins is central to proteomics. Protein sequencing is mainly conducted by insensitive mass spectroscopy because proteins cannot be amplified, which hampers applications such as single-cell proteomics and precision medicine. The commercial success of portable nanopore sequencers for single DNA molecules has inspired extensive research and development of single-molecule techniques for protein sequencing. Among them, three challenges remain: (1) discrimination of the 20 amino acids as building blocks of proteins; (2) unfolding proteins; and (3) controlling the motion of proteins with nonuniformly charged sequences. In this context, the emergence of label-free optical analysis techniques for single amino acids and peptides by solid-state nanopores shows promise for addressing the first challenge. In this Perspective, we first discuss the current challenges of single-molecule fluorescence detection and nanopore resistive pulse sensing in a protein sequencing. Then, label-free optical methods are described to show how they address the single-amino-acid identification within single peptides. They include localized surface plasmon resonance detection and surface-enhanced Raman spectroscopy on plasmonic nanopores. Notably, we report new data to show the ability of plasmon-enhanced Raman scattering to record and discriminate the 20 amino acids at a single-molecule level. In addition, we discuss briefly the manipulation of molecule translocation and liquid flow in plasmonic nanopores for controlling molecule movement to allow high-resolution reading of protein sequences. We envision that a combination of Raman spectroscopy with plasmonic nanopores can succeed in single-molecule protein sequencing in a label-free way.

Large-Area Nanosphere Self-Assembly Monolayers for Periodic Surface Nanostructures with Ultrasensitive and Spatially Uniform SERS Sensing

Colloidal lithography provides a rapid and low-cost approach to construct 2D periodic surface nanostructures. However, an impressive demonstration to prepare large-area colloidal template is still missing. Here, a high-efficient and flexible technique is proposed to fabricate self-assembly monolayers consisting of orderly-packed polystyrene spheres at air/water interface via ultrasonic spray. This "non-contact" technique exhibits great advantages in terms of scalability and adaptability due to its renitent interface dynamic balance. More importantly, this technique is not only competent for self-assembly of single-sized polystyrene spheres, but also for binary polystyrene spheres, completely reversing the current hard situation of preparing large-area self-assembly monolayers. As a representative application, hexagonal-packed silver-coated silicon nanorods array (Si-NRs@Ag) is developed as an ultrasensitive surface-enhanced Raman scattering (SERS) substrate with very low limit-of-detection for selective detection of explosive 2,4,6-trinitrotoluene down to femtomolar (10^-14 m) range. The periodicity and orderliness of the array allow hot spots to be designed and constructed in a homogeneous fashion, resulting in an incomparable uniformity and reproducibility of Raman signals. All these excellent properties come from the Si-NRs@Ag substrate based on the ordered structure, open surface, and wide-range electric field, providing a robust, consistent, and tunable platform for molecule trapping and SERS sensing for a wide range of organic molecules.

Single Step Laser-Induced Deposition of Plasmonic Au, Ag, Pt Mono-, Bi- and Tri-Metallic Nanoparticles

Multimetallic plasmonic systems usually have distinct advantages over monometallic nanoparticles due to the peculiarity of the electronic structure appearing in advanced functionality systems, which is of great importance in a variety of applications including catalysis and sensing. Despite several reported techniques, the controllable synthesis of multimetallic plasmonic nanoparticles in soft conditions is still a challenge. Here, mono-, bi- and tri-metallic nanoparticles were successfully obtained as a result of a single step laser-induced deposition approach from monometallic commercially available precursors. The process of nanoparticles formation is starting with photodecomposition of the metal precursor resulting in nucleation and the following growth of the metal phase. The deposited nanoparticles were studied comprehensively with various experimental techniques such as SEM, TEM, EDX, XPS, and UV-VIS absorption spectroscopy. The size of monometallic nanoparticles is strongly dependent on the type of metal: 140–200 nm for Au, 40–60 nm for Ag, 2–3 nm for Pt. Bi- and trimetallic nanoparticles were core-shell structures representing monometallic crystallites surrounded by an alloy of respective metals. The formation of an alloy phase took place between monometallic nanocrystallites of different metals in course of their growth and agglomeration stage.

Raman Scattering-Based Biosensing: New Prospects and Opportunities

The growing interest in the development of new platforms for the application of Raman spectroscopy techniques in biosensor technologies is driven by the potential of these techniques in identifying chemical compounds, as well as structural and functional features of biomolecules. The effect of Raman scattering is a result of inelastic light scattering processes, which lead to the emission of scattered light with a different frequency associated with molecular vibrations of the identified molecule. Spontaneous Raman scattering is usually weak, resulting in complexities with the separation of weak inelastically scattered light and intense Rayleigh scattering. These limitations have led to the development of various techniques for enhancing Raman scattering, including resonance Raman spectroscopy (RRS) and nonlinear Raman spectroscopy (coherent anti-Stokes Raman spectroscopy and stimulated Raman spectroscopy). Furthermore, the discovery of the phenomenon of enhanced Raman scattering near metallic nanostructures gave impetus to the development of the surface-enhanced Raman spectroscopy (SERS) as well as its combination with resonance Raman spectroscopy and nonlinear Raman spectroscopic techniques. The combination of nonlinear and resonant optical effects with metal substrates or nanoparticles can be used to increase speed, spatial resolution, and signal amplification in Raman spectroscopy, making these techniques promising for the analysis and characterization of biological samples. This review provides the main provisions of the listed Raman techniques and the advantages and limitations present when applied to life sciences research. The recent advances in SERS and SERS-combined techniques are summarized, such as SERRS, SE-CARS, and SE-SRS for bioimaging and the biosensing of molecules, which form the basis for potential future applications of these techniques in biosensor technology. In addition, an overview is given of the main tools for success in the development of biosensors based on Raman spectroscopy techniques, which can be achieved by choosing one or a combination of the following approaches: (i) fabrication of a reproducible SERS substrate, (ii) synthesis of the SERS nanotag, and (iii) implementation of new platforms for on-site testing.

Nanogold-based materials in medicine: from their origins to their future

The properties of gold-based materials have been explored for centuries in several research fields, including medicine. Multiple published production methods for gold nanoparticles (AuNPs) have shown that the physicochemical and optical properties of AuNPs depend on the production method used. These different AuNP properties have allowed exploration of their usefulness in countless distinct biomedical applications over the last few years. Here we present an extensive overview of the most commonly used AuNP production methods, the resulting distinct properties of the AuNPs and the potential application of these AuNPs in diagnostic and therapeutic approaches in biomedicine.

Plasmonic Core-Shell Nanomaterials and their Applications in Spectroscopies

Plasmonic core-shell nanostructures have attracted considerable attention in the scientific community recently due to their highly tunable optical properties. Plasmon-enhanced spectroscopies are one of the main applications of plasmonic nanomaterials. When excited by an incident laser of suitable wavelength, strong and highly localized electromagnetic (EM) fields are generated around plasmonic nanomaterials, which can significantly boost excitation and/or radiation processes that amplify Raman, fluorescence, or nonlinear signals and improve spectroscopic sensitivity. Herein, recent developments in plasmon-enhanced spectroscopies utilizing core-shell nanostructures are reviewed, including shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS), plasmon-enhanced fluorescence spectroscopy, and plasmon-enhanced nonlinear spectroscopy.

Silver Flowerlike Structures for Surface-Enhanced Raman Spectroscopy

Micro- and nanoflowers are a class of materials composed of particles with high surface-to-volume ratio. They have been extensively studied in the last decade due to simple preparation protocols and promising applications in biosensing, as drug delivery agents, for water purification, and so on. Flowerlike objects, due to their highly irregular surface, may act also as plasmonic materials, providing resonant coupling between optical waves and surface plasmon excitations. This fact allows us to infer the possibility to use micro- and nanoflowers as effective surface-enhanced Raman scattering (SERS) substrate materials. Here, we report on the design and Raman enhancement properties of silver flowerlike structures, deposited on aluminum surface. A simple and cost-effective fabrication method is described, which leads to SERS substrates of high developed surface area. The morphology of the silver flowers on a nanoscale is characterized by self-organized quasiperiodic stacks of nanosheets, which act as plasmonic cavity resonators. The substrates were tested against rhodamine-6G (R6G) water solutions of concentration varying between 10⁻³ M and 10⁻⁷ M. Optimal SERS enhancement factors of up to 10⁵ were established at R6G concentrations in the 10⁻⁶–10⁻⁷ M range.

Vibrational line shape effects in plasmon-enhanced stimulated Raman spectroscopies

A density matrix treatment of plasmon-enhanced (PE) stimulated Raman spectroscopies is developed. Specifically, PE stimulated Raman Gain/Loss (PE-SRG/L) and coherent anti-Stokes Raman scattering (PE-CARS) due to monochromatic excitation and PE femtosecond stimulated Raman spectroscopy (PE-FSRS) are considered. A Lorentz oscillator model is used to explicitly describe the time dependence of plasmon-enhanced optical fields. These temporal characteristics are required for a density matrix based description of all plasmon-enhanced nonlinear molecular spectroscopies. Dispersive vibrational line shapes in PE-SRG/L and PE-FSRS spectra are shown to result primarily from terms proportional to the square of the complex optical field enhancement factor. The dependence on the plasmon resonance, picosecond and femtosecond pulse characteristics, and molecular vibrational properties are evident in the density matrix derived PE-FSRS intensity expression. The difference in signal detection mechanisms accounts for the lack of dispersive line shapes in PE spontaneous Raman spectroscopy. This density matrix treatment of PE-FSRS line shapes is compared with prior coupled wave results.

Nonlinearity-modulated single molecule trapping and Raman scattering analysis

Single molecule detection and analysis play important roles in many current biomedical researches. The deep-nanoscale hotspots, being excited and confined in a plasmonic nanocavity, make it possible to simultaneously enhance the nonlinear light-matter interactions and molecular Raman scattering for label-free detections. Here, we theoretically show that a nanocavity formed in a tip-enhanced Raman scattering (TERS) system can also achieve valid optical trapping as well as TERS signal detection for a single molecule. In addition, the nonlinear responses of metallic tip and substrate film can change their intrinsic physical properties, leading to the modulation of the optical trapping force and the TERS signal. The results demonstrate a new degree of freedom brought by the nonlinearity for effectively modulating the optical trapping and Raman detection in single molecule level. This proposed platform also shows a great potential in various fields of research that need high-precision surface imaging.

Coherent Raman scattering microscopy for chemical imaging of biological systems

Coherent Raman scattering (CRS) processes, including both the coherent anti-Stokes Raman scattering and stimulated Raman scattering, have been utilized in state-of-the-art microscopy platforms for chemical imaging of biological samples. The key advantage of CRS microscopy over fluorescence microscopy is label-free, which is an attractive characteristic for modern biological and medical sciences. Besides, CRS has other advantages such as higher selectivity to metabolites, no photobleaching, and narrow peak width. These features have brought fast-growing attention to CRS microscopy in biological research. In this review article, we will first briefly introduce the history of CRS microscopy, and then explain the theoretical background of the CRS processes in detail using the classical approach. Next, we will cover major instrumentation techniques of CRS microscopy. Finally, we will enumerate examples of recent applications of CRS imaging in biological and medical sciences.

Surface-Enhanced Raman Scattering-Active Plasmonic Metal Nanoparticle-Persistent Luminescence Material Composite Films for Multiple Illegal Dye Detection

Uniform two-dimensional plasmonic nanoparticle (NP)-semiconductor composite films could retard the attenuation of electromagnetic evanescent wave and show intensive Raman activity for the multiplex monitoring of hazards in a practical food matrix. Here, an efficient Raman platform is developed by employing a plasmonic nanoparticle (NP)-persistent luminescence material (PLM) composite film. PLM show upconversion photoluminescence (UCPL) properties. The emitted photons are absorbed by plasmonic NPs, which further boost the surface plasmon resonance for the generation of high polarizability and induce strong electromagnetic strength for surface-enhanced Raman scattering (SERS) enhancement. A UCPL-assisted SERS-enhanced mechanism is proposed and verified. A plasmonic NP-PLM film with superior SERS activity and detection capability becomes an alternative candidate for the sensitive and multiple detection of illegal addition of dyes in a food matrix. The proposed UCPL-assisted SERS-enhanced mechanism provides promising future directions to this end to design a next-generation SERS-active plasmonic NP-PLM composite film for the specific detection in complex samples.

Quantum-enhanced nonlinear microscopy

The performance of light microscopes is limited by the stochastic nature of light, which exists in discrete packets of energy known as photons. Randomness in the times that photons are detected introduces shot noise, which fundamentally constrains sensitivity, resolution and speed¹. Although the long-established solution to this problem is to increase the intensity of the illumination light, this is not always possible when investigating living systems, because bright lasers can severely disturb biological processes^2-4. Theory predicts that biological imaging may be improved without increasing light intensity by using quantum photon correlations^1,5. Here we experimentally show that quantum correlations allow a signal-to-noise ratio beyond the photodamage limit of conventional microscopy. Our microscope is a coherent Raman microscope that offers subwavelength resolution and incorporates bright quantum correlated illumination. The correlations allow imaging of molecular bonds within a cell with a 35 per cent improved signal-to-noise ratio compared with conventional microscopy, corresponding to a 14 per cent improvement in concentration sensitivity. This enables the observation of biological structures that would not otherwise be resolved. Coherent Raman microscopes allow highly selective biomolecular fingerprinting in unlabelled specimens^6,7, but photodamage is a major roadblock for many applications^8,9. By showing that the photodamage limit can be overcome, our work will enable order-of-magnitude improvements in the signal-to-noise ratio and the imaging speed.

A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation

Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.

Plasmon-enhanced coherent anti-stokes Raman scattering vs plasmon-enhanced stimulated Raman scattering: Comparison of line shape and enhancement factor

Plasmon-enhanced coherent Raman scattering microscopy has reached single-molecule detection sensitivity. Due to the different driven fields, there are significant differences between a coherent Raman scattering process and its plasmon-enhanced derivative. The commonly accepted line shapes for coherent anti-Stokes Raman scattering and stimulated Raman scattering do not hold for the plasmon-enhanced condition. Here, we present a theoretical model that describes the spectral line shapes in plasmon-enhanced coherent anti-Stokes Raman scattering (PECARS). Experimentally, we measured PECARS and plasmon-enhanced stimulated Raman scattering (PESRS) spectra of 4-mercaptopyridine adsorbed on the self-assembled Au nanoparticle (NP) substrate and aggregated Au NP colloids. The PECARS spectra show a nondispersive line shape, while the PESRS spectra exhibit a dispersive line shape. PECARS shows a higher signal to noise ratio and a larger enhancement factor than PESRS from the same specimen. It is verified that the nonresonant background in PECARS originates from the photoluminescence of nanostructures. The decoupling of background and the vibrational resonance component results in the nondispersive line shape in PECARS. More local electric field enhancements are involved in the PECARS process than in PESRS, which results in a higher enhancement factor in PECARS. The current work provides new insight into the mechanism of plasmon-enhanced coherent Raman scattering and helps to optimize the experimental design for ultrasensitive chemical imaging.

Quantitative Drug Dynamics Visualized by Alkyne-Tagged Plasmonic-Enhanced Raman Microscopy

Visualizing live-cell uptake of small-molecule drugs is paramount for drug development and pharmaceutical sciences. Bioorthogonal imaging with click chemistry has made significant contributions to the field, visualizing small molecules in cells. Furthermore, recent developments in Raman microscopy, including stimulated Raman scattering (SRS) microscopy, have realized direct visualization of alkyne-tagged small-molecule drugs in live cells. However, Raman and SRS microscopy still suffer from limited detection sensitivity with low concentration molecules for observing temporal dynamics of drug uptake. Here, we demonstrate the combination of alkyne-tag and surface-enhanced Raman scattering (SERS) microscopy for the real-time monitoring of drug uptake in live cells. Gold nanoparticles are introduced into lysosomes of live cells by endocytosis and work as SERS probes. Raman signals of alkynes can be boosted by enhanced electric fields generated by plasmon resonance of gold nanoparticles when alkyne-tagged small molecules are colocalized with the nanoparticles. With time-lapse 3D SERS imaging, this technique allows us to investigate drug uptake by live cells with different chemical and physical conditions. We also perform quantitative evaluation of the uptake speed at the single-cell level using digital SERS counting under different quantities of drug molecules and temperature conditions. Our results illustrate that alkyne-tag SERS microscopy has a potential to be an alternative bioorthogonal imaging technique to investigate temporal dynamics of small-molecule uptake of live cells for pharmaceutical research.

Mammalian cell and tissue imaging using Raman and coherent Raman microscopy

Direct imaging of metabolism in cells or multicellular organisms is important for understanding many biological processes. Raman scattering (RS) microscopy, particularly, coherent Raman scattering (CRS) such as coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS), has emerged as a powerful platform for cellular imaging due to its high chemical selectivity, sensitivity, and imaging speed. RS microscopy has been extensively used for the identification of subcellular structures, metabolic observation, and phenotypic characterization. Conjugating RS modalities with other techniques such as fluorescence or infrared (IR) spectroscopy, flow cytometry, and RNA-sequencing can further extend the applications of RS imaging in microbiology, system biology, neurology, tumor biology and more. Here we overview RS modalities and techniques for mammalian cell and tissue imaging, with a focus on the advances and applications of CARS and SRS microscopy, for a better understanding of the metabolism and dynamics of lipids, protein, glucose, and nucleic acids in mammalian cells and tissues. This article is categorized under: Laboratory Methods and Technologies > Imaging Biological Mechanisms > Metabolism Analytical and Computational Methods > Analytical Methods.

Accessing Excited State Molecular Vibrations by Femtosecond Stimulated Raman Spectroscopy

Excited state vibrations are crucial for determining the photophysical and photochemical properties of molecular compounds. Stimulated Raman scattering can coherently stimulate and probe molecular vibrations with optical pulses, but it is generally restricted to ground state properties. Working under resonance conditions enables cross-section enhancement and selective excitation to a targeted electronic level but is hampered by an increased signal complexity due to the presence of overlapping spectral contributions. Here, we show how detailed information about ground and excited state vibrations can be disentangled by exploiting the relative time delay between Raman and probe pulses to control the excited state population, combined with a diagrammatic formalism to dissect the pathways concurring with the signal generation. The proposed method is then exploited to elucidate the vibrational properties of the ground and excited electronic states in the paradigmatic case of cresyl violet. We anticipate that the presented approach holds the potential for selective mapping of the reaction coordinates pertaining to transient electronic stages implied in photoactive compounds.

Time-Domain Observation of Surface-Enhanced Coherent Raman Scattering with 105-106 Enhancement

Combining surface-enhanced Raman scattering (SERS) with the coherent nonlinear Raman technique is a promising route for achieving higher sensitivity and time-resolved SERS measurements, yet such attempts have just been started. Here, we report time-domain Raman measurements of trans-1,2-bis(4-pyridyl)ethylene (BPE) adsorbed on gold nanoparticle assemblies (GNAs), which were carried out with impulsive stimulated Raman spectroscopy using sub-8 fs pulses. We observe coherent nuclear wavepacket motion of BPE on GNAs with drastic enhancement through the surface plasmon resonance, which provides information on the Raman-active vibrations in the time domain. Through Fourier transform of the measured time-domain Raman data, we obtained SERS spectra of BPE on GNAs with enhancement factors as high as 10⁵-10⁶. The present study not only demonstrates applicability of time-domain nonlinear Raman techniques in SERS, i.e., surface-enhanced impulsive stimulated Raman spectroscopy (SE-ISRS), but also provides a technical basis for femtosecond time-resolved SE-ISRS experiments to track ultrafast dynamics of the adsorbates.

Nonlinear plasmon-exciton coupling enhances sum-frequency generation from a hybrid metal/semiconductor nanostructure

The integration of metallic plasmonic nanoantennas with quantum emitters can dramatically enhance coherent harmonic generation, often resulting from the coupling of fundamental plasmonic fields to higher-energy, electronic or excitonic transitions of quantum emitters. The ultrafast optical dynamics of such hybrid plasmon-emitter systems have rarely been explored. Here, we study those dynamics by interferometrically probing nonlinear optical emission from individual porous gold nanosponges infiltrated with zinc oxide (ZnO) emitters. Few-femtosecond time-resolved photoelectron emission microscopy reveals multiple long-lived localized plasmonic hot spot modes, at the surface of the randomly disordered nanosponges, that are resonant in a broad spectral range. The locally enhanced plasmonic near-field couples to the ZnO excitons, enhancing sum-frequency generation from individual hot spots and boosting resonant excitonic emission. The quantum pathways of the coupling are uncovered from a two-dimensional spectrum correlating fundamental plasmonic excitations to nonlinearly driven excitonic emissions. Our results offer new opportunities for enhancing and coherently controlling optical nonlinearities by exploiting nonlinear plasmon-quantum emitter coupling.

Biological imaging of chemical bonds by stimulated Raman scattering microscopy

All molecules consist of chemical bonds, and much can be learned from mapping the spatiotemporal dynamics of these bonds. Since its invention a decade ago, stimulated Raman scattering (SRS) microscopy has become a powerful modality for imaging chemical bonds with high sensitivity, resolution, speed and specificity. We introduce the fundamentals of SRS microscopy and review innovations in SRS microscopes and imaging probes. We highlight examples of exciting biological applications, and share our vision for potential future breakthroughs for this technology.