Nano-chemical infrared imaging of membrane proteins in lipid bilayers

Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features

This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of 13C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of 13C-13C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.

Synchrotron infrared nanospectroscopy in fourth-generation storage rings

Fourth-generation synchrotron storage rings represent a significant milestone in synchrotron technology, offering outstandingly bright and tightly focused X-ray beams for a wide range of scientific applications. However, due to their inherently tight magnetic lattices, these storage rings have posed critical challenges for accessing lower-energy radiation, such as infrared (IR) and THz. Here the first-ever IR beamline to be installed and to operate at a fourth-generation synchrotron storage ring is introduced. This work encompasses several notable advancements, including a thorough examination of the new IR source at Sirius, a detailed description of the radiation extraction scheme, and the successful validation of our optical concept through both measurements and simulations. This optimal optical setup has enabled us to achieve an exceptionally wide frequency range for our nanospectroscopy experiments. Through the utilization of synchrotron IR nanospectroscopy on biological and hard matter samples, the practicality and effectiveness of this beamline has been successfully demonstrated. The advantages of fourth-generation synchrotron IR sources, which can now operate with unparalleled stability as a result of the stringent requirements for producing low-emittance X-rays, are emphasized.

Infrared nanoimaging of neuronal ultrastructure and nanoparticle interaction with cells

Here we introduce scattering-type scanning near-field optical microscopy (s-SNOM) as a novel tool for nanoscale chemical-imaging of sub-cellular organelles, nanomaterials and of the interactions between them. Our setup uses a tuneable mid-infrared laser and a sharp scanning probe to image at a resolution substantially surpassing the diffraction limit. The laser can be tuned to excite vibrational modes of functional groups in biomolecules, (e.g. amide moieties), in a way that enables direct chemical mapping without the need for labelling. We, for the first time, chemically image neuronal ultrastructure, identify neuronal organelles and sub-organelle structures as small as 10 nm and validate our findings using transmission electron microscopy (TEM). We produce chemical and morphological maps of neurons treated with gold nanospheres and characterize nanoparticle size and intracellular location, and their interaction with the plasma membrane. Our results show that the label-free nature of s-SNOM means it has a 'true' chemical resolution of up to 20 nm which can be further improved. We argue that it offers significant potential in nanomedicine for nanoscale chemical imaging of cell ultrastructure and the subcellular distribution of nanomaterials within tissues.

Sub-Tip-Radius Near-Field Interactions in Nano-FTIR Vibrational Spectroscopy on Single Proteins

Tip-enhanced vibrational spectroscopy has advanced to routinely attain nanoscale spatial resolution, with tip-enhanced Raman spectroscopy even achieving atomic-scale and submolecular sensitivity. Tip-enhanced infrared spectroscopy techniques, such as nano-FTIR and AFM-IR spectroscopy, have also enabled the nanoscale chemical analysis of molecular monolayers, inorganic nanoparticles, and protein complexes. However, fundamental limits of infrared nanospectroscopy in terms of spatial resolution and sensitivity have remained elusive, calling for a quantitative understanding of the near-field interactions in infrared nanocavities. Here, we demonstrate the application of nano-FTIR spectroscopy to probe the amide-I vibration of a single protein consisting of ∼500 amino acid residues. Detection with higher tip tapping demodulation harmonics up to the seventh order leads to pronounced enhancement in the peak amplitude of the vibrational resonance, originating from sub-tip-radius geometrical effects beyond dipole approximations. This quantitative characterization of single-nanometer near-field interactions opens the path toward employing infrared vibrational spectroscopy at the subnanoscale and single-molecule levels.

Correlative chemical and elemental nano-imaging of morphology and disorder at the nacre-prismatic region interface in Pinctada margaritifera

Understanding biomineralization relies on imaging chemically heterogeneous organic-inorganic interfaces across a hierarchy of spatial scales. Further, organic minority phases are often responsible for emergent inorganic structures from the atomic arrangement of different polymorphs, to nano- and micrometer crystal dimensions, up to meter size mollusk shells. The desired simultaneous chemical and elemental imaging to identify sparse organic moieties across a large field-of-view with nanometer spatial resolution has not yet been achieved. Here, we combine nanoscale secondary ion mass spectroscopy (NanoSIMS) with spectroscopic IR s-SNOM imaging for simultaneous chemical, molecular, and elemental nanoimaging. At the example of Pinctada margaritifera mollusk shells we identify and resolve ~ 50 nm interlamellar protein sheets periodically arranged in regular ~ 600 nm intervals. The striations typically appear ~ 15 µm from the nacre-prism boundary at the interface between disordered neonacre to mature nacre. Using the polymorph distinctive IR-vibrational carbonate resonance, the nacre and prismatic regions are consistently identified as aragonite ([Formula: see text] cm-1) and calcite ([Formula: see text] cm-1), respectively. We observe previously unreported morphological features including aragonite subdomains encapsulated in extensions of the prism-covering organic membrane and regions of irregular nacre tablet formation coincident with dispersed organics. We also identify a ~ 200 nm region in the incipient nacre region with less well-defined crystal structure and integrated organics. These results show with the identification of the interlamellar protein layer how correlative nano-IR chemical and NanoSIMS elemental imaging can help distinguish different models proposed for shell growth in particular, and how organic function may relate to inorganic structure in other biomineralized systems in general.

Pseudoheterodyne interferometry for multicolor near-field imaging

We report the development and characterization of a detection technique for scattering-type scanning near-field optical microscopy (s-SNOM) that enables near-field amplitude and phase imaging at two or more wavelengths simultaneously. To this end, we introduce multispectral pseudoheterodyne (PSH) interferometry, where infrared lasers are combined to form a beam with a discrete spectrum of laser lines and a time-multiplexing scheme is employed to allow for the use of a single infrared detector. We first describe and validate the implementation of multispectral PSH into a commercial s-SNOM instrument. We then demonstrate its application for the real-time correction of the negative phase contrast (NPC), which provides reliable imaging of weak IR absorption at the nanoscale. We anticipate that multispectral PSH could improve data throughput, reduce effects of sample and interferometer drift, and help to establish multicolor s-SNOM imaging as a regular imaging modality, which could be particularly interesting as new infrared light sources become available.

Label-free nanoscale mapping of intracellular organelle chemistry

The ability to image cell chemistry at the nanoscale is key for understanding cell biology, but many optical microscopies are restricted by the ~(200-250)nm diffraction limit. Electron microscopy and super-resolution fluorescence techniques beat this limit, but rely on staining and specialised labelling to generate image contrast. It is challenging, therefore, to obtain information about the functional chemistry of intracellular components. Here we demonstrate a technique for intracellular label-free chemical mapping with nanoscale (~30 nm) resolution. We use a probe-based optical microscope illuminated with a mid-infrared laser whose wavelengths excite vibrational modes of functional groups occurring within biological molecules. As a demonstration, we chemically map intracellular structures in human multiple myeloma cells and compare the morphologies with electron micrographs of the same cell line. We also demonstrate label-free mapping at wavelengths chosen to target the chemical signatures of proteins and nucleic acids, in a way that can be used to identify biochemical markers in the study of disease and pharmacology.

Identification of weak molecular absorption in single-wavelength s-SNOM images

Scattering-type scanning near-field optical microscopy (s-SNOM) allows for nanoscale optical mapping of manifold material properties. It is based on interferometric recording of the light scattered at a scanning probe tip. For dielectric samples such as biological materials or polymers, the near-field amplitude and phase signals of the scattered field reveal the local reflectivity and absorption, respectively. Importantly, absorption in s-SNOM imaging corresponds to a positive phase contrast relative to a non-absorbing reference sample. Here, we describe that in certain conditions (weakly or non- absorbing material placed on a highly reflective substrate), a slight negative phase contrast may be observed, which can hinder the recognition of materials exhibiting a weak infrared absorption. We first document this effect and explore its origin using representative test samples. We then demonstrate straightforward simple correction methods that remove the negative phase contrast and that allow for the identification of weak absorption contrasts.

Molecular vibrational imaging at nanoscale

The demand to visualize the spatial distribution of chemical species based on vibrational spectra is rapidly increasing. Driven by such a need, various Raman and infrared spectro-microscopies with a nanometric spatial resolution have been developed over the last two decades. Despite rapid progress, a large gap still exists between the general needs and what these techniques can achieve. This Perspective highlights the key challenges and recent breakthroughs of the two vibrational nano-imaging techniques, scattering-type scanning near-field optical microscopy and tip-enhanced Raman scattering.

Revealing local molecular distribution, orientation, phase separation, and formation of domains in artificial lipid layers: Towards comprehensive characterization of biological membranes

Lipids, together with molecules such as DNA and proteins, are one of the most relevant systems responsible for the existence of life. Selected lipids are able to assembly into various organized structures, such as lipid membranes. The unique properties of lipid membranes determine their complex functions, not only to separate biological environments, but also to participate in regulatory functions, absorption of nutrients, cell-cell communication, endocytosis, cell signaling, and many others. Despite numerous scientific efforts, still little is known about the reason underlying the variability within lipid membranes, and its biochemical significance. In this review, we discuss the structural complexity of lipid membranes, as well as the importance to simplify studied systems in order to understand phenomena occurring in natural, complex membranes. Such systems require a model interface to be analyzed. Therefore, here we focused on analytical studies of artificial systems at various interfaces. The molecular structure of lipid membranes, specifically the nanometric thickens of molecular bilayer, limits in a major extent the choice of highly sensitive methods suitable to study such structures. Therefore, we focused on methods that combine high sensitivity, and/or chemical selectivity, and/or nanometric spatial resolution, such as atomic force microscopy, nanospectroscopy (tip-enhanced Raman spectroscopy, infrared nanospectroscopy), phase modulation infrared reflection-absorption spectroscopy, sum-frequency generation spectroscopy. We summarized experimental and theoretical approaches providing information about molecular structure and composition, lipid spatial distribution (phase separation), organization (domain shape, molecular orientation) of lipid membranes, and real-time visualization of the influence of various molecules (proteins, drugs) on their integrity. An integral part of this review discusses the latest achievements in the field of lipid layer-based biosensors.

Broadband Near-Field Near-Infrared Spectroscopy and Imaging with a Laser-Driven Light Source

The scattering-type scanning near-field optical microscope (s-SNOM) has become a powerful imaging and nano-spectroscopy tool, which is widely used in the characterization of electronic and photonic devices, two-dimensional materials and biomolecules. However, in the published literature, nano-spectroscopy is mainly employed in the mid-infrared band, and the near-infrared (NIR) nano-spectroscopy with broadband spectral range has not been well discussed. In the present paper, we introduce a home-built near-field NIR spectroscopy and imaging set-up that is based on a laser-driven light source (LDLS). By mapping the Ge-Au periodic grating sample and the photonic topology device, a ~30 nm spatial resolution and the excellent capability of characterizing complex samples are demonstrated. Spectra obtained by experiment reveal the optical band-gap of Ge with a spectral resolution of 25 cm−1, and a spectral range from 900 to 2000 nm. This technology is expected to provide a novel and unique approach for near-field NIR spectroscopy and imaging.

Atomic Force Microscopy and Infrared Nanospectroscopy of COVID-19 Spike Protein for the Quantification of Adhesion to Common Surfaces

The COVID-19 pandemic has claimed millions of lives worldwide, sickened many more, and has resulted in severe socioeconomic consequences. As society returns to normal, understanding the spread and persistence of SARS CoV-2 on commonplace surfaces can help to mitigate future outbreaks of coronaviruses and other pathogens. We hypothesize that such an understanding can be aided by studying the binding and interaction of viral proteins with nonbiological surfaces. Here, we propose a methodology for investigating the adhesion of the SARS CoV-2 spike glycoprotein on common inorganic surfaces such as aluminum, copper, iron, silica, and ceria oxides as well as metallic gold. Quantitative adhesion was obtained from the analysis of measured forces at the nanoscale using an atomic force microscope operated under ambient conditions. Without imposing further constraints on the measurement conditions, our preliminary findings suggest that spike glycoproteins interact with similar adhesion forces across the majority of the metal oxides tested with the exception to gold, for which attraction forces ∼10 times stronger than all other materials studied were observed. Ferritin, which was used as a reference protein, was found to exhibit similar adhesion forces as SARS CoV-2 spike protein. This study results show that glycoprotein adhesion forces for similar ambient humidity, tip shape, and contact surface are nonspecific to the properties of metal oxide surfaces, which are expected to be covered by a thin water film. The findings suggest that under ambient conditions, glycoprotein adhesion to metal oxides is primarily controlled by the water capillary forces, and they depend on the surface tension of the liquid water. We discuss further strategies warranted to decipher the intricate nanoscale forces for improved quantification of the adhesion.

Developments and Ongoing Challenges for Analysis of Surface-Bound Proteins

Proteins at surfaces and interfaces play important roles in the function and performance of materials in applications ranging from diagnostic assays to biomedical devices. To improve the performance of these materials, detailed molecular structure (conformation and orientation) along with the identity and concentrations of the surface-bound proteins on those materials must be determined. This article describes radiolabeling, surface plasmon resonance, quartz crystal microbalance with dissipation, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, sum frequency generation spectroscopy, and computational techniques along with the information each technique provides for characterizing protein films. A multitechnique approach using both experimental and computation methods is required for these investigations. Although it is now possible to gain much insight into the structure of surface-bound proteins, it is still not possible to obtain the same level of structural detail about proteins on surfaces as can be obtained about proteins in crystals and solutions, especially for large, complex proteins. However, recent results have shown it is possible to obtain detailed structural information (e.g., backbone and side chain orientation) about small peptides (5-20 amino sequences) on surfaces. Current studies are extending these investigations to small proteins such as protein G B1 (∼6 kDa). Approaches for furthering the capabilities for characterizing the molecular structure of surface-bound proteins are proposed.

Highly sensitive crumpled 2D material-based plasmonic biosensors

We propose surface plasmon resonance biosensors based on crumpled graphene and molybdenum disulphide (MoS₂) flakes supported on stretchable polydimethylsiloxane (PDMS) or silicon substrates. Accumulation of specific biomarkers resulting in measurable shifts in the resonance wavelength of the plasmon modes of two-dimensional (2D) material structures, with crumpled structures demonstrating large refractive index shifts. Using theoretical calculations based on the semiclassical Drude model, combined with the finite element method, we demonstrate that the interaction between the surface plasmons of crumpled graphene/MoS₂ layers and the surrounding analyte results in high sensitivity to biomarker driven refractive index shifts, up to 7499 nm/RIU for structures supported on silicon substrates. We can achieve a high figure of merit (FOM), defined as the ratio of the refractive index sensitivity to the full width at half maximum of the resonant peak, of approximately 62.5 RIU^-1. Furthermore, the sensing properties of the device can be tuned by varying crumple period and aspect ratio through simple stretching and integrating material interlayers. By stacking multiple 2D materials in heterostructures supported on the PDMS layer, we produced hybrid plasmon resonances detuned from the PDMS absorbance region allowing higher sensitivity and FOM compared to pure crumpled graphene structures on the PDMS substrates. The high sensitivity and broad mechanical tunability of these crumpled 2D material biosensors considerable advantages over traditional refractive index sensors, providing a new platform for ultrasensitive biosensing.

Infrared Nanospectroscopy of Individual Extracellular Microvesicles

Extracellular vesicles are membrane-delimited structures, involved in several inter-cellular communication processes, both physiological and pathological, since they deliver complex biological cargo. Extracellular vesicles have been identified as possible biomarkers of several pathological diseases; thus, their characterization is fundamental in order to gain a deep understanding of their function and of the related processes. Traditional approaches for the characterization of the molecular content of the vesicles require a large quantity of sample, thereby providing an average molecular profile, while their heterogeneity is typically probed by non-optical microscopies that, however, lack the chemical sensitivity to provide information of the molecular cargo. Here, we perform a study of individual microvesicles, a subclass of extracellular vesicles generated by the outward budding of the plasma membrane, released by two cultures of glial cells under different stimuli, by applying a state-of-the-art infrared nanospectroscopy technique based on the coupling of an atomic force microscope and a pulsed laser, which combines the label-free chemical sensitivity of infrared spectroscopy with the nanometric resolution of atomic force microscopy. By correlating topographic, mechanical and spectroscopic information of individual microvesicles, we identified two main populations in both families of vesicles released by the two cell cultures. Subtle differences in terms of nucleic acid content among the two families of vesicles have been found by performing a fitting procedure of the main nucleic acid vibrational peaks in the 1000–1250 cm⁻¹ frequency range.

How did correlative atomic force microscopy and super-resolution microscopy evolve in the quest for unravelling enigmas in biology?

With the invention of the Atomic Force Microscope (AFM) in 1986 and the subsequent developments in liquid imaging and cellular imaging it became possible to study the topography of cellular specimens under nearly physiological conditions with nanometric resolution. The application of AFM to biological research was further expanded with the technological advances in imaging modes where topographical data can be combined with nanomechanical measurements, offering the possibility to retrieve the biophysical properties of tissues, cells, fibrous components and biomolecules. Meanwhile, the quest for breaking the Abbe diffraction limit restricting microscopic resolution led to the development of super-resolution fluorescence microscopy techniques that brought the resolution of the light microscope comparable to the resolution obtained by AFM. The instrumental combination of AFM and optical microscopy techniques has evolved over the last decades from integration of AFM with bright-field and phase-contrast imaging techniques at first to correlative AFM and wide-field fluorescence systems and then further to the combination of AFM and fluorescence based super-resolution microscopy modalities. Motivated by the many developments made over the last decade, we provide here a review on AFM combined with super-resolution fluorescence microscopy techniques and how they can be applied for expanding our understanding of biological processes.

Single Particle Approaches to Plasmon-Driven Catalysis

Plasmonic nanoparticles have recently emerged as a promising platform for photocatalysis thanks to their ability to efficiently harvest and convert light into highly energetic charge carriers and heat. The catalytic properties of metallic nanoparticles, however, are typically measured in ensemble experiments. These measurements, while providing statistically significant information, often mask the intrinsic heterogeneity of the catalyst particles and their individual dynamic behavior. For this reason, single particle approaches are now emerging as a powerful tool to unveil the structure-function relationship of plasmonic nanocatalysts. In this Perspective, we highlight two such techniques based on far-field optical microscopy: surface-enhanced Raman spectroscopy and super-resolution fluorescence microscopy. We first discuss their working principles and then show how they are applied to the in-situ study of catalysis and photocatalysis on single plasmonic nanoparticles. To conclude, we provide our vision on how these techniques can be further applied to tackle current open questions in the field of plasmonic chemistry.

SSNOMBACTER: A collection of scattering-type scanning near-field optical microscopy and atomic force microscopy images of bacterial cells

BACKGROUND

In recent years, a variety of imaging techniques operating at nanoscale resolution have been reported. These techniques have the potential to enrich our understanding of bacterial species relevant to human health, such as antibiotic-resistant pathogens. However, owing to the novelty of these techniques, their use is still confined to addressing very particular applications, and their availability is limited owing to associated costs and required expertise. Among these, scattering-type scanning near field optical microscopy (s-SNOM) has been demonstrated as a powerful tool for exploring important optical properties at nanoscale resolution, depending only on the size of a sharp tip. Despite its huge potential to resolve aspects that cannot be tackled otherwise, the penetration of s-SNOM into the life sciences is still proceeding at a slow pace for the aforementioned reasons.

RESULTS

In this work we introduce SSNOMBACTER, a set of s-SNOM images collected on 15 bacterial species. These come accompanied by registered Atomic Force Microscopy images, which are useful for placing nanoscale optical information in a relevant topographic context.

CONCLUSIONS

The proposed dataset aims to augment the popularity of s-SNOM and for accelerating its penetration in life sciences. Furthermore, we consider this dataset to be useful for the development and benchmarking of image analysis tools dedicated to s-SNOM imaging, which are scarce, despite the high need. In this latter context we discuss a series of image processing and analysis applications where SSNOMBACTER could be of help.

Infrared Scattering-Type Scanning Near-Field Optical Microscopy of Biomembranes in Water

Infrared (IR) absorption spectroscopy detects the state and chemical composition of biomolecules solely by their inherent vibrational fingerprints. Major disadvantages like the lack of spatial resolution and sensitivity have lately been overcome by the use of pointed probes as local sensors enabling the detection of quantities as few as hundreds of proteins with nanometer precision. However, the strong absorption of infrared radiation by liquid water still prevents simple access to the measured quantity: the light scattered at the probing atomic force microscope tip. Here we report on the local IR response of biological membranes immersed in aqueous bulk solution. We make use of a silicon solid immersion lens as the substrate and focusing optics to achieve detection efficiencies sufficient to yield IR near-field maps of purple membranes. Finally, we suggest a means to improve the imaging quality by tracing the tip by a laser-scanning approach.

Electric field stimulates production of highly conductive microbial OmcZ nanowires

Multifunctional living materials are attractive due to their powerful ability to self-repair and replicate. However, most natural materials lack electronic functionality. Here we show that an electric field, applied to electricity-producing Geobacter sulfurreducens biofilms, stimulates production of previously unknown cytochrome OmcZ nanowires with 1,000-fold higher conductivity (30 S/cm), and 3-fold higher stiffness (1.5 GPa), than the cytochrome OmcS nanowires that are important in natural environments. Using chemical imaging-based multimodal nanospectroscopy, we correlate protein structure with function, and observe pH-induced conformational switching to β-sheets in individual nanowires, which increases their stiffness and conductivity by 100-fold due to enhanced π-stacking of heme groups; this was further confirmed by computational modelling and bulk spectroscopic studies. These nanowires can transduce mechanical and chemical stimuli into electrical signals to perform sensing, synthesis and energy production. These findings of biologically-produced, highly-conductive protein nanowires may help to guide the development of seamless, bidirectional interfaces between biological and electronic systems.

Direct observation of anisotropic growth of water films on minerals driven by defects and surface tension

Knowledge of the occurrences of water films on minerals is critical for global biogeochemical and atmospheric processes, including element cycling and ice nucleation. The underlying mechanisms controlling water film growth are, however, misunderstood. Using infrared nanospectroscopy, amplitude-modulated atomic force microscopy, and molecular simulations, we show how water films grow from water vapor on hydrophilic mineral nanoparticles. We imaged films with up to four water layers that grow anisotropically over a single face. Growth usually begins from the near edges of a face where defects preferentially capture water vapor. Thicker films produced by condensation cooling completely engulf nanoparticles and form thicker menisci over defects. The high surface tension of water smooths film surfaces and produces films of inhomogeneous thickness. Nanoscale topography and film surface energy thereby control anisotropic distributions and thicknesses of water films on hydrophilic mineral nanoparticles.

In Liquid Infrared Scattering Scanning Near-Field Optical Microscopy for Chemical and Biological Nanoimaging

Imaging biological systems with simultaneous intrinsic chemical specificity and nanometer spatial resolution in their typical native liquid environment has remained a long-standing challenge. Here, we demonstrate a general approach of chemical nanoimaging in liquid based on infrared scattering scanning near-field optical microscopy (IR s-SNOM). It is enabled by combining AFM operation in a fluid cell with evanescent IR illumination via total internal reflection, which provides spatially confined excitation for minimized IR water absorption, reduced far-field background, and enhanced directional signal emission and sensitivity. We demonstrate in-liquid IR s-SNOM vibrational nanoimaging and conformational identification of catalase nanocrystals and spatio-spectral analysis of biomimetic peptoid sheets with monolayer sensitivity and chemical specificity at the few zeptomole level. This work establishes the principles of in-liquid and in situ IR s-SNOM spectroscopic chemical nanoimaging and its general applicability to biomolecular, cellular, catalytic, electrochemical, or other interfaces and nanosystems in liquids or solutions.

Visualization and measurement of the local absorption coefficients of single bilayer phospholipid membranes using scanning near-field optical microscopy

Here we report the results of shear-mode thicknesses and absorption coefficient measurements made on neat membranes using scanning near-field optical microscopy (SNOM). Biomimic neat membranes composed of two different types of phoshpholipid molecules: 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2- dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) were found to exhibit different absorption coefficients under the SNOM. The localization of the lipids could be identified and correlated to the morphology of the membrane domains indicating that SNOM can be an effective and accurate approach for the label-free characterization of the structure-function relationships in cell membranes.

Substrate Matters: Surface-Polariton Enhanced Infrared Nanospectroscopy of Molecular Vibrations

Infrared nanospectroscopy based on Fourier transform infrared near-field spectroscopy (nano-FTIR) is an emerging nanoanalytical tool with large application potential for label-free mapping and identification of organic and inorganic materials with nanoscale spatial resolution. However, the detection of thin molecular layers and nanostructures on standard substrates is still challenged by weak signals. Here, we demonstrate a significant enhancement of nano-FTIR signals of a thin organic layer by exploiting polariton-resonant tip-substrate coupling and surface polariton illumination of the probing tip. When the molecular vibration matches the tip-substrate resonance, we achieve up to nearly one order of magnitude signal enhancement on a phonon-polaritonic quartz (c-SiO₂) substrate, as compared to nano-FTIR spectra obtained on metal (Au) substrates, and up to two orders of magnitude when compared to the standard infrared spectroscopy substrate CaF₂. Our results will be of critical importance for boosting nano-FTIR spectroscopy toward the routine detection of monolayers and single molecules.

Modern Scattering-Type Scanning Near-Field Optical Microscopy for Advanced Material Research

Infrared and optical spectroscopy represents one of the most informative methods in advanced materials research. As an important branch of modern optical techniques that has blossomed in the past decade, scattering-type scanning near-field optical microscopy (s-SNOM) promises deterministic characterization of optical properties over a broad spectral range at the nanoscale. It allows ultrabroadband optical (0.5-3000 µm) nanoimaging, and nanospectroscopy with fine spatial (<10 nm), spectral (<1 cm^-1 ), and temporal (<10 fs) resolution. The history of s-SNOM is briefly introduced and recent advances which broaden the horizons of this technique in novel material research are summarized. In particular, this includes the pioneering efforts to study the nanoscale electrodynamic properties of plasmonic metamaterials, strongly correlated quantum materials, and polaritonic systems at room or cryogenic temperatures. Technical details, theoretical modeling, and new experimental methods are also discussed extensively, aiming to identify clear technology trends and unsolved challenges in this exciting field of research.

Ultrastructural and SINS analysis of the cell wall integrity response of Aspergillus nidulans to the absence of galactofuranose

With lethal opportunistic fungal infections on the rise, it is imperative to explore new methods to examine virulence mechanisms. The fungal cell wall is crucial for both the virulence and viability of Aspergillus nidulans. One wall component, Galf, has been shown to contribute to important fungal processes, integrity of the cell wall and pathogenesis. Here, we explore gene deletion strains lacking the penultimate enzyme in Galf biosynthesis (ugmAΔ) and the protein that transports Galf for incorporation into the cell wall (ugtAΔ). In applying gene deletion technology to the problem of cell wall integrity, we have employed multiple micro- and nano-scale imaging tools, including confocal fluorescence microscopy, electron microscopy, X-Ray fluorescence and atomic force microscopy. Atomic force microscopy allows quantification of ultrastructural cell wall architecture while near-field infrared spectroscopy provides spatially resolved chemical signatures, both at the nanoscale. Here, for the first time, we demonstrate correlative data collection with these two emerging modalities for the multiplexed in situ study of the nanoscale architecture and chemical composition of fungal cell walls.

Tip-Enhanced Infrared Difference-Nanospectroscopy of the Proton Pump Activity of Bacteriorhodopsin in Single Purple Membrane Patches

Photosensitive proteins embedded in the cell membrane (about 5 nm thickness) act as photoactivated proton pumps, ion gates, enzymes, or more generally, as initiators of stimuli for the cell activity. They are composed of a protein backbone and a covalently bound cofactor (e.g. the retinal chromophore in bacteriorhodopsin (BR), channelrhodopsin, and other opsins). The light-induced conformational changes of both the cofactor and the protein are at the basis of the physiological functions of photosensitive proteins. Despite the dramatic development of microscopy techniques, investigating conformational changes of proteins at the membrane monolayer level is still a big challenge. Techniques based on atomic force microscopy (AFM) can detect electric currents through protein monolayers and even molecular binding forces in single-protein molecules but not the conformational changes. For the latter, Fourier-transform infrared spectroscopy (FTIR) using difference-spectroscopy mode is typically employed, but it is performed on macroscopic liquid suspensions or thick films containing large amounts of purified photosensitive proteins. In this work, we develop AFM-assisted, tip-enhanced infrared difference-nanospectroscopy to investigate light-induced conformational changes of the bacteriorhodopsin mutant D96N in single submicrometric native purple membrane patches. We obtain a significant improvement compared with the signal-to-noise ratio of standard IR nanospectroscopy techniques by exploiting the field enhancement in the plasmonic nanogap that forms between a gold-coated AFM probe tip and an ultraflat gold surface, as further supported by electromagnetic and thermal simulations. IR difference-spectra in the 1450-1800 cm^-1 range are recorded from individual patches as thin as 10 nm, with a diameter of less than 500 nm, well beyond the diffraction limit for FTIR microspectroscopy. We find clear spectroscopic evidence of a branching of the photocycle for BR molecules in direct contact with the gold surfaces, with equal amounts of proteins either following the standard proton-pump photocycle or being trapped in an intermediate state not directly contributing to light-induced proton transport. Our results are particularly relevant for BR-based optoelectronic and energy-harvesting devices, where BR molecular monolayers are put in contact with metal surfaces, and, more generally, for AFM-based IR spectroscopy studies of conformational changes of proteins embedded in intrinsically heterogeneous native cell membranes.

Infrared Nanospectroscopy of Phospholipid and Surfactin Monolayer Domains

A main challenge in understanding the structure of a cell membrane and its interactions with drugs is the ability to chemically study the different molecular species on the nanoscale. We have achieved this for a model system consisting of mixed monolayers (MLs) of the biologically relevant phospholipid 1,2-distearoyl-sn-glycero-phosphatidylcholine and the antibiotic surfactin. By employing nano-infrared (IR) microscopy and spectroscopy in combination with atomic force microscopy imaging, it was possible to identify and chemically detect domain formation of the two constituents as well as to obtain IR spectra of these species with a spatial resolution on the nanoscale. A novel method to enhance the near-field imaging contrast of organic MLs by plasmon interferometry is proposed and demonstrated. In this technique, the organic layer is deposited on gold and ML graphene substrates, the latter of which supports propagating surface plasmons. Plasmon reflections arising from changes in the dielectric environment provided by the organic layer lead to an additional contrast mechanism. Using this approach, the interfacial region between surfactin and the phospholipid has been mapped and a transition region is identified.

Nano-spectroscopic imaging of proteins with near-field scanning optical microscopy (NSOM)

Understanding the hierarchical structure of proteins at their fundamental length scales is essential to get insights into their functions and roles in fundamental biological processes. Near-field scanning optical microscopy (NSOM), which overcomes the diffraction limits of conventional optics, provides a powerful analytical tool to image target proteins at nanoscale resolution. Especially, by combining NSOM with infrared (IR) or Raman spectroscopy, near-field nanospectroscopic imaging of a single protein is achieved. In this review, we present the recent technical progress of NSOM setup for nanospectroscopic imaging of proteins, and its application to nanospectroscopic analysis of protein structures is highlighted and critically reviewed. Finally, current challenges and perspectives on application of NSOM in emerging areas of industrial, environmental and medical biotechnology are discussed.

Elastocapillary Driven Assembly of Particles at Free-Standing Smectic-A Films

Colloidal particles at complex fluid interfaces and within films assemble to form ordered structures with high degrees of symmetry via interactions that include capillarity, elasticity, and other fields like electrostatic charge. Here we study microparticle interactions within free-standing smectic-A films, in which the elasticity arising from the director field distortion and capillary interactions arising from interface deformation compete to direct the assembly of motile particles. New colloidal assemblies and patterns, ranging from 1D chains to 2D aggregates, sensitive to the initial wetting conditions of particles at the smectic film, are reported. This work paves the way to exploiting LC interfaces as a means to direct spontaneously formed, reconfigurable, and optically active materials.

Heterogeneity of the Transmembrane Protein Conformation in Purple Membranes Identified by Infrared Nanospectroscopy

Cell membranes are intrinsically heterogeneous, as the local protein and lipid distribution is critical to physiological processes. Even in template systems embedding a single protein type, like purple membranes, there can be a different local response to external stimuli or environmental factors, resulting in heterogeneous conformational changes. Despite the dramatic advances of microspectroscopy techniques, the identification of the conformation heterogeneity is still a challenging task. Tip-enhanced infrared nanospectroscopy is here used to identify conformational changes connected to the hydration state of the transmembrane proteins contained in a 50 nm diameter cell membrane area, without the need for fluorescent labels. In dried purple membrane monolayers, areas with fully hydrated proteins are found among large numbers of molecules with randomly distributed hydration states. Infrared nanospectroscopy results are compared to the spectra obtained with diffraction-limited infrared techniques based on the use of synchrotron radiation, in which the diffraction limit still prevents the observation of nanoscale heterogeneity.

Nanoscale mapping of refractive index by using scattering-type scanning near-field optical microscopy

We present a novel method for nanoscale reconstruction of complex refractive index by using scattering-type Scanning Near-field Optical Microscopy (s-SNOM). Our method relies on correlating s-SNOM experimental image data with computational data obtained through simulation of the classical oscillating point-dipole model. This results in assigning a certain dielectric function for every pixel of the s-SNOM images, which further results in nanoscale mapping of the refractive index. This method is employed on human erythrocytes to demonstrate the approach in a biologically relevant manner. The presented results advance the current knowledge on the capabilities of s-SNOM to extract quantitative information with nanoscale resolution from optical data sets with biological application.

Nanoplasmonic mid-infrared biosensor for in vitro protein secondary structure detection

Plasmonic nanoantennas offer new applications in mid-infrared (mid-IR) absorption spectroscopy with ultrasensitive detection of structural signatures of biomolecules, such as proteins, due to their strong resonant near-fields. The amide I fingerprint of a protein contains conformational information that is greatly important for understanding its function in health and disease. Here, we introduce a non-invasive, label-free mid-IR nanoantenna-array sensor for secondary structure identification of nanometer-thin protein layers in aqueous solution by resolving the content of plasmonically enhanced amide I signatures. We successfully detect random coil to cross β-sheet conformational changes associated with α-synuclein protein aggregation, a detrimental process in many neurodegenerative disorders. Notably, our experimental results demonstrate high conformational sensitivity by differentiating subtle secondary-structural variations in a native β-sheet protein monolayer from those of cross β-sheets, which are characteristic of pathological aggregates. Our nanoplasmonic biosensor is a highly promising and versatile tool for in vitro structural analysis of thin protein layers.

Enhancing the sensitivity of nano-FTIR spectroscopy

Synchrotron radiation-based nano-FTIR spectroscopy utilizes the highly brilliant and ultra-broadband infrared (IR) radiation provided by electron storage rings for the infrared spectroscopic characterization of samples at the nanoscale. In order to exploit the full potential of this approach we investigated the influence of the properties of the radiation source, such as the electron bunch shape and spectral bandwidth of the emitted radiation, on near-field infrared spectra of silicon-carbide (SiC). The adapted configuration of the storage ring optics enables a modification of the transverse electron bunch profile allowing an increase of the measured near-field signal amplitude. Additionally, the decay of the signal amplitude due to the decreasing storage ring current is also eliminated. Further options for improving the sensitivity of nano-FTIR spectroscopy, which can also be applied to other broadband radiation sources, are the adaption of the spectral bandwidth to the wavelength range of interest or the use of polarization optics. The sensitivity enhancement emerging from these options is verified by comparing near-field spectra collected from crystalline SiC samples. The improvement in sensitivity by combining these approaches is demonstrated by acquiring nano-FTIR spectra from thin organic films, which show weak resonances in the IR-regime.

Mapping of Bernal and non-Bernal stacking domains in bilayer graphene using infrared nanoscopy

Bilayer graphene (BLG) shows great potential as a new material for opto-electronic devices because its bandgap can be controlled by varying the stacking orders, as well as by applying an external electric field. An imaging technique that can visualize and characterize various stacking domains in BLG may greatly help in fully utilizing such properties of BLG. Here we demonstrate that infrared (IR) scattering-type scanning near-field optical microscopy (sSNOM) can visualize Bernal and non-Bernal stacking domains of BLG, based on the stacking-specific inter- and intra-band optical conductivities. The method enables nanometric mapping of stacking domains in BLG on dielectric substrates, augmenting current limitations of Raman spectroscopy and electron microscopy techniques for the structural characterization of BLG.

Two Mechanisms of Tip Enhancement of Raman Scattering by Protein Aggregates

Tip-enhanced Raman spectroscopy (TERS) is a powerful tool for probing the surface of biological species with nanometer spatial resolution. Here, we report the TER spectra of an individual insulin fibril, the protein cast film and a short peptide (LVEALYL) microcrystal mimicking the fibril core. Two different types of TER spectra were acquired depending on the "roughness" of the probed surface at the molecular level. A fully reproducible, low-intensity, normal Raman-type spectrum was characteristic of the top flat surface of the microcrystal while highly variable, higher intensity TER spectra were obtained for the edges of the microcrystal, cast film, and fibril. As a result, two tip enhancement mechanisms of Raman scattering, long- and short-range, were proposed by analogy with the physical and chemical enhancement mechanisms, respectively, known for surface-enhanced Raman spectroscopy.

Octave-spanning mid-infrared pulses by plasma generation in air pumped with an Yb:KGW source

Femtosecond mid-infrared (IR) supercontinuum generation in gas media provides a broadband source suited for time-domain spectroscopies and microscopies. This technology has largely utilized <100  fs Ti:sapphire pump lasers. In this Letter, we describe the first plasma generation mid-IR source based on a 1030 nm, 171 fs Yb:KGW laser system; when its first three harmonics are focused in air, a conical mode supercontinuum is generated that spans <1000 to 2700  cm^-1 with a 190 pJ pulse energy and 0.5% RMS stability.

Compressive Broad-Band Hyperspectral Sum Frequency Generation Microscopy to Study Functionalized Surfaces

A broad-band sum frequency generation microscope has been developed for the study of molecular monolayers on surfaces. Because sum frequency generation is a vibrational spectroscopy based on a second-order optical process, it is uniquely sensitive to detecting a molecule's vibrational fingerprints specifically at interfaces. In this microscope, a structured illumination beam generated by a spatial light modulator is used to irradiate the sample with a series of sparsifying pseudorandom patterns. The spectra associated with each pattern are then input into a reconstruction algorithm to compressively recover the full hyperspectral image cube. As a proof-of-principle, this system performed molecule-specific imaging of a microcontact-printed self-assembled monolayer of alkanethiolate on copper. This hyperspectral compressive imaging effectively recovered both spatial and spectral surface features with compression greater than 80%, meaning more than a 5-fold decrease in acquisition time compared to traditional methods.

Correlative infrared nanospectroscopic and nanomechanical imaging of block copolymer microdomains

Intermolecular interactions and nanoscale phase separation govern the properties of many molecular soft-matter systems. Here, we combine infrared vibrational scattering scanning near-field optical microscopy (IR s-SNOM) with force-distance spectroscopy for simultaneous characterization of both nanoscale optical and nanomechanical molecular properties through hybrid imaging. The resulting multichannel images and correlative analysis of chemical composition, spectral IR line shape, modulus, adhesion, deformation, and dissipation acquired for a thin film of a nanophase separated block copolymer (PS-b-PMMA) reveal complex structural variations, in particular at domain interfaces, not resolved in any individual signal channel alone. These variations suggest that regions of multicomponent chemical composition, such as the interfacial mixing regions between microdomains, are correlated with high spatial heterogeneity in nanoscale material properties.

Damage-free vibrational spectroscopy of biological materials in the electron microscope

Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be ‘safely' investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope.

Use of electron microscopy to determine morphology, or find where functionally significant biomolecules are located with high spatial resolution is of great interest. Here, Rez, Cohen et al. use aloof electron beam vibrational spectroscopy to probe different bonds in biological samples with no significant radiation damage.

Infrared Vibrational Nanospectroscopy by Self-Referenced Interferometry

Infrared vibrational scattering scanning near-field optical microscopy (s-SNOM) has emerged as a new frontier in imaging science due to its potential to provide nanoscale spatially resolved chemical spectroscopy for the investigation of molecular, soft-matter, and biological materials. As a phase-sensitive technique able to yield the full complex dielectric function of materials, different interferometric schemes have been developed involving asymmetric interferometry between sample and reference arms. In this work, we take advantage of a greatly simplified symmetric geometry that uses the spatially coherent background scattered light from within the confocal sample volume as a reference field for signal amplification in both self-homodyne and self-heterodyne interferometry. On the basis of a simple model for tip-sample scattering and interferometric detection, we demonstrate the measurement of the vibrational response of molecular materials in good agreement with established values. In addition to a compact design, enhanced signal levels, and a reduced sensitivity to fluctuations and drift, including those from the light source, self-referenced interferometry brings benefits for routine s-SNOM chemical spectroscopy, remaining robust even under a wide range of challenging experimental environments.

High spatial resolution mapping of chemically-active self-assembled N-heterocyclic carbenes on Pt nanoparticles

The properties of many functional materials critically depend on the spatial distribution of surface active sites. In the case of solid catalysts, the geometric and electronic properties of different surface sites will directly impact their catalytic properties. However, the detection of catalytic sites at the single nanoparticle level cannot be easily achieved and most spectroscopic measurements are performed with ensemble-based measurements in which the reactivity is averaged over millions of nanoparticles. It is hereby demonstrated that chemically-functionalized N-heterocyclic carbene molecules can be attached to the surfaces of Pt nanoparticles and utilized as a model system for studying catalytic reactions on single metallic nanoparticles. The formation of a carbene self-assembled layer on the surface of a Pt nanoparticle and its stability under oxidizing conditions were investigated. IR nanospectroscopy measurements detected the chemical properties of surface-anchored molecules on single nanoparticles. A direct correlation was identified between IR nanospectroscopy measurements and macroscopic ATR-IR measurements. These results demonstrate that high spatial resolution mapping of the catalytic reactivity on single nanoparticles can be achieved with this approach.

Broadband infrared vibrational nano-spectroscopy using thermal blackbody radiation

Infrared vibrational nano-spectroscopy based on scattering scanning near-field optical microscopy (s-SNOM) provides intrinsic chemical specificity with nanometer spatial resolution. Here we use incoherent infrared radiation from a 1400 K thermal blackbody emitter for broadband infrared (IR) nano-spectroscopy. With optimized interferometric heterodyne signal amplification we achieve few-monolayer sensitivity in phonon polariton spectroscopy and attomolar molecular vibrational spectroscopy. Near-field localization and nanoscale spatial resolution is demonstrated in imaging flakes of hexagonal boron nitride (hBN) and determination of its phonon polariton dispersion relation. The signal-to-noise ratio calculations and analysis for different samples and illumination sources provide a reference for irradiance requirements and the attainable near-field signal levels in s-SNOM in general. The use of a thermal emitter as an IR source thus opens s-SNOM for routine chemical FTIR nano-spectroscopy.

Scattering-type scanning near-field optical microscopy with reconstruction of vertical interaction

Scattering-type scanning near-field optical microscopy provides access to super-resolution spectroscopic imaging of the surfaces of a variety of materials and nanostructures. In addition to chemical identification, it enables observations of nano-optical phenomena, such as mid-infrared plasmons in graphene and phonon polaritons in boron nitride. Despite the high lateral spatial resolution, scattering-type near-field optical microscopy is not able to provide characteristics of near-field responses in the vertical dimension, normal to the sample surface. Here, we present an accurate and fast reconstruction method to obtain vertical characteristics of near-field interactions. For its first application, we investigated the bound electromagnetic field component of surface phonon polaritons on the surface of boron nitride nanotubes and found that it decays within 20 nm with a considerable phase change in the near-field signal. The method is expected to provide characterization of the vertical field distribution of a wide range of nano-optical materials and structures.

Conventionally, scattering-type scanning near-field optical microscopy does not provide information on the vertical characteristic of near-field responses. Here, Xu et al. develop a method to reconstruct the vertical interaction response between the tip and the sample using this near-field technique.

Nanoscale probing of dynamics in local molecular environments

Vibrational spectroscopy can provide information about structure, coupling, and dynamics underlying the properties of complex molecular systems. While measurements of spectral line broadening can probe local chemical environments, the spatial averaging in conventional spectroscopies limits insight into underlying heterogeneity, in particular in disordered molecular solids. Here, using femtosecond infrared scattering scanning near-field optical microscopy (IR s-SNOM), we resolve in vibrational free-induction decay (FID) measurements a high degree of spatial heterogeneity in polytetrafluoroethylene (PTFE) as a dense molecular model system. In nanoscopic probe volumes as small as 10(3) vibrational oscillators, we approach the homogeneous response limit, with extended vibrational dephasing times of several picoseconds, that is, up to 10 times the inhomogeneous lifetime, and spatial average converging to the bulk ensemble response. We simulate the dynamics of relaxation with a finite set of local vibrational transitions subject to random modulations in frequency. The combined results suggest that the observed heterogeneity arises due to static and dynamic variations in the local molecular environment. This approach thus provides real-space and real-time visualization of the subensemble dynamics that define the properties of many functional materials.

Graphene-Based Platform for Infrared Near-Field Nanospectroscopy of Water and Biological Materials in an Aqueous Environment

Scattering scanning near-field optical microscopy (s-SNOM) has emerged as a powerful nanoscale spectroscopic tool capable of characterizing individual biomacromolecules and molecular materials. However, applications of scattering-based near-field techniques in the infrared (IR) to native biosystems still await a solution of how to implement the required aqueous environment. In this work, we demonstrate an IR-compatible liquid cell architecture that enables near-field imaging and nanospectroscopy by taking advantage of the unique properties of graphene. Large-area graphene acts as an impermeable monolayer barrier that allows for nano-IR inspection of underlying molecular materials in liquid. Here, we use s-SNOM to investigate the tobacco mosaic virus (TMV) in water underneath graphene. We resolve individual virus particles and register the amide I and II bands of TMV at ca. 1520 and 1660 cm(-1), respectively, using nanoscale Fourier transform infrared spectroscopy (nano-FTIR). We verify the presence of water in the graphene liquid cell by identifying a spectral feature associated with water absorption at 1610 cm(-1).