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.

Rapid Deposition of the Biomimetic Hydroxyapatite-Polydopamine-Amino Acid Composite Layers onto the Natural Enamel

In this work, we developed a technology that enables rapid deposition of biomimetic composite films onto natural enamel slices (known as biotemplates). These films are composed of polydopamine (PDA) and nanocrystalline carbonate-substituted hydroxyapatite (nano-cHAp) that have been functionalized with amino acid l-Arginine. We utilized atomic force microscopy (AFM) and scattering scanning near-field optical microscopy (s-SNOM) combined with infrared (IR) synchrotron to achieve nanoscale spatial resolution for both IR absorption and topography analyses. This combined analytical modality allowed us to understand how morphology connects to local changes in the chemical environment on the biotemplate surface during the deposition of the bioinspired coating. Our findings revealed that when using the proposed technology and after the deposition of the first PDA layer, the film formed on the enamel surface nearly covers the entire surface of the specimen whose thickness is larger on the surface of the emerging enamel prisms. Calculation of the crystallinity index for the biomimetic layer showed a multiple increase compared with natural enamel. This indicates regular and dense aggregation of nano-cHAp into larger crystals, imitating the morphology of natural enamel rods. The microhardness of the formed PDA-based biomimetic layer mineralized with nano-cHAp functionalized with amino acid l-Arginine deposited on natural enamel was practically the same as that of natural enamel. The characterization of nano-cHAp-amino acid-PDA layers using IR and Raman microspectroscopy showed that l-arginine acts as a conjunction agent in the formation of mineralized biomimetic composite coatings. The uniformity of the mechanisms of PDA layer formation under different deposition conditions and substrate types allows for the formation of coatings regardless of the macro- and micromorphology of the template. Therefore, the results obtained in this work have a high potential for future clinical applications in dental practice.

Changes in Dental Biofilm Proteins' Secondary Structure in Groups of People with Different Cariogenic Situations in the Oral Cavity and Using Medications by Means of Synchrotron FTIR-Microspectroscopy

This work unveils the idea that the cariogenic status of the oral cavity (the presence of active caries lesions) can be predicted via a lineshape analysis of the infrared spectral signatures of the secondary structure of proteins in dental biofilms. These spectral signatures that work as natural markers also show strong sensitivity to the application in patients of a so-called modulator-a medicinal agent (a pelleted mineral complex with calcium glycerophosphate). For the first time, according to our knowledge, in terms of deconvolution of the complete spectral profile of the amide I and amide II bands, significant intra- and intergroup differences were determined in the secondary structure of proteins in the dental biofilm of patients with a healthy oral cavity and with a carious pathology. This allowed to conduct a mathematical assessment of the spectral shifts in proteins' secondary structure in connection with the cariogenic situation in the oral cavity and with an external modulation. It was shown that only for the component parallel β-strands in the amide profile of the biofilm, a statistically significant (p < 0.05) change in its percentage weight (composition) was registered in a cariogenic situation (presence of active caries lesions). Note that no significant differences were detected in a normal situation (control) and in the presence of a carious pathology before and after the application of the modulator. The change in the frequency and percentage weight of parallel β-strands in the spectra of dental biofilms proved to be the result of the presence of cariogenic mutans streptococci in the film as well as of the products of their metabolism-glucan polymers. We foresee that the results presented here can inherently provide the basis for the infrared spectral diagnosis of changes (shifts) in the oral microbiome driven by the development of the carious process in the oral cavity as well as for the choice of optimal therapeutic treatments of caries based on microbiome-directed prevention measures.

Graphene Nano-Optics in the Terahertz Gap

Graphene nano-optics at terahertz (THz) frequencies (ν) is theoretically anticipated to feature extraordinary effects. However, interrogating such phenomena is nontrivial, since the atomically thin graphene dimensionally mismatches the THz radiation wavelength reaching hundreds of micrometers. Greater challenges happen in the THz gap (0.1-10 THz) wherein light sources are scarce. To surpass these barriers, we use a nanoscope illuminated by a highly brilliant and tunable free-electron laser to image the graphene nano-optical response from 1.5 to 6.0 THz. For ν < 2 THz, we observe a metal-like behavior of graphene, which screens optical fields akin to noble metals, since this excitation range approaches its charge relaxation frequency. At 3.8 THz, plasmonic resonances cause a field-enhancement effect (FEE) that improves the graphene imaging power. Moreover, we show that the metallic behavior and the FEE are tunable upon electrical doping, thus providing further control of these graphene nano-optical properties in the THz gap.

Review on infrared nanospectroscopy of natural 2D phyllosilicates

Phyllosilicates have emerged as a promising class of large bandgap lamellar insulators. Their applications have been explored from the fabrication of graphene-based devices to 2D heterostructures based on transition metal dichalcogenides with enhanced optical and polaritonics properties. In this review, we provide an overview of the use of infrared (IR) scattering-type scanning near-field optical microscopy (s-SNOM) for studying nano-optics and local chemistry of a variety of 2D natural phyllosilicates. Finally, we bring a brief update on applications that combine natural lamellar minerals into multifunctional nanophotonic devices driven by electrical control.

The Biochemical Mechanisms of Antimicrobial Photodynamic Therapy

The unbridled dissemination of multidrug-resistant pathogens is a major threat to global health and urgently demands novel therapeutic alternatives. Antimicrobial photodynamic therapy (aPDT) has been developed as a promising approach to treat localized infections regardless of drug resistance profile or taxonomy. Even though this technique has been known for more than a century, discussions and speculations regarding the biochemical mechanisms of microbial inactivation have never reached a consensus on what is the primary cause of cell death. Since photochemically generated oxidants promote ubiquitous reactions with various biomolecules, researchers simply assumed that all cellular structures are equally damaged. In this study, biochemical, molecular, biological, and advanced microscopy techniques were employed to investigate whether protein, membrane or DNA damage correlates better with dose-dependent microbial inactivation kinetics. We showed that although mild membrane permeabilization and late DNA damage occur, no correlation with inactivation kinetics was found. On the other hand, protein degradation was analyzed by 3 different methods and showed a dose-dependent trend that matches microbial inactivation kinetics. Our results provide a deeper mechanistic understanding of aPDT that can guide the scientific community towards the development of optimized photosensitizing drugs and also rationally propose synergistic combinations with antimicrobial chemotherapy.

Van der Waals materials as dielectric layers for tailoring the near-field photonic response of surfaces

Epsilon near-zero photonics and surface polariton nanophotonics have become major fields within optics, leading to unusual and enhanced light-matter interaction. Specific dielectric responses are required in both cases, which can be achieved, e.g., via operation near a material's electronic or phononic resonance. However, this condition restricts operation to a specific, narrow frequency range. It has been shown that using a thin dielectric layer can adjust the dielectric response of a surface and, therefore, the operating frequency for achieving specific photonic excitations. Here, we show that a surface's optical properties can be tuned via the deposition/transference of ultra-thin layered van der Waals (vdW) crystals, the thicknesses of which can easily be adjusted to provide the desired response. In particular, we experimentally and theoretically show that the surface phonon resonance of a silica surface can be tuned by ∼50 cm^-1 through the simple deposition of nanometer-thick exfoliated flakes of black phosphorus. The surface properties were probed by infrared nanospectroscopy, and results show a close agreement with the theory. The black phosphorus-silica layered structure effectively acts as a surface with a tunable effective dielectric constant that presents an infrared response dependent on the black phosphorus thickness. In contrast, with a lower dielectric constant, hexagonal boron nitride does not significantly tune the silica surface phonon polariton. Our approach also applies to epsilon near-zero surfaces, as theoretically shown, and to polaritonic surfaces operating at other optical ranges.

Nano-Infrared Imaging of Primary Neurons

Alzheimer’s disease (AD) accounts for about 70% of neurodegenerative diseases and is a cause of cognitive decline and death for one-third of seniors. AD is currently underdiagnosed, and it cannot be effectively prevented. Aggregation of amyloid-β (Aβ) proteins has been linked to the development of AD, and it has been established that, under pathological conditions, Aβ proteins undergo structural changes to form β-sheet structures that are considered neurotoxic. Numerous intensive in vitro studies have provided detailed information about amyloid polymorphs; however, little is known on how amyloid β-sheet-enriched aggregates can cause neurotoxicity in relevant settings. We used scattering-type scanning near-field optical microscopy (s-SNOM) to study amyloid structures at the nanoscale, in individual neurons. Specifically, we show that in well-validated systems, s-SNOM can detect amyloid β-sheet structures with nanometer spatial resolution in individual neurons. This is a proof-of-concept study to demonstrate that s-SNOM can be used to detect Aβ-sheet structures on cell surfaces at the nanoscale. Furthermore, this study is intended to raise neurobiologists’ awareness of the potential of s-SNOM as a tool for analyzing amyloid β-sheet structures at the nanoscale in neurons without the need for immunolabeling.

Sub-diffractional cavity modes of terahertz hyperbolic phonon polaritons in tin oxide

Hyperbolic phonon polaritons have recently attracted considerable attention in nanophotonics mostly due to their intrinsic strong electromagnetic field confinement, ultraslow polariton group velocities, and long lifetimes. Here we introduce tin oxide (SnO2) nanobelts as a photonic platform for the transport of surface and volume phonon polaritons in the mid- to far-infrared frequency range. This report brings a comprehensive description of the polaritonic properties of SnO2 as a nanometer-sized dielectric and also as an engineered material in the form of a waveguide. By combining accelerator-based IR-THz sources (synchrotron and free-electron laser) with s-SNOM, we employed nanoscale far-infrared hyper-spectral-imaging to uncover a Fabry-Perot cavity mechanism in SnO2 nanobelts via direct detection of phonon-polariton standing waves. Our experimental findings are accurately supported by notable convergence between theory and numerical simulations. Thus, the SnO2 is confirmed as a natural hyperbolic material with unique photonic properties essential for future applications involving subdiffractional light traffic and detection in the far-infrared range.

Dipole modelling for a robust description of subdiffractional polariton waves

The nanophotonics of van der Waals (vdW) materials relies critically on the electromagnetic properties of polaritons defined on sub-diffraction length scales. Here, we use a full electromagnetic Hertzian dipole antenna (HDA) model to describe the hyperbolic phonon polaritons (HP²s) in vdW crystals of hexagonal boron nitride (hBN) on a gold surface. The HP² waves are investigated by broadband synchrotron infrared nanospectroscopy (SINS) which covers the type I and type II hyperbolic bands simultaneously. Basically, polariton waves, observed by SINS, are assigned to the resultant electric field from the summation over the irradiated electric fields of dipoles distributed along the crystal edge and at the tip location and a non-propagating field. The values of polariton momenta and damping extracted from the HDA model present excellent agreement with theoretical predictions. Our analysis shows that the confinement factor of type I HP²s exceeds that of the type II ones by up to a factor of 3. We extract anti-parallel group velocities (v_g) for type I (v_g,typeI = -0.005c, c is the light velocity in a vacuum) in relation to type II (v_g,typeII = 0.05c) polaritonic pulses, with lifetimes of ∼0.6 ps and ∼0.3 ps, respectively. Furthermore, by incorporating consolidated optical-near field theory into the HDA model, we simulate real-space images of polaritonic standing waves for hBN crystals of different shapes. This approach reproduces the experiments with a minimal computational cost. Thus, it is demonstrated that the HDA modelling self-consistently explains the measured complex-valued polariton near-field, while being a general approach applicable to other polariton types, like plasmon- and exciton-polaritons, active in the wide range of vdW materials.

Inactivation of milk-borne pathogens by blue light exposure

Food safety and quality management play a pivotal role in the dairy industry. Milk is a highly nutritious food that also provides an excellent medium for growth of pathogenic microorganisms. Thus, dairy industry focuses most of their processes and costs on keeping contamination levels as low as possible. Thermal processes for microbial decontamination may be effective; however, they cannot provide excellent organoleptic, nutritional, and decontamination properties simultaneously. In this scenario, microbial inactivation by exposure to blue light is a promising alternative method in the food industry due to its intrinsic antimicrobial properties free of any thermal effect. Therefore, this study aimed to determine the inactivation kinetics induced by blue light (λ = 413 nm) against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Salmonella Typhimurium, and Mycobacterium fortuitum cells suspended in whole milk or saline solution. We also performed a series of optic spectroscopies to investigate possible degradation of milk components. All species were sensitive to photoinactivation suspended either in saline solution or milk. Inactivation kinetics differs significantly depending on the suspension medium and each species is differently affected. All bacterial species tested presented more than 5 log₁₀ of inactivation within less than 2 h of irradiation (720 J/cm²). Infrared spectroscopy did not reveal any significant alteration in any of the milk constituents (e.g., sugars, proteins, and lipids). Riboflavin (vitamin B₂) was the only significantly degraded constituent found. Therefore, we conclude that microbial inactivation performed by blue light presents extraordinary potential for processes in the dairy industry.

Synchrotron infrared nanospectroscopy on a graphene chip

A recurring goal in biology and biomedicine research is to access the biochemistry of biological processes in liquids that represent the environmental conditions of living organisms. These demands are becoming even more specific as microscopy techniques are fast evolving in the era of single cell analysis. In the modality of chemical probes, synchrotron infrared spectroscopy (μ-FTIR) is a technique that is extremely sensitive to vibrational responses of materials; however, the classical optical limits prevent the technique to access the biochemistry of specimens at the subcellular level. In addition, due to the intricate environmental requirements and strong infrared absorption of water, μ-FTIR of bioprocesses in liquids remains highly challenging. In phase with these challenges, on-chip liquid cells emerge as a versatile alternative to control the water thickness while providing a biocompatible chemical environment for analytical analyses. In this work we report the development of a liquid platform specially designed for nanoscale infrared analysis of biomaterials in wet environments. A key advantage of our designed platform is the use of graphene as an optical window that interfaces wet and dry environments in the liquid cell. By combining near-field optical microscopy and synchrotron infrared radiation, we measure the nanoscale fingerprint IR absorbance of a variety of liquids often used in biological studies. Further, we demonstrate the feasibility of the platform for the chemical analysis of protein clusters immersed in water with a clear view of the proteins' secondary structure signatures. The simplicity of the proposed platform combined with the high quality of our data makes our findings a template for future microfluidic devices targeting dynamic nanoscale-resolved chemical analysis.

Anisotropic Flow Control and Gate Modulation of Hybrid Phonon-Polaritons

Light-matter interaction in two-dimensional photonic or phononic materials allows for the confinement and manipulation of free-space radiation at sub-wavelength scales. Most notably, the van der Waals heterostructure composed of graphene (G) and hexagonal boron nitride (hBN) provides for gate-tunable hybrid hyperbolic plasmon phonon-polaritons (HP³). Here, we present the anisotropic flow control and gate-voltage modulation of HP³ modes in G-hBN on an air-Au microstructured substrate. Using broadband infrared synchrotron radiation coupled to a scattering-type near-field optical microscope, we launch HP³ waves in both hBN Reststrahlen bands and observe directional propagation across in-plane heterointerfaces created at the air-Au junction. The HP³ hybridization is modulated by varying the gate voltage between graphene and Au. This modifies the coupling of continuum graphene plasmons with the discrete hBN hyperbolic phonon polaritons, which is described by an extended Fano model. This work represents the first demonstration of the control of polariton propagation, introducing a theoretical approach to describe the breaking of the reflection and transmission symmetry for HP³ modes. Our findings augment the degree of control of polaritons in G-hBN and related hyperbolic metamaterial nanostructures, bringing new opportunities for on-chip nano-optics communication and computing.

Interplay of non-uniform charge distribution on the electrochemical modification of graphene

Graphene is considered a model material for surfaces because it is stable despite being composed of a single layer of carbon atoms. Although the thermal and electronic properties of graphene are well reported, the behavior of graphene sheets with the addition of charges to the structure is not well understood. Combining infrared spectroscopy, electrochemical analysis, and computational simulations, we report the effect of an electrochemically induced covalent anchoring of 4-carboxyphenyl (4-CP) units on the optical and electronic properties of graphene. Charges in graphene become concentrated at specific sites of the sheet when electrochemically perturbed and the functionalization occurs inhomogeneously along the graphene sheet. We observed that, when graphene is covalently functionalized, the resistance to heterogeneous electron transfer is increased by a factor of 1.4. Furthermore, scattering-type scanning near-field optical microscopy and atomic force microscopy show that the covalent functionalization affects drastically the optical and physical properties of the graphene/SiO2 system, especially the plasmon-phonon coupling after the functionalization. In addition, from these we infer that a comparatively higher degree of functionalization occurs near the electrode edges. These results are supported by computational simulations, which show that the covalent anchoring of 4-CP units weakens electron transfer because the charges are retained on the sp3-hybridized carbon atoms generated upon functionalization, suggesting that graphene properties are deeply influenced by the way the molecules are immobilized on its structure.

Infrared Nanospectroscopy Reveals the Chemical Nature of Pit Membranes in Water-Conducting Cells of the Plant Xylem

In the xylem of angiosperm plants, microscopic pits through the secondary cell walls connect the water-conducting vessels. Cellulosic meshes originated from primary walls, and middle lamella between adjacent vessels, called the pit membrane, separates one conduit from another. The intricate structure of the nano-sized pores in pit membranes enables the passage of water under negative pressure without hydraulic failure due to obstruction by gas bubbles (i.e. embolism) under normal conditions or mild drought stress. Since the chemical composition of pit membranes affects embolism formation and bubble behavior, we directly measured pit membrane composition in Populus nigra wood. Here, we characterized the chemical composition of cell wall structures by synchrotron infrared nanospectroscopy and atomic force microscopy-infrared nanospectroscopy with high spatial resolution. Characteristic peaks of cellulose, phenolic compounds, and proteins were found in the intervessel pit membranes of P. nigra wood. In addition, the vessel to parenchyma pit membranes and developing cell walls of the vascular cambium showed clear signals of cellulose, proteins, and pectin. We did not find a distinct peak of lignin and other compounds in these structures. Our investigation of the complex chemical composition of intervessel pit membranes furthers our understanding of the flow of water and bubbles between neighboring conduits. The advances presented here pave the way for further label-free studies related to the nanochemistry of plant cell components.

Low-aberration beamline optics for synchrotron infrared nanospectroscopy

Synchrotron infrared nanospectroscopy is a recently developed technique that enables new possibilities in the broadband chemical analysis of materials in the nanoscale, far beyond the diffraction limit in this frequency domain. Synchrotron infrared ports have exploited mainly the high brightness advantage provided by electron storage rings across the whole infrared range. However, optical aberrations in the beam produced by the source depth of bending magnet emission at large angles prevent infrared nanospectroscopy to reach its maximum capability. In this work we present a low-aberration optical layout specially designed and constructed for a dedicated synchrotron infrared nanospectroscopy beamline. We report excellent agreement between simulated beam profiles (from standard wave propagation and raytracing optics simulations) with experimental measurements. We report an important improvement in the infrared nanospectroscopy experiment related to the improved beamline optics. Finally, we demonstrate the performance of the nanospectroscopy endstation by measuring a hyperspectral image of a polar material and we evaluate the setup sensitivity by measuring ultra-thin polymer films down to 6 nm thick.

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.

X-ray phase measurements as a probe of small structural changes in doped nonlinear optical crystals

X-ray multiple diffraction experiments with synchrotron radiation were carried out on pure and doped nonlinear optical crystals: NH4H2PO4and KH2PO4doped with Ni and Mn, respectively. Variations in the intensity profiles were observed from pure to doped samples, and these variations correlated with shifts in the structure factor phases, also known as triplet phases. This result demonstrates the potential of X-ray phase measurements to study doping in this type of single crystal. Different methodologies for probing structural changes were developed. Dynamical diffraction simulations and curve fitting procedures were also necessary for accurate phase determination. Structural changes causing the observed phase shifts are discussed.

Detection of residual leukemia with immunologic methods: technical developments and clinical implications

The identification of immunophenotypes expressed on leukemic cells but rare or absent during normal hematopoiesis allows close monitoring of residual leukemia after treatment. Phenotypes that afford a detection level of 1 leukemic cell among 10,000 normal bone marrow cells have been identified in 90% of cases of T-lineage acute lymphoblastic leukemia (T-ALL), 25% of B lineage ALL and 40% of acute myeloid leukemia (AML). Residual disease detected with immunologic techniques in patients with acute leukemia during continuation therapy or off treatment usually anticipates overt relapse. While these data indicate the reliability of these techniques, further studies with homogeneously treated cohorts of patients, currently underway, are needed to precisely define the clinical significance of detecting occult leukemia at different points during treatment. The proportion of patients that can be studied with immunologic methods may increase through the definition of new leukemia-associated phenotypes using existing antibodies. In addition, new useful phenotypes may be identified through a) the development of novel techniques that allow cell permeabilization with preservation of surface membrane molecules and light-scattering properties; b) the generation of new antibodies that recognize leukemia-associated antigens.