Perspectives for infrared beamlines in fourth-generation synchrotron facilities.

With several fourth-generation, or diffraction-limited, storage rings and multiple beamlines in operation, the missing range of the spectrum was infrared…until recently.

Origins and consequences of asymmetric nano-FTIR interferograms.

Infrared scattering-type near-field optical microscopy, IR s-SNOM, and its broadband variant, nano-FTIR, are pioneering, flagship techniques for their ability to provide molecular identification and material optical property information at a spatial resolution well below the far-field diffraction limit, typically less than 25 nm. While s-SNOM and nano-FTIR instrumentation and data analysis have been discussed previously, there is a lack of information regarding experimental parameters for the practitioner, especially in the context of previously developed frameworks. Like conventional FTIR spectroscopy, the critical component of a nano-FTIR instrument is an interferometer. However, unlike FTIR spectroscopy, the resulting interference patterns or interferograms are typically asymmetric. Here, we unambiguously describe the origins of asymmetric interferograms recorded with nano-FTIR instruments, give a detailed analysis of potential artifacts, and recommend optimal instrument settings as well as data analysis parameters.

Diffraction-limited mid-infrared microspectroscopy to reveal a micron-thick interfacial water layer signature.

Mid-infrared microspectroscopy is a non-invasive tool for identifying the molecular structure and chemical composition at the scale of the probe, i.e. at the scale of the beam. Consequently, investigating small objects or domains (commensurable to the wavelength) requires high-resolution measurements, even down to the diffraction limit. Herein, different protocols and machines allowing high-resolution measurements in transmission mode (aperture size (i.e., beam size) from 15 × 15 µm to 3 × 3 µm) are tested using the same sample. The model sample is a closed cavity containing a water-air assemblage buried in a quartz fragment (fluid inclusion). The spectral range covers the water stretching band (3000-3800 cm-1), whose variations are followed as a function of the distance to the cavity wall. The experiments compare the performance of one focal plane array (FPA) detector associated with a Globar source with respect to a single-element mercury cadmium telluride (MCT) detector associated with a supercontinuum laser (SCL) or a synchrotron radiation source (SRS). This work also outlines the importance of post-experimental data processing, including interference fringe removal and Mie scattering correction, to ensure that the observed spectral signatures are not related to optical aberrations. We show that the SCL and the SRS-based setups detect specific spectral features along the quartz boundary (solid surface), invisible to the FPA imaging microscope. Additionally, the broadband SCL thus has the potential to substitute at the laboratory scale the SRS for conducting diffraction-limited high-resolution measurements.

Does dinocyst wall composition really reflect trophic affinity? New evidence from ATR micro-FTIR spectroscopy measurements.

Attenuated total reflection (ATR) microscope Fourier transform infrared (micro-FTIR) spectroscopy was used to investigate the dinosporin composition in the walls of modern, organic-walled dinoflagellate resting cysts (dinocysts). Variable cyst wall compositions were observed, which led to the erection of four spectrochemical groups, some with striking similarities to other resistant biomacromolecules such as sporopollenin and algaenan. Furthermore, possible proxies derivable from the spectrochemical composition of modern and fossil dinocysts were discussed. The color of the dinocyst walls was reflected in the spectral data. When comparing that color with a standard and the results of a series of bleaching experiments with oxidative agents, eumelanin was assigned as a likely pigment contributing to the observed color. Following this assignment, the role of eumelanin as an ultraviolet sunscreen in colored dinocysts was hypothesized, and its implications on the autofluorescence and morphological preservation of dinocysts were further discussed. Unlike what had previously been assumed, it was shown that micro-FTIR data from dinocysts cannot be used to unambiguously infer trophic affinities of their associated cells. Finally, using methods with high spatial resolutions (synchrotron transmission micro-FTIR and optical photothermal infrared spectroscopy), it was shown that dinocyst wall layers are chemically homogenous at the probed scales. This study fills a large knowledge gap in our understanding of the chemical nature of dinocyst walls and has nuanced certain assumptions and interpretations made in the past.

Direct Visualization of Ultrastrong Coupling between Luttinger-Liquid Plasmons and Phonon Polaritons.

Ultrastrong coupling of light and matter creates new opportunities to modify chemical reactions or develop novel nanoscale devices. One-dimensional Luttinger-liquid plasmons in metallic carbon nanotubes are long-lived excitations with extreme electromagnetic field confinement. They are promising candidates to realize strong or even ultrastrong coupling at infrared frequencies. We applied near-field polariton interferometry to examine the interaction between propagating Luttinger-liquid plasmons in individual carbon nanotubes and surface phonon polaritons of silica and hexagonal boron nitride. We extracted the dispersion relation of the hybrid Luttinger-liquid plasmon-phonon polaritons (LPPhPs) and explained the observed phenomena by the coupled harmonic oscillator model. The dispersion shows pronounced mode splitting, and the obtained value for the normalized coupling strength shows we reached the ultrastrong coupling regime with both native silica and hBN phonons. Our findings predict future applications to exploit the extraordinary properties of carbon nanotube plasmons, ranging from nanoscale plasmonic circuits to ultrasensitive molecular sensing.

Super-Resolved 3D Mapping of Molecular Orientation Using Vibrational Techniques.

When a sample has an anisotropic structure, it is possible to obtain additional information controlling the polarization of incident light. With their straightforward instrumentation approaches, infrared (IR) and Raman spectroscopies are widely popular in this area. Single-band-based determination of molecular in-plane orientation, typically used in materials science, is here extended by the concurrent use of two vibration bands, revealing the orientational ordering in three dimension. The concurrent analysis was applied to IR spectromicroscopic data to obtain orientation angles of a model polycaprolactone spherulite sample. The applicability of this method spans from high-resolution, diffraction-limited Fourier transform infrared (FT-IR) and Raman imaging to super-resolved optical photothermal infrared (O-PTIR) imaging. Due to the nontomographic experimental approach, no image distortion is visible and nanometer scale orientation domains can be observed. Three-dimensional (3D) bond orientation maps enable in-depth characterization and consequently precise control of the sample's physicochemical properties and functions.

Micro to Nano: Multiscale IR Analyses Reveal Zinc Soap Heterogeneity in a 19th-Century Painting by Corot.

Formation and aggregation of metal carboxylates (metal soaps) can degrade the appearance and integrity of oil paints, challenging efforts to conserve painted works of art. Endeavors to understand the root cause of metal soap formation have been hampered by the limited spatial resolution of Fourier transform infrared microscopy (µ-FTIR). We overcome this limitation using optical photothermal infrared spectroscopy (O-PTIR) and photothermal-induced resonance (PTIR), two novel methods that provide IR spectra with ≈500 and ≈10 nm spatial resolutions, respectively. The distribution of chemical phases in thin sections from the top layer of a 19th-century painting is investigated at multiple scales (µ-FTIR ≈ 102 µm3, O-PTIR ≈ 10-1 µm3, PTIR ≈ 10-5 µm3). The paint samples analyzed here are found to be mixtures of pigments (cobalt green, lead white), cured oil, and a rich array of intermixed, small (often ≪ 0.1 µm3) zinc soap domains. We identify Zn stearate and Zn oleate crystalline soaps with characteristic narrow IR peaks (≈1530-1558 cm-1) and a heterogeneous, disordered, water-permeable, tetrahedral zinc soap phase, with a characteristic broad peak centered at ≈1596 cm-1. We show that the high signal-to-noise ratio and spatial resolution afforded by O-PTIR are ideal for identifying phase-separated (or locally concentrated) species with low average concentration, while PTIR provides an unprecedented nanoscale view of distributions and associations of species in paint. This newly accessible nanocompositional information will advance our knowledge of chemical processes in oil paint and will stimulate new art conservation practices.

Correlative imaging to resolve molecular structures in individual cells: Substrate validation study for super-resolution infrared microspectroscopy.

Light microscopy has been a favorite tool of biological studies for almost a century, recently producing detailed images with exquisite molecular specificity achieving spatial resolution at nanoscale. However, light microscopy is insufficient to provide chemical information as a standalone technique. An increasing amount of evidence demonstrates that optical photothermal infrared microspectroscopy (O-PTIR) is a valuable imaging tool that can extract chemical information to locate molecular structures at submicron resolution. To further investigate the applicability of sub-micron infrared microspectroscopy for biomedical applications, we analyzed the contribution of substrate chemistry to the infrared spectra acquired from individual neurons grown on various imaging substrates. To provide an example of correlative immunofluorescence/O-PTIR imaging, we used immunofluorescence to locate specific organelles for O-PTIR measurement, thus capturing molecular structures at the sub-cellular level directly in cells, which is not possible using traditional infrared microspectroscopy or immunofluorescence microscopy alone.

Vitamin D and Calcium Supplementation Accelerate Vascular Calcification in a Model of Pseudoxanthoma Elasticum.

Arterial calcification is a common feature of pseudoxanthoma elasticum (PXE), a disease characterized by ABCC6 mutations, inducing a deficiency in pyrophosphate, a key inhibitor of calcium phosphate crystallization in arteries. METHODS: we analyzed whether long-term exposure of Abcc6-/- mice (a murine model of PXE) to a mild vitamin D supplementation, with or without calcium, would impact the development of vascular calcification. Eight groups of mice (including Abcc6-/- and wild-type) received vitamin D supplementation every 2 weeks, a calcium-enriched diet alone (calcium in drinking water), both vitamin D supplementation and calcium-enriched diet, or a standard diet (controls) for 6 months. Aorta and kidney artery calcification was assessed by 3D-micro-computed tomography, Optical PhotoThermal IR (OPTIR) spectroscopy, scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDS) and Yasue staining. RESULTS: at 6 months, although vitamin D and/or calcium did not significantly increase serum calcium levels, vitamin D and calcium supplementation significantly worsened aorta and renal artery calcification in Abcc6-/- mice. CONCLUSIONS: vitamin D and/or calcium supplementation accelerate vascular calcification in a murine model of PXE. These results sound a warning regarding the use of these supplementations in PXE patients and, to a larger extent, patients with low systemic pyrophosphate levels.

Optical Photothermal Infrared Microspectroscopy Discriminates for the First Time Different Types of Lung Cells on Histopathology Glass Slides.

The debate of whether a glass substrate can be used in Fourier transform infrared spectroscopy is strongly linked to its potential clinical application. Histopathology glass slides of 1 mm thickness absorb the mid-IR spectrum in the rich fingerprint spectral region. Thus, it is important to assess whether emerging IR techniques can be employed to study biological samples placed on glass substrates. For this purpose, we used optical photothermal infrared (O-PTIR) spectroscopy to study for the first time malignant and non-malignant lung cells with the purpose of identifying IR spectral differences between these cells placed on standard pathology glass slides. The data in this feasibility study showed that O-PTIR can be used to obtain good-quality IR spectra from cells from both the lipid region (3000-2700 cm-1) and the fingerprint region between 1770 and 950 cm-1 but with glass contributions from 1350 to 950 cm-1. A new single-unit dual-range (C-H/FP) quantum cascade laser (QCL) IR pump source was applied for the first time, delivering a clear synergistic benefit to the classification results. Furthermore, O-PTIR is able to distinguish between lung cancer cells and non-malignant lung cells both in the lipid and fingerprint regions. However, when these two spectral ranges are combined, classification accuracies are enhanced with Random Forest modeling classification accuracy results ranging from 96 to 99% across all three studied cell lines. The methodology described here for the first time with a single-unit dual-range QCL for O-PTIR on glass is another step toward its clinical application in pathology.

A new typology of human hair medullas based on lipid composition analysis by synchrotron FTIR microspectroscopy.

Human hair is an organ that connects fundamental and applied research with everyday life through the cosmetic industry. Yet, the accurate compositional description of the human hair medulla is lacking due to their small size and difficulty with microextraction. Medullas are thus generally classified based on morphology. We investigated the chemical composition of the human hair medulla using synchrotron based infrared microspectroscopy. We confirmed that lipid signatures dominate the medulla infrared spectrum having 3-20 times higher lipid concentration compared to their surrounding cortex. Human hair medullas contain a mixture of non-esterified and esterified lipids, and carboxylate soaps in various proportions. We reveal the first direct spectroscopic evidence that medulla carboxylates are coordinated to calcium since they exhibit the specific calcium carboxylate signature. Using a representative sample, we observed a strong compositional variability between medullas that was unreported before. We detected calcium carboxylates in 76% of the medullas with one order of magnitude concentration variability between samples. All medullas contained esters with esterification varying by a factor of 30. Moreover, we detected the presence of crystalline calcium stearate in 9% of the medullas. We described a series of spectral markers to characterize medullas based on their lipid composition and propose to classify medullas in four to five groups. Our analysis provides a more detailed understanding of the chemical composition of human hair medullas that may impact cosmetics and biology. The origin and biological meaning of these variations must still be investigated.

Nanoscale Analysis of Historical Paintings by Means of O-PTIR Spectroscopy: The Identification of the Organic Particles in L'Arlésienne (Portrait of Madame Ginoux) by Van Gogh.

Optical-photothermal infrared (O-PTIR) spectroscopy is a recently developed technique that provides spectra comparable to traditional transmission FTIR spectroscopy with nanometric spatial resolution. Hence, O-PTIR is a promising candidate for the analysis of historical paintings, as well as other cultural heritage objects, but its potential has not yet been evaluated. This work presents the first application of O-PTIR to the analysis of cultural heritage, and in particular to an extremely small fragment from Van Gogh's painting L'Arlésienne (portrait of Madame Ginoux). The striking results obtained, including the detection of geranium lake pigments as well as the complete analysis of the stratigraphy, failed with other state-of-the-art techniques, highlight the potential of this method. The integration of O-PTIR to the study of cultural heritage opens to the possibility of decreasing the amount of sample extracted, therefore contributing to the preservation of the integrity of artworks while providing a complete characterization of the materials.

Mesoporous Metal-Organic Framework MIL-101 at High Pressure.

The chromium terephthalate MIL-101 is a mesoporous metal-organic framework (MOF) with unprecedented adsorption capacities due to the presence of giant pores. The application of an external pressure can effectively modify the open structure of MOFs and its interaction with guest molecules. In this work, we study MIL-101 under pressure by synchrotron X-ray diffraction and infrared (IR) spectroscopy with several pressure transmitting media (PTM). Our experimental results clearly show that when a solid medium as NaCl is employed, an irreversible amorphization of the empty structure occurs at about 0.4 GPa. Using a fluid PTM, as Nujol or high-viscosity silicone oil, results in a slight lattice expansion and a strong modification of the peak frequency and shape of the MOF hydroxyl vibration below 0.1 GPa. Moreover, the framework stability is enhanced under pressure with the amorphization onset shifted to about 7 GPa. This coherent set of results points out the insertion of the fluid inside the MIL-101 pores. Above 7 GPa, concomitantly to the nucleation of the amorphous phase, we observe a peculiar medium-dependent lattice expansion. The behavior of the OH stretching vibrations under pressure is profoundly affected by the presence of the guest fluid, showing that OH bonds are sensitive vibrational probes of the host-guest interactions. The present study demonstrates that even a polydimethylsiloxane silicone oil, although highly viscous, can be effectively inserted into the MIL-101 pores at a pressure below 0.2 GPa. High pressure can thus promote the incorporation of large polymers in mesoporous MOFs.

Synchrotron based phase contrast X-ray imaging combined with FTIR spectroscopy reveals structural and biomolecular differences in spikelets play a significant role in resistance to Fusarium in wheat.

BACKGROUND: Fusarium head blight (FHB), a scab principally caused by Fusarium graminearum Schw., is a serious disease of wheat. The purpose of this study is to evaluate the potential of combining synchrotron based phase contrast X-ray imaging (PCI) with Fourier Transform mid infrared (FTIR) spectroscopy to understand the mechanisms of resistance to FHB by resistant wheat cultivars. Our hypothesis is that structural and biochemical differences between resistant and susceptible cultivars play a significant role in developing resistance to FHB. RESULTS: Synchrotron based PCI images and FTIR absorption spectra (4000-800 cm(-1)) of the floret and rachis from Fusarium-damaged and undamaged spikes of the resistant cultivar 'Sumai3', tolerant cultivar 'FL62R1', and susceptible cultivar 'Muchmore' were collected and analyzed. The PCI images show significant differences between infected and non-infected florets and rachises of different wheat cultivars. However, no pronounced difference between non-inoculated resistant and susceptible cultivar in terms of floret structures could be determined due to the complexity of the internal structures. The FTIR spectra showed significant variability between infected and non-infected floret and rachis of the wheat cultivars. The changes in absorption wavenumbers following pathogenic infection were mostly in the spectral range from 1800-800 cm(-1). The Principal Component Analysis (PCA) was also used to determine the significant chemical changes inside floret and rachis when exposed to the FHB disease stress to understand the plant response mechanism. In the floret and rachis samples, PCA of FTIR spectra revealed differences in cell wall related polysaccharides. In the florets, absorption peaks for Amide I, cellulose, hemicellulose and pectin were affected by the pathogenic fungus. In the rachis of the wheat cultivars, PCA underlines significant changes in pectin, cellulose, and hemicellulose characteristic absorption spectra. Amide II and lignin absorption peaks, persistent in the rachis of Sumai3, together with increased peak shift at 1245 cm(-1) after infection with FHB may be a marker for stress response in which the cell wall compounds related to pathways for lignification are increased. CONCLUSIONS: Synchrotron based PCI combined with FTIR spectroscopy show promising results related to FHB in wheat. The combined technique is a powerful new tool for internal visualisation and biomolecular monitoring before and during plant-microbe interactions to understand both the differences between cultivars and their different responses to disease stress.

Pressure induced phase transitions and metallization of a neutral radical conductor.

The crystal structure and charge transport properties of the prototypal oxobenzene-bridged 1,2,3-bisdithiazolyl radical conductor 3a are strongly dependent on pressure. Compression of the as-crystallized α-phase, space group Fdd2, to 3-4 GPa leads to its conversion into a second or ß-phase, in which F-centering is lost. The space group symmetry is lowered to Pbn21, and there is concomitant halving of the a and b axes. A third or γ-phase, also space group Pbn21, is generated by further compression to 8 GPa. The changes in packing that accompany both phase transitions are associated with an "ironing out" of the ruffled ribbon-like architecture of the α-phase, so that consecutive radicals along the ribbons are rendered more nearly coplanar. In the ß-phase the planar ribbons are propagated along the b-glides, while in the γ-phase they follow the n-glides. At ambient pressure 3a is a Mott insulator, displaying high but activated conductivity, with σ(300 K) = 6 × 10(-3) S cm(-1) and E(act) = 0.16 eV. With compression beyond 4 GPa, its conductivity is increased by 3 orders of magnitude, and the thermal activation energy is reduced to zero, heralding the formation of a metallic state. High pressure infrared absorption and reflectivity measurements are consistent with closure of the Mott-Hubbard gap near 4-5 GPa. The results are discussed in the light of DFT calculations on the molecular and band electronic structure of 3a. The presence of a low-lying LUMO in 3a gives rise to high electron affinity which, in turn, creates an electronically much softer radical with a low onsite Coulomb potential U. In addition, considerable crystal orbital (SOMO/LUMO) mixing occurs upon pressurization, so that a metallic state is readily achieved at relatively low applied pressure.

Comparing and correlating solubility parameters governing the self-assembly of molecular gels using 1,3:2,4-dibenzylidene sorbitol as the gelator.

Solvent properties play a central role in mediating the aggregation and self-assembly of molecular gelators and their growth into fibers. Numerous attempts have been made to correlate the solubility parameters of solvents and gelation abilities of molecular gelators, but a comprehensive comparison of the most important parameters has yet to appear. Here, the degree to which partition coefficients (log P), Henry's law constants (HLC), dipole moments, static relative permittivities (ε(r)), solvatochromic E(T)(30) parameters, Kamlet-Taft parameters (ß, α, and π), Catalan's solvatochromic parameters (SPP, SB, and SA), Hildebrand solubility parameters (δ(i)), and Hansen solubility parameters (δ(p), δ(d), δ(h)) and the associated Hansen distance (R(ij)) of 62 solvents (covering a wide range of properties) can be correlated with the self-assembly and gelation of 1,3:2,4-dibenzylidene sorbitol (DBS) gelation, a classic molecular gelator, is assessed systematically. The approach presented describes the basis for each of the parameters and how it can be applied. As such, it is an instructional blueprint for how to assess the appropriate type of solvent parameter for use with other molecular gelators as well as with molecules forming other types of self-assembled materials. The results also reveal several important insights into the factors favoring the gelation of solvents by DBS. The ability of a solvent to accept or donate a hydrogen bond is much more important than solvent polarity in determining whether mixtures with DBS become solutions, clear gels, or opaque gels. Thermodynamically derived parameters could not be correlated to the physical properties of the molecular gels unless they were dissected into their individual HSPs. The DBS solvent phases tend to cluster in regions of Hansen space and are highly influenced by the hydrogen-bonding HSP, δ(h). It is also found that the fate of this molecular gelator, unlike that of polymers, is influenced not only by the magnitude of the distance between the HSPs for DBS and the HSPs of the solvent, R(ij), but also by the directionality of R(ij): if the solvent has a larger hydrogen-bonding HSP (indicating stronger H-bonding) than that of the DBS, then clear gels are formed; opaque gels form when the solvent has a lower δ(h) than does DBS.

Size-dependent dissociation of carbon monoxide on cobalt nanoparticles.

In situ soft X-ray absorption spectroscopy (XAS) was employed to study the adsorption and dissociation of carbon monoxide molecules on cobalt nanoparticles with sizes ranging from 4 to 15 nm. The majority of CO molecules adsorb molecularly on the surface of the nanoparticles, but some undergo dissociative adsorption, leading to oxide species on the surface of the nanoparticles. We found that the tendency of CO to undergo dissociation depends critically on the size of the Co nanoparticles. Indeed, CO molecules dissociate much more efficiently on the larger nanoparticles (15 nm) than on the smaller particles (4 nm). We further observed a strong increase in the dissociation rate of adsorbed CO upon exposure to hydrogen, clearly demonstrating that the CO dissociation on cobalt nanoparticles is assisted by hydrogen. Our results suggest that the ability of cobalt nanoparticles to dissociate hydrogen is the main parameter determining the reactivity of cobalt nanoparticles in Fischer-Tropsch synthesis.

Step-scan IR spectroelectrochemistry with ultramicroelectrodes: nonsurface enhanced detection of near femtomole quantities using synchrotron radiation.

The result of interfacing step-scan spectroelectrochemistry with an IR microscope and synchrotron infrared (SIR) radiation is provided here. An external reflectance cell containing a 25 µm gold ultramicroelectrode is employed to achieve an electrochemical time constant less than one microsecond. The use of a prototypical electrochemical system, i.e., the mass-transport controlled reduction of ferricyanide, allows for a proof of principle evaluation of the viability of SIR for step-scan spectroelectrochemistry. An analysis of the importance of accounting for synchrotron source variation over the prolonged duration of a step-scan experiment is provided. Modeling of the material flux in the restricted diffusion space afforded by the external reflectance cell allows the quantitative IR results to be compared to theoretical predictions. The results indicate that only at very short times does linear diffusion within the cavity dominate the electrode response and the majority of the transient signal operates under conditions of quasi-hemispherical diffusion. The analytical information provided by the IR signal is found to be considerably less than that derived from the current response due the latter's pronounced edge effects. The results provide a detection limit of 36 fmol for step-scan SIR measurements of ferrocyanide. Implications for future IR spectroelectrochemical studies in the microsecond domain are discussed.

A reaction cell with sample laser heating for in situ soft X-ray absorption spectroscopy studies under environmental conditions.

A miniature (1 ml volume) reaction cell with transparent X-ray windows and laser heating of the sample has been designed to conduct X-ray absorption spectroscopy studies of materials in the presence of gases at atmospheric pressures. Heating by laser solves the problems associated with the presence of reactive gases interacting with hot filaments used in resistive heating methods. It also facilitates collection of a small total electron yield signal by eliminating interference with heating current leakage and ground loops. The excellent operation of the cell is demonstrated with examples of CO and H2 Fischer-Tropsch reactions on Co nanoparticles.

Allium fistulosum as a novel system to investigate mechanisms of freezing resistance.

Allium fistulosum was investigated as a novel model system to examine the mechanism of freezing resistance in cold hardy plants. The 250 × 50 × 90 µm average cell size and single epidermal cell layer system allowed direct observation of endoplasmic reticulum (ER), functional group localization during acclimation, freezing and thawing on an individual cell basis in live intact tissues. Cells increased freezing resistance from an LT50 of -11°C (non-acclimated) to -25°C under 2 weeks of cold acclimation. Samples were processed using Fourier transform infrared technology (FTIR) on a synchrotron light source and a focal plane array detector. In addition, confocal fluorescent microscopy combined with a cryostage using ER selective dye of ER-Tracker allowed more detailed examination of membrane responses during freezing. Cold acclimation increased the ER volume per cell, and the freeze-induced cell deformation stopped ER streaming and ER vesiculation subsequently occurred through the breakdown in the ER network. Freeze-induced ER vesicles in cold-acclimated cells were larger and more abundant than those in non-acclimated cells. According to FTIR, the carbohydrate/ester fraction and α-helical/ß-sheet secondary structure localized in the apoplast/plasma membrane region were most visibly increased during cold acclimation. Results suggest the mechanism of cold acclimation and freezing resistance in very hardy cells may be associated with both alterations in the apoplast/plasma membrane region and the ER cryodynamics. Allium fistulosum appears to be a useful system to obtain direct evidence at both intra and extracellular levels during cold acclimation and the freezing process.