Infrared Signatures for Phase Identification in Hafnium Oxide Thin Films

Phase identification in HfO2-based thin films is a prerequisite to understanding the mechanisms stabilizing the ferroelectric phase in these materials, which hold great promise in next-generation nonvolatile memory and computing technology. While grazing-incidence X-ray diffraction is commonly employed for this purpose, it has difficulty unambiguously differentiating between the ferroelectric phase and other metastable phases that may exist due to similarities in the d-spacings, their low intensities, and the overlapping of reflections. Infrared signatures provide an alternative route. However, their use in phase identification remains limited because phase control has overwhelmingly been accomplished via substituents, thereby convoluting infrared signatures between the substituents and the phase changes that they induce. Herein, we report the infrared optical responses of three undoped hafnium oxide films where annealing conditions have been used to create films consisting primarily of the ferroelectric polar orthorhombic Pca21, antipolar orthorhombic Pbca, and monoclinic P21/c phases, as was confirmed via transmission electron microscopy (TEM), UV-visible optical properties, and electrical property measurements. Vibrational signatures acquired from synchrotron nano-Fourier transform infrared spectroscopy (nano-FTIR) are shown to be capable of differentiating between the phases in a nondestructive, rapid, and nanoscale manner. The utility of nano-FTIR is illustrated for a film exhibiting an antiferroelectric polarization response. In this sample, it is proven that this behavior results from the Pbca phase rather than the often-cited tetragonal phase. By demonstrating that IR spectroscopy can unambiguously distinguish phases in this material, this work establishes a tool needed to isolate the factors dictating the ferroelectric phase stability in HfO2-based materials.

Comparing the potential of IR-spectroscopic techniques to gas chromatography coupled to ion mobility spectrometry for classifying virgin olive oil categories

Virgin olive oil (OO) can be classified into three different categories: extra virgin, virgin and lampante. The official method for this classification, based on physicochemical analysis and sensory tasting, is considered useful and effective, although it is a costly and time-consuming process. The aim of this study was to assess the potential of some analytical techniques for classifying and predicting different OO categories to support official methods and to provide olive oil companies with a rapid tool to assess product quality. Thus, mid and near infrared spectroscopies (MIR and NIR) have been compared by using different instruments and with head-space gas chromatography coupled to an ion mobility spectrometer (HS-GC-IMS). High classification success rates in validation models were obtained using IR spectrometers (>70% and > 80% in average for ternary and binary classifications, respectively), although HS-GC-IMS showed greater classification potential (>85% and > 90%).

Green Additives in Chitosan-Based Bioplastic Films: Physical, Mechanical, and Chemical Properties

To switch to alternatives for fossil-fuel-based polymer materials, renewable raw materials from green resources should be utilized. Chitosan is such a material that is a strong, but workable derivative from chitin, obtained from crustaceans. However, various applications ask for specific plastic properties, such as certain flexibility, hardness and transparency. With different additives, also obtainable from green resources, chitosan-based composites in the form of self-supporting films, ranging from very hard and brittle to soft and flexible were successfully produced. The additives turned out to belong to one of three categories, namely linear, non-linear, or crosslinking additives. The non-linear additives could only be taken up to a certain relative amount, whereas the uptake of linear additives was not limited within the range of our experiments. Additives with multiple functional groups tend to crosslink chitosan even at room temperature in an acidic medium. Finally, it was shown that dissolving the chitosan in acetic acid and subsequently drying the matrix as a film results in reacetylation compared to the starting chitosan source, resulting in a harder material. With these findings, it is possible to tune the properties of chitosan-based polymer materials, making a big step towards application of this renewable polymer within consumer goods.

Abundance and composition of microplastics in Tampico beach sediments, Tamaulipas State, southern Gulf of Mexico

The abundance and characteristics of microplastics (MPs) in coastal sediments from the Tampico beach, Gulf of Mexico was investigated. The MPs were extracted by a density separation method with saturated solutions of NaCl and ZnCl₂, the sediment-solution relationship was 1:3. MPs were classified according to its shape, color, and size under a stereoscopic microscope. Identification of MPs surface was carried out by a Scanning Electron Microscope (SEM). The polymer types were detected by a Fourier-transformed infrared (FTIR) Spectroscopy. Number of MPs in 20 g of sediments varies from 256 to 283 particles. The average abundance of MPs per kg was inferred as ∼13,392 microplastic particles. Fiber was the only MP particle identified in the Tampico beach, its size varied from 1.76 mm to 3.92 mm. Fibers identified were mostly transparent, blue, white, black, multicolor, yellow, pink, and red. Six different polymers were identified, i.e., polyester (PES), polyethylacrylate (PEA), cellophane, polyacrylonitrile (PAN), polystyrene acrylonitrile (SAN), and polyvinyl acetate ethylene (PVAE). PES is the most prevalent polymer in all samples.

Orientational deformations leading to temperature-induced structural phase transition in Prehnite using Raman, Infrared, and Terahertz spectroscopy

Understanding molecular and structural properties of naturally extracted minerals under varying thermodynamic parameters such as pressure (P) and temperature (T) helps us to explore vital information regarding various geological processes. Here, we present the comprehensive results of Raman, infrared (IR), and Terahertz (THz) spectroscopic investigations on Prehnite (Ca₂Al(AlSi₃O₁₀)(OH)₂) mineral from ambient (25 °C) to 1000 °C in the 6.6 - 4000 cm^-1 wide spectral range. The results indicate a substantial distortion in orientation between AlO₆ octahedron and SiO₄ tetrahedron layer leads to the strengthening of hydrogen bonds (HBs) in the Prehnite structure around 800 °C. Consequently, the disappearance of Raman active modes and abrupt change in frequency (ω) of Far-IR modes (obtained using THz spectroscopy) around 800 °C are spectral signatures of symmetry change in the structure. Eventually, these orientational changes at the molecular level trigger structural phase transition around 800 °C, supported by X-ray diffraction (XRD) measurements. Thus, the present study depicts the pivotal role of inter- and intra-molecular interactions in Prehnite, which determines its bonding and structural characteristics and hence its physicochemical properties under diverse environments.

Pyridine Dimers and Their Low-Temperature Isomerization: A High-Resolution Matrix-Isolation Spectroscopy Study

The bonding between two neutral aromatic compounds, especially small ones, has been controversially debated in the last decades, and terms like "π-stacking" had to be revised. Surprisingly, despite of many experimental and computational work, there is still no clear consensus about the structure of and the bonding in the pyridine dimer. In this work, for different isomeric forms of the pyridine dimer, the structures and bonding were elucidated by combining high-resolution matrix-isolation spectroscopic results with quantum-chemical calculations. High-resolution IR spectra of Ne matrices at 4 K containing pyridine were recorded for different concentrations and upon annealing to 10 and 12 K, relying on three isotopologues of pyridine. The spectra show the presence of hydrogen-bonded, T-shaped, and stacked forms of weakly-bound pyridine dimers. Among these, the hydrogen-bonded isomer is identified as the lowest-energy form. The results provide for the first time conclusive information about the interaction between two pyridine dimers.

Infrared Diffusion-Ordered Spectroscopy Reveals Molecular Size and Structure

Inspired by ideas from NMR, we have developed Infrared Diffusion-Ordered Spectroscopy (IR-DOSY), which simultaneously characterizes molecular structure and size. We rely on the fact that the diffusion coefficient of a molecule is determined by its size through the Stokes-Einstein relation, and achieve sensitivity to the diffusion coefficient by creating a concentration gradient and tracking its equilibration in an IR-frequency resolved manner. Analogous to NMR-DOSY, a two-dimensional IR-DOSY spectrum has IR frequency along one axis and diffusion coefficient (or equivalently, size) along the other, so the chemical structure and the size of a compound are characterized simultaneously. In an IR-DOSY spectrum of a mixture, molecules with different sizes are nicely separated into distinct sets of IR peaks. Extending this idea to higher dimensions, we also perform 3D-IR-DOSY, in which we combine the conformation sensitivity of femtosecond multi-dimensional IR spectroscopy with size sensitivity.

Studying the Key Intermediate of RNA Autohydrolysis by Cryogenic Gas-Phase Infrared Spectroscopy

Over the course of the COVID-19 pandemic, mRNA-based vaccines have gained tremendous importance. The development and analysis of modified RNA molecules benefit from advanced mass spectrometry and require sufficient understanding of fragmentation processes. Analogous to the degradation of RNA in solution by autohydrolysis, backbone cleavage of RNA strands was equally observed in the gas phase; however, the fragmentation mechanism remained elusive. In this work, autohydrolysis-like intermediates were generated from isolated RNA dinucleotides in the gas phase and investigated using cryogenic infrared spectroscopy in helium nanodroplets. Data from both experiment and density functional theory provide evidence for the formation of a five-membered cyclic phosphate intermediate and rule out linear or six-membered structures. Furthermore, the experiments show that another prominent condensed-phase reaction of RNA nucleotides can be induced in the gas phase: the tautomerization of cytosine. Both observed reactions are therefore highly universal and intrinsic properties of the investigated molecules.

Chemical changes induced during heating of acetonitrile-rich ice pre-irradiated by X-rays and its implication in astrochemistry

In this work, we investigate the effects induced by the heating of acetonitrile-rich ice from 13 K to 350 K. Before the heating, the sample was irradiated at 13 K by broadband X-rays (6 eV to 2 keV), which trigger the production of new molecules, such as HCN, H₂CCNH, CH₄ and CH₃NC (see Carvalho and Pilling, 2020) and also induced desorption of frozen species to gas-phase. New spectra were collected during heating to investigate whether new species, not present before at lower temperatures, appear due to thermal processing. New infrared bands were identified at temperatures around 120 K and 300 K, from which it was possible to notice the possible presence of HCN/CN radical, ammonia and C₂N₂. It was also verified that acetonitrile has a thermal desorption peak between 120 K and 200 K, which yields to the vanishing of acetonitrile within the sample for temperatures of 200 K and above. Some infrared features assigned before solely to acetonitrile remain for sample temperatures >200 K, which indicates the presence of blended species with similar infrared features. From analyzing those blended peaks, we also perceived the possible presence of aminoacetonitrile.

Meibum Lipid Composition and Conformation in Parkinsonism

PURPOSE

Patients with Parkinson's disease (PD) exhibit unstable tear films. Tear film lipid composition and structure are related to tear film stability and dry eye and tear lipids have not been characterized in people with PD. The aim of this study is to characterize Meibum tear lipids in donors with PD using ¹H-NMR and infrared spectroscopy.

METHODS

Three cohorts were compared: meibum from donors with PD (Mp) n = 10, meibum from donors with PD and dry eye (Mpd) n = 3, meibum from donors without PD (Mn) n = 29.

RESULTS

There were no significant differences, P > 0.05, in hydrocarbon branching for Mp compared with Mn. Mn contained twice as much cholesteryl esters compared with Mp, P < 0.0001. The cooperativity of the phase transition was significantly 37% lower for Mp compared with Mn, P < 0.0001. Mpd was much more ordered (stiffer) with compared with Mp and Mn, P < 0.0001.

CONCLUSION

Changes in meibum lipid composition and structure could be a marker for and/or contribute to increase the susceptibility of dry eye in patients with PD. A less cooperative phase transition for Mp compared with Mn indicates that Mp was more heterogeneous and/or contained more contaminants than Mn. The data support the idea that more ordered lipid contributes to dry eye.

ArCH2 + : A Detectable Noble Gas Molecule

The noble gas molecular cation, ArCH₂ ⁺ , has been observed in mass spectrometry experiments, and the present work is providing high-level quantum chemical predictions for the vibrational and rotational spectroscopic data necessary to observe this molecule in situ in other laboratory conditions. The Ar-C stretch in this cation is a bright fundamental vibrational frequency that should be observable in the early regions of the far-infrared at 421.2 cm^-1 for the universally most common ³⁶ Ar isotope. The near-prolate nature of this molecule and its 2.91 D dipole moment should also make it distinguishable for submillimeter detection, as well. Furthermore, the Ar-C bond strength in ArCH₂ ⁺ is greater than the global minimum for the dissociation of the experimentally known ArOH⁺ cation. As a result, the infrared spectrum of this simple organo-noble gas molecule is likely waiting to be observed and may already exist in the spectra of hydrocarbon cations in argon-matrix condensed phase experiments.

Analytical Approaches to the Characterization of Solid Drug Delivery Systems with Porous Adsorbent Carriers

A large variety of analytical techniques are available to meet the needs of characterization of solid samples. But, when solid drug delivery systems are concerned we are faced with demanding methodologies which have to compile capabilities of analytical techniques in regard to large diversity of structures and surface functionality of analyzed adsorbent carriers. In this review, the most commonly used analytical techniques are presented with their basic principles, advantages and disadvantages in applications of interest. Adsorbent carriers are widely used today as ingredients in the formulation of pharmaceutical forms, for increasing the dissolution rate of the drug and hence the bioavailability. They are also used in the formulation of substances with modified or target drug release into a specific tissue. Methods of thermal analysis (Thermogravimetry - TGA, Differential Scanning Calorimetry - DSC and Thermal microscopy - TM), spectroscopic methods (Infrared Spectroscopy - IR, especially Fourier Transform Infrared Spectroscopy - FTIR and Raman spectroscopy), crystallographic methods (Powder X-Ray Diffraction - PXRD) and finally Scanning Electron Microscopy (SEM) are the most powerful in the characterization of modern therapeutic systems with porous adsorbents. The problem-solving power of each particular analytical method is often enhanced by using simultaneous methods rather than a single technique.

Infrared Spectroscopy and Imaging in Stem Cells and Aging Research

The effect of aging process on stem cell function is crucial because of their critical role in tissue regeneration and repair. The impact of aging on stem cells needs to be understood clearly for the success of clinical application and obtaining desired therapeutic outcome throughout the novel stem cell based therapies. The existing methods used to monitor and characterize the stem cells have some unwanted effects on the properties of stem cells and these methods also do not provide real-time information about cellular conditions. These challenges enforce the usage of nondestructive, rapid, sensitive, high-quality, label-free, cheep, and innovative chemical monitoring methods. In this context, vibrational spectroscopy provides promising alternative to get new information into the field of stem cell biology for chemical analysis, quantification, and imaging of stem cells. Infrared spectroscopy and imaging coupled with chemometric methods can be used as novel and complimentary methods to obtain new insight into stem cell studies for future therapeutic and regenerative medicine.

Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region

Studies of structural changes in peptides and proteins using IR spectroscopy often rely on subtle changes in the amide I' band as a function of temperature. However, these changes can be obscured by the overlap with other absorptions, namely the side-chain and terminal carboxylic groups. The former were the subject of our previous report (Anderson et al., 2014). In this paper we investigate the IR spectra of the asymmetric stretch of α-carboxylic groups for amino acids representing all major types (Gly, Ala, Val, Leu, Ser, Thr, Asp, Glu, Lys, Asn, His, Trp, Pro) as well as the C-terminal groups of three dipeptides (Gly-Gly, Gly-Ala, Ala-Gly) in D₂O at neutral pH. Experimental temperature dependent IR spectra were analyzed by fitting of both symmetric and asymmetric pseudo-Voigt functions. Qualitatively the spectra exhibit shifts to higher frequency, loss in intensity and narrowing with increased temperature, similar to that observed previously for the side-chain carboxylic groups of Asp. The observed dependence of the band parameters (frequency, intensity, width and shape) on temperature is in all cases linear: simple linear regression is therefore used to describe the spectral changes. The spectral parameters vary between individual amino acids and show systematic differences between the free amino acids and dipeptides, particularly in the absolute peak frequencies, but the temperature variations are comparable. The relative variations between the dipeptide spectral parameters are most sensitive to the C-terminal amino acid, and follow the trends observed in the free amino acid spectra. General rules for modeling the α-carboxylic IR absorption bands in peptides and proteins as the function of temperature are proposed.

Synthesis and Protein Incorporation of Azido-Modified Unnatural Amino Acids

Two new azidophenylalanine residues (3 and 4) have been synthesized and, in combination with 4-azido-L-phenylalanine (1) and 4-azidomethyl-L-phenylalanine (2), form a series of unnatural amino acids (UAAs) containing the azide vibrational reporter at varying distances from the aromatic ring of phenylalanine. These UAAs were designed to probe protein hydration with high spatial resolution by utilizing the large extinction coefficient and environmental sensitivity of the azide asymmetric stretch vibration. The sensitivity of the azide reporters was investigated in solvents that mimic distinct local protein environments. Three of the four azido-modified phenylalanine residues were successfully genetically incorporated into a surface site in superfolder green fluorescent protein (sfGFP) utilizing an engineered, orthogonal aminoacyl-tRNA synthetase in response to an amber codon with high efficiency and fidelity. SDS-PAGE and ESI-Q-TOF mass analysis verified the site-specific incorporation of these UAAs. The observed azide asymmetric stretch in the linear IR spectra of these UAAs incorporated into sfGFP indicated that the azide groups were hydrated in the protein.

Characterization of a membrane-active peptide from the Bordetella pertussis CyaA toxin

Bordetella pertussis, the pathogenic bacteria responsible for whooping cough, secretes several virulence factors, among which is the adenylate cyclase toxin (CyaA) that plays a crucial role in the early stages of human respiratory tract colonization. CyaA invades target cells by translocating its catalytic domain directly across the plasma membrane and overproduces cAMP, leading to cell death. The molecular process leading to the translocation of the catalytic domain remains largely unknown. We have previously shown that the catalytic domain per se, AC384, encompassing residues 1-384 of CyaA, did not interact with lipid bilayer, whereas a longer polypeptide, AC489, spanning residues 1-489, binds to membranes and permeabilizes vesicles. Moreover, deletion of residues 375-485 within CyaA abrogated the translocation of the catalytic domain into target cells. Here, we further identified within this region a peptidic segment that exhibits membrane interaction properties. A synthetic peptide, P454, corresponding to this sequence (residues 454-485 of CyaA) was characterized by various biophysical approaches. We found that P454 (i) binds to membranes containing anionic lipids, (ii) adopts an α-helical structure oriented in plane with respect to the lipid bilayer, and (iii) permeabilizes vesicles. We propose that the region encompassing the helix 454-485 of CyaA may insert into target cell membrane and induce a local destabilization of the lipid bilayer, thus favoring the translocation of the catalytic domain across the plasma membrane.

Effective pumping proton collection facilitated by a copper site (CuB) of bovine heart cytochrome c oxidase, revealed by a newly developed time-resolved infrared system

X-ray structural and mutational analyses have shown that bovine heart cytochrome c oxidase (CcO) pumps protons electrostatically through a hydrogen bond network using net positive charges created upon oxidation of a heme iron (located near the hydrogen bond network) for O2 reduction. Pumping protons are transferred by mobile water molecules from the negative side of the mitochondrial inner membrane through a water channel into the hydrogen bond network. For blockage of spontaneous proton back-leak, the water channel is closed upon O2 binding to the second heme (heme a3) after complete collection of the pumping protons in the hydrogen bond network. For elucidation of the structural bases for the mechanism of the proton collection and timely closure of the water channel, conformational dynamics after photolysis of CO (an O2 analog)-bound CcO was examined using a newly developed time-resolved infrared system feasible for accurate detection of a single C=O stretch band of α-helices of CcO in H2O medium. The present results indicate that migration of CO from heme a3 to CuB in the O2 reduction site induces an intermediate state in which a bulge conformation at Ser-382 in a transmembrane helix is eliminated to open the water channel. The structural changes suggest that, using a conformational relay system, including CuB, O2, heme a3, and two helix turns extending to Ser-382, CuB induces the conformational changes of the water channel that stimulate the proton collection, and senses complete proton loading into the hydrogen bond network to trigger the timely channel closure by O2 transfer from CuB to heme a3.

Calcium ions promote superoxide dismutase 1 (SOD1) aggregation into non-fibrillar amyloid: a link to toxic effects of calcium overload in amyotrophic lateral sclerosis (ALS)?

Imbalance in metal ion homeostasis is a hallmark in neurodegenerative conditions involving protein deposition, and amyotrophic lateral sclerosis (ALS) is no exception. In particular, Ca(2+) dysregulation has been shown to correlate with superoxide dismutase-1 (SOD1) aggregation in a cellular model of ALS. Here we present evidence that SOD1 aggregation is enhanced and modulated by Ca(2+). We show that at physiological pH, Ca(2+) induces conformational changes that increase SOD1 β-sheet content, as probed by far UV CD and attenuated total reflectance-FTIR, and enhances SOD1 hydrophobicity, as probed by ANS fluorescence emission. Moreover, dynamic light scattering analysis showed that Ca(2+) boosts the onset of SOD1 aggregation. In agreement, Ca(2+) decreases SOD1 critical concentration and nucleation time during aggregation kinetics, as evidenced by thioflavin T fluorescence emission. Attenuated total reflectance FTIR analysis showed that Ca(2+) induced aggregates consisting preferentially of antiparallel β-sheets, thus suggesting a modulation effect on the aggregation pathway. Transmission electron microscopy and analysis with conformational anti-fibril and anti-oligomer antibodies showed that oligomers and amyloidogenic aggregates constitute the prevalent morphology of Ca(2+)-induced aggregates, thus indicating that Ca(2+) diverts SOD1 aggregation from fibrils toward amorphous aggregates. Interestingly, the same heterogeneity of conformations is found in ALS-derived protein inclusions. We thus hypothesize that transient variations and dysregulation of cellular Ca(2+) levels contribute to the formation of SOD1 aggregates in ALS patients. In this scenario, Ca(2+) may be considered as a pathogenic effector in the formation of ALS proteinaceous inclusions.

Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes

Phytochromes act as photoswitches between the red- and far-red absorbing parent states of phytochromes (Pr and Pfr). Plant phytochromes display an additional thermal conversion route from the physiologically active Pfr to Pr. The same reaction pattern is found in prototypical biliverdin-binding bacteriophytochromes in contrast to the reverse thermal transformation in bathy bacteriophytochromes. However, the molecular origin of the different thermal stabilities of the Pfr states in prototypical and bathy bacteriophytochromes is not known. We analyzed the structures of the chromophore binding pockets in the Pfr states of various bathy and prototypical biliverdin-binding phytochromes using a combined spectroscopic-theoretical approach. For the Pfr state of the bathy phytochrome from Pseudomonas aeruginosa, the very good agreement between calculated and experimental Raman spectra of the biliverdin cofactor is in line with important conclusions of previous crystallographic analyses, particularly the ZZEssa configuration of the chromophore and its mode of covalent attachment to the protein. The highly homogeneous chromophore conformation seems to be a unique property of the Pfr states of bathy phytochromes. This is in sharp contrast to the Pfr states of prototypical phytochromes that display conformational equilibria between two sub-states exhibiting small structural differences at the terminal methine bridges A-B and C-D. These differences may mainly root in the interactions of the cofactor with the highly conserved Asp-194 that occur via its carboxylate function in bathy phytochromes. The weaker interactions via the carbonyl function in prototypical phytochromes may lead to a higher structural flexibility of the chromophore pocket opening a reaction channel for the thermal (ZZE → ZZZ) Pfr to Pr back-conversion.