Water (H2O and D2O) molar absorptivity in the 1000-4000 cm-1 range and quantitative infrared spectroscopy of aqueous solutions

Optical photothermal infrared imaging using metabolic probes in biological systems

Infrared spectroscopy is a powerful tool for identifying biomolecules. In biological systems, infrared spectra provide information on structure, reaction mechanisms, and conformational change of biomolecules. However, the promise of applying infrared imaging to biological systems has been hampered by low spatial resolution and the overwhelming water background arising from the aqueous nature of in cell and in vivo work. Recently, optical photothermal infrared microscopy (OPTIR) has overcome these barriers and achieved both spatially and spectrally resolved images of live cells and organisms. Here, we determine the most effective modes of collection for work in biological samples. We examine three cell lines (Huh-7, differentiated 3T3-L1, and U2OS) and three organisms ( E. coli , tardigrades, and zebrafish). Our results suggest that the information provided by multifrequency imaging is comparable to hyperspectral imaging while reducing imaging times twenty-fold. We also explore the utility of IR active probes, including global and site-specific probes, for tracking metabolic pathways and protein localization, structure, and local environment. Our findings illustrate the versatility of OPTIR, and together, provide a direction for future dynamic imaging of living cells and organisms.

Nanometric determination of the thickness of aqueous samples for accurate molar absorption coefficients of water-soluble molecules in the mid-infrared region

Absorption spectra of aqueous samples measured by transmission need to be acquired using very thin cells (5-50 μm) when targeting the mid-infrared (mid-IR) region due to the strong background absorbance of liquid water. The thickness of the cell used controls the pathlength of the light through the sample, a value needed to transform absorption spectra into molar absorption coefficient spectra, or to determine solute concentrations from absorption spectra. The most accurate way to determine the thickness of an empty cell (i.e., filled with air) is from the period of an interference pattern, known as interference fringes, that arises when the cell is placed perpendicular to the path of light in the spectrometer. However, this same approach is not directly applicable to determine the thickness of a cell filled with an aqueous solution, due partially to the smaller amplitude of the interference fringes but fundamentally caused by its complex waveform, with a wavenumber-dependent oscillation period. Here, using Fresnel equations, we derived analytical expressions to model interference fringes in absorption spectra obtained by transmission, which are also valid for aqueous samples. We also present a novel Fourier-based analysis of the interference fringes that, in combination with the derived analytical expressions, allowed us to determine the pathlength of aqueous samples with an error below ∼ 50 nm. We implemented this novel approach to analyze interference fringes as a Live Script running in the software Matlab. As an application, we measured the absorption spectra of a 97 mM solution of MES buffer at pH 3.4 and pH 8.4 using cells of various nominal thicknesses (6, 25 and 50 μm), whose actual thicknesses were determined using the present approach. The derived molar absorption coefficient spectrum for both the acidic and basic forms of MES were virtually identical regardless of the cell, indicating that the determined thicknesses were likely very accurate. These results illustrate the utility of the present methodology in obtaining accurate molar absorption coefficient spectra of water-soluble molecules in the mid-IR region.

A rapid method to monitor structural perturbations of high-concentrated therapeutic antibody solutions using Intrinsic Tryptophan Fluorescence Emission spectroscopy

Drug product development of therapeutic antibody formulations is still dictated by the risk of protein particle formation during processing or storage, which can lead to loss of potency and potential immunogenic reactions. Since structural perturbations are the main driver for irreversible protein aggregation, the conformational integrity of antibodies should be closely monitored. The present study evaluated the applicability of a plate reader-based high throughput method for Intrinsic Tryptophan Fluorescence Emission (ITFE) spectroscopy to detect protein aggregation due to protein unfolding in high-concentrated therapeutic antibody samples. The impact of fluorophore concentration on the ITFE signal in microplate readers was investigated by analysis of dilution series of two therapeutic antibodies and pure tryptophan. At low antibody concentrations (< 5 mg/mL, equivalent to 0.8 mM tryptophan), the low inner filter effect suggests a quasi-linear relationship between antibody concentration and ITFE intensity. In contrast, the constant ITFE intensity at high protein concentrations (> 40 mg/mL, equivalent to 6.1 mM tryptophan) indicate that ITFE spectroscopy measurements of IgG1 antibodies are feasible in therapeutically relevant concentrations (up to 223 mg/mL). Furthermore, the capability of the method to detect low levels of unfolding (around 1 %) was confirmed by limit of detection (LOD) determination with temperature-stressed antibody samples as degradation standards. Change of fluorescence intensity at the maximum (ΔIaM) was identified as sensitive descriptor for protein degradation, providing the lowest LOD values. The results demonstrate that ITFE spectroscopy performed in a microplate reader is a valuable tool for high-throughput monitoring of protein degradation in therapeutic antibody formulations.

Orientational Behavior and Vibrational Response of Glycine at Aqueous Interfaces

Aqueous glycine plays many different roles in living systems, from being a building block for proteins to being a neurotransmitter. To better understand its fundamental behavior, we study glycine's orientational behavior near model aqueous interfaces, in the absence and presence of electric fields and biorelevant ions. To this purpose, we use a surface-specific technique called heterodyne-detected vibrational sum-frequency generation spectroscopy (HD-VSFG). Using HD-VSFG, we directly probe the symmetric and antisymmetric stretching vibrations of the carboxylate group of zwitterionic glycine. From their relative amplitudes, we infer the zwitterion's orientation near surfactant-covered interfaces and find that it is governed by both electrostatic and surfactant-specific interactions. By introducing additional ions, we observe that the net orientation is altered by the enhanced ionic strength, indicating a change in the balance of the electrostatic and surfactant-specific interactions.

Label-free mid-infrared photothermal live-cell imaging beyond video rate

Advancement in mid-infrared (MIR) technology has led to promising biomedical applications of MIR spectroscopy, such as liquid biopsy or breath diagnosis. On the contrary, MIR microscopy has been rarely used for live biological samples in an aqueous environment due to the lack of spatial resolution and the large water absorption background. Recently, mid-infrared photothermal (MIP) imaging has proven to be applicable to 2D and 3D single-cell imaging with high spatial resolution inherited from visible light. However, the maximum measurement rate has been limited to several frames s^-1, limiting its range of use. Here, we develop a significantly improved wide-field MIP quantitative phase microscope with two orders-of-magnitude higher signal-to-noise ratio than previous MIP imaging techniques and demonstrate live-cell imaging beyond video rate. We first derive optimal system design by numerically simulating thermal conduction following the photothermal effect. Then, we develop the designed system with a homemade nanosecond MIR optical parametric oscillator and a high full-well-capacity image sensor. Our high-speed and high-spatial-resolution MIR microscope has great potential to become a new tool for life science, in particular for live-cell analysis.

Combinational Vibration Modes in H2O/HDO/D2O Mixtures Detected Thanks to the Superior Sensitivity of Femtosecond Stimulated Raman Scattering

Overtones and combinational modes frequently play essential roles in ultrafast vibrational energy relaxation in liquid water. However, these modes are very weak and often overlap with fundamental modes, particularly in isotopologues mixtures. We measured VV and HV Raman spectra of H₂O and D₂O mixtures with femtosecond stimulated Raman scattering (FSRS) and compared the results with calculated spectra. Specifically, we observed the mode at around 1850 cm^-1 and assigned it to H-O-D bend + rocking libration. Second, we found that the H-O-D bend overtone band and the OD stretch + rocking libration combination band contribute to the band located between 2850 and 3050 cm^-1. Furthermore, we assigned the broad band located between 4000 and 4200 cm^-1 to be composed of combinational modes of high-frequency OH stretching modes with predominantly twisting and rocking librations. These results should help in a proper interpretation of Raman spectra of aqueous systems as well as in the identification of vibrational relaxation pathways in isotopically diluted water.

Imaging temperature and thickness of thin planar liquid water jets in vacuum

We present spatially resolved measurements of the temperature of a flat liquid water microjet for varying ambient pressures, from vacuum to 100% relative humidity. The entire jet surface is probed in a single shot by a high-resolution infrared camera. Obtained 2D images are substantially influenced by the temperature of the apparatus on the opposite side of the infrared camera; a protocol to correct for the thermal background radiation is presented. In vacuum, we observe cooling rates due to water evaporation on the order of 105 K/s. For our system, this corresponds to a temperature decrease in approximately 15 K between upstream and downstream positions of the flowing leaf. Making reasonable assumptions on the absorption of the thermal background radiation in the flatjet, we can extend our analysis to infer a thickness map. For a reference system, our value for the thickness is in good agreement with the one reported from white light interferometry.

Mid-IR dispersion spectroscopy - A new avenue for liquid phase analysis

Mid-IR dispersion spectroscopy is an attractive, novel approach to liquid phase analysis that extends the possibilities of traditional methods based on the detection of absorption via intensity attenuation. This technique detects inherent refractive index changes (phase shifts) induced by IR light interaction with absorbing matter. In contrast to classic absorption spectroscopy, it provides extended dynamic range, baseline-free detection, constant sensitivity, and inherent immunity to power fluctuation. In this paper, we provide a detailed experimental and theoretical characterization and verification of this method with special focus on broadband liquid sample analysis. For this purpose, we develop a compact benchtop dispersion spectroscopy setup based on an EC-QCL coupled to a Mach-Zehnder interferometer. Phase-locked interferometric detection enables to fully harness the advantages of the technique. By instrument operation in the quadrature point combined with balanced detection, the full immunity towards laser power fluctuations and the environmental noise can be achieved. On the example of ethanol (0.5-50% v/v) dissolved in water, it is experimentally demonstrated that changes of the refractive index function are linearly related to concentration also for strongly absorbing, highly concentrated samples beyond the validity of the Beer-Lambert law. Characterization of the sensitivity and noise behavior indicates that the optimum applicable pathlength for liquid analysis can be extended beyond the ones for absorption spectroscopy. Experimental demonstration of the advantages over classical absorption spectroscopy illuminates the potential of dispersion spectroscopy as upcoming robust and sensitive way of recording IR spectra of liquid samples.

Dentin primer based on a highly functionalized gelatin-methacryloyl hydrogel

Gelatin-methacryloyl hydrogels (GelMA) have demonstrated their utility as scaffolds in a variety of tissue engineering applications.

OBJECTIVES

In this study, a highly functionalized GelMA hydrogel was synthesized and assessed for degree of functionalization. As the proposed GelMA hydrogel was coupled to a visible-light photoinitiator, we hypothesized it might serve as base to formulate a model dentin primer for application in restorative dentistry.

METHODS

GelMA was mixed with photoinitiator lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP), photopolymerized for 0-40 s using a dental light-curing device and tested for extrudability, degree of photo-crosslinking (DPxlink), water sorption/solubility/swelling (WS/SL/SW) and apparent modulus of elasticity (AE). Model dentin primer was prepared by mixing GelMA+LAP with a primer of a commercial three-step etch-and-rinse adhesive. After application of GelMA-based primer to acid-etched dentin, samples were bonded with correspondent adhesive agent, photopolymerized and had their immediate bond strength compared to control samples primed and bonded with the same commercial material.

RESULTS

Extrudability of hydrogel was confirmed using a microsyringe to write the acronym "CDMI". DPxlink of GelMA+LAP changed significantly as a function of photopolymerization time (20 s < 30 s ≤ 40 s). WS, SL and SW were significantly reduced in hydrogels polymerized for 30 and 40 s. AE of hydrogels varied significantly as a function of photopolymerization time (20 s < 30 s ≤ 40 s; 20 s ‡ 40 s). Bond strength of dentin primed with GelMA-based primer was lower (∼29.3 MPa) but not significantly of that of control (∼34.6 MPa).

CONCLUSIONS

Optimization of a GelMA-based dentin primers can lead to the development of promising biomimetic adhesives for dentin rehabilitation.

Vibrational relaxation by methylated xanthines in solution: Insights from 2D IR spectroscopy and calculations

Two-dimensional infrared (2D IR) spectroscopy, infrared pump-infrared probe spectroscopy, and density functional theory calculations were used to study vibrational relaxation by ring and carbonyl stretching modes in a series of methylated xanthine derivatives in acetonitrile and deuterium oxide (heavy water). Isotropic signals from the excited symmetric and asymmetric carbonyl stretch modes decay biexponentially in both solvents. Coherent energy transfer between the symmetric and asymmetric carbonyl stretching modes gives rise to a quantum beat in the time-dependent anisotropy signals. The damping time of the coherent oscillation agrees with the fast decay component of the carbonyl bleach recovery signals, indicating that this time constant reflects intramolecular vibrational redistribution (IVR) to other solute modes. Despite their similar frequencies, the excited ring modes decay monoexponentially with a time constant that matches the slow decay component of the carbonyl modes. The slow decay times, which are faster in heavy water than in acetonitrile, approximately match the ones observed in previous UV pump-IR probe measurements on the same compounds. The slow component is assigned to intermolecular energy transfer to solvent bath modes from low-frequency solute modes, which are populated by IVR and are anharmonically coupled to the carbonyl and ring stretch modes. 2D IR measurements indicate that the carbonyl stretching modes are weakly coupled to the delocalized ring modes, resulting in slow exchange that cannot explain the common solvent-dependence. IVR is suggested to occur at different rates for the carbonyl vs ring modes due to differences in mode-specific couplings and not to differences in the density of accessible states.

2D-IR spectroscopy of proteins in H2O-A Perspective

The form of the amide I infrared absorption band provides a sensitive probe of the secondary structure and dynamics of proteins in the solution phase. However, the frequency coincidence of the amide I band with the bending vibrational mode of H₂O has necessitated the widespread use of deuterated solvents. Recently, it has been demonstrated that ultrafast 2D-IR spectroscopy allows the detection of the protein amide I band in H₂O-based fluids, meaning that IR methods can now be applied to study proteins in physiologically relevant solvents. In this perspective, we describe the basis of the 2D-IR method for observing the protein amide I band in H₂O and show how this development has the potential to impact areas ranging from our fundamental appreciation of protein structural dynamics to new applications for 2D-IR spectroscopy in the analytical and biomedical sciences. In addition, we discuss how the spectral response of water, rather than being a hindrance, now provides a basis for new approaches to data pre-processing, standardization of 2D-IR data collection, and signal quantification. Ultimately, we visualize a direction of travel toward the creation of 2D-IR spectral libraries that can be linked to advanced computational methods for use in high-throughput protein screening and disease diagnosis.

Layer-Stacking Sequence Governs Ion-Storage in Layered Double Hydroxides

In layered materials, the layer-stacking sequence allows the tuning of ion transport and storage properties by modulating the host-ion interactions. However, unlike in the case of cations, the relationship between the stacking sequence and anion transport and storage properties is less clearly understood. Herein, we demonstrate that the stacking sequence governs the nitrate-storage properties of layered double hydroxides (LDHs); the 2H₁ polytype enhances the nitrate-storage capacity to 400% of that of the 3R₁ polytype. A quartz crystal microbalance with dissipation monitoring combined with multimodal ex situ experiments indicated that the high ion-storage capacity of the 2H₁ polytype originates from the soft nature of LDHs lattices, which facilitates nitrate with minimal lattice changes. In contrast, the rigid lattice of the 3R₁ sequence requires a notably large lattice expansion, which is detrimental to ion storage. Our findings can aid the rational design of anion-host interaction-derived functionalities.

Nonspecific Amyloid Aggregation of Chicken Smooth-Muscle Titin: In Vitro Investigations

A giant multidomain protein of striated and smooth vertebrate muscles, titin, consists of tandems of immunoglobulin (Ig)- and fibronectin type III (FnIII)-like domains representing β-sandwiches, as well as of disordered segments. Chicken smooth muscles express several titin isoforms of ~500-1500 kDa. Using various structural-analysis methods, we investigated in vitro nonspecific amyloid aggregation of the high-molecular-weight isoform of chicken smooth-muscle titin (SMT_HMW, ~1500 kDa). As confirmed by X-ray diffraction analysis, under near-physiological conditions, the protein formed amorphous amyloid aggregates with a quaternary cross-β structure within a relatively short time (~60 min). As shown by circular dichroism and Fourier-transform infrared spectroscopy, the quaternary cross-β structure-unlike other amyloidogenic proteins-formed without changes in the SMT_HMW secondary structure. SMT_HMW aggregates partially disaggregated upon increasing the ionic strength above the physiological level. Based on the data obtained, it is not the complete protein but its particular domains/segments that are likely involved in the formation of intermolecular interactions during SMT_HMW amyloid aggregation. The discovered properties of titin position this protein as an object of interest for studying amyloid aggregation in vitro and expanding our views of the fundamentals of amyloidogenesis.

Liquid Heterostructures: Generation of Liquid-Liquid Interfaces in Free-Flowing Liquid Sheets

Chemical reactions and biological processes are frequently governed by the structure and dynamics of the interface between two liquid phases, but these interfaces are often difficult to study due to the relative abundance of the bulk liquids. Here, we demonstrate a method for generating multilayer thin film stacks of liquids, which we call liquid heterostructures. These free-flowing layered liquid sheets are produced with a microfluidic nozzle that impinges two converging jets of one liquid onto opposite sides of a third jet of another liquid. The resulting sheet consists of two layers of the first liquid enveloping an inner layer of the second liquid. Infrared microscopy, white light reflectivity, and imaging ellipsometry measurements demonstrate that the buried liquid layer has a tunable thickness and displays well-defined liquid-liquid interfaces and that this inner layer can be only tens of nanometers thick. The demonstrated multilayer liquid sheets minimize the amount of bulk liquid relative to their buried interfaces, which makes them ideal targets for spectroscopy and scattering experiments.

A mid-infrared lab-on-a-chip for dynamic reaction monitoring

Mid-infrared spectroscopy is a sensitive and selective technique for probing molecules in the gas or liquid phase. Investigating chemical reactions in bio-medical applications such as drug production is recently gaining particular interest. However, monitoring dynamic processes in liquids is commonly limited to bulky systems and thus requires time-consuming offline analytics. In this work, we show a next-generation, fully-integrated and robust chip-scale sensor for online measurements of molecule dynamics in a liquid solution. Our fingertip-sized device utilizes quantum cascade technology, combining the emitter, sensing section and detector on a single chip. This enables real-time measurements probing only microliter amounts of analyte in an in situ configuration. We demonstrate time-resolved device operation by analyzing temperature-induced conformational changes of the model protein bovine serum albumin in heavy water. Quantitative measurements reveal excellent performance characteristics in terms of sensor linearity, wide coverage of concentrations, extending from 0.075 mg ml^-1 to 92 mg ml^-1 and a 55-times higher absorbance than state-of-the-art bulky and offline reference systems.

Self-assembly pathways in a triphenylalanine peptide capped with aromatic groups

Peptide derivatives and, most specifically, their self-assembled supramolecular structures are being considered in the design of novel biofunctional materials. Although the self-assembly of triphenylalanine homopeptides has been found to be more versatile than that of homopeptides containing an even number of residues (i.e. diphenylalanine and tetraphenylalanine), only uncapped triphenylalanine (FFF) and a highly aromatic analog blocked at both the N- and C-termini with fluorenyl-containing groups (Fmoc-FFF-OFm), have been deeply studied before. In this work, we have examined the self-assembly of a triphenylalanine derivative bearing 9-fluorenylmethyloxycarbonyl and benzyl ester end-capping groups at the N- and C-termini, respectively (Fmoc-FFF-OBzl). The antiparallel arrangement clearly dominates in β-sheets formed by Fmoc-FFF-OBzl, whereas the parallel and antiparallel dispositions are almost isoenergetic in Fmoc-FFF-OFm β-sheets and the parallel one is slightly favored for FFF. The effects of both the peptide concentration and the medium on the self-assembly process have been examined considering Fmoc-FFF-OBzl solutions in a wide variety of solvent:co-solvent mixtures. In addition, Fmoc-FFF-OBzl supramolecular structures have been compared to those obtained for FFF and Fmoc-FFF-OFm under identical experimental conditions. The strength of π-π stacking interactions involving the end-capping groups plays a crucial role in the nucleation and growth of supramolecular structures, which determines the resulting morphology. Finally, the influence of a non-invasive external stimulus, ultrasounds, on the nucleation and growth of supramolecular structures has been examined. Overall, FFF-based peptides provide a wide range of supramolecular structures that can be of interest in the biotechnological field.

The effect of hydration and dehydration on the conformation, assembling behavior and photoluminescence of PBLG

Hydration and dehydration play crucial roles in hydrophobic effects (HEs) and are yet to be understood. Poly(γ-benzyl-L-glutamate) (PBLG) homopolymers in THF/water with various water contents were investigated. We discovered that PBLG was hydrated at low water contents and adopted a helical conformation. The chain became dehydrated with increasing water content, which converted the PBLG₁₀₀ helix to a PPII-helix. The variation in the conformation resulted in an alteration of the self-assembled morphologies from fibers to particles. For PBLG₁₂ with a shorter chain, the chain underwent an α-to-β transition in the conformation due to dehydration as the water content increased, and correspondingly the morphologies varied from tapes to helical ribbons, and eventually to toroids at a higher water content. We also observed that this α-to-β transition is accompanied by an increase in intensity of the fluorescence, which is attributed to the through-space-conjugation of tightly packed phenyl groups within the β-sheet. The discovered effect of hydration and dehydration on the PBLG chain conformation, self-assembling behavior and optical function is essential for the innovation of polypeptide materials and understanding of water-mediated biological systems.

Simultaneous Infrared Spectroscopy, Raman Spectroscopy, and Luminescence Sensing: A Multispectroscopic Analytical Platform

Scientific questions in fields such as catalysis, monitoring of biological processes, or environmental chemistry demand analytical technologies combining orthogonal spectroscopies. Combined spectroscopic concepts facilitate in situ online monitoring of dynamic processes providing a better understanding of the involved reaction pathways. In the present study, a low-liquid-volume multispectroscopic platform was developed based on infrared attenuated total reflection (IR-ATR) spectroscopy combined with Raman spectroscopy and luminescence sensing. To demonstrate the measurement capabilities, exemplary analyte systems including water/heavy water and aqueous solutions of ammonium sulfate were analyzed as proof-of-principle studies. It was successfully demonstrated that three optical techniques may be integrated into a single analytical platform without interference providing synchronized and complementary data sets by probing the same minute sample volume. In addition, the developed assembly provides a gastight lid sealing the headspace above the probed liquid for monitoring the concentration of molecular oxygen also in the gas phase via luminescence quenching. Hence, the entire assembly may be operated at inert conditions, as required, for example, during the analysis of photocatalytic processes.

Water does not dance as ions sing: A new approach in elucidation of ion-invariant water fluctuations

Aqueous solutions of salts composed from monovalent ions are explored using temperature-dependent FT-IR spectroscopy in transmission. Water combination band, being extremely sensitive to the network of hydrogen bonds due to the contribution of water librations (ρ_LH₂O), is analyzed in uni- and multivariate fashion. Univariate analysis of the combination band maximum (ν_max) reveals that perturbation of water hydrogen bond network by ions is primary driven by electrostatic interactions between water and ions. Using multivariate curve resolution with alternating least squares and evolving factor analysis this band is separated into two components that represent low- and high-density water. The observed asymmetry in their behavior is interpreted in terms of fluctuations of a hydrogen bond network of two water components. The significance of the found phenomenon is unambiguously confirmed by performing analogous analysis in the spectral range that contains partial signature of water linear bending (δHOH) and is free from ρ_LH₂O, in which the asymmetry is absent. Additionally, we show that this phenomenon, namely ion-invariant behavior of water fluctuations, persists even in the regime of high ionic strengths. Although ions indeed participate in shaping of water hydrogen bond network, this straightforward approach shows that its temperature-dependent fluctuations are ion-independent.

Infrared Spectroscopy in Aqueous Solutions: Capabilities and Challenges

Fourier-transform infrared (FTIR) spectroscopy provides rapid, reliable, quantitative, and qualitative analysis of samples in different aggregation states, i.e., gases, thin films, solids, liquids, etc. However, when analyzing aqueous solutions, particular issues associated with the rather pronounced IR absorption characteristics of water appear to interfere with the solute determination. In this review, Fourier-transform infrared spectroscopic techniques and their analytical capabilities for analyzing aqueous solutions are reviewed, and highlight examples are discussed.

Direct observation of protein structural transitions through entire amyloid aggregation processes in water using 2D-IR spectroscopy

Amyloid proteins that undergo self-assembly to form insoluble fibrillar aggregates have attracted much attention due to their role in biological and pathological significance in amyloidosis. This study aims to understand the amyloid aggregation dynamics of insulin (INS) in H₂O using two-dimensional infrared (2D-IR) spectroscopy. Conventional IR studies have been performed in D₂O to avoid spectral congestion despite distinct H–D isotope effects. We observed a slowdown of the INS fibrillation process in D₂O compared to that in H₂O. The 2D-IR results reveal that different quaternary structures of INS at the onset of the nucleation phase caused the distinct fibrillation pathways of INS in H₂O and D₂O. A few different biophysical analysis, including solution-phase small-angle X-ray scattering combined with molecular dynamics simulations and other spectroscopic techniques, support our 2D-IR investigation results, providing insight into mechanistic details of distinct structural transition dynamics of INS in water. We found the delayed structural transition in D₂O is due to the kinetic isotope effect at an early stage of fibrillation of INS in D₂O, i.e., enhanced dimer formation of INS in D₂O. Our 2D-IR and biophysical analysis provide insight into mechanistic details of structural transition dynamics of INS in water. This study demonstrates an innovative 2D-IR approach for studying protein dynamics in H₂O, which will open the way for observing protein dynamics under biological conditions without IR spectroscopic interference by water vibrations.

This study aims to understand the structural transition dynamics of INS during amyloid aggregation in H₂O using 2D-IR spectroscopy. The results show that distinct fibrillations in D₂O and H₂O originated from different quaternary structures of INS.

Characterization of the Conformational Properties of Soluble and Insoluble Proteins by Fourier Transform Infrared Spectroscopy

The FTIR (micro-)spectroscopy method applied to the study of the structural properties of different soluble and insoluble proteins will be illustrated. In particular, we will discuss the procedure to analyze proteins in form of hydrated films and in solution by means of attenuated total reflection (ATR) measurements. Moreover, we will describe the procedure to characterize bacterial inclusion bodies (IBs) and amyloid deposits within human tissues by means of FTIR microspectroscopy.

Thermophysical properties of water using reactive force fields

The widescale importance and rich phenomenology of water continue to motivate the development of computational models. ReaxFF force fields incorporate many characteristics desirable for modeling aqueous systems: molecular flexibility, polarization, and chemical reactivity (bond formation and breaking). However, their ability to model the general properties of water has not been evaluated in detail. We present comprehensive benchmarks of the thermophysical properties of water for two ReaxFF models, the water-2017 and CHON-2017_weak force fields. These include structural, electrostatic, vibrational, thermodynamic, coexistence, and transport properties at ambient conditions (300 K and 0.997 g cm^-3) and along the standard pressure (1 bar) isobar. Overall, CHON-2017_weak predicts more accurate thermophysical properties than the water-2017 force field. Based on our results, we recommend potential avenues for improvement: the dipole moment to quadrupole moment ratio, the self-diffusion coefficient, especially for water-2017, and the gas phase vibrational frequencies with the aim to improve the vibrational properties of liquid water.

Removal of Oily Contaminants from Water by Using the Hydrophobic Ag Nanoparticles Incorporated Dopamine Modified Cellulose Foam

The presence of oil-related contaminants in water has emerged as a severe threat to the environment. The separation of these contaminants from water has become a great challenge, and extensive efforts are being made to develop suitable, environmentally friendly materials. Highly hydrophobic materials are effective in the selective separation of oil from water. In this work, silver (Ag)-incorporated, highly hydrophobic dopamine-modified cellulose sponge was prepared by functionalizing with the range of alkyl silanes. The Ag nanoparticle-incorporated dopamine provided the appropriate roughness, whereas the alkyl component provided the low surface energy that made it selective towards oil. It was found that the alkyl groups with a longer chain length were more effective in enhancing the hydrophobicity of the Ag nanoparticle-incorporated, dopamine-modified cellulose. The developed materials were characterized by Fourier transform infrared spectroscopy (FTIR), field emission-scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (EDX), elemental mapping, and contact angle goniometry. The maximum water contact angle on the functionalized surfaces was observed at 148.4°. The surface of the C18s-Ag-DA-Cell-F showed excellent selectivity towards the oily component that rapidly permeated, and water was rejected wholly. The developed material showed a separation efficiency of 96.2% for the oil/water mixture. The C18s-Ag-DA-Cell-F material showed excellent reusability. Due to their environmentally friendly nature, excellent selectivity, and good separation efficiency, the functionalized cellulose materials can be used to separate oil and water effectively.

The effect of applied electric field on the micromorphology of Pt nanoparticles synthesized by laser ablation

In the present study, laser ablation technique (Nd:YAG) has been applied to synthesize platinum nanoparticles (NPs). Also, the effect of applied electric field on the physical, structural, and morphological properties of Pt NPs has been investigated during the nanosecond pulsed laser ablation of platinum. Based on the results extracted from TEM and scanning electron microscopy images, the formation of high percentage of NPs with spherical shape is demonstrated in all samples. The increase of applied electric field creates few rectangular, hexagonal, and rhombic NPs with the average size decreased from 20 to 9 nm. The significant influence of increasing electric field is also observed in UV-vis spectra by appearing the blue shift of the localized surface plasmon resonance peak. The UV-vis spectra also confirm the metallic nature of Pt NPs and the existence of inhomogeneous-sized particles and the coagulation of particle because of the long tail in higher wavelengths. In addition, atomic force microscopy images have been analyzed through MountainsMap Premium program and fractal dimension. As can be seen, increasing the applied electric field make the surface more irregular and the maximum value of D_f reveals the most irregular topography for sample with 50 V/cm electric field. Finally, the bending and stretching frequencies of the functional bending groups connected to the NPs surface have been characterized by Fourier transform infrared spectroscopy. Electrical field-assisted laser ablation in liquids method allows a better control of the size, morphology, structure, and chemical composition of nanoparticles.

Adsorption of Horseradish Peroxidase on Metallic Nanoparticles: Effects on Reactive Oxygen Species Detection Using 2',7'-Dichlorofluorescin Diacetate

The fluorescent probe 2',7'-dichlorofluorescein diacetate (DCFH-DA) together with the enzyme horseradish peroxidase (HRP) is widely used in nanotoxicology to study acellular reactive oxygen species (ROS) production from nanoparticles (NPs). This study examined whether HRP adsorbs onto NPs of Mn, Ni, and Cu and if this surface process influences the extent of metal release and hence the ROS production measurements using the DCFH assay in phosphate buffered saline (PBS), saline, or Dulbecco's modified Eagle's medium (DMEM). Adsorption of HRP was evident onto all NPs and conditions, except for Mn NPs in PBS. The presence of HRP resulted in an increased release of copper from the Cu NPs in PBS and reduced levels of nickel from the Ni NPs in saline. Both metal ions in solution and the adsorption of HRP onto the NPs can change the activity of HRP and thus influence the ROS results. The effect of HRP on the NP reactivity was shown to be solution chemistry dependent. Most notable was the evident affinity/adsorption of phosphate toward the metal NPs, followed by a reduced adsorption of HRP, the concomitant reduction in released manganese from the Mn NPs, and increased levels of released metals from the Cu NPs in PBS. Minor effects were observed for the Ni NPs. The solution pH should be monitored since the release of metals can change the solution pH and the activity of HRP is known to be pH-dependent. It is furthermore essential that solution pH adjustments are made following the addition of NaOH during diacetyl removal of DCFH-DA. Even though not observed for the given exposure conditions of this study, released metal ions could possibly induce agglomeration or partial denaturation of HRP, which in turn could result in steric hindrance for H2O2 to reach the active site of HRP. This study further emphasizes the influence of HRP on the background kinetics, its solution dependence, and effects on measured ROS signals. Different ways of correcting for the background are highlighted, as this can result in different interpretations of generated results. The results show that adsorption of HRP onto the metal NPs influenced the extent of metal release and may, depending on the investigated system, result in either under- or overestimated ROS signals if used together with the DCFH assay. HRP should hence be used with caution when measuring ROS in the presence of reactive metallic NPs.

Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectroscopy for the Quantitative Analysis of Deuterium in Plasma: Application to Total Body Water Determination in Humans and Other Animals

Conventional methods for measuring the concentration of deuterium in body fluids are by either isotope ratio mass spectrometry or Fourier transform infrared transmission (FT-IR) spectroscopy. The latter method is often preferred as it is less expensive and time consuming; however, having a lower sensitivity means a larger sample volume is required. This study investigated an alternative FT-IR spectroscopic method, attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR), which has the potential to provide shorter analysis times while requiring smaller sample volumes. Deuterium was assayed using ATR FT-IR in plasma in the concentration range 0.5 to 2.5 mg mL^-1, typical of those observed in tracer dilution measurements of total body water. Minimal sample preparation was required and analysis time was substantially decreased compared to transmission FT-IR. Samples were analyzed with high precision (coefficient of variation (CV) < 0.5%). Precision of assay was maintained when assaying plasma volumes of only 10 µL. The application of the method to the determination of total body water in humans and animals (horses) was demonstrated. A rapid and simple method for the measurement of deuterium in plasma is described that only requires very small sample volumes, rendering the method suitable for use in pediatrics where blood sampling is required to be kept to a minimum.

Deuteration Aiming for Neutron Scattering

The distinguished feature of neutron as a scattering probe is an isotope effect, especially the large difference in neutron scattering length between hydrogen and deuterium. The difference renders the different visibility between hydrogenated and deuterated proteins. Therefore, the combination of deuterated protein and neutron scattering enables the selective visualization of a target domain in the complex or a target protein in the multi-component system. Despite of this fascinating character, there exist several problems for the general use of this method: difficulty and high cost for protein deuteration, and control and determination of deuteration ratio of the sample. To resolve them, the protocol of protein deuteration techniques is presented in this report. It is strongly expected that this protocol will offer more opportunity for conducting the neutron scattering studies with deuterated proteins.

Binding of tyrosine kinase inhibitor to epidermal growth factor receptor: surface-enhanced infrared absorption microscopy reveals subtle protein secondary structure variations

Surface-Enhanced Infrared Absorption (SEIRA) has been proposed as a valuable tool for protein binding studies, but its performances have been often proven on model proteins undergoing severe secondary structure rearrangements, while ligand binding only marginally involves the protein backbone in the vast majority of the biologically relevant cases. In this study we demonstrate the potential of SEIRA microscopy for highlighting the very subtle secondary structure modifications associated with the binding of Lapatinib, a tyrosine kinase inhibitor (TKI), to epidermal growth factor receptor (EGFR), a well-known driver of tumorigenesis in pathological settings such as lung, breast and brain cancers. By boosting the performances of Mid-IR plasmonic devices based on nanoantennas cross-geometry, accustoming the protein purification protocols, carefully tuning the protein anchoring methodology and optimizing the data analysis, we were able to detect EGFR secondary structure modification associated with few amino acids. A nano-patterned platform with this kind of sensitivity bridges biophysical and structural characterization methods, thus opening new possibilities in studying of proteins of biomedical interest, particularly for drug-screening purposes.

Analysis of Fixed and Live Single Cells Using Optical Photothermal Infrared with Concomitant Raman Spectroscopy

This paper reports the first use of a novel completely optically based photothermal method (O-PTIR) for obtaining infrared spectra of both fixed and living cells using a quantum cascade laser (QCL) and optical parametric oscillator (OPO) laser as excitation sources, thus enabling all biologically relevant vibrations to be analyzed at submicron spatial resolution. In addition, infrared data acquisition is combined with concomitant Raman spectra from exactly the same excitation location, meaning the full vibrational profile of the cell can be obtained. The pancreatic cancer cell line MIA PaCa-2 and the breast cancer cell line MDA-MB-231 are used as model cells to demonstrate the capabilities of the new instrumentation. These combined modalities can be used to analyze subcellular structures in both fixed and, more importantly, live cells under aqueous conditions. We show that the protein secondary structure and lipid-rich bodies can be identified on the submicron scale.

FTIR Imaging of Protein Microarrays for High Throughput Secondary Structure Determination

The paper introduces a new method designed for high-throughput protein structure determination. It is based on spotting proteins as microarrays at a density of ca. 2000-4000 samples per cm² and recording Fourier transform infrared (FTIR) spectra by FTIR imaging. It also introduces a new protein library, called cSP92, which contains 92 well-characterized proteins. It has been designed to cover as well as possible the structural space, both in terms of secondary structures and higher level structures. Ascending stepwise linear regression (ASLR), partial least square (PLS) regression, and support vector machine (SVM) have been used to correlate spectral characteristics to secondary structure features. ASLR generally provides better results than PLS and SVM. The observation that secondary structure prediction is as good for protein microarray spectra as for the reference attenuated total reflection spectra recorded on the same samples validates the high throughput microarray approach. Repeated double cross-validation shows that the approach is suitable for the high accuracy determination of the protein secondary structure with root mean square standard error in the cross-validation of 4.9 ± 1.1% for α-helix, 4.6 ± 0.8% for β-sheet, and 6.3 ± 2.2% for the "other" structures when using ASLR.

In Situ Electrochemical Transformation Reaction of Ammonium-Anchored Heptavanadate Cathode for Long-Life Aqueous Zinc-Ion Batteries

Rechargeable aqueous zinc-ion batteries (ZIBs) are promising portable and large-scale grid energy storage devices, as they are safe and economical. However, developing suitable ZIB cathode materials with excellent cycling performance characteristics remains a challenging task. Here, ammonium heptavanadate (NH₄)₂V₇O₁₆·3.2H₂O (NHVO) nanosquares with mixed-valence V⁵⁺/V⁴⁺ as a cathode are developed for high-performance ZIBs. The layered NHVO shows a capacity of 362 mA h g^-1 at 0.05 A g^-1, with a high energy density of 263.5 W h kg^-1. It exhibits an initial specific capacity of 250.7 mA h g^-1 at a current density of 4 A g^-1 and retains 255 mA h g^-1 capacity after 1000 charge/discharge cycles. The V₇O₁₆-based cathode was demonstrated with a phase transition to the V₂O₅-based cathode upon initial cycling. Moreover, the in situ generated V₂O₅-based cathodes show excellent electrochemical properties, which provide a different perspective on the electrochemical reaction of cathode materials for aqueous ZIBs.

Elucidation of the mechanism of subunit exchange in αB crystallin oligomers

AlphaB crystallin (αB-crystallin) is a key protein for maintaining the long-term transparency of the eye lens. In the eye lens, αB-crystallin is a "dynamical" oligomer regulated by subunit exchange between the oligomers. To elucidate the unsettled mechanism of subunit exchange in αB-crystallin oligomers, the study was carried out at two different protein concentrations, 28.5 mg/mL (dense sample) and 0.45 mg/mL (dilute sample), through inverse contrast matching small-angle neutron scattering. Interestingly, the exchange rate of the dense sample was the same as that of the dilute sample. From analytical ultracentrifuge measurements, the coexistence of small molecular weight components and oligomers was detected, regardless of the protein concentration. The model proposed that subunit exchange could proceed through the assistance of monomers and other small oligomers; the key mechanism is attaching/detaching monomers and other small oligomers to/from oligomers. Moreover, this model successfully reproduced the experimental results for both dense and dilute solutions. It is concluded that the monomer and other small oligomers attaching/detaching mainly regulates the subunit exchange in αB-crystallin oligomer.

Developability Assessment of an Isolated CH2 Immunoglobulin Domain

The IgG C_H2 domain continues to hold promise for the development of new therapeutic entities because of its bifunctional role as a biomarker and effector protein. The need for further understanding of molecular stability and aggregation in therapeutic proteins has led to the development of a breakthrough quantum cascade laser microscope to allow for real-time comparability assessment of an array of related proteins in solution upon thermal perturbation. Our objective was to perform a comprehensive developability assessment of three similar monoclonal antibody (mAb) fragments: C_H2, C_H2s, and m01s. The C_H2 construct consists of residues Pro238 to Lys340 of the IgG1 heavy chain sequence. C_H2s has a 7-residue deletion at the N-terminus and a 16-residue C-terminal extension containing a histidine tag. The m01s construct is identical to C_H2s, except for two cysteines introduced at positions 242 and 334. A series of hyperspectral images was acquired during thermal perturbation from 28 to 60 °C for all three proteins in an array. Co-distribution and two-dimensional infrared correlation spectroscopies yielded the mechanism of aggregation and stability for these three proteins. The level of detail is unprecedented, identifying the regions within C_H2 and C_H2s that are prone to self-association and establishing the differences in stability. Furthermore, C_H2 helical segments, β-sheets, β-turns, and random coil regions were less stable than in C_H2s and m01s because of the presence of the N-terminal 3₁₀-helix and β-turn type III. The engineered disulfide bridge in m01s eliminated the self-association process and rendered this mAb fragment the most stable.

Transformation of aqueous protein attenuated total reflectance infra-red absorbance spectroscopy to transmission

Infrared (IR) spectroscopy is increasingly being used to probe the secondary structure of proteins, especially for high-concentration samples and biopharmaceuticals in complex formulation vehicles. However, the small path lengths required for aqueous protein transmission experiments, due to high water absorbance in the amide I region of the spectrum, means that the path length is not accurately known, so only the shape of the band is ever considered. This throws away a dimension of information. Attenuated total reflectance (ATR) IR spectroscopy is much easier to implement than transmission IR spectroscopy and, for a given instrument and sample, gives reproducible spectra. However, the ATR-absorbance spectrum varies with sample concentration and instrument configuration, and its wavenumber dependence differs significantly from that observed in transmission spectroscopy. In this paper, we determine, for the first time, how to transform water and aqueous protein ATR spectra into the corresponding transmission spectra with appropriate spectral shapes and intensities. The approach is illustrated by application to water, concanavalin A, haemoglobin and lysozyme. The transformation is only as good as the available water refractive index data. A hybrid of literature data provides the best results. The transformation also allows the angle of incidence of an ATR crystal to be determined. This opens the way to using both spectral shape and spectra intensity for protein structure fitting.

Quick Method to Quantify the Potassium and Sodium Content Variation in Leaves of Banana Varieties

The current study describes novel and quick methods for the quantification of K⁺ and Na⁺ in banana leaves using Horiba Laqua twin ion meters. Foliar K⁺ and Na⁺ content measured by ion meter significantly correlated with standard test values by coefficients of 0.83 and 0.46, respectively. About 48 absorbance values associated with potassium concentrations at wave numbers (1581 to 1583 and 3194 to 3410 cm^-1) and 15 sodium associated wave numbers (3773 to 3996 cm^-1) predicted potassium and sodium content with regression coefficients of 0.999 and 0.588, respectively. K⁺ and Na⁺ cations of fresh leaves in seven banana varieties were quantified using ion meters and new information of differences in the foliar potassium and sodium contents was found between banana varieties within the AAB group. The Rasbali (Silk subgroup) variety possessed greater potassium (5413 mg/L) and sodium (188 mg/L) ions than Amti (Mysore subgroup).

Concentration- and Temperature-Responsive Reversible Transition in Amide-Functionalized Surface-Active Ionic Liquids: Micelles to Vesicles to Organogel

A ubiquitous example of DNA and proteins inspires the scientific community to design synthetic systems that can construct various self-assembled complex nano-objects for high-end physiological functions. To gain insight into judiciously designed artificial amphiphilic structures that through self-assembling form various morphological architectures within a single system, herein, we have studied self-aggregation of amide-functionalized surface-active ionic liquids (AFSAILs) with different head groups in the DMSO/water mixed system. The AFSAIL forms stimuli-responsive reversible micelle and vesicle configurations that coexist with three-dimensional (3D) network structures, the organogel in the DMSO/water mixed system. The self-assembly driving forces, self-organization patterns, network morphologies, and mechanical properties of these network structures have been investigated. With the proven biodegradability and biocompatibility, one can envisage these AFSAILs as the molecules with a new dimension of versatility.

Resolution Enhancement in Wide-Field IR Imaging and Time-Domain Spectroscopy Using Dielectric Microspheres

Wide-field imaging through dielectric microspheres has emerged in recent years as a simple and effective approach for generating super-resolution images at visible wavelengths. We present, to our knowledge, the first demonstration that dielectric microspheres can be used in a wide-field infrared (IR) microscope to enhance the far field resolution. We have observed a substantial improvement in resolution and magnification when images are collected through polystyrene microspheres. In addition, we demonstrate that spectroscopic imaging with a pulse-shaper based femtosecond mid-IR laser system is possible through the dielectric microspheres, which is a promising first step toward applying this technique to ultrafast IR imaging methods such as pump-probe and 2DIR microscopy.

Biomolecular and bioanalytical applications of infrared spectroscopy - A review

Infrared (IR; or mid-infrared, MIR; 4000-400 cm^-1; 2500-25,000 nm) spectroscopy has become one of the most powerful and versatile tools at the disposal of modern bioscience. Because of its high molecular specificity, applicability to wide variety of samples, rapid measurement and non-invasivity, IR spectroscopy forms a potent approach to elucidate qualitative and quantitative information from various kinds of biological material. For these reasons, it became an established bioanalytical technique with diverse applications. This work aims to be a comprehensive and critical review of the recent accomplishments in the field of biomolecular and bioanalytical IR spectroscopy. That progress is presented on a wider background, with fundamental characteristics, the basic principles of the technique outlined, and its scientific capability directly compared with other methods being used in similar fields (e.g. near-infrared, Raman, fluorescence). The article aims to present a complete examination of the topic, as it touches the background phenomena, instrumentation, spectra processing and data analytical methods, spectra interpretation and related information. To suit this goal, the article includes a tutorial information essential to obtain a thorough perspective of bio-related applications of the reviewed methodologies. The importance of the fundamental factors to the final performance and applicability of IR spectroscopy in various areas of bioscience is explained. This information is interpreted in critical way, with aim to gain deep understanding why IR spectroscopy finds extraordinarily intensive use in this remarkably diverse and dynamic field of research and utility. The major focus is placed on the diversity of the applications in which IR biospectroscopy has been established so far and those onto which it is expanding nowadays. This includes qualitative and quantitative analytical spectroscopy, spectral imaging, medical diagnosis, monitoring of biophysical processes, and studies of physicochemical properties and dynamics of biomolecules. The application potential of IR spectroscopy in light of the current accomplishments and the future prospects is critically evaluated and its significance in the progress of bioscience is comprehensively presented.

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds

Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.

Vibrational mode frequency correction of liquid water in density functional theory molecular dynamics simulations with van der Waals correction

We develop a frequency correction scheme for the stretch and bending modes of liquid water, which substantially improves the prediction of the vibrational spectra.