Thinner, Smaller, Faster: IR Techniques To Probe the Functionality of Biological and Biomimetic Systems

Nanosecond Transient IR Spectroscopy of Halorhodopsin in Living Cells

The ability to track minute changes of a single amino acid residue in a cellular environment is causing a paradigm shift in the attempt to fully understand the responses of biomolecules that are highly sensitive to their environment. Detecting early protein dynamics in living cells is crucial to understanding their mechanisms, such as those of photosynthetic proteins. Here, we elucidate the light response of the microbial chloride pump NmHR from the marine bacterium Nonlabens marinus, located in the membrane of living Escherichia coli cells, using nanosecond time-resolved UV/vis and IR absorption spectroscopy over the time range from nanoseconds to seconds. Transient structural changes of the retinal cofactor and the surrounding apoprotein are recorded using light-induced time-resolved UV/vis and IR difference spectroscopy. Of particular note, we have resolved the kinetics of the transient deprotonation of a single cysteine residue during the photocycle of NmHR out of the manifold of molecular vibrations of the cells. These findings are of high general relevance, given the successful development of optogenetic tools from photoreceptors to interfere with enzymatic and neuronal pathways in living organisms using light pulses as a noninvasive trigger.

Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity

Cell membranes are incredibly complex environments containing hundreds of components. Despite substantial advances in the past decade, fundamental questions related to lipid-lipid interactions and heterogeneity persist. This review explores the complexity of lipid membranes, showcasing recent advances in vibrational spectroscopy to characterize the structure, dynamics, and interactions at the membrane interface. We include an overview of modern techniques such as surface-enhanced infrared spectroscopy as a steady-state technique with single-bilayer sensitivity, two-dimensional sum-frequency generation spectroscopy, and two-dimensional infrared spectroscopy to measure time-evolving structures and dynamics with femtosecond time resolution. Furthermore, we discuss the potential of multiscale molecular dynamics (MD) simulations, focusing on recently developed simulation algorithms, which have emerged as a powerful approach to interpret complex spectra. We highlight the ongoing challenges in studying heterogeneous environments in multicomponent membranes via current vibrational spectroscopic techniques and MD simulations. Overall, this review provides an up-to-date comprehensive overview of the powerful combination of vibrational spectroscopy and simulations, which has great potential to illuminate lipid-lipid, lipid-protein, and lipid-water interactions in the intricate conformational landscape of cell membranes.

Controlling Interfacial Hydrogen Bonding at a Gold Surface: The Effect of Organic Cosolvents

Water often serves as both a reactant and solvent in electrocatalytic reactions. Interfacial water networks can affect the transport and kinetics of these reactions, e.g., hydrogen evolution reaction and CO2 reduction reaction. Adding cosolvents that influence the hydrogen-bonding (H-bonding) environment, such as dimethyl sulfoxide (DMSO), has the potential to tune the reactivity of these important electrocatalytic reactions by regulating the interfacial local environment and water network. We investigate interfacial H-bonding networks in water-DMSO cosolvent mixtures on gold surfaces by using surface-enhanced infrared absorption spectroscopy and molecular dynamics simulations. Experiments and simulations show that the gold surface is enriched with dehydrated DMSO molecules and the mixture phase-separates to form water clusters. Simulations show a "buckled" water conformation at the surface, further constraining interfacial H-bonding. The small size of these water clusters and the energetically unfavorable H-bond conformations might inhibit H-bonding with bulk water, suppressing the proton diffusion required for efficient hydrogen evolution reaction processes.

Extracting accurate infrared lineshapes from weak vibrational probes at low concentrations

Fourier-transform infrared (FTIR) spectroscopy using vibrational probes is an ideal tool to detect changes in structure and local environments within biological molecules. However, challenges arise when dealing with weak infrared probes, such as thiocyanates, due to their inherent low signal strengths and overlap with solvent bands. In this protocol we demonstrate:•A streamlined approach for the precise extraction of weak infrared absorption lineshapes from a strong solvent background.•A protocol combining a spectral filter, background modeling, and subtraction.•Our methodology successfully extracts the CN stretching mode peak from methyl thiocyanate at remarkably low concentrations (0.25 mM) in water, previously a challenge for FTIR spectroscopy.This approach offers valuable insights and tools for more accurate FTIR measurements using weak vibrational probes. This enhanced precision can potentially enable new approaches to enhance our understanding of protein structure and dynamics in solution.

Sponge-phase Lipid Droplets as Synthetic Organelles: An Ultrafast Study of Hydrogen Bonding and Interfacial Environments

Bottom-up design of biomimetic organelles has gained recent attention as a route towards understanding the transition between non-living matter and life. Despite various artificial lipid membranes being developed, the specific relations between lipid structure, composition, interfacial properties, and morphology are not currently understood. Sponge-phase droplets contain dense, nonlamellar lipid bilayer networks that capture the complexities of the endoplasmic reticulum (ER), making them ideal artificial models of such organelles. Here, we combine ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics simulations to investigate the interfacial H-bond networks in sponge-phase droplets composed of glycolipid and nonionic detergents. In the sponge phase, the interfacial environments are more hydrated and water molecules confined to the nanometer-scale aqueous channels in the sponge phase exhibit dynamics that are significantly slower compared to bulk water. Surfactant configurations and microscopic phase separation play a dominant role in determining membrane curvature and slow dynamics observed in the sponge phase. The studies suggest that H-bond networks within the nanometer-scale channels are disrupted not only by confinement but also by the interactions of surfactants, which extend 1-2 nm from the bilayer surface. The results provide a molecular-level description for controlling phase and morphology in the design of synthetic lipid organelles.

Elucidating the Self-cleavage Dynamics of Hairpin Ribozyme by Mode-decomposed Infrared Spectroscopy

While catalytic reactions of biomolecular processes play an indispensable role in life, extracting the underlying molecular picture often remains challenging. Based on ab initio simulations of the self-cleavage reaction of hairpin ribozyme, mode-decomposed infrared spectra, and cosine similarity analysis to correlate the product with reactant IR spectra, we demonstrate a strategy to extract molecular details from characteristic spectral changes. Our results are in almost quantitative agreement with the experimental IR band library of nucleic acids and suggest that the spectral range of 800-1200 cm-1 is particularly valuable to monitor self-cleavage. Importantly, the cosine similarities also disclose that IR peaks subject to slight shifts due to self-cleavage might be unrelated, while strongly shifting resonances can correspond to the same structural dynamics. This framework of correlating complex IR spectra at the molecular level along biocatalytic reaction pathways is broadly applicable.

A hybrid graphene metamaterial absorber for enhanced modulation and molecular fingerprint retrieval

Surface-enhanced infrared absorption (SEIRA) has proven its ability to improve the detection performance of traditional infrared spectroscopy at unprecedented levels. However, the resonant frequency of the metamaterial absorber (MA) lacks tunability once the structure is fabricated, which poses a challenge for broadband fingerprint retrieval of molecules. Here, we propose a pixelated and electric tunable hybrid graphene MA with a broadband response for molecular fingerprint retrieval. Loss engineering is employed to optimize the sensing sensitivity of MA. The resonant frequency of MA is approximately linearly modulated with a change in the graphene Fermi level. This design allows a meta-pixel to match multiple characteristic absorption spectra, thereby establishing a one-to-many mapping relationship between spatial and spectral information. The one-to-many mapping relationship greatly reduces the number of meta-pixels. As a concept demonstration, we integrate 9 meta-pixels to achieve full spectral coverage from 1000 cm-1 to 2000 cm-1. Based on the broadband spectral properties of the sensor, we demonstrate its potential for multi-fingerprint detection, quantitative detection, chemical identification, and compositional analysis. Our proposed hybrid graphene MA can be easily integrated with other on-chip devices, providing a potential platform for optical sensing, infrared spectroscopy, and photodetection.

Introducing Aliphatic Fluoropeptides: Perspectives on Folding Properties, Membrane Partition and Proteolytic Stability

A de novo designed class of peptide-based fluoropolymers composed of fluorinated aliphatic amino acids as main components is reported. Structural characterization provided insights into fluorine-induced alterations on β-strand to α-helix transition upon an increase in SDS content and revealed the unique formation of PPII structures for trifluorinated fluoropeptides. A combination of circular dichroism, fluorescence-based leaking assays and surface enhanced infrared absorption spectroscopy served to examine the insertion and folding processes into unilamellar vesicles. While partitioning into lipid bilayers, the degree of fluorination conducts a decrease in α-helical content. Furthermore, this study comprises a report on the proteolytic stability of peptides exclusively built up by fluorinated amino acids and proved all sequences to be enzymatically degradable despite the degree of fluorination. Herein presented fluoropeptides as well as the distinctive properties of these artificial and polyfluorinated foldamers with enzyme-degradable features will play a crucial role in the future development of fluorinated peptide-based biomaterials.

Membrane Protein Activity Induces Specific Molecular Changes in Nanodiscs Monitored by FTIR Difference Spectroscopy

It is well known that lipids neighboring integral membrane proteins directly influence their function. The opposite effect is true as well, as membrane proteins undergo structural changes after activation and thus perturb the lipidic environment. Here, we studied the interaction between these molecular machines and the lipid bilayer by observing changes in the lipid vibrational bands via FTIR spectroscopy. Membrane proteins with different functionalities have been reconstituted into lipid nanodiscs: Microbial rhodopsins that act as light-activated ion pumps (the proton pumps NsXeR and UmRh1, and the chloride pump NmHR) or as sensors (NpSRII), as well as the electron-driven cytochrome c oxidase RsCcO. The effects of the structural changes on the surrounding lipid phase are compared to mechanically induced lateral tension exerted by the light-activatable lipid analogue AzoPC. With the help of isotopologues, we show that the ν(C = O) ester band of the glycerol backbone reports on changes in the lipids’ collective state induced by mechanical changes in the transmembrane proteins. The perturbation of the nanodisc lipids seems to involve their phase and/or packing state. ¹³C-labeling of the scaffold protein shows that its structure also responds to the mechanical expansion of the lipid bilayer.

Adsorption/Desorption Behaviors and SERS Chemical Enhancement of 6-Mercaptopurine on a Nanostructured Gold Surface: The Au20 Cluster Model

Computational approaches are employed to elucidate the binding mechanism and the SERS phenomenon of 6-mercaptopurine (6MP) adsorbed on the tetrahedral Au20 cluster as a simple model for a nanostructured gold surface. Computations are carried out in both vacuum and aqueous environments using a continuum model. In the gaseous phase and neutral conditions, interaction of 6MP with the gold cluster is mostly dominated by a covalent Au-S bond and partially stabilized by the Au⋅⋅⋅H-N coupling. However, in acidic solution, the nonconventional Au⋅⋅⋅H-S hydrogen-bond becomes the most favorable binding mode. The 6MP affinity for gold clusters decreases in the order of vacuum > neutral solution > acidic medium. During the adsorption, the energy gap of Au20 substantially declines, leading to an increase in its electrical conductivity, which can be converted to an electrical noise. Moreover, such interaction is likely a reversible process and triggered by either the low pH in sick tissues or the presence of cysteine residues in protein matrices. While N-H bending and stretching vibrations play major roles in the SERS phenomenon of 6MP on gold surfaces in neutral solution, the strongest enhancement in acidic environment is mostly due to an Au⋅⋅⋅H-S coupling, rather than an aromatic ring-gold surface π overlap as previously proposed.

Study of Membrane Protein Monolayers Using Surface-Enhanced Infrared Absorption Spectroscopy (SEIRAS): Critical Dependence of Nanostructured Gold Surface Morphology

Surface-enhanced infrared absorption spectroscopy (SEIRAS) is a powerful tool that allows studying the reactivity of protein monolayers at very low concentrations and independent from the protein size. In this study, we probe the surface's morphology of electroless gold deposition for optimum enhancement using two different types of immobilization adapted to two proteins. Independently from the mode of measurement (i.e., transmission or reflection) or type of protein immobilization (i.e., through electrostatic interactions or nickel-HisTag), the enhancement and reproducibility of protein signals in the infrared spectra critically depended on the gold nanostructured surface morphology deposited on silicon. Just a few seconds deviation from the optimum time in the nanoparticle deposition led to a significantly weaker enhancement. Scanning electron microscopy and atomic force microscopy measurements revealed the evolution of the nanostructured surface when comparing different deposition times. The optimal deposition time led to isolated gold nanostructures on the silicon crystal. Importantly, in the case of the immobilization using nickel-HisTag, the surface morphology is rearranged upon immobilization of linker and the protein. A complex three-dimensional (3D) network of nanoparticles decorated with the protein could be observed leading to the optimal enhancement. The electroless deposition of gold is a simple technique, which can be adapted to flow cells and used in analytical approaches.

Ultrasensitive Molecule Detection Based on Infrared Metamaterial Absorber with Vertical Nanogap

Surface-enhanced infrared absorption (SEIRA) spectroscopy is a powerful methodology for sensing and identifying small quantities of analyte molecules via coupling between molecular vibrations and an enhanced near-field induced in engineered structures. A metamaterial absorber (MA) is proposed as an efficient SEIRA platform; however, its efficiency is limited because it requires the appropriate insulator thickness and has a limited accessible area for sensing. SEIRA spectroscopy is proposed using an MA with a 10 nm thick vertical nanogap, and a record-high reflection difference SEIRA signal of 36% is experimentally achieved using a 1-octadecanethiol monolayer target molecule. Theoretical and experimental comparative studies are conducted using MAs with three different vertical nanogaps. The MAs with a vertical nanogap are processed using nanoimprint lithography and isotropic dry etching, which allow cost-effective large-area patterning and mass production. The proposed structure may provide promising routes for ultrasensitive sensing and detection applications.

Infrared spectroscopy probes ion binding geometries

Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.

Introduction to Infrared and Raman-Based Biomedical Molecular Imaging and Comparison with Other Modalities

Molecular imaging has rapidly developed to answer the need of image contrast in medical diagnostic imaging to go beyond morphological information to include functional differences in imaged tissues at the cellular and molecular levels. Vibrational (infrared (IR) and Raman) imaging has rapidly emerged among the molecular imaging modalities available, due to its label-free combination of high spatial resolution with chemical specificity. This article presents the physical basis of vibrational spectroscopy and imaging, followed by illustration of their preclinical in vitro applications in body fluids and cells, ex vivo tissues and in vivo small animals and ending with a brief discussion of their clinical translation. After comparing the advantages and disadvantages of IR/Raman imaging with the other main modalities, such as magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography/single-photon emission-computed tomography (PET/SPECT), ultrasound (US) and photoacoustic imaging (PAI), the design of multimodal probes combining vibrational imaging with other modalities is discussed, illustrated by some preclinical proof-of-concept examples.

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

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

Metasurface with metallic nanoantennas and graphene nanoslits for sensing of protein monolayers and sub-monolayers

Biomolecule sensing plays an important role in both fundamental biological studies and medical diagnostic applications. Infrared (IR) spectroscopy presents opportunities for sensing biomolecules as it allows their fingerprints to be determined by directly measuring their absorption spectra. However, the detection of biomolecules at low concentrations is difficult with conventional IR spectroscopy due to signal-to-noise considerations. This has led to recent interest on the use of nanostructured surfaces to boost the signals from biomolecules in a method termed surface enhanced infrared spectroscopy. So far, efforts have largely involved the use of metallic nanoantennas (which produce large field enhancement) or graphene nanostructures (which produce strong field confinement and provide electrical tunability). Here, we propose a nanostructured surface that combines the large field enhancement of metallic nanoantennas with the strong field confinement and electrical tunability of graphene plasmons. Our device consists of an array of plasmonic nanoantennas and graphene nanoslits on a resonant substrate. We perform systematic electromagnetic simulations to quantify the sensing performance of the proposed device and show that it outperforms designs in which only plasmons from metallic nanoantennas or plasmons from graphene are utilized. These investigations consider the model system of a representative protein-goat anti-mouse immunoglobulin G (IgG) - in monolayer or sub-monolayer form. Our findings provide guidance for future biosensors for the sensitive quantification and identification of biomolecules.

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.

IR Spectroscopy Can Reveal the Mechanism of K+ Transport in Ion Channels

Ion channels like KcsA enable ions to move across cell membranes at near diffusion-limited rates and with very high selectivity. Various mechanisms have been proposed to explain this phenomenon. Broadly, there is disagreement among the proposed mechanisms about whether ions occupy adjacent sites in the channel during the transport process. Here, using a mixed quantum-classical approach to calculate theoretical infrared spectra, we propose a set of infrared spectroscopy experiments that can discriminate between mechanisms with and without adjacent ions. These experiments differ from previous ones in that they independently probe specific ion binding sites within the selectivity filter. When ions occupy adjacent sites in the selectivity filter, the predicted spectra are significantly redshifted relative to when ions do not occupy adjacent sites. Comparisons between theoretical and experimental peak frequencies will therefore discriminate the mechanisms.

Ultrafast pH-jump two-dimensional infrared spectroscopy

We present a pH-jump two-dimensional infrared (2D IR) spectrometer to probe pH-dependent conformational changes from nanoseconds to milliseconds. The design incorporates a nanosecond 355 nm source into a pulse-shaper-based 2D IR spectrometer to trigger dissociation of a caged proton prior to probing subsequent conformational changes with femtosecond 2D IR spectroscopy. We observe a blue shift in the amide I mode (C═O stretch) of diglycine induced by protonation of the terminal amine. This method combines the bond-specific structural sensitivity of ultrafast 2D IR with triggered conformational dynamics, providing structural access to multiscale biomolecular transformations such as protein folding.

Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane

Transmembrane peptides contain polar residues in the interior of the membrane, which may alter the electrostatic environment and favor hydration in the otherwise nonpolar environment of the membrane core. Here, we demonstrate a general, nonperturbative strategy to probe hydration of the peptide backbone at specific depths within the bilayer using a combination of site-specific isotope labels, ultrafast two-dimensional infrared spectroscopy, and spectral modeling based on molecular dynamics simulations. Our results show that the amphiphilic pH-low insertion peptide supports a highly heterogeneous environment, with significant backbone hydration of nonpolar residues neighboring charged residues. For example, a leucine residue located as far as 1 nm into the hydrophobic bulk reports hydrogen-bonded populations as high as ∼20%. These findings indicate that the polar nature of these residues may facilitate the transport of water molecules into the hydrophobic core of the membrane.

Metamaterial-enhanced infrared attenuated total reflection spectroscopy

The use of Fourier transform infrared spectroscopy with attenuated total reflection (FTIR-ATR) allows solid or liquid samples to be characterised directly without specific sample preparation. In such a system, the evanescent waves generated through total internal reflection within a crystal interact with the sample under test. In this work we explore the use of a mid-infrared metasurface to enhance the interaction between molecular vibrations and the evanescent waves. A complementary ring-resonator structure was patterned onto both silicon and SiO₂/Si substrates, and the spectral properties of both devices were characterised using a FTIR-ATR system. Minima in reflectance were observed corresponding to the resonance of the metasurface on the silicon substrate, and to the hybrid resonance of phonon modes and metasurface resonances on the SiO₂/Si substrate, in good agreement with simulations. Preliminary experiments were undertaken using mixtures containing trace amounts of butyl acetate diluted with oleic acid. Without the use of a metasurface, the minimum concentration of butyl acetate that could be clearly detected was 10%, whereas the use of the metasurface on the SiO₂/Si substrate allowed the detection of 1% butyl acetate. This demonstrates the potential of using metasurfaces to enhance trace chemical detection in FTIR-ATR systems.

Water as a Universal Infrared Probe for Bioanalysis in Aqueous Solution by Attenuated Total Reflection-Surface Enhanced Infrared Absorption Spectroscopy

Monitoring the properties and reactions of biomolecules at their interface has attracted ever-growing interest. Here, we propose an approach of infrared analysis technique that utilizes water molecule as a universal probe for in situ and label free monitoring of interfacial bioevents in aqueous solution with high sensitivity. The strong infrared (IR) signal of O-H stretching vibrations from the repelled water is used to sensitively reveal the kinetics of interfacial bioevents at molecular level based on the steric displacement of water using an attenuated total reflection-surface enhanced infrared absorption spectroscopy. Using interfacial immuno-recognition and DNA hybridization as demonstrations, water IR probe offers 26 and 34 times higher sensitivity and even 200 and 86 times lower detection limit for immunosensing and DNA sensing, respectively, as compared to the traditional IR molecular fingerprints.

Real-Time In Situ Secondary Structure Analysis of Protein Monolayer with Mid-Infrared Plasmonic Nanoantennas

Dynamic detection of protein conformational changes at physiological conditions on a minute amount of samples is immensely important for understanding the structural determinants of protein function in health and disease and to develop assays and diagnostics for protein misfolding and protein aggregation diseases. Herein, we experimentally demonstrate the capabilities of a mid-infrared plasmonic biosensor for real-time and in situ protein secondary structure analysis in aqueous environment at nanoscale. We present label-free ultrasensitive dynamic monitoring of β-sheet to disordered conformational transitions in a monolayer of the disease-related α-synuclein protein under varying stimulus conditions. Our experiments show that the extracted secondary structure signals from plasmonically enhanced amide I signatures in the protein monolayer can be reliably and reproducibly acquired with second derivative analysis for dynamic monitoring. Furthermore, by using a polymer layer we show that our nanoplasmonic approach of extracting the frequency components of vibrational signatures matches with the results attained from gold-standard infrared transmission measurements. By facilitating conformational analysis on small quantities of immobilized proteins in response to external stimuli such as drugs, our plasmonic biosensor could be used to introduce platforms for screening small molecule modulators of protein misfolding and aggregation.

Potential Second-Harmonic Ghost Bands in Fourier Transform Infrared (FT-IR) Difference Spectroscopy of Proteins

Fourier transform infrared (FT-IR) difference absorption spectroscopy is a common method for studying the structural and dynamical aspects behind protein function. In particular, the 2800-1800 cm^-1 spectral range has been used to obtain information about internal (deuterated) water molecules, as well as site-specific details about cysteine residues and chemically modified and artificial amino acids. Here, we report on the presence of ghost bands in cryogenic light-induced FT-IR difference spectra of the protein bacteriorhodopsin. The presence of these ghost bands can be particularly problematic in the 2800-1900 cm^-1 region, showing intensities similar to O-D vibrations from water molecules. We demonstrate that they arise from second harmonics from genuine chromophore bands located in the 1400-850 cm^-1 region, generated by double-modulation artifacts caused from reflections of the IR beam at the sample and at the cryostat windows back to the interferometer (inter-reflections). The second-harmonic ghost bands can be physically removed by placing an optical filter of suitable cutoff in the beam path, but at the cost of losing part of the multiplexing advantage of FT-IR spectroscopy. We explored alternatives to the use of optical filters. Tilting the cryostat windows was effective in reducing the intensity of the second harmonic artifacts but tilting the sample windows was not, presumably by their close proximity to the focal point of the IR beam. We also introduce a simple numerical post-processing approach that can partially, but not fully, correct for second-harmonic ghost bands in FT-IR difference spectra.

Aptamer-based sensor for quantitative detection of mercury (II) ions by attenuated total reflection surface enhanced infrared absorption spectroscopy

A sensing platform based on the attenuated total reflection surface enhanced infrared absorption spectroscopy (ATR-SEIRAS) technique and immobilized aptamer has been proposed herein for the selective detection of mercury ions (Hg²⁺). In the proposed platform, 5' thiolated 32-mer DNA probes with methylene blue at the 3' end were immobilized on a thin gold (Au) surface layer. Following Hg²⁺ ions interacting with T bases of the aptamer, T-Hg-T bonds are formed; resulting in a hairpin-shaped formation of the DNA and a detectable change in the IR absorbance of the sensing interface. Notably, the background noise produced by external molecules (e.g., water, non-specific binding molecules and bulk solution) is reduced to a negligible level by means of the ATR detection mode. It is shown that the proposed sensor has a linear response (R² = 0.986) with high sensitivity and good selectivity over the Hg²⁺ range of 0.01 μM-50 μM.

Coordination to lanthanide ions distorts binding site conformation in calmodulin

The Ca²⁺-sensing protein calmodulin (CaM) is a popular model of biological ion binding since it is both experimentally tractable and essential to survival in all eukaryotic cells. CaM modulates hundreds of target proteins and is sensitive to complex patterns of Ca²⁺ exposure, indicating that it functions as a sophisticated dynamic transducer rather than a simple on/off switch. Many details of this transduction function are not well understood. Fourier transform infrared (FTIR) spectroscopy, ultrafast 2D infrared (2D IR) spectroscopy, and electronic structure calculations were used to probe interactions between bound metal ions (Ca²⁺ and several trivalent lanthanide ions) and the carboxylate groups in CaM's EF-hand ion-coordinating sites. Since Tb³⁺ is commonly used as a luminescent Ca²⁺ analog in studies of protein-ion binding, it is important to characterize distinctions between the coordination of Ca²⁺ and the lanthanides in CaM. Although functional assays indicate that Tb³⁺ fully activates many Ca²⁺-dependent proteins, our FTIR spectra indicate that Tb³⁺, La³⁺, and Lu³⁺ disrupt the bidentate coordination geometry characteristic of the CaM binding sites' strongly conserved position 12 glutamate residue. The 2D IR spectra indicate that, relative to the Ca²⁺-bound form, lanthanide-bound CaM exhibits greater conformational flexibility and larger structural fluctuations within its binding sites. Time-dependent 2D IR lineshapes indicate that binding sites in Ca²⁺-CaM occupy well-defined configurations, whereas binding sites in lanthanide-bound-CaM are more disordered. Overall, the results show that binding to lanthanide ions significantly alters the conformation and dynamics of CaM's binding sites.

pH-sensitive vibrational probe reveals a cytoplasmic protonated cluster in bacteriorhodopsin

Infrared spectroscopy has been used in the past to probe the dynamics of internal proton transfer reactions taking place during the functional mechanism of proteins but has remained mostly silent to protonation changes in the aqueous medium. Here, by selectively monitoring vibrational changes of buffer molecules with a temporal resolution of 6 µs, we have traced proton release and uptake events in the light-driven proton-pump bacteriorhodopsin and correlate these to other molecular processes within the protein. We demonstrate that two distinct chemical entities contribute to the temporal evolution and spectral shape of the continuum band, an unusually broad band extending from 2,300 to well below 1,700 cm^-1 The first contribution corresponds to deprotonation of the proton release complex (PRC), a complex in the extracellular domain of bacteriorhodopsin where an excess proton is shared by a cluster of internal water molecules and/or ionic E194/E204 carboxylic groups. We assign the second component of the continuum band to the proton uptake complex, a cluster with an excess proton reminiscent to the PRC but located in the cytoplasmic domain and possibly stabilized by D38. Our findings refine the current interpretation of the continuum band and call for a reevaluation of the last proton transfer steps in bacteriorhodopsin.

Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods

Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.

The Role of Water Distribution Controlled by Transmembrane Potentials in the Cytochrome c-Cardiolipin Interaction: Revealing from Surface-Enhanced Infrared Absorption Spectroscopy

The interaction of cytochrome c (cyt c) with cardiolipin (CL) plays a crucial role in apoptotic functions, however, the changes of the transmembrane potential in governing the protein behavior at the membrane-water interface have not been studied due to the difficulties in simultaneously monitoring the interaction and regulating the electric field. Herein, surface-enhanced infrared absorption (SEIRA) spectroelectrochemistry is employed to study the mechanism of how the transmembrane potentials control the interaction of cyt c with CL membranes by regulating the electrode potentials of an Au film. When the transmembrane potential decreases, the water content at the interface of the membranes can be increased to slow down protein adsorption through decreasing the hydrogen-bond and hydrophobic interactions, but regulates the redox behavior of CL-bound cyt c through a possible water-facilitated proton-coupled electron transfer process. Our results suggest that the potential drop-induced restructure of the CL conformation and the hydration state could modify the structure and function of CL-bound cyt c on the lipid membrane.

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

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

Fourier transform spectroscopy in the vibrational fingerprint region with a birefringent interferometer

We introduce a birefringent interferometer for Fourier transform (FT) spectroscopy in the mid-infrared, covering the vibrational fingerprint region (5-10 µm, 1000-2000 cm^-1), which is crucial for molecular identification. Our interferometer employs the crystal calomel (Hg₂Cl₂), which combines high birefringence (n_e-n_o≈0.55) with a broad transparency range (0.38-20 µm). We adopt a design based on birefringent wedges, which is simple and compact and guarantees excellent delay accuracy and long-term stability. We demonstrate FTIR spectroscopy, with a frequency resolution of 3 cm^-1, as well as two-dimensional IR (2DIR) spectroscopy. Our setup can be extended to other spectroscopic modalities such as vibrational circular dichroism and step-scan FT spectroscopy.

Laser Synthesis and Processing of Colloids: Fundamentals and Applications

Driven by functionality and purity demand for applications of inorganic nanoparticle colloids in optics, biology, and energy, their surface chemistry has become a topic of intensive research interest. Consequently, ligand-free colloids are ideal reference materials for evaluating the effects of surface adsorbates from the initial state for application-oriented nanointegration purposes. After two decades of development, laser synthesis and processing of colloids (LSPC) has emerged as a convenient and scalable technique for the synthesis of ligand-free nanomaterials in sealed environments. In addition to the high-purity surface of LSPC-generated nanoparticles, other strengths of LSPC include its high throughput, convenience for preparing alloys or series of doped nanomaterials, and its continuous operation mode, suitable for downstream processing. Unscreened surface charge of LSPC-synthesized colloids is the key to achieving colloidal stability and high affinity to biomolecules as well as support materials, thereby enabling the fabrication of bioconjugates and heterogeneous catalysts. Accurate size control of LSPC-synthesized materials ranging from quantum dots to submicrometer spheres and recent upscaling advancement toward the multiple-gram scale are helpful for extending the applicability of LSPC-synthesized nanomaterials to various fields. By discussing key reports on both the fundamentals and the applications related to laser ablation, fragmentation, and melting in liquids, this Article presents a timely and critical review of this emerging topic.

Time-resolved infrared spectroscopy in the study of photosynthetic systems

Time-resolved (TR) infrared (IR) spectroscopy in the nanosecond to second timescale has been extensively used, in the last 30 years, in the study of photosynthetic systems. Interesting results have also been obtained at lower time resolution (minutes or even hours). In this review, we first describe the used techniques-dispersive IR, laser diode IR, rapid-scan Fourier transform (FT)IR, step-scan FTIR-underlying the advantages and disadvantages of each of them. Then, the main TR-IR results obtained so far in the investigation of photosynthetic reactions (in reaction centers, in light-harvesting systems, but also in entire membranes or even in living organisms) are presented. Finally, after the general conclusions, the perspectives in the field of TR-IR applied to photosynthesis are described.

Scanning Fourier transform spectrometer in the visible range based on birefringent wedges

We introduce a spectrometer capable of measuring sample absorption spectra in the visible regime, based on a time-domain scanning Fourier transform (FT) approach. While infrared FT spectrometers typically employ a Michelson interferometer to create the two delayed light replicas, the proposed apparatus exploits a compact common-mode passive interferometer that relies on the use of birefringent wedges. This ensures excellent path-length stability (∼λ/300) and accuracy, with no need for active feedback or beam tracking. We demonstrate the robustness of the technique measuring the transmission spectrum of a colored bandpass filter over one octave of bandwidth and compare the results with those obtained with a commercial spectrophotometer.

High-Field High-Repetition-Rate Sources for the Coherent THz Control of Matter

Ultrashort flashes of THz light with low photon energies of a few meV, but strong electric or magnetic field transients have recently been employed to prepare various fascinating nonequilibrium states in matter. Here we present a new class of sources based on superradiant enhancement of radiation from relativistic electron bunches in a compact electron accelerator that we believe will revolutionize experiments in this field. Our prototype source generates high-field THz pulses at unprecedented quasi-continuous-wave repetition rates up to the MHz regime. We demonstrate parameters that exceed state-of-the-art laser-based sources by more than 2 orders of magnitude. The peak fields and the repetition rates are highly scalable and once fully operational this type of sources will routinely provide 1 MV/cm electric fields and 0.3 T magnetic fields at repetition rates of few 100 kHz. We benchmark the unique properties by performing a resonant coherent THz control experiment with few 10 fs resolution.

Infrared Plasmonic Biosensor for Real-Time and Label-Free Monitoring of Lipid Membranes

In this work, we present an infrared plasmonic biosensor for chemical-specific detection and monitoring of biomimetic lipid membranes in a label-free and real-time fashion. Lipid membranes constitute the primary biological interface mediating cell signaling and interaction with drugs and pathogens. By exploiting the plasmonic field enhancement in the vicinity of engineered and surface-modified nanoantennas, the proposed biosensor is able to capture the vibrational fingerprints of lipid molecules and monitor in real time the formation kinetics of planar biomimetic membranes in aqueous environments. Furthermore, we show that this plasmonic biosensor features high-field enhancement extending over tens of nanometers away from the surface, matching the size of typical bioassays while preserving high sensitivity.

Developing and understanding biofluid vibrational spectroscopy: a critical review

Biofluid vibrational spectroscopy, a promising tool for rapid disease diagnosis.

From Ultrafast Structure Determination to Steering Reactions: Mixed IR/Non-IR Multidimensional Vibrational Spectroscopies

Ultrafast multidimensional infrared spectroscopy is a powerful method for resolving features of molecular structure and dynamics that are difficult or impossible to address with linear spectroscopy. Augmenting the IR pulse sequences by resonant or nonresonant UV, Vis, or NIR pulses considerably extends the range of application and creates techniques with possibilities far beyond a pure multidimensional IR experiment. These include surface-specific 2D-IR spectroscopy with sub-monolayer sensitivity, ultrafast structure determination in non-equilibrium systems, triggered exchange spectroscopy to correlate reactant and product bands, exploring the interplay of electronic and nuclear degrees of freedom, investigation of interactions between Raman- and IR-active modes, imaging with chemical contrast, sub-ensemble-selective photochemistry, and even steering a reaction by selective IR excitation. We give an overview of useful mixed IR/non-IR pulse sequences, discuss their differences, and illustrate their application potential.

Optical nanoscopy of transient states in condensed matter

Recently, the fundamental and nanoscale understanding of complex phenomena in materials research and the life sciences, witnessed considerable progress. However, elucidating the underlying mechanisms, governed by entangled degrees of freedom such as lattice, spin, orbit, and charge for solids or conformation, electric potentials, and ligands for proteins, has remained challenging. Techniques that allow for distinguishing between different contributions to these processes are hence urgently required. In this paper we demonstrate the application of scattering-type scanning near-field optical microscopy (s-SNOM) as a novel type of nano-probe for tracking transient states of matter. We introduce a sideband-demodulation technique that allows for probing exclusively the stimuli-induced change of near-field optical properties. We exemplify this development by inspecting the decay of an electron-hole plasma generated in SiGe thin films through near-infrared laser pulses. Our approach can universally be applied to optically track ultrafast/-slow processes over the whole spectral range from UV to THz frequencies.

Chemical Functionalization of Germanium with Dextran Brushes for Immobilization of Proteins Revealed by Attenuated Total Reflection Fourier Transform Infrared Difference Spectroscopy

Protein immobilization studied by attenuated total reflection Fourier transform infrared (ATR-FT-IR) difference spectroscopy is an emerging field enabling the study of proteins at atomic detail. Gold or glass surfaces are frequently used for protein immobilization. Here, we present an alternative method for protein immobilization on germanium. Because of its high refractive index and broad spectral window germanium is the best material for ATR-FT-IR spectroscopy of thin layers. So far, this technique was mainly used for protein monolayers, which lead to a limited signal-to-noise ratio. Further, undesired protein-protein interactions can occur in a dense layer. Here, the germanium surface was functionalized with thiols and stepwise a dextran brush was generated. Each step was monitored by ATR-FT-IR spectroscopy. We compared a 70 kDa dextran with a 500 kDa dextran regarding the binding properties. All surfaces were characterized by atomic force microscopy, revealing thicknesses between 40 and 110 nm. To analyze the capability of our system we utilized N-Ras on mono-NTA (nitrilotriacetic acid) functionalized dextran, and the amount of immobilized Ras corresponded to several monolayers. The protein stability and loading capacity was further improved by means of tris-NTA for immobilization. Small-molecule-induced changes were revealed with an over 3 times higher signal-to-noise ratio compared to monolayers. This improvement may allow the observation of very small and so far hidden changes in proteins upon stimulus. Furthermore, we immobilized green fluorescent protein (GFP) and mCherry simultaneously enabling an analysis of the surface by fluorescence microscopy. The absence of a Förster resonance energy transfer (FRET) signal demonstrated a large protein-protein distance, indicating an even distribution of the protein within the dextran.

Microsecond Deprotonation of Aspartic Acid and Response of the α/β Subdomain Precede C-Terminal Signaling in the Blue Light Sensor Plant Cryptochrome

Plant cryptochromes are photosensory receptors that regulate various central aspects of plant growth and development. These receptors consist of a photolyase homology region (PHR) carrying the oxidized flavin adenine dinucleotide (FAD) cofactor, and a cryptochrome C-terminal extension (CCT), which is essential for signaling. Absorption of blue/UVA light leads to formation of the FAD neutral radical as the likely signaling state, and ultimately activates the CCT. Little is known about the signal transfer from the flavin to the CCT. Here, we investigated the photoreaction of the PHR by time-resolved step-scan FT-IR spectroscopy complemented by UV-vis spectroscopy. The first spectrum at 500 ns shows major contributions from the FAD anion radical, which is demonstrated to then be protonated by aspartic acid 396 to the neutral radical within 3.5 μs. The analysis revealed the existence of three intermediates characterized by changes in secondary structure. A marked loss of β-sheet structure is observed in the second intermediate evolving with a time constant of 500 μs. This change is accompanied by a conversion of a tyrosine residue, which is identified as the formation of a tyrosine radical in the UV-vis. The only β-sheet in the PHR is located within the α/β subdomain, ∼25 Å away from the flavin. This subdomain has been previously attributed a role as a putative antenna binding site, but is now suggested to have evolved to a component in the signaling of plant cryptochromes by mediating the interaction with the CCT.