Transient 2D IR spectroscopy from micro- to milliseconds

Novel Developments and Progress in Two-Dimensional Correlation Spectroscopy (2D-COS)

This first of the two-part series of the comprehensive survey review on the progress of the two-dimensional correlation spectroscopy (2D-COS) field during the period 2021-2022, covers books, reviews, tutorials, novel concepts and theories, and patent applications that appeared in the last two years, as well as some inappropriate use or citations of 2D-COS. The overall trend clearly shows that 2D-COS is continually growing and evolving with notable new developments. The technique is well recognized as a powerful analytical tool that provides deep insights into systems in many science fields.

Diverse Applications of Two-Dimensional Correlation Spectroscopy (2D-COS)

This second of the two-part series of a comprehensive survey review provides the diverse applications of two-dimensional correlation spectroscopy (2D-COS) covering different probes, perturbations, and systems in the last two years. Infrared spectroscopy has maintained its top popularity in 2D-COS over the past two years. Fluorescence spectroscopy is the second most frequently used analytical method, which has been heavily applied to the analysis of heavy metal binding, environmental, and solution systems. Various other analytical methods including laser-induced breakdown spectroscopy, dynamic mechanical analysis, differential scanning calorimetry, capillary electrophoresis, seismologic, and so on, have also been reported. In the last two years, concentration, composition, and pH are the main effects of perturbation used in the 2D-COS fields, as well as temperature. Environmental science is especially heavily studied using 2D-COS. This comprehensive survey review shows that 2D-COS undergoes continuous evolution and growth, marked by novel developments and successful applications across diverse scientific fields.

Phenomenology of Intermediate Molecular Dynamics at Metal-Oxide Interfaces

Reaction intermediates buried within a solid-liquid interface are difficult targets for physiochemical measurements. They are inherently molecular and locally dynamic, while their surroundings are extended by a periodic lattice on one side and the solvent dielectric on the other. Challenges compound on a metal-oxide surface of varied sites and especially so at its aqueous interface of many prominent reactions. Recently, phenomenological theory coupled with optical spectroscopy has become a more prominent tool for isolating the intermediates and their molecular dynamics. The following article reviews three examples of the SrTiO3-aqueous interface subject to the oxygen evolution from water: reaction-dependent component analyses of time-resolved intermediates, a Fano resonance of a mode at the metal-oxide-water interface, and reaction isotherms of metastable intermediates. The phenomenology uses parameters to encase what is unknown at a microscopic level to then circumscribe the clear and macroscopically tuned trends seen in the spectroscopic data.

Chirped pulse upconversion for femtosecond mid-infrared spectroscopy at 100 kHz

We demonstrate that chirped pulse up-conversion (CPU), a method routinely used with systems based on 1-kHz Titanium:Sapphire lasers, can be extended to a repetition rate of 100 kHz with an Ytterbium diode-pumped femtosecond amplifier. Individual mid-infrared spectra can thus be measured directly in the near infrared using a fast CMOS linescan camera. After an appropriate Fourier processing, a spectral resolution of 1.1 cm-1 is reported, currently limited by our spectrometer. Additionally, we demonstrate the application of CPU to a pump-probe measurement of the vibrational relaxation in carboxy-hemoglobin, and we show that the combination of fast scanning and fast acquisition enables a straightforward removal of pump scattering interference.

Biomolecular infrared spectroscopy: making time for dynamics

Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.

Structural Characterization of Boron Sheets beyond the Monolayer and Implication for Experimental Synthesis and Identification

The successful synthesis of quasi-freestanding bilayer borophene has aroused much attention for its superior physical properties and holds great promise for future electronic devices. Herein, we comprehensively explore six boron sheets beyond the monolayer and structurally characterize them via various methods using first-principles calculations for experimental references. On the basis of atomic models of borophenes, simulated scanning tunneling microscope (STM) images show different morphologies at different bias voltages and are explained by the partial densities of states and the height differences in the vertical direction. Simulated transmission electron microscope images further probe the internal atomic arrangement of boron sheets and compensate for the shortcomings of STM images to better distinguish different phases of boron sheets. The interlayer coupling strength is stronger in bilayer borophenes than in the three-layer system via the electron localization function and Mulliken bond population. In addition, simulated X-ray diffraction and infrared spectra show different characteristic peaks and corresponding vibrational modes to further characterize these boron sheets. These theoretical results can decrease the prime cost and provide vital guidance for the experimental synthesis and identification of boron sheets beyond the monolayer.

Breaking Barriers in Ultrafast Spectroscopy and Imaging Using 100 kHz Amplified Yb-Laser Systems

ConspectusUltrafast spectroscopy and imaging have become tools utilized by a broad range of scientists involved in materials, energy, biological, and chemical sciences. Commercialization of ultrafast spectrometers including transient absorption spectrometers, vibrational sum frequency generation spectrometers, and even multidimensional spectrometers have put these advanced spectroscopy measurements into the hands of practitioners originally outside the field of ultrafast spectroscopy. There is now a technology shift occurring in ultrafast spectroscopy, made possible by new Yb-based lasers, that is opening exciting new experiments in the chemical and physical sciences. Amplified Yb-based lasers are not only more compact and efficient than their predecessors but also, most importantly, operate at many times the repetition rate with improved noise characteristics in comparison to the previous generation of Ti:sapphire amplifier technologies. Taken together, these attributes are enabling new experiments, generating improvements to long-standing techniques, and affording the transformation of spectroscopies to microscopies. This Account aims to show that the shift to 100 kHz lasers is a transformative step in nonlinear spectroscopy and imaging, much like the dramatic expansion that occurred with the commercialization of Ti:sapphire laser systems in the 1990s. The impact of this technology will be felt across a great swath of scientific communities. We first describe the technology landscape of amplified Yb-based laser systems used in conjunction with 100 kHz spectrometers operating with shot-to-shot pulse shaping and detection. We also identify the range of different parametric conversion and supercontinuum techniques which now provide a path to making pulses of light optimal for ultrafast spectroscopy. Second, we describe specific instances from our laboratories of how the amplified Yb-based light sources and spectrometers are transformative. For multiple probe time-resolved infrared and transient 2D IR spectroscopy, the gain in temporal span and signal-to-noise enables dynamical spectroscopy measurements from femtoseconds to seconds. These gains widen the applicability of time-resolved infrared techniques across a range of topics in photochemistry, photocatalysis, and photobiology as well as lower the technical barriers to implementation in a laboratory. For 2D visible spectroscopy and microscopy with white light, as well as 2D IR imaging, the high repetition rates of these new Yb-based light sources allow one to spatially map 2D spectra while maintaining high signal-to-noise in the data. To illustrate the gains, we provide examples of imaging applications in the study of photovoltaic materials and spectroelectrochemistry.

Transient 2D IR Spectroscopy and Multiscale Simulations Reveal Vibrational Couplings in the Cyanobacteriochrome Slr1393-g3

Cyanobacteriochromes are bistable photoreceptor proteins with desirable photochemical properties for biotechnological applications, such as optogenetics or fluorescence microscopy. Here, we investigate Slr1393-g3, a cyanobacteriochrome that reversibly photoswitches between a red-absorbing (Pr) and green-absorbing (Pg) form. We applied advanced IR spectroscopic methods to track the sequence of intermediates during the photocycle over many orders of magnitude in time. In the conversion from Pg to Pr, we have revealed a new intermediate with distinct spectroscopic features in the IR, which precedes Pr formation using transient IR spectroscopy. In addition, stationary and transient 2D IR experiments measured the vibrational couplings between different groups of the chromophore and the protein in these intermediate states, as well as their structural disorder. Anharmonic QM/MM calculations predict spectra in good agreement with experimental 2D IR spectra of the initial and final states of the photocycle. They facilitate the assignment of the IR spectra that serve as a basis for the interpretation of the spectroscopic results and suggest structural changes of the intermediates along the photocycle.

Increasing Pump-Probe Signal toward Asymptotic Limits

Optimization of pump-probe signal requires a complete understanding of how signal scales with experimental factors. In simple systems, signal scales quadratically with molar absorptivity, and linearly with fluence, concentration, and path length. In practice, scaling factors weaken beyond certain thresholds (e.g., OD > 0.1) due to asymptotic limits related to optical density, fluence and path length. While computational models can accurately account for subdued scaling, quantitative explanations often appear quite technical in the literature. This Perspective aims to present a simpler understanding of the subject with concise formulas for estimating absolute magnitudes of signal under both ordinary and asymptotic scaling conditions. This formulation may be more appealing for spectroscopists seeking rough estimates of signal or relative comparisons. We identify scaling dependencies of signal with respect to experimental parameters and discuss applications for improving signal under broad conditions. We also review other signal enhancement methods, such as local-oscillator attenuation and plasmonic enhancement, and discuss respective benefits and challenges regarding asymptotic limits that signal cannot exceed.

The molecular mechanism of light-induced bond formation and breakage in the cyanobacteriochrome TePixJ

Cyanobacteriochromes (CBCRs) are small and versatile photoreceptor proteins with high potential for biotechnological applications. Among them, the so-called DXCF-CBCRs exhibit an intricate secondary photochemistry: miliseconds after activation with light, a covalent linkage between a conserved cysteine residue and the light-absorbing tetrapyrrole chromophore is reversibly formed or broken. We employed time-resolved IR spectroscopy over ten orders of magnitude in time in conjunction with 2D-IR spectroscopy to investigate the molecular mechanism of this intriguing reaction in the DXCF-CBCR model system TePixJ from T. elongatus. The crosspeak pattern in the 2D-IR spectrum facilitated the assignment of the dominant signals to vibrational modes of the chromophore, which in turn enabled us to construct a mechanistic model for the photocycle reactions from the time-resolved IR spectra. Here, we assigned the time-resolved signals to several proton transfer steps and distinct geometric changes of the chromophore. We propose a model that describes how these events lead to the rearrangement of charges in the chromophore binding pocket, which serves as the trigger for the light-induced bond formation and breakage with the nearby cysteine.

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.

Spectrophotometric Concentration Analysis Without Molar Absorption Coefficients by Two-Dimensional-Infrared and Fourier Transform Infrared Spectroscopy

A spectrophotometric method for determining relative concentrations of infrared (IR)-active analytes with unknown concentration and unknown molar absorption coefficient is explored. This type of method may be useful for the characterization of complex/heterogeneous liquids or solids, the study of transient species, and for other scenarios where it might be difficult to gain concentration information by other means. Concentration ratios of two species are obtained from their IR absorption and two-dimensional (2D)-IR diagonal bleach signals using simple ratiometric calculations. A simple calculation framework for deriving concentration ratios from spectral data is developed, extended to IR-pump-probe signals, and applied to the calculation of transition dipole ratios. Corrections to account for the attenuation of the 2D-IR signal caused by population relaxation, spectral overlap, wavelength-dependent pump absorption, inhomogeneous broadening, and laser intensity variations are described. A simple formula for calculating the attenuation of the 2D-IR signal due to sample absorption is deduced and by comparison with 2D-IR signals at varying total sample absorbance found to be quantitatively accurate. 2D-IR and Fourier transform infrared spectroscopy of two carbonyl containing species acetone and N-methyl-acetamide dissolved in D2O are used to experimentally confirm the validity of the ratiometric calculations. Finally, to address ambiguities over units and scaling of 2D-IR signals, a physical unit of 2D-IR spectral amplitude in mOD/c m - 1 is proposed.

Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy

Phytochromes are ubiquitous photoreceptor proteins that undergo a significant refolding of secondary structure in response to initial photoisomerization of the chromophoric group. This process is important for the signal transduction through the protein and thus its regulatory function in different organisms. Here, we employ two-dimensional infrared absorption (2D-IR) spectroscopy, an ultrafast spectroscopic technique that is sensitive to vibrational couplings, to study the photoreaction of bacterial phytochrome Agp1. By calculating difference spectra with respect to the photoactivation, we are able to isolate sharp difference cross-peaks that report on local changes in vibrational couplings between different sites of the chromophore and the protein. These results indicate inter alia that a dipole coupling between the chromophore and the so-called tongue region plays a role in stabilizing the protein in the light-activated state.

A stop-flow sample delivery system for transient spectroscopy

A stop-flow sample delivery system for transient spectroscopy is presented, which is, in particular, suited for laser-based instruments (quantum-cascade lasers or amplified femtosecond lasers) with excitation pulse repetition rates in the range 10-100 Hz. Two pulsing micro-valves are mounted onto a flow cuvette designed for transient IR spectroscopy, which is integrated into a flow cycle driven by a peristaltic pump. The performance of the system is demonstrated with transient IR experiments of the trans-to-cis photoisomerization of a water-soluble azobenzene derivative. The sample stands still when the micro-valves are closed and is pushed out from the probe beam focus on a 1 ms timescale when opening the micro-valves. The setup is extremely sample efficient. It needs only small sample volumes, and at the same time, it enables excitation of a large fraction of molecules in solution.

Computational spectroscopy of complex systems

Numerous linear and non-linear spectroscopic techniques have been developed to elucidate structural and functional information of complex systems ranging from natural systems, such as proteins and light-harvesting systems, to synthetic systems, such as solar cell materials and light-emitting diodes. The obtained experimental data can be challenging to interpret due to the complexity and potential overlapping spectral signatures. Therefore, computational spectroscopy plays a crucial role in the interpretation and understanding of spectral observables of complex systems. Computational modeling of various spectroscopic techniques has seen significant developments in the past decade, when it comes to the systems that can be addressed, the size and complexity of the sample types, the accuracy of the methods, and the spectroscopic techniques that can be addressed. In this Perspective, I will review the computational spectroscopy methods that have been developed and applied for infrared and visible spectroscopies in the condensed phase. I will discuss some of the questions that this has allowed answering. Finally, I will discuss current and future challenges and how these may be addressed.

Molecular vibrational polariton: Its dynamics and potentials in novel chemistry and quantum technology

Molecular vibrational polaritons, a hybridized quasiparticle formed by the strong coupling between molecular vibrational modes and photon cavity modes, have attracted tremendous attention in the chemical physics community due to their peculiar influence on chemical reactions. At the same time, the half-photon half-matter characteristics of polaritons make them suitable to possess properties from both sides and lead to new features that are useful for photonic and quantum technology applications. To eventually use polaritons for chemical and quantum applications, it is critical to understand their dynamics. Due to the intrinsic time scale of cavity modes and molecular vibrational modes in condensed phases, polaritons can experience dynamics on ultrafast time scales, e.g., relaxation from polaritons to dark modes. Thus, ultrafast vibrational spectroscopy becomes an ideal tool to investigate such dynamics. In this Perspective, we give an overview of recent ultrafast spectroscopic works by our group and others in the field. These recent works show that molecular vibrational polaritons can have distinct dynamics from its pure molecular counterparts, such as intermolecular vibrational energy transfer and hot vibrational dynamics. We then discuss some current challenges and future opportunities, such as the possible use of ultrafast vibrational dynamics, to understand cavity-modified reactions and routes to develop molecular vibrational polaritons as new room temperature quantum platforms.

Transparent window 2D IR spectroscopy of proteins

Proteins are complex, heterogeneous macromolecules that exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires experimental tools to characterize them with high spatial and temporal precision. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution. Two-dimensional (2D) IR methods that provide richer information are becoming more routine but remain challenging to apply to proteins. Spectral congestion typically prevents selective investigation of native vibrations; however, the problem can be overcome by site-specific introduction of amino acid side chains that have vibrational groups with frequencies in the "transparent window" of protein spectra. This Perspective provides an overview of the history and recent progress in the development of transparent window 2D IR of proteins.

Sequence of Events during Peptide Unbinding from RNase S: A Complete Experimental Description

The phototriggered unbinding of the intrinsically disordered S-peptide from the RNase S complex is studied with the help of transient IR spectroscopy, covering a wide range of time scales from 100 ps to 10 ms. To that end, an azobenzene moiety has been linked to the S-peptide in a way that its helicity is disrupted by light, thereby initiating its complete unbinding. The full sequence of events is observed, starting from unfolding of the helical structure of the S-peptide on a 20 ns time scale while still being in the binding pocket of the S-protein, S-peptide unbinding after 300 μs, and the structural response of the S-protein after 3 ms. With regard to the S-peptide dynamics, the binding mechanism can be classified as an induced fit, while the structural response of the S-protein is better described as conformational selection.

Needles in a haystack: H-bonding in an optogenetic protein observed with isotope labeling and 2D-IR spectroscopy

Recently, re-purposing of cyanobacterial photoreceptors as optogentic actuators enabled light-regulated protein expression in different host systems. These new bi-stable optogenetic tools enable interesting new applications, but their light-driven working mechanism remains largely elusive on a molecular level. Here, we study the optogenetic cyanobacteriochrome Am1-c0023g2 with isotope labeling and two dimensional infrared (2D-IR) spectroscopy. Isotope labeling allows us to isolate two site-specific carbonyl marker modes from the overwhelming mid-IR signal of the peptide backbone vibrations. Unlike conventional difference-FTIR spectroscopy, 2D-IR is sensitive to homogeneous and inhomogeneous broadening mechanisms of these two vibrational probes in the different photostates of the protein. We analyse the 2D-IR line shapes in the context of available structural models and find that they reflect the hydrogen-bonding environment of these two marker groups.