Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy

Measuring Protein Conformation at Aqueous Interfaces with 2D Infrared Spectroscopy of Emulsions

Determining the secondary and tertiary structures of proteins at aqueous interfaces is crucial for understanding their function, but measuring these structures selectively at the interface is challenging. Here we demonstrate that two-dimensional infrared (2D-IR) spectroscopy of protein stabilized emulsions offers a new route to measuring interfacial protein structure with high levels of detail. We prepared hexadecane/water oil-in-water emulsions stabilized by model LK peptides that are known to fold into either α-helix or β-sheet conformations at hydrophobic interfaces and measured 2D-IR spectra in a transmission geometry. We saw clear spectral signatures of the peptides folding at the interface, with no detectable residue from remaining bulk peptides. Using 2D spectroscopy gives us access to correlation and dynamics data, which enables structural assignment in cases where linear spectroscopy fails. Using the emulsions allows one to study interfacial spectra with standard transmission geometry spectrometers, bringing the richness of 2D-IR to the interface with no additional optical complexity.

Ionic Dynamics and Vibrational Spectral Diffusion of a Protic Alkylammonium Ionic Salt through Intrinsic Cationic N-H Vibrational Probe from FPMD Simulations

We employed density functional theory (DFT)-based molecular dynamics simulations to explore the structure, dynamics, and spectral properties of the protic ionic entity trimethylammonium chloride (TMACl). Structural investigations include calculating the site-site radial distribution functions (RDFs), the distribution of constituent cations and anions in three-dimensional space, and combined distribution functions of the hydrogen-bonded pair RDF versus angle, revealing the structural characteristics of the ionic solvation and the intermolecular interactions within ions. Further, we determined the instantaneous vibrational stretching frequencies of the intrinsic N-H stretch probe modes by applying the time-series wavelet method. The associated ionic dynamics within the protic ionic compound were investigated by calculating the time-evolution of the fluctuating frequencies and the frequency-time correlation functions (FFCFs). The time scale related to the local structural relaxation process and the average hydrogen bond lifetime, ion cage dynamics, and mean squared displacement were investigated. The faster decay component of the FFCFs, depicting the intermolecular motion of intact hydrogen bonds in TMACl, is 0.07 ps for the Perdew-Burke-Ernzerhof (PBE)-based simulation and 0.06 ps for the PBE-D2 representation. The slower time scale of the longer picosecond decay time component of PBE and PBE-D2 representations are 3.13 and 2.87 ps, respectively. These picosecond time scales represent more significant fluctuations of the hydrogen-bonding partners in the ionic entity and hydrogen-bond jump events accompanied by large angular jumps. The longest picosecond time scales represent structural relaxation, including large angular jumps and ion-pair dynamics. Also, ion cage lifetimes correlate with the slowest time scale of the associated dynamics of vibrational spectral diffusion despite the type of DFT functional. This study benchmarks DFT treatments of the exchange-correlation functional with and without the van der Waals (vdW) dispersion correction scheme. The inclusion of vdW interactions to the PBE functional represents a less structured state of the ionic entity and faster dynamics of the molecular motions relative to the one predicted by the PBE system. All the results illustrate the necessity of accurately describing the Coulomb interactions, vdW dispersive interactive forces, and localized hydrogen bonds required to sustain the energetic balance in this ionic salt.

Probing Denaturation of Protein A via Surface-Enhanced Infrared Absorption Spectroscopy

We apply surface-enhanced infrared absorption (SEIRA) spectroscopy to monitor the denaturation process of a surface-bound protein A monolayer. Our proposed platform relies on a plasmonic metasurface comprising different spatial subregions (“pixels”) that are engineered to exhibit different resonances covering the infrared region of the electromagnetic spectrum that is matched to the vibrational modes of the Amide groups. Specifically, we are able to determine changes in the Amide I and Amide II vibration coupled modes, by comparing the SEIRA reflectance spectra pertaining to the native state and a denatured state induced by a pH variation. In particular, we observe some evident red-shifts in the principal Amide I mode and the Amide II vibration coupled modes (attributable to the breaking of hydrogen bonds), which result in insurmountable barriers for refolding. Thanks to the strong field localization, and consequent enhancement of the light-matter interactions, our proposed sensing platform can operate with extremely small amounts of an analyte, with an estimated detection limit of about 3 femtomoles of molecules.

Generative Adversarial Neural Networks for Denoising Coherent Multidimensional Spectra

Ultrafast spectroscopy often involves measuring weak signals and long data acquisition times. Spectra are typically collected as a "pump-probe" spectrum by measuring differences in intensity across laser shots. Shot-to-shot intensity fluctuations are most often the primary source of noise in ultrafast spectroscopy. Here, we present a novel approach for denoising ultrafast two-dimensional infrared (2D IR) spectra using conditional generative adversarial neural networks (cGANNs). The cGANN approach is able to eliminate shot-to-shot noise and reconstruct the line shapes present in the noisy input spectrum. We present a general approach for training the cGANN using matched pairs of noisy and clean synthetic 2D IR spectra based on the Kubo-line shape model for a three-level system. Experimental shot-to-shot laser noise is added to synthetic spectra to recreate the noise profile present in measured experimental spectra. The cGANNs can recover line shapes from synthetic 2D IR spectra with signal-to-noise ratios as low as 2:1, while largely preserving the key features such as center frequencies, line widths, and diagonal elongation. In addition, we benchmark the performance of the cGANN using experimental 2D IR spectra of an ester carbonyl vibrational probe and demonstrate that, by applying the cGANN denoising approach, we can extract the frequency-frequency time correlation function (FFCF) from reconstructed spectra using a nodal-line slope analysis. Finally, we provide a set of practical guidelines for extending the denoising method to other coherent multidimensional spectroscopies.

Machine learning recognition of protein secondary structures based on two-dimensional spectroscopic descriptors

Protein secondary structure discrimination is crucial for understanding their biological function. It is not generally possible to invert spectroscopic data to yield the structure. We present a machine learning protocol which uses two-dimensional UV (2DUV) spectra as pattern recognition descriptors, aiming at automated protein secondary structure determination from spectroscopic features. Accurate secondary structure recognition is obtained for homologous (97%) and nonhomologous (91%) protein segments, randomly selected from simulated model datasets. The advantage of 2DUV descriptors over one-dimensional linear absorption and circular dichroism spectra lies in the cross-peak information that reflects interactions between local regions of the protein. Thanks to their ultrafast (∼200 fs) nature, 2DUV measurements can be used in the future to probe conformational variations in the course of protein dynamics.

Generation of intense phase-stable femtosecond hard X-ray pulse pairs

Coherent nonlinear spectroscopies and imaging in the X-ray domain provide direct insight into the coupled motions of electrons and nuclei with resolution on the electronic length scale and timescale. The experimental realization of such techniques will strongly benefit from access to intense, coherent pairs of femtosecond X-ray pulses. We have observed phase-stable X-ray pulse pairs containing more than 3 × 107 photons at 5.9 keV (2.1 Å) with ∼1 fs duration and 2 to 5 fs separation. The highly directional pulse pairs are manifested by interference fringes in the superfluorescent and seeded stimulated manganese Kα emission induced by an X-ray free-electron laser. The fringes constitute the time-frequency X-ray analog of Young’s double-slit interference, allowing for frequency domain X-ray measurements with attosecond time resolution.

Modeling amide-I vibrations of alanine dipeptide in solution by using neural network protocol

Infrared spectroscopy is a powerful tool for the understanding of molecular structure and function of polypeptides. Theoretical interpretation of IR spectra relies on ab initio calculations may be very costly in computational resources. Herein, we developed a neural network (NN) modeling protocol to evaluate a model dipeptide's backbone amide-I spectra. DFT calculations were performed for the amide-I vibrational motions and structural parameters of alanine dipeptide (ALAD) conformers in different micro-environments ranging from polar to non-polar ones. The obtained backbone dihedrals, C = O bond lengths and amide-I frequencies of ALAD were gather together for NN architecture. The applications of built NN protocols for the prediction of amide-I frequencies of ALAD in other solvation conditions are quite satisfactory with much less computational cost comparing with electronic structure calculations. The results show that this cost-effective way enables us to decipher the polypeptide's dynamic secondary structures and biological functions with their backbone vibrational probes.

Investigating the effects of N-terminal acetylation on KFE8 self-assembly with 2D IR spectroscopy

Peptide self-assembly is an exciting and robust approach to create novel nanoscale materials for biomedical applications. However, the complex interplay between intra- and intermolecular interactions in peptide aggregation means that minor changes in peptide sequence can yield dramatic changes in supramolecular structure. Here, we use two-dimensional infrared (2D IR) spectroscopy to study a model amphiphilic peptide, KFE8, and its N-terminal acetylated counterpart, AcKFE8. 2D IR spectra of isotope-labeled peptides reveal that AcKFE8 aggregates comprise two distinct β-sheet structures while KFE8 aggregates comprise only one of these structures. Using an excitonic Hamiltonian to simulate the vibrational spectra of model β-sheets, we determine that the spectra are consistent with antiparallel β-sheets with different strand alignments, specifically a two-residue shift in the register of the β-strands. These findings bring forth new insights into how N-terminal acetylation may subtly impact secondary structure, leading to larger effects on overall aggregate morphology. Additionally, these results highlight the importance of understanding the residue-level structural differences that result from changes in peptide sequence in order to facilitate the rational design of peptide materials.

Dynamic effect of polymers at the surfactant-water interface: an ultrafast study

Interfaces play a role in controlling the rates and outcomes of chemical processes. Characterizing the interactions at heterogeneous interfaces is critical to developing a comprehensive model of the role of interfaces and confinement in modulating chemical reactions. Reverse micelles are an ideal model system for exploring the effect of encapsulated species on interfacial environments. Here, we use a combination of ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics (MD) simulations to characterize the picosecond interfacial dynamics in reverse micelles (RMs) containing acrylamide monomers and polyacrylamide polymers within the aqueous phase. The ester carbonyl vibrations of the sorbitan monostearate surfactants are examined to extract interfacial hydrogen-bonding populations and dynamics. Hydrogen bond populations at the ester carbonyl positions remain unchanged with the inclusion of either polymer or monomer species. Hydrogen-bond dynamics are not altered with the addition of monomer but are slowed down twofold in the presence of encapsulated polyacrylamide polymer species as a result of polymer chains partially localizing to the interface. These findings imply that kinetics of reactions that occur at interfaces or in confined environments could be modulated by interfacial localization of the different components.

Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure

Infrared (IR) spectroscopy is a highly sensitive technique that provides complete information on chemical compositions. The IR spectra of proteins or peptides give rise to nine characteristic IR absorption bands. The amide I bands are the most prominent and sensitive vibrational bands and widely used to predict protein secondary structures. The interference of H₂O absorbance is the greatest challenge for IR protein secondary structure prediction. Much effort has been made to reduce/eliminate the interference of H₂O, simplify operation steps, and increase prediction accuracy. Progress in sampling and equipment has rendered the Fourier transform infrared (FTIR) technique suitable for determining the protein secondary structure in broader concentration ranges, greatly simplifying the operating steps. This review highlights the recent progress in sample preparation, data analysis, and equipment development of FTIR in A/T mode, with a focus on recent applications of FTIR spectroscopy in the prediction of protein secondary structure. This review also provides a brief introduction of the progress in ATR-FTIR for predicting protein secondary structure and discusses some combined IR methods, such as AFM-based IR spectroscopy, that are used to analyze protein structural dynamics and protein aggregation.

The polarization dependence of 2D IR cross-peaks distinguishes parallel-stranded and antiparallel-stranded DNA G-quadruplexes

Guanine-rich nucleic acid sequences have a tendency to form four-stranded non-canonical motifs known as G-quadruplexes. These motifs may adopt a wide range of structures characterized by size, strand orientation, guanine base conformation, and fold topology. Using three K⁺-bound model systems, we show that vibrational coupling between guanine C6 = O and ring modes varies between parallel-stranded and antiparallel-stranded G-quadruplexes, and that such structures can be distinguished by comparison of the polarization dependences of cross-peaks in their two-dimensional infrared (2D IR) spectra. Combined with previously defined vibrational frequency trends, this analysis reveals key features of a 30-nucleotide unimolecular variant of the Bcl-2 proximal promoter that are consistent with its reported structure. This study shows that 2D IR spectroscopy is a convenient method for analyzing G-quadruplex structures that can be applied to complex sequences where traditional high-resolution methods are limited by solubility and disorder.

Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded-double-stranded DNA junctions by 2D fluorescence spectroscopy

DNA replication and the related processes of genome expression require binding, assembly, and function of protein complexes at and near single-stranded (ss)-double-stranded (ds) DNA junctions. These central protein-DNA interactions are likely influenced by thermally induced conformational fluctuations of the DNA scaffold across an unknown distribution of functionally relevant states to provide regulatory proteins access to properly conformed DNA binding sites. Thus, characterizing the nature of conformational fluctuations and the associated structural disorder at ss-dsDNA junctions is critical for understanding the molecular mechanisms of these central biological processes. Here, we describe spectroscopic studies of model ss-dsDNA fork constructs that contain dimers of "internally labeled" cyanine (iCy3) chromophore probes that have been rigidly inserted within the sugar-phosphate backbones of the DNA strands. Our combined analyses of absorbance, circular dichroism, and two-dimensional fluorescence spectroscopy permit us to characterize the local conformational parameters and conformational distributions. We find that the DNA sugar-phosphate backbones undergo abrupt successive changes in their local conformations-initially from a right-handed and ordered DNA state to a disordered splayed-open structure and then to a disordered left-handed conformation-as the dimer probes are moved across the ss-dsDNA junction. Our results suggest that the sugar-phosphate backbones at and near ss-dsDNA junctions adopt specific position-dependent local conformations and exhibit varying extents of conformational disorder that deviate widely from the Watson-Crick structure. We suggest that some of these conformations can function as secondary-structure motifs for interaction with protein complexes that bind to and assemble at these sites.

Cross-α/β polymorphism of PSMα3 fibrils

Phenol soluble modulins (PSMs) are an important class of peptides secreted by Staphylococcus aureus bacteria. The toxicity to human cells and unique ability of one such peptide, PSMα3, to aggregate into an α-helical amyloid-like structure may hold a key to a better understanding of the virulence of dangerous pathogens such as methicillin resistant S. aureus. In reporting a detailed two-dimensional infrared (2DIR) analysis of PSMα3, we found direct evidence of multiple aggregate architectures existing in equilibrium with one another. We also discovered a unique and characteristic 2DIR spectroscopic signature that unambiguously reports on the presence of the unusual and highly cytotoxic cross-α amyloid structure.

The formation of ordered cross-β amyloid protein aggregates is associated with a variety of human disorders. While conventional infrared methods serve as sensitive reporters of the presence of these amyloids, the recently discovered amyloid secondary structure of cross-α fibrils presents new questions and challenges. Herein, we report results using Fourier transform infrared spectroscopy and two-dimensional infrared spectroscopy to monitor the aggregation of one such cross-α–forming peptide, phenol soluble modulin alpha 3 (PSMα3). Phenol soluble modulins (PSMs) are involved in the formation and stabilization of Staphylococcus aureus biofilms, making sensitive methods of detecting and characterizing these fibrils a pressing need. Our experimental data coupled with spectroscopic simulations reveals the simultaneous presence of cross-α and cross-β polymorphs within samples of PSMα3 fibrils. We also report a new spectroscopic feature indicative of cross-α fibrils.

Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands

Fundamental vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. Such studies started comparing vibrational changes between the initial BR state (all-trans retinal) and the K intermediate (13-cis retinal), being later extended to the rest of intermediates. They contributed to our understanding of the proton-pumping mechanism of BR by exploiting the sensitivity of fundamental vibrational transitions of the retinal to its conformation. Here, we report on new bands in the 2,500 to 1,800 cm⁻¹ region of the K-BR difference FT-IR spectrum. We show that the bands between 2,500 and 2,300 cm⁻¹ originate from overtone and combination transitions from C-C stretches of the retinal. We assigned bands below 2,300 cm⁻¹ to the combination of retinal C-C stretches with methyl rocks and with hydrogen-out-of-plane vibrations. Remarkably, experimental C-C overtone bands appeared at roughly twice the wavenumber of their fundamentals, with anharmonic mechanical constants ≤3.5 cm⁻¹, and in some cases of ∼1 cm⁻¹. Comparison of combination and fundamental bands indicates that most of the mechanical coupling constants are also very small. Despite the mechanical quasi-harmonicity of the C-C stretches, the area of their overtone bands was only ∼50 to ∼100 times smaller than of their fundamental bands. We concluded that electrical anharmonicity, the second mechanism giving intensity to overtone bands, must be particularly high for the retinal C-C stretches. We corroborated the assignments of negative bands in the K-BR difference FT-IR spectrum by ab initio anharmonic vibrational calculations of all-trans retinal in BR using a quantum-mechanics/molecular mechanics approach, reproducing reasonably well the small experimental anharmonic and coupling mechanical constants. Yet, and in spite accounting for both mechanical and electrical anharmonicities, the intensity of overtone C-C transitions was underestimated by a factor of 4–20, indicating room for improvement in state-of-the-art anharmonic vibrational calculations. The relatively intense overtone and combination bands of the retinal might open the possibility to detect retinal conformational changes too subtle to significantly affect fundamental transitions but leaving a footprint in overtone and combination transitions.

Solvent Effects on Ultrafast Photochemical Pathways

Photochemical reactions are increasingly being used for chemical and materials synthesis, for example, in photoredox catalysis, and generally involve photoexcitation of molecular chromophores dissolved in a liquid solvent. The choice of solvent influences the outcomes of the photochemistry because solute-solvent interactions modify the energies of and crossings between electronic states of the chromophores, and they affect the evolving structures of the photoexcited molecules. Ultrafast laser spectroscopy methods with femtosecond to picosecond time resolution can resolve the dynamics of these photoexcited molecules as they undergo structural and electronic changes, relax back to the ground state, dissipate their excess internal energy to the surrounding solvent, or undergo photochemical reactions. In this Account, we illustrate how experimental studies using ultrafast lasers can reveal the influences that different solvents or cosolutes exert on the photoinduced nonadiabatic dynamics of internal conversion and intersystem crossing in nonradiative relaxation pathways. Although the environment surrounding a solute molecule is rapidly changing, with fluctuations in the coordination to neighboring solvent molecules occurring on femtosecond or picosecond time scales, we show that it is possible to photoexcite selectively only those molecular chromophores transiently experiencing specific solute-solvent interactions such as intermolecular hydrogen bonding.The effects of different solvation environments on the photodynamics are illustrated using four selected examples of photochemical processes in which the solvent has a marked effect on the outcomes. We first consider two aromatic carbonyl compounds, benzophenone and acetophenone, which are known to undergo fast intersystem crossing to populate the first excited triplet state on time scales of a few picoseconds. We show that the nonadiabatic excited-state dynamics are modified by transient hydrogen bonding of the carbonyl group to a protic solvent or by coordination to a metal cation cosolute. We then examine how different solvents modify the competition between two alternative relaxation pathways in a photoexcited UVA-sunscreen molecule, diethylamino hydroxybenzoyl hexyl benzoate (DHHB). This relaxation back to the ground electronic state is an essential part of the effective operation of the sunscreen compound, but the dynamics are sensitive to the surrounding environment. Finally, we consider how solvents of different polarity affect the energies and lifetimes of excited states with locally excited or charge-transfer character in heterocyclic organic compounds used as excited-state electron donors for photoredox catalysis. With these and other examples, we seek to develop a molecular level understanding of how the choice of solution environment might be used to control the outcomes of photochemical reactions.

Distinct electrostatic frequency tuning rates for amide I and amide I' vibrations

Amide I spectroscopy probes the backbone C=O stretch vibrations of peptides and proteins. Amide I spectra are often collected in deuterated water (D₂O) since this provides a cleaner background in the amide I frequency range; such data are often referred to as amide I' spectra since deuteration induces changes in the mode structure, including a roughly ∼10 cm^-1 redshift. For biological samples, however, deuteration is often not possible. As amide I frequency maps are increasingly applied to quantitative protein structural analysis, this raises the interesting challenge of drawing direct connections between amide I and amide I' data. We here analyze amide I and amide I' peak frequencies for a series of dipeptides and related compounds. Changes in protonation state induce large electrostatic shifts in the peak frequencies, allowing us to amass a sizable library of data points for direct amide I/amide I' comparison. While we find an excellent linear correlation between amide I and amide I' peak frequencies, the deuteration-induced shift is smaller for more red-shifted vibrations, indicating different electrostatic tuning rates in the two solvents. H₂O/D₂O shifts were negligible for proline-containing dipeptides that lack exchangeable amide hydrogens, indicating that the intrinsic properties of the solvent do not strongly influence the H/D shift. These findings indicate that the distinct tuning rates observed for the two vibrations arise from modifications to the intrinsic properties of the amide bond and provide (at least for solvated dipeptides) a simple, linear "map" for translating between amide I and amide I' frequencies.

Probing Ligand Effects on the Ultrafast Dynamics of Copper Complexes via Midinfrared Pump-Probe and 2DIR Spectroscopies

The effects of ligand structural variation on the ultrafast dynamics of a series of copper coordination complexes were investigated using polarization-dependent mid-IR pump-probe spectroscopy and two-dimensional infrared (2DIR) spectroscopy. The series consists of three copper complexes [(^R3P₃tren)Cu^IIN₃]BAr₄^F (1^PR3, ^R3P₃tren = tris[2-(phosphiniminato)ethyl]amine, BAr₄^F = tetrakis(pentafluorophenyl)borate) where the number of methyl and phenyl groups in the PR₃ ligand are systematically varied across the series (PR₃ = PMe₃, PMe₂Ph, PMePh₂). The asymmetric stretching mode of azide in the 1^PR3 series is used as a vibrational probe of the small-molecule binding site. The results of the pump-probe measurements indicate that the vibrational energy of azide dissipates through intramolecular pathways and that the bulkier phenyl groups lead to an increase in the spatial restriction of the diffusive reorientation of bound azide. From 2DIR experiments, we characterize the spectral diffusion of the azide group and find that an increase in the number of phenyl groups maps to a broader inhomogeneous frequency distribution (Δ₂). This indicates that an increase in the steric bulk of the secondary coordination sphere acts to create more distinct configurations in the local environment that are accessible to the azide group. This work demonstrates how ligand structural variation affects the ultrafast dynamics of a small molecular group bound to the metal center, which could provide insight into the structure-function relationship of the copper coordination complexes and transition-metal coordination complexes in general.

Simulation of Condensed-Phase Spectroscopy with Near-Term Digital Quantum Computers

Spectroscopy is an indispensable tool for understanding the structures and dynamics of molecular systems. However, computational modeling of spectroscopy is challenging due to the exponential scaling of computational complexity with system sizes unless drastic approximations are made. Quantum computers could potentially overcome these classically intractable computational tasks, but the existing approaches using quantum computers to simulate spectroscopy can only handle isolated and static molecules. In this work, we develop a workflow that combines multi-scale modeling and a time-dependent variational quantum algorithm to compute the linear spectroscopy of systems interacting with their condensed-phase environment via the relevant time correlation function. We demonstrate the feasibility of our approach by numerically simulating the UV-vis absorption spectra of organic semiconductors. We show that our dynamical approach captures several spectral features that are otherwise overlooked by static methods. Our method can be directly used for other linear condensed-phase spectroscopy and could potentially be extended to nonlinear multi-dimensional spectroscopy.

Concerted Motions and Molecular Function: What Physical Chemistry We Can Learn from Light-Driven Ion-Pumping Rhodopsins

Transmembrane ion gradients are generated and maintained by ion-pumping proteins in cells. Light-driven ion-pumping rhodopsins are retinal-containing proteins found in archaea, bacteria, and eukarya. Photoisomerization of the retinal chromophore induces structural changes in the protein, allowing the transport of ions in a particular direction. Understanding unidirectional ion transport by ion-pumping rhodopsins is an exciting challenge for biophysical chemistry. Concerted changes in ion-binding affinities of the ion-binding sites in proteins are key to unidirectional ion transport, as is the coupling between the chromophore and the protein moiety to drive the concerted motions regulating ion-binding affinities. The commonality of ion-pumping rhodopsin protein structures and the diversity of their ion-pumping functions suggest universal principles governing ion transport, which would be widely applicable to molecular systems. In this Perspective, I review the insights obtained from previous studies on rhodopsins and discuss future perspectives.

Ultrafast Structure and Vibrational Dynamics of a Cyano-Containing Non-Fullerene Acceptor for Organic Solar Cells Revealed by Two-Dimensional Infrared Spectroscopy

Non-fullerene molecules, such as ITIC (3,9-bis(2-methylene-(3-(1,1-dicyanomethylene) indanone)-5,5,11,11-tetrakis(4-hexylphenyl)dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']-dithiophene), are among the most promising non-fullerene acceptors for organic solar cells (OSCs). In this work, using the cyano stretching mode as a vibrational marker, the structural and vibrational energy dynamics of ITIC were examined on an ultrafast time scale with two-dimensional infrared spectroscopy. Two IR-active modes studied here mainly correspond to two anti-symmetric combinations of symmetric and asymmetric stretching vibrations of two C≡N modes originating from two -C(CN)₂ chromophores that are located across the ITIC system, which were found to have significantly larger off-diagonal anharmonicity than their corresponding diagonal anharmonicities. This indicates strong anharmonic vibrational coupling between the two modes, which is supported by ab initio anharmonic frequency computations. Transient IR results indicate picosecond intramolecular vibrational energy transfer between the two C≡N modes upon excitation. The structural basis for these vibrational and energetic features is the conjugating molecular frame that is composed of a network of single/double bonds connecting the two -C(CN)₂ chromophores and may enable efficient vibration delocalization, in addition to its well-known electron delocalization capability. The importance of the results for the OSC applications is discussed.

Lanthanide-dependent coordination interactions in lanmodulin: a 2D IR and molecular dynamics simulations study

The biological importance of lanthanides, and the early lanthanides (La³⁺-Nd³⁺) in particular, has only recently been recognized, and the structural principles underlying selective binding of lanthanide ions in biology are not yet well established. Lanmodulin (LanM) is a novel protein that displays unprecedented affinity and selectivity for lanthanides over most other metal ions, with an uncommon preference for the early lanthanides. Its utilization of EF-hand motifs to bind lanthanides, rather than the Ca²⁺ typically recognized by these motifs in other proteins, has led it to be used as a model system to understand selective lanthanide recognition. Two-dimensional infrared (2D IR) spectroscopy combined with molecular dynamics simulations were used to investigate LanM's selectivity mechanisms by characterizing local binding site geometries upon coordination of early and late lanthanides as well as calcium. These studies focused on the protein's uniquely conserved proline residues in the second position of each EF-hand binding loop. We found that these prolines constrain the EF-hands for strong coordination of early lanthanides. Substitution of this proline results in a more flexible binding site to accommodate a larger range of ions but also results in less compact coordination geometries and greater disorder within the binding site. Finally, we identify the conserved glycine in the sixth position of each EF-hand as a mediator of local binding site conformation and global secondary structure. Uncovering fundamental structure-function relationships in LanM informs the development of synthetic biology technologies targeting lanthanides in industrial applications.

Structural dynamics and vibrational feature of N-Acetyl-d-glucosamine in aqueous solution

Molecular dynamics simulations and DFT calculations were performed for the demonstration of the structural dynamics and vibrational feature of N-Acetyl-d-glucosamine (NAG) in solution phase. The interactions between NAG and solvent molecules were evaluated through spatial distribution function and radial distribution function, and the preferred conformations of NAG in aqueous solution were revealed by cluster analysis. Results from normal mode analysis show that the solvent induced structural fluctuation of NAG could be reflected in the vibrational feature of specific chromophores, thus we can evaluate the molecular structure with the help of its vibrational signature based on the built correlation between molecular structure and vibrational frequencies of specific groups.

Identical Water Dynamics in Acrylamide Hydrogels, Polymers, and Monomers in Solution: Ultrafast IR Spectroscopy and Molecular Dynamics Simulations

The dynamics and structure of water in polyacrylamide hydrogels (PAAm-HG), polyacrylamide, and acrylamide solutions are investigated using ultrafast infrared experiments on the OD stretch of dilute HOD/H₂O and molecular dynamics simulations. The amide moiety of the monomer/polymers interacts strongly with water through hydrogen bonding (H-bonding). The FT-IR spectra of the three systems indicate that the range of H-bond strengths is relatively unchanged from bulk water. Vibrational population relaxation measurements show that the amide/water H-bonds are somewhat weaker but fall within the range of water/water H-bond strengths. A previous study of water dynamics in PAAm-HG suggested that the slowing observed was due to increasing confinement with concentration. Here, for the same concentrations of the amide moiety, the experimental results demonstrate that the reorientational dynamics (infrared pump-probe experiments) and structural dynamics (two-dimensional infrared spectroscopy) are identical in the three acrylamide systems studied. Molecular dynamics simulations of the water orientational relaxation in aqueous solutions of the acrylamide monomer, trimer, and pentamer are in good agreement with the experimental results and are essentially chain length independent. The simulations show that there is a slower, low-amplitude (<7%) decay component not accessible by the experiments. The simulations examine the dynamics and structure of water H-bonded to acrylamide, in the first solvent shell, and beyond for acrylamide monomers and short chains. The experiments and simulations show that the slowing of water dynamics in PAAm-HG is not caused by confinement in the polymer network but rather by interactions with individual acrylamide moieties.

Nanopore sensing: A physical-chemical approach

Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.

Ultrafast vibrational dynamics of the tyrosine ring mode and its application to enkephalin insertion into phospholipid membranes as probed by two-dimensional infrared spectroscopy

Enkephalins are small opioid peptides whose binding conformations are catalyzed by phospholipid membranes. Binding to opioid receptors is determined by the orientation of tyrosine and phenylalanine side chains. In this work, we investigate the effects of different charged phospholipid headgroups on the insertion of the tyrosine side chain into a lipid bilayer using a combination of 2D IR spectroscopy, anharmonic DFT calculations, and third order response function modeling. The insertion is probed by using the ∼1515 cm^-1 tyrosine ring breathing mode, which we found exhibits rich vibrational dynamics on the picosecond timescale. These dynamics include rapid intramolecular vibrational energy redistribution (IVR), where some of the energy ends up in a dark state that shows up as an anharmonically shifted combination band. The waiting-time dependent 2D IR spectra also show an unusual line shape distortion that affects the extraction of the frequency-frequency correlation function (FFCF), which is the dynamic observable of interest that reflects the tyrosine side chain's insertion into the lipid bilayer. We proposed three models to account for this distortion: a hot-state exchange model, a local environment dependent IVR model, and a coherence transfer model. A qualitative analysis of these models suggests that the local environment dependent IVR rate best explains the line shape distortion, while the coherence transfer model best reproduced the effects on the FFCF. Even with these complex dynamics, we found that the tyrosine ring mode's FFCF is qualitatively correlated with the degree of insertion expected from the different phospholipid headgroups.

Application of 2D IR Bioimaging: Hyperspectral Images of Formalin-Fixed Pancreatic Tissues and Observation of Slow Protein Degradation

We used two-dimensional IR bioimaging to study the structural heterogeneity of formalin-fixed mouse pancreas. Images were generated from the hyperspectral data sets by plotting quantities associated with the amide I vibrational mode, which is created by the backbone carbonyl stretch. Images that measure the fundamental vibrational frequencies, cross peaks, and anharmonic shifts are presented. Histograms are generated for each quantity, providing averaged values and distributions around the mean that serve as metrics for protein structures. Images were generated from tissue that had been stored in a formalin fixation for 3, 8, and 48 weeks. Over this period, all three metrics show that that the β-sheet content of the samples increased, consistent with protein aggregation. Our results indicate that formalin fixation does not entirely arrest the degradation of a protein structure in pancreas tissue.

Pump Slice Amplitudes: A Simple and Robust Method for Connecting Two-Dimensional Infrared and Fourier Transform Infrared Spectra

Ultrafast two-dimensional infrared (2D IR) spectroscopy and Fourier transform infrared (FTIR) spectroscopy are often performed in tandem, with FTIR typically used to interpret and provide hypotheses for 2D IR experiments. Comparisons between 2D IR and FTIR spectra can also be used to examine the structure and orientation in systems of coupled vibrational chromophores. The most common method for comparing 2D IR and FTIR lineshapes, the diagonal slice method, contains significant artifacts when applied to oscillators with low anharmonicities. Here, we introduce a new technique, the pump slice amplitude (PSA) method, for relating 2D IR lineshapes to FTIR lineshapes and compare PSAs against diagonal slices using theoretical and experimental spectra. We find that PSAs are significantly more similar to FTIR lineshapes than diagonal slices in systems with low anharmonicity.

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.

Protein Dynamics by Two-Dimensional Infrared Spectroscopy

Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.

Substituent Effects on the Vibrational Properties of the CN Stretch Mode of Aromatic Nitriles: IR Probes Useful for Time-resolved IR Spectroscopy

Developing ideal IR probes is essential to understand the structure and dynamics of biomolecules with time-resolved IR spectroscopies and imaging techniques. Especially, nitrile (CN) group has recently been proposed to serve as IR probes of the local environment of proteins. Herein, we investigated the effect of a substituent on the vibrational properties of the benzonitrile. The electron-donating and withdrawing character of p-substituent on benzonitrile are expected to modulate the vibrational frequency, molar extinction coefficient, and vibrational lifetime of CN probe. FT-IR revealed the positive correlation between electron-donating character and the molar extinction coefficient of CN stretch mode. Infrared pump-probe (IR-PP) measurements showed that the vibrational lifetime of CN stretch mode exhibits a relatively weak correlation with the electron-donating strength. Among the investigated samples, 4-dimethylamino benzonitrile with the strongest electron-donating strength shows enhanced absorption and extended vibrational lifetime. Utilizing substituent effects will be a practical strategy to improve the performance of the IR probe.

Advances in Application of Azobenzene as a Trigger in Biomedicine: Molecular Design and Spontaneous Assembly

Azobenzene is a well-known derivative of stimulus-responsive molecular switches and has shown superior performance as a functional material in biomedical applications. The results of multiple studies have led to the development of light/hypoxia-responsive azobenzene for biomedical use. In recent years, long-wavelength-responsive azobenzene has been developed. Matching the longer wavelength absorption and hypoxia-response characteristics of the azobenzene switch unit to the bio-optical window results in a large and effective stimulus response. In addition, azobenzene has been used as a hypoxia-sensitive connector via biological cleavage under appropriate stimulus conditions. This has resulted in on/off state switching of properties such as pharmacology and fluorescence activity. Herein, recent advances in the design and fabrication of azobenzene as a trigger in biomedicine are summarized.

Distinguishing steric and electrostatic molecular probe orientational ordering via their effects on reorientation-induced spectral diffusion

The theoretical framework for reorientation-induced spectral diffusion (RISD) describes the polarization dependence of spectral diffusion dynamics as measured with two-dimensional (2D) correlation spectroscopy and related techniques. Generally, RISD relates to the orientational dynamics of the molecular chromophore relative to local electric fields of the medium. The predictions of RISD have been shown to be very sensitive to both restricted orientational dynamics (generally arising from steric hindrance) and the distribution of local electric fields relative to the probe (electrostatic ordering). Here, a theory that combines the two effects is developed analytically and supported with numerical calculations. The combined effects can smoothly vary the polarization dependence of spectral diffusion from the purely steric case (least polarization dependence) to the purely electrostatic case (greatest polarization dependence). Analytic approximations of the modified RISD equations were also developed using the orientational dynamics of the molecular probe and two order parameters describing the degree of electrostatic ordering. It was found that frequency-dependent orientational dynamics are a possible consequence of the combined electrostatic and steric effects, providing a test for the applicability of this model to experimental systems. The modified RISD equations were then used to successfully describe the anomalous polarization-dependent spectral diffusion seen in 2D infrared spectroscopy in a polystyrene oligomer system that exhibits frequency-dependent orientational dynamics. The degree of polarization-dependent spectral diffusion enables the extent of electrostatic ordering in a chemical system to be quantified and distinguished from steric ordering.

Theory of two-dimensional spectroscopy with intense laser fields

Two-dimensional vibrational and electronic spectroscopic observables of isotropically oriented molecular samples in solution are sensitive to laser field intensities and polarization. The third-order response function formalism predicts a signal that grows linearly with the field strength of each laser pulse, thus lacking a way of accounting for non-trivial intensity-dependent effects, such as saturation and finite bleaching. An analytical expression to describe the orientational part of the molecular response, which, in the weak-field limit, becomes equivalent to a four-point correlation function, is presented. Such an expression is evaluated for Liouville-space pathways accounting for diagonal and cross peaks for all-parallel and cross-polarized pulse sequences, in both the weak- and strong-field conditions, via truncation of a Taylor series expansion at different orders. The results obtained in the strong-field conditions suggest how a careful analysis of two-dimensional spectroscopic experimental data should include laser pulse intensity considerations when determining molecular internal coordinates.

Coupling chemical biology and vibrational spectroscopy for studies of amyloids in vitro and in cells

Amyloid diseases are characterized by the aggregation of various proteins to form insoluble β-sheet-rich fibrils leading to cell death. Vibrational spectroscopies have emerged as attractive methods to study this process because of the rich structural information that can be extracted without large, perturbative probes. Importantly, specific vibrations such as the amide-I band directly report on secondary structure changes, which are key features of amyloid formation. Beyond intrinsic vibrations, the incorporation of unnatural vibrational probes can improve sensitivity for secondary structure determination (e.g. isotopic labeling), can provide residue-specific information of the surrounding polarity (e.g. unnatural amino acid), and are translatable into cellular studies. Here, we review the latest studies that have leveraged tools from chemical biology for the incorporation of novel vibrational probes into amyloidogenic proteins for both mechanistic and cellular studies.

Elucidating the mechanism behind the infrared spectral features and dynamics observed in the carbonyl stretch region of organic carbonates interacting with lithium ions

Ultrafast infrared spectroscopy has become a very important tool for studying the structure and ultrafast dynamics in solution. In particular, it has been recently applied to investigate the molecular interactions and motions of lithium salts in organic carbonates. However, there has been a discrepancy in the molecular interpretation of the spectral features and dynamics derived from these spectroscopies. Hence, the mechanism behind spectral features appearing in the carbonyl stretching region was further investigated using linear and nonlinear spectroscopic tools and the co-solvent dilution strategy. Lithium perchlorate in a binary mixture of dimethyl carbonate (DMC) and tetrahydrofuran was used as part of the dilution strategy to identify the changes of the spectral features with the number of carbonates in the first solvation shell since both solvents have similar interaction energetics with the lithium ion. Experiments showed that more than one carbonate is always participating in the lithium ion solvation structures, even at the low concentration of DMC. Moreover, temperature-dependent study revealed that the exchange of the solvent molecules coordinating the lithium ion is not thermally accessible at room temperature. Furthermore, time-resolved IR experiments confirmed the presence of vibrationally coupled carbonyl stretches among coordinated DMC molecules and demonstrated that this process is significantly altered by limiting the number of carbonate molecules in the lithium ion solvation shell. Overall, the presented experimental findings strongly support the vibrational energy transfer as the mechanism behind the off-diagonal features appearing on the 2DIR spectra of solutions of lithium salt in organic carbonates.

A Machine-Learning Protocol for Ultraviolet Protein-Backbone Absorption Spectroscopy under Environmental Fluctuations

Ultraviolet (UV) absorption spectra are commonly used for characterizing the global structure of proteins. However, the theoretical interpretation of UV spectra is hindered by the large number of required expensive ab initio calculations of excited states spanning a huge conformation space. We present a machine-learning (ML) protocol for far-UV (FUV) spectra of proteins, which can predict FUV spectra of proteins with comparable accuracy to density functional theory (DFT) calculations but with 3-4 orders of magnitude reduced computational cost. It further shows excellent predictive power and transferability that can be used to probe structural mutations and protein folding pathways.

Bursting the bubble: A molecular understanding of surfactant-water interfaces

Surfactant science has historically emphasized bulk, thermodynamic measurements to understand the microemulsion properties of greatest industrial significance, such as interfacial tensions, phase behavior, and thermal stability. Recently, interest in the molecular properties of surfactants has grown among the physical chemistry community. This has led to the application of cutting-edge spectroscopic methods and advanced simulations to understand the specific interactions that give rise to the previously studied bulk characteristics. In this Perspective, we catalog key findings that describe the surfactant-oil and surfactant-water interfaces in molecular detail. We emphasize the role of ultrafast spectroscopic methods, including two-dimensional infrared spectroscopy and sum-frequency-generation spectroscopy, in conjunction with molecular dynamics simulations, and the role these techniques have played in advancing our understanding of interfacial properties in surfactant microemulsions.

Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity

We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic molecular dynamics simulations and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer can be experimentally resolved. Our model reveals two significant conformations to the dimer: a dominant native state consistent with other experimental structures of the dimer and a twisted state with a structure that appears to reflect a ∼55° clockwise rotation of the native dimer interface. The twisted state primarily influences the contacts involving the C-terminus of insulin's B chain, shifting the registry of its intermolecular hydrogen bonds and reorganizing its side-chain packing. The MSM kinetics predict that these configurations exchange on a 14 μs time scale, largely passing through two Markov states with a solvated dimer interface. Computational amide I spectroscopy of site-specifically ¹³C¹⁸O labeled amides indicates that the native and twisted conformation can be distinguished through a series of single and dual labels involving the B24F, B25F, and B26Y residues. Additional structural heterogeneity and disorder is observed within the native and twisted states, and amide I spectroscopy can also be used to gain insight into this variation. This study will provide important interpretive tools for IR spectroscopic investigations of insulin structure and transient IR kinetics experiments studying the conformational dynamics of insulin dimer.

The molecular pH-response mechanism of the plant light-stress sensor PsbS

Plants need to protect themselves from excess light, which causes photo-oxidative damage and lowers the efficiency of photosynthesis. Photosystem II subunit S (PsbS) is a pH sensor protein that plays a crucial role in plant photoprotection by detecting thylakoid lumen acidification in excess light conditions via two lumen-faced glutamates. However, how PsbS is activated under low-pH conditions is unknown. To reveal the molecular response of PsbS to low pH, here we perform an NMR, FTIR and 2DIR spectroscopic analysis of Physcomitrella patens PsbS and of the E176Q mutant in which an active glutamate has been replaced. The PsbS response mechanism at low pH involves the concerted action of repositioning of a short amphipathic helix containing E176 facing the lumen and folding of the luminal loop fragment adjacent to E71 to a 310-helix, providing clear evidence of a conformational pH switch. We propose that this concerted mechanism is a shared motif of proteins of the light-harvesting family that may control thylakoid inter-protein interactions driving photoregulatory responses.

A Genetically Encoded Two-Dimensional Infrared Probe for Enzyme Active-Site Dynamics

While two-dimensional infrared (2D-IR) spectroscopy is uniquely suitable for monitoring femtosecond (fs) to picosecond (ps) water dynamics around static protein structures, its utility for probing enzyme active-site dynamics is limited due to the lack of site-specific 2D-IR probes. We demonstrate the genetic incorporation of a novel 2D-IR probe, m-azido-L-tyrosine (N3Y) in the active-site of DddK, an iron-dependent enzyme that catalyzes the conversion of dimethylsulfoniopropionate to dimethylsulphide. Our results show that both the oxidation of active-site iron to Fe^III , and the addition of denaturation reagents, result in significant decrease in enzyme activity and active-site water motion confinement. As tyrosine residues play important roles, including as general acids and bases, and electron transfer agents in many key enzymes, the genetically encoded 2D-IR probe N3Y should be broadly applicable to investigate how the enzyme active-site motions at the fs-ps time scale direct reaction pathways to facilitating specific chemical reactions.

Differentiation of bacterial spores via 2D-IR spectroscopy

Ultrafast 2D-IR spectroscopy is a powerful tool for understanding the spectroscopy and dynamics of biological molecules in the solution phase. A number of recent studies have begun to explore the utility of the information-rich 2D-IR spectra for analytical applications. Here, we report the application of ultrafast 2D-IR spectroscopy for the detection and classification of bacterial spores. 2D-IR spectra of Bacillus atrophaeus and Bacillus thuringiensis spores as dry films on CaF₂ windows were obtained. The sporulated nature of the bacteria was confirmed using 2D-IR diagonal and off-diagonal peaks arising from the calcium dipicolinate CaDP·3H₂O biomarker for sporulation. Distinctive peaks, in the protein amide I region of the spectrum were used to differentiate the two types of spore. The identified marker modes demonstrate the potential for the use of 2D-IR methods as a direct means of spore classification. We discuss these new results in perspective with the current state of analytical 2D-IR measurements, showing that the potential exists to apply 2D-IR spectroscopy to detect the spores on surfaces and in suspensions as well as in dry films. The results demonstrate how applying 2D-IR screening methodologies to spores would enable the creation of a library of spectra for classification purposes.

Dynamics underlying hydroxylation selectivity of cytochrome P450cam

Structural heterogeneity and the dynamics of the complexes of enzymes with substrates can determine the selectivity of catalysis; however, fully characterizing how remains challenging as heterogeneity and dynamics can vary at the spatial level of an amino acid residue and involve rapid timescales. We demonstrate the nascent approach of site-specific two-dimensional infrared (IR) spectroscopy to investigate the archetypical cytochrome P450, P450cam, to better delineate the mechanism of the lower regioselectivity of hydroxylation of the substrate norcamphor in comparison to the native substrate camphor. Specific locations are targeted throughout the enzyme by selectively introducing cyano groups that have frequencies in a spectrally isolated region of the protein IR spectrum as local vibrational probes. Linear and two-dimensional IR spectroscopy were applied to measure the heterogeneity and dynamics at each probe and investigate how they differentiate camphor and norcamphor recognition. The IR data indicate that the norcamphor complex does not fully induce a large-scale conformational change to a closed state of the enzyme adopted in the camphor complex. Additionally, a probe directed at the bound substrate experiences rapidly interconverting states in the norcamphor complex that explain the hydroxylation product distribution. Altogether, the study reveals large- and small-scale structural heterogeneity and dynamics that could contribute to selectivity of a cytochrome P450 and illustrates the approach of site-selective IR spectroscopy to elucidate protein dynamics.

Optical and Infrared Spectroelectrochemical Studies of CN-Substituted Bipyridyl Complexes of Ruthenium(II)

Ruthenium(II) polypyridyl complexes [Ru(CN-Me-bpy)_x(bpy)_3-x]²⁺ (CN-Me-bpy = 4,4'-dicyano-5,5'-dimethyl-2,2'-bipyridine, bpy = 2,2'-bipyridine, and x = 1-3, abbreviated as 1²⁺, 2²⁺, and 3²⁺) undergo four (1²⁺) or five (2²⁺ and 3²⁺) successive one-electron reduction steps between -1.3 and -2.75 V versus ferrocenium/ferrocene (Fc⁺/Fc) in tetrahydrofuran. The CN-Me-bpy ligands are reduced first, with successive one-electron reductions in 2²⁺ and 3²⁺ being separated by 150-210 mV; reduction of the unsubstituted bpy ligand in 1²⁺ and 2²⁺ occurs only when all CN-Me-bpy ligands have been converted to their radical anions. Absorption spectra of the first three reduction products of each complex were measured across the UV, visible, near-IR (NIR), and mid-IR regions and interpreted with the help of density functional theory calculations. Reduction of the CN-Me-bpy ligand shifts the ν(C≡N) IR band by ca. -45 cm^-1, enhances its intensity ∼35 times, and splits the symmetrical and antisymmetrical modes. Semireduced complexes containing two and three CN-derivatized ligands 2⁺, 3⁺, and 3⁰ show distinct ν(C≡N) features due to the presence of both CN-Me-bpy and CN-Me-bpy^•-, confirming that each reduction is localized on a single ligand. NIR spectra of 1⁰, 1^-, and 2^- exhibit a prominent band attributable to the CN-Me-bpy^•- moiety between 6000 and 7500 cm^-1, whereas bpy^•--based absorption occurs between 4500 and 6000 cm^-1; complexes 2⁺, 3⁺, and 3⁰ also exhibit a band at ca. 3300 cm^-1 due to a CN-Me-bpy^•- → CN-Me-bpy interligand charge-transfer transition. In the UV-vis region, the decrease of π → π* intraligand bands of the neutral ligands and the emergence of the corresponding bands of the radical anions are most diagnostic. The first reduction product of 1²⁺ is spectroscopically similar to the lowest triplet metal-to-ligand charge-transfer excited state, which shows pronounced NIR absorption, and its ν(C≡N) IR band is shifted by -38 cm^-1 and 5-7-fold-enhanced relative to the ground state.

Membrane-dependent amyloid aggregation of human BAX α9 (173-192)

Mitochondrial outer membrane permeabilization, which is a critical step in apoptosis, is initiated upon transmembrane insertion of the C-terminal α-helix (α9) of the proapoptotic Bcl-2 family protein BAX. The isolated α9 fragment (residues 173-192) is also competent to disrupt model membranes, and the structures of its membrane-associated oligomers are of interest in understanding the potential roles of this sequence in apoptosis. Here, we used ultrafast two-dimensional infrared (2D IR) spectroscopy, thioflavin T binding, and transmission electron microscopy to show that the synthetic BAX α9 peptide (α9p) forms amyloid aggregates in aqueous environments and on the surfaces of anionic small unilamellar vesicles. Its inherent amyloidogenicity was predicted by sequence analysis, and 2D IR spectra reveal that vesicles modulate the β-sheet structures of insoluble aggregates, motivating further examination of the formation or suppression of BAX amyloids in apoptosis.