Extended timescale 2D IR probes of proteins: p-cyanoselenophenylalanine

The Long and Short of Coupling and Uncoupling via 2D IR Spectroscopy

Determining dynamic structural changes along with the functional movements in biological systems has been a significant challenge for scientists for several decades. Utilizing vibrational coupling with the aid of 2D IR probe pairs has aided in uncovering structural dynamics and functional roles of chemical moieties involved in actions such as membrane peptide folding and transport, ion and water transport, and drug-protein interactions. Both native and non-native vibrational probe pairs have been developed for infrared studies, and their efficacy has been tested in various systems. With these probe pairs, 2D IR spectroscopy captures frozen snapshots of the structural events involved in biological function through vibrational coupling and correlated spectral diffusion. In this Perspective, different treatments of vibrational coupling and coupling models will be addressed, and a review of some of the specific vibrational probe pairs used to study these coupling mechanisms is presented. Overall, the intrinsic molecular dynamics detected on these ultrafast time scales will provide an atomic level view of how chosen structures traverse reaction paths. Thus, it is important to evaluate and assess the accuracy of the different vibrational coupling models and their consistency with the prediction of different molecular structures.

Facile Generation of Cyanoselenocysteine as a Vibrational Label for Measuring Protein Dynamics on Longer Time Scales by 2D IR Spectroscopy

Two-dimensional infrared (2D IR) spectroscopy is a powerful technique for measuring molecular heterogeneity and dynamics with a high spatiotemporal resolution. The methods can be applied to characterize specific residues of proteins by incorporating frequency-resolved vibrational labels. However, the time scale of dynamics that 2D IR spectroscopy can measure is limited by the vibrational label's excited-state lifetime due to the decay of 2D IR absorption bands. To extend this time scale, vibrational labels with longer lifetimes are sought. An effective approach to inhibiting intramolecular energy relaxation is to isolate the vibration from the rest of the molecule by inserting a heavy atom bridge. Although this strategy has been demonstrated through the generation of functionalized amino acids, a straightforward route to their selective incorporation into proteins is often unclear. A facile approach for the attachment of a cyano group at cysteine to generate a thiocyanate has contributed to its adoption as a vibrational label of proteins. We demonstrate that an analogous route can be used for introducing cyanoselenocysteine to generate a selenocyanate vibrational label containing a heavier bridge atom. We confirm by infrared pump-probe and 2D IR spectroscopy longer vibrational lifetimes of 100-250 ps, depending on the solvent, which enable the collection of 2D IR spectra to measure frequency dynamics on longer time scales.

Linear and Two-Dimensional Infrared Spectroscopy of the Multifunctional Vibrational Probe, 3-(4-Azidophenyl) Propiolonitrile. Deperturbing a Fermi Triad by Isotopic Substitution

Infrared probes are chemical moieties whose vibrational modes are used to obtain spectroscopic information about structural dynamics of complex systems; in particular, of biomacromolecules. Here, we explore the vibrational spectroscopy and dynamics of a reagent, 3-(4-azidophenyl)propiolonitrile (AzPPN), for selectively tagging thiols in protein environments with a multifunctional infrared probe containing both, an azide and a nitrile chromophore. The linear infrared spectrum of AzPPN is heavily perturbed in the antisymmetric azide stretching region as a result of accidental Fermi resonances. Isotopically labeling the azide group at the β-position deperturbs the spectrum considerably and reveals two combination tones that mix with the antisymmetric stretching fundamental into a Fermi triad of hybrid vibrational excitations. Moreover, two-dimensional infrared (2DIR) spectra were recorded for 15Nβ-labeled AzPPN, which reveal waiting-time-dependent spectral shifts of diagonal peaks and dynamic buildups of cross peaks. The 2DIR-spectral evolution is indicative of intramolecular distribution of the pump-induced excess vibrational energy into low-frequency modes of the molecule that are coupled to either the azide or the nitrile stretching transition dipoles. Finally, IR-pump/IR-probe spectra with selective narrowband excitation reveal a time constant of 2.3 ps for intramolecular vibrational redistribution (IVR) and 18 ps for the final energy dissipation into the solvent. The cross-peak dynamics corroborate a notion in which IVR within the AzPPN-molecule is an irreversible process.

Vibrational heavy atom effect on relaxation and solvent shell dynamics in group VIII trimetallic carbonyls

Infrared pump-probe and two-dimensional infrared (2D-IR) spectroscopies were used to study the vibrational dynamics of a homologous set of trimetallic dodecacarbonyls with increasingly heavy atomic masses in tetrahydrofuran solution. The vibrational lifetimes showed some evidence of the vibrational heavy atom effect (VHAE) but were not consistent across the sample set. Spectral diffusion was measured by 2D-IR spectroscopy to investigate whether the changes produced by the VHAE had influenced other aspects of vibrational dynamics. The triiron species was found to be more dynamic on very fast timescales and may exhibit evidence of a transient bridging CO structure. Centerline slope analysis of the high-frequency CO peak for each complex revealed that the vibrational dynamics were subtly but consistently slowed for the compounds with heavier metal atoms.

Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

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.

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.

Enhancing Alkyne-Based Raman Tags with a Sulfur Linker

Alkyne-based Raman tags have proven their utility for biological imaging. Although the alkynyl stretching mode is a relatively strong Raman scatterer, the detection sensitivity of alkyne-tagged compounds is ultimately limited by the magnitude of the probe's Raman response. In order to improve the performance of alkyne-based Raman probes, we have designed several tags that benefit from π-π conjugation as well as from additional n-π conjugation with a sulfur linker. We show that the sulfur linker provides additional enhancement and line width narrowing, offering a simple yet effective strategy for improving alkyne-based Raman tags. We validate the utility of various sulfur-linked alkyne tags for cellular imaging through stimulated Raman scattering microscopy.

Interdomain Interactions Modulate the Active Site Dynamics of Human Inducible Nitric Oxide Synthase

Nitric oxide synthase (NOS) is a homodimeric flavohemoprotein responsible for catalyzing the oxidation of l-arginine (l-Arg) to citrulline and nitric oxide. Electrons are supplied for the reaction via interdomain electron transfer between an N-terminal heme-containing oxygenase domain and a FMN-containing (sub)domain of a C-terminal reductase domain. Extensive attention has focused on elucidating how conformational dynamics regulate electron transfer between the domains. Here we investigate the impact of the interdomain FMN-heme interaction on the heme active site dynamics of inducible NOS (iNOS). Steady state linear and time-resolved two-dimensional infrared (2D IR) spectroscopy was applied to probe a CO ligand at the heme within the oxygenase domain for full-length and truncated or mutated constructs of human iNOS. Whereas the linear IR spectra of the CO ligand were identical among the constructs, 2D IR spectroscopy revealed variation in the frequency dynamics. The wild-type constructs that can properly form the FMN/oxygenase docked state due to the presence of both the FMN and oxygenase domains showed slower dynamics than the oxygenase domain alone. Introduction of the mutation (E546N) predicted to perturb electrostatic interactions between the domains resulted in measured dynamics intermediate between those for the full-length and individual oxygenase domain, consistent with perturbation to the docked/undocked equilibrium. These results indicate that docking of the FMN domain to the oxygenase domain not only brings the FMN cofactor within electron transfer distance of the heme domain but also modulates the dynamics sensed by the CO ligand within the active site in a way expected to promote efficient electron transfer.

Versatile Vibrational Energy Sensors for Proteins

Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.

Characterization of Acetonitrile Isotopologues as Vibrational Probes of Electrolytes

Acetonitrile has emerged as a solvent candidate for novel electrolyte formulations in metal-ion batteries and supercapacitors. It features a bright local C≡N stretch vibrational mode whose infrared (IR) signature is sensitive to battery-relevant cations (Li⁺, Mg²⁺, Zn²⁺, Ca²⁺) both in pure form and in the presence of water admixture across a full possible range of concentrations from the dilute to the superconcentrated regime. Stationary and time-resolved IR spectroscopy thus emerges as a natural tool to study site-specific intermolecular interactions from the solvent perspective without introducing an extrinsic probe that perturbs solution morphology and may not represent the intrinsic dynamics in these electrolytes. The metal-coordinated acetonitrile, water-separated metal-acetonitrile pair, and free solvent each have a distinct vibrational signature that allows their unambiguous differentiation. The IR band frequency of the metal-coordinated acetonitrile depends on the ion charge density. To study the ion transport dynamics, it is necessary to differentiate energy-transfer processes from structural interconversions in these electrolytes. Isotope labeling the solvent is a necessary prerequisite to separate these processes. We discuss the design principles and choice of the CD₃¹³CN label and characterize its vibrational spectroscopy in these electrolytes. The Fermi resonance between ¹³C≡N and C-D stretches complicates the spectral response but does not prevent its effective utilization. Time-resolved two-dimensional (2D) IR spectroscopy can be performed on a mixture of acetonitrile isotopologues and much can be learned about the structural dynamics of various species in these formulations.

Long Vibrational Lifetime R-Selenocyanate Probes for Ultrafast Infrared Spectroscopy: Properties and Synthesis

Ultrafast infrared vibrational spectroscopy is widely used for the investigation of dynamics in systems from water to model membranes. Because the experimental observation window is limited to a few times the probe's vibrational lifetime, a frequent obstacle for the measurement of a broad time range is short molecular vibrational lifetimes (typically a few to tens of picoseconds). Five new long-lifetime aromatic selenocyanate vibrational probes have been synthesized and their vibrational properties characterized. These probes are compared to commercial phenyl selenocyanate. The vibrational lifetimes range between ∼400 and 500 ps in complex solvents, which are some of the longest room-temperature vibrational lifetimes reported to date. In contrast to vibrations that are long-lived in simple solvents such as CCl₄, but become much shorter in complex solvents, the probes discussed here have ∼400 ps lifetimes in complex solvents and even longer in simple solvents. One of them has a remarkable lifetime of 1235 ps in CCl₄. These probes have a range of molecular sizes and geometries that can make them useful for placement into different complex materials due to steric reasons, and some of them have functionalities that enable their synthetic incorporation into larger molecules, such as industrial polymers. We investigated the effect of a range of electron-donating and electron-withdrawing para-substituents on the vibrational properties of the CN stretch. The probes have a solvent-independent linear relationship to the Hammett substituent parameter when evaluated with respect to the CN vibrational frequency and the ipso ¹³C NMR chemical shift.

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.

Computing the frequency fluctuation dynamics of highly coupled vibrational transitions using neural networks

The description of frequency fluctuations for highly coupled vibrational transitions has been a challenging problem in physical chemistry. In particular, the complexity of their vibrational Hamiltonian does not allow us to directly derive the time evolution of vibrational frequencies for these systems. In this paper, we present a new approach to this problem by exploiting the artificial neural network to describe the vibrational frequencies without relying on the deconstruction of the vibrational Hamiltonian. To this end, we first explored the use of the methodology to predict the frequency fluctuations of the amide I mode of N-methylacetamide in water. The results show good performance compared with the previous experimental and theoretical results. In the second part, the neural network approach is used to investigate the frequency fluctuations of the highly coupled carbonyl stretch modes for the organic carbonates in the solvation shell of the lithium ion. In this case, the frequency fluctuation predicted by the neural networks shows a good agreement with the experimental results, which suggests that this model can be used to describe the dynamics of the frequency in highly coupled transitions.

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.

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.

Two-dimensional IR spectroscopy reveals a hidden Fermi resonance band in the azido stretch spectrum of β-azidoalanine

Azido stretch modes in a variety of azido-derivatized nonnatural amino acids and nucleotides have been used as a site-specific infrared (IR) probe for monitoring changes in their conformations and local electrostatic environments. The vibrational bands of azide probes are often accompanied by complex line shapes with shoulder peaks, which may arise either from incomplete background subtraction, Fermi resonance, or multiple conformers. The isotope substitution in the infrared probe has thus been introduced to remove Fermi resonances without causing a significant perturbation to the structure. Here, we synthesized and labeled the mid-N atoms of aliphatic azide derivatives with 15N to study the effects of isotope labelling on their vibrational properties. The FT-IR spectra of the aliphatic azide with asymmetric lineshape became a single symmetric band upon isotope substitution, which might be an indication of the removal of the hidden Fermi resonance from the system. We also noticed that the 2D-IR spectrum of unlabeled aliphatic azide has cross-peaks, even though it is not apparently identifiable. The 1D slice spectra obtained from the 2D-IR spectra reveal the existence of a hidden Fermi resonance peak. Furthermore, we show that this weak Fermi resonance does not produce discernible oscillatory beating patterns in the IR pump-probe spectrum, which has been used as evidence of the Fermi resonance. Therefore, we confirm that isotope labelling combined with 2D-IR spectroscopy is the most efficient and incisive way to identify the origin of small shoulder peaks in the linear and nonlinear vibrational spectra of various IR probe molecules.

Extending the vibrational lifetime of azides with heavy atoms

The development of novel vibrational reporters (VRs), aka infrared (IR) probes, to study local environments and dynamic processes in biomolecules and materials continues to be an important area of research. Azides are important VRs because of their small size and large transition dipole strengths, however, their relatively short vibrational lifetimes (<2 ps) have limited their full potential. Herein we report that the vibrational lifetimes of azides can be increased by attaching them to heavy atoms and by using heavy 15N isotopes. Three group 14 atom triphenyl azides (Ph3CN3, Ph3SiN3, Ph3SnN3), and their triple-15N isotopomers, were synthesized in good yields. Tributyltin azide and its heavy isotopomer (Bu3Sn15N3) were also prepared to probe the effect of molecular scaffolding. The extinction coefficients for the natural abundance azides were determined, ranging from 900 to 1500 M-1 cm-1. The vibrational lifetimes of all azides were measured by pump-probe IR spectroscopy and each showed a major component with a short-to-moderate vibrational lifetime and a minor component with a much longer vibrational lifetime. Based on these results, the lifetime, aka the observation window, of an azide reporter can be extended from ∼2 ps to as long as ∼300 ps by a combination of isotopic labeling and heavy atom effect. 2D IR measurements of these compounds further confirmed the ability to observe these azide transitions at much longer timescales showing their utility to capture dynamic processes from tens to hundreds of picoseconds.

Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition

Proteins exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires knowledge of the populated states and thus the experimental tools to characterize them. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution, and 2D IR methods that provide richer information are becoming more routine. Although application of IR spectroscopy for investigation of proteins is challenged by spectral congestion, the issue can be overcome by site-specific introduction of amino acid side chains that have IR probe groups with frequency-resolved absorptions, which furthermore enables selective characterization of different locations in proteins. Here, we briefly introduce the biophysical methods and summarize the current progress toward the study of proteins. We then describe our efforts to apply site-specific 1D and 2D IR spectroscopy toward elucidation of protein conformations and dynamics to investigate their involvement in protein molecular recognition, in particular mediated by dynamic complexes: plastocyanin and its binding partner cytochrome f, cytochrome P450s and substrates or redox partners, and Src homology 3 domains and proline-rich peptide motifs. We highlight the advantages of frequency-resolved probes to characterize specific, local sites in proteins and uncover variation among different locations, as well as the advantage of the fast time scale of IR spectroscopy to detect rapidly interconverting states. In addition, we illustrate the greater insight provided by 2D methods and discuss potential routes for further advancement of the field of biomolecular 2D IR spectroscopy.

Heterogeneous and Highly Dynamic Interface in Plastocyanin-Cytochrome f Complex Revealed by Site-Specific 2D-IR Spectroscopy

Transient protein complexes are crucial for sustaining dynamic cellular processes. The complexes of electron-transfer proteins are a notable example, such as those formed by plastocyanin (Pc) and cytochrome f (cyt f) in the photosynthetic apparatus. The dynamic and heterogeneous nature of these complexes, however, makes their study challenging. To better elucidate the complex of Nostoc Pc and cyt f, 2D-IR spectroscopy coupled to site-specific labeling with cyanophenylalanine infrared (IR) probes was employed to characterize how the local environments at sites along the surface of Pc were impacted by cyt f binding. The results indicate that Pc most substantially engages with cyt f via the hydrophobic patch around the copper redox site. Complexation with cyt f led to an increase in inhomogeneous broadening of the probe absorptions, reflective of increased heterogeneity of interactions with their environment. Notably, most of the underlying states interconverted very rapidly (1 to 2 ps), suggesting a complex with a highly mobile interface. The data support a model of the complex consisting of a large population of an encounter complex. Additionally, the study demonstrates the application of 2D-IR spectroscopy with site-specifically introduced probes to reveal new quantitative insight about dynamic biochemical systems.

Site-specific 2D IR spectroscopy: a general approach for the characterization of protein dynamics with high spatial and temporal resolution

The conformational heterogeneity and dynamics of protein side chains contribute to function, but investigating exactly how is hindered by experimental challenges arising from the fast timescales involved and the spatial heterogeneity of protein structures. The potential of two-dimensional infrared (2D IR) spectroscopy for measuring conformational heterogeneity and dynamics with unprecedented spatial and temporal resolution has motivated extensive effort to develop amino acids with functional groups that have frequency-resolved absorptions to serve as probes of their protein microenvironments. We demonstrate the full advantage of the approach by selective incorporation of the probe p-cyanophenylalanine at six distinct sites in a Src homology 3 domain and the application of 2D IR spectroscopy to site-specifically characterize heterogeneity and dynamics and their contribution to cognate ligand binding. The approach revealed a wide range of microenvironments and distinct responses to ligand binding, including at the three adjacent, conserved aromatic residues that form the recognition surface of the protein. Molecular dynamics simulations performed for all the labeled proteins provide insight into the underlying heterogeneity and dynamics. Similar application of 2D IR spectroscopy and site-selective probe incorporation will allow for the characterization of heterogeneity and dynamics of other proteins, how heterogeneity and dynamics are affected by solvation and local structure, and how they might contribute to biological function.

Simultaneous enhancement of transition dipole strength and vibrational lifetime of an alkyne IR probe via π-d backbonding and vibrational decoupling

Alkyne IR probes 1–6 with Si and S (or Se) atoms incorporated into the CC bond were synthesized, and the vibrational properties of their CC stretch mode were studied using FTIR and femtosecond IR PP spectroscopies and quantum chemical calculations.

Linear and Nonlinear Infrared Spectroscopies Reveal Detailed Solute-Solvent Dynamic Interactions of a Nitrosyl Ruthenium Complex in Solution

In this work, the solvation of a nitrosyl ruthenium complex, [(CH₃)₄N][RuCl₃(qn)(NO)] (with qn = deprotonated 8-hydroxyquinoline), which is a potential NO-releasing molecule in the bio-environment, was studied in two bio-friendly solvents, namely deuterated dimethyl sulfoxide (dDMSO) and water (D₂O). A blue-shifted NO stretching frequency was observed in water with respect to that in dDMSO, which was believed to be due to ligand-solvent hydrogen-bonding interactions, one N═O···D and particularly three Ru-Cl···D, that show competing effects on the NO bond length. The dynamic differences of the NO stretch in these two solvents were further revealed by transient pump-probe IR and two-dimensional IR results: faster vibrational relaxation and faster spectral diffusion (SD) were observed in D₂O, confirming stronger solvent-solute interaction and also faster solvent structural dynamics in D₂O than in DMSO. Further, a significant non-decaying residual in the SD dynamics was observed in D₂O but not in DMSO, suggesting the formation of a stable solvation shell in water due to strong multi-site ligand-solvent hydrogen-bonding interactions, which is in agreement with the observed blue-shifted NO stretching frequency. This work demonstrates that small solvent molecules such as water can form a relatively rigid solvation shell for certain transition metal complexes due to cooperative ligand-solvent interactions and show slower dynamics.

Equilibrium versus Nonequilibrium Peptide Dynamics: Insights into Transient 2D IR Spectroscopy

Over the past two decades, two-dimensional infrared (2D IR) spectroscopy has evolved from the theoretical underpinnings of nonlinear spectroscopy as a means of investigating detailed molecular structure on an ultrafast time scale. The combined time and spectral resolution over which spectra can be collected on complex molecular systems has led to the precise structural resolution of dynamic species that have previously been impossible to directly observe through traditional methods. The adoption of 2D IR spectroscopy for the study of protein folding and peptide interactions has provided key details of how small changes in conformations can exert major influences on the activities of these complex molecular systems. Traditional 2D IR experiments are limited to molecules under equilibrium conditions, where small motions and fluctuations of these larger molecules often still lead to functionality. Utilizing techniques that allow the rapid initiation of chemical or structural changes in conjunction with 2D IR spectroscopy, i.e., transient 2D IR, a vast dynamic range becomes available to the spectroscopist uncovering structural content far from equilibrium. Furthermore, this allows the observation of reaction pathways of these macromolecules under quasi- and nonequilibrium conditions.

Fermi resonance as a means to determine the hydrogen-bonding status of two infrared probes

The C[double bond, length as m-dash]O/C[triple bond, length as m-dash]N stretching vibration arising from a carbonyl/nitrile functional group in various molecular systems has been frequently used to assess, for example, local hydrogen-bonding interactions, among other applications. However, in practice it is not always easy to ascertain whether the carbonyl or nitrile group in question is engaged in such interactions. Herein, we use 4-cyanoindole and cyclopentanone as models to show that, when a fundamental C[double bond, length as m-dash]O or C[triple bond, length as m-dash]N stretching mode is involved in Fermi resonance, the underlying vibrational coupling constant (W) is a convenient reporter of the hydrogen-bonding status of the corresponding carbonyl or nitrile group. Specifically, we find that for both groups a W value of 7.7 cm^-1 or greater is indicative of their involvement in hydrogen-bonding interactions. Furthermore, we find that, as observed in similar studies, the Fermi resonance coupling leads to quantum beats in the two-dimensional infrared spectra of 4-cyanoindole in isopropanol, with a period of about 1.9 ps.

A structural model of the hierarchical assembly of an amyloid nanosheet by an infrared probe technique

A hierarchical structural model of an amyloid nanosheet by IR probe technique.

Discontinuity in Fast Dynamics at the Glass Transition of ortho-Terphenyl

The dynamics of the molecular glass former ortho-terphenyl through the glass transition were observed with two-dimensional infrared vibrational spectroscopy measurements of spectral diffusion using the small probe molecule phenylselenocyanate. Although the slow diffusive motions were not visible on the experimental time scale, a picosecond-scale exponential relaxation was observed at temperatures from above to well below the glass transition temperature. The characteristic time scale has a smooth temperature dependence from the liquid into the glass phase, but the range of vibrational frequencies the probe samples displayed a discontinuity at the glass transition temperature. Complementary pump-probe experiments associate the observed motion with density fluctuations. The key features of the dynamics are reproduced with a simple corrugated well potential energy surface model. In addition, the temperature dependence of the homogeneous vibrational dephasing was found to have a T² functional form, where T is the absolute temperature.