2D IR Spectroscopy Research Articles

Vibrational Probe at the Electrochemical Interface: Dependence on Plasmon Coupling and Potential of the Lineshape in Two-Dimensional Infrared Spectroscopy.

Two-dimensional infrared spectroscopy of vibrational probes at an electrode surface shows promise for studying the structural dynamics at an active electrochemical interface. This interface is a complex environment where the solution structures in response to the applied potential. A strategy for achieving the necessary monolayer sensitivity is to use a plasmonically active electrode, which enhances the electromagnetic fields that produce the spectroscopic response. Here, we show how the coupling between the plasmon and the vibrations of the molecular monolayer impacts the FTIR and 2D IR spectroscopy, with an emphasis on the electrochemical potential difference spectra. We show how mixing between the vibrational and plasmonic states gives rise to the distortions that are observed in these measurements. This provides an important step toward 2D IR measurements of vibrational probes at the electrochemical interface as a tool for probing the structural dynamics in the double layer.

Methyl 4-pyridyl ketone thiosemicarbazone (4-PT) as an effective and safe inhibitor of mushroom tyrosinase and antibrowning agent

Enzymatic browning is of concern as it can affect food safety and quality. In this study, an effective and safe tyrosinase inhibitor and anti-browning agent, methyl 4-pyridyl ketone thiosemicarbazone (4-PT), was synthesised and characterised using Fourier-transform infrared (FTIR) spectroscopy, CHNS elemental analysis, and proton (1H) and carbon-13 (13C) nuclear magnetic resonance (NMR) spectroscopy. The vibrational frequencies of 4-PT were studied theoretically using vibrational energy distribution analysis (VEDA). Density functional theory (DFT) was applied to elucidate its chemical properties, including the Mulliken atomic charges, molecular electrostatic potential (MEP), quantum theory of atoms in molecules (QTAIM) and reduced density gradient non-covalent interactions (RDG-NCIs). Moreover, 4-PT was compared with kojic acid in terms of its effectiveness as a tyrosinase inhibitor and anti-browning agent. The toxicity and physicochemical properties of 4-PT were predicted via ADME evaluation, which proved that 4-PT is safer than kojic acid. Experimentally, 4-PT (IC50 = 5.82 μM, browning index (10 days) = 0.292 ± 0.002) was proven to be an effective tyrosinase inhibitor and anti-browning agent compared to kojic acid (IC50 = 128.17 μM, browning index (10 days) = 0.332 ± 0.002). Furthermore, kinetic analyses indicated that the type of tyrosinase inhibition is a mixed inhibition, with Km and Vmax values of 0.85 mM and 2.78 E-09 μM/s, respectively. Finally, the mechanism of 4-PT for tyrosinase inhibition was proven by 1D, second derivative and 2D IR spectroscopy, molecular docking and molecular dynamic simulation approaches.

Investigating Intramolecular H Atom Transfer Dynamics in β-Diketones with Ultrafast Infrared Spectroscopies and Theoretical Modeling.

The vibrational signatures and ultrafast dynamics of the intramolecular H-bond in a series of β-diketones are investigated with 2D IR spectroscopy and computational modeling. The chosen β-diketones exhibit a range of H atom donor-acceptor distances and asymmetry along the H atom transfer coordinate that tunes the intramolecular H-bond strength. The species with the strongest H-bonds are calculated to have very soft H atom potentials, resulting in highly red-shifted OH stretch fundamental frequencies and dislocation of the H atom upon vibrational excitation. These soft potentials lead to significant coupling to the other normal mode coordinates and give rise to the very broad vibrational signatures observed experimentally. The 2D IR spectra in both the OH and OD stretch regions of the light and deuterated isotopologues reveal broadened and long-lived ground-state bleach signatures of the vibrationally hot molecules. Polarization-sensitive transient absorption measurements in the OH and OD stretch regions reveal notable isotopic differences in orientational dynamics. Orientational relaxation was measured to occur on ∼600 fs and ∼2 ps time scales for the light and deuterated isotopologues, respectively. The orientational dynamics are interpreted in terms of activated H/D atom transfer events driven by collective intramolecular structural rearrangements.

Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy.

Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.

Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra.

Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and β-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.

Crowding alters F-actin secondary structure and hydration

Actin, an important component of eukaryotic cell cytoskeleton, regulates cell shape and transport. The morphology and biochemical properties of actin filaments are determined by their structure and protein-protein contacts. Crowded environments can organize filaments into bundles, but less is known about how they affect F-actin structure. This study used 2D IR spectroscopy and spectral calculations to examine how crowding and bundling impact the secondary structure and local environments in filaments and weakly or strongly bundled networks. The results reveal that bundling induces changes in actin’s secondary structure, leading to a decrease in β-sheet and an increase in loop conformations. Strongly bundled networks exhibit a decrease in backbone solvent exposure, with less perturbed α-helices and nearly “locked” β-sheets. Similarly, the loops become less hydrated but maintain a dynamic environment. These findings highlight the role of loop structure in actin network morphology and stability under morphology control by PEG.

Probing Ion Configurations in the KcsA Selectivity Filter with Single-Isotope Labels and 2D IR Spectroscopy.

The potassium ion (K+) configurations of the selectivity filter of the KcsA ion channel protein are investigated with two-dimensional infrared (2D IR) spectroscopy of amide I vibrations. Single 13C-18O isotope labels are used, for the first time, to selectively probe the S1/S2 or S2/S3 binding sites in the selectivity filter. These binding sites have the largest differences in ion occupancy in two competing K+ transport mechanisms: soft-knock and hard-knock. According to the former, water molecules alternate between K+ ions in the selectivity filter while the latter assumes that K+ ions occupy the adjacent sites. Molecular dynamics simulations and computational spectroscopy are employed to interpret experimental 2D IR spectra. We find that in the closed conductive state of the KcsA channel, K+ ions do not occupy adjacent binding sites. The experimental data is consistent with simulated 2D IR spectra of soft-knock ion configurations. In contrast, the simulated spectra for the hard-knock ion configurations do not reproduce the experimental results. 2D IR spectra of the hard-knock mechanism have lower frequencies, homogeneous 2D lineshapes, and multiple peaks. In contrast, ion configurations of the soft-knock model produce 2D IR spectra with a single peak at a higher frequency and inhomogeneous lineshape. We conclude that under equilibrium conditions, in the absence of transmembrane voltage, both water and K+ ions occupy the selectivity filter of the KcsA channel in the closed conductive state. The ion configuration is central to the mechanism of ion transport through potassium channels.

Counteracting Effects of Trimethylamine N-Oxide against Urea in Aqueous Solutions: Insights from Theoretical Two-Dimensional Infrared Spectroscopy.

The study of small osmolytes in their aqueous solutions has gained significant attention because of their relevance to structure and thermodynamics of proteins in aqueous media. Special attention has been given to the binary and ternary aqueous solutions of urea and trimethylamine N-oxide (TMAO). Urea is a well-known protein denaturant, while TMAO protects proteins in their native states. Interestingly, TMAO counteracts urea's ability to denature proteins when present in solutions with approximately half of the concentration of urea. Vibrational spectroscopy can improve our understanding of the molecular origin of this counteracting effect because of its sensitivity to local structure and dynamics. We present results of theoretical linear vibrational and two-dimensional infrared (2DIR) spectroscopy of water in the binary and ternary aqueous solutions of TMAO and urea. The 2DIR spectra are calculated using the electronic structure/molecular dynamics approach. The non-Condon effects in spectral transitions are incorporated in the theoretical calculations of 2DIR spectra. It is found that TMAO disrupts the local structure of water, while urea leaves it essentially unaffected. The 2DIR results show that both TMAO and urea slow down the dynamics of spectral diffusion of water. The extent of slowing down is found to be particularly significant for both hydration and bulk water in the presence of TMAO which can be attributed to strong hydrogen bonds between the water and TMAO molecules. The water molecules present in the hydration layer of the solutes in the ternary solutions are found to relax at even slower rates compared to that in their binary solutions in water. The hydrogen bonds between TMAO and urea are found to be not stable. Thus, the counteracting effect of TMAO against urea is seen to take place mainly through water-mediated interactions. Such TMAO-induced effects giving rise to more structured and slower hydrogen-bonded network are successfully captured through 2DIR spectroscopic calculations.

A new method based on pseudo-Zernike polynomials to analyze and extract dynamical and spectral information from the 2DIR spectra.

Ultrafast two-dimensional infrared (2DIR) spectroscopy is a relatively new methodology, which has now been widely used to study the molecular structure and dynamics of molecular processes occurring in solution. Typically, in 2DIR spectroscopy the dynamics of a system is inferred from the evolution of 2DIR spectral features over waiting times. One of the most important metrics derived from the 2DIR is the frequency-frequency correlation function (FFCF), which can be extracted using different methods, including center and nodal line slope. However, these methods struggle to correctly describe the dynamics in 2DIR spectra with multiple and overlapping transitions. Here, a new approach, utilizing pseudo-Zernike moments, is introduced to retrieve the FFCF dynamics of each spectral component from complex 2DIR spectra. The results show that this new method not only produces equivalent results to more established methodologies in simple spectra but also successfully extracts the FFCF dynamics of individual component from very congested and unresolved 2DIR spectra. In addition, this new methodology can be used to locate the individual frequency components from those complex spectra. Overall, a new methodology for analyzing the 2D spectra is presented here, which allows us to retrieve previously unattainable spectral features from the 2DIR spectra.

(1E)-1-(2-pyrazinyl)ethanone thiosemicarbazone (PT) as a tyrosinase inhibitor with anti-browning activity: Spectroscopy, DFT and molecular docking studies

In this study, (1E)-1-(2-Pyrazinyl)ethanone thiosemicarbazone (PT) was synthesized and characterized using Fourier-transform infrared (FTIR), ultraviolet-visible (UV–Vis), proton nuclear magnetic resonance (1HNMR ) and carbon-13 nuclear magnetic resonance (13CNMR ) spectroscopy. The vibrational frequencies were analysed using the Vibrational Energy Distribution Analysis (VEDA) program. The chemical properties of PT, including electron density distribution and intramolecular interactions, were characterized using in-silico methods based on Mulliken atomic charges, molecular electrostatic potential (MEP), quantum theory of atoms in molecules and reduced density gradient noncovalent interaction approaches. PT exhibits a significant inhibitory effect on enzymatic browning (6 and 24 h) and tyrosinase enzymes (IC50 = 7.75 μM). Kinetic analysis shows that PT is a mixed-type inhibitor, with respective Km and Vmax values of 0.632 mM and 0.0044 μM/s, and that it forms a reversible enzyme-inhibitor interaction. The PT-tyrosinase interaction was experimentally evaluated based on 1D, second derivatives of 1D, 2D and 3D IR spectroscopy. Furthermore, analysis of absorption, distribution, metabolism, excretions and toxicity properties revealed good physicochemical properties of PT according to the drug scores and Lipinski's Rule of Five. Lastly, the mechanisms of PT against tyrosinase were visualized and supported by means of a molecular docking approach.

Temperature-Induced Effects on the Structure of Gramicidin S.

We report on the structure of Gramicidin S (GS) in a model membrane mimetic environment represented by the amphipathic solvent 1-octanol using one-dimensional (1D) and two-dimensional (2D) IR spectroscopy. To explore potential structural changes of GS, we also performed a series of spectroscopic measurements at differing temperatures. By analyzing the amide I band and using 2D-IR spectral changes, results could be associated to the disruption of aggregates/oligomers, as well as structural and conformational changes happening in the concentrated solution of GS. The ability of 2D-IR to enable differentiation in melting transitions of oligomerized GS structures is attributed to the sensitivity of the technique to vibrational coupling. Two melting transition temperatures were identified; at Tm1 in the range 41-47 °C where the GS aggregates/oligomers disassemble and at Tm2 = 57 ± 2 °C where there is significant change involving GS β-sheet-type hydrogen bonds, whereby it is proposed that there is loss of interpeptide hydrogen bonds and we are left with mainly intrapeptide β-sheet and β-turn hydrogen bonds of the smaller oligomers. Further analysis with quantum mechanical/molecular mechanics (QM/MM) simulations and second derivative results highlighted the participation of active GS side chains. Ultimately, this work contributes toward understanding the GS structure and the formulation of GS analogues with improved bioactivity.

Correction to “Structural Dynamics of (RGD)4PGC Peptides in Solvated and Au Nanorod Surface-Bound Forms Examined by Ultrafast 2D IR Spectroscopy”

ADVERTISEMENT RETURN TO ARTICLES ASAPPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to “Structural Dynamics of (RGD)4PGC Peptides in Solvated and Au Nanorod Surface-Bound Forms Examined by Ultrafast 2D IR Spectroscopy”Xueqian DongXueqian DongMore by Xueqian Dong, Pengyun YuPengyun YuMore by Pengyun Yu, Juan ZhaoJuan ZhaoMore by Juan Zhao, Yue WuYue WuMore by Yue Wu, Moustafa R. K. AliMoustafa R. K. AliMore by Moustafa R. K. Alihttps://orcid.org/0000-0002-2027-1006, Mostafa A. El-SayedMostafa A. El-SayedMore by Mostafa A. El-Sayedhttps://orcid.org/0000-0002-7674-8424, and Jianping Wang*Jianping WangMore by Jianping Wanghttps://orcid.org/0000-0001-7127-869XCite this: J. Phys. Chem. C 2023, XXXX, XXX, XXX-XXXPublication Date (Web):April 24, 2023Publication History Received5 April 2023Published online24 April 2023https://doi.org/10.1021/acs.jpcc.3c02276© 2023 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views-Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (556 KB) Get e-Alerts Get e-Alerts

2D-IR Spectroscopy of Nitrosyl Stretch of Sodium Nitroprusside Reveals the Elusive Two Anomalous Regions in the DMSO–Water Mixture

DMSO-water mixtures provide an intriguing hydrogen-bonding environment which has been a subject of various theoretical and experimental investigations. The structural dynamics of aqueous DMSO solutions has been investigated, using nitrosyl stretch of sodium nitroprusside (SNP, Na2[Fe(CN)5NO]) as a local vibrational probe, with the help of infrared (IR) absorption spectroscopy, vibrational pump-probe spectroscopy, and two-dimensional IR spectroscopy (2D-IR). Fourier transform infrared spectra of the nitrosyl stretch of SNP reveals that both the peak position and spectral broadening are very sensitive to the composition of the DMSO-water mixture and the subsequent structural changes occurring due to the addition of DMSO to water. The vibrational lifetime of the nitrosyl stretch displays two different linear variation regimes as a function of mole fraction of DMSO which has been assigned presumably to two different predominant structures at these compositions. However, the rotational depolarization measurements show that the reorientational times follow a bell-shaped profile, imitating the changes in the composition-dependent physical properties (viscosity) of DMSO-water solvent mixtures. To get a holistic picture of the system, 2D-IR spectroscopy of the NO stretch of SNP has been employed to study time scales of hydrogen-bond reorganization dynamics existing at different compositions. The analysis of frequency-frequency correlation function (FFCF) decay times reveal that the dynamics gets slower in intermediate DMSO concentrations than that of pure DMSO or pure water. A careful analysis reveals two anomalous regions of hydrogen-bond dynamics: XDMSO ∼0.2 and 0.4, which indicates that different hydrogen-bonded structures exist in these regions that can be effectively probed by SNP which has remained mostly elusive to previous vibrational probe-based investigations.

2D-IR spectroscopy of carbohydrates: Characterization of thiocyanate-labeled β-glucose in CHCl3 and H2O.

Carbohydrates constitute one of the four key classes of biomacromolecules but have not been studied by 2D-IR spectroscopy so far. Similarly as for proteins, a lack of native vibrational reporter groups, combined with their huge structural diversity, leads to spectrally congested infrared spectra already for single carbohydrates. Biophysical studies are further impeded by the strong overlap between water modes and carbohydrate modes. Here, we demonstrate the application of the known vibrational reporter group thiocyanate (SCN) as a label in glucose. In this first study, we are able to perform IR and 2D-IR spectroscopy of β-glucose with SCN at the C2 position in chloroform. Upon improved synthesis and the removal of all protecting groups, we successfully performed 2D-IR spectroscopy of β-glucose in H2O. All experimental results are compared to those of methyl-thiocyanate as a reference sample. Overall, we show that the concept of using site-specific vibrational reporter groups can be transferred to carbohydrates. Thus, biophysical studies with 2D-IR spectroscopy can now expand to glycoscience.

Slow spectral diffusion of the NO stretching mode of [RuCl5(NO)]2- in D2O studied by 2D-IR spectroscopy and molecular dynamics simulations.

The vibrational dynamics of the NO stretching mode of [RuCl5(NO)]2- in D2O were investigated by nonlinear infrared (IR) spectroscopy. We performed IR pump-probe measurements to obtain the vibrational lifetime of this molecule. The lifetime is 31ps, which is sufficiently long enough to study the vibrational frequency fluctuation on a slower time scale with high precision. By two-dimensional IR spectroscopy, the frequency-frequency time correlation function (FFTCF) of the NO stretching mode was characterized with a delta function plus a double-exponential function. The time constant of the slower component was ∼10ps. We also found that the time constant does not strongly depend on temperature. In order to investigate the microscopic origin of this component, we performed classical molecular dynamics simulations. It was found that the hydration structure around the NO group was influenced by the negatively charged Cl ligands. To calculate the FFTCF decay, we employed an approximate theoretical model based on the vibrational solvatochromism theory. It was demonstrated that water fluctuations around the Cl ligands projected on the NO group correspond to the 10ps decay component in the FFTCF. The fluctuation is related to the orientational dynamics of the water molecules attracted by the Cl ligands. By comparing the FFTCF parameters of the present solute with those of previously reported metal complexes and SCN- in D2O, we conclude that the presence of different electrostatic environments around the vibrational probe and the other interaction sites of the solute is important for understanding the slow decay component in the FFTCFs.

Multidimensional infrared diffusion-ordered spectroscopy in depletion mode distinguishes protein amyloids and monomers.

Conventional and two-dimensional infrared (2D-IR) spectroscopy are well suited to study amyloid aggregates, because the amide I mode is a sensitive probe of the aggregate structure. However, these methods are not so useful to study mixtures of aggregates and monomers, which generally have overlapping amide I spectra. Here, we show that IR-Diffusion-Ordered Spectroscopy can disentangle the contributions of protein monomers and aggregates (amyloids) in FTIR and 2D-IR spectra by separating the spectral contributions based on molecular size. We rely on the fact that the diffusion coefficient of a molecule is determined by its size through the Stokes-Einstein relation, and achieve sensitivity to the diffusion coefficient by creating a concentration gradient inside an IR sample cell and tracking its equilibration in an IR-frequency-resolved manner. The amyloid diffusion is too slow to be experimentally observable, so instead of tracking the arrival of molecular species diffusing into the initially empty region of the sample cell, we track the depletion of the more rapidly diffusing species as they leave the sample-filled region. This way, we can still obtain the spectrum of very slowly diffusing species, although we cannot determine their diffusion coefficient. We first demonstrate this depletion method on a mixture of two small organic molecules and then show how it can be used to separate the spectrum of a mixture of bovine-serum-albumin amyloids and monomers into its component spectra, both in the FTIR and 2D-IR case.

Molecular Vibrational Polariton Dynamics: What Can Polaritons Do?

ConspectusWhen molecular vibrational modes strongly couple to virtual states of photonic modes, new molecular vibrational polariton states are formed, along with a large population of dark reservoir modes. The polaritons are much like the bonding and antibonding molecular orbitals when atomic orbitals form molecular bonds, while the dark modes are like nonbonding orbitals. Because the polariton states are half-matter and half-light, whose energy is shifted from the parental states, polaritons are predicted to modify chemistry under thermally activated conditions, leading to an exciting and emerging field known as polariton chemistry that could potentially shift paradigms in chemistry. Despite several published results supporting this concept, the chemical physics and mechanism of polariton chemistry remain elusive. One reason for this challenge is that previous works cannot differentiate polaritons from dark modes. This limitation makes delineating the contributions to chemistry from polaritons and dark states difficult. However, this level of insight is critical for developing a solid mechanism for polariton chemistry to design and predict the outcome of strong coupling with any given reaction. My group addressed the challenge of differentiating the dynamics of polaritons and dark modes by ultrafast two-dimensional infrared (2D IR) spectroscopy. Specifically, (1) we found that polaritons can facilitate intra- and intermolecular vibrational energy transfer, opening a pathway to control vibrational energy flow in liquid-phase molecular systems, and (2) by studying a single-step isomerization event, we verified that indeed polaritons can modify chemical dynamics under strong coupling conditions, but in contrast, the dark modes behave like uncoupled molecules and do not change the dynamics. This finding confirmed the central concept of polariton chemistry: polaritons modify the potential energy landscape of reactions. The result also clarified the role of dark modes, which lays a critical foundation for designing cavities for future polariton chemistry. Aside from using 2D IR spectroscopy to study polariton chemistry, we also used the same technique to develop molecular polaritons into a potential quantum simulation platform. We demonstrated that polaritons have Rabi oscillations, and using a checkerboard cavity design, we showed that polaritons could have large nonlinearity across space. We further used the checkerboard polaritons to simulate coherence transfer and visualize it. A unidirectional coherence transfer was observed, indicating non-Hermitian dynamics. The highlighted efforts in this Account provide a solid understanding of the capability of polaritons for chemistry and quantum information science. I conclude this Account by discussing a few challenges for moving polariton chemistry toward being predictable and making the polariton quantum platform a complement to existing systems.

Narrow homogeneous linewidths and slow cooling dynamics across infrared intra-band transitions in n-doped HgSe colloidal quantum dots.

Intra-band transitions in colloidal quantum dots (QDs) are promising for opto-electronic applications in the mid-IR spectral region. However, such intra-band transitions are typically very broad and spectrally overlapping, making the study of individual excited states and their ultrafast dynamics very challenging. Here, we present the first full spectrum two-dimensional continuum infrared (2D CIR) spectroscopy study of intrinsically n-doped HgSe QDs, which exhibit mid-infrared intra-band transitions in their ground state. The obtained 2D CIR spectra reveal that underneath the broad absorption line shape of ∼500cm-1, the transitions exhibit surprisingly narrow intrinsic linewidths with a homogeneous broadening of 175-250cm-1. Furthermore, the 2D IR spectra are remarkably invariant, with no signof spectral diffusion dynamics at waiting times up to 50ps. Accordingly, we attribute the large static inhomogeneous broadening to the distribution of size and doping level of the QDs. In addition, the two higher-lying P-states of the QDs can be clearly identified in the 2D IR spectra along the diagonal with a cross-peak. However, there is no indication of cross-peak dynamics indicating that, despite the strong spin-orbit coupling in HgSe, transitions between the P-states must be longer than our maximum waiting time of 50ps. This study illustrates a new frontier of 2D IR spectroscopy enabling the study of intra-band carrier dynamics in nanocrystalline materials across the entire mid-infrared spectrum.

Ultrafast 2D-IR spectroscopy of intensely optically scattering pelleted solid catalysts.

Solid, powdered samples are often prepared for infrared (IR) spectroscopy analysis in the form of compressed pellets. The intense scattering of incident light by such samples inhibits applications of more advanced IR spectroscopic techniques, such as two-dimensional (2D)-IR spectroscopy. We describe here an experimental approach that enables the measurement of high-quality 2D-IR spectra from scattering pellets of zeolites, titania, and fumed silica in the OD-stretching region of the spectrum under flowing gas and variable temperature up to ∼500 ◦C. In addition to known scatter suppression techniques, such as phase cycling and polarization control, we demonstrate how a bright probe laser beam comparable in strength with the pump beam provides effective scatter suppression. The possible nonlinear signals arising from this approach are discussed and shown to be limited in consequence. In the intense focus of 2D-IR laser beams, a free-standing solid pellet may become elevated in temperature compared with its surroundings. The effects of steady state and transient laser heating effects on practical applications are discussed.

Probing local changes to α-helical structures with 2D IR spectroscopy and isotope labeling

α-Helical secondary structures impart specific mechanical and physiochemical properties to peptides and proteins, enabling them to perform a vast array of molecular tasks ranging from membrane insertion to molecular allostery. Loss of α-helical content in specific regions can inhibit native protein function or induce new, potentially toxic, biological activities. Thus, identifying specific residues that exhibit loss or gain of helicity is critical for understanding the molecular basis of function. Two-dimensional infrared (2D IR) spectroscopy coupled with isotope labeling is capable of capturing detailed structural changes in polypeptides. Yet, questions remain regarding the inherent sensitivity of isotope-labeled modes to local changes in α-helicity, such as terminal fraying; the origin of spectral shifts (hydrogen-bonding versus vibrational coupling); and the ability to definitively detect coupled isotopic signals in the presence of overlapping side chains. Here, we address each of these points individually by characterizing a short, model α-helix (DPAEAAKAAAGR-NH2) with 2D IR and isotope labeling. These results demonstrate that pairs of 13C18O probes placed three residues apart can detect subtle structural changes and variations along the length of the model peptide as the α-helicity is systematically tuned. Comparison of singly and doubly labeled peptides affirm that frequency shifts arise primarily from hydrogen-bonding, while vibrational coupling between paired isotopes leads to increased peak areas that can be clearly differentiated from underlying side-chain modes or uncoupled isotope labels not participating in helical structures. These results demonstrate that 2D IR in tandem with i,i+3 isotope-labeling schemes can capture residue-specific molecular interactions within a single turn of an α-helix.