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The dynamics of excess protons in the protic ionic liquid ethylammonium formate (EAF) have been investigated from femtosecond to microseconds using visible pump mid-infrared probe spectroscopy. The pH-jump following visible photoexcitation of a photoacid (8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt, HPTS) results in proton transfer to the formate of the EAF. The proton transfer predominantly occurs over picoseconds through a pre-formed hydrogen-bonded complex between HPTS and EAF. We investigate the longer range and longer timescale proton transport processes in the ionic liquid by obtaining the ground-state conjugate base (RO-) dynamics from the congested transient-infrared spectra. The spectral kinetics indicate that the protons diffuse only a few solvent shells from the parent photoacid before recombining with RO-. A kinetic isotope effect of near unity (kH/kD~1) suggests vehicular transfer and transport of excess protons in this ionic liquid. Our findings provide a comprehensive insight into the complete photoprotolytic cycle of excess protons in a protic ionic liquid.

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.

Time-resolved IR spectra of porphyrins bound to biomolecules are reported. DFT calculations aid porphyrin vibration assignment while distinctive IR bands reveal interactions with therapeutic targets such as quadruplex DNA and proteins in HeLa cells.

Ultrafast two-dimensional infrared (2D-IR) spectra can now be obtained in a matter of seconds, opening up the possibility of high-throughput screening applications of relevance to the biomedical and pharmaceutical sectors. Determining quantitative information from 2D-IR spectra recorded on different samples and different instruments is however made difficult by variations in beam alignment, laser intensity, and sample conditions. Recently, we demonstrated that 2D-IR spectroscopy of the protein amide I band can be performed in aqueous (H2O) rather than deuterated (D2O) solvents, and we now report a method that uses the magnitude of the associated thermal response of H2O as an internal normalization standard for 2D-IR spectra. Using the water response, which is temporally separated from the protein signal, to normalize the spectra allows significant reduction of the impact of measurement-to-measurement fluctuations on the data. We demonstrate that this normalization method enables creation of calibration curves for measurement of absolute protein concentrations and facilitates reproducible difference spectroscopy methodologies. These advances make significant progress toward the robust data handling strategies that will be essential for the realization of automated spectral analysis tools for large scale 2D-IR screening studies of protein-containing solutions and biofluids.

Break down of the Born–Oppenheimer approximation is caused by mixing of electronic and vibrational transitions in the radical cations of some conjugated polymers, resulting in unusually intense vibrational bands known as infrared active vibrations (IRAVs). Here, we investigate the mechanism of this amplification, and show that it provides insights into intramolecular charge migration. Spectroelectrochemical time-resolved infrared (TRIR) and two-dimensional infrared (2D-IR) spectroscopies were used to investigate the radical cations of two butadiyne-linked conjugated porphyrin oligomers, a linear dimer and a cyclic hexamer. The 2D-IR spectra reveal strong coupling between all the IRAVs and the electronic π–π* polaron band. Intramolecular vibrational energy redistribution (IVR) and vibrational relaxation occur within ∼0.1–7 ps. TRIR spectra show that the transient ground state bleach (GSB) and excited state absorption (ESA) signals have anisotropies of 0.31 ± 0.07 and 0.08 ± 0.04 for the linear dimer and cyclic hexamer cations, respectively. The small TRIR anisotropy for the cyclic hexamer radical cation indicates that the vibrationally excited polaron migrates round the nanoring on a time scale faster than the measurement, i.e. within 0.5 ps, at 298 K. Density functional theory (DFT) calculations qualitatively reproduce the emergence of the IRAVs. The first singlet (S1) excited states of the neutral porphyrin oligomers exhibit similar IRAVs to the radical cations, implying that the excitons have similar electronic structures to polarons. Our results show that IRAVs originate from the strong coupling of charge redistribution to nuclear motion, and from the similar energies of electronic and vibrational transitions., Break down of the Born–Oppenheimer approximation is caused by mixing of electronic and vibrational transitions in the radical cations of some conjugated polymers, resulting in unusually intense vibrational bands known as infrared active vibrations (IRAVs).

Infrared (IR) and Raman spectroscopy are fundamental techniques in chemistry, allowing the convenient determination of bond specific chemical composition and structure. Over the last decades, ultrafast multidimensional IR approaches using sequences of femtosecond IR pulses have begun to provide a new means of gaining additional information on molecular vibrational couplings, distributions of molecular structures and ultrafast molecular structural dynamics. In this contribution, new approaches to measuring multidimensional spectra involving IR and Raman processes are presented and applied to the study of the amide I band of proteins. Rephasing of the amide I band is observed using dispersed IR-Raman photon echoes and frequency domain 2D-IR-Raman spectra are measured by use of a mid-IR pulse shaper or over a broader spectral range using a tuneable picosecond laser. A simple pulse shaping approach to performing heterodyned time-domain Fourier Transform 2D-IR-Raman spectroscopy is introduced, revealing that the 2D-IR-Raman spectra distinguish homogeneous and inhomogeneous broadening in the same way as the well-established methods of 2D-IR spectroscopy. Across all datasets, the unique dependence of the amide I data on the IR and Raman strengths, vibrational anharmonicities and inhomogeneous broadening provides a fascinating spectroscopic view of the amide I band., New ultrafast 2D-IR-Raman photon echo spectroscopy techniques are introduced and applied to the structural analysis of proteins.

The electrocatalytic reduction of CO2 using [fac-Mn(bpy)(CO)3Br] (bpy = 2,2'-bipyridine) and its derivatives has been the subject of numerous recent studies. However the mechanisms of catalysis are still debated. Here we carry out in situ vibrational sum-frequency generation (VSFG) spectroelectrochemistry to examine how this catalyst behaves at an electrode surface. In particular, a low overpotential pathway involving a dimeric manganese has been reported in several studies using substituted bipyridine ligands. Here, we find that the "dimer pathway" can also occur with the unsubstuituted bipyridine complexes. Specifically we can observe spectroscopic evidence of the interaction between [Mn2(bpy)2(CO)6] with CO2 in the presence of a suitable acid. Detailed VSFG studies of [Mn2(bpy)2(CO)6], including of the potential dependence of the surface ν(CO) mode, allow us to construct a model of how it accumulates and behaves at the electrode surface under potentiostatic control.

Glycine (Gly) is used as a model system to evaluate the ability of ultrafast two-dimensional infrared (2D-IR) spectroscopy to detect and quantify the low-molecular-weight proteinaceous components of blood serum. Combining data acquisition schemes to suppress absorption bands of H2O that overlap with the protein amide I band with analysis of peak patterns appearing in the off-diagonal region of the 2D-IR spectrum allows separation of the Gly spectral signature from that of the dominant protein fraction of serum in a transmission-mode 2D-IR measurement without any sample manipulation, e.g., filtration or drying. 2D-IR spectra of blood serum samples supplemented with varying concentrations of Gly were obtained, and a range of data analysis methods compared, leading to a detection limit of ∼3 mg/mL for Gly. The reported methodology provides a platform for a critical assessment of the sensitivity of 2D-IR for measuring the concentrations of amino acids, peptides, and low-molecular-weight proteins present in serum samples. We conclude that, in the case of several clinically relevant diagnostic molecules and their combinations, the potential exists for 2D-IR to complement IR absorption methods as the benefits of the second frequency dimension offered by 2D-IR spectroscopy outweigh the added technical complexity of the measurement.

The effect of oligomer length on the vibrational mode coupling and energy relaxation mechanisms of AT-rich DNA oligomers in double- and single-stranded conformations has been investigated using two-dimensional infrared spectroscopy. Vibrational coupling of modes of the DNA bases to the symmetric stretching vibration of the backbone phosphate group was observed for oligomers long enough to form duplex-DNA structures. The coupling was lost upon melting of the duplex. No significant effect of oligomer length or DNA secondary structure was found on either the timescale for vibrational relaxation of the base modes or the mechanism, which was consistent with a cascade process from base modes to intermediate modes, some of which are located on the deoxyribose group, and subsequently to the phosphate backbone. The study shows that vibrational coupling between base and backbone requires formation of the double-helix structure while vibrational energy management is an inherent property of the nucleotide.

Group 6 metal carbonyl complexes ([M(bpy)(CO)4], M = Cr, Mo, W) are potentially promising CO2 reduction electrocatalysts. However, catalytic activity onsets at prohibitively negative potentials and is highly dependent on the nature of the working electrode. Here we report in situ vibrational SFG (VSFG) measurements of the electrocatalyst [Mo(bpy)(CO)4] at platinum and gold electrodes. The greatly improved onset potential for electrocatalytic CO2 reduction at gold electrodes is due to the formation of the catalytically active species [Mo(bpy)(CO)3]2– via a second pathway at more positive potentials, likely avoiding the need for the generation of [Mo(bpy)(CO)4]2–. VSFG studies demonstrate that the strength of the interaction between initially generated [Mo(bpy)(CO)4]•– and the electrode is critical in enabling the formation of the active catalyst via the low energy pathway. By careful control of electrode material, solvent and electrolyte salt, it should therefore be possible to attain levels of activity with group 6 complexes equivalent to their much more widely studied group 7 analogues.

The mechanism of the thiol-ene reaction induced by 330-nm ultraviolet excitation of 1,2-di(quinolin-2-yl)disulfide (QSSQ) in the presence of methyl methacrylate (MMA) is investigated by sub-picosecond to microsecond transient absorption spectroscopy. The measurements, spanning more than seven orders of magnitude of time, directly reveal multiple radical reaction steps. The ground state quinoliene-2-thiyl radical (QS) is formed with a time constant of ~200 fs by photolysis of QSSQ, followed by (64 ± 1)% decay of the initially formed QS radical because of solvent cage induced geminate recombination and QS dimer formation with a rate coefficient of (3.4 ± 0.2) × 1010 M-1 s-1 in methanol solution. In MMA solution, the carbon centered radical QS-MMA forms with a bimolecular reaction rate coefficient of (2.8 ± 0.2) × 107 M-1 s-1. The distinct infrared band at 1653 cm-1 assigned to the C=O stretch mode of the QS-MMA radical decays rapidly in aerated solution, in contrast to observations in a solution purged of O2 by N2 bubbling. This decay is attributed to reaction of the QS-MMA radicals with molecular oxygen, producing peroxy radicals. Kinetic analysis of the intensity of the band at 1653 cm-1 reveals a bimolecular reaction rate coefficient of (3.3 ± 0.3) × 109 M-1 s-1 for the reaction of the QS-MMA radicals with molecular oxygen, and indicates that this reaction step is reversible.

Using ultrafast two-dimensional infrared spectroscopy (2D-IR), a vibrational probe (thiocyanate, SCN-) was used to investigate the hydrogen bonding network of a molten salt (ethyl-ammonium nitrate, EAN) compared to that of H2O. The 2D-IR experiments were performed in both parallel () and perpendicular () conditions along with temperature dependence for both EAN (14-130 ˚C) and H2O (5-89 ˚C). With polarization control, the frequency fluctuation correlation function can be separated into structural and rotational components. An Arrhenius analysis lead to independent activation energies for the isotropic, and anisotropic signals, structural spectral diffusion, and rotational induced spectral diffusion. The rotational Eas were similar for both EAN and H2O suggesting that SCN- is experiencing a similar jump model, i.e. where hydrogen bond reorientation is dominated by large angular jumps stemming from molecular rotation dynamics. The frequency pre-factors, however, were different where the more rigid and vicious EAN had a slower rate. Furthermore, the 2D-IR anisotropy and vibrational relaxation rates of EAN are frequency dependent, revealing that SCN- experiences two subensembles. We suggest that the sub-ensemble with a faster rotational timescale correlates to SCN- with more, weaker hydrogen bonds, and the sub-ensemble with a slower rotational timescale correlates to SCN- with a stronger, more directional hydrogen bond.

The amide I infrared band of proteins is highly sensitive to secondary structure, but studies under physiological conditions are prevented by strong, overlapping water absorptions, motivating the widespread use of deuterated solutions. H/D exchange raises fundamental questions regarding the impact of increased mass on protein dynamics, while deuteration is impractical for biomedical or commercial applications of protein IR spectroscopy. We show that 2D-IR spectroscopy can avoid this problem because the 2D-IR amide I signature of proteins dominates that of water even at sub-millimolar protein concentrations. Using equine blood serum as a test system, we investigate the significant implications of being able to measure the spectroscopy and dynamics of proteins in water, demonstrating relevance in areas ranging from fundamental science to the clinic. Measurements of vibrational relaxation dynamics of serum proteins reveals that deuteration slows down the rate of amide I vibrational relaxation by > 10%, indicating a dynamic impact of isotopic exchange in some proteins. The unique link between protein secondary structure and 2D-IR amide I lineshape allows differentiation of signals due to albumin and globulin protein fractions in serum leading to measurements of the biomedically-important albumin to globulin ratio (AGR) with an accuracy of ±4% across a clinically-relevant range. Furthermore, we demonstrate that 2D-IR spectroscopy enables differentiation of the structurally-similar globulin proteins IgG, IgA and IgM, opening up a straightforward spectroscopic approach to measuring levels of serum proteins that are currently only accessible via biomedical laboratory testing.

The high charge carrier mobilities of hybrid inorganic-organic lead halide perovskites has previously been linked to ferroelectric domain formation due to alignment of organic cations within films. [1], [2] Our two-dimensional infrared ultrafast spectroscopy studies reveal that organic cations re-orient within several picoseconds, and therefore ferroelectric domain formation is very unlikely and unable to account for the observed long carrier lifetimes.[3] Complimentary time-resolved infrared measurements examined the electron-phonon coupling in the conduction band. Analysis of the spectral line shapes indicates that carriers form polarons within the instrument response.

Using ultrafast two-dimensional infrared spectroscopy (2D-IR), a vibrational probe (thiocyanate, SCN-) was used to investigate the hydrogen bonding network of the protic ionic liquid ethyl-ammonium nitrate (EAN) in comparison to H2O. The 2D-IR experiments were performed in both parallel (⟨ZZZZ⟩) and perpendicular (⟨ZZXX⟩) polarizations at room temperature. In EAN, the non-Gaussian lineshape in the FTIR spectrum of SCN- suggests two sub-ensembles. Vibrational relaxation rates extracted from the 2D-IR spectra provide evidence of the dynamical differences between the two sub-ensembles. We support the interpretation of two sub-ensembles with response function simulations of two overlapping bands with different vibrational relaxation rates and, otherwise, similar dynamics. The measured rates for spectral diffusion depend on polarization, indicating reorientation-induced spectral diffusion (RISD). A model of restricted molecular rotation (wobbling in a cone) fully describes the observed spectral diffusion in EAN. In H2O, both RISD and structural spectral diffusion contribute with similar timescales. This complete characterization of the dynamics at room temperature provides the basis for the temperature-dependent measurements in Paper II of this series.

Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA.

The electrocatalytic reduction of CO2 offers a sustainable route to the many carbon fuels and feedstocks that society relies on. [fac-Mn(bpy)(CO)3Br] (bpy, 2,2-bipyridine) is one of the most promising and intensely studied CO2 reduction electrocatalysts. However, the catalytic mechanism remains experimentally unproven and many key intermediates of the prototypical catalyst have not been observed. Here we report the use of vibrational sum-frequency generation spectroscopy to study the catalytic intermediates during CO2 reduction in situ at the electrode surface. We explore the complex applied-potential and acid-dependent mechanistic pathways and provide evidence of the theoretically derived mechanisms. Demonstrating the ability to detect the key species that are only transiently present at the electrode surface is important as the need for an improved mechanistic understanding is a common theme throughout the field of molecular electrocatalysis.

Photochromic fluorescent proteins play key roles in super-resolution microscopy and optogenetics. The light-driven structural changes that modulate the fluorescence involve both trans-to-cis isomerization and proton transfer. The mechanism, timescale and relative contribution of chromophore and protein dynamics are currently not well understood. Here, the mechanism of off-to-on-state switching in dronpa is studied using femtosecond-to-millisecond time-resolved infrared spectroscopy and isotope labelling. Chromophore and protein dynamics are shown to occur on multiple timescales, from picoseconds to hundreds of microseconds. Following excitation of the trans chromophore, a ground-state primary product is formed within picoseconds. Surprisingly, the characteristic vibrational spectrum of the neutral cis isomer appears only after several tens of nanoseconds. Further fluctuations in protein structure around the neutral cis chromophore are required to form a new intermediate, which promotes the final proton-transfer reaction. These data illustrate the interplay between chromophore dynamics and the protein environment underlying fluorescent protein photochromism.

Organic cation rotation in hybrid organic−inorganic lead halide perovskites has previously been associated with low charge recombination rates and (anti)ferroelectric domain formation. Two-dimensional infrared spectroscopy (2DIR) was used to directly measure 470 ± 50 fs and 2.8 ± 0.5 ps time constants associated with the reorientation of formamidinium cations (FA+, NH2CHNH2+) in formamidinium lead iodide perovskite thin films. Molecular dynamics simulations reveal the FA+ agitates about an equilibrium position, with NH2 groups pointing at opposite faces of the inorganic lattice cube, and undergoes 90° flips on picosecond time scales. Time-resolved infrared measurements revealed a prominent vibrational transient feature arising from a vibrational Stark shift: photogenerated charge carriers increase the internal electric field of perovskite thin films, perturbing the FA+ antisymmetric stretching vibrational potential, resulting in an observed 5 cm-1 shift. Our 2DIR results provide the first direct measurement of FA+ rotation inside thin perovskite films, and cast significant doubt on the presence of long-lived (anti)ferroelectric domains, which the observed low charge recombination rates have been attributed to.

Two-dimensional infrared spectroscopy (2D-IR) is well established as a specialized, high-end technique for measuring structural and solvation dynamics of biological molecules. Recent technological developments now make it possible to acquire time-resolved 2D-IR spectra within seconds, and this opens up the possibility of screening-type applications comparing spectra spanning multiple samples. However, such applications bring new challenges associated with finding accurate, efficient methodologies to analyze large data sets in a timely, informative manner. Here, we demonstrate such an application by screening 2016 2D-IR spectra of 12 double-stranded DNA oligonucleotides obtained in the presence and absence of binding therapeutic molecule Hoechst 33258. By applying analysis of variance combined with principal component analysis (ANOVA-PCA) to 2D-IR data for the first time, we demonstrate the ability to efficiently retrieve the base composition of a DNA sequence and discriminate ligand-DNA complexes from unbound sequences. We further show accurate differentiation of the induced-fit and rigid-body binding modes that is key to identifying optimal binding interactions of Hoechst 33258, while ANOVA-PCA results across the full sequence range correlate directly with thermodynamic indicators of ligand-binding strength that require significantly longer data acquisition times to obtain.

A high-speed, high-sensitivity and compact two-dimensional infrared (2D-IR) spectrometer based on 100 kHz Yb:KGW regenerative amplifier technology is described and demonstrated. The setup is three color, using an independent pump OPA and two separately tunable probe OPAs. The spectrometer uses 100 kHz acousto-optic pulse shaping on the pump beam for rapid 2D-IR acquisitions. The shot-to-shot stability of the laser system yields excellent signal-to-noise figures (∼10 μOD noise on 5000 laser shots). We show that the reduced bandwidth of the Yb:KGW amplifiers in comparison with conventional Ti:sapphire systems does not compromise the ability of the setup to generate high-quality 2D-IR data. Instrument responses of

For the first time, infrared spectra on the sub-wavelength scale have been delivered by a synchrotron-radiation-induced thermal expansion technique [1]. The novel experimental result was achieved by coupling an atomic force microscope (AFM) to an infrared (IR) beamline at the UK's national synchrotron facility, Diamond Light Source. Via broadband synchrotron illumination and an AFM sub-micron tip, molecular IR spectra were obtained by detecting a resonance-enhanced (RE) photothermal signal with spatial resolution beyond the diffraction limit. Together with results on synchrotron IR nanoscopy in scattering mode from the IR beamline at the Advanced Light Source two years ago, the Diamond photothermal nanoprobe approach moves vibrational analysis beyond the diffraction limit and into nanoscale absorption spectroscopy.

Revealing the details of biomolecular processes in solution needs tools that can monitor structural dynamics over a range of time and length scales. We assess the ability of 2D-IR spectroscopy in combination with multivariate data analysis to quantify changes in secondary structure of the multifunctional calcium-binding messenger protein Calmodulin (CaM) as a function of temperature and Ca2+ concentration. Our approach produced quantitative agreement with circular dichroism (CD) spectroscopy in detecting the domain melting transitions of Ca2+-free (apo) CaM (reduction in α-helix structure by 13% (CD) and 15% (2D)). 2D-IR also allows accurate differentiation between melting transitions and generic heating effects observed in the more thermally-stable Ca2+-bound (holo-) CaM. The functionally-relevant random-coil-α-helix transition associated with Ca2+ uptake that involves just 7-8 out of a total of 148 amino acid residues was clearly detected. Temperature-dependent Molecular Dynamics (MD) simulations show that apo-CaM exists in dynamic equilibrium with holo-like conformations while Ca2+ uptake reduces conformational flexibility. The ability to combine quantitative structural insight from 2D-IR with MD simulations thus offers a powerful approach for measuring subtle protein conformational changes in solution.

Group 6 metal carbonyl complexes ([M(bpy)(CO)

Time-resolved spectroscopy developments are presented focussing on ultrafast IR laser techniques probing molecular dynamics. These developments at the ULTRA laboratory focus on improving sensitivity, expanding data collection parameters and widening application to a diverse array of samples. The techniques presented apply high repetition rate lasers, 1–100 kHz, based on cryo-cooled, titanium sapphire, ytterbium (Yb:KGW) and an ytterbium-pumped optical parametric chirped pulse (OPCPA) amplifiers. The outputs are used directly in experiments or via wavelength conversion devices in the ultraviolet to infrared (200–16000 nm).

Changes in the structural and solvation dynamics of a 15mer AT DNA duplex upon melting of the double-helix are observed by a combination of ultrafast two-dimensional infrared (2D-IR) and optical Kerr-effect (OKE) spectroscopies. 2D-IR spectroscopy of the vibrational modes of the DNA bases reveal signature off-diagonal peaks arising from coupling and energy transfer across Watson–Crick paired bases that are unique to double-stranded DNA (ds-DNA). Spectral diffusion of specific base vibrational modes report on the structural dynamics of the duplex and the minor groove, which is predicted to contain a spine of hydration. Changes in these dynamics upon melting are assigned to increases in the degree of mobile solvent access to the bases in single-stranded DNA (ss-DNA) relative to the duplex. OKE spectra exhibit peaks that are assigned to specific long-range phonon modes of ds- and ss-DNA. Temperature-related changes in these features correlate well with those obtained from the 2D-IR spectra although the melting temperature of the ds-DNA phonon band is slightly higher than that for the Watson–Crick modes, suggesting that a degree of long-range duplex structure survives the loss of Watson–Crick hydrogen bonding. These results demonstrate that the melting of ds-DNA disrupts helix-specific structural dynamics encompassing length scales ranging from mode delocalisation in the Watson–Crick base pairs to long-range phonon modes that extend over multiple base pairs and which may play a role in molecular recognition of DNA.

The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced noncovalent interactions between the ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a suboptimal alternating A-T sequence. Results from two-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of the minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favorable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.

In this paper, we experimentally demonstrate the use of infrared synchrotron radiation (IR-SR) as a broadband source for photothermal near-field infrared spectroscopy. We assess two methods of signal transduction; cantilever resonant thermal expansion and scanning thermal microscopy. By means of rapid mechanical chopping (50-150 kHz), we modulate the IR-SR at rates matching the contact resonance frequencies of atomic force microscope (AFM) cantilevers, allowing us to record interferograms yielding Fourier transform infrared (FT-IR) photothermal absorption spectra of polystyrene and cyanoacrylate films. Complementary offline measurements using a mechanically chopped CW IR laser confirmed that the resonant thermal expansion IR-SR measurements were below the diffraction limit, with a spatial resolution better than 500 nm achieved at a wavelength of 6 μm, i.e. λ/12 for the samples studied. Despite achieving the highest signal to noise so far for a scanning thermal microscopy measurement under conditions approaching near-field (dictated by thermal diffusion), the IR-SR resonant photothermal expansion FT-IR spectra measured were significantly higher in signal to noise in comparison with the scanning thermal data.

We present a dual-amplifier laser system for time-resolved multiple-probe infrared (IR) spectroscopy based on the ytterbium potassium gadolinium tungstate (Yb:KGW) laser medium. Comparisons are made between the ytterbium-based technology and titanium sapphire laser systems for time-resolved IR spectroscopy measurements. The 100 kHz probing system provides new capability in time-resolved multiple-probe experiments, as more information is obtained from samples in a single experiment through multiple-probing. This method uses the high repetition-rate probe pulses to repeatedly measure spectra at 10 µs intervals following excitation allowing extended timescales to be measured routinely along with ultrafast data. Results are presented showing the measurement of molecular dynamics over >10 orders of magnitude in timescale, out to 20 ms, with an experimental time response of

Amyloid aggregates are highly ordered fibrillar assemblies of polypeptides involved in a number of neurodegenerative diseases. Very little is known on the pathways of self-assembly of peptides into the final amyloid fibrils, which is due in part to the difficulty of triggering the aggregation process in a controlled manner. Here we present the design and validation of a cross-linked hexapeptide that reversibly aggregates and dissociates under ultraviolet light irradiation control. First molecular dynamics simulations were carried out to identify, among hundreds of possible sequences, those with the highest propensity to form ordered (β-sheet) oligomers in the trans state of the azobenzene cross-linker, and at the same time with the highest solubility in the cis state. In the simulations, the peptides were observed to spontaneously form ordered oligomers with cross-β contacts when the cross-linker was in the trans state, whereas in the cis state they self-assemble into amorphous aggregates. For the most promising sequence emerging from the simulations (Ac-Cys-His-Gly-Gln-Cys-Lys-NH(2) cross-linked at the two cysteine residues), the photoisomerization of the azobenzene group was shown to induce reversible aggregation by time-resolved light scattering and fluorescence measurements. The amyloid-like fibrillar topology was confirmed by electron microscopy. Potential applications of minimally designed peptides with photoswitchable amyloidogenic propensity are briefly discussed.

A series of photoswitchable, alpha-helical peptides were studied using two-dimensional infrared spectroscopy (2D-IR). Single-isotope labeling with (13)C(18)O at various positions in the sequence was employed to spectrally isolate particular backbone positions. We show that a single (13)C(18)O label can give rise to two bands along the diagonal of the 2D-IR spectrum, one of which is from an amide group that is hydrogen-bonded internally, or to a solvent molecule, and the other from a non-hydrogen-bonded amide group. The photoswitch enabled examination of both the folded and unfolded state of the helix. For most sites, unfolding of the peptide caused a shift of intensity from the hydrogen-bonded peak to the non-hydrogen-bonded peak. The relative intensity of the two diagonal peaks gives an indication of the fraction of molecules hydrogen-bonded at a certain location along the sequence. As this fraction varies quite substantially along the helix, we conclude that the helix is not uniformly folded. Furthermore, the shift in hydrogen bonding is much smaller than the change of helicity measured by CD spectroscopy, indicating that non-native hydrogen-bonded or mis-folded loops are formed in the unfolded ensemble.

The authors thank the EPSRC (Grant Number: EP/J02077X/1), CONACYT Mexico, and the University of Edinburgh for funding this research. Synchrotron radiation (SR) IR microspectroscopy has enabled determination of the thermodynamics, kinetics, and molecular orientation of CO2 adsorbed in single microcrystals of a functionalized metal–organic framework (MOF) under conditions relevant to carbon capture from flue gases. Single crystals of the small-pore MOF, Sc2(BDC-NH2)3, (BDC-NH2=2-amino-1,4-benzenedicarboxylate), with well-defined crystal form have been investigated during CO2 uptake at partial pressures of 0.025-0.2 bar at 298–373 K. The enthalpy and diffusivity of adsorption determined from individual single crystals are consistent with values obtained from measurements on bulk samples. The brilliant SR IR source permits rapid collection of polarized spectra. Strong variations in absorbance of the symmetric stretch of the NH2 groups of the MOF and the asymmetric stretch of the adsorbed CO2 at different orientations of the crystals relative to the polarized IR light show that CO2 molecules align along channels in the MOF. Publisher PDF

Surface analysis: Two-dimensional infrared spectroscopy (2D-IR) was used to probe amide and carboxylate functional groups in the vicinity of gold nanoparticles and their aggregates. The data presented shows that the unique ability of 2D-IR spectroscopy to characterize broadening mechanisms and cross peaks offers new insights into gold nanoparticle capping layer structure and dynamics (see picture).

2D-IR spectroscopy is used to quantify gold nanoparticle IR surface enhancement. Changes in 2D lineshapes and the appearance of surface group cross peaks demonstrate that 2D-IR offers a unique sensitivity to nanoparticle cappant structure/dynamics.

The well-known and prominent marker bands of aromatic amino acids in Raman spectra of protein and peptide films are revisited in the frequency and time domains using three-color picosecond coherent anti-Stokes Raman spectroscopy (CARS). We show here that control of the probe delay allows the narrow width/long lifetime states to be observed free not only from nonresonant background and fluorescence contamination but also free from the spectral congestion that arises from the complex background of spectrally broader (shorter lifetime) vibrational modes. The reasonable limits of detection obtained indicate that such CARS methods may be useful for quantitative analysis of protein composition.

In the last 10 years, several forms of two-dimensional infrared (2DIR) spectroscopy have been developed, such as IR pump−probe spectroscopy and photon-echo techniques. In this Account, we describe a doubly vibrationally enhanced four-wave mixing method, in which a third-order nonlinear signal is generated from the interaction of two independently tunable IR beams and an electron-polarizing visible beam at 790 nm. When the IR beams are independently in resonance with coupled vibrational transitions, the signal is enhanced and cross-peaks appear in the spectrum. This method is known as either DOVE (doubly vibrationally enhanced) four-wave mixing or EVV (electron−vibration−vibration) 2DIR spectroscopy. We begin by discussing the basis and properties of EVV 2DIR. We then discuss several biological and potential biomedical applications. These include protein identification and quantification, as well as the potential of this label-free spectroscopy for protein and peptide structural analysis. In proteomics, we...

We design and characterize spherical gold nanoparticles, which are covalently linked to and completely covered by 3(10)-helical peptides. These helices provide a scaffold to place (13)C=O isotope labels at defined distances from the gold surface, which we employ as local thermometers. Probing these reporter groups with transient infrared spectroscopy, we monitor the vibrational energy flow across the peptide capping layer following excitation of the nanoparticle plasmon resonance.

We study gold nanoparticles capped with a layer of helical peptides. Energy transport through the peptides is initiated by exciting the plasmon resonance. 2-D-IR spectroscopy is used to gain structural information about the capping layer.

Electrical interactions between molecular vibrations can be non-linear and thereby produce intermolecular coupling even in the absence of a chemical bond. We use this fact to detect the formation of an intermolecular complex using electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) and also to determine the distance and angle between the two molecular species.

In the last 10 years, several forms of two-dimensional infrared (2DIR) spectroscopy have been developed, such as IR pump-probe spectroscopy and photon-echo techniques. In this Account, we describe a doubly vibrationally enhanced four-wave mixing method, in which a third-order nonlinear signal is generated from the interaction of two independently tunable IR beams and an electron-polarizing visible beam at 790 nm. When the IR beams are independently in resonance with coupled vibrational transitions, the signal is enhanced and cross-peaks appear in the spectrum. This method is known as either DOVE (doubly vibrationally enhanced) four-wave mixing or EVV (electron-vibration-vibration) 2DIR spectroscopy. We begin by discussing the basis and properties of EVV 2DIR. We then discuss several biological and potential biomedical applications. These include protein identification and quantification, as well as the potential of this label-free spectroscopy for protein and peptide structural analysis. In proteomics, we also show how post-translational modifications in peptides (tyrosine phosphorylation) can be detected by EVV 2DIR spectroscopy. The feasibility of EVV 2DIR spectroscopy for tissue imaging is also evaluated. Preliminary results were obtained on a mouse kidney histological section that was stained with hematoxylin (a small organic molecule). We obtained images by setting the IR frequencies to a specific cross-peak (the strongest for hematoxylin was obtained from its analysis in isolation; a general CH(3) cross-peak for proteins was also used) and then spatially mapping as a function of the beam position relative to the sample. Protein and hematoxylin distribution in the tissue were measured and show differential contrast, which can be entirely explained by the different tissue structures and their functions. The possibility of triply resonant EVV 2DIR spectroscopy was investigated on the retinal chromophore at the centre of the photosynthetic protein bacteriorhodopsin (bR). By putting the visible third beam in resonance with an electronic transition, we were able to enhance the signal and increase the sensitivity of the method by several orders of magnitude. This increase in sensitivity is of great importance for biological applications, in which the number of proteins, metabolites, or drug molecules to be detected is low (typically pico- to femtomoles). Finally, we present theoretical investigations for using EVV 2DIR spectroscopy as a structural analysis tool for inter- and intramolecular interaction geometries.

Electron-vibration-vibration two-dimensional coherent spectroscopy, a variant of 2DIR, is shown to be a useful tool to differentiate a set of 10 proteins based on their amino acid content. Two-dimensional vibrational signatures of amino acid side chains are identified and the corresponding signal strengths used to quantify their levels by using a methyl vibrational feature as an internal reference. With the current apparatus, effective differentiation can be achieved in four to five minutes per protein, and our results suggest that this can be reduced to

We employ a particular form of two-dimensional infrared four-wave mixing (2DIR FWM) as a vibrational spectroscopic tool to quantify the amino acid content of a number of peptides. Vibrational features corresponding to ring modes of the aromatic groups of phenylalanine (Phe) and tyrosine (Tyr), as well as a methylene mode that is used as an internal reference, are identified. We show that the ratios of the integrated intensities, and the amplitudes, of the aromatic peaks of Phe and Tyr relative to the methylene integrated intensity, and amplitude, are proportional to the actual ratio of Phe and Tyr to CH2 in the samples within a precision of ±12.5%. This precision is shown to be sufficient to use this form of 2DIR spectroscopy as a possible proteins fingerprinting tool.

We show that it is possible to both directly measure and directly calculate Fermi resonance couplings in benzene. The measurement method used was a particular form of two-dimensional infrared spectroscopy (2D-IR) known as doubly vibrationally enhanced four wave mixing. By using different pulse orderings, vibrational cross peaks could be measured either purely at the frequencies of the base vibrational states or split by the coupling energy. This capability is a feature currently unique to this particular form of 2D-IR and can be helpful in the decongestion of complex spectra. Five cross peaks of the ring breathing mode nu13 with a range of combination bands were observed spanning a region of 1500-4550 cm(-1). The coupling energy was measured for two dominant states of the nu13+nu16 Fermi resonance tetrad. Dephasing rates were measured in the time domain for nu13 and the two (nu13+nu16) Fermi resonance states. The electronic and mechanical vibrational anharmonic coefficients were calculated to second and third orders, respectively, giving information on relative intensities of the cross peaks and enabling the Fermi resonance states of the combination band nu13+nu16 at 3050-3100 cm(-1) to be calculated. The excellent agreement between calculated and measured spectral intensities and line shapes suggests that assignment of spectral features from ab initio calculations is both viable and practicable for this form of spectroscopy.

We describe here a high sensitivity means of performing time resolved UV/Visible pump, infrared probe spectroscopy using optically Heterodyne Detected UV-IR Transient Gratings. The experiment design employed is simple, robust and includes a novel means of generating phase locked pulse pairs that relies on only mirrors and a beamsplitter. A signal to noise ratio increase of 24 compared with a conventional pump-probe arrangement is demonstrated.

We demonstrate how quasi-phase-cycling achieved by sub-cycle delay modulation can be used to replace optical chopping in a box-CARS 2D IR experiment in order to enhance the signal size, and, at the same time, completely eliminate any scattering contamination. Two optical devices are described that can be used for this purpose, a wobbling Brewster window and a photoelastic modulator. They are simple to construct, easy to incorporate into any existing 2D IR setup, and have attractive features such as a high optical throughput and a fast modulation frequency needed to phase cycle on a shot-to-shot basis.

The transient grating technique is applied to UV/VIS-pump IR-probe measurements to obtain a background free transient infrared signal. In comparison with conventional UV/VIS-pump IR-probe measurements the S/N is enhanced by a factor of 25.