Potential Dependent Reorientation Controlling Activity of a Molecular Electrocatalyst.

The activity of molecular electrocatalysts depends on the interplay of electrolyte composition near the electrode surface, the composition and morphology of the electrode surface, and the electric field at the electrode-electrolyte interface. This interplay is challenging to study and often overlooked when assessing molecular catalyst activity. Here, we use surface specific vibrational sum frequency generation (VSFG) spectroscopy to study the solvent and potential dependent activation of Mo(bpy)(CO)4, a CO2 reduction catalyst, at a polycrystalline Au electrode. We find that the parent complex undergoes potential dependent reorientation at the electrode surface when a small amount of N-methyl-2-pyrrolidone (NMP) is present. This preactivates the complex, resulting in greater yields at less negative potentials, of the active electrocatalyst for CO2 reduction.

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

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

The 2D-IR spectrum of hydrogen-bonded silanol groups in pyrogenic silica.

Pyrogenic silica is a form of amorphous silica with a high surface area and a heterogeneous distribution of silanol hydroxyl terminations and defects. In this work, the interesting and unusual form of the hydroxyl-stretch 2D-IR spectrum of pyrogenic silica is presented and explored in the deuterated (deuteroxyl) form. Transition dipole couplings between hydrogen-bonded and non-hydrogen-bonded silanol groups give a distinct cross-peak in the 2D-IR spectrum, displaying interstate coherence oscillations during the 2D-IR experimental waiting time. The strong asymmetry about the diagonal is proposed to be the result of both the relatively small transition dipole coupling strength and the extreme differences in the width of the hydrogen-bonded and non-hydrogen-bonded silanol bands. The resulting interference of negative and positive cross-peaks has minimal intensity in the below-diagonal ω3 < ω1 region of the spectrum. An additional strong positive cross-peak is observed at a position in the 2D-IR spectrum inconsistent with transition dipole coupling. An assignment as a fifth order effect is proposed.

Correction: Time-resolved infra-red studies of photo-excited porphyrins in the presence of nucleic acids and in HeLa tumour cells: insights into binding site and electron transfer dynamics.

Correction for 'Time-resolved infra-red studies of photo-excited porphyrins in the presence of nucleic acids and in HeLa tumour cells: insights into binding site and electron transfer dynamics' by Páraic M. Keane et al., Phys. Chem. Chem. Phys., 2022, 24, 27524-27531, https://doi.org/10.1039/D2CP04604K.

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.

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

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

Time-resolved infra-red studies of photo-excited porphyrins in the presence of nucleic acids and in HeLa tumour cells: insights into binding site and electron transfer dynamics.

Cationic porphyrins based on the 5,10,15,20-meso-(tetrakis-4-N-methylpyridyl) core (TMPyP4) have been studied extensively over many years due to their strong interactions with a variety of nucleic acid structures, and their potential use as photodynamic therapeutic agents and telomerase inhibitors. In this paper, the interactions of metal-free TMPyP4 and Pt(II)TMPyP4 with guanine-containing nucleic acids are studied for the first time using time-resolved infrared spectroscopy (TRIR). In D2O solution (where the metal-free form exists as D2TMPyP4) both compounds yielded similar TRIR spectra (between 1450-1750 cm-1) following pulsed laser excitation in their Soret B-absorption bands. Density functional theory calculations reveal that vibrations centred on the methylpyridinium groups are responsible for the dominant feature at ca. 1640 cm-1. TRIR spectra of D2TMPyP4 or PtTMPyP4 in the presence of guanosine 5'-monophosphate (GMP), double-stranded {d(GC)5}2 or {d(CGCAAATTTGCG)}2 contain negative-going signals, 'bleaches', indicative of binding close to guanine. TRIR signals for D2TMPyP4 or PtTMPyP bound to the quadruplex-forming cMYC sequence {d(TAGGGAGGG)}2T indicate that binding occurs on the stacked guanines. For D2TMPyP4 bound to guanine-containing systems, the TRIR signal at ca. 1640 cm-1 decays on the picosecond timescale, consistent with electron transfer from guanine to the singlet excited state of D2TMPyP4, although IR marker bands for the reduced porphyrin/oxidised guanine were not observed. When PtTMPyP is incorporated into HeLa tumour cells, TRIR studies show protein binding with time-dependent ps/ns changes in the amide absorptions demonstrating TRIR's potential for studying light-activated molecular processes not only with nucleic acids in solution but also in biological cells.

Detection of Glycine as a Model Protein in Blood Serum Using 2D-IR Spectroscopy.

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.

An ultrafast vibrational study of dynamical heterogeneity in the protic ionic liquid ethyl-ammonium nitrate. I. Room temperature dynamics.

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.

2D-Infrared Spectroscopy of Proteins in Water: Using the Solvent Thermal Response as an Internal Standard.

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.

In situ study of the low overpotential "dimer pathway" for electrocatalytic carbon dioxide reduction by manganese carbonyl complexes.

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.

Rapid Screening of DNA-Ligand Complexes via 2D-IR Spectroscopy and ANOVA-PCA.

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.

The Role of Electrode-Catalyst Interactions in Enabling Efficient CO2 Reduction with Mo(bpy)(CO)4 As Revealed by Vibrational Sum-Frequency Generation Spectroscopy.

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.

Quantifying Secondary Structure Changes in Calmodulin Using 2D-IR 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.

Femtosecond to microsecond observation of the photochemical reaction of 1,2-di(quinolin-2-yl)disulfide with methyl methacrylate.

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[double bond, length as m-dash]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.

Ultrafast 2D-IR and optical Kerr effect spectroscopy reveal the impact of duplex melting on the structural dynamics of DNA.

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.

Broadband near-field infrared spectromicroscopy using photothermal probes and synchrotron radiation.

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.

In situ synchrotron IR microspectroscopy of CO2 adsorption on single crystals of the functionalized MOF Sc2(BDC-NH2)3.

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.

Laser induced temperature-jump time resolved IR spectroscopy of zeolites.

Combining pulsed laser heating and time-resolved infrared (TR-IR) absorption spectroscopy provides a means of initiating and studying thermally activated chemical reactions and diffusion processes in heterogeneous catalysts on timescales from nanoseconds to seconds. To this end, we investigated single pulse and burst laser heating in zeolite catalysts under realistic conditions using TR-IR spectroscopy. 1 ns, 70 µJ, 2.8 µm laser pulses from a Nd:YAG-pumped optical parametric oscillator were observed to induce temperature-jumps (T-jumps) in zeolite pellets in nanoseconds, with the sample cooling over 1-3 ms. By adopting a tightly focused beam geometry, T-jumps as large as 145 °C from the starting temperature were achieved, demonstrated through comparison of the TR-IR spectra with temperature dependent IR absorption spectra and three dimensional heat transfer modelling using realistic experimental parameters. The simulations provide a detailed understanding of the temperature distribution within the sample and its evolution over the cooling period, which we observe to be bi-exponential. These results provide foundations for determining the magnitude of a T-jump in a catalyst/adsorbate system from its absorption spectrum and physical properties, and for applying T-jump TR-IR spectroscopy to the study of reactive chemistry in heterogeneous catalysts.

Gold nanoparticle capping layers: structure, dynamics, and surface enhancement measured using 2D-IR spectroscopy.

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.