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Transient IR and X-Ray spectroscopies were used to investigate excited state delocalization of a mixed valence Ru based donor-bridge-acceptor complex on a femtosecond timescale revealing the role of the electron density on the Ru-CN-Ru fragment
Proteins are complex, heterogeneous macromolecules that exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires experimental tools to characterize them with high spatial and temporal precision. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution. Two-dimensional (2D) IR methods that provide richer information are becoming more routine but remain challenging to apply to proteins. Spectral congestion typically prevents selective investigation of native vibrations; however, the problem can be overcome by site-specific introduction of amino acid side chains that have vibrational groups with frequencies in the “transparent window” of protein spectra. This Perspective provides an overview of the history and recent progress in the development of transparent window 2D IR of proteins.
This paper presents a re-examination of the conclusions of a study reported in The Journal of Physical Chemistry Letters (Saparbaev et al., 2021, 12, 907) that compared the structure of microsolvated ions formed by electrospray ionization to those formed in the gas-phase via a previously published cryogenic ion trap approach. We conducted additional experiments that clearly show that most of the observed differences in the IR spectra can be accounted for by considering the different spectroscopic action schemes used to obtain them. In particular, the presence of the D 2 -tag induces shifts in some of the N-H and O-H peaks which need to be carefully considered before comparing spectra. Furthermore, once these spectral effects are taken into account, we show that both clustering approaches yields similar clusters structures for the small GlyH + (H 2 O)n species. Using unimolecular reaction rate theory, we also show that for the small complexes considered here, only the gas-phase equilibrium distribution of conformers should be expected in both experimental approaches. In addition, the barrier heights necessary to kinetically trap high-energy conformers at 298K is explored using a series of model polyalanine chains.
We report the generation and characterization of microjoule level, broad bandwidth femtosecond pulses in the mid-infrared (MIR) using optical parametric amplification of continuum MIR seed pulses in GaSe. The signal (3 μm) and idler (6 μm) pulses have energies of 6 μJ and 3 μJ with bandwidths of ∼950 cm −1 and 650 cm −1 FWHM and pulse lengths of 34 fs and 80 fs. Broadband 2D IR spectra of O-H and N-H transitions are acquired with the signal beam demonstrating the capabilities of this source for cross peak and line shape measurements.
Characterizing surface intermediates during catalysis is essential for developing mechanistic models of catalytic reactions and for identifying rate-controlling steps. Here, in this work, we used polarization-dependent reflection absorption infrared spectroscopy (PD-RAIRS) to investigate surface intermediates that form on IrO 2 (1 1 0) during the catalytic oxidation of C 2 H 6 at pressures near 0.5 Torr. Our results show that adsorbed CO and HCO 2 are the only intermediates detectable with PD-RAIRS across a wide range of temperatures and reactant compositions during complete C 2 H 6 oxidation, giving rise to dominant peaks at about 2093 and 1310 cm −1 , respectively. These assignments were corroborated by RAIRS measurements following CO and HCOOH adsorption in ultrahigh vacuum, RAIRS with C 2 H 6 – 18 O 2 mixtures during catalysis and vibrational frequencies and IR intensities computed using density functional theory. We find that increasing the C 2 H 6 mole fraction in the reaction mixture raises the CO surface coverage relative to HCO 2 , correlating with increasing catalytic oxidation rates. The formation of CO and HCO 2 surface species at temperatures well below catalytic ignition indicates that the overall rate of C 2 H 6 oxidation on IrO 2 (1 1 0) is governed by steps late in the reaction sequence, such as H 2 O formation, CO oxidation and HCO 2 dehydrogenation. These findings provide key insight into the mechanism of alkane oxidation on IrO 2 (1 1 0) and valuable input for first-principles microkinetic modeling.
The reactions of acetone and hydroxyacetone over heteroatom doped BEA zeolites (Sn, Mo, and W) in the presence and absence of H 2 O vapor are investigated using infrared spectroscopy. Acetone is converted to mesityl oxide over Sn-BEA exclusively. At higher temperatures, larger oxygenates such as phorones, aromatics, and coke form. The presence of co-adsorbed water in Sn-BEA suppresses tautomerization. H 2 O vapor is also beneficial for minimizing coke formation at high temperatures. Hydroxyacetone is converted into 2-hydroxypropanal over Sn-BEA, exhibiting high affinity to Sn sites up to 400 °C. Sn-BEA catalyzes conversion of hydroxyacetone into the enol in the absence of H 2 O, but exposure to H 2 O induces the formation of 2-hydroxypropanal and subsequent conversion to acrolein. Furthermore, the Lewis acid descriptors are used to rationalize the reaction pathways. For the isomerization of hydroxyacetone into 2-hydroxypropanal, the hardness of acid sites influences the reaction and correlates with the overall Lewis acidity of the catalysts, respectively. However, the size of the exchanged metal significantly affects aldol condensation, where keto and enol forms of acetone adsorb to active sites simultaneously.
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Diffraction images were collected using an MX300-HS CCD detector. For each cryoloop, 2D raster scan with 50 μm step in each direction was performed twice. In the second pass, the raster-scan grid was shifted 25 μm in each direction. In cheetah directory, - {puck_name}/{pin_id}_hits.h5 correspond to the first scan, and - {puck_name}/{pin_id}-2_hits.h5 correspond to the second scan.
Eleven 2,2'-bipyridine (bpy) ligands functionalized with attachment groups for covalent immobilization on silicon surfaces were prepared. Five of the ligands feature silatrane functional groups for attachment to metal oxide coatings on the silicon surfaces, while six contain either alkene or alkyne functional groups for attachment to hydrogen-terminated silicon surfaces. The bpy ligands were coordinated to Re(CO) 5 Cl to form complexes of the type Re(bpy)(CO) 3 Cl, which are related to known catalysts for CO 2 reduction. Six of the new complexes were characterized using X-ray crystallography. As proof of principle, four molecular Re complexes were immobilized on either a thin layer of TiO 2 on silicon or hydrogen-terminated silicon. The surface-immobilized complexes were characterized using X-ray photoelectron spectroscopy, IR spectroscopy, and cyclic voltammetry (CV) in the dark and for one representative example in the light. The CO stretching frequencies of the attached complexes were similar to those of the pure molecular complexes, but the CVs were less analogous. For two of the complexes, comparison of the electrocatalytic CO 2 reduction performance showed lower CO Faradaic efficiencies for the immobilized complexes than the same complex in solution under similar conditions. In particular, a complex containing a silatrane linked to bpy with an amide linker showed poor catalytic performance and control experiments suggest that amide linkers in conjugation with a redox-active ligand are not stable under highly reducing conditions and alkyl linkers are more stable. So a conclusion of this work is that understanding the behavior of molecular Re catalysts attached to semiconducting silicon is more complicated than related complexes, which have previously been immobilized on metallic electrodes.
Cyclometalated platinum(II) compounds with both C^N chelating iminic ligands and isocyanide ligands were synthesized. Two sets of compounds from the reaction of two separate HC^N ligands (derived from thiophene or benzene) with [Pt2Me4(μ-SMe 2 ) 2 ] were obtained, resulting in square planar compounds with an anionic C^N ligand, a methyl ligand, and a dimethyl sulfide (dms) ligand completing the coordination sphere. Subsequently, the dms ligand was easily substituted by several isocyanide ligands (2-naphthyl, adamantyl, 2,6-dimethylphenyl, ptoluenesulfonylmethyl). The compounds were characterized by multinuclear NMR spectroscopy, IR spectroscopy, and singlecrystal X-ray diffraction (SCXRD). Their photophysical properties were explored using UV/vis, emission, and transient absorption (TA) spectroscopy. The emission spectra for the thiophene-derived compounds showed well-defined dual emission peaks, while the benzene-derived compounds’ bands appeared less resolved. DFT and TDDFT calculations were performed, and results were compared to the observed spectroscopic properties of the newly synthesized complexes.
Metal borohydride complexes have long been the subject of intense fundamental interest because of their unconventional metal–ligand bonding that occurs via three-center, two-electron M–H–B bonds. This type of bonding implies significant delocalization of electron density over all three atoms, but the degree of orbital mixing between the metal and boron has been difficult to assess by direct experimental means. Herein, we demonstrate how ligand K-edge X-ray absorption spectroscopy (XAS) conducted at the B K-edge yields evidence of significant covalent M–H–B bonding with Zr and Hf. To accommodate the B K-edge XAS studies, which were conducted under ultra-high vacuum (<10 −8 torr), we prepared a series of new [Zr(RBH 3 ) 4 ] and [Hf(RBH 3 ) 4 ] complexes with substituents that attenuate volatility (R = benzyl, phenyl, mesityl, 2,4,6-triisopropylphenyl, and anthryl). 1 H and 11 B NMR spectroscopy, IR spectroscopy, and single-crystal X-ray diffraction (XRD) studies revealed metal and ligand dependent differences in the BH 3 chemical shifts that correlate to changes in M−B distances and select B–H vibrational stretching modes. The B K-edge XAS spectra of the Zr and Hf complexes yielded a pre-edge feature that was assigned as B 1s → M–H–B π* based on comparison to time-dependent density functional theory (TDDFT) calculations. The pre-edge transitions appear due to covalent mixing between boron and the metal, thereby demonstrating how B K-edge XAS can provide direct evidence of covalent three-center, two electron M–H–B bonding in borohydride complexes using boron as a spectroscopic reporter.
Infrared (IR) spectroscopy is a powerful method for mapping chemical heterogeneity on the microscale. Synchrotron IR radiation uniquely provides a high brightness and broad bandwidth to further extend the capabilities of IR spectroscopic imaging. However, the diffraction-limited spatial resolution of IR spectroscopy is insufficient for studies requiring submicrometer spatial differentiation. Optical photothermal IR (O-PTIR) microscopy is a powerful, emerging method that overcomes the IR diffraction limit in IR hyperspectral imaging by employing a modulated IR beam and a visible probe laser beam to detect local temperature-induced modulation at the visible diffraction limit. In this work, we extend the spectral range of photothermal infrared measurements by incorporating a synchrotron IR source, demonstrating a combined synchrotron-based O-PTIR modality that enables high spatial resolution far-field chemical imaging spanning the entire mid-IR range. Both optical- and fluorescence-detected photothermal modalities were performed using a step-scan interferometer, demonstrating improved spectral range (541-4000 cm-1) when compared to optical photothermal microscopy with commercial laser sources (800-1800 cm-1 for this particular source) and improved spatial resolution, when compared to synchrotron microspectroscopy measurements. Following these initial validation studies, synchrotron Fourier-transform fluorescence-detected photothermal IR spectroscopy in combination with synchrotron microspectroscopy measurements was used to differentiate cells in mouse brain tissue sections, which requires submicron spatial resolutions beyond those accessible by IR spectroscopy alone.
Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.
Ion pair formation is a fundamental molecular process that occurs in a wide variety of systems, including electrolytes, biological systems, and materials. In solution, the thiocyanate (SCN–) anion interacts with cations to form contact ion pairs (CIPs). Due to its ambidentate nature, thiocyanate can bind through either its sulfur or nitrogen atoms, depending on the solvent. This study focuses on the binding nature of thiocyanate with lithium ions as a function of the solvents using FTIR, 2D infrared spectroscopy (2DIR) spectroscopies, and theoretical calculations. The study reveals that the SCN– binding mode (S or N end) in CIPs can be identified through 2DIR spectroscopy but not by linear IR spectroscopy. Linear IR spectroscopy shows that the CN stretch frequencies are too close to one another to separate N- and S-bound CIPs. Moreover, the IR spectrum shows that the S–C stretch presents different frequencies for the salt in different solvents, but it is related to the anion speciation rather than to its binding mode. A similar trend is observed for the anion bend. 2DIR spectra show different dynamics for N-bound and S-bound thiocyanate. In particular, the frequency–frequency correlation function (FFCF) dynamics extracted from the 2DIR spectra have a single picosecond exponential decay for N-bound thiocyanate and a biexponential decay for S-bound thiocyanate, consistent with the binding mode of the anion. Lastly, it is also observed that the binding mode also affects the line shape parameters, probably due to the different molecular mechanisms of the FFCF for N- and S-bound CIPs.
As graphene enjoys worldwide research and deployment, the biological impact, geologic degradation, environmental retention, and even some physical phenomena remain less well studied. Bulk production of 13 C-graphene yields a powerful route to study all of these questions. Gram scale synthesis of high quality and high purity turbostratic flash graphene with varying amounts of 13 C-enrichment, from 5% to 99% is reported here. Here, the material is characterized by solid state nuclear magnetic resonance spectroscopy, Raman spectroscopy, infrared (IR) spectroscopy, X-ray photoelectron spectroscopy and inductively coupled plasma mass spectrometry. Notably, an unusual enhancement in the Raman spectroscopic D’ peak is observed, resulting from the modification in vibrational frequency through isotopic enrichment favoring intravalley phonon scattering modes. While the IR absorbance spectrum of graphene is for the most part silent, we prepare here 13 C-enhanced graphene samples that show a large aromatic 12 C= 13 C stretch that reveals this IR-active mode.
Surface grafted organozirconium catalyzes C─H/Et─Al exchange reactions, involving saturated hydrocarbons and AlEt 3 , to afford organoaluminum compounds and ethane. The Zr(O t Bu) 3 @SiO 2 -Al 2 O 3 –700 (1) catalyst contains monopodal ≡SiO─Zr(O t Bu) 3 and only a few residual silanols (<5%). Nonetheless, these silanols are the Achille's heel of 1, providing a pathway for surface and catalyst degradation during catalysis, limiting the alkylaluminum yield and catalyst turnover. Support degradation, involving the cleavage of Si─O bonds by activated surface organometallics, is inhibited by capping silanols with ─SiMe 3 . Residual silanols in 1 react with allyltrimethylsilane, as determined by solid-state 13 C and 29 Si nuclear magnetic resonance (NMR) spectroscopy, infrared (IR) spectroscopy, and reaction stoichiometry, to form Zr(O t Bu) 3 /SiMe 3 @SiO 2 -Al 2 O 3–700 (2), which is resistant to degradation by AlEt 3 . C─H alumination of dodecane catalyzed by 2 produces higher yields of the 1-dodecylaluminum product in comparison to 1, and in >95% selectivity. Additionally, methane undergoes 2-catalyzed C─H alumination, providing a route to AlMe 3 .