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Correction for ‘Infrared spectroscopy for understanding the structure of Nafion and its associated properties’ by Tanya Agarwal et al. , J. Mater. Chem. A , 2024, https://doi.org/10.1039/D3TA05653H.
When surface states (SSs) form in topological insulators (TIs), they inherit the properties of bulk bands, including the electron–hole (e–h) asymmetry but with much more profound impacts. Here via combining magneto-infrared spectroscopy with theoretical analysis, we show that e–h asymmetry significantly modifies the SS electronic structures when interplaying with the quantum confinement effect. Compared with the case without e–h asymmetry, the SSs now bear not only a band asymmetry, such as that in the bulk, but also a shift of the Dirac point relative to the bulk bands and a reduction of the hybridization gap of up to 70%. Here, our results signify the importance of e–h asymmetry in the band engineering of TIs in the thin-film limit.
The cell wall integrity (CWI) signaling pathway regulates yeast cell wall biosynthesis, cell division, and responses to external stress. The cell wall, comprised of a dense network of chitin, β-1,3- and β-1,6- glucans, and mannoproteins, is very thin, <100 nm. Alterations in cell wall composition may activate the CWI pathway. Saccharomyces cerevisiae, a model yeast, was used to study the role of individual wall components in altering the structure and biophysical properties of the yeast cell wall. Near-field Fourier transform infrared spectroscopy (nano-FT-IR) was used for the first direct, spectrochemical identification of cell wall composition in a background (wild-type) strain and two deletion mutants from the yeast knock-out collection: kre6Δ and knr4Δ. Killer toxin resistant 6 (Kre6) is an integral membrane protein required for biosynthesis of β-1,6-glucan, while Knr4 is a cell signaling protein involved in the control of cell wall biosynthesis, in particular, biosynthesis and deposition of chitin. Complementary spectral data were obtained with far-field (FF)-FT-IR, in transmission, and with attenuated total reflectance (ATR) spectromicroscopy with 3 –10 μm wavelength-dependent spatial resolution. The FF-FT-IR spectra of cells and spectra of isolated cell wall components showed that components of the cell body dominated transmission spectra and were still evident in ATR spectra. In contrast, the nano-FT-IR at ~25 nm spatial resolution could be used to characterize the yeast wall chemical structure. Our results show that the β-1,6-glucan content is decreased in kre6Δ, while all glucan content is decreased in the knr4Δ cell wall. The latter may be thinner than in wild type, since not only are mannan and chitin detectable by nano-FT-IR, but also lipid membranes and protein, indicative of cell interior.
The ability to uniquely identify a compound requires highly precise and orthogonal measurements. Here we describe a newly developed analytical platform that integrates high resolution ion mobility and cryogenic vibrational ion spectroscopy for high-precision structural characterizations. This platform allows for the temporal separation of isomeric/isobaric ions and provides a highly sensitive description of the ion’s adopted geometry in the gas phase. The combination of these orthogonal structural measurements yields precise descriptors that can be used to resolve between and confidently identify highly similar ions. The unique benefits of our instrument, which integrates a structures for lossless ion manipulations ion mobility (SLIM IM) device with messenger tagging infrared spectroscopy, include the ability to perform high-resolution ion mobility separations and to record the IR spectra of all ions simultaneously. The SLIM IM device, with its 13 m separation path length, allows for multipass experiments to be performed for increased resolution as needed. It is integrated with an Agilent qTOF MS where the collision cell was replaced with a cryogenically held (30 K) TW-SLIM module. The cryo-SLIM is operated in a novel manner that allows ions to be streamed through the device and collisionally cooled to a temperature where they can form noncovalently bound N 2 complexes that are maintained as they exit the device and are detected by the TOF mass analyzer. The instrument can be operated in two modes: IMS+IR where the IR spectra for mobility-selected ions can be recorded and IR-only mode where the IR spectra for all mass-resolved ions can be recorded. In IR-only mode, IR spectra (400 cm –1 spectral range) can be recorded in as short as 2 s for high throughput measurements. Further, this work details the construction of the instrument and modes of operation. It provides initial benchmarking of CCS and IR measurements to demonstrate the utility of this instrument for targeted and untargeted approaches.
Herein we employ synchrotron-based near-field infrared spectroscopy to image the phononic properties of ferroelectric domain walls in hexagonal ( h ) Lu 0.6 Sc 0.4 FeO 3 , and we compare our findings with a detailed symmetry analysis, lattice dynamics calculations, and prior models of domain-wall structure. Rather than metallic and atomically thin as observed in the rare-earth manganites, ferroelectric walls in h -Lu 0.6 Sc 0.4 FeO 3 are broad and semiconducting, a finding that we attribute to the presence of an A -site substitution-induced intermediate phase that reduces strain and renders the interior of the domain wall nonpolar. Mixed Lu/Sc occupation on the A site also provides compositional heterogeneity over micron-sized length scales, and we leverage the fact that Lu and Sc cluster in different ratios to demonstrate that the spectral characteristics at the wall are robust even in different compositional regimes. This work opens the door to broadband imaging of physical and chemical heterogeneity in ferroics and represents an important step toward revealing the rich properties of these flexible defect states.
Photothermal atomic force microscopy coupled with infrared spectroscopy (AFM-IR) brings significant value as a spatially resolved surface analysis technique for disordered oxide materials such as glasses, but additional development and fundamental understanding of governing principles is needed to interpret AFM-IR spectra, since the existing theory described for organic materials does not work for materials with high extinction coefficients for infrared (IR) absorption. This paper describes theoretical calculation of a transient temperature profile inside the IR-absorbing material considering IR refraction at the interface as well as IR adsorption and heat transfer inside the sample. Furthermore, this calculation explains the differences in peak positions and amplitudes of AFM-IR spectra from those of specular reflectance and extinction coefficient spectra. It also addresses the information depth of the AFM-IR characterization of bulk materials. AFM-IR applied to silica and silicate glass surfaces has demonstrated novel capability of characterizing subsurface structural changes and surface heterogeneity due to mechanical stresses from physical contacts, as well as chemical alterations manifested in surface layers through aqueous corrosion.
In September and October of 2022, soil samples were collected at the Kougarok Fire Complex near mile marker 86 of the Nome-Taylor Highway on the Seward Peninsula of Alaska. This study site was chosen due to its unique fire history, as the Kougarok Fire Complex has experienced multiple wildfires since 1971. As the Arctic warms, the risk of Arctic tundra fires continues to increase due to warmer summer temperatures and higher frequency of lightning. Burned soil carbon or pyrogenic carbon (PyC) is an important component of C cycling after wildfire, and one that is often overlooked in tundra systems where wildfires are historically rare. To better understand PyC signatures and quantify PyC presence in post-regeneration permafrost regions, soils were sampled from soil pits within the 1971, 2002, and 2019 burn sites, as well as two unburned control sites. At each site, three soil pits were dug to the permafrost table. Soil samples were collected with a trowel from the face of each pit at 10 cm increments down to the permafrost table. Thaw depth, maximum vegetation height, vegetation species composition, and O horizon depth were also collected at each soil pit. An HS2 Hydrosense II Handheld Soil Moisture Sensor was used to collect volumetric soil moisture content at each 10 cm sampling increment. This dataset includes one *.csv of middle infrared spectroscopy measurements of soil samples, one *.csv of field observations, one *.csv of carbon and nitrogen analysis of soil samples, and one *.kml of sampling locations.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic) was a 15-year research effort (2012-2027) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy’s Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy’s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
Abstract Microsecond time-resolved step-scan FTIR difference spectroscopy was used to study photosystem I (PSI) from Thermosynechococcus vestitus BP-1 ( T. vestitus, formerly known as T. elongatus ) at 77 K. In addition, photoaccumulated (P700 + –P700) FTIR difference spectra were obtained at both 77 and 293 K. The FTIR difference spectra are presented here for the first time. To extend upon these FTIR studies nanosecond time-resolved infrared difference spectroscopy was also used to study PSI from T. vestitus at 296 K. Nanosecond infrared spectroscopy has never been used to study PSI samples at physiological temperatures, and here it is shown that such an approach has great value as it allows a direct probe of electron transfer down both branches in PSI. In PSI at 296 K, the infrared flash-induced absorption changes indicate electron transfer down the B- and A-branches is characterized by time constants of 33 and 364 ns, respectively, in good agreement with visible spectroscopy studies. These time constants are associated with forward electron transfer from A 1 – to F X on the B- and A-branches, respectively. At several infrared wavelengths flash-induced absorption changes at 296 K recover in tens to hundreds of milliseconds. The dominant decay phase is characterized by a lifetime of 128 ms. These millisecond changes are assigned to radical pair recombination reactions, with the changes being associated primarily with P700 + rereduction. This conclusion follows from the observation that the millisecond infrared spectrum is very similar to the photoaccumulated (P700 + –P700) FTIR difference spectrum.
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.
Probing vibrations at the single-molecule level is essential for achieving bond-specific chemical control in realistic heterogeneous environments. Here, we introduce a new measurement scheme that integrates frequency-tunable infrared excitation with scanning tunneling microscopy to characterize vibration-mediated nuclear motions of single molecules. We first validated the technique by monitoring the infrared-induced rotation of the ethynyl radical and then applied it to mapping pyrrolidine’s conformational dynamics. The resulting broadband spectra captured fundamental vibrational modes together with rich overtone and combination bands inaccessible by conventional methods, which we confirmed with isotopic substitutions. Density functional theory calculations showed that delocalized modes coupled with pyrrolidine ring puckering drive the structural transition, revealing altered selection rules compared with traditional infrared spectroscopy. Here, this new experimental platform enables molecular vibrations and transformations to be probed with atomic precision.
The activation of CO 2 on nickel surfaces is the first step of various CO 2 conversion processes. Consequently, understanding the surface intermediates formed during this step and their adsorption sites is crucial for elucidating reaction mechanisms. In this study, we employ in situ infrared spectroscopy to investigate the interaction of 1 mbar CO 2 with a model Ni(111) catalyst between 25°C and 300°C. Under these conditions, CO 2 is activated via a direct dissociation into CO and atomic oxygen, while the oxidation state of the Ni(111) surface is primarily determined by residual H 2 and O 2 . The high surface coverage of CO and oxygen at ambient CO 2 pressure induces a competitive adsorption mechanism on the energetically favored hollow sites. This mechanism leads to a temperature-dependent distribution of CO between top and hollow sites, potentially explaining the effect of reaction conditions on the adsorption site of CO intermediates in CO 2 conversion reactions.
The hydrolysis and subsequent acidic dehydration of biomass leads to the production of smaller oxygenates, including furfural, which can undergo subsequent reactions such as hydrogenation to produce value-added products. Palladium has been found to be an active catalyst for this process. As a result, the surface chemistry of furfural is investigated on a Pd(111) single-crystal surface using reflection-absorption infrared spectroscopy as a basis for understanding the catalytic conversion of furfural to value-added products. Following adsorption at 90 K, furfural adopts a flat-lying geometry at low coverages, but converts to a tilted species as the coverage approaches saturation. Heating to ~175 K forms a tilted η 1 (O) species that appears to deprotonate on heating to above 200 K to form an intermediate with a tilted furyl ring and a carbonyl group close to parallel to the surface. Further heating to ~250 K and above caused this species to decarbonylate to form adsorbed carbon monoxide and an infrared invisible furyl intermediate. This can then undergo a ring-opening reaction to produce further CO and form a C 3 H 3 intermediate that can hydrogenate to produce propylene. Finally, this reaction sequence is in good agreement with previous density functional theory calculations and with the products observed in temperature-programmed desorption.
Infiltration of inorganic oxides inside polymers using sequential infiltration synthesis (SIS) is an effective method for creating materials for a broad range of applications. The reactions between various polymer functional groups and organometallic/inorganic precursors are unique, which makes it essential to understand the specific interactions for a range of precursors and polymers to enable predictive process design and to extend the utility of SIS to applications. In this paper, in situ Fourier transform infrared spectroscopy (FTIR) measurements have been performed during Al 2 O 3 and TiO 2 SIS in three different homopolymers: poly(methyl methacrylate) (PMMA), poly(epsilon-caprolactone) (PCL), and poly(2-vinylpyridine) (P2VP). From the FTIR intensity changes after precursor exposure and during the subsequent purge times, it is demonstrated quantitatively that the interaction dynamics and the stability of the intermediate complexes of these polymers with the metal precursors are substantially different. A key finding from this comparative study is that PCL interacts far more strongly with metal precursors, even though its carbonyl (C=O) and ester (C-O-R) functional groups are similar to those of the more weakly interacting PMMA. This behavior suggests that additional factors beyond the identity of the functional groups dictate how polymers interact with metal compounds in SIS. PCL, which has not previously been reported in SIS processes, may be an attractive polymeric template for implementing SIS with improved uniformity and cost-effectiveness.
A polycrystalline copper, surface-terminated by a well-defined (511)-oriented facet, was electrochemically generated by a series of step-wise surface reconstruction and iterations of mild oxidative-reductive processes in 0.1 M KOH. The electrochemical reduction of CO on the resultant stepped surface was investigated by four surface-sensitive operando methodologies: electrochemical scanning tunneling microscopy (STM), electrochemical quartz crystal nanobalance (EQCN), differential electrochemical mass spectrometry (DEMS), and polarization-modulation infrared spectroscopy (PMIRS). The stepped surface catalyzed the facile conversion of CO into ethanol, the exclusive alcohol product at a low overpotential of -1.06 V (SHE) or - 0.3 V (RHE). Additionally, the chemisorption of CO was found to be a necessary prelude to ethanol production; i.e. the surface coverages, rather than solution concentrations, of CO and its surface-bound intermediates primarily dictate the reaction rates (current densities). Contrary to the expected predominance of undercoordinated step-site reactivity over the coordination chemistry of vicinal surfaces, vibrational spectroscopic evidence reveals the involvement of terrace-bound CO adsorbates during the multi-atomic transformations associated with the production of ethanol.
Multi-scale problems are commonly known in many scientific and engineering fields where microscopic behaviors are coupled with macroscopic processes. This is also an unsolved problem in low-temperature plasma chemistry where hundreds of chemical species are involved in thousands of chemical reactions. To address this problem, a physics-informed data-driven modeling is developed to solve such a multi-scale problem using the experimental Fourier-transform infrared spectroscopy (FTIR) measurements of several species’ concentrations. The modeling based on modern machine learning techniques provides concentrations of other relevant species along with the electron temperature and gas temperature at the location of FTIR measurements. For example, the concentrations O, OH, and H 2 O 2 play key roles in plasma-based cancer therapy. This approach overcomes the multi-scale difficulties of microscopic low-temperature plasma chemistry coupling with macroscopic gas flow and allows the acquisition of a full picture of output species concentrations. Presented here for the helium-air jet at atmospheric pressure, the ML-based modeling can be used to describe and possibly control multiscale systems using partial experimental data sets.
Rapid characterization of biomass composition is a key enabling technology for biorefineries—the ability to measure the chemical composition of biomass materials entering the biorefinery as well as the composition of key process intermediate streams would allow real-time process control and the development of robust models to predict process performance. The utility of near-infrared (NIR) spectroscopy for rapid characterization requires multivariate algorithms for building calibration models. The most prevalent algorithm used for building calibration models using NIR spectra is the linear modeling algorithm Partial Least Squares Regression (PLS). Nonlinear regression algorithms (which are typically more computationally intensive than linear modeling approaches) have gained popularity in recent years due to their ability to solve a wide variety of classification and regression problems and the dramatic increase in available computational resources. In this work, we demonstrate that a calibration model can predict the composition of corn stover process intermediate samples pretreated with three different treatments—hot water (HW), dilute acid (DA), and deacetylation followed by dilute acid (DDA). We quantitatively compare three different algorithms for building prediction models based on near-infrared spectroscopy—partial least squares (PLS), support vector machines (SVM), and random forests (RF). We demonstrate the utility of improving model performance by accounting for instrument performance variability using repeated measurements of standard materials (e.g., the “repeatability file” strategy) and investigate its performance with nonlinear regression techniques, and we discuss methods for quantifying the uncertainties of specific predictions among the three methods.
The goal of this research is to further our understanding of biological electron transfer in photosynthesis through the development and application of new methods for studying proteins with high spatial and temporal detail. Biological electron transfer occurs between metal sites imbedded in proteins where the environment and its motions can be very different from those of normal bulk liquids. Moreover, electron transfer between two proteins typically involves short-lived binding interactions within a highly mobile complex. We have directed our studies at photosynthetic electron transfer proteins plastocyanin and cytochrome f. We have labeled two key ligands to the copper ion of plastocyanin with carbon deuterium probe vibrations that enable their selective analysis by infrared spectroscopy. This analysis has shown that association of plastocyanin with cytochrome f leads to large changes in the bonding between the copper ion and ligands. In addition, the probes have been used to assess the contribution of the protein scaffold of plastocyanin in dictating the copper coordination geometry. We also have made progress to extend our experiments from equilibrium to non-equilibrium studies. The studies help to illuminate how proteins are tuned to control biological electron transfer. A better understanding of electron transfer reactions in natural photosynthesis will bolster efforts to develop artificial systems for energy production.
We report gas-phase cyclobutyl radical (c-C 4 H 7 ) is generated at a rotational temperature of T rot = 26(1) K in a slit-jet discharge mixture of 70% Ne/30% He and 0.5–0.6% cyclobromobutane (c-C 4 H 7 Br). A fully rovibrationally resolved absorption spectrum of the α-CH stretch fundamental band between 3062.9 cm −1 to 3075.7 cm −1 is obtained and analyzed, yielding first precision structural and dynamical information for this novel radical species. The α-CH stretch band origin is determined to be 3068.7887(4) cm −1 , which implies only a modest (≈0.8 cm −1 ) blue shift from rotationally unresolved infrared spectroscopic studies of cyclobutyl radicals in liquid He droplets [ A. R. Brown, P. R. Franke and G. E. Douberly, J. Phys. Chem. A , 2017, 121 , 7576–7587]. Of particular dynamical interest, a one-dimensional potential energy surface with respect to the ring puckering coordinate is computed at CCSD(T)/ANO2 level of theory and reveals a double minimum C s puckered geometry, separated by an exceedingly shallow planar C 2v transition state barrier (E barr ≈ 1 cm −1 ). Numerical solutions on this double minimum potential yield a zero-point energy for the ground state (E zero-point ≈ 27 cm −1 ) greatly in excess of the interconversion barrier. This is indicative of highly delocalized, large amplitude motion of the four-membered ring structure, for which proper vibrationally averaging of the moment of inertia tensor reproduces the experimentally determined inertial defect remarkably well. Finally, intensity alternation in the experimental spectrum due to nuclear spin statistics upon exchange of three indistinguishable H atom pairs (IH = ½) matches K a + K c = even : odd = 36 : 28 predictions, implying that the unpaired electron in the radical center lies in an out-of-plane p π orbital. Thus, high-resolution infrared spectroscopy provides first experimental confirmation of a shallow double minimum ring puckering potential with a highly delocalized ground state wave function peaked at a planar C 2v transition state geometry consistent with a cyclobutyl π radical.