Two-dimensional Spectroscopy Research Articles

Tracking structural changes of protein residues by two-dimensional correlation surface-enhanced Raman spectroscopy

In-situ tracking structural changes of protein residues was developed by two-dimensional correlation surface-enhanced Raman spectroscopy (2DC-SERS). The change order of SERS fingerprints during artificial nitrification of edible bird's nest (EBN) was interpreted as the structural changes of amino acid residues. It inherently realizes reliable recognition of natural EBN and artificially dyed fakes. Both this direct structural tracking of protein residues and the indirect azo dye testing of nitrites/nitrosamines could be used as indicators for discriminating different EBN before and after the artificial dyeing. Limit of detection (LOD) for nitrite and NDMA is about 40.6 ppb and 88.1 ppb, respectively. A conceptual logical circuit of the OR gate was constructed by considering the protein structural indicator (INPUT1) and the nitrite indicator (INPUT2) as two independent inputs for automatic recognition of different EBN samples. A data-driven analog soft independent modeling (DD-SIMCA) model could quickly distinguish normal EBN from A-EBN with 98% specificity.

Vertical characteristics of NO2 and HCHO, and the ozone formation regimes in Hefei, China

The research on the mechanism of combined air pollution in the Yangtze–Huaihe region, which is characterized by unique meteorological and geographical conditions and pollution emission characteristics, is still insufficient. We performed an experiment on key pollutants and an ozone formation study in Hefei, which is a pivotal city in the Yangtze–Huaihe region, from September 1 to 20, 2020. The aerosols retrieved via two-dimensional Multi-axis Differential Optical Absorption Spectroscopy (2D-MAX-DOAS) with a Boltzmann-shaped a priori profile had the best agreement with the results of Light Detection and Ranging (LIDAR) and sun-photometer measurements among the three typical a priori profiles (Gaussian, Boltzmann, and exponential shapes). The correlation coefficients of the near-surface gas concentrations retrieved using both 2D-MAX-DOAS and in situ measurements were 0.86 (NO2) and 0.61 (HCHO). The high NO2 and HCHO concentrations were observed at azimuths of 180° and 315° at heights of 0.8–1.5 km, and they may have been emitted by aircrafts. Importantly, the ratio of HCHO to NO2 during a typical pollution episode revealed that the factors controlling the O3 formation changed with altitude: VOCs (surface) to NOx (0.4 km) to transition (1.0 km) to VOCs (1.6 km). Moreover, the effect of VOCs on the O3 generation was stronger than that of NOx, especially in the downtown area of Hefei. When the ratio of HCHO to NO2 was 3.55–7.46, the ozone concentration in Hefei could be controlled well, especially at the optimal value of 5.50.

Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded-double-stranded DNA junctions by 2D fluorescence spectroscopy.

DNA replication and the related processes of genome expression require binding, assembly, and function of protein complexes at and near single-stranded (ss)-double-stranded (ds) DNA junctions. These central protein-DNA interactions are likely influenced by thermally induced conformational fluctuations of the DNA scaffold across an unknown distribution of functionally relevant states to provide regulatory proteins access to properly conformed DNA binding sites. Thus, characterizing the nature of conformational fluctuations and the associated structural disorder at ss-dsDNA junctions is critical for understanding the molecular mechanisms of these central biological processes. Here, we describe spectroscopic studies of model ss-dsDNA fork constructs that contain dimers of "internally labeled" cyanine (iCy3) chromophore probes that have been rigidly inserted within the sugar-phosphate backbones of the DNA strands. Our combined analyses of absorbance, circular dichroism, and two-dimensional fluorescence spectroscopy permit us to characterize the local conformational parameters and conformational distributions. We find that the DNA sugar-phosphate backbones undergo abrupt successive changes in their local conformations-initially from a right-handed and ordered DNA state to a disordered splayed-open structure and then to a disordered left-handed conformation-as the dimer probes are moved across the ss-dsDNA junction. Our results suggest that the sugar-phosphate backbones at and near ss-dsDNA junctions adopt specific position-dependent local conformations and exhibit varying extents of conformational disorder that deviate widely from the Watson-Crick structure. We suggest that some of these conformations can function as secondary-structure motifs for interaction with protein complexes that bind to and assemble at these sites.

Two-dimensional and Third-order Nonlinear Laser Spectroscopy of Fused Heterocyclic Derivatives

In optical research, the birth of laser has brought unprecedented development to the field of optics. This technology has been fully developed and applied when lasers have been developed and studied for a long time in the field of traditional spectroscopy. In addition, a lot of very important information can be received that cannot be obtained by these classical methods. The purpose of this paper is to study the two-dimensional third-order nonlinear laser spectroscopy of fused heterocyclic derivatives. A new method for third-order nonlinear laser spectroscopy, and in order to judge the accuracy of the method, the cascaded equation of motion method is used for comparison. The experimental results show that the time non-local quantum master equation is a relatively accurate method for solving the time evolution of the density matrix, so the matching method can obtain accurate two-dimensional third-order spectrum when solving the spectrum.

Liquid–Liquid membrane contactors incorporating surface skin asymmetric hollow fibres of poly(4-methyl-1-pentene) for ammonium recovery as liquid fertilisers

Two novel hollow-fibre liquid–liquid membrane contactor (HF-LLMC) modules, containing S-type (skin layer with low porosity) and Q-type (skin layer with higher porosity) fibres, have been evaluated. Both fibres, with asymmetric, porous, and hydrophobic membranes, made from poly(4-methyl-1-pentene) (PMP), were used as efficient technology for ammonia recovery to produce liquid fertilisers. The ammonia-rich stream was fed into the shell side of the PMP-HF-LLMC, while nitric acid or phosphoric acid were fed separately into the lumen to produce N-type (NO3–-NH4+) and N-P-type (NH4+-P2O5) fertilisers, respectively. The maximum NH3 recovery (>95%) was achieved in a closed-loop configuration with S-type fibres, while Q-type fibres showed a better performance in terms of the production of more concentrated N-type liquid fertiliser. With Q-type fibres, the highest values of N-P-type liquid fertilisers were achieved (8.0 % N (NH4+) and 20.3% P2O5 (w/w)) using phosphoric acid, while the highest value of water flux across the PMP fibres was < 0.01 kg m–2h−1. The highest overall mass transfer coefficient (Km), measured for solutions containing 5.0 gNH3 L–1 with a feed/stripping volume ratio of 60:1, was (2.9 ± 0.2) × 10−7 m s−1. Additionally, ultraviolet–visible spectroscopy and two-dimensional excitation-emission matrix fluorescence spectroscopy were employed to monitor the absence of pore-wetting events and the stability of the PMP-HF-LLMC under strongly acidic and basic conditions.

Binding of the substrate analog methanol in the oxygen-evolving complex of photosystem II in the D1-N87A genetic variant of cyanobacteria.

The solar water-splitting protein complex, photosystem II (PSII), catalyzes one of the most energetically demanding reactions in nature by using light energy to drive a catalyst capable of oxidizing water. The water oxidation reaction is catalyzed at the Mn4Ca-oxo cluster in the oxygen-evolving complex (OEC), which cycles through five light-driven S-state intermediates (S0-S4). A detailed mechanism of the reaction remains elusive as it requires knowledge of the delivery and binding of substrate water in the higher S-state intermediates. In this study, we use two-dimensional (2D) hyperfine sublevel correlation spectroscopy, in conjunction with quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT), to probe the binding of the substrate analog, methanol, in the S2 state of the D1-N87A variant of PSII from Synechocystis sp. PCC 6803. The results indicate that the size and specificity of the "narrow" channel is altered in D1-N87A PSII, allowing for the binding of deprotonated 13C-labeled methanol at the Mn4(IV) ion of the catalytic cluster in the S2 state. This has important implications on the mechanistic models for water oxidation in PSII.

Moisture Content Measurement Technique by Imaging-Type Two-Dimensional Fourier Spectroscopy Before and After Wiping with Wet Towels

Moisture Content Measurement Technique by Imaging-Type Two-Dimensional Fourier Spectroscopy Before and After Wiping with Wet Towels

Structural insights into Lewis acid- and F4TCNQ-doped conjugated polymers by solid-state magnetic resonance spectroscopy.

Molecular doping strategies facilitate orders of magnitude enhancement in the charge carrier mobility of organic semiconductors (OSCs). Understanding the different doping mechanisms and molecular-level constraints on doping efficiency related to the material energy levels is crucial to develop versatile dopants for OSCs. Given the compositional and structural heterogeneities associated with OSC thin films, insight into dopant-polymer interactions by long-range techniques such as X-ray scattering and electron microscopy is exceedingly challenging to obtain. This study employs short-range probes, solid-state (ss)NMR and EPR spectroscopy, to resolve local structures and intermolecular interactions between dopants such as F4TCNQ (2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane), Lewis acid BCF (tris[pentafluorophenyl] borane) and Lewis base conjugated polymer, PCPDTBT (P4) (poly[2,6-(4,4-bis(2-hexadecyl)-4H-cyclopenta[2,1-b;3,4-b']dithiophene)-alt-4,7(2,1,3-benzothiadiazole)]). Analysis of 1H and 13C ssNMR spectra of P4, P4 : F4TCNQ and P4 : BCF blends indicates that the addition of dopants induces local structural changes in the P4 polymer, and causes paramagnetism-induced signal broadening and intensity losses. The hyperfine interactions in P4 : BCF and P4 : F4TCNQ are characterized by two-dimensional pulsed EPR spectroscopy. For P4 : F4TCNQ, 19F ssNMR analysis indicates that the F4TCNQ molecules are distributed and aggregated into different local chemical environments. By comparison, BCF molecules are intermixed with the P4 polymer and interact with traces of water molecules to form BCF-water complexes that serve as Brønsted acid sites, as revealed by 11B ssNMR spectroscopy. These results indicate that the P4-dopant blends exhibit complex morphology with different distributions of dopants, whereby the combined use of ssNMR and EPR provides essential insights into how higher doping efficiency is observed with BCF and a mediocre efficiency is associated with F4TCNQ molecules.

Acidogenic Fermentation of Brewers' Spent Grain: Performance and Monitoring Through Two-Dimensional Fluorescence Spectroscopy

Acidogenic Fermentation of Brewers' Spent Grain: Performance and Monitoring Through Two-Dimensional Fluorescence Spectroscopy

Direct observation of reversible bond homolysis by 2D EXSY NMR.

Bond homolysis is one of the most fundamental bond cleavage mechanisms. Thus, understanding of bond homolysis influences the development of a wide range of chemistry. Photolytic bond homolysis and its reverse process have been observed directly using time-resolved spectroscopy. However, direct observation of reversible bond homolysis remains elusive. Here, we report the direct observation of reversible Co–Co bond homolysis using two-dimensional nuclear magnetic resonance exchange spectroscopy (2D EXSY NMR). The characterization of species involved in this homolysis is firmly supported by diffusion ordered NMR spectroscopy (DOSY NMR). The unambiguous characterization of the Co–Co bond homolysis process enabled us to study ligand steric and electronic factors that influence the strength of the Co–Co bond. Understanding of these factors will contribute to rational design of multimetallic complexes with desired physical properties or catalytic activity.

A Robust Man-Made Target Detection Method Based on Relative Spectral Stationarity for High-Resolution SAR Images

The generality and robustness of a man-made target detection method are of high practical value in SAR applications. However, current methods hardly adapt to different SAR images simultaneously because data property and target characteristics are not identical in images with various resolutions and scenes. The key to achieving high generality and robustness is extracting stable and invariant information in different SAR images. This paper analyzes the scattering of man-made targets and natural backgrounds in SAR images and assumes that the noise characteristics are relatively stable and invariant when resolution and observing background change. Then the Relative Spectral Stationarity (RSS) is proposed based on two-dimensional spectrum analysis to measure the distance between the observed data and a manually generated noise. RSS takes the manually generated noise with known and definite properties as a standard, so it is irrelevant to image parameters and scenes. A low RSS indicates that the characteristics of observing data are dominated by noise, whereas a high value means there may be targets in the observing data weakening the noise characteristics. An efficient segmentation algorithm Sparsity-based Format-free Segmentation within error <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</i> (SFFe) is proposed to process the RSS map and complete the detection method. SAR images with resolutions ranging from 0.1m to 8m are employed as testing data. Various testing scenes are constructed to simulate different practical conditions. Experimental results validate that the proposed RSS-based method works well in SAR images with different resolutions, bands, and observing scenes, obtaining reliable and robust detection results and outperforming canonical methods on various criteria.

Tomographic imaging for solar extreme ultraviolet He II 30.4 nm and spectral data inversion

Highly dynamic solar eruptive activities occurring over the corona and transition region, triggered off by magnetic field reconnection, are the driving source of disastrous space weather, and the space imaging and spectroscopic measurements of solar eruptive activities are a key data source for accurate space weather forecasting. The He II 30.4 nm resonance line comes from the Lyman &lt;i&gt;α&lt;/i&gt; transition of singly ionized helium, which has an anomalous intensity, an order of magnitude higher than the intensities of other transition region lines. In this paper, we propose and design a two-dimensional spectroscopic tomographic imaging instrument operating at He II 30.4 nm wavelength to make up for the shortcomings of conventional solar extreme ultraviolet imager and imaging spectrometer, and adopt a slitless three-order (–1, 0, +1) simultaneous diffraction imaging configuration with a single snapshot to achieve two-dimensional spectroscopy instantaneous imaging with a large field of view. Owing to the confusion of spatial and spectral information of the three orders of images, the three-dimensional data cube &lt;i&gt;I&lt;/i&gt; (&lt;i&gt;x&lt;/i&gt;, &lt;i&gt;y&lt;/i&gt;, &lt;i&gt;λ&lt;/i&gt;) of the observed target is reconstructed using a spectral data inversion algorithm with a limited tomographic projection angle.

Phytochemical and biological study of phenolic fraction from Geoffroea decorticans bark

The stem bark of Geoffroea decorticans (Gill.ex Hook. et Arn.) Burk. (Fabaceae) was used medicinally to cure several skin affections; however, previous phytochemical and biological antecedents that supported its vulnerary property were not found yet. A purified methanolic fraction from G. decorticans bark (PFGB), was derivatized by silylation for GC/MS analysis, and complementary analyses by two-dimensional TLC and UV-Vis spectroscopy against detected standards compounds. Nine phenolic compounds were characterized as gallic acid, quercetin, kaempferol, apigenin, protocatechuic acid, taxifolin, 4-Hydroxybenzoic acid; among these two methoxy-flavonoids. PFGB showed significant antibacterial activity (MICs= 125 μg/mL) against Staphylococcus aureus (25923) and Enterococcus faecalis (29212) ATCC strains. Cytotoxic effects on human lymphocytes activated or not by LPS were not observed up to 100 μg/mL, by MTT colorimetric assay. The resultsobtained through the ethnopharmacological approach of this work contribute to the scientific validation of the vulnerary medicinal use of G. decorticans.

Identification of synthetic cannabinoid methyl 2-{[1-(cyclohexylmethyl)-1H-indol-3-yl] formamido}-3-methylbutanoate using modern mass spectrometry and nuclear magnetic resonance techniques

Abstract The samples of plant material suspected to contain new psychoactive substances are very often the subject of chemical-toxicological analyses. Gas chromatography-mass spectrometry (MS), liquid chromatography-quadrupole time-of-flight-MS, and liquid chromatography-tandem MS were applied with the aim to identify synthetic cannabinoid, methyl 2-{[1-(cyclohexylmethyl)-1H-indol-3-yl] formamido}-3-methylbutanoate (MMB-CHMICA) without the analytical standard, which is very often the case when a new drug arrives. The structure of compound was also confirmed by one-dimensional and two-dimensional nuclear magnetic resonance spectroscopy and conformational analysis. After identification, methanolic extract of plant material containing MMB-CHMICA was successfully used for developing a multiple reaction monitoring method on liquid chromatography-tandem MS instrument. The optimization procedure is shown in detail. The complete fragmentation pattern and also the optimization of the extraction procedure of MMB-CHMICA from plant material were shown. The obtained data are useful for forensic, toxicological, and clinical purposes.

Theoretical reconsideration of the mechanism of the excited state proton transfer of indigo carmine in water

The excited state proton transfer process is critical for biocatalysis and the photostability of dye molecules. Fleming et al. deemed intramolecular proton transfer of Indigo carmine (InC) in water using two-dimensional electron vibration spectroscopy combined with implicit model calculation [J. Phys. Chem. Lett. 11 (2020) 415–4162]. Alternatively, water can form intermolecular hydrogen bonds with the amino groups of InC, and there is the possibility of intermolecular proton transfer, so the accuracy of this conclusion remains to be discussed. In this work, density functional theory and time-dependent density functional theory were used to investigate the mechanism of excited proton transfer of InC in both display and implicit models. The analysis of hydrogen bond length, transition density matrix and infrared vibration spectrum state that the InC is more prone to proton transfer in the display model. According to the analysis results of non-covalent bond strength, only the peak position of the display model changes, stating that the proton transfer process of InC can only occur in the display model. In addition, the calculated results of potential energy curves manifest that the barrier height is 6.41 kcal/mol in the display model and 9.71 kcal/mol in the implicit model. It is convinced that the proton transfer of InC in aqueous solution is intermolecular rather than intramolecular. This work provides new ideas for the design and development of novel organic fluorescent molecules.

Characterization of Acetonitrile Isotopologues as Vibrational Probes of Electrolytes.

Acetonitrile has emerged as a solvent candidate for novel electrolyte formulations in metal-ion batteries and supercapacitors. It features a bright local C≡N stretch vibrational mode whose infrared (IR) signature is sensitive to battery-relevant cations (Li+, Mg2+, Zn2+, Ca2+) both in pure form and in the presence of water admixture across a full possible range of concentrations from the dilute to the superconcentrated regime. Stationary and time-resolved IR spectroscopy thus emerges as a natural tool to study site-specific intermolecular interactions from the solvent perspective without introducing an extrinsic probe that perturbs solution morphology and may not represent the intrinsic dynamics in these electrolytes. The metal-coordinated acetonitrile, water-separated metal–acetonitrile pair, and free solvent each have a distinct vibrational signature that allows their unambiguous differentiation. The IR band frequency of the metal-coordinated acetonitrile depends on the ion charge density. To study the ion transport dynamics, it is necessary to differentiate energy-transfer processes from structural interconversions in these electrolytes. Isotope labeling the solvent is a necessary prerequisite to separate these processes. We discuss the design principles and choice of the CD313CN label and characterize its vibrational spectroscopy in these electrolytes. The Fermi resonance between 13C≡N and C–D stretches complicates the spectral response but does not prevent its effective utilization. Time-resolved two-dimensional (2D) IR spectroscopy can be performed on a mixture of acetonitrile isotopologues and much can be learned about the structural dynamics of various species in these formulations.

Measuring time-dependent induced quantum coherences via two-dimensional coherence spectroscopy

We propose a two-dimensional spectroscopic protocol for measuring the time-dependent coherences between the stationary states of a system induced by a time-dependent system-bath interaction. We also investigate the role of temporally-correlated noise on coherence dephasing. This protocol enables dynamical information about the system and its coupling to the environment to be determined. Our results are based on the quantum-trajectory method, and are obtained from both approximate, analytical and exact, numerical solutions of the time-dependent Schroedinger equation. As an example, we show how this protocol can be used to investigate exciton dynameds in conjugated polymers induced by the coupling of their torsional modes with the environment.

Mono-cycle terahertz pulses from intersubband shift currents in asymmetric semiconductor quantum wells

Both second-order frequency mixing in nonlinear optical media and photoconductive antennas have provided terahertz (THz) transients in a wide parameter range. Here, we demonstrate a novel type of ultrafast nonlinear optical response in asymmetric semiconductor quantum wells, originating from electron shift currents. Resonant intersubband excitation by a femtosecond mid-infrared pulse induces a transient spatial shift of electronic charge, which leads to the emission of a mono-cycle THz pulse. This mechanism is characterized and separated from conventional difference frequency mixing by nonlinear two-dimensional THz spectroscopy. The amplitude of the THz electric field emitted by the shift current reaches several percent of the mid-infrared driving field, significantly higher than in difference frequency mixing. Changes in time structure of the THz pulse upon nonlinear saturation of intersubband absorption allow for generating tailored THz transients. The present concept can be implemented in highly compact devices driven by mid-infrared pulses at megahertz repetition rates to provide versatile THz pulses for spectroscopy and optoelectronics.

Laser-induced fluorescence experimental spectroscopy and theoretical calculations of uranium monoxide

As a model molecule of actinide chemistry, UO molecule plays an important role in understanding the electronic structure and chemical bonding of actinide-containing species. We report a study of the laser-induced fluorescence spectra of the U16O and U18O using two-dimensional spectroscopy. Several rotationally resolved excitation spectra were investigated. Accurate molecular rotational constants and equilibrium internuclear distances were reported. Low-lying electronic states information was extracted from high resolution dispersed fluorescence spectra and analyzed by the ligand field theory model. The configuration of the ground state was determined as U2+(5f37s)O2−. The branching ratios, and the vibrational harmonic and anharmonic parameters were also obtained. Radiative lifetimes were determined by recording the time-resolved fluorescence spectroscopy. Transition dipole moments were calculated using the branching ratios and the radiative lifetimes. These findings were elucidated by using quantum-chemical calculations, and the chemical bonding was also analyzed. The findings presented in this work will enrich our understanding of actinide-containing molecules.

Stable Diarylamine-Substituted Tris(2,4,6-trichlorophenyl)methyl Radicals: One-Step Synthesis, Near-Infrared Emission, and Redox Chemistry

Stable Diarylamine-Substituted Tris(2,4,6-trichlorophenyl)methyl Radicals: One-Step Synthesis, Near-Infrared Emission, and Redox Chemistry