Two-dimensional Spectroscopy Research Articles

Rapid and accurate bacteria identification through deep-learning-based two-dimensional Raman spectroscopy

Surface-enhanced Raman spectroscopy (SERS) offers a distinctive vibrational fingerprint of the molecules and has led to widespread applications in medical diagnosis, biochemistry, and virology. With the rapid development of artificial intelligence (AI) technology, AI-enabled Raman spectroscopic techniques, as a promising avenue for biosensing applications, have significantly boosted bacteria identification. By converting spectra into images, the dataset is enriched with more detailed information, allowing AI to identify bacterial isolates with enhanced precision. However, previous studies usually suffer from a trade-off between high-resolution spectrograms for high-accuracy identification and short training time for data processing. Here, we present an efficient bacteria identification strategy that combines deep learning models with a spectrogram encoding algorithm based on wavelet packet transform and Gramian angular field techniques. In contrast to the direct analysis of raw Raman spectra, our approach utilizes wavelet packet transform techniques to compress the spectra by a factor of 1/15, while concurrently maintaining state-of-the-art accuracy by amplifying the subtle differences via Gramian angular field techniques. The results demonstrate that our approach can achieve a 99.64 % and a 90.55 % identification accuracy for two types of bacterial isolates and thirty types of bacterial isolates, respectively, while a 90 % reduction in training time compared to the conventional methods. To verify the model's stability, Gaussian noises were superimposed on the testing dataset, showing a specific generalization ability and superior performance. This algorithm has the potential for integration into on-site testing protocols and is readily updatable with new bacterial isolates. This study provides profound insights and contributes to the current understanding of spectroscopy, paving the way for accurate and rapid bacteria identification in diverse applications of environment monitoring, food safety, microbiology, and public health.

Exploring two-dimensional coherent spectroscopy with exact diagonalization: Spinons and confinement in one-dimensional quantum magnets

Exploring two-dimensional coherent spectroscopy with exact diagonalization: Spinons and confinement in one-dimensional quantum magnets

In vitro spectroscopic analysis of the chemical interaction between calcium hypochlorite and chlorhexidine.

This study aimed to identify the chemical composition resulting from the chemical interaction between calcium hypochlorite [Ca(OCl)2] and chlorhexidine (CHX) using different 1H and 13C nuclear magnetic resonance spectrometry (NMR), correlated two-dimensional spectroscopy (2D COSY), heteronuclear single quantum coherence (HSQC), and Fourier Transform Infrared Spectroscopy (FTIR) experiments. The 5.25% Ca(OCl)2 was mixed with 2% CHX in a 1:1 ratio, obtaining an orange-brown precipitate that was filtered, washed in ultrapure water, dried and characterized by 1H and 13C NMR, 2D COSY, HSQC and FTIR. One-dimensional and two-dimensional NMR spectra demonstrated the chemical changes around the protons and carbon atoms of the initial CHX and after reacted with Ca(OCl)2. These techniques and FTIR show that the interaction generated two by-products from the degradation of CHX, none of which were parachloroaniline (PCA) despite both products obtained being substituted benzene compounds. Using NMR and FTIR data together with a previously proposed catalytic cleavage degradation mechanism for CHX, the products appear to be parachlorophenylurea (PCU) and parachlorophenylguanidyl-1,6-diguanidyl-hexane (PCGH). Therefore, this in vitro study demonstrated that the precipitate formed from the chemical interaction between Ca(OCl)₂ and CHX results in two by-products, PCU and PCGH, neither of which is PCA. Due to the absence of cytotoxicity studies on the products generated from the combination of Ca(OCl)₂ and CHX, an intermediate rinse with an inert solution is recommended to remove these compounds from the root canals.

The development and applications of multidimensional biomolecular spectroscopy illustrated by photosynthetic light harvesting.

The parallel and synergistic developments of atomic resolution structural information, new spectroscopic methods, their underpinning formalism, and the application of sophisticated theoretical methods have led to a step function change in our understanding of photosynthetic light harvesting, the process by which photosynthetic organisms collect solar energy and supply it to their reaction centers to initiate the chemistry of photosynthesis. The new spectroscopic methods, in particular multidimensional spectroscopies, have enabled a transition from recording rates of processes to focusing on mechanism. We discuss two ultrafast spectroscopies - two-dimensional electronic spectroscopy and two-dimensional electronic-vibrational spectroscopy - and illustrate their development through the lens of photosynthetic light harvesting. Both spectroscopies provide enhanced spectral resolution and, in different ways, reveal pathways of energy flow and coherent oscillations which relate to the quantum mechanical mixing of, for example, electronic excitations (excitons) and nuclear motions. The new types of information present in these spectra provoked the application of sophisticated quantum dynamical theories to describe the temporal evolution of the spectra and provide new questions for experimental investigation. While multidimensional spectroscopies have applications in many other areas of science, we feel that the investigation of photosynthetic light harvesting has had the largest influence on the development of spectroscopic and theoretical methods for the study of quantum dynamics in biology, hence the focus of this review. We conclude with key questions for the next decade of this review.

Deciphering Spectroscopic Signatures of Competing Ca2+ - Peptide Interactions.

Calcium-protein interactions are of paramount importance in biochemistry. They are a key element in a number of biological processes, such as neuronal signaling. Therefore, an understanding of the interaction at the molecular level is highly desirable. Here, we study the zwitterionic model peptide l-alanyl-l-alanine (2Ala), which has two distinct and competing binding sites for Ca2+: The carbonyl of the peptide bond and the C-terminus, the carboxylate group. We perform linear and two-dimensional IR spectroscopy experiments and find that the spectroscopic signatures of both moieties in the IR spectra change in amplitude and peak position upon the addition of CaCl2: A blueshift of the asymmetric carboxylate band and a redshift for the amide I mode. Ab initio molecular dynamics simulations confirm the direct interaction of the Ca2+ ion at both the carboxylate and the amide CO site leading to different spectral responses. The blueshift of the asymmetric carboxylate band is caused by a localization of the charge, leading to a decoupling of the CO stretching modes of the carboxylate group. The slight redshift of the amide I mode of 2Ala upon the addition of CaCl2 contrasts the blueshift that has been observed for isolated amide motifs, such as N-methylacetamide (NMA). This difference is caused by the smaller number of water molecules being replaced by the Ca2+ ion for 2Ala's amide compared to less sterically hindered, isolated amide carbonyls, in conjunction with vibrational Stark effects. Our results highlight the importance of considering potential competing binding sites, such as the amide CO backbone, the termini and residues, as well as the nature of the hydration of both peptide and ion, when exploring ions' interacting with small peptides and larger proteins.

Ultrasound-assisted low-temperature extraction of polysaccharides from Lavandula angustifolia Mill.: optimization, structure characterization, and anti-inflammatory activity

Lavandula angustifolia Mill. is a traditional Chinese medicinal herb with high economic and pharmacological value. In this study, we optimized the conditions for low-temperature ultrasound-assisted extraction of L. angustifolia Mill. polysaccharides using response surface methodology (RSM), and two homopolysaccharides LAPW1 (33.6 kDa) and LAPS1 (95.9 kDa) were obtained after isolation and purification by DEAE-650 M and Superdex™ 200 chromatography. The primary structure of LAPS1 was determined using “partial acid hydrolysis, methylation, two-dimensional (2D NMR) spectroscopy” as the core method. The results revealed that LAPS1 is a heteropolysaccharide whose main chain consists of [-1)-β-Galp-(6→1)-α-Araf-(5→]3-1-α-Araf-(3→1)-α-Araf-(5→[1)-β-Galp-(6→1)-α-Araf-(5→]3-1-α-Araf-(5→1)-α-Araf-(5→[-1)-β-Galp-(6→1)-α-Araf-(5→]3. In vitro experiments revealed that LAPW1 and LAPS1 significantly reduced the production of the inflammatory cytokines Interleukin-1β (IL-1β), Interleukin-6 (IL-6), and Tumor Necrosis Factor (TNF), as well as the expression of Nitric Oxide Synthase 2 (NOS2) and release of nitric oxide (.NO) free radical in the inflammatory model established by lipopolysaccharide (LPS) stimulated RAW264.7. Besides, the zebrafish inflammatory model, stimulated by CuSO4, was employed to assess the impact of polysaccharides on neutrophil migration, indicating a notable decrease in zebrafish neutrophils and confirming their potential anti-inflammatory activity. These results indicate that polysaccharides from L. angustifolia Mill. be used in the development of functional foods and pharmaceutical products.

Macroscopic perspective on phase transition behavior of natural single-crystal graphite under different pressure environments

Comprehensive understanding of the direct transformation pathway from graphite to diamond under high temperature and high pressure has long been one of the fundamental goals in materials science. Despite considerable experimental and theoretical progress, current experimental studies have mainly focused on the local microstructural characterizations of recovered samples, which has certain limitations for high-temperature and high-pressure products, which often exhibit diversity. Here, we report on the pressure-induced phase transition behavior of natural single-crystal graphite under three distinct pressure-transmitting media from a macroscopic perspective using in situ two-dimensional Raman spectroscopy, scanning electron microscopy, and atomic force microscopy. The surface evolution process of graphite before and after the phase transition is captured, revealing that pressure-induced surface textures can impede the continuity of the phase transition process across the entire single crystal. Our results provide a fresh perspective for studying the phase transition behavior of graphite and greatly deepen our understanding of this behavior, which will be helpful in guiding further high-temperature and high-pressure syntheses of carbon allotropes.

The Insecticidal Activity of Secondary Metabolites Produced by Streptomyces sp. SA61 against Trialeurodes vaporariorum (Hemiptera: Aleyrodidae).

Trialeurodes vaporariorum Westwood poses a significant threat to vegetable and ornamental crops in temperate zones, resulting in notable reductions in yield and substantial economic burdens. In order to find compounds with high insecticidal activity against T. vaporariorum, five compounds were isolated and identified from the crude extract of Streptomyces sp. SA61. These include three new polyketides, named strekingmycins F-H (1-3); one new diterpenoid, named phenalinolactone CD8 (4); and one known compound, strekingmycin A (5). Their structures were analyzed using high-resolution electrospray ionization mass spectrometry and one-dimensional and two-dimensional nuclear magnetic resonance spectroscopy data and by comparing them with previously reported data. The insecticidal activities of compounds 1-5 against T. vaporariorum were evaluated. Among them, compound 5 exhibited the highest insecticidal activity, with an LC50 of 6.949 mg/L against T. vaporariorum at 72 h using the leaf-dip method. Lower insecticidal activities were found in compounds 1-4, with LC50 values of 22.817, 19.150, 16.981 and 41.501 mg/L, respectively. These data indicate that strekingmycin could be a potential candidate for a novel insecticide to control T. vaporariorum.

Fluorescence-Detected Two-Dimensional Electronic Spectroscopy of a Single Molecule.

Single-molecule fluorescence spectroscopy is a powerful method that avoids ensemble averaging, but its temporal resolution is limited by the fluorescence lifetime to nanoseconds at most. At the ensemble level, two-dimensional spectroscopy provides insight into ultrafast femtosecond processes, such as energy transfer and line broadening, even beyond the Fourier limit, by correlating pump and probe spectra. Here, we combine these two techniques and demonstrate coherent 2D spectroscopy of individual dibenzoterrylene (DBT) molecules at room temperature. We excite the molecule in a confocal microscope with a phase-modulated train of femtosecond pulses and detect the emitted fluorescence with single-photon counting detectors. Using a phase-sensitive detection scheme, we were able to measure the nonlinear 2D spectra of most of the DBT molecules that we studied. Our method is applicable to a wide range of single emitters and opens new avenues for understanding energy transfer in single quantum objects on ultrafast time scales.

Adaptive Variational Quantum Computing Approaches for Green's Functions and Nonlinear Susceptibilities.

We present and benchmark quantum computing approaches for calculating real-time single-particle Green's functions and nonlinear susceptibilities of Hamiltonian systems. The approaches leverage adaptive variational quantum algorithms for state preparation and propagation. Using automatically generated compact circuits, the dynamical evolution is performed over sufficiently long times to achieve adequate frequency resolution of the response functions. We showcase accurate Green's function calculations using a statevector simulator on classical hardware for Fermi-Hubbard chains of 4 and 6 sites, with maximal ansatz circuit depths of 65 and 424 layers, respectively, and for the molecule LiH with a maximal ansatz circuit depth of 81 layers. Additionally, we consider an antiferromagnetic quantum spin-1 model that incorporates the Dzyaloshinskii-Moriya interaction to illustrate calculations of the third-order nonlinear susceptibilities, which can be measured in two-dimensional coherent spectroscopy experiments. These results demonstrate that real-time approaches using adaptive parametrized circuits to evaluate linear and nonlinear response functions can be feasible with near-term quantum processors.

Response functions for electric field induced two-dimensional nonlinear spectroscopy in a Kitaev magnet

We study the dynamical response functions relevant for electric field induced two-dimensional (2D) coherent nonlinear optical spectroscopy in a Kitaev magnet at finite temperature. We show that these response functions are susceptible to both types of fractional quasiparticles of this quantum spin-liquid, i.e. fermions and flux visons. Focusing on the second order response, we find a strong antidiagonal feature in the 2D frequency plane, related to the galvanoelectric effect of the fractional fermions. Perpendicular to the antidiagonal, the width of this feature is set by quasiparticle relaxation rates beyond the bare Kitaev magnet, thereby providing access to single-particle characteristics within a multi-particle continuum. While the 2D spectrum of the response is set by the fermionic quasiparticles and displays Fermi blocking versus temperature, the emergent bond randomness which arises due to thermally populated visons strongly modifies the fermionic spectrum. Therefore also the presence of gauge excitations is manifest in the 2D nonlinear response as the temperature is increased beyond the flux proliferation crossover.

Theoretical Description of Pump-Probe Experiments in Charge-Density-Wave Materials out to Long Times

We describe coupled nonequilibrium electron-phonon systems semiclassically—Ehrenfest dynamics for the phonons and quantum mechanics for the electrons—using a classical Monte Carlo approach that determines the nonequilibrium response to a large pump field. The semiclassical approach is expected to be accurate, because the phonons are excited to average energies much higher than the phonon frequency, eliminating the need for a quantum description. The numerical efficiency of this method allows us to perform a self-consistent time evolution out to very long times (tens of picoseconds), enabling us to model pump-probe experiments of a charge-density-wave (CDW) material. Our system is a half-filled, one-dimensional (1D) Holstein chain that exhibits CDW ordering due to a Peierls transition. The chain is subjected to a time-dependent electromagnetic pump field that excites it out of equilibrium, and then a second probe pulse is applied after a time delay. By evolving the system to long times, we capture the complete process of lattice excitation and subsequent relaxation to a new equilibrium, due to an exchange of energy between the electrons and the lattice, leading to lattice relaxation at finite temperatures. We employ an indirect (impulsive) driving mechanism of the lattice by the pump pulse due to the direct driving of the electrons. We identify two driving regimes, where the pump can either cause small perturbations or completely invert the initial CDW order. Our work successfully describes the ringing of the amplitude mode in CDW systems that has long been seen in experiment but never successfully explained by microscopic theory. We also describe the fluence-dependent crossover that inverts the CDW order parameter and changes the phonon dynamics. Finally, we illustrate how this method can examine a number of different types of experiments including photoemission, x-ray diffraction, and two-dimensional (2D) spectroscopy. Published by the American Physical Society 2024

Probing Majorana Wave Functions in Kitaev Honeycomb Spin Liquids with Second-Order Two-Dimensional Spectroscopy.

Two-dimensional coherent terahertz spectroscopy (2DCS) emerges as a valuable tool to probe the nature, couplings, and lifetimes of excitations in quantum materials. It thus promises to identify unique signatures of spin liquid states in quantum magnets by directly probing properties of their exotic fractionalized excitations. Here, we calculate the second-order 2DCS of the Kitaev honeycomb model and demonstrate that distinct spin liquid fingerprints appear already in this lowest-order nonlinear response χ_{yzx}^{(2)}(ω_{1},ω_{2}) when using crossed light polarizations. We further relate the off-diagonal 2DCS peaks to the localized nature of the matter Majorana excitations trapped by Z_{2} flux excitations and show that 2DCS thus directly probes the inverse participation ratio of Majorana wave functions. By providing experimentally observable features of spin liquid states in the 2D spectrum, our Letter can guide future 2DCS experiments on Kitaev magnets.

Principles of two-dimensional terahertz spectroscopy of collective excitations: The case of Josephson plasmons in layered superconductors

Principles of two-dimensional terahertz spectroscopy of collective excitations: The case of Josephson plasmons in layered superconductors

Exploring the Local Environment Effect on Properties of all-Trans-Retinal by Two-Dimensional Correlation Resonance Raman Spectroscopy

Exploring the Local Environment Effect on Properties of all-Trans-Retinal by Two-Dimensional Correlation Resonance Raman Spectroscopy

Probing inhomogeneous cuprate superconductivity by terahertz Josephson echo spectroscopy

AbstractInhomogeneities crucially influence the properties of quantum materials, yet methods that can measure them remain limited and can access only a fraction of relevant observables. For example, local probes such as scanning tunnelling microscopy have documented that the electronic properties of cuprate superconductors are inhomogeneous over nanometre length scales. However, complementary techniques that can resolve higher-order correlations are needed to elucidate the nature of these inhomogeneities. Furthermore, local tunnelling probes are often effective only far below the critical temperature. Here we develop a two-dimensional terahertz spectroscopy method to measure Josephson plasmon echoes from an interlayer superconducting tunnelling resonance in a near-optimally doped cuprate. The technique allows us to study the multidimensional optical response of the interlayer Josephson coupling in the material and disentangle intrinsic lifetime broadening from extrinsic inhomogeneous broadening for interlayer superconducting tunnelling. We find that inhomogeneous broadening persists up to a substantial fraction of the critical temperature, above which this is overcome by the thermally increased lifetime broadening.

19F NMR Reveals the Dynamics of Substrate Binding and Lid Closure for Iodotyrosine Deiodinase as a Complement to Steady-State Kinetics and Crystallography.

Active site lids are common features of enzymes and typically undergo conformational changes upon substrate binding to promote catalysis. Iodotyrosine deiodinase is no exception and contains a lid segment in all of its homologues from human to bacteria. The solution-state dynamics of the lid have now been characterized using 19F NMR spectroscopy with a CF3-labeled enzyme and CF3O-labeled ligands. From two-dimensional 19F-19F NMR exchange spectroscopy, interconversion rates between the free and bound states of a CF3O-substituted tyrosine (45 ± 10 s-1) and the protein label (40 ± 3 s-1) are very similar and suggest a correlation between ligand binding and conformational reorganization of the lid. Both occur at rates that are ∼100-fold faster than turnover, and therefore these steps do not limit catalysis. A simple CF3O-labeled phenol also binds to the active site and induces a conformational change in the lid segment that was not previously detectable by crystallography. Exchange rates of the ligand (130 ± 20 s-1) and protein (98 ± 8 s-1) in this example are faster than those above but remain self-consistent to affirm a correlation between ordering of the lid and binding of the ligand. Both ligands also protect the protein from limited proteolysis, as expected from their ability to stabilize a compact lid structure. However, the minimal turnover of simple phenol substrates indicates that such stabilization may be necessary but is not sufficient for efficient catalysis.

Time-domain interferometry of electron weak localization through terahertz nonlinear response

We study theoretically the nonlinear optical response of disordered electrons in the regime of weak (anti)localization. Our analytical and numerical calculations reveal that in orthogonal/symplectic class systems, two consecutive, phase-coherent optical pulses generate an electric current echo that appears after the second pulse, and at a time equal to the pulse delay time. The current echo reflects the quantum interference between a self-intersecting electron path and its time-reversal partner, and, therefore, provides a time-domain interferometry of weak (anti)localization. Our results can be potentially tested on disordered metal films by using terahertz two-dimensional coherent spectroscopy or ultrafast transport measurements. Published by the American Physical Society 2024

Research on Water-Soluble Constituents and Anti-Aging Effect of the Leaves of Nelumbo nucifera Gaertn

Objective: This study aimed to isolate and elucidate the structure of water-soluble constituents from Nelumbo nucifera Gaertn. leaves and evaluate their anti-aging effect. Methods: The natural products were isolated from the 60% aqueous acetone extract of the leaves of N. nucifera by column chromatography on MCI gel CHP 20P, YMC-Gel ODS-AQ-HG, and TSK gel Toyopearl HW-40F. Their structures were elucidated using high-resolution-electrospray ionization-mass spectrometry, one-dimensional and two-dimensional nuclear magnetic resonance spectroscopy, and electronic circular dichroism spectroscopy. The anti-aging activity was evaluated in the Caenorhabditis elegans model. Results/Conclusion: One novel flavonoid nuciferanoid (1), together with eleven known compounds, were isolated from the extract of the leaves of N. nucifera. Among them, compound 1 could be a starting point for further development of anti-aging drugs.

Excitation-dependent features and artifacts in 2-D terahertz spectroscopy.

Recently, two-dimensional terahertz spectroscopy (2DTS) has attracted increasing attention for studying complex solids. A number of recent studies have applied 2DTS either with long pulses or away from any material resonances, situations that yield unconventional 2DTS spectra that are often difficult to interpret. Here, we clarify the generic origins of observed spectral features by examining 2DTS spectra of ZnTe, a model system with a featureless optical susceptibility at low terahertz frequencies. These results also reveal possible artifacts that may arise from electro-optic sampling in collinear 2DTS experiments, including the observation of spurious rectified or second harmonic signals.