Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Diffuse Reflectance-Based Femtosecond Stimulated Raman Spectroscopy of Opaque Suspensions.

ABSTRACT: By augmentation of the collection optics utilized in transmission-based femtosecond stimulated Raman spectroscopy (FSRS), two novel diffuse reflectance-based femtosecond stimulated Raman spectroscopy (drFSRS) techniques were developed. These techniques were then used to collect the Raman spectra of opaque systems, those being cyclohexane-intercalated poly(tetrafluoroethylene) microbeads and ethanol in 1% intralipid solutions. The resulting drFSRS data from the cyclohexane:PTFE system show significant distortion of the depolarization ratio of the 803 cm^-1 cyclohexane peak, indicating a loss of incident pump:probe polarization in a scattering environment. The drFSRS data from the ethanol in 1% intralipid solution demonstrate less signal strength but equal spectral resolution when compared to transmission-based FSRS of the same sample. The results presented in this Technical Note demonstrate the current capabilities of collecting stimulated Raman spectra of opaque systems using drFSRS.

SUBMITTER: Diaz SA

PROVIDER: S-EPMC10620773 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Diffuse Reflectance-Based Femtosecond Stimulated Raman Spectroscopy of Opaque Suspensions.

Diaz Steven A SA McCamant David W DW

Analytical chemistry 20231018 43

By augmentation of the collection optics utilized in transmission-based femtosecond stimulated Raman spectroscopy (FSRS), two novel diffuse reflectance-based femtosecond stimulated Raman spectroscopy (drFSRS) techniques were developed. These techniques were then used to collect the Raman spectra of opaque systems, those being cyclohexane-intercalated poly(tetrafluoroethylene) microbeads and ethanol in 1% intralipid solutions. The resulting drFSRS data from the cyclohexane:PTFE system show signif ...[more]

PMID: 37852269

Similar Datasets

Ultrafast charge separation dynamics in opaque, operational dye-sensitized solar cells revealed by femtosecond diffuse reflectance spectroscopy.

Project description:Efficient dye-sensitized solar cells are based on highly diffusive mesoscopic layers that render these devices opaque and unsuitable for ultrafast transient absorption spectroscopy measurements in transmission mode. We developed a novel sub-200 femtosecond time-resolved diffuse reflectance spectroscopy scheme combined with potentiostatic control to study various solar cells in fully operational condition. We studied performance optimized devices based on liquid redox electrolytes and opaque TiO2 films, as well as other morphologies, such as TiO2 fibers and nanotubes. Charge injection from the Z907 dye in all TiO2 morphologies was observed to take place in the sub-200 fs time scale. The kinetics of electron-hole back recombination has features in the picosecond to nanosecond time scale. This observation is significantly different from what was reported in the literature where the electron-hole back recombination for transparent films of small particles is generally accepted to occur on a longer time scale of microseconds. The kinetics of the ultrafast electron injection remained unchanged for voltages between +500 mV and -690 mV, where the injection yield eventually drops steeply. The primary charge separation in Y123 organic dye based devices was clearly slower occurring in two picoseconds and no kinetic component on the shorter femtosecond time scale was recorded.

| S-EPMC4837338 | biostudies-literature

Accessing Excited State Molecular Vibrations by Femtosecond Stimulated Raman Spectroscopy.

Project description:Excited state vibrations are crucial for determining the photophysical and photochemical properties of molecular compounds. Stimulated Raman scattering can coherently stimulate and probe molecular vibrations with optical pulses, but it is generally restricted to ground state properties. Working under resonance conditions enables cross-section enhancement and selective excitation to a targeted electronic level but is hampered by an increased signal complexity due to the presence of overlapping spectral contributions. Here, we show how detailed information about ground and excited state vibrations can be disentangled by exploiting the relative time delay between Raman and probe pulses to control the excited state population, combined with a diagrammatic formalism to dissect the pathways concurring with the signal generation. The proposed method is then exploited to elucidate the vibrational properties of the ground and excited electronic states in the paradigmatic case of cresyl violet. We anticipate that the presented approach holds the potential for selective mapping of the reaction coordinates pertaining to transient electronic stages implied in photoactive compounds.

| S-EPMC7735730 | biostudies-literature

Structural Characterization of Fluorescent Proteins Using Tunable Femtosecond Stimulated Raman Spectroscopy.

Project description:The versatile functions of fluorescent proteins (FPs) as fluorescence biomarkers depend on their intrinsic chromophores interacting with the protein environment. Besides X-ray crystallography, vibrational spectroscopy represents a highly valuable tool for characterizing the chromophore structure and revealing the roles of chromophore-environment interactions. In this work, we aim to benchmark the ground-state vibrational signatures of a series of FPs with emission colors spanning from green, yellow, orange, to red, as well as the solvated model chromophores for some of these FPs, using wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in conjunction with quantum calculations. We systematically analyzed and discussed four factors underlying the vibrational properties of FP chromophores: sidechain structure, conjugation structure, chromophore conformation, and the protein environment. A prominent bond-stretching mode characteristic of the quinoidal resonance structure is found to be conserved in most FPs and model chromophores investigated, which can be used as a vibrational marker to interpret chromophore-environment interactions and structural effects on the electronic properties of the chromophore. The fundamental insights gained for these light-sensing units (e.g., protein active sites) substantiate the unique and powerful capability of wavelength-tunable FSRS in delineating FP chromophore properties with high sensitivity and resolution in solution and protein matrices. The comprehensive characterization for various FPs across a colorful palette could also serve as a solid foundation for future spectroscopic studies and the rational engineering of FPs with diverse and improved functions.

| S-EPMC10418586 | biostudies-literature

Ultrafast excited-state isomerization in phytochrome revealed by femtosecond stimulated Raman spectroscopy.

Project description:Photochemical interconversion between the red-absorbing (P(r)) and the far-red-absorbing (P(fr)) forms of the photosensory protein phytochrome initiates signal transduction in bacteria and higher plants. The P(r)-to-P(fr) transition commences with a rapid Z-to-E photoisomerization at the C(15)=C(16) methine bridge of the bilin prosthetic group. Here, we use femtosecond stimulated Raman spectroscopy to probe the structural changes of the phycocyanobilin chromophore within phytochrome Cph1 on the ultrafast time scale. The enhanced intensity of the C(15)-H hydrogen out-of-plane (HOOP) mode, together with the appearance of red-shifted C=C stretch and N-H in-plane rocking modes within 500 fs, reveal that initial distortion of the C(15)=C(16) bond occurs in the electronically excited I* intermediate. From I*, 85% of the excited population relaxes back to P(r) in 3 ps, whereas the rest goes on to the Lumi-R photoproduct consistent with the 15% photochemical quantum yield. The C(15)-H HOOP and skeletal modes evolve to a Lumi-R-like pattern after 3 ps, thereby indicating that the C(15)=C(16) Z-to-E isomerization occurs on the excited-state surface.

| S-EPMC2644115 | biostudies-literature

Molecular Origin of Photoprotection in Cyanobacteria Probed by Watermarked Femtosecond Stimulated Raman Spectroscopy.

Project description:Photoprotection is fundamental in photosynthesis to avoid oxidative photodamage upon excess light exposure. Excited chlorophylls (Chl) are quenched by carotenoids, but the precise molecular origin remains controversial. The cyanobacterial HliC protein belongs to the Hlip family ancestral to plant light-harvesting complexes, and binds Chl a and β-carotene in 2:1 ratio. We analyzed HliC by watermarked femtosecond stimulated Raman spectroscopy to follow the time evolution of its vibrational modes. We observed a 2 ps rise of the C═C stretch band of the 2Ag- (S1) state of β-carotene upon Chl a excitation, demonstrating energy transfer quenching and fast excess-energy dissipation. We detected two distinct β-carotene conformers by the C═C stretch frequency of the 2Ag- (S1) state, but only the β-carotene whose 2Ag- energy level is significantly lowered and has a lower C═C stretch frequency is involved in quenching. It implies that the low carotenoid S1 energy that results from specific pigment-protein or pigment-pigment interactions is the key property for creating a dissipative energy channel. We conclude that watermarked femtosecond stimulated Raman spectroscopy constitutes a promising experimental method to assess energy transfer and quenching mechanisms in oxygenic photosynthesis.

| S-EPMC5942868 | biostudies-literature

Neural network-based inverse model for diffuse reflectance spectroscopy.

Project description:In diffuse reflectance spectroscopy, the retrieval of the optical properties of a target requires the inversion of a measured reflectance spectrum. This is typically achieved through the use of forward models such as diffusion theory or Monte Carlo simulations, which are iteratively applied to optimize the solution for the optical parameters. In this paper, we propose a novel neural network-based approach for solving this inverse problem, and validate its performance using experimentally measured diffuse reflectance data from a previously reported phantom study. Our inverse model was developed from a neural network forward model that was pre-trained with data from Monte Carlo simulations. The neural network forward model then creates a lookup table to invert the diffuse reflectance to the optical coefficients. We describe the construction of the neural network-based inverse model and test its ability to accurately retrieve optical properties from experimentally acquired diffuse reflectance data in liquid optical phantoms. Our results indicate that the developed neural network-based model achieves comparable accuracy to traditional Monte Carlo-based inverse model while offering improved speed and flexibility, potentially providing an alternative for developing faster clinical diagnosis tools. This study highlights the potential of neural networks in solving inverse problems in diffuse reflectance spectroscopy.

| S-EPMC10545200 | biostudies-literature

Femtosecond stimulated Raman spectroscopy of the cyclobutane thymine dimer repair mechanism: a computational study.

Project description:Cyclobutane thymine dimer, one of the major lesions in DNA formed by exposure to UV sunlight, is repaired in a photoreactivation process, which is essential to maintain life. The molecular mechanism of the central step, i.e., intradimer C-C bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (C═O and C═C/C-C stretch vibrations) of cyclobutane thymine dimer and thymine dinucleotide radical anion, thymidylyl(3'→5')thymidine, can be directly probed with femtosecond stimulated Raman spectroscopy (FSRS). We construct a DFT(M05-2X) potential energy surface with two minor barriers for the intradimer C₅-C₅' splitting and a main barrier for the C₆-C₆' splitting, and identify the appearance of two C₅═C₆ stretch vibrations due to the C₆-C₆' splitting as a spectroscopic signature of the underlying bond splitting mechanism. The sequential mechanism shows only absorptive features in the simulated FSRS signals, whereas the fast concerted mechanism shows characteristic dispersive line shapes.

| S-EPMC4210081 | biostudies-literature

Instrument independent diffuse reflectance spectroscopy.

Project description:Diffuse reflectance spectroscopy with a fiber optic probe is a powerful tool for quantitative tissue characterization and disease diagnosis. Significant systematic errors can arise in the measured reflectance spectra and thus in the derived tissue physiological and morphological parameters due to real-time instrument fluctuations. We demonstrate a novel fiber optic probe with real-time, self-calibration capability that can be used for UV-visible diffuse reflectance spectroscopy in biological tissue in clinical settings. The probe is tested in a number of synthetic liquid phantoms over a wide range of tissue optical properties for significant variations in source intensity fluctuations caused by instrument warm up and day-to-day drift. While the accuracy for extraction of absorber concentrations is comparable to that achieved with the traditional calibration (with a reflectance standard), the accuracy for extraction of reduced scattering coefficients is significantly improved with the self-calibration probe compared to traditional calibration. This technology could be used to achieve instrument-independent diffuse reflectance spectroscopy in vivo and obviate the need for instrument warm up and post∕premeasurement calibration, thus saving up to an hour of precious clinical time.

| S-EPMC3041242 | biostudies-other

Femtosecond stimulated Raman spectroscopy - guided library mining leads to efficient singlet fission in rubrene derivatives.

Project description:Chromophores undergoing singlet fission are promising candidates for harnessing solar energy as they can generate a pair of charge carriers by the absorption of one photon. However, photovoltaic devices employing singlet fission are still lacking practical applications due to the limitations within the existing molecules undergoing singlet fission. Chemical modifications to acenes can lead to efficient singlet fission devices, but the influence of changes to molecular structure on the rate of singlet fission is challenging to model and predict. Using femtosecond stimulated Raman spectroscopy we have previously demonstrated that the triplet separation process during singlet fission in crystalline rubrene is associated with the loss of electron density from its tetracene core. Based on this knowledge, we mined a library of new rubrene derivatives with electron withdrawing substituents that prime the molecules for efficient singlet fission, without impacting their crystal packing. Our rationally chosen crystalline chromophores exhibit significantly improved singlet fission rates. This study demonstrates the utility and strength of a structurally sensitive spectroscopic technique in providing insights to spectroscopy-guided materials selection and design guidelines that go beyond energy arguments to design new singlet fission-capable chromophores.

| S-EPMC8549787 | biostudies-literature

Ultrafast Dynamics and Vibrational Relaxation in Six-Coordinate Heme Proteins Revealed by Femtosecond Stimulated Raman Spectroscopy.

Project description:Identifying the structural rearrangements during photoinduced reactions is a fundamental challenge for understanding from a microscopic perspective the dynamics underlying the functional mechanisms of heme proteins. Here, femtosecond stimulated Raman spectroscopy is applied to follow the ultrafast evolution of two different proteins, each bearing a six-coordinate heme with two amino acid axial ligands. By exploiting the sensitivity of Raman spectra to the structural configuration, we investigate the effects of photolysis and the binding of amino acid residues in cytochrome c and neuroglobin. By comparing the system response for different time delays and Raman pump resonances, we show how detailed properties of atomic motions and energy redistribution can be unveiled. In particular, we demonstrate substantially faster energy flow from the dissociated heme to the protein moiety in cytochrome c, which we assign to the presence of covalent heme-protein bonds.

| S-EPMC7735705 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data