Specific Molecular Vibrations Research Articles

Isotopomeric Peak Assignment for N2O in Cross-Labeling Experiments by Fiber-Enhanced Raman Multigas Spectroscopy.

Human intervention in nature, especially fertilization, greatly increased the amount of N2O emission. While nitrogen fertilizer is used to improve nitrogen availability and thus plant growth, one negative side effect is the increased emission of N2O. Successful regulation and optimization strategies require detailed knowledge of the processes producing N2O in soil. Nitrification and denitrification, the main processes responsible for N2O emissions, can be differentiated using isotopic analysis of N2O. The interplay between these processes is complex, and studies to unravel the different contributions require isotopic cross-labeling and analytical techniques that enable tracking of the labeled compounds. Fiber-enhanced Raman spectroscopy (FERS) was exploited for sensitive quantification of N2O isotopomers alongside N2, O2, and CO2 in multigas compositions and in cross-labeling experiments. FERS enabled the selective and sensitive detection of specific molecular vibrations that could be assigned to various isotopomer peaks. The isotopomers 14N15N16O (2177 cm-1) and 15N14N16O (2202 cm-1) could be clearly distinguished, allowing site-specific measurements. Also, isotopomers containing different oxygen isotopes, such as 14N14N17O, 14N14N18O, 15N15N16O, and 15N14N18O could be identified. A cross-labeling showed the capability of FERS to disentangle the contributions of nitrification and denitrification to the total N2O fluxes while quantifying the total sample headspace composition. Overall, the presented results indicate the potential of FERS for isotopic studies of N2O, which could provide a deeper understanding of the different pathways of the nitrogen cycle.

Solvent effects on spectroscopic, electronic, and topological analyses, Hirshfeld surface, ADME, and molecular docking studies on antiviral pyridine carboxamide derivatives

A theoretical study of three pyridine carboxamide derivatives in conjunction with the Density Functional Theory (DFT) approach at the 6-311+G(d,p) basis set is presented along with X-ray results. The pyridine carboxamide derivatives were analyzed with the help of FT-IR, UV–Vis, 1H and 13C NMR investigation. The spectral characterizations were made by vibrational energy distribution analysis (VEDA4), which helps to assign vibrational frequencies to specific molecular vibrations. A comparative analysis of computed 1H and 13C NMR chemical shift values with experimental chemical shifts for the pyridine carboxamide compounds by applying the gauge-including atomic orbitals method in chloroform and acetone solvents was carried out. UV–Vis spectroscopy and electronic transitions were conducted on both chloroform and acetone solvents through the assistance of the TD-DFT methodology. Hirshfeld Surface analysis was employed to analyze the intermolecular hydrogen bonds of the type N-H⋯N to the crystal packing. The chemical properties of frontier molecular orbital and global reactivity descriptors were analyzed for the different solvents such as chloroform and acetone. The Fukui functions were used to identify reactive sites in a molecule, including those susceptible to nucleophilic and electrophilic outbreaks. The weak interactions were analyzed using reduced density gradient (RDG) analysis, a computational method used to study noncovalent interactions, including hydrogen bonding. The Absorption, Distribution, Metabolism, and Excretion (ADME) attributes of the studied compounds have been evaluated for drug discovery initiatives. Molecular docking studies with antiviral SARS-CoV-2 Mpro and Omicron variant containing the Q493R mutation proteins of three pyridine carboxamide derivatives (L3–L5) have been performed, and L5 has maximum binding energy values of −7.13 kcal/mol for 6LU7.

Selective Detection in Impulsive Low-Frequency Raman Imaging Using Shaped Probe Pulses

Impulsive stimulated Raman scattering (ISRS) using a single short femtosecond pump pulse to excite molecular vibrations offers an elegant pump-probe approach to perform vibrational imaging below $200\phantom{\rule{0.2em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$. One shortcoming of ISRS is its inability to offer vibrational selectivity as all the vibrational bonds whose frequencies lie within the short pump-pulse bandwidth are excited. To date, several coherent control techniques have been explored to address this issue and selectively excite a specific molecular vibration by shaping the pump pulse. There has not been any systematic work that reports an analogous shaping of the probe pulse to implement preferential detection. In this work, we focus on vibrational imaging and report vibrational selective detection by shaping the probe pulse in time. We demonstrate numerically and experimentally two pulse-shaping strategies with one functioning as a vibrational notch filter and the other functioning as a vibrational low-pass filter. This enables fast ($25\phantom{\rule{0.2em}{0ex}}\text{\ensuremath{\mu}}\mathrm{s}/$pixel) and selective hyperspectral imaging in the low-frequency regime ($<200\phantom{\rule{0.2em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$).

Quantification of Chemical Uptake into the Skin by Vibrational Spectroscopies and Stratum Corneum Sampling.

Evaluation of the bioavailability of drugs intended to act within the skin following the application of complex topical products requires the application of multiple experimental tools, which must be quantitative, validated, and, ideally and ultimately, sufficiently minimally invasive to permit use in vivo. The objective here is to show that both infrared (IR) and Raman spectroscopies can assess the uptake of a chemical into the stratum corneum (SC) that correlates directly with its quantification by the adhesive tape-stripping method. Experiments were performed ex vivo using excised porcine skin and measured chemical disposition in the SC as functions of application time and formulation composition. The quantity of chemicals in the SC removed on each tape-strip was determined from the individually measured IR and Raman signal intensities of a specific molecular vibration at a frequency where the skin is spectroscopically silent and by a subsequent conventional extraction and chromatographic analysis. Correlations between the spectroscopic results and the chemical quantification on the tape-strips were good, and the effects of longer application times and the use of different vehicles were clearly delineated by the different measurement techniques. Based on this initial investigation, it is now possible to explore the extent to which the spectroscopic approach (and Raman in particular) may be used to interrogate chemical disposition deeper in the skin and beyond the SC.

The Raman Active Vibrations of Flavone and Quercetin: The Impact of Conformers and Hydrogen Bonding on Fingerprint Modes

The detection and analysis of flavonoids by Raman spectroscopy are of interest in many fields, including medicinal chemistry, food science, and astrobiology. Spectral interpretation would benefit from better identification of the fingerprint vibrational peaks of different flavonoids and how they are affected by intermolecular interactions. The Raman spectra of two flavonoids, flavone and quercetin, were investigated through comparisons between spectra recorded from pure powders and spectra calculated with time dependent density functional theory (TDDFT). For both flavone and quercetin, 17 peaks were assigned to specific molecular vibrations. Both flavonoids were found to have a split peak between 1250-1350 cm-1 that is not predicted by TDDFT calculations on isolated molecules. In each case, it is shown that the addition of hydrogen bonded molecules arranged based on crystal structures reproduces the split peaks. These peaks were due to a stretching vibration of the bond between benzopyrone and phenyl rings and represent a characteristic spectral feature of flavonoids. Spectra of pollen grains from Quercus virginiana were also recorded and exhibit several peaks that correspond to the quercetin spectrum.

Vibration‐Assisted Charge Transport through Positively Charged Dimer Junctions

AbstractIntermolecular charge transport plays a vital role in the fields of electronics, as well as biochemical systems. Here, we design supramolecular dimer junctions and investigate the effects of charge state and energy level alignment on charge transport under nanoconfinement. Incoherent tunneling caused by thermally‐induced vibrations is enhanced in positively charged systems. The transition between coherent and incoherent tunneling is associated with specific molecular vibration modes. Positively charged systems with smaller torsional barriers and vibrational frequencies result in lower transition temperatures. Multiple thermal effects have a great impact on the conductance in the off‐resonant tunneling, while thermally‐induced vibron‐assisted tunneling contributes more to the transport in the resonant tunneling. These investigations offer a deep mechanism understanding of intermolecular charge transport and facilitate the development of practical functional molecular devices.

Vibration-Assisted Charge Transport through Positively Charged Dimer Junctions.

Intermolecular charge transport plays a vital role in the fields of electronics, as well as biochemical systems. Here, we design supramolecular dimer junctions and investigate the effects of charge state and energy level alignment on charge transport under nanoconfinement. Incoherent tunneling caused by thermally-induced vibrations is enhanced in positively charged systems. The transition between coherent and incoherent tunneling is associated with specific molecular vibration modes. Positively charged systems with smaller torsional barriers and vibrational frequencies result in lower transition temperatures. Multiple thermal effects have a great impact on the conductance in the off-resonant tunneling, while thermally-induced vibron-assisted tunneling contributes more to the transport in the resonant tunneling. These investigations offer a deep mechanism understanding of intermolecular charge transport and facilitate the development of practical functional molecular devices.

Field-Induced Funneling of Vibrational Energy into High-Frequency Modes in Molecular Junctions Far from Equilibrium

The ability to control the energy content of specific molecular vibrations is essential for realizing mode-selective chemistry. Single-molecule junctions far from equilibrium were proposed as potential platforms for this purpose by utilizing different bias polarities for funneling energy into different molecular modes. Here, we show that vibrational energy can be funneled into (or out of) a specific molecular mode even under a fixed static bias, via external periodic driving (or changing the temperature) of the fermion reservoirs in the molecular junction. Indeed, changes in the charge-carrier distributions within the driven reservoirs induce changes in the balance between vibrational cooling and heating pathways (induced by charge transport), in a way which depends sensitively on the different mode frequencies and vibronic couplings. Conditions under which this proposed mechanism should induce pronounced mode-selective excitation are demonstrated and discussed.

Data-Driven Identification of Biomarkers for In Situ Monitoring of Drug Treatment in Bladder Cancer Organoids.

Three-dimensional (3D) organoid culture recapitulating patient-specific histopathological and molecular diversity offers great promise for precision medicine in cancer. In this study, we established label-free imaging procedures, including Raman microspectroscopy (RMS) and fluorescence lifetime imaging microscopy (FLIM), for in situ cellular analysis and metabolic monitoring of drug treatment efficacy. Primary tumor and urine specimens were utilized to generate bladder cancer organoids, which were further treated with various concentrations of pharmaceutical agents relevant for the treatment of bladder cancer (i.e., cisplatin, venetoclax). Direct cellular response upon drug treatment was monitored by RMS. Raman spectra of treated and untreated bladder cancer organoids were compared using multivariate data analysis to monitor the impact of drugs on subcellular structures such as nuclei and mitochondria based on shifts and intensity changes of specific molecular vibrations. The effects of different drugs on cell metabolism were assessed by the local autofluorophore environment of NADH and FAD, determined by multiexponential fitting of lifetime decays. Data-driven neural network and data validation analyses (k-means clustering) were performed to retrieve additional and non-biased biomarkers for the classification of drug-specific responsiveness. Together, FLIM and RMS allowed for non-invasive and molecular-sensitive monitoring of tumor-drug interactions, providing the potential to determine and optimize patient-specific treatment efficacy.

A better way to do infrared microspectroscopy

A promising microspectroscopy technique has just become even more promising thanks to an improvement that increases the technique’s sensitivity and spatial resolution. The advance, which combines fluorescence microscopy and infrared (IR) spectroscopy, enables scientists to probe chemistry inside living cells and within tiny domains of heterogeneous materials. Barely 5 years old, mid-IR photothermal microscopy provides molecular information from a microscopic region of a specimen by monitoring the temperature changes that result from IR-induced sample heating. The sample absorbs select bands of IR light, which triggers specific molecular vibrations that can be detected as temperature changes and used for chemical fingerprinting and sample mapping. Researchers typically probe the temperature change by monitoring how a beam of visible light scatters from the sample. But scattering depends weakly on temperature, so imaging can be slow and the image quality poor. Working independently, two research teams have come up with a way to sidestep

NWU‐RSIT: An integrated graphical user interface for biomedical Raman spectral imaging with both univariate and multivariate modules

AbstractWhen consecutively acquiring Raman spectra at a given number, Raman imaging could be applied to extract the compositional and structural information from the selected sampling region. By compacting both univariate and multivariate algorithms, an integrated Raman spectral imaging toolbox (NWU‐RSIT) was developed for spectral analysis, image reconstruction, and feature recognition. Using an example hyperspectral dataset from a single living mouse osteosarcoma cell, univariate imaging method reveals spatial distributions of some specific molecular vibration modes; multivariate algorithms, including principal component analysis (PCA), hierarchical clustering analysis (HCA), k‐means clustering analysis (KCA), vertex component analysis (VCA), and N‐FINDR algorithm, were realized to extract more detailed constitution information from the acquired hyperspectral dataset. After comparing and evaluating the system performance of NWU‐RSIT, it will make Raman spectral imaging more accessible to all related fields, especially for the biomedical studies.

Ultrafast time-resolved x-ray absorption spectroscopy of ionized urea and its dimer through ab initio nonadiabatic dynamics.

Investigating the early dynamics of chemical systems following ionization is essential for our understanding of radiation damage. However, experimental as well as theoretical investigations are very challenging due to the complex nature of these processes. Time-resolved x-ray absorption spectroscopy on a femtosecond timescale, in combination with appropriate simulations, is able to provide crucial insights into the ultrafast processes that occur upon ionization due to its element-specific probing nature. In this theoretical study, we investigate the ultrafast dynamics of valence-ionized states of urea and its dimer employing Tully's fewest switches surface hopping approach using Koopmans' theorem to describe the ionized system. We demonstrate that following valence ionization through a pump pulse, the time-resolved x-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges reveal rich insights into the dynamics. Excited states of the ionized system give rise to time-delayed blueshifts in the x-ray absorption spectra as a result of electronic relaxation dynamics through nonadiabatic transitions. Moreover, our statistical analysis reveals specific structural dynamics in the molecule that induce time-dependent changes in the spectra. For the urea monomer, we elucidate the possibility to trace effects of specific molecular vibrations in the time-resolved x-ray absorption spectra. For the urea dimer, where ionization triggers a proton transfer reaction, we show how the x-ray absorption spectra can reveal specific details on the progress of proton transfer.

Raman image-activated cell sorting

The advent of image-activated cell sorting and imaging-based cell picking has advanced our knowledge and exploitation of biological systems in the last decade. Unfortunately, they generally rely on fluorescent labeling for cellular phenotyping, an indirect measure of the molecular landscape in the cell, which has critical limitations. Here we demonstrate Raman image-activated cell sorting by directly probing chemically specific intracellular molecular vibrations via ultrafast multicolor stimulated Raman scattering (SRS) microscopy for cellular phenotyping. Specifically, the technology enables real-time SRS-image-based sorting of single live cells with a throughput of up to ~100 events per second without the need for fluorescent labeling. To show the broad utility of the technology, we show its applicability to diverse cell types and sizes. The technology is highly versatile and holds promise for numerous applications that are previously difficult or undesirable with fluorescence-based technologies.

Washing Durability and Photo-Stability of NanoTiO2-SiO2 Coatings Exhausted onto Cotton and Cotton/Polyester Fabrics

The purpose of this study was to assess and compare the durability of TiO2-SiO2 coatings applied in three concentrations onto two lightweight cellulose-based fabrics diverse in the composition against two external factors, repeated washings and prolonged intensive UV irradiation, by observing the changes in surface morphology, investigation of optical properties, and identification of specific molecular vibrations. The scanning electron microscopy (SEM) micrographs, diffuse reflectance spectroscopy (DRS) profiles and fourier transform-infrared (FT-IR) spectra implied equal distribution of TiO2-SiO2 nanoparticles over the surfaces of both fabrics after exhaustion procedures, regarding the concentration of colloidal paste and the type of material used, followed by a slight reduction of nanoparticles after twenty washing cycles. Moreover, the newly gained, good to very good UV protective functionality proved the suitability of the employed procedure and the sufficient durability of the selected coatings. Additionally, UV irradiation mainly caused damages to the cotton. Cotton/polyester became yellower under UV, although the application of TiO2-SiO2 protected the material against yellowness.

Metasurface based on cross-shaped plasmonic nanoantennas as chemical sensor for surface-enhanced infrared absorption spectroscopy

Infrared spectroscopy is an effective technique extensively used in research and industry for the label-free and unambiguous identification of molecular species. However, the sensitivity of this technique is severely limited as a result of Beer’s law and, the small infrared absorption cross-section that make prohibitively weak the absorption signals, of minute amounts of analyte as those present in monolayers. This limitation can be overcome by enhancing the infrared vibration of molecules through the enhancement of the electromagnetic (EM) field. Surface Enhanced InfraRed Absorption (SEIRA) using resonant metal Nano-scale Antennas (NAs) can provide huge electromagnetic fields on the nanometer scale featuring localized collective oscillations of electrons, an effect named Localized Surface Plasmonic Resonances (LSPRsWe here report on a series of 2D arrays of cross-shaped NAs having several mm2 area coverage (metasurface) as SEIRA optimized antennas, which can be used in practical applications such as the vibrational sensing of chemical and biological analytes. Cross-shape designed NAs are insensitive to the polarization of the electromagnetic radiation impinging the active area. Due to the random orientation of the dipole moments of molecules they are particularly suitable for the construction of bio-molecular sensors. At the same time, the 2D-array configuration ensures a good near-field signal enhancement arising from the coupling between neighbour NAs Moreover, SEIRA NAs can be easily integrated with micrometre-sized channels and be suitable for the high sensitivity, real time analysis of IR emitting samples, in matrices where IR spectroscopy is severely limited due to absorption bands of liquid water. We present the design, fabrication and experimental characterization of large-area metasurfaces based on cross-shaped plasmonic NAs for the spectroscopic characterization of various types of compounds and for sensing applications in the mid-infrared range. The cross-shaped NAs we have designed exhibit SEIRA phenomena which are very sensitive to both refractive index changes in the surrounding medium and to the specific molecular vibration band emerging from surface adsorbed molecules. To test this effect on our device, we have used as model compounds small molecules (molecular weight (MW) < 500 g/mol) containing triple bond groups resonating at about 2100 cm−1 and a large polymer (MW ˜ 950,000 g/mol) containing carbonyl groups resonating at wavenumbers of about 1700 cm−1. We show a sensitivity of 600 nm/RIU at different wavelengths at a maximum amount of immobilized small molecule of 0.7 fmoles and a SEIRA enhancement factor of 48,000. We also show the device potential to reveal chemical reactions, occurring on the sensor surface at the same scale, where the nitrile group is converted to a triazole ring.

Illuminating Fermi Resonances that Trigger Reaction in a Complex Molecule

Transferring energy to specific molecular vibrations remains a challenge in the quest to control chemical reactions with light. In this issue of Chem, Rafiq et al. show that a quantum-mechanical Fermi resonance between a light-absorbing terpyridine-molybdenum complex and dinitrogen bridge directs energy to vibrations associated with bond activation.

Mode-Selective Laser Control of Palladium Catalyst Decomposition.

It is generally assumed that molecules behave ergodically during chemical reactions, that is, reactivities depend only on the total energy content and not on the initial state of the molecule. While there are a few examples of nonergodic behavior in small (usually electronically excited) species, to date there have been no reports of such behavior in larger covalently bound species composed of several tens of atoms. Here, we demonstrate vibrational mode-selective behavior in a series of palladium catalysts. When we excite solvent-tagged gas-phase Pd catalysts with an infrared laser that is tuned to be resonant with specific molecular vibrations, depending on which vibration we excite, we can select different reaction pathways. We also demonstrate that this behavior can be "turned off" via chemical substitution.

Joint Space-Time Coherent Vibration Driven Conformational Transitions in a Single Molecule.

We report single-molecule conformational transitions with joint angstrom-femtosecond resolution by irradiating the junction of a scanning tunneling microscope with femtosecond laser pulses. An isolated pyrrolidine molecule adsorbed on a Cu(001) surface undergoes reversible transitions between two conformational states. The transition rate decays in time and exhibits sinusoidal oscillations with periods of specific molecular vibrations. The dynamics of this transition depends sensitively on the molecular environment, as exemplified by the effects of another molecule in proximity.

Near infrared spectroscopic imaging assessment of cartilage composition: Validation with mid infrared imaging spectroscopy

Disease or injury to articular cartilage results in loss of extracellular matrix components which can lead to the development of osteoarthritis (OA). To better understand the process of disease development, there is a need for evaluation of changes in cartilage composition without the requirement of extensive sample preparation. Near infrared (NIR) spectroscopy is a chemical investigative technique based on molecular vibrations that is increasingly used as an assessment tool for studying cartilage composition. However, the assignment of specific molecular vibrations to absorbance bands in the NIR spectrum of cartilage, which arise from overtones and combinations of primary absorbances in the mid infrared (MIR) spectral region, has been challenging. In contrast, MIR spectroscopic assessment of cartilage is well-established, with many studies validating the assignment of specific bands present in MIR spectra to specific molecular vibrations. In the current study, NIR imaging spectroscopic data were obtained for compositional analysis of tissues that served as an in vitro model of OA. MIR spectroscopic data obtained from the identical tissue regions were used as the gold-standard for collagen and proteoglycan (PG) content. MIR spectroscopy in transmittance mode typically requires a much shorter pathlength through the sample (≤10 microns thick) compared to NIR spectroscopy (millimeters). Thus, this study first addressed the linearity of small absorbance bands in the MIR region with increasing tissue thickness, suitable for obtaining a signal in both the MIR and NIR regions. It was found that the linearity of specific, small MIR absorbance bands attributable to the collagen and PG components of cartilage (at 1336 and 856 cm−1, respectively) are maintained through a thickness of 60 μm, which was also suitable for NIR data collection. MIR and NIR spectral data were then collected from 60 μm thick samples of cartilage degraded with chondroitinase ABC as a model of OA. Partial least squares (PLS) regression using NIR spectra as input predicted the MIR-determined compositional parameters of PG/collagen within 6% of actual values. These results indicate that NIR spectral data can be used to assess molecular changes that occur with cartilage degradation, and further, the data provide a foundation for future clinical studies where NIR fiber optic probes can be used to assess the progression of cartilage degradation.

Electron momentum spectroscopy of dimethyl ether taking account of nuclear dynamics in the electronic ground state.

The influence of nuclear dynamics in the electronic ground state on the (e,2e) momentum profiles of dimethyl ether has been analyzed using the harmonic analytical quantum mechanical and Born-Oppenheimer molecular dynamics approaches. In spite of fundamental methodological differences, results obtained with both approaches consistently demonstrate that molecular vibrations in the electronic ground state have a most appreciable influence on the momentum profiles associated to the 2b1, 6a1, 4b2, and 1a2 orbitals. Taking this influence into account considerably improves the agreement between theoretical and newly obtained experimental momentum profiles, with improved statistical accuracy. Both approaches point out in particular the most appreciable role which is played by a few specific molecular vibrations of A1, B1, and B2 symmetries, which correspond to C-H stretching and H-C-H bending modes. In line with the Herzberg-Teller principle, the influence of these molecular vibrations on the computed momentum profiles can be unraveled from considerations on the symmetry characteristics of orbitals and their energy spacing.