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Introduction
Valdas Sablinskas currently works at the Institute of Chemical Physics, Vilnius University. Valdas does research in Biophysics. Their current projects are 'Cluster structure of hydrogen-bonded liquids' and "Stop fake food".
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Vilnius University
Institute of Chemical Physics
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Director
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Iryna Doroshenko
Taras Shevchenko National University of Kyiv
Valeriy Pogorelov
Taras Shevchenko National University of Kyiv
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Iuliu Haţieganu University of Medicine and Pharmacy
Vilnius University
Vilnius University
Northeastern University
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Vilnius University
Center for Physical Sciences and Technology
Vilnius University
Vilnius University
Vilnius University
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Projects (2)
Cluster structure of hydrogen-bonded liquids
FTIR spectroscopy, matrix isolation
Stop fake food (http://stopfakefood.com/)
The project is dealing with following problems in food production: (i) Meat products are counterfeited with much cheaper substitute to increase profits. (ii) There are many cases when extra virgin olive oil is fake (iii) Some seafood wholesalers are using formalin to prevent fish from deteriorating during transportation and keep it longer fresh. We do qualitative and quantitative analysis of meat, oil and fish by means of Raman and SERS spectroscopy.
Research
Research Items (149)
1-chloromethyl-1-fluorosilacyclopentane (1-ClM-1-FSiCP) was synthesized for the first time and investigated by means of vibrational spectroscopy and theoretical calculations. FT-IR and Raman spectroscopic methods were implemented to collect vibrational spectra of 1-ClM-1-FSiCP. The conformational analysis was performed utilizing FT-IR matrix isolation technique and theoretical methods such as density functional theory and ab initio calculations. The spectra of the 1-ClM-1-FSiCP isolated in the argon and nitrogen matrices, were collected before and after the annealing process. During the conformational analysis the envelope (E) and twisted (T) ring shapes with the position of the fluorine atom and chloromethyl group in terms of axial/equatorial and cis/trans/gauche-/gauche+ positions were investigated utilizing MP2/aug-cc-pVTZ and DFT/B3LYP/aug-cc-pVTZ level of theory. Results indicate three stable conformers: twisted trans (global energy minimum), twisted gauche– and twisted gauche+. The potential energy surface scans were performed to trace the energy changes and the presence of transition state structures during ring conversion and rotation of the CH2Cl group.
Vibrational spectroscopy provides the possibility for sensitive and precise detection of chemical changes in biomolecules due to development of cancers. In this work, label-free near-infrared surface enhanced Raman spectroscopy (SERS) was applied for the differentiation between cancerous and normal human bladder tissues via analysis of the extracellular fluid of the tissue. Specific cancer-related SERS marker bands were identified by using a 1064 nm excitation wavelength. The prominent spectral marker band was found to be located near 1052 cm-1 and was assigned to the C-C, C-O, and C-N stretching vibrations of lactic acid and/or cysteine molecules. The correct identification of 80% of samples is achieved with even limited data set and could be further improved. The further development of such a detection method could be implemented in clinical practice for the aid of surgeons in determining of boundaries of malignant tumors during the surgery.
The widespread use of plastic without the sustainable management of the plastic waste has led to its accumulation in the environment. The presence of microplastics even in drinking water and food products is of immense concern. This situation is getting even more complicated due to the limited knowledge about the sources of microplastics and their impact on the environment and human health. This article focuses on a poorly understood but potentially significant source of microplastic-treated organic waste. Quantitative and qualitative analyses of microplastics down to 50 µm in the stabilised organic waste (SOW) output after mixed municipal solid waste (MSW) processing and green and food composts are presented in the article. Nile Red staining and FTIR analysis were adopted for the identification of microplastics. The highest average microplastic abundance was found in the SOW: 17407 ± 1739 particles kg−1 in autumn and 15400 ± 1217 particles kg−1 in winter. Nevertheless, even separately collected treated organic waste contained a significant amount of microplastics. Green compost contained 5733 ± 850 particles kg−1 in autumn and 6433 ± 751 particles kg−1 in winter, while food compost 3783 ± 351 particles kg−1 in autumn and 4066 ± 658 particles kg−1 in winter. Microplastics < 1 mm accounted for 83.8–94.9% of all microplastics, which reflects the need to control not only large but also small microplastics in organic waste fertilisers to prevent soil pollution. The dominant shape of microplastics in compost samples was films, while in the SOW, it was fragments. Based on morphological and FTIR analyses, the majority of microplastics in green and food composts were considered as the residuals of plastic bags and packaging materials.
Keywords: multi-walled carbon nanotubes (MWCNT), iridium-doped, nanohybrid composite, Raman spectrum, energy-dispersive X-ray spectroscopy Multi-walled carbon nanotubes have been prepared by chemical vapour deposition pyrolysis of ethyl alcohol at 665°C. The addition of atoms other than carbon to the nanostructure, in our case the iridium component, leads to the formation of defects that contribute to changes in the electrical and optoelectrical properties. The formation and structural changes of multi-walled nanotubes were studied using an electron microscope, Raman and energydisperse spectrometry. Using the Raman and X-ray spectrum, a clear difference between the synthesis without and with the addition of iridium impurities was found.
1-chloro-1-chloromethylsilacyclohexane (1-Cl-1-ClMSiCH) is a newly synthesized molecular compound whose conformational analysis was performed by means of vibrational spectroscopy and theoretical calculations. Conventional ATR-FTIR and Raman spectroscopic methods were used to obtain vibrational spectra of the liquid sample. Additionally, FTIR spectra of the compound isolated in low-temperature neon and nitrogen matrices were registered to make a complete assignment of the experimental vibrational spectral bands. All theoretically possible 38 canonical ring conformations considering axial/equatorial and cis/trans/gauche-/gauche+ positions of the Cl and CH2Cl group were analyzed by utilizing MP2 and B3LYP at aug-cc-pVTZ theory level. The most stable local energy minima were investigated in detail, with the global energy minimum structure being in the chair axial trans conformation. Detailed analysis of the potential energy surface revealed the transition states (TS) and the energy barriers. The conformational path was found to be the chair→ envelope/half-chair (TS)→ skew-boat C1→ boat (TS)→ skew-boat C2. The energy barrier for ¹C4 to ¹S3 conversion was found to be 4.94 kcal/mol while for the reverse process – it was calculated to be 0.26 kcal/mol. The vibrational analysis and the experimental spectra suggest that the four lowest energy (chair ring) conformers coexist at room temperature. The energy barrier for gauche to trans conversion is 1.15 kcal/mol for axial and 1.04 kcal/mol for equatorial conformers, and it is possible to observe these processes in low-temperature matrices.
In this research, we have demonstrated that 2D Ti3C2Xn-based MXene (MXene) films are suitable for the design of surface-enhanced Raman spectroscopy (SERS)-based sensors. The enhanced SERS signal was observed for a salicylic acid molecule on Ti3C2Tx-based MXene film. Confirmation of the adsorption of the salicylic acid molecule and the formation of a salicylic acid–MXene complex were determined by experimental SERS-based spectral observations such as greatly enhanced out-of-plane bending modes of salicylic acid at 896 cm−1 and a band doublet at 681 cm−1 and 654 cm−1. Additionally, some other spectral features indicate the adsorption of salicylic acid on the MXene surface, namely, a redshift of vibrational modes and the disappearance of the carboxyl deformation spectral band at 771 cm−1. The determined enhancement factor indicates the value that can be expected for the chemical enhancement mechanism in SERS of 220 for out-of-plane vibrational modes. Theoretical modeling based on density functional theory (DFT) calculations using B3LYP/6311G++ functional were performed to assess the formation of the salicylic acid/MXene complex. Based on the calculations, salicylic acid displays affinity of forming a chemical bond with titanium atom of Ti3C2(OH)2 crystal via oxygen atom in hydroxyl group of salicylic acid. The electron density redistribution of the salicylic acid–MXene complex leads to a charge transfer effect with 2.2 eV (428 nm) and 2.9 eV (564 nm) excitations. The experimentally evaluated enhancement factor can vary from 220 to 60 when different excitation wavelengths are applied.
The goal of this study is development of ultra-sensitive and reproducible SERS platform based on novel magnetoplasmonic nanoparticles produced by laser ablation. The magnetic part of hybrid nanoparticles ensures manipulation of the nanoparticles by magnetic field by arranging them at biological surfaces in a special geometry resulting in high and reproducible SERS. Magneto-plasmonic Au-Fe nanoparticles in colloidal suspension were prepared by picosecond laser ablation of evaporated iron and gold films on glass. The nanoparticles were characterized by UV-visible extinction, high resolution electronic microscopy, and Raman spectroscopy. EDX analysis revealed that the shell of nanoparticles (2−20 nm) consist of iron and the core is composed mostly of gold. The plasmonic behavior of nanoparticles was accessed by analysis of SERS spectra from adsorbed adenine as probe ligand. The fabrication of hybrid nanoparticles by laser ablation offers a new possibility for construction of SERS substrates with tunable optical and magnetic properties for biomedical sensing.
This work presents the application of EC-SERS spectroscopy for the detection of caffeine consumption from human saliva. Caffeine and paraxanthine as the major metabolite of caffeine were tested. Model samples of saliva spiked with caffeine were investigated, and detection of caffeine in real-life saliva samples was tested in order to ensure the viability of the method for clinical applications. Two doses of caffeine (2 mg/kg and 3.5 mg/kg) were ingested by volunteers, and their saliva samples were taken at different time periods ranging from 1 h to 10 h after the consumption. Density functional theory calculations of caffeine and paraxanthine adsorbed on the silver surface were performed in order to better understand the adsorption of the investigated molecules and to make a correct assignment of the experimental spectral bands of the EC-SERS spectra. It was determined that a low dose caffeine consumption can be detected by the appearance of the SERS spectral marker band of caffeine and paraxanthine at 692 cm⁻¹. The intensity of this band is mostly reasoned by the paraxanthine concentration since the intensity changes of the band over time correlates to the concentration changes of paraxanthine determined by the pharmacokinetic studies of paraxanthine and caffeine in the human saliva. It was found that the limit of detection paraxanthine in saliva by means of EC-SERS is as low as 15 μM and can be further improved.
Pathogenic strains of bacteria are causing various illnesses all around the world and have a major socio‐economic impact. Thus, fast and low‐cost methods for the microbial control of foods are needed. One of them might be photosensitization. This study looks deeper into the mechanism of E. coli damage by Chlorophyllin‐based photosensitization. Fluorimetric data indicate that after 15 min incubation with chlorophyllin (Chl) (1.5 × 10⁻⁵ M Chl) 0.73 ± 0.03 μM of this compound was associated with E. coli cell surface. After photoactivation (405 nm, 6–30 J/cm²) significant reduction (88.2%) of bacterial viability was observed. Higher concentration of Chl (5 × 10⁻⁴ M Chl) reduced viability of bacteria more than by 98%. Results indicated that reactive oxygen species (ROS) took place in this inactivation. Colloidal surface enhanced Raman scattering (SERS) spectroscopy was employed to detect the molecular changes in the the treated bacteria. It was found that Chl‐based based photosensitization triggers multiple surface structure changes in E. coli what induce lethal unrepairable damages and inactivation of pathogen. This article is protected by copyright. All rights reserved.
Cesium–lead–bromide (CsPbBr3) is the simplest all inorganic halide perovskite. It serves as a reference material for understanding the exceptional solar cell properties of the organic–inorganic hybrid halide perovskites and is itself discussed as an alternative absorber material. Broadband dielectric spectroscopy has proven to yield an in depth understanding of charge screening mechanisms in the halide solar cell absorbers based on methylammonium and modifications hereof. For a deeper understanding of charge carrier screening, we have investigated CsPbBr3 across wide temperature (120 K–450 K) and frequency ranges. Besides the two known phase transitions at 403 K and 361 K, the dielectric data show another anomaly around 220 K, which can be interpreted as another phase transition. XRD and EPR studies confirm the presence of this anomaly, but Raman scattering spectra do not show any lattice anomalies in the vicinity of 220 K. This additional anomaly is of first order character (different transition temperatures upon cooling and heating) but hardly influences the lattice dynamics. Our broadband dielectric investigations of CsPbBr3 display the same microwave limit permittivity as for MAPbX3 (εr ≈ 30, X = Cl, Br, I, MA = CH3NH3⁺) but do not afford a second permittivity relaxation up to this frequency. Our prior assignment of the second contribution in the methylammonium compounds being due to the relaxation dynamics of the methylammonium ion as a dipole is herewith proven. Nevertheless, CsPbBr3 shows large charge carrier screening up to very high frequencies which can still play a vital role in charge carrier dynamics and exciton behaviour in this material as well.
Since 1-chloromethyl-1-fluorosilacyclohexane is a newly synthesized molecular compound its structural parameters and conformational stability is unknown. Raman and infrared vibrational spectroscopy methods were employed for analysis of this molecule. IR spectra were recorded for both gas phase and liquid sample, whereas the Raman experiments were performed in the liquid state. Additionally, low temperature matrix isolation infrared spectra were recorded after isolating the molecule in argon and nitrogen matrices. For the assignment of the experimental spectral bands, theoretical DFT/B3LYP/aug-cc-pVDZ and MP2/aug-cc-pVDZ calculations were performed. From the calculations it was found that 1-chloromethyl-1-fluorosilacyclohexane may exist in twelve different conformational forms out of which the chair axial trans conformer is the most stable form. However, there are three more chair type conformers – equatorial trans, equatorial gauche and axial gauche that are stable enough to be observed in the experimental spectra.
We present the infrared spectroscopy study of three types of human healthy and cancerous tissues using standard ATR and fiber optics based ATR techniques. The use of fiber based ATR probes eliminates the need to bring the sample under the study to the spectroscopic instrument and opens the path for the application of infrared spectroscopy for the studies in situ and in vivo. The study revealed that conventional portable FTIR spectrometers with room temperature DTGS detectors cannot be readily used when coupled with fiber probes due to the high loses of the optical signal, but this problem can be overcome by combining an additional more sensitive liquid nitrogen cooled MCT detector to the system. The potential of the system is demonstrated in the cases of the studies of three types of tumorous tissues: kidney, bladder and brain. The studies of the tissue smears and untreated (wet) tissues indicated that “water free” fingerprint region has clear spectral signatures for the tumor identification. Depending on the tissue, the signatures are based on the glycogen infrared absorption bands for kidney tissue and the collagen absorption bands for bladder tissue. Brain tissue examination also shows some promising spectral markers for which precise establishment the higher data sets are still needed.
Tetrahydrofuran (THF) is a widely used chemical compound, in particular as a solvent in organic and inorganic synthesis. The THF molecule has also an interesting property, namely, undergoes pseudorotation, similar to the case of the cyclopentane. Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. We study the influence of the molecular environment (N2) on the Cs–C2 equilibrium of tetrahydrofuran in the [email protected]2 system utilizing nitrogen matrix isolation infrared spectroscopy. We observe a different ratio between envelope (Cs) and twisted (C2) conformations with respect to a change of the temperature. FTIR experimental studies are supported by the results of the static density functional theory calculations and Car-Parrinello molecular dynamics simulations. We focus on the dynamics of the pseudorotation process, in particular, the lifetime of the THF conformations and their mutual rearrangements. On the basis of the [email protected]2 matrix model, with explicit nitrogen molecules, the anharmonic infrared spectra are generated from the Fourier transformation of the dipole moment autocorrelation function.
More than 90% of solid kidney tumors are cancerous and have to be treated by surgical resection where surgical outcomes and patient prognosis are dependent on the tumor discrimination. The development of alternative approaches based on a new generation of fiber attenuated total reflection (ATR) probes could aid tumor identification even under intra‐surgical conditions. Herein, fiber ATR IR spectroscopy is employed to distinguish normal and cancerous kidney tissues. Freshly resected tissue samples from thirty four patients are investigated under nearly native conditions. Spectral marker bands that allow a reliable discrimination between tumor and normal tissue is identified by a supervised classification algorithm. The absorbance values of the bands at 1025, 1155 and 1240 cm⁻¹ assigned to glycogen and fructose 1,6‐bisphosphatase are used as the clearest markers for the tissue discrimination. Absorbance threshold values for tumor and normal tissue are determined by discriminant analysis. This new approach allows the surgeon to make a clinical diagnosis. This article is protected by copyright. All rights reserved.
Aspirin being freely available as an over the counter drug has a high overdose risk and can cause severe health symptoms. The methods used in clinics for the detection of such drugs (pharmaceuticals) in bodily fluids are mostly based on liquid chromatography and mass spectroscopy. These methods are known to be precise; however, they both require long and laborious sample preparation; thus, it takes time to acquire the required information. Because in the case of an overdose, the time has high importance, and faster methods would be beneficial. This work presents an application of a Surface‐enhanced Raman scattering (SERS) spectroscopic method for the detection of salicylic acid as a metabolite of aspirin in the blood serum of the patient under examination. In this research, the various colloidal solutions were employed for the preparation of SERS active substrates. The choice of the most efficient colloidal solution and the challenges of collecting SERS spectra of whole blood or its components are discussed. The spectra of both the model and the real‐life blood samples containing metabolite of aspirin were collected with a Fourier transform Raman spectrometer. The analysis of the collected spectra revealed that label‐free SERS can be used for the detection of salicylic acid with concentration down to 3 mM in blood serum corresponding to consumption of at least eight standard pills of aspirin (equivalent to mild toxicity). The proposed diagnostic method could be applied faster than the standard methods and could allow sensitive and fast diagnosis of aspirin consumption in the human blood. We propose a method for fast and sensitive detection of salicylic acid in blood and blood serum using label‐free Surface‐enhanced Raman scattering spectroscopy by employing colloidal solutions. Samples simulating real‐life conditions (consumption of aspirin dose) were used for testing the sensitivity of the method and its application for point‐of‐care analysis.
The structure of trifluoroacetylacetone in argon and nitrogen matrices and association with water molecules were studied by the means of Fourier transform infrared absorption spectroscopy (FTIR) aided with density functional theory (DFT) calculations. The absorption bands of trifluoroacetylacetone isolated in argon can be attributed to the single conformer 1,1,1-trifluoro-4-hydroxy-3-penten-2-one (AcAcF3(CO)) which is in good agreement with previous studies. Absorption bands of trifluoroacetylacetone isolated in nitrogen matrix cannot be explained by the presence of only one conformer and with the aid of DFT calculations both conformers 1,1,1-tri-fluoro-4-hydroxy-3-penten-2-one and 5,5,5-trifluoro-4-hydroxy-3-penten-2-one (AcAcF3(OH)) are confirmed to coexist in the nitrogen matrix. Addition of water to the trifluoroacetylacetone–matrix mixture resulted in appearance of new spectral bands not belonging either to trifluoroacetylacetone or water monomers confirming the formation of trifluoroacetylacetone–water complexes. The most abundant isomer out of trifluoroacetylacetone–water complexes was found to be the one formed from 5,5,5-trifluoro-4-hydroxy-3-penten-2-one and water attached to its C=O group in both matrices, the other one isomer of 1,1,1-trifluoro-4-hydroxy-3-penten-2-one–water complex is also observed in smaller amounts. © Rasa Platakyte, Alejandro Gutiérrez-Quintanilla, Valdas Sablinskas, and Justinas Ceponkus, 2019
Different configurations of (H5O2)⁺− Ar, (H5O2)⁺− Ne and (H5O2)⁺− He complexes were calculated using DFT methods and series of Dunning and Pople basis sets. The possibility of the existence of an equilibrium configuration with C2 symmetry for complexes analyzed was in focus of the studies carried out. DFT methods that do not take into account dispersion interactions, as a rule, define (H5O2)⁺− X (X = Ar, Ne, He) configurations with C2 symmetry as transitional states. At the same time, such DFT methods as B1B95, B98, and WB97X make it possible to determine geometric parameters of these complexes with C2 symmetry in equilibrium configurations. Taking into account dispersion interactions in the framework of D3 Grimme approach and using density functionals, including dispersion interactions (such as M06-2X, wB97XD, etc.), leads to the situation, when configurations of the complexes such as (H5O2)⁺− X (X = Ar, Ne, He) with C2 symmetry calculated using most of the basis sets turn out to be equilibrium. However, calculations within the framework of MP2, MP4, and CCSD (T) methods determine configurations of complexes with C2 symmetry as transition states, while the experimental data on the IR spectra of (H5O2)⁺− Ar complex probably point out to the existence of an equilibrium configuration of this complex with C2 symmetry. In addition to structural analysis for equilibrium configurations found, IR spectra were calculated in harmonic and in some cases also in anharmonic approximations. Calculated IR spectra were compared to protonated water dimer IR spectra calculated at the same level of theory in equilibrium configuration and in the transition state.
Effects of the dispersion interactions on the parameters of the water dimer equilibrium configuration and IR spectra are analyzed in the paper. Dimer equilibrium geometry was calculated using a series of the density functionals, both with (B3LYP-D3, B2PLYPD, B2PLYP-D3, mPW2PLYPD, wB97XD) and without (B3LYP, B2PLYP, mPW2PLYP, wB97X) accounting of the dispersion interactions and using density functional M-06-2X that include the dispersion interaction effects. For the determined equilibrium configurations of the water dimer, IR spectra in harmonic and anharmonic (VPT2) approximations were calculated at the corresponding levels of theory. Additional analysis of the donor hydroxyl group vibrations was performed using the 3D potential energy surfaces, calculated at B3LYP/cc-pVTZ, B3LYP-D3/cc-pVTZ, B2PLYP/cc-pVTZ, B2PLYPD/cc-pVTZ, M06-2X/cc-pVTZ, wB97XD/cc-pVTZ levels of theory. Moreover, double anharmonic couplings of the analyzed modes with other vibrational modes were accounted using the “hybrid” method. Comparison of the calculated results with the experimental and theoretical data from the literature was performed.
Polymer composite materials are used increasingly in material and engineering science. They provide outstanding mechanical and optical properties. The linkage between the polymer materials is crucial for achieving the desired properties. Understanding the linkage and structure of the polymer-polymer interface layer is a key for utilization polymer composite materials as well as for their fabrication. When analyzing the thin polymer-polymer interface it is important to achieve clear identification of molecular linker structures. One reliable analytical technique allowing this is surface enhanced Raman scattering (SERS) spectroscopy. This study aims at the in-situ evaluation of SERS spectra recorded from the Polycarbonate (PC) –Octadecylamine (ODA) interface to identify the formation of urethane bonds. The detailed analysis of SERS spectra taken before and after the chemical linkage reaction reveals the formation of urethane structures, indicating a chemical bond between PC and ODA. The spectral pattern of urethane groups was identified and evaluated by a reference Raman spectrum.
Association of acetylacetone molecules with water was studied by means of infrared absorption spectroscopy aided by matrix isolation technique. The spectra of acetylacetone–water mixtures isolated in low temperature argon and nitrogen matrices revealed additional spectral bands, not observed in the spectra of pure substances, thus confirming the formation of hydrogen bonded complexes. The precise assignment of the spectral bands was performed by varying the sample concentration, performing annealing experiments and DFT B3LYP 6-311++G(3df, 3pd) calculations. Positions of the associated water bands indicate a medium strength hydrogen bond comparable to the one observed in the water trimers. The effect of hydrogen bond formation is rather minimal for the acetylacetone molecule and our experiments confirm no significant influence on an internal hydrogen bond structure or dynamics in the acetylacetone molecule. Similar conclusions are valid in the case of the D2O D2-acetylacetone complex. Different situation is observed when CH3 groups in acetylacetone are replaced with CF3 groups. The calculated energy of the complex is twice as small. This is also confirmed by a very small bounded OH stretch shift. This observation confirms that the electronic structure of the molecular groups even relatively far away from the hydrogen bond accepting atom has a large influence on its possibility to form a hydrogen bond.
Raman spectra of liquid water and ice were measured at different temperatures. The intensity of the band assigned to bending vibrations of water molecules was observed to decrease at the liquid-to-solid transition, while the Raman line near 2200cm-1showed an anomalously high intensity in the solid phase. A tetrahedral model was used for computer analysis of the observed spectral changes. Quantum-chemical calculations of the structure, normal vibrations and Raman spectra in the harmonic approximation, as well as frequencies and intensities of some vibrations using 1D and 2D potential energy surfaces, were carried out using B3LYP with the cc-pVTZ basis set. The influence of the number of hydrogen bonds on the frequency and Raman activity of the bending vibrations was analyzed. The possibility of hydrogen bond weakening upon excitation of the combined bending-rocking vibration due to the large amplitude of this vibration is considered.
Herein, a technique to analyze air-dried kidney tissue impression smears by means of Attenuated Total Reflection Infrared (ATR-IR) spectroscopy is presented. Spectral tumor markers - absorption bands of glycogen - are identified in the ATR-IR spectra of the kidney tissue smear samples. Thin kidney tissue cryo-sections currently used for IR spectroscopic analysis lack such spectral markers as the sample preparation causes irreversible molecular changes in the tissue. In particular, freeze-thaw cycle results in degradation of the glycogen and reduction or complete dissolution of its content. Supervised spectral classification was applied to the recorded spectra of the smears and the test spectra were classified with a high accuracy of 92 % for normal tissue and 94 % for tumor tissue, respectively. For further development, we propose that combination of the method with optical fiber ATR probes could potentially be used for rapid real-time intra-operative tissue analysis without interfering with either the established protocols of pathological examination or the ordinary workflow of operating surgeon. Such approach could ensure easier transition of the method to clinical applications where it may complement the results of gold standard histopathology examination and aid in more precise resection of kidney tumors.
We present a novel approach for detection of cancerous kidney tissue areas by measuring surface enhanced Raman scattering (SERS) spectra of extracellular fluid taken from kidney tissue. The method is based on spectral analysis of the cancerous and normal tissue areas in order to find the specific spectral markers. The samples were prepared by sliding the kidney tissue over a substrate—calcium fluoride optical window. For producing the SERS signal, the dried extracellular fluid film was covered by silver nanoparticle colloidal solution. In order to suppress fluorescence background, the measurements of the dried samples were performed in the NIR spectral region with the Raman excitation wavelength of 1,064 nm. The most significant spectral differences—spectral markers—were found in the wavenumber region between 400 and 1,800 cm−1, where spectral bands related to various vibrations of carbohydrates, amino acids, and nucleic acids are located. Spectral markers in the SERS spectra are different from those in IR absorption spectra. The SERS spectroscopic method has a potential to be used directly during the surgery.
The frequencies and intensities of vibration–rotational transitions of water molecules in an argon matrix were calculated for temperatures of 6 and 30 K. The rigid asymmetric top approximation was used with available literature values of the effective rotational constants in the ground and excited vibrational states. The calculations were carried out by taking into account the existence of a non-equilibrium population distribution between the rotational levels of ortho- and para-water isomers. It was assumed that the temperature relaxation of the population of rotational levels is independent of the ortho- and para-isomers. Comparison of the results of the theoretical calculations with experimental literature data shows good agreement for the majority of the rotational structure lines for symmetric and antisymmetric stretching vibrations both in the frequency values and in the values of the relative intensities.
Surface enhanced Raman scattering (SERS) spectroscopy is a useful method for detection of trace amounts of molecules. It has already been successfully implemented for detection of explosives, food additives, biomarkers in blood or urine, etc. In the last decade, SERS spectroscopy was introduced into the field of health sciences and has been especially focused on early disease detection. In the recent years, application of SERS spectroscopy for detection of various types of human cancerous tissues emerged. Furthermore, SERS spectroscopy of extracellular fluid shows great potential for the differentiation of normal and cancerous tissues; however, due to high variety of molecules present in such biological samples, the experimental spectrum is a combination of many different overlapping vibrational spectral bands. Thus, precise assignment of these bands to the corresponding molecular vibrations is a difficult task. In most cases, researchers try to avoid this task satisfying just with tentative assignment. In this study, low temperature SERS measurements of extracellular fluid of cancerous and healthy kidney tissue samples were carried out in order to get a deeper understanding of the nature of vibrational spectral bands present in the experimental spectrum. The SERS spectra were measured in temperature range from 300 K down to 100 K. SERS method was implemented using silver nanoparticle colloidal solution. The results of the low temperature SERS experiment were analysed and compared with the results of theoretical calculations. The analysis showed that the SERS spectrum of extracellular fluid of kidney tissue is highly influenced by the vibrational bands of adenine and Lcystine molecules.
The structure and harmonic- and anharmonic IR spectra of the protonated water dimer (PWD) were calculated in C1, C2 and CS symmetry at the MP4/acc-pVTZ level of theory. We found that structure and IR spectra are practically identical in C2 and C1 symmetry demonstrating that an equilibrium С1 configuration of the PWD is not realized. Anharmonic coupling of the shared proton stretching vibration with all other modes in the PWD in C2 and CS symmetry was the focus of this investigation. For this purpose 28 two-dimensional potential energy surfaces (2D PES) were built at the MP4/acc-pVTZ level of theory and the corresponding vibrational Schrödinger equations were solved using the DVR method. Differences in the coupling of the investigated mode with other modes in the C2 and CS configurations, along with some factors that determine the red- or blue-shift of the stretching vibration frequency, were analyzed. We obtained a rather reasonable value of the stretching frequency of the bridging proton (1058.4 cm⁻¹) unperturbed by Fermi resonance. The Fermi resonance between the fundamental vibration ν7 and the combined vibration ν2+ν6 of the same symmetry was analyzed through anharmonic second-order perturbation theory calculations, as well as by 3D PES constructed using Q2, Q6 and Q7 as normal coordinates. A significant (up to 50%) transfer of intensity from the fundamental vibration to the combined one was found. We have estimated the frequency of the bridging proton stretching vibration in CS configuration of the PWD based on calculations of the intrinsic anharmonicity and anharmonic double modes interactions at MP4/acc-pVTZ level of theory (1261 cm⁻¹).
A new mechanism for combinatorial broadening of donor-OH stretching-vibration absorption bands in molecular clusters with H-bonds is proposed. It enables the experimentally observed increase of the O–H stretching-vibration bandwidth with increasing number of molecules in H-bonded clusters to be explained. Knowledge of the half-width of the OH stretching-vibration absorption band in the dimer and the number of H-bonds in the analyzed cluster is suffi cient in the zeroth-order approximation to estimate the O–H stretching-absorption bands in clusters containing several molecules. Good agreement between the calculated and published experimental half-widths of the OH stretching-vibration absorption bands in MeOH and PrOH clusters was obtained using this approach.
Tracing aetiology and pathogenesis of urinary stone disease is of great importance in order to prescribe appropriate treatment and prevent recurrences. For this purpose, morphological examination combined with determination of chemical composition of urinary stones is fundamental. In this work, we have evaluated the potential of multimodal nonlinear optical imaging for investigation of (micro)structure and chemical composition of human urinary stones. The method provides high-resolution multimodal images of the cross-sectioned stones without any labelling or some other pretreatment of the samples. We have shown that various constituents of urinary stones can be well discriminated in the multimodal images according to their optical signals. In addition, small structures (1–5 µm in size) were observed in the cross-sections of urinary stones of various types. These structures were identified as crystallites of uric acid. They could either act as an active element during formation of urinary stones or, more probably, be accidentally incorporated into their structure, as it is suggested by random distribution of the crystallites. The results of this work show that multimodal nonlinear optical imaging can provide relevant information about growth processes of urinary stones and deliver useful insights in aetiology and pathogenesis of urolithiasis. Copyright
Uric acid concentration in human bodily fluids is an important marker for disorders such as gout, pre-eclamsia or cardiovascular disease. However, currently used methods for its detection either lack sensitivity or require sophisticated, bulky and expensive equipment. In this work, we show that by using surface-enhanced Raman scattering spectroscopy (SERS) on dried Ag colloidal drops and with 1064 nm excitation, concentrations of uric acid in aqueous solutions down to 10−6 M can be detected. Such sensitivity is sufficient for medical applications as concentration of uric acid in various bodily fluids are in the range of 10−3–10−4 M. Drying of the colloidal drops is known to result in the formation of ‘coffee-ring’ structures that allow obtaining high enhancements but poor reproducibility. Here, the formation of the structures was avoided by choosing aluminum oxide as a base substrate and by controlling environment conditions. Despite the fact that variations of signal enhancement from sample to sample prevent quantitative analysis from being performed, the results of this work imply that strict control of sample preparation conditions could lead to obtaining reproducible SERS enhancements. Results of density functional theory calculations of uric acid tautomer – five-atom silver cluster complexes performed for the first time show that the differences between Raman and SERS spectra of uric acid can be mainly explained by tautomerization of the molecule and its bonding to the silver surface. Assignment of spectral bands is important for correct SERS signal interpretation and detection of uric acid in biological fluids in the future studies. Copyright
Determination of cancerous and normal kidney tissues during partial, simple or radical nephrectomy surgery was performed by using differences in the IR absorption spectra of extracellular fluid taken from the corresponding tissue areas. The samples were prepared by stamping of the kidney tissue on ATR diamond crystal. The spectral measurements were performed directly in the OR during surgery for 58 patients. It was found that intensities of characteristic spectral bands of glycogen (880-1200 cm⁻¹) in extracellular fluid are sensitive to the type of the tissue and can be used as spectral markers of tumours. Characteristic spectral band of lactic acid (1730 cm⁻¹) - product of the anaerobic glycolysis, taking place in the cancer cells is not suitable for use as a spectral marker of cancerous tissue, since it overlaps with the band of carbonyl stretch in phospholipids and fatty acids. Results of hierarchical cluster analysis of the spectra show that the spectra of healthy and tumour tissue films can be reliably separated into two groups. On the other hand, possibility to differentiate between tumours of different types and grades remains in question. While the fluid from highly malignant G3 tumour tissue contains highly pronounced glycogen spectral bands and can be well separated from benign and G1 tumours by principal component analysis, the variations between spectra from sample to sample prevent from obtaining conclusive results about the grouping between different tumour types and grades. The proposed method is instant and can be used in situ and even in vivo.
FTIR spectra of monohydric alcohols 1-nonanol (C9H19OH) and 1-decanol (C10H21OH) were registered in the spectral region from 500 cm-1 to 4000 cm-1 at temperatures from -50 to + 25 {\deg}C for 1-nonanol and +100 {\deg}C for 1-decanol. Temperature-induced spectra changes were compared for these two alcohols. The authors link the observed changes with the transformations of cluster structure occurring during phase transitions.
H&E stained sections of SCI in rat models with and without alginate hydrogel implant at one and six months after injury. (JPG)
Analysis of the contralateral nervous tissue. IR spectroscopic images of SCI in rat models with and without alginate hydrogel implant at one and six months after injury, obtained plotting the intensity of the lipid-related band at 1735 cm-1. (JPG)
Analysis of the fibrotic lesion. IR spectroscopic images of SCI in rat models with and without alginate hydrogel implant at one and six months after injury, obtained plotting the intensity of the collagen-related band at 1242 cm-1. (JPG)
Matrix isolation method allows investigating individual molecules and clusters. Basing on the registered spectra, one can obtain the information on cluster structures in n-hexanol and the changing of these structures during phase transitions. Using quantum chemical methods, the energy of hydrogen bonds for clusters of different sizes and their spatial parameters were calculated. A comparison of experimentally registered and theoretically calculated IR spectra of n-hexanol was made.
Molecular vibrational spectra of methanol in argon and nitrogen matrices have been studied. Since methanol belongs to a class of substances with hydrogen bonds, there is a possibility of forming molecular associations and clusters with various numbers of molecules. IR spectra of methanol in Ar and N2 matrices experimentally obtained in the temperature range from 10 to 50 K are compared with the results of computer simulation using the ab initio Car– Parrinello molecular dynamics (CPMD) method. The results obtained for small clusters in model calculations demonstrate a good correlation with experimental data for various matrices at the corresponding temperatures.
Spinal cord injury (SCI) induces complex biochemical changes, which result in inhibition of nervous tissue regeneration abilities. In this study, Fourier-transform infrared (FT-IR) spectroscopy was applied to assess the outcomes of implants made of a novel type of non-functionalized soft calcium alginate hydrogel in a rat model of spinal cord hemisection (n = 28). Using FT-IR spectroscopic imaging, we evaluated the stability of the implants and the effects on morphology and biochemistry of the injured tissue one and six months after injury. A semi-quantitative evaluation of the distribution of lipids and collagen showed that alginate significantly reduced injury-induced demyelination of the contralateral white matter and fibrotic scarring in the chronic state after SCI. The spectral information enabled to detect and localize the alginate hydrogel at the lesion site and proved its long-term persistence in vivo. These findings demonstrate a positive impact of alginate hydrogel on recovery after SCI and prove FT-IR spectroscopic imaging as alternative method to evaluate and optimize future SCI repair strategies.
Raman spectra of liquid, and infrared spectra of gaseous as well as matrix isolated 1,1,2,2-tetrachloro-1,3-disilacyclopentane were recorded and analyzed with the aid of DFT calculations. Complete assignment of the experimental vibrational spectral bands is made. Experimental results and DFT calculations confirm that 1,1,2,2-tetrachloro-1,3-disilacyclopentane exists as single twist conformer in gaseous and liquid states as well as isolated in Ar and N2 matrices. Fast dissociation of 1,1,2,2-tetrachloro-1,3-disilacyclopentane takes place in gas phase, while the molecule remains stabile in condensed phase. The spectral data and results of DFT calculations in anharmonic approximation confirm that dissociation of 1,1,2,2-tetrachloro-1,3-disilacyclopentane starts with the cleavage of C-C bond of the five membered ring. Dichlorodimethylsilane and HCl were found to be the main products of the dissociation. The geometry and stability of the title molecule is discussed in the light of recent publications on the studies of similar substituted disilacyclapentanes.
Molecular vibrational spectra of methanol in argon and nitrogen matrices have been studied. Since methanol belongs to a class of substances with hydrogen bonds, there is a possibility of forming molecular associations and clusters with various numbers of molecules. IR spectra of methanol in Ar and N2 matrices experimentally obtained in the temperature range from 10 to 50 K are compared with the results of computer simulation using the ab initio Ca-Parrinello molecular dynamics (CPMD) method. The results obtained for small clusters in model calculations demonstrate a good correlation with experimental data for various matrices at the corresponding temperatures. © YE.A. CHERNOLEVSKA, I.YU. DOROSHENKO, V.E. POGORELOV, YE.V. VASKIVSKYI, V. SABLINSKAS, V. BALEVICIUS, A. ISAEV, 2015.
Raman spectroscopy is known to provide information about the quality of the single walled carbon nanotubes (SWCNT). The information is based on the intensity ratio of D and G spectral modes and the frequency of RBM modes. However due to resonance nature of Raman spectrum of the nanotubes this method is not suitable to detect functionalization of the nanotubes. Surface enhanced Raman spectroscopy (SERS) is known to enhance the Raman bands up to fourteen orders of magnitude. Preferable adsorption sites for small silver nanoparticles are expected to be the functional groups of SWCNT; therefore SERS technique allows detecting small amounts of functional groups despite strong resonance Raman from backbone of SWCNT. In this study functionalized nanotubes were dispersed in silver colloid and dried on the standard silver plate for Raman measurements. Spectra of SWCNT without colloid in the spectral range between 50 and 1800 cm⁻¹ exhibit only four main spectral features: G, D, and RBM modes between 200 and 400 cm⁻¹. Spectra of SWCNT with the colloid exhibit several additional spectral bands which do not belong to the colloid. These bands attributed to vibrations of C-O, C-C and O-H from the functional groups and the carbon atom of the SWCNT attached to the corresponding group. The bands associated with the vibrations involving O atom is an indication that silver nanoparticles interact with the functional group attached to SWCNT.
Alcohol molecules can form hydrogen bonds and arrange in different structures named clusters. The aim of this work is to study the behavior of a cluster structure of alcohols at phase transitions and to elucidate the structure of clusters in the solid and liquid states. The objects of investigation are monohydric alcohols n-pentanol (CH2)4CH3–OH and n-octanol (CH2)7CH3–OH. For the structural analysis of the clusters, the matrix isolation FTIR spectroscopy is used, while the spectroscopic studies of the behavior of different clusters at the solid-liquid phase transition are performed in the liquid and solid states. In order to interpret the experimental spectra, the quantum-chemical calculations with the use of Gaussian03 software (approximation DFT/B3LYP, 6–31G (d, p) are carried out. © A. VASYLIEVA, I. DOROSHENKO, V. POGORELOV, V. SABLINSKAS, V. BALEVICIUS, 2015.
We present a novel approach to the detection of cancerous kidney tissue areas by measuring vibrational spectra (IR absorption or SERS) of intercellular fluid taken from the tissue. The method is based on spectral analysis of cancerous and normal tissue areas in order to find specific spectral markers. The samples were prepared by sliding the kidney tissue over a substrate - surface of diamond ATR crystal in case of IR absorption or calcium fluoride optical window in case of SERS. For producing the SERS signal the dried fluid film was covered by silver nanoparticle colloidal solution. In order to suppress fluorescence background the measurements were performed in the NIR spectral region with the excitation wavelength of 1064 nm. The most significant spectral differences – spectral markers - were found in the region between 400 and 1800 cm⁻¹, where spectral bands related to various vibrations of fatty acids, glycolipids and carbohydrates are located. Spectral markers in the IR and SERS spectra are different and the methods can complement each other. Both of them have potential to be used directly during surgery. Additionally, IR absorption spectroscopy in ATR mode can be combined with waveguide probe what makes this method usable in vivo.
The structure and IR absorption spectrum of the formic acid dimer (FAD) were calculated using the B3LYP DFT functional and cc-pVTZ basis set. Matrices of force and anharmonic constants were calculated in order to find the fundamental frequencies more accurately. The 1D and 2D potential energy surfaces (PES) were built using symmetry coordinates and stretching coordinates of С-Н and O-H bonds. For O-H stretching coordinates, the 2D PES were built with and without optimization of the remaining geometric parameters. It was shown that in the second case besides the global minimum, an additional local minimum on the unrelaxed PES is formed with the energy more than 4000 cm-1 higher than the energy of the ground state. A numerical solution of Schrödinger equations gives the values of O-H and C-H stretching vibrations. Comparison of the obtained theoretical results with the experimental data presented in the literature allowed us to make new assignments for IR and Raman spectral bands related to hydroxyl groups stretching vibrations in FAD.
Raman spectra of germacyclohexane in liquid and solid states were recorded and depolarization data obtained. Infrared absorption spectra of the vapor and liquid have been studied. The wavenumbers of the vibrational modes were derived in the harmonic and anharmonic approximation in B3LYP/ccpVTZ calculations. According to the calculations, germacyclohexane exists in the stable chair conformation, whereas a possible twist form should have more than 15 kJ·mol-1 higher enthalpy of formation what makes this conformer experimentally not observable. The 27 A&apos; and 21 A&apos;&apos; fundamentals were assigned on the basis of the calculations and infrared and Raman band intensities, contours of gas phase infrared spectral bands and Raman depolarization measurements. An average discrepancy of ca. 0.77 % was found between the observed and the calculated anharmonic wavenumbers for the 48 modes. Substitution of carbon atom with Ge atom in the cyclohexane ring is reasoning flattening of the ring.
IR and Raman spectra of the malonaldehyde molecule and its deuterated analogues were calculated in the B3LYP/cc-pVQZ approximation. Anharmonicity effects were taken into account both in the context of a standard model of the second order perturbation theory and by constructing the potential energy surfaces (PES) with a limited number of dimensions using the Cartesian coordinates of the hydroxyl hydrogen atom and the stretching coordinates of С-Н, C-D, O-H, and O-D bonds. It was shown that in each of the two equivalent forms of the molecule, besides the global minimum, an additional local minimum at the PES is formed with the energy more than 3000cm(-1) higher than the energy in the global minimum. Calculations carried out by constructing the 2D and 3D PESs indicate a high anharmonicity level and multiple manifestations of the stretching О-Н vibrations, despite the fact that the model used does not take into account the splitting of the ground-state and excited vibrational energy levels. In particular, the vibration with the frequency 3258cm(-1) may be associated with proton transfer to the region of a local minimum of energy. Comparing the results obtained with the experimental data presented in the literature allowed us to propose a new variant of bands assignments in IR and Raman spectra of the molecule in the spectral region 2500-3500cm(-1). Copyright © 2015 Elsevier B.V. All rights reserved.
Infrared spectra of gaseous, liquid and matrix isolated samples of newly synthesized 1,1-dimethyl-2-oxy-1-silacyclohexane were recorded. Raman spectra of 1,1-dimethyl-2-oxy-1-silacyclohexane in liquid and solid states were obtained in the temperature range from 170 to 340 K. Ab initio HF and DFT B3LYP calculations were performed in order to determine the possible conformations of 1,1-dimethyl-2-oxy-1-silacyclohexane and to make accurate assignment of the vibrational spectral bands. The study confirms existence of only one chair type conformer of 1,1-dimethyl-2-oxy-1-silacyclohexane.
FTIR spectra of 1-propanol in an argon matrix were studied in the range 11–30 K. Principal component analysis of dynamic FTIR spectra and nonlinear band shape fitting has been carried out. The peaks of monomer, open dimer, mixed propanol-water dimer and those of higher H-bond clusters have been resolved and analyzed. The attribution of certain FTIR peaks has been supported by proper density functional theory calculations. Analyzing dependences of the integral band intensities of various aggregates on temperature it has been deduced that in the initial stage of clustering monomers and dimers are the basic building blocks forming higher H-bond clusters. The peaks assigned to two conformers of monomers and mixed propanol-water dimers were investigated processing the temperature dependences of their integral intensities in Arrhenius plot. The obtained values of 0.18 kJ·mol−1 for propanol monomer and 0.26 kJ·mol−1 for mixed dimer are well comparable with the energy differences between the global minimum conformation of 1-propanol (Gt) and some other energetically higher structures (Tt or Tg).
The aim of the study was to investigate the prevalence of metabolic syndrome in patients with uric acid and calcium–based kidney stones and to investigate the relationship between metabolic syndrome and type of kidney stone using infrared spectroscopy to evaluate the chemical composition of kidney stones Sixty patients with urolithiasis were examined. Metabolic syndrome was diagnosed according to clinical and laboratory criteria. Weight, height, body mass index, waist circumference, and blood pressure of patients were measured. Blood tests were performed. Concentrations of total cholesterol, low density lipoprotein cholesterol, high density lipoprotein cholesterol, triglycerides, glucose and uric acid in blood, were analyzed. The kidney stones of patients were removed and the composition of each kidney stone was analyzed using Fourier transform infrared spectroscopy. Metabolic syndrome was diagnosed in 55% of the patients; 86.7% of patients with uric acid (UA) kidney stones and 44.4% of patients with calcium (Ca) based stones had metabolic syndrome. All patients diagnosed with metabolic syndrome were overweight or obese. Even though there were no statistically significant differences observed concerning the anthropometrical measures and arterial blood pressure (BP) between the UA stone formers and Ca–based stone formers, the results show a trend that failed to reach significance: higher waist size, BMI and arterial BP means in the group of patients with UA stones than in the patients with Ca–based stones. No statistically significant differences in lipid profile between the groups were found. Concentration of UA in blood serum was significantly higher in patients with UA kidney stones than it was in patients with Ca–based kidney stones. Significant positive correlation between triglycerides and serum UA concentrations, as well as body mass index and serum UA concentration, and negative correlation between concentrations of high-density lipoprotein cholesterol and UA was found. Conclusion: Metabolic syndrome was more prevalent in patients with uric acid stones than in the patients with calcium–based kidney stones, even though this relationship was not statistically significant, most likely because of the limited number of patients investigated.
Fourier transform infrared (FT-IR) spectroscopy was applied to characterize the extracellular matrix (ECM) of kidney tumor tissue and normal kidney tissue. Freshly resected tissue samples from 31 patients were pressed on a CaF2 substrate. FT-IR spectra obtained from ECM of tumor tissue exhibit stronger absorption bands in the spectral region from 1000 to 1200 cm(-1) and around 1750 cm(-1) than those obtained from normal tissue. It is likely that the spectra of ECM of kidney tumor tissue with large increases in the intensities of these bands represent a higher concentration of fatty acids and glycerol. Amide I and amide II bands are stronger in the spectra of ECM from normal tissue, indicating a higher level of proteins. Our results suggest that FT-IR spectroscopy of the ECM is an innovative emerging technology for real-time intraoperative tumor diagnosis, which may improve margin clearance in renal cancer surgery. (C) 2014 Society of Photo-Optical Instrumentation Engineers (SPIE)
Long-wave Raman spectra of some normal alcohols (from n-pentanol to n-decanol) in the liquid phase were registered. The regularities in the dependencies of Raman bands frequencies on the number of carbon atoms in the hydrocarbon chain were deduced. The calculations of Raman spectra of the studied molecules, their equilibrium structures and possible conformers were carried out in the approximation B3LYP/cc-pVDZ. These results in combination with the analysis of literature data allowed to explain the observed regularities in Raman band positions in the spectral range of 200 - 600 сm−1 and their shifts upon increasing length of the chains. It was found that the plane configurations dominate in the liquid phase for molecules with short- and moderate chain lengths. The elongation of the chain leads to the decrease of the fraction of plane conformers and in n-decanol the plane structure is completely absent.
The investigation of the temperature dependence of FTIR spectrum of n-octanol in the temperature range from −150°C to 50°C is presented. The observed changes in the registered spectra during gradual heating of the sample were analysed. The structure transformation at the phase transition from solid to liquid phase is detected.
The investigation of the temperature dependence of FTIR spectrum of n-octanol in the temperature range from −150°C to 50°C is presented. The observed changes in the registered spectra during gradual heating of the sample were analysed. The structure transformation at the phase transition from solid to liquid phase is detected.
Mid-Infrared (MIR) Spectroscopy Near Infrared Spectroscopy Raman Spectroscopy UV/vis Spectroscopy Fluorescence Spectroscopy References
In this work the infrared absorption spectra of intercellular fluid of normal and tumor kidney tissue were recorded and analyzed. The samples were prepared by stamping freshly resected tissue onto a CaF2 substrate. FT-IR spectra obtained from intracellular fluid of tumor tissue exhibit stronger absorption bands in the spectral region from 1000-1200 cm-1 and around 1750 cm-1 than those obtained from normal tissue. It is likely the spectra of extracellular matrix of kidney tumor tissue with large increases in the intensities of these bands represent a higher concentration of fatty acids and glycerol. Amide I and amide II bands are stronger in spectra of normal tissue indicating a higher level of proteins. The results demonstrate that FT-IR spectroscopy of intercellular fluids is a novel approach for a quick diagnosis during surgical resection, which can improve the therapy of kidney tumors.
Surface-enhanced Raman scattering (SERS) spectroscopy can be a useful tool in regard to disease diagnosis and prevention. Advantage of SERS over conventional Raman spectroscopy is its significantly increased signal (up to factor of 106-108) which allows detection of trace amounts of substances in the sample. So far, this technique is successfully used for analysis of food, pieces of art and various biochemical/biomedical samples. In this work, we survey the possibility of applying SERS spectroscopy for detection of trace components in urinary deposits. Early discovery together with the identification of the exact chemical composition of urinary sediments could be crucial for taking appropriate preventive measures that inhibit kidney stone formation or growth processes. In this initial study, SERS spectra (excitation wavelength - 1064 nm) of main components of urinary deposits (calcium oxalate, uric acid, cystine, etc.) were recorded by using silver (Ag) colloid. Spectra of 10-3-10-5 M solutions were obtained. While no/small Raman signal was detected without the Ag colloid, characteristic peaks of the substances could be clearly separated in the SERS spectra. This suggests that even small amounts of the components could be detected and taken into account while determining the type of kidney stone forming in the urinary system. We found for the first time that trace amounts of components constituting urinary deposits could be detected by SERS spectroscopy. In the future study, the analysis of centrifuged urine samples will be carried out.
The unregulated cancer cell growth leads to strong alterations in morphology and composition of the tissue. The combination of coherent anti-Stokes Raman scattering, two-photon excited fluorescence and second harmonic generation enables a high resolution imaging with strong information on tissue composition and can then provide useful information for tumour diagnosis. Here we present the potential of multimodal non-linear microscopy for imaging of renal tumours. Using cryosections of human oncocytoma and carcinoma, the method gave a detailed insight in cancer morphology and composition, enabling to discern between normal kidney tissue, tumour and necrosis. Several features significant for the diagnosis were clearly visualised without use of any staining. Translation of this method in clinical pathology will greatly improve speed and quality of the analyses. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).
Specular reflection infrared microspectroscopy was used for chemical imaging of cross-sectioned urinary stones to determine their chemical composition and morphology simultaneously. Absorption spectral bands were recovered from reflection spectra by Kramers-Kronig transform. FUse of far-infrared radiation provides high-contrast images and allows more precise constituent distribution determinations than mid-infrared because band asymmetry after the transform caused by diffuse reflection is less in the far-infrared.
MIR Spectrometers Dispersive SpectrometersFourier-Transform SpectrometersNIR Spectrometers FT-NIR SpectrometersScanning-Grating SpectrometersDiode Array SpectrometersFilter SpectrometersLED SpectrometersAOTF SpectrometersRaman Spectrometers Raman Grating Spectrometer with Single Channel DetectorFT-Raman Spectrometers with Near-Infrared ExcitationRaman Grating Polychromator with Multichannel DetectorUV/VIS Spectrometers SourcesMonochromatorsDetectorsFluorescence Spectrometers Dispersive SpectrometersFourier-Transform Spectrometers FT-NIR SpectrometersScanning-Grating SpectrometersDiode Array SpectrometersFilter SpectrometersLED SpectrometersAOTF Spectrometers Raman Grating Spectrometer with Single Channel DetectorFT-Raman Spectrometers with Near-Infrared ExcitationRaman Grating Polychromator with Multichannel Detector SourcesMonochromatorsDetectors
FTIR spectra of pyridine N-oxide and trichloroacetic acid H-bonded complex in acetonitrile were studied at 20 and 50°C. The calculations of equilibrium configurations of the complex and their IR spectra in harmonic- and anharmonic approximations were carried out at the level of B3LYP/cc-pVTZ/PCM. However both approximations turned out to be incompetent determining the frequency of the O-Н stretching vibration. In order to reveal the causes of essential discrepancies between calculated and experimental data one-, two- and three-dimensional potential energy surfaces (PES) of the O-H…O bridge proton motion in the frame of fixed other atoms in the complex were calculated. The frequencies of O-H…O stretching and bending vibrations were calculated by numerical solution of the Schrödinger equation. It is shown that only the approach of proton motion on the 3D PES allows obtaining a good agreement between the calculated and the experimental values of the frequencies of the О-Н stretching vibrations.
We have used infrared microspectroscopy for chemical analysis of urinary sediments. We showed that Mie scattering from urinary sediments as small as 10-100 μm is influencing the spectra and the influence can be suppressed and quality of the spectra can be improved by applying RMieS-EMSC procedure.
We used infrared reflection microspectroscopy for chemical imaging of urinary calculi and showed that contribution of diffuse reflection, influencing the imaging results, can be suppressed by decreasing surface roughness and (or) increasing wavelength of infrared radiation applied for the imaging.
Low-temperature infrared absorption spectra are obtained for ethanol isolated in an argon matrix at temperatures of 20–45 K range for ratios of the numbers of the molecules being studied to the numbers of matrix atoms of 1:1000 and 1:2000. A preliminary interpretation of the spectra is obtained on the basis of the temperature variations in the spectra and published data. The structure of the ethanol conformers, rotational constants, and internal rotation barriers of the methyl and hydroxyl groups are calculated in the B3LYP/cc-pVQZ approximation. The harmonic and anharmonic IR spectra of the gauche- and trans-conformers are calculated in the same approximation. The force fields of the two conformers and the distributions of the potential energy of the normal vibrations are calculated and compared for a general set of dependent coordinates. Anharmonicity effects are taken into account by introducing spectroscopic masses for the hydrogen atoms when calculating the normal vibrations in the harmonic approximation.
Results of the structural analysis of urinary sediments by means of infrared spectral microscopy are presented. The results are in good agreement with the results of standard optical microscopy in the case of single-component and crystalline urinary sediments. It is found that for noncrystalline or multicomponent sediments, the suggested spectroscopic method is superior to optical microscopy. The chemical structure of sediments of any molecular origin can be elucidated by this spectroscopic method. The method is sensitive enough to identify solid particles of drugs present in urine. Sulfamethoxazole and traces of other medicines are revealed in this study among the other sediments. We also show that a rather good correlation exists between the type of urinary sediments and the renal stones removed from the same patient. Spectroscopic studies of urinary stones and corresponding sediments from 76 patients suffering from renal stone disease reveal that in 73% of cases such correlation exists. This finding is a strong argument for the use of infrared spectral microscopy to prevent kidney stone disease because stones can be found in an early stage of formation by using the nonintrusive spectroscopic investigation of urinary sediments. Some medical recommendations concerning the overdosing of certain pharmaceuticals can also be derived from the spectroscopic studies of urinary sediments.
The geometry optimization for the pyridine N-oxide/trichloroacetic acid complex is realized in B3LYP/cc-pVTZ approximation. Computations of IR absorption spectra for the optimized configuration are performed in harmonic and anharmonic approximations. It is found that taking into account the anharmonicity effects leads to the red shift of the stretching vibration frequency of O–H bond by more than 600 $cm^{-1}$. At the same time, the red shift of the in-plane and out-of-plane bending vibrations of the hydroxyl group does not exceed 70 $cm^{-1}$. The 1D potential curves and 2D potential surfaces associated with stretching and bending vibrations of a hydroxyl group are computed. The vibrational frequencies of O–H bonds are derived by numerical solution of Schrödinger equations. The frequencies are compared to those of anharmonic computations for this complex. A combined method including the advantages of both approaches is proposed.
Distribution of chemical components in the mixed oxalatic, phosphatic and uratic urinary stones was analysed by means of infrared microspectroscopy. The specular reflection from the surface of the cross-sectioned stones was used for the infrared spectroscopic imaging. It was found that the reflection spectra consist from specular and diffuse reflection components and the former one exhibit Reststrahlen bands which resemble first derivative of the spectral bands in the absorption spectrum. In order to use the measured spectra for the chemical imaging they were corrected for asymmetry by subtracting the diffuse reflection component and applying Kramers–Kronig transform to the specular reflection component. The Kramers–Kronig transformed spectrum was then combined with the diffuse reflection component. Spectra corrected in this manner were used to create false-colour images of the stones. It was found that the images obtained after applying the correction procedure to the spectra differ substantially from the ones obtained from the raw spectra. They are in good agreement with the stones’ images obtained from the FT-Raman spectra.
The dependence of FTIR spectrum of pure ethanol on the temperature was investigated. The measurements were performed for frozen (the minimum temperature −180°C) and liquid ethanol (the maximum temperature 40°C). All changes in IR spectrum of ethanol during gradual warming were detected and analyzed. On the bases of preset observations, the conclusions concerning the evolution of cluster structures in ethanol during transition from solid (frozen) state to liquid state were made.
FTIR spectra of homologous series of monohydric alcohols which belong to the class of partly ordered liquids were registered. The molecules of monohydric alcohols containing hydroxyl group are able to form hydrogen-bonded clusters in the condensed phase. The existence of clusters is clearly observed from the position and the contour of the stretch OH band in the vibrational spectra of liquid alcohols. In this work, the experimentally registered FTIR spectra of liquid n-alcohols from methanol to decanol are presented as well as the same spectra of methanol, ethanol, propanol, butanol, pentanol, and hexanol in gas phase.
Single-walled carbon nanotubes (SWCNT) as well as functionalized nanotubes were studied by means of low temperature Fourier transform infrared (FTIR) absorption spectros-copy. Embedment of carbon nanotubes into KBr (potassium bromide) pellets was found to be one of the most convenient methods to study the nanotubes at room and low temperatures. Low temperature allows us to observe several spectral bands associated with vibrations in the nanotubes. These vibrations were found to be sensitive to the ordering of the carbon atoms in the nanotube therefore it could be used as a signature of the nanotube quality. Infrared spectroscopy was found to be sensitive enough for the monitoring of na-notube functionalization and identification of the particular functional groups attached to the nanotubes. Assignment of spectral bands to particular vibrations of atoms localized in the functional groups attached to the nanotube is supported by ab initio calculations.
The dependence of FTIR spectrum of pure ethanol on the temperature was investigated. The measurements were performed for frozen (the minimum temperature −180°C) and liquid ethanol (the maximum temperature 40°C). All changes in IR spectrum of ethanol during gradual warming were detected and analyzed. On the bases of preset observations, the conclusions concerning the evolution of cluster structures in ethanol during transition from solid (frozen) state to liquid state were made.
FTIR spectra of homologous series of monohydric alcohols which belong to the class of partly ordered liquids were registered. The molecules of monohydric alcohols containing hydroxyl group are able to form hydrogen-bonded clusters in the condensed phase. The existence of clusters is clearly observed from the position and the contour of the stretch OH band in the vibrational spectra of liquid alcohols. In this work, the experimentally registered FTIR spectra of liquid n-alcohols from methanol to decanol are presented as well as the same spectra of methanol, ethanol, propanol, butanol, pentanol, and hexanol in gas phase.
The silver nanoparticle colloid was used to obtain surface enhanced Raman spectra of Listeria monocy-togenes, Salmonela enterica, and Esherichia coli bacteria. The SERS spectra were captured using for excita-tion the near-infrared (1064 nm) laser radiation with reduced intensity, which ensured the prevention of the fluorescence background as well as photo-and thermal decomposition of the samples. It was found that the optimal size of silver nanoparticles for the enhancement of the Raman signal in the near-infrared spectral region is ca. 50 nm. The spectral data obtained in this study indicate that relative intensities of SERS spectral bands of bacteria can be used for spectral differentiation of bacteria. In case of Listeria, Salmonela, and Esherichia cells, the intensity ratio of spectral bands of adenine and cysteine can be used as a spectral marker for differentiation of the bacteria.
The silver nanoparticle colloid was used to obtain surface enhanced Raman spectra of Listeria monocy-togenes, Salmonela enterica, and Esherichiacoli bacteria. The SERS spectra were captured using for excita-tion the near-infrared (1064nm) laser radiation with reduced intensity, which ensured the prevention of the fluorescence background as well as photo-and thermal decomposition of the samples. It was found that the op-timal size of silver nanoparticles for the enhancement of the Raman signal in the near-infrared spectral region is ca. 50nm. The spectral data obtained in this study indicate that relative intensities of SERS spectral bands of bacteria can be used for spectral differentiation of bacteria. In case of Listeria, Salmonela, and Esherichia cells, the intensity ratio of spectral bands of adenine and cysteine can be used as a spectral marker for differentiation of the bacteria.
Theoretical calculations of structures, stability and vibrational spectra of 1-butene secondary ozonide (SOZ) conformers were performed using DFT method B3LYP with a 6-311++G(3df, 3pd) basis set. The calculations predict six staggered structures of 1-butene SOZ. The FTIR spectra of 1-butene SOZ isolated in Ar, N2 and Xe matrices were recorded. It was found that nitrogen is the best suited for the matrix isolation of 1-butene SOZ. The bandwidth of the spectral bands of the ozonide isolated in nitrogen was as narrow as 2 cm−1. For the first time the existence of five conformers of 1-butene SOZ were confirmed experimentally by means of matrix isolation infrared absorption spectroscopy. The equatorial gauche (∠OCCC=−66.1°) conformer was proved theoretically and experimentally to be the most stable. It was found that due to high potential barriers of the conformational transitions annealing of the matrix is useless for the assignment of spectral bands to various conformers of 1-butene SOZ. Using the hot nozzle technique the van’t Hoff experimental plots were made for three additional conformers of 1-butene SOZ and experimental ΔH values for these additional conformers were established. The crystallization problems of 1-butene SOZ are discussed which accounts for the rich conformational diversity of the ozonide as well as high conformational barriers for axial-equatorial transitions.
Low-temperature FTIR spectra of ethanol in the argon matrix have been recorded in the spectral interval 2800-4000 cm-1. The spectra were obtained for several temperatures over the range 20-50 К and for the number ratios 1:1000 and 1:2000 of the mo lecules studied and atoms in the matrix. A tentative interpretation has been performed on the basis of the temperature and concentration changes in FTIR spectra with the use of the relevant literature data. The co mputations of harmonic and anharmonic IR spectra for gauche-and trans-rotamers of the ethanol molecule and its two deuterated derivatives (СD 3 CH 2 OH and CH 3 CD 2 OH) have been carried out in the appro ximation B3LYP/cc-p VQZ. An interpretation of the bands and lines in the region of stretching С-Н vibrations has been proposed with regard to the anharmonicity effects and Fermi resonances using the literature data on IR and Raman spectra of the molecule under study.
Fourier transform infrared (FT-IR) spectroscopic imaging has been used to characterize different types of pituitary gland tumors and normal pituitary tissue. Freshly resected tumor tissue from surgery was prepared as thin cryosections and examined by FT-IR spectroscopic imaging. Tissue types were discriminated via k-means cluster analysis and a supervised classification algorithm based on linear discriminant analysis. Spectral classification allowed us to discriminate between tumor and non-tumor cells, as well as between tumor cells that produce human growth hormone (hGH+) and tumor cells that do not produce that hormone (hGH-). The spectral classification was compared and contrasted with a histological PAS and orange G stained image. It was further shown that hGH+ pituitary tumor cells show stronger amide bands than tumor cells that do not produce hGH. This study demonstrates that FT-IR spectroscopic imaging can not only potentially serve as a fast and objective approach for discriminating pituitary gland tumors from normal tissue, but that it can also detect hGH-producing tumor cells.
The spectroscopic method of measurement of the internal diameter of carbon nanotubes is suggested. For this purpose, the infrared (IR) absorption spectrum of the mixture containing both the carbon nanotube powder and the methyl alcohol is registered. From comparison of the IR spectra of an investigated sample and methanol clusters, the conclusion about the value of internal diameter of the nanotubes is made.
Fourier transform infrared (FTIR) spectroscopic imaging has been used to probe the biochemical composition of human renal tumor tissue and adjacent normal tissue. Freshly resected renal tumor tissue from surgery was prepared as a thin cryosection and examined by FTIR spectroscopic imaging. Tissue types could be discriminated by utilizing a combination of fuzzy k-means cluster analysis and a supervised classification algorithm based on a linear discriminant analysis. The spectral classification is compared and contrasted with the histological stained image. It is further shown that renal tumor cells have spread in adjacent normal tissue. This study demonstrates that FTIR spectroscopic imaging can potentially serve as a fast and objective approach for discrimination of renal tumor tissue from normal tissue and even in the detection of tumor infiltration in adjacent tissue.
Each year, billions of day-old layer chicks are produced in the world. Since only female chicks are reared for egg production, the chicks must be sexed and the unwanted male layer chicks are culled. The culling of male chicks is a serious problem, both in terms of animal welfare and waste disposal. The germinal disc in fertilized but unincubated eggs contains already several thousands of blastoderm cells. The cellular DNA in birds is different for male and female chicks. The difference in DNA content between male and female chicks is around 2% and is measurable by Fourier transform infrared (FT-IR) spectroscopy. In this study, small amounts of blastoderm cells from 22 chicken eggs were characterized by attenuated total reflection FT-IR spectroscopic imaging and classified by linear discriminant analysis. Polymerase chain reaction (PCR) was used as a reference method to determine the gender. The spectroscopic results demonstrate that male blastoderm cells exhibit a higher content of DNA than cells from female blastoderm. The spectroscopic-based gender determination led to the same result as the PCR analysis. FT-IR spectroscopic imaging allows the gender determination of unincubated eggs within a few seconds based on the accurate determination of the different DNA contents in blastoderm cells of both sexes.
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