Surface enhanced Raman spectroscopy and quantum chemical studies on glycine single crystal

Rapid discrimination of four Salmonella enterica serovars: A performance comparison between benchtop and handheld Raman spectrometers

Foodborne illnesses, particularly those caused by Salmonella enterica with its extensive array of over 2600 serovars, present a significant public health challenge. Therefore, prompt and precise identification of S. enterica serovars is essential for clinical relevance, which facilitates the understanding of S. enterica transmission routes and the determination of outbreak sources. Classical serotyping methods via molecular subtyping and genomic markers currently suffer from various limitations, such as labour intensiveness, time consumption, etc. Therefore, there is a pressing need to develop new diagnostic techniques. Surface-enhanced Raman spectroscopy (SERS) is a non-invasive diagnostic technique that can generate Raman spectra, based on which rapid and accurate discrimination of bacterial pathogens could be achieved. To generate SERS spectra, a Raman spectrometer is needed to detect and collect signals, which are divided into two types: the expensive benchtop spectrometer and the inexpensive handheld spectrometer. In this study, we compared the performance of two Raman spectrometers to discriminate four closely associated S. enterica serovars, that is, S. enterica subsp. enterica serovar dublin, enteritidis, typhi and typhimurium. Six machine learning algorithms were applied to analyse these SERS spectra. The support vector machine (SVM) model showed the highest accuracy for both handheld (99.97%) and benchtop (99.38%) Raman spectrometers. This study demonstrated that handheld Raman spectrometers achieved similar prediction accuracy as benchtop spectrometers when combined with machine learning models, providing an effective solution for rapid, accurate and cost-effective identification of closely associated S. enterica serovars.

Spectroscopic, quantum chemical investigation and molecular docking studies on N-(2-benzoylamino) phenyl benzamide: A novel SARS-CoV-2 drug

The present work describes the structural and spectral properties of N-(2-benzoylamino) phenyl benzamide (NBPB). The geometrical parameters of NBPB molecule such as bond lengths, bond angles and dihedral angles are calculated and compared with experimental values. The assigned vibrational wave numbers are in good agreement with the experimental FTIR and FT Raman spectra. The vibrational frequency of C=O stretching was downshifted to a lower wave number (red shift) due to mesomeric effect. The UV-Vis spectrum of the title compound was simulated and validated experimentally. The energy gap and charge transfer interaction of the title molecule were studied using frontier molecular orbital analysis. The electrophilic and nucleophilic reactivity sites of NBPB were investigated through the analysis of the molecular electrostatic potential surface and the Fukui function. An assessment of the intramolecular stabilization interactions of the molecule was performed using natural bond orbital analysis. The drug-likeness parameter was calculated. To investigate the inhibitory potential of the molecule, molecular docking analysis was conducted against SARS-CoV-2 proteins, revealing its capability to serve as a novel inhibitor against SARS-CoV-2. The high binding affinity of NBPB molecule was due to the presence of hydrogen bonds along with different hydrophobic interactions between the drug and the SARS-CoV-2 protein receptor. Hence, the title molecule is identified to be a potential candidate for SARS-CoV-2.

Quantum chemical, spectroscopic and molecular docking investigations of potential pulmonary fibrosis drug methyl 2-chloro 4-iodonicotinate

In this work, the methyl 2-chloro 4-iodonicotinate (MCIN) was investigated to study the structural, spectroscopic and electronic properties using density functional theory (DFT) quantum chemical calculations. The most stable structure of MCIN was optimized by DFT/B3LYP method with a LanLD2Z basis set. The optimized parameters and vibrational wavenumbers were determined. The vibrational task of the molecule was done by potential energy distribution calculations. The ¹³ C NMR spectrum of the MCIN molecule was simulated by the Gauge-Invariant-Atomic Orbital method using a dimethyl sulfoxide solution and the isotropic chemical shift values of the molecule were calculated and observed. Ultraviolet-visible spectra were simulated and observed. The pharmaceutical activity was predicted using frontier molecular orbital and natural bond orbital analysis. The reactive sites of the MCIN molecule were determined using Mulliken atomic charge distribution, molecular electrostatic potential surface and the local reactivity analysis. The molecular docking analysis confirms that the title molecule can be used in drug design for the treatment of pulmonary fibrosis.

A Collection of Molecular Fingerprints of Single Aerosol Particles in Air for Potential Identification and Detection Using Optical Trapping-Raman Spectroscopy

Characterization, identification, and detection of aerosol particles in their native atmospheric states remain a challenge. Recently, optical trapping-Raman spectroscopy (OT-RS) has been developed and demonstrated for characterization of single, airborne particles. Such particles in different chemical groups have been characterized by OT-RS in recent years and many more are being studied. In this work, we collected single-particle Raman spectra measured using the OT-RS technique and began construction of a library of OT-RS fingerprints that may be used as a reference for potential detection and identification of aerosol particles in the atmosphere. We collected OT-RS fingerprints of aerosol particles from eight different categories including carbons, bioaerosols (pollens, fungi, vitamins, spores), dusts, biological warfare agent surrogates, etc. Among the eight categories, spectral fingerprints of six groups of aerosol particles have been published previously and two other groups are new. We also discussed challenges, limitations, and advantages of using single-particle optical trapping-Raman spectroscopy for aerosol-particle characterization, identification, and detection.

Phase changes of tris(glycinato)chromium(III) monohydrate crystal systematically studied by thermal analyses, XRPD, FTIR, and Raman combined with ab initio calculations

Tris(glycinato)chromium(III) monohydrate [Cr(C₂H₄NO₂)₃·H₂O] crystals were grown through the slow solvent evaporation method. The crystals were studied by Fourier transform infrared (FTIR) and Raman spectroscopy at room temperature. The assignments of vibration modes were performed using the Density Functional Theory (DFT). Thermal analyses (TGA, DTA, and DSC), X-ray diffraction (XRD), and Raman were used to study the phase changes on the crystals under high- and low-temperature conditions. Temperature-dependent XRPD measurements were carried out in the interval of 473-12 K. Several changes were observed in the patterns, like the appearance of new peaks and the disappearance of peaks occurring within 373-393 K due to water loss. In addition, the Raman measurements were performed in the 423-10 K interval. Several changes on the inter and intramolecular vibration bands during the cooling, such as decreasing bands' intensities, the appearance of vibration modes, and discontinuities on the modes' behavior, were observed. These spectral modifications occurred at about 370 K and within 120-220 K, thus, confirming that the crystals undergo two phase changes, one being structural and the other one conformational, respectively, at high- temperature and low-temperature conditions. Finally, thermal investigations corroborated the structural and vibrational results under high temperatures.

Glycine amino acid transformation under impacts by small solar system bodies, simulated via high-pressure torsion method

Impacts by small solar system bodies (meteoroids, asteroids, comets and transitional objects) are characterized by a combination of energy dynamics and chemical modification on both terrestrial and small solar system bodies. In this context, the discovery of glycine amino acid in meteorites and comets has led to a hypothesis that impacts by astronomical bodies could contribute to delivery and polymerization of amino acids in the early Earth to generate proteins as essential molecules for life. Besides the possibility of abiotic polymerization of glycine, its decomposition by impacts could generate reactive groups to form other essential organic biomolecules. In this study, the high-pressure torsion (HPT) method, as a new platform for simulation of impacts by small solar system bodies, was applied to glycine. In comparison with high-pressure shock experiments, the HPT method simultaneously introduces high pressure and deformation strain. It was found that glycine was not polymerized in the experimental condition assayed, but partially decomposed to ethanol under pressures of 1 and 6 GPa and shear strains of < 120 m/m. The detection of ethanol implies the inherent availability of remaining nitrogen-containing groups, which can incorporate to the formation of other organic molecules at the impact site. In addition, this finding highlights a possibility of the origin of ethanol previously detected in comets.

Tracking the Amide I and αCOO- Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue's amide I ν(C=O) and the αCOO- terminal ν(C=O) bands on the neighboring side chain, the length of the peptide fragment, and the extent of intramolecular hydrogen bonding in the structure are investigated here via the EGEDEA peptide. The hexapeptide is broken down into fragments increasing in size from dipeptides to hexapeptides, including EG, ED, EA, EGE, EDE, DEA, EGED, EDEA, EGEDE, GEDEA, and, finally, EGEDEA, which are investigated with experimental Raman spectroscopy and density functional theory (DFT) computations to model the zwitterionic crystalline solids (in vacuo). The molecular geometries and Boltzmann sum of the simulated Raman spectra for a set of energetic minima corresponding to each peptide fragment are computed with full geometry optimizations and corresponding harmonic vibrational frequency computations at the B3LYP/6-311++G(2df,2pd) level of theory. In absence of the crystal structure, geometry sampling is performed to approximate solid phase behavior. Natural bond order (NBO) analyses are performed on each energetic minimum to quantify the magnitude of the intramolecular hydrogen bonds. The extent of the intramolecular charge transfer is dependent on the overall polarity of the fragment considered, with larger and more polar fragments exhibiting the greatest extent of intramolecular charge transfer. A steady blue shift arises when considering the amide I band position moving linearly from ED to EDE to EDEA to GEDEA and, finally, to EGEDEA. However, little variation is observed in the αCOO- ν(C=O) band position in this family of fragments.

Explosive vapour/particles detection using SERS substrates and a hand-held Raman detector

We developed and optimized surface-enhanced Raman spectrometry (SERS) methods for trace analysis of explosive vapour and particles using a hand-held Raman spectrometer in the field. At first, limits of detection (LODs) using SERS methods based on a colloidal suspension of gold nanoparticles were measured under alkaline conditions and are as follows: pentaerythritol tetranitrate (PETN) (1.5 × 10⁻⁶ M, 6.9 ng), 1,3,5,7-tetranitro-1,3,5,7-tetrazoctane (HMX), 8.1 × 10⁻⁶ M, 35 ng; urea nitrate (UN), 9.2 × 10⁻⁴ M, 165 ng; 2,4,6-trinitrotoluene (TNT), 1.1 × 10⁻⁷ M, 0.35 ng. We developed SERS substrates that demonstrate the wide applicability of this technique for use in the field for explosive vapour and particles adsorbed on a surface based on Au nanoparticles that were optimal for the detection of the target materials in solution. Au nanoparticles were modified onto quartz fibres or a polyurethane sponge for vapour/particles detection. SERS detection of vapours of 2,4-dinitrotoluene (2,4-DNT) and 1,3-dinitrobenzene (1,3-DNB) was shown by sampling vapours onto Au-modified quartz fibres followed by hand-held Raman analysis with estimated minimum detection levels of 3.6 ng and 54 ng, respectively. The detection of 2,4-DNT using sponge-based SERS decorated with Au nanoparticles was also demonstrated; however, the sensitivity was lower than that observed using quartz fibres. The detection of TNT on a surface was performed by utilizing quartz-fibres precoated with alumina and modified with Au nanoparticles, and the detection of 10 μg (0.53 μg cm⁻²) of TNT was demonstrated.

We developed and optimized surface-enhanced Raman spectrometry (SERS) methods for trace analysis of explosive vapour and particles using a hand-held Raman spectrometer in the field.

Determination of vibrational band positions in the E-hook of β-tubulin

Raman spectral characterization of the β-TUBB2A E-hook hexapeptide, EGEDEA, is determined through experimental analysis combined with full geometry optimizations and corresponding harmonic vibrational frequency computations employing DFT methods. The hexapeptide is first broken down into di- and tetrapeptide fragments which are analyzed both quantum chemically and experimentally, and then combined to achieve an energetic minimum of the large EGEDEA hexapeptide. The Raman spectral characterization of EGEDEA band positions are then verified via the literature and comparison to the small fragment's similarly located band positions. The approach employed provides further evidence for the use of fragments as a helpful tool in characterization of the vibrational band positions of large peptides. STATEMENT OF SIGNIFICANCE: To investigate β-TUBB2A E-hook hexapeptide, a unique approach is employed whereby the hexapeptide is broken into fragments, EG, ED, EA, EGED, and EDEA and analyzed via experimental Raman spectroscopy of the crystalline solids. The experimentally observed vibrational band positions are compared to those computed using and scaled from DFT methods and Pople's 6-311+G(2df,2pd) basis set. The reported vibrational band positions are also confirmed by previously reported bands of similar peptides in the literature. This methodology facilitates differentiation between the behaviors of various side chains and their influence on the structure of the hexapeptide, providing insight into not only the nature of the peptide but also defining regions for potential protein and cytoplasmic interactions, without requiring excessive computing resources or overly-sensitive experimental methods.