Conformational change in the C form of palmitic acid investigated by Raman spectroscopy and X-ray diffraction

New polymorphic phase of arachidic acid crystal: structure, intermolecular interactions, low-temperature stability and Raman spectroscopy combined with DFT calculations

Saturated monocarboxylic fatty acids with long carbon chains are organic compounds widely used in several applied fields, such as energy production, thermal energy storage, antibactericidal, antimicrobial, among others. In this research, a new polymorphic phase of arachidic acid (AA) crystal was synthesized and its structural and vibrational properties were studied by single-crystal X-ray diffraction (XRD) and polarized Raman scattering. The new structure of AA was solved at two different temperature conditions (100 and 300 K). XRD analysis indicated that this polymorph belongs to the monoclinic space group P21/c (C2h5), with four molecules per unit cell (Z = 4). All molecules in the crystal lattice adopt a gauche configuration, exhibiting a R22(8) hydrogen bond pattern. Consequently, this new polymorphic phase, labeled as B form, is a polytype belonging to the monoclinic symmetry, i.e., Bm form. Complementarily, Hirshfeld's surfaces were employed to analyze the intermolecular interactions within the crystal lattice of this polymorph at temperatures of 100 and 300 K. Additionally, density functional theory (DFT) calculations were performed to assign all intramolecular vibration modes related to experimental Raman-active bands, which were properly calculated using a dimer model, considering a pair of AA molecules in the gauche configuration, according to the solved-crystal structure.

Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.

Elucidating the phase transitions of decanoic-acid crystal by XRD, Raman, group theory and Gibbs energy analyses combined with DFT calculations

This research reports a series of phase transitions in the decanoic-acid (DA) crystal under low-temperature conditions, which were elucidated by XRD, Raman scattering and DFT calculations in a dimer of DA in the C form (monoclinic structure). The first phase change was noticed within the 210-190 K interval duly characterized as a transition of second-order type, as indicated by Gibbs energy behavior, suggesting that the monoclinic structure (P2₁/c) of the crystal is not changed. The second change was observed nearly 110-90 K, whose transition is first-order type occurring from the C form to an A form (triclinic), possibly belonging to the P1 space group. This new polymorphic phase was duly predicted through DFT calculations. According to Gibbs energy behavior, the third phase change (∼30-10 K) is proposed to be a transition from the A form to a new polymorphic phase that probably is a first-order transition, likely associated with a change from the P1 space group to P-1. Furthermore, group theory and wavenumber vs temperature plots' analyses corroborated the phase transitions undergone by DA crystal. In addition, anharmonicity effects in several Raman bands' behavior were noticed during the cooling. A correct assignment for the Raman and IR modes via DFT calculations at room-temperature conditions is also provided herein.

Computational structural, electronic and optical properties of the palmitic acid in its C form

In this work, we report a theoretical study of the structural, electronic, and optical properties of palmitic acid crystal in its C form under DFT calculations level. Palmitic acid is a fatty acid that constitutes the large majority of vegetable oils with recognized potential applications in medicine, pharmaceuticals, cosmetics technology, foods, and fuel. As a main result, we have found that the electronic bandstructure reveals an indirect gap given by 3.713 eV (E→B andE→Γ), as a main bandgap, while the secondary bandgaps found were 4.175 eV (γ₁→Γ) and 4.172 eV (γ₂→B). It behaves like a wide bandgap semiconductor, which points to potential applications in optoelectronic devices.

Fatty acids as biomimetic replication agents for luminescent metal-organic framework patterns

Luminescent metal-organic frameworks (MOFs) are known to spontaneously self-assemble on human fingerprints. Here, we investigate the different chemical components of fingerprints and determine that MOF growth is predominantly induced by insoluble fatty acids. This finding shows that these simple biomolecules can be employed for the precise positioning of luminescent MOFs.

Detection of Potential Lipid Biomarkers in Oxidative Environments by Raman Spectroscopy and Implications for the ExoMars 2020-Raman Laser Spectrometer Instrument Performance

The aim of the European Space Agency's ExoMars rover mission is to search for potential traces of present or past life in the swallow subsurface (2 m depth) of Mars. The ExoMars rover mission relies on a suite of analytical instruments envisioned to identify organic compounds with biological value (biomarkers) associated with a mineralogical matrix in a highly oxidative environment. We investigated the feasibility of detecting basic organics (linear and branched lipid molecules) with Raman laser spectroscopy, an instrument onboard the ExoMars rover, when exposed to oxidant conditions. We compared the detectability of six lipid molecules (alkanes, alkanols, fatty acid, and isoprenoid) before and after an oxidation treatment (15 days with hydrogen peroxide), with and without mineral matrix support (amorphous silica rich vs. iron rich). Raman and infrared spectrometry was combined with gas chromatography-mass spectrometry to determine detection limits and technical constraints. We observed different spectral responses to degradation depending on the lipid molecule and mineral substrate, with the silica-rich material showing better preservation of organic signals. These findings will contribute to the interpretation of Raman laser spectroscopy results on cores from the ExoMars rover landing site, the hydrated silica-enriched delta fan on Cogoon Vallis (Oxia Planum).

New structural phases of [bis(L-alaninato) diaqua] nickel(II) dihydrate crystal

The study of [bis(L‑alaninato) diaqua] nickel(II) dihydrate crystal using Raman scattering and X-ray diffraction as a function of temperature is reported in this paper. Thermal analysis (TGA and DSC) complementary measurements were also performed in order to obtain information on structural changes and mass loss occurred in this material. It was identified that the crystal undergoes loss of water at two different temperatures: ~340 and 393 K. X-ray diffraction measurements showed two phase transformations related to these two water loss events. After heating up to 423 K, the sample was cooled down to 298 K and its diffraction pattern presented the same pattern at 423 K, evidencing an irreversible phase transformation. The diffraction results also showed that crystal goes to monohydrate and anhydrous phases. Furthermore, cell lattice parameters and space groups of both phases were determined by applying Rietveld refinement through Le Bail method, demonstrating that their structures belong to the P2₁ and C2/c space groups, both with monoclinic symmetry. In addition, assignments of Raman spectra vibrational bands (at 300 K) are provided. The high-temperature Raman spectra were obtained in the 100-3500 cm^-1 range, where it was observed several abrupt changes in the intensity of low-wavenumber bands and the appearance/disappearance of some vibrational modes that have coupling with OH⋯O hydrogen bonds. These spectral changes are in good agreement with X-ray diffraction and thermal analyses data. Finally, we obtained Raman measurements at low temperatures, from which we identified that the crystal structure is extremely stable throughout the temperature range of 293-10 K.

Phase transformation in the C form of myristic-acid crystals and DFT calculations

In this study, the vibrational frequencies of myristic acid (CH₃(CH₂)₁₂COOH) were obtained using density functional theory calculations, and the results were compared with experimental Raman and infrared data. Additionally, Raman spectra of crystalline myristic acid were recorded in the 300-20 K range. Raman spectroscopy gives important insights into the effect of low temperatures on its monoclinic phase. X-ray diffraction was performed from 298 to 133 K to provide additional information about the cryogenic behavior of the crystals. These undergo a phase transformation, which was confirmed by differential scanning calorimetry through an enthalpy anomaly observed at low temperatures. Raman spectra and X-ray diffraction refinement of the cell parameters in combination with differential scanning calorimetry at low temperatures revealed slight modifications, confirming a conformational change in the myristic acid molecules involving rearrangement of dimers within the unit cell.