Abstract Raman spectroscopy provides label‐free, specific analysis of biomolecular structure and interactions. It could have a greater impact with improved characterization of complex fingerprint vibrations. Many Raman peaks have been assigned to cholesterol, for example, but the molecular vibrations associated with those peaks are not known. In this report, time‐dependent density functional theory calculations of the Raman spectrum of cholesterol are compared to measurements on microcrystalline powder to identify 23 peaks in the Raman spectrum. Among them, a band of six peaks is found to be sensitive to the conformational structure of cholesterol's iso‐octyl chain. Calculations on 10 conformers in this spectral band are fit to experimental spectra to probe the cholesterol chain structure in purified powder and in phospholipid vesicles. In vesicles, the chain is found to bend perpendicular to the steroid rings, supporting the case that the chain is a dynamic structure that contributes to lipid condensation and other effects of cholesterol in biomembranes. Statement of Significance: Here we use density functional theory to identify a band of six peaks in cholesterol's Raman spectrum that is sensitive to the conformational structure of cholesterol's chain. Raman spectra were analyzed to show that in fluid‐phase lipid membranes, about half of the cholesterol chains point perpendicular to the steroid rings. This new method of label‐free structural analysis could make significant contributions to our understanding of cholesterol's critical role in biomembrane structure and function. More broadly, the results show that computational quantum chemistry Raman spectroscopy can make significant new contributions to molecular structure when spectra are interpreted with computational quantum chemistry.
more »
« less
This content will become publicly available on January 1, 2026
Raman Match: Application for automated identification of minerals from Raman spectroscopy data
Abstract Raman spectroscopy is a rapid, nondestructive analysis technique used in various scientific disciplines, including mineralogy, chemistry, materials science, and biology. The analysis of Raman spectra and the identification of specific substances in unknown samples can be complex and time-consuming due to the large database of Raman spectra. The Raman Match application was developed to simplify and automate the sample identification process through a search and match method. The application integrates the well-established RRUFF Raman database with the Python programming language. It provides a user-friendly graphical interface to load Raman spectra, identify and fit peaks, match peaks to the reference libraries, visualize the results, and generate publication-ready figures. The application offers a swift and automated method for mineral identification using Raman spectroscopy in laboratory and field settings and during planetary exploration missions to extraterrestrial environments with constraints on time and resources.
more »
« less
- PAR ID:
- 10567538
- Editor(s):
- Kung, Jennifer
- Publisher / Repository:
- Mineralogical Society of America
- Date Published:
- Journal Name:
- American Mineralogist
- Volume:
- 110
- Issue:
- 1
- ISSN:
- 0003-004X
- Page Range / eLocation ID:
- 25 to 33
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
The detection and analysis of flavonoids by Raman spectroscopy are of interest in many fields, including medicinal chemistry, food science, and astrobiology. Spectral interpretation would benefit from better identification of the fingerprint vibrational peaks of different flavonoids and how they are affected by intermolecular interactions. The Raman spectra of two flavonoids, flavone and quercetin, were investigated through comparisons between spectra recorded from pure powders and spectra calculated with time dependent density functional theory (TDDFT). For both flavone and quercetin, 17 peaks were assigned to specific molecular vibrations. Both flavonoids were found to have a split peak between 1250 – 1350 cm-1 that is not predicted by TDDFT calculations on isolated molecules. In each case, it is shown that the addition of hydrogen bonded molecules arranged based on crystal structures reproduce the split peaks. These peaks were due to a stretching vibration of the bond between the benzopyrone and phenyl rings and represent a characteristic spectral feature of the flavonoids. Spectra of pollen grains from Quercus virginiana were also recorded and exhibit several peaks that correspond to the quercetin spectrum.more » « less
-
null (Ed.)Abstract Raman spectra were collected for an extensive set of well-characterized layer-structure Mn oxide mineral species (phyllomanganates) employing a range of data collection conditions. We show that the application of various laser wavelengths, such as 785, 633, and 532 nm, at low power levels (30–500 μW) in conjunction with the comprehensive database of standard spectra presented here, makes it possible to distinguish and identify the various phyllomanganate minerals. The Raman mode relative intensities can vary significantly as a function of crystal orientation relative to the incident laser light polarization direction as well as incident laser light wavelength. Consequently, phase identification success is enhanced when using a standards database that includes multiple spectra collected for different crystal orientations and with different laser light wavelengths. The position of the highest frequency Raman mode near 630–665 cm–1 shows a strong linear correlation with the fraction of Mn3+ in the octahedral Mn sites. With the comprehensive Raman database of well-characterized Mn oxide standards provided here (and available online as Online Material1), and use of appropriate data collection conditions, micro-Raman is a powerful tool for identification and characterization of biotic and abiotic Mn oxide phases from diverse natural settings, including on other planets, as well as for laboratory and industrial materials.more » « less
-
Background subtraction is a general problem in spectroscopy often addressed with application-specific techniques, or methods that introduce a variety of implementation barriers such as having to specify peak-free regions of the spectrum. An iterative dual-tree complex wavelet transform-based background subtraction method (DTCWT-IA) was recently developed for the analysis of ultrafast electron diffraction patterns. The method was designed to require minimal user intervention, to support streamlined analysis of many diffraction patterns with complex overlapping peaks and time-varying backgrounds, and is implemented in an open-source computer program. We examined the performance of DTCWT-IA for the analysis of spectra acquired by a range of optical spectroscopies including ultraviolet–visible spectroscopy (UV–Vis), X-ray photoelectron spectroscopy (XPS), and surface-enhanced Raman spectroscopy (SERS). A key benefit of the method is that the user need not specify regions of the spectrum where no peaks are expected to occur. SER spectra were used to investigate the robustness of DTCWT-IA to signal-to-noise levels in the spectrum and to user operation, specifically to two of the algorithm parameter settings: decomposition level and iteration number. The single, general DTCWT-IA implementation performs well in comparison to the different conventional approaches to background subtraction for UV–Vis, XPS, and SERS, while requiring minimal input. The method thus holds the same potential for optical spectroscopy as for ultrafast electron diffraction, namely streamlined analysis of spectra with complex distributions of peaks and varying signal levels, thus supporting real-time spectral analysis or the analysis of data acquired from different sources.more » « less
-
Abstract BackgroundBreast cancer poses a significant health risk to women worldwide, with approximately 30% being diagnosed annually in the United States. The identification of cancerous mammary tissues from non-cancerous ones during surgery is crucial for the complete removal of tumors. ResultsOur study innovatively utilized machine learning techniques (Random Forest (RF), Support Vector Machine (SVM), and Convolutional Neural Network (CNN)) alongside Raman spectroscopy to streamline and hasten the differentiation of normal and late-stage cancerous mammary tissues in mice. The classification accuracy rates achieved by these models were 94.47% for RF, 96.76% for SVM, and 97.58% for CNN, respectively. To our best knowledge, this study was the first effort in comparing the effectiveness of these three machine-learning techniques in classifying breast cancer tissues based on their Raman spectra. Moreover, we innovatively identified specific spectral peaks that contribute to the molecular characteristics of the murine cancerous and non-cancerous tissues. ConclusionsConsequently, our integrated approach of machine learning and Raman spectroscopy presents a non-invasive, swift diagnostic tool for breast cancer, offering promising applications in intraoperative settings.more » « less
An official website of the United States government
