Structural Motifs, Conformational Patterns, and Noncovalent Interactions in Isolated Flexible Molecules and Hydrates by Laser Spectroscopies and Quantum Chemical Calculations

by Mr. Rami Rahimi

Ben-Gurion University of the Negev

at Quantum optics seminar

Wed, 29 May 2024, 16:00
Sacta-Rashi Building for Physics (54), room 207

Abstract

This is a student seminar.
(The seminar will be held in Hebrew.)
It will take place in person in room 207.

Abstract:
Exposing the dynamics, three-dimensional structures, and conformational landscapes of isolated biomolecules and the role played by their inter- and intra-molecular non-covalent interactions (NCIs) with each other and with solvents attracts considerable interest. Here, we use our novel and difficult-to-implement laser-based spectroscopic technique of ionization-loss stimulated Raman spectroscopy (ILSRS) combined with quantum calculations to study the structural motifs and NCIs in selected isolated neurotransmitter model molecules, analogues, and hydrates [1-3]. For some species we provide the first comprehensive study while for others there exists ambiguity regarding their identification. We identify the structures by comparing the measured spectra to scaled harmonic Raman spectra and obtain the best matching spectrum visually. The finding of the optimized structures opens the door to their deeper investigation, including relative energy calculations, NCI analysis, and other properties. To improve the predictions and data analysis, we established a new database based on our measured ILSR spectra, allowing us to obtain scaling factors for better agreement with measured spectra. We further developed a quantitative method for spectral comparison and structural identification [4], which uses the Kuhn-Munkres assignment algorithm, with Euclidean and Manhattan distance measures, or optimal transport. This new database/approach can reveal subtle structural changes, quantitatively assign spectra, and recover structures, holding great promise for future studies and benchmarking other predicted signatures.

1. Rahimi, R.; Shachar, A.; Bar, I. J. Am. Chem. Soc. 2022, 144, 8337−8346.
2. Rahimi, R.; Saban, N.; Bar, I. J. Am. Chem. Soc. 2023, 145, 18455–18467.
3. Rahimi, R.; Saban, N.; Bar, I. J. Phys. Chem. Lett. 2024, 15, 3658–3667.
4. Rahimi, R.; Saban, N.; Bar, I. in preparation.

Created on 22-05-2024 by Folman, Ron (folman)
Updaded on 22-05-2024 by Folman, Ron (folman)