It is commonly believed that solvation of a polar molecule in a polar solvent has the only effect of red shifting all of his spectroscopical features, similarly solvating a polar molecule in a non polar solvent has the opposite effect. Naturally this can be retained valid for very simple molecular systems, but what are the effects of solvation to more complex molecular systems ?. A theoretical analysis of different kind of systems can be helpful to give atomistic insights to answer these questions, and also help develope a model which can be used to take in consideration solvation effects for complex kind of molecular systems. With this work [1] our goal is to try to understand the effects of solvation on vibrational features, in particular our work focuses on the differences that occurs between gas phase spectroscopic simulations and simulations carried on in a box of solvent. The latest one should also permit us to show that the use of an appropriate explicit solvent in this kind of simulations, is fundamental to catch the right shifts [2] caused by interaction of the system with the solvent molecule. We started our work with a simple molecule of 2'-deoxyguanosine, the informations gained from the first set of simulations has been used to show how solvation acts differently when the same molecule is found in a quadruplex geometry. In the end we will also show how the use of both classical and semiclassical [3] approaches combined with the use of Force Fields, [4,5] are able to give a good qualitative reproduction of experimental data. [1] Davide Moscato, Fabio Gabas, Riccardo Conte, and Michele Ceotto. A theoretical vibrational spectroscopy approach on the study of solvation effects in the g-quadruplex. To be submitted, TBD. [2] Cynthia V. Pagba, Stephen M. Lane, and Sebastian Wachsmann-Hogiu. J. Raman Spectrosc., 41(3):241–247, 2010. [3] R. Conte and M. Ceotto. Semiclassical Molecular Dynamics for Spectroscopic Calculations, chapter 19, pages 595–628. John Wiley & Sons, Ltd, 2020. [4] Changsheng Zhang, Chao Lu, Zhifeng Jing, Chuanjie Wu, Jean-Philip Piquemal, Jay W. Ponder, and Pengyu Ren. J. Chem. Theory Comput., 14(4):2084–2108, April 2018. [5] Fabio Gabas, Riccardo Conte, and Michele Ceotto. Quantum vibrational spectroscopy of explicitly solvated thymidine in semiclassical approximation. J. Phys. Chem. Lett., 13(5):1350–1355, February 2022.

Vibrational spectroscopy simulation of solvation effects on the g-quadruplex / D. Moscato, F. Gabas, R. Conte, M. Ceotto. ((Intervento presentato al convegno Challenges of molecular spectroscopy: Theory meets experiment tenutosi a Lausanne nel 2022.

Vibrational spectroscopy simulation of solvation effects on the g-quadruplex

D. Moscato
Primo
Writing – Original Draft Preparation
;
F. Gabas
Secondo
;
R. Conte
Penultimo
;
M. Ceotto
Ultimo
Supervision
2022-06-19

Abstract

It is commonly believed that solvation of a polar molecule in a polar solvent has the only effect of red shifting all of his spectroscopical features, similarly solvating a polar molecule in a non polar solvent has the opposite effect. Naturally this can be retained valid for very simple molecular systems, but what are the effects of solvation to more complex molecular systems ?. A theoretical analysis of different kind of systems can be helpful to give atomistic insights to answer these questions, and also help develope a model which can be used to take in consideration solvation effects for complex kind of molecular systems. With this work [1] our goal is to try to understand the effects of solvation on vibrational features, in particular our work focuses on the differences that occurs between gas phase spectroscopic simulations and simulations carried on in a box of solvent. The latest one should also permit us to show that the use of an appropriate explicit solvent in this kind of simulations, is fundamental to catch the right shifts [2] caused by interaction of the system with the solvent molecule. We started our work with a simple molecule of 2'-deoxyguanosine, the informations gained from the first set of simulations has been used to show how solvation acts differently when the same molecule is found in a quadruplex geometry. In the end we will also show how the use of both classical and semiclassical [3] approaches combined with the use of Force Fields, [4,5] are able to give a good qualitative reproduction of experimental data. [1] Davide Moscato, Fabio Gabas, Riccardo Conte, and Michele Ceotto. A theoretical vibrational spectroscopy approach on the study of solvation effects in the g-quadruplex. To be submitted, TBD. [2] Cynthia V. Pagba, Stephen M. Lane, and Sebastian Wachsmann-Hogiu. J. Raman Spectrosc., 41(3):241–247, 2010. [3] R. Conte and M. Ceotto. Semiclassical Molecular Dynamics for Spectroscopic Calculations, chapter 19, pages 595–628. John Wiley & Sons, Ltd, 2020. [4] Changsheng Zhang, Chao Lu, Zhifeng Jing, Chuanjie Wu, Jean-Philip Piquemal, Jay W. Ponder, and Pengyu Ren. J. Chem. Theory Comput., 14(4):2084–2108, April 2018. [5] Fabio Gabas, Riccardo Conte, and Michele Ceotto. Quantum vibrational spectroscopy of explicitly solvated thymidine in semiclassical approximation. J. Phys. Chem. Lett., 13(5):1350–1355, February 2022.
Theoretical chemistry; G-Quadruplex; Vibrational spectrscopy; Semiclassical dynamics
Settore CHIM/02 - Chimica Fisica
Cecam
ETH
https://www.cecam.org/workshop-details/1034
Vibrational spectroscopy simulation of solvation effects on the g-quadruplex / D. Moscato, F. Gabas, R. Conte, M. Ceotto. ((Intervento presentato al convegno Challenges of molecular spectroscopy: Theory meets experiment tenutosi a Lausanne nel 2022.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/933629
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