Séminaire de l'équipe PCMT: Jessica Bowles (Vrije Universiteit Brussel; VUB)

Vibrational Spectroscopy through Molecular Dynamics with a Polarisable Force Field

To support the interpretation of experimental measurements and to further the understanding of structure and spectra, theoretical predictions of vibrational spectra are crucial. As an alternative to computational methods based on explicit descriptions of electronic structure such as density functional theory and ab initio molecular dynamics (AIMD) [1], and to circumvent their limited sampling capabilities in time and space, we have attempted to simulate vibrational circular dichroism (VCD) and Raman spectra directly from molecular dynamics trajectories employing a polarisable force field called AMOEBA [2]. This force field offers a refined description of electrostatic interactions by accounting for both permanent atomic multipoles and induced atomic dipoles, the latter being essential for simulating Raman spectroscopy.

In this presentation, the initial segment will describe my implementation of VCD spectroscopy using the AMOEBA polarisable force field in the Tinker software package [3]. This implementation, performed in collaboration with Dr. Sascha Jähnigen, Dr. Florent Calvo and Dr. Carine Clavaguéra, was utilized to examine the VCD spectrum of alanine in the gaseous, hydrated and solid phases.

In the second part, the expansion of the implementation of Raman spectroscopy [4] with the same force field to silicic acids in solution will be shown. In this work, additional parameters for hydrated Silicic acids were determined through the Force Balance software [5] and the Polarize utility of Tinker was adapted to obtain the molecular polarisability tensor rather than the total tensor. This work was carried out with the help of Fileto Rodriguez and Prof. Frederik Tielens.

References:

[1] Fischer SA, Ueltschi TW, El-Khoury PZ, Mifflin AL, Hess WP, Wang HF, et al. J Phys Chem B. 120, 1429–36 (2016).

[2] Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, et al. Current status of the AMOEBA polarizable force field. J Phys Chem B. 114, 2549–64 (2010).

[3] Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, et al. J Chem. Theory Comput. 14 5273–89 (2018).

[4] Binninger T, Saraç D, Marsh L, Picard T, Doublet ML, Raynaud C. J Chem. Theory Comput. 19, 1023–34 (2023).

[5] Wang L-P., Chen J., and Van Voorhis T.. J Chem. Theory Comput., 9, 452–460, 2013; Wang L-P, Martinez T. J., Pande V. S. J. Phys. Chem. Letters, 5, 1885, 2014; Wang L-P, McKiernan K. A, Gomes J., Beauchamp K. A., Head-Gordon T., Rice J. E., Swope W. C, Martínez T. J., Pande V. S. J. Phys. Chem. B, 121, 4023, 2017