Semiclassical Vibrational Spectroscopy of Biological Molecules Using Force Fields

Abstract

Semiclassical spectroscopy is a practical way to get an accurately approximate quantum description of spectral features starting from ab initio molecular dynamics simulations. The computational bottleneck for the method is represented by the cost of ab initio potential, gradient, and Hessian matrix estimates. This drawback is particularly severe for biological systems due to their unique complexity and large dimensionality. The main goal of this manuscript is to demonstrate that quantum dynamics and spectroscopy, at the level of semiclassical approximation, are doable even for sizable biological systems. To this end, we investigate the possibility of performing semiclassical spectroscopy simulations when ab initio calculations are replaced by computationally cheaper force field evaluations. Both polarizable (AMOEBABIO18) and nonpolarizable (AMBER14SB) force fields are tested. Calculations of some particular vibrational frequencies of four nucleosides, i.e., uridine, thymidine, deoxyguanosine, and adenosine, show that ab initio simulations are accurate and widely applicable. Conversely, simulations based on AMBER14SB are limited to harmonic approximations, but those relying on AMOEBABIO18 yield acceptable semiclassical values if the investigated conformation has been included in the force field parametrization. The main conclusion is that AMOEBABIO18 may provide a viable route to assist semiclassical spectroscopy in the study of large biological molecules for which an ab initio approach is not computationally affordable.

How many water molecules are needed to solvate one?

“…Semiclassical methods have been applied successfully in a range going from small molecules, [32][33][34] including fluxional ones, 35 to medium-large systems. 36 For this work we employed the multiple coherent states divide-and-conquer semiclassical initial value representation technique (MC-DC SCIVR), 37 which has permitted to solve open issues concerning protonated glycine supramolecular systems 38 and has already been applied to the vibrational in-vestigation of small water clusters. 39 The interested reader may find more theoretical information on semiclassical dynamics and spectroscopy in Section 1 of the ESI †.…”

Qual È La Più Piccola Goccia D’acqua?

“…Nel mio gruppo di ricerca (https://sites.unimi.it/ceotto/) abbiamo recentemente sviluppato dei metodi basati sulla meccanica semiclassica [5][6][7][8][9][10][11][12][13], grazie ad un finanziamento dell'European Research Council. In particolare, abbiamo esteso le teorie semiclassiche al calcolo degli spettri vibrazionali di sistemi molecolari complessi e supramolecolari [14][15][16][17][18][19][20][21]. La meccanica semiclassica, come si può comprendere dalla Fig.…”

Machine learning for vibrational spectroscopy via divide-and-conquer semiclassical initial value representation molecular dynamics with application to N-methylacetamide

“…This method, named MC-DC SCIVR, can deal with very high-dimensional systems. Notable applications of MC-DC SCIVR include dipeptide derivatives, 59 nucleobases 60 and nucleosides, 61 and molecules adsorbed on titania surfaces. 62 The most relevant issue to deal with for a successful DC-SCIVR calculation is the choice of the optimal subspace decomposition.…”