Many‐body meets QM/MM: Application to indole in water solution

Abstract

Aromatic chromophores are used as optical probes to investigate the structure of complex biological systems. For this purpose, it is crucial to understand the role of the bio‐chemical environment in the modification of their optical properties. Here we present a theoretical method to analyze this aspect on large scale systems, like biologically relevant molecules in aqueous solution. We combine many body perturbation theory with a quantum‐mechanics/molecular‐mechanics (QM/MM) approach. We include quasi‐particle and excitonic effects for the calculation of optical absorption spectra in a QM/MM scheme. In agreement with the experiments, we find that the solvent induces a redshift in the main spectral peak of indole, and we demonstrate this shift originates both from electrostatic and geometrical effects.magnified image

Explaining Level Inversion of the La and Lb States of Indole and Indole Derivatives in Polar Solvents

“…[18][19][20] Indeed, there are only a few theoretical studies of indole that accounted for the presence of a solvent. [21][22][23] To the best of our knowledge, the only study on indole emission using a combined ab initio approach and a continuum solvation model was done in Ref. [23].…”

Chapter 9. First Principles Methods in Biology: From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanics

“…As yet, most QM/MM investigations on optical chromophore properties have been focused on solvent effects on absorption spectra, [242][243][244] whereas studies on biomolecular environmental shifts on optical spectra are still relatively rare. [245][246][247][248][249][250][251][252] That is, the full conformational flexibility of large protein environments at ambient temperature based on MD and its influence on absorption or emission band positions and shapes, e.g.…”

“…QM/MM simulations are well suited to investigate the factors that control photochemical excitation and reactivity. In excited-state QM/MM schemes, the QM part is either described via multiconfigurational wave functionbased quantum chemical methods, [253][254][255][256] or by many-body perturbation theory 243,[257][258][259] or through excited-state extensions of DFT. 242,243,[259][260][261] Whereas the former two types of approaches are still limited to fairly small systems and relatively small basis sets, the latter one is also extendible to rather large systems.…”

“…Indeed, QM/MM methods have also been explored for excited-state dynamics governing photochemical reactions. 242,[253][254][255][256]261,[263][264][265][266][267][268][269] DFT for ground states or time-dependent DFT (TD-DFT) 270 for the description of electronically excited states are computationally very efficient and have been used successfully, in particular in conjunction with Car-Parrinello MD methods 243,249,250,[271][272][273][274][275] including non-adiabatic dynamics. 251,265,266,[276][277][278][279] Nevertheless, the quality of results obtained by TD-DFT calculations depends on the system under investigation and on the functional used to reproduce the exchange and correlation interactions.…”

Structural prediction of a rhodamine-based biosensor and comparison with biophysical data

“…This approach has been shown to give fairly good results for a variety of solutes in aqueous solution. [22][23][24][25][26]…”