Importance of Accurate Structures for Quantum Chemistry Embedding Methods: Which Strategy Is Better?

Abstract

Quantum chemistry embedding methods have become a popular approach to calculate molecular properties of larger systems. In order to account for finite temperature effects, including both configurational and conformational averaging, embedding methods are often combined with molecular dynamics (MD) simulations either in a direct or sequential manner. One of the decisive factors for a successful application of embedding methods is that that the underlying structures provided by the MD simulation are accurate, if not this will result in low-quality prediction of the molecular properties in question. Here we investigate different approaches for generating a set of molecular structures to be used in subsequent embedding calculations ranging from classical MD using a standard molecular mechanics (MM) force field to combined quantum mechanics/molecular mechanics (QM/MM) MD. Overall, we find an intermediate approach relying on classical MD followed by a constrained QM/MM geometry optimization to be a fairly accurate and very cost-effective approach, although this procedure naturally leads to underestimation of, for example, spectral bandwidths.

QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra

“…This improves the agreement with experiments, where the second absorption band of both forms also appears broad without much fine structure [13,14]. Overall, the photoproduct tuning might be already described with one or few selected structures, whereas sampling is necessary to describe the shape of the absorption bands and their broadening due to temperature effects, which was also stated in a recent study investigating chromophores in solution with QM/MM [89]. We note that with the approaches employed by us, it is not possible to describe vibronic effects as reviewed recently [90,91].…”

Assessing Configurational Sampling in the Quantum Mechanics/Molecular Mechanics Calculation of Temoporfin Absorption Spectrum and Triplet Density of States

“…The large discrepancy between the experimental and the theoretical absorption spectra obtained with classical MD followed by QM/MM excited-state calculations ( Figure 1 ) could be attributed to a failure of the force field that describes the vibrational motion of the chromophore during the classical sampling [ 46 ]. To investigate whether this is the case, the classical MD sampling is refined with subsequent QM/MM-MD simulations, where mTHPC is treated at QM level with the B3LYP functional.…”

Unraveling the molecular mechanisms of color expression in anthocyanins

“…Indeed, an accurate modelisation of the optical properties in principle requires taking into account the different molecular states, their possible conformations, thermal fluctuations, and the effects of the solvent. Previous works have gone as far as taking into account thermal fluctuations in the minimum energy conformer, 9,10,20,21 however realistically many conformers will coexist in solution, and each of their contributions to the final color should be taken into account. Such a systematic study is lacking, and the present work intends to be a first step in this direction by applying a multi-scale simulation protocol to the simulation of anthocyanins.…”