TD-DFT absorption spectrum of (poly)threonine in water: A study combining molecular dynamics and quantum mechanics calculations

Mendanha, Karinna; Prado, R.; Oliveira, Leonardo Bruno Assis; Colherinhas, Guilherme

doi:10.1016/j.cplett.2021.138876

Cited by 5 publications

(1 citation statement)

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“…Photo-induced phenomena and optical properties are the grounds to investigate electronic states and their interactions with the environment . Experimental spectra can be interpreted via computational approaches at the molecular scale, understanding the microscopic characteristics that determine the position, width and shape of absorption bands [23][24][25][26][27][28][29][30][31][32][33][34]. However, a number of challenges remain open and mainly concern the modeling of either floppy molecules or non-covalent complexes in solution.…”

Section: Introductionmentioning

confidence: 99%

An Expedited Route to Optical and Electronic Properties at Finite Temperature via Unsupervised Learning

et al. 2023

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Electronic properties and absorption spectra are the grounds to investigate molecular electronic states and their interactions with the environment. Modeling and computations are required for the molecular understanding and design strategies of photo-active materials and sensors. However, the interpretation of such properties demands expensive computations and dealing with the interplay of electronic excited states with the conformational freedom of the chromophores in complex matrices (i.e., solvents, biomolecules, crystals) at finite temperature. Computational protocols combining time dependent density functional theory and ab initio molecular dynamics (MD) have become very powerful in this field, although they require still a large number of computations for a detailed reproduction of electronic properties, such as band shapes. Besides the ongoing research in more traditional computational chemistry fields, data analysis and machine learning methods have been increasingly employed as complementary approaches for efficient data exploration, prediction and model development, starting from the data resulting from MD simulations and electronic structure calculations. In this work, dataset reduction capabilities by unsupervised clustering techniques applied to MD trajectories are proposed and tested for the ab initio modeling of electronic absorption spectra of two challenging case studies: a non-covalent charge-transfer dimer and a ruthenium complex in solution at room temperature. The K-medoids clustering technique is applied and is proven to be able to reduce by ∼100 times the total cost of excited state calculations on an MD sampling with no loss in the accuracy and it also provides an easier understanding of the representative structures (medoids) to be analyzed on the molecular scale.

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