Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure

Abstract

Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical spectra. For chromophores in the condensed phase, the large number of atoms needed to simulate the environment has traditionally prohibited the use of high-level excited-state electronic structure methods. By leveraging transfer learning, we show how to construct machinelearned models to accurately predict the high-level excitation energies of a chromophore in solution from only 400 high-level calculations. We show that when the electronic excitations of the green fluorescent protein chromophore in water are treated using EOM-CCSD embedded in a DFT description of the solvent the optical spectrum is correctly captured and that this improvement arises from correctly treating the coupling of the electronic transition to electric fields, which leads to a larger response upon hydrogen bonding between the chromophore and water.

Mapping electronic decoherence pathways in molecules

“…We envision the application of this strategy to elucidate the role of diverse chemical and biological environments to the decoherence, and to establish decoherence pathways for localized and delocalized, spin-specific and charge-transfer electronic excitations, and in molecules of varying size and rigidity. Further, the extracted spectral densities will be of general utility to characterize the dynamics of molecular chromophores with full chemical complexity using quantum master equations ( 42 – 44 ) of increasing sophistication, and to advance our computational capabilities to accurately capture electron-nuclear interactions in condensed phase environments ( 49 – 51 , 55 ).…”

“…Specifically, in quantum master equations the interaction between the molecular chromophore and its thermal environment is characterized by a spectral density, ( 48 ), which quantifies the frequencies of the nuclear environment, , and their coupling strength with the electronic excitations. Unfortunately, the quantitative determination of has remained elusive to theory ( 49 – 55 ), and its experimental characterization is limited ( 56 – 60 ). For this reason, most studies of molecular decoherence based on quantum master equations rely on simple models of the spectral density that do not capture the interactions of realistic chemical problems ( 45 – 47 ).…”

Taming The Third Order Cumulant Approximation to Linear Optical Spectroscopy

“…6,[16][17][18][19][21][22][23][24][25][26]57 Additionally, the computational cost of sampling energy gap fluctuations can be significantly reduced using machine learning (ML) techniques. 58,59 However, in practical calculations, the cumulant expansion is generally truncated at second order, corresponding to mapping energy gap fluctuations onto a bath of linearly coupled harmonic oscillators (Brownian Oscillator Model or BOM). This truncation is only exact for systems where energy-gap fluctuations follow Gaussian statistics, and already leads to errors in the harmonic GBOM Hamiltonian including changes in PES curvature and Duschinsky mode mixing effects, 39,60 that are captured exactly by the FC approach.…”

Axial H-bonding Solvent Controls Inhomogeneous Spectral Broadening, Peripheral H-bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol

“…The energy gap correlation function can then be used to compute the spectral density, 21 which shows how vibrational modes couple to the optical excitation and the resulting optical spectra, such as the resonance Raman spectrum and the absorption spectrum. 18,20,[22][23][24][25][26][27][28][29][30] This trajectory-based approach is able to capture both vibronic effects and specific environmental effects on the optical spectrum on an equal footing. Specific solvent interactions are known to cause spectral changes.…”