arXiv subjects

Yuezhi Mao

Publications and source records attributed to Yuezhi Mao.

7 recordsLinked to original sources

arXiv2024

Environmentally driven symmetry-breaking quenches dual fluorescence in proflavine

Nonadiabatic couplings between several electronic excited states are ubiquitous in many organic chromophores and can significantly influence optical properties. A recent experimental study demonstrated that the proflavine molecule exhibits surprising dual fluorescence in the gas phase, that is suppressed in polar solvent environments. Here, we uncover the origin of this phenomenon by parameterizing a linear-vibronic coupling (LVC) Hamiltonian from spectral densities of system-bath coupling constructed along molecular dynamics trajectories, fully accounting for interactions with the condensed-phase environment. The finite-temperature absorption, steady-stat emission, and time-resolved emission spectra are then computed using powerful, numerically exact tensor network approaches. We find that the dual fluorescence in vacuum is driven by a single well-defined coupling mode, but is quenched in solution due to dynamic solvent-driven symmetry-breaking that mixes the two low-lying electronic states. We expect the computational framework developed here to be widely applicable to the study of non-Condon effects in complex condensed-phase environments.

physics.chem-ph↗

arXiv2023

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

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 machine-learned models to accurately predict 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.

physics.chem-ph↗

arXiv2022

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials

Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecules interacting with proteins. It contains over 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and uncharged molecules, and a wide range of covalent and non-covalent interactions. It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, along with other useful quantities such as multipole moments and bond orders. We train a set of machine learning potentials on it and demonstrate that they can achieve chemical accuracy across a broad region of chemical space. It can serve as a valuable resource for the creation of transferable, ready to use potential functions for use in molecular simulations.

physics.chem-ph↗

arXiv2022

Relativistic Orbital Optimized Density Functional Theory for Accurate Core-Level Spectroscopy

Core-level spectra of 1s electrons of elements heavier than Ne show significant relativistic effects. We combine advances in orbital optimized DFT (OO-DFT) with the spin-free exact two-component (X2C) model for scalar relativistic effects, to study K-edge spectra of third period elements. OO-DFT/X2C is found to be quite accurate at predicting energies, yielding $\sim 0.5$ eV RMS error vs experiment with the modern SCAN (and related) functionals. This marks a significant improvement over the $>50$ eV deviations that are typical for the popular time-dependent DFT (TDDFT) approach. Consequently, experimental spectra are quite well reproduced by OO-DFT/X2C, sans empirical shifts for alignment. OO-DFT/X2C combines high accuracy with ground state DFT cost and is thus a promising route for computing core-level spectra of third period elements. We also explored K and L edges of 3d transition metals to identify limitations of the OO-DFT/X2C approach in modeling the spectra of heavier atoms.

physics.chem-ph↗

arXiv2020

A Non-Perturbative Pairwise-Additive Analysis of Charge Transfer Contributions to Intermolecular Interaction Energies

Energy decomposition analysis (EDA) based on absolutely localized molecular orbitals (ALMOs) decomposes the interaction energy between molecules into physically interpretable components like geometry distortion, frozen interactions, polarization, and charge transfer (CT, also sometimes called charge delocalization) interactions. In this work, a numerically exact scheme to decompose the CT interaction energy into pairwise additive terms is introduced for the ALMO-EDA using density functional theory. Unlike perturbative pairwise charge-decomposition analysis, the new approach does not break down for strongly interacting systems, or show significant exchange-correlation functional dependence in the decomposed energy components. Both the energy lowering and the charge flow associated with CT can be decomposed. Complementary occupied-virtual orbital pairs (COVPs) that capture the dominant donor and acceptor CT orbitals are obtained for the new decomposition. It is applied to systems with different types of interactions including DNA base-pairs, borane-ammonia adducts, and transition metal hexacarbonyls. While consistent with most existing understanding of the nature of CT in these systems, the results also reveal some new insights into the origin of trends in donor-acceptor interactions.

physics.chem-ph↗

arXiv2020

Excited state diabatization on the cheap using DFT: Photoinduced electron and hole transfer

Excited state electron and hole transfer underpin fundamental steps in processes such as exciton dissociation at photovoltaic heterojunctions, photoinduced charge transfer at electrodes, and electron transfer in photosynthetic reaction centers. Diabatic states corresponding to charge or excitation localized species, such as locally excited and charge transfer states, provide a physically intuitive framework to simulate and understand these processes. However, obtaining accurate diabatic states and their couplings from adiabatic electronic states generally leads to inaccurate results when combined with low-tier electronic structure methods, such as time dependent density functional theory (TDDFT), and exorbitant computational cost when combined with high-level wavefunction-based methods. Here we introduce a DFT-based diabatization scheme, Δ-ALMO(MSDFT2), which directly constructs the diabatic states using absolutely localized molecular orbitals (ALMOs). We demonstrate that our method, which combines ALMO calculations with the ΔSCF technique to construct electronically excited diabatic states and obtains their couplings with charge-transfer states using our MSDFT2 scheme, gives accurate results for excited state electron and hole transfer in both charged and uncharged systems that underlie DNA repair, charge separation in donor-acceptor dyads, chromophore-to-solvent electron transfer, and singlet fission. This framework for the accurate and efficient construction of excited state diabats and evaluation of their couplings directly from DFT thus offers a route to simulate and elucidate photoinduced electron and hole transfer in large disordered systems, such as those encountered in the condensed phase.

physics.chem-ph↗

arXiv2019

Accurate and efficient DFT-based diabatization for hole and electron transfer using absolutely localized molecular orbitals

Diabatic states and the couplings between them are important for quantifying, elucidating, and predicting the rates and mechanisms of many chemical and biochemical processes. Here, we propose and investigate approaches to accurately compute diabatic couplings from density functional theory (DFT) using absolutely localized molecular orbitals (ALMOs). ALMOs provide an appealing approach to generate variationally optimized diabatic states and obtain their associated forces that allows for the relaxation of the donor and acceptor orbitals in a way that is internally consistent in how the method treats both the donor and acceptor states. Here, we show that one can obtain more accurate electronic couplings between ALMO-based diabats by employing the symmetrized transition density matrix to evaluate the exchange-correlation contribution. We demonstrate that this approach yields accurate results in comparison to other commonly used DFT-based diabatization methods across a wide array of electron and hole transfer processes occurring in systems ranging from conjugated organic molecules, such as thiophene and pentacene, to DNA base pairs. We also show that this approach yields accurate diabatic couplings even when combined with lower tiers of the DFT hierarchy, opening the door to combining it with quantum dynamics approaches to provide an ab initio treatment of nonadiabatic processes in the condensed phase.

physics.chem-ph↗