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Exploiting Machine Learning to Efficiently Predict Multidimensional Optical Spectra in Complex Environments

Journal Article · · Journal of Physical Chemistry Letters

The excited-state dynamics of chromophores in complex environments determine a range of vital biological and energy capture processes. Time-resolved, multidimensional optical spectroscopies provide a key tool to investigate these processes. Although theory has the potential to decode these spectra in terms of the electronic and atomistic dynamics, the need for large numbers of excited-state electronic structure calculations severely limits first-principles predictions of multidimensional optical spectra for chromophores in the condensed phase. In this work, we leverage the locality of chromophore excitations to develop machine learning models to predict the excited-state energy gap of chromophores in complex environments for efficiently constructing linear and multidimensional optical spectra. By analyzing the performance of these models, which span a hierarchy of physical approximations, across a range of chromophore–environment interaction strengths, we provide strategies for the construction of machine learning models that greatly accelerate the calculation of multidimensional optical spectra from first principles.

Research Organization:
Univ. of California, Merced, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF)
Grant/Contract Number:
SC0020203
OSTI ID:
1803922
Journal Information:
Journal of Physical Chemistry Letters, Journal Name: Journal of Physical Chemistry Letters Journal Issue: 18 Vol. 11; ISSN 1948-7185
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English

References (105)

Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review journal September 2018
Atomistic Study of the Long-Lived Quantum Coherences in the Fenna-Matthews-Olson Complex journal February 2012
Two-Dimensional Electronic Spectroscopy Reveals Dynamics and Mechanisms of Solvent-Driven Inertial Relaxation in Polar BODIPY Dyes journal February 2018
Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units journal May 2011
Coherent wavepackets in the Fenna–Matthews–Olson complex are robust to excitonic-structure perturbations caused by mutagenesis journal January 2018
Quantum-chemical insights from deep tensor neural networks journal January 2017
The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach journal January 2018
Atom-centered symmetry functions for constructing high-dimensional neural network potentials journal February 2011
Operators in quantum machine learning: Response properties in chemical space journal February 2019
How van der Waals interactions determine the unique properties of water journal July 2016
Local protein solvation drives direct down-conversion in phycobiliprotein PC645 via incoherent vibronic transport journal March 2018
A Theory of Intensity Distribution in Band Systems journal December 1926
Neural Networks and the Bias/Variance Dilemma journal January 1992
How Proteins Trigger Excitation Energy Transfer in the FMO Complex of Green Sulfur Bacteria journal October 2006
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost text January 2017
Symmetry-Adapted Machine Learning for Tensorial Properties of Atomistic Systems. text January 2018
Symmetry-Adapted Machine Learning for Tensorial Properties of Atomistic Systems dataset January 2018
Machine Learning Molecular Dynamics for the Simulation of Infrared Spectra text January 2017
Using Gaussian Process Regression to Simulate the Vibrational Raman Spectra of Molecular Crystals text January 2019
Deep Learning Spectroscopy: Neural Networks for Molecular Excitation Spectra journal January 2019
Hybrid molecular dynamics-quantum mechanics simulations of solute spectral properties in the condensed phase: Evaluation of simulation parameters: Evaluation of Simulation Parameters for a Hybrid MD-QM Method journal March 2007
Calculation of pigment transition energies in the FMO protein: From simplicity to complexity and back journal October 2007
Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations journal November 2018
Machine learning of two-dimensional spectroscopic data journal April 2019
An implementation of artificial neural-network potentials for atomistic materials simulations: Performance for TiO2 journal March 2016
Molecular Chromophore–Catalyst Assemblies for Solar Fuel Applications journal August 2015
Quantum Chemical Modeling of the Photoinduced Activity of Multichromophoric Biosystems: Focus Review journal July 2019
Solvent Effects on Electronic Excitations of an Organic Chromophore journal March 2016
Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent journal April 2017
Transferable Dynamic Molecular Charge Assignment Using Deep Neural Networks journal July 2018
PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges journal April 2019
Machine Learning for Vibrational Spectroscopic Maps journal October 2019
Extending the Representation of Multistate Coupled Potential Energy Surfaces To Include Properties Operators Using Neural Networks: Application to the 1,2 1 A States of Ammonia journal November 2019
Machine-Learning Energy Gaps of Porphyrins with Molecular Graph Representations journal April 2018
Methylene Blue Exciton States Steer Nonradiative Relaxation: Ultrafast Spectroscopy of Methylene Blue Dimer journal January 2016
Convergence of Excitation Energies in Mixed Quantum and Classical Solvent: Comparison of Continuum and Point Charge Models journal November 2016
Influence of Electronic Polarization on the Spectral Density journal December 2019
Deep Learning for Optoelectronic Properties of Organic Semiconductors journal March 2020
Combining SchNet and SHARC: The SchNarc Machine Learning Approach for Excited-State Dynamics journal April 2020
Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes journal August 2016
The Interplay of Structure and Dynamics in the Raman Spectrum of Liquid Water over the Full Frequency and Temperature Range journal February 2018
Discovering a Transferable Charge Assignment Model Using Machine Learning journal July 2018
Deep Learning for Nonadiabatic Excited-State Dynamics journal November 2018
Multiresolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography journal July 2019
Hiding in the Crowd: Spectral Signatures of Overcoordinated Hydrogen-Bond Environments journal September 2019
Integrating Machine Learning with the Multilayer Energy-Based Fragment Method for Excited States of Large Systems journal November 2019
Coherent Two-Dimensional Optical Spectroscopy journal April 2008
Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein journal September 2012
Fluorescence and absorption of large anharmonic molecules - spectroscopy without eigenstates journal March 1985
Finding the Way to Solar Fuels with Dye-Sensitized Photoelectrosynthesis Cells journal September 2016
First-Principles Models for Biological Light-Harvesting: Phycobiliprotein Complexes from Cryptophyte Algae journal June 2017
A Quantum Chemical Interpretation of Two-Dimensional Electronic Spectroscopy of Light-Harvesting Complexes journal May 2017
Ultrafast Solvation Dynamics and Vibrational Coherences of Halogenated Boron-Dipyrromethene Derivatives Revealed through Two-Dimensional Electronic Spectroscopy journal October 2017
Polar Solvation Dynamics in the Femtosecond Evolution of Two-Dimensional Fourier Transform Spectra journal August 2002
The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules journal October 2013
Quantum Coherence Enabled Determination of the Energy Landscape in Light-Harvesting Complex II journal December 2009
Theory and Simulation of the Environmental Effects on FMO Electronic Transitions journal June 2011
Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems journal April 2007
Lessons from nature about solar light harvesting journal September 2011
In situ mapping of the energy flow through the entire photosynthetic apparatus journal May 2016
Chemical shifts in molecular solids by machine learning journal October 2018
A molecular movie of ultrafast singlet fission journal September 2019
Observation of dissipative chlorophyll-to-carotenoid energy transfer in light-harvesting complex II in membrane nanodiscs journal March 2020
Primary Charge Separation in the Photosystem II Reaction Center Revealed by a Global Analysis of the Two-dimensional Electronic Spectra journal September 2017
Highly Improved Solar Energy Harvesting for Fuel Production from CO2 by a Newly Designed Graphene Film Photocatalyst journal November 2018
Open quantum system parameters for light harvesting complexes from molecular dynamics journal January 2015
Machine learning exciton dynamics journal January 2016
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost journal January 2017
Machine learning molecular dynamics for the simulation of infrared spectra journal January 2017
The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics journal January 2018
Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory journal January 2018
The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach journal January 2018
Modeling multidimensional spectral lineshapes from first principles: application to water-solvated adenine journal January 2020
Accurate prediction of chemical shifts for aqueous protein structure on “Real World” data journal January 2020
Raman spectrum and polarizability of liquid water from deep neural networks journal January 2020
Two-dimensional Fourier transform electronic spectroscopy journal October 2001
Electronic spectra from TDDFT and machine learning in chemical space journal August 2015
Hierarchical modeling of molecular energies using a deep neural network journal June 2018
wACSF—Weighted atom-centered symmetry functions as descriptors in machine learning potentials journal June 2018
Atom-density representations for machine learning journal April 2019
Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches journal August 2019
Machine learning approach for describing vibrational solvatochromism journal May 2020
 -Helices direct excitation energy flow in the Fenna Matthews Olson protein journal October 2007
Molecular bases for the selection of the chromophore of animal rhodopsins journal November 2015
Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism journal March 2017
Accurate molecular polarizabilities with coupled cluster theory and machine learning journal February 2019
A neural network protocol for electronic excitations of N -methylacetamide journal May 2019
Machine learning of molecular electronic properties in chemical compound space journal September 2013
Using Gaussian process regression to simulate the vibrational Raman spectra of molecular crystals journal October 2019
Machine learning for the modeling of interfaces in energy storage and conversion materials journal July 2019
Principles of light harvesting from single photosynthetic complexes journal June 2015
Deep neural network for the dielectric response of insulators journal July 2020
High-dimensional neural-network potentials for multicomponent systems: Applications to zinc oxide journal April 2011
On representing chemical environments journal May 2013
Efficient and accurate machine-learning interpolation of atomic energies in compositions with many species journal July 2017
Gaussian Approximation Potentials: The Accuracy of Quantum Mechanics, without the Electrons journal April 2010
Symmetry-Adapted Machine Learning for Tensorial Properties of Atomistic Systems journal January 2018
Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics journal April 2018
Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces journal April 2007
Delocalized excitons in natural light-harvesting complexes journal August 2018
Capturing intensive and extensive DFT/TDDFT molecular properties with machine learning journal August 2018
M ULTIDIMENSIONAL F EMTOSECOND C ORRELATION S PECTROSCOPIES OF E LECTRONIC AND V IBRATIONAL E XCITATIONS journal October 2000
T WO -D IMENSIONAL F EMTOSECOND S PECTROSCOPY journal October 2003
How van der Waals interactions determine the unique properties of water dataset January 2015
How van der Waals interactions determine the unique properties of water dataset January 2015