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Title: Making machine learning a useful tool in the accelerated discovery of transition metal complexes

Journal Article · · Wiley Interdisciplinary Reviews: Computational Molecular Science
DOI:https://doi.org/10.1002/wcms.1439· OSTI ID:1546100
ORCiD logo [1]
  1. Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts

Abstract As machine learning (ML) has matured, it has opened a new frontier in theoretical and computational chemistry by offering the promise of simultaneous paradigm shifts in accuracy and efficiency. Nowhere is this advance more needed, but also more challenging to achieve, than in the discovery of open‐shell transition metal complexes. Here, localized d or f electrons exhibit variable bonding that is challenging to capture even with the most computationally demanding methods. Thus, despite great promise, clear obstacles remain in constructing ML models that can supplement or even replace explicit electronic structure calculations. In this article, I outline the recent advances in building ML models in transition metal chemistry, including the ability to approach sub‐kcal/mol accuracy on a range of properties with tailored representations, to discover and enumerate complexes in large chemical spaces, and to reveal opportunities for design through analysis of feature importance. I discuss unique considerations that have been essential to enabling ML in open‐shell transition metal chemistry, including (a) the relationship of data set size/diversity, model complexity, and representation choice, (b) the importance of quantitative assessments of both theory and model domain of applicability, and (c) the need to enable autonomous generation of reliable, large data sets both for ML model training and in active learning or discovery contexts. Finally, I summarize the next steps toward making ML a mainstream tool in the accelerated discovery of transition metal complexes. This article is categorized under: Electronic Structure Theory > Density Functional Theory Software > Molecular Modeling Computer and Information Science > Chemoinformatics

Sponsoring Organization:
USDOE
OSTI ID:
1546100
Journal Information:
Wiley Interdisciplinary Reviews: Computational Molecular Science, Journal Name: Wiley Interdisciplinary Reviews: Computational Molecular Science Vol. 10 Journal Issue: 1; ISSN 1759-0876
Publisher:
Wiley Blackwell (John Wiley & Sons)Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 29 works
Citation information provided by
Web of Science

References (143)

Do CCSD and approximate CCSD-F12 variants converge to the same basis set limits? The case of atomization energies journal October 2018
UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations journal December 1992
Representing potential energy surfaces by high-dimensional neural network potentials journal April 2014
The Shrinking World of Innocent Ligands: Conventionaland Non-Conventional Redox-Active Ligands journal January 2012
Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation journal January 2008
Density functional theory embedding for correlated wavefunctions: Improved methods for open-shell systems and transition metal complexes journal December 2012
Nudged elastic band calculations accelerated with Gaussian process regression journal October 2017
Porphyrin-Sensitized Solar Cells with Cobalt (II/III)-Based Redox Electrolyte Exceed 12 Percent Efficiency journal November 2011
Machine learning for heterogeneous catalyst design and discovery journal May 2018
Auxiliary basis sets to approximate Coulomb potentials journal June 1995
ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules journal December 2017
Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space journal June 2015
Prediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error journal October 2017
Less is more: Sampling chemical space with active learning journal June 2018
Machine learning in catalysis journal April 2018
Predicting electronic structure properties of transition metal complexes with neural networks journal January 2017
Perspective: Treating electron over-delocalization with the DFT+U method journal June 2015
Machine-Learning-Augmented Chemisorption Model for CO 2 Electroreduction Catalyst Screening journal August 2015
Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB) journal May 2014
SchNet – A deep learning architecture for molecules and materials journal June 2018
molSimplify: A toolkit for automating discovery in inorganic chemistry journal July 2016
Fast and Accurate Uncertainty Estimation in Chemical Machine Learning journal November 2018
Computational studies of the O2-evolving complex of photosystem II and biomimetic oxomanganese complexes journal February 2008
Unifying Exchange Sensitivity in Transition-Metal Spin-State Ordering and Catalysis through Bond Valence Metrics journal October 2017
Harnessing Organic Ligand Libraries for First-Principles Inorganic Discovery: Indium Phosphide Quantum Dot Precursor Design Strategies journal April 2017
Accelerating Chemical Discovery with Machine Learning: Simulated Evolution of Spin Crossover Complexes with an Artificial Neural Network journal February 2018
Materials Synthesis Insights from Scientific Literature via Text Extraction and Machine Learning journal October 2017
Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules journal January 2018
Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations journal February 2018
A simple DFT-based diagnostic for nondynamical correlation journal December 2012
Perspective: Multireference coupled cluster theories of dynamical electron correlation journal July 2018
Discovering a Transferable Charge Assignment Model Using Machine Learning journal July 2018
Electrocatalytic Hydrogen Evolution under Acidic Aqueous Conditions and Mechanistic Studies of a Highly Stable Molecular Catalyst journal July 2016
Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning journal January 2012
Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals journal April 2017
Communication: Evaluating non-empirical double hybrid functionals for spin-state energetics in transition-metal complexes journal January 2018
Resolving Transition Metal Chemical Space: Feature Selection for Machine Learning and Structure–Property Relationships journal November 2017
Quantum Machine Learning in Chemical Compound Space journal March 2018
The Elements of Statistical Learning book January 2009
The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics journal January 2018
Catalytic Functionalization of C(sp 2 )H and C(sp 3 )H Bonds by Using Bidentate Directing Groups journal September 2013
Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction journal July 2017
When Hartree-Fock exchange admixture lowers DFT-predicted barrier heights: Natural bond orbital analyses and implications for catalysis journal June 2018
Understanding and Breaking Scaling Relations in Single-Site Catalysis: Methane to Methanol Conversion by Fe IV ═O journal January 2018
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density journal January 1988
Learning from Failure: Predicting Electronic Structure Calculation Outcomes with Machine Learning Models journal March 2019
Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach journal April 2015
Phosphorescent Nanocluster Light-Emitting Diodes journal November 2015
Blue-Light Emission of Cu(I) Complexes and Singlet Harvesting journal September 2011
Multi-fidelity machine learning models for accurate bandgap predictions of solids journal March 2017
Thermally Activated Delayed Fluorescence (TADF) and Enhancing Photoluminescence Quantum Yields of [Cu I (diimine)(diphosphine)] + Complexes—Photophysical, Structural, and Computational Studies journal July 2014
Comparison of density functionals for differences between the high- (T2g5) and low- (A1g1) spin states of iron(II) compounds. IV. Results for the ferrous complexes [Fe(L)(‘NHS4’)] journal June 2005
Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces journal April 2007
DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB) journal March 2011
Accelerating the search for global minima on potential energy surfaces using machine learning journal October 2016
Hierarchical visualization of materials space with graph convolutional neural networks journal November 2018
Assessment of density functional theory for iron(II) molecules across the spin-crossover transition journal September 2012
A Survey on Transfer Learning journal October 2010
Brightly Blue and Green Emitting Cu(I) Dimers for Singlet Harvesting in OLEDs journal May 2013
Machine learning molecular dynamics for the simulation of infrared spectra journal January 2017
Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields journal November 1994
Unsupervised machine learning in atomistic simulations, between predictions and understanding journal April 2019
Machine learning for molecular and materials science journal July 2018
Gaussian process regression for geometry optimization journal March 2018
SBH10: A Benchmark Database of Barrier Heights on Transition Metal Surfaces journal September 2017
Density Functional Theory in Transition-Metal Chemistry: A Self-Consistent Hubbard U Approach journal September 2006
Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis journal February 2013
Solar Synthesis: Prospects in Visible Light Photocatalysis journal February 2014
Machine learning meets volcano plots: computational discovery of cross-coupling catalysts journal January 2018
Neural Networks in Chemistry journal April 1993
Tensor hypercontraction density fitting. I. Quartic scaling second- and third-order Møller-Plesset perturbation theory journal July 2012
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost journal January 2017
Low-order scaling local electron correlation methods. I. Linear scaling local MP2 journal October 1999
How Much Can Density Functional Approximations (DFA) Fail? The Extreme Case of the FeO 4 Species journal March 2016
Visible Light Photoredox Catalysis with Transition Metal Complexes: Applications in Organic Synthesis journal March 2013
The atomic simulation environment—a Python library for working with atoms journal June 2017
Designing in the Face of Uncertainty: Exploiting Electronic Structure and Machine Learning Models for Discovery in Inorganic Chemistry journal March 2019
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs journal January 2006
Density functional theory for transition metals and transition metal chemistry journal January 2009
Computational Discovery of Hydrogen Bond Design Rules for Electrochemical Ion Separation journal August 2016
Linear scaling computation of the Fock matrix journal April 1997
Ligand-Field-Dependent Behavior of Meta-GGA Exchange in Transition-Metal Complex Spin-State Ordering journal October 2016
Reduced scaling CASPT2 using supporting subspaces and tensor hyper-contraction journal July 2018
Triplet Harvesting with 100% Efficiency by Way of Thermally Activated Delayed Fluorescence in Charge Transfer OLED Emitters journal May 2013
Synthesis, Structure, and Characterization of Dinuclear Copper(I) Halide Complexes with P^N Ligands Featuring Exciting Photoluminescence Properties journal October 2012
Calculation of Ligand Dissociation Energies in Large Transition-Metal Complexes journal March 2018
Addressing uncertainty in atomistic machine learning journal January 2017
A Density Functional Tight Binding Layer for Deep Learning of Chemical Hamiltonians journal October 2018
Towards quantifying the role of exact exchange in predictions of transition metal complex properties journal July 2015
Machine learning in materials informatics: recent applications and prospects journal December 2017
The ligand field molecular mechanics model and the stereoelectronic effects of d and s electrons journal February 2001
Transferability in Machine Learning for Electronic Structure via the Molecular Orbital Basis journal July 2018
Ironing out the photochemical and spin-crossover behavior of Fe(II) coordination compounds with computational chemistry journal April 2017
Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials
  • Eichkorn, Karin; Weigend, Florian; Treutler, Oliver
  • Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 97, Issue 1-4 https://doi.org/10.1007/s002140050244
journal October 1997
Predicting the Band Gaps of Inorganic Solids by Machine Learning journal March 2018
Representations in neural network based empirical potentials journal July 2017
Perspective: Machine learning potentials for atomistic simulations journal November 2016
Development and testing of a general amber force field journal January 2004
Multireference Character for 4d Transition Metal-Containing Molecules journal November 2015
Ab Initio Reactive Computer Aided Molecular Design journal March 2017
Automated Construction of Molecular Active Spaces from Atomic Valence Orbitals journal August 2017
Towards operando computational modeling in heterogeneous catalysis journal January 2018
Computational Ligand Descriptors for Catalyst Design journal October 2018
Comparing molecules and solids across structural and alchemical space journal January 2016
The AFLOW standard for high-throughput materials science calculations journal October 2015
Feed-forward neural networks in chemistry: mathematical systems for classification and pattern recognition journal December 1993
Density‐functional thermochemistry. III. The role of exact exchange journal April 1993
Accelerating materials property predictions using machine learning journal September 2013
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids journal January 1996
Open Babel: An open chemical toolbox journal October 2011
Spin-state diversity in a series of Co( ii ) PNP pincer bromide complexes journal January 2016
Embedded Correlated Wavefunction Schemes: Theory and Applications journal May 2014
The performance of nonhybrid density functionals for calculating the structures and spin states of Fe(II) and Fe(III) complexes journal November 2004
High-Dimensional Neural Network Potentials for Organic Reactions and an Improved Training Algorithm journal April 2015
Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics journal August 2009
Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations journal October 2017
Multiconfiguration Pair-Density Functional Theory Predicts Spin-State Ordering in Iron Complexes with the Same Accuracy as Complete Active Space Second-Order Perturbation Theory at a Significantly Reduced Computational Cost journal April 2017
MN15: A Kohn–Sham global-hybrid exchange–correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions journal January 2016
Strategies and Software for Machine Learning Accelerated Discovery in Transition Metal Chemistry journal September 2018
Reduction of Systematic Uncertainty in DFT Redox Potentials of Transition-Metal Complexes journal March 2012
Tuning the Electronic Structure of Fe(II) Polypyridines via Donor Atom and Ligand Scaffold Modifications: A Computational Study journal August 2015
Benchmarking Semiempirical Methods for Thermochemistry, Kinetics, and Noncovalent Interactions: OMx Methods Are Almost As Accurate and Robust As DFT-GGA Methods for Organic Molecules journal August 2011
Assessment and Validation of Machine Learning Methods for Predicting Molecular Atomization Energies journal July 2013
Density functional theory for modelling large molecular adsorbate–surface interactions: a mini-review and worked example journal November 2016
AFLOW: An automatic framework for high-throughput materials discovery journal June 2012
Multiconfiguration Pair-Density Functional Theory for Iron Porphyrin with CAS, RAS, and DMRG Active Spaces journal February 2019
Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements journal September 2007
Application of Semiempirical Methods to Transition Metal Complexes: Fast Results but Hard-to-Predict Accuracy journal May 2018
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules journal February 1988
The promise of artificial intelligence in chemical engineering: Is it here, finally? journal December 2018
Ruthenium(II)-Catalyzed C–H Bond Activation and Functionalization journal August 2012
Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities journal October 2018
Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation journal March 2009
A Shape Index from Molecular Graphs journal January 1985
Communication: Understanding molecular representations in machine learning: The role of uniqueness and target similarity journal October 2016
Spin State Energetics in First-Row Transition Metal Complexes: Contribution of (3s3p) Correlation and Its Description by Second-Order Perturbation Theory journal January 2017
Automated Selection of Active Orbital Spaces journal March 2016
Combining Linear-Scaling DFT with Subsystem DFT in Born–Oppenheimer and Ehrenfest Molecular Dynamics Simulations: From Molecules to a Virus in Solution journal June 2016
Local treatment of electron correlation in coupled cluster theory journal April 1996
A general-purpose machine learning framework for predicting properties of inorganic materials journal August 2016
Quantum chemistry structures and properties of 134 kilo molecules journal August 2014
Bridging the Homogeneous-Heterogeneous Divide: Modeling Spin for Reactivity in Single Atom Catalysis journal April 2019
Random Forests journal January 2001

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