Exploration of Reaction Pathways and Chemical Transformation Networks

Abstract

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.

arXiv comment48 pages, 4 figures

References in corpus (24)

• Escaping free-energy minima
• A nonequilibrium equality for free energy differences
• String Method for the Study of Rare Events
• Dynamics of Lennard-Jones clusters: A characterization of the activation-relaxation technique
• Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods
• Heuristics-Guided Exploration of Reaction Mechanisms
• Sampling molecular conformations and dynamics in a multi-user virtual reality framework
• Context-Driven Exploration of Complex Chemical Reaction Networks
• Error-Controlled Exploration of Chemical Reaction Networks with Gaussian Processes
• Semiempirical Molecular Orbital Models based on the Neglect of Diatomic Differential Overlap Approximation
• Reliable estimation of prediction uncertainty for physico-chemical property models
• Interactive Chemical Reactivity Exploration
• Mechanism Deduction from Noisy Chemical Reaction Networks
• Error Assessment of Computational Models in Chemistry
• Minimum Energy Paths and Transition States by Curve Optimization
• Comprehensive Analysis of the Neglect of Diatomic Differential Overlap Approximation
• Real-time Quantum Chemistry
• Steering Orbital Optimization out of Local Minima and Saddle Points Toward Lower Energy
• Statistical Analysis of Semiclassical Dispersion Corrections
• Real-time feedback from iterative electronic structure calculations
• Accelerating Wave Function Convergence in Interactive Quantum Chemical Reactivity Studies
• Molecular propensity as a driver for explorative reactivity studies
• Integrated Reaction Path Processing from Sampled Structure Sequences
• Mode-Tracking Based Stationary-Point Optimization

Cited by in corpus (35)

• Autonomous discovery in the chemical sciences part I: Progress
• Quantum computing enhanced computational catalysis
• The Exploration of Chemical Reaction Networks
• autoCAS: a program for fully automated multi-configurational calculations
• Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks
• Systematic Microsolvation Approach with a Cluster-Continuum Scheme and Conformational Sampling
• Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis
• Universal QM/MM Approaches for General Nanoscale Applications
• Expansive Quantum Mechanical Exploration of Chemical Reaction Paths
• Automated construction of quantum-classical hybrid models
• Self-Parametrizing System-Focused Atomistic Models
• Pathfinder -- Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-based Approach
• Blind search for complex chemical pathways using Harmonic Linear Discriminant Analysis
• Molecule-specific Uncertainty Quantification in Quantum Chemical Studies
• Enhancing automated reaction discovery with boxed molecular dynamics in energy space
• High-throughput ab initio reaction mechanism exploration in the cloud with automated multi-reference validation
• Navigating chemical reaction space with a steering wheel
• Automated Exploration of Reaction Network and Mechanism via Meta-dynamics Nanoreactor
• On the Predictive Power of Chemical Concepts
• Concentration-Flux-Steered Mechanism Exploration with an Organocatalysis Application
• SCINE -- Software for Chemical Interaction Networks
• Quantum chemical roots of machine-learning molecular similarity descriptors
• Finding reaction pathways with optimal atomic index mappings
• Uncertainty-aware First-principles Exploration of Chemical Reaction Networks
• Automated Microsolvation for Minimum Energy Path Construction in Solution
• The chemistry of AlF and CaF production in buffer gas sources
• Molecular relaxation by reverse diffusion with time step prediction
• Heron: Visualizing and Controlling Chemical Reaction Explorations and Networks
• Lifelong Machine Learning Potentials for Chemical Reaction Network Explorations
• Ultra-fast Spectroscopy for High-Throughput and Interactive Quantum Chemistry
• Initial estimate for minimum energy pathways and transition states using velocities in internal coordinates
• Heuristics and Uncertainty Quantification in Rational and Inverse Compound and Catalyst Design
• Locating Ab Initio Transition States via Approximate Geodesics on Machine Learned Potential Energy Surfaces
• Automated Exploration of Radical-Molecule Chemistry: The Case of Oxirane + CH in the ISM
• Solving intractable chemical problems by tensor decomposition