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RESEARCH PAPER · Nature Reviews Methods Primers · 2021

Automation and computer-assisted planning for chemical synthesis

Yuning Shen, Julia E. Borowski, Melissa A. Hardy, Richmond Sarpong, Abigail G. Doyle, Tim Cernak

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Automation and computer-assisted planning for chemical synthesisOriginalPredicting Reaction Yields via Supervised Learning187Ultrahigh-Throughput Experimentation for Information-Rich Chemical Synthesis110Combining generative artificial intelligence and on-chip synthesis for de novo drug design187A general reactivity map for predicting outcomes in palladium-catalyzed cross-coupling0FAIR and Open Data in Science: The Opportunity for IUPAC12Masthead - Full issue pdf0Towards Data‐Driven Design of Asymmetric Hydrogenation of Olefins: Database and Hierarchical Learning78Towards Data‐Driven Design of Asymmetric Hydrogenation of Olefins: Database and Hierarchical Learning6Site-Selective Cross-Coupling of Polyhalogenated Arenes and Heteroarenes with Identical Halogen Groups137A reactivity map for oxidative addition enables quantitative predictions for multiple catalytic reaction classes0Highly accurate prediction of reaction performance and enantioselectivity with a uniform machine learning protocol0Deep learning in retrosynthesis planning: datasets, models and tools99The Formal Cross‐Coupling of Amines and Carboxylic Acids to Form sp 3 –sp 3 Carbon–Carbon Bonds48The Formal Cross‐Coupling of Amines and Carboxylic Acids to Form sp3–sp3 Carbon–Carbon Bonds7Molecular size and molecular structure: Discriminating their changes upon chemical reactions in terms of information entropy18The roles of computer-aided drug synthesis in drug development29Strategic elements in computer-assisted retrosynthesis: A case study of the pupukeanane natural products12A broadly applicable quantitative relative reactivity model for nucleophilic aromatic substitution (S N Ar) using simple descriptors43A reactivity model for oxidative addition to palladium enables quantitative predictions for catalytic cross-coupling reactions63Accelerating manufacturing for biomass conversion via integrated process and bench digitalization: a perspective29Machine learning for design principles for single atom catalysts towards electrochemical reactions116Modern machine learning for tackling inverse problems in chemistry: molecular design to realization50Predicting reaction conditions from limited data through active transfer learning78The way to AI-controlled synthesis: how far do we need to go?13Third-harmonic Mie scattering from semiconductor nanohelices70Small molecules and their impact in drug discovery: A perspective on the occasion of the 125th anniversary of the Bayer Chemical Research Laboratory198ARTIFICIAL INTELLIGENCE IN PHARMACY DRUG DESIGN9Digitizing Chemical Synthesis in 3D Printed Reactionware6Digitizing Chemical Synthesis in 3D Printed Reactionware33The case for data science in experimental chemistry: examples and recommendations83Quantum Chemical Calculations to Trace Back Reaction Paths for the Prediction of Reactants41GraphRXN: A Novel Representation for Reaction Prediction0On-the-Fly Mass Spectrometry in Digital Microfluidics Enabled by a Microspray Hole: Toward Multidimensional Reaction Monitoring in Automated Synthesis Platforms49Network search algorithms and scoring functions for advanced‐level computerized synthesis planning18Leveraging Regio- and Stereoselective C(sp 3 )–H Functionalization of Silyl Ethers to Train a Logistic Regression Classification Model for Predicting Site-Selectivity Bias33Probing the properties of molecules and complex materials using machine learning5Chemistry-informed molecular graph as reaction descriptor for machine-learned retrosynthesis planning52Enabling Technologies in Carbohydrate Chemistry: Automated Glycan Assembly, Flow Chemistry and Data Science28AI-assisted reaction impurity prediction and inverse structure elucidation1Merging enzymatic and synthetic chemistry with computational synthesis planning81Autonomous Drug Design with Multi-Armed Bandits7Experimental and Computational Approaches to Sulfonated Poly(arylene ether sulfone) Synthesis Using Different Halogen Atoms at the Reactive Site0Digital advancements in smart materials design and multifunctional coating manufacturing46A comprehensive machine learning strategy for designing high-performance photoanode catalysts21A field guide to flow chemistry for synthetic organic chemists393Amenamevir by Ugi-4CR12Drug discovery: Standing on the shoulders of giants0Model-based evaluation and data requirements for parallel kinetic experimentation and data-driven reaction identification and optimization13On the use of real-world datasets for reaction yield prediction141Parallel multi-droplet platform for reaction kinetics and optimization23Retrosynthesis from transforms to predictive sustainable chemistry and nanotechnology: a brief tutorial review19Synthesize in a Smart Way: A Brief Introduction to Intelligence and Automation in Organic Synthesis1The future of metal–organic frameworks and covalent organic frameworks: rational synthesis and customized applications35A Review on Artificial Intelligence Enabled Design, Synthesis, and Process Optimization of Chemical Products for Industry 4.076Knowledge-integrated machine learning for materials: lessons from gameplaying and robotics137Porous Molecular Materials1Toward Ab Initio Reaction Discovery Using the Artificial Force Induced Reaction Method26Exploring Spectrum‐based Molecular Descriptors for Reaction Performance Prediction5Genetic Algorithms for the Discovery of Homogeneous Catalysts14A Brief Introduction to Chemical Reaction Optimization437A neural network model informs the total synthesis of clovane sesquiterpenoids33Artificial intelligence in molecular de novo design: Integration with experiment23Retention time prediction for chromatographic enantioseparation by quantile geometry-enhanced graph neural network78It Is Not All about the Ligands: Exploring the Hidden Potentials of tBu3P through Its Oxidative Addition Complex as the Precatalyst17A miniaturized toolkit for medicinal chemists0Miniaturization of popular reactions from the medicinal chemists’ toolbox for ultrahigh-throughput experimentation42Machine Learning Methods for Small Data Challenges in Molecular Science499Unbiasing Retrosynthesis Language Models with Disconnection Prompts39Designing Chemical Reaction Arrays Using Phactor and ChatGPT39A deep learning framework for accurate reaction prediction and its application on high-throughput experimentation data46Structural design of organic battery electrode materials: from DFT to artificial intelligence42Accelerating Scientific Discovery With AI-Aided Automation0Development of high‐throughput wet‐chemical synthesis techniques for material research38Computer‐aided evaluation and exploration of chemical spaces constrained by reaction pathways14Advances in AI-Driven Retention Prediction for Different Chromatographic Techniques: Unraveling the Complexity25Complex molecule synthesis by electrocatalytic decarboxylative cross-coupling85Natural Product Synthesis: The Endless Quest for Unreachable Perfection18Exploration and Insights on Topology Adjustment of Giant Heterometallic Cages Featuring Inorganic Skeletons Assisted by Machine Learning32Autonomous closed-loop mechanistic investigation of molecular electrochemistry via automation7PolyID: Artificial Intelligence for Discovering Performance-Advantaged and Sustainable Polymers56Organopalladium Catalysis as a Proving Ground for Data-Rich Approaches to Reaction Development and Quantitative Predictions8Enabling late-stage drug diversification by high-throughput experimentation with geometric deep learning89Intelligent design and synthesis of energy catalytic materials25Quantitative Structure–Reactivity Relationships for Synthesis Planning: The Benzhydrylium Case15Autonomous Synthesis and Self-optimizing Reactors1Part III: Data Intelligence and Industrial Applications0Design of new dipeptide inhibitors against SARS-CoV 3CLpro: 3D-QSAR, molecular docking, MD simulation, ADMET studies and retrosynthesis strategy10Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products67Emergent Entanglement in Evolution of Biological Networks2Harnessing GPT-3.5 for text parsing in solid-state synthesis – case study of ternary chalcogenides26Monitoring and Mass Trapping of Fruit Flies (Diptera: Tephritidae) in the Americas6Exploring the combinatorial explosion of amine–acid reaction space via graph editing17Evolving drug discovery using AI, automation, and ASMS through an integrated D-preMTA-MTA strategy for target-focused library exploration2Surface energy prediction and Winterbottom morphology evolution analysis in Winterbottom construction on various crystal orientations using machine learning4A Semi‐Automated, High‐Throughput Approach for the Synthesis and Identification of Highly Photo‐Cytotoxic Iridium Complexes30A Semi‐Automated, High‐Throughput Approach for the Synthesis and Identification of Highly Photo‐Cytotoxic Iridium Complexes4Baldwin and Whitehead’s Manzamine Alkaloids Biosynthesis Hypothesis Involves a Finely Tuned Reactivity of Acrolein: Automated Extraction of Reactivity Patterns from LC-MS2 Data2Enhancing Nanocrystal Synthesis: A Comparative Study of Online Artificial Intelligence Optimization and Offline High-Throughput Experimentation in Chemical Material Discovery11RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries7Autonomous closed-loop mechanistic investigation of molecular electrochemistry via automation64Toward Making Polymer Chemistry Autonomous24Deep reinforcement learning in chemistry: A review26Computational Prediction of Spiropyrazoline Derivatives as Potential Acetylcholinesterase Inhibitors for Alzheimer’s Disease Treatment2Foundations of Generative AI14Vertebral Column Pathology Diagnosis Using Ensemble Strategies Based on Supervised Machine Learning Techniques3Relevance and Potential Applications of C2‐Carboxylated 1,3‐Azoles1Computer‐Aided Synthesis Planning (CASP) and Machine Learning: Optimizing Chemical Reaction Conditions15Printed polymer platform empowering machine-assisted chemical synthesis in stacked droplets11Pyrrole: An Essential Framework in the Development of Therapeutic Agents and Insightful Analysis of Structure‐Active Relationships16Coupling digital microfluidics with mass spectrometry0Computer-Aided Retrosynthesis for Greener and Optimal Total Synthesis of a Helicase-Primase Inhibitor Active Pharmaceutical Ingredient20Generative Design and Experimental Validation of Non-Fullerene Acceptors for Photovoltaics8Machine learning-guided strategies for reaction conditions design and optimization49Prediction of organic sulfur solubility in mixed solvent using feature-based transfer learning and a hybrid Henry's law constant calculation method1Impact of C–H Cross-Coupling Reactions in the One-Step Retrosynthesis of Drug Molecules9molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction11Trends of Artificial Intelligence (AI) Use in Drug Targets, Discovery and Development: Current Status and Future Perspectives48Machine learning in advancing anode materials for Lithium-Ion batteries – A review17Rapid Exploration of Chemical Space by High-Throughput Desorption Electrospray Ionization Mass Spectrometry34Reaction blueprints and logical control flow for parallelized chiral synthesis in the Chemputer14Artificial Intelligence-Driven Development of Nickel-Catalyzed Enantioselective Cross-Coupling Reactions25Computational methods for asymmetric catalysis14A review of large language models and autonomous agents in chemistry269Chemoenzymatic Synthesis Planning Guided by Reaction Type Score5Intelligent Experiment Robotic Systems Design for Material Preparation and Detection2Modulating the Potency of BRD4 PROTACs at the Systems Level with Amine-Acid Coupling Reactions11Accelerating climate technologies through the science of scale-up4Total synthesis of 25 picrotoxanes by virtual library selection19Artificial intelligence in drug development498Direct-To-Biology Chemistry2Simple User‐Friendly Reaction Format16Predicting and Explaining Yields with Machine Learning for Carboxylated Azoles and Beyond6Parametrization of κ 2 - N , O -Oxazoline Preligands for Enantioselective Cobaltaelectro-Catalyzed C–H Activations20Design and optimization of a shared synthetic route for multiple active pharmaceutical ingredients through combined computer aided retrosynthesis and flow chemistry11Design, optimization and performance Evaluation of a fully automatic electrochemical disc electrode polishing robot0Carbohydrate Synthesis is Entering the Data‐Driven Digital Era3Electron-Informed Coarse-Graining Molecular Representation Learning for Real-World Molecular Physics0DeepSyn: Operable Chemical Retrosynthetic Design with the DeepSeek R1 Model4Invasive Species Management Through the Lens of Chemistry1One-Pot Multisubstrate Screening for Asymmetric Catalysis Enabled by 19F NMR-Based Simultaneous Chiral Analysis12Exploring New Reactions with an Accessible High-throughput Screening (Open-HTS) Chemical Robotic System2Regulating strategies of localized alkaline microenvironment in various electrocatalytic applications2Artificial Intelligence in Chemistry: A Transformative Review1Large language models to accelerate organic chemistry synthesis48Material intelligence by the convergence of artificial intelligence and robotic platforms16Semi‐Automated Pipeline for Transition State Search of Molecular Photoswitches1Accelerated Discovery of Energy Transfer-Catalyzed Dearomative Cycloadditions through a Data-Driven Three-Layer Screening Strategy25$\texttt {DiffER}$: categorical diffusion ensembles for single-step chemical retrosynthesis0Machine Learning Guided Assembly of a Nested Gd 20 @Gd 32 @Ni 36 Cluster via Urea Controlled Carbonate Release7Machine Learning Guided Assembly of a Nested Gd 20 @Gd 32 @Ni 36 Cluster via Urea Controlled Carbonate Release0

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