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  • Primer
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Automation and computer-assisted planning for chemical synthesis

Nature Reviews Methods Primers volume 1, Article number: 23 (2021) Cite this article

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Abstract

The molecules of today — the medicines that cure diseases, the agrochemicals that protect our crops, the materials that make life convenient — are becoming increasingly sophisticated thanks to advancements in chemical synthesis. As tools for synthesis improve, molecular architects can be bold and creative in the way they design and produce molecules. Several emerging tools at the interface of chemical synthesis and data science have come to the forefront in recent years, including algorithms for retrosynthesis and reaction prediction, and robotics for autonomous or high-throughput synthesis. This Primer covers recent additions to the toolbox of the data-savvy organic chemist. There is a new movement in retrosynthetic logic, predictive models of reactivity and chemistry automata, with considerable recent engagement from contributors in diverse fields. The promise of chemical synthesis in the information age is to improve the quality of the molecules of tomorrow through data-harnessing and automation. This Primer is written for organic chemists and data scientists looking to understand the software, hardware, data sets and tactics that are commonly used as well as the capabilities and limitations of the field. The Primer is split into three main components covering retrosynthetic logic, reaction prediction and automated synthesis. The former of these topics is about distilling the strategy of multistep synthesis to a logic that can be taught to a computer. The section on reaction prediction details modern tools and models for developing reaction conditions, catalysts and even new transformations based on information-rich data sets and statistical tools such as machine learning. Finally, we cover recent advances in the use of liquid handling robotics and autonomous systems that can physically perform experiments in the chemistry laboratory.

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Fig. 1: General tools underlying chemical synthesis with information theory.
Fig. 2: Retrosynthetic planners, reaction prediction and automated synthesis workflows.
Fig. 3: Results from retrosynthetic planning programs.
Fig. 4: Applications of retrosynthetic planning validated by laboratory efforts.
Fig. 5: Retrosynthetic planning, reaction prediction and automated synthesis platform directed by ASKCOS.
Fig. 6: Prediction of reaction enantioselectivities for chiral phosphoric acid-catalysed nucleophilic additions to imines94.
Fig. 7: Prediction of reaction yields for palladium-catalysed Buchwald–Hartwig aminations93.
Fig. 8: Probing reaction selectivity using high-throughput experimentation177.
Fig. 9: Reaction miniaturization and validation114.
Fig. 10: Organic synthesis using a modular automated robotic system144.

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Acknowledgements

A.G.D., R.S., M.A.H. and J.E.B. were supported by the National Science Foundation (NSF) under the Center for Computer Aided Synthesis (C-CAS) (CHE-1925607). M.A.H. is grateful for funding from the NSF graduate research fellowship program (DGE-1752814). Y.S. and T.C. were supported by the University of Michigan College of Pharmacy.

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Author notes

  1. These authors contributed equally: Yuning Shen, Julia E. Borowski, Melissa A. Hardy.

Authors and Affiliations

  1. Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA

    Yuning Shen & Tim Cernak

  2. Department of Chemistry, Princeton University, Princeton, NJ, USA

    Julia E. Borowski & Abigail G. Doyle

  3. Department of Chemistry, University of California, Berkeley, CA, USA

    Melissa A. Hardy & Richmond Sarpong

Authors
  1. Yuning Shen
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Contributions

Introduction (Y.S., J.E.B., M.A.H., R.S., A.G.D. and T.C.); Experimentation (Y.S., J.E.B., M.A.H., R.S., A.G.D. and T.C.); Results (Y.S., J.E.B., M.A.H., R.S., A.G.D. and T.C.); Applications (Y.S., J.E.B., M.A.H., R.S., A.G.D. and T.C.); Reproducibility and data deposition (Y.S., J.E.B., M.A.H., R.S., A.G.D. and T.C.); Limitations and optimizations (Y.S., J.E.B., M.A.H., R.S., A.G.D. and T.C.); Outlook (Y.S., J.E.B., M.A.H., R.S., A.G.D. and T.C.); Overview of the Primer (T.C.).

Corresponding authors

Correspondence to Richmond Sarpong, Abigail G. Doyle or Tim Cernak.

Ethics declarations

Competing interests

T.C. has received mosquito robotics from SPT Labtech and Merck & Co., Inc. T.C. and R.S. receive research support from MilliporeSigma, the company that owns the retrosynthetic software SYNTHIA. All other authors declare no competing interests.

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Peer review information

Nature Reviews Methods Primers thanks O. Ravitz, M. Segler, S. Trice and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Related links

AiZynthFinder: https://github.com/MolecularAI/aizynthfinder

ASKCOS: https://github.com/connorcoley/ASKCOS

Chemical.AI: https://Chemical.AI

IBM RXN for Chemistry: https://rxn.res.ibm.com/

ICSYNTH: https://www.deepmatter.io/products/icsynth/

Iktos spaya.ai: https://beta.spaya.ai/

RDKit: https://www.rdkit.org/

Reaxys: https://www.elsevier.com/solutions/reaxys/features-and-capabilities/synthesis-planner

SciFindern: https://www.cas.org/products/scifinder

SciKit-learn: https://scikit-learn.org/stable/

SYNTHIA: https://www.sigmaaldrich.com/chemistry/chemical-synthesis/synthesis-software.html

Glossary

Linear free energy relationships

Linear relationships between the free energy of activation or free energy change of a reaction induced by a substituent of a molecule and a parameter that describes the electronic or steric properties of that substituent. Linear free energy relationships are a subset of structure–function (or structure–activity) relationships.

Simplified molecular input line entry system

(SMILES). A string notation to represent chemical structures that can be generated from a two-dimensional or three-dimensional graph notation. Notably, the same molecule can sometimes be represented by multiple different SMILES codes depending on the drawing that was input. These notations are human understandable and variable in length.

International Chemical Identifier

(InChI). A fixed-length, 27-character line notation that is designed to allow easy searches of chemical compounds. These are derived from the full length that encodes layers of information about a given molecular structure including connectivity, charge, stereochemistry and atomic isotopes. These notations are not human understandable.

SMILES arbitrary target specification

(SMARTS). An extension of the simplified molecular input line entry system (SMILES) notations that allows for the specification of generic atoms and bonds to allow for substructures for searching databases.

Reaction rules

Descriptions of chemical transforms that can be applied in a retrosynthetic module. These encode the substructures of the products and starting materials for a given synthetic step, and also include additional layers to express the scope and limitations of when the transform can be applied.

Reaction templates

Descriptions of chemical transforms that include the substructures of the reactants and products and highlight structural changes. These contain somewhat less context than a reaction rule and often require additional strategy to select which of the numerous templates to apply in a retrosynthetic module to minimize computational cost.

Sequence-to-sequence

A family of machine learning algorithms developed for natural language processing (language translation, image captioning and so on) that relies on recurrent neural networks to transform one sequence into another sequence.

Transformer

An algorithm developed for natural language processing (language translation, image captioning and so on). This algorithm does not rely on recurrent neural networks and can process data in any order, thus allowing for reduced training times .

Monte Carlo tree search

An algorithm for navigating search trees in which search steps are selected randomly, without branching, until a solution has been found or a maximum depth is reached. Algorithms of this type have emerged as strategic in applications of sequential decision problems without clear heuristics.

Quantitative structure–activity relationship

A statistical modelling method used to relate molecular structure to biological and physico-chemical properties and predict these properties in new molecules.

Density functional theory

(DFT). A computational method for modelling the electronic structure of atoms and molecules using quantum mechanics. In synthetic chemistry, density functional theory is used to compute and study molecular structures and their corresponding energies that cannot be obtained through experimental methods.

Molecular mechanics

A computational method for modelling molecular structure using classical mechanics. Bonds are treated as springs from which a potential energy can be determined. Molecular mechanics is a less computationally expensive method relative to density functional theory.

HOMO–LUMO energies

(Highest-occupied molecular orbital–lowest-unoccupied molecular orbital energies). These values correspond to the energetics of the molecular orbitals that are most involved in bond-making and bond-breaking processes, commonly referred to as the frontier molecular orbitals.

Sterimol parameters

Three steric parameters — B1, B5 and L — for molecular substituents determined from three-dimensional structures. B1 and B5 represent the minimum and maximum widths, respectively, of the molecule perpendicular to the primary bond axis. L is the total length of the substituent measured along the primary bond axis.

Buried volume

A steric parameter for ligands in transition metal complexes. The volume of a ligand, bonded to a metal at a fixed distance, enclosed by a sphere of a defined radius r. Provided as a percentage, representing the percentage of the sphere that is filled by a single bound ligand.

Conformers

(Also known as conformational isomers). Structures of a molecule that differ by the rotation of groups about one or more single bonds in the molecule. Conformers can interconvert without making or breaking bonds and will have different relative energies based on the presence of attractive or repulsive interactions.

High-throughput experimentation

(HTE). A technique used for screening chemical experiments, typically in a miniaturized format. Common formats for HTE include 24-well, 96-well and 384-well arrays, whereas ultraHTE refers to arrays of 1,536 experiments or more.

k-fold cross-validation

A method for evaluating model performance on limited data. The data are split into k groups; one group is a test set, whereas the other is used as the training set. This is repeated k times to train and test the several groupings of the data.

R 2 value

(Also known as the coefficient of determination). A measure of how well a model fits the data when comparing the measured values against predicted values for the training set. An R2 value of 0.8 means that the model can account for 80% of the observed variance in the data.

Acoustic droplet ejection

A technology that uses precise ultrasound waves to move or transfer nanolitre volumes of solutions. Acoustic droplet ejection transfers the droplets from the source plate into an inverted receiving plate above the source plate.

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Shen, Y., Borowski, J.E., Hardy, M.A. et al. Automation and computer-assisted planning for chemical synthesis. Nat Rev Methods Primers 1, 23 (2021). https://doi.org/10.1038/s43586-021-00022-5

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