1
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Schnitzer T, Schnurr M, Zahrt AF, Sakhaee N, Denmark SE, Wennemers H. Machine Learning to Develop Peptide Catalysts-Successes, Limitations, and Opportunities. ACS CENTRAL SCIENCE 2024; 10:367-373. [PMID: 38435528 PMCID: PMC10906243 DOI: 10.1021/acscentsci.3c01284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 03/05/2024]
Abstract
Peptides have been established as modular catalysts for various transformations. Still, the vast number of potential amino acid building blocks renders the identification of peptides with desired catalytic activity challenging. Here, we develop a machine-learning workflow for the optimization of peptide catalysts. First-in a hypothetical competition-we challenged our workflow to identify peptide catalysts for the conjugate addition reaction of aldehydes to nitroolefins and compared the performance of the predicted structures with those optimized in our laboratory. On the basis of the positive results, we established a universal training set (UTS) containing 161 catalysts to sample an in silico library of ∼30,000 tripeptide members. Finally, we challenged our machine learning strategy to identify a member of the library as a stereoselective catalyst for an annulation reaction that has not been catalyzed by a peptide thus far. We conclude with a comparison of data-driven versus expert-knowledge-guided peptide catalyst optimization.
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Affiliation(s)
- Tobias Schnitzer
- Laboratory
of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Martin Schnurr
- Laboratory
of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Andrew F. Zahrt
- Roger
Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Nader Sakhaee
- Roger
Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott E. Denmark
- Roger
Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Helma Wennemers
- Laboratory
of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
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2
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Aucar JJ, Stroppa A, Aucar GA. A Relationship between the Molecular Parity-Violation Energy and the Electronic Chirality Measure. J Phys Chem Lett 2024; 15:234-240. [PMID: 38158620 DOI: 10.1021/acs.jpclett.3c03038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
When the weak forces producing parity-violating effects are taken into account, there is a tiny energy difference between the total electronic energies of two enantiomers (ΔEPV), which might be the key to understanding the evolution of the biological homochirality. We focus on the electronic chirality measure (ECM), a powerful descriptor based on the electronic charge density, for quantifying the chirality degree of a molecule, in a representative set of chiral molecules, together with their EPV energies. Our results show a novel, strong, and positive correlation between ΔEPV and ECM, supporting a subtle interplay between the weak forces acting within the nuclei of a given molecule and its chirality. These findings suggest that experimental investigations for molecular parity violation detection should consider molecules with ECM values as large as possible and may support that a chiral signature is imprinted on life by fundamental physics via the parity-violating weak interactions.
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Affiliation(s)
- Juan J Aucar
- Physics Department, Natural and Exact Science Faculty, National Northeastern University of Argentina, Avda Libertad, W3404AAS 5460, Corrientes, Argentina
- Institute for Modelling and Innovative Technology, IMIT (CONICET-UNNE), Avda Libertad, W3404AAS 5460, Corrientes, Argentina
| | - Alessandro Stroppa
- CNR-SPIN, c/o Dip.to di Scienze Fisiche e Chimiche 67100, Coppito (AQ), Via Vetoio, Italy
| | - Gustavo A Aucar
- Physics Department, Natural and Exact Science Faculty, National Northeastern University of Argentina, Avda Libertad, W3404AAS 5460, Corrientes, Argentina
- Institute for Modelling and Innovative Technology, IMIT (CONICET-UNNE), Avda Libertad, W3404AAS 5460, Corrientes, Argentina
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3
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Abraham E, Dinpajooh M, Climent C, Nitzan A. Heat transport with a twist. J Chem Phys 2023; 159:174904. [PMID: 37916592 DOI: 10.1063/5.0171680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023] Open
Abstract
Despite the desirability of polymers for use in many products due to their flexibility, light weight, and durability, their status as thermal insulators has precluded their use in applications where thermal conductors are required. However, recent results suggest that the thermal conductance of polymers can be enhanced and that their heat transport behaviors may be highly sensitive to nanoscale control. Here we use non-equilibrium molecular dynamics simulations to study the effect of mechanical twist on the steady-state thermal conductance across multi-stranded polyethylene wires. We find that a highly twisted double-helical polyethylene wire can display a thermal conductance up to three times that of its untwisted form, an effect which can be attributed to a structural transition in the strands of the double helix. We also find that in thicker wires composed of many parallel strands, adding just one twist can increase its thermal conductance by over 30%. However, we find that unlike stretching a polymer wire, which causes a monotonic increase in thermal conductance, the effect of twist is highly non-monotonic, and certain amounts of twist can actually decrease the thermal conductance. Finally, we apply the Continuous Chirality Measure (CCM) in an attempt to explore the correlation between heat conductance and chirality. The CCM is found to correlate with twist as expected, but we attribute the observed heat transport behaviors to structural factors other than chirality.
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Affiliation(s)
- Ethan Abraham
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mohammadhasan Dinpajooh
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Clàudia Climent
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Abraham Nitzan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
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4
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Yang L, Zhu L, Zhang S, Hong X. Machine Learning Prediction of
Structure‐Performance
Relationship in Organic Synthesis. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Li‐Cheng Yang
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University Hangzhou Zhejiang 310027 China
| | - Lu‐Jing Zhu
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University Hangzhou Zhejiang 310027 China
| | - Shuo‐Qing Zhang
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University Hangzhou Zhejiang 310027 China
| | - Xin Hong
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University Hangzhou Zhejiang 310027 China
- Beijing National Laboratory for Molecular Sciences, Zhongguancun North First Street NO. 2 Beijing 100190 China
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road Hangzhou Zhejiang 310024 China
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5
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Towards Data‐Driven Design of Asymmetric Hydrogenation of Olefins: Database and Hierarchical Learning. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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6
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Voronoi Entropy vs. Continuous Measure of Symmetry of the Penrose Tiling: Part I. Analysis of the Voronoi Diagrams. Symmetry (Basel) 2021. [DOI: 10.3390/sym13091659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A continuous measure of symmetry and the Voronoi entropy of 2D patterns representing Voronoi diagrams emerging from the Penrose tiling were calculated. A given Penrose tiling gives rise to a diversity of the Voronoi diagrams when the centers, vertices, and the centers of the edges of the Penrose rhombs are taken as the seed points (or nuclei). Voronoi diagrams keep the initial symmetry group of the Penrose tiling. We demonstrate that the continuous symmetry measure and the Voronoi entropy of the studied sets of points, generated by the Penrose tiling, do not necessarily correlate. Voronoi diagrams emerging from the centers of the edges of the Penrose rhombs, considered nuclei, deny the hypothesis that the continuous measure of symmetry and the Voronoi entropy are always correlated. The Voronoi entropy of this kind of tiling built of asymmetric convex quadrangles equals zero, whereas the continuous measure of symmetry of this pattern is high. Voronoi diagrams generate new types of Penrose tiling, which are different from the classical Penrose tessellation.
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8
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Xu LC, Zhang SQ, Li X, Tang MJ, Xie PP, Hong X. Towards Data-driven Design of Asymmetric Hydrogenation of Olefins: Database and Hierarchical Learning. Angew Chem Int Ed Engl 2021; 60:22804-22811. [PMID: 34370892 DOI: 10.1002/anie.202106880] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/14/2021] [Indexed: 11/09/2022]
Abstract
Asymmetric hydrogenation of olefins is one of the most powerful asymmetric transformations in molecular synthesis. Although several privileged catalyst scaffolds are available, the catalyst development for asymmetric hydrogenation is still a time- and resource-consuming process due to the lack of predictive catalyst design strategy. Targeting the data-driven design of asymmetric catalysis, we herein report the development of a standardized database that contains the detailed information of over 12000 literature asymmetric hydrogenations of olefins. This database provides a valuable platform for the machine learning applications in asymmetric catalysis. Based on this database, we developed a hierarchical learning approach to achieve predictive machine leaning model using only dozens of enantioselectivity data with the target olefin, which offers a useful solution for the few-shot learning problem and will facilitate the reaction optimization with new olefin substrate in catalysis screening.
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Affiliation(s)
- Li-Cheng Xu
- Zhejiang University, Department of Chemistry, CHINA
| | | | - Xin Li
- Zhejiang University, Department of Chemistry, CHINA
| | | | - Pei-Pei Xie
- Zhejiang University, Department of Chemistry, CHINA
| | - Xin Hong
- Zhejiang University, Department of Chemistry, 38 Zheda Road, 310028, Hangzhou, CHINA
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9
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Rinehart NI, Zahrt AF, Henle JJ, Denmark SE. Dreams, False Starts, Dead Ends, and Redemption: A Chronicle of the Evolution of a Chemoinformatic Workflow for the Optimization of Enantioselective Catalysts. Acc Chem Res 2021; 54:2041-2054. [PMID: 33856771 DOI: 10.1021/acs.accounts.0c00826] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Catalyst design in enantioselective catalysis has historically been driven by empiricism. In this endeavor, experimentalists attempt to qualitatively identify trends in structure that lead to a desired catalyst function. In this body of work, we lay the groundwork for an improved, alternative workflow that uses quantitative methods to inform decision making at every step of the process. At the outset, we define a library of synthetically accessible permutations of a catalyst scaffold with the philosophy that the library contains every potential catalyst we are willing to make. To represent these chiral molecules, we have developed general 3D representations, which can be calculated for tens of thousands of structures. This defines the total chemical space of a given catalyst scaffold; it is constructed on the basis of catalyst structure only without regard to a specific reaction or mechanism. As such, any algorithmic subset selection method, which is unsupervised (i.e., only considers catalyst structure), should provide an ideal initial screening set for any new reaction that can be catalyzed by that scaffold. Notably, because this design strategy, the same set of catalysts can be used for any reaction that can be catalyzed with that parent catalyst scaffold. These are tested experimentally, and statistical learning tools can be used to create a model relating catalyst structure to catalyst function. Further, this model can be used to predict the performance of each catalyst candidate in the greater database of virtual catalyst candidates. In this way, it is possible estimate the performance of tens of thousands of catalysts by experimentally testing a smaller subset. Using error assessment metrics, it is possible to understand the confidence in new predictions. An experimentalist using this tool can balance the predicted results (reward) with the prediction confidence (risk) when deciding which catalysts to synthesize next in an optimization campaign. These catalysts are synthesized and tested experimentally. At this stage, either the optimization is a success or the predicted values were incorrect and further optimization is required. In the case of the latter, the information can be fed back into the statistical learning model to refine the model, and this iterative process can be used to determine the optimal catalyst. In this body of work, we not only establish this workflow but quantitatively establish how best to execute each step. Herein, we evaluate several 3D molecular representations to determine how best to represent molecules. Several selection protocols are examined to best decide which set of molecules can be used to represent the library of interest. In addition, the number of reactions needed to make accurate, statistical learning models is evaluated. Taken together these components establish a tool ready to progress from the development stage to the utility stage. As such, current research endeavors focus on applying these tools to optimize new reactions.
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Affiliation(s)
- N. Ian Rinehart
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Andrew F. Zahrt
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Jeremy J. Henle
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott E. Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
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10
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Shrestha B, Rose BT, Olen CL, Roth A, Kwong AC, Wang Y, Denmark SE. A Unified Strategy for the Asymmetric Synthesis of Highly Substituted 1,2-Amino Alcohols Leading to Highly Substituted Bisoxazoline Ligands. J Org Chem 2021; 86:3490-3534. [PMID: 33539091 DOI: 10.1021/acs.joc.0c02899] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general procedure for the asymmetric synthesis of highly substituted 1,2-amino alcohols in high yield and diastereoselectivity is described that uses organometallic additions of a wide range of nucleophiles to tert-butylsulfinimines as the key step. The addition of organolithium reagents to these imines follows a modified Davis model. The diastereoselectivity for this reaction depends significantly on both the nucleophile and electrophile. These highly substituted 1,2-amino alcohols are used to synthesize stereochemically diverse and structurally novel, polysubstituted 2,2'-methylene(bisoxazoline) ligands in high yields.
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Affiliation(s)
- Bijay Shrestha
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Brennan T Rose
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Casey L Olen
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Aaron Roth
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Adon C Kwong
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Yang Wang
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott E Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
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11
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Fossépré M, Tuvi-Arad I, Beljonne D, Richeter S, Clément S, Surin M. Binding Mode Multiplicity and Multiscale Chirality in the Supramolecular Assembly of DNA and a π-Conjugated Polymer. Chemphyschem 2020; 21:2543-2552. [PMID: 32910539 DOI: 10.1002/cphc.202000630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/04/2020] [Indexed: 02/04/2023]
Abstract
Water-soluble π-conjugated polymers are increasingly considered for DNA biosensing. However, the conformational rearrangement, supramolecular organization and dynamics upon interaction with DNA have been overlooked, which prevents the rational design of such detection tools. To elucidate the binding of a cationic polythiophene (CPT) to DNA with atomistic resolution, we performed molecular simulations of their supramolecular assembly. Comparison of replicated simulations show a multiplicity of CPT binding geometries that contribute to the wrapping of CPT around DNA. The different binding geometries are stabilized by both electrostatic interactions between CPT lateral cations and DNA phosphodiesters and van der Waals interactions between the CPT backbone and the DNA grooves. Simulated circular dichroism (CD) spectra show that the induced CD signal stems from a conserved geometrical feature across the replicated simulations, i. e. the presence of segments of syn configurations between thiophene units along the CPT chain. At the macromolecular scale, we inspected the different shapes related to the CPT binding modes around the DNA through symmetry metrics. Altogether, molecular dynamics (MD) simulations, model Hamiltonian calculations of the CD spectra, and symmetry indices provide insights into the origin of induced chirality from the atomic to the macromolecular scale. Our multidisciplinary approach points out the hierarchical aspect of CPT chiral organization induced by DNA.
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Affiliation(s)
- Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 20 Place du Parc, Mons, 7000, Belgium
| | - Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - David Beljonne
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 20 Place du Parc, Mons, 7000, Belgium
| | | | | | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 20 Place du Parc, Mons, 7000, Belgium
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12
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Kaspi-Kaneti AW, Barroso J, Merino G, Avnir D, Garzón IL, Tuvi-Arad I. Head to Tail Distortion Wave Characterizes the Enantiomerization of Helicenes. J Org Chem 2020; 85:15415-15421. [PMID: 33210538 DOI: 10.1021/acs.joc.0c02196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A fresh look on helicenes' enantiomerization process with a focus on ring conformation reveals that it can be described as a step-by-step mechanism in which maximal distortion is consecutively transferred along the helicene skeleton, head to tail. Density functional theory methods were used to compute the enantiomerization pathway, and continuous symmetry measures were applied to quantify the distortion of even-number helicenes with 8-14 rings. Our findings show that the distortion wave is additive-the process always starts from one edge of the helicene and progresses along the rings until the other edge is reached. As more rings are added to the helicene, extra steps are appended to the distortion wave. Implications of this fundamental process are discussed in light of similar natural phenomena from polymer dynamics to snake locomotion.
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Affiliation(s)
- Ariela W Kaspi-Kaneti
- Department of Natural Sciences, The Open University of Israel, Raanana 4353701, Israel.,Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Jorge Barroso
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida, Mérida, Yucatán 97310, México
| | - Gabriel Merino
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida, Mérida, Yucatán 97310, México
| | - David Avnir
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ignacio L Garzón
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana 4353701, Israel
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13
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Morphometric Analysis of Surface Utricles in Halimeda tuna (Bryopsidales, Ulvophyceae) Reveals Variation in Their Size and Symmetry within Individual Segments. Symmetry (Basel) 2020. [DOI: 10.3390/sym12081271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Calcifying marine green algae of genus Halimeda have siphonous thalli composed of repeated segments. Their outer surface is formed by laterally appressed peripheral utricles which often form a honeycomb structure, typically with varying degrees of asymmetry in the individual polygons. This study is focused on a morphometric analysis of the size and symmetry of these polygons in Mediterranean H. tuna. Asymmetry of surface utricles is studied using a continuous symmetry measure quantifying the deviation of polygons from perfect symmetry. In addition, the segment shapes are also captured by geometric morphometrics and compared to the utricle parameters. The area of surface utricles is proved to be strongly related to their position on segments, where utricles near the segment bases are considerably smaller than those located near the apical and lateral margins. Interestingly, this gradient is most pronounced in relatively large reniform segments. The polygons are most symmetric in the central parts of segments, with asymmetry uniformly increasing towards the segment margins. Mean utricle asymmetry is found to be unrelated to segment shapes. Systematic differences in utricle size across different positions might be related to morphogenetic patterns of segment development, and may also indicate possible small-scale variations in CaCO3 content within segments.
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14
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Li Y, Lidskog A, Armengol‐Relats H, Pham TH, Favraud A, Nicolas M, Dawaigher S, Xiao Z, Ma D, Lindbäck E, Strand D, Wärnmark K. Enantiotopic Discrimination by Coordination‐Desymmetrized
meso
‐Ligands. ChemCatChem 2020. [DOI: 10.1002/cctc.201902243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yutang Li
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
| | - Anna Lidskog
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
| | - Helena Armengol‐Relats
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
| | - Thanh Huong Pham
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
| | - Antoine Favraud
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
| | - Maxime Nicolas
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
| | - Sami Dawaigher
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
| | - Zeyun Xiao
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
| | - Dayou Ma
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
| | - Emil Lindbäck
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
- Present address: Department of Chemistry Bioscience and Environmental Engineering Faculty of Science and TechnologyUniversity of Stavanger Stavanger NO-4036 Norway
| | - Daniel Strand
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
| | - Kenneth Wärnmark
- Centre for Analysis and Synthesis Department of ChemistryLund University Lund SE-22100 Sweden
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15
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Zahrt AF, Athavale SV, Denmark SE. Quantitative Structure-Selectivity Relationships in Enantioselective Catalysis: Past, Present, and Future. Chem Rev 2020; 120:1620-1689. [PMID: 31886649 PMCID: PMC7018559 DOI: 10.1021/acs.chemrev.9b00425] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The dawn of the 21st century has brought with it a surge of research related to computer-guided approaches to catalyst design. In the past two decades, chemoinformatics, the application of informatics to solve problems in chemistry, has increasingly influenced prediction of activity and mechanistic investigations of organic reactions. The advent of advanced statistical and machine learning methods, as well as dramatic increases in computational speed and memory, has contributed to this emerging field of study. This review summarizes strategies to employ quantitative structure-selectivity relationships (QSSR) in asymmetric catalytic reactions. The coverage is structured by initially introducing the basic features of these methods. Subsequent topics are discussed according to increasing complexity of molecular representations. As the most applied subfield of QSSR in enantioselective catalysis, the application of local parametrization approaches and linear free energy relationships (LFERs) along with multivariate modeling techniques is described first. This section is followed by a description of global parametrization methods, the first of which is continuous chirality measures (CCM) because it is a single parameter derived from the global structure of a molecule. Chirality codes, global, multivariate descriptors, are then introduced followed by molecular interaction fields (MIFs), a global descriptor class that typically has the highest dimensionality. To highlight the current reach of QSSR in enantioselective transformations, a comprehensive collection of examples is presented. When combined with traditional experimental approaches, chemoinformatics holds great promise to predict new catalyst structures, rationalize mechanistic behavior, and profoundly change the way chemists discover and optimize reactions.
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Affiliation(s)
- Andrew F. Zahrt
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Soumitra V. Athavale
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Scott E. Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL 61801
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16
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Singh S, Pareek M, Changotra A, Banerjee S, Bhaskararao B, Balamurugan P, Sunoj RB. A unified machine-learning protocol for asymmetric catalysis as a proof of concept demonstration using asymmetric hydrogenation. Proc Natl Acad Sci U S A 2020; 117:1339-1345. [PMID: 31915295 PMCID: PMC6983389 DOI: 10.1073/pnas.1916392117] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Design of asymmetric catalysts generally involves time- and resource-intensive heuristic endeavors. In view of the steady increase in interest toward efficient catalytic asymmetric reactions and the rapid growth in the field of machine learning (ML) in recent years, we envisaged dovetailing these two important domains. We selected a set of quantum chemically derived molecular descriptors from five different asymmetric binaphthyl-derived catalyst families with the propensity to impact the enantioselectivity of asymmetric hydrogenation of alkenes and imines. The predictive power of the random forest (RF) built using the molecular parameters of a set of 368 substrate-catalyst combinations is found to be impressive, with a root-mean-square error (rmse) in the predicted enantiomeric excess (%ee) of about 8.4 ± 1.8 compared to the experimentally known values. The accuracy of RF is found to be superior to other ML methods such as convolutional neural network, decision tree, and eXtreme gradient boosting as well as stepwise linear regression. The proposed method is expected to provide a leap forward in the design of catalysts for asymmetric transformations.
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Affiliation(s)
- Sukriti Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, 400076 Mumbai, India
| | - Monika Pareek
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, 400076 Mumbai, India
| | - Avtar Changotra
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, 400076 Mumbai, India
| | - Sayan Banerjee
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, 400076 Mumbai, India
| | - Bangaru Bhaskararao
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, 400076 Mumbai, India
| | - P Balamurugan
- Industrial Engineering and Operations Research, Indian Institute of Technology Bombay, Powai, 400076 Mumbai, India
| | - Raghavan B Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, 400076 Mumbai, India;
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Ligand Design for Asymmetric Catalysis: Combining Mechanistic and Chemoinformatics Approaches. TOP ORGANOMETAL CHEM 2020. [DOI: 10.1007/3418_2020_47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kilinkissa OEY, Govender KK, Báthori NB. Melting point–solubility–structure correlations in chiral and racemic model cocrystals. CrystEngComm 2020. [DOI: 10.1039/d0ce00014k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Comparison of chiral and racemic binary cocrystals showed that the chiral building block limits the formation of certain intermolecular interactions, decreases the packing efficiency, lowers the melting point and increases aqueous solubility.
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Affiliation(s)
| | - Krishna K. Govender
- Department of Chemical Sciences
- University of Johannesburg
- Johannesburg
- South Africa
- Council for Scientific and Industrial Research
| | - Nikoletta B. Báthori
- Department of Chemistry
- Cape Peninsula University of Technology
- Cape Town
- South Africa
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Dommaschk M, Echavarren J, Leigh DA, Marcos V, Singleton TA. Dynamic Control of Chiral Space Through Local Symmetry Breaking in a Rotaxane Organocatalyst. Angew Chem Int Ed Engl 2019; 58:14955-14958. [PMID: 31454135 DOI: 10.1002/anie.201908330] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Indexed: 12/21/2022]
Abstract
We report on a switchable rotaxane molecular shuttle that features a pseudo-meso 2,5-disubstituted pyrrolidine catalytic unit on the axle whose local symmetry is broken according to the position of a threaded benzylic amide macrocycle. The macrocycle can be selectively switched (with light in one direction; with catalytic acid in the other) with high fidelity between binding sites located to either side of the pyrrolidine unit. The position of the macrocycle dictates the facial bias of the rotaxane-catalyzed conjugate addition of aldehydes to vinyl sulfones. The pseudo-meso non-interlocked thread does not afford significant selectivity as a catalyst (2-14 % ee), whereas the rotaxane affords selectivities of up to 40 % ee with switching of the position of the macrocycle changing the handedness of the product formed (up to 60 % Δee).
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Affiliation(s)
- Marcel Dommaschk
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Javier Echavarren
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - David A Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Vanesa Marcos
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Thomas A Singleton
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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Dommaschk M, Echavarren J, Leigh DA, Marcos V, Singleton TA. Dynamic Control of Chiral Space Through Local Symmetry Breaking in a Rotaxane Organocatalyst. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908330] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Marcel Dommaschk
- School of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
| | - Javier Echavarren
- School of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
| | - David A. Leigh
- School of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
| | - Vanesa Marcos
- School of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
| | - Thomas A. Singleton
- School of Chemistry University of Manchester Oxford Road Manchester M13 9PL UK
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