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Journal articles on the topic 'Retrosynthesis'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Williams, Craig M., and Madeleine A. Dallaston. "The Future of Retrosynthesis and Synthetic Planning: Algorithmic, Humanistic or the Interplay?" Australian Journal of Chemistry 74, no. 5 (2021): 291. http://dx.doi.org/10.1071/ch20371.

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The practice of deploying and teaching retrosynthesis is on the cusp of considerable change, which in turn forces practitioners and educators to contemplate whether this impending change will advance or erode the efficiency and elegance of organic synthesis in the future. A short treatise is presented herein that covers the concept of retrosynthesis, along with exemplified methods and theories, and an attempt to comprehend the impact of artificial intelligence in an era when freely and commercially available retrosynthetic and forward synthesis planning programs are increasingly prevalent. Will the computer ever compete with human retrosynthetic design and the art of organic synthesis?

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2

Smith, Joel M., Stephen J. Harwood, and Phil S. Baran. "Radical Retrosynthesis." Accounts of Chemical Research 51, no. 8 (August 2, 2018): 1807–17. http://dx.doi.org/10.1021/acs.accounts.8b00209.

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3

Turner, Nicholas J., and Elaine O'Reilly. "Biocatalytic retrosynthesis." Nature Chemical Biology 9, no. 5 (April 17, 2013): 285–88. http://dx.doi.org/10.1038/nchembio.1235.

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4

SS, Fatahala. "Retrosynthesis analysis; a way to design a retrosynthesis map for Pyridine and pyrimidine ring." Annals of Advances in Chemistry 1, no. 2 (2017): 057–60. http://dx.doi.org/10.29328/journal.aac.1001007.

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5

Nair, Vishnu H., Philippe Schwaller, and Teodoro Laino. "Data-driven Chemical Reaction Prediction and Retrosynthesis." CHIMIA International Journal for Chemistry 73, no. 12 (December 18, 2019): 997–1000. http://dx.doi.org/10.2533/chimia.2019.997.

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The synthesis of organic compounds, which is central to many areas such as drug discovery, material synthesis and biomolecular chemistry, requires chemists to have years of knowledge and experience. The development of technologies with the potential to learn and support experts in the design of synthetic routes is a half-century-old challenge with an interesting revival in the last decade. In fact, the renewed interest in artificial intelligence (AI), driven mainly by data availability, is profoundly changing the landscape of computer-aided chemical reaction prediction and retrosynthetic analysis. In this article, we briefly review different approaches to predict forward reactions and retrosynthesis, with a strong focus on data-driven ones. While data-driven technologies still need to demonstrate their full potential compared to expert rule-based systems in synthetic chemistry, the acceleration experienced in the last decade is a convincing sign that where we use software today, there will be AI tomorrow. This revolution will help and empower bench chemists, driving the transformation of chemistry towards a high-tech business over the next decades.

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6

Guo, Zhongliang, Stephen Wu, Mitsuru Ohno, and Ryo Yoshida. "Bayesian Algorithm for Retrosynthesis." Journal of Chemical Information and Modeling 60, no. 10 (September 25, 2020): 4474–86. http://dx.doi.org/10.1021/acs.jcim.0c00320.

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7

Proudfoot, John R. "Molecular Complexity and Retrosynthesis." Journal of Organic Chemistry 82, no. 13 (June 12, 2017): 6968–71. http://dx.doi.org/10.1021/acs.joc.7b00714.

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8

Turner, Nicholas J., and Elaine O'Reilly. "ChemInform Abstract: Biocatalytic Retrosynthesis." ChemInform 44, no. 29 (July 1, 2013): no. http://dx.doi.org/10.1002/chin.201329258.

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9

Rother, Dörte, and Stephan Malzacher. "Computer-aided enzymatic retrosynthesis." Nature Catalysis 4, no. 2 (February 2021): 92–93. http://dx.doi.org/10.1038/s41929-021-00582-5.

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10

Chen, Lihua, Joseph Kern, Jordan P. Lightstone, and Rampi Ramprasad. "Data-assisted polymer retrosynthesis planning." Applied Physics Reviews 8, no. 3 (September 2021): 031405. http://dx.doi.org/10.1063/5.0052962.

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11

Duan, Hongliang, Ling Wang, Chengyun Zhang, Lin Guo, and Jianjun Li. "Retrosynthesis with attention-based NMT model and chemical analysis of “wrong” predictions." RSC Advances 10, no. 3 (2020): 1371–78. http://dx.doi.org/10.1039/c9ra08535a.

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12

AZARIO, P., M. ARBELOT, A. BALDY, R. MEYER, R. BARONE, and M. CHANON. "ChemInform Abstract: Microcomputer Assisted Retrosynthesis (MARS)." ChemInform 22, no. 14 (August 23, 2010): no. http://dx.doi.org/10.1002/chin.199114355.

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13

Schwaller, Philippe, Riccardo Petraglia, Valerio Zullo, Vishnu H. Nair, Rico Andreas Haeuselmann, Riccardo Pisoni, Costas Bekas, Anna Iuliano, and Teodoro Laino. "Predicting retrosynthetic pathways using transformer-based models and a hyper-graph exploration strategy." Chemical Science 11, no. 12 (2020): 3316–25. http://dx.doi.org/10.1039/c9sc05704h.

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14

Lee, Alpha A., Qingyi Yang, Vishnu Sresht, Peter Bolgar, Xinjun Hou, Jacquelyn L. Klug-McLeod, and Christopher R. Butler. "Molecular Transformer unifies reaction prediction and retrosynthesis across pharma chemical space." Chemical Communications 55, no. 81 (2019): 12152–55. http://dx.doi.org/10.1039/c9cc05122h.

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15

Yang, Ming Jun, Yong Gang Wang, Xiao Feng Liu, and Jing Wu. "Synthesis and Anti-Tumor Activity of Cyclodepsipeptides Paecilodepsipeptide A." Advanced Materials Research 643 (January 2013): 92–95. http://dx.doi.org/10.4028/www.scientific.net/amr.643.92.

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paecilodepsipeptide A was first synthesized by retrosynthesis methods. the structures were determined by Mass Spectrometry and NMR spectroscopy, and the anti-tumor activities on human hepatocellular carcinoma cell line (SMMC-7721) and human lymphoma cell line (Raji) were examined by MTT. The result showed that the rate of Paecilodepsipeptide A was 72% by retrosynthesis methods. The structures of the synthesized product were identified by 1H NMR and 13C NMR spectra, which is identical to the natural product. The product has remarkable anti-proliferation activity on SMMC-7721 and Raji, which showed good anti-tumor activity. IC50 was 8.97 μmol/L and 11.13 μmol/L respectively, The total synthesis of Paecilodepsipeptide A is significant to further study its derivatives and develop novel antitumor drugs.

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16

Delépine, Baudoin, Thomas Duigou, Pablo Carbonell, and Jean-Loup Faulon. "RetroPath2.0: A retrosynthesis workflow for metabolic engineers." Metabolic Engineering 45 (January 2018): 158–70. http://dx.doi.org/10.1016/j.ymben.2017.12.002.

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17

Gehrke, Nicole, Nadine Nassif, Nicola Pinna, Markus Antonietti, Himadri S. Gupta, and Helmut Cölfen. "Retrosynthesis of Nacre via Amorphous Precursor Particles." Chemistry of Materials 17, no. 26 (December 2005): 6514–16. http://dx.doi.org/10.1021/cm052150k.

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18

Coley, Connor W., Luke Rogers, William H. Green, and Klavs F. Jensen. "Computer-Assisted Retrosynthesis Based on Molecular Similarity." ACS Central Science 3, no. 12 (November 16, 2017): 1237–45. http://dx.doi.org/10.1021/acscentsci.7b00355.

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19

Hönig, Moritz, Philipp Sondermann, Nicholas J. Turner, and Erick M. Carreira. "Enantioselective Chemo- and Biocatalysis: Partners in Retrosynthesis." Angewandte Chemie International Edition 56, no. 31 (June 26, 2017): 8942–73. http://dx.doi.org/10.1002/anie.201612462.

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20

Mao, Kelong, Xi Xiao, Tingyang Xu, Yu Rong, Junzhou Huang, and Peilin Zhao. "Molecular graph enhanced transformer for retrosynthesis prediction." Neurocomputing 457 (October 2021): 193–202. http://dx.doi.org/10.1016/j.neucom.2021.06.037.

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21

Taulelle, Francis, Corine Gérardin, Mohamed Haouas, Clarisse Huguenard, Vincent Munch, Thierry Loiseau, and Gérard Férey. "Fluorine-19 NMR from retrosynthesis to NMR crystallography." Journal of Fluorine Chemistry 101, no. 2 (February 2000): 269–72. http://dx.doi.org/10.1016/s0022-1139(99)00169-4.

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22

de Souza, Rodrigo O. M. A., Leandro S. M. Miranda, and Uwe T. Bornscheuer. "A Retrosynthesis Approach for Biocatalysis in Organic Synthesis." Chemistry - A European Journal 23, no. 50 (June 22, 2017): 12040–63. http://dx.doi.org/10.1002/chem.201702235.

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23

Rao, Ashit, José Arias, and Helmut Cölfen. "On Mineral Retrosynthesis of a Complex Biogenic Scaffold." Inorganics 5, no. 1 (March 15, 2017): 16. http://dx.doi.org/10.3390/inorganics5010016.

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24

Green, Anthony P., and Nicholas J. Turner. "Biocatalytic retrosynthesis: Redesigning synthetic routes to high-value chemicals." Perspectives in Science 9 (December 2016): 42–48. http://dx.doi.org/10.1016/j.pisc.2016.04.106.

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25

Nicolaou, K. C., P. G. Nantermet, H. Ueno, R. K. Guy, E. A. Couladouros, and E. J. Sorensen. "Total Synthesis of Taxol. 1. Retrosynthesis, Degradation, and Reconstitution." Journal of the American Chemical Society 117, no. 2 (January 1995): 624–33. http://dx.doi.org/10.1021/ja00107a006.

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26

Segler, Marwin H. S., and Mark P. Waller. "Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction." Chemistry - A European Journal 23, no. 25 (February 22, 2017): 5966–71. http://dx.doi.org/10.1002/chem.201605499.

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27

Bjerrum, Esben Jannik, Amol Thakkar, and Ola Engkvist. "Artificial applicability labels for improving policies in retrosynthesis prediction." Machine Learning: Science and Technology 2, no. 1 (December 31, 2020): 017001. http://dx.doi.org/10.1088/2632-2153/abcf90.

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28

Bedford, Simon, and Jon Mason. "How to impart tacit knowledge: “Blending Chess and Chemistry”." New Directions in the Teaching of Physical Sciences, no. 3 (February 23, 2016): 59–63. http://dx.doi.org/10.29311/ndtps.v0i3.421.

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Retrosynthesis has been likened to the game of chess. There are relatively simple rules to learn, but only through experience and practice can a learner acquire the tacit knowledge required for mastery of the subject. This makes it a challenging topic to teach effectively to a large and diverse cohort of learners. Lectures are a good way of transmitting knowledge, but do not provide the engagement and training that is essential in developing a deep understanding of retrosynthesis. Therefore, students tend to struggle to achieve success in this topic. This project aimed to alleviate this problem by producing online learning resources to be combined with traditional face-to-face teaching methods to develop a blended learning approach. These resources included animated videos, quizzes, worked examples and other interactive learning materials. Analysis of examination results and learner feedback showed that the supplementary resources not only improved student performance and understanding, but also provided a more satisfactory learning experience. External evaluation suggested that the learning package has significant potential and development should be continued. The package of learning resources can be viewed online at: people.bath.ac.uk/ch3jhm

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29

Christ, Clara D., Matthias Zentgraf, and Jan M. Kriegl. "Mining Electronic Laboratory Notebooks: Analysis, Retrosynthesis, and Reaction Based Enumeration." Journal of Chemical Information and Modeling 52, no. 7 (June 15, 2012): 1745–56. http://dx.doi.org/10.1021/ci300116p.

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30

Henry, Marc. "Retrosynthesis in inorganic crystal structures: application to nesosilicate and inosilicate networks." Coordination Chemistry Reviews 178-180 (December 1998): 1109–63. http://dx.doi.org/10.1016/s0010-8545(98)00167-2.

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31

Horinouchi, Nobuyuki, Jun Ogawa, Takako Kawano, Takafumi Sakai, Kyota Saito, Seiichiro Matsumoto, Mie Sasaki, Yoichi Mikami, and Sakayu Shimizu. "Biochemical retrosynthesis of 2′-deoxyribonucleosides from glucose, acetaldehyde, and a nucleobase." Applied Microbiology and Biotechnology 71, no. 5 (November 11, 2005): 615–21. http://dx.doi.org/10.1007/s00253-005-0205-5.

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32

Yirik, Mehmet Aziz, and Christoph Steinbeck. "Chemical graph generators." PLOS Computational Biology 17, no. 1 (January 5, 2021): e1008504. http://dx.doi.org/10.1371/journal.pcbi.1008504.

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Chemical graph generators are software packages to generate computer representations of chemical structures adhering to certain boundary conditions. Their development is a research topic of cheminformatics. Chemical graph generators are used in areas such as virtual library generation in drug design, in molecular design with specified properties, called inverse QSAR/QSPR, as well as in organic synthesis design, retrosynthesis or in systems for computer-assisted structure elucidation (CASE). CASE systems again have regained interest for the structure elucidation of unknowns in computational metabolomics, a current area of computational biology.

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33

Thalladi, Venkat R., B. Satish Goud, Vanessa J. Hoy, Frank H. Allen, Judith A. K. Howard, and Gautam R. Desiraju. "Supramolecular synthons in crystal engineering. Structure simplification, synthon robustness and supramolecular retrosynthesis." Chemical Communications, no. 3 (1996): 401. http://dx.doi.org/10.1039/cc9960000401.

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34

Geng, Xin, Yuanqiang Sun, Zhaohui Li, Ran Yang, Yanmin Zhao, Yifei Guo, Jinjin Xu, et al. "Retrosynthesis of Tunable Fluorescent Carbon Dots for Precise Long‐Term Mitochondrial Tracking." Small 15, no. 48 (June 4, 2019): 1901517. http://dx.doi.org/10.1002/smll.201901517.

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35

NICOLAOU, K. C., P. G. NANTERMET, H. UENO, R. K. GUY, E. A. COULADOUROS, and E. J. SORENSEN. "ChemInform Abstract: Total Synthesis of Taxol. Part 1. Retrosynthesis, Degradation, and Reconstitution." ChemInform 26, no. 27 (August 17, 2010): no. http://dx.doi.org/10.1002/chin.199527226.

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36

Warrener, RN, IG Pitt, KDV Weerasuria, and RA Russell. "Acetylene Stacking: a New Concept for the Synthesis of Cyclic Polyenes. Application to the Preparation of a 1,6-Bridged Bicyclo[4.2.0]octa-2,4,7-triene and Some Novel Oxepins." Australian Journal of Chemistry 45, no. 1 (1992): 155. http://dx.doi.org/10.1071/ch9920155.

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A new protocol for a general synthesis of cyclic polyenes is presented; in this protocol two new concepts are introduced. The first, acetylene stacking, is the generic term covering both the synthesis of a target molecule and the specific retrosynthesis upon which it is based. This retrosynthetic analysis involves conversion of the target molecule, through a series of transannular [ π2s+π2s] valence isomerizations , into a key polycyclobutanoid intermediate (24). This intermediate is cleaved, in turn, through a similar number of [ σ2s+ σ2s] electrocyclic fragmentations, to yield a set of acetylene synthons . The synthetic phase is based on the recombination of the corresponding acetylene synthetic equivalents in a stacking mode which leads to the target molecule by way of the same polycyclobutanoid intermediate (24). To achieve the ordered assembly of the acteylene synthons, in the required stacking mode, it has been necessary to develop the second concept, namely transfer technology. This involves the use of special transfer reagents, to act as synthetic equivalents and provide the molecular equivalent of acetylenes without ever producing acetylenes per se. Similar transfer reagents are described for cyclobutadienes which serves to demonstrate the wider implications of this new concept in organic synthesis. The bridged bicyclic polyene 8-oxatricyclo [4.3.2.01,6]undeca-2,4,10-triene (73), and the heterocycle 2,4,5,7,8-pentamethyl-1H-oxepino[4,5-c]pyrrole-1,3(2H)- dione (91) are used as the target molecules to illustrate this new synthesis protocol involving sets of stacked acetylenes (or cyclobutadienes ) as the synthetic base. The conversion of the oxepin (91) into isomeric oxepins, and the role of their tautomeric benzene oxides, present as equilibrium partners, is discussed.

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37

Tao, Yongfeng, Keighley N. Reisenauer, Marco Masi, Antonio Evidente, Joseph H. Taube, and Daniel Romo. "Pharmacophore-Directed Retrosynthesis Applied to Ophiobolin A: Simplified Bicyclic Derivatives Displaying Anticancer Activity." Organic Letters 22, no. 21 (October 9, 2020): 8307–12. http://dx.doi.org/10.1021/acs.orglett.0c02938.

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38

Kim, Eunji, Dongseon Lee, Youngchun Kwon, Min Sik Park, and Youn-Suk Choi. "Valid, Plausible, and Diverse Retrosynthesis Using Tied Two-Way Transformers with Latent Variables." Journal of Chemical Information and Modeling 61, no. 1 (January 7, 2021): 123–33. http://dx.doi.org/10.1021/acs.jcim.0c01074.

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39

Wang, Xiaorui, Yuquan Li, Jiezhong Qiu, Guangyong Chen, Huanxiang Liu, Benben Liao, Chang-Yu Hsieh, and Xiaojun Yao. "RetroPrime: A Diverse, plausible and Transformer-based method for Single-Step retrosynthesis predictions." Chemical Engineering Journal 420 (September 2021): 129845. http://dx.doi.org/10.1016/j.cej.2021.129845.

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40

Gao, Hanyu, Connor W. Coley, Thomas J. Struble, Linyan Li, Yujie Qian, William H. Green, and Klavs F. Jensen. "Combining retrosynthesis and mixed-integer optimization for minimizing the chemical inventory needed to realize a WHO essential medicines list." Reaction Chemistry & Engineering 5, no. 2 (2020): 367–76. http://dx.doi.org/10.1039/c9re00348g.

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41

Parmeggiani, Fabio, Arnau Rué Casamajo, Danilo Colombo, Maria Chiara Ghezzi, James L. Galman, Roberto A. Chica, Elisabetta Brenna, and Nicholas J. Turner. "Biocatalytic retrosynthesis approaches to d-(2,4,5-trifluorophenyl)alanine, key precursor of the antidiabetic sitagliptin." Green Chemistry 21, no. 16 (2019): 4368–79. http://dx.doi.org/10.1039/c9gc01902b.

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42

Muthukrishnan, S., J. H. Franklin Benjamin, G. Sathishkannan, T. Senthil Kumar, and M. V. Rao. "ChemInform Abstract: In Vitro Propagation of Genus Ceropegia and Retrosynthesis of Cerpegin - a Review." ChemInform 46, no. 3 (December 22, 2014): no. http://dx.doi.org/10.1002/chin.201503265.

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43

Truax, Nathanyal J., Safiat Ayinde, Khoi Van, Jun O. Liu, and Daniel Romo. "Pharmacophore-Directed Retrosynthesis Applied to Rameswaralide: Synthesis and Bioactivity of Sinularia Natural Product Tricyclic Cores." Organic Letters 21, no. 18 (September 9, 2019): 7394–99. http://dx.doi.org/10.1021/acs.orglett.9b02713.

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44

King, Jason R., Steven Edgar, Kangjian Qiao, and Gregory Stephanopoulos. "Accessing Nature’s diversity through metabolic engineering and synthetic biology." F1000Research 5 (March 24, 2016): 397. http://dx.doi.org/10.12688/f1000research.7311.1.

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In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents.

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45

Hasic, Haris, and Takashi Ishida. "Single-Step Retrosynthesis Prediction Based on the Identification of Potential Disconnection Sites Using Molecular Substructure Fingerprints." Journal of Chemical Information and Modeling 61, no. 2 (February 3, 2021): 641–52. http://dx.doi.org/10.1021/acs.jcim.0c01100.

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46

Warsito, Warsito, Edi Priyo Utomo, Achmad Ashadi, and Satriyo Santosa. "THE USE OF GRIGNARD REAGENT IN PHEROMONE SYNTHESIS FOR PALM WEEVIL (Rhynchorus, Sp)." Indonesian Journal of Chemistry 3, no. 3 (June 9, 2010): 141–44. http://dx.doi.org/10.22146/ijc.21878.

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In an integrated controlling system of palm weevil, using of synthetic feromoid is strickly needed. The research is aimed to synthesize pheromone which secreted by the weevil, e.g. 4-methyl-5-nonanol (R. ferrugineus) and 3-methyl-4-octanol (R. schach) through Grignard reagent which formed in situ. The synthesis was proceded by retrosynthesis to determine the precursor, valeraldehyde. The precursor was reacted with Grignard reagent of sec-amyl magnesium bromide (R. ferrugenieus) and sec-butyl magnesium bromide (R. shach) which made in situ. Characterization of the synthetic molecular pheromone was performed by Gas Chromatography-mass spectroscopy and Fourier Transformed Infra Red. The bioassay of the molecule was carried out by olfactometer. The result showed that the conversion of the reactions were 51.28% (4-methyl-5-nonanol) and 85.90% (3-methyl-4-octanol). The character of physico-chemical and bioactivity of the synthetic pheromone are identic with natural pheromones. Keywords: palm weevil, pheromone, grignard reagent

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47

Singh, Monika, Jency Thomas, and Arunachalam Ramanan. "Understanding Supramolecular Interactions Provides Clues for Building Molecules into Minerals and Materials: a Retrosynthetic Analysis of Copper-Based Solids." Australian Journal of Chemistry 63, no. 4 (2010): 565. http://dx.doi.org/10.1071/ch09427.

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The influence of non-covalent interactions on the crystal packing of molecules is well documented in the literature. Unlike molecular solids, crystal engineering of non-molecular solids is difficult to interpret as aggregation is complicated by the presence of neutral as well as ionic species and a range of forces operating, from weak hydrogen bonding to strong covalent interactions. In this perspective, we demonstrate for the first time the role of non-bonding interactions in the occurrence of oxide, hydroxide, or chloride linkages in oxides, hydroxychlorides, and chlorides of copper-based minerals and coordination polymers in terms of a mechanistic approach based on supramolecular retrosynthesis. The model proposed here visualizes the crystal nucleus as a supramolecular analogue of a transition state wherein appropriate tectons (chemically reasonable molecules) aggregate through non-bonding forces that can be perceived through well-known supramolecular synthons. The mechanistic approach provides chemical insights into the occurrence of different topologies and solid-state phenomena like polymorphism.

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48

Neira-Carrillo, Andrónico, María Soledad Fernández, Gonzalo Poblete Hevia, José Luis Arias, Denis Gebauer, and Helmut Cölfen. "Retrosynthesis of CaCO 3 via amorphous precursor particles using gastroliths of the Red Claw lobster ( Cherax quadricarinatus )." Journal of Structural Biology 199, no. 1 (July 2017): 46–56. http://dx.doi.org/10.1016/j.jsb.2017.05.004.

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49

Huang, Qi, Lin-Li Li, and Sheng-Yong Yang. "RASA: A Rapid Retrosynthesis-Based Scoring Method for the Assessment of Synthetic Accessibility of Drug-like Molecules." Journal of Chemical Information and Modeling 51, no. 10 (September 21, 2011): 2768–77. http://dx.doi.org/10.1021/ci100216g.

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50

Geng, Xin, Yuanqiang Sun, Zhaohui Li, Ran Yang, Yanmin Zhao, Yifei Guo, Jinjin Xu, et al. "Carbon Dots: Retrosynthesis of Tunable Fluorescent Carbon Dots for Precise Long‐Term Mitochondrial Tracking (Small 48/2019)." Small 15, no. 48 (November 2019): 1970259. http://dx.doi.org/10.1002/smll.201970259.

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