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Organic Synthesis: Handout 1
Prof Tim Donohoe: Strategies and Taccs in Organic Synthesis: Handout 1 Organic Synthesis III 8 x 1hr Lectures: Michaelmas Term Weeks 5-8 2016 Mon at 10am; Wed at 9am Dyson Perrins lecture theatre Copies of this handout will be available at hEp://donohoe.chem.ox.ac.uk/page16/index.html 1/33 Prof Tim Donohoe: Strategies and Taccs in Organic Synthesis: Handout 1 Organic Synthesis III Synopsis 1) Introduc5on to synthesis: (i) Why do we want to synthesise molecules- what sort of molecules do we need to make? (ii) What aspects of selecvity do we need to accomplish a good synthesis (chemo-, regio- and stereoselecvity)? (iii) Protecng group chemistry is central to any syntheAc effort (examples and principles) (iv) What is the perfect synthesis (performed in industry versus academia)? 2) The chiral pool: where does absolute stereochemistry come from? 3) Retrosynthesis- learning to think backwards (revision from first and second year). Importance of making C-C bonds and controlling oxidaAon state. Umpolung 4) Some problems to think about 5) Examples of retrosynthesis/synthesis in ac5on. 6) Ten handy hints for retrosynthesis 7) Soluons to the problems Recommended books: General: Organic Chemistry (Warren et al) Organic Synthesis: The DisconnecRon Approach (S. Warren) Classics in Total Synthesis Volumes I and II (K. C. Nicolaou) The Logic of Chemical Synthesis (E. J. Corey) 2/33 View Article Online / Journal Homepage / Table of Contents for this issue 619461 Strychniqae and BYucine. Pavt XLII. 903 Prof Tim Donohoe: Strategies and Taccs in Organic Synthesis: Handout 1 (i) Why do we want to synthesise complex molecules? Isolated from the Pacific Yew in 1962 Prescribed for prostate, breast and ovarian cancer Unique mode of acRon 1x 100 year old tree = 300 mg Taxol Isolated in 1818- poisonous Stuctural elucidaon took R. -
Artificial Intelligence for Computer-Aided Synthesis
ORIGINAL RESEARCH published: 04 August 2020 doi: 10.3389/fceng.2020.00005 Artificial Intelligence for Computer-Aided Synthesis In Flow: Analysis and Selection of Reaction Components Pieter P. Plehiers 1,2, Connor W. Coley 1, Hanyu Gao 1, Florence H. Vermeire 1, Maarten R. Dobbelaere 2, Christian V. Stevens 3, Kevin M. Van Geem 2* and William H. Green 1* 1 Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States, 2 Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University, Ghent, Belgium, 3 SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent Edited by: University, Ghent, Belgium René Schenkendorf, Technische Universitat Braunschweig, Germany Computer-aided synthesis has received much attention in recent years. It is a challenging Reviewed by: topic in itself, due to the high dimensionality of chemical and reaction space. It becomes Richard Anthony Bourne, even more challenging when the aim is to suggest syntheses that can be performed in University of Leeds, United Kingdom Alexei Lapkin, continuous flow. Though continuous flow offers many potential benefits, not all reactions University of Cambridge, are suited to be operated continuously. In this work, three machine learning models United Kingdom have been developed to provide an assessment of whether a given reaction may benefit *Correspondence: from continuous operation, what the likelihood of success in continuous flow is for a Kevin M. Van Geem [email protected] certain set of reaction components (i.e., reactants, reagents, solvents, catalysts, and William H. Green products) and, if the likelihood of success is low, which alternative reaction components [email protected] can be considered. -
Retrosynthetic Design of Metabolic Pathways to Chemicals Not Found in Nature
Retrosynthetic design of metabolic pathways to chemicals not found in nature The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Lin, Geng-Min et al. "Retrosynthetic design of metabolic pathways to chemicals not found in nature." Biology 14 (April 2019): 82-107 © 2019 The Authors As Published http://dx.doi.org/10.1016/J.COISB.2019.04.004 Publisher Elsevier BV Version Final published version Citable link https://hdl.handle.net/1721.1/125854 Terms of Use Creative Commons Attribution-NonCommercial-NoDerivs License Detailed Terms http://creativecommons.org/licenses/by-nc-nd/4.0/ Available online at www.sciencedirect.com Current Opinion in ScienceDirect Systems Biology Retrosynthetic design of metabolic pathways to chemicals not found in nature Geng-Min Lin1, Robert Warden-Rothman1 and Christopher A. Voigt Abstract simpler chemical building blocks derived from pe- Biology produces a universe of chemicals whose precision and troleum or other sources [1]. Chemicals that are large complexity is the envy of chemists. Over the last 30 years, the and complex with many functional groups and ster- expansive field of metabolic engineering has many successes eocenters have required Herculean efforts to build; in optimizing the overproduction of metabolites of industrial in- for example, halichondrin B has 32 stereocenters (4 terest, including moving natural product pathways to production billion isomers) and requires a sprawling total syn- hosts (e.g., plants to yeast). However, there are stunningly few thesis whose longest linear path is 47 reactions [2]. examples where enzymes are artificially combined to make a Solutions have been found to incredibly challenging chemical that is not found somewhere in nature. -
Organic Synthesis: New Vistas in the Brazilian Landscape
Anais da Academia Brasileira de Ciências (2018) 90(1 Suppl. 1): 895-941 (Annals of the Brazilian Academy of Sciences) Printed version ISSN 0001-3765 / Online version ISSN 1678-2690 http://dx.doi.org/10.1590/0001-3765201820170564 www.scielo.br/aabc | www.fb.com/aabcjournal Organic Synthesis: New Vistas in the Brazilian Landscape RONALDO A. PILLI and FRANCISCO F. DE ASSIS Instituto de Química, UNICAMP, Rua José de Castro, s/n, 13083-970 Campinas, SP, Brazil Manuscript received on September 11, 2017; accepted for publication on December 29, 2017 ABSTRACT In this overview, we present our analysis of the future of organic synthesis in Brazil, a highly innovative and strategic area of research which underpins our social and economical progress. Several different topics (automation, catalysis, green chemistry, scalability, methodological studies and total syntheses) were considered to hold promise for the future advance of chemical sciences in Brazil. In order to put it in perspective, contributions from Brazilian laboratories were selected by the citations received and importance for the field and were benchmarked against some of the most important results disclosed by authors worldwide. The picture that emerged reveals a thriving area of research, with new generations of well-trained and productive chemists engaged particularly in the areas of green chemistry and catalysis. In order to fulfill the promise of delivering more efficient and sustainable processes, an integration of the academic and industrial research agendas is to be expected. On the other hand, academic research in automation of chemical processes, a well established topic of investigation in industrial settings, has just recently began in Brazil and more academic laboratories are lining up to contribute. -
Peptide Synthesis: Chemical Or Enzymatic
Electronic Journal of Biotechnology ISSN: 0717-3458 Vol.10 No.2, Issue of April 15, 2007 © 2007 by Pontificia Universidad Católica de Valparaíso -- Chile Received June 6, 2006 / Accepted November 28, 2006 DOI: 10.2225/vol10-issue2-fulltext-13 REVIEW ARTICLE Peptide synthesis: chemical or enzymatic Fanny Guzmán Instituto de Biología Pontificia Universidad Católica de Valparaíso Avenida Brasil 2950 Valparaíso, Chile Fax: 56 32 212746 E-mail: [email protected] Sonia Barberis Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis Ejército de los Andes 950 (5700) San Luis, Argentina E-mail: [email protected] Andrés Illanes* Escuela de Ingeniería Bioquímica Pontificia Universidad Católica de Valparaíso Avenida Brasil 2147 Fax: 56 32 2273803 E-mail: [email protected] Financial support: This work was done within the framework of Project CYTED IV.22 Industrial Application of Proteolytic Enzymes from Higher Plants. Keywords: enzymatic synthesis, peptides, proteases, solid-phase synthesis. Abbreviations: CD: circular dichroism CLEC: cross linked enzyme crystals DDC: double dimer constructs ESI: electrospray ionization HOBT: hydroxybenzotriazole HPLC: high performance liquid hromatography KCS: kinetically controlled synthesis MALDI: matrix-assisted laser desorption ionization MAP: multiple antigen peptide system MS: mass spectrometry NMR: nuclear magnetic resonance SPS: solution phase synthesis SPPS: solid-phase peptide synthesis t-Boc: tert-butoxycarbonyl TCS: thermodynamically controlled synthesis TFA: trifluoroacetic acid Peptides are molecules of paramount importance in the medium, biocatalyst and substrate engineering, and fields of health care and nutrition. Several technologies recent advances and challenges in the field are analyzed. for their production are now available, among which Even though chemical synthesis is the most mature chemical and enzymatic synthesis are especially technology for peptide synthesis, lack of specificity and relevant. -
Peptide Services090320.Ai
FlexPeptideTM Ensures Delivery & Quality! cGMP Peptide: Up to kilograms can be synthesized Mirror-Image Peptide Drug Discovery Services (Cat.No. SC1211) GenScript constructs libraries with natural L-peptides, which are easily amendable. These libraries are then screened with synthetic mirror-image D-forms of the target proteins to identify potent leads that can guide the synthesis of their mirror-image D-peptides. Competitive Advantages Services Include Delivery Specifications Synthesis and purification of D-enantiomers of target protein Chemically synthesized and purified D-enantiomers of the target protein Synthesis and screening of L-peptide libraries Libraries of chemically synthesized L-peptides Construction and screening of L-peptide phage display libraries Libraries of L-peptide phage display Synthesis of D-enantiomers of isolated peptide leads D-enantiomers of the isolated L-peptide leads Functional characterization data of the leads (if applicable) QC reports Custom Recombinant Peptide Services (Cat.No. SC1082) Due to the fact that long peptides (> 150 residues) or complicated peptides (multiple disulfide bonds) are prohibitively expensive to synthesize chemically. GenScript has developed a proprietary recombinant peptide system that complements our standard chemical peptide synthesis service. The powerful combination of these two-protocol allows GenScript to provide our customers with any peptide of any length on any scale. Competitive Advantages Services Include Key Features • Any length • Superior precision • Any sequence • Outstanding procedure • Any scale • Scalable system Custom Peptide Services • Low cost • Batch-to-Batch consistency FlexPeptideTM Ensures Delivery & Quality! Recommended Purity Levels Standard Peptide Synthesis GenScript proposes a range of different purity levels to help you make the right choice for your application. -
Synthesis of Proteins by Automated Flow Chemistry
Synthesis of Proteins by Automated Flow Chemistry Authors: N. Hartrampf1, A. Saebi1†, M. Poskus1†, Z. P. Gates1, A. J. Callahan1, A. E. Cowfer1, S. Hanna1, S. Antilla1, C. K. Schissel1, A. J. Quartararo1, X. Ye1, A. J. Mijalis1,2, M. D. Simon1, A. Loas1, S. Liu1,3, C. Jessen4, T. E. Nielsen4 and B. L. Pentelute1* 5 Affiliations: 1 Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. 2 Current address: Harvard Medical School, Department of Genetics, 77 Avenue Louis Pasteur, Boston, 10 MA 02115, USA. 3 Current address: Department of Chemistry, East China Normal University, 3663 North Zhongshan Rd., Shanghai, 200062, China. 4 Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark. *Correspondence to: [email protected] 15 † authors contributed equally. Abstract: Ribosomes produce most proteins of living cells in seconds. Here we report highly efficient 20 chemistry matched with an automated fast-flow instrument for the direct manufacturing of peptide chains up to 164 amino acids over 328 consecutive reactions. The machine is rapid - the peptide chain elongation is complete in hours. We demonstrate the utility of this approach by the chemical synthesis of nine different protein chains that represent enzymes, structural units, and regulatory factors. After purification and folding, the synthetic materials display biophysical and enzymatic 25 properties comparable to the biologically expressed proteins. High-fidelity automated flow chemistry is an alternative for producing single-domain proteins without the ribosome. One Sentence Summary: A benchtop automated machine synthesizes protein chains in hours. 30 Main Text: Mechanical pumps, valves, solid supports and computers have transformed the way we perform chemical reactions. -
Highly Enantioselective Synthesis of Γ-, Δ-, and E-Chiral 1-Alkanols Via Zr-Catalyzed Asymmetric Carboalumination of Alkenes (ZACA)–Cu- Or Pd-Catalyzed Cross-Coupling
Highly enantioselective synthesis of γ-, δ-, and e-chiral 1-alkanols via Zr-catalyzed asymmetric carboalumination of alkenes (ZACA)–Cu- or Pd-catalyzed cross-coupling Shiqing Xu, Akimichi Oda, Hirofumi Kamada, and Ei-ichi Negishi1 Department of Chemistry, Purdue University, West Lafayette, IN 47907 Edited by Chi-Huey Wong, Academia Sinica, Taipei, Taiwan, and approved May 2, 2014 (received for review January 21, 2014) Despite recent advances of asymmetric synthesis, the preparation shown in Schemes 1 and 2 illustrate the versatility of ZACA of enantiomerically pure (≥99% ee) compounds remains a chal- represented by the organoaluminum functionality of the ini- lenge in modern organic chemistry. We report here a strategy tially formed ZACA products. Introduction of the OH group for a highly enantioselective (≥99% ee) and catalytic synthesis by oxidation of initially formed alkylalane intermediates in of various γ- and more-remotely chiral alcohols from terminal Scheme 2 is based on two considerations: (i) the proximity of the alkenes via Zr-catalyzed asymmetric carboalumination of alkenes OH group to a stereogenic carbon center is highly desirable for (ZACA reaction)–Cu- or Pd-catalyzed cross-coupling. ZACA–in situ lipase-catalyzed acetylation to provide ultrapure (≥99% ee) di- oxidation of tert-butyldimethylsilyl (TBS)-protected ω-alkene-1-ols functional intermediates, and (ii) the versatile OH group can R S α ω produced both ( )- and ( )- , -dioxyfunctional intermediates (3) be further transformed to a wide range of carbon groups by – ee ≥ ee in 80 88% , which were readily purified to the 99% level tosylation or iodination followed by Cu- or Pd-catalyzed cross- by lipase-catalyzed acetylation through exploitation of their high α ω coupling. -
Complex Organic Synthesis: Structure, Properties, And/Or 5 Function? 6
Essays 1 DOI: 10.1002/ijch.201800016 2 3 4 Complex Organic Synthesis: Structure, Properties, and/or 5 Function? 6 7 [a] 8 George M. Whitesides 9 10 In 1956 – the year R. B. Woodward’s famous Perspective[1] addition to performing research, university research groups 11 was published – I was a senior in high school. The next year, have the important obligation to teach students what they need 12 when I started college and joined a research group, it was still to know for their intended careers. Is the training that students 13 all the (I thought, hopefully and in anticipation, “we”) organic currently receive in organic synthesis the one that best 14 chemistry graduate students talked about. The vision was so prepares them for their future (and which may possibly be 15 astonishing, and the ambition so grand, that it was transfixing. entirely different than their research director’s past)? 16 It clearly marked the transformation of the field of synthesis 17 from one state into something entirely different – one marked 18 by disciplined, elegant, complexity. I never actually met “Organic Synthesis:” What Is It? 19 Woodward (other than secondarily, through one of his 20 postdocs, to let me know of his intense displeasure at my use The phrase “Organic Synthesis” is a complicated one, and 21 of his IR spectrometers in the middle of the night), but I did means different things to different people. It is always risky, 22 go to Woodward group seminars, where I learned humility, as semantically, to use a single phrase to describe many different 23 well as new definitions of “endurance” and bladder control things. -
Peptide Synthesis and Modification As a Versatile Strategy for Probes Construction
University of Pennsylvania ScholarlyCommons Master of Chemical Sciences Capstone Projects Department of Chemistry 8-11-2017 Peptide Synthesis and Modification as a ersatileV Strategy for Probes Construction Jieliang Wang University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/mcs_capstones Part of the Chemistry Commons Wang, Jieliang, "Peptide Synthesis and Modification as a ersatileV Strategy for Probes Construction" (2017). Master of Chemical Sciences Capstone Projects. 7. https://repository.upenn.edu/mcs_capstones/7 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/mcs_capstones/7 For more information, please contact [email protected]. Peptide Synthesis and Modification as a ersatileV Strategy for Probes Construction Abstract Peptide synthesis and modification is a ersatilev chemical biology strategy to construct probes and sensors of a variety of types of biological activity, including protein/protein interactions, protein localization, and proteolysis. In my thesis work, I have made probes for three distinct biological applications. To do so, I have used a combination of solid phase peptide synthesis (SPPS), native chemical ligation (NCL), protein expression, and S-alkylation to construct probes with desired functional groups, while minimizing the perturbation to the native structure. In the first project, I constructed photo- crosslinking probes to study the difference in protein-protein interactions of N-terminal acetylated (N-ac) histone H4 peptide versus non-acetylated histone H4 peptide. One protein was identified yb Western blot with binding preference to N-Ace histone H4 peptide. In the second separate project, I constructed probes to study the toxicity mechanism of proline/arginine dipeptide PRx from amyotrophic lateral sclerosis (ALS) associated gene C9ORF72. -
M.Sc. (Organic Chemistry) Part II Pattern 2019
M.Sc. (Organic Chemistry) Part II Pattern 2019 Deccan Education Society’s FERGUSSON COLLEGE (AUTONOMOUS), PUNE Syllabus for M. Sc. (Organic Chemistry) Part II (Semester-III and Semester-IV) [Pattern 2019] from Academic Year 2020-21 1 Department of Chemistry, Fergusson College (Autonomous), Pune M.Sc. (Organic Chemistry) Part II Pattern 2019 Program Structure of M.Sc. (Organic Chemistry) Part-II Particulars Paper Paper Title of Paper Type of No. of code Paper Credits Paper- 1 CHO5301 Stereochemistry of Organic Molecules CORE-1 4 Paper - 2 CHO5302 Structure Determination by Analytical CORE- 2 4 Methods Paper - 3 CHO5303 Chemistry of Heterocycles and Medicinal D. elective Chemistry CHO5304 Pharmaceutical Chemistry G. Elective M.Sc. CHO5305 MOOC Course MOOC1 4 Semester- III Paper -4 CHO5306 Organic Chemistry Practical V PCORE-1 4 Paper -5 CHO5307 Organic Chemistry Practical VI PCORE-1 4 Chemistry of Natural Products and CHO5401 Paper -1 Chiron Approach D. elective CHO5402 Forensic Science and Toxicology G. Elective 4 CHO5403 MOOC Course MOOC2 Paper - 2 CHO5404 Advanced Synthetic Organic Chemistry D. elective CHO5405 Analytical Spectroscopy G. Elective 4 M. Sc. CHO5409 MOOC Course MOOC3 Semester- Paper - 3 Designing of Organic Synthesis and D. elective CHO5407 IV Asymmetric Synthesis 4 CHO5408 Polymer Chemistry G. Elective CHO5409 MOOC Course MOOC4 Paper -4 CHO5410 Organic Chemistry Practical VII PCORE-3 4 Paper -5 CHO5411 Organic Chemistry Practical VIII PCORE-4 4 OR Paper -6 Project / Internship (Optional for practical 8 CHO5412 courses CHO5410 and CHO5411) * 1 P * Course- 1 CHO-01 Environmental Chemistry MOOCs 4 Course- 2 CHO-02 MOOCs 4 MOOC Biophysical Chemistry courses Course-3 CHO-03 Environmental soil chemistry MOOCs 4 Course- 4 CHO-04 Food Analysis MOOCs 4 CHO5301: Stereochemistry of Organic Molecules [Credits – 4] 2 Department of Chemistry, Fergusson College (Autonomous), Pune M.Sc. -
Organic Synthesis - Gian Paolo Chiusoli
FUNDAMENTALS OF CHEMISTRY – Vol. II - Organic Synthesis - Gian Paolo Chiusoli ORGANIC SYNTHESIS Gian Paolo Chiusoli University of Parma, Italy Keywords: asymmetric synthesis, catalysis, combinatorial chemistry, chirality amplification, electrochemical synthesis, electrocyclic reactions, electrophilic reagents, enzymes, metallacyclic reactions, nucleophilic reagents, oligomerization, organic reactions, organic sequences, phase transfer, photochemical synthesis, polymerization, protective groups, retrosynthetic analysis, selectivity, self-assembly, self-replication, solid-state reactions, stereoselectivity, supercritical fluids Contents 1. Introduction 2. Organic Reactions 2.1. Reactions of Nucleophilic Reagents with Electrophilic Substrates 2.2. Reactions of Electrophilic Reagents with Nucleophilic Substrates 2.3. Electrocyclic Reactions 2.4. Metallacyclic Reactions: Metathesis 3. Rate and Selectivity Control 3.1. Rational Use of Chemical and Physical Parameters 3.2. Catalysis 3.3. Selectivity 3.4. Asymmetric Synthesis 3.5. Protective Groups 3.6. Heterogeneous and Solid-State Reactions 3.7. Phase-Transfer Techniques 3.8. Syntheses in Special Fluids 3.8.1. Synthesis in Fluorous Phase 3.8.2. Synthesis in Supercritical Fluids 3.8.3. Synthesis in Ionic Liquids 3.9. Photochemical Synthesis 3.10. Electrochemical Synthesis 4. Multistep UNESCOReactions – EOLSS 4.1. Oligomerization and Polymerization of Organic Compounds 4.2. Stepwise Reactions Involving Group Protection and Deprotection 4.3. Chain-Growth Organic Reactions 5. Organic SynthesisSAMPLE based on Weak Interactions: CHAPTERS Self-Assembly 6. Bio-Inspired Organic Synthesis 6.1. Enzyme Models 6.2. Antibody-Catalyzed Reactions 6.3. Self-Replication 6.4. Amplification of Chirality 7. Synthetic Planning and Strategies 7.1. Target Identification and Modeling 7.1.1. New Structures 7.1.2. New Structures with Function ©Encyclopedia of Life Support Systems (EOLSS) FUNDAMENTALS OF CHEMISTRY – Vol.