{"id":6859,"date":"2012-05-28T13:06:57","date_gmt":"2012-05-28T12:06:57","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=6859"},"modified":"2017-07-09T14:55:17","modified_gmt":"2017-07-09T13:55:17","slug":"streptomycin-a-case-study-in-the-progress-of-science","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6859","title":{"rendered":"Streptomycin: a case study in the progress of science."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"6859\">\n<p>Streptomycin is an antibiotic active against tuberculosis, and its discovery has become something of a cause c\u00e9l\u00e8bre. It was first isolated on October 19, 1943 by a graduate student <a href=\"http:\/\/www.albertschatzphd.com\/?cat=articles&amp;subcat=streptomycin&amp;itemnum=001\" target=\"_blank\">Albert Schatz<\/a> in the laboratory of Selman Waksman at Rutgers University. I want to concentrate in this post on its molecular structure. Its initial isolation was followed by an extraordinarily concentrated period of about three years devoted to identifying that structure, culminating in a review of this chemistry in 1948 by Lemieux and Wolfram.<span id=\"cite_ITEM-6859-0\" name=\"citation\"><a href=\"#ITEM-6859-0\">[1]<\/a><\/span> This review presents the structure as shown below (left). The modern rendering on the right is based on a crystal structure done in 1978.<span id=\"cite_ITEM-6859-1\" name=\"citation\"><a href=\"#ITEM-6859-1\">[2]<\/a><\/span><sup>&Dagger;<\/sup><\/p>\n<table border=\"0\">\n<tbody>\n<tr>\n<td><a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/05\/streptomycin.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-6861\" title=\"streptomycin\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/05\/streptomycin.jpg\" alt=\"\" width=\"236\" height=\"546\" \/><\/a><\/td>\n<td><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter  wp-image-6862\" title=\"streptomycin\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('white');jmolApplet([450,450],'load wp-content\/uploads\/2012\/05\/STOSEH10.cif;frame 19; zoom 100;');\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/05\/streptomycin.svg\" alt=\"\" width=\"285\" height=\"250\" \/><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>My interest in this was kindled by wondering how elucidating such a structure would be accomplished during the 1940s. None of the modern structural techniques were available then (NMR, MS, X-Ray); only IR and polarimetry (optical rotation). So how was it done? Well, the same way it had been done for the previous 100 years or so; degradation. In this case, into three smaller fragments, labelled <strong>A-C<\/strong> in the rhs diagram, and named <em>streptidine<\/em>, <em>streptose<\/em> and<em> glucosamine<\/em> in the original analysis.<\/p>\n<ol>\n<li>This reduction to smaller fragments is set out on page 338 of the Lemieux and Wolfram\u00a0article.<span id=\"cite_ITEM-6859-0\" name=\"citation\"><a href=\"#ITEM-6859-0\">[1]<\/a><\/span><\/li>\n<li>The procedure to isolate streptomycin is described from p343 and the purification on p345, which concludes with the molecular formula C<sub>21<\/sub>H<sub>37-39<\/sub>N<sub>7<\/sub>O<sub>12<\/sub><\/li>\n<li>On p346, after evaluating other methods for determining the molecular weight,\u00a0C<sub>21<\/sub>H<sub>39<\/sub>N<sub>7<\/sub>O<sub>12 <\/sub>is the final candidate for its formula.<\/li>\n<li>Next, &#8220;strongly basic&#8221; degradation yields streptidine (Ring C), with the formula C<sub>8<\/sub>H<sub>18<\/sub>N<sub>6<\/sub>O<sub>4<\/sub>. Likewise, formulae were established for the other components.<\/li>\n<li>On p347, the odyssey to assemble a structure from this information begins. I will not dwell on the details. But by p359, a partial structure of Streptidine-streptose-N-methyl-L-glucosamine is suggested.<\/li>\n<li>By p366, they have boiled it down to two possibilities (they call XXXIX and XL), and they abandon the hydrolytic procedures used up to that point and adopt oxidative reactions, which narrow it down to\u00a0XXXIX.<\/li>\n<li>The next property to be used to determine the structure is optical rotation. They knew it incorporates an L-sugar (whose absolute configuration was not known in 1948), and of course there are 15 stereogenic centres in the entire system (32768 possibilities). P368 -375 continues discussion of the stereochemistry, and in particular the need to demonstrate that none of the degradative\/oxidative procedures have interfered with it, so to speak.<\/li>\n<li>By p375, it has all boiled down to the stereochemistry of the glycosidic bonds (marked with a red ring above). This was assigned on the basis of optical rotations and the use of additive rules (Table 1 of their article). This discussion ends with the stereochemistry shown above. Although\u00a0initially assigned <em>trans<\/em>, it was subsequently revised to <em>cis<\/em>, and then back to <em>trans<\/em> again.<\/li>\n<li>On p382, the wrap up has started. Table III there shows the properties of the 18 products obtained merely from the preparation of ring A (for comparison with the product obtained by degradation). Some 127 articles have been cited for supporting information and around 50 pages of tight logical argument presented as evidence, similar in length indeed to the longer mathematical proofs!<\/li>\n<li>There was one residual uncertainty (green ring above) that had to wait for the crystal structure in 1978 to resolve. It took so long because of the challenge of finding a crystalline derivative.<\/li>\n<\/ol>\n<p>I cannot help but note that the skills required to assemble a structure by degradation, and no use of NMR, MS or X-ray, were formidable, and very probably there are few chemists alive nowadays who could do a similar job (the motivation to do so would also be lacking). Assuming good crystals were available, solving such a structure nowadays using crystallography would only take 24 hours or so. And structures with 100+ stereogenic centres can now be done. When Woodward\u00a0<a href=\"http:\/\/www.youtube.com\/watch?v=ph19KFpllDU\">muse<\/a>d\u00a0about the progress in chemistry, he might have had streptomycin in mind. I think it is worth remembering that the structural chemistry of 60 years ago was quite an intellectual achievement.<\/p>\n<hr \/>\n<p><sup>&Dagger;<\/sup>In fact the structure was first reported in 1968<span id=\"cite_ITEM-6859-2\" name=\"citation\"><a href=\"#ITEM-6859-2\">[3]<\/a><\/span> but the coordinates in the CSD (Cambridge structure database) derive from the 1978 report.<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-6859-0\">R. Lemieux, and M. Wolfrom, \"The Chemistry of Streptomycin\", <i>Advances in Carbohydrate Chemistry<\/i>, pp. 337-384, 1948. <a href=\"https:\/\/doi.org\/10.1016\/s0096-5332(08)60034-x\">https:\/\/doi.org\/10.1016\/s0096-5332(08)60034-x<\/a>\n\n<\/li>\n<li id=\"ITEM-6859-1\">S. Neidle, D. Rogers, and M.B. Hursthouse, \"The crystal and molecular structure of streptomycin oxime selenate tetrahydrate\", <i>Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences<\/i>, vol. 359, pp. 365-388, 1978. <a href=\"https:\/\/doi.org\/10.1098\/rspa.1978.0047\">https:\/\/doi.org\/10.1098\/rspa.1978.0047<\/a>\n\n<\/li>\n<li id=\"ITEM-6859-2\">S. Neidle, D. Rogers, and M. Hursthouse, \"The crystal and molecular structure of streptomycin oxime selenate\", <i>Tetrahedron Letters<\/i>, vol. 9, pp. 4725-4728, 1968. <a href=\"https:\/\/doi.org\/10.1016\/s0040-4039(00)75942-9\">https:\/\/doi.org\/10.1016\/s0040-4039(00)75942-9<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 6859 -->","protected":false},"excerpt":{"rendered":"<p>Streptomycin is an antibiotic active against tuberculosis, and its discovery has become something of a cause c\u00e9l\u00e8bre. It was first isolated on October 19, 1943 by a graduate student Albert Schatz in the laboratory of Selman Waksman at Rutgers University. I want to concentrate in this post on its molecular structure. Its initial isolation was [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":5,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[4],"tags":[845,1178,2651,847,849,850,74,846,848,42],"ppma_author":[2661],"class_list":["post-6859","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-albert-schatz","tag-candidate-for-its-formula","tag-historical","tag-laboratory-of-selman-waksman","tag-ms","tag-muse","tag-pence","tag-rutgers-university","tag-tuberculosis","tag-x-ray"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.7 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Streptomycin: a case study in the progress of science. - Henry Rzepa&#039;s Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6859\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Streptomycin: a case study in the progress of science. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Streptomycin is an antibiotic active against tuberculosis, and its discovery has become something of a cause c\u00e9l\u00e8bre. 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&#8220;Mee&#8221;  and &#8220;Mellor&#8221;.","author":"Henry Rzepa","date":"November 11, 2023","format":false,"excerpt":"I am a member of the \u00a0Royal Society of \u00a0Chemistry's Historical group. Amongst other activities, it publishes two editions\u00a0of a newsletter each year for its members. A new theme was recently launched asking for contributions on the topic of \u00a0\"two influential books\" and shortly to appear in the winter 2023\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":13136,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13136","url_meta":{"origin":6859,"position":1},"title":"Halogen bonds 3: &#8220;Nitrogen tri-iodide&#8221;","author":"Henry Rzepa","date":"December 1, 2014","format":false,"excerpt":"Nitrogen tri-iodide, or more accurately the complex between it and ammonia ranks amongst the oldest known molecules (1812). I became familiar with it around the age of 12-13, in an era long gone when boys (and very possibly girls too) were allowed to make such substances in their parent's back\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":6438,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6438","url_meta":{"origin":6859,"position":2},"title":"Confirming the Fischer convention as a structurally correct representation of absolute configuration.","author":"Henry Rzepa","date":"March 13, 2012","format":false,"excerpt":"I wrote in an earlier post\u00a0how Pauling's\u00a0Nobel prize-winning suggestion in February 1951 of a (left-handed)\u00a0\u03b1-helical structure for proteins was based on the wrong absolute configuration of the amino acids (hence his helix should really have been the right-handed enantiomer). This was most famously established a few months later by Bijvoet's\u2026","rel":"","context":"In &quot;Chiroptics&quot;","block_context":{"text":"Chiroptics","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2644"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":17633,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17633","url_meta":{"origin":6859,"position":3},"title":"George Olah and the norbornyl cation.","author":"Henry Rzepa","date":"March 10, 2017","format":false,"excerpt":"George Olah passed away on March 8th. He was part of the generation of scientists in the post-war 1950s who had access to chemical instrumentation that truly revolutionised chemistry. In particular he showed how the then newly available NMR spectroscopy illuminated structures of cations in solvents such \"Magic acid\". The\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":2828,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2828","url_meta":{"origin":6859,"position":4},"title":"Can a cyclobutadiene and carbon dioxide co-exist in a calixarene cavity?","author":"Henry Rzepa","date":"November 19, 2010","format":false,"excerpt":"On 8th August this year, I posted on a fascinating article that had just appeared in Science in which the crystal structure was reported of two small molecules,\u00a01,3-dimethyl cyclobutadiene\u00a0and\u00a0carbon dioxide, entrapped together inside a calixarene cavity. Other journals (e.g.\u00a0Nature Chemistry ran the article as a research highlight (where the purpose\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/11\/cbd.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17122,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17122","url_meta":{"origin":6859,"position":5},"title":"Long C=C bonds.","author":"Henry Rzepa","date":"December 1, 2016","format":false,"excerpt":"Following on from a search for long C-C bonds, here is the same repeated for C=C double bonds. The query restricts the search to each carbon having just two non-metallic substituents. To avoid conjugation with these, they each are 4-coordinated; the carbons themselves are three-coordinated. Further constraints are the usual\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"sq","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/12\/sq-1024x415.jpg?resize=350%2C200","width":350,"height":200},"classes":[]}],"jetpack_likes_enabled":false,"authors":[{"term_id":2661,"user_id":1,"is_guest":0,"slug":"admin","display_name":"Henry Rzepa","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/6859","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=6859"}],"version-history":[{"count":14,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/6859\/revisions"}],"predecessor-version":[{"id":18628,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/6859\/revisions\/18628"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=6859"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=6859"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=6859"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=6859"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}