{"id":28802,"date":"2025-06-06T11:29:43","date_gmt":"2025-06-06T10:29:43","guid":{"rendered":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28802"},"modified":"2025-07-22T09:02:51","modified_gmt":"2025-07-22T08:02:51","slug":"how-many-of-the-compounds-that-appear-in-the-chemical-literature-are-mentioned-just-once","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28802","title":{"rendered":"How many of the compounds that appear in the chemical literature are mentioned just once?"},"content":{"rendered":"
\n

Tom recently emailed me this question: Do you know how to find out how many of the compounds that appear in the chemical literature are mentioned just once?<\/i>\u00a0Intrigued, I first set out to find out how many substances<\/b>, as Chemical Abstracts refers to the them, there were as of 5 June, 2025<\/strong>. There is a static estimate here<\/a> (219 million), but to get the most up to date information, I asked CAS directly. They responded immediately (thanks Lee!) with 294,778,693<\/em><\/strong> on the date mentioned above. It is not actually possible to answer the first question itself using CAS SciFinder, but again CAS came up with a value: “there are 113,383,649<\/strong> substances in CAS Registry with only one CAplus citation<\/em>” equivalent to \u00a0“38.5% of the current substances have only 1 reference<\/em>.” I should add this estimate was qualified\u00a0by “that can be misleading, since that includes salts, multicomponents, etc. But that’s a first pass.”<\/em> I am actually impressed that as many as 61.5% are mentioned more than once, since before learning the answer, I had intuitively guessed that percentage as being much lower.<\/p>\n

My mind then went back to the year 1974, when my PhD thesis was published.[1]<\/a><\/span> As part of this research, I had managed to synthesize several sterically hindered indoles, culminating in the preparations of 2-Methyl-3,5-di-t-butylindole<\/strong> (3<\/strong>, R=Me)and \u00a02,4,6-tri-t-butylindole <\/strong>(3<\/strong>, R=t-Butyl) by the route shown below (R= Me, t-Butyl – \u00a0a different route also gave the same product). I was very proud of this, since my research supervisor intimated to me a few years later that he had not believed I would succeed, on the grounds that making sterically hindered systems can be quite challenging! This work was published in a journal in 1975.[2]<\/a><\/span><\/p>\n

\"\"<\/a><\/p>\n

Next, to find out what “impact” this work has had in the intervening 50 years. Well, a CAS SciFinder search revealed that 2-Methyl-3,5-di-t-butylindole (3<\/strong>, R=Me) was one of the 38.5% of the current substances that have only 1 reference, to just our own work. Zero impact then! But worse was to come – \u00a02,4,6-tri-t-butylindole (3<\/strong>, R=t-Butyl) did not even have 1 reference – as far as CAS was concerned, it was an unknown compound! So too were the precursors 2-methyl-3,5-di-t-butylaniline (1<\/strong>) and the anilides\u00a02<\/strong> (R=Me, t-butyl).<\/p>\n

The explanation can be found – at least \u00a0in part – by reading our article[2]<\/a><\/span> and from \u00a0the computational modelling I did some forty years later.[3]<\/a><\/span> We were measuring kinetic isotope effects on the rate of diazo-coupling of these indoles and had noted in the article that 2,4,6-tri-t-butylindole was so hindered it simply did not diazo-couple at any measurable rate. As a result, it was not included by us in the experimental section detailing its synthesis (we really should have). The absence of the anilides 2<\/strong> in the CAS database is perhaps understandable, since they are merely precursors to the final cyclisation and these are not always characterised as fully as final products. I have retrieved the experimental information in my PhD thesis[1]<\/a><\/span> \u00a0and reproduce it here so that you can see it as well. \u00a0I note that the anilide\u00a02<\/strong>, R=Me) is mentioned only in passing (red text below) whilst for 2<\/strong>, R=t-Butyl, only an m.p. and mass spec weight are included.<\/p>\n

I have now set myself the challenge of whether substances 1<\/strong> and especially\u00a03<\/strong> (R=t-Butyl) at least can\u00a0be retrospectively added to the CAS database. Watch this space!<\/p>\n

\n

2-Methyl-3,5-di-t-butylaniline.<\/h3>\n

Bromine (8g) was added to dimethylsulfide (3.2g) in dichloromethane (40 ml) at -46\u00b0 (chorobenzene\/N2<\/sub> cooling bath) with no precautions taken to exclude moisture. A yellow crystalline precipitate of bromosulfonium bromide salt was formed. 3,5-Di-t-butyl aniline (10g) and triethylamine (5g) in dichoromethane (10 ml) were added dropwise, during the course of which the yellow salt dissolved and white crystals of triethylammonium bromide were deposited. After 2 hours at -46\u00b0, a solution of sodium (2.5g) in methanol (15 ml) was added, resulting in the production of a white precipitate of sodium bromide. After 8 hours at 20\u00b0 the rearrangement was essentially complete and the solution was shaken with water, the solvent separated and evaporated to give a yellow oil (12g, 95%) which crystallised on standing. \u03b4 1.30 (9H, s), 1.47 (9H, s) 2.13 (3H, s), 4.12 (4H, br), 6.53, 6.83 (2H, dd, JAB<\/sub> 2Hz). m\/e 265 (M+<\/sup>), 218 (M+<\/sup>-CH3<\/sub>S+<\/sup>).<\/p>\n

Raney nickel (prepared from 210g of 50% Na\/Al alloy) was stirred with a solution of the 2-methylthiomethyl-3,5-di-t-butylaniline (32g) in ethanol (150 ml) at 70\u00b0 for 1 hour. Filtration and evaporation of the solvent gave an oil which on distillation gave 2-methyl-3,5-di-t-butylaniline (66%), b.p. 126\u00b0\/2.7 mm. \u03b4 1.25, 1.38 (18H, d), 2.17 (3H, s), 3.27 (2H, s), 6.43, 6.75 (2H, dd, JAB<\/sub> 2Hz).<\/p>\n

2-Methyl-3,5-di-t-butylindole.<\/h3>\n

2-Methyl-3,5-di-t-butylaniline (2g) in ether (20 ml) and triethylamine (1g) was mixed with acetyl chloride (1.2 g) in ether. After 1 hour the ether was washed with 0.01N HCl and the solvent removed to give the acetyl derivative (90%). The acetyl derivative<\/b> was cyclised by potassium t-butoxide at 360\u00b0 to give a melt which was boiled up with water. Ether extraction followed by crystallisation from hexane gave 2-methyl-4,6-di-t-butylindole (30%), m.p. 176\u00b0. \u03bdmax<\/sub> 3370, 1617, 1538, 849, 784, 755 cm-1<\/sup>. \u03b4 1.35, 1.45 (18H, d), 2.37 (3H, s), 6.27 (1H, m), 6.97 (1H, s), 7.4 (1H, br, exchanges with D2<\/sub>O). \u03bbmax<\/sub> (log \u03b5) 223 (4.35), 272 (3.95). m\/e 243 (M+<\/sup>), 225 (M+<\/sup>-15). Found C, 81.95; H, 11.41; N, 6.19%. C15<\/sub>H25<\/sub>N requires C, 82.12; H, 11.48; N 6.38%.<\/p>\n

2,4,6-Tri-t-butyl indole.<\/h3>\n

2-Methyl-3,5-di-t-butyl aniline was acylated with trimethyl acetyl chloride in ether to give the anilide (97%), m.p. (ether) 215\u00b0, m\/e 303 (M+<\/sup>).<\/b> Fusion with potassium t-butoxide at 350C gave on cooling a solid which was treated with water, giving brown crystals of the 1:1 t-butanol complex. These were dried and sublimed very slowly at 70\u00b0 to give a colourless glass (25%), pure by nmr and tlc. \u03bdmax<\/sub> 3450, 3310, 2960, 2870, 1645, 1600, 1370, 800 cm-1<\/sup>. \u03b4 1.30, 1.35, 1.48 (27H, t), 6.25 (1H, d, 2Hz), 6.95 (1H, d, 2Hz, 7.72 (1H, s, exchanges with D2<\/sub>O). m\/e 285 (M+<\/sup>), 270 (M+<\/sup>-15). Found C, 84.12; H, 10.97; N, 4.76%. C20<\/sub>H31<\/sub>N requires C, 84.14; H, 10.94; N 4.90%.<\/p>\n

\n

References<\/h2>\n
  1. H.S. Rzepa, \"Hydrogen transfer reactions of indoles\", 1974. https:\/\/doi.org\/10.14469\/spiral\/20860<\/a>\n\n<\/li>\n
  2. B.C. Challis, and H.S. Rzepa, \"The mechanism of diazo-coupling to indoles and the effect of steric hindrance on the rate-limiting step\", Journal of the Chemical Society, Perkin Transactions 2<\/i>, pp. 1209, 1975. https:\/\/doi.org\/10.1039\/p29750001209<\/a>\n\n<\/li>\n
  3. H. Rzepa, \"I've started so I'll finish. The mechanism of diazo coupling to indoles \u2013 forty (three) years on!\", 2015. https:\/\/doi.org\/10.59350\/1jhn9-9v717<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    Tom recently emailed me this question: Do you know how to find out how many of the compounds that appear in the chemical literature are mentioned just once?\u00a0Intrigued, I first set out to find out how many substances, as Chemical Abstracts refers to the them, there were as of 5 June, 2025. There is a […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[2],"tags":[],"ppma_author":[2661],"class_list":["post-28802","post","type-post","status-publish","format-standard","hentry","category-chemical-it"],"yoast_head":"\nHow many of the compounds that appear in the chemical literature are mentioned just once? - Henry Rzepa'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=28802\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"How many of the compounds that appear in the chemical literature are mentioned just once? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Tom recently emailed me this question: Do you know how to find out how many of the compounds that appear in the chemical literature are mentioned just once?\u00a0Intrigued, I first set out to find out how many substances, as Chemical Abstracts refers to the them, there were as of 5 June, 2025. 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Synthetic chemists imply it when they describe a synthetic product with an observable enantiomeric excess or ee (which can range from close to 0% to almost 100%). There are two cheminformatics questions of interest to\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":15869,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15869","url_meta":{"origin":28802,"position":1},"title":"Earth’s missing chemistry.","author":"Henry Rzepa","date":"February 24, 2016","format":false,"excerpt":"At the precise moment I write this, there is information about 108,230,950 organic and inorganic chemical substances from the World's disclosed chemistry. So it was with a sense of curiosity\u00a0that I came across this article in the American Mineralogist entitled \"Earth\u2019s \u201cmissing\u201d minerals\" (the first in a series of articles\u2026","rel":"","context":"In "Interesting chemistry"","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":17951,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17951","url_meta":{"origin":28802,"position":2},"title":"Supporting information: chemical graveyard or invaluable resource for chemical structures.","author":"Henry Rzepa","date":"March 31, 2017","format":false,"excerpt":"Nowadays, data supporting\u00a0most publications relating to the synthesis of organic compounds is more likely than not to be found in associated \"supporting information\" rather than the (often page limited) article itself. For example, this article has an SI which is paginated at 907; almost a mini-database in its own right!\u2020\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1459,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1459","url_meta":{"origin":28802,"position":3},"title":"How long will a blog last? ArchivePress","author":"Henry Rzepa","date":"January 9, 2010","format":false,"excerpt":"After around 40 posts here, I decided to take a look at the whole effort and ask some questions. For example Should (scientific) blogs be used to report new science, or merely opinion on existing science (see this blog also)? If the former, should they be abstracted in the manner\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":3723,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3723","url_meta":{"origin":28802,"position":4},"title":"Chemicalizing a blog.","author":"Henry Rzepa","date":"March 30, 2011","format":false,"excerpt":"I am at the ACS meeting, attending a session on chemistry and the Internet. This post was inspired by Chemicalize, a service offered by ChemAxon, which scans a post like this one, and identifies molecules named. I had previously used generic post taggers, which frankly did not work well in\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":19472,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19472","url_meta":{"origin":28802,"position":5},"title":"What are the highest bond indices for main group and transition group elements?","author":"Henry Rzepa","date":"March 4, 2018","format":false,"excerpt":"A bond index (BI) approximately measures the totals of the bond orders at any given atom in a molecule. Here I ponder what the maximum values might be for elements with filled valence shells. Following Lewis in 1916 who proposed that the full valence shell for main group elements should\u2026","rel":"","context":"In "Interesting chemistry"","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":[]}],"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","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/28802","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=28802"}],"version-history":[{"count":43,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/28802\/revisions"}],"predecessor-version":[{"id":28848,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/28802\/revisions\/28848"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=28802"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=28802"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=28802"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=28802"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}