{
  "version": "https://jsonfeed.org/version/1.1",
  "title": "chem-bla-ics",
  "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.",
  "home_page_url": "https://chem-bla-ics.linkedchemistry.info/",
  "feed_url": "https://chem-bla-ics.linkedchemistry.info/2006/12/17/counting-stereoisomers-from-molecular_17.json",
  "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png",
  "language": "en",
  "authors": [
    {
      "name": "Egon Willighagen",
      "url": "https://orcid.org/0000-0001-7542-0286",
      "_orcid": "0000-0001-7542-0286"
    }
  ],
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    {
      "id": "https://doi.org/10.59350/r9gwr-k2s81",
      "url": "https://chem-bla-ics.linkedchemistry.info/2006/12/17/counting-stereoisomers-from-molecular_17.html",
      "title": "Counting constitutional isomers from the molecular formula",
      "content_html": "<p><strong>Update</strong>: check <a href=\"https://doi.org/10.1186/s13321-022-00604-9\">these</a> <a href=\"https://doi.org/10.1186/s13321-021-00529-9\">two</a> papers.</p>\n\n<p>We all know the combinatorial explosion when calculating the number of possible constitutional\nisomers (see <a href=\"http://en.wikipedia.org/wiki/Structural_isomerism\">wp:structural isomorphism</a>) of\na certain molecular formula. For example, C2H6 has only one constitutional isomer (ethane,\n<span class=\"chem:inchi\" xmlns:chem=\"http://www.blueobelisk.org/chemistryblogs/\">InChI=1/C2H6/c1-2/h1-2H3</span>),\nand C4H10 has only two. Especially, breaking symmetry by replacing one\ncarbon by another element, or replacing a single by a double bond, increases the number sharply.\nFor example, C7H16 has only nine constitutional isomers, while replacing two single bonds by two\ndouble bonds, creating C7H10, increases this number to 499! Then, replacing in the last formula,\none carbon by an oxygen adds another few, totaling 747 isomers.</p>\n\n<p>Now, C8H8NBr has at least <strong>649 thousand</strong> constitutional isomers, and I am quite interested in\nbeing able to know the number of isomers beforehand, without having to generate the structures\nitself (for example, using <a href=\"http://cdk.sf.net/\">CDK</a>’s <code class=\"language-plaintext highlighter-rouge\">GENMDeterministicGenerator</code>).\n<span class=\"chem:inchi\" xmlns:chem=\"http://www.blueobelisk.org/chemistryblogs/\">InChI=1/C8H8BrN/c9-7-1-2-8-6(5-7)3-4-10-8/h1-2,5,10H,3-4H2</span>\nis one of the isomers.</p>\n\n<p>So, my question: is anyone aware of free code (in order of preference: 1. LGPL, 2. BSD/MIT,</p>\n<ol>\n  <li>opensource, 4. free) to calculate or estimate the number of constitutional isomers for a\ncertain molecular formula. An estimate would already be nice. Ideally, I would implement this bit\nof code into the CDK, but otherwise, just knowing the number of isomers for C8H8NBr would be\nnice :)</li>\n</ol>\n\n<p>Additionally, any relevant, recent literature recommendations are most welcomed. I am aware of the\nuse of polynomials, but literature I have seen so far just focuses on molecules of a certain\narchitecture, and it not able to come up with a guess based on the molecular formula alone.</p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">McKay, B. D., Yirik, M. A., &#38; Steinbeck, C. (2022). Surge: a fast open-source chemical graph generator. <i>Journal of Cheminformatics</i>, <i>14</i>(1). https://doi.org/10.1186/s13321-022-00604-9 <a href=\"https://doi.org/10.1186/s13321-022-00604-9\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1186/s13321-022-00604-9\">Scholia</a></div>\n    <div class=\"csl-entry\">Yirik, M. A., Sorokina, M., &#38; Steinbeck, C. (2021). MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle. <i>Journal of Cheminformatics</i>, <i>13</i>(1). https://doi.org/10.1186/s13321-021-00529-9 <a href=\"https://doi.org/10.1186/s13321-021-00529-9\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1186/s13321-021-00529-9\">Scholia</a></div>\n  </div>",
      "summary": "Update: check these two papers.",
      
      "date_published": "2006-12-17T00:00:00+00:00",
      "date_modified": "2025-02-23T00:00:00+00:00",
      "tags": ["cheminf","cdk"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1186/s13321-021-00529-9", "doi": "10.1186/s13321-021-00529-9"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.1186/s13321-022-00604-9", "doi": "10.1186/s13321-022-00604-9"
             }
            
          
        ],
      
      
      "_citations": [
        
          
          
            { "url": "https://doi.org/10.1186/1471-2105-8-487", "doi": "10.1186/1471-2105-8-487"
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        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

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}