{
  "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/2009/03/20/preferential-positions-of-phophate.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"
    }
  ],
  "items": [

    {
      "id": "https://doi.org/10.59350/e7wjx-fvr63",
      "url": "https://chem-bla-ics.linkedchemistry.info/2009/03/20/preferential-positions-of-phophate.html",
      "title": "Preferential positions of phophate counter ions",
      "content_html": "<p>A long time ago (‘96 or so?), as a student with the no longer existing CAOS/CAMM (Google shows some traces, like\n<a href=\"https://doi.org/10.3233/CMI-2014-000003\">this chapter describing the centre</a>), I did a short internship\nwith Hilbert Bruijn-Slot (I hope I remember his name correctly), where has asked me to look at data in the CSD, and in\nparticular the prefered position of phosphate counter ions. It was a fun research, and almost made it into a paper, if we\nwere not just beating by a few months by a group of Russians who just published the same.</p>\n\n<p>Today, <a href=\"http://chem-bla-ics.blogspot.com/2009/03/nature-chemistry-improves-publishing.html?showComment=1237542960000#c7670910429973706274\">Neil asked me</a> <!-- keep link -->\nto look at another Nature Chemistry paper (DOI:<a href=\"http://dx.doi.org/10.1038/nchem.100\">10.1038/nchem.100</a>), and in particular\n<a href=\"http://www.nature.com/nchem/journal/v1/n1/compound/nchem.100_ci.html\">its Chemical Compounds table</a>. I could not directly\nspot the thing not in the table I discussed, but did notice the phosphate salts in the table. Not uncommonly, the counter ions are not near the phosphate in this diagram and I wondered how they did this in 3D.</p>\n\n<p>Well, bringing back good memories to that internship I mentioned, <a href=\"http://www.nature.com/nchem/journal/v1/n1/compound/nchem.100_comp5_3d.html\">the 3D model</a>\nshown by <a href=\"http://www.jmol.org/\">Jmol</a> actually does show the salt, and with the two sodiums near the phosphate;\neven better, they sit at very recognisable positions :)</p>\n\n<p><img src=\"/assets/images/phosphateSalt.png\" alt=\"\" /></p>\n\n<h4>References</h4>\n<div class=\"csl-bib-body\">\n    <div class=\"csl-entry\">Noordik, J. H. (2004). The CAOS/CAMM Center: The Dutch national academic facility for computer-assisted organic synthesis and modeling. <i>Cheminformatics</i>, <i>1</i>(1–2), 7–36. https://doi.org/10.3233/cmi-2014-000003 <a href=\"https://doi.org/10.3233/CMI-2014-000003\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.3233/CMI-2014-000003\">Scholia</a></div>\n    <div class=\"csl-entry\">Sawada, T., Yoshizawa, M., Sato, S., &#38; Fujita, M. (2009). Minimal nucleotide duplex formation in water through enclathration in self-assembled hosts. <i>Nature Chemistry</i>, <i>1</i>(1), 53–56. https://doi.org/10.1038/nchem.100 <a href=\"https://doi.org/10.1038/nchem.100\">CrossRef</a> <a href=\"https://qlever.scholia.wiki/doi/10.1038/nchem.100\">Scholia</a></div>\n  </div>",
      "summary": "A long time ago (‘96 or so?), as a student with the no longer existing CAOS/CAMM (Google shows some traces, like this chapter describing the centre), I did a short internship with Hilbert Bruijn-Slot (I hope I remember his name correctly), where has asked me to look at data in the CSD, and in particular the prefered position of phosphate counter ions. It was a fun research, and almost made it into a paper, if we were not just beating by a few months by a group of Russians who just published the same.",
      "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/phosphateSalt.png",
      "date_published": "2009-03-20T00:00:00+00:00",
      "date_modified": "2025-11-19T00:00:00+00:00",
      "tags": ["chemistry","jmol"],
      "_references": [
        
          
          
            { "url": "https://doi.org/10.1038/nchem.100", "doi": "10.1038/nchem.100"
             }
            ,
          
        
          
          
            { "url": "https://doi.org/10.3233/CMI-2014-000003", "doi": "10.3233/CMI-2014-000003"
             }
            
          
        ],
      
      
      
      
      
      
        "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ]
      
    }

  ]
}