Preferential positions of phophate counter ions
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.
Today, Neil asked me to look at another Nature Chemistry paper (DOI:10.1038/nchem.100), and in particular its Chemical Compounds table. I could not directly spot 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.
Well, bringing back good memories to that internship I mentioned, the 3D model shown by Jmol actually does show the salt, and with the two sodiums near the phosphate; even better, they sit at very recognisable positions :)

Additional details
Description
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.
Identifiers
- GUID
- https://doi.org/10.59350/e7wjx-fvr63
- URL
- https://chem-bla-ics.linkedchemistry.info/2009/03/20/preferential-positions-of-phophate.html
Dates
- Issued
-
2009-03-20T01:00:00
- Updated
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2025-11-19T01:00:00
References
- Sawada, T., Yoshizawa, M., Sato, S., & Fujita, M. (2009). Minimal nucleotide duplex formation in water through enclathration in self-assembled hosts. Nature Chemistry, 1(1), 53–56. https://doi.org/10.1038/nchem.100
- Noordik, J. H. (2004). The CAOS/CAMM Center: The Dutch national academic facility for computer-assisted organic synthesis and modeling. Cheminformatics, 1(1-2), 7–36. https://doi.org/10.3233/cmi-2014-000003