From dias at usp.br Tue Aug 10 01:17:52 2021 From: dias at usp.br (Fabio Ramos Dias de Andrade) Date: Mon, 9 Aug 2021 19:17:52 -0300 Subject: [Cod-bugs] meaning of 'At' and 'Ow" in zeolite structure Message-ID: Dear colleagues, I kinldy ask for your help! I have a question regarding chemical composition of zeolites in CIF files. what is the meaning of 'At', in a formula such as Reference code: 96-900-6365 Mineral name: Laumontite Compound name: Laumontite Common name: Laumontite Chemical formula: Si16.00Al8.00O48.00Ca4.00*At23.08*H37.60 thank you for your support! with best regards, F?bio Ramos Dias de Andrade University of S?o Paulo, Brazil -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From grazulis at ibt.lt Tue Aug 10 10:13:56 2021 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Tue, 10 Aug 2021 10:13:56 +0300 Subject: [Cod-bugs] meaning of 'At' and 'Ow" in zeolite structure In-Reply-To: References: Message-ID: Dear Fabio! On 2021-08-10 01:17, Fabio Ramos Dias de Andrade wrote: > what is the meaning of 'At', in a formula such as? > > Reference code: 96-900-6365 The reference code (aka database ID) does not seem to belong to any of our curated or related databases (COD, PCOD, TCOD, AMCSD). For the experimental databases (COD, AMCSD), the IDs are 7-digit numbers, but you quote nine digits. We can not trace back that data. Please either provide the COD ID for the data you are working with, or the database designator from which you reference code was taken; only then the data provenance can be established. > Mineral name: Laumontite > Compound name: Laumontite > Common name: Laumontite > Chemical formula: Si16.00Al8.00O48.00Ca4.00*At23.08*H37.60 > Usually, "At" in CIFs means Astatine, or Astatium [1]. It is strange however to see this element in such abundances in an X-ray experimental structure, since all isotopes of AT are unstable, and the most stable has half-life of just 8.3 hours [1]. It would be difficult (although not impossible) to obtain crystals containing At for long enough to measure their structure. For zeolites, of course, At could be a "guest" component that was diffused rapidly (as a solute or in gaseous form) into the structure and the measured on a synchrotron or on a neutron source. Another possibility could be that "At" is mistyped "Al", although this is unlikely since Al is already present in the formula. In any case you should refer to the original publication that reported the structure ? you should find there exact description of the sample and its preparation. Hope this helps! Refs.: [1] https://www.webelements.com/astatine/ [2021-08-10 10:07:00+03:00] -- Dr. Saulius Gra?ulis Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OpenPGP_signature Type: application/pgp-signature Size: 665 bytes Desc: OpenPGP digital signature URL: From grazulis at ibt.lt Tue Aug 10 10:22:03 2021 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Tue, 10 Aug 2021 10:22:03 +0300 Subject: [Cod-bugs] meaning of 'At' and 'Ow" in zeolite structure In-Reply-To: References: Message-ID: <6fe82a2f-db32-0f02-8662-901420a8c470@ibt.lt> On 2021-08-10 01:17, Fabio Ramos Dias de Andrade wrote: > I have a question regarding chemical composition of zeolites in CIF files. > Regarding the 'Ow' designator which you mention in your Subject ? this is most probably a water molecule. It is definitely a water molecule if the CIF specifies '_atom_site_type_symbol' as 'O' and has '_atom_site_attached_hydrogens' specified as 2. An example of a structure with such markup can be found here: http://www.crystallography.net/cod/3500013.html Regards, Saulius -- Dr. Saulius Gra?ulis Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366 -------------- next part -------------- A non-text attachment was scrubbed... Name: OpenPGP_signature Type: application/pgp-signature Size: 665 bytes Desc: OpenPGP digital signature URL: