{"id":88,"date":"2012-11-06T15:48:11","date_gmt":"2012-11-06T15:48:11","guid":{"rendered":"http:\/\/nextmovesoftware.com\/blog\/?p=88"},"modified":"2015-06-22T17:08:01","modified_gmt":"2015-06-22T16:08:01","slug":"radioactivity-its-in-the-air-for-you-and-me","status":"publish","type":"post","link":"https:\/\/nextmovesoftware.com\/blog\/2012\/11\/06\/radioactivity-its-in-the-air-for-you-and-me\/","title":{"rendered":"Radioactivity — It’s in the air for you and me"},"content":{"rendered":"

\"Radioactive<\/a>Radioactivity, discovered by Madame Curie, is the process by which the nucleus of an “unstable” atom decays to a different form.\u00a0 As mentioned in a previous blog post<\/a>, atoms are composed of protons, neutrons and electrons; protons are easy to handle in cheminformatics, electrons are incredibly difficult and here we discuss the neutrons.<\/p>\n

Checking whether the number of neutrons specified with an atom (the isotope) is plausible and reasonable is a non-trivial challenge.\u00a0 At the most simplistic level, many cheminformatics applications and file formats ignore isotopes altogether and assume every atom has the default terrestrial isotopic composition\/abundance as prescribed\/recommended by IUPAC<\/a>. The next level of sophistication is to treat the atomic symbols “D” and “T” as corresponding to deuterium, [2H]<\/code>, and tritium, [3H]<\/code> respectively.<\/p>\n

More usually, such as with MDL’s SD files or SMILES, allow the optional specification of a mass number (number of nucleons, i.e. protons+neutrons, in the nucleus).\u00a0 If not specified, the element again has the IUPAC recommended composition.\u00a0 A common misunderstanding with these semantics is that [12C]<\/code> is not the same as [C]<\/code>.\u00a0 Although terrestrial carbon is predominantly carbon-12 (98.89% by the latest 2009 recommendations) the presence of trace amounts of [13C]<\/code> keep these distinct.\u00a0 Having said that, 22 elements do have a unique isotope officially used to determine their atomic weight and hence [4Be]<\/code>, [9F]<\/code>, [11Na]<\/code>, [13Al]<\/code>, [15P]<\/code>, [21Sc]<\/code>, [25Mn]<\/code>, [27Co]<\/code>, [33As]<\/code>, [39Y]<\/code>, [41Nb]<\/code>, [45Rh]<\/code>, [53I]<\/code>, [55Cs]<\/code>, [59Pr]<\/code>, [65Tb]<\/code>, [67Ho]<\/code>, [69Tm]<\/code>, [79Au]<\/code>, [83Bi]<\/code>, [90Th]<\/code> and [91Pa]<\/code> may legitimately be canonicalised without the isotopic specification, i.e. [Be]<\/code>, F<\/code>, [Na]<\/code> and so on.<\/p>\n

The most advanced cheminformatics file formats, such as Perkin Elmer Informatics’ (formerly CambridgeSoft’s) ChemDraw CDX and CDXML file format<\/a> can even specify enrichment and depletion in specific isotopes.\u00a0 <\/p>\n

Unfortunately, having a specified isotope is often confused with being radioactive.\u00a0 For example, RSC’s ChemSpider abuses the international icon for radioactivity to actually mean “Non-standard isotope”, though this is clearly stated.\u00a0 This is because testing for a specified mass number is relatively easy, with many toolkits supporting the SMARTS semantics that [!0*]<\/code> matches any specified isotope.\u00a0 Although this is useful for identifying compounds whose isotopes need to be checked, it doesn’t correspond to radioactivity.\u00a0 For example, deuterium, [2H]<\/code> has a specified isotope but isn’t radioactive, whilst uranium, [U]<\/code>, even without a specified isotope is radioactive.<\/p>\n

To address this I’ll describe how to ascertain whether a compound is radioactive, a useful descriptor especially when dealing with the “Health & Safety” parts of a pharmaceutical company.\u00a0 A molecule is radioactive if any of its atoms is radioactive, and an atom is radioactive if it isn’t stable.\u00a0 If an isotope isn’t specified, the element must have at least one stable isotope to be considered stable (these are the elements from hydrogen, [#1]<\/code>, to lead, [#82]<\/code>, with the exceptions of technetium [#43]<\/code> and prometium [#61]<\/code>), otherwise the specified isotope must correspond to one of the 255 known stable nuclides.\u00a0 Hence, SMARTS pattern is_stable<\/em> corresponds to [0#1,1#1,2#1,0#2,3#2,4#2,...]<\/code>.\u00a0 Using De Morgan’s laws<\/a> this atom expression can be negated to produce is_radioactive<\/em> as [!0,!#1;!1,!#1;!2,!#2;\u2026]<\/code>.<\/p>\n

The complete SMARTS pattern for is_radioactive<\/em> is shown below:<\/p>\n

\r\n[!0,!#1;!1,!#1;!2,!#1;!0,!#2;!3,!#2;!4,!#2;!0,!#3;!6,!#3;!7,!#3;!0,!#4;!9,!#4;!0,!#5;!10,!#5;!11,!#5;!0,!#6;!12,!#6;!13,!#6;!0,!#7;!14,!\r\n#7;!15,!#7;!0,!#8;!16,!#8;!17,!#8;!18,!#8;!0,!#9;!19,!#9;!0,!#10;!20,!#10;!21,!#10;!22,!#10;!0,!#11;!23,!#11;!0,!#12;!24,!#12;!25,!\r\n#12;!26,!#12;!0,!#13;!27,!#13;!0,!#14;!28,!#14;!29,!#14;!30,!#14;!0,!#15;!31,!#15;!0,!#16;!32,!#16;!33,!#16;!34,!#16;!36,!#16;!0,\r\n!#17;!35,!#17;!37,!#17;!0,!#18;!36,!#18;!38,!#18;!40,!#18;!0,!#19;!39,!#19;!41,!#19;!0,!#20;!40,!#20;!42,!#20;!43,!#20;!44,!#20;\r\n!46,!#20;!0,!#21;!47,!#21;!0,!#22;!46,!#22;!47,!#22;!48,!#22;!49,!#22;!50,!#22;!0,!#23;!51,!#23;!0,!#24;!50,!#24;!52,!#24;!53,!#\r\n24;!54,!#24;!0,!#25;!55,!#25;!0,!#26;!54,!#26;!56,!#26;!57,!#26;!58,!#26;!0,!#27;!59,!#27;!0,!#28;!58,!#28;!60,!#28;!61,!#28;!62,\r\n!#28;!64,!#28;!0,!#29;!63,!#29;!65,!#29;!0,!#30;!64,!#30;!66,!#30;!67,!#30;!68,!#30;!70,!#30;!0,!#31;!69,!#31;!71,!#31;!0,!#32;!\r\n70,!#32;!72,!#32;!73,!#32;!74,!#32;!0,!#33;!75,!#33;!0,!#34;!74,!#34;!76,!#34;!77,!#34;!78,!#34;!80,!#34;!0,!#35;!79,!#35;!81,!#\r\n35;!0,!#36;!79,!#36;!80,!#36;!82,!#36;!83,!#36;!84,!#36;!86,!#36;!0,!#37;!85,!#37;!0,!#38;!84,!#38;!86,!#38;!87,!#38;!88,!#38;!0,\r\n!#39;!89,!#39;!0,!#40;!90,!#40;!91,!#40;!92,!#40;!94,!#40;!96,!#40;!0,!#41;!93,!#41;!0,!#42;!92,!#42;!94,!#42;!95,!#42;!96,!#42;\r\n!97,!#42;!98,!#42;!0,!#44;!96,!#44;!98,!#44;!99,!#44;!100,!#44;!101,!#44;!102,!#44;!104,!#44;!0,!#45;!103,!#45;!0,!#46;!102,!#4\r\n6;!104,!#46;!105,!#46;!106,!#46;!108,!#46;!110,!#46;!0,!#47;!107,!#47;!109,!#47;!0,!#48;!106,!#48;!108,!#48;!110,!#48;!111,!#\r\n48;!112,!#48;!114,!#48;!0,!#49;!113,!#49;!0,!#50;!112,!#50;!114,!#50;!115,!#50;!116,!#50;!117,!#50;!118,!#50;!119,!#50;!120,!\r\n#50;!122,!#50;!124,!#50;!0,!#51;!121,!#51;!123,!#51;!0,!#52;!120,!#52;!122,!#52;!123,!#52;!124,!#52;!125,!#52;!126,!#52;!0,!#5\r\n3;!127,!#53;!0,!#54;!124,!#54;!126,!#54;!128,!#54;!129,!#54;!130,!#54;!131,!#54;!132,!#54;!134,!#54;!136,!#54;!0,!#55;!133,!#\r\n55;!0,!#56;!130,!#56;!132,!#56;!134,!#56;!135,!#56;!136,!#56;!137,!#56;!138,!#56;!0,!#57;!139,!#57;!0,!#58;!136,!#58;!138,!#5\r\n8;!140,!#58;!142,!#58;!0,!#59;!141,!#59;!0,!#60;!142,!#60;!143,!#60;!145,!#60;!146,!#60;!148,!#60;!0,!#62;!144,!#62;!149,!#62;\r\n!150,!#62;!152,!#62;!154,!#62;!0,!#63;!153,!#63;!0,!#64;!154,!#64;!155,!#64;!156,!#64;!157,!#64;!158,!#64;!160,!#64;!0,!#65;!1\r\n59,!#65;!0,!#66;!156,!#66;!158,!#66;!160,!#66;!161,!#66;!162,!#66;!163,!#66;!164,!#66;!0,!#67;!165,!#67;!0,!#68;!162,!#68;!16\r\n4,!#68;!166,!#68;!167,!#68;!168,!#68;!170,!#68;!0,!#69;!169,!#69;!0,!#70;!168,!#70;!170,!#70;!171,!#70;!172,!#70;!173,!#70;!1\r\n74,!#70;!176,!#70;!0,!#71;!175,!#71;!0,!#72;!176,!#72;!177,!#72;!178,!#72;!179,!#72;!180,!#72;!0,!#73;!180,!#73;!181,!#73;!0,!\r\n#74;!182,!#74;!183,!#74;!184,!#74;!186,!#74;!0,!#75;!185,!#75;!0,!#76;!184,!#76;!187,!#76;!188,!#76;!189,!#76;!190,!#76;!192,\r\n!#76;!0,!#77;!191,!#77;!193,!#77;!0,!#78;!192,!#78;!194,!#78;!195,!#78;!196,!#78;!198,!#78;!0,!#79;!197,!#79;!0,!#80;!196,!#80\r\n;!198,!#80;!199,!#80;!200,!#80;!201,!#80;!202,!#80;!204,!#80;!0,!#81;!203,!#81;!205,!#81;!0,!#82;!204,!#82;!206,!#82;!207,!#8\r\n2;!208,!#82]\r\n<\/pre>\n
Image credit:<\/b> LimeTech<\/a> on Flickr<\/p>\n","protected":false},"excerpt":{"rendered":"
Radioactivity, discovered by Madame Curie, is the process by which the nucleus of an “unstable” atom decays to a different form.\u00a0 As mentioned in a previous blog post, atoms are composed of protons, neutrons and electrons; protons are easy to handle in cheminformatics, electrons are incredibly difficult and here we discuss the neutrons. Checking whether … Continue reading Radioactivity — It’s in the air for you and me<\/span><\/a><\/p>\n","protected":false},"author":4,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"_links":{"self":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/88"}],"collection":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/comments?post=88"}],"version-history":[{"count":17,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/88\/revisions"}],"predecessor-version":[{"id":1472,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/88\/revisions\/1472"}],"wp:attachment":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/media?parent=88"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/categories?post=88"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/tags?post=88"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}