&& aliphaticAtom(ratom(1))

User 870ab5b546

27-09-2006 18:45:02

Consider this reaction:





[H][C:1][#8,Cl,Br,I:3].[#6,#7,#8,F,#15,#16,Cl,#33,#34,Br,#52,I;-:2]>>[#8,Cl,Br,I;-:3].[H][C:1][#6,#7,#8,F,#15,#16,Cl,#33,#34,Br,#52,I:2]





with this reactivity rule:





(match(ratom(3), "[Cl:1]", 1)


|| match(ratom(3), "[Br:1]", 1)


|| match(ratom(3), "", 1)


|| match(ratom(3), "[O:1]S(=O)(=O)", 1))


&& aliphaticAtom(ratom(1))





and substrates reactant(0): [C-]#CC1CCCC1, reactant(1): CCI and C=CBr, combinatorial combination method. I get an Invalid parameter error upon pressing the react button.





However, this reactivity rule:





aliphaticAtom(ratom(1))





does not give an Invalid parameter error. Nor does the reactivity rule:





(match(ratom(3), "[Cl:1]", 1)


|| match(ratom(3), "[Br:1]", 1)


|| match(ratom(3), "", 1)


|| match(ratom(3), "[O:1]S(=O)(=O)", 1))





???

ChemAxon d76e6e95eb

29-09-2006 08:47:41

The reaction scheme is not too clear for me. Would you please specify the products you expect from each example reaction?

User 870ab5b546

29-09-2006 12:06:46

Yeah, it's pretty general, so it's hard to read, but it's simply an SN2 substitution reaction in which the leaving group can be Cl, Br, I, or a sulfonate, and the nucleophile can be C, N, O, F, P, S, Cl, As, Se, Br, Te, or I.





The electrophilic C atom C(1) should not be aromatic. (Actually, it needs to be sp3-hybridized, but I need to use a different match rule for that.)





The point of my post, though, was that the two rules that I cited work individually, but when I combined them with &&, I get an Invalid parameter error. I think it is a bug.





Oh, to answer your question, the expected products are CCC#CC1CCCC1 and C=CC#CC1CCCC1.

ChemAxon d76e6e95eb

02-10-2006 15:44:01

Thanks, Bob, I could reproduce it and my collegue is looking for the reason.

ChemAxon e08c317633

24-10-2007 09:18:34

We have fixed this bug. The fix will be available in JChem 3.2.12 version.





Zsolt