&& aliphaticAtom(ratom(1))

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))





???

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

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.

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

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





Zsolt