cdk
diff --git a/‎base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/Expr.java‎
Lines changed: 5 additions & 1 deletion b/‎base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/Expr.java‎
Lines changed: 5 additions & 1 deletion
@@ -462,6 +462,8 @@ public Expr and(Expr expr) {
             if (type.isLogical() && !expr.type.isLogical()) {
                 if (type == AND)
                     right.and(expr);
+                else if (type != NOT)
+                    setLogical(Type.AND, expr, new Expr(this));
                 else
                     setLogical(Type.AND, expr, new Expr(this));
             } else {
@@ -488,8 +490,10 @@ public Expr or(Expr expr) {
             if (type.isLogical() && !expr.type.isLogical()) {
                 if (type == OR)
                     right.or(expr);
-                else
+                else if (type != NOT)
                     setLogical(Type.OR, expr, new Expr(this));
+                else
+                    setLogical(Type.OR, new Expr(this), expr);
             }
             else
                 setLogical(Type.OR, new Expr(this), expr);