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Homopolymer with 2 head and 2 tail atoms (PIM-1) not possible to construct


I try to construct PIM-1, which is connected via a dioxane-ring. The endgroups are two oxygen-atoms that are bonded to a benzene ring (see attached picture). I can only define one oxygen-bonded hydrogen atom as the head atom and one aromatic hydrogen-atom as the tail atom. The result is a single-bonded polymer. Does anyone knows how I might construct the homopolymer properly? Thank you for your help !! 


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CarstenCarsten (Accelrys) 
This is not possible out of the box.

The only idea I have is to name the atoms which from the bond accordingly and to make a bond between them when they are close enough to each other. I think then I would already start with monomers which do not have protons at this positions.

Or do this manually.
Hi DaveM,

The topic Building polymers with two head and tail atoms has a script to create ladder-like polymers.
Unfortunately when I tried it for PIM-1 the bonding wasn’t right. I think it expects the connection points to be further apart.

A quicker option might be to build it using a single head/tail pair first, and then fix it up with a script. For example if you name the connecting atoms R1 and R2 this should do it:
       DistanceCriterionMode => "Absolute",
       MaxAbsoluteDistance => 5,
       PathLength => 4,
       ExclusionMode => "Bonded"]);
my $doc = $Documents{"PolyPIM-1.xsd"};
my $atoms = $doc->Atoms;
foreach my $atom (@$atoms)
       next if $atom->Name ne "R1";
       my $contacts = $atom->CalculateCloseContacts();
       foreach my $contact (@$contacts)
              my $atom1 = $contact->Atom1;
              my $atom2 = $contact->Atom2;
              if($atom1->Name eq "R2" or $atom2->Name eq "R2")
                     $doc->CreateBond($atom1, $atom2, "Single");
Jason DeJoannisJason DeJoannis
Hi DaveM,

Here is a script you can use. It seems to work well on a 10mer. I was hoping that it would not introduce any ring spearing and it looks ok.
Jason DeJoannisJason DeJoannis
Oops, looks like Reinier already solved it using a very similar approach. The main difference is his method uses the CloseContacts feature with a path length included, which is nice.
Hi Jason,

I also need PIM-1 to construct, I used your script but it seems that it does not work for older version of yours.
Do you have any suggestion for that?