Author Topic: how to draw fullerene and porphyrin  (Read 13287 times)

0 Members and 1 Guest are viewing this topic.

Offline shank

  • Heavy QuantumATK user
  • ***
  • Posts: 33
  • Reputation: 0
    • View Profile
how to draw fullerene and porphyrin
« on: August 10, 2009, 10:27 »
Dear all
please help me to draw fullerene and porphyrin  between two elecytrode to measure IV.

with regards
shank

Offline zh

  • QuantumATK Support
  • Supreme QuantumATK Wizard
  • *****
  • Posts: 1141
  • Reputation: 24
    • View Profile
Re: how to draw fullerene and porphyrin
« Reply #1 on: August 10, 2009, 13:36 »
First, you can search the xyz or pdf files for their molecule structures from internet by Google. Of Course, you may build them by yourself using "Molecule Builder" of VNL. Then you can use the "Atomic manipulator" to build their two-probe systems.
For example: porphyrin fe(iii) can be found here:
http://xray.bmc.uu.se/hicup//POR/index.html
http://www.3dchem.com/inorganicmolecule.asp?id=1403


Offline Anders Blom

  • QuantumATK Staff
  • Supreme QuantumATK Wizard
  • *****
  • Posts: 5411
  • Country: dk
  • Reputation: 89
    • View Profile
    • QuantumATK at Synopsys
Re: how to draw fullerene and porphyrin
« Reply #2 on: August 10, 2009, 14:03 »
A C60 molecule as XYZ is attached, perhaps it helps a bit. The new VNL (2009.06) has an entire cupboard of various fullerenes.

Offline shank

  • Heavy QuantumATK user
  • ***
  • Posts: 33
  • Reputation: 0
    • View Profile
Re: how to draw fullerene and porphyrin
« Reply #3 on: August 12, 2009, 10:05 »
Thanks for reply.Is it possible to import the structure drwan in chem draw  to VNL for I-V
with regards

Offline Anders Blom

  • QuantumATK Staff
  • Supreme QuantumATK Wizard
  • *****
  • Posts: 5411
  • Country: dk
  • Reputation: 89
    • View Profile
    • QuantumATK at Synopsys
Re: how to draw fullerene and porphyrin
« Reply #4 on: August 12, 2009, 10:18 »
As far as I recall, ChemDraw is an illustration program. To run a calculation in ATK, you need the actual coordinates of the atoms, e.g. in an XYZ file. Perhaps ChemDraw has such an export function, and in that case you could do it. I would doubt that it does, but on the other hand it does have "interfaces" to QM software like MOPAC, so perhaps...

Otherwise I suggest you use a real molecular editor, like those in VNL or some external software that can produce an XYZ file.