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How do I calculate the enthalpy of formation of a gaseous metal cation for a given oxidation state?

Asked by [ Admin ] , Edited by Egon Willighagen [ Admin ]

The context of my recent question about a toolkit rosetta for quantum chemistry is a recent nanoQSAR paper by Puzyn et al, where the enthalpy of formation of a gaseous metal cation for a given oxidation state turns out to be an important descriptor the toxicity of the nanomaterials studied. They used a PM6 method, and I’m going to ask the author this week how they calculated it. However, I like to ask the community too, how would you calculate (with Open tools; e.g. Mopac with PM3) this enthalpy? I am seeking to reproduce your exact calculation, so please be verbose on input files, scripts, etc.

NN comments
steve wathen
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Mopac2009 has PM6, so it would probably be able to reproduce the results you are interested in. Mopac7 only has PM3 and might not give the same number.

In an earlier question you asked about calculations on Ubuntu – are you still using Ubuntu? Have you gotten Mopac to run on Ubuntu? Which version of Mopac? Mopac7 is in the Ubuntu repository, but I haven’t been able to get it to run.

chem-bla-ics
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And Ghemical 2.99.2 doesn’t allow me to do this calculation on a charged metal :(

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2 answers

0

chem-bla-ics [ Admin ] from Maastricht, Nederland

I recently ported Ambit2’s Mopac7 code to the CDK, allowing me to create a Mopac7 input file with this CDK groovy code:


    import org.openscience.cdk.io.program.;
    import org.openscience.cdk.modeling.builder3d.;
    import org.openscience.cdk.silent.;
    import org.openscience.cdk.smiles.;
    
    metal = args[0]
    
    parser = new SmilesParser(
       SilentChemObjectBuilder.newInstance()
    )
    mol = parser.parseSmiles(“[\$metal]”)
    
    fileWriter = new FileWriter(metal + “.dat”)
    writer = new Mopac7Writer(fileWriter)
    writer.write(mol)
    writer.close()

This program (if saved as createInput) is then called with:

    groovy createInput Al+++

This creates an Al+++.dat input file. Unfortunately, the current Mopac7 writer code in the CDK does not output the charge, so you have to add to the end of the line the additional command “CHARGE=3”.

This code can be run with the Mopac7 runmopac7 program:

    runmopac7 Al+++

Which creates a Al+++.OUT file listing the HEAT OF FORMATION.

HoF values with PM3 will deviate from those calculated with PM6, as implemenented in the closed-source-but-free-for-academics Mopac2009. The same input can be used for that version, after replacing PM3 by PM6 in the input file.
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1

steve wathen [ Editor ]

I can get the calculation to run in Ghemical 2.98, but not with pm3.


Note: in Ubuntu turn off Visual Effects or the molecule window will not display correctly
always start with new – I get inconsistent results when 
        I change the current molecule and try to re-calculate

Click the periodic table button and select an element
Make sure the Draw (Pencil) Icon is selected, then click in the molecule window to add an atom
Click the Setup (MM) button (or right click in the molecule window)   select Compute, Setup 
Select the “all QM” tab
set charge
select Engine Class – you need to use one of the MPQC methods 
(the others will give the energy as zero)
click OK

Right click in window – select: Compute – Energy

The energy will be displayed in the text panel below the molecule window

I don’t know how to interpret the resulting numbers.  I tried methane and the result did not match the “textbook” number.  I don’t know how good the results will be for metal ions.
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