[ase-users] thermochemistry module

[John Kitchin]

>
> Message: 1
> Date: Mon, 5 Mar 2018 19:44:09 -1000
> From: John Casey <jrcasey at hawaii.edu>
> To: Jens J?rgen Mortensen <jjmo at dtu.dk>,
>         ase-users at listserv.fysik.dtu.dk
> Subject: Re: [ase-users] thermochemistry module
> Message-ID:
>         <CAPvatJQXWTrWa8f=ELpNsKdAv0V82tCu7zoun-MdSmem=J
> XxTw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Jens and ASE Users,
>      First of all... kudos to you all for this amazing resource and sorry
> for the rookie question!
>
> Disclaimer - I am an oceanographer and a recreational computational
> biologist, not a card-carrying chemist.
>
> Background - I am working with large metabolic networks for a variety of
> microbes, and more specifically I'm making some attempt to relate
> stoichiometric flux models to calorimetry experiments. Somewhere in
> between, I would like to calculate the enthalpy of each reaction going on
> in each of my virtual cells (calculated fluxes and reaction enthalpies can
> be combined to calculate heat flow). When I was working with just one
> strain, I took the painstaking approach of literally printing out molecular
> structures of something like 800 metabolites and manually counting various
> bonds and groups and then implementing some simplified version of the
> so-called Kharash equation (empirical formula of the enthalpy of combustion
> of organic compounds). As the size of my problem has grown, this approach
> has become untenable (actually it was then too- try counting the C-C bonds
> in cobamide). So, I was thrilled to find the thermochemistry calculator in
> the ASE distribution!
>
> Problem - I've made some attempts with compounds with standard enthalpy of
> formation entries that are readily found in lookup tables (like glucose),
> but have not managed to reproduce those with the thermochemistry module.
> I've attached an example of my simple alteration to the tutorial code
> provided in the ASE wiki. Basically, I am providing a 3D .sdf structure
> (attached) retrieved from PubChem (
> https://pubchem.ncbi.nlm.nih.gov/compound/5793) and importing it to an
> 'atoms' object. From there, nothing has changed from the tutorial example.
> ASE calculates the enthalpy to be +5.168 eV, or equivalently +498 KJ mol-1.
> The dHf of glucose should be -1273 KJ mol-1. Where have I gone wrong? Or
> maybe this is some kind of ideal gas approximation issue?
>


The enthalpy is in the ideal gas limit.  This enthalpy is not a formation
enthalpy though. That has to be calculated by differences of enthalpy, and
would require a calculator. I wouldn't expect it to give good results with
the EMT calculator if that is what you used. It is not designed for
molecules.



>
> Config - Mac OSX 13.3, python 3.6.4 implemented in spyder 3.2.7, ASE
> v3.15.0
>
> Thank you in advance for any help - I realize that this is probably a
> cursory application of ASE, but it will really save me some enormous
> headaches in the future!
>
> Aloha,
> John
>
>
>
>
> On Thu, Mar 1, 2018 at 12:57 AM, Jens J?rgen Mortensen <jjmo at dtu.dk>
> wrote:
>
> > On 02/28/2018 10:32 PM, John Casey via ase-users wrote:
> >
> >> Dear ASE user group,
> >>        Sorry for the global email. I have a question regarding the
> >> thermochemistry calculator - if there is someone here who is familiar, I
> >> would appreciate a few of your minutes!
> >>
> >
> > Go ahead and ask!
> >
> > Jens J?rgen
> >
> >
> >> Aloha,
> >> John
> >>
> >>
> >> --
> >> John R. Casey
> >>
> >>
> >> Center for Microbial Oceanography: Research and Education
> >> School of Ocean and Earth Science and Technology
> >> University of Hawaii, Manoa
> >> 1950 East-West Rd., Honolulu, HI 96822
> >> Tel: (808) 956-0577
> >>
> >>
> >>
> >> _______________________________________________
> >> ase-users mailing list
> >> ase-users at listserv.fysik.dtu.dk
> >> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> >>
> >
> >
>
>
> --
> John R. Casey
>
>
> Center for Microbial Oceanography: Research and Education
> School of Ocean and Earth Science and Technology
> University of Hawaii, Manoa
> 1950 East-West Rd., Honolulu, HI 96822
> Tel: (808) 956-0577
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