[ase-users] thermochemistry module

[John Casey]

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?

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 Jørgen 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 Jørgen
>
>
>> 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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