[ase-users] thermochemistry module

[John Casey]

Thank you Jens, I’m not sure what he meant but will contact him directly. If you happen to run across anyone with a suggestion on how to calculate the formation entropies and enthalpies of molecules, that would be a huge help. 

Best,
John

Sent from my iPhone

> On Apr 12, 2018, at 8:49 PM, Jens Jørgen Mortensen <jjmo at dtu.dk> wrote:
> 
>> On 03/24/2018 03:41 AM, John Casey wrote:
>> Hi Jens,
>>      Sorry for the bother, just wanted to reach out in case you're back from vacation.
> 
> There was one reply to your question:
> 
> https://listserv.fysik.dtu.dk/pipermail/ase-users/2018-March/004259.html
> 
> I don't know if that answered your question.
> 
> Jens Jørgen
> 
>> 
>> Cheers,
>> John
>> 
>> 
>> On Mon, Mar 5, 2018 at 7:44 PM, John Casey <jrcasey at hawaii.edu <mailto:jrcasey at hawaii.edu>> wrote:
>> 
>>    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
>>    <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 <mailto: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 <tel:%28808%29%20956-0577>
>> 
>> 
>> 
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>>            <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 <tel:%28808%29%20956-0577>
>> 
>> 
>> 
>> 
>> -- 
>> 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
>> 
>