CCL:G: energy for proton
- From: steinbrt..rci.rutgers.edu
- Subject: CCL:G: energy for proton
- Date: Fri, 13 Apr 2012 03:24:49 -0400 (EDT)
Sent to CCL by: steinbrt!A!rci.rutgers.edu
Dear CCLers,
I found the most recent comments on this by Alexander suprising. This is a
particularly interesting discussion thread and I hope someone else will
comment more on this.
Why would thermodynamic parameters for a proton not make sense? As a free
particle in vacuum it exists, and for any particle with a mass I can
compute ideal values for its enthalpy, entropy and temperature (well, for
one particle, kinetic energy at least).
Moving from a description of a single particle in vacuum to a mol of
(ideal) particles at standard state is then at least conceptually
possible.
The fact that a mol of H+ does not exist any more than a mol of Ac-
doesn't change the fact that I can use it as a reference in computing
thermodynamic properties of the reaction HAc -> H+ + Ac- from the
properties of its constituent molecules.
Furthermore, why can a deprotonation reaction not be described by
thermodynamics? The fragmentation of e.g. HF -> F- + H+ in vacuum will
have an equilibrium that lies exceptionally far to the left, but at high
temperature some fragmentation would occur (disregarding the alternative
radical cleavage for now, which would be more likely but shouldn't stop
the heterolytic cleavage from happening)
If I am wrong in any of the above, I would be happy to be corrected :-)
Kind Regards,
Thomas
On Thu, April 12, 2012 1:17 pm, Alexander Bagaturyants sasha#photonics.ru
wrote:
>
> Sent to CCL by: "Alexander Bagaturyants" [sasha .. photonics.ru]
> A good comment by Prof. Sukumar!
> However, it seems that it was not too straightforward,
> because some misleading comments still appear and appear.
> The matter of fact is that neither enthalpy, nor entropy, nor temperature
> of
> a free proton makes physical sense. One cannot construct a (thermodynamic)
> ensemble of free protons. A reaction in which a proton is detached from a
> molecule can proceed only under nonequilibrium conditions, it is a dynamic
> rather than thermodynamic process.
> That is, it senseless to calculate formally any thermodynamic function of
> a
> free (individual) proton.
> Hope this will make things a little bit more clear.
> Best regards
> Alexander
>
>> -----Original Message-----
>> From: owner-chemistry+sasha==photonics.ru===ccl.net [mailto:owner-
>> chemistry+sasha==photonics.ru===ccl.net] On Behalf Of N. Sukumar
>> nagams(a)rpi.edu
>> Sent: 12 April, 2012 15:27
>> To: Alexander Bagaturyants
>> Subject: CCL:G: energy for proton
>>
>>
>> Sent to CCL by: "N. Sukumar" [nagams~~rpi.edu] "Why not
perform the
>> calculation on proton?"
>>
>> This is an interesting philosophical/pedagogical question. My answer
>> would be: because for many students (and others), the output from a
>> computer is the end of the problem, not the beginning of the question!
>> If the computation is used as an aid to understand the chemistry, well
>> and good. But many people these days will not believe a numerical
>> answer unless it is produced by a calculator or a computer. And they
>> may see no need to question those numbers/output any further.
>>
>> N. Sukumar
>> Rensselaer Exploratory Center for Cheminformatics Research Professor of
>> Chemistry Shiv Nadar University
>> --------------------------
>> "When you get exactly the opposite result to what you predict, you
know
>> it is right, because there is no bias." -- David Nutt, Imperial
>> College, London.
>>
>> ==============Original message text=============== On Thu, 12 Apr 2012
>> 4:13:44 EDT "Peeter Burk peeter.burk^ut.ee" wrote:
>>
>>
>> Sent to CCL by: Peeter Burk [peeter.burk * ut.ee] Why not perform the
>> calculation on prorton? With Gaussian 09 (if I remember correctly, then
>> with g03 you had to use Freq=NoRaman to get the same results) you will
>> get:
>>
>> -------------------
>> - Thermochemistry -
>> -------------------
>> Temperature 298.150 Kelvin. Pressure 1.00000 Atm.
>> Atom 1 has atomic number 1 and mass 1.00783
>> Molecular mass: 1.00783 amu.
>> Zero-point vibrational energy 0.0 (Joules/Mol)
>> 0.00000 (Kcal/Mol)
>> Vibrational temperatures:
>> (Kelvin)
>>
>> Zero-point correction= 0.000000
>> (Hartree/Particle)
>> Thermal correction to Energy= 0.001416
>> Thermal correction to Enthalpy= 0.002360
>> Thermal correction to Gibbs Free Energy= -0.010000
>> Sum of electronic and zero-point Energies= 0.000000
>> Sum of electronic and thermal Energies= 0.001416
>> Sum of electronic and thermal Enthalpies= 0.002360
>> Sum of electronic and thermal Free Energies= -0.010000
>>
>>
>> Peeter Burk
>> University of Tartu
>>
>> On 04/12/2012 10:17 AM, Tymofii Nikolaienko tim_mail*_*ukr.net wrote:
>> >
>> > Sent to CCL by: Tymofii Nikolaienko [tim_mail{=}ukr.net] Yes, ZPE
is
>> > zero.
>> > However, if considering temperatures higher than 0 K, we can NOT
>> > neglect the kinetic energy of the proton, since its thermal
avarage
>> is
>> > 3 * kT / 2 !
>> >
>> > It is easy to demonstrate if you run the following for example
with H
>> atom:
>> >
>> > # opt freq b3lyp/aug-cc-pVQZ int=ultrafine
>> >
>> > H atom
>> >
>> > 0 2
>> > H 0.0 0.0 0.0
>> >
>> > And than you read in the output file:
>> > ...
>> > - Thermochemistry -
>> > -------------------
>> > Temperature 298.150 Kelvin. Pressure 1.00000 Atm.
>> > ...
>> > Zero-point correction= 0.000000 (Hartree/Particle) Thermal
correction
>> > to Energy= 0.001416 Thermal correction to Enthalpy= 0.002360
Thermal
>> > correction to Gibbs Free Energy= -0.010654
>> >
>> > These thermal corrections would be just that same for the proton
>> since
>> > when calculating thermochemistry Gaussian assumes ground electron
>> > state only (so no electronic degrees of freedom contribute to
thermal
>> > corrections; see http://www.gaussian.com/g_whitepap/thermo.htm ).>
>> > Note that "0.001416" (the "Thermal correction to
Energy") equals
>> > 3/2*k*T for T = 298.15 K, while "0.002360" ("
Thermal correction to
>> > Enthalpy") equals 3/2*k*T + k*T since the enthalpy is H = U +
P*v
>> > while P*v = k*T for ideal gas - the model for calculating
>> > thermochemistry Gaussian assumes (where v is the gas volume per
>> > particle). To obtain Gibbs free energy use the -T*s term where s
is
>> > the entropy of ideal gas per particle at given temperature.
>> >
>> > Yours sincerely
>> > Tymofii Nikolaienko
>> >
>> >
>> > 12.04.2012 8:30, Alexander Bagaturyants bagaturyants-.-gmail.com
>> wrote:
>> >> Sent to CCL by: "Alexander Bagaturyants"
[bagaturyants_-_gmail.com]
>> >> Dear Arturo, Proton has no internal degrees of freedom;
therefore,
>> >> its energy is zero, if we neglect its kinetic energy.
>> >> Naturally, the kinetic energy (of a free proton) can take on
any
>> >> value, so that we may speak about so-called dissociation
threshold.
>> >> A piece of advice: when you consider chemistry, you should not
>> >> sometimes forget about physics.
>> >> Best regards
>> >> Alexander
>> >>
>> >>> -----Original Message-----
>> >>> From: owner-chemistry+sasha==photonics.ru|,|ccl.net [mailto:owner-
>> >>> chemistry+sasha==photonics.ru|,|ccl.net] On Behalf Of
Arturo
>> >>> chemistry+Espinosa
>> >>> artuesp|*|um.es
>> >>> Sent: 11 April, 2012 21:12
>> >>> To: Alexander Bagaturyants
>> >>> Subject: CCL: energy for proton
>> >>>
>> >>>
>> >>> Sent to CCL by: Arturo Espinosa [artuesp(_)um.es] Dear CCL
users:
>> >>>
>> >>> I am trying to compute ZPE-corrected dissociation energies
for some
>> >>> particular bonds, in order to correlate these values with
other
>> >>> properties computed at the same level (starting from,
let's say,
>> >>> B3LYP- D/def2-TZVP). My problem (perhaps a bit stupid)
comes when
>> >>> dealing with heterolytic dissociations of a A-H bond to
give A-
>> >>> (anion) and H+ (a proton). Moreover I am intending to
compare this
>> >>> dissociation with the other possible heterolytic
dissociation and
>> >>> even with the homolytic one. Calculation of the A-H and A-
species
>> >>> is straighforward (no matter what level of calculation),
but the
>> >>> problem is what value (in atomic
>> >>> units) should I assign to the H+ species. No QC
calculation is
>> >>> possible as there are no electrons. I recognize that I am
a bit
>> lost.
>> >>> Suggestions are wellcome.
>> >>> Thank you in advance and best regards,
>> >>> Arturo> To recover the email address of the author of
the message,
>> >>> please
>> >>> change the strange characters on the top line to the |,|
sign. You
>> >>> can alsohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:>;
>> >>>
>> http://server.ccl.net/chemistry/announcements/conferences/http-:-//www
>> >>> .ccl.net/cgi-
>> bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/su
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>> >>> original message text===========> To recover the email
address of
>> the author of the message, please
>> change the strange characters on the top line to the === sign. You can
>> also>
>
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854