From owner-chemistry@ccl.net Fri Apr 13 09:46:00 2012 From: "Bruce Palfey brupalf(-)umich.edu" To: CCL Subject: CCL:G: energy for proton Message-Id: <-46692-120413094427-17390-w7cKBpxAa3daA/RbQ5k0ow(0)server.ccl.net> X-Original-From: Bruce Palfey Content-Type: multipart/alternative; boundary=Apple-Mail-5--464836113 Date: Fri, 13 Apr 2012 09:44:09 -0400 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Bruce Palfey [brupalf+/-umich.edu] --Apple-Mail-5--464836113 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii I think the forest is being missed for the trees. The heterolytic = dissociation energies that are to be calculated are very much analogous = to reduction potentials - thermodynamic parameters referring to a = fictional chemical reaction involving free electrons. In the present = case, a proton would be produced in all the dissociation reactions. Its = fate, whether realistic or fictional, whether involving chemistry = (transfer to a base) or physics (a plasma), would be the same for all = reactions. Its energy would be the same, so it needn't be calculated. = Assume it's zero for convenience. Regardless, the calculated differences = between HA and A- can be compared to gain chemical insight on = reactivities of compounds, just like reduction potentials can be. And = two (fictional?) reactions can be combined after reversing one to give a = net reaction without a dodgy ill-defined species, and an associated = energy could be calculated with the fictional part canceling; it could = possibly be measured. ciao, Bruce Bruce A. Palfey Associate Professor of Biological Chemistry & Associate Director, Program in Chemical Biology Department of Biological Chemistry University of Michigan Medical School 5220E MSRB III 1150 W. Medical Center Drive Ann Arbor, MI 48109-0606 (734) 615-2452 brupalf!=!umich.edu On Apr 13, 2012, at 8:14 AM, Alex A. Granovsky = gran,+,classic.chem.msu.su wrote: >=20 > Sent to CCL by: "Alex A. Granovsky" [gran[a]classic.chem.msu.su] > Dear Pedro, >=20 > Thermodynamics is only applicable to macroscopic systems with additive = energies. > Charged plasma like gas of protons does not satisfy this requirement = due to long-range nature of Coulomb interaction. >=20 > Kind regards, > Alex Granovsky >=20 >=20 >=20 > -----Original Message-----=20 >> From: Pedro Silva pedros%%ufp.edu.pt > Sent: Friday, April 13, 2012 2:39 PM > To: Granovsky, Alex, A. Subject: CCL:G: energy for proton >=20 >=20 > Sent to CCL by: Pedro Silva [pedros[*]ufp.edu.pt] > Dear Alexander, >=20 > Your argument " one can never consider a proton as an ideal particle." > applies equally to every molecule, even to noble gases. We all know > that the theory involves approximations, so why should one "pick" on > the proton as a uniquely problematic case for statistical > thermodynamics? >=20 > I also cannot understand why "One can never consider a mole of protons > in a finite volume or a mole of protons at a finite pressure", as it > is possible to generate a mole of protons by bombarding H atoms with > x-rays with the appropriate wavelength to eject all electrons. That > system does not contain A-, and its thermodynamics must be describable > in some way :-) > On the other hand, if the issue at hand on " "One can never consider a > mole of protons in a finite volume" is that of electrostatic > repulsion, the same argumnent would also apply to one mole of Na+, H-, > or any other charged species. >=20 >=20 > Pedro S. >=20 > 2012/4/13 Alexander Bagaturyants bagaturyants-.-gmail.com > : >>=20 >> Sent to CCL by: "Alexander Bagaturyants" [bagaturyants%gmail.com] >> Dear Thomas, >> Of course, a proton can exist as a free particle in vacuum, and you = also can >> calculate some formal quantities using some standard equations, but = (!) >> One can never consider a mole of protons in a finite volume or a mole = of >> protons at a finite pressure, and one can never consider a proton as = an >> ideal particle. >>=20 >> A free proton can have any possible kinetic energy, but it cannot = exist in a >> thermodynamic equilibrium and its kinetic energy depends not on the = bath >> temperature but on conditions of its generation. It cannot be = characterized >> by a temperature, because temperature relates to an ensemble rather = than an >> individual particle. >>=20 >> One cannot consider an equilibrium like AH -> A(-) + H(+), and the >> equilibrium constant for this reaction makes no sense. >>=20 >> Sorry for these trivial explanations. >>=20 >> PS: I would not like to discuss here de Broglie's concept of hidden >> thermodynamics of an isolated particle, because this is a different = story. >>=20 >> Best regards >> Alexander >>=20 >>=20 >>> -----Original Message----- >>> From: owner-chemistry+sasha=3D=3Dphotonics.ru-*-ccl.net = [mailto:owner- >>> chemistry+sasha=3D=3Dphotonics.ru-*-ccl.net] On Behalf Of steinbrt=3D-= >>> =3Drci.rutgers.edu >>> Sent: 13 April, 2012 11:25 >>> To: Alexander Bagaturyants >>> Subject: CCL:G: energy for proton >>>=20 >>>=20 >>> Sent to CCL by: steinbrt!A!rci.rutgers.edu Dear CCLers, >>>=20 >>> 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. >>>=20 >>> 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). >>>=20 >>> 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. >>>=20 >>> 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. >>>=20 >>> 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) >>>=20 >>> If I am wrong in any of the above, I would be happy to be corrected = :-) >>>=20 >>> Kind Regards, >>>=20 >>> Thomas >>>=20 >>> 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=3D=3Dphotonics.ru=3D=3D=3Dccl.net = [mailto:owner- >>> >> chemistry+sasha=3D=3Dphotonics.ru=3D=3D=3Dccl.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. >>> >> >>> >> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3DOriginal message = text=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 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=3DNoRaman 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=3D 0.000000 >>> >> (Hartree/Particle) >>> >> Thermal correction to Energy=3D 0.001416 >>> >> Thermal correction to Enthalpy=3D 0.002360 >>> >> Thermal correction to Gibbs Free Energy=3D -0.010000 >>> >> Sum of electronic and zero-point Energies=3D = 0.000000 >>> >> Sum of electronic and thermal Energies=3D = 0.001416 >>> >> Sum of electronic and thermal Enthalpies=3D = 0.002360 >>> >> Sum of electronic and thermal Free Energies=3D = -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{=3D}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=3Dultrafine >>> >> > >>> >> > 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=3D 0.000000 (Hartree/Particle) Thermal >>> >> > correction to Energy=3D 0.001416 Thermal correction to = Enthalpy=3D >>> >> > 0.002360 Thermal correction to Gibbs Free Energy=3D -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 =3D 298.15 K, while "0.002360" (" Thermal correction to >>> >> > Enthalpy") equals 3/2*k*T + k*T since the enthalpy is H =3D U + = P*v >>> >> > while P*v =3D 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=3D=3Dphotonics.ru|,|ccl.net >>> >> >>> [mailto:owner- >>> >> >>> chemistry+sasha=3D=3Dphotonics.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 >>> >> >>> Arturo> 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 >>> >> >>> b_unsub.shtmlhttp://www.ccl.net/spammers.txt=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3DEnd of >>> >> >>> original message text=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D> To = recover the email address >>> of >>> >> the author of the message, please >>> >> change the strange characters on the top line to the =3D=3D=3D = sign. You >>> >> can >>> >> also> >>> > >>> > >>>=20 >>>=20 >>> Dr. Thomas Steinbrecher >>> formerly at the >>> BioMaps Institute >>> Rutgers University >>> 610 Taylor Rd. >>> Piscataway, NJ 08854> 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> >>=20 >=20 >=20 >=20 > --=20 > Pedro J. Silva > Associate Professor > Universidade Fernando Pessoa > Porto - Portugal > http://homepage.ufp.pt/pedros/science/science.htm > = http://biochemicalmatters.blogspot.comhttp://www.ccl.net/cgi-bin/ccl/send_= ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/= spammers.txt >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20=>=20>=20Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 >=20 >=20 --Apple-Mail-5--464836113 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Bruce A. Palfey
Associate = Professor of Biological Chemistry &
Associate Director, Program in Chemical = Biology
Department of Biological Chemistry
University of Michigan = Medical School
5220E MSRB III
1150 W. Medical Center Drive
Ann = Arbor, MI 48109-0606
(734) 615-2452
brupalf!=!umich.edu
On Apr 13, 2012, at 8:14 AM, Alex A. Granovsky = gran,+,classic.chem.msu.su wrote:


Sent to CCL by: "Alex A. Granovsky" = [gran[a]classic.chem.msu.su]
Dear Pedro,

Thermodynamics is = only applicable to macroscopic systems with additive = energies.
Charged plasma like gas of protons does not satisfy this = requirement due to long-range nature of Coulomb interaction.

Kind = regards,
Alex Granovsky



-----Original Message----- =
From: Pedro Silva = pedros%%ufp.edu.pt
Sent: Friday, April 13, 2012 2:39 = PM
To: Granovsky, Alex, A. Subject: CCL:G: energy for = proton


Sent to CCL by: Pedro Silva = [pedros[*]ufp.edu.pt]
Dear Alexander,

Your argument " one can = never consider a proton as an ideal particle."
applies equally to = every molecule, even to noble gases. We all know
that the theory = involves approximations, so why should one "pick" on
the proton as a = uniquely problematic case for statistical
thermodynamics?

I = also cannot understand why "One can never consider a mole of = protons
in a finite volume or a mole of protons at a finite = pressure", as  it
is possible to generate a mole of protons by = bombarding H atoms with
x-rays with the appropriate wavelength to = eject all electrons. That
system does not contain A-, and its = thermodynamics must be describable
in some way :-)
On the other = hand, if the issue at hand on " "One can never consider a
mole of = protons in a finite volume" is that of electrostatic
repulsion, the = same argumnent would also apply to one mole of Na+, H-,
or any other = charged species.


Pedro S.

2012/4/13 Alexander = Bagaturyants bagaturyants-.-gmail.com
&= lt;owner-chemistry|*|ccl.net>:

Sent to CCL by: = "Alexander Bagaturyants" = [bagaturyants%gmail.com]
Dear = Thomas,
Of course, a proton = can exist as a free particle in vacuum, and you also = can
calculate some formal = quantities using some standard equations, but = (!)
One can never consider a = mole of protons in a finite volume or a mole = of
protons at a finite = pressure, and one can never consider a proton as = an
ideal = particle.

A free proton = can have any possible kinetic energy, but it cannot exist in = a
thermodynamic equilibrium = and its kinetic energy depends not on the = bath
temperature but on = conditions of its generation. It cannot be = characterized
by a = temperature, because temperature relates to an ensemble rather than = an
individual = particle.

One cannot = consider an equilibrium like AH -> A(-) + H(+), and = the
equilibrium constant for = this reaction makes no sense.

Sorry for these = trivial explanations.

PS: I would not = like to discuss here de Broglie's concept of = hidden
thermodynamics of an = isolated particle, because this is a different = story.

Best = regards
Alexander


-----Original = Message-----
From: = owner-chemistry+sasha=3D=3Dphotonics.ru-*-ccl.net = [mailto:owner-
chemistry+sasha=3D=3Dphotonics.ru-*-ccl.net] On Behalf Of = steinbrt=3D-
=3Drci.rutgers.edu
Sent: 13 April, 2012 = 11:25
To: Alexander = Bagaturyants
Subject: CCL:G: energy for = proton


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=3D=3Dphotonics.ru=3D=3D=3Dccl.net = [mailto:owner-
>> = chemistry+sasha=3D=3Dphotonics.ru=3D=3D=3Dccl.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.
>>
>> =3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3DOriginal message text=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D 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=3DNoRaman 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)
>> =             &n= bsp;           &nbs= p;            = 0.00000 (Kcal/Mol)
>>   Vibrational = temperatures:
>> =            (Kelvin)=
>>
>>   Zero-point = correction=3D =             &n= bsp;           &nbs= p; 0.000000
>> = (Hartree/Particle)
>>   Thermal = correction to Energy=3D =             &n= bsp;      0.001416
>> =   Thermal correction to Enthalpy=3D =             &n= bsp;    0.002360
>>   Thermal = correction to Gibbs Free Energy=3D =        -0.010000
>> =   Sum of electronic and zero-point Energies=3D =             &n= bsp;0.000000
>>   Sum of = electronic and thermal Energies=3D =             &n= bsp;   0.001416
>>   Sum of = electronic and thermal Enthalpies=3D =             &n= bsp; 0.002360
>>   Sum of = electronic and thermal Free Energies=3D =           -0.010000
<= /blockquote>
>>
>>
>> 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{=3D}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=3Dultrafine
>> = >
>> > 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=3D 0.000000 (Hartree/Particle) = Thermal
>> > correction to Energy=3D 0.001416 Thermal = correction to Enthalpy=3D
>> > 0.002360 Thermal = correction to Gibbs Free Energy=3D = -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 =3D 298.15 K, = while "0.002360" (" Thermal correction = to
>> > Enthalpy") equals 3/2*k*T + k*T since the = enthalpy is H =3D U + P*v
>> > while P*v =3D 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
<= /blockquote>
>> 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=3D=3Dphotonics.ru|,|ccl.net
>> = >>> [mailto:owner-
>> >>> = chemistry+sasha=3D=3Dphotonics.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
>> >>> Arturo> = message,
>> >>> = please
>> >>> change the strange characters on the = top line to the |,| sign.
>> >>> You = can
>> >>> also=Conferences:>
>> = >>>
>> http://server.ccl.net/chemistry/announcements/conferences/http://www
>> >>> = .ccl.net/cgi-
>> = bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/su
>> = >>> b_unsub.shtmlhttp://www.ccl.net/spammers.txt=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3DEnd of
>> >>> original = message text=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D> To recover the email = address
of
>> the author of the = message, please
>> change the strange = characters on the top line to the =3D=3D=3D sign. = You
>> can
>> = also>
>
>


Dr. Thomas = Steinbrecher
formerly at = the
BioMaps Institute
Rutgers = University
610 Taylor = Rd.
Piscataway, NJ 08854> 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>




--
Pedro J. = Silva
Associate Professor
Universidade Fernando Pessoa
Porto - = Portugal
http://homepage= .ufp.pt/pedros/science/science.htm
http://biochemicalmatters.blogsp= ot.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/ch= emistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


-=3D = This is automatically added to each message by the mailing script = =3D-
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
look up the X-Original-From: line in the mail = header.
=     http://www.ccl.net/cgi-bin/ccl/send_ccl_message =     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
Before posting, check wait time at: = http://www.ccl.net

Search = Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

If = your mail bounces from CCL with 5.7.1 error, check:
=     http://www.ccl.net/spammers.txt

RTFI: = http://www.ccl.net/chemistry/aboutccl/instructions/






= --Apple-Mail-5--464836113--