From owner-chemistry@ccl.net Sat Apr 8 04:46:00 2017 From: "Andreas Klamt klamt^^^cosmologic.de" To: CCL Subject: CCL:G: Thermodynamic Data & Solvation - Calculation Questions: Message-Id: <-52733-170408044449-23436-Q/GEDb3XjfzlBllfq5urCA(!)server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Sat, 8 Apr 2017 10:44:37 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt-.-cosmologic.de] Hi together, it is surely true that the most fundamental way to separate H and TS is doing a temperature derivative. But that requires that the free energy has the correct temperature dependence. Please note that the 2nd derivatives in solution, if calculate from a continuum solvation model, are not the true vibrational frequencies. It is pure fiction to assume that in this way you would end up the correct enthalpy and entropy. In COSMO-RS we have a consistent, although not completely ab initio (no practically usable solvation model is completely ab initio!), scheme for temperature and mixture dependent free energies, and thus for H and TS. Best regards Andreas Am 07.04.2017 um 09:12 schrieb adon cumi adonmage- -gmail.com: > Sent to CCL by: adon cumi [adonmage .. gmail.com] > HI TO ALL! > > > The most *robust* way of separating enthalpic and entropic > contributions would be to calculate the full value of the free energy > at a variety of different temperatures, then numerically evaluating > dG/dT to find the entropy > > The JAGUAR program from SCHRODINGER Inc. It provide a tool via > jaguar-->single point energy-->vibrational frequencies. in the tab > below you should be able to increment the temperature to do your > "dG/dT" ! > > BEST REGARDS, > > 2017-04-06 17:08 UTC+02:00, Eric Hermes erichermes**gmail.com > : >> Sent to CCL by: Eric Hermes [erichermes!^!gmail.com] >> Dr. Mielczarek, >> >> As always, the free energy of a species is defined with respect to some >> choice of reference state, such that for a reaction of the form: >> >> (1) A + B -> C >> >> with a standard state free energy of reaction ΔG°, one can write the >> equilibrium constant as: >> >> (2) Keq = exp[-ΔG°/(kB T)] = a_C / (a_A a_C) >> >> Where a is the *activity* of a species. In the case of an ideal gas, >> the activity is simply the density divided by the *standard state* >> density: >> >> (3) a = ρ/ρ° >> >> The numerical value of Keq then depends on choice of reference state, >> but the equilibrium densities do not. Eq. 2 satisfies this requirement. >> One can show that the free energy of a species at an *arbitrary* >> reference state is given by: >> >> (4) G = G° + kB T ln[ρ/ρ°] >> >> This is *general*, but you can show that for an ideal gas the >> expression derives from the translational entropy. >> >> Now, when we are discussing free energy of solvation, the reaction >> becomes: >> >> (5) A_g -> A_soln >> >> Which of course brings with it changes to both the enthalpy and the >> entropy. These issues are *orthogonal* to the reference state issue, >> though. The standard state for species in the gas phase is usually >> taken to be 1 bar (occasionally 1 atm is chosen instead), but the >> standard state for species in *solution* is typically chosen to be 1 M, >> which is very different! With these choices of reference state, the >> free energy of solvation ΔG°solv can be used to calculate the >> equilibrium constant like this (using P for pressure to visually >> distinguish from the density ρ): >> >> (6) Keq = exp[-ΔG°solv/(kB T)] = (ρ_A/(1 M)) / (P_A / (1 bar)) >> >> As before, the numerical value of Keq depends on the choice of >> reference state, but the equilibrium density and pressure do not. >> >> So, if your goal is to determine the equilibrium properties of a >> solvation process, then you do not need to be concerned about the >> choice of reference state -- you need to be *aware* of it in order to >> calculate the properties directly, but whichever choice you make you >> will get the same answer. On the other hand, if you wish to compare >> your free energies of solvation to experimental values, you should most >> definitely ensure that the value you are calculating uses a reference >> state of 1 M for solution-phase species and 1 bar for gas-phase >> species. >> >> In the case of SMD, by default it will use the *same* reference state >> for the gas-phase and solution-phase species. The actual value of the >> reference state is irrelevant, as ΔGsolv has the same value for any >> choice of reference state so long as the reactants and products have >> the *same* reference state (if you are not convinced, stare at eqs 2, >> 3, and 4 in the context of eq 5 until you believe me :) ). >> >> This means you can arbitrarily say what reference state ΔGsolv is at, >> say 1 bar, for both reactants and products. Then, if you want to >> calculate ΔG°solv (the *experimental* standard state value), you just >> need to use eq 4: >> >> (7) ΔGsolv = Gsoln - G°gas (we choice a reference state of 1 bar) >> (8) Gsoln = G°soln + kB T ln[(1 bar / (kB T))/1 M] (ideal gas law) >> (9) ΔG°solv = G°soln - G°gas = ΔGsolv - kB T ln[(1 bar / (kB T))/1 M] >> >> Note that you would have gotten the *exact same result* if you had >> arbitrarily chosen a reference state of 1 M instead for ΔGsolv (if you >> don't believe me, try it yourself -- start with ΔGsolv = G°soln - >> Ggas). >> >> --- >> >> Now, as to your point about the entropy of solution phase species -- >> I'm not sure the paper you are linking is making the claim you are >> saying it does. It is an *unarguable fact* that (at the typical choice >> of standard states) a species in solution has less entropy than the >> same species in the gas phase. This *must* be the case because the >> molecules in an ideal gas are non-interacting, uncorrelated, and >> undergoing ballistic motion, whereas in solution molecules are *caged* >> by the solvent and undergoing diffusive motion, which means they have >> significantly less freedom of motion. >> >> The paper you link talks about *vibrational* motion, which is going to >> be *significantly* less perturbed by the presence of solvent. The >> *vast* majority of entropy for gas-phase species comes from >> translational motion, not vibrational motion. >> >> --- >> >> Finally, I'm not sure SMD is well-suited to give a *breakdown* of >> enthalpic and entropic terms to the free energy of solvation. The >> procedure you discuss will get *some* of that breakdown, but ultimately >> several contributions to ΔGsolv are all entangled with one another. >> >> What I mean by that is if you simply perform two *single point* >> calculations on the same species, one with and one without SMD >> correction, the difference in the potential energies between those two >> calculations will include a mixture of enthalpic and entropic effects. >> >> Doing the full thermodynamic calculations (i.e. doing a frequency >> calculation and reading the thermodynamic data printed in the Gaussian >> output file) will give you a *full* estimate for ΔGsolv. But, in both >> calculations (with and without SMD) the calculated enthalpic and >> entropic contributions are arising from the same set of approximations >> -- harmonic oscillator for vibration, rigid rotor for rotation, and >> *ideal gas* for translation. >> >> This works because the *potential energy* difference between the >> systems is parameterized such that the free energy difference >> calculated by Gaussian is a good approximatino of the total free energy >> of solvation. Since the enthalpy and entropy calculated by Gaussian for >> both calculations are using the same approximations, they will have >> very similar (but not identical!) values. All of those complicated >> factors such as the loss of translational entropy due to solvation are >> baked into the *electronic energy* that is calculated by the SMD >> method. >> >> The most *robust* way of separating enthalpic and entropic >> contributions would be to calculate the full value of the free energy >> at a variety of different temperatures, then numerically evaluating >> dG/dT to find the entropy. However, SMD as implemented in Gaussian is >> not temperature-dependent, so you cannot actually do this. There are >> other continuum solvation models developed by Cramer and Truhlar which >> do have temperature-dependence, which would allow you to do this, but >> as far as I can tell they are not included in Gaussian. >> >> --- >> >> I hope this answers all of the questions that you had. Please let me >> know if anything I said was unclear or you want additional assistance. >> >> Eric Hermes >> >> On Thu, 2017-04-06 at 06:24 +0000, MIELCZAREK Detlev Conrad detlev- >> conrad.mielczarek-.-ifpen.fr wrote: >>> Sent to CCL by: MIELCZAREK Detlev Conrad [detlev- >>> conrad.mielczarek]^[ifpen.fr] >>> Dear CCL, a question on thermodynamic data & solvation from me, maybe >>> you can help me. >>> >>> So, the basic problem for me is, that I am calculating/want to >>> calculate thermodynamic data (Hf, S - hence also dG) in solvation, >>> using implicit solvation models, SMD with a COSMO cavity to be >>> specific. For my application, these should be accurate enough. (So no >>> molecular dynamics simulations etc.) >>> >>> Solvation models are normally parametrised for dGsolv - so this value >>> can be extracted from the quantum chemistry calculation as the >>> difference in the calculated Gibbs Free Enthalpy. >>> Hf can calculated easily in the gas phase, and a re-optimisation of >>> the structure with solvation should capture the majority of the >>> impact of solvation on the enthalpy. (Which is dominated by molecular >>> structure.) >>> (I guess there is the case of stabilisation and complexes, such as >>> are reported for water. However this is currently beyond the scope of >>> my work.) >>> >>> The topic of solvation has been discussed previously on the CCL here: >>> http://www.ccl.net/chemistry/resources/messages/2011/12/01.001-dir/ >>> http://www.ccl.net/chemistry/resources/messages/2011/10/06.005-dir/ >>> http://www.ccl.net/chemistry/resources/messages/2014/05/01.004-dir/ >>> And there is the book "Essentials of Computational Chemistry Theories >>> and Models" from Professor Cramer with a section on phase change (the >>> source of my confusion). >>> >>> Specifically, the discussion concerning the energy change related to >>> the state conversion causes me some grief. >>> >>> On the one hand, the CCL responses read as if this should be applied >>> in the case of any phase change, but then others suggest this is >>> applicable only if the process is a second order reaction and thus >>> the total number of mols changes? - The latter view seems to agree >>> with the book... >>> >>> So if I have compound A in both the gas and liquid phase (from a >>> quantum chemistry calculation), do I need to account for the phase >>> change/change of state or not? Or is it something that can be >>> included in the parametrisation of the solvation model/the quantum >>> chemistry code already? >>> >>> Just to add more confusion to the topic: I have trialled a commercial >>> product which gives the Gibbs Enthalpy of Solvation in kcal/mol for >>> mol/L concentrations and using a very low end/fast functional, it >>> gives values similar to when a correction term is added... on the >>> other hand, where available, the calculated values without correction >>> agree with the published values in the SMD paper: http://pubs.acs.org >>> /doi/abs/10.1021/jp810292n (Supplementary Data) >>> >>> In addition, a regular computational chemistry calculation sees very >>> little (virtually no) difference in the entropy between the gaseous >>> and solvated phase. This would agree with the CCL-linked paper here h >>> ttp://pubs.acs.org/doi/abs/10.1021/jp205508z . But this would clash >>> with the common expectation that entropy in the liquid phase is >>> reduced... >>> >>> Hence, I would highly appreciate if someone knowledgeable in the >>> field of solvation could guide me onto the correct track. >>> >>> Detlev Conrad Mielczarek >>> Scientific Visitor/Post Doctorant >>> IFP Energies nouvelles >>> France >>> >>> www.ifpenergiesnouvelles.fr >>> >>> __________________________ >>> Avant d'imprimer, pensez à l'environnement ! Please consider the >>> environment before printing ! >>> Ce message et toutes ses pièces jointes sont confidentiels et établis >>> à l'intention exclusive de ses destinataires. Toute utilisation non >>> conforme à sa destination, toute diffusion ou toute publication, >>> totale ou partielle, est interdite, sauf autorisation expresse. IFP >>> Energies nouvelles décline toute responsabilité au titre de ce >>> message. This message and any attachments are confidential and >>> intended solely for the addressees. Any unauthorised use or >>> dissemination is prohibited. IFP Energies nouvelles should not be >>> liable for this message. >>> __________________________ >>> >>> >>> >>> -= This is automatically added to each message by the mailing script >>> =- >>> To recover the email address of the author of the message, please >>> change>> Conferences: http://server.ccl.net/chemistry/announcements/conference >>> s/> > > -- -------------------------------------------------- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt_+_cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Sat Apr 8 08:34:00 2017 From: "may abdelghani may01dz(~)yahoo.fr" To: CCL Subject: CCL:G: Re : CCL:G: service for GAUSSIAN CALCULATION Message-Id: <-52734-170408033204-19332-oV/HMGKZ5WJ4WuqSfBbeFw|-|server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Sat, 8 Apr 2017 07:31:56 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz_-_yahoo.fr] Hello, GAMMES and , NWCHEM on https://www.crunchyard.com/ -------------------------------------------- En date de : Ven 7.4.17, AXEL LONTSI adonmage .. gmail.com a écrit : Objet: CCL:G: service for GAUSSIAN CALCULATION À: "Abdelghani, May " Date: Vendredi 7 avril 2017, 21h43 Sent to CCL by: "AXEL  LONTSI" [adonmage-x-gmail.com] HI TO ALL!!! it is been a while that I have start a opt freq simulation of an organic molecule in my laptop using GAUSSIAN 09. but it take too much time!!! I WANT TO KNOW IF THERE ARE SITES WEB OR SERVICES WHICH PROVIDE SERVERS FOR COMPUTATIONAL CHEMISTRY WITH GAUSSIAN (OR JAGUAR) SO THAT I CAN START COMPUTATION ON THEIR SERVERS AND PAY FOR THAT. THIS SOLUTION CAN HELP ME SPEED UP MY RESEARCH!!!! THANK YOU FOR ANY ANSWER!!! AXEL LONTSI TIWA MINISTRY OF RESEARCH AND INNOVATION , CAMEROON                     From owner-chemistry@ccl.net Sat Apr 8 09:58:00 2017 From: "Peter Jarowski peterjarowski!^!gmail.com" To: CCL Subject: CCL:G: Re : CCL:G: service for GAUSSIAN CALCULATION Message-Id: <-52735-170408095417-32528-uHalG+FTxdWSa4tS6x3LWA * server.ccl.net> X-Original-From: Peter Jarowski Content-Type: multipart/alternative; boundary=001a114b0a72a7ea47054ca81391 Date: Sat, 08 Apr 2017 13:54:00 +0000 MIME-Version: 1.0 Sent to CCL by: Peter Jarowski [peterjarowski[A]gmail.com] --001a114b0a72a7ea47054ca81391 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Yes. www.chemalive.com using an nwchem and Gamess backbone. Also offering automation and interactive data presentation. We are launching our ab initio comformational analysis module this month. 2D structure to full conformationsl space calculation with energy diagram display for easy navigation of the results. Downloadable coordinates and image generation. Best, Peter Sign up to the mailing list. On Sat, 8 Apr 2017 at 15:38, may abdelghani may01dz(~)yahoo.fr < owner-chemistry++ccl.net> wrote: > > Sent to CCL by: may abdelghani [may01dz_-_yahoo.fr] > Hello, > > GAMMES and , NWCHEM on https://www.crunchyard.com/ > -------------------------------------------- > En date de : Ven 7.4.17, AXEL LONTSI adonmage .. gmail.com > a =C3=A9crit : > > Objet: CCL:G: service for GAUSSIAN CALCULATION > =C3=80: "Abdelghani, May " > Date: Vendredi 7 avril 2017, 21h43 > > > Sent to CCL by: "AXEL LONTSI" > [adonmage-x-gmail.com] > HI TO ALL!!! > > it is been a while that I have start a > opt freq simulation of an organic > > molecule in my laptop using GAUSSIAN > 09. but it take too much time!!! > > I WANT TO KNOW IF THERE ARE SITES WEB > OR SERVICES WHICH PROVIDE > > SERVERS FOR COMPUTATIONAL CHEMISTRY > WITH GAUSSIAN (OR JAGUAR) SO THAT I CAN START COMPUTATION ON > THEIR SERVERS AND PAY FOR THAT. > > THIS SOLUTION CAN HELP ME SPEED UP MY > RESEARCH!!!! > > THANK YOU FOR ANY ANSWER!!! > > AXEL LONTSI TIWA > > MINISTRY OF RESEARCH AND INNOVATION , > CAMEROON > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a114b0a72a7ea47054ca81391 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Yes.=C2=A0


using an nwchem and= Gamess backbone. Also offering automation and interactive data presentatio= n.=C2=A0

We are launching our ab initio comformati= onal analysis module this month.=C2=A0

2D structur= e to full conformationsl space calculation with energy diagram display for = easy navigation of the results.=C2=A0

Downloadable= coordinates and image generation.

Best,

Peter=C2=A0

Sign up to the mailing= list.
On Sat, 8 Apr 2017 at 15:3= 8, may abdelghani may01dz(~)yahoo.fr <owner-chemistry++ccl.net> wr= ote:

Sent to CCL by: may abdelghani [may01dz_-_yahoo.fr]
Hello,

GAMMES and , NWCHEM on https://www.crunchyard.com/
--------------------------------------------
En date de=C2=A0: Ven 7.4.17, AXEL LONTSI adonmage .. gmail.com<= /a> <owner-chemistry_._ccl.net> a =C3=A9crit=C2=A0:

=C2=A0Objet: CCL:G: service for GAUSSIAN CALCULATION
=C2=A0=C3=80: "Abdelghani, May " <may01dz_._yahoo.fr= >
=C2=A0Date: Vendredi 7 avril 2017, 21h43


=C2=A0Sent to CCL by: "AXEL=C2=A0 LONTSI"
=C2=A0[adonmage-x-gmail.com]
=C2=A0HI TO ALL!!!

=C2=A0it is been a while that I have start a
=C2=A0opt freq simulation of an organic

=C2=A0molecule in my laptop using GAUSSIAN
=C2=A009. but it take too much time!!!

=C2=A0I WANT TO KNOW IF THERE ARE SITES WEB
=C2=A0OR SERVICES WHICH PROVIDE

=C2=A0SERVERS FOR COMPUTATIONAL CHEMISTRY
=C2=A0WITH GAUSSIAN (OR JAGUAR) SO THAT I CAN START COMPUTATION ON
=C2=A0THEIR SERVERS AND PAY FOR THAT.

=C2=A0THIS SOLUTION CAN HELP ME SPEED UP MY
=C2=A0RESEARCH!!!!

=C2=A0THANK YOU FOR ANY ANSWER!!!

=C2=A0AXEL LONTSI TIWA

=C2=A0MINISTRY OF RESEARCH AND INNOVATION ,
=C2=A0CAMEROON=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0


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