From owner-chemistry@ccl.net Fri Aug 6 01:23:00 2010 From: "Kalju Kahn kalju(~)chem.ucsb.edu" To: CCL Subject: CCL:G: Conformation of trication Message-Id: <-42457-100805193943-23673-Ms/PdcpmMXkvKWOQtTzA7g^^server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 5 Aug 2010 16:39:28 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju---chem.ucsb.edu] Hi Vijay: To add to points mentioned by Thomas and Andreas, keep in mind that standard minimization will not give you the lowest energy conformer unless you start with a structure that is structurally similar to the lowest energy conformer. You need a conformational search, which does a large number of minimizations starting with different initial structures. This is implemented in many molecular mechanics programs (Macromodel in Schrodinger Suite, SYBYL, TINKER, BOSS ... I would think Discovery Studio has something like this, too). With 86 atoms you probably do not want to use ab initio methods, and only a few QM programs offer conformational search anyways. As Andreas pointed out, you need to treat your solvent. As a quicker alternative to the rigorous approach he mentioned, one can specify a dielectric constant. This is a standard option in most molecular mechanics programs. Keep in mind that "quicker" in computational chemistry usually translates to "less accurate". A more rigorous (but also more time-consuming) approach is to set up a Monte Carlo or Molecular Dynamics simulation (Discovery Studio allows the latter). You'll still using classical force fields (i.e. not quantum mechanics) but now with explicit solvent you'll be able to take into account specific interactions between the solvent ans solute. I am not sure how the conformations from explicit solvent simulation compare to COSMO-RS. Quite frankly, unless the molecule you are looking at is very flexible, you may have a better luck taking some NMR (E-COSY, NOESY) spectra, and figuring out the conformation from this data. Good luck, Kalju > > Sent to CCL by: Andreas Klamt [klamt..cosmologic.de] > Hi Vijay, > > Thomas is basically right, but I think he missed to mention an important > aspect, i.e. solvation. It is quite unlikely that you are interested in > your trication in vacuum or gasphase. Most likely you are interested in > the aqueous solvation. Hence you need to use a combination of a QM with > a solvation model. Implicit solvation models are most efficient. I am > convinced that COSMO-RS is most reliable in this regard. > > Years ago some Danish people did a comparison on the accuracy of the > prediction of the right conformers of > „Conformational analysis of cyclic acidic a-amino acids in aqueous > solution - an evaluation of different continuum hydration models." > by Peter Aadal Nielsen, Per-Ola Norrby, Jerzy W. Jaroszewski, and Tommy > Liljefors (I am currently not sure whether and where this finally got > published.) > Several of the species were ions. COSMO-RS had by far the smallest error > in this blind prediction test. I am not aware of other method > comparisons in this regard. Quite surely there are none for triply > charged species. > > Best regards > > Andreas > > > > > Am 05.08.2010 07:52, schrieb Gkourmpis, Thomas > Thomas.Gkourmpis[A]borealisgroup.com: >> Sent to CCL by: "Gkourmpis, Thomas" >> [Thomas.Gkourmpis---borealisgroup.com] >> Hi Vijay >> >> If the minimum energy configuration is the only thing you're interested >> in any computational chemistry/physics program will do the job. They all >> work on similar ways and have routines that do the same things (though >> in different ways but that's beside the point and does not concern you >> at this stage). If you use quantum mechanical methods (I assume that's >> what you're looking for) then the only issues you need to think about is >> which theory level and basis set will be the best and most efficient way >> for your particular problem. If you are not interested in electronic >> properties like wavefunctions, orbitals etc you can always use >> semiempirical methods that are very fast and relatively accurate. >> Personally I am using Gaussian, but all other software packages >> available should be able to perform the energy minimisation task without >> any problems. >> >> I hope this helps >> >> Thomas >> >> >> -----Original Message----- >> >>> From: owner-chemistry+thomas.gkourmpis==borealisgroup.com() ccl.net >>> [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com() ccl.net] >>> On Behalf Of Vijay Tak takvijay(~)gmail.com >>> >> Sent: Wednesday, August 04, 2010 7:42 PM >> To: Gkourmpis, Thomas >> Subject: CCL: Conformation of trication >> >> >> Sent to CCL by: "Vijay Tak" [takvijay%x%gmail.com] >> Hi CCL, >> I am very new to computational chemistry. Please help me out.I would >> like to find the minimum energy conformation of imidazolium based >> trication ( total 86 atoms).Let me know which software is suitable in >> this case. Is Discovery studio is appropriate for for this task. >> Thanks, >> Vijay Tak >> takvijay|a|gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> >> >> >> > > > -- > PD. Dr. Andreas Klamt > CEO / Geschäftsführer > COSMOlogic GmbH& Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt!=!cosmologic.de > web www.cosmologic.de > > HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Fri Aug 6 01:58:00 2010 From: "Simmie, John john.simmie[#]nuigalway.ie" To: CCL Subject: CCL:G: Reaction Rate as a function of Pressure Message-Id: <-42458-100805233032-10199-ukfTVaid+fWGtFGNhdJBCQ-.-server.ccl.net> X-Original-From: "Simmie, John" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CB3517.B44B3B5D" Date: Fri, 6 Aug 2010 04:25:42 +0100 MIME-Version: 1.0 Sent to CCL by: "Simmie, John" [john.simmie]-[nuigalway.ie] This is a multi-part message in MIME format. ------_=_NextPart_001_01CB3517.B44B3B5D Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Thomas You are already calculating the reaction rate at the high-pressure limit to get the pressue dependent rate constants you need to employ = RRKM/master equation theory ... which lies outside the province of Gaussian, Molpro, = etc J Simmie::Combustion Chemistry Centre::NUI Galway Ireland -----Original Message----- > From: owner-chemistry+john.simmie=3D=3Dnuigalway.ie!=!ccl.net on behalf of = Thomas Gkourmpis thomas.gkourmpis(~)borealisgroup.com Sent: Thu 05/08/2010 14:37 To: Simmie, John Subject: CCL:G: Reaction Rate as a function of Pressure =20 Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis * = borealisgroup.com] Hello everyone I have a question to ask regarding the pressure and temperature = dependence on the reaction rate. I am trying to calculate the rate = constant of a beta scission in a radical (tertbutoxy radical) obtained = by the decomposition of a peroxide. I am using Gaussian for this job and = I have no problem in locating the minimum energy configurations for = products, reactant(s) and transition states. After the final structures = have been obtained I am running a frequency calculation as a function of = pressure and temperature to obtain the relevant frequencies, Gibbs Free = Energies and partition functions I need for the Arrhenius equation. This is where I have a problem. The frequency outcome as a function of = temperature is fine and I have no problems with it, but the pressure = outcome is really puzzling. My results seem to indicate that all the = thermodynamic quantities that I calculate have almost negligible = dependence on pressure (especially the frequencies that remain unchanged = for the same temperature). I am interested in temperature ranges of the = order 300K-800K and pressures from 1bar to 3000bars. I know from = experimental data that the reaction constant does change as a function = of pressure (it gets shifted towards the right as pressure increases), = but my calculations does not seem to be able to reproduce this = phenomenon. One of the reasons I can think about this is the fact that all the = thermochemical calculations in Gaussian are done under the = Born-Oppenheimer approximation, but I am not sure if this is the only = reason (I might be missing something else). Therefore the favour I want to ask is this: Can anyone tell me if this = is an effect due only to the approximation I am using? Furthermore if = this is the case can anybody please suggest any possible ways to apply = corrections to this approximation for high pressures? Thanks a lot in advance Thomas -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------_=_NextPart_001_01CB3517.B44B3B5D-- From owner-chemistry@ccl.net Fri Aug 6 04:08:00 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis-,-borealisgroup.com" To: CCL Subject: CCL:G: Reaction Rate as a function of Pressure Message-Id: <-42459-100806040621-13286-8HkSkQgTYHIV/8rk8x1ntA(~)server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 6 Aug 2010 10:06:07 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis . borealisgroup.com] Thanks for the answer. I was actually afraid that Gaussian will not be up to the job to get these types of correlations. Are you aware of a software that can perform the RRKM/master equation analysis? Thanks again Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com^ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com^ccl.net] On Behalf Of Simmie, John john.simmie[#]nuigalway.ie Sent: Friday, August 06, 2010 5:26 AM To: Gkourmpis, Thomas Subject: CCL:G: Reaction Rate as a function of Pressure Thomas You are already calculating the reaction rate at the high-pressure limit to get the pressue dependent rate constants you need to employ RRKM/master equation theory ... which lies outside the province of Gaussian, Molpro, etc J Simmie::Combustion Chemistry Centre::NUI Galway Ireland -----Original Message----- > From: owner-chemistry+john.simmie==nuigalway.ie-.-ccl.net on behalf of Thomas Gkourmpis thomas.gkourmpis(~)borealisgroup.com Sent: Thu 05/08/2010 14:37 To: Simmie, John Subject: CCL:G: Reaction Rate as a function of Pressure Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis * borealisgroup.com] Hello everyone I have a question to ask regarding the pressure and temperature dependence on the reaction rate. I am trying to calculate the rate constant of a beta scission in a radical (tertbutoxy radical) obtained by the decomposition of a peroxide. I am using Gaussian for this job and I have no problem in locating the minimum energy configurations for products, reactant(s) and transition states. After the final structures have been obtained I am running a frequency calculation as a function of pressure and temperature to obtain the relevant frequencies, Gibbs Free Energies and partition functions I need for the Arrhenius equation. This is where I have a problem. The frequency outcome as a function of temperature is fine and I have no problems with it, but the pressure outcome is really puzzling. My results seem to indicate that all the thermodynamic quantities that I calculate have almost negligible dependence on pressure (especially the frequencies that remain unchanged for the same temperature). I am interested in temperature ranges of the order 300K-800K and pressures from 1bar to 3000bars. I know from experimental data that the reaction constant does change as a function of pressure (it gets shifted towards the right as pressure increases), but my calculations does not seem to be able to reproduce this phenomenon. One of the reasons I can think about this is the fact that all the thermochemical calculations in Gaussian are done under the Born-Oppenheimer approximation, but I am not sure if this is the only reason (I might be missing something else). Therefore the favour I want to ask is this: Can anyone tell me if this is an effect due only to the approximation I am using? Furthermore if this is the case can anybody please suggest any possible ways to apply corrections to this approximation for high pressures? Thanks a lot in advance Thomashttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt------_=extPart_001_01CB3517.B44B3B5D-- -=is is automatically added to each message by the mailing script =http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Aug 6 04:42:01 2010 From: "Alain Borel alain.borel,+,epfl.ch" To: CCL Subject: CCL:G: Reaction Rate as a function of Pressure Message-Id: <-42460-100806043435-30338-O9+p9lcyjwp4GuSk7vJ/XA-$-server.ccl.net> X-Original-From: Alain Borel Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 06 Aug 2010 10:34:22 +0200 MIME-Version: 1.0 Sent to CCL by: Alain Borel [alain.borel]~[epfl.ch] On 05.08.10 15:37, Thomas Gkourmpis wrote: > I have a question to ask regarding the pressure and temperature dependence on the reaction rate. I am trying to calculate the rate constant of a beta scission in a radical (tertbutoxy radical) obtained by the decomposition of a peroxide. I am using Gaussian for this job and I have no problem in locating the minimum energy configurations for products, reactant(s) and transition states. After the final structures have been obtained I am running a frequency calculation as a function of pressure and temperature to obtain the relevant frequencies, Gibbs Free Energies and partition functions I need for the Arrhenius equation. > > This is where I have a problem. The frequency outcome as a function of temperature is fine and I have no problems with it, but the pressure outcome is really puzzling. My results seem to indicate that all the thermodynamic quantities that I calculate have almost negligible dependence on pressure (especially the frequencies that remain unchanged for the same temperature). I am interested in temperature ranges of the order 300K-800K and pressures from 1bar to 3000bars. I know from experimental data that the reaction constant does change as a function of pressure (it gets shifted towards the right as pressure increases), but my calculations does not seem to be able to reproduce this phenomenon. How do your calculations model the environment of your system? Pressure really affects how the molecules of interest interact with the solvent, for example. Best regards, Alain Borel From owner-chemistry@ccl.net Fri Aug 6 06:09:00 2010 From: "ABHISHEK SHAHI shahi.abhishek1984[A]gmail.com" To: CCL Subject: CCL:G: Reaction Rate as a function of Pressure Message-Id: <-42461-100806060803-25139-l0o1/zYzWwGvVfzY6L4t+Q###server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=0016367fadb111d113048d24d737 Date: Fri, 6 Aug 2010 15:37:53 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984__gmail.com] --0016367fadb111d113048d24d737 Content-Type: text/plain; charset=ISO-8859-1 Hi Thomas Fortran codes are available for temperature dependence rate constant (TST theory) and energy dependence rate constant (RRKM theory).But I don't know any pressure dependence program for rate constant calculation.let me know if you get something. For RRKM calculation, follow the following LINK. And if its not helpfull to you then write to auther for Program(free) ONLINE RRKM CALCULATOR . With regards; ABHISHEK SHAHI Ph. D. student Department of Inorganic and Physical Chemistry IISc bangalore-12 : 080-2293-2384(lab) Official E-mail: shahi###ipc.iisc.ernet.in CC: shahi.abhishek1984###gmail.com On Fri, Aug 6, 2010 at 1:36 PM, Gkourmpis, Thomas Thomas.Gkourmpis-,- borealisgroup.com wrote: > > Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis . borealisgroup.com] > Thanks for the answer. I was actually afraid that Gaussian will not be up > to the job to get these types of correlations. Are you aware of a software > that can perform the RRKM/master equation analysis? > > Thanks again > > Thomas > > -----Original Message----- > > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com_._ccl.net[mailto: > owner-chemistry+thomas.gkourmpis > ==borealisgroup.com_._ccl.net] On Behalf Of Simmie, John john.simmie[#] > nuigalway.ie > Sent: Friday, August 06, 2010 5:26 AM > To: Gkourmpis, Thomas > Subject: CCL:G: Reaction Rate as a function of Pressure > > Thomas > You are already calculating the reaction rate at the high-pressure limit > to get the pressue dependent rate constants you need to employ RRKM/master > equation theory ... which lies outside the province of Gaussian, Molpro, > etc > > J Simmie::Combustion Chemistry Centre::NUI Galway Ireland > > > -----Original Message----- > > From: owner-chemistry+john.simmie==nuigalway.ie-.-ccl.net on behalf of > Thomas Gkourmpis thomas.gkourmpis(~)borealisgroup.com > Sent: Thu 05/08/2010 14:37 > To: Simmie, John > Subject: CCL:G: Reaction Rate as a function of Pressure > > > Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis * borealisgroup.com] > Hello everyone > > I have a question to ask regarding the pressure and temperature dependence > on the reaction rate. I am trying to calculate the rate constant of a beta > scission in a radical (tertbutoxy radical) obtained by the decomposition of > a peroxide. I am using Gaussian for this job and I have no problem in > locating the minimum energy configurations for products, reactant(s) and > transition states. After the final structures have been obtained I am > running a frequency calculation as a function of pressure and temperature to > obtain the relevant frequencies, Gibbs Free Energies and partition functions > I need for the Arrhenius equation. > > This is where I have a problem. The frequency outcome as a function of > temperature is fine and I have no problems with it, but the pressure outcome > is really puzzling. My results seem to indicate that all the thermodynamic > quantities that I calculate have almost negligible dependence on pressure > (especially the frequencies that remain unchanged for the same temperature). > I am interested in temperature ranges of the order 300K-800K and pressures > from 1bar to 3000bars. I know from experimental data that the reaction > constant does change as a function of pressure (it gets shifted towards the > right as pressure increases), but my calculations does not seem to be able > to reproduce this phenomenon. > > One of the reasons I can think about this is the fact that all the > thermochemical calculations in Gaussian are done under the Born-Oppenheimer > approximation, but I am not sure if this is the only reason (I might be > missing something else). > > Therefore the favour I want to ask is this: Can anyone tell me if this is > an effect due only to the approximation I am using? Furthermore if this is > the case can anybody please suggest any possible ways to apply corrections > to this approximation for high pressures? > > Thanks a lot in advance > > Thomashttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt------_=extPart_001_01CB3517.B44B3B5D-- > > > > -=is is automatically added to each message by the mailing script =http://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > --0016367fadb111d113048d24d737 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Thomas
=A0=A0 Fortran codes are available for temperature dependence = rate constant (TST theory) and energy dependence rate constant (RRKM theory= ).But I don't know any pressure dependence program for rate constant ca= lculation.let me know if you get something. For RRKM calculation, follow th= e following LINK. And if its not helpfull to you then write to auther for P= rogram(free)

ONLINE RRKM CALCULATOR.


With regards;
=A0 ABHISHEK SHAHI
=A0 Ph. D. student
=A0 Department of Inorganic and Physical Chemistry=A0 IISc bangalore-12
=A0=A0:=A0 080-2293-2384(lab)=A0 Official E-mail: shahi###ipc.iisc.ernet.in
=A0 CC:=A0 shahi.abhishek1984###gmail.com


On Fri, Aug 6, 2010 at 1:36 PM, Gkourmpi= s, Thomas Thomas.Gkourmpis-,-borealisg= roup.com <owner-chemistry###ccl.net> wrote:

Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis . borealisgroup.com]
Thanks for the answer. I was actually afraid that Gaussian will not be up t= o the job to get these types of correlations. Are you aware of a software t= hat can perform the RRKM/master equation analysis?

Thanks again

Thomas

-----Original Message-----
> From: owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com_._ccl.net [mailto:owner-chemistry+thomas.gkourmpis= =3D=3Dborealisgroup.com_._ccl.= net] On Behalf Of Simmie, John john.simmie[#]nuigalway.ie
Sent: Friday, August 06, 2010 5:26 AM
To: Gkourmpis, Thomas
Subject: CCL:G: Reaction Rate as a function of Pressure

Thomas
You are already calculating the reaction rate at the high-pressure limit to get the pressue dependent rate constants you need to employ RRKM/master<= br> equation theory ... which lies outside the province of Gaussian, Molpro, et= c

J Simmie::Combustion Chemistry Centre::NUI Galway Ireland


-----Original Message-----
> From: owner-chemistry+john.simmie=3D=3Dnuigalway.ie-.-ccl.net on behalf of Thomas Gkourmpis thom= as.gkourmpis(~)borea= lisgroup.com
Sent: Thu 05/08/2010 14:37
To: Simmie, John
Subject: CCL:G: Reaction Rate as a function of Pressure


Sent to CCL by: "Thomas =A0Gkourmpis" [thomas.gkourmpis * borealisgroup.com]
Hello everyone

I have a question to ask regarding the pressure and= temperature dependence on the reaction rate. I am trying to calculate the = rate constant of a beta scission in a radical (tertbutoxy radical) obtained= by the decomposition of a peroxide. I am using Gaussian for this job and I= have no problem in locating the minimum energy configurations for products= , reactant(s) and transition states. After the final structures have been o= btained I am running a frequency calculation as a function of pressure and = temperature to obtain the relevant frequencies, Gibbs Free Energies and par= tition functions I need for the Arrhenius equation.

This is where I have a problem. The frequency outcome as a function of temp= erature is fine and I have no problems with it, but the pressure outcome is= really puzzling. My results seem to indicate that all the thermodynamic qu= antities that I calculate have almost negligible dependence on pressure (es= pecially the frequencies that remain unchanged for the same temperature). I= am interested in temperature ranges of the order 300K-800K and pressures f= rom 1bar to 3000bars. I know from experimental data that the reaction const= ant does change as a function of pressure (it gets shifted towards the righ= t as pressure increases), but my calculations does not seem to be able to r= eproduce this phenomenon.

One of the reasons I can think about this is the fa= ct that all the thermochemical calculations in Gaussian are done under the = Born-Oppenheimer approximation, but I am not sure if this is the only reaso= n (I might be missing something else).

Therefore the favour I want to ask is this: Can anyone tell me if this is a= n effect due only to the approximation I am using? Furthermore if this is t= he case can anybody please suggest any possible ways to apply corrections t= o this approximation for high pressures?

Thanks a lot in advance

Thomashttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.n= et/spammers.txt------_=3DextPart_001_01CB3517.B44B3B5D--



-=3Dis is automatically added to each message by the mailing script =3Dh= ttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/= sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

--0016367fadb111d113048d24d737-- From owner-chemistry@ccl.net Fri Aug 6 07:56:00 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis[-]borealisgroup.com" To: CCL Subject: CCL:G: Reaction Rate as a function of Pressure Message-Id: <-42462-100806075418-15780-I7rmrCuHlO0Y8xZVHakJzg]_[server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_2BD27C21A5B53C4AB53F403FC915A182014610579ACMS02mignetwo_" Date: Fri, 6 Aug 2010 13:53:00 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis:_:borealisgroup.com] --_000_2BD27C21A5B53C4AB53F403FC915A182014610579ACMS02mignetwo_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Thanks a lot for all the answers guys=2E They're most appreciated=2E I will= look for the relevant software you recommended and I will also check the l= iterature on the subject again to see what I can dig up=2E=0D=0A=0D=0AAlain= the calculations that I have done so far are in the gas phase, and I am do= ing them in a solvent as we speak=2E I can imagine that the solvent will be= heavily affected by the pressure, but I was expecting to see some effect (= a bit smaller but still measurable) in the gas as well=2E=0D=0A=0D=0AAgain = thanks a lot=0D=0A=0D=0AThomas=0D=0A=0D=0A=0D=0AFrom: owner-chemistry+thoma= s=2Egkourmpis=3D=3Dborealisgroup=2Ecom]^[ccl=2Enet [mailto:owner-chemistry+th= omas=2Egkourmpis=3D=3Dborealisgroup=2Ecom]^[ccl=2Enet] On Behalf Of ABHISHEK = SHAHI shahi=2Eabhishek1984[A]gmail=2Ecom=0D=0ASent: Friday, August 06, 2010= 12:08 PM=0D=0ATo: Gkourmpis, Thomas=0D=0ASubject: CCL:G: Reaction Rate as = a function of Pressure=0D=0A=0D=0AHi Thomas=0D=0A Fortran codes are avail= able for temperature dependence rate constant (TST theory) and energy depen= dence rate constant (RRKM theory)=2EBut I don't know any pressure dependenc= e program for rate constant calculation=2Elet me know if you get something= =2E For RRKM calculation, follow the following LINK=2E And if its not helpf= ull to you then write to auther for Program(free)=0D=0A=0D=0AONLINE RRKM CA= LCULATOR=2E=0D=0A=0D=0A=0D=0AWith= regards;=0D=0A ABHISHEK SHAHI [http://e/softbank_ne_jp=2E7D9]=0D=0A Ph= =2E D=2E student=0D=0A Department of Inorganic and Physical Chemistry=0D= =0A IISc bangalore-12=0D=0A [http://e/ezweb_ne_jp=2E523] : 080-2293-2384= (lab)=0D=0A Official E-mail: shahi() ipc=2Eiisc=2Eernet=2Ein=0D=0A CC: shahi=2Eabhishek1984() gmail=2Ecom= =0D=0A=0D=0AOn Fri, Aug 6, 201= 0 at 1:36 PM, Gkourmpis, Thomas Thomas=2EGkourmpis-,-borealisgroup=2Ecom > wrote:=0D=0A=0D=0ASent to CCL by: "Gkourmpis, Thomas" [T= homas=2EGkourmpis =2E borealisgroup=2Ecom]=0D= =0AThanks for the answer=2E I was actually afraid that Gaussian will not be= up to the job to get these types of correlations=2E Are you aware of a sof= tware that can perform the RRKM/master equation analysis?=0D=0A=0D=0AThanks= again=0D=0A=0D=0AThomas=0D=0A=0D=0A-----Original Message-----=0D=0A> From:= owner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ecom_=2E_ccl=2Enet<= http://ccl=2Enet> [mailto:owner-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ecom_=2E_ccl=2Enet] On Behalf Of Simmie, John john=2Esimmie[#]nuigalway=2Eie=0D=0ASent: Friday, August 06, 2010 5:26 AM=0D=0ATo: Gkou= rmpis, Thomas=0D=0ASubject: CCL:G: Reaction Rate as a function of Pressure= =0D=0A=0D=0AThomas=0D=0AYou are already calculating the reaction rate at th= e high-pressure limit=0D=0Ato get the pressue dependent rate constants you = need to employ RRKM/master=0D=0Aequation theory =2E=2E=2E which lies outsid= e the province of Gaussian, Molpro, etc=0D=0A=0D=0AJ Simmie::Combustion Che= mistry Centre::NUI Galway Ireland=0D=0A=0D=0A=0D=0A-----Original Message---= --=0D=0A> From: owner-chemistry+john=2Esimmie=3D=3Dnuigalway=2Eie-=2E-ccl= =2Enet on behalf of Thomas Gkourmpis thomas=2Egkourmpis(~= )borealisgroup=2Ecom=0D=0ASent: Thu 05/08/2010 = 14:37=0D=0ATo: Simmie, John=0D=0ASubject: CCL:G: Reaction Rate as a functio= n of Pressure=0D=0A=0D=0A=0D=0ASent to CCL by: "Thomas Gkourmpis" [thomas= =2Egkourmpis * borealisgroup=2Ecom]=0D=0AHello = everyone=0D=0AI have a question to ask regarding the pressure and temperatu= re dependence on the reaction rate=2E I am trying to calculate the rate con= stant of a beta scission in a radical (tertbutoxy radical) obtained by the = decomposition of a peroxide=2E I am using Gaussian for this job and I have = no problem in locating the minimum energy configurations for products, reac= tant(s) and transition states=2E After the final structures have been obtai= ned I am running a frequency calculation as a function of pressure and temp= erature to obtain the relevant frequencies, Gibbs Free Energies and partiti= on functions I need for the Arrhenius equation=2E=0D=0A=0D=0AThis is where = I have a problem=2E The frequency outcome as a function of temperature is f= ine and I have no problems with it, but the pressure outcome is really puzz= ling=2E My results seem to indicate that all the thermodynamic quantities t= hat I calculate have almost negligible dependence on pressure (especially t= he frequencies that remain unchanged for the same temperature)=2E I am inte= rested in temperature ranges of the order 300K-800K and pressures from 1bar= to 3000bars=2E I know from experimental data that the reaction constant do= es change as a function of pressure (it gets shifted towards the right as p= ressure increases), but my calculations does not seem to be able to reprodu= ce this phenomenon=2E=0D=0AOne of the reasons I can think about this is the= fact that all the thermochemical calculations in Gaussian are done under t= he Born-Oppenheimer approximation, but I am not sure if this is the only re= ason (I might be missing something else)=2E=0D=0A=0D=0ATherefore the favour= I want to ask is this: Can anyone tell me if this is an effect due only to= the approximation I am using? Furthermore if this is the case can anybody = please suggest any possible ways to apply corrections to this approximation= for high pressures?=0D=0A=0D=0AThanks a lot in advance=0D=0AThomashttp://w= ww=2Eccl=2Enet/cgi-bin/ccl/send_ccl_messagehttp://www=2Eccl=2Enet/spammers= =2Etxt------_=3DextPart_001_01CB3517=2EB44B3B5D--=0D=0A=0D=0A=0D=0A=0D=0A-=3Dis is automatica= lly added to each message by the mailing script =3Dhttp://www=2Eccl=2Enet/c= gi-bin/ccl/send_ccl_messagehttp://www=2Eccl=2Enet/chemistry/sub_unsub=2Esht= mlhttp://www=2Eccl=2Enet/spammers=2Etxt=0D=0A=0D=0A=0D=0A-=3D This is automatically ad= ded to each message by the mailing script =3D- or use= :=0D=0A http://www=2Eccl=2Enet/cgi-bin/ccl/send_ccl_message=0D=0A=0D=0A= E-mail to administrators: CHEMISTRY-REQUEST() ccl=2Enet or use=0D=0A http://www=2Eccl=2Enet/cgi-bin/ccl/se= nd_ccl_message=0D=0A=0D=0ASubscribe/Unsubscribe:=0D=0A http://www=2Eccl= =2Enet/chemistry/sub_unsub=2Eshtml=0D=0A=0D=0ABefore posting, check wait ti= me at: http://www=2Eccl=2Enet=0D=0A=0D=0AJob: http://www=2Eccl=2Enet/jobs= =0D=0AConferences: http://server=2Eccl=2Enet/chemistry/announcements/confer= ences/=0D=0A=0D=0ASearch Messages: http://www=2Eccl=2Enet/chemistry/searchc= cl/index=2Eshtml=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A=0D=0A