From owner-chemistry@ccl.net Thu Sep 8 04:58:41 2005 From: "CCL" To: CCL Subject: CCL: W:GTO and STO Message-Id: <-29095-050908045734-4493-sY0f/B+VKit+lcn3g2/sLw~~server.ccl.net> X-Original-From: Stan van Gisbergen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Date: Thu, 8 Sep 2005 10:51:27 +0200 Mime-Version: 1.0 (Apple Message framework v619.2) Sent to CCL by: Stan van Gisbergen [vangisbergen~~scm.com] Dear Dr. McKelvey and others interested in STO code performance, Thank you for your compliments regarding ADF's capabilities. As there seems to be some doubt regarding the efficiency of STO-based codes, such as ADF, I would like to give one timing example to make the discussion less theoretical. An 8-CPU job on a Linux cluster (http://www.sara.nl/userinfo/lisa/description/index.html) for a geometry step at the GGA level of a Pt-complex with 105 atoms in a DZP basis set (1021 STO's) takes 17.5 minutes elapsed time. My conclusion is that this is fast enough to do a lot of useful chemistry with ADF during one coffee break. I can provide the input file upon request so you can check if other DFT codes are similarly efficient. Further information on the efficiency of ADF is available in our brochure (http://www.scm.com/SCMForms/BrochureRequest.jsp) and can be tested through a free trial. Best regards, Stan van Gisbergen, Scientific Computing & Modelling (www.scm.com), provider of ADF On Sep 7, 2005, at 4:17 PM, CCL wrote: > > Sent to CCL by: John McKelvey [jmmckel;;attglobal.net] > All, > > I have not seen any timing benchmarks of ADF and Slater functions > versus a gaussian based code. With intent to compare accuracy I > suppose one could start by comparing a D-Z Slater calculation in ADF > with an equivalent D-Z/STO-6G basis in a gaussian based code. The cusp > conditions and hence energies would be off some, but I would guess > that geometries might be very similar.... Not sure of codes that > have STO-NG for d functions.. > I have to say that after sitting through the ADF seminar at the recent > ACS meeting I am quite impressed with it's capabilities. CPU times > may not be the only issue; after all understanding chemistry is the > main point. :-) > > Best regards, > > John McKelvey > > > CCL wrote: > >> Sent to CCL by: Laurence Cuffe [Laurence.Cuffe^ucd.ie] >> >> >> ----- Original Message ----- >> >>> From: CCL >>> >> Date: Tuesday, September 6, 2005 6:31 pm >> Subject: CCL: W:GTO and STO >> >> >>> Sent to CCL by: Serguei Patchkovskii [ps:+:ned.sims.nrc.ca] >>> >>>> Sent to CCL by: Laurence Cuffe [Laurence.Cuffe]*[ucd.ie] >>>> The short answer is that calculating the overlap between two >>>> Gaussiantype -Orbitals can be done in closed form. That is given two >>>> GTO's A and B you can write an relatively simple algebraic >>>> expression >>>> for the size of the overlap between them. This is not possible with >>>> Slater type orbitals. >>>> >>> This statement, of course, is false. Closed-form expressions for >>> overlap integrals in terms of exponential integral-type functions >>> are very well known. For example:…(cut) >>> Dr. Serguei Patchkovskii >>> >> A fair point Dr Patchkovskii. In hindsight I should, perhaps, have put >> more emphasis on “relatively simple” As Ahmed. Bouferguene wrote: >> The "flip side of the coin" is, multi-center integrals (which is the >> heart >> of ab initio calculations) over STOs is much much more difficult than >> with >> GTOs. I think I’d trust his judgment in this area, as its one where >> he’s >> published a number of papers e.g. >> Ahmed Bouferguene 2005 J. Phys. A: Math. Gen. 38 2899-2916 “Addition >> theorem of Slater type orbitals: a numerical evaluation of >> Barnett–Coulson/Löwdin functions” >> Historically evaluating GTO’s was faster, and while there are now >> claims >> that highly optimised STO codes can beat GTO codes, I remain to be >> convinced that highly optimised STO codes can beat highly optimised >> GTO >> codes. >> In the wider sense original question was about the popularity of >> Gaussian type orbital codes over STO based ones. Here I think the >> reason >> is also historical, and is based on the early popularity of the >> gaussian >> program as a collaborative venture among a number of theoretical >> chemists. The use of GTO’s was, I think, first suggested by S.F. >> Boys, in Proc. >> Roy. Soc. A200, 542 (1950) >> >> ADF (using STO’s) has been around for a long time, and I know that the >> Zeigler group has made many substantial contributions to it. It has >> not >> (yet) overtaken Gaussian in popularity, but maybe if( or when) it does >> we’ll be wondering what the advantages of GTO’s are. I’m not holding >> my >> breath. >> All the best >> Dr Laurence Cuffe> To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST~~ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > Dr. S.J.A. van Gisbergen       Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands                                 vangisbergen~~scm.com   http://www.scm.com Please note NEW FAX AND TELEPHONE NUMBERS: T: +31-20-5987626     F: +31-20-5987629       From owner-chemistry@ccl.net Thu Sep 8 09:25:08 2005 From: "CCL" To: CCL Subject: CCL: Hydration ONIOM Message-Id: <-29096-050908055947-23118-sY0f/B+VKit+lcn3g2/sLw{}server.ccl.net> X-Original-From: "Tomasz Grabarkiewicz" Content-Type: multipart/alternative; boundary="----=_NextPart_000_003C_01C5B466.7E403C50" Date: Thu, 8 Sep 2005 11:14:34 +0200 MIME-Version: 1.0 Sent to CCL by: "Tomasz Grabarkiewicz" [grabar{}man.poznan.pl] This is a multi-part message in MIME format. ------=_NextPart_000_003C_01C5B466.7E403C50 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable Hi, Does anyone has any experince with ONIOM based calculations of solvated = systems? Recently, I'm trying to refine some data from MD simulations, but so far = without success. My system contains of a small RNA fragment (4nt) and few (5-8) water = molecules + 2 Na+ ions (RNA structure is kept rigid, while the rest is = optimised). Water molecules and ions are the long-residence ones from MD - I simply = want to check if their positions change substantially when a more = accurate method is used. =20 I have tried different methods (from semiempirical to DFT) but still = haven't manage to achieve convergence in any case. I'm using Gaussian = and I tried different iop's but it didn't help. Can anyone suggest anything? Perhaps I've chosen a wrong way/method or = it doesn't make any sense to do such calculations. My intention is to = show specyfic hydrogen bonding scheme between RNA and water. I still = have a feeling that we can only deduce about such scheme from MD = results. Any suggestions will be greatly appreciated. Thanks Tomasz =20 ------=_NextPart_000_003C_01C5B466.7E403C50 Content-Type: text/html; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable
Hi,
Does anyone has any experince with = ONIOM based=20 calculations of solvated systems?
Recently, I'm trying to refine some = data from MD=20 simulations, but so far without success.
My system contains of a small RNA=20 fragment (4nt) and few (5-8) water molecules + 2 Na+ ions (RNA = structure is kept rigid, while the rest is optimised).
Water molecules and ions are the = long-residence=20 ones from MD - I simply want to check if their positions = change=20 substantially when a more accurate method is used.  
I have tried different methods (from = semiempirical=20 to DFT) but still haven't manage to achieve convergence in any = case. I'm=20 using Gaussian and I tried different iop's but it didn't = help.
Can anyone suggest anything? Perhaps = I've=20 chosen a wrong way/method or it doesn't make any sense to do such=20 calculations. My intention is to show specyfic hydrogen bonding scheme = between=20 RNA and water. I still have a feeling that we can only deduce about = such=20 scheme from MD results.
 
Any suggestions will be greatly=20 appreciated.
Thanks
Tomasz  
 

 
------=_NextPart_000_003C_01C5B466.7E403C50-- From owner-chemistry@ccl.net Thu Sep 8 10:46:45 2005 From: "CCL" To: CCL Subject: CCL: W:GTO and STO Message-Id: <-29097-050908103147-22556-hrkl3wo+uWKlJqfCv20ZGw{:}server.ccl.net> X-Original-From: "Ahmed" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 8 Sep 2005 08:42:06 -0600 MIME-Version: 1.0 Sent to CCL by: "Ahmed" [ahmed.bouferguene{:}ualberta.ca] Hi all, Thanks a lot for the links you've provided. In fact, ADF is a density functional code and in this case it is not strange to have high efficient codes since the most difficult integrals needed for such code are the so called three-center nuclear attraction integrals (these are one-electron integrals). However, it is in the ab-initio that the damage is visible since in this case one needs ALL the integrals (including the infamous 4-center 2 electron integrals). Cheers -----Original Message----- > From: owner-chemistry{:}ccl.net [mailto:owner-chemistry{:}ccl.net] Sent: Thursday, September 08, 2005 2:51 AM To: Bouferguene, Ahmed Subject: CCL: W:GTO and STO Sent to CCL by: Stan van Gisbergen [vangisbergen~~scm.com] Dear Dr. McKelvey and others interested in STO code performance, Thank you for your compliments regarding ADF's capabilities. As there seems to be some doubt regarding the efficiency of STO-based codes, such as ADF, I would like to give one timing example to make the discussion less theoretical. An 8-CPU job on a Linux cluster (http://www.sara.nl/userinfo/lisa/description/index.html) for a geometry step at the GGA level of a Pt-complex with 105 atoms in a DZP basis set (1021 STO's) takes 17.5 minutes elapsed time. My conclusion is that this is fast enough to do a lot of useful chemistry with ADF during one coffee break. I can provide the input file upon request so you can check if other DFT codes are similarly efficient. Further information on the efficiency of ADF is available in our brochure (http://www.scm.com/SCMForms/BrochureRequest.jsp) and can be tested through a free trial. Best regards, Stan van Gisbergen, Scientific Computing & Modelling (www.scm.com), provider of ADF On Sep 7, 2005, at 4:17 PM, CCL wrote: > > Sent to CCL by: John McKelvey [jmmckel;;attglobal.net] > All, > > I have not seen any timing benchmarks of ADF and Slater functions > versus a gaussian based code. With intent to compare accuracy I > suppose one could start by comparing a D-Z Slater calculation in ADF > with an equivalent D-Z/STO-6G basis in a gaussian based code. The cusp > conditions and hence energies would be off some, but I would guess > that geometries might be very similar.... Not sure of codes that > have STO-NG for d functions.. > I have to say that after sitting through the ADF seminar at the recent > ACS meeting I am quite impressed with it's capabilities. CPU times > may not be the only issue; after all understanding chemistry is the > main point. :-) > > Best regards, > > John McKelvey > > > CCL wrote: > >> Sent to CCL by: Laurence Cuffe [Laurence.Cuffe^ucd.ie] >> >> >> ----- Original Message ----- >> >>> From: CCL >>> >> Date: Tuesday, September 6, 2005 6:31 pm >> Subject: CCL: W:GTO and STO >> >> >>> Sent to CCL by: Serguei Patchkovskii [ps:+:ned.sims.nrc.ca] >>> >>>> Sent to CCL by: Laurence Cuffe [Laurence.Cuffe]*[ucd.ie] >>>> The short answer is that calculating the overlap between two >>>> Gaussiantype -Orbitals can be done in closed form. That is given two >>>> GTO's A and B you can write an relatively simple algebraic >>>> expression >>>> for the size of the overlap between them. This is not possible with >>>> Slater type orbitals. >>>> >>> This statement, of course, is false. Closed-form expressions for >>> overlap integrals in terms of exponential integral-type functions >>> are very well known. For example:…(cut) >>> Dr. Serguei Patchkovskii >>> >> A fair point Dr Patchkovskii. In hindsight I should, perhaps, have put >> more emphasis on “relatively simple” As Ahmed. Bouferguene wrote: >> The "flip side of the coin" is, multi-center integrals (which is the >> heart >> of ab initio calculations) over STOs is much much more difficult than >> with >> GTOs. I think I’d trust his judgment in this area, as its one where >> he’s >> published a number of papers e.g. >> Ahmed Bouferguene 2005 J. Phys. A: Math. Gen. 38 2899-2916 “Addition >> theorem of Slater type orbitals: a numerical evaluation of >> Barnett–Coulson/Löwdin functions” >> Historically evaluating GTO’s was faster, and while there are now >> claims >> that highly optimised STO codes can beat GTO codes, I remain to be >> convinced that highly optimised STO codes can beat highly optimised >> GTO >> codes. >> In the wider sense original question was about the popularity of >> Gaussian type orbital codes over STO based ones. Here I think the >> reason >> is also historical, and is based on the early popularity of the >> gaussian >> program as a collaborative venture among a number of theoretical >> chemists. The use of GTO’s was, I think, first suggested by S.F. >> Boys, in Proc. >> Roy. Soc. A200, 542 (1950) >> >> ADF (using STO’s) has been around for a long time, and I know that the >> Zeigler group has made many substantial contributions to it. It has >> not >> (yet) overtaken Gaussian in popularity, but maybe if( or when) it does >> we’ll be wondering what the advantages of GTO’s are. I’m not holding >> my >> breath. >> All the best >> Dr Laurence Cuffe> To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST{:}ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > Dr. S.J.A. van Gisbergen       Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands                                 vangisbergen{:}scm.com   http://www.scm.com Please note NEW FAX AND TELEPHONE NUMBERS: T: +31-20-5987626     F: +31-20-5987629       From owner-chemistry@ccl.net Thu Sep 8 11:39:24 2005 From: "CCL" To: CCL Subject: CCL: Dual core processor Message-Id: <-29099-050908113644-20197-85r0OIhW4KZ7sC5L52weEQ{}server.ccl.net> X-Original-From: Marcel Torok Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Thu, 08 Sep 2005 16:43:07 +0200 MIME-Version: 1.0 Sent to CCL by: Marcel Torok [mtorok{}kosice.upjs.sk] Dear CCL'ers, has somebody experience with dual core processor solutions for computational chemistry, mainly G03 and GAMESS? Are there some computation benchmarks comparing them with standard SMP configurations? Thank you Marcel -- ================================================= RNDr. Marcel Torok, PhD. Katedra organickej chemie Ustav chemickych vied, Prirodovedecka fakulta Universita P.J Safarika Moyzesova 11 SK-041 54 Kosice Tel.: +421 (0)55 62 283 32 FAX: +421 (0)55 62 221 24 email: mtorok{}kosice.upjs.sk ================================================= From owner-chemistry@ccl.net Thu Sep 8 11:39:24 2005 From: "CCL" To: CCL Subject: CCL: need the free energy values of water species Message-Id: <-29098-050908110008-13459-85r0OIhW4KZ7sC5L52weEQ[-]server.ccl.net> X-Original-From: Laurynas Riauba Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 08 Sep 2005 17:03:42 +0300 MIME-Version: 1.0 Sent to CCL by: Laurynas Riauba [laurynas.Riauba[-]chf.vu.lt] You can get some numbers at http://webbook.nist.gov For liquid water, formation enthalpy is -285.84 kJ*mol-1, entropy -69.96 J *mol-1*K-1 In "Smith B. J.,Calculation of aqueous proton dissociation constants of quinoline and hydroxyquinolines : A comparison of solvation models, Phys. Chem. Chem. Phys., 2000, 2, 5383-5388" following values are mentioned (according a reference, data is from NIST page): "Experimental values for the proton enthalpy of formation (1530 kJ mol~1), entropy (108.95 J mol~1 K~1) and solvation Gibbs energy (1085.8 kJ mol~1)" Note: I suppose solvation Gibbs energy should have negative sign. For calculations of solvation energy you can look also at http://www.chemistry.ohio-state.edu/~coe/Coe_review.pdf Laurynas Riauba, PhD student, Vilnius University, Vilnius, Lithuania CCL wrote: > Dear all, > > I would like to know the experimental values of free energy of > > 1. Water > 2. Hydronium (H3O+) ion > 3. Hydroxide (OH-) ion > 4. Proton (H+) > > in gas-phase and condensed phase (solvate-phase) > > If someone know, or the source that I can retrieve these values, > could you please inform me. > Thank you very much for your kind consideration. > > Best regards, > Pong Jaturong > jr_pk2001[-]yahoo.com > > > Send instant messages to your online friends http://uk.messenger.yahoo.com > From owner-chemistry@ccl.net Thu Sep 8 13:49:57 2005 From: "CCL" To: CCL Subject: CCL: Dual core processor Message-Id: <-29100-050908131809-24021-IkdSsI0o7bIbaeY2FfAFuw : server.ccl.net> X-Original-From: "S.I.Gorelsky" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 8 Sep 2005 09:34:58 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "S.I.Gorelsky" [gorelsky : stanford.edu] For the information about the dual-core Opteron performance with G03 please refer to http://www.sg-chem.net/cluster/ Best regards, S. Gorelsky > > Sent to CCL by: Marcel Torok [mtorok{}kosice.upjs.sk] > Dear CCL'ers, > has somebody experience with dual core processor solutions for > computational chemistry, mainly G03 and GAMESS? Are there some > computation benchmarks comparing them with standard SMP configurations? > > Thank you > > Marcel > -- > ================================================= > RNDr. Marcel Torok, PhD. > Katedra organickej chemie > Ustav chemickych vied, Prirodovedecka fakulta > Universita P.J Safarika > Moyzesova 11 > SK-041 54 Kosice > > Tel.: +421 (0)55 62 283 32 > FAX: +421 (0)55 62 221 24 > email: mtorok : kosice.upjs.sk > =================================================> > > ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From owner-chemistry@ccl.net Thu Sep 8 14:32:54 2005 From: "CCL" To: CCL Subject: CCL: W:Smarts patterns for functional groups Message-Id: <-29101-050908143219-10232-IkdSsI0o7bIbaeY2FfAFuw-,-server.ccl.net> X-Original-From: "Andrew Smellie" Sent to CCL by: "Andrew Smellie" [asmellie-,-arqule.com] Can anyone recommend a good source of smarts patterns that describe functional groups, especially hydrogen bond donors, acceptors etc ? I'm especially interested in patterns that encode many of the exclusions to the more generic rules Thanks Andrew From owner-chemistry@ccl.net Thu Sep 8 15:51:36 2005 From: "CCL" To: CCL Subject: CCL: need the free energy values of water species Message-Id: <-29103-050908153343-28616-IkdSsI0o7bIbaeY2FfAFuw/./server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-2--279157581 Date: Thu, 8 Sep 2005 13:33:34 -0500 Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Christopher Cramer [cramer/./chem.umn.edu] --Apple-Mail-2--279157581 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed The recentt discussion of thermodynamic quantities for water, the proton, etc., in aqueous solution prompts me to offer a caveat to the experimental numbers that have so far been listed. Each number that I have seen from the list thus far has LACKED any specification of standard state. This is a common flaw in the published literature, too (and a less understandable one since we are not talking about quick email messages) and can introduce fairly large errors if thermodynamic cycles are constructed without careful attention to common standard states. I and several coauthors published a paper recently in J. Chem. Ed. discussing the standard-state issue in some detail, and moreover providing what we consider to be the best consensus assignment of the free energy of solvation of the proton (which is equivalent to defining the absolute potential of the normal hydrogen electrode, incidentally). That reference is Lewis, A.; Bumpus, J. A.; Truhlar, D. G.; Cramer, C. J. "Molecular Modeling of Environmentally Important Processes: Reduction Potentials" J. Chem. Ed. 2004, 81, 596. I suspect that it would violate copyright agreement for me to attach that article to this email, but for those who do not have access to the journal, I would be happy to reply to personal requests for reprints (as a pdf). I also note that an erratum has been submitted that indicates that even after all our efforts, we too made a small standard-state, ahem..., error. It turns out that we were lucky, because our error was essentially exactly equal to the difference between the best estimate at the time and a better estimate that subsequently appeared (so that we regard all numbers in the published paper to still be correct), but it illustrates just how tricky the standard-state issue can sometimes be. The erratum has not yet appeared, and I'd be happy to send a preprint of that, too, but note again that the bottom line is that the published article contains only correct data -- the issue is more one of discussion. Chris Cramer P.S. In the 1 atm (gas) to 1 M (aq) standard state, the free energy of solvation for the proton that we recommend is -1096.6 kJ/mol. The two most recent estimates from simulation and an interpretation of ion-cluster data (for the same standard state choice) are -1097.9 +/- 4.2 and -1104.5 +/- 8.4 kJ/mol, respectively. See Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. H.; Earhart, A. D.; Coe, J. V.; Tuttle, T. R. J. Phys. Chem. A 1998, 102, 7787-7794 and Zhan, C.-G.; Dixon, D. A. J. Phys. Chem. A 2001, 105, 11534-11540. > Sent to CCL by: Laurynas Riauba [laurynas.Riauba[-]chf.vu.lt] > You can get some numbers at http://webbook.nist.gov > > For liquid water, formation enthalpy is -285.84 kJ*mol-1, entropy > -69.96 J *mol-1*K-1 > > In "Smith B. J.,Calculation of aqueous proton dissociation constants > of quinoline and hydroxyquinolines : A comparison of solvation models, > Phys. Chem. Chem. Phys., 2000, 2, 5383-5388" following values are > mentioned (according a reference, data is from NIST page): > > "Experimental values for the proton enthalpy of formation > (1530 kJ mol~1), entropy (108.95 J mol~1 K~1) and solvation > Gibbs energy (1085.8 kJ mol~1)" > > Note: I suppose solvation Gibbs energy should have negative sign. > > For calculations of solvation energy you can look also at > http://www.chemistry.ohio-state.edu/~coe/Coe_review.pdf > > > Laurynas Riauba, > PhD student, > Vilnius University, > Vilnius, Lithuania > > CCL wrote: >> Dear all, >> I would like to know the experimental values of free energy of >> 1. Water >> 2. Hydronium (H3O+) ion >> 3. Hydroxide (OH-) ion >> 4. Proton (H+) >> in gas-phase and condensed phase (solvate-phase) >> If someone know, or the source that I can retrieve these values, >> could you please inform me. >> Thank you very much for your kind consideration. >> Best regards, >> Pong Jaturong >> jr_pk2001/./yahoo.com >> > To=jr_pk2001/./yahoo.com&YY=74978&order=down&sort=date&pos=0> >> Send instant messages to your online friends >> http://uk.messenger.yahoo.com> To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST/./ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer/./pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-2--279157581 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII The recentt discussion of thermodynamic quantities for water, the proton, etc., in aqueous solution prompts me to offer a caveat to the experimental numbers that have so far been listed. Each number that I have seen from the list thus far has LACKED any specification of standard state. This is a common flaw in the published literature, too (and a less understandable one since we are not talking about quick email messages) and can introduce fairly large errors if thermodynamic cycles are constructed without careful attention to common standard states. I and several coauthors published a paper recently in J. Chem. Ed. discussing the standard-state issue in some detail, and moreover providing what we consider to be the best consensus assignment of the free energy of solvation of the proton (which is equivalent to defining the absolute potential of the normal hydrogen electrode, incidentally). That reference is TimesLewis, A.; Bumpus, J. A.; Truhlar, D. G.; Cramer, C. J. "Molecular Modeling of Environmentally Important Processes: Reduction Potentials" J. Chem. Ed. 2004, 81, 596. I suspect that it would violate copyright agreement for me to attach that article to this email, but for those who do not have access to the journal, I would be happy to reply to personal requests for reprints (as a pdf). I also note that an erratum has been submitted that indicates that even after all our efforts, we too made a small standard-state, ahem..., error. It turns out that we were lucky, because our error was essentially exactly equal to the difference between the best estimate at the time and a better estimate that subsequently appeared (so that we regard all numbers in the published paper to still be correct), but it illustrates just how tricky the standard-state issue can sometimes be. The erratum has not yet appeared, and I'd be happy to send a preprint of that, too, but note again that the bottom line is that the published article contains only correct data -- the issue is more one of discussion. Chris Cramer P.S. In the 1 atm (gas) to 1 M (aq) standard state, the free energy of solvation for the proton that we recommend is -1096.6 kJ/mol. The two most recent estimates from simulation and an interpretation of ion-cluster data (for the same standard state choice) are -1097.9 +/- 4.2 and -1104.5 +/- 8.4 kJ/mol, respectively. See Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. H.; Earhart, A. D.; Coe, J. V.; Tuttle, T. R. J. Phys. Chem. A 1998, 102, 7787-7794 and Zhan, C.-G.; Dixon, D. A. J. Phys. Chem. A 2001, 105, 11534-11540. Sent to CCL by: Laurynas Riauba [laurynas.Riauba[-]chf.vu.lt] You can get some numbers at http://webbook.nist.gov For liquid water, formation enthalpy is -285.84 kJ*mol-1, entropy -69.96 J *mol-1*K-1 In "Smith B. J.,Calculation of aqueous proton dissociation constants of quinoline and hydroxyquinolines : A comparison of solvation models, Phys. Chem. Chem. Phys., 2000, 2, 5383-5388" following values are mentioned (according a reference, data is from NIST page): "Experimental values for the proton enthalpy of formation (1530 kJ mol~1), entropy (108.95 J mol~1 K~1) and solvation Gibbs energy (1085.8 kJ mol~1)" Note: I suppose solvation Gibbs energy should have negative sign. For calculations of solvation energy you can look also at http://www.chemistry.ohio-state.edu/~coe/Coe_review.pdf Laurynas Riauba, PhD student, Vilnius University, Vilnius, Lithuania CCL wrote: Dear all, I would like to know the experimental values of free energy of 1. Water 2. Hydronium (H3O+) ion 3. Hydroxide (OH-) ion 4. Proton (H+) in gas-phase and condensed phase (solvate-phase) If someone know, or the source that I can retrieve these values, could you please inform me. Thank you very much for your kind consideration. Best regards, Pong Jaturong jr_pk2001/./yahoo.com < Send instant messages to your online friends http://uk.messenger.yahoo.com -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer/./pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-2--279157581-- From owner-chemistry@ccl.net Thu Sep 8 15:51:36 2005 From: "CCL" To: CCL Subject: CCL: Dual core processor Message-Id: <-29102-050908143935-20415-IkdSsI0o7bIbaeY2FfAFuw_-_server.ccl.net> X-Original-From: jle_-_theworld.com Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 8 Sep 2005 14:30:55 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: jle_-_theworld.com > > Sent to CCL by: Marcel Torok [mtorok{}kosice.upjs.sk] > Dear CCL'ers, > has somebody experience with dual core processor solutions for > computational chemistry, mainly G03 and GAMESS? Are there some > computation benchmarks comparing them with standard SMP configurations? I would be interested in hearing about this as well. Our admittedly unscientific experimentation with running 1 CPU-intensive job on a 2-processor machine vs. 2 suggests that the PC platform's not fully able to support 2 heavy-load jobs. Possibly a memory or i/o bandwidth problem, as it IS a cheap, desktop machine and all that. I would LOVE to be proven wrong over this... Since it seems the same kind(s) of motherboards are used in built-clusters vs. desktop machines, it seems useful to know whether one should buy 1-proc or >1-proc cards for the rack. Joe Leonard jle_-_theworld.com > > Thank you > > Marcel > -- > ================================================= > RNDr. Marcel Torok, PhD. > Katedra organickej chemie > Ustav chemickych vied, Prirodovedecka fakulta > Universita P.J Safarika > Moyzesova 11 > SK-041 54 Kosice > > Tel.: +421 (0)55 62 283 32 > FAX: +421 (0)55 62 221 24 > email: mtorok_-_kosice.upjs.sk > =================================================> To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST_-_ccl.net> > > From owner-chemistry@ccl.net Thu Sep 8 17:14:05 2005 From: "CCL" To: CCL Subject: CCL: W:GTO and STO Message-Id: <-29104-050908165608-30350-IkdSsI0o7bIbaeY2FfAFuw|*|server.ccl.net> X-Original-From: "Dmitri G. Goussev" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="Windows-1252"; reply-type=response Date: Thu, 8 Sep 2005 10:53:12 -0400 MIME-Version: 1.0 Sent to CCL by: "Dmitri G. Goussev" [dgoussev|*|wlu.ca] I would be good if someone could make a brief critical comparative evaluation of the Gaussian 03 and ADF packages. Some questions in particular can be raised about the choice of hybrid DFT (used mostly in Gaussian 03) and pure DFT functionals (used typically in ADF), and which give better reaction energies and barriers. I have heard that frequency calculations are so much longer in ADF that they are not practical for medium to large system, leaving the question open as to whether the optimized geometries are minimums or not. Relativistic effects are also treated differently in the two packages, with the use of ECP's in Gaussian and ZORA- corrections in ADF. It would be interesting to know what difference this could make. Regards, Dmitri Dmitri G. Goussev (Gusev) Associate Professor of Chemistry Wilfrid Laurier University Department of Chemistry Waterloo, Ontario N2L 3C5 Canada Tel.: (519) 884-1970, ext. 2736 Fax: (519) 746-0677 ----- Original Message ----- > From: "CCL" To: "Goussev, Dmitri " Sent: Thursday, September 08, 2005 4:51 AM Subject: CCL: W:GTO and STO > > Sent to CCL by: Stan van Gisbergen [vangisbergen~~scm.com] > Dear Dr. McKelvey and others interested in STO code performance, > > Thank you for your compliments regarding ADF's capabilities. > > As there seems to be some doubt regarding the efficiency of STO-based > codes, > such as ADF, I would like to give one timing example to make the > discussion less theoretical. > > An 8-CPU job on a Linux cluster > (http://www.sara.nl/userinfo/lisa/description/index.html) > for a geometry step at the GGA level of a Pt-complex with 105 atoms in a > DZP basis set > (1021 STO's) takes 17.5 minutes elapsed time. My conclusion is that this > is fast enough > to do a lot of useful chemistry with ADF during one coffee break. I can > provide the input > file upon request so you can check if other DFT codes are similarly > efficient. > > Further information on the efficiency of ADF is available in our brochure > (http://www.scm.com/SCMForms/BrochureRequest.jsp) > and can be tested through a free trial. > > Best regards, > Stan van Gisbergen, > Scientific Computing & Modelling (www.scm.com), provider of ADF > > On Sep 7, 2005, at 4:17 PM, CCL wrote: > >> >> Sent to CCL by: John McKelvey [jmmckel;;attglobal.net] >> All, >> >> I have not seen any timing benchmarks of ADF and Slater functions versus >> a gaussian based code. With intent to compare accuracy I suppose one >> could start by comparing a D-Z Slater calculation in ADF with an >> equivalent D-Z/STO-6G basis in a gaussian based code. The cusp >> conditions and hence energies would be off some, but I would guess that >> geometries might be very similar.... Not sure of codes that have STO-NG >> for d functions.. >> I have to say that after sitting through the ADF seminar at the recent >> ACS meeting I am quite impressed with it's capabilities. CPU times may >> not be the only issue; after all understanding chemistry is the main >> point. :-) >> >> Best regards, >> >> John McKelvey >> >> >> CCL wrote: >> >>> Sent to CCL by: Laurence Cuffe [Laurence.Cuffe^ucd.ie] >>> >>> >>> ----- Original Message ----- >>> >>>> From: CCL >>>> >>> Date: Tuesday, September 6, 2005 6:31 pm >>> Subject: CCL: W:GTO and STO >>> >>> >>>> Sent to CCL by: Serguei Patchkovskii [ps:+:ned.sims.nrc.ca] >>>> >>>>> Sent to CCL by: Laurence Cuffe [Laurence.Cuffe]*[ucd.ie] >>>>> The short answer is that calculating the overlap between two >>>>> Gaussiantype -Orbitals can be done in closed form. That is given two >>>>> GTO's A and B you can write an relatively simple algebraic expression >>>>> for the size of the overlap between them. This is not possible with >>>>> Slater type orbitals. >>>>> >>>> This statement, of course, is false. Closed-form expressions for >>>> overlap integrals in terms of exponential integral-type functions >>>> are very well known. For example:…(cut) >>>> Dr. Serguei Patchkovskii >>>> >>> A fair point Dr Patchkovskii. In hindsight I should, perhaps, have put >>> more emphasis on “relatively simple” As Ahmed. Bouferguene wrote: >>> The "flip side of the coin" is, multi-center integrals (which is the >>> heart >>> of ab initio calculations) over STOs is much much more difficult than >>> with >>> GTOs. I think I’d trust his judgment in this area, as its one where he’s >>> published a number of papers e.g. >>> Ahmed Bouferguene 2005 J. Phys. A: Math. Gen. 38 2899-2916 “Addition >>> theorem of Slater type orbitals: a numerical evaluation of >>> Barnett–Coulson/Löwdin functions” >>> Historically evaluating GTO’s was faster, and while there are now >>> claims >>> that highly optimised STO codes can beat GTO codes, I remain to be >>> convinced that highly optimised STO codes can beat highly optimised GTO >>> codes. >>> In the wider sense original question was about the popularity of >>> Gaussian type orbital codes over STO based ones. Here I think the >>> reason >>> is also historical, and is based on the early popularity of the >>> gaussian >>> program as a collaborative venture among a number of theoretical >>> chemists. The use of GTO’s was, I think, first suggested by S.F. Boys, >>> in Proc. >>> Roy. Soc. A200, 542 (1950) >>> >>> ADF (using STO’s) has been around for a long time, and I know that the >>> Zeigler group has made many substantial contributions to it. It has >>> not >>> (yet) overtaken Gaussian in popularity, but maybe if( or when) it does >>> we’ll be wondering what the advantages of GTO’s are. I’m not holding my >>> breath. >>> All the best >>> Dr Laurence Cuffe> To send e-mail to subscribers of CCL put the string >>> CCL: on your >> Subject: line> >> Send your subscription/unsubscription requests to: >> CHEMISTRY-REQUEST|*|ccl.net HOME Page: http://www.ccl.net | Jobs Page: >> http://www.ccl.net/jobs >> If your is mail bouncing from ccl.net domain due to spam filters, >> please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >> +-+ >> >> >> >> > Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV > Theoretical Chemistry, Vrije Universiteit > De Boelelaan 1083 > 1081 HV Amsterdam > The Netherlands vangisbergen|*|scm.com http://www.scm.com > > Please note NEW FAX AND TELEPHONE NUMBERS: > T: +31-20-5987626 F: +31-20-5987629> To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST|*|ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs> use the Web based form from CCL Home > Page> > > From owner-chemistry@ccl.net Thu Sep 8 18:44:09 2005 From: "CCL" To: CCL Subject: CCL: Dual core processor Message-Id: <-29105-050908183646-17123-IkdSsI0o7bIbaeY2FfAFuw{:}server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Thu, 8 Sep 2005 14:56:00 -0700 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross{:}rosswalker.co.uk] I did some a long time ago with AMD chips and Gaussian. Things are reasonably similar now. If you run two single processor jobs at once each will run around 85 to 90% of a single cpu. Depending on how much memory / disk they are fighting for. Running a single dual processor job very much depends on what type of simulation you are doing. Some routines in Gaussian are not multithreaded for example. On a typical optimisation you can expect to get performance between 155 and 165% of a single cpu. This can depend on chipset, memory speed etc. So some motherboards do better than others. Anyway, here's the site with the data on: http://www.rosswalker.co.uk/benchmarks/ All the best Ross /\ \/ |\oss Walker | Department of Molecular Biology TPC15 | | The Scripps Research Institute | | Tel: +1 858 784 8889 | EMail:- ross{:}rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. > -----Original Message----- > From: owner-chemistry{:}ccl.net [mailto:owner-chemistry{:}ccl.net] > Sent: Thursday, September 08, 2005 07:43 > To: Walker, Ross > Subject: CCL: Dual core processor > > > Sent to CCL by: Marcel Torok [mtorok{}kosice.upjs.sk] > Dear CCL'ers, > has somebody experience with dual core processor solutions for > computational chemistry, mainly G03 and GAMESS? Are there some > computation benchmarks comparing them with standard SMP > configurations? > > Thank you > > Marcel > -- > ================================================= > RNDr. Marcel Torok, PhD. > Katedra organickej chemie > Ustav chemickych vied, Prirodovedecka fakulta > Universita P.J Safarika > Moyzesova 11 > SK-041 54 Kosice > > Tel.: +421 (0)55 62 283 32 > FAX: +421 (0)55 62 221 24 > email: mtorok{:}kosice.upjs.sk > ================================================= > > > > -= This is automatically added to each message by the mailing > script =- > To send e-mail to subscribers of CCL put the string CCL: on > your Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST{:}ccl.net> > If your is mail bouncing from ccl.net domain due to spam > filters, please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > From owner-chemistry@ccl.net Thu Sep 8 19:12:06 2005 From: "CCL" To: CCL Subject: CCL: W:GTO and STO Message-Id: <-29106-050908185205-26226-IkdSsI0o7bIbaeY2FfAFuw-$-server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 08 Sep 2005 17:50:23 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel-$-attglobal.net] All, The test would be to compare two different programs using the same DFT functional and as similar basis sets as possible. In a Slater sense STO-6G _might_ be a near equivalent to a Slater; the question would be then what would be the flop count for a DZ Slater basis using two Slaters vs 2*STO-6G gaussian Slater mimics... Cheers, John McKelvey CCL wrote: >Sent to CCL by: "Ahmed" [ahmed.bouferguene{:}ualberta.ca] >Hi all, > >Thanks a lot for the links you've provided. In fact, ADF is a density >functional code and in this case it is not strange to have high efficient >codes since the most difficult integrals needed for such code are the so >called three-center nuclear attraction integrals (these are one-electron >integrals). > >However, it is in the ab-initio that the damage is visible since in this >case one needs ALL the integrals (including the infamous 4-center 2 electron >integrals). > >Cheers > >-----Original Message----- > > >>From: owner-chemistry-$-ccl.net [mailto:owner-chemistry-$-ccl.net] >> >> >Sent: Thursday, September 08, 2005 2:51 AM >To: Bouferguene, Ahmed >Subject: CCL: W:GTO and STO > > >Sent to CCL by: Stan van Gisbergen [vangisbergen~~scm.com] >Dear Dr. McKelvey and others interested in STO code performance, > >Thank you for your compliments regarding ADF's capabilities. > >As there seems to be some doubt regarding the efficiency of STO-based >codes, >such as ADF, I would like to give one timing example to make the >discussion less theoretical. > >An 8-CPU job on a Linux cluster >(http://www.sara.nl/userinfo/lisa/description/index.html) >for a geometry step at the GGA level of a Pt-complex with 105 atoms in >a DZP basis set >(1021 STO's) takes 17.5 minutes elapsed time. My conclusion is that >this is fast enough >to do a lot of useful chemistry with ADF during one coffee break. I can >provide the input >file upon request so you can check if other DFT codes are similarly >efficient. > >Further information on the efficiency of ADF is available in our >brochure >(http://www.scm.com/SCMForms/BrochureRequest.jsp) >and can be tested through a free trial. > >Best regards, >Stan van Gisbergen, >Scientific Computing & Modelling (www.scm.com), provider of ADF > >On Sep 7, 2005, at 4:17 PM, CCL wrote: > > > >>Sent to CCL by: John McKelvey [jmmckel;;attglobal.net] >>All, >> >>I have not seen any timing benchmarks of ADF and Slater functions >>versus a gaussian based code. With intent to compare accuracy I >>suppose one could start by comparing a D-Z Slater calculation in ADF >>with an equivalent D-Z/STO-6G basis in a gaussian based code. The cusp >>conditions and hence energies would be off some, but I would guess >>that geometries might be very similar.... Not sure of codes that >>have STO-NG for d functions.. >>I have to say that after sitting through the ADF seminar at the recent >>ACS meeting I am quite impressed with it's capabilities. CPU times >>may not be the only issue; after all understanding chemistry is the >>main point. :-) >> >>Best regards, >> >>John McKelvey >> >> >>CCL wrote: >> >> >> >>>Sent to CCL by: Laurence Cuffe [Laurence.Cuffe^ucd.ie] >>> >>> >>>----- Original Message ----- >>> >>> >>> >>>>From: CCL >>>> >>>> >>>> >>>Date: Tuesday, September 6, 2005 6:31 pm >>>Subject: CCL: W:GTO and STO >>> >>> >>> >>> >>>>Sent to CCL by: Serguei Patchkovskii [ps:+:ned.sims.nrc.ca] >>>> >>>> >>>> >>>>>Sent to CCL by: Laurence Cuffe [Laurence.Cuffe]*[ucd.ie] >>>>>The short answer is that calculating the overlap between two >>>>>Gaussiantype -Orbitals can be done in closed form. That is given two >>>>>GTO's A and B you can write an relatively simple algebraic >>>>>expression >>>>>for the size of the overlap between them. This is not possible with >>>>>Slater type orbitals. >>>>> >>>>> >>>>> >>>>This statement, of course, is false. Closed-form expressions for >>>>overlap integrals in terms of exponential integral-type functions >>>>are very well known. For example:…(cut) >>>>Dr. Serguei Patchkovskii >>>> >>>> >>>> >>>A fair point Dr Patchkovskii. In hindsight I should, perhaps, have put >>>more emphasis on “relatively simple” As Ahmed. Bouferguene wrote: >>>The "flip side of the coin" is, multi-center integrals (which is the >>>heart >>>of ab initio calculations) over STOs is much much more difficult than >>>with >>>GTOs. I think I’d trust his judgment in this area, as its one where >>>he’s >>>published a number of papers e.g. >>>Ahmed Bouferguene 2005 J. Phys. A: Math. Gen. 38 2899-2916 “Addition >>>theorem of Slater type orbitals: a numerical evaluation of >>>Barnett–Coulson/Löwdin functions” >>>Historically evaluating GTO’s was faster, and while there are now >>>claims >>>that highly optimised STO codes can beat GTO codes, I remain to be >>>convinced that highly optimised STO codes can beat highly optimised >>>GTO >>>codes. >>>In the wider sense original question was about the popularity of >>>Gaussian type orbital codes over STO based ones. Here I think the >>>reason >>>is also historical, and is based on the early popularity of the >>>gaussian >>>program as a collaborative venture among a number of theoretical >>>chemists. The use of GTO’s was, I think, first suggested by S.F. >>>Boys, in Proc. >>>Roy. Soc. A200, 542 (1950) >>> >>>ADF (using STO’s) has been around for a long time, and I know that the >>>Zeigler group has made many substantial contributions to it. It has >>>not >>>(yet) overtaken Gaussian in popularity, but maybe if( or when) it does >>>we’ll be wondering what the advantages of GTO’s are. I’m not holding >>>my >>>breath. >>>All the best >>>Dr Laurence Cuffe> To send e-mail to subscribers of CCL put the string >>> >>> >CCL: on your > > >>Subject: line> >>Send your subscription/unsubscription requests to: >>CHEMISTRY-REQUEST-$-ccl.net HOME Page: http://www.ccl.net | Jobs Page: >>http://www.ccl.net/jobs >>If your is mail bouncing from ccl.net domain due to spam filters, >>please> >> >> >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > >>+-+ >> >> >> >> >> >> >Dr. S.J.A. van Gisbergen >Scientific Computing & Modelling NV >Theoretical Chemistry, Vrije Universiteit >De Boelelaan 1083 >1081 HV Amsterdam >The Netherlands >vangisbergen-$-scm.com >http://www.scm.com > >Please note NEW FAX AND TELEPHONE NUMBERS: >T: +31-20-5987626 >F: +31-20-5987629> > > > > > > From owner-chemistry@ccl.net Thu Sep 8 20:27:50 2005 From: "CCL" To: CCL Subject: CCL: need the free energy values of water species Message-Id: <-29107-050908180011-13263-IkdSsI0o7bIbaeY2FfAFuw]![server.ccl.net> X-Original-From: "luo" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0008_01C5B49A.1EF71640" Date: Thu, 8 Sep 2005 17:24:08 -0400 MIME-Version: 1.0 Sent to CCL by: "luo" [luo]![marine.usf.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0008_01C5B49A.1EF71640 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLs, I collected thermodynamic data you required. This new database, = "Comprehensive Handbook of Chemical Bond Energies", will be published by = CRC Press 2006. I would show you the detailed values in advance if you need some.=20 Yu-Ran Luo, Ph.D. luo]![marine.usf.edu =3D=3D=3D=3D ----- Original Message -----=20 From: CCL=20 To: Luo, Yu-Ran =20 Sent: Thursday, September 08, 2005 2:33 PM Subject: CCL: need the free energy values of water species The recentt discussion of thermodynamic quantities for water, the = proton, etc., in aqueous solution prompts me to offer a caveat to the = experimental numbers that have so far been listed. Each number that I have seen from the list thus far has LACKED any = specification of standard state. This is a common flaw in the published = literature, too (and a less understandable one since we are not talking = about quick email messages) and can introduce fairly large errors if = thermodynamic cycles are constructed without careful attention to common = standard states. I and several coauthors published a paper recently in J. Chem. Ed. = discussing the standard-state issue in some detail, and moreover = providing what we consider to be the best consensus assignment of the = free energy of solvation of the proton (which is equivalent to defining = the absolute potential of the normal hydrogen electrode, incidentally). = That reference is Lewis, A.; Bumpus, J. A.; Truhlar, D. G.; Cramer, C. J. "Molecular = Modeling of Environmentally Important Processes: Reduction Potentials" = J. Chem. Ed. 2004, 81, 596. I suspect that it would violate copyright agreement for me to attach = that article to this email, but for those who do not have access to the = journal, I would be happy to reply to personal requests for reprints (as = a pdf). I also note that an erratum has been submitted that indicates = that even after all our efforts, we too made a small standard-state, = ahem..., error. It turns out that we were lucky, because our error was = essentially exactly equal to the difference between the best estimate at = the time and a better estimate that subsequently appeared (so that we = regard all numbers in the published paper to still be correct), but it = illustrates just how tricky the standard-state issue can sometimes be. = The erratum has not yet appeared, and I'd be happy to send a preprint of = that, too, but note again that the bottom line is that the published = article contains only correct data -- the issue is more one of = discussion. Chris Cramer P.S. In the 1 atm (gas) to 1 M (aq) standard state, the free energy of = solvation for the proton that we recommend is -1096.6 kJ/mol. The two = most recent estimates from simulation and an interpretation of = ion-cluster data (for the same standard state choice) are -1097.9 +/- = 4.2 and -1104.5 +/- 8.4 kJ/mol, respectively. See Tissandier, M. D.; = Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. H.; Earhart, A. D.; Coe, J. V.; Tuttle, T. R. J. Phys. Chem. A 1998, 102, 7787-7794 = and Zhan, C.-G.; Dixon, D. A. J. Phys. Chem. A 2001, 105, 11534-11540. Sent to CCL by: Laurynas Riauba [laurynas.Riauba[-]chf.vu.lt] You can get some numbers at http://webbook.nist.gov For liquid water, formation enthalpy is -285.84 kJ*mol-1, entropy = -69.96 J *mol-1*K-1 In "Smith B. J.,Calculation of aqueous proton dissociation constants = of quinoline and hydroxyquinolines : A comparison of solvation models, = Phys. Chem. Chem. Phys., 2000, 2, 5383-5388" following values are = mentioned (according a reference, data is from NIST page): "Experimental values for the proton enthalpy of formation (1530 kJ mol~1), entropy (108.95 J mol~1 K~1) and solvation Gibbs energy (1085.8 kJ mol~1)" Note: I suppose solvation Gibbs energy should have negative sign. For calculations of solvation energy you can look also at = http://www.chemistry.ohio-state.edu/~coe/Coe_review.pdf Laurynas Riauba, PhD student, Vilnius University, Vilnius, Lithuania CCL wrote: Dear all, I would like to know the experimental values of free energy of 1. Water 2. Hydronium (H3O+) ion 3. Hydroxide (OH-) ion 4. Proton (H+) in gas-phase and condensed phase (solvate-phase) If someone know, or the source that I can retrieve these values, could you please inform me. Thank you very much for your kind consideration. Best regards, Pong Jaturong jr_pk2001]![yahoo.com = Send instant messages to your online friends = http://uk.messenger.yahoo.com -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer]![pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") ------=_NextPart_000_0008_01C5B49A.1EF71640 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLs,
 
I collected thermodynamic data you = required. This=20 new database, "Comprehensive Handbook of Chemical Bond = Energies", will=20 be published by CRC Press 2006.
 
I would show you the detailed values in = advance if=20 you need some.
 
Yu-Ran Luo, Ph.D.
luo]![marine.usf.edu
=3D=3D=3D=3D
----- Original Message -----
From:=20 CCL=20
Sent: Thursday, September 08, = 2005 2:33=20 PM
Subject: CCL: need the free = energy values=20 of water species

The recentt discussion of thermodynamic quantities for = water,=20 the proton, etc., in aqueous solution prompts me to offer a caveat to = the=20 experimental numbers that have so far been listed.

Each number = that I=20 have seen from the list thus far has LACKED any specification of = standard=20 state. This is a common flaw in the published literature, too (and a = less=20 understandable one since we are not talking about quick email = messages) and=20 can introduce fairly large errors if thermodynamic cycles are = constructed=20 without careful attention to common standard states.

I and = several=20 coauthors published a paper recently in J. Chem. Ed. discussing the=20 standard-state issue in some detail, and moreover providing what we = consider=20 to be the best consensus assignment of the free energy of solvation of = the=20 proton (which is equivalent to defining the absolute potential of the = normal=20 hydrogen electrode, incidentally). That reference = is

Lewis, A.; Bumpus, J. A.;=20 Truhlar, D. G.; Cramer, C. J. "Molecular Modeling of Environmentally = Important=20 Processes: Reduction Potentials" J. Chem. Ed. 2004, = 81,=20 596.

I suspect that it would violate = copyright=20 agreement for me to attach that article to this email, but for those = who do=20 not have access to the journal, I would be happy to reply to personal = requests=20 for reprints (as a pdf). I also note that an erratum has been = submitted that=20 indicates that even after all our efforts, we too made a small = standard-state,=20 ahem..., error. It turns out that we were lucky, because our error was = essentially exactly equal to the difference between the best estimate = at the=20 time and a better estimate that subsequently appeared (so that we = regard all=20 numbers in the published paper to still be correct), but it = illustrates just=20 how tricky the standard-state issue can sometimes be. The erratum has = not yet=20 appeared, and I'd be happy to send a preprint of that, too, but note = again=20 that the bottom line is that the published article contains only = correct data=20 -- the issue is more one of discussion.

Chris = Cramer

P.S. In the=20 1 atm (gas) to 1 M (aq) standard state, the free energy of solvation = for the=20 proton that we recommend is -1096.6 kJ/mol. The two most recent = estimates from=20 simulation and an interpretation of ion-cluster data (for the same = standard=20 state choice) are -1097.9 +/- 4.2 and -1104.5 +/- 8.4 kJ/mol, = respectively.=20 See Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, = M. H.;=20 Earhart,
A. D.; Coe, J. V.; Tuttle, T. R. J. Phys. Chem. A 1998, = 102,=20 7787-7794 and Zhan, C.-G.; Dixon, D. A. J. Phys. Chem. A 2001, 105,=20 11534-11540.


Sent to CCL by: Laurynas Riauba=20 [laurynas.Riauba[-]chf.vu.lt]
You can get some numbers at=20 http://webbook.nist.gov

For liquid water, formation enthalpy = is=20 -285.84 kJ*mol-1, entropy -69.96 J *mol-1*K-1

In "Smith B.=20 J.,Calculation of aqueous proton dissociation constants of quinoline = and=20 hydroxyquinolines : A comparison of solvation models, Phys. Chem. = Chem.=20 Phys., 2000, 2, 5383-5388" following values are mentioned (according = a=20 reference, data is from NIST page):

"Experimental values for = the=20 proton enthalpy of formation
(1530 kJ mol~1), entropy (108.95 J = mol~1=20 K~1) and solvation
Gibbs energy (1085.8 kJ mol~1)"

Note: I = suppose=20 solvation Gibbs energy should have negative sign.

For = calculations of=20 solvation energy you can look also at=20 = http://www.chemistry.ohio-state.edu/~coe/Coe_review.pdf


Lauryn= as=20 Riauba,
PhD student,
Vilnius University,
Vilnius,=20 Lithuania

CCL wrote:
Dear all,
I would like to know the experimental = values of=20 free energy of
1. Water
2. Hydronium (H3O+) ion
3. = Hydroxide=20 (OH-) ion
4. Proton (H+)
in gas-phase and condensed phase=20 (solvate-phase)
If someone know, or the source that I can = retrieve=20 these values,
could you please inform me.
Thank you very = much for=20 your kind consideration.
Best regards,
Pong=20 Jaturong
jr_pk2001]![yahoo.com=20 = <http://aa.f516.mail.yahoo.com/ym/Compose?To=3Djr_pk2001]![yahoo.com&= ;YY=3D74978&order=3Ddown&sort=3Ddate&pos=3D0>
Send=20 instant messages to your online friends=20 = http://uk.messenger.yahoo.com

--

Christ= opher=20 J. Cramer
University of Minnesota
Department of = Chemistry
207=20 Pleasant St. SE
Minneapolis, MN=20 55455-0431
--------------------------
Phone: (612) 624-0859 = || FAX:=20 (612) 626-2006
Mobile: (952)=20 = 297-2575
cramer]![pollux.chem.umn.edu
http://pollux.chem.umn.edu/~cra= mer
(website=20 includes information about the textbook "Essentials
of = Computational=20 Chemistry: Theories and Models, 2nd=20 Edition")

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