From owner-chemistry@ccl.net Thu Feb 9 01:26:01 2006 From: "Hugo Martiniano hugomartiniano(-)sapo.pt" To: CCL Subject: CCL:G: Solvation Enthalpy with PCM__CCL Message-Id: <-30823-060209005646-19781-RSfF1FVInX/bKweCTc2DOA*o*server.ccl.net> X-Original-From: "Hugo Martiniano" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 9 Feb 2006 04:55:44 -0000 MIME-Version: 1.0 Sent to CCL by: "Hugo Martiniano" [hugomartiniano---sapo.pt] Hello ralf Yes, my question was how to calculate solvation enthalpies from gaussian output. Unfortunately the method I found (from chem. phys. 65 (1982) 239-245 and JACS 106, 7 (1984) 1945-1950) didn't work very well and I abandoned the idea after a just a few tries, as it was more trouble than it was worth. -----Original Message----- > From: Ralf Tonner [mailto:Tonner(!)chemie.uni-marburg.de] Sent: quarta-feira, 1 de Fevereiro de 2006 16:42 To: hugomartiniano(!)sapo.pt Subject: Solvation Enthalpy with PCM__CCL Dear Hugo, I read your thread on the CCL from last month because I have the same problem and want to calculate solvation enthalpies with the CPCM model using Gaussian03. As I read your thread you solved that problem succesfully. May I ask if it is possible to calculate this entity out of the Gaussian-Output (as this was your initial question, too) ? Or is a more sophisticated treatment needed to obtain meaningful results ? Thanks in advance Ralf -- Ralf Tonner Philipps Universität Marburg Fachbereich Chemie AK Frenking Hans-Meerwein-Straße 35032 Marburg Germany Tel.: +49-6421/28-27030 Tonner(!)chemie.uni-marburg.de From owner-chemistry@ccl.net Thu Feb 9 02:01:01 2006 From: "Joop van lenthe joop|a|chem.uu.nl" To: CCL Subject: CCL: PES vs. # of CPUs Message-Id: <-30824-060208192625-24283-rcRRmzEPqNgFcY5EVzbQ2Q|server.ccl.net> X-Original-From: Joop van lenthe Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 9 Feb 2006 00:19:48 +0100 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Joop van lenthe [joop^-^chem.uu.nl] Hi Jozsef could you send the data you used as input I would like to try to make it less theoretical Joop On 1-feb-06, at 23:41, Jozsef Csontos jozsefcsontos~~creighton.edu wrote: > Sent to CCL by: Jozsef Csontos [jozsefcsontos]|[creighton.edu] > Hi, > > my short question is: > is it possible to get different optimized final structures using the > same input and architecture, OS, software (and so on), but different > number of processors? > > My longer comments are: > I understand that we use approximations (in QM and in life too:) and > there might be error accumulations and our number representation > depends > on the hardware etc. But, I'm quite sure the answer is no. Maybe I'm > wrong, so I tell you the story. > > The story: > I have been using a commercial quantum package, which uses the MPI > libraries (MPICH) for parallelization. I was about to map the PES of > several tripeptides in water using DFT. (Of course, the molecules are > flexible and the PESs are flat and more more approximations) I'm not > totally surprised that the results are different on 1 node with 1 > processor and 6 node with 6 processors. (In the first case there is no > MPI and in the second one there is.) Interestingly, the results are > different on 3 nodes with 6 processors (2CPUs/node) and on 6 nodes with > 6 processors (1CPU/node), in addition the calculation using the > previous > 6 processor configuration (2CPUs/node) differs from the 4 CPUs config > (2CPUs/node) ones. > The energy differences between the structures are small about > 1kcal/mol, > however, the rmsd is quite large 1.9 Angstrom considering heavy atoms > and one of these structures is the deepest minimum on the PES, so these > structures belong to the low energy region. I haven't checked all the > structures whether they are minima or other stationary points. I guess > this is not related to the question, but if all of them were minima my > question would be louder. > > I'm wondering what your opinions are? > > Best wishes, > > Jozsef > > -- > Jozsef Csontos, Ph.D. > > Department of Biomedical Sciences > Creighton University, > Omaha, NE> To recover the email address of the author of the message, please > change> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > =============================== Joop van Lenthe Theoretical Chemistry Group Utrecht tel. -31-30-2532733 joop- -chem.uu.nl =============================== From owner-chemistry@ccl.net Thu Feb 9 02:36:01 2006 From: "fuji yama yamafuji6__yahoo.com" To: CCL Subject: CCL:G: What is the difference between ab inito and DFT? Message-Id: <-30825-060208221313-5702-POE+HMywT4oVjPdm1VBwFw]_[server.ccl.net> X-Original-From: "fuji yama" Sent to CCL by: "fuji yama" [yamafuji6__yahoo.com] Hello All, Can you please tell me the difference between ab initio and DFT methods? It seems for both the calculations people are using the same basis set and same method (like B3Lyp). Can you please tell me how to do ab initio calculation in g03? Please give me model inputfile, if possible. Thank you very much. Fujiyama. From owner-chemistry@ccl.net Thu Feb 9 04:57:00 2006 From: "Marcel Swart m.swart|few.vu.nl" To: CCL Subject: CCL:G: What is the difference between ab inito and DFT? Message-Id: <-30826-060209042730-29892-yWOzGPw9yPL7qoCuEGDOdg*o*server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Date: Thu, 9 Feb 2006 10:26:01 +0100 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Marcel Swart [m.swart ~ few.vu.nl] Hello Fujiyama, see any textbook dealing with these things, like (among many others): Jensen - Introduction to computational chemistry The basic consensus nowadays is, I think, that people refer to "wavefunction based" methods (RHF, MP2, CCSD(T), QCISD(T), CASSCF, CASPT2, MR-CI) as "ab initio", as opposed to Density Functional Theory (DFT) methods. B3LYP you mention belongs to the DFT methods. On Feb 9, 2006, at 8:52 AM, fuji yama yamafuji6__yahoo.com wrote: > Sent to CCL by: "fuji yama" [yamafuji6__yahoo.com] > Hello All, > Can you please tell me the difference between ab initio and DFT > methods? It seems for both the calculations people are using the same > basis set and same method (like B3Lyp). Can you please tell me how to > do ab initio calculation in g03? Please give me model inputfile, if > possible. Thank you very much. > Fujiyama.> To recover the email address of the author of the message, please > change> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > –––––––––––––––––––––––––––––––––––––––––––– dr. Marcel Swart Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E m.swart[A]few.vu.nl W http://www.few.vu.nl/~swart –––––––––––––––––––––––––––––––––––––––––––– Starting May 1, 2006: ICREA researcher at Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) –––––––––––––––––––––––––––––––––––––––––––– From owner-chemistry@ccl.net Thu Feb 9 07:14:01 2006 From: "Pierre Archirel pierre.archirel],[lcp.u-psud.fr" To: CCL Subject: CCL: ab initio and DFT Message-Id: <-30827-060209065705-6504-QB42uEgMSeBpRNGmPa3poQ:_:server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 09 Feb 2006 12:03:56 +0100 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel~!~lcp.u-psud.fr] Dear collegues, Ab initio and DFT methods can be nicely differentiated with the following statement: 1- in ab initio we correlate the wave-function 2- in DFT we correlate the hamiltonian This can be seen as follows: E_exact= (no doubt about it...) Now if Psi_D is a simple determinant, it can be transformed to the exact wave function: Psi_exact=U Psi_D and you get: E_exact== with H_mod=aU H_exact U This means that the exact energy can be obtained with a simple determinant and a modified hamiltonian. DFT is looking for this new hamiltonian. Note that this is also the spirit of semi-empirical theories, who also postulate that the wave-function is a simple determinant, and parametrise H, so as to get the exact energy. DFT and semi-empirical methods both correlate the hamiltonian. Best wishes, P.A. __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel-x-lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Thu Feb 9 09:54:00 2006 From: "nokophala+*+aim.com" To: CCL Subject: CCL: Aquous electrochemistry Message-Id: <-30828-060209093858-11022-mftR0zm+Dd9NSA32QrLp7Q=-=server.ccl.net> X-Original-From: nokophala[-]aim.com Content-Type: multipart/alternative; boundary="--------MailBlocks_8C7FB9DAA5BEEF8_1E8_101_MBLK-M11.sysops.aol.com" Date: Thu, 09 Feb 2006 09:38:45 -0500 MIME-Version: 1.0 Sent to CCL by: nokophala{=}aim.com ----------MailBlocks_8C7FB9DAA5BEEF8_1E8_101_MBLK-M11.sysops.aol.com Content-Type: text/plain; charset="us-ascii" just to add again on thuis issue: Some (most?) anions have positive homo energies. I suppose this means they do not really exist in isolation. I wonder what the correct way of calculating the energis in solution for such species would be. I was thinking of I want to calculate the energy of an anionic species, A-(aq), then I can consider the cycle: AH = A-(aq) +H+(aq). Both AH (which is neutral) and H+ obviously hav epositive homos and so can be considered stable, so E(AH-H+(aq)) can be considered the true energy of A- in solution, and it may/may not differ from a direct calculation of a hypothetical A- in solution. But then, the energy of A- can easily depend on the nature of the counterion. Is that not a true picture of reality, i.e. energy of an anion in solution should depend on the nature of the surounding cation (even if it is not strongly bound)? I hope the argument that species with positive HOMOs (think HF energies to avoid the issue of meaning of DFT orbitals) do not exist is true irrespective of the belief about whether orbitals are reality or not (i do not want to re-start that debate). Noko -----Original Message----- > From: nokophala##aim.com To: Phala, Noko Sent: Tue, 7 Feb 2006 14:51:45 -0500 Subject: CCL: Aquous electrochemistry Sent to CCL by: nokophala-$-aim.com ----------MailBlocks_8C7FA093983A4F3_1630_19F3_FWM-D25.sysops.aol.com Content-Type: text/plain; charset="us-ascii" Thanks for responses so far, everyone. From my current calcs it does seem that one must have the correct structure of the first shell, especially for cationic ions. For H+ is is almost mandatory, but already a single water molecules brings the solvation energy to within an eV of the correct value. Anionic species seem ok'yish even without a shell. Dr Noko Phala E-mail: nokophala ~~ aim.com -----Original Message----- > From: Goedele Roos groos[]vub.ac.be To: Phala, Noko Sent: Mon, 6 Feb 2006 14:54:03 -0500 Subject: CCL: Aquous electrochemistry Sent to CCL by: Goedele Roos [groos^-^vub.ac.be] Yes, the first solvatation shell is important, see Uudsemaa, M., Tamm, T., J. Phys. Chem. A 2003, 107, 9997. or see: M. Namazian, Siahrostami, s., Noorbala, M. R., Coote, m. L., J. Mol. Struct.: Theochem, 759,(2006), 245. or: Shamsipur, M., Alizadeh, Arshadi, S., J. Mol. Struct.: Theochem, 758, (2005), 71 also a very good paper Dutton, A., S., Fukuto, J. M., Kendall, N. H., J. Inorg. Chem. 2005, 44, 4024. Baik, M.-H., Friesner, A. J. Phys. Chem. A 2002, 106, 7407. Patterson, E, Cramer, C., Truhlar, D, JACS, 123 (2001) 2025. Greetz, Goedele >Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com] >Here's an interesting link: > >http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html > > >Jim > >> -----Original Message----- >> From: nokophala. ~ .aim.com [mailto:owner-chemistry ~ ccl.net] >> Sent: Sunday, February 05, 2006 10:22 AM >> To: Kress, Jim >> Subject: CCL: Aquous electrochemistry >> >> Sent to CCL by: nokophala++aim.com >> >> Hi There, >> Is anyone aware of successes in reproducing some of the >> tabulated redox potentials of electrochemical reactions that >> ar elisted i standard electrochemical tables, especiall those >> involving single ions? e.g. Cu >> --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the >> selection of appropriate solvation models. I doubt if >> continuum models would require inclusion of at least the >> first shell of water molecules, as these are strongly bound. >> As a starting point I am trying to reproduce the experimental >> value of the 'reference' reaction 2H+ +2e = H2. Even this >> appears tricky. >> >> Thanks in advance, >> >> Noko Phala, Anglo Research >> ______________________________________________________________ >> __________ >> Check Out the new free AIM(R) Mail -- 2 GB of storage and >> industry-leading spam and email virus protection. >> >> >> >> -= 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/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search)> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> -+-+-+-+-+> > > > Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________________________________________________ Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. ----------MailBlocks_8C7FA093983A4F3_1630_19F3_FWM-D25.sysops.aol.com Content-Type: text/html; charset="us-ascii"
Thanks for responses so far, everyone. From my current calcs it does seem that one must have the correct structure of the first shell, especially for cationic ions. For H+ is is almost mandatory, but already a single water molecules brings the solvation energy to within an eV of the correct value. Anionic species seem ok'yish even without a shell.



Dr Noko Phala
E-mail: nokophala ~~ aim.com

-----Original Message-----
From: Goedele Roos groos[]vub.ac.be
To: Phala, Noko
Sent: Mon, 6 Feb 2006 14:54:03 -0500
Subject: CCL: Aquous electrochemistry

Sent 
to CCL by: Goedele Roos [groos^-^vub.ac.be]

Yes, the first solvatation shell is important,
see Uudsemaa, M., Tamm, T., J. Phys. Chem. A 2003, 107, 9997.
or see: M. Namazian, Siahrostami, s., Noorbala, M. R., Coote, m. L., J. Mol. 
Struct.: Theochem, 759,(2006), 245.
or: Shamsipur, M., Alizadeh, Arshadi, S., J. Mol. Struct.: Theochem, 758, 
(2005), 71

also a very good paper Dutton, A., S., Fukuto, J. M., Kendall, N. H., J. Inorg. 
Chem. 2005, 44, 4024.

Baik, M.-H., Friesner, A. J. Phys. Chem. A 2002, 106, 7407.

Patterson, E, Cramer, C., Truhlar, D, JACS, 123 (2001) 2025.


Greetz, Goedele

>Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com]
>Here's an interesting link:
>
>http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html
>
>
>Jim 
>
>> -----Original Message-----
>> From: nokophala. ~ .aim.com [mailto:owner-chemistry 
~ ccl.net] 
>> Sent: Sunday, February 05, 2006 10:22 AM
>> To: Kress, Jim 
>> Subject: CCL: Aquous electrochemistry
>> 
>> Sent to CCL by: nokophala++aim.com
>> 
>> Hi There,
>> Is anyone aware of successes in reproducing some of the 
>> tabulated redox potentials of electrochemical reactions that 
>> ar elisted i standard electrochemical tables, especiall those 
>> involving single ions? e.g. Cu 
>> --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the
>> selection of appropriate solvation models. I doubt if 
>> continuum models would require inclusion of at least the 
>> first shell of water molecules, as these are strongly bound. 
>> As a starting point I am trying to reproduce the experimental 
>> value of the 'reference' reaction 2H+ +2e = H2. Even this 
>> appears tricky.
>> 
>> Thanks in advance,
>> 
>> Noko Phala, Anglo Research
>> ______________________________________________________________
>> __________
>> Check Out the new free AIM(R) Mail -- 2 GB of storage and 
>> industry-leading spam and email virus protection.
>> 
>> 
>> 
>> -= 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/conferences/
>> 
>> Search Messages: http://www.ccl.net/htdig  
(login: ccl, 
>> Password: search)> 
>> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>> -+-+-+-+-+>
>
>
>

Drs. Goedele Roos
Dienst Algemene Chemie (ALGC)
Vrije Universiteit Brussel (VUB)
Pleinlaan 2
B-1050 Brussels
Tel: 0032-2-629 35 16
Fax: 0032-2-629 33 17E-mail to subscribers: CHEMISTRY 
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just to add again on thuis issue: Some (most?) anions have positive homo energies. I suppose this means they do not really exist in isolation. I wonder what the correct way of calculating the energis in solution for such species would be. I was thinking of I want to calculate the energy of an anionic species, A-(aq),  then I can consider the cycle:
AH = A-(aq) +H+(aq). Both AH (which is neutral) and H+ obviously hav epositive homos and so can be considered stable, so E(AH-H+(aq)) can be considered the true energy of A- in solution, and it may/may not differ from a direct calculation of a hypothetical A- in solution. But then, the energy of A- can easily depend on the nature of the counterion. Is that not a true picture of reality, i.e. energy of an anion in solution should depend on the nature of the surounding cation (even if it is not strongly bound)?
 
I hope the argument that species with positive HOMOs (think HF energies to avoid the issue of meaning of DFT orbitals) do not exist is true irrespective of the belief about whether orbitals are reality or not (i do not want to re-start that debate). 
 
Noko
 
-----Original Message-----
From: nokophala##aim.com <owner-chemistry++ccl.net>
To: Phala, Noko <nokophala++aim.com>
Sent: Tue, 7 Feb 2006 14:51:45 -0500
Subject: CCL: Aquous electrochemistry

Sent to CCL by: nokophala-$-aim.com

----------MailBlocks_8C7FA093983A4F3_1630_19F3_FWM-D25.sysops.aol.com
Content-Type: text/plain; charset="us-ascii"

Thanks for responses so far, everyone. From my current calcs it does seem that 
one must have the correct structure of the first shell, especially for cationic 
ions. For H+ is is almost mandatory, but already a single water molecules brings 
the solvation energy to within an eV of the correct value. Anionic species seem 
ok'yish even without a shell.  
 



Dr Noko Phala
E-mail: nokophala ~~ aim.com

 
 
-----Original Message-----
> From: Goedele Roos groos[]vub.ac.be <owner-chemistry ~~ ccl.net>
To: Phala, Noko  <nokophala ~~ aim.com>
Sent: Mon, 6 Feb 2006 14:54:03 -0500
Subject: CCL: Aquous electrochemistry


Sent to CCL by: Goedele Roos [groos^-^vub.ac.be]

Yes, the first solvatation shell is important,
see Uudsemaa, M., Tamm, T., J. Phys. Chem. A 2003, 107, 9997.
or see: M. Namazian, Siahrostami, s., Noorbala, M. R., Coote, m. L., J. Mol. 
Struct.: Theochem, 759,(2006), 245.
or: Shamsipur, M., Alizadeh, Arshadi, S., J. Mol. Struct.: Theochem, 758, 
(2005), 71

also a very good paper Dutton, A., S., Fukuto, J. M., Kendall, N. H., J. Inorg. 
Chem. 2005, 44, 4024.

Baik, M.-H., Friesner, A. J. Phys. Chem. A 2002, 106, 7407.

Patterson, E, Cramer, C., Truhlar, D, JACS, 123 (2001) 2025.


Greetz, Goedele

>Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com]
>Here's an interesting link:
>
>http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html
>
>
>Jim 
>
>> -----Original Message-----
>> From: nokophala. ~ .aim.com [mailto:owner-chemistry ~ ccl.net] 
>> Sent: Sunday, February 05, 2006 10:22 AM
>> To: Kress, Jim 
>> Subject: CCL: Aquous electrochemistry
>> 
>> Sent to CCL by: nokophala++aim.com
>> 
>> Hi There,
>> Is anyone aware of successes in reproducing some of the 
>> tabulated redox potentials of electrochemical reactions that 
>> ar elisted i standard electrochemical tables, especiall those 
>> involving single ions? e.g. Cu 
>> --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the
>> selection of appropriate solvation models. I doubt if 
>> continuum models would require inclusion of at least the 
>> first shell of water molecules, as these are strongly bound. 
>> As a starting point I am trying to reproduce the experimental 
>> value of the 'reference' reaction 2H+ +2e = H2. Even this 
>> appears tricky.
>> 
>> Thanks in advance,
>> 
>> Noko Phala, Anglo Research
>> ______________________________________________________________
>> __________
>> Check Out the new free AIM(R) Mail -- 2 GB of storage and 
>> industry-leading spam and email virus protection.
>> 
>> 
>> 
>> -= 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/conferences/
>> 
>> Search Messages: http://www.ccl.net/htdig  (login: ccl, 
>> Password: search)> 
>> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>> -+-+-+-+-+>
>
>
>

Drs. Goedele Roos
Dienst Algemene Chemie (ALGC)
Vrije Universiteit Brussel (VUB)
Pleinlaan 2
B-1050 Brussels
Tel: 0032-2-629 35 16
Fax: 0032-2-629 33 17http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________________________________________________
Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam 
and email virus protection.

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Content-Type: text/html; charset="us-ascii"

<HTML><BODY><DIV style='font-family: "Verdana"; font-size: 10pt;'><DIV>
<DIV>Thanks for responses so far, everyone. From my current calcs it does seem 
that one must have the correct structure of the first shell, especially for 
cationic ions. For H+ is is almost mandatory, but already a single water 
molecules brings the solvation energy to within an eV of the correct value. 
Anionic species seem ok'yish even without a shell.  </DIV>
<DIV> </DIV>
<DIV><BR><BR><BR>Dr Noko Phala<BR>E-mail: nokophala ~~ aim.com<BR></DIV>
<DIV> </DIV> <BR>-----Original Message-----<BR>From: Goedele Roos 
groos[]vub.ac.be <owner-chemistry ~~ ccl.net><BR>To: Phala, Noko  <nokophala ~~ 
aim.com><BR>Sent: Mon, 6 Feb 2006 14:54:03 -0500<BR>Subject: CCL: Aquous 
electrochemistry<BR><BR>
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<DIV class=AOLPlainTextBody id=AOLMsgPart_0_5b1d94a5-e3d2-4048-b182-b236a00316f8><PRE><TT>Sent 
to CCL by: Goedele Roos [groos^-^vub.ac.be]

Yes, the first solvatation shell is important,
see Uudsemaa, M., Tamm, T., J. Phys. Chem. A 2003, 107, 9997.
or see: M. Namazian, Siahrostami, s., Noorbala, M. R., Coote, m. L., J. Mol. 
Struct.: Theochem, 759,(2006), 245.
or: Shamsipur, M., Alizadeh, Arshadi, S., J. Mol. Struct.: Theochem, 758, 
(2005), 71

also a very good paper Dutton, A., S., Fukuto, J. M., Kendall, N. H., J. Inorg. 
Chem. 2005, 44, 4024.

Baik, M.-H., Friesner, A. J. Phys. Chem. A 2002, 106, 7407.

Patterson, E, Cramer, C., Truhlar, D, JACS, 123 (2001) 2025.


Greetz, Goedele

>Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com]
>Here's an interesting link:
>
><A href="http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html" 
target=_blank>http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html</A>
>
>
>Jim 
>
>> -----Original Message-----
>> From: nokophala. ~ .aim.com [<A href="mailto:owner-chemistry">mailto:owner-chemistry</A> 
~ ccl.net] 
>> Sent: Sunday, February 05, 2006 10:22 AM
>> To: Kress, Jim 
>> Subject: CCL: Aquous electrochemistry
>> 
>> Sent to CCL by: nokophala++aim.com
>> 
>> Hi There,
>> Is anyone aware of successes in reproducing some of the 
>> tabulated redox potentials of electrochemical reactions that 
>> ar elisted i standard electrochemical tables, especiall those 
>> involving single ions? e.g. Cu 
>> --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the
>> selection of appropriate solvation models. I doubt if 
>> continuum models would require inclusion of at least the 
>> first shell of water molecules, as these are strongly bound. 
>> As a starting point I am trying to reproduce the experimental 
>> value of the 'reference' reaction 2H+ +2e = H2. Even this 
>> appears tricky.
>> 
>> Thanks in advance,
>> 
>> Noko Phala, Anglo Research
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>

Drs. Goedele Roos
Dienst Algemene Chemie (ALGC)
Vrije Universiteit Brussel (VUB)
Pleinlaan 2
B-1050 Brussels
Tel: 0032-2-629 35 16
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----------MailBlocks_8C7FB9DAA5BEEF8_1E8_101_MBLK-M11.sysops.aol.com-- From owner-chemistry@ccl.net Thu Feb 9 10:29:02 2006 From: "MSSC mssc]_[unito.it" To: CCL Subject: CCL: MSSC2006 - Ab initio Modeling in Solid State Chemistry Message-Id: <-30829-060209030320-16958-6WkL0TEU5CnYbBHk0CZeRw^_^server.ccl.net> X-Original-From: MSSC Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 09 Feb 2006 08:24:24 +0100 MIME-Version: 1.0 Sent to CCL by: MSSC [mssc:unito.it] The Theoretical Chemistry Group of the Torino University is organizing a new edition of the Summer School: Ab initio Modeling in Solid State Chemistry MSSC2006 http://www.crystal.unito.it/mssc2006 E-mail: mssc()unito.it September 3-8, 2006 - Torino, Italy Director: R. Dovesi The school is addressed to PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis. It will provide an overview of the possibilities offered by ab initio quantum mechanical techniques when applied to characterize materials. The new capabilities of CRYSTAL06 ( http://www.crystal.unito.it ) will be illustrated: - vibration frequencies and IR intensities of solids at Gamma - full geometry optimization (atom coordinates and cell parameters). On behalf of the organizing Committee Bartolomeo Civalleri From owner-chemistry@ccl.net Thu Feb 9 11:04:00 2006 From: "Ojwang, J.G.O. j.g.o.ojwang{:}tue.nl" To: CCL Subject: CCL:G: [Bad Mail] RE: G: What is the difference between ab inito and DFT? Message-Id: <-30830-060209065705-12345-F1WiSuggyjI6krYwNtN1wg**server.ccl.net> X-Original-From: "Ojwang, J.G.O." Date: Thu, 9 Feb 2006 09:16:58 +0100 Sent to CCL by: "Ojwang, J.G.O." [j.g.o.ojwang ~ tue.nl] [The MS winmail.dat attachment removed by jkl _ ccl.net] Dear Fujiyama, ab initio means from first principles. DFT is essentially an ab initio = method although the XC is not exactly known and most of the values were = obtained from fitting to atomisation energies of phosphorus etc. One of = the true ab initio methods is like Moller Plesset pertubation theory = where everything is obtained from calculations without a fit to = experimental data. But all said and done, roughly speaking DFT is = normally taken as an ab initio method. I hope that answers your qn. -----Original Message----- From: fuji yama yamafuji6__yahoo.com [mailto:owner-chemistry _ ccl.net] Sent: Thu 2/9/2006 8:49 AM To: Ojwang, J.G.O. Cc:=09 Subject: CCL:G: What is the difference between ab inito and DFT? Sent to CCL by: "fuji yama" [yamafuji6__yahoo.com] Hello All, Can you please tell me the difference between ab initio and DFT methods? = It seems for both the calculations people are using the same basis set = and same method (like B3Lyp). Can you please tell me how to do ab initio = calculation in g03? Please give me model inputfile, if possible. Thank = you very much. Fujiyama. From owner-chemistry@ccl.net Thu Feb 9 11:39:00 2006 From: "Godefroid Gahungu ggahungu##yahoo.fr" To: CCL Subject: CCL:G: Fukui functions Message-Id: <-30831-060209034345-25320-ewP6+t5sa4wd4z+6VdIvMg.@.server.ccl.net> X-Original-From: "Godefroid Gahungu" Sent to CCL by: "Godefroid Gahungu" [ggahungu__yahoo.fr] Hello CCNeters, I am attempting a calculation of the condensed Fuikui functions and to my knowledge, these can be calculated using the simple procedure (based on. Mulliken population analysis) given by Yang and Mortier [W. Yang, W. J. Mortier, J. Am. Chem. Soc. 1986, 108, 5708-5711]. It seems that for a system of N electrons, independent calculations are to be made for corresponding N-1, N, and N+1 electron systems with the same molecular geometry. Mulliken population analysis should yield (gross charges) qk(N-1), qk(N),and qk(N + 1) for all atoms k which are to be used in these calculations. So, could anyone provide me with some details (from the preparation of the Gaussian input file to the extraction of the necessary data from the output) to be executed in order to do this!!! Thanks ahead for you coming help!! From owner-chemistry@ccl.net Thu Feb 9 13:38:00 2006 From: "Nuno A. G. Bandeira nuno.bandeira|ist.utl.pt" To: CCL Subject: CCL:G: Fukui functions Message-Id: <-30832-060209130829-13753-pp8Ev+FSnO+OYJOaOQAMvw#,#server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 09 Feb 2006 18:08:17 +0000 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira:+:ist.utl.pt] Godefroid Gahungu ggahungu##yahoo.fr wrote: > I am attempting a calculation of the condensed Fuikui functions and to my knowledge, these can be calculated using the simple procedure (based on. Mulliken population analysis) given by Yang and Mortier [W. Yang, W. J. Mortier, J. Am. Chem. Soc. 1986, 108, 5708-5711]. It seems that for a system of N electrons, independent calculations are to be made for corresponding N-1, N, and N+1 electron systems with the same molecular geometry. Mulliken population analysis should yield (gross charges) > qk(N-1), qk(N),and qk(N + 1) for all atoms k which are to be used in these calculations. > So, could anyone provide me with some details (from the preparation of the Gaussian input file to the extraction of the necessary data from the output) to be executed in order to do this!!! Arguslab (www.planaria-software.com) can automatically make you an input file for Gaussian. I wouldn't trust Mulliken charges if I were you. It's better that you use NPA or Hirshfeld charges. cheers, -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student . IST,Lisbon -- From owner-chemistry@ccl.net Thu Feb 9 14:20:48 2006 From: "Nathan Yoder n-yoder[*]northwestern.edu" To: CCL Subject: CCL: Reaction Path Problems and Memory Questions in Q-CHEM Message-Id: <-30833-060208133250-26211-oFUubBI8b8HYIDholY4Ciw[a]server.ccl.net> X-Original-From: "Nathan Yoder" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 8 Feb 2006 11:28:02 -0600 MIME-Version: 1.0 Sent to CCL by: "Nathan Yoder" [n-yoder]*[northwestern.edu] Hi, I am having some problems running reaction path calculations in qchem on a "molecule" containing silicon, carbon, and hydrogen (30-40 atoms total) using DFT (B3LYP) with 6-31G** and 6-311G** basis sets. The calculations will run for a while, between 1-16 reaction path steps, and then will just quit, normally in the middle of an SCF cycle, although sometimes during the computation of the analytic gradient. Approximately 20% of the runs will give the error message: "Q-Chem fatal error occurred in module NewQAlloc.C, line 268: Unsuccessful malloc of 1678112 bytes of double storage" Which I took to mean a memory issue, so I played around with my memory settings. I generally have used a MEM_STATIC between 300 and 1000. (listed in the manual as # of MB) and a MEM_TOTAL of 1000-3000 (Also listed as MB). However, when I used MEM_TOTAL = 1000, I got the following error: "Q-Chem memory limit of 1000 bytes exceeded on allocation of 543232 bytes of INTEGER storage (chunk #721, address 610f6008) Q-Chem fatal error occurred in module NewQAlloc.C, line 316: Q-Chem total memory limit exceeded" This indicates that that MEM_TOTAL is specified in BYTES, not MB ???? Does anyone have some insight into this? I also tried setting MEM_TOTAL to a really large value (~1000000000) and still have the same problem. The computer has over 2 GB of memory. In all of the cases, I am doing three consecutive Calculations: Transition structure --> Frequency --> Reaction Path. Both the Transition Strucure search and the Frequency calculation run fine, the problem is always in the Reaction path calculation. Reaction Path Settings ($REM): EXCHANGE B3LYP CORRELATION None BASIS 6-31G** JOBTYPE RPATH SCF_PRINT 0 PRINT_ORBITALS FALSE SCF_FINAL_PRINT 0 MEM_TOTAL 1000 MEM_STATIC 300 SCF_GUESS READ GEOM_OPT_HESSIAN READ RPATH_MAX_CYCLES 200 RPATH_COORDS 0 RPATH_DIRECTION 1 RPATH_TOL_DISPLACEMENT 50 RPATH_MAX_STEPSIZE 450 Any ideas are welcome.... Nathan Yoder Northwestern University n-yoder#,#northwestern.edu From owner-chemistry@ccl.net Thu Feb 9 14:39:00 2006 From: "Miklos Kertesz kertesz%georgetown.edu" To: CCL Subject: CCL: NSF-sponsored Research Experiences for Undergraduates (REU) program Message-Id: <-30834-060209141639-5191-38Pe7fmOgiRS0g/8Q3xFcw-,-server.ccl.net> X-Original-From: "Miklos Kertesz" Sent to CCL by: "Miklos Kertesz" [kertesz+*+georgetown.edu] Georgetown University will host its annual NSF-sponsored Research Experiences for Undergraduates (REU) program in chemistry and biochemistry. The ten-week program runs from May 30 to Aug 4 and is open to students who have completed a full year of chemistry by the end of spring term 2005. Students interested in theoretical and/or computational projects will work with Professors Miklos Kertesz, Angel deDios and/or Toshiko Ichiye. The research experience is supplemented by a series of professional development workshops and terminates with a final poster presentation. Successful applicants will receive a stipend of 4000, a travel allowance, and housing. Further details are available at http://www.georgetown.edu/departments/chemistry/ The deadline for applications is March 10, 2006. For more information, contact chemreu()georgetown.edu. From owner-chemistry@ccl.net Thu Feb 9 15:23:01 2006 From: "J. Rui Rodrigues jrui,+,ci.uc.pt" To: CCL Subject: CCL: LINUX system problem Message-Id: <-30836-060209151906-13822-oi5U55ZMI6MpbsYRzXcN3w_._server.ccl.net> X-Original-From: "J. Rui Rodrigues" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 09 Feb 2006 18:50:54 +0000 MIME-Version: 1.0 Sent to CCL by: "J. Rui Rodrigues" [jrui%ci.uc.pt] Dear Ulrike , We had a problem with a linux box that was crashing frequently. Memory tests were ok. Hard drives tests reported both drives as defective. We changed both drives, but the computer was still crashing and the brand new drives (strangely) reported problems. Finally, a careful visual inspection of the motherboard revealed a burned tiny component. We replaced the motherboard and the computer is ok since then. Hope this helps, Rui Rodrigues Ulrike Salzner salzner-x-fen.bilkent.edu.tr wrote: >Sent to CCL by: Ulrike Salzner [salzner:+:fen.bilkent.edu.tr] >Dear all, >we have one PC that is a real lemon. It made problems after about 7 >months of usage and crashes very often. One thing that happens is that >after crashing, all the file systems have changed their lables by adding >a 1. For instance / goes to /1, /usr to /usr1 and so on. Is this some >kind rescue attempt by LINUX (Fedora Core 3) or by the SATA disk? What >can be done to restore the file system? I can log in but if I start a >job it runs for minute or two and then the computer crashes. >Reinstalling the systems help until the next crash occurs ... >Can someone give a hint? > >Thanks, >Ulrike > > From owner-chemistry@ccl.net Thu Feb 9 17:40:00 2006 From: "Jeffrey L Nauss jnauss++accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training for March 2006 Message-Id: <-30837-060209173519-29791-Ea4Sq7G4rMZEo+GmGI/yVA\a/server.ccl.net> X-Original-From: "Jeffrey L Nauss" Sent to CCL by: "Jeffrey L Nauss" [jnauss,,accelrys.com] Accelrys Inc. are holding the following training workshops at during March. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs for the scheduled workshops are 500 per day for all customers. For the on-line presentations, the price is 175 per three hour session for all customers. CAMBRIDGE, UK Introduction to MS Modeling 6 Mar Introduction to Nanomaterials Modeling 7-8 Mar Introduction to Crystal Structure Modeling 9-10 Mar Introduction to MS Modeling 13 Mar Introduction to Polymer Modeling 14-15 Mar Introduction to Quantum Mechanics Modeling 16-17 Mar Structure-Based Design in Discovery Studio 21 Mar Protein Design in Discovery Studio 22 Mar Simulation in Discovery Studio 23 Mar PARIS, FRANCE Pharmacophore Generation with Catalyst 7-8 Mar Structure Based Drug Design with Cerius2 9-10 Mar Library Design and Analysis with Cerius2 13-14 Mar QSAR with Cerius2 15-16 Mar ONLINE TRAINING Introduction to General Modeling using Cerius2 2 Mar (4pm GMT) DS ViewerPro 9 Mar (4pm GMT) DS Gene 13 Mar (3pm PST) DS Gene 14 Mar (7am PST) Introduction to Discovery Studio 14 Mar (7am PST) Solvation Models in CHARMm 15 Mar (7am PST) MacVector 15 Mar (3pm PST) MacVector 16 Mar (7am PST) Accord for Excel Desktop 21 Mar (7am GMT) Accord for Excel Desktop 21 Mar (4pm GMT) Accord for Excel CombiChem 22 Mar (7am GMT) Accord for Excel CombiChem 22 Mar (4pm GMT) DIVA 23 Mar (7am GMT) DIVA 23 Mar (4pm GMT) Further details can be found on our website at http://www.accelrys.com/services/training/general/calendar.html and http://www.accelrys.com/services/training/general/calendar_online.html. Questions regarding scheduling and content should be directed to workshops_._accelrys.com Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training