From owner-chemistry@ccl.net Thu Nov 22 01:17:01 2007 From: "Markus Thut markus.thut[*]iac.unibe.ch" To: CCL Subject: CCL:G: AW: G: AW: G: AW: CIS Optimization for the First Singlet Excited State Message-Id: <-35689-071122011427-3286-vDpx8FKaL3zOS5txcu0HxQ,server.ccl.net> X-Original-From: "Markus Thut" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C82CD7.4144D540" Date: Thu, 22 Nov 2007 07:14:00 +0100 MIME-Version: 1.0 Sent to CCL by: "Markus Thut" [markus.thut]![iac.unibe.ch] This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C82CD7.4144D540 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Yes, we did, usually applying the CalcAll keyword for better = convergence. =20 Hope this helps. =20 Cheers =20 Markus _____ =20 Von: owner-chemistry**ccl.net [mailto:owner-chemistry**ccl.net]=20 Gesendet: Mittwoch, 21. November 2007 10:53 An: Thut, Markus Betreff: CCL:G: AW: G: AW: CIS Optimization for the First Singlet = Excited State =20 Dear Markus, =20 It is a local minimum. =20 After you found the excited state with symmetry constraint, did you reoptimize your system into a C1 symmtery? =20 Thanks, Sue "Markus Thut markus.thut..iac.unibe.ch" = wrote: The _calcall_ calculates the forces at each point in the optimization. = Thus, the minimization algorithm can easily step into the direction of the = largest force contribution. This speeds up convergence (or makes it possible for shallow potentials), but strongly slows down your calculations. So use = it just in case you have convergence problems. =20 Cheers =20 Markus =20 =20 _____ =20 Von: owner-chemistry[A]ccl.net [mailto:owner-chemistry[A]ccl.net]=20 Gesendet: Dienstag, 20. November 2007 04:04 An: Thut, Markus=20 Betreff: CCL:G: AW: CIS Optimization for the First Singlet Excited State =20 Dear Markus Thank you very much for your suggestion.=20 =20 The compound that I have studied do not have any symmetry. In my case, = the LUMO and LUMO+1 is mixed. That might caused the problem for the = interchange of the excited states. =20 The basis set that I used is 6-31g* for all atoms. Is the optimization = more easiler to get converged with Calcall keyword? =20 Best regards, Sue =20 "Markus Thut markus.thut[-]iac.unibe.ch" = wrote: Sent to CCL by: "Markus Thut" [markus.thut+/-iac.unibe.ch] Dear Sue We usedd to encounter this problem too. What we found is that i) upon interchange of the excited states, the electronic character of = the two states interchange. Thus, a "major" change in geometry occurs upon = this change. Please check the evolution of your optimized molecule. ii) Usually, such interchanges occur due to symmetry-breaking = optimization steps. Sometimes, you can prevent interchanges by restricting the optimization to e.g. Cs instead of C1, even though the cluster/molecule = you are optimizing is presumably C1. iii) if you have a symmetry wich allows optimizations for a' or a" transitions, try to optimize for the desired transition (you can do this = in TURBOMOLE, I'm not sure about Gaussian03). In this case, you should get = a minima for the a' and on for the a" transition. Comparing these two geometries, you should find the structural change responsible for the interchange of the two states. We found, for example thath for hydroxyquinolines, such an interchage is induced by a significant change = of the angle of the quinone-N. iv) there might be some problems with your basis set (inducing = structural changes and so on), maybe you first choose a standard basis set? v) try the CalcAll parameter for the opt command. Cheers, Markus > -----Urspr=FCngliche Nachricht----- > Von: owner-chemistry .. ccl.net [mailto:owner-chemistry .. ccl.net] > Gesendet: Samstag, 17. November 2007 03:05 > An: Thut, Markus > Betreff: CCL: CIS Optimization for the First Singlet Excited State >=20 >=20 > Sent to CCL by: "Sue L" [chsue2004 ~~ yahoo.com] > Hi all, >=20 > I have performed a CIS optimization for the first singlet excited = state > with the keywords #n cis(root=3D1,direct) gen opt >=20 > However, the optimization cannot be converged. I found that in the = middle > of the optimization, the first- and second- excited state swapped, as > indicated in the section of Excitation energies and oscillator = strength > (as below). >=20 > --------- > Excited State 1: Singlet-A 3.7320 eV 332.22 nm f=3D0.1634 > 93 -> 94 0.67286 > This state for optimization and/or second-order correction. > Copying the excited state density for this state as the 1-particle = RhoCI > density. >=20 > Excited State 2: Singlet-A 5.5654 eV 222.78 nm f=3D0.2648 > 91 -> 94 -0.12140 > 91 -> 96 -0.14274 > 92 -> 94 0.46889 > 92 -> 95 -0.14756 > 93 -> 95 -0.35249 > --------- >=20 > --------- > Excited State 1: Singlet-A 5.5227 eV 224.50 nm f=3D0.2035 > 91 -> 94 -0.11890 > 91 -> 95 -0.11553 > 91 -> 96 -0.13341 > 92 -> 94 0.46589 > 92 -> 95 -0.17450 > 93 -> 95 -0.35340 > This state for optimization and/or second-order correction. > Copying the excited state density for this state as the 1-particle = RhoCI > density. >=20 > Excited State 2: Singlet-A 4.0937 eV 302.86 nm f=3D0.1943 > 92 -> 95 -0.11059 > 93 -> 94 0.66385 > -------- >=20 > Could anyone know what the problem is? >=20 > Thank you very much. >=20 > Sue >=20 >=20 >=20 > >> > > > > > >=20 > > > >=20 > =3D>=20 >=20 your = homepage. =20 =20 _____ =20 Never miss a thing. Make Yahoo your = homepage. ------=_NextPart_000_0001_01C82CD7.4144D540 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Yes, we did, = usually applying the CalcAll keyword for better = convergence.

 =

Hope this = helps.

 =

Cheers=

 =

Markus=

Von: owner-chemistry**ccl.net [mailto:owner-chemistry**ccl.net]
Gesendet: Mittwoch, 21. = November 2007 10:53
An: Thut, Markus =
Betreff: CCL:G: AW: G: = AW: CIS Optimization for the First Singlet Excited = State

 

Dear Markus,

 

It is a local minimum.

 

After you found the excited state with symmetry = constraint, did you reoptimize your system into a C1 = symmtery?

 

Thanks,

Sue

"Markus = Thut markus.thut..iac.unibe.ch" <owner-chemistry * = ccl.net> wrote:

The _calcall_ calculates the forces at = each point in the optimization. Thus, the minimization algorithm can easily = step into the direction of the largest force contribution. This speeds up convergence (or makes it possible for shallow potentials), but strongly = slows down your calculations. So use it just in case you have convergence = problems.

 

 Cheers

 

Markus

 

 

Von: owner-chemistry[A]ccl.net [mailto:owner-chemistry[A]ccl.net]
Gesendet: Dienstag, 20. = November 2007 04:04
An: Thut, Markus
Betreff: CCL:G: AW: CIS = Optimization for the First Singlet Excited State

 

Dear Markus

Thank you very much for your suggestion. =

 

The compound that I have studied do not have any = symmetry. In my case, the LUMO and LUMO+1 is mixed. That might caused the problem = for the interchange of the excited = states.

 

The basis set that I used is 6-31g* for all atoms. Is the = optimization more easiler to get converged with Calcall keyword?

 

Best regards,

Sue

 



"Markus = Thut markus.thut[-]iac.unibe.ch" = <owner-chemistry|-|ccl.net> wrote:


Sent to CCL by: "Markus Thut" [markus.thut+/-iac.unibe.ch]
Dear Sue

We usedd to encounter this problem too. What we found is that

i) upon interchange of the excited states, the electronic character of = the
two states interchange. Thus, a "major" change in geometry = occurs upon this
change. Please check the evolution of your optimized molecule.

ii) Usually, such interchanges occur due to symmetry-breaking = optimization
steps. Sometimes, you can prevent interchanges by restricting the
optimization to e.g. Cs instead of C1, even though the cluster/molecule = you
are optimizing is presumably C1.

iii) if you have a symmetry wich allows optimizations for a' or = a"
transitions, try to optimize for the desired transition (you can do this = in
TURBOMOLE, I'm not sure about Gaussian03). In this case, you should get = a
minima for the a' and on for the a" transition. Comparing these = two
geometries, you should find the structural change responsible for = the
interchange of the two states. We found, for example thath for
hydroxyquinolines, such an interchage is induced by a significant change = of
the angle of the quinone-N.

iv) there might be some problems with your basis set (inducing = structural
changes and so on), maybe you first choose a standard basis set?

v) try the CalcAll parameter for the opt command.

Cheers,

Markus


> -----Urspr=FCngliche Nachricht-----
> Von: owner-chemistry .. ccl.net [mailto:owner-chemistry .. = ccl.net]
> Gesendet: Samstag, 17. November 2007 03:05
> An: Thut, Markus
> Betreff: CCL: CIS Optimization for the First Singlet Excited = State
>
>
> Sent to CCL by: "Sue L" [chsue2004 ~~ yahoo.com]
> Hi all,
>
> I have performed a CIS optimization for the first singlet excited = state
> with the keywords #n cis(root=3D1,direct) gen opt
>
> However, the optimization cannot be converged. I found that in the = middle
> of the optimization, the first- and second- excited state swapped, = as
> indicated in the section of Excitation energies and oscillator = strength
> (as below).
>
> ---------
> Excited State 1: Singlet-A 3.7320 eV 332.22 nm f=3D0.1634
> 93 -> 94 0.67286
> This state for optimization and/or second-order correction.
> Copying the excited state density for this state as the 1-particle = RhoCI
> density.
>
> Excited State 2: Singlet-A 5.5654 eV 222.78 nm f=3D0.2648
> 91 -> 94 -0.12140
> 91 -> 96 -0.14274
> 92 -> 94 0.46889
> 92 -> 95 -0.14756
> 93 -> 95 -0.35249
> ---------
>
> ---------
> Excited State 1: Singlet-A 5.5227 eV 224.50 nm f=3D0.2035
> 91 -> 94 -0.11890
> 91 -> 95 -0.11553
> 91 -> 96 -0.13341
> 92 -> 94 0.46589
> 92 -> 95 -0.17450
> 93 -> 95 -0.35340
> This state for optimization and/or second-order correction.
> Copying the excited state density for this state as the 1-particle = RhoCI
> density.
>
> Excited State 2: Singlet-A 4.0937 eV 302.86 nm f=3D0.1943
> 92 -> 95 -0.11059
> 93 -> 94 0.66385
> --------
>
> Could anyone know what the problem is?
>
> Thank you very much.
>
> Sue
>
>
>
>
>> > > > > >
>
>
> > >
> =3D>
>


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------=_NextPart_000_0001_01C82CD7.4144D540-- From owner-chemistry@ccl.net Thu Nov 22 02:12:01 2007 From: "Andreas Klamt klamt:-:cosmologic.de" To: CCL Subject: CCL:G: PCM for DMF Message-Id: <-35690-071122021019-28474-Tixf4Kam84fPqpXBXzr6kg!=!server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Nov 2007 08:10:09 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt : cosmologic.de] As I already have pointed out several times, it is a poor assumption that all the non-dielectric features of solvents can be described by changing the dilectric constant and maybe some "solvent radii". COSMO-RS provides a statistical thermodynamics based on the information of the COSMO surface polarization charges. By that solutes and solvents get treated on the same, thermodynamically consistent footing. Thus it can describe almost any solvent (includig ionic liquids) at variable temperature. COSMO-RS is widely used meanwhile in chemical engineering and drug development to calculate free energies, partition coefficients, activity coefficients, solubilities and phase diagrams of solutes in most diverse solvents and mixtures. For literature on COSMO-RS see my book (Klamt, "COSMO-RS: From quantum chemistry to fluid phase thermodynamics and drug design", Elsevier, 2005, or the literature on www.cosmologic.de/publications.html. Best regards Andreas P.S.: If you are luccky you are using an older version of Gaussian03 which supports writing COSMO files for COSMO-RS. Unfortunately since about 1.5 years this has been removed from Gaussian03, since we are kind of "banned by Gaussian". Michael Lanci mpl[A]jhu.edu schrieb: > > I need to run a PCM calculation with dimethylformamide(DMF) as the > solvent. From what I can find in the Gaussian user manuals the > internal parameters are not defined for DMF and changing the > dielectric constant will not sufficiently describe the system. Does > anyone know how I could go about addressing this issue, or are there > parameters that are available elsewhere? > > > > -Mike > > > > > > Michael Lanci > > Department of Chemistry > > Johns Hopkins University > > Baltimore, MD 21218 > > > > Phone: 410.516.7145 > > Fax: 410.516.8420 > > E-mail: mpl]_[jhu.edu > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt~!~cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Nov 22 02:46:00 2007 From: "Shrin Pal spalindia%gmail.com" To: CCL Subject: CCL:G: QMMD Message-Id: <-35691-071122020840-28081-aMOuE/hDbfYqLlMe5JkzbA,+,server.ccl.net> X-Original-From: "Shrin Pal" Content-Type: multipart/alternative; boundary="----=_Part_34808_2390668.1195711424557" Date: Thu, 22 Nov 2007 11:33:44 +0530 MIME-Version: 1.0 Sent to CCL by: "Shrin Pal" [spalindia|a|gmail.com] ------=_Part_34808_2390668.1195711424557 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Subscribers, Can I get a sample Gaussian input (.com) file that describes how I can implement QM and MD in two layers of a QMMD study? Thanks for your support, SP JNCASR India ------=_Part_34808_2390668.1195711424557 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Subscribers,

Can I get a sample Gaussian input (.com) file that describes how I can implement QM and MD in two layers of a QMMD study?

Thanks for your support,

SP
JNCASR
India
------=_Part_34808_2390668.1195711424557-- From owner-chemistry@ccl.net Thu Nov 22 04:11:01 2007 From: "Ulrich Scharfenort scharfenort{=}ltt.rwth-aachen.de" To: CCL Subject: CCL:G: Strange Error in Gaussian Message-Id: <-35692-071122040916-11241-5QGIKkhQf/0u6MisCydo7g!^!server.ccl.net> X-Original-From: Ulrich Scharfenort Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Thu, 22 Nov 2007 10:09:04 +0100 MIME-version: 1.0 Sent to CCL by: Ulrich Scharfenort [scharfenort,,ltt.rwth-aachen.de] Hello, yes i using Linux as well as Windows. should have guessed that this is Windows trouble. My thanks to all who provided that input. Regards Ulrich Scharfenort Close, David M. CLOSED+/-mail.etsu.edu schrieb: > Sent to CCL by: "Close, David M." [CLOSED:_:mail.etsu.edu] > Ulrich: > You don't say how you prepared the original file. However the failure > is in Link1, so Gaussian is having trouble reading the input file. > Sometimes this results from using a DOS editor to input information to a > UNIX environment. UNIX tends to have troubles with old DOS characters > such a carriage returns. These characters are hidden, so you editor > doesn't show them. If this is your problem, you can find useful DOS to > Unix conversion programs that come with the usual FORTRAN editors on the > www. > Regards, Dave Close. > > -----Original Message----- > >> From: owner-chemistry]^[ccl.net [mailto:owner-chemistry]^[ccl.net] >> > Sent: Wednesday, November 21, 2007 5:25 AM > To: Close, David M. > Subject: CCL:G: Strange Error in Gaussian > > > Sent to CCL by: Ulrich Scharfenort [scharfenort+*+ltt.rwth-aachen.de] > > Hello, > > i hope someone has an solution for this strange problem. > > When i copy the *.chk file and the *.com file with an program and try to > start it directly with Gaussian i get the following error: > > Unrecognized layer " > ". > C 1.27522 -0.25922 0. > Error termination via Lnk1e in > /opt/GAUSSIAN/LINUX_amd64/g03.d02/l101.exe at Wed Nov 21 > > but if i open the *.com file with an text editor and just save it > (without any changes). Gaussian starts without any problem. > > I would be grateful for an solution to this strange problem. > > sincerly > > Ulrich Scharfenorthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt > > > -=his is automatically added to each message by the mailing script =-> > > > > From owner-chemistry@ccl.net Thu Nov 22 06:01:01 2007 From: "Andrew Turner andrew.turner],[ed.ac.uk" To: CCL Subject: CCL: solar cells efficiency parameters Message-Id: <-35693-071122055919-15326-JtA0oc4p6NXAzzogeimbEw-*-server.ccl.net> X-Original-From: Andrew Turner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Nov 2007 10:59:15 +0000 MIME-Version: 1.0 Sent to CCL by: Andrew Turner [andrew.turner*ed.ac.uk] Daniel, I got this reply from one of our members of staff who is working in this area. Hope it is useful. Andy --- Andy It is important to realise that the power conversion efficiency is a function of the complete system rather than being attributable to any component material. The nanocrystalline metal oxide, the dye, the redox electrolyte (or hole-transport material), the additives to the electrolyte, the electrode materials, any additional blocking layers and the interactions between all these determine the light harvesting and the kinetic parameters that ultimately control efficiency. Computational comparisons within a given series of dyes, for example, can give insight into factors such as redox potentials, dye-TiO2 binding or light harvesting however this is just one part of a complex system. See for example J. Phys. Chem. C. 2007, 111, 7539-7547 and refs therein. Also of course, gas phase calculations on a dye might not represent well the behaviour in a complex electrolyte mixture while bound to a metal oxide - there have been very few computational studies of dyes actually in situ. As well as the electronic properties, other factors such as dye size and shape can play a role in blocking the dark current (good) or catalysing the dark current (bad). Overall, from the dye perspective, modifications are likely to enhance some aspects (light-harvesting or kinetics) and make others worse so it can be pretty complex. So in summary, within a closely-related series, some insight can be gained > from computational work into the possible effects of small modifications on one of the components, however the system is too complex to be able to predict efficiencies for a general case. Neil Dr. Neil Robertson School of Chemistry University of Edinburgh King's Buildings, West Mains Road Edinburgh EH9 3JJ Tel: +44 131 650 4755 http://www.chem.ed.ac.uk/staff/academic/robertson.html Daniel Glossman-Mitnik dglossman||gmail.com wrote: > Sent to CCL by: "Daniel Glossman-Mitnik" [dglossman:-:gmail.com] > Dear netters: > > When studying solar cells, specially DSSCs, one needs to estimate the efficiency of the materials used for the construction of that solar cell. > The way that this is usually performed is by constructing the I-V curve under standard illumination for a given molecule or material. From this curve it is possible to get some parameters like the short-circuit photocurrent Isc, the open-circuit voltage Voc, of course I and V, the fill factor FF, etc. With all this parameters one is able to estimate the efficiency of the solar cell. From the theoretical point of view, there are programs that can simulate computationally the I-V curve, and from there, to extract the needed parameters. > > My question is: Is it possible to calculate the needed parameters to emitate the efficiency based solely in terms of quantum chemistry calculations? I am thinking that something can be done in terms of orbitals or the ionization potential and electron affinity. > > I will be grateful if you can send me informations about literature (journal, books, web pages) where this problem has been considered. > > Best regards, > > Daniel Glossman-Mitnik> > > > -- ================================== Dr Andrew R. Turner Research Computing Officer e: andrew.turner_+_ed.ac.uk t: +44 (0)131 650 7748 w: http://www.eastchem.ac.uk/rcf icq: 370-899-715 p: School of Chemistry University of Edinburgh EH9 3JJ ================================== From owner-chemistry@ccl.net Thu Nov 22 06:35:01 2007 From: "akef afaneh akef_afnh##yahoo.com" To: CCL Subject: CCL:G: PCM for DMF Message-Id: <-35694-071122062041-24630-35fPAQyuEpBo8i2akzbSsg*server.ccl.net> X-Original-From: akef afaneh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-136823743-1195730425=:22403" Date: Thu, 22 Nov 2007 03:20:25 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: akef afaneh [akef_afnh\a/yahoo.com] --0-136823743-1195730425=:22403 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I doubt that there is an plausible answer to your question. I think you can use the following link: http://www.gaussian.com/g_ur/k_scrf.htm then go down to the SPECIFYING THE SOLVENT and SPECIFYING THE MOLECULAR CAVITY. If you need to build up the cavity you can use United Atom (UA0) model. For example: PBE/6-31G(d) level of theory can be used with RADII=UAKS. "Andreas Klamt klamt:-:cosmologic.de" wrote: Sent to CCL by: Andreas Klamt [klamt : cosmologic.de] As I already have pointed out several times, it is a poor assumption that all the non-dielectric features of solvents can be described by changing the dilectric constant and maybe some "solvent radii". COSMO-RS provides a statistical thermodynamics based on the information of the COSMO surface polarization charges. By that solutes and solvents get treated on the same, thermodynamically consistent footing. Thus it can describe almost any solvent (includig ionic liquids) at variable temperature. COSMO-RS is widely used meanwhile in chemical engineering and drug development to calculate free energies, partition coefficients, activity coefficients, solubilities and phase diagrams of solutes in most diverse solvents and mixtures. For literature on COSMO-RS see my book (Klamt, "COSMO-RS: From quantum chemistry to fluid phase thermodynamics and drug design", Elsevier, 2005, or the literature on www.cosmologic.de/publications.html. Best regards Andreas P.S.: If you are luccky you are using an older version of Gaussian03 which supports writing COSMO files for COSMO-RS. Unfortunately since about 1.5 years this has been removed from Gaussian03, since we are kind of "banned by Gaussian". Michael Lanci mpl[A]jhu.edu schrieb: > > I need to run a PCM calculation with dimethylformamide(DMF) as the > solvent. From what I can find in the Gaussian user manuals the > internal parameters are not defined for DMF and changing the > dielectric constant will not sufficiently describe the system. Does > anyone know how I could go about addressing this issue, or are there > parameters that are available elsewhere? > > > > -Mike > > > > > > Michael Lanci > > Department of Chemistry > > Johns Hopkins University > > Baltimore, MD 21218 > > > > Phone: 410.516.7145 > > Fax: 410.516.8420 > > E-mail: mpl]_[jhu.edu > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt|*|cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -----------------------------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Get easy, one-click access to your favorites. Make Yahoo! your homepage. --0-136823743-1195730425=:22403 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
I doubt that there is an plausible answer to your question. I think you can use the following link:
then go down to the SPECIFYING THE SOLVENT and SPECIFYING THE MOLECULAR CAVITY. If you need to build up the cavity you can use United Atom (UA0) model. For example: PBE/6-31G(d) level of theory can be used with RADII=UAKS.
 


"Andreas Klamt klamt:-:cosmologic.de" <owner-chemistry^^ccl.net> wrote:

Sent to CCL by: Andreas Klamt [klamt : cosmologic.de]
As I already have pointed out several times, it is a poor assumption
that all the non-dielectric features of solvents can be described by
changing the dilectric constant and maybe some "solvent radii". COSMO-RS
provides a statistical thermodynamics based on the information of the
COSMO surface polarization charges. By that solutes and solvents get
treated on the same, thermodynamically consistent footing. Thus it can
describe almost any solvent (includig ionic liquids) at variable
temperature. COSMO-RS is widely used meanwhile in chemical engineering
and drug development to calculate free energies, partition coefficients,
activity coefficients, solubilities and phase diagrams of solutes in
most diverse solvents and mixtures.

For literature on COSMO-RS see my book (Klamt, "COSMO-RS: From quantum
chemistry to fluid phase thermodynamics and drug design", Elsevier,
2005, or the literature on www.cosmologic.de/publications.html.

Best regards

Andreas

P.S.: If you are luccky you are using an older version of Gaussian03
which supports writing COSMO files for COSMO-RS. Unfortunately since
about 1.5 years this has been removed from Gaussian03, since we are kind
of "banned by Gaussian".

Michael Lanci mpl[A]jhu.edu schrieb:
>
> I need to run a PCM calculation with dimethylformamide(DMF) as the
> solvent. From what I can find in the Gaussian user manuals the
> internal parameters are not defined for DMF and changing the
> dielectric constant will not sufficiently describe the system. Does
> anyone know how I could go about addressing this issue, or are there
> parameters that are available elsewhere?
>
>
>
> -Mike
>
>
>
>
>
> Michael Lanci
>
> Department of Chemistry
>
> Johns Hopkins University
>
> Baltimore, MD 21218
>
>
>
> Phone: 410.516.7145
>
> Fax: 410.516.8420
>
> E-mail: mpl]_[jhu.edu
>
>
>


--
-----------------------------------------------------------------------------
Dr. habil. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9
e-mail: klamt|*|cosmologic.de
web: www.cosmologic.de
-----------------------------------------------------------------------------
COSMOlogic
Your Competent Partner for
Computational Chemistry and Fluid Thermodynamics
-----------------------------------------------------------------------------


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Get easy, one-click access to your favorites. Make Yahoo! your homepage. --0-136823743-1195730425=:22403-- From owner-chemistry@ccl.net Thu Nov 22 07:10:00 2007 From: "elite 158 elite158#,#gmail.com" To: CCL Subject: CCL: MD Simulation of nanotube Message-Id: <-35695-071121131455-28550-r0WtUc0cu3KQJ0sCan23UQ_+_server.ccl.net> X-Original-From: "elite 158" Content-Type: multipart/alternative; boundary="----=_Part_28131_30183038.1195665413612" Date: Wed, 21 Nov 2007 22:46:53 +0530 MIME-Version: 1.0 Sent to CCL by: "elite 158" [elite158*|*gmail.com] ------=_Part_28131_30183038.1195665413612 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Tried NAMD and VMD? elite158 On Nov 21, 2007 12:48 AM, Tanusree Sarkar sarkar.tanusree{}gmail.com < owner-chemistry[A]ccl.net> wrote: > Dear CCL Users, > I want to simulate growth of carbon nanotube using > MD simulation. Can you please refer > some MD software for this? > Any kind of help is greatly appreciated > Thanking you > With best regards > Tanusree > ------=_Part_28131_30183038.1195665413612 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Tried NAMD and VMD?
elite158
On Nov 21, 2007 12:48 AM, Tanusree Sarkar sarkar.tanusree{}gmail.com <owner-chemistry[A]ccl.net> wrote:
Dear CCL Users,
                        I want to simulate growth of carbon nanotube using MD simulation. Can you please refer
some MD software for this?
Any kind of help is greatly appreciated
Thanking you
With best regards
Tanusree

------=_Part_28131_30183038.1195665413612-- From owner-chemistry@ccl.net Thu Nov 22 11:40:01 2007 From: "mohamed aish mhmdaish ~~ yahoo.com" To: CCL Subject: CCL: Warning!!: Message-Id: <-35696-071122113807-24392-beJZc+Pasg1+Vp2shwhUaQ_+_server.ccl.net> X-Original-From: mohamed aish Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-2146083764-1195749457=:92520" Date: Thu, 22 Nov 2007 08:37:37 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: mohamed aish [mhmdaish(a)yahoo.com] --0-2146083764-1195749457=:92520 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear All; I am doing a job with MP2 method and 6-31G* (opt.) for compounds containing Br atoms. There is a warning massage, with each compound, appear during running the job. This warning was: **** Warning!!: The largest alpha MO coefficient is 0.19655825D+02 Can anyone tell me why this warning appears? In addition, how can I cancel it? Thanks --------------------------------- Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. --0-2146083764-1195749457=:92520 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear All;
I am doing a job with MP2 method and 6-31G* (opt.) for compounds containing Br atoms. There is a warning massage, with each compound, appear during running the job. This warning was:
**** Warning!!: The largest alpha MO coefficient is  0.19655825D+02
Can anyone tell me why this warning appears? In addition, how can I cancel it?
 
Thanks 
 

Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. --0-2146083764-1195749457=:92520-- From owner-chemistry@ccl.net Thu Nov 22 12:32:01 2007 From: "Guanna Li gnli-$-dicp.ac.cn" To: CCL Subject: CCL:G: PCM for DMF Message-Id: <-35697-071121213722-8660-mDNFcwQC/VKkPqH+CA4kDQ-*-server.ccl.net> X-Original-From: "Guanna Li" Date: Thu, 22 Nov 2007 10:01:57 +0800 Sent to CCL by: "Guanna Li" [gnli##dicp.ac.cn] I think you can use the scrf=read , then define EPS, RSOLV, DENSITY value to last line of the inputfile. you can find these keyword in g03 user manual. hope this is helpful for you ------ Guanna Li 2007-11-22 -------------- Michael Lanci mpl[A]jhu.edu wrote: CCL:G: PCM for DMF I need to run a PCM calculation with dimethylformamide(DMF) as the solvent. From what I can find in the Gaussian user manuals the internal parameters are not defined for DMF and changing the dielectric constant will not sufficiently describe the system. Does anyone know how I could go about addressing this issue, or are there parameters that are available elsewhere? .... From owner-chemistry@ccl.net Thu Nov 22 13:05:01 2007 From: "ilknurca41#gmail.com" To: CCL Subject: CCL: statistical methods Message-Id: <-35698-071121025713-10707-zk9/zljzZKd9C+XUq/XRUA%%server.ccl.net> X-Original-From: ilknurca41*gmail.com Date: Wed, 21 Nov 2007 08:51:38 +0200 Sent to CCL by: ilknurca41*o*gmail.com Hi everybody, What do you think about which is the most effective statistical method in drug design using QSAR?(Multiple Lineer Regression, Partial Least Square, Principle Component Analysis, Neural Networks, etc....) Thanks for attention. Kind regards... ilknurca41^^gmail.com From owner-chemistry@ccl.net Thu Nov 22 13:45:01 2007 From: "Mohamed Imran imranpkm * gmail.com" To: CCL Subject: CCL:G: NBO view Message-Id: <-35699-071122131037-2174-qg7wiMGDx65Y0TFj817OWw+/-server.ccl.net> X-Original-From: Mohamed Imran Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Nov 2007 22:59:40 +0530 MIME-Version: 1.0 Sent to CCL by: Mohamed Imran [imranpkm(_)gmail.com] Hi Related to NBO view I got the following reply and thanks for the same. gOpenMol works for Gaussian only and I would appreciate any method related to GAMESS output. For Molden, switching over to Linux helps. regards Imran ysubboti###ucalgary.ca wrote: > Sent to CCL by: ysubboti%a%ucalgary.ca > Hi Imran > You can use those programms: > gOpenMol > http://www.csc.fi/gopenmol/ > http://www.csc.fi/english/pages/g0penMol/gallery/aspirin_mo.jpg > > and > http://www.cmbi.ru.nl/molden/molden.html > > Just be sure that you have stored NBO orbitals in your chk file. > then use this manual to visualize > http://educ.gaussian.com/visual/Orbs/index.htm > > My best > Julia > > > >> Sent to CCL by: "Imran Predhanekar" [imranpkm+/-gmail.com] >> Hi all >> >> Is there any free software availble to view NBO orbitals/results? >> Help will be gratefully acknowledged. >> >> regards >> Imran> > > > > From owner-chemistry@ccl.net Thu Nov 22 14:57:01 2007 From: "Bob Snyder Noordwijkerhout,comcast.net" To: CCL Subject: CCL: Call for Papers: 8th International Conference on Chemical Structures Message-Id: <-35700-071122145441-13044-OaGWYa/oN2V+ngBrcEu8uA-*-server.ccl.net> X-Original-From: "Bob Snyder" Date: Thu, 22 Nov 2007 14:54:37 -0500 Sent to CCL by: "Bob Snyder" [Noordwijkerhout.---.comcast.net] C A L L F O R P A P E R S 8th International Conference on Chemical Structures NH Leeuwenhorst Conference Hotel, Noordwijkerhout, The Netherlands 1 - 5 June 2008 Visit the conference website at www.int-conf-chem-structures.org for more information. Joint Organizers: o Division of Chemical Information of the American Chemical Society (CINF) o Chemical Structure Association Trust (CSA Trust) o Division of Chemical Information and Computer Science of the Chemical Society of Japan (CSJ) o Chemistry-Information-Computer Division of the Society of German Chemists (GDCh) o Royal Netherlands Chemical Society (KNCV) o Chemical Information Group of the Royal Society of Chemistry (RSC) o Swiss Chemical Society (SCS) The 8th International Conference on Chemical Structures is seeking presentations of novel research and emerging technologies for the following plenary sessions: o Cheminformatics > molecular similarity and diversity > library analysis and profiling > chemical information visualization > representation and searching of conformationally flexible compounds o Structure-Activity and Structure-Property Prediction > data fusion, consensus modeling and multi-property optimization > prediction of ADME/Tox properties > industrialized and large-scale QSAR/QSPR model building o Structure-Based Drug Design and Virtual Screening > protein flexibility in docking > improved chemical models and scoring functions > integration of virtual and high-throughput screening o Analysis of Large Data Sets > data mining of HTS data > analysis of large chemistry spaces > machine learning o Informatics for Bridging Between Chemistry and Biology > integrative discovery informatics > virtual pharmacology > target family based approaches to drug discovery o Virtual Chemistry > structure- and ligand-based de-novo design > synthesis planning and design > mining electronic lab journals > reaction networks, reaction databases and reaction retrieval We encourage the submission of papers on both applications and case studies as well as on method development and algorithmic work. The final program will be a balance of these two aspects. Posters can be submitted for any of the above and related areas, but we also welcome contributions in any aspect of the computer handling of chemical structure information, such as: o representation and manipulation of organic and inorganic compounds, biomacromolecules and polymers o new algorithms for searching and managing chemical structures and reactions o 3D databases and pharmacophore modeling o (automatic) structure elucidation o combinatorial chemistry, diversity analysis o web technology and its effect on chemical information o electronic publishing o searching/dealing with patent spaces o MM or QM/MM simulations o practical free energy calculations o material sciences The conference will feature a new product review session for commercial presentations. Visit the conference website at www.int-conf-chem-structures.org for more information, including details on procedures for online abstract submission and conference registration. The deadline for the submission of abstracts is 15 February 2008. We hope to see you in Noordwijkerhout. Bob Snyder, ICCS Program Chair Markus Wagener, ICCS Vice Chair