Dear Krishna,<= /div>

If memory serves you can use PO= TWRT and ESP keywords to generate a esp file that will display very well in= Molden.

James Robi= nson

From: Krishna Go= vender kk.govender=3D-=3Dgmail.com <owner-chemistry[-]ccl.net>
To: "Robinson, James " = <jameschums[-]yahoo.com>
Sent:= Wednesday, June 1, 2011 9:54 AM
Subject: CCL: Display ESP MOPAC

=0A
Sen= t to CCL by: "Krishna Govender" [kk.govender^gmail.com]
Good day C= CL users.

I was wondering if anyone knows how to display electrostat= ic potentials generated from MOPAC.
I am currently performing the ESP ca= lculation with MOPAC using a single SCF, but i don't know of any software p= ackages that maybe able to display these ESPs.
Any assistance will be g= reatly appreciated.
Thanks.

PhD(Chemistry) Student
Krishna Kub= en Govender
University of Cape Town
Scientific Computing Research Uni= t
Cape Town
Rondebosch
7701

-=3D This is automatica= lly added to each message by the mailing script =3D-
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--0-1163391243-1306940055=:40875-- From owner-chemistry@ccl.net Wed Jun 1 12:22:01 2011 From: "Hao-Bo Guo guohaobo a gmail.com" To: CCL Subject: CCL: Solvation entropy Message-Id: <-44805-110601121946-5457-tRlRr7LyhrposhgyEt+6Mg*|*server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=bcaec548a445f0d1c604a4a8e2bf Date: Wed, 1 Jun 2011 12:19:35 -0400 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo(!)gmail.com] --bcaec548a445f0d1c604a4a8e2bf Content-Type: text/plain; charset=ISO-8859-1 Hi Archirel, Here I want to point out that the Wertz's point is simply wrong! Please carefully read the paper by Ben-Naim and Marcus (J. Chem. Phys. 1984, 81, 2016-2027). Hao-Bo Guo On Wed, Jun 1, 2011 at 10:14 AM, Pierre Archirel pierre.archirel]^[u-psud.fr wrote: > > Sent to CCL by: "Pierre Archirel" [pierre.archirel,,u-psud.fr] > Dear Andreas, > Many thanks for your helpful comment. I was saying a mistake, but > apparently in the language only. My point is as follows: > > 1- there is a paper by D. Wertz (JACS,102 (1980) 5316) showing > empiricaly that the relative entropy loss of a molecule due to solvation > does not depend on the molecule itself and therefore can be taken in > the solvent molecule, taken in the right standard state. Comparing the > entropies of gaseous and liquid water, Wertz deduces the formula for > solvation entropy of any molecule in water: > > DeltaS_solv = S_sol-S_g = -0.46(S_g-14.3) (in kcal/mol) > > where S_g is the standard (1/24.5M) gas-phase entropy of the solute and > Delta_S the solvation entropy between 1/24.5M gas and solution. > In the mind of Wertz S_g and DeltaS_solv are total entropies. > This paper has been cited 95 times, until 2011, and used with some success. > > 2- working on experimental results in acetonitrile I have used a similar > formula and found that a better correlation is found between measurement > and calculation if I subtract the (harmonic analysis) vibration entropy > > from the gas phase entropy. S_g is now the gas phase translation-rotation > entropy. For the consistency I must consider that the resulting DeltaS is > also "vibration free" and I abusively called S_sol the > "translation-rotation" > entropy in solution. > > As you explain to us it is a more subtle quantity, including translation, > rotation, solute-solvent vibration, and configuration entropy. > > Any opinion about the formula of D. Wertz will be welcome. I will > also appreciate references about configuration entropy in solvation. > > Pierre Archirel > LCP, Universite Paris-Sud > France > pierre.archirel:-:u-psud.fr> > > --bcaec548a445f0d1c604a4a8e2bf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Archirel,

Here I want to point out that the Wertz's point is = simply wrong!
Please carefully read the paper by Ben-Naim and Marcus (J.= Chem. Phys. 1984, 81, 2016-2027).

Hao-Bo Guo

On Wed, Jun 1, 2011 at 10:14 AM, Pierre Archirel pierre.archirel]^[u-psud.fr <owner-chemistry%ccl.net> wrote:
=

Sent to CCL by: "Pierre =A0Archirel" [pierre.archirel,,u-psud.fr]
Dear Andreas,
Many thanks for your helpful comment. I was saying a mistake, but
apparently in the language only. My point is as follows:

1- there is a paper by D. Wertz (JACS,102 (1980) 5316) showing
empiricaly that the relative entropy loss of a molecule due to solvation does not depend on the molecule itself and therefore can be taken in
the solvent molecule, taken in the right standard state. Comparing the
entropies of gaseous and liquid water, Wertz deduces the formula for
solvation entropy of any molecule in water:

DeltaS_solv =3D S_sol-S_g =3D -0.46(S_g-14.3) (in kcal/mol)

where S_g is the standard (1/24.5M) gas-phase entropy of the solute and
Delta_S the solvation entropy between 1/24.5M gas and solution.
In the mind of Wertz S_g and DeltaS_solv are total entropies.
This paper has been cited 95 times, until 2011, and used with some success.=

2- working on experimental results in acetonitrile I have used a similar formula and found that a better correlation is found between measurement and calculation if I subtract the (harmonic analysis) vibration entropy
> from the gas phase entropy. S_g is now the gas phase translation-rotat= ion
entropy. For the consistency I must consider that the resulting DeltaS is also "vibration free" and I abusively called S_sol the "tran= slation-rotation"
entropy in solution.

As you explain to us it is a more subtle quantity, including translation, rotation, solute-solvent vibration, and configuration entropy.

Any opinion about the formula of D. Wertz will be welcome. I will
also appreciate references about configuration entropy in solvation.

Pierre Archirel
LCP, Universite Paris-Sud
France
pierre.archirel:-:u-psud.fr<= /a>

-=3D This is automatically added to each message by the mailing script =3D-=
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--bcaec548a445f0d1c604a4a8e2bf-- From owner-chemistry@ccl.net Wed Jun 1 12:57:00 2011 From: "Andreas Klamt klamt===cosmologic.de" To: CCL Subject: CCL: Solvation entropy Message-Id: <-44806-110601123848-18235-1o9enmOXiGEeBxE4sfyklw() server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 01 Jun 2011 18:38:38 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt%%cosmologic.de] Dear Piere, let us make the following simple virtual experiment: Le tus consider two molecules A being a spherical non-polar compound, let us say neopentane D being a spherical compound of the same size with a strong dipole Now let us consider both as solutes and solvents: A in A: A can freely rotate in its spherical cavity A in D: A can freely rotate in its spherical cavity D in A: D can freely rotate in its spherical cavity D in D: D is fixed along the local electric field of the cavity provided by the solvent D The rotational entropy of solvation will be zero in the first three cases, but there will be a considerable entropy loss in the last case. How do you describe this in the language of Wertz? Best regards Andreas Am 01.06.2011 16:14, schrieb Pierre Archirel pierre.archirel]^[u-psud.fr: > Sent to CCL by: "Pierre Archirel" [pierre.archirel,,u-psud.fr] > Dear Andreas, > Many thanks for your helpful comment. I was saying a mistake, but > apparently in the language only. My point is as follows: > > 1- there is a paper by D. Wertz (JACS,102 (1980) 5316) showing > empiricaly that the relative entropy loss of a molecule due to solvation > does not depend on the molecule itself and therefore can be taken in > the solvent molecule, taken in the right standard state. Comparing the > entropies of gaseous and liquid water, Wertz deduces the formula for > solvation entropy of any molecule in water: > > DeltaS_solv = S_sol-S_g = -0.46(S_g-14.3) (in kcal/mol) > > where S_g is the standard (1/24.5M) gas-phase entropy of the solute and > Delta_S the solvation entropy between 1/24.5M gas and solution. > In the mind of Wertz S_g and DeltaS_solv are total entropies. > This paper has been cited 95 times, until 2011, and used with some success. > > 2- working on experimental results in acetonitrile I have used a similar > formula and found that a better correlation is found between measurement > and calculation if I subtract the (harmonic analysis) vibration entropy >> from the gas phase entropy. S_g is now the gas phase translation-rotation > entropy. For the consistency I must consider that the resulting DeltaS is > also "vibration free" and I abusively called S_sol the "translation-rotation" > entropy in solution. > > As you explain to us it is a more subtle quantity, including translation, > rotation, solute-solvent vibration, and configuration entropy. > > Any opinion about the formula of D. Wertz will be welcome. I will > also appreciate references about configuration entropy in solvation. > > Pierre Archirel > LCP, Universite Paris-Sud > France > pierre.archirel:-:u-psud.fr> > > -- PD. Dr. Andreas Klamt CEO / Gesch�ftsf�hrer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt###cosmologic.de web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Wed Jun 1 13:34:00 2011 From: "Alejandro Pisanty apisan++servidor.unam.mx" To: CCL Subject: CCL: Solvation entropy Message-Id: <-44807-110601133151-29446-mtFPxK2BtqZhSIRTJ5gzpQ#,#server.ccl.net> X-Original-From: Alejandro Pisanty Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 1 Jun 2011 17:31:23 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Alejandro Pisanty [apisan ~ servidor.unam.mx] Hi, is libration also important in these studies? It gets your water boiling under microwaves... If solvation energies and entropies are significant for a given system, other than with very simple ions (metal cations), does that not increase the importance of constrained rotation? Is this easy to calculate or estimate? Negligible quantitatively? (Feedback welcome.) Yours, Alejandro Pisanty . . . . . . . . . . . . . . . . . . . . . . . . . . Dr. Alejandro Pisanty UNAM, Av. Universidad 3000, 04510 Mexico DF Mexico Tels. +52-(1)-55-5105-6044, +52-(1)-55-5418-3732 * Mi blog/My blog: http://pisanty.blogspot.com * LinkedIn profile: http://www.linkedin.com/in/pisanty * Twitter: http://twitter.com/apisanty * Unete al grupo UNAM en LinkedIn, http://www.linkedin.com/e/gis/22285/4A106C0C8614 * Ven a ISOC Mexico, http://www.isoc.org.mx, ISOC http://www.isoc.org *Participa en ICANN, http://www.icann.org . . . . . . . . . . . . . . . . . . . . . . . . . . On Wed, 1 Jun 2011, Pierre Archirel pierre.archirel]^[u-psud.fr wrote: > Date: Wed, 1 Jun 2011 10:14:42 -0400 > From: "Pierre Archirel pierre.archirel]^[u-psud.fr" > Reply-To: CCL Subscribers > To: "Pisanty, Alejandro " > Subject: CCL: Solvation entropy > > > Sent to CCL by: "Pierre Archirel" [pierre.archirel,,u-psud.fr] > Dear Andreas, > Many thanks for your helpful comment. I was saying a mistake, but > apparently in the language only. My point is as follows: > > 1- there is a paper by D. Wertz (JACS,102 (1980) 5316) showing > empiricaly that the relative entropy loss of a molecule due to solvation > does not depend on the molecule itself and therefore can be taken in > the solvent molecule, taken in the right standard state. Comparing the > entropies of gaseous and liquid water, Wertz deduces the formula for > solvation entropy of any molecule in water: > > DeltaS_solv = S_sol-S_g = -0.46(S_g-14.3) (in kcal/mol) > > where S_g is the standard (1/24.5M) gas-phase entropy of the solute and > Delta_S the solvation entropy between 1/24.5M gas and solution. > In the mind of Wertz S_g and DeltaS_solv are total entropies. > This paper has been cited 95 times, until 2011, and used with some success. > > 2- working on experimental results in acetonitrile I have used a similar > formula and found that a better correlation is found between measurement > and calculation if I subtract the (harmonic analysis) vibration entropy >> from the gas phase entropy. S_g is now the gas phase translation-rotation > entropy. For the consistency I must consider that the resulting DeltaS is > also "vibration free" and I abusively called S_sol the "translation-rotation" > entropy in solution. > > As you explain to us it is a more subtle quantity, including translation, > rotation, solute-solvent vibration, and configuration entropy. > > Any opinion about the formula of D. Wertz will be welcome. I will > also appreciate references about configuration entropy in solvation. > > Pierre Archirel > LCP, Universite Paris-Sud > France > pierre.archirel:-:u-psud.fr> > > From owner-chemistry@ccl.net Wed Jun 1 14:17:00 2011 From: "Bradley Kenneth Welch bwelch5%%slu.edu" To: CCL Subject: CCL: CBS extrapolation formulas Message-Id: <-44808-110601141619-9942-AwYmHlWwywaDr900rWo5Hw^^^server.ccl.net> X-Original-From: "Bradley Kenneth Welch" Date: Wed, 1 Jun 2011 14:16:16 -0400 Sent to CCL by: "Bradley Kenneth Welch" [bwelch5=slu.edu] Hey CCL readers, We want to do the CBS for a set of energies done with the dunning basis sets from double zeta to 6 zeta. What are some of the commonly used formulas for this? Which ones allow for 5 energies to be used in extrapolation? Sincerely, Bradley Welch Saint Louis University Room 218 From owner-chemistry@ccl.net Wed Jun 1 15:33:01 2011 From: "=?ISO-8859-1?Q?Mart=EDn_Lavecchia?= lavecchia*gmail.com" To: CCL Subject: CCL: Display ESP MOPAC Message-Id: <-44809-110601133612-930-2Ozon3e3d5AZcBjkFLwqEA[#]server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Mart=EDn_Lavecchia?= Content-Type: multipart/alternative; boundary=0015174c151050531604a4a9f44e Date: Wed, 1 Jun 2011 14:35:42 -0300 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Mart=EDn_Lavecchia?= [lavecchia!^!gmail.com] --0015174c151050531604a4a9f44e Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Krishna, You can visualizate ESP results with Jmol. In MOPAC add GRAPHF option. This generates a file with extension mgf. Then open it. I hope it helps. Regards Martin Lavecchia Centro de Qu=EDmica Inorg=E1nica (CEQUINOR) UNLP - CONICET La Plata, Argentina > > ------------------------------ > *From:* Krishna Govender kk.govender=3D-=3Dgmail.com ccl.net> > *To:* "Robinson, James " > *Sent:* Wednesday, June 1, 2011 9:54 AM > *Subject:* CCL: Display ESP MOPAC > > > Sent to CCL by: "Krishna Govender" [kk.govender^gmail.com] > Good day CCL users. > > I was wondering if anyone knows how to display electrostatic potentials > generated from MOPAC. > I am currently performing the ESP calculation with MOPAC using a single > SCF, but i don't know of any software packages that maybe able to display > these ESPs. > Any assistance will be greatly appreciated. > Thanks. > > PhD(Chemistry) Student > Krishna Kuben Govender > University of Cape Town > Scientific Computing Research Unit > Cape Town > Rondebosch > 7701 > > > > -=3D This is automatically added to each message by the mailing script = =3D-> the strange characters on the top line to the ^^^ sign. You can also > look up the X-Original-> From: line in the mail header. > > E-mail to subscribers: CHEMISTRY^^^ccl.net or use: > > > E-mail to administrators: CHEMISTRY-REQUEST^^^ccl.net or use> > > > > --0015174c151050531604a4a9f44e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Krishna,
You can visualizate ESP results with Jmol. In MOPAC add GR= APHF option. This generates a file with extension mgf. Then open it. I hope= it helps.

Regards
Martin Lavecchia
Centro de Qu=EDmica Inorg= =E1nica (CEQUINOR)
UNLP - CONICET
La Plata, Argentina

From: Krishna Govender kk.= govender=3D-=3Dgmail.com= <owner-chemistry^^^ccl.net= >
To: "Robinson, James = " <jameschums^^^yaho= o.com>
Sent: Wed= nesday, June 1, 2011 9:54 AM
Subject: CCL: Display ESP = MOPAC

Sent to CCL by: "Krishna=A0 Govender" [kk.govender^gmail.com]
Good day CCL users.<= br>
I was wondering if anyone knows how to display electrostatic potenti= als generated from MOPAC.
I am currently performing the ESP calculation with MOPAC using a single SCF= , but i don't know of any software packages that maybe able to display = these ESPs.
Any assistance will be greatly appreciated.
Thanks.

PhD(Chemistry) Student
Krishna Kuben Govender
University of Cape = Town
Scientific Computing Research Unit
Cape Town
Rondebosch
77= 01

-=3D This is automatically added to each messa= ge by the mailing script =3D-the strange characters on the top line to the ^^^ sign. You can also
lo= ok up the X-Original-> From: line in the mail header.

E-mail to s= ubscribers: = CHEMISTRY^^^ccl.net or use:
=A0 =A0 =A0

E-mail to administrators: CHEMISTRY-REQUEST^^^ccl= .net or use
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=
Before posting, check wait time at: http://www.ccl.net

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Search Messages: http://www.ccl.net/= chemistry/searchccl/index.shtml
=A0 =A0 =A0 <= a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank">http://www.ccl= .net/spammers.txt

--0015174c151050531604a4a9f44e-- From owner-chemistry@ccl.net Wed Jun 1 17:14:00 2011 From: "Gerald Knizia knizia*|*cornell.edu" To: CCL Subject: CCL: CBS extrapolation formulas Message-Id: <-44810-110601160317-28595-pen4Ayea7c0XNvnsA8/2ZQ###server.ccl.net> X-Original-From: Gerald Knizia Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 01 Jun 2011 16:03:08 -0400 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia]-[cornell.edu] Bradley Kenneth Welch bwelch5%%slu.edu wrote: > We want to do the CBS for a set of energies done with the dunning > basis sets from double zeta to 6 zeta. What are some of the commonly > used formulas for this? Which ones allow for 5 energies to be used in > extrapolation? > 1) In general, you don't want to include any calculations except for the two largest ones in the extrapolation, because including smaller sets usually makes the result worse. This particularly applies to double-zeta basis sets, which cannot provide more than a qualitative (correlated) calculation. If you include them in the extrapolation, you are basically including trash, as such sets strongly violate the approximations under which the extrapolation formulas hold. 2) There are plenty of extrapolation formulas. The most popular is the l3 extrapolation of Helgaker and coworkers (J. Chem. Phys 106 9639 (1997) and J. Chem. Phys. 112 9229 (2000)), where you assume that the correlation energy behaves as E_n \approx E_cbs + a/n3 (with n the cardinality). This gives you E_cbs[n-1,n] = (n3 E_n - (n-1)3 E_{n-1})/(n3 - (n-1)3) if you solve E_cbs putting in the two largest calculations (n and n-1). But if you want, you can also include more calculations; in that case you would curve-fit E_cbs to the E_n/n pairs you got (you can easily do it, it's just that the results don't get better). The l3 formula (and the l3/l5 formula of Klopper (Mol.Phys. 99 481 (2001)) for separate extrapolation of singlet/triplet pairs) is founded on theoretical arguments, not on fitting. In principle it assumes that each angular momentum up to l=n is saturated (that's why it doesn't work well when including VDZ), but it works very well for cc-pVnZ sets, nevertheless. 3) If you search the literature, you will find *lots* of different extrapolation formulas, each claiming to be better than l3 or the other ones. One notable example are the fitted formulas of Schwenke (J. Chem. Phys. 122**, 014107 (2005)) which have found much attention. Our own experimentation with such formulas during the development of explicitly correlated methods showed that using other formulas than l3 generally gains you either exactly nothing or almost nothing in relative energies, apart from the special case of DZ/TZ extrapolation. This holds especially if large basis sets (QZ and larger) are involved. Despite claims of greater accuracy of such formulas, we found almost identical statistical behavior in almost all cases when the results are averaged over large sets of different compounds (see, for example, the comments on extrapolation in and supplementary material of J. Chem. Phys. 130 054104 (2009)). As always, the fitted formulas work best for the set they are fitted to... 4) Note that in multi-reference calculations you generally want to extrapolate total energies (e.g., MCSCF+MRCI) with the correlation energy formulas, not just correlation energies (e.g., only MRCI). That is the case because MCSCF reference functions already contain a significant fraction of dynamic correlation, and you cannot easily separate the different contributions. You get away with extrapolating the total energies, because the actual reference contribution to the total energy (i.e., the "SCF" part) converges very quickly with the basis set cardinality, and doesn't really contribute much. -- Gerald Knizia From owner-chemistry@ccl.net Wed Jun 1 18:44:00 2011 From: "Miguel Quiliano Meza rifaximina|,|gmail.com" To: CCL Subject: CCL:G: How to build a linux cluster for computational chemistry purposes?, HELP Message-Id: <-44811-110601181549-15934-T+Nwv5iGwiCuGP7BH5+Fkg]|[server.ccl.net> X-Original-From: Miguel Quiliano Meza Content-Type: multipart/alternative; boundary=001485ea3c9e641f5104a4addc1a Date: Wed, 1 Jun 2011 18:15:40 -0400 MIME-Version: 1.0 Sent to CCL by: Miguel Quiliano Meza [rifaximina~!~gmail.com] --001485ea3c9e641f5104a4addc1a Content-Type: text/plain; charset=ISO-8859-1 Dear community. After... talk.. and talk.. with my boss, I convinced him to build a linux cluster for computational chemistry purposes, in other words... to use Gaussian03. So now I have 80 cores at my disposal. We also have TCP/LINDA. Could you please recommend me, one operative system and some online guide to build it or book? Personal experiences are welcome. Thanks in advance. Miguel Quiliano. --001485ea3c9e641f5104a4addc1a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear community.

After... talk.. and talk.. with my boss, I convinced him to build a linux cluster for computation= al chemistry purposes, in other words... to use Gaussian03. <= span id=3D"yiv634381530result_box" class=3D"yiv634381530short_text">So now I have 80 c= ores at my disposal. We also have TCP/LINDA.

Could you please recommend me, one operative system and some online gui= de to build it or book? Personal experiences are welcome.

Thanks in = advance.

Miguel Quiliano.
--001485ea3c9e641f5104a4addc1a--