From owner-chemistry@ccl.net Tue Dec 12 11:00:00 2006
From: "Bala krishna baluchembioinf%gmail.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL: help
Message-Id: <-33227-061211074024-21973-KSvuA2Sy/W+X/LkBREO++g..server.ccl.net>
X-Original-From: "Bala  krishna" <baluchembioinf]|[gmail.com>
Date: Mon, 11 Dec 2006 07:40:23 -0500


Sent to CCL by: "Bala  krishna" [baluchembioinf|-|gmail.com]
Dear Sir /Friends
     I am computational chemistry student and I am working on quantum chemical descriptors for QSAR in that concern I need help in calculating the HOMO and LUMO values. I had seen Mopac is giving the values but I want to do calculations on my own amd then I want to include them in further work.
  I had used a formula 

 E=n2h2/8mv


which is giving me the values which are nearly equal to the HOMO but it is giving me the positive  values  but maximum HOMO values are negative values .
  LUMO calculations are not so good  I know that this formula does not work for HOMO LUMO calculations.

 please help me by guiding  to solve this  problem .


Aspiring student
G.Balakrishna


From owner-chemistry@ccl.net Tue Dec 12 11:35:01 2006
From: "Torsten Bruhn bruhn%x%chemie.uni-wuerzburg.de" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL:G: Unit of Rotatory strength in gaussian and turbomole
Message-Id: <-33228-061212095648-23599-RdwntQokrVXNo6DyqM1SHA:-:server.ccl.net>
X-Original-From: "Torsten  Bruhn" <bruhn__chemie.uni-wuerzburg.de>
Date: Tue, 12 Dec 2006 09:56:47 -0500


Sent to CCL by: "Torsten  Bruhn" [bruhn###chemie.uni-wuerzburg.de]
Hi,

we recently did some TD DFT calculations with turbomole and gaussian 03 in order to get rotatory strength values. Whereas gaussian uses the cgs unit 10^-40 erg-esu-cm/Gauss TM uses 10^-40 erg*cm^3. Does anyone know how to convert these units to each other or are they the same?

Best regards


From owner-chemistry@ccl.net Tue Dec 12 12:09:00 2006
From: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?= reynier.suardiaz..gmail.com" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL:G: pbe functional in gaussian
Message-Id: <-33229-061212111813-25591-uKWEKcgoaIGbM1wTTtE1xw(!)server.ccl.net>
X-Original-From: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?=" <reynier.suardiaz===gmail.com>
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Date: Tue, 12 Dec 2006 16:13:41 +0100
MIME-Version: 1.0


Sent to CCL by: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?=" [reynier.suardiaz(0)gmail.com]
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Hi
i would like to know if is correct to report that pbe functional was used
when i put pbepbe as keyword in gaussian. My doubt is if PBE term is not
used  as some other combination of exchanges or correlation functional where
pbe was used as one of them.
thanks in advance
reynier

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<div>Hi</div>
<div>i would like to know if is&nbsp;correct to report that pbe functional was used when i put pbepbe as keyword in gaussian. My doubt is if PBE term is not used&nbsp; as some other combination of exchanges or correlation functional where pbe was used as one of them. 
</div>
<div>thanks in advance</div>
<div>reynier</div>
<div>&nbsp;</div>
<div>&nbsp;</div>

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From owner-chemistry@ccl.net Tue Dec 12 12:44:00 2006
From: "Fabienne Bessac fbessac(0)iciq.es" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian and forcefield
Message-Id: <-33230-061212110336-10669-o5dLekg51a8hy2VhuJ3v4A*_*server.ccl.net>
X-Original-From: "Fabienne  Bessac" <fbessac/a\iciq.es>
Date: Tue, 12 Dec 2006 11:03:36 -0500


Sent to CCL by: "Fabienne  Bessac" [fbessac%%iciq.es]
Hello everyone,

  I would like to have the different terms which contribute to the MM energy in a Gaussian 03 calculation. I mean :
                   Total Energy
                        Stretch
                           Bend
                        Torsion
               Improper Torsion
                            VDW
                  Electrostatic
        Explicit Hydrogen Bonds
                    Cross Terms
Is it possible? Does anyone have modified the Gaussian code in order to print that?

  Thanks  a lot for your help.

Fabienne.


From owner-chemistry@ccl.net Tue Dec 12 13:20:00 2006
From: "Noko Phala nokophala[a]aim.com" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: help
Message-Id: <-33231-061212124847-25316-XnHnDmaKnB/kXR+85E3e3w,server.ccl.net>
X-Original-From: "Noko Phala" <nokophala+/-aim.com>
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Date: Tue, 12 Dec 2006 19:47:11 +0200
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Sent to CCL by: "Noko Phala" [nokophala(0)aim.com]
Perhaps I dont understand your question (you want to do hand calculations of 
orbital energies and compare with Mopac), but as far as I know it is almost 
impossible to do paper calculations of HOMO/LUMO for molecules at a given 
level of theory, the computers solve the difficult calculations  for 
us.Let's say your maths skills are great and you get same values as Mopac 
when you use the same theory in you rhand calcs, why the effort?

Noko Phala
Anglo Research
----- Original Message ----- 
> From: "Bala krishna baluchembioinf%gmail.com" <owner-chemistry(_)ccl.net>
To: "Phala, Noko " <nokophala(_)aim.com>
Sent: Tuesday, December 12, 2006 6:15 PM
Subject: CCL: help


> Sent to CCL by: "Bala  krishna" [baluchembioinf|-|gmail.com]
> Dear Sir /Friends
>     I am computational chemistry student and I am working on quantum 
> chemical descriptors for QSAR in that concern I need help in calculating 
> the HOMO and LUMO values. I had seen Mopac is giving the values but I want 
> to do calculations on my own amd then I want to include them in further 
> work.
>  I had used a formula
>
> E=n2h2/8mv
>
>
> which is giving me the values which are nearly equal to the HOMO but it is 
> giving me the positive  values  but maximum HOMO values are negative 
> values .
>  LUMO calculations are not so good  I know that this formula does not work 
> for HOMO LUMO calculations.
>
> please help me by guiding  to solve this  problem .
>
>
> Aspiring student
> G.Balakrishna>
>
>
>


From owner-chemistry@ccl.net Tue Dec 12 13:55:00 2006
From: "Steve Williams willsd*appstate.edu" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: help
Message-Id: <-33232-061212125753-31128-EgZGS1w7L2XvRj2t/gfgkg . server.ccl.net>
X-Original-From: Steve Williams <willsd-#-appstate.edu>
Content-transfer-encoding: 7bit
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Date: Tue, 12 Dec 2006 11:57:52 -0500
MIME-version: 1.0


Sent to CCL by: Steve Williams [willsd[#]appstate.edu]
This looks similar to the formula for th energy eigenvalues for a 
particle in a one-dimensional box.  There is no good reason to think 
that this would be appropriate for an arbitrary molecule... might be 
useful for some conjugated dye molecules, but not much else.  There 
really is nothing like this formula that will be useful for molecules 
with their interacting electrons.  If there were, there would be no need 
for molecular electronic structure codes (mopac is an example of one of 
these).
Steve Williams

Bala krishna baluchembioinf%gmail.com wrote:
> Sent to CCL by: "Bala  krishna" [baluchembioinf|-|gmail.com]
> Dear Sir /Friends
>      I am computational chemistry student and I am working on quantum chemical descriptors for QSAR in that concern I need help in calculating the HOMO and LUMO values. I had seen Mopac is giving the values but I want to do calculations on my own amd then I want to include them in further work.
>   I had used a formula 
>
>  E=n2h2/8mv
>
>
> which is giving me the values which are nearly equal to the HOMO but it is giving me the positive  values  but maximum HOMO values are negative values .
>   LUMO calculations are not so good  I know that this formula does not work for HOMO LUMO calculations.
>
>  please help me by guiding  to solve this  problem .
>
>
> Aspiring student
> G.Balakrishna>
>
>
>


From owner-chemistry@ccl.net Tue Dec 12 15:35:01 2006
From: "Kramer Campen campen#,#geosc.psu.edu" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL:G: pbe functional in gaussian
Message-Id: <-33233-061212141244-23489-UpOvAv3pUx4OZIgXcZ0gZg _ server.ccl.net>
X-Original-From: Kramer Campen <campen|-|geosc.psu.edu>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Date: Tue, 12 Dec 2006 13:06:04 -0500
Mime-Version: 1.0


Sent to CCL by: Kramer Campen [campen^^geosc.psu.edu]
Reynier:

That combination will give you the exchange and correlation functionals 
> from the 1996 and 1997 papers (nothing else).  This is explained in a 
little more detail on http://www.gaussian.com/g_ur/k_dft.htm where you can 
also find the original references if you're interested.

Kramer


At 12:13 PM 12/12/2006 -0500, you wrote:
>Sent to CCL by: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?=" 
>[reynier.suardiaz(0)gmail.com]
>------=_Part_48909_4791134.1165936421032
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>Content-Transfer-Encoding: 7bit
>Content-Disposition: inline
>
>Hi
>i would like to know if is correct to report that pbe functional was used
>when i put pbepbe as keyword in gaussian. My doubt is if PBE term is not
>used  as some other combination of exchanges or correlation functional where
>pbe was used as one of them.
>thanks in advance
>reynier
>
>------=_Part_48909_4791134.1165936421032
>Content-Type: text/html; charset=ISO-8859-1
>Content-Transfer-Encoding: 7bit
>Content-Disposition: inline
>
><div>Hi</div>
><div>i would like to know if is&nbsp;correct to report that pbe functional 
>was used when i put pbepbe as keyword in gaussian. My doubt is if PBE term 
>is not used&nbsp; as some other combination of exchanges or correlation 
>functional where pbe was used as one of them.
></div>
><div>thanks in advance</div>
><div>reynier</div>
><div>&nbsp;</div>
><div>&nbsp;</div>
>
>------=_Part_48909_4791134.1165936421032--

From owner-chemistry@ccl.net Tue Dec 12 16:13:00 2006
From: "Wayne Steinmetz WES04747[-]pomona.edu" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian and forcefield
Message-Id: <-33234-061212161021-11218-w0OTmlK8tzb5w6a91DEmag,+,server.ccl.net>
X-Original-From: "Wayne Steinmetz" <WES04747-.-pomona.edu>
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Date: Tue, 12 Dec 2006 11:39:27 -0800
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Sent to CCL by: "Wayne Steinmetz" [WES04747-#-pomona.edu]
SYBYL's implementation of molecular mechanics provides the breakdown
that you require.  

Wayne E. Steinmetz
Carnegie Professor of Chemistry
Woodbadge Course Director
Chemistry Department
Pomona College
645 North College Avenue
Claremont, California 91711-6338
USA
phone: 1-909-621-8447
FAX: 1-909-607-7726
Email: wsteinmetz%pomona.edu
WWW: pages.pomona.edu/~wsteinmetz
 
-----Original Message-----
> From: owner-chemistry%ccl.net [mailto:owner-chemistry%ccl.net] 
Sent: Tuesday, December 12, 2006 9:48 AM
To: Wayne Steinmetz
Subject: CCL:G: Gaussian and forcefield

Sent to CCL by: "Fabienne  Bessac" [fbessac%%iciq.es]
Hello everyone,

  I would like to have the different terms which contribute to the MM
energy in a Gaussian 03 calculation. I mean :
                   Total Energy
                        Stretch
                           Bend
                        Torsion
               Improper Torsion
                            VDW
                  Electrostatic
        Explicit Hydrogen Bonds
                    Cross Terms
Is it possible? Does anyone have modified the Gaussian code in order to
print that?

  Thanks  a lot for your help.

Fabienne.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-------------------------------------------------------------
This message has been scanned by Postini anti-virus software.


From owner-chemistry@ccl.net Tue Dec 12 17:12:00 2006
From: "Markus Weingarth m.weingarth a web.de" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL:G: Displaying of of shielding
Message-Id: <-33235-061212151648-14454-PcTPJrlzvequagDd2H6MuQ-.-server.ccl.net>
X-Original-From: "Markus  Weingarth" <m.weingarth_-_web.de>
Date: Tue, 12 Dec 2006 15:16:48 -0500


Sent to CCL by: "Markus  Weingarth" [m.weingarth*_*web.de]
Dear CCL users,

I have calculated the shielding density with G03 and I am a little bit disappointed about the displaying in GaussView. 

I am not really interested in maintaining the shielding of individually nuclei but more of whole functions like a benzene moiety. The shielding of the drug is to some extent well know and all I want is a fine presentation.

To take that benzene as an example - we all know that shielding picture with the shielding cone above the molecular plane. I is feasible to derive such a display?

With best regards

M. Weingarth


From owner-chemistry@ccl.net Tue Dec 12 21:59:00 2006
From: "Ana Maria Mendoza mwilson||ciad.mx" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL:G: Question about dielectric constant
Message-Id: <-33236-061212211802-4632-Ciysd3D8KLD8RIvOT7bgyQ-x-server.ccl.net>
X-Original-From: "Ana Maria Mendoza" <mwilson^ciad.mx>
Date: Tue, 12 Dec 2006 21:18:02 -0500


Sent to CCL by: "Ana Maria Mendoza" [mwilson|*|ciad.mx]

Hi,   
I am working with the Gaussian 03W computational package. As you know, in this package it is not possible to simulate the pH of the medium, so I would like to know if it is feasible to employ HCl and/or acetic acid for simulating an acidic medium, water for a neutral medium, and ammonia for an alkaline medium by utilizing their respective dielectric constants,in order to calculate the molecular properties of two molecules of interest by simulating an acidic, neutral and alkaline medium.

Is there anybody who can help me?

Thanks in advance

Ana Maria


From owner-chemistry@ccl.net Tue Dec 12 22:51:00 2006
From: "Yi LUO yi_luo/a\riken.jp" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL:G: postprocessing of ADMP result from G03
Message-Id: <-33237-061212224939-3732-qs7eJe5ZisnjNn415rTyoA{}server.ccl.net>
X-Original-From: "Yi LUO" <yi_luo-*-riken.jp>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0061_01C71EB5.20665640"
Date: Wed, 13 Dec 2006 12:49:28 +0900
MIME-Version: 1.0


Sent to CCL by: "Yi LUO" [yi_luo]|[riken.jp]
This is a multi-part message in MIME format.

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Hi, Dear all,

 I performed ADMP simulation by using G03 program. To analysis the result, 
GaussianView can give the plot of energy vs simulation time. I am also 
interested in the change of selected interatomic distances (or angles among 
selected atoms) against simulation time.

 Could anybody tell me how to plot the distance vs simulation time profile? 
Is there any free software to do it?

Thank you in advance

Luo

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	charset="iso-2022-jp"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-2022-jp">
<META content=3D"MSHTML 6.00.2900.2995" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DCentury>Hi, Dear all,</FONT></DIV>
<DIV><FONT face=3DCentury></FONT>&nbsp;</DIV>
<DIV><FONT face=3DCentury>&nbsp;I performed ADMP simulation by using G03 =
program.=20
To analysis the result, GaussianView can give the plot of energy vs =
simulation=20
time. I am also interested in&nbsp;the change of selected interatomic =
distances=20
(or angles among selected atoms) against=20
simulation&nbsp;time.&nbsp;</FONT></DIV>
<DIV><FONT face=3DCentury></FONT>&nbsp;</DIV>
<DIV><FONT face=3DCentury>&nbsp;Could anybody tell me how to&nbsp;plot=20
the&nbsp;distance vs&nbsp;simulation time&nbsp;profile? Is there any =
free=20
software to do it?&nbsp;&nbsp;</FONT></DIV>
<DIV><FONT face=3DCentury></FONT>&nbsp;</DIV>
<DIV><FONT face=3DCentury>Thank you in advance</FONT></DIV>
<DIV><FONT face=3DCentury></FONT>&nbsp;</DIV>
<DIV><FONT face=3DCentury>Luo</FONT></DIV>
<DIV><FONT face=3DCentury></FONT>&nbsp;</DIV></BODY></HTML>

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From owner-chemistry@ccl.net Tue Dec 12 23:25:00 2006
From: "silviu polosan Spol68]~[yahoo.com" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: electrostatic repulsion
Message-Id: <-33238-061212225850-23785-4xzKZMdWJhGoBVu6HWM1Fg(_)server.ccl.net>
X-Original-From: "silviu  polosan" <Spol68]-[yahoo.com>
Date: Tue, 12 Dec 2006 22:58:49 -0500


Sent to CCL by: "silviu  polosan" [Spol68\a/yahoo.com]
Hi friends,

I would like to know if someone can advice me about the calculation of electrostatic repulsion between two molecules (two rings actuually).

Thank you veru much.