From owner-chemistry@ccl.net Mon Sep  2 12:02:00 2013
From: "Mark Zottola mzottola(-)gmail.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL:G: Dipole Moment Calculation within Gaussian
Message-Id: <-49126-130902115816-25550-61ExEcgEI6Yy2M6+alOZKA+*+server.ccl.net>
X-Original-From: Mark Zottola <mzottola^-^gmail.com>
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Date: Mon, 2 Sep 2013 11:58:08 -0400
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Sent to CCL by: Mark Zottola [mzottola{}gmail.com]
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Are the cartesian components of the dipole moment shown in the gaussian
output based on a center of mass, center of charge, or geometric center for
the origin?  If the last, is that based on the "Input Orientation" or the
"Standard Orientation"?

I did not find this info when I dove Gaussian's web pages nor a simple
google search.  Any help would be greatly appreciated.

Thanks,


Mark

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<div dir=3D"ltr">Are the cartesian components of the dipole moment shown in=
 the gaussian output based on a center of mass, center of charge, or geomet=
ric center for the origin? =A0If the last, is that based on the &quot;Input=
 Orientation&quot; or the &quot;Standard Orientation&quot;?<div>
<br></div><div>I did not find this info when I dove Gaussian&#39;s web page=
s nor a simple google search. =A0Any help would be greatly appreciated.</di=
v><div><br></div><div>Thanks,</div><div><br></div><div><br></div><div>Mark<=
/div>
</div>

--001a11332252763bb404e568a3f2--


From owner-chemistry@ccl.net Mon Sep  2 14:16:00 2013
From: "Andrew Voronkov drugdesign,yandex.ru" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: software for toxicity analysis
Message-Id: <-49127-130902055950-13016-H4GfxyatwKBbp35/necG+g:-:server.ccl.net>
X-Original-From: Andrew Voronkov <drugdesign**yandex.ru>
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Date: Mon, 02 Sep 2013 13:59:40 +0400
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Sent to CCL by: Andrew Voronkov [drugdesign:+:yandex.ru]
Dear CCL, I am looking for software, which can be used to analyze the fragments of the substance which cause gastrointestinal toxicity.
I have a compound, which displays gastrointestinal toxicity. I would like to analyze groups which may cause it.
Please recommend which free online or offline software services can be used for that purpose.

Best regards,
Andrew


From owner-chemistry@ccl.net Mon Sep  2 14:51:00 2013
From: "Cina Foroutan-Nejad canyslopus\a/yahoo.co.uk" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL:G: Dipole Moment Calculation within Gaussian
Message-Id: <-49128-130902144347-8951-6dD2hHqUl/P2Cm92Acg5lQ(~)server.ccl.net>
X-Original-From: Cina Foroutan-Nejad <canyslopus^_^yahoo.co.uk>
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Date: Mon, 2 Sep 2013 19:43:38 +0100 (BST)
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Sent to CCL by: Cina Foroutan-Nejad [canyslopus(a)yahoo.co.uk]
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Dear Mark,=0A=0AThe dipole moment in Gaussian is defined with respect to th=
e center of positive charge. However, if your molecule is neutral changing =
the origin for defining the dipole moment does not change the dipole moment=
 itself. If your system is charged then changing the origin from R1 to R2 w=
ill change the dipole by (R1-R2)q. Where q is the molecular charge.=0AIf yo=
u have more questions feel free to contact me directly.=0A=0AGood luck,=0AC=
ina=0A=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0ACina Foro=
utan-Nejad, PhD=0Ahttp://muni.academia.edu/CinaForoutanNejad=0A=0A=0A=0A___=
_____________________________=0A From: Mark Zottola mzottola(-)gmail.com <o=
wner-chemistry~~ccl.net>=0ATo: "Foroutan-Nejad, Cina " <canyslopus~~y=
ahoo.co.uk> =0ASent: Monday, 2 September 2013, 17:58=0ASubject: CCL:G: Dipo=
le Moment Calculation within Gaussian=0A =0A=0A=0AAre the cartesian compone=
nts of the dipole moment shown in the gaussian output based on a center of =
mass, center of charge, or geometric center for the origin? =A0If the last,=
 is that based on the "Input Orientation" or the "Standard Orientation"?=0A=
=0AI did not find this info when I dove Gaussian's web pages nor a simple g=
oogle search. =A0Any help would be greatly appreciated.=0A=0AThanks,=0A=0A=
=0AMark
---361436947-1906821009-1378147418=:23067
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<html><body><div style=3D"color:#000; background-color:#fff; font-family:bo=
okman old style, new york, times, serif;font-size:12pt"><div id=3D"yiv83311=
65213"><div><div style=3D"color: rgb(0, 0, 0); background-color: rgb(255, 2=
55, 255); font-family: 'bookman old style', 'new york', times, serif; font-=
size: 12pt;"><div id=3D"yiv8331165213yui_3_7_2_39_1378143232124_55"><span i=
d=3D"yiv8331165213yui_3_7_2_39_1378143232124_72">Dear Mark,</span></div><di=
v id=3D"yiv8331165213yui_3_7_2_39_1378143232124_55" style=3D"color: rgb(0, =
0, 0); font-size: 16px; font-family: 'bookman old style', 'new york', times=
, serif; background-color: transparent; font-style: normal;"><span id=3D"yi=
v8331165213yui_3_7_2_39_1378143232124_75"><br></span></div><div id=3D"yiv83=
31165213yui_3_7_2_39_1378143232124_55" style=3D"color: rgb(0, 0, 0); font-s=
ize: 16px; font-family: 'bookman old style', 'new york', times, serif; back=
ground-color: transparent; font-style: normal;"><span
 id=3D"yiv8331165213yui_3_7_2_39_1378143232124_80">The dipole moment in Gau=
ssian is defined with respect to the center of positive charge. However, if=
 your molecule is neutral changing the origin for defining the dipole momen=
t does not change the dipole moment itself. If your system is charged then =
changing the origin from R1 to R2 will change the dipole by (R1-R2)q. Where=
 q is the molecular charge.</span></div><div id=3D"yiv8331165213yui_3_7_2_3=
9_1378143232124_55" style=3D"color:rgb(0, 0, 0);font-size:16px;font-family:=
'bookman old style', 'new york', times, serif;background-color:transparent;=
font-style:normal;" class=3D"yui_3_7_2_35_1378147065174_57"><span>If you ha=
ve more questions feel free to contact me directly.</span></div><div id=3D"=
yiv8331165213yui_3_7_2_39_1378143232124_55" style=3D"color:rgb(0, 0, 0);fon=
t-size:16px;font-family:'bookman old style', 'new york', times, serif;backg=
round-color:transparent;font-style:normal;"
 class=3D"yui_3_7_2_35_1378147065174_57"><span><br></span></div><div id=3D"=
yiv8331165213yui_3_7_2_39_1378143232124_55" style=3D"color:rgb(0, 0, 0);fon=
t-size:16px;font-family:'bookman old style', 'new york', times, serif;backg=
round-color:transparent;font-style:normal;" class=3D"yui_3_7_2_35_137814706=
5174_57"><span>Good luck,</span></div><div id=3D"yiv8331165213yui_3_7_2_39_=
1378143232124_55" style=3D"color:rgb(0, 0, 0);font-size:16px;font-family:'b=
ookman old style', 'new york', times, serif;background-color:transparent;fo=
nt-style:normal;" class=3D"yui_3_7_2_35_1378147065174_57"><span>Cina</span>=
</div><div id=3D"yiv8331165213yui_3_7_2_39_1378143232124_55" style=3D"color=
:rgb(0, 0, 0);font-size:16px;font-family:'bookman old style', 'new york', t=
imes, serif;background-color:transparent;font-style:normal;" class=3D"yui_3=
_7_2_35_1378147065174_57"><span>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D</span></div><div
 id=3D"yiv8331165213yui_3_7_2_39_1378143232124_55" style=3D"color:rgb(0, 0,=
 0);font-size:16px;font-family:'bookman old style', 'new york', times, seri=
f;background-color:transparent;font-style:normal;" class=3D"yui_3_7_2_35_13=
78147065174_57"><span>Cina Foroutan-Nejad, PhD</span></div><div id=3D"yiv83=
31165213yui_3_7_2_39_1378143232124_55" style=3D"color:rgb(0, 0, 0);font-siz=
e:16px;font-family:'bookman old style', 'new york', times, serif;background=
-color:transparent;font-style:normal;" class=3D"yui_3_7_2_35_1378147065174_=
57"><span><a href=3D"http://muni.academia.edu/CinaForoutanNejad">http://mun=
i.academia.edu/CinaForoutanNejad</a><br></span></div><div><br id=3D"yiv8331=
165213yui_3_7_2_39_1378143232124_57"></div>  <div style=3D"font-family: 'bo=
okman old style', 'new york', times, serif; font-size: 12pt;" id=3D"yiv8331=
165213yui_3_7_2_39_1378143232124_60" class=3D"yiv8331165213yui_3_7_2_39_137=
8143232124_59"> <div style=3D"font-family: 'times new roman', 'new york', t=
imes, serif;
 font-size: 12pt;" class=3D"yiv8331165213yui_3_7_2_39_1378143232124_63"> <d=
iv dir=3D"ltr"> <hr size=3D"1">  <font size=3D"2" face=3D"Arial"> <b><span =
style=3D"font-weight:bold;">From:</span></b> Mark Zottola mzottola(-)gmail.=
com &lt;owner-chemistry~~ccl.net&gt;<br> <b><span style=3D"font-weight:bold;=
">To:</span></b> "Foroutan-Nejad, Cina " &lt;canyslopus~~yahoo.co.uk=
&gt; <br> <b><span style=3D"font-weight:bold;">Sent:</span></b> Monday, 2 S=
eptember 2013, 17:58<br> <b><span style=3D"font-weight:bold;">Subject:</spa=
n></b> CCL:G: Dipole Moment Calculation within Gaussian<br> </font> </div> =
<div class=3D"yiv8331165213y_msg_container"><br><div id=3D"yiv8331165213"><=
div dir=3D"ltr">Are the cartesian components of the dipole moment shown in =
the gaussian output based on a center of mass, center of charge, or geometr=
ic center for the origin? &nbsp;If the last, is=0A that based on the "Input=
 Orientation" or the "Standard Orientation"?<div>=0A<br></div><div>I did no=
t find this info when I dove Gaussian's web pages nor a simple google searc=
h. &nbsp;Any help would be greatly appreciated.</div><div><br></div><div>Th=
anks,</div><div><br></div><div><br></div><div>Mark</div>=0A</div></div><br>=
<br></div> </div> </div>  </div></div></div></div></body></html>
---361436947-1906821009-1378147418=:23067--


From owner-chemistry@ccl.net Mon Sep  2 20:01:00 2013
From: "Susi Lehtola susi.lehtola%a%alumni.helsinki.fi" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL:G: Dipole Moment Calculation within Gaussian
Message-Id: <-49129-130902153326-13713-ug93JOAl7scf95XWomMw/w#%#server.ccl.net>
X-Original-From: Susi Lehtola <susi.lehtola]~[alumni.helsinki.fi>
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Date: Mon, 2 Sep 2013 22:33:17 +0300
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Sent to CCL by: Susi Lehtola [susi.lehtola/a\alumni.helsinki.fi]
On Mon, 2 Sep 2013 19:43:38 +0100 (BST)
"Cina Foroutan-Nejad canyslopus\a/yahoo.co.uk"
<owner-chemistry|,|ccl.net> wrote:
> From: Mark Zottola mzottola(-)gmail.com <owner-chemistry-#-ccl.net>
>> Are the cartesian components of the dipole moment shown in the
>> gaussian output based on a center of mass, center of charge, or
>> geometric center for the origin?  If the last, is that based on the
>> "Input Orientation" or the "Standard Orientation"?
> 
> The dipole moment in Gaussian is defined with respect to the center
> of positive charge. However, if your molecule is neutral changing the
> origin for defining the dipole moment does not change the dipole
> moment itself. If your system is charged then changing the origin
> from R1 to R2 will change the dipole by (R1-R2)q. Where q is the
> molecular charge. If you have more questions feel free to contact me
> directly.

... but the cartesian components of the dipole moment *are* dependent
on the orientation of the molecule. AFAIK everything is reported in the
Standard Orientation, but you might want to ask Gaussian Inc support
about that.
-- 
---------------------------------------------------------------
Mr. Susi Lehtola, PhD             Postdoctoral researcher
susi.lehtola|,|alumni.helsinki.fi   Department of Applied Physics
http://www.helsinki.fi/~jzlehtol  Aalto University
                                  Finland
---------------------------------------------------------------
Susi Lehtola, FT                  Tutkijatohtori
susi.lehtola|,|alumni.helsinki.fi   Fysiikan laitos
http://www.helsinki.fi/~jzlehtol  Aalto-yliopisto
---------------------------------------------------------------


From owner-chemistry@ccl.net Mon Sep  2 20:49:00 2013
From: "Salter-Duke, Brian James - brian.james.duke[]gmail.com" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL:G: Dipole Moment Calculation within Gaussian
Message-Id: <-49130-130902202814-20119-m7udjB4GaPS+csnGzn4xLw : server.ccl.net>
X-Original-From: "Salter-Duke, Brian James -" <brian.james.duke]=[gmail.com>
Content-Disposition: inline
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Date: Tue, 3 Sep 2013 10:28:03 +1000
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Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke:_:gmail.com]
On Mon, Sep 02, 2013 at 11:58:08AM -0400, Mark Zottola mzottola(-)gmail.com wrote:
> Are the cartesian components of the dipole moment shown in the gaussian
> output based on a center of mass, center of charge, or geometric center for
> the origin?  If the last, is that based on the "Input Orientation" or the
> "Standard Orientation"?
> 
> I did not find this info when I dove Gaussian's web pages nor a simple
> google search.  Any help would be greatly appreciated.

I got an answer to this exact question from Gaussian only last week. The
dipole integrals are evaluated with whatever origin Gaussian is using
for the coordinates . These are normally the "Standard Orientation"
coordinates and these are based on the origin at the centre of charge.
There is an IOP code to use the centre of mass.

As another poster has said, this does not affect the dipole moment, but
it defines the x, y, z axis for the cartesian components.

Brian.
 
> Thanks,
> 
> 
> Mark

-- 
   Brian Salter-Duke (Brian Duke)   Brian.Salter-Duke()monash.edu
                    Adjunct Associate Professor
            Monash Institute of Pharmaceutical Sciences
      Monash University Parkville Campus, VIC 3052, Australia