From owner-chemistry@ccl.net Mon Nov 29 11:36:01 2010 From: "James Eilers jeilers!^!siue.edu" To: CCL Subject: CCL:G: Question on calculation of charge center of electrons in a molecule Message-Id: <-43237-101129100357-1506-hUf/xn1d7Drf0aZ6EbEGzA]=[server.ccl.net> X-Original-From: James Eilers Content-Type: multipart/alternative; boundary=Apple-Mail-2--796939897 Date: Mon, 29 Nov 2010 09:01:12 -0600 Mime-Version: 1.0 (Apple Message framework v624) Sent to CCL by: James Eilers [jeilers-,-siue.edu] --Apple-Mail-2--796939897 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Mulliken charges also include the "shared" electron density or cross =20 terms between atomic orbitals on different centers. On Nov 27, 2010, at 8:02 PM, Jiabo Li jiaboli/./yahoo.com wrote: > To understand what is wrong, you can look at a simple example: the =20 > hydrogen atom in its excited state with the single electron on a SP =20= > hydride orbital. In this case, the electron density is not central =20 > symmetric but polarized, and the dipole moment is not zero (a big =20 > dipole moment), while in this case the net atomic charge is zero =20 > (neutral). > =A0 > Jiabo > > --- On Fri, 11/26/10, Herbert Fruchtl =20 > herbert.fruchtl[#]st-andrews.ac.uk wrote: > > >> From: Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk =20 >> > Subject: CCL:G: Question on calculation of charge center of electrons =20= > in a molecule > To: "Li, Jiabo " > Date: Friday, November 26, 2010, 6:25 AM > > > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl::st-andrews.ac.uk] > The centre of charge of each Gaussian function is its origin, i.e. the = =20 > nucleus if you have atom-centred basis functions. The Mulliken charge =20= > is the sum of those functions, multiplied with their occupation =20 > number. Shouldn't this sum have its centre on the nucleus as well? And = =20 > the sum of all of them (over all atoms) gives the complete charge =20 > distribution. Where am I going wrong? > > =A0 Herbert > > Ulf Ekstr=F6m ulfek(~)few.vu.nl wrote: >> Sent to CCL by: =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D = [ulfek],[few.vu.nl] >> On Thu, Nov 25, 2010 at 9:56 AM, Herbert Fruchtl >> herbert.fruchtl-.-st-andrews.ac.uk wrote: >>> Sent to CCL by: Herbert Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk] >>> I don't have time to look at the maths of it, but I think the centre = =20 >>> of >>> charge of the electron density should be identical to the centre of =20= >>> the >>> Mulliken charges, which would be easy to calculate (analogous to the = =20 >>> centre >>> of mass). >> >> This will not work, for example if you have a single centre basis set = =20 >> all >> Mulliken charge would be on that center. What you should do is to =20 >> compute >> the dipole moment of the molecule and use that to work out the center >> of charge. >> >> Sincerely, >> Ulf Ekstrom> > > -- Herbert Fruchtl > Senior Scientific Computing Officer > School of Chemistry, School of Mathematics and Statistics > University of St Andrews > -- > The University of St Andrews is a charity registered in Scotland: > No SC013532 > > > > -=3D This is automatically added to each message by the mailing script = =20 > =3D-=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =20= > =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message > > Subscribe/Unsubscribe:=A0 =A0 =A0 =20Conferences: =20 > http://server.ccl.net/chemistry/announcements/conferences/=A0 =20 > =A0=A0=A0http://www.ccl.net/spammers.txt--0-160776249-1290909739=3D:8785= 1 > Content-Type: text/html; charset=3Diso-8859-1 > Content-Transfer-Encoding: quoted-printable > >
valign=3D"top" style=3D"font: inherit;">
To understand what is = wrong, =20 > you can look at a simple example: the hydrogen atom in its excited =20 > state with the single electron on a SP hydride orbital. In this case, =20= > the electron density is not central symmetric but polarized, and the =20= > dipole moment is not zero (a big dipole moment), while in this case =20= > the net atomic charge is zero (neutral).
>
 
>
Jiabo

--- On Fri, 11/26/10, Herbert Fruchtl =20 > herbert.fruchtl[#]st-andrews.ac.uk =20 > <owner-chemistry]*[ccl.net> wrote:
>
rgb(16,16,255) 2px solid">
From: Herbert Fruchtl =20 > herbert.fruchtl[#]st-andrews.ac.uk =20 > <owner-chemistry]*[ccl.net>
Subject: CCL:G: Question on =20 > calculation of charge center of electrons in a molecule
To: "Li, =20= > Jiabo " <jiaboli]*[yahoo.com>
Date: Friday, November =20= > 26, 2010, 6:25 AM

>

Sent to CCL by: Herbert Fruchtl =20 > [herbert.fruchtl::st-andrews.ac.uk]
The centre of charge of each =20= > Gaussian function is its origin, i.e. the nucleus if you have =20 > atom-centred basis functions. The Mulliken charge is the sum of those =20= > functions, multiplied with their occupation number. Shouldn't this sum = =20 > have its centre on the nucleus as well? And the sum of all of them =20 > (over all atoms) gives the complete charge distribution. Where am I =20= > going wrong?

  Herbert

Ulf Ekstr=F6m =20 > ulfek(~)few.vu.nl wrote:
> Sent to CCL by: =20 > =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek],[few.vu.nl]
> On = Thu, Nov =20 > 25, 2010 at 9:56 AM, Herbert Fruchtl
> =20 > herbert.fruchtl-.-st-andrews.ac.uk <owner-chemistry . ccl.net> =20= > wrote:
>> Sent to CCL by: Herbert Fruchtl =20 > [herbert.fruchtl*_*st-andrews.ac.uk]
>> I don't have time to =20= > look at the maths of it, but I think the centre of
>> charge =20= > of the electron density > should be identical to the centre of the
>> Mulliken =20 > charges, which would be easy to calculate (analogous to the =20 > centre
>> of mass).
>
> This will not work, for =20= > example if you have a single centre basis set all
> Mulliken =20 > charge would be on that center. What you should do is to =20 > compute
> the dipole moment of the molecule and use that to work = =20 > out the center
> of charge.
>
> Sincerely,
> =20= > Ulf Ekstrom>

-- Herbert Fruchtl
Senior Scientific =20 > Computing Officer
School of Chemistry, School of Mathematics and =20= > Statistics
University of St Andrews
--
The University of St =20= > Andrews is a charity registered in Scotland:
No =20 > SC013532



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James E. Eilers Professor Chemistry Department Southern Illinois University Edwardsville (618)650-3559 --Apple-Mail-2--796939897 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=ISO-8859-1 Mulliken charges also include the "shared" electron density or cross terms between atomic orbitals on different centers. On Nov 27, 2010, at 8:02 PM, Jiabo Li jiaboli/./yahoo.com wrote: To understand what is wrong, you can look at a simple example: the hydrogen atom in its excited state with the single electron on a SP hydride orbital. In this case, the electron density is not central symmetric but polarized, and the dipole moment is not zero (a big dipole moment), while in this case the net atomic charge is zero (neutral). =A0 Jiabo --- On Fri, 11/26/10, Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk < wrote: From: Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk < Subject: CCL:G: Question on calculation of charge center of electrons in a molecule To: "Li, Jiabo " < Date: Friday, November 26, 2010, 6:25 AM Sent to CCL by: Herbert Fruchtl [herbert.fruchtl::st-andrews.ac.uk] The centre of charge of each Gaussian function is its origin, i.e. the nucleus if you have atom-centred basis functions. The Mulliken charge is the sum of those functions, multiplied with their occupation number. Shouldn't this sum have its centre on the nucleus as well? And the sum of all of them (over all atoms) gives the complete charge distribution. Where am I going wrong? =A0 Herbert Ulf Ekstr=F6m ulfek(~)few.vu.nl wrote: Sent to CCL by: =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek],[few.vu.nl] On Thu, Nov 25, 2010 at 9:56 AM, Herbert Fruchtl herbert.fruchtl-.-st-andrews.ac.uk < wrote: Sent to CCL by: Herbert Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk] I don't have time to look at the maths of it, but I think the centre of charge of the electron density should be identical to the centre of the Mulliken charges, which would be easy to calculate (analogous to the centre of mass). This will not work, for example if you have a single centre basis set all Mulliken charge would be on that center. What you should do is to compute the dipole moment of the molecule and use that to work out the center of charge. Sincerely, Ulf Ekstrom>=20 -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=A0 =A0 =A0=A0 =A0=A0=A0http://www.ccl.net/spammers.txt--0-160776249-1290909739=3D:87851 Content-Type: text/html; charset=3Diso-8859-1 Content-Transfer-Encoding: quoted-printable <<<<<
<
To understand what is = wrong, you can look at a simple example: the hydrogen atom in its excited state with the single electron on a SP hydride orbital. In this case, the electron density is not central symmetric but polarized, and the dipole moment is not zero (a big dipole moment), while in this case the net atomic charge is zero (neutral).<
<
 <
<
Jiabo<
<
--- On <Fri, 11/26/10, Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk <<owner-chemistry]*[ccl.net><< wrote:<
<
<
<
From: Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk <owner-chemistry]*[ccl.net><
Subject: CCL:G: Question on calculation of charge center of electrons in a molecule<
To: "Li, Jiabo " <jiaboli]*[yahoo.com><
Date: Friday, November 26, 2010, 6:25 AM<
<
<
<
Sent to CCL by: Herbert Fruchtl [herbert.fruchtl::st-andrews.ac.uk]<
The centre of charge of each Gaussian function is its origin, i.e. the nucleus if you have atom-centred basis functions. The Mulliken charge is the sum of those functions, multiplied with their occupation number. Shouldn't this sum have its centre on the nucleus as well? And the sum of all of them (over all atoms) gives the complete charge distribution. Where am I going wrong?<
<
  Herbert<
<
Ulf Ekstr=F6m ulfek(~)few.vu.nl wrote:<
> Sent to CCL by: =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek],[few.vu.nl]<
> On = Thu, Nov 25, 2010 at 9:56 AM, Herbert Fruchtl<
> herbert.fruchtl-.-st-andrews.ac.uk <owner-chemistry . ccl.net> wrote:<
>> Sent to CCL by: Herbert Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk]<
>> I don't have time to look at the maths of it, but I think the centre of<
>> charge of the electron density should be identical to the centre of the<
>> Mulliken charges, which would be easy to calculate (analogous to the centre<
>> of mass).<
> <
> This will not work, for example if you have a single centre basis set all<
> Mulliken charge would be on that center. What you should do is to compute<
> the dipole moment of the molecule and use that to work out the center<
> of charge.<
> <
> Sincerely,<
> Ulf Ekstrom> <
<
-- Herbert Fruchtl<
Senior Scientific Computing Officer<
School of Chemistry, School of Mathematics and Statistics<
University of St Andrews<
--<
The University of St Andrews is a charity registered in Scotland:<
No SC013532<
<
<
<
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HelveticaJames E. Eilers Professor Chemistry Department Southern Illinois University Edwardsville (618)650-3559 --Apple-Mail-2--796939897-- From owner-chemistry@ccl.net Mon Nov 29 12:33:00 2010 From: "John McKelvey jmmckel-,-gmail.com" To: CCL Subject: CCL:G: Question on calculation of charge center of electrons in a molecule Message-Id: <-43238-101129122938-17162-9J/w6p7JMO8ejdcqRLj7Hg++server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 29 Nov 2010 12:29:28 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel++gmail.com] On the other hand the NBO program can compute ZDO type charges which are atom-centered and are along the diagonal of the density matrix and for which the sum is the same as the number of electrons in the system. John McKelvey On Mon, Nov 29, 2010 at 10:01 AM, James Eilers jeilers!^!siue.edu wrote: > Mulliken charges also include the "shared" electron density or cross terms > between atomic orbitals on different centers. > > On Nov 27, 2010, at 8:02 PM, Jiabo Li jiaboli/./yahoo.com wrote: > >> To understand what is wrong, you can look at a simple example: the >> hydrogen atom in its excited state with the single electron on a SP hydride >> orbital. In this case, the electron density is not central symmetric but >> polarized, and the dipole moment is not zero (a big dipole moment), while in >> this case the net atomic charge is zero (neutral). >> >> Jiabo >> >> --- On Fri, 11/26/10, Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk >> wrote: >> >> >>> From: Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk >>> >> >> Subject: CCL:G: Question on calculation of charge center of electrons in a >> molecule >> To: "Li, Jiabo " >> Date: Friday, November 26, 2010, 6:25 AM >> >> >> >> Sent to CCL by: Herbert Fruchtl [herbert.fruchtl::st-andrews.ac.uk] >> The centre of charge of each Gaussian function is its origin, i.e. the >> nucleus if you have atom-centred basis functions. The Mulliken charge is the >> sum of those functions, multiplied with their occupation number. Shouldn't >> this sum have its centre on the nucleus as well? And the sum of all of them >> (over all atoms) gives the complete charge distribution. Where am I going >> wrong? >> >>   Herbert >> >> Ulf Ekström ulfek(~)few.vu.nl wrote: >>> >>> Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek],[few.vu.nl] >>> On Thu, Nov 25, 2010 at 9:56 AM, Herbert Fruchtl >>> herbert.fruchtl-.-st-andrews.ac.uk wrote: >>>> >>>> Sent to CCL by: Herbert Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk] >>>> I don't have time to look at the maths of it, but I think the centre of >>>> charge of the electron density should be identical to the centre of the >>>> Mulliken charges, which would be easy to calculate (analogous to the >>>> centre >>>> of mass). >>> >>> This will not work, for example if you have a single centre basis set all >>> Mulliken charge would be on that center. What you should do is to compute >>> the dipole moment of the molecule and use that to work out the center >>> of charge. >>> >>> Sincerely, >>> Ulf Ekstrom> >> >> -- Herbert Fruchtl >> Senior Scientific Computing Officer >> School of Chemistry, School of Mathematics and Statistics >> University of St Andrews >> -- >> The University of St Andrews is a charity registered in Scotland: >> No SC013532>>    http://www.ccl.net/cgi-bin/ccl/send_ccl_message >>    http://www.ccl.net/cgi-bin/ccl/send_ccl_message >> >> Subscribe/Unsubscribe:       Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >>    http://www.ccl.net/spammers.txt--0-160776249-1290909739=:87851 >> Content-Type: text/html; charset=iso-8859-1 >> Content-Transfer-Encoding: quoted-printable >> >>
> style="font: inherit;">
To understand what is wrong, you can look at a >> simple example: the hydrogen atom in its excited state with the single >> electron on a SP hydride orbital. In this case, the electron density is not >> central symmetric but polarized, and the dipole moment is not zero (a big >> dipole moment), while in this case the net atomic charge is zero >> (neutral).
>>
 
>>
Jiabo

--- On Fri, 11/26/10, Herbert Fruchtl >> herbert.fruchtl[#]st-andrews.ac.uk >> <owner-chemistry]*[ccl.net> wrote:
>>

From: Herbert Fruchtl >> herbert.fruchtl[#]st-andrews.ac.uk >> <owner-chemistry]*[ccl.net>
Subject: CCL:G: Question on calculation >> of charge center of electrons in a molecule
To: "Li, Jiabo " >> <jiaboli]*[yahoo.com>
Date: Friday, November 26, 2010, 6:25 >> AM

>>

Sent to CCL by: Herbert Fruchtl >> [herbert.fruchtl::st-andrews.ac.uk]
The centre of charge of each Gaussian >> function is its origin, i.e. the nucleus if you have atom-centred basis >> functions. The Mulliken charge is the sum of those functions, multiplied >> with their occupation number. Shouldn't this sum have its centre on the >> nucleus as well? And the sum of all of them (over all atoms) gives the >> complete charge distribution. Where am I going wrong?

  >> Herbert

Ulf Ekström ulfek(~)few.vu.nl wrote:
> Sent to CCL by: >> =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek],[few.vu.nl]
> On Thu, Nov 25, >> 2010 at 9:56 AM, Herbert Fruchtl
> herbert.fruchtl-.-st-andrews.ac.uk >> <owner-chemistry . ccl.net> wrote:
>> Sent to CCL by: Herbert >> Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk]
>> I don't have time >> to look at the maths of it, but I think the centre of
>> charge of >> the electron density >>  should be identical to the centre of the
>> Mulliken charges, >> which would be easy to calculate (analogous to the centre
>> of >> mass).
>
> This will not work, for example if you have a single >> centre basis set all
> Mulliken charge would be on that center. What >> you should do is to compute
> the dipole moment of the molecule and >> use that to work out the center
> of charge.
>
> >> Sincerely,
> Ulf Ekstrom>

-- Herbert Fruchtl
Senior >> Scientific Computing Officer
School of Chemistry, School of Mathematics >> and Statistics
University of St Andrews
--
The University of St >> Andrews is a charity registered in Scotland:
No >> SC013532



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> > James E. Eilers > Professor > Chemistry Department > Southern Illinois University Edwardsville > (618)650-3559 > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel###gmail.com From owner-chemistry@ccl.net Mon Nov 29 13:41:00 2010 From: "Radoslaw Kaminski rkaminski.rk-x-gmail.com" To: CCL Subject: CCL:G: Question on calculation of charge center of electrons in a molecule Message-Id: <-43239-101129133714-29566-7jq+J5JjBhj9qQY+IcucEw{}server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=0016369d0217c921ee0496355b1a Date: Mon, 29 Nov 2010 19:37:04 +0100 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk*_*gmail.com] --0016369d0217c921ee0496355b1a Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, For the calculation of the center of charge wouldn't it be just to integrat= e the electron density multiplied by the position over the whole space and divide this by the number of electrons? The first are just components of th= e dipole moment printed by every QM program. For a molecule it's straightforward. I see the problem when the species is charged and the dipole moment depends on the origin choice, but I'm not a specialist. Radek 2010/11/29 John McKelvey jmmckel-,-gmail.com > > Sent to CCL by: John McKelvey [jmmckel++gmail.com] > On the other hand the NBO program can compute ZDO type charges which > are atom-centered and are along the diagonal of the density matrix and > for which the sum is the same as the number of electrons in the > system. > > John McKelvey > > On Mon, Nov 29, 2010 at 10:01 AM, James Eilers jeilers!^!siue.edu > wrote: > > Mulliken charges also include the "shared" electron density or cross > terms > > between atomic orbitals on different centers. > > > > On Nov 27, 2010, at 8:02 PM, Jiabo Li jiaboli/./yahoo.com wrote: > > > >> To understand what is wrong, you can look at a simple example: the > >> hydrogen atom in its excited state with the single electron on a SP > hydride > >> orbital. In this case, the electron density is not central symmetric b= ut > >> polarized, and the dipole moment is not zero (a big dipole moment), > while in > >> this case the net atomic charge is zero (neutral). > >> > >> Jiabo > >> > >> --- On Fri, 11/26/10, Herbert Fruchtl herbert.fruchtl[#] > st-andrews.ac.uk > >> wrote: > >> > >> > >>> From: Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk > >>> > >> > >> Subject: CCL:G: Question on calculation of charge center of electrons = in > a > >> molecule > >> To: "Li, Jiabo " > >> Date: Friday, November 26, 2010, 6:25 AM > >> > >> > >> > >> Sent to CCL by: Herbert Fruchtl [herbert.fruchtl::st-andrews.ac.uk] > >> The centre of charge of each Gaussian function is its origin, i.e. the > >> nucleus if you have atom-centred basis functions. The Mulliken charge = is > the > >> sum of those functions, multiplied with their occupation number. > Shouldn't > >> this sum have its centre on the nucleus as well? And the sum of all of > them > >> (over all atoms) gives the complete charge distribution. Where am I > going > >> wrong? > >> > >> Herbert > >> > >> Ulf Ekstr=F6m ulfek(~)few.vu.nl wrote: > >>> > >>> Sent to CCL by: =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek],[few.vu.= nl] > >>> On Thu, Nov 25, 2010 at 9:56 AM, Herbert Fruchtl > >>> herbert.fruchtl-.-st-andrews.ac.uk wrote: > >>>> > >>>> Sent to CCL by: Herbert Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk] > >>>> I don't have time to look at the maths of it, but I think the centre > of > >>>> charge of the electron density should be identical to the centre of > the > >>>> Mulliken charges, which would be easy to calculate (analogous to the > >>>> centre > >>>> of mass). > >>> > >>> This will not work, for example if you have a single centre basis set > all > >>> Mulliken charge would be on that center. What you should do is to > compute > >>> the dipole moment of the molecule and use that to work out the center > >>> of charge. > >>> > >>> Sincerely, > >>> Ulf Ekstrom> > >> > >> -- Herbert Fruchtl > >> Senior Scientific Computing Officer > >> School of Chemistry, School of Mathematics and Statistics > >> University of St Andrews > >> -- > >> The University of St Andrews is a charity registered in Scotland: > >> No SC013532Conferences: > >> http://server.ccl.net/chemistry/announcements/conferences/--0-160776249-1290909739=3D:87851 > >> Content-Type: text/html; charset=3Diso-8859-1 > >> Content-Transfer-Encoding: quoted-printable > >> > >>
>> style=3D"font: inherit;">
To understand what is wrong, you can loo= k at > a > >> simple example: the hydrogen atom in its excited state with the single > >> electron on a SP hydride orbital. In this case, the electron density i= s > not > >> central symmetric but polarized, and the dipole moment is not zero (a > big > >> dipole moment), while in this case the net atomic charge is zero > >> (neutral).
> >>
 
> >>
Jiabo

--- On Fri, 11/26/10, Herbert Fruchtl > >> herbert.fruchtl[#]st-andrews.ac.uk > >> <owner-chemistry]*[ccl.net> wrote:
> >>
>> rgb(16,16,255) 2px solid">
From: Herbert Fruchtl > >> herbert.fruchtl[#]st-andrews.ac.uk > >> <owner-chemistry]*[ccl.net>
Subject: CCL:G: Question on > calculation > >> of charge center of electrons in a molecule
To: "Li, Jiabo " > >> <jiaboli]*[yahoo.com>
Date: Friday, November 26, 2010, 6:25 > >> AM

> >>

Sent to CCL by: Herbert Fruchtl > >> [herbert.fruchtl::st-andrews.ac.uk]
The centre of charge of each > Gaussian > >> function is its origin, i.e. the nucleus if you have atom-centred basi= s > >> functions. The Mulliken charge is the sum of those functions, multipli= ed > >> with their occupation number. Shouldn't this sum have its centre on th= e > >> nucleus as well? And the sum of all of them (over all atoms) gives the > >> complete charge distribution. Where am I going wrong?

  > >> Herbert

Ulf Ekstr=F6m ulfek(~)few.vu.nl wrote:
> Sent to = CCL > by: > >> =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek],[few.vu.nl]
> On Th= u, Nov > 25, > >> 2010 at 9:56 AM, Herbert Fruchtl
> herbert.fruchtl-.- > st-andrews.ac.uk > >> <owner-chemistry . ccl.net> wrote:
>> Sent to CCL by: > Herbert > >> Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk]
>> I don't have > time > >> to look at the maths of it, but I think the centre of
>> char= ge > of > >> the electron density > >> should be identical to the centre of the
>> Mulliken charges= , > >> which would be easy to calculate (analogous to the centre
>> = of > >> mass).
>
> This will not work, for example if you have a > single > >> centre basis set all
> Mulliken charge would be on that center. > What > >> you should do is to compute
> the dipole moment of the molecule > and > >> use that to work out the center
> of charge.
>
> > >> Sincerely,
> Ulf Ekstrom>

-- Herbert Fruchtl
Senio= r > >> Scientific Computing Officer
School of Chemistry, School of > Mathematics > >> and Statistics
University of St Andrews
--
The University of = St > >> Andrews is a charity registered in Scotland:
No > >> SC013532



-=3D This is automatically added to each messa= ge > by > >> the mailing script =3D-
To recover the email address of the author = of > the > >> message, please change
the strange characters on the top line to th= e > ]*[ > >> sign. You can also
E-mail to subscribers: >> href=3D"http://us.mc369.mail.yahoo.com/mc/compose?to=3DCHEMISTRY]*[ccl= .net" > >> ymailto=3D"mailto:CHEMISTRY]*[ccl.net">CHEMISTRY]*[ccl.net or > >> use:
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Job: >> href=3D"http://www.ccl.net/jobs" target=3D_blank>http://www.ccl.net/jo= bs > > >> Conferences: >> href=3D"http://server.ccl.net/chemistry/announcements/conferences/" > >> target=3D_blank> > http://server.ccl.net/chemistry/announcements/conferences/ >

Search > >> Messages: >> target=3D_blank>http://www.ccl.net/chemistry/searchccl/index.shtml >
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> > > > James E. Eilers > > Professor > > Chemistry Department > > Southern Illinois University Edwardsville > > (618)650-3559 > > > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel],[gmail.com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Radoslaw Kaminski, M.Sc. Eng. Ph.D. Student Crystallochemistry Laboratory Department of Chemistry University of Warsaw Pasteura 1, 02-093 Warszawa, Poland http://www.chem.uw.edu.pl/people/RKaminski/ --0016369d0217c921ee0496355b1a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

For the calculation of the center of charge wouldn't it be j= ust to integrate the electron density multiplied by the position over the w= hole space and divide this by the number of electrons? The first are just c= omponents of the dipole moment printed by every QM program. For a molecule = it's straightforward. I see the problem when the species is charged and= the dipole moment depends on the origin choice, but I'm not a speciali= st.

Radek


2010/11/29 John McKelvey jm= mckel-,-gmail.com <owner-chemistry..ccl.net>

Sent to CCL by: John McKelvey [jmmckel++gmail.com]
On the other hand the NBO program can compute ZDO type charges which
are atom-centered and are along the diagonal of the density matrix and
for which the sum is the same as the number of electrons in the
system.

John McKelvey

On Mon, Nov 29, 2010 at 10:01 AM, James Eilers jeilers!^!siue.edu
<owner-chemistry],[ccl.net> wrote:
> Mulliken charges also include the "shared" electron density = or cross terms
> between atomic orbitals on different centers.
>
> On Nov 27, 2010, at 8:02 PM, Jiabo Li jiaboli/./yahoo.com wrote:
>
>> To understand what is wrong, you can look at a simple example: the=
>> hydrogen atom in its excited state with the single electron on a S= P hydride
>> orbital. In this case, the electron density is not central symmetr= ic but
>> polarized, and the dipole moment is not zero (a big dipole moment)= , while in
>> this case the net atomic charge is zero (neutral).
>>
>> Jiabo
>>
>> --- On Fri, 11/26/10, Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk
>> <owner-chemistry]*[ccl.net> wrote:
>>
>>
>>> From: Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk
>>> <owner-chemistry]*[ccl.net>
>>
>> Subject: CCL:G: Question on calculation of charge center of electr= ons in a
>> molecule
>> To: "Li, Jiabo " <jiaboli]*[yahoo.com>
>> Date: Friday, November 26, 2010, 6:25 AM
>>
>>
>>
>> Sent to CCL by: Herbert Fruchtl [herbert.fruchtl::st-andrews.ac.uk]
>> The centre of charge of each Gaussian function is its origin, i.e.= the
>> nucleus if you have atom-centred basis functions. The Mulliken cha= rge is the
>> sum of those functions, multiplied with their occupation number. S= houldn't
>> this sum have its centre on the nucleus as well? And the sum of al= l of them
>> (over all atoms) gives the complete charge distribution. Where am = I going
>> wrong?
>>
>> =A0 Herbert
>>
>> Ulf Ekstr=F6m ulfek(~)few.vu.nl wrote:
>>>
>>> Sent to CCL by: =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek],[= few.vu.nl]
>>> On Thu, Nov 25, 2010 at 9:56 AM, Herbert Fruchtl
>>> herbert.fruchtl-.-st-andrews.ac.uk <owner-chemistry . ccl.net> wrote:
>>>>
>>>> Sent to CCL by: Herbert Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk]
>>>> I don't have time to look at the maths of it, but I th= ink the centre of
>>>> charge of the electron density should be identical to the = centre of the
>>>> Mulliken charges, which would be easy to calculate (analog= ous to the
>>>> centre
>>>> of mass).
>>>
>>> This will not work, for example if you have a single centre ba= sis set all
>>> Mulliken charge would be on that center. What you should do is= to compute
>>> the dipole moment of the molecule and use that to work out the= center
>>> of charge.
>>>
>>> Sincerely,
>>> Ulf Ekstrom>
>>
>> -- Herbert Fruchtl
>> Senior Scientific Computing Officer
>> School of Chemistry, School of Mathematics and Statistics
>> University of St Andrews
>> --
>> The University of St Andrews is a charity registered in Scotland:<= br>
>> No SC013532>> =A0=A0=A0http://www.ccl.net/cgi= -bin/ccl/send_ccl_message
>> =A0=A0=A0http://www.ccl.net/c= gi-bin/ccl/send_ccl_message
>>
>> Subscribe/Unsubscribe:=A0 =A0 =A0 =A0Conferences:
>> http://server.ccl.net/chemistry/announcements/confer= ences/
>> =A0=A0=A0http://www.ccl.net/spammers.txt--0-16= 0776249-1290909739=3D:87851
>> Content-Type: text/html; charset=3Diso-8859-1
>> Content-Transfer-Encoding: quoted-printable
>>
>> <table cellspacing=3D"0" cellpadding=3D"0" = border=3D"0" ><tr><td valign=3D"top"
>> style=3D"font: inherit;"><DIV>To understand wha= t is wrong, you can look at a
>> simple example: the hydrogen atom in its excited state with the si= ngle
>> electron on a SP hydride orbital. In this case, the electron densi= ty is not
>> central symmetric but polarized, and the dipole moment is not zero= (a big
>> dipole moment), while in this case the net atomic charge is zero >> (neutral).</DIV>
>> <DIV>&nbsp;</DIV>
>> <DIV>Jiabo<BR><BR>--- On <B>Fri, 11/26/10,= Herbert Fruchtl
>> herbert.fruchtl[#]st-andrews.ac.uk
>> <I>&lt;owner-chemistry]*[ccl.net&gt;</I></B> wrote:<BR></= DIV>
>> <BLOCKQUOTE style=3D"PADDING-LEFT: 5px; MARGIN-LEFT: 5px; = BORDER-LEFT:
>> rgb(16,16,255) 2px solid"><BR>From: Herbert Fruchtl<= br> >> herbert.fruchtl[#]st-andrews.ac.uk
>> &lt;owner-chemistry]*[ccl.net&gt;<BR>Subject: CCL:G: Question on calculation >> of charge center of electrons in a molecule<BR>To: "Li,= Jiabo "
>> &lt;jiaboli]*[y= ahoo.com&gt;<BR>Date: Friday, November 26, 2010, 6:25
>> AM<BR><BR>
>> <DIV class=3DplainMail><BR>Sent to CCL by: Herbert Fru= chtl
>> [herbert.fruchtl::st-andrews.ac.uk]<BR>The centre of charge of each Gaussian<= br> >> function is its origin, i.e. the nucleus if you have atom-centred = basis
>> functions. The Mulliken charge is the sum of those functions, mult= iplied
>> with their occupation number. Shouldn't this sum have its cent= re on the
>> nucleus as well? And the sum of all of them (over all atoms) gives= the
>> complete charge distribution. Where am I going wrong?<BR><= ;BR>&nbsp;
>> Herbert<BR><BR>Ulf Ekstr=F6m ulfek(~)few.vu.nl wrote:<BR>&gt; Sent t= o CCL by:
>> =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek],[few.vu.nl]<BR>&gt; On Thu, Nov 25,=
>> 2010 at 9:56 AM, Herbert Fruchtl<BR>&gt; herbert.fruchtl= -.-st-andrews.ac.uk
>> &lt;owner-chemistry . ccl.net&gt; wrote:<BR>&gt;&gt; Sent to CCL by: H= erbert
>> Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk]<BR>&gt;&gt; I don't = have time
>> to look at the maths of it, but I think the centre of<BR>&am= p;gt;&gt; charge of
>> the electron density
>> =A0should be identical to the centre of the<BR>&gt;&= gt; Mulliken charges,
>> which would be easy to calculate (analogous to the centre<BR>= ;&gt;&gt; of
>> mass).<BR>&gt; <BR>&gt; This will not work, fo= r example if you have a single
>> centre basis set all<BR>&gt; Mulliken charge would be on= that center. What
>> you should do is to compute<BR>&gt; the dipole moment of= the molecule and
>> use that to work out the center<BR>&gt; of charge.<BR= >&gt; <BR>&gt;
>> Sincerely,<BR>&gt; Ulf Ekstrom&gt; <BR><BR&= gt;-- Herbert Fruchtl<BR>Senior
>> Scientific Computing Officer<BR>School of Chemistry, School = of Mathematics
>> and Statistics<BR>University of St Andrews<BR>--<BR= >The University of St
>> Andrews is a charity registered in Scotland:<BR>No
>> SC013532<BR><BR><BR><BR>-=3D This is autom= atically added to each message by
>> the mailing script =3D-<BR>To recover the email address of t= he author of the
>> message, please change<BR>the strange characters on the top = line to the ]*[
>> sign. You can also<BR<BR><BR>E-mail to subscribers:= <A
>> href=3D"http://us.mc369.mail.yahoo.com/= mc/compose?to=3DCHEMISTRY]*[ccl.net"
>> ymailto=3D"mailto:CHEMISTRY]= *[ccl.net">CHEMIST= RY]*[ccl.net</A> or<= br> >> use:<BR>&nbsp; &nbsp;&nbsp;&nbsp;<A
>> href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message"
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>> ymailto=3D"mailto:CHEMIS= TRY-REQUEST]*[ccl.net&= quot;>CHEMISTRY-REQUEST]*[c= cl.net</A>
>> or use<BR>&nbsp; &nbsp;&nbsp;&nbsp;<A
>> href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message"
>> target=3D_blank>http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age</A><BR><BR>Subscribe/Unsubscribe:&nbsp;
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>> posting, check wait time at: <A href=3D"http://www.ccl.net/"
>> =A0target=3D_blank>http://www.ccl.net</A><BR><BR>Job: <A
>> href=3D"http://www.ccl.net/jobs" target=3D_blank>http://www.ccl.net/jobs</A>
>> Conferences: <A
>> href=3D"http://server.ccl.net/chemistry/announc= ements/conferences/"
>> target=3D_blank>http://server.ccl.net/chemistry/a= nnouncements/conferences/</A><BR><BR>Search
>> Messages: <A href=3D"http://www.ccl.net/chemistry/se= archccl/index.shtml"
>> target=3D_blank>http://www.ccl.net/chemistry/searchccl/in= dex.shtml</A><BR><BR<BR>&nbsp;
>> &nbsp;&nbsp;&nbsp;<A href=3D"http://www.ccl.net/spammers.tx= t"
>> target=3D_blank>http://www.ccl.net/spammers.txt</A><BR><B= R>RTFI: <A
>> href=3D"http://www.ccl.net/chemistry/aboutccl/instruct= ions/"
>> target=3D_blank>http://www.ccl.net/chemistry/aboutccl/in= structions/</A><BR><BR><BR></DIV></BLO= CKQUOTE></td></tr></table>
>
> James E. Eilers
> Professor
> Chemistry Department
> Southern Illinois University Edwardsville
> (618)650-3559
>



--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel],[gmail.com



-=3D This is automatically added to each message by the mailing script =3D-=
To recover the email address of the author of the m= essage, please change
the strange characters on the top line to the .. sig= n. You can also

E-mail to subscribers: CHEMISTRY..ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_me= ssage

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--
Radoslaw Kaminski, M.Sc= . Eng.
Ph.D. Student
Crystallochemistry Laboratory
Department of C= hemistry
University of Warsaw
Pasteura 1, 02-093 Warszawa, Poland
h= ttp://www.chem.uw.edu.pl/people/RKaminski/
--0016369d0217c921ee0496355b1a-- From owner-chemistry@ccl.net Mon Nov 29 17:21:00 2010 From: "Shirley Peng speng .. chemcomp.com" To: CCL Subject: CCL: CCG ANNOUNCES THE NEW VERSION OF MOE - MOLECULAR OPERATING ENVIRONMENT Message-Id: <-43240-101129152148-19502-kUVK9JsSt7gUrbvj1Qs8pg++server.ccl.net> X-Original-From: "Shirley Peng" Date: Mon, 29 Nov 2010 15:21:47 -0500 Sent to CCL by: "Shirley Peng" [speng#chemcomp.com] CHEMICAL COMPUTING GROUP ANNOUNCES THE NEW VERSION OF MOE - MOLECULAR OPERATING ENVIRONMENT MONTREAL, Canada November 30, 2010 Chemical Computing Group (CCG) is pleased to announce the release of MOE 2010.10. MOE is a fully integrated multi-platform (Windows/Linux/Unix/Mac) drug discovery software package. MOE 2010.10 includes the following new and enhanced capabilities: Streamlined Interactive Modeling Interface Integration of NAMD Engine in MOE Kinase Database and Explorer Structure-Based Medicinal Chemistry Transformations Enhanced Graphics Non-bonded Interaction Visualization The MOE interface has been redesigned with the objective of simplifying and streamlining the modeling process for computational as well as medicinal chemists. As Paul Labute, President and CEO of CCG, explained, We put considerable effort into making the modeling process more efficient. Many of the new enhancements were the result of close collaboration with our clients who expressed interest in optimizing the modeling experience. In MOE 2010.10, multiple complexes can be handled simultaneously more effectively, with quick toggling on and off of active atom sets, surfaces and rendering styles. The new interface also provides fast access to harmonized application panels, enabling researchers to streamline their modeling and simulation efforts. Another highlight of the 2010.10 version is the integration of the NAMD engine into MOEs suite of dynamics tools. Such integration offers MOE users the flexibility to farm out molecular dynamic simulations to NAMD and import trajectories back into MOE for subsequent analysis, observed Paul Labute. NAMD is a high-performance parallelized MD engine that is extensively used and has been validated over the years. Being able to include NAMD easily into the workflow will greatly benefit the MOE user community, simplifying the setup of complex MD runs and reducing the effort involved in preparing parameter files. MOE 2010.10 also features a new kinase structural database and explorer/browser. The new Kinase Search interface allows MOE users to extract potentially complex data sets quickly and efficiently by searching and visualizing ligand topologies and ligand:receptor structural domain information. Paul Labute added, Researchers will be able to include proprietary structures to expand and update the knowledge base to enhance their understanding of complicated issues such as selectivity. About Chemical Computing Group Chemical Computing Group (CCG) is a leading supplier of software solutions for Life Sciences. CCG has been in business since 1994, always providing state-of-the-art applications in Drug Discovery for Pharmaceutical, Biotech and Academic research. CCGs products and services are used by biologists, medicinal chemists and computational chemists throughout the world. Chemical Computing Group has a proven track record in scientific innovation, consistently producing releases and upgrades for all their products. CCG has a very strong reputation for collaborative scientific support, with offices in both North America and Europe. CCG headquarter is in Montreal, Canada. For more information visit: www.chemcomp.com For additional information please contact: Raul Alvarez Senior Marketing Manager (514) 393-1055 | ralvarez/./chemcomp.com From owner-chemistry@ccl.net Mon Nov 29 17:56:00 2010 From: "omer Sicimogullari omer4444(~)hotmail.com" To: CCL Subject: CCL: 3D visulisation software for components created by PCA. Like Spotfire. Message-Id: <-43241-101129073306-19926-59a5THnHrrIeHiZjy7dtDg!A!server.ccl.net> X-Original-From: "omer Sicimogullari" Date: Mon, 29 Nov 2010 07:33:04 -0500 Sent to CCL by: "omer Sicimogullari" [omer4444[#]hotmail.com] Hello I am looking for a software like Spotfire but for free. I want to use it to create 3D graphs using the component matrix numbers created from Factor analysis/PCA in SPSS. I would be greatful if someone can help me? Thank you From owner-chemistry@ccl.net Mon Nov 29 18:31:00 2010 From: "masomeh - gharabaghi gharabaghimasume66**gmail.com" To: CCL Subject: CCL: getting homo and lumo energies Message-Id: <-43242-101129074827-22075-u9tGJiZjnb+6cnPNmzyCHA|a|server.ccl.net> X-Original-From: "masomeh - gharabaghi" Date: Mon, 29 Nov 2010 07:48:24 -0500 Sent to CCL by: "masomeh - gharabaghi" [gharabaghimasume66!=!gmail.com] Hi all; Can you recommend me how I can get the homo and lumo energies of each group of atoms by my output, running via DFT method and TD keyword? Thank you masume gharabaghi email address:gharabaghimasume66__gmail.com From owner-chemistry@ccl.net Mon Nov 29 19:06:00 2010 From: "omer sicimogullari omer4444],[hotmail.com" To: CCL Subject: CCL: 3D graphical software Message-Id: <-43243-101129150735-20253-oZxhrTzQV+8BE9HOYcjBnw..server.ccl.net> X-Original-From: "omer sicimogullari" Date: Mon, 29 Nov 2010 15:07:32 -0500 Sent to CCL by: "omer sicimogullari" [omer4444!A!hotmail.com] Hello I am looking for a software like Spotfire but for free. I want to use it to create 3D graphs using the component matrix numbers created from Factor analysis/PCA in SPSS. I would be greatful if someone can help me? Thank you From owner-chemistry@ccl.net Mon Nov 29 20:12:01 2010 From: "Jiabo Li jiaboli,,yahoo.com" To: CCL Subject: CCL: 3D graphical software Message-Id: <-43244-101129201059-13245-fzYkB2w7oYhv4v55sza02A###server.ccl.net> X-Original-From: Jiabo Li Content-Type: multipart/alternative; boundary="0-1983512611-1291079451=:92905" Date: Mon, 29 Nov 2010 17:10:51 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Jiabo Li [jiaboli(~)yahoo.com] --0-1983512611-1291079451=:92905 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Try Accelrys' Discovery Studio Visualizer. The latest version 3.0 has super= graphic quality=A0 and performance. It also has =A0many=A0new functionalit= ies. Check the following link: =A0 http://accelrys.com/products/discovery-studio/visualization-download.php =A0 Jiabo --- On Mon, 11/29/10, omer sicimogullari omer4444],[hotmail.com wrote: > From: omer sicimogullari omer4444],[hotmail.com Subject: CCL: 3D graphical software To: "Li, Jiabo " Date: Monday, November 29, 2010, 12:07 PM Sent to CCL by: "omer=A0 sicimogullari" [omer4444!A!hotmail.com] Hello I am looking for a software like Spotfire but for free.=A0 I want to use it= to create 3D graphs using the component matrix numbers created from Factor= analysis/PCA in SPSS.=A0 I would be greatful if someone can help me? Thank you -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0--0-1983512611-1291079451=:92905 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Try Accelrys' Discovery Studio Visualize= r. The latest version 3.0 has super graphic quality  and performance. = It also has  many new functionalities. Check the following link:<= /DIV>
 
 
Jiabo

--- On Mon, 11/29/10, omer sicimogullari omer4444],[ho= tmail.com <owner-chemistry|a|ccl.net> wrote:

From: omer sicimogullari omer4444],[hotmail.com &= lt;owner-chemistry|a|ccl.net>
Subject: CCL: 3D graphical software
To= : "Li, Jiabo " <jiaboli|a|yahoo.com>
Date: Monday, November = 29, 2010, 12:07 PM


Sent to CCL by: "omer  sicimogullari" [omer= 4444!A!hotmail.com]
Hello

I am looking for a software like Spotfi= re but for free.  I want to use it to create 3D graphs using the compo= nent matrix numbers created from Factor analysis/PCA in SPSS.  I would= be greatful if someone can help me?

Thank you



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