From owner-chemistry@ccl.net Wed May 8 08:23:00 2013 From: "Reis Heribert hreis:_:eie.gr" To: CCL Subject: CCL:G: Dipole moment of charged species in Gaussian Message-Id: <-48655-130508075836-513-TgxvOZtq55jQeyuUnv6xjA .. server.ccl.net> X-Original-From: Reis Heribert Content-Type: multipart/alternative; boundary=047d7b15b17dd24a5804dc33a6ef Date: Wed, 8 May 2013 13:58:27 +0200 MIME-Version: 1.0 Sent to CCL by: Reis Heribert [hreis=-=eie.gr] --047d7b15b17dd24a5804dc33a6ef Content-Type: text/plain; charset=ISO-8859-1 Hello John, In my opinion the choice of the origin for multipoles is most of the time just a matter of what one is trying to investigate. So a choice like the one you propose may be interesting in questions related to, say, chemical reactivity. But apart from that, it is not quite clear to me how you would go about computing such an origin. Computing the electron density due to the valence orbitals on a grid? Or do you have another idea in mind? Maybe something related to Hirshfelds' free atom densities? Heribert On Tue, May 7, 2013 at 8:53 PM, John McKelvey jmmckel===gmail.com < owner-chemistry%x%ccl.net> wrote: > Hello, > > Perhaps there is another way to look at it, and it is a subset of looking > at the center of nuclear charge. Perhaps it is more sensitive (?) to look > at the center of constituent free atom valence electrons? > > John McKelvey > > > On Tue, May 7, 2013 at 12:26 PM, Reis Heribert hreis_-_eie.gr < > owner-chemistry/./ccl.net> wrote: > >> Hello >> >> The definition of the dipole moment of a charged species is well defined. >> The only problem with it (and with all higher multipoles) is, that its >> value depends on the origin of the coordinate system. Thus for comparison >> purposes the origin of the coordinate system of different molecules should >> be comparable. A very common choice is the centre of mass; another >> possibility is the center of nuclear charge, which is the standard origin >> in Gaussian09, if one does not specify the 'Nosymm' keyword. You can also >> turn the problem on its head and define the origin as that point where the >> dipole is zero... >> >> I'm assuming that you want to compare the absolute value of the dipole >> between different molecules. In case you also want to compare the >> components, you also should use comparable orientations of the coordinate >> systems (e.g the coordinate system where e.g. the inertia (or >> polarizability or ...) tensor is diagonal). This, however, is independent >> of being charged or uncharged. >> >> Heribert >> > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel/./gmail.com > --047d7b15b17dd24a5804dc33a6ef Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello John,

In my opinion the choic= e of the origin for multipoles is most of the time just a matter of what on= e is trying to investigate. So a choice like the one you propose may be int= eresting in questions related to, say, chemical reactivity.

But apart from that, it is not quite clear to me how you would go about= computing such an origin. Computing the electron density due to the valenc= e orbitals on a grid? Or do you have another idea in mind? Maybe something = related to Hirshfelds' free atom densities?

Heribert


On Tue, May 7, 2013 at 8:53 PM, John McKelvey jmmckel=3D= =3D=3Dgmail.com <owner-chemistry%x%cc= l.net> wrote:
Hello,

Perhaps there is another way to look at it, and it is a subset of lookin= g at the center of nuclear charge.=A0 Perhaps it is more sensitive (?) to l= ook at the center of=A0 constituent free atom valence electrons?

John McKelvey


On Tue, May 7, 2013 at 12:26 PM,= Reis Heribert hreis_-_= eie.gr <owner-chemistry/./ccl.net> wrote:
Hello
The definition of the dipole moment of a charged species is well def= ined. The only problem with it (and with all higher multipoles) is, that it= s value depends on the origin of the coordinate system. Thus for comparison= purposes the origin of the coordinate system of different molecules should= be comparable. A very common choice is the centre of mass; another possibi= lity is the center of nuclear charge, which is the standard origin in Gauss= ian09, if one does not specify the 'Nosymm' keyword. You can also t= urn the problem on its head and define the origin as that point where the d= ipole is zero...

I'm assuming that you want to compare the absolute value of t= he dipole between different molecules. In case you also want to compare the= components, you also should use comparable orientations of the coordinate = systems (e.g the coordinate system where e.g. the inertia (or polarizabilit= y or ...) tensor is diagonal). This, however, is independent of being charg= ed or uncharged.

Heribert



--
John McKelvey
10819 Middleford PlFt Wayne, IN 46818
260-489-2160
jmmckel/./gmail.co= m

--047d7b15b17dd24a5804dc33a6ef-- From owner-chemistry@ccl.net Wed May 8 10:06:00 2013 From: "Herbert Fruchtl herbert.fruchtl,+,st-andrews.ac.uk" To: CCL Subject: CCL:G: Dipole moment of charged species in Gaussian Message-Id: <-48656-130508100352-21722-1fx+URo898bPntoSSJugRA _ server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 08 May 2013 15:03:25 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl%%st-andrews.ac.uk] Intuitively, I would center any multipole analysis at the centre of charge. The centre of atomic (not just nuclear!) charges, calculated in any partition scheme (Mulliken, Hirshfeld, Bader, ...) should be a reasonable approximation of this. Herbert On 08/05/13 12:58, Reis Heribert hreis:_:eie.gr wrote: > Hello John, > > In my opinion the choice of the origin for multipoles is most of the time just a > matter of what one is trying to investigate. So a choice like the one you > propose may be interesting in questions related to, say, chemical reactivity. > > But apart from that, it is not quite clear to me how you would go about > computing such an origin. Computing the electron density due to the valence > orbitals on a grid? Or do you have another idea in mind? Maybe something related > to Hirshfelds' free atom densities? > > Heribert > > > On Tue, May 7, 2013 at 8:53 PM, John McKelvey jmmckel===gmail.com > > wrote: > > Hello, > > Perhaps there is another way to look at it, and it is a subset of looking at > the center of nuclear charge. Perhaps it is more sensitive (?) to look at > the center of constituent free atom valence electrons? > > John McKelvey > > > On Tue, May 7, 2013 at 12:26 PM, Reis Heribert hreis_-_eie.gr > > wrote: > > Hello > > The definition of the dipole moment of a charged species is well > defined. The only problem with it (and with all higher multipoles) is, > that its value depends on the origin of the coordinate system. Thus for > comparison purposes the origin of the coordinate system of different > molecules should be comparable. A very common choice is the centre of > mass; another possibility is the center of nuclear charge, which is the > standard origin in Gaussian09, if one does not specify the 'Nosymm' > keyword. You can also turn the problem on its head and define the origin > as that point where the dipole is zero... > > I'm assuming that you want to compare the absolute value of the dipole > between different molecules. In case you also want to compare the > components, you also should use comparable orientations of the > coordinate systems (e.g the coordinate system where e.g. the inertia (or > polarizability or ...) tensor is diagonal). This, however, is > independent of being charged or uncharged. > > Heribert > > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel/./gmail.com > > -- 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 From owner-chemistry@ccl.net Wed May 8 12:09:00 2013 From: "John McKelvey jmmckel%gmail.com" To: CCL Subject: CCL:G: Dipole moment of charged species in Gaussian Message-Id: <-48657-130508111556-21059-uRlgOZSmmZU8pBEASO4SAQ%a%server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=047d7b66f68bb775e504dc366883 Date: Wed, 8 May 2013 11:15:49 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel : gmail.com] --047d7b66f68bb775e504dc366883 Content-Type: text/plain; charset=ISO-8859-1 Heribert, Thanks for your comment. I'm not familiar with Hirschfelds approach, but I could be doing something related. I could have better stated my approach. Instead of using atomic mass, or atomic core charge, I use the "atomic valence shell" core charge, i.e. the number of valence electrons a given neutral atom *typically* contributes to a molecule. Occasionally I omit the hydrogen valence-electron core. Before people using VDW surface type of solvation, i.e. PVM or COSMO, non spherical molecules, say iodo-benzene, the center-of-mass could have a portion of charge outside an ellipse or spherical cavity. Using the valence-core-charge minimized this issue, and with respect core electrons, it is the valence electron shifts that shift shift around most. On Wed, May 8, 2013 at 7:58 AM, Reis Heribert hreis:_:eie.gr < owner-chemistry(!)ccl.net> wrote: > Hello John, > > In my opinion the choice of the origin for multipoles is most of the time > just a matter of what one is trying to investigate. So a choice like the > one you propose may be interesting in questions related to, say, chemical > reactivity. > > But apart from that, it is not quite clear to me how you would go about > computing such an origin. Computing the electron density due to the valence > orbitals on a grid? Or do you have another idea in mind? Maybe something > related to Hirshfelds' free atom densities? > > Heribert > > > On Tue, May 7, 2013 at 8:53 PM, John McKelvey jmmckel===gmail.com < > owner-chemistry!^!ccl.net> wrote: > >> Hello, >> >> Perhaps there is another way to look at it, and it is a subset of looking >> at the center of nuclear charge. Perhaps it is more sensitive (?) to look >> at the center of constituent free atom valence electrons? >> >> John McKelvey >> >> >> On Tue, May 7, 2013 at 12:26 PM, Reis Heribert hreis_-_eie.gr < >> owner-chemistry/./ccl.net> wrote: >> >>> Hello >>> >>> The definition of the dipole moment of a charged species is well >>> defined. The only problem with it (and with all higher multipoles) is, that >>> its value depends on the origin of the coordinate system. Thus for >>> comparison purposes the origin of the coordinate system of different >>> molecules should be comparable. A very common choice is the centre of mass; >>> another possibility is the center of nuclear charge, which is the standard >>> origin in Gaussian09, if one does not specify the 'Nosymm' keyword. You can >>> also turn the problem on its head and define the origin as that point where >>> the dipole is zero... >>> >>> I'm assuming that you want to compare the absolute value of the dipole >>> between different molecules. In case you also want to compare the >>> components, you also should use comparable orientations of the coordinate >>> systems (e.g the coordinate system where e.g. the inertia (or >>> polarizability or ...) tensor is diagonal). This, however, is independent >>> of being charged or uncharged. >>> >>> Heribert >>> >> >> >> >> -- >> John McKelvey >> 10819 Middleford Pl >> Ft Wayne, IN 46818 >> 260-489-2160 >> jmmckel/./gmail.com >> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel(!)gmail.com --047d7b66f68bb775e504dc366883 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Heribert,

Thanks for your comment.=A0 I&= #39;m not familiar with Hirschfelds approach, but I could be doing somethin= g related. =A0

I could have better stated my approach.=A0 Instead o= f using atomic mass, or atomic core charge, I use the "atomic valence= =A0 shell" core charge, i.e. the number of valence electrons a given n= eutral atom *typically* contributes to a molecule.=A0=A0=A0 Occasionally I = omit the hydrogen valence-electron=A0=A0=A0=A0 core.

Before people using VDW surface type of solvation, i.e. PVM or COSMO, n= on spherical molecules, say iodo-benzene, the center-of-mass could have a p= ortion of charge outside an ellipse or spherical cavity.=A0 Using the valen= ce-core-charge minimized this issue, and with respect core electrons, it is= the valence electron shifts that shift shift around most.=A0
=A0


On Wed, May 8, 2013 at 7:58 AM, Reis Heribert hreis:_:eie.gr <owner-chemistry(!)ccl.net> wrote:
Hello John,
In my opinion the choice of the origin for multipoles is most of th= e time just a matter of what one is trying to investigate. So a choice like= the one you propose may be interesting in questions related to, say, chemi= cal reactivity.

But apart from that, it is not quite clear to me how you would go about= computing such an origin. Computing the electron density due to the valenc= e orbitals on a grid? Or do you have another idea in mind? Maybe something = related to Hirshfelds' free atom densities?

Heribert


On Tue, May 7, 2013 at 8:53 PM, John McKelvey jmmckel=3D= =3D=3Dgmail.com <owner-chemistry!^!ccl.net> wrote:
Hello,

Perhaps there is another way to look at it, and it is a subset of lookin= g at the center of nuclear charge.=A0 Perhaps it is more sensitive (?) to l= ook at the center of=A0 constituent free atom valence electrons?

John McKelvey

<= br>
On Tue, May 7, 2013 at 12:26 PM, Reis Heriber= t hreis_-_eie.gr <owner-chemistry/./ccl.net> wrote:
Hello
The definition of the dipole moment of a charged species is well def= ined. The only problem with it (and with all higher multipoles) is, that it= s value depends on the origin of the coordinate system. Thus for comparison= purposes the origin of the coordinate system of different molecules should= be comparable. A very common choice is the centre of mass; another possibi= lity is the center of nuclear charge, which is the standard origin in Gauss= ian09, if one does not specify the 'Nosymm' keyword. You can also t= urn the problem on its head and define the origin as that point where the d= ipole is zero...

I'm assuming that you want to compare the absolute value of t= he dipole between different molecules. In case you also want to compare the= components, you also should use comparable orientations of the coordinate = systems (e.g the coordinate system where e.g. the inertia (or polarizabilit= y or ...) tensor is diagonal). This, however, is independent of being charg= ed or uncharged.

Heribert



--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel/./gmail.co= m




--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel(!)gmail.com
--047d7b66f68bb775e504dc366883-- From owner-chemistry@ccl.net Wed May 8 14:38:00 2013 From: "Reis Heribert hreis.:.eie.gr" To: CCL Subject: CCL:G: Dipole moment of charged species in Gaussian Message-Id: <-48658-130508142944-16523-ftJKOUwlFLBFyDKJ/RP3bg%server.ccl.net> X-Original-From: Reis Heribert Content-Type: multipart/alternative; boundary=e89a8f923c7ac21f6a04dc391db5 Date: Wed, 8 May 2013 20:29:37 +0200 MIME-Version: 1.0 Sent to CCL by: Reis Heribert [hreis[*]eie.gr] --e89a8f923c7ac21f6a04dc391db5 Content-Type: text/plain; charset=ISO-8859-1 On Wed, May 8, 2013 at 4:03 PM, Herbert Fruchtl herbert.fruchtl,+, st-andrews.ac.uk wrote: > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl%%st-andrews.**ac.uk > ] > Intuitively, I would center any multipole analysis at the centre of > charge. The centre of atomic (not just nuclear!) charges, calculated in any > partition scheme (Mulliken, Hirshfeld, Bader, ...) should be a reasonable > approximation of this. > Herbert, This can only work when you have an overall charged molecule, as for the calculation of the origin for all of these quantities (nuclear charge, mass, charge etc) one divides by the total quantity, which is zero for an uncharged molecule. In the case of an ion, 'the centre of charge' incidentally is defined as that origin, for which the total dipole is zero (see Stone, The Theory of Intermolecular Forces, p. 33) Heribert > > Herbert > > > On 08/05/13 12:58, Reis Heribert hreis:_:eie.gr wrote: > >> Hello John, >> >> In my opinion the choice of the origin for multipoles is most of the time >> just a >> matter of what one is trying to investigate. So a choice like the one you >> propose may be interesting in questions related to, say, chemical >> reactivity. >> >> But apart from that, it is not quite clear to me how you would go about >> computing such an origin. Computing the electron density due to the >> valence >> orbitals on a grid? Or do you have another idea in mind? Maybe something >> related >> to Hirshfelds' free atom densities? >> >> Heribert >> >> >> On Tue, May 7, 2013 at 8:53 PM, John McKelvey jmmckel===gmail.com >> > >> >> wrote: >> >> Hello, >> >> Perhaps there is another way to look at it, and it is a subset of >> looking at >> the center of nuclear charge. Perhaps it is more sensitive (?) to >> look at >> the center of constituent free atom valence electrons? >> >> John McKelvey >> >> >> On Tue, May 7, 2013 at 12:26 PM, Reis Heribert hreis_-_eie.gr >> > >> >> wrote: >> >> Hello >> >> The definition of the dipole moment of a charged species is well >> defined. The only problem with it (and with all higher >> multipoles) is, >> that its value depends on the origin of the coordinate system. >> Thus for >> comparison purposes the origin of the coordinate system of >> different >> molecules should be comparable. A very common choice is the >> centre of >> mass; another possibility is the center of nuclear charge, which >> is the >> standard origin in Gaussian09, if one does not specify the >> 'Nosymm' >> keyword. You can also turn the problem on its head and define the >> origin >> as that point where the dipole is zero... >> >> I'm assuming that you want to compare the absolute value of the >> dipole >> between different molecules. In case you also want to compare the >> components, you also should use comparable orientations of the >> coordinate systems (e.g the coordinate system where e.g. the >> inertia (or >> polarizability or ...) tensor is diagonal). This, however, is >> independent of being charged or uncharged. >> >> Heribert >> >> >> >> >> -- >> John McKelvey >> 10819 Middleford Pl >> Ft Wayne, IN 46818 >> 260-489-2160 >> jmmckel/./gmail.com >> >> >> > -- > 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 chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --e89a8f923c7ac21f6a04dc391db5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable



On Wed, May 8, 2013 at 4:03 PM, Herbert Fruchtl herbert.fruchtl,+,<= a href=3D"http://st-andrews.ac.uk">st-andrews.ac.uk &= lt;owner-chemi= stry##ccl.net> wrote:

Sent to CCL by: Herbert Fruchtl [herbert.fruchtl%%st-andrews.ac.uk]
Intuitively, I would center any multipole analysis at the centre of charge.= The centre of atomic (not just nuclear!) charges, calculated in any partit= ion scheme (Mulliken, Hirshfeld, Bader, ...) should be a reasonable approxi= mation of this.

Herbert,

This= can only work when you have an overall charged molecule, as for the calcul= ation of the origin for all of these quantities (nuclear charge, mass, char= ge etc) one divides by the total quantity, which is zero for an uncharged m= olecule. In the case of an ion, 'the centre of charge' incidentally= is defined as that origin, for which the total dipole is zero (see Stone, = The Theory of Intermolecular Forces, p. 33)

Heribert
=A0

=A0 Herbert


On 08/05/13 12:58, Reis Heribert hreis:_:eie.gr wrote:
Hello John,

In my opinion the choice of the origin for multipoles is most of the time j= ust a
matter of what one is trying to investigate. So a choice like the one you propose may be interesting in questions related to, say, chemical reactivit= y.

But apart from that, it is not quite clear to me how you would go about
computing such an origin. Computing the electron density due to the valence=
orbitals on a grid? Or do you have another idea in mind? Maybe something re= lated
to Hirshfelds' free atom densities?

Heribert


On Tue, May 7, 2013 at 8:53 PM, John McKelvey jmmckel=3D=3D=3Dgmail.com
<http://gmail.com>= <owner-chemistry!^!ccl.net=

<mailto:owner-chemi= stry!^!ccl.net&= gt;> wrote:

=A0 =A0 Hello,

=A0 =A0 Perhaps there is another way to look at it, and it is a subset of l= ooking at
=A0 =A0 the center of nuclear charge. =A0Perhaps it is more sensitive (?) t= o look at
=A0 =A0 the center of =A0constituent free atom valence electrons?

=A0 =A0 John McKelvey


=A0 =A0 On Tue, May 7, 2013 at 12:26 PM, Reis Heribert hreis_-_eie.gr
=A0 =A0 <http://hrei= s_-_eie.gr> <owner-chemistry/./ccl.net

=A0 =A0 <mailto:own= er-chemistry/./ccl.= net>> wrote:

=A0 =A0 =A0 =A0 Hello

=A0 =A0 =A0 =A0 The definition of the dipole moment of a charged species is= well
=A0 =A0 =A0 =A0 defined. The only problem with it (and with all higher mult= ipoles) is,
=A0 =A0 =A0 =A0 that its value depends on the origin of the coordinate syst= em. Thus for
=A0 =A0 =A0 =A0 comparison purposes the origin of the coordinate system of = different
=A0 =A0 =A0 =A0 molecules should be comparable. A very common choice is the= centre of
=A0 =A0 =A0 =A0 mass; another possibility is the center of nuclear charge, = which is the
=A0 =A0 =A0 =A0 standard origin in Gaussian09, if one does not specify the = 'Nosymm'
=A0 =A0 =A0 =A0 keyword. You can also turn the problem on its head and defi= ne the origin
=A0 =A0 =A0 =A0 as that point where the dipole is zero...

=A0 =A0 =A0 =A0 I'm assuming that you want to compare the absolute valu= e of the dipole
=A0 =A0 =A0 =A0 between different molecules. In case you also want to compa= re the
=A0 =A0 =A0 =A0 components, you also should use comparable orientations of = the
=A0 =A0 =A0 =A0 coordinate systems (e.g the coordinate system where e.g. th= e inertia (or
=A0 =A0 =A0 =A0 polarizability or ...) tensor is diagonal). This, however, = is
=A0 =A0 =A0 =A0 independent of being charged or uncharged.

=A0 =A0 =A0 =A0 Heribert




=A0 =A0 --
=A0 =A0 John McKelvey
=A0 =A0 10819 Middleford Pl
=A0 =A0 Ft Wayne, IN 46818
=A0 =A0 260-489-2160 <tel:260-489-2160>
=A0 =A0 jmmckel/./gmail.com<= /a> <mailto:jmmckel/./<= a href=3D"http://gmail.com" target=3D"_blank">gmail.com>



--
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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--e89a8f923c7ac21f6a04dc391db5-- From owner-chemistry@ccl.net Wed May 8 15:12:00 2013 From: "Reis Heribert hreis]|[eie.gr" To: CCL Subject: CCL:G: Dipole moment of charged species in Gaussian Message-Id: <-48659-130508144812-20867-G183IfcDOQ57ObZyiVQ41w]~[server.ccl.net> X-Original-From: Reis Heribert Content-Type: multipart/alternative; boundary=047d7b676476df0aeb04dc395f86 Date: Wed, 8 May 2013 20:48:06 +0200 MIME-Version: 1.0 Sent to CCL by: Reis Heribert [hreis- -eie.gr] --047d7b676476df0aeb04dc395f86 Content-Type: text/plain; charset=ISO-8859-1 John, Just to make sure I understand your procedure correctly: you assign the valence electrons of each atom to the position of the nucleus of that atom in the molecule and then compute the center of those charges? That's interesting, but what about ions? Heribert On Wed, May 8, 2013 at 5:15 PM, John McKelvey jmmckel%gmail.com < owner-chemistry],[ccl.net> wrote: > Heribert, > > Thanks for your comment. I'm not familiar with Hirschfelds approach, but > I could be doing something related. > > I could have better stated my approach. Instead of using atomic mass, or > atomic core charge, I use the "atomic valence shell" core charge, i.e. the > number of valence electrons a given neutral atom *typically* contributes to > a molecule. Occasionally I omit the hydrogen valence-electron core. > > Before people using VDW surface type of solvation, i.e. PVM or COSMO, non > spherical molecules, say iodo-benzene, the center-of-mass could have a > portion of charge outside an ellipse or spherical cavity. Using the > valence-core-charge minimized this issue, and with respect core electrons, > it is the valence electron shifts that shift shift around most. > > > > On Wed, May 8, 2013 at 7:58 AM, Reis Heribert hreis:_:eie.gr < > owner-chemistry###ccl.net> wrote: > >> Hello John, >> >> In my opinion the choice of the origin for multipoles is most of the time >> just a matter of what one is trying to investigate. So a choice like the >> one you propose may be interesting in questions related to, say, chemical >> reactivity. >> >> But apart from that, it is not quite clear to me how you would go about >> computing such an origin. Computing the electron density due to the valence >> orbitals on a grid? Or do you have another idea in mind? Maybe something >> related to Hirshfelds' free atom densities? >> >> Heribert >> >> >> On Tue, May 7, 2013 at 8:53 PM, John McKelvey jmmckel===gmail.com < >> owner-chemistry!^!ccl.net> wrote: >> >>> Hello, >>> >>> Perhaps there is another way to look at it, and it is a subset of >>> looking at the center of nuclear charge. Perhaps it is more sensitive (?) >>> to look at the center of constituent free atom valence electrons? >>> >>> John McKelvey >>> >>> >>> On Tue, May 7, 2013 at 12:26 PM, Reis Heribert hreis_-_eie.gr < >>> owner-chemistry/./ccl.net> wrote: >>> >>>> Hello >>>> >>>> The definition of the dipole moment of a charged species is well >>>> defined. The only problem with it (and with all higher multipoles) is, that >>>> its value depends on the origin of the coordinate system. Thus for >>>> comparison purposes the origin of the coordinate system of different >>>> molecules should be comparable. A very common choice is the centre of mass; >>>> another possibility is the center of nuclear charge, which is the standard >>>> origin in Gaussian09, if one does not specify the 'Nosymm' keyword. You can >>>> also turn the problem on its head and define the origin as that point where >>>> the dipole is zero... >>>> >>>> I'm assuming that you want to compare the absolute value of the dipole >>>> between different molecules. In case you also want to compare the >>>> components, you also should use comparable orientations of the coordinate >>>> systems (e.g the coordinate system where e.g. the inertia (or >>>> polarizability or ...) tensor is diagonal). This, however, is independent >>>> of being charged or uncharged. >>>> >>>> Heribert >>>> >>> >>> >>> >>> -- >>> John McKelvey >>> 10819 Middleford Pl >>> Ft Wayne, IN 46818 >>> 260-489-2160 >>> jmmckel/./gmail.com >>> >> >> > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel###gmail.com > --047d7b676476df0aeb04dc395f86 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
John,

Just to make sure I understa= nd your procedure correctly: you assign the valence electrons of each atom = to the position of the nucleus of that atom in the molecule and then comput= e the center of those charges? That's interesting, but what about ions?=

Heribert


On Wed,= May 8, 2013 at 5:15 PM, John McKelvey jmmckel%gmail.com <owner-chemistry],[ccl.net> wrote:
Heribert,

Thanks for your comment.=A0 I'm not familiar with Hirschfelds approach= , but I could be doing something related. =A0

I could have better stated my approach.=A0 Instead of using atomic mass= , or atomic core charge, I use the "atomic valence=A0 shell" core= charge, i.e. the number of valence electrons a given neutral atom *typical= ly* contributes to a molecule.=A0=A0=A0 Occasionally I omit the hydrogen va= lence-electron=A0=A0=A0=A0 core.

Before people using VDW surface type of solvation, i.e. PVM or COSMO, n= on spherical molecules, say iodo-benzene, the center-of-mass could have a p= ortion of charge outside an ellipse or spherical cavity.=A0 Using the valen= ce-core-charge minimized this issue, and with respect core electrons, it is= the valence electron shifts that shift shift around most.=A0
=A0


On Wed, May 8, 2013 at 7:58 AM, Reis Heribert hreis:_:eie.gr <= owner-ch= emistry###ccl.net> wrote:
Hello John,

In my opinion the choice of the origin for = multipoles is most of the time just a matter of what one is trying to inves= tigate. So a choice like the one you propose may be interesting in question= s related to, say, chemical reactivity.

But apart from that, it is not quite clear to me how you would go about= computing such an origin. Computing the electron density due to the valenc= e orbitals on a grid? Or do you have another idea in mind? Maybe something = related to Hirshfelds' free atom densities?

Heribert


On Tue, May 7, 2013 at 8:53 PM, John= McKelvey jmmckel=3D=3D=3Dgm= ail.com <owner-chemistry!^!ccl.net> wrote:
Hello,

Perhaps there is another way to look at it, and = it is a subset of looking at the center of nuclear charge.=A0 Perhaps it is= more sensitive (?) to look at the center of=A0 constituent free atom valen= ce electrons?

John McKelvey


On Tue, May 7, 2013 a= t 12:26 PM, Reis Heribert hreis_-_eie.gr <owner-chemistry/./ccl.net> wr= ote:
Hello
The definition of the dipole moment of a charged species is well def= ined. The only problem with it (and with all higher multipoles) is, that it= s value depends on the origin of the coordinate system. Thus for comparison= purposes the origin of the coordinate system of different molecules should= be comparable. A very common choice is the centre of mass; another possibi= lity is the center of nuclear charge, which is the standard origin in Gauss= ian09, if one does not specify the 'Nosymm' keyword. You can also t= urn the problem on its head and define the origin as that point where the d= ipole is zero...

I'm assuming that you want to compare the absolute value of t= he dipole between different molecules. In case you also want to compare the= components, you also should use comparable orientations of the coordinate = systems (e.g the coordinate system where e.g. the inertia (or polarizabilit= y or ...) tensor is diagonal). This, however, is independent of being charg= ed or uncharged.

Heribert



=
--
John McKelvey
10819 Middleford= Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel/./gm= ail.com




--
John = McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel###g= mail.com

--047d7b676476df0aeb04dc395f86-- From owner-chemistry@ccl.net Wed May 8 17:22:00 2013 From: "John McKelvey jmmckel#%#gmail.com" To: CCL Subject: CCL:G: Dipole moment of charged species in Gaussian Message-Id: <-48660-130508172111-32258-TSV2hu6xlMayg7/XHIT1vQ^-^server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001a11c33d14d11ec104dc3b82ea Date: Wed, 8 May 2013 17:21:02 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel a gmail.com] --001a11c33d14d11ec104dc3b82ea Content-Type: text/plain; charset=ISO-8859-1 Hi!, No, not the number of electrons "per-se" but what would be the charge on each neutral constituent atom with all valence electrons removed, i.e. 4 for C, 5 for N, etc, regardless of the molecular charge. John On Wed, May 8, 2013 at 2:48 PM, Reis Heribert hreis]|[eie.gr < owner-chemistry++ccl.net> wrote: > John, > > Just to make sure I understand your procedure correctly: you assign the > valence electrons of each atom to the position of the nucleus of that atom > in the molecule and then compute the center of those charges? That's > interesting, but what about ions? > > Heribert > > > On Wed, May 8, 2013 at 5:15 PM, John McKelvey jmmckel%gmail.com < > owner-chemistry%%ccl.net > wrote: > >> Heribert, >> >> Thanks for your comment. I'm not familiar with Hirschfelds approach, but >> I could be doing something related. >> >> I could have better stated my approach. Instead of using atomic mass, or >> atomic core charge, I use the "atomic valence shell" core charge, i.e. the >> number of valence electrons a given neutral atom *typically* contributes to >> a molecule. Occasionally I omit the hydrogen valence-electron core. >> >> Before people using VDW surface type of solvation, i.e. PVM or COSMO, non >> spherical molecules, say iodo-benzene, the center-of-mass could have a >> portion of charge outside an ellipse or spherical cavity. Using the >> valence-core-charge minimized this issue, and with respect core electrons, >> it is the valence electron shifts that shift shift around most. >> >> >> >> On Wed, May 8, 2013 at 7:58 AM, Reis Heribert hreis:_:eie.gr < >> owner-chemistry###ccl.net> wrote: >> >>> Hello John, >>> >>> In my opinion the choice of the origin for multipoles is most of the >>> time just a matter of what one is trying to investigate. So a choice like >>> the one you propose may be interesting in questions related to, say, >>> chemical reactivity. >>> >>> But apart from that, it is not quite clear to me how you would go about >>> computing such an origin. Computing the electron density due to the valence >>> orbitals on a grid? Or do you have another idea in mind? Maybe something >>> related to Hirshfelds' free atom densities? >>> >>> Heribert >>> >>> >>> On Tue, May 7, 2013 at 8:53 PM, John McKelvey jmmckel===gmail.com < >>> owner-chemistry!^!ccl.net> wrote: >>> >>>> Hello, >>>> >>>> Perhaps there is another way to look at it, and it is a subset of >>>> looking at the center of nuclear charge. Perhaps it is more sensitive (?) >>>> to look at the center of constituent free atom valence electrons? >>>> >>>> John McKelvey >>>> >>>> >>>> On Tue, May 7, 2013 at 12:26 PM, Reis Heribert hreis_-_eie.gr < >>>> owner-chemistry/./ccl.net> wrote: >>>> >>>>> Hello >>>>> >>>>> The definition of the dipole moment of a charged species is well >>>>> defined. The only problem with it (and with all higher multipoles) is, that >>>>> its value depends on the origin of the coordinate system. Thus for >>>>> comparison purposes the origin of the coordinate system of different >>>>> molecules should be comparable. A very common choice is the centre of mass; >>>>> another possibility is the center of nuclear charge, which is the standard >>>>> origin in Gaussian09, if one does not specify the 'Nosymm' keyword. You can >>>>> also turn the problem on its head and define the origin as that point where >>>>> the dipole is zero... >>>>> >>>>> I'm assuming that you want to compare the absolute value of the dipole >>>>> between different molecules. In case you also want to compare the >>>>> components, you also should use comparable orientations of the coordinate >>>>> systems (e.g the coordinate system where e.g. the inertia (or >>>>> polarizability or ...) tensor is diagonal). This, however, is independent >>>>> of being charged or uncharged. >>>>> >>>>> Heribert >>>>> >>>> >>>> >>>> >>>> -- >>>> John McKelvey >>>> 10819 Middleford Pl >>>> Ft Wayne, IN 46818 >>>> 260-489-2160 >>>> jmmckel/./gmail.com >>>> >>> >>> >> >> >> -- >> John McKelvey >> 10819 Middleford Pl >> Ft Wayne, IN 46818 >> 260-489-2160 >> jmmckel###gmail.com >> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel++gmail.com --001a11c33d14d11ec104dc3b82ea Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi!,

No, not the number of electron= s "per-se" but what would be the charge on each neutral constitue= nt atom with all valence electrons removed,=A0 i.e. 4 for C, 5 for N, etc, = regardless of the molecular charge.

John


On Wed, May 8, 2013 at 2:48 PM, Reis Heribert hreis]|[eie.gr <owner-chemistry++ccl.net> w= rote:
John,

Just to make sure I understand your procedure correctly: you assign the = valence electrons of each atom to the position of the nucleus of that atom = in the molecule and then compute the center of those charges? That's in= teresting, but what about ions?

Heribert


On Wed, May 8, 2013 at 5:15 PM, John McKelvey jmmckel%gmail.com <owner-chemist= ry%%ccl.net> wrote:
Heribert,

Thanks for your comment.=A0 I'm not familiar w= ith Hirschfelds approach, but I could be doing something related. =A0

I could have better stated my approach.=A0 Instead of using atomic mass= , or atomic core charge, I use the "atomic valence=A0 shell" core= charge, i.e. the number of valence electrons a given neutral atom *typical= ly* contributes to a molecule.=A0=A0=A0 Occasionally I omit the hydrogen va= lence-electron=A0=A0=A0=A0 core.

Before people using VDW surface type of solvation, i.e. PVM or COSMO, n= on spherical molecules, say iodo-benzene, the center-of-mass could have a p= ortion of charge outside an ellipse or spherical cavity.=A0 Using the valen= ce-core-charge minimized this issue, and with respect core electrons, it is= the valence electron shifts that shift shift around most.=A0
=A0


On Wed, May 8, 2013 at 7:58 AM, Reis Heribert= hreis:_:eie.gr <owner-chemistry###ccl.net> wrote:
Hello John,

In my opinion the choice of the= origin for multipoles is most of the time just a matter of what one is try= ing to investigate. So a choice like the one you propose may be interesting= in questions related to, say, chemical reactivity.

But apart from that, it is not quite clear to me how you would go about= computing such an origin. Computing the electron density due to the valenc= e orbitals on a grid? Or do you have another idea in mind? Maybe something = related to Hirshfelds' free atom densities?

Heribert


=
On Tue, May 7, 2013 at 8:= 53 PM, John McKelvey jmmckel=3D=3D=3Dgmail.com <owner-chemistry!^!ccl.net>= wrote:
Hello,

Perhaps there is another way to look= at it, and it is a subset of looking at the center of nuclear charge.=A0 P= erhaps it is more sensitive (?) to look at the center of=A0 constituent fre= e atom valence electrons?

John McKelvey


On Tue, Ma= y 7, 2013 at 12:26 PM, Reis Heribert hreis_-_eie.gr <owner-chemistry/./ccl.net>= ; wrote:
Hello
The definition of the dipole moment of a charged species is well def= ined. The only problem with it (and with all higher multipoles) is, that it= s value depends on the origin of the coordinate system. Thus for comparison= purposes the origin of the coordinate system of different molecules should= be comparable. A very common choice is the centre of mass; another possibi= lity is the center of nuclear charge, which is the standard origin in Gauss= ian09, if one does not specify the 'Nosymm' keyword. You can also t= urn the problem on its head and define the origin as that point where the d= ipole is zero...

I'm assuming that you want to compare the absolute value of t= he dipole between different molecules. In case you also want to compare the= components, you also should use comparable orientations of the coordinate = systems (e.g the coordinate system where e.g. the inertia (or polarizabilit= y or ...) tensor is diagonal). This, however, is independent of being charg= ed or uncharged.

Heribert



=
<= font color=3D"#888888">
--
John McKelvey
10819= Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmcke= l/./gmail.com




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




--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel++gmail.com --001a11c33d14d11ec104dc3b82ea-- From owner-chemistry@ccl.net Wed May 8 18:27:00 2013 From: "Val Gillet v.gillet.++.sheffield.ac.uk" To: CCL Subject: CCL: Sheffield Conference on Chemoinformatics: Registration Open Message-Id: <-48661-130508154329-8657-EDGcmBdDGcxuOgjYbhqXxw++server.ccl.net> X-Original-From: "Val Gillet" Date: Wed, 8 May 2013 15:43:28 -0400 Sent to CCL by: "Val Gillet" [v.gillet_._sheffield.ac.uk] *Sixth Joint Sheffield Conference on Chemoinformatics, The Edge, University of Sheffield, 22nd-24th July 2013* http://cisrg.shef.ac.uk/shef2013 Registration: Registration is now open with early bird discounts available until May 31st. Programme: The oral presentations are now listed. Note that there will also be a large number of high quality posters (details to be posted later). Exhibition booths are available for exhibiting organisations. For inquiries with regard to exhibiting at the conference, please contact the conference organisers at cheminf2013(_)sheffield.ac.uk. Organised on behalf of the Molecular Graphics and Modelling Society and the Chemical Structure Association Trust. From owner-chemistry@ccl.net Wed May 8 21:09:00 2013 From: "Anjan Roy aroy6|,|uic.edu" To: CCL Subject: CCL:G: Gausian 09 Easiest way to subtract structures/coordinates Message-Id: <-48662-130508155859-19420-0Sb+Gg2zYe5jj1z2sBK0jg[A]server.ccl.net> X-Original-From: "Anjan Roy" Date: Wed, 8 May 2013 15:58:57 -0400 Sent to CCL by: "Anjan Roy" [aroy6!^!uic.edu] Hello, My Gaussian 09 opimization returns a negative frequency, one solution suggested was to distort the molecule in the direction if the negative freq motion. Could someone kindly suggest how I can do this by subtracting structures in the command line or by way of a GUI. thank you Anjan