From owner-chemistry@ccl.net Tue Jan 6 00:38:01 2015 From: "Utpal Sarkar utpalchemiitkgp-.-gmail.com" To: CCL Subject: CCL: Assignment of electronic charges on different atoms Message-Id: <-50854-150106001940-23369-h6P+rXqnKPKWX/+o5pWWbA#,#server.ccl.net> X-Original-From: Utpal Sarkar Content-Type: multipart/alternative; boundary=001a1134d2289d9380050bf4f372 Date: Tue, 6 Jan 2015 10:49:30 +0530 MIME-Version: 1.0 Sent to CCL by: Utpal Sarkar [utpalchemiitkgp#%#gmail.com] --001a1134d2289d9380050bf4f372 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable But if an electron is attached fully (100%) to any atom of a molecule or functional group, then the porbablity of finding that electron in that region should be ONE if and only if that electron is bound by infinite potential. But is there any existence of infinite potential within a molecule? utpal On Mon, Jan 5, 2015 at 4:17 PM, V=C3=ADctor Lua=C3=B1a Cabal victor** fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor() > fluor.quimica.uniovi.es] > On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp ~~ > gmail.com wrote: > > How do you localize an electron at a specific point ? doesn't it > contradict > > uncertainty principle? > > Why do you identify an aton with a point? > First, you can use QTAIM to assign a charge > to an atom of a functional group. > There are other possibilities of localization too. > > Do you need/want references? > > Regards, > Dr. V=C3=ADctor Lua=C3=B1a > > -- > \|/a "Have no fear of perfection, you will never attain it!" > |^.^| "No tengas miedo de la perfecci=C3=B3n, nunca la alcanzar=C3= =A1s" > +-!OO--\_/--OO!--------------------------------+---------------------- > ! Dr.V=C3=ADctor Lua=C3=B1a ! (Salvador Dal= =C3=AD) > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor * fluor.quimica.uniovi.es ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +----------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a1134d2289d9380050bf4f372 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

But if an electron is attached fully (100%) to any at= om of a molecule or functional group, then the porbablity of finding that e= lectron=C2=A0in=C2=A0that region should be ONE if and only if that electron= is bound by infinite potential. =C2=A0=C2=A0But is there any existence of = infinite potential within a molecule?

utpal

<= div>=C2=A0=C2=A0

On Mon, Jan 5, 2015 at 4:17 PM, V=C3=ADctor Lua=C3=B1a Cabal vic= tor**fluor.quimica.uniovi.es= <owner-chemistry-*-ccl.net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor() <= a href=3D"http://fluor.quimica.uniovi.es" target=3D"_blank">fluor.quimica.u= niovi.es]
On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp ~~ <= a href=3D"http://gmail.com" target=3D"_blank">gmail.com wrote:
> How do you localize an electron at a specific point ? doesn't it c= ontradict
> uncertainty principle?

Why do you identify an aton with a point?
First, you can use QTAIM to assign a charge
to an atom of a functional group.
There are other possibilities of localization too.

Do you need/want references?

Regards,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua=C3=B1a

--
=C2=A0 =C2=A0 =C2=A0 =C2=A0\|/a=C2=A0 "Have no fear of perfection, you= will never attain it!"
=C2=A0 =C2=A0 =C2=A0 |^.^|=C2=A0 "No tengas miedo de la perfecci=C3=B3= n, nunca la alcanzar=C3=A1s"
+-!OO--\_/--OO!--------------------------------+----------------------
!=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr.V=C3=ADctor Lua=C3=B1a=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0! (Salvador D= al=C3=AD)
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica=C2=A0 =C2=A0! ! Universidad de Oviedo, 33006-Oviedo, Spain=C2=A0 =C2=A0!
! e-mail:=C2=A0 =C2=A0victor * fluor.quimica.uniovi.es=C2=A0 =C2=A0 =C2=A0!
! phone: +34-985-103491=C2=A0 fax: +34-985-103125=C2=A0 =C2=A0!
+----------------------------------------------+
=C2=A0GroupPage : http://azufre.quimica.uniovi.es/=C2=A0 (being reworked)

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--001a1134d2289d9380050bf4f372-- From owner-chemistry@ccl.net Tue Jan 6 06:56:00 2015 From: "Partha Sengupta anapspsmo%%gmail.com" To: CCL Subject: CCL:G: Assignment of electronic charges on different atoms Message-Id: <-50855-150106065504-20759-bDNXHchLbTzCaChYSw15RA!A!server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=001a11c2a5c4dfa5d2050bfa79ce Date: Tue, 6 Jan 2015 17:24:57 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo!^!gmail.com] --001a11c2a5c4dfa5d2050bfa79ce Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable In Density Functional calculation with Gaussian 09W, I want to assign certain charge assigned on different atom For the determination of hyperpolarizablity/optimized/non optimized parameter of a molecular system we get the Mulliken atomic charges: like 1 1 N -0.627468 2 C -0.089856 3 C -0.123465 4 C -0.188188 5 C -0.269616 .... etc. In the same way, is it possible to assign the charges on the atoms according to users choice (my choice) as a command 1 1 N -0.727468 2 C -0.009856 3 C -0.123465 4 C -0.188188 5 C -0.269616 Here the charge of N is changed from -0.627468 to -0727468. Does it Possible within the frame work of Gaussian 09W? On Tue, Jan 6, 2015 at 10:49 AM, Utpal Sarkar utpalchemiitkgp-.-gmail.com < owner-chemistry===ccl.net> wrote: > But if an electron is attached fully (100%) to any atom of a molecule or > functional group, then the porbablity of finding that electron in that > region should be ONE if and only if that electron is bound by infinite > potential. But is there any existence of infinite potential within a > molecule? > utpal > > > > On Mon, Jan 5, 2015 at 4:17 PM, V=C3=ADctor Lua=C3=B1a Cabal victor** > fluor.quimica.uniovi.es wrote: > >> >> Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor(= ) >> fluor.quimica.uniovi.es] >> On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp ~= ~ >> gmail.com wrote: >> > How do you localize an electron at a specific point ? doesn't it >> contradict >> > uncertainty principle? >> >> Why do you identify an aton with a point? >> First, you can use QTAIM to assign a charge >> to an atom of a functional group. >> There are other possibilities of localization too. >> >> Do you need/want references? >> >> Regards, >> Dr. V=C3=ADctor Lua=C3=B1a >> >> -- >> \|/a "Have no fear of perfection, you will never attain it!" >> |^.^| "No tengas miedo de la perfecci=C3=B3n, nunca la alcanzar= =C3=A1s" >> +-!OO--\_/--OO!--------------------------------+---------------------- >> ! Dr.V=C3=ADctor Lua=C3=B1a ! (Salvador Dal= =C3=AD) >> ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! >> ! Universidad de Oviedo, 33006-Oviedo, Spain ! >> ! e-mail: victor * fluor.quimica.uniovi.es ! >> ! phone: +34-985-103491 fax: +34-985-103125 ! >> +----------------------------------------------+ >> GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY*|*ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST*|*ccl.net or use>> >> >> > --=20 Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --001a11c2a5c4dfa5d2050bfa79ce Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

In Density Functional calculation with Gaus= sian 09W,=C2=A0 I want to assign certain charge assigned on different atom =

For the determination of hyperpolarizablity/optimized/no= n optimized parameter=C2=A0 of a molecular system we get the Mulliken atomi= c charges: like
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 1
=C2=A0=C2=A0=C2=A0=C2=A0 1=C2=A0 N=C2=A0=C2= =A0 -0.627468
=C2=A0=C2=A0=C2=A0=C2=A0 2=C2=A0 C=C2=A0=C2=A0 -0.089856=C2=A0=C2=A0=C2=A0=C2=A0 3=C2=A0 C=C2=A0=C2=A0 -0.123465
=C2=A0=C2=A0= =C2=A0=C2=A0 4=C2=A0 C=C2=A0=C2=A0 -0.188188
=C2=A0=C2=A0=C2=A0=C2=A0 5= =C2=A0 C=C2=A0=C2=A0 -0.269616
....

etc.

In the same = way, is it possible to assign

the charges on the atoms according = to users choice (my choice) as a command=C2=A0
1
=C2=A0=C2=A0=C2=A0= =C2=A0 1=C2=A0 N=C2=A0=C2=A0 -0.727468
=C2=A0=C2=A0=C2=A0=C2=A0 2=C2=A0 = C=C2=A0=C2=A0 -0.009856
=C2=A0=C2=A0=C2=A0=C2=A0 3=C2=A0 C=C2=A0=C2=A0 -= 0.123465
=C2=A0=C2=A0=C2=A0=C2=A0 4=C2=A0 C=C2=A0=C2=A0 -0.188188
=C2= =A0=C2=A0=C2=A0=C2=A0 5=C2=A0 C=C2=A0=C2=A0 -0.269616

Here the cha= rge of N is changed from -0.627468 to -0727468.

Does it Possible w= ithin the frame work of Gaussian 09W?

On Tue, Jan 6, 2015 at 10:49 AM, Ut= pal Sarkar utpalchemiitkgp-.-gmail.com <owner-chemistry===ccl.net> wrote:

But if an electron is attached fully (100%)= to any atom of a molecule or functional group, then the porbablity of find= ing that electron=C2=A0in=C2=A0that region should be ONE if and only if tha= t electron is bound by infinite potential. =C2=A0=C2=A0But is there any exi= stence of infinite potential within a molecule?
utpal
<= br>
=C2=A0=C2=A0

On Mon, Jan 5, 2015 at 4:17 PM, V=C3= =ADctor Lua=C3=B1a Cabal victor**fluor.quimica.uniovi.es <owner-chemistry*= |*ccl.net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor() <= a href=3D"http://fluor.quimica.uniovi.es" target=3D"_blank">fluor.quimica.u= niovi.es]
On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp ~~ <= a href=3D"http://gmail.com" target=3D"_blank">gmail.com wrote:
> How do you localize an electron at a specific point ? doesn't it c= ontradict
> uncertainty principle?

Why do you identify an aton with a point?
First, you can use QTAIM to assign a charge
to an atom of a functional group.
There are other possibilities of localization too.

Do you need/want references?

Regards,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua=C3=B1a

--
=C2=A0 =C2=A0 =C2=A0 =C2=A0\|/a=C2=A0 "Have no fear of perfection, you= will never attain it!"
=C2=A0 =C2=A0 =C2=A0 |^.^|=C2=A0 "No tengas miedo de la perfecci=C3=B3= n, nunca la alcanzar=C3=A1s"
+-!OO--\_/--OO!--------------------------------+----------------------
!=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr.V=C3=ADctor Lua=C3=B1a=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0! (Salvador D= al=C3=AD)
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica=C2=A0 =C2=A0! ! Universidad de Oviedo, 33006-Oviedo, Spain=C2=A0 =C2=A0!
! e-mail:=C2=A0 =C2=A0victor * fluor.quimica.uniovi.es=C2=A0 =C2=A0 =C2=A0!
! phone: +34-985-103491=C2=A0 fax: +34-985-103125=C2=A0 =C2=A0!
+----------------------------------------------+
=C2=A0GroupPage : http://azufre.quimica.uniovi.es/=C2=A0 (being reworked)

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY*|*ccl.net or use:
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Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda M= ahavidyalaya, Burdwan

--001a11c2a5c4dfa5d2050bfa79ce-- From owner-chemistry@ccl.net Tue Jan 6 07:31:01 2015 From: "Partha Sengupta anapspsmo~!~gmail.com" To: CCL Subject: CCL: Assignment of electronic charges on different atoms Message-Id: <-50856-150106065540-20884-OJSpghFBbmnSkXBjUNEsyQ%%server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=001a11c3d124129e42050bfa7cfa Date: Tue, 6 Jan 2015 17:25:34 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo++gmail.com] --001a11c3d124129e42050bfa7cfa Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable For the determination of hyperpolarizablity/optimized parameter of a molecular system we get the Mulliken atomic charges: like 1 1 N -0.627468 2 C -0.089856 3 C -0.123465 4 C -0.188188 5 C -0.269616 .... etc. In the same way, is it possible to assign the charges on the atoms according to users choice as a command 1 1 N -0.727468 2 C -0.009856 3 C -0.123465 4 C -0.188188 5 C -0.269616 On Mon, Jan 5, 2015 at 11:29 PM, Partha Sengupta wrote: > Sir, I want to know the structural deformation of drug molecule working i= n > the synaptic node. > I really need the references. > I have no knowledge about > *QTAIM .* > > *Please clarify that.* > > *Sincerely,* > *Partha * > > On Mon, Jan 5, 2015 at 4:17 PM, V=C3=ADctor Lua=C3=B1a Cabal victor** > fluor.quimica.uniovi.es wrote: > >> >> Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor(= ) >> fluor.quimica.uniovi.es] >> On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp ~= ~ >> gmail.com wrote: >> > How do you localize an electron at a specific point ? doesn't it >> contradict >> > uncertainty principle? >> >> Why do you identify an aton with a point? >> First, you can use QTAIM to assign a charge >> to an atom of a functional group. >> There are other possibilities of localization too. >> >> Do you need/want references? >> >> Regards, >> Dr. V=C3=ADctor Lua=C3=B1a >> >> -- >> \|/a "Have no fear of perfection, you will never attain it!" >> |^.^| "No tengas miedo de la perfecci=C3=B3n, nunca la alcanzar= =C3=A1s" >> +-!OO--\_/--OO!--------------------------------+---------------------- >> ! Dr.V=C3=ADctor Lua=C3=B1a ! (Salvador Dal= =C3=AD) >> ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! >> ! Universidad de Oviedo, 33006-Oviedo, Spain ! >> ! e-mail: victor * fluor.quimica.uniovi.es ! >> ! phone: +34-985-103491 fax: +34-985-103125 ! >> +----------------------------------------------+ >> GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D->> >> >> > > > -- > Dr. Partha Sarathi Sengupta > Associate Professor > Vivekananda Mahavidyalaya, Burdwan > --=20 Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --001a11c3d124129e42050bfa7cfa Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

For the determination of hyperpolarizablity= /optimized parameter=C2=A0 of a molecular system we get the Mulliken atomic= charges: like
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 1
=C2=A0=C2=A0=C2=A0=C2=A0 1=C2=A0 N=C2=A0=C2=A0 -= 0.627468
=C2=A0=C2=A0=C2=A0=C2=A0 2=C2=A0 C=C2=A0=C2=A0 -0.089856
=C2= =A0=C2=A0=C2=A0=C2=A0 3=C2=A0 C=C2=A0=C2=A0 -0.123465
=C2=A0=C2=A0=C2=A0= =C2=A0 4=C2=A0 C=C2=A0=C2=A0 -0.188188
=C2=A0=C2=A0=C2=A0=C2=A0 5=C2=A0 = C=C2=A0=C2=A0 -0.269616
....

etc.

In the same way, is= it possible to assign

the charges on the atoms according to user= s choice as a command=C2=A0
1
=C2=A0=C2=A0=C2=A0=C2=A0 1=C2=A0 N=C2= =A0=C2=A0 -0.727468
=C2=A0=C2=A0=C2=A0=C2=A0 2=C2=A0 C=C2=A0=C2=A0 -0.00= 9856
=C2=A0=C2=A0=C2=A0=C2=A0 3=C2=A0 C=C2=A0=C2=A0 -0.123465
=C2=A0= =C2=A0=C2=A0=C2=A0 4=C2=A0 C=C2=A0=C2=A0 -0.188188
=C2=A0=C2=A0=C2=A0=C2= =A0 5=C2=A0 C=C2=A0=C2=A0 -0.269616

On Mon, Jan 5, 2015 at 11:29 PM, Partha Sen= gupta <anapspsmo]~[gmail.com> wrote:

Sir, I want to know= the structural deformation of drug molecule working in the synaptic node.<= br>
I really need the references.
I have no knowledge about= =C2=A0QTAIM .
Please clarify that.
Since= rely,
Partha

On Mon, Jan 5, 2015 at 4:= 17 PM, V=C3=ADctor Lua=C3=B1a Cabal victor**fluor.quimica.uniovi.es <owner-che= mistry]~[ccl.net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor() <= a href=3D"http://fluor.quimica.uniovi.es" target=3D"_blank">fluor.quimica.u= niovi.es]
On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp ~~ <= a href=3D"http://gmail.com" target=3D"_blank">gmail.com wrote:
> How do you localize an electron at a specific point ? doesn't it c= ontradict
> uncertainty principle?

Why do you identify an aton with a point?
First, you can use QTAIM to assign a charge
to an atom of a functional group.
There are other possibilities of localization too.

Do you need/want references?

Regards,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua=C3=B1a

--
=C2=A0 =C2=A0 =C2=A0 =C2=A0\|/a=C2=A0 "Have no fear of perfection, you= will never attain it!"
=C2=A0 =C2=A0 =C2=A0 |^.^|=C2=A0 "No tengas miedo de la perfecci=C3=B3= n, nunca la alcanzar=C3=A1s"
+-!OO--\_/--OO!--------------------------------+----------------------
!=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr.V=C3=ADctor Lua=C3=B1a=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0! (Salvador D= al=C3=AD)
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica=C2=A0 =C2=A0! ! Universidad de Oviedo, 33006-Oviedo, Spain=C2=A0 =C2=A0!
! e-mail:=C2=A0 =C2=A0victor * fluor.quimica.uniovi.es=C2=A0 =C2=A0 =C2=A0!
! phone: +34-985-103491=C2=A0 fax: +34-985-103125=C2=A0 =C2=A0!
+----------------------------------------------+
=C2=A0GroupPage : http://azufre.quimica.uniovi.es/=C2=A0 (being reworked)

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY]~[ccl.net or use:
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--
Dr. Partha Sarathi Sengupta
Ass= ociate Professor
Vivekananda Mahavidyalaya, Burdwan

Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda M= ahavidyalaya, Burdwan

--001a11c3d124129e42050bfa7cfa-- From owner-chemistry@ccl.net Tue Jan 6 08:06:01 2015 From: "Jean Jules Fifen julesfifen\a/gmail.com" To: CCL Subject: CCL:G: Assignment of electronic charges on different atoms Message-Id: <-50857-150106074040-12890-cAxdac+z2cmC44+ppphDfg/./server.ccl.net> X-Original-From: Jean Jules Fifen Content-Type: multipart/alternative; boundary=20cf301b67c90b4f2c050bfb1dd4 Date: Tue, 6 Jan 2015 13:40:35 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules Fifen [julesfifen[A]gmail.com] --20cf301b67c90b4f2c050bfb1dd4 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable It is not possible because the electron is delocalized within the molecule. Even though you do this, after optimization, the appropriate charge will be assigned instead. Regards, On Tue, Jan 6, 2015 at 12:54 PM, Partha Sengupta anapspsmo%%gmail.com < owner-chemistry() ccl.net> wrote: > In Density Functional calculation with Gaussian 09W, I want to assign > certain charge assigned on different atom > For the determination of hyperpolarizablity/optimized/non optimized > parameter of a molecular system we get the Mulliken atomic charges: like > 1 > 1 N -0.627468 > 2 C -0.089856 > 3 C -0.123465 > 4 C -0.188188 > 5 C -0.269616 > .... > etc. > In the same way, is it possible to assign > the charges on the atoms according to users choice (my choice) as a > command > 1 > 1 N -0.727468 > 2 C -0.009856 > 3 C -0.123465 > 4 C -0.188188 > 5 C -0.269616 > Here the charge of N is changed from -0.627468 to -0727468. > Does it Possible within the frame work of Gaussian 09W? > > > On Tue, Jan 6, 2015 at 10:49 AM, Utpal Sarkar utpalchemiitkgp-.-gmail.com > wrote: > >> But if an electron is attached fully (100%) to any atom of a molecule or >> functional group, then the porbablity of finding that electron in that >> region should be ONE if and only if that electron is bound by infinite >> potential. But is there any existence of infinite potential within a >> molecule? >> utpal >> >> >> >> On Mon, Jan 5, 2015 at 4:17 PM, V=C3=ADctor Lua=C3=B1a Cabal victor** >> fluor.quimica.uniovi.es wrote: >> >>> >>> Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor= () >>> fluor.quimica.uniovi.es] >>> On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp >>> ~~ gmail.com wrote: >>> > How do you localize an electron at a specific point ? doesn't it >>> contradict >>> > uncertainty principle? >>> >>> Why do you identify an aton with a point? >>> First, you can use QTAIM to assign a charge >>> to an atom of a functional group. >>> There are other possibilities of localization too. >>> >>> Do you need/want references? >>> >>> Regards, >>> Dr. V=C3=ADctor Lua=C3=B1a >>> >>> -- >>> \|/a "Have no fear of perfection, you will never attain it!" >>> |^.^| "No tengas miedo de la perfecci=C3=B3n, nunca la alcanzar= =C3=A1s" >>> +-!OO--\_/--OO!--------------------------------+---------------------- >>> ! Dr.V=C3=ADctor Lua=C3=B1a ! (Salvador Da= l=C3=AD) >>> ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! >>> ! Universidad de Oviedo, 33006-Oviedo, Spain ! >>> ! e-mail: victor * fluor.quimica.uniovi.es ! >>> ! phone: +34-985-103491 fax: +34-985-103125 ! >>> +----------------------------------------------+ >>> GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) >>> >>> >>> >>> -=3D This is automatically added to each message by the mailing script = =3D- >>> E-mail to subscribers: CHEMISTRY*|*ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST*|*ccl.net or use>>> >>> >>> >> > > > -- > Dr. Partha Sarathi Sengupta > Associate Professor > Vivekananda Mahavidyalaya, Burdwan > --=20 Jean Jules FIFEN --20cf301b67c90b4f2c050bfb1dd4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

It is not possible because the electron is d=
elocalized within the molecule.

Even though you do t=
his, after optimization, the appropriate charge will be assigned instead.

Regards,

On Tue, Jan 6, 2015 at 12:54 PM, Partha Se= ngupta anapspsmo%%gmail.com <owner-= chemistry() ccl.net> wrote:

<= div dir=3D"ltr">
In Density Functional calculation with Gauss= ian 09W,=C2=A0 I want to assign certain charge assigned on different atom <= br>
For the determination of hyperpolarizablity/optimized/non= optimized parameter=C2=A0 of a molecular system we get the Mulliken atomic= charges: like
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 1
=C2=A0=C2=A0=C2=A0=C2=A0 1=C2=A0 N=C2=A0=C2=A0 -= 0.627468
=C2=A0=C2=A0=C2=A0=C2=A0 2=C2=A0 C=C2=A0=C2=A0 -0.089856
=C2= =A0=C2=A0=C2=A0=C2=A0 3=C2=A0 C=C2=A0=C2=A0 -0.123465
=C2=A0=C2=A0=C2=A0= =C2=A0 4=C2=A0 C=C2=A0=C2=A0 -0.188188
=C2=A0=C2=A0=C2=A0=C2=A0 5=C2=A0 = C=C2=A0=C2=A0 -0.269616
....
etc.
In the same way, is= it possible to assign
the charges on the atoms according to user= s choice (my choice) as a command=C2=A0
1
=C2=A0=C2=A0=C2=A0=C2=A0 = 1=C2=A0 N=C2=A0=C2=A0 -0.727468
=C2=A0=C2=A0=C2=A0=C2=A0 2=C2=A0 C=C2=A0= =C2=A0 -0.009856
=C2=A0=C2=A0=C2=A0=C2=A0 3=C2=A0 C=C2=A0=C2=A0 -0.12346= 5
=C2=A0=C2=A0=C2=A0=C2=A0 4=C2=A0 C=C2=A0=C2=A0 -0.188188
=C2=A0=C2= =A0=C2=A0=C2=A0 5=C2=A0 C=C2=A0=C2=A0 -0.269616
Here the charge of= N is changed from -0.627468 to -0727468.
Does it Possible within = the frame work of Gaussian 09W?

On Tue, Jan 6, 2015 at 10:49 AM, Utpal Sa= rkar utpalchemiitkgp-.-gmail= .com <owner-chemistry-*-ccl.net> wrote:

But if an electron is attac= hed fully (100%) to any atom of a molecule or functional group, then the po= rbablity of finding that electron=C2=A0in=C2=A0that region should be ONE if= and only if that electron is bound by infinite potential. =C2=A0=C2=A0But = is there any existence of infinite potential within a molecule?

u= tpal

=C2=A0=C2=A0

On Mon, Jan 5, 2015 at 4:17 PM, = V=C3=ADctor Lua=C3=B1a Cabal victor**fluor.quimica.uniovi.es <owner-chemis= try*|*ccl.net> wrote:

fluor.quimica.u= niovi.es]
On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp ~~ <= a href=3D"http://gmail.com" target=3D"_blank">gmail.com wrote:
> How do you localize an electron at a specific point ? doesn't it c= ontradict
> uncertainty principle?

Why do you identify an aton with a point?
First, you can use QTAIM to assign a charge
to an atom of a functional group.
There are other possibilities of localization too.

Do you need/want references?

Regards,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua=C3=B1a

--
=C2=A0 =C2=A0 =C2=A0 =C2=A0\|/a=C2=A0 "Have no fear of perfection, you= will never attain it!"
=C2=A0 =C2=A0 =C2=A0 |^.^|=C2=A0 "No tengas miedo de la perfecci=C3=B3= n, nunca la alcanzar=C3=A1s"
+-!OO--\_/--OO!--------------------------------+----------------------
!=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr.V=C3=ADctor Lua=C3=B1a=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0! (Salvador D= al=C3=AD)
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica=C2=A0 =C2=A0! ! Universidad de Oviedo, 33006-Oviedo, Spain=C2=A0 =C2=A0!
! e-mail:=C2=A0 =C2=A0victor * fluor.quimica.uniovi.es=C2=A0 =C2=A0 =C2=A0!
! phone: +34-985-103491=C2=A0 fax: +34-985-103125=C2=A0 =C2=A0!
+----------------------------------------------+
=C2=A0GroupPage : http://azufre.quimica.uniovi.es/=C2=A0 (being reworked)

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY*|*ccl.net or use:
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Dr. Partha Sarathi Sengupta
A= ssociate Professor
Vivekananda Mahavidyalaya, Burdwan

Jean Jules FIFEN

=C2=A0

--20cf301b67c90b4f2c050bfb1dd4-- From owner-chemistry@ccl.net Tue Jan 6 09:02:00 2015 From: "Kalyanashis Jana kalyan.chem.in*|*gmail.com" To: CCL Subject: CCL:G: Quantum Mechanical Tunneling Message-Id: <-50858-150106042723-4688-GJnmTvHm6J2K79ySz+UR4w() server.ccl.net> X-Original-From: "Kalyanashis Jana" Date: Tue, 6 Jan 2015 04:27:22 -0500 Sent to CCL by: "Kalyanashis Jana" [kalyan.chem.in*o*gmail.com] This is Kalyanashis Jana, working under Dr. B. Ganguly, CSIR-CSMCRI, Gujarat, India. I am interested to work on proton tunneling. I have installed Polyrate-2010 and Gaussrate-2009. I have run the polyrate-testrun files successfully. When I tried to run different input files, I could not run them. I got the following error. "gmake -s ../exe/polyrate2010-A.ch4o.serial.exe rm: cannot remove `esp.fu61': No such file or directory mv: cannot stat `poly.fu14': No such file or directory mv: cannot stat `poly.fu15': No such file or directory" Again, when I have tried to run the same input file (which has successfully run) from different directory, has not completed successfully. (Hessian recalculated *** mxlneq *** k = 1 at step k a gauss-jordan pivot value was zero) Can you please tell me, what does it exactly need to run a polyrate job ( except xx.dat and xx.jc files)?? I think, potential energy surface data required to calculate the polyrate job. How do I get potential energy surface data for an arbitrary reaction? I could able to run the gaussrate-testrun files. I has generated the "GRTEMPFILES" but the esp.fu82 file empty and the .fu6 file ended with Error searching Gaussian checkpoint file for gradient. Please help me.. From owner-chemistry@ccl.net Tue Jan 6 09:37:01 2015 From: "uekstrom/./gmail.com uekstrom/./gmail.com" To: CCL Subject: CCL: Any regrets open-sourcing your programs? Message-Id: <-50859-150106071327-28414-FgBBO3pa2QpcLDeJyx47FA]*[server.ccl.net> X-Original-From: "uekstrom^^^gmail.com" Content-Type: multipart/alternative; boundary=f46d043bdf142f444d050bfabb2a Date: Tue, 6 Jan 2015 13:13:13 +0100 MIME-Version: 1.0 Sent to CCL by: "uekstrom^^^gmail.com" [uekstrom^^^gmail.com] --f46d043bdf142f444d050bfabb2a Content-Type: text/plain; charset=UTF-8 Dear all, I am involved in a discussion about open source scientific software. Of course there are well known arguments on "both sides" in this debate. Is there anyone on CCL who regret publishing their code under an open source* license? Did it affect your scientific or commercial career negatively in any way? *) By open source I mean one of the well known licenses which have been examined by real lawyers. Regards, Ulf Ekstrom, University of Oslo --f46d043bdf142f444d050bfabb2a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear all,

I am involved in a discussion about open sou= rce scientific software. Of course there are well known arguments on "= both sides" in this debate. Is there anyone on CCL who regret publishi= ng their code under an open source* license? Did it affect your scientific = or commercial career negatively in any way?

*) By = open source I mean one of the well known licenses which have been examined = by real lawyers.=C2=A0

Regards,

Ulf Ekst= rom, University of Oslo

--f46d043bdf142f444d050bfabb2a-- From owner-chemistry@ccl.net Tue Jan 6 10:11:01 2015 From: "Marcel Swart marcel.swart#,#icrea.cat" To: CCL Subject: CCL: Assignment of electronic charges on different atoms Message-Id: <-50860-150106095108-21306-q/1HiNs5Wg21IDKrdsoXFA^^server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary="Apple-Mail=_3284C611-CD3B-44CF-9828-63797B8EB15A" Date: Tue, 6 Jan 2015 15:50:57 +0100 Mime-Version: 1.0 (Mac OS X Mail 8.1 \(1993\)) Sent to CCL by: Marcel Swart [marcel.swart]|[icrea.cat] --Apple-Mail=_3284C611-CD3B-44CF-9828-63797B8EB15A Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Partha, the answer is simple: No, you cannot. In more detail: Atomic charges are not observables, but are obtained through charge = analyses, that depend on the wave-function and/or charge density. These analyses = then assign a point charge to a specific point in space (usually the nuclei = of atoms), and that=E2=80=99s that. You cannot modify them, they are the result. The same happens with the energy, you calculate it (using QM, MM, or = ..), and when you have it, that=E2=80=99s the result. In both cases you cannot adjust it =E2=80=9Caccording to users = choice=E2=80=9D. The only thing you can do is have a look with different charge analyses, e.g. Mulliken, NBO, Hirshfeld, MDC-d, CHELPG, because each of them has its own benefits (and followers). Marcel > On 2015-01-06, at 12:55, Partha Sengupta anapspsmo~!~gmail.com = wrote: >=20 > For the determination of hyperpolarizablity/optimized parameter of a = molecular system we get the Mulliken atomic charges: like > 1 > 1 N -0.627468 > 2 C -0.089856 > 3 C -0.123465 > 4 C -0.188188 > 5 C -0.269616 > .... > etc.=20 > In the same way, is it possible to assign=20 > the charges on the atoms according to users choice as a command =20 > 1 > 1 N -0.727468 > 2 C -0.009856 > 3 C -0.123465 > 4 C -0.188188 > 5 C -0.269616 >=20 >=20 > On Mon, Jan 5, 2015 at 11:29 PM, Partha Sengupta = > wrote: > Sir, I want to know the structural deformation of drug molecule = working in the synaptic node. > I really need the references. > I have no knowledge about QTAIM . > Please clarify that. > Sincerely, > Partha=20 >=20 > On Mon, Jan 5, 2015 at 4:17 PM, V=C3=ADctor Lua=C3=B1a Cabal = victor**fluor.quimica.uniovi.es = > wrote: >=20 > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal = [victor() fluor.quimica.uniovi.es ] > On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp = ~~ gmail.com wrote: > > How do you localize an electron at a specific point ? doesn't it = contradict > > uncertainty principle? >=20 > Why do you identify an aton with a point? > First, you can use QTAIM to assign a charge > to an atom of a functional group. > There are other possibilities of localization too. >=20 > Do you need/want references? >=20 > Regards, > Dr. V=C3=ADctor Lua=C3=B1a >=20 > -- > \|/a "Have no fear of perfection, you will never attain it!" > |^.^| "No tengas miedo de la perfecci=C3=B3n, nunca la = alcanzar=C3=A1s" > +-!OO--\_/--OO!--------------------------------+---------------------- > ! Dr.V=C3=ADctor Lua=C3=B1a ! (Salvador = Dal=C3=AD) > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor * fluor.quimica.uniovi.es = ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +----------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ = (being reworked) >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- >=20 >=20 >=20 > E-mail to subscribers: CHEMISTRY_._ccl.net = or use:= >=20 > E-mail to administrators: CHEMISTRY-REQUEST_._ccl.net = or use= >=20= >=20= >=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ = >=20= >=20 >=20= >=20= >=20 >=20 >=20 >=20 >=20 > --=20 > Dr. Partha Sarathi Sengupta > Associate Professor > Vivekananda Mahavidyalaya, Burdwan >=20 >=20 >=20 > --=20 > Dr. Partha Sarathi Sengupta > Associate Professor > Vivekananda Mahavidyalaya, Burdwan =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 Prof. Dr. Marcel Swart ICREA Research Professor at Institut de Qu=C3=ADmica Computacional i Cat=C3=A0lisi Universitat de Girona Facultat de Ci=C3=A8ncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart~!~icrea.cat marcel.swart~!~udg.edu web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf =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 --Apple-Mail=_3284C611-CD3B-44CF-9828-63797B8EB15A Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Partha,

the= answer is simple: No, you cannot.

In more detail:

Atomic charges are not observables, but are obtained through = charge analyses,

that depend on the wave-function = and/or charge density. These analyses then

assign a = point charge to a specific point in space (usually the nuclei of = atoms),

and that=E2=80=99s that. You cannot modify = them, they are the result.

The same happens with = the energy, you calculate it (using QM, MM, or ..),

and when you have it, that=E2=80=99s the result.

In both cases you cannot = adjust it =E2=80=9Caccording to users choice=E2=80=9D.

The only thing you can = do is have a look with different charge analyses,

e.g. Mulliken, NBO, Hirshfeld, MDC-d, CHELPG, because each of = them

has its own benefits (and = followers).

Marcel

On 2015-01-06, at 12:55, Partha = Sengupta anapspsmo~!~gmail.com= <owner-chemistry~!~ccl.net> wrote:

For the = determination of hyperpolarizablity/optimized parameter of a = molecular system we get the Mulliken atomic charges: like
          &nb= sp;   1
     1 = N   -0.627468
     2 = C   -0.089856
     3 = C   -0.123465
     4 = C   -0.188188
     5 = C   -0.269616
....
etc.
In the same way, is it possible to assign
the charges on the atoms according to users choice as a = command
1
     = 1 N   -0.727468
     = 2 C   -0.009856
     = 3 C   -0.123465
     = 4 C   -0.188188
     = 5 C   -0.269616

On Mon, = Jan 5, 2015 at 11:29 PM, Partha Sengupta <anapspsmo_._gmail.com> wrote:
Sir, I want to know the structural = deformation of drug molecule working in the synaptic node.
I really need the references.
I = have no knowledge about QTAIM .
Please clarify that.
Sincerely,
Partha

On Mon, Jan 5, 2015 at 4:17 PM, = V=C3=ADctor Lua=C3=B1a Cabal victor**fluor.quimica.uniovi.es <owner-chemistry_._ccl.net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal = [victor() fluor.quimica.uniovi.es]
On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp = ~~ gmail.com wrote:
> How do you localize an electron at a specific point ? doesn't it = contradict
> uncertainty principle?

Why do you identify an aton with a point?
First, you can use QTAIM to assign a charge
to an atom of a functional group.
There are other possibilities of localization too.

Do you need/want references?

Regards,
Dr. V=C3=ADctor Lua=C3=B1a

--
\|/a "Have no fear of perfection, you = will never attain it!"
|^.^| "No tengas miedo de la perfecci=C3=B3n, = nunca la alcanzar=C3=A1s"
= +-!OO--\_/--OO!--------------------------------+----------------------
! Dr.V=C3=ADctor Lua=C3=B1a = ! = (Salvador Dal=C3=AD)
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica = !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail: victor * fluor.quimica.uniovi.es = !
! phone: +34-985-103491 fax: +34-985-103125 !
+----------------------------------------------+
GroupPage : http://azufre.quimica.uniovi.es/ = (being reworked)

-=3D This is automatically added to each message by the mailing script = =3D-

E-mail to subscribers: CHEMISTRY_._ccl.net or use:
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--
Dr. Partha Sarathi = Sengupta
Associate Professor
Vivekananda = Mahavidyalaya, Burdwan

--
Dr. Partha = Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan

=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
Prof. Dr. Marcel Swart

ICREA = Research Professor at
Institut de Qu=C3=ADmica = Computacional i Cat=C3=A0lisi
Universitat de Girona

Facultat de Ci=C3=A8ncies
Campus = Montilivi
17071 Girona
Catalunya (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mail
marcel.swart~!~icrea.cat
marcel.swart~!~udg.edu
web
http://www.marcelswart.eu
vCard

=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

= --Apple-Mail=_3284C611-CD3B-44CF-9828-63797B8EB15A-- From owner-chemistry@ccl.net Tue Jan 6 12:02:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor]*[fluor.quimica.uniovi.es" To: CCL Subject: CCL: Assignment of electronic charges on different atoms Message-Id: <-50861-150106114353-25665-9BGHuwkY1fveVVdk5+YRjQ-,-server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Tue, 06 Jan 2015 17:25:24 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor- -fluor.quimica.uniovi.es] On Mon, Jan 05, 2015 at 11:29:48PM +0530, Partha Sengupta anapspsmo*o*gmail.com wrote: > Sir, I want to know the structural deformation of drug molecule working in > the synaptic node. > I really need the references. > I have no knowledge about > *QTAIM .* QTAIM = Quantum Theory of Atoms in Molecules. The theory was initially developed by Richard F W Bader, a Canadian of familiar origin in the german part of Switzerland. The theory is nicely exposed in this book: R. F. W. Bader Atoms in Molecules. A Quantum Theory. Oxford University Press, 1990 A short description of the theory can be found in the In the wikipedia page you can find some more references to start with. The QTAIM community is in good help and growing. The aim behind QTAIM is that chemical bonding is nothing but the application of physics to explain the chemical properties. Some properties are simple to explain, some not so simple, but everything in chemistry is the result of the physical laws. In Spain, but not only, you can find a strong school of developers of QTAIM ideas. Best regards Dr. V�ctor Lua�a -- \|/a "After years of working on a problem the genius shout: |^.^| what an idiot I am ... the solution is trivial!' +-!OO--\_/--OO!--------------------------------+----------------------- ! Dr.V�ctor Lua�a ! ! Departamento de Qu�mica F�sica y Anal�tica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor#%#fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Tue Jan 6 12:37:01 2015 From: "Gilles Frapper gilles.frapper%univ-poitiers.fr" To: CCL Subject: CCL: DN-NSM 2015: 10th USPEX workshop + ES'PA 2015 / june, Poitiers, France Message-Id: <-50862-150106085649-12074-2vGP9xSDdykErxznrQ88Lw]~[server.ccl.net> X-Original-From: "Gilles Frapper" Date: Tue, 6 Jan 2015 08:56:48 -0500 Sent to CCL by: "Gilles Frapper" [gilles.frapper-x-univ-poitiers.fr] Dear friends, It is a pleasure to announce the 10th hands-on workshop on Crystal Structure Prediction and Materials Discovery with the USPEX code, which will take place in Poitiers University (France) on june 22-26, 2015. Morning sessions will consist of lectures by developers and advanced users of USPEX and some key figures in this field, whereas afternoons will be dedicated to hands-on exercises. Participants will have an opportunity to solve problems related to their research and to present their work. For beginners in periodic DFT we will hold a special three-day hands-on tutorials based both on the Vienna Ab initio Simulation Package code (VASP), and on the opensource and freeware QUANTUM ESPRESSO (QE). ES'PA 2015 - Electronic Structures: a Practical Approach - will take place in Poitiers University on june 18-20, 2015. DN-NSM 2015 - ES'PA + 10th USPEX workshop - will include an excursion to the Loire river (wine tasting, Fontevraud abbay, Castles...) and to others historical places in and around Poitiers. For summer day, The "Fte de la Musique" in Poitiers will celebrate the end of ES'PA 2015 and beginning of 10th USPEX! The DN-NSM 2015 international workshop is supported by Poitiers university, CNRS and Stony Brook University. Thanks to generous support, registration fees (inclusive of accommodation, meals and excursion) are low. For program and registration details, please see http://dnnsm2015.conference.univ-poitiers.fr. The number of seats is limited, so pre-register early! Gilles Frapper and Artem R. Oganov (organizers) P.S. For those who don't know, USPEX is a powerful code, enabling prediction of 3D (crystals), 2D (surfaces, interfaces, 2D-crystals), 1D (polymers) and 0D (clusters) structures by global optimization. It has unique efficiency, especially for large and complex systems. USPEX is used by more than 2100 researchers and several major companies, and is free for academic researchers. contact: dnnsm2015*gmail.com Website DN-NSM 2015 "Discovery of Novel Nanoparticles, Surfaces and bulk Materials": http://dnnsm2015.conference.univ-poitiers.fr USPEX site: http://uspex.stonybrook.edu From owner-chemistry@ccl.net Tue Jan 6 13:12:00 2015 From: "Breneman, Curt brenec^^^rpi.edu" To: CCL Subject: CCL: Assignment of electronic charges on different atoms Message-Id: <-50863-150106113140-20173-PWlqtuVU/ZAyH9JH3gU5EA|*|server.ccl.net> X-Original-From: "Breneman, Curt" Content-Language: en-US Content-Type: multipart/mixed; boundary="_004_00344A8866D0451EAEBB6A17DBBCB5D0rpiedu_" Date: Tue, 6 Jan 2015 16:31:32 +0000 MIME-Version: 1.0 Sent to CCL by: "Breneman, Curt" [brenec]|[rpi.edu] --_004_00344A8866D0451EAEBB6A17DBBCB5D0rpiedu_ Content-Type: multipart/alternative; boundary="_000_00344A8866D0451EAEBB6A17DBBCB5D0rpiedu_" --_000_00344A8866D0451EAEBB6A17DBBCB5D0rpiedu_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear Folks, Please note that QTAIM doesn=92t attempt to assign a location to any specif= ic electron(s), but rather is used to characterize electron density distrib= ution properties (including surfaces of zero net flux that separate atomic = basins) that allow electron populations to be assigned to atoms. When inte= grated electron populations within a basin are taken together with the atom= ic nuclear charges, the net charge within an atomic basin should not be con= fused with the results of point charge models, because the basins are not s= pherical within a molecular environment. When basin electron populations (= and their multipole moments) are combined with nuclear charges, the resulti= ng molecular dipoles=85etc will be accurate to the level of integration err= or. Cheers, Curt M. Breneman, Ph.D. Dean, School of Science Rensselaer Polytechnic Institute 110 8th St Troy, NY 12180-3590 Tel: (518) 276-6305 Fax (518) 276-4887 Email: brenec+*+rpi.edu [cid:77D52C07-AAAB-4311-8E42-432F7C974280] On Jan 6, 2015, at 12:19 AM, Utpal Sarkar utpalchemiitkgp-.-gmail.com

> wrot= e: But if an electron is attached fully (100%) to any atom of a molecule or fu= nctional group, then the porbablity of finding that electron in that region= should be ONE if and only if that electron is bound by infinite potential.= But is there any existence of infinite potential within a molecule? utpal On Mon, Jan 5, 2015 at 4:17 PM, V=EDctor Lua=F1a Cabal victor**fluor.quimic= a.uniovi.es

> wrote: Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor() f= luor.quimica.uniovi.es] On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp ~~ g= mail.com wrote: > How do you localize an electron at a specific point ? doesn't it contradi= ct > uncertainty principle? Why do you identify an aton with a point? First, you can use QTAIM to assign a charge to an atom of a functional group. There are other possibilities of localization too. Do you need/want references? Regards, Dr. V=EDctor Lua=F1a -- \|/a "Have no fear of perfection, you will never attain it!" |^.^| "No tengas miedo de la perfecci=F3n, nunca la alcanzar=E1s" +-!OO--\_/--OO!--------------------------------+---------------------- ! Dr.V=EDctor Lua=F1a ! (Salvador Dal=ED) ! Departamento de Qu=EDmica F=EDsica y Anal=EDtica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor * fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY*|*ccl.net or u= se:E-mail to administrators: CHEMISTRY-REQUEST*|*ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml Content-Transfer-Encoding: quoted-printable Dear Folks,

Please note that QTAIM doesn=92t attempt to assign a location to any s= pecific electron(s), but rather is used to characterize electron density di= stribution properties (including surfaces of zero net flux that separate at= omic basins) that allow electron populations to be assigned to atoms. When integrated electron populations within= a basin are taken together with the atomic nuclear charges, the net charge= within an atomic basin should not be confused with the results of point ch= arge models, because the basins are not spherical within a molecular environment. When basin electron popula= tions (and their multipole moments) are combined with nuclear charges, the = resulting molecular dipoles=85etc will be accurate to the level of integrat= ion error.

Cheers,

Curt M. Breneman, Ph.D.
Dean, School of Science
Rensselaer Polytechnic Institute
110 8th St
Troy, NY 12180-3590
Tel: (518) 276-6305
Fax (518) 276-4887
Email: brenec+*+rpi.edu

On Jan 6, 2015, at 12:19 AM, Utpal Sarkar utpalchemiitkgp-.-gmail.com <owner-chemistry+*+ccl.net> wrote:

But if an electron is attached fully (100%) to any atom of a molecule = or functional group, then the porbablity of finding that electron in&n= bsp;that region should be ONE if and only if that electron is bound by infi= nite potential. But is there any existence of infinite potential within a molecule?

utpal

On Mon, Jan 5, 2015 at 4:17 PM, V=EDctor Lua=F1a= Cabal victor**fluor.quimica.un= iovi.es <owner-chemistry*|*ccl.net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor() <= a href=3D"http://fluor.quimica.uniovi.es/" target=3D"_blank"> fluor.quimica.uniovi.es]
On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp = ~~ gmail.com wrote:
> How do you localize an electron at a specific point ? doesn't it contr= adict
> uncertainty principle?

Why do you identify an aton with a point?
First, you can use QTAIM to assign a charge
to an atom of a functional group.
There are other possibilities of localization too.

Do you need/want references?

Regards,
Dr. V=EDctor Lua=F1a

--
\|/a "Have no fear of perfection, you= will never attain it!"
|^.^| "No tengas miedo de la perfecci=F3n, = nunca la alcanzar=E1s"
+-!OO--\_/--OO!--------------------------------+-------------------= ---
! Dr.V=EDctor Lua=F1a = ! (Salvador Dal=ED)=
! Departamento de Qu=EDmica F=EDsica y Anal=EDtica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail: victor * fluor.quimica.uniovi.es !
! phone: +34-985-103491 fax: +34-985-103125 !
+----------------------------------------------+
GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)

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4+vkc+T85YTmDeaW5x/nqegy6LzpRunQ6lvq5etw6/vshu0R7ZzuKO6070DvzPBY8OXxcvH/8ozz GfOn9DT0wvVQ9d72bfb794r4Gfio+Tj5x/pX+uf7d/wH/Jj9Kf26/kv+3P9t//8= --_004_00344A8866D0451EAEBB6A17DBBCB5D0rpiedu_-- From owner-chemistry@ccl.net Tue Jan 6 13:47:00 2015 From: "Marko Tomic tomic#,#physik.tu-berlin.de" To: CCL Subject: CCL: Excessive mixing of frozen core and valence orbitals (Gaussian 09) Message-Id: <-50864-150106115204-28282-6cwTnnXz5SpwvuxTkRdOXA#%#server.ccl.net> X-Original-From: "Marko Tomic" Date: Tue, 6 Jan 2015 11:52:02 -0500 Sent to CCL by: "Marko Tomic" [tomic++physik.tu-berlin.de] Hello everybody, first post, first problem... I got after some different TD-DFT calculation following error message at the end of the output-file; "Excessive mixing of frozen core and valence orbitals" The input-file looks like following examples; # B3LYP/Gen TD=(Nstates=10) Pseudo=Read geom=connectivity or # B3LYP/ccpVDZ TD=(Nstates=10) geom=connectivity I try to calculate a cluster [flavin-molecule + alkali metal kation (charge +1)]. I optimized the structure before with the same level of theory. If somebody could help me, I would be very grateful! Marko Tomic Technische Universitt Institut fr Optik und Atomare Physik Hardenbergstrae 36 tomic*_*physik.tu-berlin.de From owner-chemistry@ccl.net Tue Jan 6 14:22:00 2015 From: "Chang, Christopher Christopher.Chang_._nrel.gov" To: CCL Subject: CCL: Assignment of electronic charges on different atoms Message-Id: <-50865-150106124805-26028-ZhcOyNEMt7ZcUhuppo7I5w|a|server.ccl.net> X-Original-From: "Chang, Christopher" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Tue, 6 Jan 2015 17:47:58 +0000 MIME-Version: 1.0 Sent to CCL by: "Chang, Christopher" [Christopher.Chang^_^nrel.gov] It sounds like Partha is asking for van Voorhis’ constrained DFT http://pubs.acs.org/doi/pdfplus/10.1021/cr200148b (Sorry if that’s behind a paywall, you can Google “constrained DFT” for a variety of open results). I don’t know if people often use it to constrain charges atom-by-atom, normally more to define diabatic states of fragments/molecules, but it might be do-able. Chemical interpretation of what comes out is a whole ‘nother story, though. Caveat emptor. Chris > From: owner-chemistry+christopher.chang==nrel.gov(_)ccl.net [mailto:owner-chemistry+christopher.chang==nrel.gov(_)ccl.net] On Behalf Of Marcel Swart marcel.swart#,#icrea.cat Sent: Tuesday, January 06, 2015 7:51 AM To: Chang, Christopher Subject: CCL: Assignment of electronic charges on different atoms Partha, the answer is simple: No, you cannot. In more detail: Atomic charges are not observables, but are obtained through charge analyses, that depend on the wave-function and/or charge density. These analyses then assign a point charge to a specific point in space (usually the nuclei of atoms), and that’s that. You cannot modify them, they are the result. The same happens with the energy, you calculate it (using QM, MM, or ..), and when you have it, that’s the result. In both cases you cannot adjust it “according to users choice”. The only thing you can do is have a look with different charge analyses, e.g. Mulliken, NBO, Hirshfeld, MDC-d, CHELPG, because each of them has its own benefits (and followers). Marcel On 2015-01-06, at 12:55, Partha Sengupta anapspsmo~!~gmail.com wrote: For the determination of hyperpolarizablity/optimized parameter of a molecular system we get the Mulliken atomic charges: like 1 1 N -0.627468 2 C -0.089856 3 C -0.123465 4 C -0.188188 5 C -0.269616 .... etc. In the same way, is it possible to assign the charges on the atoms according to users choice as a command 1 1 N -0.727468 2 C -0.009856 3 C -0.123465 4 C -0.188188 5 C -0.269616 On Mon, Jan 5, 2015 at 11:29 PM, Partha Sengupta wrote: Sir, I want to know the structural deformation of drug molecule working in the synaptic node. I really need the references. I have no knowledge about QTAIM . Please clarify that. Sincerely, Partha On Mon, Jan 5, 2015 at 4:17 PM, Víctor Luaña Cabal victor**fluor.quimica.uniovi.es wrote: Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor() fluor.quimica.uniovi.es] On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp ~~ gmail.com wrote: > How do you localize an electron at a specific point ? doesn't it contradict > uncertainty principle? Why do you identify an aton with a point? First, you can use QTAIM to assign a charge to an atom of a functional group. There are other possibilities of localization too. Do you need/want references? Regards, Dr. Víctor Luaña -- \|/a "Have no fear of perfection, you will never attain it!" |^.^| "No tengas miedo de la perfección, nunca la alcanzarás" +-!OO--\_/--OO!--------------------------------+---------------------- ! Dr.Víctor Luaña ! (Salvador Dalí) ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor * fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)E-mail to subscribers: CHEMISTRY_._ccl.net or use: E-mail to administrators: CHEMISTRY-REQUEST_._ccl.net or use -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan =================================== Prof. Dr. Marcel Swart ICREA Research Professor at Institut de Química Computacional i Catàlisi Universitat de Girona Facultat de Ciències Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart*icrea.cat marcel.swart*udg.edu web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf =================================== From owner-chemistry@ccl.net Tue Jan 6 14:57:00 2015 From: "Partha Sengupta anapspsmo[*]gmail.com" To: CCL Subject: CCL: Assignment of electronic charges on different atoms Message-Id: <-50866-150106130926-8833-LX5aV4xwimDbvA+RIKWjJQ]*[server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=001a11340cacc0b1d1050bffb4c9 Date: Tue, 6 Jan 2015 23:39:20 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo()gmail.com] --001a11340cacc0b1d1050bffb4c9 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Sir, Thank you for your answer. It help me to think to the right direction for the computational calculation. Regards, PSSengupta On Tue, Jan 6, 2015 at 8:20 PM, Marcel Swart marcel.swart#,#icrea.cat < owner-chemistry#,#ccl.net> wrote: > Partha, > > the answer is simple: No, you cannot. > > In more detail: > Atomic charges are not observables, but are obtained through charge > analyses, > that depend on the wave-function and/or charge density. These analyses th= en > assign a point charge to a specific point in space (usually the nuclei of > atoms), > and that=E2=80=99s that. You cannot modify them, they are the result. > The same happens with the energy, you calculate it (using QM, MM, or ..), > and when you have it, that=E2=80=99s the result. > > In both cases you cannot adjust it =E2=80=9Caccording to users choice=E2= =80=9D. > > The only thing you can do is have a look with different charge analyses, > e.g. Mulliken, NBO, Hirshfeld, MDC-d, CHELPG, because each of them > has its own benefits (and followers). > > Marcel > > On 2015-01-06, at 12:55, Partha Sengupta anapspsmo~!~gmail.com < > owner-chemistry*ccl.net> wrote: > > For the determination of hyperpolarizablity/optimized parameter of a > molecular system we get the Mulliken atomic charges: like > 1 > 1 N -0.627468 > 2 C -0.089856 > 3 C -0.123465 > 4 C -0.188188 > 5 C -0.269616 > .... > etc. > In the same way, is it possible to assign > the charges on the atoms according to users choice as a command > 1 > 1 N -0.727468 > 2 C -0.009856 > 3 C -0.123465 > 4 C -0.188188 > 5 C -0.269616 > > > On Mon, Jan 5, 2015 at 11:29 PM, Partha Sengupta > wrote: > >> Sir, I want to know the structural deformation of drug molecule working >> in the synaptic node. >> I really need the references. >> I have no knowledge about >> *QTAIM .* >> >> *Please clarify that.* >> >> *Sincerely,* >> *Partha * >> >> On Mon, Jan 5, 2015 at 4:17 PM, V=C3=ADctor Lua=C3=B1a Cabal victor** >> fluor.quimica.uniovi.es wrote: >> >>> >>> Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor= () >>> fluor.quimica.uniovi.es] >>> On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp >>> ~~ gmail.com wrote: >>> > How do you localize an electron at a specific point ? doesn't it >>> contradict >>> > uncertainty principle? >>> >>> Why do you identify an aton with a point? >>> First, you can use QTAIM to assign a charge >>> to an atom of a functional group. >>> There are other possibilities of localization too. >>> >>> Do you need/want references? >>> >>> Regards, >>> Dr. V=C3=ADctor Lua=C3=B1a >>> >>> -- >>> \|/a "Have no fear of perfection, you will never attain it!" >>> |^.^| "No tengas miedo de la perfecci=C3=B3n, nunca la alcanzar= =C3=A1s" >>> +-!OO--\_/--OO!--------------------------------+---------------------- >>> ! Dr.V=C3=ADctor Lua=C3=B1a ! (Salvador Da= l=C3=AD) >>> ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! >>> ! Universidad de Oviedo, 33006-Oviedo, Spain ! >>> ! e-mail: victor * fluor.quimica.uniovi.es ! >>> ! phone: +34-985-103491 fax: +34-985-103125 ! >>> +----------------------------------------------+ >>> GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) >>> >>> >>> >>> -=3D This is automatically added to each message by the mailing script = =3D- >>> >>> >>> >>> E-mail to subscribers: CHEMISTRY_._ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST_._ccl.net or use>>> >>> >>> >> >> >> -- >> Dr. Partha Sarathi Sengupta >> Associate Professor >> Vivekananda Mahavidyalaya, Burdwan >> > > > > -- > Dr. Partha Sarathi Sengupta > Associate Professor > Vivekananda Mahavidyalaya, Burdwan > > > > =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 > Prof. Dr. Marcel Swart > > ICREA Research Professor at > Institut de Qu=C3=ADmica Computacional i Cat=C3=A0lisi > Universitat de Girona > > Facultat de Ci=C3=A8ncies > Campus Montilivi > 17071 Girona > Catalunya (Spain) > > tel > +34-972-418861 > fax > +34-972-418356 > e-mail > marcel.swart*icrea.cat > marcel.swart*udg.edu > web > http://www.marcelswart.eu > vCard > addressbook://www.marcelswart.eu/MSwart.vcf > =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 > > > > > > --=20 Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --001a11340cacc0b1d1050bffb4c9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Sir, Thank you for your answer. It help me to th= ink to the right direction for the computational calculation.

Rega= rds,

PSSengupta

On Tue, Jan 6, 2015 at 8:20 PM, Marcel Swart marcel.swart#= ,#icrea.cat <owner-chemistry#,#ccl.n= et> wrote:

Partha,

the answer is simple: No, yo= u cannot.

In more detail:
Atomic charges= are not observables, but are obtained through charge analyses,
t= hat depend on the wave-function and/or charge density. These analyses then<= /div>
assign a point charge to a specific point in space (usually the n= uclei of atoms),
and that=E2=80=99s that. You cannot modify them,= they are the result.
The same happens with the energy, you calcu= late it (using QM, MM, or ..),
and when you have it, that=E2=80= =99s the result.

In both cases you cannot adjust i= t =E2=80=9Caccording to users choice=E2=80=9D.

The= only thing you can do is have a look with different charge analyses,
=
e.g. Mulliken, NBO, Hirshfeld, MDC-d, CHELPG, because each of them
has its own benefits (and followers).

Marce= l

= On 2015-01-06, at 12:55, Partha Sengupta anapspsmo~!~gmail.com <owner-chemistry*ccl.net> wrote:
For the determination of hyperpolari= zablity/optimized parameter=C2=A0 of a molecular system we get the Mulliken= atomic charges: like
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1
=C2=A0=C2=A0=C2=A0=C2=A0 1=C2=A0 N=C2= =A0=C2=A0 -0.627468
=C2=A0=C2=A0=C2=A0=C2=A0 2=C2=A0 C=C2=A0=C2=A0 -0.08= 9856
=C2=A0=C2=A0=C2=A0=C2=A0 3=C2=A0 C=C2=A0=C2=A0 -0.123465
=C2=A0= =C2=A0=C2=A0=C2=A0 4=C2=A0 C=C2=A0=C2=A0 -0.188188
=C2=A0=C2=A0=C2=A0=C2= =A0 5=C2=A0 C=C2=A0=C2=A0 -0.269616
....
etc.
In the = same way, is it possible to assign
the charges on the atoms accor= ding to users choice as a command=C2=A0
1
=C2=A0=C2=A0=C2=A0=C2=A0 = 1=C2=A0 N=C2=A0=C2=A0 -0.727468
=C2=A0=C2=A0=C2=A0=C2=A0 2=C2=A0 C=C2=A0= =C2=A0 -0.009856
=C2=A0=C2=A0=C2=A0=C2=A0 3=C2=A0 C=C2=A0=C2=A0 -0.12346= 5
=C2=A0=C2=A0=C2=A0=C2=A0 4=C2=A0 C=C2=A0=C2=A0 -0.188188
=C2=A0=C2= =A0=C2=A0=C2=A0 5=C2=A0 C=C2=A0=C2=A0 -0.269616

On Mon, Jan 5, 2015 at 11:29 PM= , Partha Sengupta <anapspsmo_._gmail.com> wrote:
Sir, I= want to know the structural deformation of drug molecule working in the sy= naptic node.
I really need the references.
I have no know= ledge about=C2=A0QTAIM .
Please clarify that.
Sincerely,
Partha

On Mon, Jan 5, 2015 at 4:17= PM, V=C3=ADctor Lua=C3=B1a Cabal victor**fluor.quimica.uniovi.es = <owner-ch= emistry_._ccl.net> wrote:
<= br> Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor() <= a href=3D"http://fluor.quimica.uniovi.es/" target=3D"_blank">fluor.quimica.= uniovi.es]
On Mon, Jan 05, 2015 at 01:17:31PM +0530, Utpal Sarkar utpalchemiitkgp ~~ <= a href=3D"http://gmail.com/" target=3D"_blank">gmail.com wrote:
> How do you localize an electron at a specific point ? doesn't it c= ontradict
> uncertainty principle?

Why do you identify an aton with a point?
First, you can use QTAIM to assign a charge
to an atom of a functional group.
There are other possibilities of localization too.

Do you need/want references?

Regards,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua=C3=B1a

--
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! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica=C2=A0 =C2=A0! ! Universidad de Oviedo, 33006-Oviedo, Spain=C2=A0 =C2=A0!
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--
Dr. Partha Sarathi Sengupta
Associate Pro= fessor
Vivekananda Mahavidyalaya, Burdwan

--
Dr. Partha Sarathi= Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan

=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
Prof. Dr= . Marcel Swart

ICREA Research Professor at
Institut de Qu=C3=ADmi= ca Computacional i Cat=C3=A0lisi
Universitat de Girona

Facultat d= e Ci=C3=A8ncies
Campus Montilivi
17071 Girona
Catalunya (Spain)
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marcel.swart*udg.edu<= br>web
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=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

<= br>

Dr. Partha Sarathi Sengupta
Associate Professor<= br>Vivekananda Mahavidyalaya, Burdwan

--001a11340cacc0b1d1050bffb4c9-- From owner-chemistry@ccl.net Tue Jan 6 15:32:01 2015 From: "Susi Lehtola susi.lehtola!A!alumni.helsinki.fi" To: CCL Subject: CCL: Assignment of electronic charges on different atoms Message-Id: <-50867-150106133703-1915-PJAWtyAU9It1tkWpbfaBHA#server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 06 Jan 2015 10:36:50 -0800 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola---alumni.helsinki.fi] On 01/06/2015 03:55 AM, Partha Sengupta anapspsmo~!~gmail.com wrote: > For the determination of hyperpolarizablity/optimized parameter of a > molecular system we get the Mulliken atomic charges: like > 1 > 1 N -0.627468 > 2 C -0.089856 > 3 C -0.123465 > 4 C -0.188188 > 5 C -0.269616 > .... > etc. > In the same way, is it possible to assign > the charges on the atoms according to users choice as a command > 1 > 1 N -0.727468 > 2 C -0.009856 > 3 C -0.123465 > 4 C -0.188188 > 5 C -0.269616 > I guess this would be possible using a formalism such as Constrained DFT, but then you'll anyway need a definition for obtaining the atomic charge, e.g. Mulliken, Löwdin, AIM (Bader), IAO, Voronoi, ... But, IIRC in CDFT you usually constrain the charge on functional groups, not the individual atoms. Also, if the charges are nonsense, the method you have chosen just might not apply to the system you want to study. For instance, reproducing charge localization with DFT is often impossible due to self-interaction effects. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola,alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Jan 6 16:07:01 2015 From: "Van Dam, Hubertus J HubertusJJ.vanDam * pnnl.gov" To: CCL Subject: CCL: Any regrets open-sourcing your programs? Message-Id: <-50868-150106143339-23428-brIY9QqGpauglyPcbP7rnA%a%server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_99ABE4E57F52104B9121AAE22D07CE301E919B4CEX10MBOX02pnnlg_" Date: Tue, 6 Jan 2015 19:33:31 +0000 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam#pnnl.gov] --_000_99ABE4E57F52104B9121AAE22D07CE301E919B4CEX10MBOX02pnnlg_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SGkgVWxmLA0KDQpJIGd1ZXNzIHRoaXMgaXMgb25lIG9mIHRob3NlIHBlcnBldHVhbGx5IHJlY3Vy cmluZyB0b3BpY3MgYnV0IG1heWJlIEkgY2FuIG1ha2UgYSBmZXcgdW51c3VhbCBwb2ludHMuIEkg aGF2ZSB3b3JrZWQgZm9yIG92ZXIgYSBkZWNhZGUgb24gYSBjbG9zZWQgc291cmNlIGNvZGUgKEdB TUVTUy1VSykuIEFib3V0IDUgeWVhcnMgYWdvIEkgY2hhbmdlZCBlbXBsb3llciB0byBqb2luIGEg dGVhbSB3b3JraW5nIG9uIGFuIG9wZW4gc291cmNlIGNvZGUgKE5XQ2hlbSBzZWU6IGh0dHA6Ly93 d3cubndjaGVtLXN3Lm9yZykuDQoNCkZpcnN0IG9mIGFsbCBJIGhhdmUgdG8gYWRtaXQgdGhhdCBJ 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bmVkIGJ5IHJlYWwgbGF3eWVycy4mbmJzcDs8bzpwPjwvbzpwPjwvcD4NCjwvZGl2Pg0KPGRpdj4N CjxwIGNsYXNzPSJNc29Ob3JtYWwiPjxvOnA+Jm5ic3A7PC9vOnA+PC9wPg0KPC9kaXY+DQo8ZGl2 Pg0KPHAgY2xhc3M9Ik1zb05vcm1hbCI+UmVnYXJkcyw8bzpwPjwvbzpwPjwvcD4NCjwvZGl2Pg0K PGRpdj4NCjxwIGNsYXNzPSJNc29Ob3JtYWwiPlVsZiBFa3N0cm9tLCBVbml2ZXJzaXR5IG9mIE9z bG88bzpwPjwvbzpwPjwvcD4NCjwvZGl2Pg0KPC9kaXY+DQo8L2Rpdj4NCjwvYm9keT4NCjwvaHRt bD4NCg== --_000_99ABE4E57F52104B9121AAE22D07CE301E919B4CEX10MBOX02pnnlg_-- From owner-chemistry@ccl.net Tue Jan 6 16:42:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor~~fluor.quimica.uniovi.es" To: CCL Subject: CCL: Assignment of electronic charges on different atoms Message-Id: <-50869-150106154244-12499-x4GkV8HXvqmDowXtnTLnQQ##server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Tue, 06 Jan 2015 21:24:15 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor:fluor.quimica.uniovi.es] On Tue, Jan 06, 2015 at 10:49:30AM +0530, Utpal Sarkar utpalchemiitkgp-.-gmail.com wrote: > But if an electron is attached fully (100%) to any atom of a molecule or > functional group, then the porbablity of finding that electron in that > region should be ONE if and only if that electron is bound by infinite > potential. But is there any existence of infinite potential within a > molecule? Your idea of QTAIM is quite wrong. The objective is analyzing the real electron density of a system measured or computed with the best quality that it can be achieved. In QTAIM an atom or a functional group is wiewed as a basin receiving the electron density from a region of space in a molecule or solid. The electron density, i.e. the first order density matrix (see McWeeny book) is a well defined property be it for a non-relativistic or relativistic calculation, be it for an inmovil part of a system or a vibrating molecule or solid. Maybe you are more interested in the partioning of n-electron density functions and I invite you to read the work of Andreas Savin, Angel Martin Pend�s and many others. Savin uses to organize an international meeting on the subject. Let me show you our starting work on the ions in crystals series: Phys. Rev. B 55 (1997) 4275; 4285; 62 (2000) 12028 J. Phys. Chem. B 102 (1998) 6937; 107 (2003) 4912 Phys. Rev. Lett. 83 (1999) 1930 Best regards, Dr. V�ctor Lua�a -- \|/a "Have no fear of perfection, you will never attain it!" |^.^| "No tengas miedo de la perfecci�n, nunca la alcanzar�s" +-!OO--\_/--OO!--------------------------------+---------------------- ! Dr.V�ctor Lua�a ! (Salvador Dal�) ! Departamento de Qu�mica F�sica y Anal�tica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor:-:fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Tue Jan 6 20:32:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor##fluor.quimica.uniovi.es" To: CCL Subject: CCL: Any regrets open-sourcing your programs? Message-Id: <-50870-150106151207-13986-C4WQPSe/VkUrw2mPduGHwQ]=[server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Tue, 06 Jan 2015 20:53:34 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor]^[fluor.quimica.uniovi.es] On Tue, Jan 06, 2015 at 01:13:13PM +0100, uekstrom/./gmail.com uekstrom/./gmail.com wrote: > Dear all, > I am involved in a discussion about open source scientific software. Of > course there are well known arguments on "both sides" in this debate. Is > there anyone on CCL who regret publishing their code under an open source* > license? Did it affect your scientific or commercial career negatively in > any way? > > *) By open source I mean one of the well known licenses which have been > examined by real lawyers. I expect that you may receive only answers from people observing problems, so I have always published my codes as freeware from my web pages or as open source codes under a creative commons license and I've found no problem whatsoever. Best regards, Dr. V�ctor Lua�a -- \|/a "Have no fear of perfection, you will never attain it!" |^.^| "No tengas miedo de la perfecci�n, nunca la alcanzar�s" +-!OO--\_/--OO!--------------------------------+---------------------- ! Dr.V�ctor Lua�a ! (Salvador Dal�) ! Departamento de Qu�mica F�sica y Anal�tica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor~!~fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Tue Jan 6 21:07:01 2015 From: "Susi Lehtola susi.lehtola++alumni.helsinki.fi" To: CCL Subject: CCL: Any regrets open-sourcing your programs? Message-Id: <-50871-150106201530-22131-uvQzj3GqZ5FEXaaNlnanjA ~~ server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 06 Jan 2015 17:15:18 -0800 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola=alumni.helsinki.fi] On 01/06/2015 11:33 AM, Van Dam, Hubertus J HubertusJJ.vanDam * pnnl.gov wrote: > Hi Ulf, > > I guess this is one of those perpetually recurring topics but maybe I > can make a few unusual points. I have worked for over a decade on a > closed source code (GAMESS-UK). About 5 years ago I changed employer to > join a team working on an open source code (NWChem see: > http://www.nwchem-sw.org). I wholeheartedly agree with Hub's posting. IMHO maybe the most important points for open-sourcing have to do with availability. If you are developing new methods and you want people to use them, it makes complete sense to open-source your programs, as this will minimize the impediment to adopt them. On the other hand, if people already want your method and you have a significant competitive advantage, it may make more sense to not publish it as open source. But, most open source science projects don't have a fully open development cycle anyway. New features are developed in-house, and published in the open source part of the code only after most of the possible papers have been cranked out by the group. As already stated by Hub, selling closed-source software introduces a lot of hassle with handling licenses and providing user support. The overhead is rather significant and the amount of users so small, that there are really no large successful quantum chemistry companies. By open-sourcing you will guarantee that you'll have access to your work in the future, as well, and possibly even get other people to maintain and develop your code, should your interests move elsewhere. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola%alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA -----------------------------------------------------------------------