From owner-chemistry@ccl.net Tue Jun 15 01:25:00 2010
From: "Jamin Krinsky jamink++berkeley.edu" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL:G: TDDFT
Message-Id: <-42111-100615012157-11991-6EzMuIDat9IbTSE1t7eSYg],[server.ccl.net>
X-Original-From: Jamin Krinsky <jamink_._berkeley.edu>
Content-Type: multipart/alternative; boundary=00163630f3cf1d484804890ac8c6
Date: Mon, 14 Jun 2010 22:21:46 -0700
MIME-Version: 1.0


Sent to CCL by: Jamin Krinsky [jamink+/-berkeley.edu]
--00163630f3cf1d484804890ac8c6
Content-Type: text/plain; charset=ISO-8859-1

A vanishing oscillator strength does mean that the transition is predicted
to be unobserved. Whether or not it is technically forbidden depends on the
molecular symmetry, etc., and I don't know what your system is. In TD-DFT it
is fairly common to get low-lying, spurious (non-physical) states with
little or no oscillator strength. Also, if you were calculating triplet
states from a singlet ground state than all of those will obviously be
forbidden (but you mentioned that you were studying open-shell systems so
that's probably not the case).
Jamin


On Mon, Jun 14, 2010 at 6:37 PM, Liu Jing jliu]^[cuhk.edu.hk <
owner-chemistry(-)ccl.net> wrote:

> Dear Jamin,
>     Thank you for your quick reply.
>     Would you like to say sth about the oscillator strengths. In my
> calculation this value is equal to zero for the first excited state, does
> it mean this transition is forbidden?
>
> Regards
> Liu, Jing
> 2010/6/15 Jamin Krinsky jamink()berkeley.edu <owner-chemistry%ccl.net>
>
> Dear Jing,
>>
>> If you are using Gaussian, you cannot request excited-state multiplicities
>> different from the ground state for open-shell molecules (the "singlets" and
>> "triplets" options are ignored). You can of course calculate the
>> ground-state configuration for each multiplicity and compare energies of
>> those... Some other programs (Q-Chem included I think) will let you do
>> spin-flip TDDFT, but you'd want to read up on the subject before attempting
>> it (I don't know much about it).
>>
>> Regards,
>> Jamin
>>
>>
>> On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/./cuhk.edu.hk <
>> owner-chemistry]~[ccl.net <owner-chemistry]%7E[ccl.net>> wrote:
>>
>>> Dear all,
>>>
>>>   Can you tell me how to set the spin multiplicity of the excited states
>>> when a open-
>>> shell system is concerned?
>>>
>>>  Thank you and good luck.
>>>
>>> Yours Jing
>>>
>>
>>
>>
>> --
>> Jamin L Krinsky, Ph.D.
>> Molecular Graphics and Computation Facility
>> 175 Tan Hall, University of California, Berkeley, CA 94720
>> jamink]~[berkeley.edu <jamink]%7E[berkeley.edu>, 510-643-0616
>> http://glab.cchem.berkeley.edu
>>
>>
>


-- 
Jamin L Krinsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, University of California, Berkeley, CA 94720
jamink(-)berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--00163630f3cf1d484804890ac8c6
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

A vanishing oscillator strength does mean that the transition is predicted =
to be unobserved. Whether or not it is technically forbidden depends on the=
 molecular symmetry, etc., and I don&#39;t know what your system is. In TD-=
DFT it is fairly common to get low-lying, spurious (non-physical) states wi=
th little or no oscillator strength. Also, if you were calculating triplet =
states from a singlet ground state than all of those will obviously be forb=
idden (but you mentioned that you were studying open-shell systems so that&=
#39;s probably not the case).<br>
Jamin<br><br><br><div class=3D"gmail_quote">On Mon, Jun 14, 2010 at 6:37 PM=
, Liu Jing jliu]^[<a href=3D"http://cuhk.edu.hk">cuhk.edu.hk</a> <span dir=
=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry(-)ccl.net">owner-chemistry(-)ccl=
.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div>Dear Jamin,<=
/div>
<div>=A0=A0=A0 Thank you for your quick reply.</div>
<div>=A0=A0=A0 Would you like to say sth about the oscillator strengths. In=
 my</div>
<div>calculation this value is equal to zero for the first excited state, d=
oes</div>
<div>it mean this transition is forbidden?</div>
<div>=A0</div>
<div>Regards</div>
<div>Liu, Jing<br></div>
<div class=3D"gmail_quote">2010/6/15 Jamin Krinsky jamink()<a href=3D"http:=
//berkeley.edu" target=3D"_blank">berkeley.edu</a> <span dir=3D"ltr">&lt;<a=
 href=3D"mailto:owner-chemistry%ccl.net" target=3D"_blank">owner-chemistry%=
ccl.net</a>&gt;</span><div>
<div></div><div class=3D"h5"><br>
<blockquote class=3D"gmail_quote" style=3D"padding-left: 1ex; margin: 0px 0=
px 0px 0.8ex; border-left: 1px solid rgb(204, 204, 204);">Dear Jing,<br><br=
>If you are using Gaussian, you cannot request excited-state multiplicities=
 different from the ground state for open-shell molecules (the &quot;single=
ts&quot; and &quot;triplets&quot; options are ignored). You can of course c=
alculate the ground-state configuration for each multiplicity and compare e=
nergies of those... Some other programs (Q-Chem included I think) will let =
you do spin-flip TDDFT, but you&#39;d want to read up on the subject before=
 attempting it (I don&#39;t know much about it).<br>

<br>Regards,<br>Jamin<br><br><br>
<div class=3D"gmail_quote">On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/.=
/<a href=3D"http://cuhk.edu.hk/" target=3D"_blank">cuhk.edu.hk</a> <span di=
r=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry]%7E[ccl.net" target=3D"_bla=
nk">owner-chemistry]~[ccl.net</a>&gt;</span> wrote:<br>


<blockquote class=3D"gmail_quote" style=3D"padding-left: 1ex; margin: 0pt 0=
pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);">
<div>Dear all,</div>
<div>=A0=A0 </div>
<div>=A0=A0Can you tell me how to set the spin multiplicity of the excited =
states when a open-</div>
<div>shell system is concerned? </div>
<div>=A0</div>
<div>=A0Thank you and good luck.</div>
<div>=A0</div>
<div>Yours Jing </div></blockquote></div><br><font color=3D"#888888"><br cl=
ear=3D"all"><br>-- <br>Jamin L Krinsky, Ph.D.<br>Molecular Graphics and Com=
putation Facility<br>175 Tan Hall, University of California, Berkeley, CA 9=
4720<br>

<a href=3D"mailto:jamink]%7E[berkeley.edu" target=3D"_blank">jamink]~[berke=
ley.edu</a>, 510-643-0616<br><a href=3D"http://glab.cchem.berkeley.edu/" ta=
rget=3D"_blank">http://glab.cchem.berkeley.edu</a><br><br></font></blockquo=
te>
</div></div></div>
<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Jamin L Krinsky, Ph.D.<=
br>Molecular Graphics and Computation Facility<br>175 Tan Hall, University =
of California, Berkeley, CA 94720<br><a href=3D"mailto:jamink(-)berkeley.edu"=
>jamink(-)berkeley.edu</a>, 510-643-0616<br>
<a href=3D"http://glab.cchem.berkeley.edu">http://glab.cchem.berkeley.edu</=
a><br><br>

--00163630f3cf1d484804890ac8c6--


From owner-chemistry@ccl.net Tue Jun 15 03:10:00 2010
From: "Liu Jing jliu a cuhk.edu.hk" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL:G: TDDFT
Message-Id: <-42112-100615030817-11765-v5B1TeLk40DyAuqWPw6+SA_+_server.ccl.net>
X-Original-From: Liu Jing <jliu:+:cuhk.edu.hk>
Content-Type: multipart/alternative; boundary=00c09ffb50c5528f0c04890c4455
Date: Tue, 15 Jun 2010 15:08:05 +0800
MIME-Version: 1.0


Sent to CCL by: Liu Jing [jliu~~cuhk.edu.hk]
--00c09ffb50c5528f0c04890c4455
Content-Type: text/plain; charset=ISO-8859-1

Dear Jamin,

  What i want to do is to add the first excited energy to the electron
detachment enery and then get the total energy from ground state of
parent ions to the first excited state of product ion.So i'm confused
whehter it is meaningful when oscillator strength =0, can you give me
some hint, thank you.

Regards
Liu,Jing

2010/6/15 Jamin Krinsky jamink++berkeley.edu <owner-chemistry-$-ccl.net>

> A vanishing oscillator strength does mean that the transition is predicted
> to be unobserved. Whether or not it is technically forbidden depends on the
> molecular symmetry, etc., and I don't know what your system is. In TD-DFT it
> is fairly common to get low-lying, spurious (non-physical) states with
> little or no oscillator strength. Also, if you were calculating triplet
> states from a singlet ground state than all of those will obviously be
> forbidden (but you mentioned that you were studying open-shell systems so
> that's probably not the case).
> Jamin
>
>
>
> On Mon, Jun 14, 2010 at 6:37 PM, Liu Jing jliu]^[cuhk.edu.hk <
> owner-chemistry|a|ccl.net <owner-chemistry%7Ca%7Cccl.net>> wrote:
>
>> Dear Jamin,
>>     Thank you for your quick reply.
>>     Would you like to say sth about the oscillator strengths. In my
>> calculation this value is equal to zero for the first excited state, does
>> it mean this transition is forbidden?
>>
>> Regards
>> Liu, Jing
>> 2010/6/15 Jamin Krinsky jamink()berkeley.edu <owner-chemistry%ccl.net>
>>
>> Dear Jing,
>>>
>>> If you are using Gaussian, you cannot request excited-state
>>> multiplicities different from the ground state for open-shell molecules (the
>>> "singlets" and "triplets" options are ignored). You can of course calculate
>>> the ground-state configuration for each multiplicity and compare energies of
>>> those... Some other programs (Q-Chem included I think) will let you do
>>> spin-flip TDDFT, but you'd want to read up on the subject before attempting
>>> it (I don't know much about it).
>>>
>>> Regards,
>>> Jamin
>>>
>>>
>>> On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/./cuhk.edu.hk <
>>> owner-chemistry]~[ccl.net> wrote:
>>>
>>>> Dear all,
>>>>
>>>>   Can you tell me how to set the spin multiplicity of the excited states
>>>> when a open-
>>>> shell system is concerned?
>>>>
>>>>  Thank you and good luck.
>>>>
>>>> Yours Jing
>>>>
>>>
>>>
>>>
>>> --
>>> Jamin L Krinsky, Ph.D.
>>> Molecular Graphics and Computation Facility
>>> 175 Tan Hall, University of California, Berkeley, CA 94720
>>> jamink]~[berkeley.edu, 510-643-0616
>>> http://glab.cchem.berkeley.edu
>>>
>>>
>>
>
>
> --
> Jamin L Krinsky, Ph.D.
> Molecular Graphics and Computation Facility
> 175 Tan Hall, University of California, Berkeley, CA 94720
> jamink|a|berkeley.edu <jamink%7Ca%7Cberkeley.edu>, 510-643-0616
>
> http://glab.cchem.berkeley.edu
>
>

--00c09ffb50c5528f0c04890c4455
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<div>Dear=A0Jamin,</div>
<div>=A0=A0=A0</div>
<div>=A0 What i want to do is to add the first=A0excited energy to the elec=
tron</div>
<div>detachment enery and then=A0get=A0the total energy from ground state o=
f</div>
<div>parent ions to the first excited state of product ion.So i&#39;m confu=
sed </div>
<div>whehter it is meaningful when oscillator strength =3D0, can you give m=
e</div>
<div>some hint, thank you.</div>
<div>=A0</div>
<div>Regards</div>
<div>Liu,Jing <br><br></div>
<div class=3D"gmail_quote">2010/6/15 Jamin Krinsky jamink++<a href=3D"http:=
//berkeley.edu">berkeley.edu</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:ow=
ner-chemistry-$-ccl.net">owner-chemistry-$-ccl.net</a>&gt;</span><br>
<blockquote class=3D"gmail_quote" style=3D"PADDING-LEFT: 1ex; MARGIN: 0px 0=
px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">A vanishing oscillator strength =
does mean that the transition is predicted to be unobserved. Whether or not=
 it is technically forbidden depends on the molecular symmetry, etc., and I=
 don&#39;t know what your system is. In TD-DFT it is fairly common to get l=
ow-lying, spurious (non-physical) states with little or no oscillator stren=
gth. Also, if you were calculating triplet states from a singlet ground sta=
te than all of those will obviously be forbidden (but you mentioned that yo=
u were studying open-shell systems so that&#39;s probably not the case).<br=
>
Jamin=20
<div>
<div></div>
<div class=3D"h5"><br><br><br>
<div class=3D"gmail_quote">On Mon, Jun 14, 2010 at 6:37 PM, Liu Jing jliu]^=
[<a href=3D"http://cuhk.edu.hk/" target=3D"_blank">cuhk.edu.hk</a> <span di=
r=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry%7Ca%7Cccl.net" target=3D"_b=
lank">owner-chemistry|a|ccl.net</a>&gt;</span> wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"PADDING-LEFT: 1ex; MARGIN: 0pt 0=
pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<div>Dear Jamin,</div>
<div>=A0=A0=A0 Thank you for your quick reply.</div>
<div>=A0=A0=A0 Would you like to say sth about the oscillator strengths. In=
 my</div>
<div>calculation this value is equal to zero for the first excited state, d=
oes</div>
<div>it mean this transition is forbidden?</div>
<div>=A0</div>
<div>Regards</div>
<div>Liu, Jing<br></div>
<div class=3D"gmail_quote">2010/6/15 Jamin Krinsky jamink()<a href=3D"http:=
//berkeley.edu/" target=3D"_blank">berkeley.edu</a> <span dir=3D"ltr">&lt;<=
a href=3D"mailto:owner-chemistry%ccl.net" target=3D"_blank">owner-chemistry=
%ccl.net</a>&gt;</span>=20
<div>
<div></div>
<div><br>
<blockquote class=3D"gmail_quote" style=3D"PADDING-LEFT: 1ex; MARGIN: 0px 0=
px 0px 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">Dear Jing,<br><br>If=
 you are using Gaussian, you cannot request excited-state multiplicities di=
fferent from the ground state for open-shell molecules (the &quot;singlets&=
quot; and &quot;triplets&quot; options are ignored). You can of course calc=
ulate the ground-state configuration for each multiplicity and compare ener=
gies of those... Some other programs (Q-Chem included I think) will let you=
 do spin-flip TDDFT, but you&#39;d want to read up on the subject before at=
tempting it (I don&#39;t know much about it).<br>
<br>Regards,<br>Jamin<br><br><br>
<div class=3D"gmail_quote">On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/.=
/<a href=3D"http://cuhk.edu.hk/" target=3D"_blank">cuhk.edu.hk</a> <span di=
r=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry]~[ccl.net" target=3D"_blank=
">owner-chemistry]~[ccl.net</a>&gt;</span> wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"PADDING-LEFT: 1ex; MARGIN: 0pt 0=
pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<div>Dear all,</div>
<div>=A0=A0 </div>
<div>=A0=A0Can you tell me how to set the spin multiplicity of the excited =
states when a open-</div>
<div>shell system is concerned? </div>
<div>=A0</div>
<div>=A0Thank you and good luck.</div>
<div>=A0</div>
<div>Yours Jing </div></blockquote></div><br><font color=3D"#888888"><br cl=
ear=3D"all"><br>-- <br>Jamin L Krinsky, Ph.D.<br>Molecular Graphics and Com=
putation Facility<br>175 Tan Hall, University of California, Berkeley, CA 9=
4720<br>
<a href=3D"mailto:jamink]~[berkeley.edu" target=3D"_blank">jamink]~[berkele=
y.edu</a>, 510-643-0616<br><a href=3D"http://glab.cchem.berkeley.edu/" targ=
et=3D"_blank">http://glab.cchem.berkeley.edu</a><br><br></font></blockquote=
></div>
</div></div><br></blockquote></div><br><br clear=3D"all"><br>-- <br>Jamin L=
 Krinsky, Ph.D.<br>Molecular Graphics and Computation Facility<br>175 Tan H=
all, University of California, Berkeley, CA 94720<br></div></div><a href=3D=
"mailto:jamink%7Ca%7Cberkeley.edu" target=3D"_blank">jamink|a|berkeley.edu<=
/a>, 510-643-0616=20
<div>
<div></div>
<div class=3D"h5"><br><a href=3D"http://glab.cchem.berkeley.edu/" target=3D=
"_blank">http://glab.cchem.berkeley.edu</a><br><br></div></div></blockquote=
></div><br>

--00c09ffb50c5528f0c04890c4455--


From owner-chemistry@ccl.net Tue Jun 15 09:40:00 2010
From: "zouzou adnani zinebeladnani%%hotmail.com" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: optimisation problem
Message-Id: <-42113-100615093822-22933-vTcxVJlN6W//A84TbFkzeA:_:server.ccl.net>
X-Original-From: "zouzou  adnani" <zinebeladnani#%#hotmail.com>
Date: Tue, 15 Jun 2010 09:37:57 -0400


Sent to CCL by: "zouzou  adnani" [zinebeladnani%a%hotmail.com]
hi,
I'm trying to study the interaction between one iron atom and some quinoxaline  derivatives, each time I end up with some very odd geometries even though  I changed the iron position several times and I tried some of the propositions I found in the CCL archive (Maxcycle, Vshift, QC...).
here is one of my input files, please help me:
 
%chk=mol2fer-dft-cep121g.chk
%nproc=1
 
#p opt freq b3lyp nosymm guess=save cep-121g
 
0 1
 
 C
 C                  1              B1
 H                  1              B2    2              A1
 C                  1              B3    2              A2    3              D1
 C                  2              B4    1              A3    4              D2
 H                  2              B5    1              A4    4              D3
 C                  5              B6    2              A5    1              D4
 C                  4              B7    1              A6    2              D5
 H                  5              B8    2              A7    1              D6
 H                  7              B9    5              A8    2              D7
 H                  8             B10    4              A9    1              D8
 N                  2             B11    1             A10    4              D9
 C                 12             B12    2             A11    1             D10
 O                 13             B13   12             A12    2             D11
 C                 13             B14   12             A13    2             D12
 O                 15             B15   13             A14   12             D13
 N                 15             B16   13             A15   12             D14
 H                 17             B17   15             A16   13             D15
 Fe                15             B18   13             A17   12             D16
 
   B1             1.40644101
   B2             2.14928644
   B3             1.39759508
   B4             1.39765674
   B5             2.08511317
   B6             1.39253612
   B7             1.39257680
   B8             1.08638027
   B9             1.08486967
   B10            1.08486443
   B11            1.39557266
   B12            1.38144585
   B13            1.21473476
   B14            1.53434602
   B15            1.21479365
   B16            1.38128209
   B17            1.01319508
   B18            2.48818517
   A1           145.95140520
   A2           119.79706010
   A3           119.77892540
   A4           143.20945469
   A5           120.09436720
   A6           120.08836427
   A7           119.29734053
   A8           119.58833605
   A9           119.59281559
   A10          118.07480691
   A11          126.52180143
   A12          122.62536055
   A13          115.40288341
   A14          121.97364409
   A15          115.41203166
   A16          114.40037764
   A17           74.26757538
   D1            -0.00336246
   D2             0.00283977
   D3          -179.98326314
   D4             0.00000000
   D5            -0.00385223
   D6          -180.00000000
   D7           179.99662248
   D8          -179.99638223
   D9          -180.00000000
   D10           -0.02573946
   D11         -179.98395853
   D12            0.01264207
   D13         -179.98079972
   D14            0.03738560
   D15         -179.99076401
   D16          -83.15595137


From owner-chemistry@ccl.net Tue Jun 15 11:06:00 2010
From: "Rinderspacher, Berend (Cont, ARL/WMRD) berend.rinderspacher%%us.army.mil" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL:G: optimisation problem (UNCLASSIFIED)
Message-Id: <-42114-100615105722-32379-OY5BHCn8kkdRbyzhRUcRaA_-_server.ccl.net>
X-Original-From: "Rinderspacher, Berend (Cont, ARL/WMRD)" <berend.rinderspacher(a)us.army.mil>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset="US-ASCII"
Date: Tue, 15 Jun 2010 10:56:50 -0400
MIME-Version: 1.0


Sent to CCL by: "Rinderspacher, Berend (Cont, ARL/WMRD)" [berend.rinderspacher%a%us.army.mil]
Classification: UNCLASSIFIED
Caveats: NONE

Dear Zouzou,

Can you send the "odd" geometries as well? I have seen Gaussian converge
smoothly on a geometry only for the energy and forces to explode
(seemingly randomly) in the past.

-----Original Message-----
> From: owner-chemistry+berend.rinderspacher=3D=3Dus.army.mil---ccl.net
[mailto:owner-chemistry+berend.rinderspacher=3D=3Dus.army.mil---ccl.net] =
On
Behalf Of zouzou adnani zinebeladnani%%hotmail.com
Sent: Tuesday, June 15, 2010 9:38 AM
To: Rinderspacher, Berend (Cont, ARL/WMRD)
Subject: CCL: optimisation problem


Sent to CCL by: "zouzou  adnani" [zinebeladnani%a%hotmail.com]
hi,
I'm trying to study the interaction between one iron atom and some
quinoxaline  derivatives, each time I end up with some very odd
geometries even though  I changed the iron position several times and I
tried some of the propositions I found in the CCL archive (Maxcycle,
Vshift, QC...).
here is one of my input files, please help me:
=20
%chk=3Dmol2fer-dft-cep121g.chk
%nproc=3D1
=20
#p opt freq b3lyp nosymm guess=3Dsave cep-121g
=20
0 1
=20
 C
 C                  1              B1
 H                  1              B2    2              A1
 C                  1              B3    2              A2    3
D1
 C                  2              B4    1              A3    4
D2
 H                  2              B5    1              A4    4
D3
 C                  5              B6    2              A5    1
D4
 C                  4              B7    1              A6    2
D5
 H                  5              B8    2              A7    1
D6
 H                  7              B9    5              A8    2
D7
 H                  8             B10    4              A9    1
D8
 N                  2             B11    1             A10    4
D9
 C                 12             B12    2             A11    1
D10
 O                 13             B13   12             A12    2
D11
 C                 13             B14   12             A13    2
D12
 O                 15             B15   13             A14   12
D13
 N                 15             B16   13             A15   12
D14
 H                 17             B17   15             A16   13
D15
 Fe                15             B18   13             A17   12
D16
=20
   B1             1.40644101
   B2             2.14928644
   B3             1.39759508
   B4             1.39765674
   B5             2.08511317
   B6             1.39253612
   B7             1.39257680
   B8             1.08638027
   B9             1.08486967
   B10            1.08486443
   B11            1.39557266
   B12            1.38144585
   B13            1.21473476
   B14            1.53434602
   B15            1.21479365
   B16            1.38128209
   B17            1.01319508
   B18            2.48818517
   A1           145.95140520
   A2           119.79706010
   A3           119.77892540
   A4           143.20945469
   A5           120.09436720
   A6           120.08836427
   A7           119.29734053
   A8           119.58833605
   A9           119.59281559
   A10          118.07480691
   A11          126.52180143
   A12          122.62536055
   A13          115.40288341
   A14          121.97364409
   A15          115.41203166
   A16          114.40037764
   A17           74.26757538
   D1            -0.00336246
   D2             0.00283977
   D3          -179.98326314
   D4             0.00000000
   D5            -0.00385223
   D6          -180.00000000
   D7           179.99662248
   D8          -179.99638223
   D9          -180.00000000
   D10           -0.02573946
   D11         -179.98395853
   D12            0.01264207
   D13         -179.98079972
   D14            0.03738560
   D15         -179.99076401
   D16          -83.15595137



-=3D This is automatically added to each message by the mailing script =
=3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txtClassification: UNCLASSIFIED
Caveats: NONE


From owner-chemistry@ccl.net Tue Jun 15 11:41:01 2010
From: "Jim Kress ccl_nospam:_:kressworks.com" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL:G: TDDFT
Message-Id: <-42115-100615002710-1264-ad+1GNE3jQhWx4rW1xOZcQ|-|server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam(_)kressworks.com>
Content-Language: en-us
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0010_01CB0C1C.69EA4710"
Date: Mon, 14 Jun 2010 23:50:45 -0400
MIME-Version: 1.0


Sent to CCL by: "Jim Kress" [ccl_nospam(-)kressworks.com]
This is a multi-part message in MIME format.

------=_NextPart_000_0010_01CB0C1C.69EA4710
Content-Type: text/plain;
	charset="us-ascii"
Content-Transfer-Encoding: 7bit

Have you tried ORCA?  It is quite complete when it comes to calculations
involving virtually any kind of spectroscopy.

 

http://www.thch.uni-bonn.de/tc/orca/

 

Jim Kress

 

> From: owner-chemistry+ccl_nospam==kressworks.com ~~ ccl.net
[mailto:owner-chemistry+ccl_nospam==kressworks.com ~~ ccl.net] On Behalf Of Liu
Jing jliu]^[cuhk.edu.hk
Sent: Monday, June 14, 2010 9:38 PM
To: Kress, Jim 
Subject: CCL:G: TDDFT

 

Dear Jamin,

    Thank you for your quick reply.

    Would you like to say sth about the oscillator strengths. In my

calculation this value is equal to zero for the first excited state, does

it mean this transition is forbidden?

 

Regards

Liu, Jing

2010/6/15 Jamin Krinsky jamink()berkeley.edu <owner-chemistry%ccl.net>

Dear Jing,

If you are using Gaussian, you cannot request excited-state multiplicities
different from the ground state for open-shell molecules (the "singlets" and
"triplets" options are ignored). You can of course calculate the
ground-state configuration for each multiplicity and compare energies of
those... Some other programs (Q-Chem included I think) will let you do
spin-flip TDDFT, but you'd want to read up on the subject before attempting
it (I don't know much about it).

Regards,
Jamin



On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/./cuhk.edu.hk
<http://cuhk.edu.hk/>  <owner-chemistry]~[ccl.net> wrote:

Dear all,

   

  Can you tell me how to set the spin multiplicity of the excited states
when a open-

shell system is concerned? 

 

 Thank you and good luck.

 

Yours Jing 




-- 
Jamin L Krinsky, Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, University of California, Berkeley, CA 94720
jamink]~[berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu <http://glab.cchem.berkeley.edu/> 

 


------=_NextPart_000_0010_01CB0C1C.69EA4710
Content-Type: text/html;
	charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:v=3D"urn:schemas-microsoft-com:vml" =
xmlns:o=3D"urn:schemas-microsoft-com:office:office" =
xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns:m=3D"http://schemas.microsoft.com/office/2004/12/omml" =
xmlns=3D"http://www.w3.org/TR/REC-html40">

<head>
<meta http-equiv=3DContent-Type content=3D"text/html; =
charset=3Dus-ascii">
<meta name=3DGenerator content=3D"Microsoft Word 12 (filtered medium)">
<style>
<!--
 /* Font Definitions */
  ~~ font-face
	{font-family:"Cambria Math";
	panose-1:2 4 5 3 5 4 6 3 2 4;}
 ~~ font-face
	{font-family:Calibri;
	panose-1:2 15 5 2 2 2 4 3 2 4;}
 ~~ font-face
	{font-family:Tahoma;
	panose-1:2 11 6 4 3 5 4 4 2 4;}
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{margin:0in;
	margin-bottom:.0001pt;
	font-size:12.0pt;
	font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
	{mso-style-priority:99;
	color:blue;
	text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
	{mso-style-priority:99;
	color:purple;
	text-decoration:underline;}
span.EmailStyle17
	{mso-style-type:personal-reply;
	font-family:"Calibri","sans-serif";
	color:#1F497D;}
.MsoChpDefault
	{mso-style-type:export-only;}
 ~~ page WordSection1
	{size:8.5in 11.0in;
	margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
	{page:WordSection1;}
-->
</style>
<!--[if gte mso 9]><xml>
 <o:shapedefaults v:ext=3D"edit" spidmax=3D"1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
 <o:shapelayout v:ext=3D"edit">
  <o:idmap v:ext=3D"edit" data=3D"1" />
 </o:shapelayout></xml><![endif]-->
</head>

<body lang=3DEN-US link=3Dblue vlink=3Dpurple>

<div class=3DWordSection1>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Have you tried ORCA?&nbsp; It is quite complete when it =
comes to
calculations involving virtually any kind of =
spectroscopy.<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><a =
href=3D"http://www.thch.uni-bonn.de/tc/orca/">http://www.thch.uni-bonn.de=
/tc/orca/</a><o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Jim Kress<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt =
0in 0in 0in'>

<p class=3DMsoNormal><b><span =
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span>=
</b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
owner-chemistry+ccl_nospam=3D=3Dkressworks.com ~~ ccl.net
[mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com ~~ ccl.net] <b>On =
Behalf Of </b>Liu
Jing jliu]^[cuhk.edu.hk<br>
<b>Sent:</b> Monday, June 14, 2010 9:38 PM<br>
<b>To:</b> Kress, Jim <br>
<b>Subject:</b> CCL:G: TDDFT<o:p></o:p></span></p>

</div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

<div>

<p class=3DMsoNormal>Dear Jamin,<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;&nbsp;&nbsp; Thank you for your quick =
reply.<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;&nbsp;&nbsp; Would you like to say sth about =
the
oscillator strengths. In my<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>calculation this value is equal to zero for the =
first
excited state, does<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>it mean this transition is =
forbidden?<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>Regards<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>Liu, Jing<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>2010/6/15 Jamin Krinsky jamink()<a =
href=3D"http://berkeley.edu">berkeley.edu</a>
&lt;<a =
href=3D"mailto:owner-chemistry%ccl.net">owner-chemistry%ccl.net</a>&gt;<o=
:p></o:p></p>

<p class=3DMsoNormal style=3D'margin-bottom:12.0pt'>Dear Jing,<br>
<br>
If you are using Gaussian, you cannot request excited-state =
multiplicities
different from the ground state for open-shell molecules (the
&quot;singlets&quot; and &quot;triplets&quot; options are ignored). You =
can of
course calculate the ground-state configuration for each multiplicity =
and
compare energies of those... Some other programs (Q-Chem included I =
think) will
let you do spin-flip TDDFT, but you'd want to read up on the subject =
before
attempting it (I don't know much about it).<br>
<br>
Regards,<br>
Jamin<br>
<br>
<o:p></o:p></p>

<div>

<p class=3DMsoNormal>On Mon, Jun 14, 2010 at 1:25 AM, Liu Jing jliu/./<a
href=3D"http://cuhk.edu.hk/" target=3D"_blank">cuhk.edu.hk</a> &lt;<a
href=3D"mailto:owner-chemistry]~[ccl.net" =
target=3D"_blank">owner-chemistry]~[ccl.net</a>&gt;
wrote:<o:p></o:p></p>

<div>

<p class=3DMsoNormal>Dear all,<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;&nbsp; <o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;&nbsp;Can you tell me how to set the spin =
multiplicity
of the excited states when a open-<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>shell system is concerned? <o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;Thank you and good luck.<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>&nbsp;<o:p></o:p></p>

</div>

<div>

<p class=3DMsoNormal>Yours Jing <o:p></o:p></p>

</div>

</div>

<p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><br>
<span style=3D'color:#888888'><br clear=3Dall>
<br>
-- <br>
Jamin L Krinsky, Ph.D.<br>
Molecular Graphics and Computation Facility<br>
175 Tan Hall, University of California, Berkeley, CA 94720<br>
<a href=3D"mailto:jamink]~[berkeley.edu" =
target=3D"_blank">jamink]~[berkeley.edu</a>,
510-643-0616<br>
<a href=3D"http://glab.cchem.berkeley.edu/" =
target=3D"_blank">http://glab.cchem.berkeley.edu</a></span><o:p></o:p></p=
>

</div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

</div>

</body>

</html>

------=_NextPart_000_0010_01CB0C1C.69EA4710--


From owner-chemistry@ccl.net Tue Jun 15 15:05:00 2010
From: "Deskins, N Aaron nadeskins,+,WPI.EDU" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: Constructing nanoparticles
Message-Id: <-42116-100615150344-25320-i8B95ybVcWd4sX7+ogk/5w_+_server.ccl.net>
X-Original-From: "Deskins, N Aaron" <nadeskins^-^WPI.EDU>
Content-Language: en-US
Content-Type: multipart/alternative;
	boundary="_000_A43FA9C6AD151B4BB262595A1B438A60237BF7879EEXCHANGEMAILa_"
Date: Tue, 15 Jun 2010 15:03:33 -0400
MIME-Version: 1.0


Sent to CCL by: "Deskins, N Aaron" [nadeskins .. WPI.EDU]
--_000_A43FA9C6AD151B4BB262595A1B438A60237BF7879EEXCHANGEMAILa_
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

I haven't received any responses to my request, so I thought I should be mo=
re specific. Here are some examples where highly-crystalline nanoparticles =
were modeled. I suppose you could create these by hand, but some software i=
nterface would go faster. Any ideas?

Han, Miranda, and Ceder, Physical Review B, "Effect of particle size and su=
rface structure on adsorption of O and OH on platinum nanoparticles: A firs=
t-principles study" 77, 075410, 2008.
Yudanov et al., JACS, "How the C-O bond breaks during Methanol Decompositio=
n on Nanocrystallites of Palladium Catalysts", 130, 9342-9352, 2008.
Barnard et al., Physical Review B, "Modeling the structure and electronic p=
roperties of TiO2 nanoparticles", 73, 205405, 2006.

> From: owner-chemistry+nadeskins=3D=3Dwpi.edu/./ccl.net [mailto:owner-chemistr=
y+nadeskins=3D=3Dwpi.edu/./ccl.net]

Hello all,
  Is there software (free or commercial) that can be used to construct atom=
ic models of crystalline nanoparticles  - not clusters, but real nanopartic=
les (5-50 nm) for molecular dynamics simulations? I'm mostly interested in =
particles with well-defined faces.

Thank you,
Aaron

--_000_A43FA9C6AD151B4BB262595A1B438A60237BF7879EEXCHANGEMAILa_
Content-Type: text/html; charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:v=3D"urn:schemas-microsoft-com:vml" xmlns:o=3D"urn:schemas-micr=
osoft-com:office:office" xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns:x=3D"urn:schemas-microsoft-com:office:excel" xmlns:p=3D"urn:schemas-m=
icrosoft-com:office:powerpoint" xmlns:a=3D"urn:schemas-microsoft-com:office=
:access" xmlns:dt=3D"uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns:s=3D"=
uuid:BDC6E3F0-6DA3-11d1-A2A3-00AA00C14882" xmlns:rs=3D"urn:schemas-microsof=
t-com:rowset" xmlns:z=3D"#RowsetSchema" xmlns:b=3D"urn:schemas-microsoft-co=
m:office:publisher" xmlns:ss=3D"urn:schemas-microsoft-com:office:spreadshee=
t" xmlns:c=3D"urn:schemas-microsoft-com:office:component:spreadsheet" xmlns=
:odc=3D"urn:schemas-microsoft-com:office:odc" xmlns:oa=3D"urn:schemas-micro=
soft-com:office:activation" xmlns:html=3D"http://www.w3.org/TR/REC-html40" =
xmlns:q=3D"http://schemas.xmlsoap.org/soap/envelope/" xmlns:rtc=3D"http://m=
icrosoft.com/officenet/conferencing" xmlns:D=3D"DAV:" xmlns:Repl=3D"http://=
schemas.microsoft.com/repl/" xmlns:mt=3D"http://schemas.microsoft.com/share=
point/soap/meetings/" xmlns:x2=3D"http://schemas.microsoft.com/office/excel=
/2003/xml" xmlns:ppda=3D"http://www.passport.com/NameSpace.xsd" xmlns:ois=
=3D"http://schemas.microsoft.com/sharepoint/soap/ois/" xmlns:dir=3D"http://=
schemas.microsoft.com/sharepoint/soap/directory/" xmlns:ds=3D"http://www.w3=
.org/2000/09/xmldsig#" xmlns:dsp=3D"http://schemas.microsoft.com/sharepoint=
/dsp" xmlns:udc=3D"http://schemas.microsoft.com/data/udc" xmlns:xsd=3D"http=
://www.w3.org/2001/XMLSchema" xmlns:sub=3D"http://schemas.microsoft.com/sha=
repoint/soap/2002/1/alerts/" xmlns:ec=3D"http://www.w3.org/2001/04/xmlenc#"=
 xmlns:sp=3D"http://schemas.microsoft.com/sharepoint/" xmlns:sps=3D"http://=
schemas.microsoft.com/sharepoint/soap/" xmlns:xsi=3D"http://www.w3.org/2001=
/XMLSchema-instance" xmlns:udcs=3D"http://schemas.microsoft.com/data/udc/so=
ap" xmlns:udcxf=3D"http://schemas.microsoft.com/data/udc/xmlfile" xmlns:udc=
p2p=3D"http://schemas.microsoft.com/data/udc/parttopart" xmlns:wf=3D"http:/=
/schemas.microsoft.com/sharepoint/soap/workflow/" xmlns:dsss=3D"http://sche=
mas.microsoft.com/office/2006/digsig-setup" xmlns:dssi=3D"http://schemas.mi=
crosoft.com/office/2006/digsig" xmlns:mdssi=3D"http://schemas.openxmlformat=
s.org/package/2006/digital-signature" xmlns:mver=3D"http://schemas.openxmlf=
ormats.org/markup-compatibility/2006" xmlns:m=3D"http://schemas.microsoft.c=
om/office/2004/12/omml" xmlns:mrels=3D"http://schemas.openxmlformats.org/pa=
ckage/2006/relationships" xmlns:spwp=3D"http://microsoft.com/sharepoint/web=
partpages" xmlns:ex12t=3D"http://schemas.microsoft.com/exchange/services/20=
06/types" xmlns:ex12m=3D"http://schemas.microsoft.com/exchange/services/200=
6/messages" xmlns:pptsl=3D"http://schemas.microsoft.com/sharepoint/soap/Sli=
deLibrary/" xmlns:spsl=3D"http://microsoft.com/webservices/SharePointPortal=
Server/PublishedLinksService" xmlns:Z=3D"urn:schemas-microsoft-com:" xmlns:=
st=3D"&#1;" xmlns=3D"http://www.w3.org/TR/REC-html40">

<head>
<meta http-equiv=3DContent-Type content=3D"text/html; charset=3Dus-ascii">
<meta name=3DGenerator content=3D"Microsoft Word 12 (filtered medium)">
<style>
<!--
 /* Font Definitions */
 /./font-face
	{font-family:"Cambria Math";
	panose-1:2 4 5 3 5 4 6 3 2 4;}
/./font-face
	{font-family:Calibri;
	panose-1:2 15 5 2 2 2 4 3 2 4;}
/./font-face
	{font-family:Tahoma;
	panose-1:2 11 6 4 3 5 4 4 2 4;}
 /* Style Definitions */
 p.MsoNormal, li.MsoNormal, div.MsoNormal
	{margin:0in;
	margin-bottom:.0001pt;
	font-size:12.0pt;
	font-family:"Times New Roman","serif";}
h1
	{mso-style-priority:9;
	mso-style-link:"Heading 1 Char";
	mso-margin-top-alt:auto;
	margin-right:0in;
	mso-margin-bottom-alt:auto;
	margin-left:0in;
	font-size:24.0pt;
	font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
	{mso-style-priority:99;
	color:blue;
	text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
	{mso-style-priority:99;
	color:purple;
	text-decoration:underline;}
span.apple-style-span
	{mso-style-name:apple-style-span;}
span.EmailStyle18
	{mso-style-type:personal;
	font-family:"Arial","sans-serif";
	color:blue;}
span.EmailStyle19
	{mso-style-type:personal-reply;
	font-family:"Arial","sans-serif";
	color:blue;}
span.Heading1Char
	{mso-style-name:"Heading 1 Char";
	mso-style-priority:9;
	mso-style-link:"Heading 1";
	font-weight:bold;}
.MsoChpDefault
	{mso-style-type:export-only;
	font-size:10.0pt;}
/./page WordSection1
	{size:8.5in 11.0in;
	margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
	{page:WordSection1;}
-->
</style>
<!--[if gte mso 9]><xml>
 <o:shapedefaults v:ext=3D"edit" spidmax=3D"1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
 <o:shapelayout v:ext=3D"edit">
  <o:idmap v:ext=3D"edit" data=3D"1" />
 </o:shapelayout></xml><![endif]-->
</head>

<body lang=3DEN-US link=3Dblue vlink=3Dpurple>

<div class=3DWordSection1>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Arial","s=
ans-serif";
color:black'>I haven&#8217;t received any responses to my request, so I tho=
ught
I should be more specific. Here are some examples where highly-crystalline
nanoparticles were modeled. I suppose you could create these by hand, but s=
ome
software interface would go faster. Any ideas?<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Arial","s=
ans-serif";
color:black'><o:p>&nbsp;</o:p></span></p>

<h1><span style=3D'font-size:11.0pt;font-family:"Arial","sans-serif";color:=
black;
font-weight:normal'>Han, Miranda, and Ceder, Physical Review B,</span><span
style=3D'font-size:11.0pt;font-family:"Arial","sans-serif";color:black'> &#=
8220;</span><span
style=3D'font-size:11.0pt;font-family:"Arial","sans-serif";color:black;
font-weight:normal'>Effect of particle size and surface structure on adsorp=
tion
of O and OH on platinum nanoparticles: A first-principles study&#8221; 77,
075410, 2008.<o:p></o:p></span></h1>

<h1><span style=3D'font-size:11.0pt;font-family:"Arial","sans-serif";color:=
black;
font-weight:normal'>Yudanov et al., JACS, &#8220;How the C-O bond breaks du=
ring
Methanol Decomposition on Nanocrystallites of Palladium Catalysts&#8221;, 1=
30, 9342-9352,
2008.<o:p></o:p></span></h1>

<h1><span style=3D'font-size:11.0pt;font-family:"Arial","sans-serif";font-w=
eight:
normal'>Barnard et al., Physical Review B, &#8220;Modeling the structure an=
d
electronic properties of TiO2 nanoparticles&#8221;, 73, 205405, 2006.<o:p><=
/o:p></span></h1>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Arial","s=
ans-serif";
color:blue'><o:p>&nbsp;</o:p></span></p>

<div>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in =
0in 0in'>

<p class=3DMsoNormal><b><span style=3D'font-size:10.0pt;font-family:"Tahoma=
","sans-serif"'>From:</span></b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
owner-chemistry+nadeskins=3D=3Dwpi.edu/./ccl.net
[mailto:owner-chemistry+nadeskins=3D=3Dwpi.edu/./ccl.net] <o:p></o:p></span><=
/p>

</div>

</div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

<div>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Arial","s=
ans-serif"'>Hello
all,<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Arial","s=
ans-serif"'>&nbsp;
Is there software (free or commercial) that can be used to construct atomic
models of crystalline nanoparticles &nbsp;&#8211; not clusters, but real
nanoparticles (5-50 nm) for molecular dynamics simulations? I&#8217;m mostl=
y
interested in particles with well-defined faces.<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Arial","s=
ans-serif"'><o:p>&nbsp;</o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Arial","s=
ans-serif"'>Thank
you,<o:p></o:p></span></p>

<p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Arial","s=
ans-serif"'>Aaron
<o:p></o:p></span></p>

</div>

</div>

</body>

</html>

--_000_A43FA9C6AD151B4BB262595A1B438A60237BF7879EEXCHANGEMAILa_--


From owner-chemistry@ccl.net Tue Jun 15 15:39:01 2010
From: "Geoffrey Hutchison geoffh#pitt.edu" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL:G: CNDO or INDO parameters for Se?
Message-Id: <-42117-100615153041-3229-mKI274xTM/GlE+JF9f3mZA|-|server.ccl.net>
X-Original-From: Geoffrey Hutchison <geoffh||pitt.edu>
Content-transfer-encoding: quoted-printable
Content-type: text/plain; charset=us-ascii
Date: Tue, 15 Jun 2010 15:30:30 -0400
MIME-version: 1.0 (Apple Message framework v1078)


Sent to CCL by: Geoffrey Hutchison [geoffh]-[pitt.edu]
Dear CCL,

Here's a non-Gaussian question!

Zerner's implementation of INDO/S is remarkably good for UV/Vis spectra, =
particularly of organic conjugated molecules. Most of us use it for =
undergrad labs -- a quick way to compute an optical absorption spectra.

Sadly, I can't find any parameters for common fourth-row main-block =
elements like As and Se, even though Br and I parameters exist. Thanks =
to a few people, I've examined Zerner's original Fortran code, and it =
has most everything needed (e.g., Slater exponent) for both As and Se.

What's missing is the "Gamma AA" parameter for ZINDO. Now, if you refer =
to Pople's book (Approximate MO Theory), Gamma-AA should be the Coulomb =
( AA | AA ) integral. Pople helpfully gives the derivation in an =
appendix.

Here's my worry:
1) The CNDO Slater exponents you find in the literature for Se are =
*VERY* different from Zerner's.
2) When I use Pople's derivation for ( AA | AA ) with Zerner's =
exponents, I get strange numbers for carbon and hydrogen (i.e., they =
don't match Zerner's tabulated Gamma-AA).

So I'm curious about a few things:
1) Whether anyone knows of an INDO parameter (published or =
non-published) for the Gamma-AA integral for fourth-row elements, =
particularly Se. I'd like to make sure the method can handle molecules =
like selenocysteine, but arsenic is OK too.
2) Why Zerner used different Slater exponents than CNDO? Pople's book =
indicates that INDO should generally use the same parameters as CNDO/2. =
I can't find a discussion in Zerner's papers about this.
3) Whether INDO uses a different derivation for (AA | AA) somehow.

I'd settle for a code in any form which evaluates Gamma-AA given a =
Slater exponent -- preferably one which matches Zerner's evaluations for =
1st and 2nd row elements.

Thanks very much,
-Geoff

P.S. If you're curious, the results will be going into an open source =
INDO implementation eventually.

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh^pitt.edu
web: http://hutchison.chem.pitt.edu/


From owner-chemistry@ccl.net Tue Jun 15 17:14:00 2010
From: "John McKelvey jmmckel#%#gmail.com" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL:G: CNDO or INDO parameters for Se?
Message-Id: <-42118-100615165800-10418-v0ZqeUJ8NCpUtujr8TwsUQ]=[server.ccl.net>
X-Original-From: John McKelvey <jmmckel-$-gmail.com>
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset=ISO-8859-1
Date: Tue, 15 Jun 2010 16:57:50 -0400
MIME-Version: 1.0


Sent to CCL by: John McKelvey [jmmckel-$-gmail.com]
Geoff,

The theoretical <aa|aa> in indo/s is defined to be the number I-A,
where I is the atomic ionization potential, and A is the electron
affinity.  Zerner's exponents for this are different from Slater's
rules because at this point in the periodiv table they are from the
single-zeta contraction of high level double-zeta ab initio
calculations.  Without this approach the orbital would fall off to
quickly with distance.

So,  plug in the I-A values, and then vary Beta-S, Beta-P, and Beta-D
to suit your needs.

Best regards,

John McKelvey

On Tue, Jun 15, 2010 at 3:30 PM, Geoffrey Hutchison geoffh#pitt.edu
<owner-chemistry^ccl.net> wrote:
>
> Sent to CCL by: Geoffrey Hutchison [geoffh]-[pitt.edu]
> Dear CCL,
>
> Here's a non-Gaussian question!
>
> Zerner's implementation of INDO/S is remarkably good for UV/Vis spectra, =
particularly of organic conjugated molecules. Most of us use it for undergr=
ad labs -- a quick way to compute an optical absorption spectra.
>
> Sadly, I can't find any parameters for common fourth-row main-block eleme=
nts like As and Se, even though Br and I parameters exist. Thanks to a few =
people, I've examined Zerner's original Fortran code, and it has most every=
thing needed (e.g., Slater exponent) for both As and Se.
>
> What's missing is the "Gamma AA" parameter for ZINDO. Now, if you refer t=
o Pople's book (Approximate MO Theory), Gamma-AA should be the Coulomb ( AA=
 | AA ) integral. Pople helpfully gives the derivation in an appendix.
>
> Here's my worry:
> 1) The CNDO Slater exponents you find in the literature for Se are *VERY*=
 different from Zerner's.
> 2) When I use Pople's derivation for ( AA | AA ) with Zerner's exponents,=
 I get strange numbers for carbon and hydrogen (i.e., they don't match Zern=
er's tabulated Gamma-AA).
>
> So I'm curious about a few things:
> 1) Whether anyone knows of an INDO parameter (published or non-published)=
 for the Gamma-AA integral for fourth-row elements, particularly Se. I'd li=
ke to make sure the method can handle molecules like selenocysteine, but ar=
senic is OK too.
> 2) Why Zerner used different Slater exponents than CNDO? Pople's book ind=
icates that INDO should generally use the same parameters as CNDO/2. I can'=
t find a discussion in Zerner's papers about this.
> 3) Whether INDO uses a different derivation for (AA | AA) somehow.
>
> I'd settle for a code in any form which evaluates Gamma-AA given a Slater=
 exponent -- preferably one which matches Zerner's evaluations for 1st and =
2nd row elements.
>
> Thanks very much,
> -Geoff
>
> P.S. If you're curious, the results will be going into an open source IND=
O implementation eventually.
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geoffh%pitt.edu
> web: http://hutchison.chem.pitt.edu/
>
>
>
> - This is automatically added to each message by the mailing script -> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt>
>
>



--=20
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel^gmail.com


From owner-chemistry@ccl.net Tue Jun 15 18:02:00 2010
From: "W Agnessi witch.of.agnessi*gmail.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: Program for enzyme design
Message-Id: <-42119-100615163823-19366-5yEiJFSpWRD6xA5X8eka8w{=}server.ccl.net>
X-Original-From: "W  Agnessi" <witch.of.agnessi{=}gmail.com>
Date: Tue, 15 Jun 2010 16:38:22 -0400


Sent to CCL by: "W  Agnessi" [witch.of.agnessi[]gmail.com]
Hello CCLers,

I'm working on computational design of an enzyme to increase it's affinity for a non-natural substrate. I wish to mutate 2-3 residues at the ligand binding site such that it can bind better a non-natural substrate. Quite a few X-ray structures are available for the apo as well as holo enzyme,with different ligands. However no structure with that non-natural substrate is available.

I'm looking  for freely available softwares, which would be able to computationally re-design the active site. My input to the program would be a (badly) docked structure of the enzyme and my ligand of interest.

Any suggestions, comments, pointers, relevant literature links are most welcome.

Thanks in advance

-WoA


From owner-chemistry@ccl.net Tue Jun 15 22:10:00 2010
From: "Brian Salter-Duke brian.james.duke]_[gmail.com" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL:G: CNDO or INDO parameters for Se?
Message-Id: <-42120-100615192716-12583-hIpLNh51mGC+FRYbN9Gk/g]~[server.ccl.net>
X-Original-From: Brian Salter-Duke <brian.james.duke.]~[.gmail.com>
Content-Disposition: inline
Content-Type: text/plain; charset=us-ascii
Date: Wed, 16 Jun 2010 08:28:35 +1000
MIME-Version: 1.0


Sent to CCL by: Brian Salter-Duke [brian.james.duke/a\gmail.com]
On Tue, Jun 15, 2010 at 03:30:30PM -0400, Geoffrey Hutchison geoffh#pitt.edu wrote:
> 
> Sent to CCL by: Geoffrey Hutchison [geoffh]-[pitt.edu]
> Dear CCL,

> Here's a non-Gaussian question!

> Zerner's implementation of INDO/S is remarkably good for UV/Vis spectra, particularly of organic conjugated molecules. Most of us use it for undergrad labs -- a quick way to compute an optical absorption spectra.

> Sadly, I can't find any parameters for common fourth-row main-block
> elements like As and Se, even though Br and I parameters exist. Thanks
> to a few people, I've examined Zerner's original Fortran code, and it
> has most everything needed (e.g., Slater exponent) for both As and Se.

> What's missing is the "Gamma AA" parameter for ZINDO. Now, if you
> refer to Pople's book (Approximate MO Theory), Gamma-AA should be the
> Coulomb ( AA | AA ) integral. Pople helpfully gives the derivation in
> an appendix.

> Here's my worry:
> 1) The CNDO Slater exponents you find in the literature for Se are 
> *VERY* different from Zerner's.

ZINDO has two methods - for geometries (essentially) and for
spectroscopy. Does he use different exponents for both? If they are
different from each other, are you sure you found the INDO-S ones?

> 2) When I use Pople's derivation for ( AA | AA ) with Zerner's 
> exponents, I get strange numbers for carbon and hydrogen (i.e., they 
> don't match Zerner's tabulated Gamma-AA).  

CNDO was intended to match Hartree-Fock minimum basis STO resuts, not
spectroscopy. Pople's INDO was the same. All attempts to use INDO for
spectroscopy (often called INDO-S) use quite different parameters for 
( AA | AA ). This started of course with Pariser/Parr/Pople for aromatic
systems. The C ( AA | AA ) used there is different to that calculated
exactly from a C Pi orbital.

> So I'm curious about a few things:
> 1) Whether anyone knows of an INDO parameter (published or non-published) 
> for the Gamma-AA integral for fourth-row elements, particularly Se. I'd 
> like to make sure the method can handle molecules like selenocysteine, 
> but arsenic is OK too.
> 2) Why Zerner used different Slater exponents than CNDO? Pople's book 
> indicates that INDO should generally use the same parameters as CNDO/2. 
> I can't find a discussion in Zerner's papers about this.
> 3) Whether INDO uses a different derivation for (AA | AA) somehow.

For (2) and (3) see above.
 
> I'd settle for a code in any form which evaluates Gamma-AA given a 
> Slater exponent -- preferably one which matches Zerner's evaluations 
> for 1st and 2nd row elements.

About 15 years ago or so, I had an Honours student try to parameterize
ZINDO for the atoms Ga - Br but for the geometries ZINDO, not the
spectroscopy ZINDO. The latter is of course much more widely used, but
we had reasons why we wanted parameters for the geometries version. The
results were not very good and the project needed more work that was
never done. There was also another major problem. We used Mike Zerner's
original code. After the student had left, I added the new parameters to
the HyperChem data files and ran a series of compounds with HyperChem,
as at that time HyperChem seemed to be the code that everyone used for
ZINDO.  The results did not agree with Zerner's code, so I decided not
to publish them. They are not what you want anyway!

I did have an idea at that time to look at the parameters for the SINDO
method. I suggest you try to look at the code for that. It might give
you some ideas.

Regards, Brian. 

> Thanks very much,
> -Geoff
> 
> P.S. If you're curious, the results will be going into an open source 
> INDO implementation eventually.
> 
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geoffh%pitt.edu
> web: http://hutchison.chem.pitt.edu/
> 

-- 
Brian Salter-Duke (Brian Duke)  Brian.Salter-Duke*_*pharm.monash.edu.au 
                     Honorary Researcher Fellow 
            Monash Institute of Pharmaceutical Sciences,
      Monash University Parkville Campus, VIC 3052, Australia.