Can you also suggest a free software for the con= struction and preparing input file of fe complex for MOPAC.

I use Discovery Studio DS Visualizer = > from Accelrys for building similar compounds - http:= //accelrys.com/downloads/freeware/ . It is free for academics an= d has a number of templates for metal ion coordination.

Cheers,

Flick

_______________

William F. Coleman

Professor of Chemistry

Wellesley College

Wellesley MA 02481

www.wellesley.edu/Chemist= ry/colemanw.html

Editor, JCE WebWare and JCE Featured = Molecules

http://www.jce.divched.org/JCE= DLib/WebWare/

h= ttp://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html=

----=_--1dfb0ef0.1dfb0dbb.c69dddff-- From owner-chemistry@ccl.net Tue Aug 4 09:49:00 2009 From: "irfan ahmad irfaahmad[a]gmail.com" To: CCL Subject: CCL: reorganization energy Message-Id: <-39920-090804075128-8199-rrywwblmWNfTIHntHQ+4RQ**server.ccl.net> X-Original-From: irfan ahmad Content-Type: multipart/alternative; boundary=0016368324ea95a49104704e0c07 Date: Tue, 4 Aug 2009 18:07:07 +0800 MIME-Version: 1.0 Sent to CCL by: irfan ahmad [irfaahmad!^!gmail.com] --0016368324ea95a49104704e0c07 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks Prof. Geoffrey Hutchison i understand that solvent reorganization energy means the internal reorganization energy in solvent. that can be calculated easily. As you mentioned that "If you want to calculate the real external reorganization in a lattice, you have to consider how the lattice would change upon charge transfer (polarization, polaron deformation, etc.) " , can you tell me about some references (published work) where they calculated external reorganization energy. I have one paper of JL Bredas who calculated it (=EF=BB=BFJ. AM. CHEM. SOC.= 2008, 130, 12377=E2=80=9312384) but i couldnot understand properly. If you explai= n it how to calculate, i will be thankful to you Irfan Ahmad Northeast Normal university China On 8/3/09, Geoffrey Hutchison geoffh..pitt.edu wrote: > > > Sent to CCL by: Geoffrey Hutchison [geoffh||pitt.edu] > >> I want to calculate the total reorganization energy of a molecule (from >> the family of organic field effect transistors). The total reorganizatio= n >> energy can be divided into two terms (1) internal reorganization energy = (2) >> external reorganization energy. >> > > Well, you mention that you're looking at OFET molecules, so it gets > slightly complicated to define the external reorganization energy. Are yo= u > looking at the reorganization energy for a solid-state charge transfer --= if > so, there's no solvent. > > my 2nd question is that if i calculate reorganization energy in solvent, >> can i say it is solvent reorganization energy >> > > From the way you wrote that, you would be calculating the reorganization > energy of the molecule using a solvation model. The solvent reorganizatio= n > energy is created by the change in the geometry of the solvent (or other > environment). Certainly if you're considering charge transfer in solution= , > the internal reorganization energy will be calculated more accurately in = a > solvent model. > > If you want to calculate the real external reorganization in a lattice, y= ou > have to consider how the lattice would change upon charge transfer > (polarization, polaron deformation, etc.) > > Hope that helps, > -Geoff > > --- > Prof. Geoffrey Hutchison > Assistant Professor, Department of Chemistry > University of Pittsburgh > http://hutchison.chem.pitt.edu/ > Office: (412) 648-0492 > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --0016368324ea95a49104704e0c07 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Thanks Prof. Geoffrey Hutchison

i understand that solvent reorganization energy means the internal reo= rganization energy in solvent. that can be calculated easily.

As you mentioned that "If you want to calculate the real external= reorganization in a lattice, you have to consider how the lattice would ch= ange upon charge transfer (polarization, polaron deformation, etc.)
" , can you=C2=A0tell me about some references (published work) where = they calculated external reorganization energy.

I have one paper of JL Bredas who calculated it (=EF=BB=BFJ. AM. CHEM.= SOC. 2008, 130, 12377=E2=80=9312384) but i couldnot understand properly. I= f you explain it how to calculate, i will be thankful to you

=C2=A0

Irfan Ahmad

Northeast Normal university

China
=C2=A0

On 8/3/09, G= eoffrey Hutchison geoffh..pitt.edu <= owner-chemistry#,#ccl.net> = wrote:

Sent to CCL by: Geoffrey Hut= chison [geoffh||pitt.edu]

I want to calculate the total re= organization energy of a molecule (from the family of organic field effect = transistors). The total reorganization energy can be divided into two terms= (1) internal reorganization energy (2) external reorganization energy.

Well, you mention that you're looking at OFET molecule= s, so it gets slightly complicated to define the external reorganization en= ergy. Are you looking at the reorganization energy for a solid-state charge= transfer -- if so, there's no solvent.

my 2nd question is that if i cal= culate reorganization energy in solvent, can i say it is solvent reorganiza= tion energy

From the way you wrote that, you would be calculating the = reorganization energy of the molecule using a solvation model. The solvent = reorganization energy is created by the change in the geometry of the solve= nt (or other environment). Certainly if you're considering charge trans= fer in solution, the internal reorganization energy will be calculated more= accurately in a solvent model.

If you want to calculate the real external reorganization in a lattice,= you have to consider how the lattice would change upon charge transfer (po= larization, polaron deformation, etc.)

Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Assistant Professor, Department of C= hemistry
University of Pittsburgh
http://hutchison.chem.pitt.edu/
Office: (412) 648-0492

-=3D This is automatically added to e= ach message by the mailing script =3D-
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--0016368324ea95a49104704e0c07-- From owner-chemistry@ccl.net Tue Aug 4 11:32:00 2009 From: "Stephen Bowlus chezbowlus * comcast.net" To: CCL Subject: CCL: Query regarding iron complex optimization using MOPAC Message-Id: <-39921-090804110814-8725-3NSFZ6+BCRtBysZ7gxY3hw*server.ccl.net> X-Original-From: Stephen Bowlus Content-Type: multipart/alternative; boundary=Apple-Mail-1-506366928 Date: Tue, 4 Aug 2009 07:35:06 -0700 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Stephen Bowlus [chezbowlus-x-comcast.net] --Apple-Mail-1-506366928 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit MOPAC input can be built with AVOGADRO, an open source program distributed under GPL. See http://sourceforge.net/projects/avogadro/ -sb On Aug 3, 2009, at 10:50 PM, Nilesh Tawari tawari.nilesh.:.gmail.com wrote: > Hello Gallagher, > Can you also suggest a free software for the construction and > preparing input file of fe complex for MOPAC. > > thanks in advance > -nilesh > > On Mon, Aug 3, 2009 at 9:54 PM, Nilesh Tawari [gmail.com> wrote: > Hello Gallagher, > Thanks a lot for the reply as suggested will be using PM6 method for > optimization using UHF keyword can you please suggest other keywords > necessary beside charge and mutiplicity for transition metal complex > calculation and additional keywords which can be used to get various > properties of complex. > > thanks in advance > -nilesh > > On Tue, Aug 4, 2009 at 5:50 AM, David Gallagher gallagher.da-*- > gmail.com wrote: > Hi Nilesh, > > Unless you have a good reason to stick with PM3, I would recommend > MOPAC2009 with PM6, as it has higher accuracy for geometries and > heats of formation. MOPAC2009 is free for academics. > > The 'UHF' keyword generally gives the most reliable results for > transition metal complexes. > > You can find links for the MOPAC manual and download (free for > academics) at: > http://cacheresearch.com/mopac.html#mopac-support > > Good luck, > David Gallagher > CACheResearch.com > > > On Mon, Aug 3, 2009 at 10:45 AM, Nilesh Tawari > tawari.nilesh*_*gmail.com wrote: > > Sent to CCL by: "Nilesh Tawari" [tawari.nilesh[*]gmail.com] > Hello everyone, > I want to optimize an iron (Fe+++) hexacoordinated complex with my > molecule using MOPAC using PM3 can you please suggest the essential > keywords and the precautions to be taken in this calculations and > get some properties like energy and heat of formation. As i am > beginner for MOPAC any help would be of great importance to me. If > possible please suggest any tutorial for the same. > Thanks in advance > -nilesh > > > > -= This is automatically added to each message by the mailing script > =- > E-mail to subscribers: CHEMISTRY^ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST^ccl.net or use> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > > > > > > -- > Mr. Nilesh R. Tawari > PhD (Tech) Medicinal Chemistry > ICT, Matunga (E), Mumbai-19 > > > > -- > Mr. Nilesh R. Tawari > PhD (Tech) Medicinal Chemistry > ICT, Matunga (E), Mumbai-19 --Apple-Mail-1-506366928 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable

MOPAC input can be built = with AVOGADRO, an open source program distributed under GPL. = See http://sourceforge.net/= projects/avogadro/

-sb

On = Aug 3, 2009, at 10:50 PM, Nilesh Tawari tawari.nilesh.:.gmail.com = wrote:

Hello Gallagher,
Can you = also suggest a free software for the construction and preparing input = file of fe complex for MOPAC.

thanks in = advance
-nilesh

On Mon, Aug 3, 2009 at 9:54 PM, Nilesh Tawari = <tawari.nilesh]|[gmail.com>= ; wrote:

Hello = Gallagher,

Thanks a lot for the reply as suggested will be = using PM6 method for optimization using UHF keyword can you please = suggest other keywords necessary beside charge and mutiplicity for = transition metal complex calculation and additional keywords which can = be used to get various properties of complex.

=
thanks in advance
=
-nilesh

On Tue, Aug 4, 2009 at 5:50 AM, David Gallagher = gallagher.da-*-gmail.com <owner-chemistry]|[ccl.net> wrote:
=
Hi Nilesh,

=
Unless you have a good reason to stick with PM3, I would recommend = MOPAC2009 with PM6, as it has higher accuracy for geometries and heats = of formation. MOPAC2009 is free for academics.
=

The 'UHF' keyword generally gives the most reliable = results for transition metal complexes.

=
You can find links for the MOPAC manual and download (free for = academics) at:

http://cacheresearch.com/mopac.html#mopac-support

Good luck,

David Gallagher
=
CACheResearch.com

=
On Mon, Aug 3, 2009 at 10:45 AM, Nilesh Tawari tawari.nilesh*_*gmail.com <owner-chemistry^ccl.net> wrote:
=

Sent to CCL by: "Nilesh Tawari" = [tawari.nilesh[*]gmail.com]
Hello everyone,
I want to = optimize an iron (Fe+++) hexacoordinated complex with my molecule using = MOPAC using PM3 can you please suggest the essential keywords and the = precautions to be taken in this calculations and get some properties = like energy and heat of formation. As i am beginner for MOPAC any help = would be of great importance to me. If possible please suggest any = tutorial for the same.
Thanks in = advance
-nilesh

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

E-mail to = subscribers: CHEMISTRY^ccl.net or use:
= http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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= http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=
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http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/<= br> =

-- =
Mr. Nilesh R. Tawari
PhD (Tech) Medicinal Chemistry
ICT, = Matunga (E), Mumbai-19

--
Mr. Nilesh R. Tawari
PhD (Tech) Medicinal = Chemistry
ICT, Matunga (E), Mumbai-19
=

= --Apple-Mail-1-506366928-- From owner-chemistry@ccl.net Tue Aug 4 12:06:01 2009 From: "clara song clarasong83|*|gmail.com" To: CCL Subject: CCL:G: Gaussian03 TDDFT calculation for excited states Message-Id: <-39922-090803132847-15188-/ZZR8PJ1rFaatSBWR74oTA^^^server.ccl.net> X-Original-From: "clara song" Date: Mon, 3 Aug 2009 13:28:44 -0400 Sent to CCL by: "clara song" [clarasong83:-:gmail.com] Anyone could help? Thanks > "clara song clarasong83++gmail.com" wrote: > > Sent to CCL by: "clara song" [clarasong83]![gmail.com] > Hi, > > I am using the TD keyword in G03 to calculation the excited states for gold clusters. And I experienced two problems with the following: > > #p TD(50-50,Nstates=10) b3lyp/gen pseudo=read pop=full gfinput, > > And in the output file I got, there are following excited states: > > Excitation energies and oscillator strengths: > Excited State 1: Triplet-B2 1.4373 eV 862.60 nm f=0.0000 > 44 -> 45 0.75598 > This state for optimization and/or second-order correction. > Total Energy, E(RPA) = -276.707873393 > Copying the excited state density for this state as the 1-particle RhoCI density. > Excited State 2: Triplet-B2 2.0939 eV 592.12 nm f=0.0000 > 44 -> 46 0.72285 > Excited State 3: Singlet-B2 2.1324 eV 581.44 nm f=0.0000 > 44 -> 45 0.61976 > Excited State 4: Singlet-B2 2.3489 eV 527.83 nm f=0.0000 > 44 -> 46 0.68672 > ..... > > So > (1) As you can see the first several states have f=0.0, should I still treat the one with lowest excitation energy as the first excited state, or I need to find the one with a non zero f value? > > (2) there is another structure having no sysmmetry as in the output: > > Initial guess orbital symmetries: > Occupied (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) > Virtual (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A).... > > So in this case, what should we do in order to get other electronic state(for example, from ground state 1A1-->1B2) for further calculation? > > Thanks a lot for your help. > > From owner-chemistry@ccl.net Tue Aug 4 13:06:00 2009 From: "John McKelvey jmmckel(!)gmail.com" To: CCL Subject: CCL:G: Gaussian03 TDDFT calculation for excited states Message-Id: <-39923-090804124741-6974-+m1ecpn6xlSAAH9JpGHqwA=-=server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=0016368325b445aeca047053a4aa Date: Tue, 4 Aug 2009 12:47:27 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel]-[gmail.com] --0016368325b445aeca047053a4aa Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit 10 states were requested. Would be good to see the rest. Which state to select as a point of interest depends on what your purpose is. Computed Singlet->Triplets will always have a zero computed oscillator strength, [in the absence of spin-orbit coupling] though experimentally they may be observed with very low extinction coefficients. For singlets if you are comparing with experiment and the observed extinction coeff is a thousand or more then one should look for a computed osc str > 0. There are no hard and fast rules here for mapping computed values versus computed values; the user has to perform this mapping though experience (in most cases.) [It is noted that your data shows no symmetry, so that issue can be ignored here.] If there are no experimental data it would be useful to see if there are singlet states with osc > 0; this might require expanding the number of states sought. If there is no interest in triplets then they need not be solved for [check documenattion to do this] Hope this helps, John McKelvey On Mon, Aug 3, 2009 at 1:28 PM, clara song clarasong83|*|gmail.com < owner-chemistry||ccl.net> wrote: > > Sent to CCL by: "clara song" [clarasong83:-:gmail.com] > > Anyone could help? > Thanks > > > "clara song clarasong83++gmail.com" wrote: > > > > Sent to CCL by: "clara song" [clarasong83]![gmail.com] > > Hi, > > > > I am using the TD keyword in G03 to calculation the excited states for > gold clusters. And I experienced two problems with the following: > > > > #p TD(50-50,Nstates=10) b3lyp/gen pseudo=read pop=full gfinput, > > > > And in the output file I got, there are following excited states: > > > > Excitation energies and oscillator strengths: > > Excited State 1: Triplet-B2 1.4373 eV 862.60 nm f=0.0000 > > 44 -> 45 0.75598 > > This state for optimization and/or second-order correction. > > Total Energy, E(RPA) = -276.707873393 > > Copying the excited state density for this state as the 1-particle RhoCI > density. > > Excited State 2: Triplet-B2 2.0939 eV 592.12 nm f=0.0000 > > 44 -> 46 0.72285 > > Excited State 3: Singlet-B2 2.1324 eV 581.44 nm f=0.0000 > > 44 -> 45 0.61976 > > Excited State 4: Singlet-B2 2.3489 eV 527.83 nm f=0.0000 > > 44 -> 46 0.68672 > > ..... > > > > So > > (1) As you can see the first several states have f=0.0, should I still > treat the one with lowest excitation energy as the first excited state, or I > need to find the one with a non zero f value? > > > > (2) there is another structure having no sysmmetry as in the output: > > > > Initial guess orbital symmetries: > > Occupied (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > > (A) (A) (A) (A) (A) (A) (A) (A) > > Virtual (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A).... > > > > So in this case, what should we do in order to get other electronic > state(for example, from ground state 1A1-->1B2) for further calculation? > > > > Thanks a lot for your help.> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel||gmail.com --0016368325b445aeca047053a4aa Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 10 states were requested.=A0 Would be good to see the rest.=A0 Which state = to select as a point of interest depends on what your purpose is.=A0 Comput= ed Singlet->Triplets will always have a zero computed oscillator strengt= h, [in the absence of spin-orbit coupling] though experimentally they may b= e observed with very low extinction coefficients.=A0

For singlets if you are comparing with experiment and the observed exti= nction coeff is a thousand or more then one should look for a computed osc = str > 0.=A0 There are no hard and fast rules here for mapping computed v= alues versus computed values; the user has to perform this mapping though e= xperience (in most cases.)=A0 [It is noted that your data shows no symmetry= , so that issue can be ignored here.]

If there are no experimental data it would be useful to see if there ar= e singlet states with osc > 0; this might require expanding the number o= f states sought.=A0 If there is no interest in triplets then they need not = be solved for [check documenattion to do this]

Hope this helps,

John McKelvey

On Mon, Aug 3, 2009 at 1:28 PM, clara song clarasong83|*|gmail.com <owner-chemistry||ccl.net> wrote:

Sent to CCL by: "clara =A0song" [clarasong83:-:gmail.com]

Anyone could help?
Thanks

> "clara song clarasong83++gmail.com" =A0wrote:
>
> Sent to CCL by: "clara =A0song" [clarasong83]![gmail.com]
> Hi,
>
> I am using the TD keyword in G03 to calculation the excited states for= gold clusters. And I experienced two problems with the following:
>
> #p TD(50-50,Nstates=3D10) b3lyp/gen pseudo=3Dread =A0pop=3Dfull gfinpu= t,
>
> And in the output file I got, there are following excited states:
>
> =A0Excitation energies and oscillator strengths:
> =A0Excited State =A0 1: =A0 Triplet-B2 =A0 =A0 1.4373 eV =A0862.60 nm = =A0f=3D0.0000
> =A0 =A0 =A0 44 -> 45 =A0 =A0 =A0 =A0 0.75598
> =A0This state for optimization and/or second-order correction.
> =A0Total Energy, E(RPA) =3D =A0-276.707873393
> =A0Copying the excited state density for this state as the 1-particle = RhoCI density.
> =A0Excited State =A0 2: =A0 Triplet-B2 =A0 =A0 2.0939 eV =A0592.12 nm = =A0f=3D0.0000
> =A0 =A0 =A0 44 -> 46 =A0 =A0 =A0 =A0 0.72285
> =A0Excited State =A0 3: =A0 Singlet-B2 =A0 =A0 2.1324 eV =A0581.44 nm = =A0f=3D0.0000
> =A0 =A0 =A0 44 -> 45 =A0 =A0 =A0 =A0 0.61976
> =A0Excited State =A0 4: =A0 Singlet-B2 =A0 =A0 2.3489 eV =A0527.83 nm = =A0f=3D0.0000
> =A0 =A0 =A0 44 -> 46 =A0 =A0 =A0 =A0 0.68672
> .....
>
> So
> (1) As you can see =A0the first several states have f=3D0.0, should I = still treat the one with lowest excitation energy as the first excited stat= e, or I need to find the one with a non zero f value?
>
> (2) there is another structure having no sysmmetry as in the output: >
> Initial guess orbital symmetries:
> =A0 =A0 =A0 =A0Occupied =A0(A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0(A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0(A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0(A) (A) (A) (A) (A) (A) (A) (A)
> =A0 =A0 =A0 =A0Virtual =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0(A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)....
>
> So in this case, what should we do in order to get other electronic st= ate(for example, from ground state 1A1-->1B2) for further calculation? >
> Thanks a lot for your help.
>
>

-=3D This is automatically added to each message by the mailing script =3D-=
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--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel||gmail.com
--0016368325b445aeca047053a4aa-- From owner-chemistry@ccl.net Tue Aug 4 15:07:00 2009 From: "Ardie Lee cclreading*_*googlemail.com" To: CCL Subject: CCL:G: about G03 solvation optimization error Message-Id: <-39924-090804073256-6567-gMbwaR/kkwxAvQSw39PSgw.:.server.ccl.net> X-Original-From: "Ardie Lee" Date: Tue, 4 Aug 2009 07:32:52 -0400 Sent to CCL by: "Ardie Lee" [cclreading() googlemail.com] Dear all, My G03 solvation opimization job ends with the following errors: BldSpC: Error generating genealogic tree for sphere 5211 at level 15 Error termination via Lnk1e in /usr/users/g03/l301.exe at Fri Jul 31 22:22:11 2009. Job cpu time: 2 days 13 hours 10 minutes 29.7 seconds. File lengths (MBytes): RWF= 6534 Int= 0 D2E= 0 Chk= 196 Scr= 1 Does anybody know the reason and how to resolve it? Thanks. The input file is: %nproc=8 %chk=cdigmpmg4h2o_iefpcm %mem=10GB # b3lyp/6-31g** nosymm opt scrf=(iefpcm,solvent=water,read) test -2 1 ..... .... (xyz coordinates ) (blank line) radii=uff Ardie Lee cclreading^_^googlemail.com ctc of xmu university, China From owner-chemistry@ccl.net Tue Aug 4 23:31:01 2009 From: "David Gallagher gallagher.da++gmail.com" To: CCL Subject: CCL: Query regarding iron complex optimization using MOPAC Message-Id: <-39925-090804232902-18988-RvZnAiFlmAjjWyWOIJrVrQ%a%server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary=0022152d61819db47004705c8072 Date: Tue, 4 Aug 2009 20:21:43 -0700 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da/a\gmail.com] --0022152d61819db47004705c8072 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Nilesh, As already suggested, Avogadro and Discovery Studio are worth considering, and there is a list of other free GUIs at http://openmopac.net/resellers.html. "FORCE" and "THERMO" keywords can provide thermodynamic properties, and the "C.I.=..." keyword may be useful for studying configurations of transition metal complexes. All the keywords and their functions are listed in the on-line manual at http://www.cacheresearch.com/mopac.html#mopac-support David Gallagher CACheResearch.com On Mon, Aug 3, 2009 at 10:50 PM, Nilesh Tawari tawari.nilesh.:.gmail.com < owner-chemistry:-:ccl.net> wrote: > Hello Gallagher,Can you also suggest a free software for the construction > and preparing input file of fe complex for MOPAC. > > thanks in advance > -nilesh > > On Mon, Aug 3, 2009 at 9:54 PM, Nilesh Tawari > > wrote: > >> Hello Gallagher, >> Thanks a lot for the reply as suggested will be using PM6 method for >> optimization using UHF keyword can you please suggest other keywords >> necessary beside charge and mutiplicity for transition metal complex >> calculation and additional keywords which can be used to get various >> properties of complex. >> >> thanks in advance >> -nilesh >> >> On Tue, Aug 4, 2009 at 5:50 AM, David Gallagher gallagher.da-*-gmail.com >> > wrote: >> >>> Hi Nilesh, >>> Unless you have a good reason to stick with PM3, I would recommend >>> MOPAC2009 with PM6, as it has higher accuracy for geometries and heats of >>> formation. MOPAC2009 is free for academics. >>> >>> The 'UHF' keyword generally gives the most reliable results for >>> transition metal complexes. >>> >>> You can find links for the MOPAC manual and download (free for academics) >>> at: >>> http://cacheresearch.com/mopac.html#mopac-support >>> >>> Good luck, >>> David Gallagher >>> CACheResearch.com >>> >>> >>> On Mon, Aug 3, 2009 at 10:45 AM, Nilesh Tawari tawari.nilesh*_* >>> gmail.com > wrote: >>> >>>> >>>> Sent to CCL by: "Nilesh Tawari" [tawari.nilesh[*]gmail.com] >>>> Hello everyone, >>>> I want to optimize an iron (Fe+++) hexacoordinated complex with my >>>> molecule using MOPAC using PM3 can you please suggest the essential keywords >>>> and the precautions to be taken in this calculations and get some properties >>>> like energy and heat of formation. As i am beginner for MOPAC any help would >>>> be of great importance to me. If possible please suggest any tutorial for >>>> the same. >>>> Thanks in advance >>>> -nilesh>>>> E-mail to subscribers: CHEMISTRY^ccl.net or use:>>>> >>>> E-mail to administrators: CHEMISTRY-REQUEST^ccl.netor use>>>> >>>> >>>> >>> >> >> >> -- >> Mr. Nilesh R. Tawari >> PhD (Tech) Medicinal Chemistry >> ICT, Matunga (E), Mumbai-19 >> > > > > -- > Mr. Nilesh R. Tawari > PhD (Tech) Medicinal Chemistry > ICT, Matunga (E), Mumbai-19 > --0022152d61819db47004705c8072 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Nilesh,

As already suggested, Avogadro and Discovery = Studio are worth considering, and there is a list of other free GUIs at=A0<= a href=3D"http://openmopac.net/resellers.html">http://openmopac.net/reselle= rs.html.

"FORCE" and "THERMO" keywords can = =A0provide thermodynamic properties, and the "C.I.=3D..." keyword= may be useful for studying configurations of transition metal complexes. = =A0All the keywords and their functions are listed in the on-line manual at= =A0http:= //www.cacheresearch.com/mopac.html#mopac-support

David Gallagher

CACheResearch.com

On Mon, Aug 3, 2009 at 10:50 PM, Nile= sh Tawari tawari.nilesh.:.gmail.com <owner-chemistry:-:= ccl.net> wrote:

Hello=A0Gallagher,
Can yo= u also suggest a free software for the construction and preparing input fil= e of fe complex for MOPAC.

thanks in advance
-nilesh

On Mon, Aug 3, 2009 at 9:54 PM, Nilesh Tawari <tawari.nile= sh]|[gmail.com> wrote:

Hello Gallagher,

Thanks a lot for the reply as suggested will be using PM6 method for o= ptimization using UHF keyword can you please suggest other keywords necessa= ry beside charge and mutiplicity for transition metal complex calculation a= nd additional keywords which can be used to get various properties of compl= ex.

=A0

thanks in advance

-nilesh

On Tue, Aug 4, 2009 at 5:50 AM, David Gallagher = gallagher.da-*-gmail.com= <owner-chemistry]|[ccl.net> wrote:

Hi Nilesh,=20

Unless you have a good reason to stick with PM3, I would recommend MOP= AC2009 with PM6, as it has higher accuracy for geometries and heats of form= ation. =A0MOPAC2009 is free for academics.

The 'UHF' keyword generally gives the most reliable results fo= r transition metal complexes.=A0

You can find links for the MOPAC manual and download (free for academi= cs) at:=A0

http://cacheresearch.com/mopac.html#mopac-support

Good luck,

David Gallagher

CACheResearch.com

On Mon, Aug 3, 2009 at 10:45 AM, Nilesh Tawari tawari.nilesh*_*gmail.com &l= t;owner-chem= istry^ccl.net> wrote:

Sent to CCL by: "Nilesh =A0Tawari" [tawari.nilesh[*]gmail.com]
Hello everyon= e,
I want to optimize an iron (Fe+++) hexacoordinated complex with my mo= lecule using MOPAC using PM3 can you please suggest the essential keywords = and the precautions to be taken in this calculations and get some propertie= s like energy and heat of formation. As i am beginner for MOPAC any help wo= uld be of great importance to me. If possible please suggest any tutorial f= or the same.
Thanks in advance
-nilesh

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

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--
Mr. Nilesh R. Taw= ari
PhD (Tech) Medicinal Chemistry
ICT, Matunga (E), Mumbai-19

--
Mr. Nilesh R. Ta= wari
PhD (Tech) Medicinal Chemistry
ICT, Matunga (E), Mumbai-19

--0022152d61819db47004705c8072--