On Tue, Oct 25, 2011 at 2:20 PM, Elda= r Mamin yeldar443-$-MAIL.RU <owner-chemistry_+_ccl.net> wrote:

Sent to CCL by: "Eldar =A0Mamin" [yeldar443_-_MAIL.RU]
Dear CCL-community

Can someone give me references of the approach of calculating reaction path= ?

the approach is well known, but references is not -

do the MCSCF IRC job, and then MRMP2 energies of each(or selected) points o= f irc.

do the (u)MP2 IRC job, and then MRMP2 energies of each(or selected) points = of irc.

(it helps when we unable to do the MRMP2 gradient in searching stationary o= r saddle points )

Thanks.

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--001636426ab5fa5e3c04b01cad0d-- From owner-chemistry@ccl.net Tue Oct 25 09:25:00 2011 From: "=?ISO-8859-1?Q?Jo=E3o_Henriques?= jmhenriques:fc.ul.pt" To: CCL Subject: CCL: Macro or something for Gaussian 03 Message-Id: <-45738-111025062754-22523-HkmEub7IhojocbVikFbplg(a)server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jo=E3o_Henriques?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 25 Oct 2011 11:27:45 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_Henriques?= [jmhenriques.-*-.fc.ul.pt] I'll have a chat with my boss in order to discuss the possibility of publishing them online on our group's website. Still, has someone said after this email, there are quite a few tools to do this type of tasks that have already been published online. I did mine just for the fun of it and also because I wanted my data to be printed/stored in a particular way. Best regards, On Tue, Oct 25, 2011 at 12:54 AM, Geoffrey Hutchison geoffh{=}pitt.edu wrote: > > Sent to CCL by: Geoffrey Hutchison [geoffh[]pitt.edu] >> Would it be possible to publish this on-line somewhere? I'm currently in the progress of writing similar python scripts and it seems foolish to duplicate efforts! > > There are already a wide variety of such scripts. I suggest python users look at GaussSum and cclib: > http://gausssum.sf.net/ > http://cclib.sf.net/ > > They work to extract data in a wide range of comp-chem packages. > > Best regards, > -Geoff > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geoffh[A]pitt.edu > web: http://hutchison.chem.pitt.edu/> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/cgi-bin/ccl/send_ccl_message> http://www.ccl.net/chemistry/sub_unsub.shtml> http://www.ccl.net/spammers.txt> > > -- João Henriques, MSc in Biochemistry Faculty of Science of the University of Lisbon Department of Chemistry and Biochemistry C8 Building, Room 8.5.47 Campo Grande, 1749-016 Lisbon, Portugal E-mail: joao.henriques.32353-*-gmail.com / jmhenriques-*-fc.ul.pt http://intheochem.fc.ul.pt/members/joaoh.html From owner-chemistry@ccl.net Tue Oct 25 09:59:00 2011 From: "John McKelvey jmmckel/./gmail.com" To: CCL Subject: CCL:G: MOPAC input file Message-Id: <-45739-111025090910-16406-lph1d/9M5cpjiJA+e9QFsw[a]server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=e89a8f646f8131f7a904b01f3ed7 Date: Tue, 25 Oct 2011 09:09:00 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel]_[gmail.com] --e89a8f646f8131f7a904b01f3ed7 Content-Type: text/plain; charset=ISO-8859-1 Since at least as early as MOPAC93 MOPAC allows Gaussian input Z-Matrix input using the keyword AIGIN. Conversley one can output a Gaussian Z-Matrix using AIGOUT. So to do the conversion either way without any additional computation add the additional keyword 0SCF [zeroSCF]... I have used it successfully both ways. John McKelvey On Tue, Oct 25, 2011 at 12:22 AM, Utpal Sarkar utpalchemiitkgp|a|gmail.com < owner-chemistry%ccl.net> wrote: > one way to use gaussian input file is to first save the gaussian input file > in cartisian coordinate then using utility program under gaussian chnage it > to mopac format. > best > utpal > > On Tue, Oct 25, 2011 at 2:35 AM, A. Anglea a.anglea90 _ yahoo.com < > owner-chemistry*o*ccl.net> wrote: > >> >> Sent to CCL by: "A. Anglea" [a.anglea90{:}yahoo.com] >> Hi all >> I am a new user of MOPAC program. >> For mopac, can I used the z matrix input file as following >> ********* >> AM1 1SCF >> Water >> Water single point >> O >> H 1 B1 >> H 1 B2 2 A1 >> >> B1 0.96000000 >> B2 0.96000000 >> A1 109.50000019 >> >> 1 3 1.0 2 1.0 >> 2 >> 3 >> ********* >> >> I got the Gaussian input file and modified it. Or it has to be converted >> using >> openbabel. >> Cheers** >> E-mail to subscribers: CHEMISTRY*o*ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST*o*ccl.net or use>> **>> >> >> > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel%gmail.com --e89a8f646f8131f7a904b01f3ed7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Since at least as early as MOPAC93 MOPAC allows Gaussian input Z-Matrix inp= ut using the keyword AIGIN.=A0 Conversley one can output a Gaussian Z-Matri= x using AIGOUT.=A0 So to do the conversion either way without any additiona= l computation add the additional keyword 0SCF [zeroSCF]...=A0 I have used i= t successfully both ways.

John McKelvey

On Tue, Oct 25, 2011 at= 12:22 AM, Utpal Sarkar utpalchemiitkgp|a|gmai= l.com <= owner-chemistry%ccl.net> wrote:

one way to use gaussian input file is to fi= rst save the gaussian input file in cartisian coordinate then using utility= program under gaussian chnage it to mopac format.
best
utpal

On Tue, Oct 25, 2011 at 2:35 AM, A. Anglea a.anglea90 _ yahoo.com <owner-chemistry*o*ccl.net> wrote:

Sent to CCL by: "A. =A0Anglea" [a.anglea90{:}yahoo.com]
Hi all
I am a new user of MOPAC program.
For mopac, can I used the z matrix input file as following
*********
AM1 1SCF
Water
Water single point
=A0O
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B1
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B2 =A0= =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A1

=A0 B1 =A0 =A0 =A0 =A0 =A0 =A0 0.96000000
=A0 B2 =A0 =A0 =A0 =A0 =A0 =A0 0.96000000
=A0 A1 =A0 =A0 =A0 =A0 =A0 109.50000019

=A01 3 1.0 2 1.0
=A02
=A03
*********

I got the Gaussian input file and modified it. Or it has to be converted us= ing
openbabel.
Cheers

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--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel%gmail.com
--e89a8f646f8131f7a904b01f3ed7-- From owner-chemistry@ccl.net Tue Oct 25 15:55:00 2011 From: "Sujit Kumar Mondal sujitharvard|,|gmail.com" To: CCL Subject: CCL: IRC-TS-PES Message-Id: <-45740-111025154328-28407-q/1HiNs5Wg21IDKrdsoXFA^^server.ccl.net> X-Original-From: Sujit Kumar Mondal Content-Type: multipart/alternative; boundary=bcaec520efa73fd4f604b024c00a Date: Tue, 25 Oct 2011 14:43:17 -0500 MIME-Version: 1.0 Sent to CCL by: Sujit Kumar Mondal [sujitharvard|a|gmail.com] --bcaec520efa73fd4f604b024c00a Content-Type: text/plain; charset=ISO-8859-1 Hi I am working on Intrinsic Reaction Co-ordinate for hetero cycle organic molecules and transition metal system. I performed IRC calculation which produced 21 step of a reaction profile path, I would like to optimized all the 21 structures obtained in IRC path including the transition state individually. 1) Can any one tell me the keywords for optimizing all the structures obtained in IRC? I do not know how to do that, please help me out. 2) secondly, I tried to optimize my transition state using keywords opt=(Calcfc,TS,noeigentest,maxcycle=200) Scf=(conver=5,maxcycle=200) but I found that my optimized transition state has changed all the atomic property including delocalization inside the 5membered ring compare to the transition state I build up (as input file). Can anyone tell me what should be done here? i need help...... 3) I would like to perform a potential energy scan, could someone tell me the keywords for a potential energy scan of a particular system? Looking forward for your reply Sujit --bcaec520efa73fd4f604b024c00a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

I am working on Intrinsic Reaction Co-ordinate for hetero cycle organi= c molecules and transition metal system. I performed IRC calculation which = produced 21 step of a reaction profile path, I would like to optimized all = the 21 structures obtained in IRC path including the transition state indiv= idually.

1) Can any one tell me the keywords for optimizing all the structures = obtained in IRC?=A0I do not know how to do that, please help me out.

=A0

2) secondly,=A0I tried to optimize my transition state using keywords = opt=3D(Calcfc,TS,noeigentest,maxcycle=3D200) Scf=3D(conver=3D5,maxcycle=3D2= 00) but=A0I found that my optimized transition state has changed all the at= omic property including delocalization inside the 5membered ring compare to= the transition state=A0I build up (as input file). Can anyone tell me what= should be done here?

i need help......

=A0

3) I would like to perform a potential energy scan, could=A0someone te= ll me the keywords for a potential energy scan of a particular system?=A0

=A0

Looking forward for your reply

Sujit

=A0

--bcaec520efa73fd4f604b024c00a-- From owner-chemistry@ccl.net Tue Oct 25 16:31:00 2011 From: "Sujit Kumar Mondal sujitharvard..gmail.com" To: CCL Subject: CCL: IRC-TS-PES Message-Id: <-45741-111025162848-856-59a5THnHrrIeHiZjy7dtDg|*|server.ccl.net> X-Original-From: Sujit Kumar Mondal Content-Type: multipart/alternative; boundary=bcaec520efa78e6a9904b025623e Date: Tue, 25 Oct 2011 15:28:40 -0500 MIME-Version: 1.0 Sent to CCL by: Sujit Kumar Mondal [sujitharvard!A!gmail.com] --bcaec520efa78e6a9904b025623e Content-Type: text/plain; charset=ISO-8859-1 Hi I am working on Intrinsic Reaction Co-ordinate for hetero cycle organic molecules and transition metal system. I performed IRC calculation which produced 21 step of a reaction profile path, I would like to optimized all the 21 structures obtained in IRC path including the transition state individually. 1) Can any one tell me the keywords for optimizing all the structures obtained in IRC? I do not know how to do that, please help me out. 2) secondly, I tried to optimize my transition state using keywords opt=(Calcfc,TS,noeigentest,maxcycle=200) Scf=(conver=5,maxcycle=200) but I found that my optimized transition state has changed all the atomic property including delocalization inside the 5membered ring compare to the transition state I build up (as input file). Can anyone tell me what should be done here? i need help...... 3) I would like to perform a potential energy scan, could someone tell me the keywords for a potential energy scan of a particular system? Looking forward for your reply Sujit --bcaec520efa78e6a9904b025623e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

1) Can any one tell me the keywords for optimizing all the structures = obtained in IRC?=A0I do not know how to do that, please help me out.

=A0

i need help......

=A0

3) I would like to perform a potential energy scan, could=A0someone te= ll me the keywords for a potential energy scan of a particular system?=A0

=A0

Looking forward for your reply

Sujit

=A0

--bcaec520efa78e6a9904b025623e-- From owner-chemistry@ccl.net Tue Oct 25 17:17:00 2011 From: "Tapas Kar tapas.kar||usu.edu" To: CCL Subject: CCL: o-hydroquinone to o-quinone reaction mechanism Message-Id: <-45742-111025171559-14703-d+AWwi+JC4K7+KPGADzFbQ+/-server.ccl.net> X-Original-From: "Tapas Kar" Date: Tue, 25 Oct 2011 17:15:51 -0400 Sent to CCL by: "Tapas Kar" [tapas.kar()usu.edu] Hello, I am looking for o-hydroquinone to o-quinone reaction mechanism in O2/H2O. I checked literature but could not found any paper describing step-by-step reaction mechanism and kinetics. Is there any theoretical/computation study reported on this reaction? I am interested to know how this reaction takes place I guess some oxygen based radical is involved but what kind? Is singlet O2 or triplet O2 facilitated the reaction? Thanks TK From owner-chemistry@ccl.net Tue Oct 25 17:52:00 2011 From: "Arne Dieckmann adieckma * googlemail.com" To: CCL Subject: CCL:G: DFT-D3 Message-Id: <-45743-111025171820-16711-x/DI9dy06er9F1Z7VOcGag-*-server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 25 Oct 2011 14:18:03 -0700 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Arne Dieckmann [adieckma[]googlemail.com] Hi all, how would I use DFT-D3 in Gaussian 09? If it is available the option seems to be very well hidden in the user's reference. I would like to include dispersion effects in the optimization process and not just add the dispersion energy correction afterwards. Cheers, Arne From owner-chemistry@ccl.net Tue Oct 25 18:27:00 2011 From: "Bruce Palfey brupalf~~umich.edu" To: CCL Subject: CCL: o-hydroquinone to o-quinone reaction mechanism Message-Id: <-45744-111025175837-31732-o2me5X82r6JwgOxWqD42tA{}server.ccl.net> X-Original-From: Bruce Palfey Content-Type: multipart/alternative; boundary=Apple-Mail-136--177205704 Date: Tue, 25 Oct 2011 17:58:14 -0400 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Bruce Palfey [brupalf(0)umich.edu] --Apple-Mail-136--177205704 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Generally, O2 (a triplet) reacts with singlet organics by an initial = single-electron transfer, forming a solvent-caged superoxide-organic = radical pair. Depending on relative rates of the possible processes, a = second electron transfer, coupled to proton transfer (s) could occur, = giving the oxidized organic and H2O2. Or, the radical intermediate = could couple, forming a peroxide which is protonated to the = hydroperoxide. Depending on the organic moiety (like an o-quinone), = that could eliminate H2O2 leaving the unsaturated organic. Or, the = radical pair could separate by diffusion, and these radicals could = oxidize the reduced organic (SET again) in a chain reaction. Another = link in a chain reaction could be the the reaction of oxidized and = reduced organic to form to radicals - especially possible with quinones. = I don't know if the specifics of what actually occurs have been = addressed for o-quinones; the relative rates of these possible reactions = are likely to depend on the reduction potentials (which will vary with = substituents) and solvent. ciao, Bruce Bruce A. Palfey Associate Professor of Biological Chemistry & Associate Director, Program in Chemical Biology Department of Biological Chemistry University of Michigan Medical School 5220E MSRB III 1150 W. Medical Center Drive Ann Arbor, MI 48109-0606 (734) 615-2452 brupalf*umich.edu http://www.biochem.med.umich.edu/?q=3Dpalfey http://www.chembio.umich.edu/people/palfey.html On Oct 25, 2011, at 5:15 PM, Tapas Kar tapas.kar||usu.edu wrote: >=20 > Sent to CCL by: "Tapas Kar" [tapas.kar()usu.edu] > Hello, >=20 > I am looking for o-hydroquinone to o-quinone reaction mechanism in = O2/H2O. I checked literature but could not found any paper describing = step-by-step reaction mechanism and kinetics. Is there any = theoretical/computation study reported on this reaction? I am interested = to know how this reaction takes place I guess some oxygen based radical = is involved but what kind? Is singlet O2 or triplet O2 facilitated the = reaction?=20 >=20 >=20 > Thanks >=20 > TK >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 >=20 >=20 --Apple-Mail-136--177205704 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii

Bruce A. Palfey
Associate Professor of = Biological Chemistry &

Associate Director, Program in = Chemical Biology
Department of Biological Chemistry
University of = Michigan Medical School
5220E MSRB III
1150 W. Medical Center = Drive
Ann Arbor, MI 48109-0606
(734) 615-2452
brupalf*umich.edu

http://www.biochem.m= ed.umich.edu/?q=3Dpalfey
http://www.chembi= o.umich.edu/people/palfey.html

On = Oct 25, 2011, at 5:15 PM, Tapas Kar tapas.kar||usu.edu wrote:

Sent to CCL by: "Tapas Kar" = [tapas.kar()usu.edu]
Hello,

I am looking for o-hydroquinone to = o-quinone reaction mechanism in O2/H2O. I checked literature but could = not found any paper describing step-by-step reaction mechanism and = kinetics. Is there any theoretical/computation study reported on this = reaction? I am interested to know how this reaction takes place I = guess some oxygen based radical is involved but what kind? Is singlet O2 = or triplet O2 facilitated the reaction? =

Thanks

TK

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= --Apple-Mail-136--177205704-- From owner-chemistry@ccl.net Tue Oct 25 20:49:00 2011 From: "Kalju Kahn kalju+*+chem.ucsb.edu" To: CCL Subject: CCL: o-hydroquinone to o-quinone reaction mechanism Message-Id: <-45745-111025204501-21714-w7RyEMaYdOsAaLg5KAa0Bw===server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 25 Oct 2011 17:44:51 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju+/-chem.ucsb.edu] Kar, Bruce's reply reminded me of an old theoretical work where I looked how triplet O2 may react with urate (hydroquinone in disguise) to yield something called dehydroisourate (quinone in disguise). Reactivity in this system was a strong function of the ionic form (as one would guess, anion was better e-donor than acid) and solvent (radical-ion pair stabilized by polar solvent). The work was published in Bioorganic Chemistry, 27(5), 351-362, 1999. There are couple of newer studies of the same reaction, that explore some of alternative mechanisms. Other systems with similar chemistry (but with possibly more stable radicals) are tetrahydropterin and the reduced flavin. Best wishes, Kalju > Generally, O2 (a triplet) reacts with singlet organics by an initial > single-electron transfer, forming a solvent-caged superoxide-organic > radical pair. Depending on relative rates of the possible processes, a > second electron transfer, coupled to proton transfer (s) could occur, > giving the oxidized organic and H2O2. Or, the radical intermediate could > couple, forming a peroxide which is protonated to the hydroperoxide. > Depending on the organic moiety (like an o-quinone), that could eliminate > H2O2 leaving the unsaturated organic. Or, the radical pair could separate > by diffusion, and these radicals could oxidize the reduced organic (SET > again) in a chain reaction. Another link in a chain reaction could be the > the reaction of oxidized and reduced organic to form to radicals - > especially possible with quinones. I don't know if the specifics of what > actually occurs have been addressed for o-quinones; the relative rates of > these possible reactions are likely to depend on the reduction potentials > (which will vary with substituents) and solvent. > > ciao, > Bruce > > Bruce A. Palfey > Associate Professor of Biological Chemistry & > Associate Director, Program in Chemical Biology > Department of Biological Chemistry > University of Michigan Medical School > 5220E MSRB III > 1150 W. Medical Center Drive > Ann Arbor, MI 48109-0606 > (734) 615-2452 > brupalf^^umich.edu > > http://www.biochem.med.umich.edu/?q=palfey > http://www.chembio.umich.edu/people/palfey.html > > > On Oct 25, 2011, at 5:15 PM, Tapas Kar tapas.kar||usu.edu wrote: > >> >> Sent to CCL by: "Tapas Kar" [tapas.kar()usu.edu] >> Hello, >> >> I am looking for o-hydroquinone to o-quinone reaction mechanism in >> O2/H2O. I checked literature but could not found any paper describing >> step-by-step reaction mechanism and kinetics. Is there any >> theoretical/computation study reported on this reaction? I am interested >> to know how this reaction takes place I guess some oxygen based radical >> is involved but what kind? Is singlet O2 or triplet O2 facilitated the >> reaction? >> >> >> Thanks >> >> TK>> To recover the email address of the author of the message, please >> change>> > > > >> >> >> > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106