From owner-chemistry@ccl.net Sat Aug 28 07:49:01 2010 From: "abhishekdc~!~iitb.ac.in" To: CCL Subject: CCL:G: need opinion Message-Id: <-42623-100828070028-781-IT5yU+aQlyxYptlx98PlNA**server.ccl.net> X-Original-From: abhishekdc*|*iitb.ac.in Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=utf-8 Date: Sat, 28 Aug 2010 16:30:08 +0530 MIME-Version: 1.0 Sent to CCL by: abhishekdc**iitb.ac.in Dear All, Let consider that there is a possibility of formation of two product > from any reaction: A (charge=1, multiplicity=1) and B (charge=2, multiplicity=1) but actually only A is formed. Is there any way to explain above phenomenon computationally ?? Can I compare there energies under equivalent atom condition (Probably not) ?? Can I say something > from there computed delta G value ?? Is there any other way to handle these situation computationally?? I am using Gaussian 03 and many thanks in advance. Sincerely, Abhishek From owner-chemistry@ccl.net Sat Aug 28 09:15:00 2010 From: "ABHISHEK SHAHI shahi.abhishek1984]![gmail.com" To: CCL Subject: CCL:G: need opinion Message-Id: <-42624-100828091412-30001-DzBlHoqvt+P3281U3zTEAQ!A!server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=0016e64c1dc25bbdca048ee201ca Date: Sat, 28 Aug 2010 18:44:03 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984 * gmail.com] --0016e64c1dc25bbdca048ee201ca Content-Type: text/plain; charset=ISO-8859-1 DEAR Abhishek There are several method to predict the major product.You can check the branching ratio by thermodynamical study and transition state calculation and see the height of barrier. G2 level calculation is found to be good for such kind of matter or you can go for other. you can see this paper for more details CPL ,406, 2005,60-74, By Wang ................and follow its references. With regards; *ABHISHEK SHAHI* IPC,IISc bangalore-12 Official E-mail: shahi[#]ipc.iisc.ernet.in CC: shahi.abhishek1984[#]gmail.com On Sat, Aug 28, 2010 at 4:30 PM, abhishekdc~!~iitb.ac.in < owner-chemistry[#]ccl.net> wrote: > > Sent to CCL by: abhishekdc**iitb.ac.in > Dear All, > Let consider that there is a possibility of formation of two product > > from any reaction: A (charge=1, multiplicity=1) and B (charge=2, > multiplicity=1) but actually only A is formed. Is there any way to > explain above phenomenon computationally ?? Can I compare there energies > under equivalent atom condition (Probably not) ?? Can I say something > > from there computed delta G value ?? Is there any other way to handle > these situation computationally?? > > I am using Gaussian 03 and many thanks in advance. > > Sincerely, > Abhishek> > > --0016e64c1dc25bbdca048ee201ca Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable DEAR Abhishek


=A0There are several method to predict the major = product.You can check the branching ratio by thermodynamical study and tran= sition state calculation and see the height of barrier. G2 level calculatio= n is found to be good for such kind of matter or you can go for other. you = can see this paper for more details
CPL ,406, 2005,60-74, By Wang ................and follow its references.





With regards;
=A0= ABHISHEK SHAHI
=A0 IPC,IISc bangalore-12
=A0 Official E-mail: shahi[#]ipc.iisc.ernet.in
=A0 CC:= =A0 shahi= .abhishek1984[#]gmail.com


On Sat, Aug 28, 2010 at 4:30 PM, abhishe= kdc~!~iitb.ac.in <owner-chemistry[#]ccl.net> wrote:

Sent to CCL by: abhishekdc**iitb.ac.in
Dear All,
=A0Let consider that there is a possibility of formation of two product > from any reaction: A (charge=3D1, multiplicity=3D1) and B (charge=3D2,=
multiplicity=3D1) but actually only A is formed. Is there any way to
explain above phenomenon computationally ?? Can I compare there energies under equivalent atom condition (Probably not) ?? =A0Can I say something > from there computed delta G value ?? Is there any other way to handle<= br> these situation computationally??

I am using Gaussian 03 and many thanks in advance.

Sincerely,
Abhishek



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY[#]ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST[#]ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--0016e64c1dc25bbdca048ee201ca-- From owner-chemistry@ccl.net Sat Aug 28 10:52:00 2010 From: "David Gallagher gallagher.da^_^gmail.com" To: CCL Subject: CCL:G: need opinion Message-Id: <-42625-100828104755-11212-zAf661SsH3X55gS09N0HhQ|server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary=0050450171806286d3048ee350fe Date: Sat, 28 Aug 2010 07:47:44 -0700 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da[a]gmail.com] --0050450171806286d3048ee350fe Content-Type: text/plain; charset=ISO-8859-1 Hi Abhishek, Assuming the reaction is reversible then the reaction should be thermodynamically controlled and product(s) should be those with the lowest free energies. However, you would need to include any counter ions, etc. in the calculation to maintain the stoichiometry (total atoms and charges must be the same). It would also be important to consider the appropriate solvent, if relevant, particularly with ions. If the prevailing product(s) does not have the lowest free energy, then the reaction may be kinetically controlled, so you would need to characterize the transition states to compare the barrier heights. There is a guide to reaction modelling at http://www.cacheresearch.com/presentations.html David Gallagher CAChe Research On Sat, Aug 28, 2010 at 4:00 AM, abhishekdc~!~iitb.ac.in < owner-chemistry^ccl.net> wrote: > > Sent to CCL by: abhishekdc**iitb.ac.in > Dear All, > Let consider that there is a possibility of formation of two product > > from any reaction: A (charge=1, multiplicity=1) and B (charge=2, > multiplicity=1) but actually only A is formed. Is there any way to > explain above phenomenon computationally ?? Can I compare there energies > under equivalent atom condition (Probably not) ?? Can I say something > > from there computed delta G value ?? Is there any other way to handle > these situation computationally?? > > I am using Gaussian 03 and many thanks in advance. > > Sincerely, > Abhishek> > > --0050450171806286d3048ee350fe Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Abhishek,
Assuming the reaction is reversible then the re= action should be thermodynamically controlled and product(s) should be thos= e with the lowest free energies. =A0However, you would need to include any = counter ions, etc. in the calculation to maintain the stoichiometry (total = atoms and charges must be the same). =A0It would also be important to consi= der the appropriate solvent, if relevant, particularly with ions. =A0

If the prevailing product(s) does not have the lowest f= ree energy, then the reaction may be kinetically controlled, so you would n= eed to characterize the transition states to compare the barrier heights. = =A0There is a guide to reaction modelling at http://www.cacheresearch.com/presentations.ht= ml

David Gallagher
CAChe Research

On Sat, Aug 28, 2010 at 4:00 AM, abhishekdc~!~iitb.ac.in <owner-chemistry^ccl.net> wrote:

Sent to CCL by: abhishekdc**iitb.ac.in
Dear All,
=A0Let consider that there is a possibility of formation of two product > from any reaction: A (charge=3D1, multiplicity=3D1) and B (charge=3D2,=
multiplicity=3D1) but actually only A is formed. Is there any way to
explain above phenomenon computationally ?? Can I compare there energies under equivalent atom condition (Probably not) ?? =A0Can I say something > from there computed delta G value ?? Is there any other way to handle<= br> these situation computationally??

I am using Gaussian 03 and many thanks in advance.

Sincerely,
Abhishek



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY^ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST^ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--0050450171806286d3048ee350fe-- From owner-chemistry@ccl.net Sat Aug 28 12:47:00 2010 From: "ABHISHEK SHAHI shahi.abhishek1984!^!gmail.com" To: CCL Subject: CCL:G: Visualization of G09 output Message-Id: <-42626-100828122051-27410-ZYTHldgG3BcBP2czlrZ18Q_+_server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=001485f6c762e3daa5048ee49cdd Date: Sat, 28 Aug 2010 21:50:42 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984]_[gmail.com] --001485f6c762e3daa5048ee49cdd Content-Type: text/plain; charset=ISO-8859-1 Dear All I am facing problem in visualizing G09 output. Gaussview (not reading vibration),Avagadro (not reading optimisation steps),chemcraft(not reading vibration and optimization steps).These all were suitable for G03 output.Please suggest me that what should I do.Is there any free software for visualizing all results. Your suggestions will be appreciated and helpful for others too......... With regards; *ABHISHEK SHAHI* IISc bangalore-12 Official E-mail: shahi#,#ipc.iisc.ernet.in CC: shahi.abhishek1984#,#gmail.com --001485f6c762e3daa5048ee49cdd Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All

=A0=A0 I am facing problem in visualizing G09 output. Gauss= view (not reading vibration),Avagadro (not reading optimisation steps),chem= craft(not reading vibration and optimization steps).These all were suitable= for G03 output.Please suggest me that what should I do.Is there any free s= oftware for visualizing all results.

=A0Your suggestions will be=A0 appreciated and helpful for=A0 others to= o.........









With regard= s;
=A0ABHISHEK SHAHI
=A0 IISc bangalore-12
=A0 Official E-mail: shahi#,#ipc.iisc.ernet.in
=A0 CC:=A0 <= a href=3D"mailto:shahi.abhishek1984#,#gmail.com" target=3D"_blank">shahi.abhi= shek1984#,#gmail.com
--001485f6c762e3daa5048ee49cdd-- From owner-chemistry@ccl.net Sat Aug 28 13:34:00 2010 From: "John McKelvey jmmckel- -gmail.com" To: CCL Subject: CCL:G: need opinion Message-Id: <-42627-100828120638-31789-PJt8ydCk2WxgzvfEA1Aeog,,server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 28 Aug 2010 12:06:30 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel ~~ gmail.com] I would add one comment to Dave's comment... Catalysis can also be considered an issue, and this may well be covered by Dave's comment on "reversibility." If I remember correctly the classical case of the reaction of N2 + 3H2 --> 2NH3. It is thermodynamically favored, but a catalyst is required. John McKelvey On Sat, Aug 28, 2010 at 10:47 AM, David Gallagher gallagher.da^_^gmail.com wrote: > Hi Abhishek, > Assuming the reaction is reversible then the reaction should be > thermodynamically controlled and product(s) should be those with the lowest > free energies.  However, you would need to include any counter ions, etc. in > the calculation to maintain the stoichiometry (total atoms and charges must > be the same).  It would also be important to consider the appropriate > solvent, if relevant, particularly with ions. > If the prevailing product(s) does not have the lowest free energy, then the > reaction may be kinetically controlled, so you would need to characterize > the transition states to compare the barrier heights.  There is a guide to > reaction modelling at http://www.cacheresearch.com/presentations.html > David Gallagher > CAChe Research > On Sat, Aug 28, 2010 at 4:00 AM, abhishekdc~!~iitb.ac.in > wrote: >> >> Sent to CCL by: abhishekdc**iitb.ac.in >> Dear All, >>  Let consider that there is a possibility of formation of two product >> > from any reaction: A (charge=1, multiplicity=1) and B (charge=2, >> multiplicity=1) but actually only A is formed. Is there any way to >> explain above phenomenon computationally ?? Can I compare there energies >> under equivalent atom condition (Probably not) ??  Can I say something >> > from there computed delta G value ?? Is there any other way to handle >> these situation computationally?? >> >> I am using Gaussian 03 and many thanks in advance. >> >> Sincerely, >> Abhishek>> E-mail to subscribers: CHEMISTRY!A!ccl.net or use: >>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message >> >> E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net or use >>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>>      http://www.ccl.net/chemistry/sub_unsub.shtml>>      http://www.ccl.net/spammers.txt>> >> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel!A!gmail.com From owner-chemistry@ccl.net Sat Aug 28 14:10:00 2010 From: "Yi (Yves) Wang yves.wang * duke.edu" To: CCL Subject: CCL:G: Visualization of G09 output Message-Id: <-42628-100828140903-8157-vJ1oUVjmt6fW3CfAPuWaJQ^-^server.ccl.net> X-Original-From: "Yi (Yves) Wang" Content-Type: multipart/alternative; boundary=Apple-Mail-2--230941433 Date: Sat, 28 Aug 2010 14:08:56 -0400 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: "Yi (Yves) Wang" [yves.wang/./duke.edu] --Apple-Mail-2--230941433 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Have you tried Gabedit and Molden? = __________________________________________________________________________= ___ Yi (Yves) Wang Department of Biochemistry Structural Biology & Biophysics Program Duke University BS: University of Science and Technology of China School of Life Sciences, National Laboratory for Physical Sciences at = Microscale Tel: +1-919-236-3307 (Cell) +1-919-684-0235 (Lab 1) +1-919-660-1634 (Lab 2) Office: A20 LSRC / 5301 FFSC E-Mail: yves.wang(~)duke.edu Mail: Box 90317, Chemistry Department =D4=DA 2010-8-28=A3=AC=CF=C2=CE=E712:20=A3=AC ABHISHEK SHAHI = shahi.abhishek1984!^!gmail.com =D0=B4=B5=C0=A3=BA > Dear All >=20 > I am facing problem in visualizing G09 output. Gaussview (not = reading vibration),Avagadro (not reading optimisation = steps),chemcraft(not reading vibration and optimization steps).These all = were suitable for G03 output.Please suggest me that what should I do.Is = there any free software for visualizing all results. >=20 > Your suggestions will be appreciated and helpful for others = too......... >=20 >=20 >=20 >=20 >=20 >=20 >=20 >=20 >=20 > With regards; > ABHISHEK SHAHI > IISc bangalore-12 > Official E-mail: shahi()ipc.iisc.ernet.in > CC: shahi.abhishek1984()gmail.com --Apple-Mail-2--230941433 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=GB2312 Have = you tried Gabedit and Molden?


Yi (Yves) Wang
Department of Biochemistry
Structural Biology & Biophysics = Program
Duke = University
BS: University = of Science and Technology of China
   +1-919-660-1634 (Lab 2)
Office: A20 LSRC / 5301 = FFSC
Mail: Box 90317, Chemistry = Department

=D4=DA 2010-8-28=A3=AC=CF=C2=CE=E712:20=A3=AC ABHISHEK = SHAHI shahi.abhishek1984!^!gmail.com =D0=B4=B5=C0=A3=BA

Dear = All

   I am facing problem in visualizing G09 output. = Gaussview (not reading vibration),Avagadro (not reading optimisation = steps),chemcraft(not reading vibration and optimization steps).These all = were suitable for G03 output.Please suggest me that what should I do.Is there any free software for visualizing = all results.

 Your suggestions will be  appreciated and helpful = for  others too.........









With regards;
 ABHISHEK = SHAHI
  IISc bangalore-12
  Official E-mail: shahi()ipc.iisc.ernet.in
  CC:  shahi.abhishek1984()gmail.com

= --Apple-Mail-2--230941433-- From owner-chemistry@ccl.net Sat Aug 28 15:30:00 2010 From: "Ol Ga eurisco1() pochta.ru" To: CCL Subject: CCL:G: Visualization of G09 output Message-Id: <-42629-100828150817-10702-3zryq7rk0oc3Cgf8+qRnqA * server.ccl.net> X-Original-From: "Ol Ga" Date: Sat, 28 Aug 2010 15:08:15 -0400 Sent to CCL by: "Ol Ga" [eurisco1%%pochta.ru] Dear ABHISHEK SHAHI, Concerning ChemCraft : Maybe you are working with outdated version of ChemCraft. It is better to update your installation. Actual version of ChemCraft supports g09 and g03 output files very well. Sincerely, Ol Ga ============ > From: ABHISHEK SHAHI shahi.abhishek1984!^!gmail.com Sent: Saturday, August 28, 2010 8:20 PM To: Ga, Ol Subject: CCL:G: Visualization of G09 output Dear All I am facing problem in visualizing G09 output. Gaussview (not reading vibration),Avagadro (not reading optimisation steps),chemcraft(not reading vibration and optimization steps).These all were suitable for G03 output.Please suggest me that what should I do.Is there any free software for visualizing all results. Your suggestions will be appreciated and helpful for others too......... With regards; ABHISHEK SHAHI IISc bangalore-12 Official E-mail: shahi()ipc.iisc.ernet.in CC: shahi.abhishek1984()gmail.com From owner-chemistry@ccl.net Sat Aug 28 20:24:00 2010 From: "Haibin Scopus lihb734.===.yahoo.com" To: CCL Subject: CCL:G: Visualization of G09 output Message-Id: <-42630-100828202235-3581-Qb5gXz4GR2o5eVdNVUCCrA===server.ccl.net> X-Original-From: Haibin Scopus Content-Type: multipart/alternative; boundary="0-1606556357-1283041348=:33980" Date: Sat, 28 Aug 2010 17:22:28 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Haibin Scopus [lihb734*_*yahoo.com] --0-1606556357-1283041348=:33980 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear ABHISHEK SHAHI, =A0 You may notice the difference between G03 and G09 output for frequency = calculations. There two blanks in =A0"Atom=A0 AN" for G09, only one for G03= . If you relplace two blanks by one for all, you can visulize your frequenc= ies output. =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 sincerely: Haibin =A0 Haibin Li Institute of Functional Material Chemistry, Faculty of Chemistry Northeast Normal University=20 changchun, Jilin, 130024 PR CHINA E-mail: lihb734+*+nenu.edu.cn; lihb734+*+yahoo.com http://www.nenu.edu.cn =0A=0A=0A --0-1606556357-1283041348=:33980 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear ABHISHEK SHAHI,
  You may notice= the difference between G03 and G09 output for frequency calculations. Ther= e two blanks in  "Atom  AN" for G09, only one for G03. If you rel= place two blanks by one for all, you can visulize your frequencies output.<= BR>            =             &nb= sp;            =             &nb= sp;            =             &nb= sp;   sincerely: Haibin
 
Haibin Li
Institute of Functional Material Chemistry, Faculty of Chemistry
Northeast Normal University
changchun, Jilin, 130024 PR = CHINA

E-mail: lihb734+*+nenu.edu.cn; lihb734+*+yahoo.com
http://www.n= enu.edu.cn



=0A=0A --0-1606556357-1283041348=:33980--