Dear Kalyan,

Thanks for your answer. So= what solvent do you think would be better to simulate solid phase?
regards.

Parth= a P. Kundu
PhD student
Light Scattering Laboratory
Chemistry & Physics of M= aterials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research (= JNCASR), Bangalore,=A0 560064 INDIA
Phone +91 80 2208 2811/2853 (Lab)

On Sun, Aug 25, 2013 at 1:16 PM, kalyan = onekalyan^^^yahoo.com &l= t;owner-chemis= try_-_ccl.net> wrote:

Probably since I am doing the calculation in gas phase adding B= Ph4- close to Na+ causing the Na to go little distant from catalyst and shi= ft in catalyst frequency is diminished.

________________________= _________________________________________________-

How come you will run your cal= culation for a complex in gas phase .?=A0

Molecule in gas phase did firs= t then run its in liquid phase . then their is a meaning . But only gas pha= se is meaningless or no sense=A0

Best regar= ds

kalyan .=A0

From: partha kundu partha1kundu[]gmail.com <owner-chemistry%x%ccl.net>
To: "Dhar, Kalyan kuma= r " <kalyan.dhar%x%mail.polimi.it>
Sent: Sunday, August 25, 2013 8:21 AM
Subject: CCL: Experimental = Raman and IR not matching with theory

Dear All,
I am trying to simulate IR and Rama= n of a catalyst and=20 trying to see the effect of Na+ on the frequency. For catalyst I am=20 getting very good match for Raman (after converting to intensity), but=20 for IR some strong experimentally observed modes (like S=3DO str.) are=20 appearing as medium or weak band in theory. I am taking a dimer=20 (obtained from crystal structure and then optimized) in gas phase to=20 simulate the solid. I know IR intensity strongly depends upon=20 intermolecular interaction which is not described properly by taking=20 dimer. How to match the intensity better?
Then I tried to add Na+=20 cation to the catalyst to see the shift in frequency. Shift in frequency is qualitatively changing as observed in experiment. Now I want to add a counter ion (BPh4), to get the contribution from it as seen in=20 experiment. Probably since I am doing the calculation in gas phase=20 adding BPh4- close to Na+ causing the Na to go little distant from=20 catalyst and shift in catalyst frequency is diminished. The crystal=20 structure of the complex is not known, so I do not have any idea of=20 where to add it. I do see interaction of BPh4 with the catalyst, 4=20 Phenyl ring breathing mode is split in the complex. Could you suggest=20 how to solve the problem?
Thanks and regards.
Partha

=

--90e6ba61493e3963e204e4c1cc61-- From owner-chemistry@ccl.net Sun Aug 25 06:31:00 2013 From: "kalyan onekalyan,yahoo.com" To: CCL Subject: CCL: Experimental Raman and IR not matching with theory Message-Id: <-49110-130825062708-28975-3Bjxq7+2oPwdyOjhL1hcBA~~server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="_44DDFC4C-E9B1-768E-9158-2041D8806C9F_" Date: Sun, 25 Aug 2013 12:27:02 +0200 MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan^^yahoo.com] --_44DDFC4C-E9B1-768E-9158-2041D8806C9F_ Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Could you please send me the experimental paper ? Eventually try to do rum = your calculation in g09 smd model with 6-31+g(d,p) set. And run cation only= both gas and water as well as run anion too. You can get Reaction energy a= s well as binding energy. So it will be your supporting information. =20 Best Regards=20 Kalyan -----Original Message----- > From: partha kundu partha1kundu{}gmail.com Sent: 25/08/2013 12:15 To: Dhar, Kalyan kumar Subject: CCL: Experimental Raman and IR not matching with theory Dear Kalyan, Thanks for your answer. So what solvent do you think would be better to sim= ulate solid phase? regards. Partha P. Kundu=20 PhD student Light Scattering Laboratory=20 Chemistry & Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalor= e, 560064 INDIA Phone +91 80 2208 2811/2853 (Lab) On Sun, Aug 25, 2013 at 1:16 PM, kalyan onekalyan^^^yahoo.com wrote: Probably since I am doing the calculation in gas phase adding BPh4- close t= o Na+ causing the Na to go little distant from catalyst and shift in cataly= st frequency is diminished. _________________________________________________________________________- How come you will run your calculation for a complex in gas phase .?=20 Molecule in gas phase did first then run its in liquid phase . then their i= s a meaning . But only gas phase is meaningless or no sense=20 Best regards kalyan .=20 =20 > From: partha kundu partha1kundu[]gmail.com To: "Dhar, Kalyan kumar " =20 Sent: Sunday, August 25, 2013 8:21 AM Subject: CCL: Experimental Raman and IR not matching with theory =20 Dear All, I am trying to simulate IR and Raman of a catalyst and trying to see the ef= fect of Na+ on the frequency. For catalyst I am getting very good match for= Raman (after converting to intensity), but for IR some strong experimental= ly observed modes (like S=3DO str.) are appearing as medium or weak band in= theory. I am taking a dimer (obtained from crystal structure and then opti= mized) in gas phase to simulate the solid. I know IR intensity strongly dep= ends upon intermolecular interaction which is not described properly by tak= ing dimer. How to match the intensity better? Then I tried to add Na+ cation to the catalyst to see the shift in frequenc= y. Shift in frequency is qualitatively changing as observed in experiment. = Now I want to add a counter ion (BPh4), to get the contribution from it as = seen in experiment. Probably since I am doing the calculation in gas phase = adding BPh4- close to Na+ causing the Na to go little distant from catalyst= and shift in catalyst frequency is diminished. The crystal structure of th= e complex is not known, so I do not have any idea of where to add it. I do = see interaction of BPh4 with the catalyst, 4 Phenyl ring breathing mode is = split in the complex. Could you suggest how to solve the problem? Thanks and regards. Partha = --_44DDFC4C-E9B1-768E-9158-2041D8806C9F_ Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="iso-8859-1"
Could you please send me the experimental paper ? Ev= entually try to do rum your calculation in g09 smd model with 6-31+g(d,p) s= et. And run cation only both gas and water as well as run anion too. You ca= n get Reaction energy as well as binding energy. So it will be your s= upporting information.

Best Regards
Kalyan
From: partha kundu partha1kundu{}gmail.com
Se= nt: 25/08/2013 12:15
To: Dhar, Kalyan kumar Subject: CCL: Experimental Raman and IR not matching with theory

Dear Kalyan,
Thanks for your= answer. So what solvent do you think would be better to simulate solid pha= se?
regards.

Partha P. Kundu
=0A= =0A= PhD student
Light Scattering Laboratory
Chemistry & Physics of M= aterials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research (= JNCASR), Bangalore, 560064 INDIA
Phone +91 80 2208 2811/2853 (Lab)=
=0A= =0A= =0A=

On Sun, Aug 25, 2013 at 1:16 PM, kalyan = onekalyan^^^yahoo.com &l= t;owner-chem= istry^-^ccl.net> wrote:
=0A= =0A=
=0A= =0A=
= Probably since I am doing the calculation in gas phase adding BPh4- close t= o Na+ causing the Na to go little distant from catalyst and shift in cataly= st frequency is diminished.
=0A= =0A=
__________________= _______________________________________________________-=0A= =0A=
How come you will run yo= ur calculation for a complex in gas phase .?
=0A= =0A=
Molecule in gas phase di= d first then run its in liquid phase . then their is a meaning . But only g= as phase is meaningless or no sense
=0A= =0A=

=0A= =0A=
Best= regards
=0A= =0A=
kalyan .
=0A= =0A=
=0A= =0A=

=0A= =0A= From:<= /b> partha kundu partha1kundu[]gmail.com <owner-chemistry%x%ccl.net>
=0A= =0A= To: "Dhar, Kalyan kumar "= <kalyan.dhar%x%mail= .polimi.it>
Sent:<= /b> Sunday, August 25, 2013 8:21 AM
=0A= =0A= Subject: CCL: Experimenta= l Raman and IR not matching with theory

=0A=
Dear All,
I am trying to simulate IR and Rama= n of a catalyst and =0A= trying to see the effect of Na+ on the frequency. For catalyst I am =0A= getting very good match for Raman (after converting to intensity), but =0A= for IR some strong experimentally observed modes (like S=3DO str.) are =0A= appearing as medium or weak band in theory. I am taking a dimer =0A= (obtained from crystal structure and then optimized) in gas phase to =0A= simulate the solid. I know IR intensity strongly depends upon =0A= intermolecular interaction which is not described properly by taking =0A= dimer. How to match the intensity better?
Then I tried to add Na+ =0A= cation to the catalyst to see the shift in frequency. Shift in frequency=0A= is qualitatively changing as observed in experiment. Now I want to add a= =0A= counter ion (BPh4), to get the contribution from it as seen in =0A= experiment. Probably since I am doing the calculation in gas phase =0A= adding BPh4- close to Na+ causing the Na to go little distant from =0A= catalyst and shift in catalyst frequency is diminished. The crystal =0A= structure of the complex is not known, so I do not have any idea of =0A= where to add it. I do see interaction of BPh4 with the catalyst, 4 =0A= Phenyl ring breathing mode is split in the complex. Could you suggest =0A= how to solve the problem?
Thanks and regards.
Partha=0A= =0A= =0A=
=0A=
=0A=

=

=0A= = --_44DDFC4C-E9B1-768E-9158-2041D8806C9F_-- From owner-chemistry@ccl.net Sun Aug 25 08:04:01 2013 From: "partha kundu partha1kundu^gmail.com" To: CCL Subject: CCL: Experimental Raman and IR not matching with theory Message-Id: <-49111-130825080305-2458-hUgihbumPdBvL1sdKODyEA]^[server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary=bcaec52d5773b6bd6c04e4c46ba7 Date: Sun, 25 Aug 2013 17:32:17 +0530 MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu]-[gmail.com] --bcaec52d5773b6bd6c04e4c46ba7 Content-Type: text/plain; charset=ISO-8859-1 Dear Kalyan, Thank you for your suggestion. Actually I am trying to simulate some experimental results which is not published. Could you send me any paper where authors has followed similar approach. It will be easier for me to understand then. One question I have, will taking water not affect the position and intensity of vibrational bands, some references will help me for supporting the approach. Thanks and kind regards. Partha. On Sun, Aug 25, 2013 at 3:57 PM, kalyan onekalyan,yahoo.com < owner-chemistry##ccl.net> wrote: > Could you please send me the experimental paper ? Eventually try to do rum > your calculation in g09 smd model with 6-31+g(d,p) set. And run cation only > both gas and water as well as run anion too. You can get Reaction energy as > well as binding energy. So it will be your supporting information. > > Best Regards > Kalyan > ------------------------------ > From: partha kundu partha1kundu{}gmail.com > Sent: 25/08/2013 12:15 > To: Dhar, Kalyan kumar > Subject: CCL: Experimental Raman and IR not matching with theory > > Dear Kalyan, > Thanks for your answer. So what solvent do you think would be better to > simulate solid phase? > regards. > > Partha P. Kundu > PhD student > Light Scattering Laboratory > Chemistry & Physics of Materials Unit > Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), > Bangalore, 560064 INDIA > Phone +91 80 2208 2811/2853 (Lab) > > > On Sun, Aug 25, 2013 at 1:16 PM, kalyan onekalyan^^^yahoo.com < > owner-chemistry^-^ccl.net> wrote: > >> >> Probably since I am doing the calculation in gas phase adding BPh4- close >> to Na+ causing the Na to go little distant from catalyst and shift in >> catalyst frequency is diminished. >> _________________________________________________________________________- >> How come you will run your calculation for a complex in gas phase .? >> Molecule in gas phase did first then run its in liquid phase . then their >> is a meaning . But only gas phase is meaningless or no sense >> >> Best regards >> kalyan . >> >> ------------------------------ >> *From:* partha kundu partha1kundu[]gmail.com >> *To:* "Dhar, Kalyan kumar " >> *Sent:* Sunday, August 25, 2013 8:21 AM >> *Subject:* CCL: Experimental Raman and IR not matching with theory >> >> Dear All, >> I am trying to simulate IR and Raman of a catalyst and trying to see the >> effect of Na+ on the frequency. For catalyst I am getting very good match >> for Raman (after converting to intensity), but for IR some strong >> experimentally observed modes (like S=O str.) are appearing as medium or >> weak band in theory. I am taking a dimer (obtained from crystal structure >> and then optimized) in gas phase to simulate the solid. I know IR intensity >> strongly depends upon intermolecular interaction which is not described >> properly by taking dimer. How to match the intensity better? >> Then I tried to add Na+ cation to the catalyst to see the shift in >> frequency. Shift in frequency is qualitatively changing as observed in >> experiment. Now I want to add a counter ion (BPh4), to get the contribution >> from it as seen in experiment. Probably since I am doing the calculation in >> gas phase adding BPh4- close to Na+ causing the Na to go little distant >> from catalyst and shift in catalyst frequency is diminished. The crystal >> structure of the complex is not known, so I do not have any idea of where >> to add it. I do see interaction of BPh4 with the catalyst, 4 Phenyl ring >> breathing mode is split in the complex. Could you suggest how to solve the >> problem? >> Thanks and regards. >> Partha >> >> >> > --bcaec52d5773b6bd6c04e4c46ba7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Kalyan,
Thank you for your su= ggestion. Actually I am trying to simulate some experimental results which = is not published. Could you send me any paper where authors has followed si= milar approach. It will be easier for me to understand then. One question I= have, will taking water not affect the position and intensity of vibration= al bands, some references will help me for supporting the approach.

Thanks and kind regards.
Partha.

On Sun, Aug 25, 20= 13 at 3:57 PM, kalyan onekalyan,yahoo.com = <owner-chemistry##ccl.net> wrote:

Could you please send me the experimental paper = ? Eventually try to do rum your calculation in g09 smd model with 6-31+g(d,= p) set. And run cation only both gas and water as well as run anion too. Yo= u can get Reaction energy as well as=A0 binding energy. So it will be your = supporting information.=A0

Best Regards
Kalyan
From: <= /span>partha k= undu partha1kundu{}gmail.com=

Sent: 25/08/2013 12:15
To: Dhar, Kalyan kumar

Subject: CCL: Experimental Raman and IR not matching wit= h theory

Dear Kalyan,
Thanks for your answer= . So what solvent do you think would be better to simulate solid phase?
=
regards.

P= artha P. Kundu
PhD student
Light Scattering Laboratory
Chemistry & Physics of M= aterials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research (= JNCASR), Bangalore,=A0 560064 INDIA
Phone +91 80 2208 2811/2853 (Lab)

On Sun, Aug 25, 2013 at 1:16 PM, kalyan = onekalyan^^^yahoo.com <owner-chemistry^-^ccl.net> wrote:

Probably since I am doing the calculation in gas phase ad= ding BPh4- close to Na+ causing the Na to go little distant from catalyst a= nd shift in catalyst frequency is diminished.

______________________= ___________________________________________________-

How come you will run your c= alculation for a complex in gas phase .?=A0

Molecule in gas phase did fi= rst then run its in liquid phase . then their is a meaning . But only gas p= hase is meaningless or no sense=A0

Best reg= ards

kalyan .=A0

From: partha kundu partha1kundu[]gmail.com <owner-chemistry%x%ccl.net>
To: "Dhar, Kalyan kuma= r " <kalyan.dhar%x%mail.polimi.it>
Sent: Sunday, August 25, 2013 8:21 AM
Subject: CCL: Experimental = Raman and IR not matching with theory

Dear All,
I am trying to simulate IR and Rama= n of a catalyst and=20 trying to see the effect of Na+ on the frequency. For catalyst I am=20 getting very good match for Raman (after converting to intensity), but=20 for IR some strong experimentally observed modes (like S=3DO str.) are=20 appearing as medium or weak band in theory. I am taking a dimer=20 (obtained from crystal structure and then optimized) in gas phase to=20 simulate the solid. I know IR intensity strongly depends upon=20 intermolecular interaction which is not described properly by taking=20 dimer. How to match the intensity better?
Then I tried to add Na+=20 cation to the catalyst to see the shift in frequency. Shift in frequency is qualitatively changing as observed in experiment. Now I want to add a counter ion (BPh4), to get the contribution from it as seen in=20 experiment. Probably since I am doing the calculation in gas phase=20 adding BPh4- close to Na+ causing the Na to go little distant from=20 catalyst and shift in catalyst frequency is diminished. The crystal=20 structure of the complex is not known, so I do not have any idea of=20 where to add it. I do see interaction of BPh4 with the catalyst, 4=20 Phenyl ring breathing mode is split in the complex. Could you suggest=20 how to solve the problem?
Thanks and regards.
Partha

=

--bcaec52d5773b6bd6c04e4c46ba7-- From owner-chemistry@ccl.net Sun Aug 25 10:22:00 2013 From: "darren.rhodes darren.rhodes*gmail.com" To: CCL Subject: CCL: Getting short contact data for molecule built with Gaussview Message-Id: <-49112-130825055430-16600-2hQZ+RF71l3bthYGcDRFJA]^[server.ccl.net> X-Original-From: "darren.rhodes" Content-Type: multipart/alternative; boundary=001a11c1ba4ade270904e4c29f68 Date: Sun, 25 Aug 2013 10:54:23 +0100 MIME-Version: 1.0 Sent to CCL by: "darren.rhodes" [darren.rhodes.:.gmail.com] --001a11c1ba4ade270904e4c29f68 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable This blog post may help if you want to take up Willy Offermans' suggestion, http://molecularmodelingbasics.blogspot.co.uk/2013/07/a-python-program-for-= reading.html Darren. On 24 August 2013 13:59, Willy Offermans Willy*Offermans.Rompen.nl < owner-chemistry * ccl.net> wrote: > > Sent to CCL by: Willy Offermans [Willy^^Offermans.Rompen.nl > ] > Hello Adedapo, > > Write a script to calculate all possible distances between the atoms in a > molecule and order the list by length. For an experienced person, it is > half an hour work, for the unexperienced a good lesson in programming. > > On Fri, Aug 23, 2013 at 11:25:49AM +0200, Adedapo Adeyinka u11335132._+_. > tuks.co.za wrote: > > Dear All, > > I want to determine the distances of all the short > contacts > > in a molecule I built with Gaussview and saved as a mol2 file. Does > anyone > > know how to get this information automatically using gaussview or > mercury? > > or is there any software that I can get for free to extract this data > for > > me. > > I will be glad if anyone can help me out. > > > > > > Thanks > > > > Adedapo. > > > > -- > > This message and attachments are subject to a disclaimer. Please refer = to > > http://www.it.up.ac.za/documentation/governance/disclaimer/ for full > > details. > > -- > Met vriendelijke groeten, > With kind regards, > Mit freundlichen Gruessen, > > Willy > > ************************************* > Dr. W.K. Offermans > CAT Fellow > CAT Catalytic Center > Institut f=FCr Technische und Makromolekulare Chemie > RWTH Aachen > Worringerweg 1, Raum 38C-150 > D-52074 Aachen, Germany > Phone: +49 241 80 28592 > Fax: +49 241 80 22593 > Home: +31 45 544 49 44 > Mobile: +31 681 15 87 68 > e-mail: Willy_+_Offermans.Rompen.nl > e-mail: Willy.Offermans_+_CatalyticCenter.RWTH-Aachen.de > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 "I have no doubt that if a party creates and sends an electronically created document then he will be treated as having signed it to the same extent that he would in law be treated as having signed a hard copy of the same document. The fact that the document is created electronically as opposed to as a hard copy can make no difference." Pelling J in Mehta v J Pereira Fernandes SA [2006] EWHC 813 (Ch) Key ID:- 0xB76FE0B9 http://pgpkeys.mit.edu:11371/ --001a11c1ba4ade270904e4c29f68 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
This blog post may help if you want to take up Willy Offermans&#= 39; suggestion,

http://molecularmodelingbasics.blogspot.c= o.uk/2013/07/a-python-program-for-reading.html

Darren.

On 24 August 2013 13:59, Willy Offermans Willy*<= a href=3D"http://Offermans.Rompen.nl">Offermans.Rompen.nl <owner= -chemistry * ccl.net> wrote:

Sent to CCL by: Willy Offermans [= Willy^^Offermans.= Rompen.nl]
Hello Adedapo,

Write a script to calculate all possible distances be= tween the atoms in a
molecule and order the list by length. For an exper= ienced person, it is
half an hour work, for the unexperienced a good les= son in programming.

On Fri, Aug 23, 2013 at 11:25:49AM +0200, Adedapo Adeyinka u11335132._+= _.tuks.co.za wrote:> Dear All,
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I want to determine = the distances of all the short contacts
> in a molecule I built with Gaussview and saved as a mol2 file. Does an= yone
> know how to get this information automatically using gaussview= or mercury?
> =A0or is there any software that I can get for free to= extract this data for
> me.
> I will be glad if anyone can help me out.
>
><= br>> Thanks
>
> Adedapo.
>
> --
> This mes= sage and attachments are subject to a disclaimer. Please refer to
> <= a href=3D"http://www.it.up.ac.za/documentation/governance/disclaimer/" targ= et=3D"_blank">http://www.it.up.ac.za/documentation/governance/disclaimer/ for full
> details.

--
Met vriendelijke groeten,
With kind regards,<= br>Mit freundlichen Gruessen,

Willy

*************************= ************
Dr. W.K. Offermans
CAT Fellow
CAT Catalytic Center Institut f=FCr Technische und Makromolekulare Chemie
RWTH Aachen
Worr= ingerweg 1, Raum 38C-150
D-52074 Aachen, Germany
Phone: =A0+49 241 80 28592=
Fax: =A0 =A0+49 241 80 22593
Home: =A0 +31 45 544 49 44
Mobile: +31 681 15 87 68
e-mail: Willy_+_O= ffermans.Rompen.nl
e-mail: Willy.Offermans_+_CatalyticCenter.RWTH-Aachen.d= e

-=3D This is automatically added to each message by the mailing= script =3D-
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--
"I have n= o doubt that if a party creates and sends an electronically created documen= t then he will be treated as having signed it to the same extent that he wo= uld in law be treated as having signed a hard copy of the same document. Th= e fact that the document is created electronically as opposed to as a hard = copy can make no difference." =A0Pelling J in Mehta v J Pereira Fernan= des SA [2006] EWHC 813 (Ch)

Key ID:- 0xB76FE0B9 http://pgpkeys.mit.edu:11371/=20 --001a11c1ba4ade270904e4c29f68-- From owner-chemistry@ccl.net Sun Aug 25 11:37:00 2013 From: "kalyan onekalyan]^[yahoo.com" To: CCL Subject: CCL: Experimental Raman and IR not matching with theory Message-Id: <-49113-130825112311-29705-yIgmlsPbdLkoOFI1nheGcg^server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="_3F7F0B75-05AE-8357-CDC6-6E1B539B9063_" Date: Sun, 25 Aug 2013 17:23:07 +0200 MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan^_^yahoo.com] --_3F7F0B75-05AE-8357-CDC6-6E1B539B9063_ Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" I am following this approach last 2 years. The things that I wrote its very easy in computational chemistry=20 You can trust me. Best Regards=20 Kalyan -----Original Message----- > From: partha kundu partha1kundu^gmail.com Sent: 25/08/2013 15:01 To: Dhar, Kalyan kumar Subject: CCL: Experimental Raman and IR not matching with theory Dear Kalyan, Thank you for your suggestion. Actually I am trying to simulate some experi= mental results which is not published. Could you send me any paper where au= thors has followed similar approach. It will be easier for me to understand= then. One question I have, will taking water not affect the position and i= ntensity of vibrational bands, some references will help me for supporting = the approach. Thanks and kind regards. Partha. On Sun, Aug 25, 2013 at 3:57 PM, kalyan onekalyan,yahoo.com wrote: Could you please send me the experimental paper ? Eventually try to do rum = your calculation in g09 smd model with 6-31+g(d,p) set. And run cation only= both gas and water as well as run anion too. You can get Reaction energy a= s well as binding energy. So it will be your supporting information. =20 Best Regards=20 Kalyan > From: partha kundu partha1kundu{}gmail.com Sent: 25/08/2013 12:15 To: Dhar, Kalyan kumar=20 Subject: CCL: Experimental Raman and IR not matching with theory Dear Kalyan, Thanks for your answer. So what solvent do you think would be better to sim= ulate solid phase? regards. Partha P. Kundu=20 PhD student Light Scattering Laboratory=20 Chemistry & Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalor= e, 560064 INDIA Phone +91 80 2208 2811/2853 (Lab) On Sun, Aug 25, 2013 at 1:16 PM, kalyan onekalyan^^^yahoo.com wrote: Probably since I am doing the calculation in gas phase adding BPh4- close t= o Na+ causing the Na to go little distant from catalyst and shift in cataly= st frequency is diminished. _________________________________________________________________________- How come you will run your calculation for a complex in gas phase .?=20 Molecule in gas phase did first then run its in liquid phase . then their i= s a meaning . But only gas phase is meaningless or no sense=20 Best regards kalyan .=20 =20 > From: partha kundu partha1kundu[]gmail.com To: "Dhar, Kalyan kumar " =20 Sent: Sunday, August 25, 2013 8:21 AM Subject: CCL: Experimental Raman and IR not matching with theory =20 Dear All, I am trying to simulate IR and Raman of a catalyst and trying to see the ef= fect of Na+ on the frequency. For catalyst I am getting very good match for= Raman (after converting to intensity), but for IR some strong experimental= ly observed modes (like S=3DO str.) are appearing as medium or weak band in= theory. I am taking a dimer (obtained from crystal structure and then opti= mized) in gas phase to simulate the solid. I know IR intensity strongly dep= ends upon intermolecular interaction which is not described properly by tak= ing dimer. How to match the intensity better? Then I tried to add Na+ cation to the catalyst to see the shift in frequenc= y. Shift in frequency is qualitatively changing as observed in experiment. = Now I want to add a counter ion (BPh4), to get the contribution from it as = seen in experiment. Probably since I am doing the calculation in gas phase = adding BPh4- close to Na+ causing the Na to go little distant from catalyst= and shift in catalyst frequency is diminished. The crystal structure of th= e complex is not known, so I do not have any idea of where to add it. I do = see interaction of BPh4 with the catalyst, 4 Phenyl ring breathing mode is = split in the complex. Could you suggest how to solve the problem? Thanks and regards. Partha = --_3F7F0B75-05AE-8357-CDC6-6E1B539B9063_ Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="iso-8859-1"
I am following this approach last 2 years.
The&nb= sp; things that I wrote its very easy in computational chemistry
You ca= n trust me.

Best Regards
Kalyan
Fr= om: partha kundu partha1kundu^gmail.com
Sent: 25/08/2013 15:01=
To: Dhar, Kalyan kumar
Subject= : C= CL: Experimental Raman and IR not matching with theory

Dear Kalyan,
Thank you for your suggesti= on. Actually I am trying to simulate some experimental results which is not= published. Could you send me any paper where authors has followed similar = approach. It will be easier for me to understand then. One question I have,= will taking water not affect the position and intensity of vibrational ban= ds, some references will help me for supporting the approach.
=0A= =0A=
Thanks and kind regards.
Partha.

On Sun, Aug 25, 20= 13 at 3:57 PM, kalyan onekalyan,yahoo.com = <owner-chemistry=3Dccl.net> wrote:
=0A= =0A=
Could you please send me the experimental pape= r ? Eventually try to do rum your calculation in g09 smd model with 6-31+g(= d,p) set. And run cation only both gas and water as well as run anion too. = You can get Reaction energy as well as binding energy. So it will be = your supporting information.
=0A= =0A=
Best Regards
Kalyan
F= rom: gmail.com
=0A= =0A=
Sent: 25/08/2013 12:15
To: Dhar, Kalyan kumar <= /span>
=0A= =0A=
Subject: CCL: Experimental Raman and IR not ma= tching with theory
=0A= =0A=
Dear Kalyan,
Thanks for your answer= . So what solvent do you think would be better to simulate solid phase?
=
regards.

P= artha P. Kundu
=0A= =0A= =0A= =0A= PhD student
Light Scattering Laboratory
Chemistry & Physics of M= aterials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research (= JNCASR), Bangalore, 560064 INDIA
Phone +91 80 2208 2811/2853 (Lab)=
=0A= =0A= =0A= =0A= =0A=

On Sun, Aug 25, 2013 at 1:16 PM, kalyan = onekalyan^^^yahoo.com <owner-chemistry^-^ccl.net> wrote:
=0A= =0A= =0A= =0A=
=0A= =0A=
=0A= =0A=
= Probably since I am doing the calculation in gas phase adding BPh4- close t= o Na+ causing the Na to go little distant from catalyst and shift in cataly= st frequency is diminished.
=0A= =0A= =0A= =0A=
__________________= _______________________________________________________-=0A= =0A= =0A= =0A=
How come you will run yo= ur calculation for a complex in gas phase .?
=0A= =0A= =0A= =0A=
Molecule in gas phase di= d first then run its in liquid phase . then their is a meaning . But only g= as phase is meaningless or no sense
=0A= =0A= =0A= =0A=

=0A= =0A= =0A= =0A=
Best= regards
=0A= =0A= =0A= =0A=
kalyan .
=0A= =0A= =0A= =0A=
=0A= =0A= =0A= =0A=

=0A= =0A=
=0A= =0A= From:<= /b> partha kundu partha1kundu[]gmail.com <owner-chemistry%x%ccl.net>
=0A= =0A= =0A= =0A= To: "Dhar, Kalyan kumar "= <kalyan.dhar%x%mail= .polimi.it>
Sent:<= /b> Sunday, August 25, 2013 8:21 AM
=0A= =0A= =0A= =0A= Subject: CCL: Experimenta= l Raman and IR not matching with theory

<= br>=0A=
Dear All,
I am trying to simulate IR and Rama= n of a catalyst and =0A= trying to see the effect of Na+ on the frequency. For catalyst I am =0A= getting very good match for Raman (after converting to intensity), but =0A= for IR some strong experimentally observed modes (like S=3DO str.) are =0A= appearing as medium or weak band in theory. I am taking a dimer =0A= (obtained from crystal structure and then optimized) in gas phase to =0A= simulate the solid. I know IR intensity strongly depends upon =0A= intermolecular interaction which is not described properly by taking =0A= dimer. How to match the intensity better?
Then I tried to add Na+ =0A= cation to the catalyst to see the shift in frequency. Shift in frequency=0A= is qualitatively changing as observed in experiment. Now I want to add a= =0A= counter ion (BPh4), to get the contribution from it as seen in =0A= experiment. Probably since I am doing the calculation in gas phase =0A= adding BPh4- close to Na+ causing the Na to go little distant from =0A= catalyst and shift in catalyst frequency is diminished. The crystal =0A= structure of the complex is not known, so I do not have any idea of =0A= where to add it. I do see interaction of BPh4 with the catalyst, 4 =0A= Phenyl ring breathing mode is split in the complex. Could you suggest =0A= how to solve the problem?
Thanks and regards.
Partha=0A= =0A= =0A=
=0A=
=0A=

=

=0A=

=0A= = --_3F7F0B75-05AE-8357-CDC6-6E1B539B9063_-- From owner-chemistry@ccl.net Sun Aug 25 14:42:00 2013 From: "Sharmistha karmakar sharmisthakarmakarr^_^gmail.com" To: CCL Subject: CCL:G: Error in QCISD Calculation Message-Id: <-49114-130825122200-2314-onAxmDwc3IKV9idYYARXAw|a|server.ccl.net> X-Original-From: "Sharmistha karmakar" Date: Sun, 25 Aug 2013 12:21:59 -0400 Sent to CCL by: "Sharmistha karmakar" [sharmisthakarmakarr^gmail.com] Dear All, I am trying to calculate frequency calculations at QCISD/tzvp method using Gaussian 09. But it failed showing following eror: ................................................................... DD1Dir will call FoFDir 1 times, MxPair= 552 NAB= 276 NAA= 0 NBB= 0 NumPrc= 6. DE(Corr)= -1.2204516 E(CORR)= -563.35323981 Delta=-1.16D-09 NORM(A)= 0.12234534D+01 ************* *MAX. CYCLES* ************* Largest amplitude= 3.70D-02 Error termination via Lnk1e in /home/rameswar/g09/l913.exe at Sun Aug 25 14:27:37 2013. ........................................................................ What does it means?How can i restart the job to get normal termination . Any help or suggestion is highly appreciated. With best regards, Sharmistha From owner-chemistry@ccl.net Sun Aug 25 15:16:00 2013 From: "Mark Zottola mzottola:gmail.com" To: CCL Subject: CCL:G: Experimental Raman and IR not matching with theory Message-Id: <-49115-130825145940-5705-4SOFCPkZnE0bgOWw+gdDMQ===server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=047d7b2e52e091d09404e4ca3df9 Date: Sun, 25 Aug 2013 14:59:34 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola%x%gmail.com] --047d7b2e52e091d09404e4ca3df9 Content-Type: text/plain; charset=ISO-8859-1 Have you considered doing periodic QM? A solid state calculation on an appropriate unit cell should solve your intensity and interaction issues. There are many QM codes which can do this - Gaussian, VASP, and ESPRESSO are but a few of the codes available. Good luck! On Sun, Aug 25, 2013 at 11:23 AM, kalyan onekalyan]^[yahoo.com < owner-chemistry++ccl.net> wrote: > I am following this approach last 2 years. > The things that I wrote its very easy in computational chemistry > You can trust me. > > Best Regards > Kalyan > ------------------------------ > From: partha kundu partha1kundu^gmail.com > Sent: 25/08/2013 15:01 > > To: Dhar, Kalyan kumar > Subject: CCL: Experimental Raman and IR not matching with theory > > Dear Kalyan, > Thank you for your suggestion. Actually I am trying to simulate some > experimental results which is not published. Could you send me any paper > where authors has followed similar approach. It will be easier for me to > understand then. One question I have, will taking water not affect the > position and intensity of vibrational bands, some references will help me > for supporting the approach. > Thanks and kind regards. > Partha. > > > > On Sun, Aug 25, 2013 at 3:57 PM, kalyan onekalyan,yahoo.com < > owner-chemistry=ccl.net> wrote: > >> Could you please send me the experimental paper ? Eventually try to do >> rum your calculation in g09 smd model with 6-31+g(d,p) set. And run cation >> only both gas and water as well as run anion too. You can get Reaction >> energy as well as binding energy. So it will be your supporting >> information. >> >> Best Regards >> Kalyan >> ------------------------------ >> From: partha kundu partha1kundu{}gmail.com >> Sent: 25/08/2013 12:15 >> To: Dhar, Kalyan kumar >> Subject: CCL: Experimental Raman and IR not matching with theory >> >> Dear Kalyan, >> Thanks for your answer. So what solvent do you think would be better to >> simulate solid phase? >> regards. >> >> Partha P. Kundu >> PhD student >> Light Scattering Laboratory >> Chemistry & Physics of Materials Unit >> Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), >> Bangalore, 560064 INDIA >> Phone +91 80 2208 2811/2853 (Lab) >> >> >> On Sun, Aug 25, 2013 at 1:16 PM, kalyan onekalyan^^^yahoo.com < >> owner-chemistry^-^ccl.net> wrote: >> >>> >>> Probably since I am doing the calculation in gas phase adding BPh4- >>> close to Na+ causing the Na to go little distant from catalyst and shift in >>> catalyst frequency is diminished. >>> >>> _________________________________________________________________________- >>> How come you will run your calculation for a complex in gas phase .? >>> Molecule in gas phase did first then run its in liquid phase . then >>> their is a meaning . But only gas phase is meaningless or no sense >>> >>> Best regards >>> kalyan . >>> >>> ------------------------------ >>> *From:* partha kundu partha1kundu[]gmail.com >> > >>> *To:* "Dhar, Kalyan kumar " >>> *Sent:* Sunday, August 25, 2013 8:21 AM >>> *Subject:* CCL: Experimental Raman and IR not matching with theory >>> >>> Dear All, >>> I am trying to simulate IR and Raman of a catalyst and trying to see the >>> effect of Na+ on the frequency. For catalyst I am getting very good match >>> for Raman (after converting to intensity), but for IR some strong >>> experimentally observed modes (like S=O str.) are appearing as medium or >>> weak band in theory. I am taking a dimer (obtained from crystal structure >>> and then optimized) in gas phase to simulate the solid. I know IR intensity >>> strongly depends upon intermolecular interaction which is not described >>> properly by taking dimer. How to match the intensity better? >>> Then I tried to add Na+ cation to the catalyst to see the shift in >>> frequency. Shift in frequency is qualitatively changing as observed in >>> experiment. Now I want to add a counter ion (BPh4), to get the contribution >>> from it as seen in experiment. Probably since I am doing the calculation in >>> gas phase adding BPh4- close to Na+ causing the Na to go little distant >>> from catalyst and shift in catalyst frequency is diminished. The crystal >>> structure of the complex is not known, so I do not have any idea of where >>> to add it. I do see interaction of BPh4 with the catalyst, 4 Phenyl ring >>> breathing mode is split in the complex. Could you suggest how to solve the >>> problem? >>> Thanks and regards. >>> Partha >>> >>> >>> >> > --047d7b2e52e091d09404e4ca3df9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Have you considered doing periodic QM? A solid state calcu= lation on an appropriate unit cell should solve your intensity and interact= ion issues. =A0There are many QM codes which can do this - Gaussian, VASP, = and ESPRESSO are but a few of the codes available.

Good luck!

On Sun, Aug 25, 2013 at 11:23 AM, kalyan onekalyan]= ^[yahoo.com <owner-chemistry++ccl.n= et> wrote:

I am following this approach last 2 years.
Th= e=A0 things that I wrote its very easy in computational chemistry
You can trust me.

Best Regards
Kalyan
From= : parth= a kundu partha1kundu^gmail.c= om
Sent: 25/08/2013 15:01

To: Dhar, Kalyan kumar Subject: CCL: Experimental Raman and IR not matching with theory

Dear Kalyan,
Thank you for your suggestion. Actually I am trying to simulate some exp= erimental results which is not published. Could you send me any paper where= authors has followed similar approach. It will be easier for me to underst= and then. One question I have, will taking water not affect the position an= d intensity of vibrational bands, some references will help me for supporti= ng the approach.

Thanks and kind regards.
Partha.

On Sun, Aug 25, 2013 at 3:= 57 PM, kalyan onekalyan,yaho= o.com <owner-chemistry=3Dccl.net> wrote:

Could you please send me the experimental paper ? Eventually try to do rum = your calculation in g09 smd model with 6-31+g(d,p) set. And run cation only= both gas and water as well as run anion too. You can get Reaction energy a= s well as=A0 binding energy. So it will be your supporting information.=A0 =

Best Regards
Kalyan
From: partha kundu partha1k= undu{}gmail.com
Sent: 25/08/2013 12:15
To: Dhar, Kalyan kumar

Subject: CCL: Experimental Raman and IR not matching with theory

Dear Kalyan,
Thanks for your answer= . So what solvent do you think would be better to simulate solid phase?
=
regards.

P= artha P. Kundu
PhD student
Light Scattering Laboratory
Chemistry & Physics of M= aterials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research (= JNCASR), Bangalore,=A0 560064 INDIA
Phone +91 80 2208 2811/2853 (Lab)

On Sun, Aug 25, 2013 at 1:16 PM, kalyan = onekalyan^^^yahoo.com <owner-chemistry^-^ccl.net> wrote:

Probably since I am doing the calculation in gas phase ad= ding BPh4- close to Na+ causing the Na to go little distant from catalyst a= nd shift in catalyst frequency is diminished.

______________________= ___________________________________________________-

How come you will run your c= alculation for a complex in gas phase .?=A0

Molecule in gas phase did fi= rst then run its in liquid phase . then their is a meaning . But only gas p= hase is meaningless or no sense=A0

Best reg= ards

kalyan .=A0

From: partha kundu partha1kundu[]gmail.com <owner-chemistry%x%ccl.net>
To: "Dhar, Kalyan kuma= r " <kalyan.dhar%x%mail.polimi.it>
Sent: Sunday, August 25, 2013 8:21 AM
Subject: CCL: Experimental = Raman and IR not matching with theory

Dear All,
I am trying to simulate IR and Rama= n of a catalyst and=20 trying to see the effect of Na+ on the frequency. For catalyst I am=20 getting very good match for Raman (after converting to intensity), but=20 for IR some strong experimentally observed modes (like S=3DO str.) are=20 appearing as medium or weak band in theory. I am taking a dimer=20 (obtained from crystal structure and then optimized) in gas phase to=20 simulate the solid. I know IR intensity strongly depends upon=20 intermolecular interaction which is not described properly by taking=20 dimer. How to match the intensity better?
Then I tried to add Na+=20 cation to the catalyst to see the shift in frequency. Shift in frequency is qualitatively changing as observed in experiment. Now I want to add a counter ion (BPh4), to get the contribution from it as seen in=20 experiment. Probably since I am doing the calculation in gas phase=20 adding BPh4- close to Na+ causing the Na to go little distant from=20 catalyst and shift in catalyst frequency is diminished. The crystal=20 structure of the complex is not known, so I do not have any idea of=20 where to add it. I do see interaction of BPh4 with the catalyst, 4=20 Phenyl ring breathing mode is split in the complex. Could you suggest=20 how to solve the problem?
Thanks and regards.
Partha

=

--047d7b2e52e091d09404e4ca3df9-- From owner-chemistry@ccl.net Sun Aug 25 15:52:01 2013 From: "kalyan onekalyan#%#yahoo.com" To: CCL Subject: CCL:G: Error in QCISD Calculation Message-Id: <-49116-130825153346-26529-zvT0ekXmdg2902tM78871g : server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="_B49167F2-65BE-72B7-4F69-4A6C8BC4268F_" Date: Sun, 25 Aug 2013 21:33:41 +0200 MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan!^!yahoo.com] --_B49167F2-65BE-72B7-4F69-4A6C8BC4268F_ Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="Windows-1252" Restart the job use chk point file. And use scf=3Dqc as well as you can use= iop(5/6) .hope it will help.=20 Best Regards=20 Kalyan -----Original Message----- > From: Sharmistha karmakar sharmisthakarmakarr^_^gmail.com Sent: 25/08/2013 21:00 To: Dhar, Kalyan kumar Subject: CCL:G: Error in QCISD Calculation Sent to CCL by: "Sharmistha karmakar" [sharmisthakarmakarr^gmail.com] Dear All, I am trying to calculate frequency calculations at QCISD/tzvp method using Gaussian 09. But it failed showing following eror: ...................................................................=20 DD1Dir will call FoFDir 1 times, MxPair=3D 552 NAB=3D 276 NAA=3D 0 NBB=3D 0 NumPrc=3D 6. DE(Corr)=3D -1.2204516 E(CORR)=3D -563.35323981 Delta=3D-1.16= D-09 NORM(A)=3D 0.12234534D+01 ************* *MAX. CYCLES* ************* Largest amplitude=3D 3.70D-02 Error termination via Lnk1e in /home/rameswar/g09/l913.exe at Sun Aug 25 1= 4:27:37 2013. ........................................................................ What does it means?How can i restart the job to get normal termination . Any help or suggestion is highly appreciated. With best regards, Sharmistha -=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.txt--_B49167F2-65BE-72B7-4F69-4A6C8BC4268F_ Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="Windows-1252"
Restart the job use chk point file. And use scf= =3Dqc as well as you can use iop(5/6) .hope it will help.

Best Rega= rds
Kalyan
From: Sharmistha karmakar sharmisth= akarmakarr^_^gmail.com
Sent: 25/08/2013 21:00
To: Dhar, Kalyan kumar
Subject: CCL:G: Error in= QCISD Calculation

Sent to CCL by: "Sharmistha karm= akar" [sharmisthakarmakarr^gmail.com]
Dear All,
I am trying to calcu= late frequency calculations at
QCISD/tzvp method using Gaussian 09. But= it failed showing following
eror:
.................................= ..................................
DD1Dir will call FoFDir   = 1 times, MxPair=3D       552
NAB=3D = 276 NAA=3D     0 NBB=3D     = 0 NumPrc=3D 6.
DE(Corr)=3D -1.2204516   &nbs= p; E(CORR)=3D     -563.35323981    = Delta=3D-1.16D-09
NORM(A)=3D   0.12234534D+01
**********= ***
*MAX. CYCLES*
*************
Largest amplitude=3D 3.70D-02 Error termination via Lnk1e in /home/rameswar/g09/l913.exe at Sun Aug 25= 14:27:37 2013.
........................................................= ................

What does it means?How can i restart the job to get= normal termination .
Any help or suggestion is highly appreciated.
W= ith best regards,
Sharmistha

-=3D This is automatically a= dded to each message by the mailing script =3D-
To recover the email add= ress of the author of the message, please change
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= --_B49167F2-65BE-72B7-4F69-4A6C8BC4268F_--