From owner-chemistry@ccl.net Fri Dec 6 03:18:00 2013 From: "Jean Jules Fifen julesfifen]|[gmail.com" To: CCL Subject: CCL: scaling factor in frequency calculation Message-Id: <-49406-131206031512-18131-jlsBqsrksjwoQqzdwmEt4Q%a%server.ccl.net> X-Original-From: Jean Jules Fifen Content-Type: multipart/alternative; boundary=001a11c1e98063cd6204ecd93e28 Date: Fri, 6 Dec 2013 09:15:05 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules Fifen [julesfifen:+:gmail.com] --001a11c1e98063cd6204ecd93e28 Content-Type: text/plain; charset=ISO-8859-1 Dear Partha, In my knowledge, I think there is no precise rule. You can get the reverse trend or any other trend. It is true that I did not investigate frequencies scale factors deeply. Thus, I suggest you to write directly to those who worked in such a field, if you are still in doubt. Try writting to George Shields: george.shields||bucknell.edu. Best regards, On Thu, Dec 5, 2013 at 9:45 PM, partha kundu partha1kundu|*|gmail.com < owner-chemistry||ccl.net> wrote: > Dear Jean, > What do I see is if I add scaling factor 0.9 for 1000-1400 , 0.96 for > 1400-1500 and 1 for 1500-1700 I getting good matches with theory. However, > I saw that generally people use scaling factor close to 1 in the lower > wave region and ~0.98 in the upper region. Is it okay to choose the > scaling factor like that? Do you know any work where this kind of behavior > has been seen? > Regards. > > Partha > > > On Tue, Dec 3, 2013 at 12:56 PM, Jean Jules Fifen julesfifen : gmail.com < > owner-chemistry#ccl.net> wrote: > >> >> Sent to CCL by: Jean Jules Fifen [julesfifen#,#gmail.com] >> Scaling factors are better when they are applied differently in >> different frequencies ranges. Thus, it is okay to use dual or more >> scaling factors for matching experimental data. For more convenience, >> I can suggest you to read the paper of Robert Shields (J. Chem. Theor. >> Comput. 2011, 7, 2804-2817) entitled, The Role of Anharmonicity in >> Hydrogen-Bonded Systems: The Case of water clusters. >> >> Best regards. >> >> On 12/2/13, partha kundu partha1kundu{:}gmail.com >> wrote: >> > Dear All, >> > I am trying to see the effect of Cu2+ binding on a ligand by Raman >> > spectroscopy and trying to match those results with DFT. For the ligand, >> I >> > got a very good match with the experimental spectrum after applying a >> > scaling factor. However for the complex if I use the same scaling >> factor, I >> > see some modes in the 1500-1700 cm-1 regions are underestimated. If I >> do >> > not use any scaling factor in that the match is better. I am using >> lanl2dz >> > ECP and basis set combination for Cu. Is it okay to use dual scaling >> (0.961 >> > for 1000-1500 and 1 for the 1500-1700 region) for matching the >> experimental >> > data. Then I can not directly compare my theoretical results with the >> > experiment. Any suggestion would be of great help. >> > Partha >> > >> >> >> -- >> >> *-------------------------------------- >> * Jean Jules FIFEN, |* >> ** Ph. D. in Molecular Physics, |* >> ** Department of Physics, |* >> ** Faculty of Science, |* >> ** University of Ngaoundere, Cameroon |* >> ** P.O. BOX 454 Ngaoundere | >> * >> ** Phone number: 00237 75 21 61 39 | >> * >> **--------------------------------------------------------->> the strange characters on the top line to the # sign. You can also>> >> E-mail to subscribers: CHEMISTRY#ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST#ccl.net or use>> >> >> > -- *--------------------------------------* Jean Jules FIFEN, |* ** Ph. D. in Molecular Physics, |* ** Department of Physics, |* ** Faculty of Science, |* ** University of Ngaoundere, Cameroon |* ** P.O. BOX 454 Ngaoundere |* ** Phone number: 00237 75 21 61 39 |* --------------------------------------------------------- --001a11c1e98063cd6204ecd93e28 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Partha,
In my kn= owledge, I think there is no precise rule. You can get the reverse trend or= any other trend. It is true that I did not investigate frequencies scale f= actors deeply. Thus, I suggest you to write directly to those who worked in= such a field, if you are still in doubt. Try writting to George Shields:= =A0 george.shields||bucknell.= edu.

Best regards,


On Thu, Dec 5, 2013 at 9:45 PM, par= tha kundu partha1kundu|*|gmail.com <owner-chemistry||ccl.net> wrote:
Dear Jean,
What do I see is if I add scaling factor 0.9 for 1000-1400 , 0.96 for 14= 00-1500 and 1 for 1500-1700 I getting good matches with theory. However, I = saw that generally people use scaling factor close to 1=A0 in the lower wav= e region and=A0 ~0.98 in the upper region. Is it okay to choose the scaling= factor like that? Do you know any work where this kind of behavior has bee= n seen?
Regards.

Partha


On Tue, Dec 3, 2013 at 12:56 PM, Jean Ju= les Fifen julesfifen : gmail.com <owner-chemistry#ccl.net><= /span> wrote:

Sent to CCL by: Jean Jules Fifen [julesfifen#,#gmail.com]
Scaling factors are better when they are applied differently i= n
different frequencies ranges. Thus, it is okay to= use dual or more
scaling factors for matching experimental data. For more conve= nience,
I can suggest you to read the paper of Robert Shields (J. Chem. Theor= .
Comput. 2011, 7, 2804-2817) entitled, The Role of Anharmonicity in
Hydrogen-Bonded Systems: The Case of water clusters.

Best regards.

On 12/2/13, partha kundu partha1kundu{:}gmail.com
<owner-chemistry**ccl.net> wrote:
> Dear All,
> I am trying to see the effect of Cu2+ binding on a ligand= by Raman
> spectroscopy and trying to match those results with DFT. = For the ligand, I
> got a very good match with the experimental spectrum afte= r applying a
> scaling factor. However for the complex if I use the same= scaling factor, I
> see some modes in the 1500-1700 cm-1 regions are underest= imated. If I do
> not use any scaling factor in that the match is better. I= am using lanl2dz
> ECP and basis set combination for Cu. Is it okay to use dual scaling (= 0.961
> for 1000-1500 and 1 for the 1500-1700 region) for matchin= g the experimental
> data. Then I can not directly compare my theoretical resu= lts with the
> experiment. Any suggestion would be of great help.
> Partha
>


--

*--------------------------------------
* Jean Jules FIFEN, =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0|*
** Ph. D. in Molecular Physics, =A0 =A0 =A0 |* ** Department of Physics, =A0 =A0 =A0 =A0 =A0 =A0 |*
** Faculty of Science, =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0|*
** University of Ngaoundere, Cameroon |*
** P.O. BOX 454 Ngaoundere =A0 =A0 =A0 =A0 =A0 =A0|
*
** Phone number: 00237 75 21 61 39 =A0 =A0|
*
**---------------------------------------------------------



-=3D This is automatically added to each message by the mailing script =3D-= the strange characters on the top line to the # sign. You can = also
look up the X-Original-From: line in the mail header.

E-mail to subscribers: CHEMISTRY#ccl.net or use:
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST#ccl.net or use
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0 http://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 =A0 h= ttp://www.ccl.net/spammers.txt

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






--
= =A0
=
------------------------------= --------
* Jean Jules FIFEN,=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 |
* Ph. D. in Mol= ecular Physics,=A0=A0=A0=A0=A0=A0 |
* Department of Physics,=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 |
* Faculty of Science,=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 |
* University of Ngaoundere, Cameroon |<= /b>
* P.O. BOX 454 Ngaou= ndere=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 |
* Phone numb= er: 00237 75 21 61 39=A0=A0=A0 |
---------------------------------------------------= ------
=A0
--001a11c1e98063cd6204ecd93e28-- From owner-chemistry@ccl.net Fri Dec 6 08:07:00 2013 From: "Kunal Roy kroy- -pharma.jdvu.ac.in" To: CCL Subject: CCL: Basic QSAR tools Message-Id: <-49407-131206080228-778-YJjz8cI0Fg0VAt1OESUXZQ*|*server.ccl.net> X-Original-From: Kunal Roy Content-Type: multipart/alternative; boundary="----=_Part_1043971_731049394.1386334954291" Date: Fri, 6 Dec 2013 18:32:34 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Kunal Roy [kroy]^[pharma.jdvu.ac.in] ------=_Part_1043971_731049394.1386334954291 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit Some basic QSAR tools are available at http://dtclab.webs.com/software-tools which may be helpful for beginners. Kunal Roy, Ph.D. Associate Professor, Drug Theoretics and Cheminformatics Lab, Department of Pharmaceutical Technology, JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) & Fellow, MANCHESTER INSTITUTE OF BIOTECHNOLOGY, 131 Princess Street, Manchester M1 7DN (UK) Email : kroy..pharma.jdvu.ac.in , kunalroy_in..yahoo.com ; Phone: +91 33 2457 2051 (Off.) URL : http://sites.google.com/site/kunalroyindia/ , http://www.jaduniv.edu.in/profile.php?uid=550 Google scholar citation page: http://scholar.google.com/citations?user=j5iRuhwAAAAJ&hl=en Publication list: http://www.researcherid.com/rid/B-1673-2009 ORCID: http://orcid.org/0000-0003-4486-8074 ------=_Part_1043971_731049394.1386334954291 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Some basic QSAR tools are available at http://dtclab.webs.com/software-tools which may be helpful for beginners.
Kunal Roy, Ph.D. Associate Professor= , Drug Theoretics and Cheminformatics Lab, Department of Pharmaceutical Tec= hnology, 
JADAVPUR UNIVERSITY, Kolkata 700 032 (IN= DIA)
& Fellow, MANCHESTER INSTITUTE OF BIOTECHNO= LOGY, 131 Princess Street, Manchester M1 7DN (UK)
Email : kroy..pharma.jdvu.ac.in , kunalroy_in..yahoo.com ; Phone: +91 33 2457 2051 (Off.) 
------=_Part_1043971_731049394.1386334954291-- From owner-chemistry@ccl.net Fri Dec 6 08:41:00 2013 From: "darren.rhodes darren.rhodes^^gmail.com" To: CCL Subject: CCL: calculation of hydrophillic factor Message-Id: <-49408-131205124054-10095-YCwBaDNTD828zT9H2EJ4Kw+/-server.ccl.net> X-Original-From: "darren.rhodes" Content-Type: multipart/alternative; boundary=047d7bf109fe9d13d104eccd07ee Date: Thu, 5 Dec 2013 17:40:46 +0000 MIME-Version: 1.0 Sent to CCL by: "darren.rhodes" [darren.rhodes+/-gmail.com] --047d7bf109fe9d13d104eccd07ee Content-Type: text/plain; charset=ISO-8859-1 Try http://www.epa.gov/nrmrl/std/qsar/MolecularDescriptorsGuide-v102.pdfp45-46. Darren. On 5 December 2013 16:28, Victor Rosas Garcia rosas.victor]_[gmail.com < owner-chemistry|a|ccl.net> wrote: > Hello everybody, > > I am looking for the formula or algorithm used to calculate the > hydrophillic factor (symbol Hy) used as molecular descriptor in QSAR > studies. So far, the only reference I've got is this > > Todeschini, R. & Consonni, V. Handbook of Molecular Descriptors. > Wlley-VCH.Weinheim (Germany), (2000). > > unfortunately, I don't have access to this handook. > > Are there any papers that describe how to calculate this? > > Regards > > Victor > -- "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/ --047d7bf109fe9d13d104eccd07ee Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable


= On 5 December 2013 16:28, Victor Rosas Garcia rosas.victor]_[gmail.com <owner-chemistry|a|ccl.net>= wrote:
Hello e= verybody,

I am looking for the formula or algorithm used to ca= lculate the hydrophillic factor (symbol Hy) used as molecular descriptor in= QSAR studies. So far, the only reference I've got is this

Todeschini, R. & Consonni, V. Handbook of Molecular Descriptors. Wl= ley-VCH.Weinheim (Germany), (2000).

unfortunately, I don't have access to this handook.

Are there any papers that describe how to calculate this?

= Regards

Victor



--
"I have no doubt t= hat 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 la= w be treated as having signed a hard copy of the same document. The fact th= at the document is created electronically as opposed to as a hard copy can = make no difference." =A0Pelling J in Mehta v J Pereira Fernandes SA [2= 006] EWHC 813 (Ch)

Key ID:- 0xB76FE0B9 http://pgpkeys.mit.edu:11371/
--047d7bf109fe9d13d104eccd07ee-- From owner-chemistry@ccl.net Fri Dec 6 10:37:01 2013 From: "George Fitzgerald George.Fitzgerald%%accelrys.com" To: CCL Subject: CCL: Dipole derivative unit vector Message-Id: <-49409-131206102709-5784-0O1aswGTABT4NzJmNpMu6A++server.ccl.net> X-Original-From: George Fitzgerald Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 6 Dec 2013 07:26:50 -0800 MIME-Version: 1.0 Sent to CCL by: George Fitzgerald [George.Fitzgerald(a)accelrys.com] Dipole derivatives are used in the calculation of infra-red intensities. George Fitzgerald, Ph.D. George.Fitzgerald%%accelrys.com +1 858 799 5360 -----Original Message----- > From: owner-chemistry+gfitzgerald==accelrys.com%%ccl.net [mailto:owner-chemistry+gfitzgerald==accelrys.com%%ccl.net] On Behalf Of Gabriela Arias De la Rosa gabriela.arias*yorkmail.cuny.edu Sent: Wednesday, December 04, 2013 12:58 PM To: George Fitzgerald Subject: CCL: Dipole derivative unit vector Sent to CCL by: "Gabriela Arias De la Rosa" [gabriela.arias]=[yorkmail.cuny.edu] Can anyone please tell me what is the purpose of a Dipole derivative unit vector? I am using Gaussview to analyze vibrational modes and I saw that function, but I am not sure for what this function is used.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Dec 6 11:24:00 2013 From: "Victor Rosas Garcia rosas.victor~~gmail.com" To: CCL Subject: CCL: calculation of hydrophillic factor Message-Id: <-49410-131206094809-30299-AMnHvqgEBU7lD0WFLWn85w~!~server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=089e0111e0dab6f39904ecdebba5 Date: Fri, 6 Dec 2013 08:48:03 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor!^!gmail.com] --089e0111e0dab6f39904ecdebba5 Content-Type: text/plain; charset=ISO-8859-1 Thanx! Got it. Victor 2013/12/5 darren.rhodes darren.rhodes^^gmail.com > Try http://www.epa.gov/nrmrl/std/qsar/MolecularDescriptorsGuide-v102.pdfp45-46. > > Darren. > > > On 5 December 2013 16:28, Victor Rosas Garcia rosas.victor]_[gmail.com < > owner-chemistry*|*ccl.net> wrote: > >> Hello everybody, >> >> I am looking for the formula or algorithm used to calculate the >> hydrophillic factor (symbol Hy) used as molecular descriptor in QSAR >> studies. So far, the only reference I've got is this >> >> Todeschini, R. & Consonni, V. Handbook of Molecular Descriptors. >> Wlley-VCH.Weinheim (Germany), (2000). >> >> unfortunately, I don't have access to this handook. >> >> Are there any papers that describe how to calculate this? >> >> Regards >> >> Victor >> > > > > -- > "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/ > --089e0111e0dab6f39904ecdebba5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Thanx! Got it.

Victor


2013/12/5 darren.rhode= s darren.rhodes^^gmail.com <owner-c= hemistry_._ccl.net>


On 5 December 2013 16:28, Victor Rosas Garcia rosas.= victor]_[gmail.com <owner-chemistry*|*ccl.net> wrote:
Hello e= verybody,

I am looking for the formula or algorithm used to ca= lculate the hydrophillic factor (symbol Hy) used as molecular descriptor in= QSAR studies. So far, the only reference I've got is this

Todeschini, R. & Consonni, V. Handbook of Molecular Descriptors. Wl= ley-VCH.Weinheim (Germany), (2000).

unfortunately, I don't have access to this handook.

Are there any papers that describe how to calculate this?

= Regards

Victor



--
"I have no doubt that if a party c= reates 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 differen= ce." =A0Pelling J in Mehta v J Pereira Fernandes SA [2006] EWHC 813 (C= h)

Key ID:- 0xB76FE0B9 http://pgpkeys.mit.edu:11371/

--089e0111e0dab6f39904ecdebba5--