From owner-chemistry@ccl.net Mon Jun 29 05:08:01 2009 From: "irfan ahmad irfaahmad~!~gmail.com" To: CCL Subject: CCL: can absorption and emission spectra have the same value Message-Id: <-39634-090629050553-31043-m6VWmdFjB/aCbWohtgqdOA===server.ccl.net> X-Original-From: "irfan ahmad" Date: Mon, 29 Jun 2009 05:05:48 -0400 Sent to CCL by: "irfan ahmad" [irfaahmad%a%gmail.com] Dear chemists i got the absorption spectra of compoundfs A,B and C 400, 450, 475 nm. the emission spectra for these compound are 401, 452, 476 nm. I checked the optimized structures at ground and excitd states, there is no problem. My question is this that, can absorption and emission spectra have the same values? any reference or comments will be highly appriciated thanks ahead Irfan Ahmad china From owner-chemistry@ccl.net Mon Jun 29 05:42:01 2009 From: "Jeremy Besnard j10b84%a%hotmail.com" To: CCL Subject: CCL: Find a lead from a drug Message-Id: <-39635-090629051529-2244-RW0Y2I1bb1XY8dnYJsgzNA|server.ccl.net> X-Original-From: "Jeremy Besnard" Date: Mon, 29 Jun 2009 05:15:25 -0400 Sent to CCL by: "Jeremy Besnard" [j10b84[-]hotmail.com] Dear colleagues, I have a list of drugs which are on the market and I'd like to find the lead compound which was used as starting point for the lead optimization process. But the artciles related a story of a drug are not easy to find. An easy one is The Discovery of Tadalafil: A Novel and Highly Selective PDE5 Inhibitor. 2: 2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4-dione Analogues. But by looking for name of drug + discovery in a search engine I don't get hits. I also tried with lead, SAR... I'd like to know if you have some hints and tips to help find a lead with the name of the drug. Also if you know a relatively recent set of leads and drugs that could be very useful. Thank you. Jeremy From owner-chemistry@ccl.net Mon Jun 29 06:16:00 2009 From: "Rafael =?iso-8859-1?q?Rodr=EDguez_Pappalardo?= rafapa * us.es" To: CCL Subject: CCL: gar2ped Message-Id: <-39636-090629045833-29564-+Lk+K66HgDGt8834xYcRGw|*|server.ccl.net> X-Original-From: Rafael =?iso-8859-1?q?Rodr=EDguez_Pappalardo?= Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: Text/Plain; charset="iso-8859-1" Date: Mon, 29 Jun 2009 09:58:00 +0200 MIME-Version: 1.0 Sent to CCL by: Rafael =?iso-8859-1?q?Rodr=EDguez_Pappalardo?= [rafapa .. us.es] On Tuesday 23 June 2009 06:05:36 yarasi rao gnsmmg * yahoo.com wrote: > Sent to CCL by: "yarasi rao" [gnsmmg(_)yahoo.com] > I downloaded gar2ped from ccl.net. After compiling two executable, pullarc > and gar2ped.x were created. Though pullarc is working the command to run > gar2ped.x to generate *.apt.xyz, nomos.xyz and nomo.nn.xyz is not working. > I am not able to run this command even for test file, triazine.arch given > in the program.. Can I have help in this regards > > thanks > Yarasi > > Dear Yarasi, Maybe I could help but I need to know which operating system are you running on. Also the compiler used and the compilation options will be useful. I have been able to run gar2ped without problems in the past. What's the sequence of commands you are doing? Best regards, Rafael -- Dr. Rafael R. Pappalardo Dept. of Physical Chemistry, Univ. de Sevilla (Spain) e-mail: rafapa#,#us.es From owner-chemistry@ccl.net Mon Jun 29 07:50:00 2009 From: "may abdelghani may01dz{=}yahoo.fr" To: CCL Subject: CCL: Re : CCL: transition states for fluxional molecules Message-Id: <-39637-090629052145-4976-wsnrIz4h9JBtcKiA0WIDVg#,#server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-1894905013-1246267289=:58958" Date: Mon, 29 Jun 2009 09:21:29 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz---yahoo.fr] --0-1894905013-1246267289=:58958 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable yes, an LDA calculations were carried out using the Amsterdam Density Functional= (ADF) =0Aprogram,The basis functions for describing the valence electrons = of each atom are double -=CE=B6=C2=A0 Slater type orbitals,large core froze= n, The value of the numerical integration parameter used to determine the p= recision =0Aof numerical integrals was 4.0,the molecule containes 3 Ru atom= s, acetylide fragment C2, 3 ph and 6 CO.=20 --- En date de=C2=A0: Dim 28.6.09, Morad El-Hendawy m80elhendawy^_^yahoo.co= m a =C3=A9crit=C2=A0: De: Morad El-Hendawy m80elhendawy^_^yahoo.com Objet: CCL: transition states for fluxional molecules =C3=80: "Abdelghani, May " Date: Dimanche 28 Juin 2009, 12h52 Dear May,=0AYour question is not so clear.=C2=A0 Please=C2=A0give us a hint= about=C2=A0the used method,=C2=A0 basis set,=C2=A0 molecular structure, et= c.=C2=A0because there are=C2=A0some methods=C2=A0give overestimated results= .=0AThanks=0AMorad M. El-Hendawy =0A =C2=A0 --- On Tue, 6/23/09, may abdelghani may01dz,+,yahoo.fr wrote: =0A > From: may abdelghani may01dz,+,yahoo.fr Subject: CCL: transition states for fluxional molecules To: "El-Hendawy, Morad Metwally " Date: Tuesday, June 23, 2009, 10:30 PM =0A=0A=0A=0A=0A=0Adear CCL'ers=0AI study the fluxional behavior of a molecu= le. I find that the energy of the transition states is fare from that of th= e ground one by 20 kcal/mole. I ask if this quantity of energy is big for s= uch reaction: this king of reaction, spend small energy to "transfer" from = one isomer to other, like I know. =0AThe easy exchange between the tow isom= ers manifest clearly on the Walsh diagram: no crossing between the orbital,= no hug different, in energy of the frontier orbital, between that of react= ion, TS and product structure. =0AI don=E2=80=99t know, in what extend the = 20 kcal/mol is big, or, it is a big cost, to spend a 20 kcal/mol of energy,= to transfer from one isomer to another, in such a reaction. I need your he= lp. =C2=A0=C2=A0 =0AMay abdelghani, Algeria =0A=0A=0A=0A =0A=0A=0A --0-1894905013-1246267289=:58958 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
yes,
an LDA calculations were carried out = using the Amsterdam Density Functional (ADF) =0Aprogram,The basis functions= for describing the valence electrons of each atom are double -=CE=B6 = Slater type orbitals,large core frozen, The value of the numerical integra= tion parameter used to determine the precision =0Aof numerical integrals wa= s 4.0,the molecule containes 3 Ru atoms, acetylide fragment C2, 3 ph and 6 = CO.

--- En date de : Dim 28.6.09, Morad El-Hendawy m80elhen= dawy^_^yahoo.com <owner-chemistry|ccl.net> a =C3=A9crit&nb= sp;:

De: Morad El-Hendawy m80elhendawy^_^ya= hoo.com <owner-chemistry|ccl.net>
Objet: CCL: transition states fo= r fluxional molecules
=C3=80: "Abdelghani, May " <may01dz|yah= oo.fr>
Date: Dimanche 28 Juin 2009, 12h52

Dear May,
=0A
Your question is not so clear.  Please=  give us a hint about the used method,  basis set,  mol= ecular structure, etc. because there are some methods give o= verestimated results.
=0A
Thanks
=0A
Morad M.= El-Hendawy
=0A

 


--- On Tue, 6/23/09, may abdelghani may01dz,+,yahoo.fr <owner-chemistry++cc= l.net> wrote:
=0A

From: may abdel= ghani may01dz,+,yahoo.fr <owner-chemistry++ccl.net>
Subject: CCL: = transition states for fluxional molecules
To: "El-Hendawy, Morad Metwall= y " <m80elhendawy++yahoo.com>
Date: Tuesday, June 23, 2009, 10:30 = PM

=0A
=0A
=0A=0A=0A
=0A
dear CC= L'ers
=0A

I study the flux= ional behavior of a molecule. I find that the energy of the transition stat= es is fare from that of the ground one by 20 kcal/mole. I ask if this quant= ity of energy is big for such reaction: this king of reaction, spend small = energy to "transfer" from one isomer to other, like I know. =0A

The easy exchange b= etween the tow isomers manifest clearly on the Walsh diagram: no crossing b= etween the orbital, no hug different, in energy of the frontier orbital, be= tween that of reaction, TS and product structure. =0A<= /p>

I don=E2=80=99t know, in what= extend the 20 kcal/mol is big, or, it is a big cost, to spend a 20 kcal/mo= l of energy, to transfer from one isomer to another, in such a reaction. I = need your help.    =0A

= May abdelghani, Algeria


=0A=0A=0A=0A =
=0A=0A=0A=0A --0-1894905013-1246267289=:58958-- From owner-chemistry@ccl.net Mon Jun 29 08:45:01 2009 From: "Robert Hinde rhinde() utk.edu" To: CCL Subject: CCL:G: DN error in IniRep (follow-up) Message-Id: <-39638-090629084213-5018-fh1ZCi+j4gZsvO4qTr/p7w^server.ccl.net> X-Original-From: "Robert Hinde" Date: Mon, 29 Jun 2009 08:42:09 -0400 Sent to CCL by: "Robert Hinde" [rhinde() utk.edu] Thanks to those who offered suggestions about the "DN error #2 in IniRep" message that I encountered using G03 for Windows. Although I wasn't able to find out what this message meant, or to complete the calculation using Gaussian, I was able to perform the calculation on NWChem using the same initial Cartesian coordinates that I provided to Gaussian. RJH From owner-chemistry@ccl.net Mon Jun 29 10:06:01 2009 From: "William F. Coleman wcoleman+*+wellesley.edu" To: CCL Subject: CCL: can absorption and emission spectra have the same value Message-Id: <-39639-090629100500-12003-+gEolFXpKDC4Q7iroNOiTg%x%server.ccl.net> X-Original-From: "William F. Coleman" Content-Type: multipart/alternative; boundary="--=_--1dc55f7f.1dc55cac.c66e7a7a" Date: Mon, 29 Jun 2009 10:04:42 -0400 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman,,wellesley.edu] This is a multi-part message in MIME format. ----=_--1dc55f7f.1dc55cac.c66e7a7a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit "CCL Subscribers" on Monday, June 29, 2009 at 5:05 AM -0400 wrote: >Sent to CCL by: "irfan ahmad" [irfaahmad%a%gmail.com] >Dear chemists >i got the absorption spectra of compoundfs A,B and C 400, 450, 475 nm. >the emission spectra for these compound are 401, 452, 476 nm. I checked >the optimized structures at ground and excitd states, there is no >problem. My question is this that, can absorption and emission spectra >have the same values? >any reference or comments will be highly appriciated >thanks ahead >Irfan Ahmad >china The 0,0 band of absorption and emission, the transition from the lowest vibrational level of the ground state to the lowest vibrational level of the excited state, should occur at the same energy. This will be the most prominent band in both spectra if the geometries of the two states are very similar. Cheers, Flick Coleman _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html ----=_--1dc55f7f.1dc55cac.c66e7a7a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>
"CCL Subscribers" <chemistry=40ccl.net> on Monday,= June 29, 2009 at 5:05 AM -0400 wrote:
Sent to CCL by: "irfan  ahmad" =5Birfaahmad%a%gmail= .com=5D
Dear chemists
i got the absorption spectra of compoundfs A,B and C 400, 450, 475= nm. the emission spectra for these compound are 401, 452, 476 nm. I checke= d the optimized structures at ground and excitd states, there is no problem= . My question is this that, can absorption and emission spectra have the sa= me values?
any reference or comments will be highly appriciated=
thanks ahead
Irfan Ahmad
china

The 0,0 band of absorption and emissi= on, the transition from the lowest vibrational level of the ground state to= the lowest vibrational level of the excited state, should occur at the sam= e energy.  This will be the most prominent band in both spectra if the= geometries of the two states are very similar.

Cheers,

Flick Coleman



_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481


Editor, JCE WebWare and JCE Featured = Molecules

----=_--1dc55f7f.1dc55cac.c66e7a7a-- From owner-chemistry@ccl.net Mon Jun 29 11:05:00 2009 From: "Delwar Hossain hossaind2004++yahoo.com" To: CCL Subject: CCL: can absorption and emission spectra have the same value Message-Id: <-39640-090629101913-18391-zfr6i50Ech0EWm5iQn4bbA . server.ccl.net> X-Original-From: Delwar Hossain Content-Type: multipart/alternative; boundary="0-853522751-1246281537=:12743" Date: Mon, 29 Jun 2009 06:18:57 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Delwar Hossain [hossaind2004 . yahoo.com] --0-853522751-1246281537=:12743 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable The absortion and emission are different electronic transition phenomena. W= hen molecules/atoms are in the excited state and reverse to the ground stat= e by emmitiing energy some energy is lossed. Hence, the absortion and emiss= ion spectra should not be same. From your value it looks these values are r= esonable. If you search in the=A0Journal of Chemical Education (ACAS) you w= ill find many articles explaining the findamental idea on electronic transi= tion on molecues and atoms. Thank you. Delwar Hossain --- On Mon, 6/29/09, irfan ahmad irfaahmad~!~gmail.com wrote: > From: irfan ahmad irfaahmad~!~gmail.com Subject: CCL: can absorption and emission spectra have the same value To: "Hossain, Delwar " Date: Monday, June 29, 2009, 4:05 AM Sent to CCL by: "irfan=A0 ahmad" [irfaahmad%a%gmail.com] Dear chemists i got the absorption spectra of compoundfs A,B and C 400, 450, 475 nm. the = emission spectra for these compound are 401, 452, 476 nm. I checked the opt= imized structures at ground and excitd states, there is no problem. My ques= tion is this that, can absorption and emission spectra have the same values= ?=20 any reference or comments will be highly appriciated thanks ahead Irfan Ahmad china -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-853522751-1246281537=:12743 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
The absortion and emission are different= electronic transition phenomena. When molecules/atoms are in the excited s= tate and reverse to the ground state by emmitiing energy some energy is los= sed. Hence, the absortion and emission spectra should not be same. From you= r value it looks these values are resonable. If you search in the Jour= nal of Chemical Education (ACAS) you will find many articles explaining the= findamental idea on electronic transition on molecues and atoms.
Thank you.
Delwar Hossain

--- On Mon, 6/29/09, irfan ahmad irfaahmad~!~gmail.com <o= wner-chemistry%x%ccl.net> wrote:

From: irfan ahmad irfaahmad~!~gmail.com <owner= -chemistry%x%ccl.net>
Subject: CCL: can absorption and emission spectra= have the same value
To: "Hossain, Delwar " <hossaind2004%x%yah= oo.com>
Date: Monday, June 29, 2009, 4:05 AM


Sent to CCL by: "irfan  ahmad" [irfaahmad%a= %gmail.com]
Dear chemists
i got the absorption spectra of compoundfs = A,B and C 400, 450, 475 nm. the emission spectra for these compound are 401= , 452, 476 nm. I checked the optimized structures at ground and excitd stat= es, there is no problem. My question is this that, can absorption and emiss= ion spectra have the same values?
any reference or comments will be hig= hly appriciated
thanks ahead
Irfan Ahmad
china



-=3D= This is automatically added to each message by the mailing script =3D-
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=0A=0A --0-853522751-1246281537=:12743-- From owner-chemistry@ccl.net Mon Jun 29 11:53:01 2009 From: "David Gallagher gallagher.da__gmail.com" To: CCL Subject: CCL: can absorption and emission spectra have the same value Message-Id: <-39641-090629114953-2190-YtojAK7F0qQud68CROfmnw.:.server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary=0022152d5dc924dc18046d7e903d Date: Mon, 29 Jun 2009 08:44:18 -0700 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da+*+gmail.com] --0022152d5dc924dc18046d7e903d Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Irfan, If the optimized geometries of the ground and excited states are identical, then the pure electronic transition (S0-S1) would be the same in both absorption and fluorescence. Of course, the vibrational fine structure would be at different wavelengths. There are some slides illustrating fluorescence at http://cacheresearch.com/presentations.html David Gallagher CACheResearch.com On Mon, Jun 29, 2009 at 2:05 AM, irfan ahmad irfaahmad~!~gmail.com < owner-chemistry,,ccl.net> wrote: > > Sent to CCL by: "irfan ahmad" [irfaahmad%a%gmail.com] > Dear chemists > i got the absorption spectra of compoundfs A,B and C 400, 450, 475 nm. the > emission spectra for these compound are 401, 452, 476 nm. I checked the > optimized structures at ground and excitd states, there is no problem. My > question is this that, can absorption and emission spectra have the same > values? > any reference or comments will be highly appriciated > thanks ahead > Irfan Ahmad > china> > > --0022152d5dc924dc18046d7e903d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Irfan,

If the optimized geometries of the ground and = excited states are identical, then the pure electronic transition (S0-S1) w= ould be the same in both absorption and fluorescence. =A0Of course, the vib= rational fine structure would be at different wavelengths.

There are some slides illustrating fluorescence at=A0http://cacheresearch.= com/presentations.html

David Gallagher
CACheResearch.com


On Mon,= Jun 29, 2009 at 2:05 AM, irfan ahmad irfaahmad~!~gmail.com <owner-chemistry,,ccl.net> wrote:

Sent to CCL by: "irfan =A0ahmad" [irfaahmad%a%gmail.com]
Dear chemists
i got the absorption spectra of compoundfs A,B and C 400, 450, 475 nm. the = emission spectra for these compound are 401, 452, 476 nm. I checked the opt= imized structures at ground and excitd states, there is no problem. My ques= tion is this that, can absorption and emission spectra have the same values= ?
any reference or comments will be highly appriciated
thanks ahead
Irfan Ahmad
china



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--0022152d5dc924dc18046d7e903d-- From owner-chemistry@ccl.net Mon Jun 29 13:38:00 2009 From: "Babak Khalili khalili.babak(~)gmail.com" To: CCL Subject: CCL: Contour map Message-Id: <-39642-090629133359-11490-j8kt1egSn+HN11jh5UgsEw^^^server.ccl.net> X-Original-From: Babak Khalili Content-Type: multipart/alternative; boundary=001636c5b6dabdbf90046d8017d2 Date: Mon, 29 Jun 2009 22:03:48 +0430 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak(a)gmail.com] --001636c5b6dabdbf90046d8017d2 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Subscribers, You will be so appreciated to help me find a software to determine phi and psi of a certain designed peptide and also, to draw the contour map. Thank you in advance , Babak Khalili, PhD Candidate of Biochemistry Khalili.babak%x%gmail.com --001636c5b6dabdbf90046d8017d2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Subscribers,

You will be so appreciated to help me find a software to determine phi and psi of a certain designed peptide and also, to draw the contour map.
Thank you in advance ,

Babak Khalili,
PhD Candidate of Biochemistry
Khalili.babak%x%gmail.com
--001636c5b6dabdbf90046d8017d2-- From owner-chemistry@ccl.net Mon Jun 29 15:02:01 2009 From: "Carlos F. Lagos carlos-.-cbuc.cl" To: CCL Subject: CCL: Find a lead from a drug Message-Id: <-39643-090629132557-10716-FKO5Y/sSYtKfNpHpx/lWTw a server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Mon, 29 Jun 2009 12:30:12 -0400 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos*_*cbuc.cl] You might search into the patents databases, you can use http://www.freepatentsonline.com/surechem/ or Scifinder to find the core of the molecule you´re looking for. Usually the patents cover the molecule > from the lead structure. On Mon, 29 Jun 2009 05:15:25 -0400, "Jeremy Besnard j10b84%a%hotmail.com" wrote: > > Sent to CCL by: "Jeremy Besnard" [j10b84[-]hotmail.com] > Dear colleagues, > > I have a list of drugs which are on the market and I'd like to find the > lead compound which was used as starting point for the lead optimization > process. > > But the artciles related a story of a drug are not easy to find. An easy > one is The Discovery of Tadalafil: A Novel and Highly Selective PDE5 > Inhibitor. 2: > 2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4-dione > Analogues. But by looking for name of drug + discovery in a search engine I > don't get hits. I also tried with lead, SAR... > > I'd like to know if you have some hints and tips to help find a lead with > the name of the drug. Also if you know a relatively recent set of leads and > drugs that could be very useful. > > Thank you. > > Jeremy-- QF Carlos F. Lagos Centre for Bioinformatics CBUC, Faculty of Biological Sciences Medicinal Chemistry Laboratory MCL, Faculty of Chemistry P. Universidad Catolica de Chile Portugal 49, Zocalo 6513492 Santiago-Chile Phone: +56 2 3541911 http://www.cbuc.cl From owner-chemistry@ccl.net Mon Jun 29 15:36:01 2009 From: "Pavle Mocilac pavle.mocilac2!=!mail.dcu.ie" To: CCL Subject: CCL:G: Free Gibbs energy... Message-Id: <-39644-090629150148-14785-AVIXLLfmBQqoYybXziKeGA^_^server.ccl.net> X-Original-From: "Pavle Mocilac" Date: Mon, 29 Jun 2009 15:01:44 -0400 Sent to CCL by: "Pavle Mocilac" [pavle.mocilac2{}mail.dcu.ie] Dear chemists, I'm trying to calculate pKa for some compounds. I found some interesting papers about that, but still, I can not find some simple method of extracting G values from Gaussian output. I made optimisations of the protonated and unprotonated forms of molecule along with freq calculations. Now, how to calculate G from this: Zero-point vibrational energy 277338.6 (Joules/Mol) 66.28551 (Kcal/Mol) Warning -- explicit consideration of 7 degrees of freedom as vibrations may cause significant error Vibrational temperatures: 317.83 553.84 558.29 574.22 578.31 (Kelvin) 777.81 785.26 1000.10 1076.29 1216.10 1223.95 1244.51 1413.69 1426.86 1446.77 1502.24 1562.29 1642.07 1803.34 1857.84 1940.16 2009.30 2104.88 2195.57 2285.82 2347.09 2446.93 4543.58 4544.54 4570.03 4579.43 5199.03 5384.27 Zero-point correction= 0.105633 (Hartree/Particle) Thermal correction to Energy= 0.111300 Thermal correction to Enthalpy= 0.112244 Thermal correction to Gibbs Free Energy= 0.076555 Sum of electronic and zero-point Energies= -303.532426 Sum of electronic and thermal Energies= -303.526759 Sum of electronic and thermal Enthalpies= -303.525815 Sum of electronic and thermal Free Energies= -303.561504 E (Thermal) CV S KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin Total 69.842 22.169 75.114 Electronic 0.000 0.000 0.000 Translational 0.889 2.981 39.535 Rotational 0.889 2.981 26.860 Vibrational 68.064 16.207 8.719 Vibration 1 0.648 1.809 1.952 Vibration 2 0.754 1.502 1.020 Vibration 3 0.756 1.496 1.008 Vibration 4 0.765 1.472 0.966 Vibration 5 0.768 1.466 0.956 Vibration 6 0.896 1.160 0.564 Vibration 7 0.901 1.149 0.553 From owner-chemistry@ccl.net Mon Jun 29 16:11:01 2009 From: "Wayne Steinmetz WES04747#,#pomona.edu" To: CCL Subject: CCL: Contour map Message-Id: <-39645-090629152901-27647-XBT8h2NpYnYvnOzPtFlqxA::server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C9F8EA.5B854A53" Date: Mon, 29 Jun 2009 11:49:39 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747*|*pomona.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C9F8EA.5B854A53 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I use SYBYL for this purpose. If the structure is drawn using the Biopolymers module or if a pdf file is used, SYBYL has all the tools that you require. =20 Wayne E. Steinmetz=20 Professor Emeritus of Chemistry=20 USFS Volunteer=20 Chemistry Department=20 Pomona College=20 645 North College Avenue=20 Claremont, California 91711-6338=20 USA=20 phone: 1-909-621-8447=20 FAX: 1-909-607-7726=20 Email: wsteinmetz/a\pomona.edu=20 WWW: pages.pomona.edu/~wsteinmetz=20 =20 ________________________________ > From: owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu/a\ccl.net [mailto:owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu/a\ccl.net] On Behalf Of Babak Khalili khalili.babak(~)gmail.com Sent: Monday, June 29, 2009 10:34 AM To: Wayne Steinmetz Subject: CCL: Contour map =20 Dear Subscribers, You will be so appreciated to help me find a software to determine phi and psi of a certain designed peptide and also, to draw the contour map. Thank you in advance , Babak Khalili, PhD Candidate of Biochemistry Khalili.babak|gmail.com ------------------------------------------------------------- This message has been scanned by Postini anti-virus software. =0D ------_=_NextPart_001_01C9F8EA.5B854A53 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I use SYBYL for this purpose.  = If the structure is drawn using the Biopolymers module or if a pdf file is used, SYBYL = has all the tools that you require.

 

Wayne E. Steinmetz
Professor Emeritus of Chemistry
USFS Volunteer
Chemistry Department
Pomona College
645 North College Avenue
Claremont, California 91711-6338
USA
phone: 1-909-621-8447
FAX: 1-909-607-7726
Email: wsteinmetz/a\pomona.edu
WWW: pages.pomona.edu/~wsteinmetz
 

From: owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu/a\ccl.net [mailto:owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu/a\ccl.net] = On Behalf Of Babak Khalili khalili.babak(~)gmail.com
Sent: Monday, June 29, = 2009 10:34 AM
To: Wayne Steinmetz
Subject: CCL: Contour = map

 

Dear Subscribers,

You will be so appreciated to help me find a software to determine phi = and psi of a certain designed peptide and also, to draw the contour map.
Thank you in advance ,

Babak Khalili,
PhD Candidate of Biochemistry
Khalili.babak|gmail.com<= /o:p>

-------------------------------------------------------------
This message has been scanned by Postini anti-virus software.
=0D
------_=_NextPart_001_01C9F8EA.5B854A53--


From owner-chemistry@ccl.net Mon Jun 29 16:56:00 2009
From: "Barry Hardy barry.hardy+*+vtxmail.ch" 
To: CCL
Subject: CCL: Drug Discovery and Predictive ADME/tox Case Studies
Message-Id: <-39646-090629165327-29140-ww3Y/YDiW707xdxzrmwppw+/-server.ccl.net>
X-Original-From: Barry Hardy 
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 29 Jun 2009 22:53:09 +0200
MIME-Version: 1.0


Sent to CCL by: Barry Hardy [barry.hardy===vtxmail.ch]

We will support and extend virtually the eCheminfo workshop activity and
discussion for both the upcoming eCheminfo drug discovery and predictive
ADME/tox workshop weeks at Oxford through the eCheminfo LinkedIn
Discussion area.

I have posted initial summary information and links for the Drug
Discovery and Predictive ADME/tox Case Studies to be worked on there.

If you are not a member of the eCheminfo LinkedIn group, you can
initiate joining by copying and pasting the following link in your browser:
https://www.linkedin.com/e/gis/1173/77EB680070FF/

best regards
Barry


Barry Hardy PhD
Director, Community of Practice & Research Activities
and OpenTox Project Coordinator (http://www.opentox.org/)
Douglas Connect LLC, Switzerland
Email: barry.hardy -(at)- douglasconnect.com
Tel: +41 61 851 0170


From owner-chemistry@ccl.net Mon Jun 29 17:29:00 2009
From: "Elaine Meng meng]~[cgl.ucsf.edu" 
To: CCL
Subject: CCL: contour map
Message-Id: <-39647-090629162528-8745-Y5+oUadUOy67oy/c9PuRrg^-^server.ccl.net>
X-Original-From: "Elaine  Meng" 
Date: Mon, 29 Jun 2009 16:25:24 -0400


Sent to CCL by: "Elaine  Meng" [meng%x%cgl.ucsf.edu]
Dear Babak,
If you don't mind uploading your structure to a Web site, this server is convenient for getting a phi/psi plot or raw values:

http://helixweb.nih.gov/structbio/basic.html

It can also perform several other useful calculations such as surface area. 
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                         
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html


From owner-chemistry@ccl.net Mon Jun 29 18:04:01 2009
From: "Spitaleri Andrea spitaleri.andrea:+:hsr.it" 
To: CCL
Subject: CCL: R: Contour map
Message-Id: <-39648-090629155521-15296-K0H6fmH09svLzZmAjboa7w=server.ccl.net>
X-Original-From: Spitaleri Andrea 
Content-Language: it-IT
content-transfer-encoding: quoted-printable
Content-Type: text/plain; charset="iso-8859-1"
Date: Mon, 29 Jun 2009 21:38:00 +0200
MIME-Version: 1.0


Sent to CCL by: Spitaleri Andrea [spitaleri.andrea|-|hsr.it]
Hi there,
have a try to gnuplot with the function 'splot'

regards

and
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://sites.google.com/site/andreaspitaleri/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
-------------------------------
________________________________________
Da: owner-chemistry+spitaleri.andrea=3D=3Dhsr.it#,#ccl.net [owner-chemistry+sp=
italeri.andrea=3D=3Dhsr.it#,#ccl.net] per conto di Babak Khalili khalili.babak=
(~)gmail.com [owner-chemistry#,#ccl.net]
Inviato: luned=EC 29 giugno 2009 19.33
A: Spitaleri Andrea
Oggetto: CCL: Contour map

Dear Subscribers,

You will be so appreciated to help me find a software to determine phi and p=
si of a certain designed peptide and also, to draw the contour map.
Thank you in advance ,

Babak Khalili,
PhD Candidate of Biochemistry
Khalili.babak|gmail.com

-----------------------------------------------------------------=0A=
=0A=
La tua mano puo' lasciare un segno importante.=0A=
Dona il tuo 5 per mille al San Raffaele di Milano.=0A=
=0A=
E' SEMPLICE E NON COSTA NULLA.=0A=
Basta indicare nell'apposito riquadro della dichiarazione dei redditi "Finan=
ziamento della ricerca sanitaria"=0A=
il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor:=0A=
03 06 42 80 153 e ricordarsi di firmare.=0A=
Per saperne di piu':  5permille#,#hsr.it o vai sul sito  http://www.5xmille.or=
g.


From owner-chemistry@ccl.net Mon Jun 29 18:41:01 2009
From: "Block, John john.block() oregonstate.edu" 
To: CCL
Subject: CCL: Find a lead from a drug
Message-Id: <-39649-090629143305-9237-EYzDy1PlYpuGoNN37fB/BA.:.server.ccl.net>
X-Original-From: "Block, John" 
Content-class: urn:content-classes:message
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset="us-ascii"
Date: Mon, 29 Jun 2009 10:36:25 -0700
MIME-Version: 1.0


Sent to CCL by: "Block, John" [john.block.:.oregonstate.edu]
One approach is to use Chemical Abstract's SciFinder Scholar.  Enter the
drug, request the references and filter for articles that describe the
synthesis or early pharmacological evaluation.  If you are lucky, you
will find the desired journal article.  Otherwise, it probably is buried
in the patent literature.

John Block

John H. Block                    Phone:  541-737-5779
College of Pharmacy         Fax:      541-737-3999
Oregon State University
Corvallis, OR 97331
John.Block~!~oregonstate.edu
blockj~!~onid.orst.edu
=20
-----Original Message-----
> From: owner-chemistry+john.block=3D=3Dorst.edu~!~ccl.net
[mailto:owner-chemistry+john.block=3D=3Dorst.edu~!~ccl.net] On Behalf Of
Jeremy Besnard j10b84%a%hotmail.com
Sent: Monday, June 29, 2009 2:15 AM
To: Block, John H. 
Subject: CCL: Find a lead from a drug


Sent to CCL by: "Jeremy  Besnard" [j10b84[-]hotmail.com]
Dear colleagues,

I have a list of drugs which are on the market and I'd like to find the
lead compound which was used as starting point for the lead optimization
process.

But the artciles related a story of a drug are not easy to find. An easy
one is The Discovery of Tadalafil:  A Novel and Highly Selective PDE5
Inhibitor. 2:
2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4-dione
Analogues. But by looking for name of drug + discovery in a search
engine I don't get hits. I also tried with lead, SAR...

I'd like to know if you have some hints and tips to help find a lead
with the name of the drug. Also if you know a relatively recent set of
leads and drugs that could be very useful.

Thank you.

Jeremy



-=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

From owner-chemistry@ccl.net Mon Jun 29 19:14:00 2009
From: "Pedro Silva pedros-x-ufp.edu.pt" 
To: CCL
Subject: CCL: Free Gibbs energy...
Message-Id: <-39650-090629182326-1401-EV16zmG/JrE6hstG/BVXJA * server.ccl.net>
X-Original-From: Pedro Silva 
Content-Type: multipart/alternative; boundary=001636c5baafaca997046d842206
Date: Mon, 29 Jun 2009 23:23:11 +0100
MIME-Version: 1.0


Sent to CCL by: Pedro Silva [pedros**ufp.edu.pt]
--001636c5baafaca997046d842206
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

The line you are interested in is the one labelled:


>  Sum of electronic and thermal Free Energies=         -303.561504

Get those lines from the output files on the acid and baisc forms. Then
subtract them and convert the values from hartree to kJ.mol-1 (the
conversion factor is approximately 627.51*4.184)
Then convert the energies to pKa using the DeltaG=-RT ln K

Remember that the computed values are gas phase ones.... In solution you
have to take account of solvation of both forms AND solvation of the proton.

Cheers!
Pedro

-- 
Pedro J. Silva
Assistant Professor
Universidade Fernando Pessoa
Porto - Portugal
http://www2.ufp.pt/~pedros/science/science.htm

--001636c5baafaca997046d842206
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

The line you are interested in is the one labelled:


> =A0Sum =
of electronic and thermal Free Energies=3D =A0 =A0 =A0 =A0 -303.561504
<=
br>Get those lines from the output files on the acid and baisc forms. Then =
subtract them and convert the values from hartree to kJ.mol-1 (the conversi=
on factor is approximately 627.51*4.184)

Then convert the energies to pKa using the DeltaG=3D-RT ln K

Remembe=
r that the computed values are gas phase ones.... In solution you have to t=
ake account of solvation of both forms AND solvation of the proton.


Cheers!
Pedro

-- 
Pedro J. Silva
Assistant Professor
Uni=
versidade Fernando Pessoa
Porto - Portugal
http://www2.ufp.pt/~pedros/science/science=
.htm




--001636c5baafaca997046d842206--


From owner-chemistry@ccl.net Mon Jun 29 20:26:00 2009
From: "Venable, Richard (NIH/NHLBI) E venabler .. nhlbi.nih.gov" 
To: CCL
Subject: CCL: Find a lead from a drug
Message-Id: <-39651-090629202235-20371-c7QS/mImtPmBxmPzNWNOgg : server.ccl.net>
X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" 
Content-Language: en
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset="iso-8859-1"
Date: Mon, 29 Jun 2009 19:50:27 -0400
MIME-Version: 1.0


Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#%#nhlbi.nih.gov]
It should also be noted that some lead compounds and others investigated ma=
y not be public knowledge; drug companies do not have to release informatio=
n about molecules they've made and studied unless they wish to put one of t=
hem on the market.  Certainly, the FDA gets involved before human tests are=
 conducted, but if the drug never goes to market, it's chemical structure a=
nd biological action do not become public knowledge.  That information is r=
egarded as confidential trade secrets, owned by the company that developed =
it.

--
Rick Venable      5635FL/T906
Membrane Biophysics Section
NIH/NHLBI Lab. of Computational Biology
Bethesda, MD  20892-9314   U.S.A.
(301) 496-1905   venabler AT nhlbi*nih*gov




On 6/29/09 1:36 PM, "Block, John john.block() oregonstate.edu"  wrote:



Sent to CCL by: "Block, John" [john.block.:.oregonstate.edu]
One approach is to use Chemical Abstract's SciFinder Scholar.  Enter the
drug, request the references and filter for articles that describe the
synthesis or early pharmacological evaluation.  If you are lucky, you
will find the desired journal article.  Otherwise, it probably is buried
in the patent literature.

John Block

John H. Block                    Phone:  541-737-5779
College of Pharmacy         Fax:      541-737-3999
Oregon State University
Corvallis, OR 97331
John.Block : oregonstate.edu
blockj : onid.orst.edu

-----Original Message-----
> From: owner-chemistry+john.block=3D=3Dorst.edu : ccl.net
[mailto:owner-chemistry+john.block=3D=3Dorst.edu : ccl.net] On Behalf Of
Jeremy Besnard j10b84%a%hotmail.com
Sent: Monday, June 29, 2009 2:15 AM
To: Block, John H.
Subject: CCL: Find a lead from a drug


Sent to CCL by: "Jeremy  Besnard" [j10b84[-]hotmail.com]
Dear colleagues,

I have a list of drugs which are on the market and I'd like to find the
lead compound which was used as starting point for the lead optimization
process.

But the artciles related a story of a drug are not easy to find. An easy
one is The Discovery of Tadalafil:  A Novel and Highly Selective PDE5
Inhibitor. 2:
2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4-dione
Analogues. But by looking for name of drug + discovery in a search
engine I don't get hits. I also tried with lead, SAR...

I'd like to know if you have some hints and tips to help find a lead
with the name of the drug. Also if you know a relatively recent set of
leads and drugs that could be very useful.

Thank you.

Jeremy



-=3D This is automatically added to each message by the mailing script =3D-=Job: =
http://www.ccl.net/jobs-=3Dis is automatically added to each message by the mailing script =3Dhttp://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 Mon Jun 29 23:47:01 2009
From: "Todd J Martinez tjm|-|spawn.scs.uiuc.edu" 
To: CCL
Subject: CCL: GPU Summer School
Message-Id: <-39652-090629161835-2366-pgNHo7nZvZobGrHtZjBPdA]*[server.ccl.net>
X-Original-From: "Todd J Martinez" 
Date: Mon, 29 Jun 2009 16:18:31 -0400


Sent to CCL by: "Todd J Martinez" [tjm . spawn.scs.uiuc.edu]
The University of Tennessee will offer a summer school course in accelerating computational 
chemistry with general-purpose graphics processing units (GPGPUs) from Aug. 10-14. The course 
is offered in coordination with the Virtual School of Computational Science and Engineering.

This course will provide students with the knowledge and practical skills necessary to start 
exploiting the power of GPGPUs in real chemistry applications. The course is especially designed for 
graduate students and advanced undergraduate students in chemistry and related disciplines.

Applications are due by July 15, 2009, and should be addressed to gpgpuschool++ion.chem.utk.edu. 
In the application please clearly indicate:
Full name
Home institution and department
Email address
Status: (graduate student, postdoc, other)
Research topic
Algorithms of interest
Programming experience

Limited funds are available for partial or full support of the travel and local expenses of a few 
students, in particular to enable participation of underrepresented or disadvantaged groups. To 
apply for support, please include a brief paragraph in the application email to request and explain 
the need for support, and to describe the benefits that attending the workshop would have for 
both you and your institution.

Further information is available at: http://illinois.edu/pc/article/2101/26850/page=1/list=list

Organizers:
University of Tennessee: Robert J. Harrison, R.J. Hinde, Gregory D. Peterson
University of Illinois at Urbana-Champaign: Volodymyr Kindratenko, Thom Dunning
Stanford University: Todd Martinez
University of Pennsylvania: Michael L. Klein, Axel Kohlmeyer

This workshop is supported by the National Science Foundation through the cyberenabled 
chemistry project "Future Computing in Chemistry."