Website for = the workshop is=20 http://www.uom.ac.mu/Faculties/FOS/Chemistry/cca/

Workshop Organisers are =

Dr Ponnadurai = Ramasami and=20 Prof Henry Schaefer III

------=_NextPart_000_00D0_01C94E75.0B521A40-- From owner-chemistry@ccl.net Mon Nov 24 11:19:01 2008 From: "Saurabh Agrawal Saurabh.Agrawal^^ucdconnect.ie" To: CCL Subject: CCL:G: van der Waals parameters for Ti Message-Id: <-38162-081124090215-530-gTFjY/jBE/pKXL9RFB0YNA[A]server.ccl.net> X-Original-From: "Saurabh Agrawal" Date: Mon, 24 Nov 2008 09:02:11 -0500 Sent to CCL by: "Saurabh Agrawal" [Saurabh.Agrawal/./ucdconnect.ie] Dear CCl users, I am trying to get non bonded parameters (van der Waals' radius and well depth) for Ti atom (rutile). I appreciate if some one could provide these parameters to me or let me know the way (tutorial) to calculate these parameters using Gaussian. Thanking you in advance. Best, Saurabh Agrawal, PhD student, University College Dublin, Ireland From owner-chemistry@ccl.net Mon Nov 24 11:54:01 2008 From: "Conley, Michael mconley~~leadscope.com" To: CCL Subject: CCL: failed drugs Message-Id: <-38163-081124111032-28322-h6GbZ8AjmzIw6ZYiPq2vSQ---server.ccl.net> X-Original-From: "Conley, Michael" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 24 Nov 2008 10:22:53 -0500 MIME-Version: 1.0 Sent to CCL by: "Conley, Michael" [mconley#,#leadscope.com] Leadscope has the FDA Marketed Drugs database that shows discontinued drugs; however, it doesn't specifically list why the was discontinued. More information is available on this database at http://www.leadscope.com/product_info.php?products_id=3D53=20 including a short pre-recorded demonstration. Mike Conley -----Original Message----- > From: owner-chemistry+mconley=3D=3Dleadscope.com * ccl.net [mailto:owner-chemistry+mconley=3D=3Dleadscope.com * ccl.net] On Behalf Of = Joe Corkery jcorkery|a|eyesopen.com Sent: Sunday, November 23, 2008 4:01 PM To: Conley, Michael Subject: CCL: failed drugs Sent to CCL by: Joe Corkery [jcorkery() eyesopen.com] I am not aware of a single database which contains this information, but most of the prominent medical journals (e.g. NEJM, JAMA, Lancet, Annals of Internal Medicine, etc) began requiring in 2005 that all clinical trials be registered at their initiation in order for them to be considered for publication at a later date. www.clinicaltrials.gov was referenced back in the original article as being the only registry at that time (2004) which met their criteria. This site is relatively new (i.e. will only have data from this decade) but going forward this could be a valuable resource. From the follow up article in these journals regarding trial registration (2007) it stated that an additional four registries were created or became compliant since the original publication that met their criteria (sadly, they don't list these registries). One of these might be the WHO registry which can be found at: http://www.who.int/ictrp/en/. If you go to either of the sites and simply search for the terms terminated or withdrawn it gives you a long list of studies which can be viewed. You can pair these terms with therapeutic areas as well for more detailed searches. With regards to approved drugs, the FDA reported a list of drugs withdrawn up to 2005 in the following document: http://www.fda.gov/CDER/reports/rtn/2005/rtn2005-4.htm And active post-market studies can be found here: http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfPMA/pma_pas.cfm Hopefully, you will be able to find some or all of these sites useful. Best of luck, Joe Corkery OpenEye Scientific Software -----Original Message----- > From: owner-chemistry+jcorkery=3D=3Deyesopen.com~!~ccl.net [mailto:owner-chemistry+jcorkery=3D=3Deyesopen.com~!~ccl.net] On Behalf = Of James T Metz James.Metz]_[Abbott.com Sent: Friday, November 21, 2008 5:00 PM To: Joe Corkery Subject: CCL: failed drugs Sent to CCL by: "James T Metz" [James.Metz .. Abbott.com] CCL, Does anyone maintain a well-curated list of failed drugs or failed drug candidates and when they failed e.g., Phase II, Phase III, market, etc. Such a list might be useful for making comparisons to drugs which did not fail. Useful literature references or other sources of information would be much appreciated. Regards, Jim Metz Abbott Laboratories -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/che= m istry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt -=3Dhis is automatically added to each message by the mailing script =3Dhttp://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 Nov 24 12:29:01 2008 From: "Kalju Kahn kalju:-:chem.ucsb.edu" To: CCL Subject: CCL:G: exercises resolved, for teaching Message-Id: <-38164-081124122400-16117-Su6PSnpgL+44fomx1Q5LfQ(!)server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 24 Nov 2008 09:23:45 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju^chem.ucsb.edu] Hi, For the H-atom problem, you may find the PDF copy of a Mathematica notebook at http://www.chem.ucsb.edu/~kalju/chem126/public/Solve_HAtom_AtomicUnit.pdf useful. One neat thing is that the solution to the radial Schrodinger equation in spherical coordinates takes less than a page! Depending on your view on how much should chemistry students know about solving differential equations, this may or may not be a good thing :) I used this then as a template and asked our students to explore: 1) Solution in the SI units leading to the calculation of the Bohr radius and spectral lines in the Balmer series. 2) The error due to Born-Oppenheimer approximation (i.e. what happens when you change the mass of electron with the reduced mass of hydrogen). 3) How to approximate the ground state wave function by Gaussian function, i.e. to generate radial STO-3G, STO-4G ... basis sets. Note that these are only the radial functions, you can't take these exponents and contraction coefficients and plug them directly into Gaussian or Gamess, and expect to get the H-atom energy right. The H atom lends itself nicely to a variational calculation. In our case I gave students the wavefunction and its derivatives with undetermined exponent: \[CapitalPsi][r] = 2(E^(-\[Zeta] r)) \[CapitalPsi]'[r] = D[2 E^(-\[Zeta] r), r] \[CapitalPsi]''[r] = D[2 E^(-\[Zeta] r), {r, 2}] set up the equations in Dirac braket notation, atomic units: bra = \[CapitalPsi][r] ket = -(1/2 ) \[CapitalPsi]''[r] - 1/r \[CapitalPsi]'[r] - 1/r \[CapitalPsi][r] and hinted that they need to integrate over (r**2 bra ket) The students then used their knowledge of the steepest descent and Newton-Rhapson algorithms (http://www.chem.ucsb.edu/~kalju/chem126/public/minim_intro.html) to write a code that minimizes the energy starting with an arbitrary initial guess for zeta. Hope this helps, Kalju > dear CCLers, > I am a teacher of theoritical chemistry, Â and i loock forÂ exercises > resolved on the folowing subjects( if it is a possible): > 1- solution of the Schrodinger equation for the hydrogen atom > 2- Variation method > 3- huckel simple > thanks > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Mon Nov 24 15:37:00 2008 From: "may abdelghani may01dz * yahoo.fr" To: CCL Subject: CCL: Re : CCL: exercises resolved, for teaching Message-Id: <-38165-081124111905-32026-7q4kQbJAoDVmMy33BG3Rng|*|server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-2043808607-1227543530=:39586" Date: Mon, 24 Nov 2008 16:18:50 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz{:}yahoo.fr] --0-2043808607-1227543530=:39586 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable thank you sir, very much --- En date de=C2=A0: Dim 23.11.08, William F. Coleman wcoleman_+_wellesley= .edu a =C3=A9crit=C2=A0: De: William F. Coleman wcoleman_+_wellesley.edu Objet: CCL: exercises resolved, for teaching =C3=80: "Abdelghani, May " Date: Dimanche 23 Novembre 2008, 15h50 Sent to CCL by: "William F. Coleman" [wcoleman[]wellesley.edu] "CCL Subscribers" on Sunday, November 23, 2008 at 2:48 AM -0500 wrote: >dear CCLers, >I am a teacher of theoritical chemistry, =C3=82 and i loock for=C3=82 exer= cises >resolved on the folowing subjects( if it is a possible): >1- solution of the Schrodinger equation for the hydrogen atom=20 >2- Variation method >3- huckel simple >thanks I would suggest starting with the Journal of Chemical Education. There is a web-based collection of exercises using computer algebra systems that address all areas of chemistry, including a number directed toward theoretical chemistry. Included are topics such as: Symbolic Math Approach To Solve Particle-in-the-Box and H-Atom Problems Construction of the Electronic Angular Wave Functions and Probability Distributions of the Hydrogen Atom Exploring Orthonormal Functions Exploring the Harmonic Oscillator Wave Function Components Potential Barriers and Tunneling Visualization of Wavefunctions of the Ionized Hydrogen Molecule Variational Methods Applied to the Particle in a Box and many others - these are all part of the SymMath Collection - http://jchemed.chem.wisc.edu/JCEDLib/SymMath/collection/index.php One of the features I edit for the Journal, the WebWare feature, also has some theoretical chemistry applications including: Restricted Hartree-Fock SCF Calculations Using Microsoft Excel Self-Consistent Field Calculations Spreadsheet The Effect of Anharmonicity on Diatomic Vibration: A Spreadsheet Simulation H=C3=83=C2=BCckel Determinant Solver These are at http://jchemed.chem.wisc.edu/JCEDLib/WebWare/collection/reviewed/index.html The print version of the Journal also contains many articles dealing with theoretical chemistry topics. All of these are part of the National Science Digital Library - http://nsdl.org/ I hope this helps, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College=20 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 -=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=0A=0A=0A --0-2043808607-1227543530=:39586 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

thank you sir, very much

--- En date d= e : Dim 23.11.08, William F. Coleman wcoleman_+_wellesley.edu &l= t;owner-chemistry(~)ccl.net> a =C3=A9crit :

De: William F. Coleman wcoleman_+_wellesley.edu <owner-chemis= try(~)ccl.net>
Objet: CCL: exercises resolved, for teaching
=C3=80: = "Abdelghani, May " <may01dz(~)yahoo.fr>
Date: Dimanche 23 No= vembre 2008, 15h50

Sent to CCL by: "William F. Coleman" [wcolem=
an[]wellesley.edu]
"CCL Subscribers" <chemistry{}ccl.net> on Sunda=
y, November 23,
2008 at 2:48
AM -0500 wrote:
>dear CCLers,
&=
gt;I am a teacher of theoritical chemistry, =C3=82 and i loock for=C3=82 ex=
ercises
>resolved on the folowing subjects( if it is a possible):
=
>1- solution of
 the Schrodinger equation for the hydrogen atom 
>2- Variation method=

>3- huckel simple
>thanks

I would suggest starting with=
 the Journal of Chemical Education.  There is
a web-based collection of =
exercises using computer algebra systems that
address all areas of chemi=
stry, including a number directed toward
theoretical chemistry.  Include=
d are topics such as:

Symbolic Math Approach To Solve Particle-in-th=
e-Box and H-Atom Problems

Construction of the Electronic Angular Wav=
e Functions and Probability
Distributions of the Hydrogen Atom

Ex=
ploring Orthonormal Functions

Exploring the Harmonic Oscillator Wave=
 Function Components

Potential Barriers and Tunneling

Visuali=
zation of Wavefunctions of the Ionized Hydrogen Molecule

Variational=
 Methods Applied to the Particle in a Box

and many others - these ar=
e all part of the SymMath Collection
 -
http://jchemed.chem.wisc.edu/JCEDLib/SymMath/collection/index.php
=

One of the features I edit for the Journal, the WebWare feature, also h=
as
some theoretical chemistry applications including:

Restricted =
Hartree-Fock SCF Calculations Using Microsoft Excel

Self-Consistent =
Field Calculations Spreadsheet

The Effect of Anharmonicity on Diatom=
ic Vibration: A Spreadsheet Simulation

H=C3=83=C2=BCckel Determinant=
 Solver

These are at
http://jchemed.chem.wisc.edu/JCEDLib/WebWare=
/collection/reviewed/index.html

The print version of the Journal als=
o contains many articles dealing with
theoretical chemistry topics.
<=
br>All of these are part of the National Science Digital Library -
http:=
//nsdl.org/

I hope this helps,

Flick



_________=
______
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/We=
bWare/
http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/ind=
ex.html



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=0A=0A=0A=0A = --0-2043808607-1227543530=:39586-- From owner-chemistry@ccl.net Mon Nov 24 22:16:00 2008 From: "Peter Schmidtke pschmidtke*|*mmb.pcb.ub.es" To: CCL Subject: CCL: PDB: structures with approved drugs Message-Id: <-38166-081124180003-24738-QQy4IEwT9EjYoHn+quN3Bw(-)server.ccl.net> X-Original-From: Peter Schmidtke Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="UTF-8" Date: Mon, 24 Nov 2008 23:27:16 +0100 MIME-Version: 1.0 Sent to CCL by: Peter Schmidtke [pschmidtke%x%mmb.pcb.ub.es] Dear CCLers, I have certainly a standard question that might appear often. Anyway, I would like to know if there is a comprehensive list of approved and marketed drugs with a corresponding PDB structure with the drug actually inside? The Drugbank only provides information about the targets, but not this detail. Thanks in advance. Best regards. --=20 Peter Schmidtke ---------------------- PhD Student at the Molecular Modeling and Bioinformatics Group Dep. Physical Chemistry Faculty of Pharmacy University of Barcelona