From owner-chemistry@ccl.net Tue Jul 24 04:03:00 2007 From: "Dr. Alexander Hofmann ah^-^chemie.hu-berlin.de" To: CCL Subject: CCL: SURFACE ENERGY CALCULATION FROM FORCITE Message-Id: <-34785-070724035711-21908-tU4U4YUR734TGvaTKHH6Ng(!)server.ccl.net> X-Original-From: "Dr. Alexander Hofmann" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 24 Jul 2007 09:25:33 +0200 MIME-Version: 1.0 Sent to CCL by: "Dr. Alexander Hofmann" [ah**chemie.hu-berlin.de] Hi Donald, I cannot exactly answer the question, but I like the way they do in the following article: V. Fiorentini and M. Methfessel, J. Phys.: Condens. Matter, 1996, 8, 6525. They compare different approaches and discuss the convergence behaviour. Very useful and general! Best regards Alexander Donald mkhonto mkhonto_._wisc.edu wrote: > Sent to CCL by: "Donald mkhonto" [mkhonto**wisc.edu] > Does anyone know how to calculate surface energy using the FORCITE software from accelrys materials studio. The surface energy is U = (U-surface - U-bulk)/Area, where U-surface is the energy of the surface and U-bulk is the energy of the bulk (species equal in number to the species contained in the surface) and is devided by the surface area. I am trying to figure out how the energy of the bulk can be calculated from FORCITE when the surface has been constructed to be a 3D crystal with a vaccum slab. Could be the same with a 2D slab I guess. Programes like METADISE and MRVIN would reprouce "the same" surface energy and am looking at ways of using accelrys to do the same and add some organic adsorbates on surfaces. I'll appreciate your help and I hope my question will be clear to everyone. > > Donald > mkhonto|,|wisc.edu> > > -- Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie Arbeitsgruppe Quantenchemie Post: Unter den Linden 6 10099 Berlin Visitors: Brook-Taylor-Strasse 2 12489 Berlin ah chemie.hu-berlin.de +*+ Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35 From owner-chemistry@ccl.net Tue Jul 24 05:11:00 2007 From: "Ramon Crehuet rcsqtc__iiqab.csic.es" To: CCL Subject: CCL:G: electric field and MP2 Message-Id: <-34786-070724041414-27748-APXAUPT2ISiNCRvfz8GO2A*server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 23 Jul 2007 16:40:38 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc%iiqab.csic.es] Dear all, We would like to perform an MP2 calculation under an external uniform electric field (FIELD keyword) in gaussian 03. Although the manual does not state that this is impossible, we get an error message saying that only single point, force and scan calculations are possible (which seems to suggest that gradients are available...) Besides, other groups seem to have performed geometry optimisations with MP2 and a field (JCP, 124, 094308, (2006)). I was wondering if it may depend on the gaussian version, though I could not find anything on the on-line release notes. In our supercomputing center we have the Gaussian 03 C02. Thanks for your attention, Ramon PS. This is the problematic input: #N MPDear all, We would like to perform an MP2 calculation under an external uniform electric field (FIELD keyword) in gaussian 03. Although the manual does not state that this is impossible, we get an error message saying that only single point, force and scan calculations are possible (which seems to suggest that gradients are available...) Besides, other groups seem to have performed geometry optimisations with MP2 and a field (JCP, 124, 094308, (2006)). I was wondering if it may depend on the gaussian version, though I could not find anything on the on-line release notes. In our supercomputing center we have the Gaussian 03 C02. Thanks for your attention, Ramon PS. This is the problematic input: #N MP2/6-31+G(d) opt=z-matrix nosymm field=z+120 h2 0 1 H H r1 r1 0.8 2/6-31+G(d) opt=z-matrix nosymm field=z+120 h2 0 1 H H 1 r1 r1 0.8 From owner-chemistry@ccl.net Tue Jul 24 08:53:01 2007 From: "ilknur cavusoglu ilknurca() kou.edu.tr" To: CCL Subject: CCL: new chemistry software Message-Id: <-34787-070724043913-8347-7LlRFuJa3nke9jUdC3W28A- -server.ccl.net> X-Original-From: "ilknur cavusoglu" Date: Tue, 24 Jul 2007 04:39:10 -0400 Sent to CCL by: "ilknur cavusoglu" [ilknurca|a|kou.edu.tr] I want to ask you that f anyone knows any software program that calculate logP parameters for metallo phthalocyanines. Kind regards... Ilknur Cavusoglu ilknurca*o*kou.edu.tr From owner-chemistry@ccl.net Tue Jul 24 09:28:01 2007 From: "Mazen Ahmad mazen2010{=}googlemail.com" To: CCL Subject: CCL: Where to find FDA drug database Message-Id: <-34788-070721194127-27859-0X5ofbA/di9P722Br2ihdw : server.ccl.net> X-Original-From: "Mazen Ahmad" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 22 Jul 2007 00:45:58 +0200 MIME-Version: 1.0 Sent to CCL by: "Mazen Ahmad" [mazen2010*|*googlemail.com] Hi all, Maybe youmean this data. http://www.fda.gov/cder/Offices/OPS_IO/MRTD.htm Regards Mazen Ahmad On 7/13/07, Rick Venable venabler|nhlbi.nih.gov wrote: > > There are ca. 21,000 formulations in the "orange book"; a given drug > substance will have many formulations (different dosages, tablet vs. caplet, > single-use vs. multi-use vials, etc.). One of the earlier posts (included > below) indicated that these 21,000 formulations represent ca. 1300-1400 drug > substances, comparable in number and scope to those listed in DrugBank. > > -- > Rick Venable 29/500 > Membrane Biophysics Section > NIH/NHLBI Lab. of Computational Biology > Bethesda, MD 20892-8014 U.S.A. > (301) 496-1905 venabler AT nhlbi*nih*gov > > > > On 7/13/07 11:33 AM, "HarryBGottlieb#comcast.net" > wrote: > > A recent overview of DrugBank by John Proudfoot appeared in CHEMISTRY > International, May-June 2007, page 24. He wrote that, "This free resource > pulls together a surprisingly comprehensive amount of information on drugs > and drug targets and contains data on over 1 000 marketed and over 3 000 > additional experimental drug substances." That is about the size of the > Comprehensive Medicinal Chemistry 3D (CMC3D) database that I was familiar > with from MDL in the early-mid 1990's. > > I'd also guess that "pieces of information" exceeds the count of "drugs" in > the other source. > > Best, > Harry Gottlieb > > > -------------- Original message -------------- > > From: "Yuan Zhao ccl|-|mail.sioc.ac.cn" > > > > > Sent to CCL by: "Yuan Zhao" [ccl ~~ mail.sioc.ac.cn] > > Thanks! > > I've downloaded the database in DrugBank. It contains 1066 molecules in > the > > sdf file, of which 11 are blank molecules and 10 contain '*' in atomic > > name. However, I searched in google and found a software named as > "Synapse > > EMR Express SERVER" which seemed to be able to download and install FDA > > drug database. It imported about 21000 pieces of infomation but I could > not > > find them. Does it mean that there are over 21000 drugs in FDA database? > If > > it is the truth, the molecules in DrugBank seem too few to summarize the > > property of FDA database. > > > > Steven > > ======================================= > > CCL: Where to find FDA drug database > > Sent to CCL by: [DSprous*redpointbio.com] > > In reply to "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] query summarized as: > > > > "I wonder how many drugs FDA have approved till now or this year?" > > > > To my knowledge: > > > > The FDA Orange Book (http://www.fda.gov/cder/ob/) is closest publicly > > available answer to this question. It is a list of approved drug > > formulations and does not have structures. Further, since it is a list > > of approved formulations, children's motrin is distinct from adult > > strength which is different from extra strength. The FDA apparently > > simply does not seem to be interested in an actual molecular database of > > approved active ingredients. You would need to download a copy of the > > list, develop a script to generate a unique list of active ingredients ! > > ; and then use something like LexiChem to convert the chemical and trade > > names to SMILES. This gives one about 1300 to 1400 compounds. > > > > An alternative which is easier to work with is the DrugBank > > (http://redpoll.pharmacy.ualberta.ca/drugbank/) datasets > maintained by > > Wishart [University of Alberta]. This too is a list of ~1300 to 1400 > > compounds. > > > > If anyone knows better public sources, please post. > > > > Dennis G. Sprous, PhD > > Chemoinformatics/Computational Chemistry > > RedPointBio Inc. > > 7 Graphics Drive Ewing NJ 08628 > > 609-637-9700 > > -----Original Message----- > > > From: owner-chemistry],[ccl.net > [mailto:owner-chemistry],[ccl.net] > > Sent: Wednesday, July 11, 2007 10:40 AM > > To: Dennis Sprous > > Subject: CCL: Where to find FDA drug database > > > > > > Sent to CCL by: "Yuan Zhao" [ccl=-=mail.sioc.ac.cn] > > Hi a! ll, > > > > I wonder how many drugs FDA have approved till now or this year. > > If possible, where can I download the FDA drug database in sd, mol > > or other chemical formats? Does anyone know how many drugs in FDA > > are fit for Lipinski rule of five? Any clue will be appreciate. > From owner-chemistry@ccl.net Tue Jul 24 10:58:01 2007 From: "Andreas Klamt klamt##cosmologic.de" To: CCL Subject: CCL: new chemistry software Message-Id: <-34789-070724103908-26599-W2OYbZhCPGGDsppjaLWivg-*-server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 24 Jul 2007 16:05:50 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt||cosmologic.de] Our COSMOtherm program (see www.cosmologic.de) can do so, if the metal atom is not much solvent exposed. I do not know exactly whether this is the case for for your compounds. Best regards Andreas Klamt ilknur cavusoglu ilknurca() kou.edu.tr schrieb: > Sent to CCL by: "ilknur cavusoglu" [ilknurca|a|kou.edu.tr] > I want to ask you that f anyone knows any software program that calculate logP parameters for metallo phthalocyanines. > Kind regards... > Ilknur Cavusoglu > ilknurca^-^kou.edu.tr> > > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt=-=cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Jul 24 13:23:00 2007 From: "Dr David N Haney haney^-^edusoft-lc.com" To: CCL Subject: CCL: new chemistry software logP Message-Id: <-34790-070724132048-4631-cRlD16hKitVtnexxggq5qw-$-server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Tue, 24 Jul 2007 13:24:34 -0400 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney[*]edusoft-lc.com] Ilknur Cavusoglu, On Tue, Jul 24, 2007 at 04:39:10AM -0400, ilknur cavusoglu ilknurca() kou.edu.tr wrote: > > Sent to CCL by: "ilknur cavusoglu" [ilknurca|a|kou.edu.tr] > I want to ask you that f anyone knows any software program that calculate logP parameters for metallo phthalocyanines. > Kind regards... > Ilknur Cavusoglu > ilknurca^-^kou.edu.tr The program HintLogP available from EduSoft (http://www.edusoft-lc.com/) will calculate LogP values, as well as atomic values and logP descriptor values. For many metalo atoms there are not good parameters (although you could develop them and add them to the database), so those atoms will be assigned as "dummy" atoms and a neutral value of 0.0. For the SMILES structures from the EPA website, the following results are obtained: 1. Cuprate(2-), [29H,31H-phthalocyanine-C,C-disulfonato(4-)-.kappa.N29,.kappa.N30,.kappa.N31,.kappa.N32]-, disodium (CAS#1330-38-7) [Cu+2].c12c3[n-]c(c1cccc2S(=O)(=O)[O-])nc1nc(c2c1cccc2S(=O)(=O)[O-])nc1c2c(cccc2)c(nc2nc(n3)c3ccccc23)[n-]1.[Na+].[Na+] HINTlogP=0.473966 2. 29H,31H-Phthalocyanine (CAS#574-93-6) n1c2nc(c3c2cccc3)nc2nc(c3c2cccc3)nc2nc(c3c2cccc3)[nH]c2c3c(c1[nH]2)cccc3 HINTlogP=6.854949 -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney**edusoft-lc.com # ################# ##################### From owner-chemistry@ccl.net Tue Jul 24 18:01:00 2007 From: "Reaz Uddin riaasuddin:+:yahoo.com" To: CCL Subject: CCL: Arranging electric charges to manage Dipole moment ..???? Message-Id: <-34791-070724160440-10747-EsNfr6an51/cN72tvjlIVA{}server.ccl.net> X-Original-From: Reaz Uddin Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1805566923-1185303848=:54428" Date: Tue, 24 Jul 2007 12:04:08 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Reaz Uddin [riaasuddin##yahoo.com] --0-1805566923-1185303848=:54428 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit David, its the reply of Sukumar not Kumar, I am sorry about that. Thanks for the reply. It helps me, I appreciate you guys.. REAZ "Shobe, David David.Shobe]=[sud-chemie.com" wrote: v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} Sometimes you can use a symmetry argument to show that the dipole moment is zero. But in general? Not that I know of. (I haven’t seen Kumar’s reply). Example: The arrangement: + - - + - + + - + - - + has a center of symmetry, and so must have a zero dipole moment; any dipole-moment vector of positive length would be incompatible with the symmetry. --David --------------------------------- From: owner-chemistry###ccl.net [mailto:owner-chemistry###ccl.net] Sent: Monday, July 23, 2007 12:36 PM To: Shobe, David Subject: CCL: Arranging electric charges to manage Dipole moment ..???? Thanks for the reply. Isn't it possible to say the system has net dipole or not just seeing the arrangement of charges.? Without calculating this components??? As Kumar replied me. Thanks REAZ "Shobe, David David.Shobe-.-sud-chemie.com" wrote: Sent to CCL by: "Shobe, David" [David.Shobe{}sud-chemie.com] REAZ, You can calculate the x component of the dipole moment as follows: calculate the sum over charges .SIGMA. qi xi where qi is the magnitude of the i'th charge and (xi, yi, zi) is the position of the i'th charge. All those i's are supposed to be subscripts. The y and z components of the dipole moment are calculated analogously. It may appear at first that this formula is dependent on the choice of origin, but it really isn't, as long as the ensemble of charges is neutral overall. Changing the origin will change each xi in the sum, but the changes will cancel out for positive and negative charges. For a continuous charge density, one replaces the sums with integrals. Regards, --David Shobe -----Original Message----- > From: owner-chemistry[#]ccl.net [mailto:owner-chemistry[#]ccl.net] Sent: Friday, July 20, 2007 9:23 PM To: Shobe, David Subject: CCL: Arranging electric charges to manage Dipole moment ..???? Sent to CCL by: "Reaz Uddin" [riaasuddin : yahoo.com] Hi, Can anybody explain me the arrangement of charges with respect to the dipole moment. I mean, How can I arrange a small number(lets say 8 or 12) of charges where I could find at certain arrangement no dipole moment (like they cancel out each other) or at certain arrangement they show the dipole moment. Take an example of 12 charges in which 4 are + and 4 are -. I would say I arranged them in the following manner: +-+- ++-- +--+ Does the above arrangement show dipole moment,? if yes then please arrange it in a way so that they dont show any dipole moment. Hope I'd get an explanatory answer in this regard. Thanks in advance. I appreciate you guys. REAZhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. David, its the reply of Sukumar not Kumar, I am sorry about that.
Thanks for the reply.
It helps me, I appreciate you guys..
REAZ
"Shobe, David David.Shobe]=[sud-chemie.com" <owner-chemistry() ccl.net> wrote:
Sometimes you can use a symmetry argument to show that the dipole moment is zero.  But in general?  Not that I know of.  (I haven’t seen Kumar’s reply).
 
Example: The arrangement:
+ - - +
- + + -
+ - - +  
has a center of symmetry, and so must have a zero dipole moment; any dipole-moment vector of positive length would be incompatible with the symmetry.
 
--David
 
From: owner-chemistry###ccl.net [mailto:owner-chemistry###ccl.net]
Sent: Monday, July 23, 2007 12:36 PM
To: Shobe, David
Subject: CCL: Arranging electric charges to manage Dipole moment ..????
 
Thanks for the reply.
Isn't it possible to say the system has net dipole or not just seeing the arrangement of charges.? Without calculating this components??? As Kumar replied me.
 
Thanks
REAZ

"Shobe, David David.Shobe-.-sud-chemie.com" <owner-chemistry{=}ccl.net> wrote:

Sent to CCL by: "Shobe, David" [David.Shobe{}sud-chemie.com]
REAZ,

You can calculate the x component of the dipole moment as follows:
calculate the sum over charges .SIGMA. qi xi where qi is the magnitude
of the i'th charge and (xi, yi, zi) is the position of the i'th charge.
All those i's are supposed to be subscripts. The y and z components of
the dipole moment are calculated analogously.

It may appear at first that this formula is dependent on the choice of
origin, but it really isn't, as long as the ensemble of charges is
neutral overall. Changing the origin will change each xi in the sum,
but the changes will cancel out for positive and negative charges.

For a continuous charge density, one replaces the sums with integrals.

Regards,
--David Shobe

-----Original Message-----
> From: owner-chemistry[#]ccl.net [mailto:owner-chemistry[#]ccl.net]
Sent: Friday, July 20, 2007 9:23 PM
To: Shobe, David
Subject: CCL: Arranging electric charges to manage Dipole moment ..????


Sent to CCL by: "Reaz Uddin" [riaasuddin : yahoo.com]
Hi,
Can anybody explain me the arrangement of charges with respect to the
dipole moment. I mean, How can I arrange a small number(lets say 8 or
12) of charges where I could find at certain arrangement no dipole
moment (like they cancel out each other) or at certain arrangement they
show the dipole moment. Take an example of 12 charges in which 4 are +
and 4 are -.
I would say I arranged them in the following manner:
+-+-
++--
+--+
Does the above arrangement show dipole moment,? if yes then please
arrange it in a way so that they dont show any dipole moment.
Hope I'd get an explanatory answer in this regard.
Thanks in advance. I appreciate you guys.
REAZhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message.
Thank you.


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