From owner-chemistry@ccl.net Mon Jul 16 01:16:00 2007 From: "Antony Williams antony.williams-,-chemspider.com" To: CCL Subject: CCL: Where to find FDA drug database Message-Id: <-34742-070716005431-25270-dkjwq3nhUP+ilLT9vJfziA(0)server.ccl.net> X-Original-From: "Antony Williams" Content-Type: multipart/alternative; boundary="----=_NextPart_000_050A_01C7C73F.B9629060" Date: Mon, 16 Jul 2007 00:24:51 -0400 MIME-Version: 1.0 Sent to CCL by: "Antony Williams" [antony.williams:chemspider.com] This is a multi-part message in MIME format. ------=_NextPart_000_050A_01C7C73F.B9629060 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Re: CCL: Where to find FDA drug databaseJust to let everyone know that = both the HMDB and Drugbank databases have recently been added to the = ChemSpider Index online. It is possible to search them independently or = simultaneously. This is explained in the recent blog postings at: http://www.chemspider.com/news/?p=3D17 and=20 http://www.chemspider.com/blog/?p=3D81 Best wishes. Antony Williams, Host of ChemSpider (www.chemspider.com) Email: antony.williams*chemspider.com ----- Original Message -----=20 From: Rick Venable venabler|nhlbi.nih.gov=20 To: Williams, Antony John =20 Sent: Friday, July 13, 2007 5:05 PM Subject: CCL: Where to find FDA drug database 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. --=20 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. =20 I'd also guess that "pieces of information" exceeds the count of = "drugs" in the other source. =20 Best, Harry Gottlieb -------------- Original message --------------=20 > From: "Yuan Zhao ccl|-|mail.sioc.ac.cn" = =20 >=20 > Sent to CCL by: "Yuan Zhao" [ccl ~~ mail.sioc.ac.cn]=20 > Thanks!=20 > I've downloaded the database in DrugBank. It contains 1066 = molecules in the=20 > sdf file, of which 11 are blank molecules and 10 contain '*' in = atomic=20 > name. However, I searched in google and found a software named = as "Synapse=20 > EMR Express SERVER" which seemed to be able to download and = install FDA=20 > drug database. It imported about 21000 pieces of infomation but = I could not=20 > find them. Does it mean that there are over 21000 drugs in FDA = database? If=20 > it is the truth, the molecules in DrugBank seem too few to = summarize the=20 > property of FDA database.=20 >=20 > Steven=20 = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20 > CCL: Where to find FDA drug database=20 > Sent to CCL by: [DSprous*redpointbio.com]=20 > In reply to "Yuan Zhao" [ccl=3D-=3Dmail.sioc.ac.cn] query = summarized as:=20 >=20 > "I wonder how many drugs FDA have approved till now or this = year?"=20 >=20 > To my knowledge:=20 >=20 > The FDA Orange Book (http://www.fda.gov/cder/ob/) is closest = publicly=20 > available answer to this question. It is a list of approved drug = > formulations and does not have structures. Further, since it is = a list=20 > of approved formulations, children's motrin is distinct from = adult=20 > strength which is different from extra strength. The FDA = apparently=20 > simply does not seem to be interested in an actual molecular = database of=20 > approved active ingredients. You would need to download a copy = of the=20 > list, develop a script to generate a unique list of active = ingredients !=20 > ; and then use something like LexiChem to convert the chemical = and trade=20 > names to SMILES. This gives one about 1300 to 1400 compounds.=20 >=20 > An alternative which is easier to work with is the DrugBank=20 > (http://redpoll.pharmacy.ualberta.ca/drugbank/) datasets = maintained by=20 > Wishart [University of Alberta]. This too is a list of ~1300 to = 1400=20 > compounds.=20 >=20 > If anyone knows better public sources, please post.=20 >=20 > Dennis G. Sprous, PhD=20 > Chemoinformatics/Computational Chemistry=20 > RedPointBio Inc.=20 > 7 Graphics Drive Ewing NJ 08628=20 > 609-637-9700=20 > -----Original Message-----=20 > > From: owner-chemistry],[ccl.net = [mailto:owner-chemistry],[ccl.net]=20 > Sent: Wednesday, July 11, 2007 10:40 AM=20 > To: Dennis Sprous=20 > Subject: CCL: Where to find FDA drug database=20 >=20 >=20 > Sent to CCL by: "Yuan Zhao" [ccl=3D-=3Dmail.sioc.ac.cn]=20 > Hi a! ll,=20 >=20 > 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=20 > or other chemical formats? Does anyone know how many drugs in = FDA=20 > are fit for Lipinski rule of five? Any clue will be appreciate.=20 ------=_NextPart_000_050A_01C7C73F.B9629060 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Re: CCL: Where to find FDA drug database
Just to let everyone know that both the = HMDB and=20 Drugbank databases have recently been added to the ChemSpider Index = online. It=20 is possible to search them independently or simultaneously. This is = explained in=20 the recent blog postings at:
 
http://www.chemspider.com= /news/?p=3D17 and=20
http://www.chemspider.com= /blog/?p=3D81
 
Best wishes.
 
Antony Williams,
Host of ChemSpider = (www.chemspider.com)
Email: antony.williams*chemspider= .com
----- Original Message -----
From:=20 Rick=20 Venable venabler|nhlbi.nih.gov
To: Williams, Antony John=20
Sent: Friday, July 13, 2007 = 5:05 PM
Subject: CCL: Where to find FDA = drug=20 database

There are ca.=20 21,000 formulations in the =93orange book=94; a given drug substance = will have=20 many formulations (different dosages, tablet vs. caplet, single-use = vs.=20 multi-use vials, etc.).   One of the earlier posts (included = below)=20 indicated that these 21,000 formulations represent ca. 1300-1400 drug=20 substances, comparable in number and scope to those listed in=20 DrugBank.

--
Rick Venable=20        29/500
Membrane = Biophysics=20 Section
NIH/NHLBI Lab. of Computational Biology
Bethesda, MD=20  20892-8014   U.S.A.
(301) 496-1905 =   venabler AT=20 nhlbi*nih*gov


On 7/13/07 11:33 AM, = "HarryBGottlieb#comcast.net"=20 <owner-chemistry#,#ccl.net> wrote:
A = recent=20 overview of DrugBank by John Proudfoot appeared in CHEMISTRY = International,=20 May-June 2007, page 24.  He wrote that, "This free resource = pulls=20 together a surprisingly comprehensive amount of information on drugs = and=20 drug targets and contains data on over 1 000 marketed and over 3 000 = additional experimental drug substances."  That is about the = size of=20 the Comprehensive Medicinal Chemistry 3D (CMC3D) database that I was = familiar with from MDL in the early-mid 1990's.
 
I'd = also guess=20 that "pieces of information" exceeds the count of "drugs" in the = other=20 source.
 
Best,
Harry Gottlieb
-------------- Original message = --------------=20
> From: "Yuan Zhao ccl|-|mail.sioc.ac.cn"=20 <owner-chemistry-.-ccl.net>

>
> Sent to = CCL by:=20 "Yuan Zhao" [ccl ~~ mail.sioc.ac.cn]
> Thanks!
> = I've=20 downloaded the database in DrugBank. It contains 1066 molecules in = the=20
> sdf file, of which 11 are blank molecules and 10 contain = '*' in=20 atomic
> name. However, I searched in google and found a = software=20 named as "Synapse
> EMR Express SERVER" which seemed to be = able to=20 download and install FDA
> drug database. It imported about = 21000=20 pieces of infomation but I could not
> find them. Does it = mean that=20 there are over 21000 drugs in FDA database? If
> it is the = truth,=20 the molecules in DrugBank seem too few to summarize the
> = property=20 of FDA database.
>
> Steven=20 =

 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> CCL: = Where=20 to find FDA drug database
> Sent to CCL by:=20 [DSprous*redpointbio.com]
> In reply to "Yuan Zhao"=20 [ccl=3D-=3Dmail.sioc.ac.cn] query summarized as:
>
> = "I wonder=20 how many drugs FDA have approved till now or this year?"
> =
>=20 To my knowledge:
>
> The FDA Orange Book (http://www.fda.gov/cder/ob/) = is=20 closest publicly
> available answer to this question. It is = a list=20 of approved drug
> formulations and does not have = structures.=20 Further, since it is a list
> of approved formulations, = children's=20 motrin is distinct from adult
> strength which is different = > from=20 extra strength. The FDA apparently
> simply does not seem = to be=20 interested in an actual molecular database of
> approved = active=20 ingredients. You would need to download a copy of the
> = list,=20 develop a script to generate a unique list of active ingredients ! =
> ; and then use something like LexiChem to convert the = chemical=20 and trade
> names to SMILES. This gives one about 1300 to = 1400=20 compounds.
>
> An alternative which is easier to = work with=20 is the DrugBank
> (http://redpoll.ph= armacy.ualberta.ca/drugbank/)=20 datasets maintained by
> Wishart [University of Alberta]. = This too=20 is a list of ~1300 to 1400
> compounds.
>
> = If anyone=20 knows better public sources, please post.
>
> Dennis = G.=20 Sprous, PhD
> Chemoinformatics/Computational Chemistry =
>=20 RedPointBio Inc.
> 7 Graphics Drive Ewing NJ 08628
> = 609-637-9700
> -----Original Message-----
> > = > From:=20 owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.n= et]=20
> Sent: Wednesday, July 11, 2007 10:40 AM
> To: = Dennis=20 Sprous
> Subject: CCL: Where to find FDA drug database =
>=20
>
> Sent to CCL by: "Yuan Zhao" = [ccl=3D-=3Dmail.sioc.ac.cn]=20
> Hi a! ll,
>
> I wonder how many drugs FDA = have=20 approved till now or this year.
> If possible, where can I = download=20 the FDA drug database in sd, mol
> or other chemical = formats? Does=20 anyone know how many drugs in FDA
> are fit for Lipinski = rule of=20 five? Any clue will be appreciate.=20
------=_NextPart_000_050A_01C7C73F.B9629060-- From owner-chemistry@ccl.net Mon Jul 16 05:30:01 2007 From: "=?ISO-8859-1?Q?=C5smund_Rinnan?= asmundrinnan[*]gmail.com" To: CCL Subject: CCL:G: Restarting a Gaussian03 job Message-Id: <-34743-070716051414-15021-JFyKs65igYhOLBw3p6ydlQ ~~ server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?=C5smund_Rinnan?=" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 16 Jul 2007 10:09:17 +0200 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?=C5smund_Rinnan?=" [asmundrinnan ~~ gmail.com] Hi, I am a bit of a rookie in Gaussian, and I have a problem as there was a power failure this weekend, causing several long running frequency jobs to do die on me. The job description is as follows: '#p b3lyp/6-311+g(3df,2p) freq scf=tight'. I have saved both the chk and the rwf-file, but I cannot seem to figure out what to write in order to restart my calculations. (They have been running for several months...) Best regards, Åsmund Rinnan Post-doc chemometrics Quality & Technology Food Science Faculty of Life Sciences University of Copenhagen Denmark From owner-chemistry@ccl.net Mon Jul 16 10:22:00 2007 From: "Shobe, David David.Shobe[a]sud-chemie.com" To: CCL Subject: CCL:G: Restarting a Gaussian03 job Message-Id: <-34744-070716101643-13383-U8S5dE6NcecHXrJ3Sk0TsA * server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 16 Jul 2007 16:16:07 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe=sud-chemie.com] Åsmund, I hate to tell you this but there's no way to restart a freq job in Gaussian. Several months? I admire your patience. I would have killed the jobs and settled for a lower level of theory a long time ago. :-) You may want to consider a two-part job: The first job using the command line: #p b3lyp/6-31+G(d,p) opt freq scf=tight --Link1-- to separate the two parts The second job using the command line: #p b3lyp/6-311+G(3df,2p) opt=readfc geom=check guess=read scf=tight This two-part procedure gives you frequencies at the b3lyp/6-31+G(d,p) level, still accurate enough for nearly all purposes geometry at the b3lyp/6-311+G(3df,2p) level, without violating the rule that when one calculates frequencies, one must use a geometry which is a stationary point at the level of theory being used for the freq calculation. Also, there is a limit on the accuracy of b3lyp and other density functional theory methods, and above this limit additional basis functions don't help. The integration grid comes into play here too: a finer grid is more accurate, but there is a point beyond which increasing the fineness of the grid does not give an improvement in accuracy. Regards, --David Shobe -----Original Message----- > From: owner-chemistry=ccl.net [mailto:owner-chemistry=ccl.net] Sent: Monday, July 16, 2007 4:09 AM To: Shobe, David Subject: CCL:G: Restarting a Gaussian03 job Sent to CCL by: "=?ISO-8859-1?Q?=C5smund_Rinnan?=" [asmundrinnan ~~ gmail.com] Hi, I am a bit of a rookie in Gaussian, and I have a problem as there was a power failure this weekend, causing several long running frequency jobs to do die on me. The job description is as follows: '#p b3lyp/6-311+g(3df,2p) freq scf=tight'. I have saved both the chk and the rwf-file, but I cannot seem to figure out what to write in order to restart my calculations. (They have been running for several months...) Best regards, Rinnan Post-doc chemometrics Quality & Technology Food Science Faculty of Life Sciences University of Copenhagen Denmarkhttp://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. From owner-chemistry@ccl.net Mon Jul 16 10:57:01 2007 From: "Barbara Jagoda-Cwiklik barbara.cwiklik/a\uochb.cas.cz" To: CCL Subject: CCL:G: Restarting a Gaussian03 job Message-Id: <-34745-070716094620-8768-IswKAodyLVcrj0lj7gdZkg^^server.ccl.net> X-Original-From: "Barbara Jagoda-Cwiklik" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 16 Jul 2007 15:46:12 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Barbara Jagoda-Cwiklik" [barbara.cwiklik%uochb.cas.cz] Hi Åsmund, There was the discussion on the CCL on the problem 2 months ago. You can find it here: http://www.ccl.net/cgi-bin/ccl/day-index.cgi?2007+05+18 Maybe it will help you... Regards :) Basia > Sent to CCL by: "Åsmund Rinnan" [asmundrinnan ~~ > gmail.com] > Hi, > I am a bit of a rookie in Gaussian, and I have a problem as there was > a power failure this weekend, causing several long running frequency > jobs to do die on me. The job description is as follows: '#p > b3lyp/6-311+g(3df,2p) freq scf=tight'. I have saved both the chk and > the rwf-file, but I cannot seem to figure out what to write in order > to restart my calculations. (They have been running for several > months...) > > Best regards, > Åsmund Rinnan > Post-doc chemometrics > Quality & Technology > Food Science > Faculty of Life Sciences > University of Copenhagen > Denmark> > > > -- Barbara Jagoda-Cwiklik, Ph.D Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Prague, Czech Republic e-mail: barbara.cwiklik ~~ uochb.cas.cz From owner-chemistry@ccl.net Mon Jul 16 11:32:01 2007 From: "Shobe, David David.Shobe!A!sud-chemie.com" To: CCL Subject: CCL: MP2 Calculation Error Message-Id: <-34746-070716104438-26132-wyHnzV6jNE4KS/7no6CETA^server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7C7B7.D171A52E" Date: Mon, 16 Jul 2007 16:44:30 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe**sud-chemie.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7C7B7.D171A52E Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Yousef, =20 It looks like you either ran out of disk space or (more likely) ran into a file size limit. 1 word =3D 8 bytes , so 350596100 words =3D about 2.8 GB. The file size limit depends on the operating system, but for Windows it's 2.0 GB. 2GB is a common limit because it's 2^31 bytes. You can, however, specify additional files using the %rwf command (see manual for details) so that when one file gets too big, the additional data can be stored in the next file listed after %rwf. =20 Regards, --David Shobe =20 ________________________________ > From: owner-chemistry/a\ccl.net [mailto:owner-chemistry/a\ccl.net]=20 Sent: Friday, July 13, 2007 6:36 PM To: Shobe, David Subject: CCL: MP2 Calculation Error =20 =20 I am trying to run MP2/6-31g optimization on Benzene molecule but it exits with no specific reason. I would really appreciate any comments. Here are the last couple of lines: =20 ExpMin=3D 1.03D-01 ExpMax=3D 4.56D+03 ExpMxC=3D 6.82D+02 IAcc=3D1 IRadAn=3D 1 AccDes=3D 1.00D-06 HarFok: IExCor=3D 205 AccDes=3D 1.00D-06 IRadAn=3D 1 IDoV=3D1 ScaDFX=3D 1.000000 1.000000 1.000000 1.000000 Range of M.O.s used for correlation: 7 144 NBasis=3D 144 NAE=3D 21 NBE=3D 21 NFC=3D 6 NFV=3D 0 NROrb=3D 138 NOA=3D 15 NOB=3D 15 NVA=3D 123 NVB=3D 123 =20 **** Warning!!: The largest alpha MO coefficient is 0.17744602D+02 =20 Estimate disk for full transformation 350596100 words. Semi-Direct transformation. ModeAB=3D 2 MOrb=3D 138 LenV=3D 99146315 LASXX=3D 75467172 LTotXX=3D 104541297 LenRXX=3D 108618075 LTotAB=3D 18624915 MaxLAS=3D 108618075 LenRXY=3D 18624915 NonZer=3D 150934344 LenScr=3D 315701760 LnRSAI=3D 0 LnScr1=3D 0 LExtra=3D 0 Total=3D 442944750 MaxDsk=3D -1 SrtSym=3D F ITran=3D 5 JobTyp=3D0 Pass 1: I=3D 1 to 138. writwa =20 Best regards, =20 Yousef Sharifi =20 =20 This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, 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 an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C7C7B7.D171A52E Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Yousef,

 

It looks like you either ran out of di= sk space or (more likely) ran into a file size limit.  1 word =3D 8 bytes= , so 350596100 words =3D about 2.8 GB.  The file size limit depends on the operating system, but for Windows it’s 2.0 GB.  2GB is a common limit beca= use it’s 2^31 bytes.  You can, however, specify additional files usi= ng the %rwf command (see manual for details) so that when one file gets too bi= g, the additional data can be stored in the next file listed after %rwf.<= /o:p>

 

Regards,

--David Shobe=

 

From: owner-chemistry/a\ccl.net [mailto:owner-chemistry/a\ccl.net]
Sent: Friday, July 13, 2007 = 6:36 PM
To: Shobe, David
Subject: CCL: MP2 Calculation Error

 

 

I am trying to r= un MP2/6-31g optimization on Benzene molecule but it exits with no specific reason.  I would really appreciate any comments. Here are the last cou= ple of lines:

 

ExpMin=3D 1.03D-= 01 ExpMax=3D 4.56D+03 ExpMxC=3D 6.82D+02 IAcc=3D1 IRadAn=3D         1 AccDes=3D 1.00D= -06

 HarFok:&nb= sp; IExCor=3D 205 AccDes=3D 1.00D-06 IRadAn=3D         1 IDoV=3D1

 ScaDFX=3D&= nbsp; 1.000000  1.000000  1.000000  1.000000

 Range of M.O.s used for correlation:     7   144

 NBasis=3D&= nbsp;  144 NAE=3D    21 NBE=3D    21 NFC=3D     6 NFV=3D     0

 NROrb=3D&n= bsp;   138 NOA=3D    15 NOB=3D    15 NVA=3D &nb= sp; 123 NVB=3D   123

 

 **** Warni= ng!!: The largest alpha MO coefficient is  0.17744602D+02<= /font>

 

 Estimate d= isk for full transformation   350596100 words.

 Semi-Direct transformation.

 ModeAB=3D&= nbsp;          2 MOrb=3D           138 LenV=3D      99146315

 LASXX=3D&n= bsp;    75467172 LTotXX=3D   104541297 LenRXX=3D   108618075

 LTotAB=3D&= nbsp;   18624915 MaxLAS=3D   108618075 LenRXY=3D    186249= 15

 NonZer=3D&= nbsp;  150934344 LenScr=3D   315701760 LnRSAI=3D     = ;      0

 LnScr1=3D&= nbsp;          0 LExtra=3D           0 Total=3D    442944750

 MaxDsk=3D&= nbsp;         -1 SrtSym=3D           F ITran=3D            = 5

 JobTyp=3D0 Pass  1:  I=3D   1 to 138.

writwa

 

Best regards,

 

Yousef Sharifi

 

 

This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, 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 an= d delete this message.
Thank you.
------_=_NextPart_001_01C7C7B7.D171A52E-- From owner-chemistry@ccl.net Mon Jul 16 12:06:00 2007 From: "Bachrach, Steven STEVEN.BACHRACH]~[Trinity.edu" To: CCL Subject: CCL: Computational Organic Chemistry - the Book, the Web site, and the Blog Message-Id: <-34747-070716101537-13169-u512Y/WY8aiW/DAwk9eLrg-*-server.ccl.net> X-Original-From: "Bachrach, Steven" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7C7AF.3C96FA88" Date: Mon, 16 Jul 2007 08:43:04 -0500 MIME-Version: 1.0 Sent to CCL by: "Bachrach, Steven" [STEVEN.BACHRACH|a|Trinity.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7C7AF.3C96FA88 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I would like to announce the publication of my book, "Computational Organic Chemistry" through Wiley (http://www.wiley.com/WileyCDA/WileyTitle/productCd-0471713422,subjectCd -CH65,descCd-tableOfContents.html). This book surveys the field of computational organic chemistry, presenting case studies of the application of ab initio and DFT computations to organic chemistry problems, along with interviews of six major figures in the field. =20 I am also providing two services on the web that augment the book. First, the book's web site (http://www.trinity.edu/sbachrac/coc/ ), besides containing a brief description of the book and the table of contents, includes every reference cited in the book with a direct link to that source (where available). Also, all 3-D molecular structures that are presented in the book as static images are available as interactive molecules using Jmol (and they can be downloaded for reuse). =20 Any book that hopes to capture the status of a dynamic field like computational chemistry is destined to become out-of-date. Even between the time the manuscript was completed and when the book was printed and distributed, research continued on, and the book is by definition incomplete. To address this, I have created a blog that serves as a mechanism to update the book, providing brief posts commenting on recent articles that touch on or expand upon the subjects discussed in the printed book. In addition, the blog provides an avenue for feedback from the readers. I welcome readers to comment on the book and the blog posts. The blog is available at http://hackberry.chem.trinity.edu/blog . =20 Both the book's auxiliary web site and the blog are operational and can be accessed for free. Enjoy! =20 Steven Bachrach =20 -- Steven Bachrach, Chair ph: (210)999-7379 Department of Chemistry fax: (210)999-7569 Trinity University =20 1 Trinity Place San Antonio, TX 78212 steven.bachrach+*+trinity.edu =20 =20 ------_=_NextPart_001_01C7C7AF.3C96FA88 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I would like = to announce the publication of my book, "Computational Organic Chemistry" = through Wiley (http://www.wiley.com/Wile= yCDA/WileyTitle/productCd-0471713422,subjectCd-CH65,des= cCd-tableOfContents.html). This book surveys the field of computational organic chemistry, = presenting case studies of the application of ab initio and DFT computations to organic chemistry problems, along with interviews of six major figures in the = field.

 

I am also = providing two services on the web that augment the book. First, the book's web site = (http://www.trinity.edu/sb= achrac/coc/), besides containing a brief description of the book and the table of = contents, includes every reference cited in the book with a direct link to that = source (where available). Also, all 3-D molecular structures that are presented = in the book as static images are available as interactive molecules using Jmol = (and they can be downloaded for reuse).

 

Any book that = hopes to capture the status of a dynamic field like computational chemistry is = destined to become out-of-date. Even between the time the manuscript was = completed and when the book was printed and distributed, research continued on, and = the book is by definition incomplete. To address this, I have created a blog that = serves as a mechanism to update the book, providing brief posts commenting on = recent articles that touch on or expand upon the subjects discussed in the = printed book. In addition, the blog provides an avenue for feedback from the = readers. I welcome readers to comment on the book and the blog posts. The blog is available at http://hackberry.chem.tri= nity.edu/blog.

 

Both the = book's auxiliary web site and the blog are operational and can be accessed for free. = Enjoy!

 

Steven Bachrach

 

--

Steven Bachrach, = Chair           &n= bsp; ph: (210)999-7379

Department of = Chemistry          fax: = (210)999-7569

Trinity University    = ;            =             &= nbsp;

1 Trinity = Place

San = Antonio, TX 78212

steven.bachrach+*+trinity.edu

 

 

------_=_NextPart_001_01C7C7AF.3C96FA88-- From owner-chemistry@ccl.net Mon Jul 16 12:42:00 2007 From: "Laurent Favaro laurent.favaro(~)u-psud.fr" To: CCL Subject: CCL: Inverse Raman Message-Id: <-34748-070716114639-10250-NJCERXyXLJgcOr6eoKMvog ~~ server.ccl.net> X-Original-From: Laurent Favaro Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Mon, 16 Jul 2007 17:34:58 +0200 MIME-Version: 1.0 Sent to CCL by: Laurent Favaro [laurent.favaro*u-psud.fr] Dear All, I would appreciate any idea about the inverse Raman problem, i.e. solving a structure from the knowledge of the Raman spectrum. > From the experimental spectrum we should be able to rebuilt the hessian matrix. The hessian matrix should reflect the symetry of the compound. How can we extract this symetry ? The hessian being the second derivative of the energy with respect to coordinates, around equilibrium position, > from the knowledge of this matrix, we cannot obtain directly the position of the atoms. But can multiple spectra at different pressure, (and then multiple hessians with different equilibrium position) bring any help ? Intensities being given by the derivative of the dipolar moment with respect to coordinates, can this data be helpful to obtain equilibrium positions ? Has anybody heard about previous research on this topic ? Thank you very much for your help. Best regards. Dr L. Favaro From owner-chemistry@ccl.net Mon Jul 16 13:17:00 2007 From: "Demetrios Xenides xenides**uop.gr" To: CCL Subject: CCL:G: Restarting a Gaussian03 job Message-Id: <-34749-070716082104-28406-Pta1e2IITl73tnqPI1HRBg__server.ccl.net> X-Original-From: Demetrios Xenides Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-7 Date: Mon, 16 Jul 2007 14:01:52 +0300 MIME-Version: 1.0 Sent to CCL by: Demetrios Xenides [xenides|-|uop.gr] Hi, the scf(tight,restart) instead of scf=tight should be adequate. D p.s rwf files only coccupying space in this time. In other words I would suggested you to delete them. Áñ÷éêü ìÞíõìá áðü "Åsmund Rinnan asmundrinnan[*]gmail.com" : > > Sent to CCL by: "=?ISO-8859-1?Q?=C5smund_Rinnan?=" [asmundrinnan ~~ > gmail.com] > Hi, > I am a bit of a rookie in Gaussian, and I have a problem as there was > a power failure this weekend, causing several long running frequency > jobs to do die on me. The job description is as follows: '#p > b3lyp/6-311+g(3df,2p) freq scf=tight'. I have saved both the chk and > the rwf-file, but I cannot seem to figure out what to write in order > to restart my calculations. (They have been running for several > months...) > > Best regards, > Åsmund Rinnan > Post-doc chemometrics > Quality & Technology > Food Science > Faculty of Life Sciences > University of Copenhagen > Denmark> > > > From owner-chemistry@ccl.net Mon Jul 16 18:47:00 2007 From: "David Hose anthrax_brothers:+:hotmail.com" To: CCL Subject: CCL: Restarting a Gaussian03 job Message-Id: <-34750-070716184531-27615-BtDTh5VEM6DS1zO811ALQw++server.ccl.net> X-Original-From: "David Hose" Date: Mon, 16 Jul 2007 18:45:27 -0400 Sent to CCL by: "David Hose" [anthrax_brothers]-[hotmail.com] Rinnan, I have to go with David's comment about 'several months'. The longest single job I've run is 15 days and that drove me up the wall! I would be looking to rerun the calculation at a lower level of theory to get the ZPE etc for any subsequent calculations, followed by a single point calculation with the larger basis set. Why do you need the vibrational analysis with this large basis set? If you want use the analysis to compare with experimental IR spectra, I would be inclined to look at a frequency scaling factor. The Computational Chemistry Comparison and Benchmark DataBase (http://srdata.nist.gov/cccbdb/) has a section of vibrational correction factors that might be worth looking into. Regards. Dave. From owner-chemistry@ccl.net Mon Jul 16 20:47:00 2007 From: "David Gallagher gallagher.da[a]gmail.com" To: CCL Subject: CCL: Micelles and Biomembranes: new modelling tool Message-Id: <-34751-070716204340-28080-rNRnCFiiyV7ZwWtS63fJ2Q a server.ccl.net> X-Original-From: David Gallagher Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 16 Jul 2007 16:50:31 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da*gmail.com] Micelles and Biomembranes: new modelling tool COSMOmic, a new software package for modelling micelles and biomembranes, has just been released by COSMOlogic. COSMOmic models surfactant micelles or biomembranes as inhomogeneous, layered liquids, allowing the calculation of properties such as free energy profiles and membrane partition coefficients of solutes. COSMOmic can deal with neutral or ionic solutes in spherical, cylindrical or lamellar type membranes. There is more information at http://www.cacheresearch.com/cosmo.html David Gallagher CAChe Research From owner-chemistry@ccl.net Mon Jul 16 23:48:01 2007 From: "Bingxing Wang wangbx_._dicp.ac.cn" To: CCL Subject: CCL: recieve many strange emails Message-Id: <-34752-070716210154-3197-sXWv6zCFLUbBRLDabqUdVw+*+server.ccl.net> X-Original-From: "Bingxing Wang" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Tue, 17 Jul 2007 08:29:41 +0800 Mime-Version: 1.0 Sent to CCL by: "Bingxing Wang" [wangbx__dicp.ac.cn] Dear CCLers: recently i recieve many strange email from owner-chemistry+wangbx==dicp.ac.cn[-]ccl.net. and it only write "aaazzzaaazzzaaazzzaaazzzaaazzz". what's wrong? thank you. With best regards, Sincerely yours, Bingxing Wang 2007-07-17 email: wangbx[-]dicp.ac.cn