From owner-chemistry@ccl.net Wed May 18 02:52:00 2011 From: "Arne Dieckmann adieckma~~googlemail.com" To: CCL Subject: CCL: iPhone & iPad 3D Molecule Browser - iMolview Message-Id: <-44686-110518025051-9773-iM9bJ+Tcx8fz3SgFPJj/4A]-[server.ccl.net> X-Original-From: "Arne Dieckmann" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: 18 May 2011 08:50:44 +0200 MIME-Version: 1.0 Sent to CCL by: "Arne Dieckmann" [adieckma%a%googlemail.com] Great, I have already bought it and will test it soon. Cheers, Arne ----------------------- Dr. Arne Dieckmann Bioorganic Chemistry (Room: NC 2/125) Ruhr-University Bochum Universitätsstraße 150 44780 Bochum, Germany phone: +49 234 3224216 email: adieckma:_:googlemail.com http://www.ruhr-uni-bochum.de/oc1/mitarbeiter/Arne-Dieckmann.html On Wednesday, May 18, 2011 at 3:28 AM, Andrew Orry andy-*-molsoft.com wrote: > > Sent to CCL by: Andrew Orry [andy]![molsoft.com] > On 5/7/2011 2:43 AM, Arne Dieckmann adieckma-$-googlemail.com wrote: > > Sent to CCL by: Arne Dieckmann [adieckma],[googlemail.com] > > Dear Andrew, > > > > how about loading in your own pdb files? I'd buy it if that will be possible. > The latest version of iMolview (v1.2) is now synced with iTunes so you can load in your own PDB files from there. We also fixed a graphics issue with older iPhone/iPod devices and introduced a number of other features and improvements. Please see the app page for the full release notes:http://www.molsoft.com/iMolview.html > Thanks, > Andrew > > -- > Andrew Orry Ph.D. > MolSoft LLC > Senior Research Scientist > 11199 Sorrento Valley Road, S209 > San Diego > CA 92121 > Tel: 858-625-2000 x108 > Fax: 828-625-2888 > www.molsoft.com> From owner-chemistry@ccl.net Wed May 18 07:08:01 2011 From: "Yonggang Yang ygyang() chemie.fu-berlin.de" To: CCL Subject: CCL:G: question about correlation energy Message-Id: <-44687-110518070436-9713-B86S2//H1WHzFDNfxZFKRQ^-^server.ccl.net> X-Original-From: "Yonggang Yang" Date: Wed, 18 May 2011 07:04:33 -0400 Sent to CCL by: "Yonggang Yang" [ygyang(!)chemie.fu-berlin.de] Dear Gaussian users, I want to calculate the pose-HF energy of a single Na atom by only including the most outside one electron. From theory the correction energy is not zero no matter by MP2 or CCSD. But Gaussian will simply say correlation is zero if only one electron is involved. Is there any possible way to calculate this pose-HF energy? Best regards, Yonggang Yang From owner-chemistry@ccl.net Wed May 18 07:45:01 2011 From: "Sebastian Kozuch kozuchs*yahoo.com" To: CCL Subject: CCL:G: basis sets Message-Id: <-44688-110518073450-23965-soeyZvYaGV439UAMqSy5PQ(a)server.ccl.net> X-Original-From: Sebastian Kozuch Content-Type: multipart/alternative; boundary="0-1860551574-1305718477=:57291" Date: Wed, 18 May 2011 04:34:37 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [kozuchs%yahoo.com] --0-1860551574-1305718477=:57291 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Regarding all this debate on small basis sets, I also have some doubts and = =0Acomments.=0A=0A1) SDD should be faster than 6-31g, having an ECP. But so= me programs can take =0Aadvantage of the fact that 6-31g has shared exponen= ts for S and P functions. In =0Athis case, Pople's is faster than Stuttgart= 's.=0A=0A2) For the same as before (shared exponentials) plus other reasons= , 6-31g can be =0Aless accurate. But someone told me that large ECP, as SDD= has, is not the best =0Achoice (of course small ECP for carbon means an al= l electron basis set). Does =0Asomeone know if this small/large basis set i= ssue is a general rule, a rule for =0Atransition metals, or not an accurate= rule at all?=0A=0A3) For the 6-31g family, it can be found everywhere disp= ersion and polarization =0Afunctions. For the SDD it=E2=80=99s not that sim= ple. This is a point for Pople=E2=80=99s.=0A=0A4) 6-31g is certainly an old= basis set, optimized for the almost obsolete HF =0Amethod. I=E2=80=99m sur= e that this is not a reason to disqualify this basis, but I=E2=80=99m =0Aal= so sure that in the last 40 years something better must have appeared. This= =0Aprobably includes SDD, def2 and cc-pVnZ (although the last two are way = heavier).=0A=0A5) Accuracy of a basis set depends heavily on the method. An= d, as was pointed =0Aout before, DFT is less sensitive. In my short experie= nce, choosing the right =0Amethod (or functional) may be more important, as= long as the basis set is good =0Aenough for that method (for instance don= =E2=80=99t use a double zeta basis for couple =0Acluster).=0A=0A =0APlease = someone with more knowledge/experience correct me or comment on this. =0ATh= is issue is important for too many people on CCL.=0A =0ABest,=0A xxxxxxxxxx= xxxxxxxxxxxxxxxxxxxxxxxxxxx=0A..........Sebastian Kozuch...........=0Axxxxx= xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx=0A....Weizmann Institute of Science....=0A= ...........Rehovot, Israel...........=0A.. sebastian.kozuch!A!weizmann.ac.il = ..=0Ahttp://yfaat.ch.huji.ac.il/kozuch.htm=0Axxxxxxxxxxxxxxxxxxxxxxxxxxxxxx= xxxxxxx=0A=0A=0A=0A=0A________________________________=0AFrom: Gerald Knizi= a knizia * theochem.uni-stuttgart.de =0ATo: "Kozuc= h, Sebastian " =0ASent: Tue, May 17, 2011 9:08:5= 9 PM=0ASubject: CCL:G: basis sets=0A=0A=0ASent to CCL by: Gerald Knizia [kn= izia{}theochem.uni-stuttgart.de]=0APierre Archirel pierre.archirel#u-psud.f= r wrote:=0A> Sent to CCL by: "Pierre Archirel" [pierre.archirel**u-psud.fr= ]=0A> This is a comment on a recent question about basis sets:=0A> 1- one c= olleague is looking for the best basis set for a CNOH molecule=0A> 2- sever= al colleagues state that 6-31g(d) works rather well and is largely =0Aused= =0A> 3- I state that SDD (Stuttgart-Dresden) bases are smaller and more acc= urate =0A>than any Pople basis, and that I have published a comparison of t= he bases in the =0A>conformation analysis of a CNOH molecule (Tetrahedron 6= 4 (2008) 1743)=0A> I acknowledge that this comparison is for one molecule o= nly, not a list.=0A> 4- the first colleagues thanks for advices and will ch= oose 6-31g(d) bases.=0A> =0A=0AWell, first: Basis set issues are complicat= ed, and data on only one molecule =0Adoes not say very much at all. When de= veloping basis sets, you will often find =0Athat a set works well for 19 di= verse molecules and then gives large errors for =0Athe 20th. This is not to= say that the SSD sets are bad; the people who made them =0Aknow what they = are doing. Just a general comment on the comparison you cite.=0A=0AApart fr= om that, there are other basis sets which are known to be superior to =0Ath= e Pople sets. E.g., Weigends def2 sets (the Turbomole sets) are superior on= =0Aall accounts, especially for SCF calculations. And they even come with = auxiliary =0Afitting sets for all elements. The cc-pVnZ families are certai= nly better for =0Acorrelated calculations than Pople sets and allow for app= roaching basis set =0Alimits systematically and closely. While I can unders= tand why the cc-sets are =0Anot often used in Gaussian calculations (they a= re not optimal for SCF, and a =0Aprogram which can't deal well with general= contractions certainly doesn't like =0Acc-sets), I do wonder why people do= n't simply stop using Pople sets and use def2 =0Asets instead. I hope the m= ain reason is that for DFT calculations the basis sets =0Areally don't matt= er that much, and you're more or less fine with the Pople sets, =0Atoo. Of = course this kind of defeats the point of asking about basis sets in the =0A= first place.=0A-- Gerald Knizia=0A=0A=0A=0A-=3D This is automatically added= to each message by the mailing script =3D-=0ATo recover the email address = of the author of the message, please change=0Athe strange characters on the= top line to the !A! sign. You can also=0Alook up the X-Original-From: line i= n the mail header.=0A=0A=0A==0A=0AE-mail to administ= rators: CHEMISTRY-REQUEST!A!ccl.net or use=0A http://www.ccl.net/cgi-bin/c= cl/send_ccl_message=0A=0Ahttp://www.ccl.net/che= mistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http://www.= ccl.net=0A=0AConferences: =0Ahttp://server.ccl= .net/chemistry/announcements/conferences/=0A=0ASearch Messages: http://www.= ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from CCL = with 5.7.1 error, check:=0A=0A=0ARTFI: h= ttp://www.ccl.net/chemistry/aboutccl/instructions/ --0-1860551574-1305718477=:57291 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
=0A=0A

Regarding all this debate on small bas= is sets, I also have=0Asome doubts and comments.
=0A
=0A1) SDD should= be faster than 6-31g, having an ECP. But some programs can take=0Aadvantag= e of the fact that 6-31g has shared exponents for S and P functions. In=0At= his case, Pople's is faster than Stuttgart's.
=0A
=0A2) For the same = as before (shared exponentials) plus other reasons, 6-31g can=0Abe less acc= urate. But someone told me that large ECP, as SDD has, is not the=0Abest ch= oice (of course small ECP for carbon means an all electron basis set). Does= =0Asomeone know if this small/large basis set issue is a general rule, a ru= le for=0Atransition metals, or not an accurate rule at all?

=0A=0A


3) For the 6-31g family, it= can be found everywhere=0Adispersion and polarization functions. For the S= DD it=E2=80=99s not that simple. This=0Ais a point for Pople=E2=80=99s.

= =0A=0A


4) 6-31g is cer= tainly an old basis set, optimized for the=0Aalmost obsolete HF method. I= =E2=80=99m sure that this is not a reason to disqualify=0Athis basis, but I= =E2=80=99m also sure that in the last 40 years something better must=0Ahave= appeared. This probably includes SDD, def2 and cc-pVnZ (although the last= =0Atwo are way heavier).

=0A=0A


5) Accuracy of a basis set depends heavily on the method.=0A= And, as was pointed out before, DFT is less sensitive. In my short experien= ce,=0Achoosing the right method (or functional) may be more important, as l= ong as the=0Abasis set is good enough for that method (for instance don=E2= =80=99t use a double zeta=0Abasis for couple cluster).

=0A=0A


 

=0A=0A

Please someone with more knowledge/experience correct me or=0Acommen= t on this. This issue is important for too many people on CCL.

=0A=0A

 

=0A=0A

Best,

=0A=0A<= div> 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........<= /span>
xxxxxxxxxx= xxxxxxxxxxxxxxxxxxxxxxxxxxx
....Weizmann Institute of Science....
...........Rehovot, Israel...= ........
.. sebastian= .kozuch!A!weizmann.ac.il ..
http://yfaat.ch.huji.ac.il/kozuch.htm<= br style=3D"font-family:courier, monaco, monospace, sans-serif;">xxxxxxxxxxxxxxxxx= xxxxxxxxxxxxxxxxxxxx


From: Gerald Kn= izia knizia * theochem.uni-stuttgart.de <owner-chemistry!A!ccl.net>
= To: "Kozuch, Sebastian -id= #3qn-" <kozuchs!A!yahoo.com>
Sent: Tue, May 17, 2011 9:08:59 PM
Subject: CCL:G: basis sets


Sent to CCL by= : Gerald Knizia [knizia{}theochem.uni-stuttgart.de]
Pierre Archirel pier= re.archirel#u-psud.fr wrote:
> Sent to CCL by: "Pierre  Archirel= " [pierre.archirel**u-psud.fr]
> This is a comment on a recent questi= on about basis sets:
> 1- one colleague is looking for the best basis= set for a CNOH molecule
> 2- several colleagues state that 6-31g(d) = works rather well and is largely used
> 3- I state that SDD (Stuttgar= t-Dresden) bases are smaller and more accurate than any Pople basis, and th= at I have published a comparison of the bases in the conformation analysis = of a CNOH molecule (Tetrahedron 64 (2008) 1743)
> I acknowledge that = this comparison is for one molecule only, not a list.
> 4- the first colleagues thanks for advices and will choose 6-31g(d) bases.
>= ; 

Well, first: Basis set issues are complicated, and data on= only one molecule does not say very much at all. When developing basis set= s, you will often find that a set works well for 19 diverse molecules and t= hen gives large errors for the 20th. This is not to say that the SSD sets a= re bad; the people who made them know what they are doing. Just a general c= omment on the comparison you cite.

Apart from that, there are other = basis sets which are known to be superior to the Pople sets. E.g., Weigends= def2 sets (the Turbomole sets) are superior on all accounts, especially fo= r SCF calculations. And they even come with auxiliary fitting sets for all = elements. The cc-pVnZ families are certainly better for correlated calculat= ions than Pople sets and allow for approaching basis set limits systematica= lly and closely. While I can understand why the cc-sets are not often used in Gaussian calculations (they are not optimal for SCF, and a p= rogram which can't deal well with general contractions certainly doesn't li= ke cc-sets), I do wonder why people don't simply stop using Pople sets and = use def2 sets instead. I hope the main reason is that for DFT calculations = the basis sets really don't matter that much, and you're more or less fine = with the Pople sets, too. Of course this kind of defeats the point of askin= g about basis sets in the first place.
-- Gerald Knizia



-= =3D This is automatically added to each message by the mailing script =3D-<= br= l= ook up the X-Original-From: line in the mail header.

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=0A=0A= =0A=0A --0-1860551574-1305718477=:57291-- From owner-chemistry@ccl.net Wed May 18 09:17:01 2011 From: "Chris Swain swain..mac.com" To: CCL Subject: CCL: Interactive plots Message-Id: <-44689-110518082950-14034-WI5AIzLbD0N3mGXveWPlkg(_)server.ccl.net> X-Original-From: Chris Swain Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=windows-1252 Date: Wed, 18 May 2011 13:29:17 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain%x%mac.com] Dear All, Apologies if this is a little off topic but I thought it might be of interest to some readers. I have a regular need to share results from my work and historically this has been via a paper reports that have more recently been replaced by electronic versions. Whilst useful, these reports lack the interactivity, in particular it is extremely useful to be able to easily link data points on a scatter plot with the corresponding chemical structure. So I’ve started using web-based reports to add extra functionality. Unfortunately it has often required the addition of applets or plugins that I can’t be sure the viewer will have available so with the advent of HTML5 I’ve been exploring writing the reports using just HTML and javascript. One of the major challenges is to produce interactive plots instead of using static images, (I did try image maps but generating them is really tedious), so I’ve been exploring the use of Flot to produce a plot with chemical structures produced using either a web-service like Chemspider or a javascript library of web components developed by ChemDoodle. You can read more from here http://homepage.mac.com/swain/Macinchem/page5/files/0b6bb2f60d2783f5f06af88d1df9f887-737.html Cheers, Chris From owner-chemistry@ccl.net Wed May 18 09:52:00 2011 From: "Andras Borosy andras.borosy^^^givaudan.com" To: CCL Subject: CCL: Chemoinformatics Message-Id: <-44690-110518030518-10094-CrBb7T2Hj1q2gv+hhBcqgg:server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 0026E7A3C1257894_=" Date: Wed, 18 May 2011 09:05:04 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy**givaudan.com] This is a multipart message in MIME format. --=_alternative 0026E7A3C1257894_= Content-Type: text/plain; charset="US-ASCII" Dear Mr. Marcou, Might you publish a salary and/or employment survey of your chemoinf graduates? Many thanks, Andras Borosy "Gilles MARCOU g.marcou.:.unistra.fr" Sent by: owner-chemistry+andras.borosy==givaudan.com]~[ccl.net 17.05.2011 20:45 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: Chemoinformatics Sent to CCL by: "Gilles MARCOU" [g.marcou*o*unistra.fr] Dear all, Chemoinformatics is young discipline with a curiculum organized around molecular descriptors, chemical space and data mining. It is different > from Molecular Modeling and Quantum Chemistry although it boroughs from these disciplines. It is different also from Bioinformatics although it has proven its usefullness mostly in the area of drug design. The University of Strasbourg in France, is organizing since 2000, a master level diploma in chemoinformatics. You can find a complete description of this master on its web site ( http://infochimie.u-strasbg.fr/master/master_home.htm). Beside, we organize also a 5 days short courses "Introduction to chemoinformatics ( http://infochim.u-strasbg.fr/spip.php?rubrique123). This could also be seen as a an example of Chemoinformatics curriculum. Furthermore, we organize every two year a summer school in chemoinformatics, the last session being in 2010 (http://infochim.u-strasbg.fr/spip.php?rubrique12) and the next session will be in June 2012. Finaly, there exists a French Society of Chemoinformatics (http://www.chemoinformatique.fr/) which is close to the Internation Chemoinformatics and QSAR Society ( http://www.chemoinformatique.fr/modules/weblinks/visit.php?lid=5). I hope those links will be helpful to clarify the picture of Chemoinformatics today. Yours Faithfully, Gilles Marcouhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 0026E7A3C1257894_= Content-Type: text/html; charset="US-ASCII"
Dear Mr. Marcou,

Might you publish a salary and/or employment survey of your chemoinf graduates?

Many thanks,

Andras Borosy



"Gilles MARCOU g.marcou.:.unistra.fr" <owner-chemistry]~[ccl.net>
Sent by: owner-chemistry+andras.borosy==givaudan.com]~[ccl.net

17.05.2011 20:45
Please respond to
"CCL Subscribers" <chemistry]~[ccl.net>
To
"Borosy, Andras " <andras.borosy]~[givaudan.com>
cc
Subject
CCL: Chemoinformatics






Sent to CCL by: "Gilles  MARCOU" [g.marcou*o*unistra.fr]
Dear all,

Chemoinformatics is young discipline with a curiculum organized around molecular descriptors, chemical space and data mining. It is different > from Molecular Modeling and Quantum Chemistry although it boroughs from these disciplines. It is different also from Bioinformatics although it has proven its usefullness mostly in the area of drug design.

The University of Strasbourg in France, is organizing since 2000, a master level diploma in chemoinformatics. You can find a complete description of this master on its web site (http://infochimie.u-strasbg.fr/master/master_home.htm). Beside, we organize also a 5 days short courses "Introduction to chemoinformatics (http://infochim.u-strasbg.fr/spip.php?rubrique123). This could also be seen as a an example of Chemoinformatics curriculum.

Furthermore, we organize every two year a summer school in chemoinformatics, the last session being in 2010
(http://infochim.u-strasbg.fr/spip.php?rubrique12) and the next session will be in June 2012. Finaly, there exists a French Society of Chemoinformatics (http://www.chemoinformatique.fr/) which is close to the Internation Chemoinformatics and QSAR Society (http://www.chemoinformatique.fr/modules/weblinks/visit.php?lid=5).

I hope those links will be helpful to clarify the picture of Chemoinformatics today.

Yours Faithfully,
Gilles Marcou


     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
     http://www.ccl.net/chemistry/sub_unsub.shtml
     http://www.ccl.net/spammers.txt
--=_alternative 0026E7A3C1257894_=-- From owner-chemistry@ccl.net Wed May 18 10:28:01 2011 From: "Ksenia Romanova ksenia248- -gmail.com" To: CCL Subject: CCL:G: INDO/S-CI Message-Id: <-44691-110518081539-427-3Bgv28Vz/0h018aNY8dyaA]~[server.ccl.net> X-Original-From: "Ksenia Romanova" Date: Wed, 18 May 2011 08:15:37 -0400 Sent to CCL by: "Ksenia Romanova" [ksenia248%%gmail.com] I would like to calculate singlets and triplets levels of the ligands for the lanthanide complexes. I know that it could be done by the INDO/S-CI model implemented in the ZINDO program by replacing the lanthanide ion by a point charge. But it is hard to find this program, can anyone recommend me how to get this program? ZINDO method is also implemented in HyperChem and, in part, in GAUSSIAN, but they can not handle with lanthanides. How can I cope with my task? Any suggestions on any programs and methods will be appreciated. From owner-chemistry@ccl.net Wed May 18 11:02:01 2011 From: "Marcel Swart marcel.swart=-=icrea.cat" To: CCL Subject: CCL:G: basis sets Message-Id: <-44692-110518091113-8646-kRyqbnSY3xwllk9zW4ndpQ^^^server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-5-999590858 Date: Wed, 18 May 2011 15:11:45 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Marcel Swart [marcel.swart..icrea.cat] --Apple-Mail-5-999590858 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Dear Sebastian, for spin-states of transition-metals it is indeed clear that ECPs do not = give the same answer as GTO or STO basis sets, and is thus not accurate. At the same time, I = must stress also that geometries and reactivities may be less affected. See e.g. M. G=FCell, J.M. Luis, M. Sol=E0 and M. Swart "Importance of the basis set for the spin-state energetics of iron = complexes" J. Phys. Chem. A 2008, 112, 6384-6391 Note also that the 6-31G* basis can be adjusted quite easily for better = performance for spin-states (to give the s6-31G* basis sets): M. Swart, M. G=FCell, J.M. Luis and M. Sol=E0 "Spin-state corrected Gaussian-type orbital basis sets" J. Phys. Chem. A 2010, 114, 7191-7197 Marcel On 18 May 2011, at 13:34, Sebastian Kozuch kozuchs*yahoo.com wrote: > Regarding all this debate on small basis sets, I also have some doubts = and comments. >=20 > 1) SDD should be faster than 6-31g, having an ECP. But some programs = can take advantage of the fact that 6-31g has shared exponents for S and = P functions. In this case, Pople's is faster than Stuttgart's. >=20 > 2) For the same as before (shared exponentials) plus other reasons, = 6-31g can be less accurate. But someone told me that large ECP, as SDD = has, is not the best choice (of course small ECP for carbon means an all = electron basis set). Does someone know if this small/large basis set = issue is a general rule, a rule for transition metals, or not an = accurate rule at all? >=20 > 3) For the 6-31g family, it can be found everywhere dispersion and = polarization functions. For the SDD it=92s not that simple. This is a = point for Pople=92s. >=20 > 4) 6-31g is certainly an old basis set, optimized for the almost = obsolete HF method. I=92m sure that this is not a reason to disqualify = this basis, but I=92m also sure that in the last 40 years something = better must have appeared. This probably includes SDD, def2 and cc-pVnZ = (although the last two are way heavier). >=20 > 5) Accuracy of a basis set depends heavily on the method. And, as was = pointed out before, DFT is less sensitive. In my short experience, = choosing the right method (or functional) may be more important, as long = as the basis set is good enough for that method (for instance don=92t = use a double zeta basis for couple cluster). >=20 > Please someone with more knowledge/experience correct me or comment on = this. This issue is important for too many people on CCL. >=20 > Best, >=20 > Sebastian Kozuch =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 dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Facultat de Ci=E8ncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart:icrea.cat marcel.swart:udg.edu web http://www.marcelswart.eu =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 --Apple-Mail-5-999590858 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252 Dear = Sebastian,

for spin-states of transition-metals it is = indeed clear that ECPs do not give the same answer
as GTO or = STO basis sets, and is thus not accurate. At the same time, I must = stress also that
geometries and reactivities may be less = affected.

See e.g.

M. = G=FCell, J.M. Luis, M. Sol=E0 and M. Swart
"Importance of the basis = set for the spin-state energetics of iron complexes"
J. Phys. Chem. = A 2008, 112, 6384-6391

Note also that = the 6-31G* basis can be adjusted quite easily for better = performance
for spin-states (to give the s6-31G* basis = sets):

M. Swart, M. G=FCell, J.M. Luis and M. = Sol=E0
"Spin-state corrected Gaussian-type orbital basis sets"
J. = Phys. Chem. A 2010, 114, = 7191-7197

Marcel

On 18 May 2011, at 13:34, Sebastian Kozuch kozuchs*yahoo.com = wrote:

Regarding all this debate on = small basis sets, I also have some doubts and comments.

1) SDD = should be faster than 6-31g, having an ECP. But some programs can take = advantage of the fact that 6-31g has shared exponents for S and P = functions. In this case, Pople's is faster than Stuttgart's.

2) = For the same as before (shared exponentials) plus other reasons, 6-31g = can be less accurate. But someone told me that large ECP, as SDD has, is = not the best choice (of course small ECP for carbon means an all = electron basis set). Does someone know if this small/large basis set = issue is a general rule, a rule for transition metals, or not an = accurate rule at all?

3) For the 6-31g = family, it can be found everywhere dispersion and polarization = functions. For the SDD it=92s not that simple. This is a point for = Pople=92s.

4) 6-31g is certainly an old = basis set, optimized for the almost obsolete HF method. I=92m sure that = this is not a reason to disqualify this basis, but I=92m also sure that = in the last 40 years something better must have appeared. This probably = includes SDD, def2 and cc-pVnZ (although the last two are way = heavier).

5) Accuracy of a basis set = depends heavily on the method. And, as was pointed out before, DFT is = less sensitive. In my short experience, choosing the right method (or = functional) may be more important, as long as the basis set is good = enough for that method (for instance don=92t use a double zeta basis for = couple cluster).

Please someone with more = knowledge/experience correct me or comment on this. This issue is = important for too many people on CCL.

 


=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

Institut de Qu=EDmica = Computacional
Universitat de Girona

Facultat de Ci=E8ncies
Campus = Montilivi
17071 Girona
Catalunya = (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mailmarcel.swart:udg.edu




= --Apple-Mail-5-999590858-- From owner-chemistry@ccl.net Wed May 18 11:47:00 2011 From: "Jim Kress ccl_nospam|a|kressworks.com" To: CCL Subject: CCL: iPhone & iPad 3D Molecule Browser - iMolview Message-Id: <-44693-110518110318-4391-9kIutPp3Myu4rg5PXvBREw{:}server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 18 May 2011 11:02:48 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam{=}kressworks.com] Is this going to be done for the Android OS, too? Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com#ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com#ccl.net] On Behalf Of Andrew Orry > andy-*-molsoft.com > Sent: Tuesday, May 17, 2011 9:29 PM > To: Kress, Jim > Subject: CCL: iPhone & iPad 3D Molecule Browser - iMolview > > > Sent to CCL by: Andrew Orry [andy]![molsoft.com] > On 5/7/2011 2:43 AM, Arne Dieckmann adieckma-$-googlemail.com wrote: > > Sent to CCL by: Arne Dieckmann [adieckma],[googlemail.com] > > Dear Andrew, > > > > how about loading in your own pdb files? I'd buy it if that will be > possible. > > > The latest version of iMolview (v1.2) is now synced with iTunes so you > can load in your own PDB files from there. We also fixed a graphics > issue with older iPhone/iPod devices and introduced a number of other > features and improvements. Please see the app page for the full release > notes:http://www.molsoft.com/iMolview.html > Thanks, > Andrew > > -- > Andrew Orry Ph.D. > MolSoft LLC > Senior Research Scientist > 11199 Sorrento Valley Road, S209 > San Diego > CA 92121 > Tel: 858-625-2000 x108 > Fax: 828-625-2888 > www.molsoft.com> To recover the email address of the author of the message, please > change> From owner-chemistry@ccl.net Wed May 18 12:28:00 2011 From: "Gustavo Laureano Coelho de Moura gustavo.moura . ufpe.br" To: CCL Subject: CCL:G: INDO/S-CI Message-Id: <-44694-110518122531-14159-qYPvde3Cql8hH/nWrZi9Rg^^server.ccl.net> X-Original-From: Gustavo Laureano Coelho de Moura Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8 Date: Wed, 18 May 2011 13:24:15 -0300 (BRT) MIME-Version: 1.0 Sent to CCL by: Gustavo Laureano Coelho de Moura [gustavo.moura ~ ufpe.br] Dear Ksenia, the free program ORCA can perform the type of calculation you want. Please refer to the page http://sparkle.pro.br/tutorial/uv-vis for an explanation on how to to calculate the UV/vis spectra of lanthanide complexes using INDO/S-CI in ORCA. Please bear in mind that ORCA calculates the transition dipole moments using an approach that is different from the one employed by ZINDO. Sincerely yours, Gustavo L.C. Moura ----- Mensagem original ----- De: "Ksenia Romanova ksenia248- -gmail.com" Para: "Gustavo L.C. Moura" Enviadas: Quarta-feira, 18 de Maio de 2011 9:15:37 Assunto: CCL:G: INDO/S-CI Sent to CCL by: "Ksenia Romanova" [ksenia248%%gmail.com] I would like to calculate singlets and triplets levels of the ligands for the lanthanide complexes. I know that it could be done by the INDO/S-CI model implemented in the ZINDO program by replacing the lanthanide ion by a point charge. But it is hard to find this program, can anyone recommend me how to get this program? ZINDO method is also implemented in HyperChem and, in part, in GAUSSIAN, but they can not handle with lanthanides. How can I cope with my task? Any suggestions on any programs and methods will be appreciated.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed May 18 13:03:00 2011 From: "Angela Bruneau amb458 * cornell.edu" To: CCL Subject: CCL:G: MP2 sp energy corrections to lower-level theory calcs Message-Id: <-44695-110517141116-6868-tU4U4YUR734TGvaTKHH6Ng_-_server.ccl.net> X-Original-From: "Angela Bruneau" Date: Tue, 17 May 2011 14:11:13 -0400 Sent to CCL by: "Angela Bruneau" [amb458[*]cornell.edu] Good afternoon, I am asked to do MP2 energy corrections on ground and transition structures that have been optimized at the B3LYP level and their frequencies calculated. I have read a ton of documents, and am still unclear as to exactly how to combine these numbers to maximize accuracy. In the optimization at B3LYP level, the energies reported are: E(B3LYP) = -1207.39398963 Zero-point correction= 0.532390 (Hartree/Particle) Thermal correction to Energy= 0.553276 Thermal correction to Enthalpy= 0.553951 Thermal correction to Gibbs Free Energy= 0.487806 Sum of electronic and zero-point Energies= -1206.861599 Sum of electronic and thermal Energies= -1206.840714 Sum of electronic and thermal Enthalpies= -1206.840039 Sum of electronic and thermal Free Energies= -1206.906184 Does E(B3LYP) already contain thermal and zero point corrections? In the optimization at the MP2 level for a single point frozen core, the energies are: E(RHF) = -1199.89828488 E2 = -0.3530251644D+01 EUMP2 = -0.12034285365186D+04 MP2= -1203.4285365 So, how do I extract the vibrational/translational/rotational energy that I calculated at the B3LYP level, and combine that with the electronic energy calculated at the RHF level with MP2 correlation correction? This is the best document Ive come across: http://www.gaussian.com/g_whitepap/thermo.htm But I still have the questions posed above. Thanks for any help. From owner-chemistry@ccl.net Wed May 18 13:38:01 2011 From: "Kirk Peterson kipeters^wsu.edu" To: CCL Subject: CCL:G: basis sets Message-Id: <-44696-110518122621-14883-JSfeA78kOgd9k7u4iZ8KCA-#-server.ccl.net> X-Original-From: Kirk Peterson Content-Type: multipart/alternative; boundary=Apple-Mail-25-1011247218 Date: Wed, 18 May 2011 09:26:01 -0700 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Kirk Peterson [kipeters|a|wsu.edu] --Apple-Mail-25-1011247218 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Dear Marcel, It would be prudent to probably not make such sweeping statements about = the accuracy of ECP-based results based solely on your previous small = basis set calculations. Were these previous results due to the basis set = or the ECP? It is not possible to tell without expanding the basis set = with the ECP. Certainly a modern small-core ECP with a quality basis set = (sorry, for example the cc-pVnZ-PP family of sets) is perfectly capable = of reproducing some of the best relativistic all-electron calculations, = including the spin-states of transition metals. -Kirk On May 18, 2011, at 6:11 AM, Marcel Swart marcel.swart=3D-=3Dicrea.cat = wrote: > Dear Sebastian, >=20 > for spin-states of transition-metals it is indeed clear that ECPs do = not give the same answer > as GTO or STO basis sets, and is thus not accurate. At the same time, = I must stress also that > geometries and reactivities may be less affected. >=20 > See e.g. >=20 > M. G=FCell, J.M. Luis, M. Sol=E0 and M. Swart > "Importance of the basis set for the spin-state energetics of iron = complexes" > J. Phys. Chem. A 2008, 112, 6384-6391 >=20 > Note also that the 6-31G* basis can be adjusted quite easily for = better performance > for spin-states (to give the s6-31G* basis sets): >=20 > M. Swart, M. G=FCell, J.M. Luis and M. Sol=E0 > "Spin-state corrected Gaussian-type orbital basis sets" > J. Phys. Chem. A 2010, 114, 7191-7197 >=20 > Marcel >=20 > On 18 May 2011, at 13:34, Sebastian Kozuch kozuchs*yahoo.com wrote: >=20 >> Regarding all this debate on small basis sets, I also have some = doubts and comments. >>=20 >> 1) SDD should be faster than 6-31g, having an ECP. But some programs = can take advantage of the fact that 6-31g has shared exponents for S and = P functions. In this case, Pople's is faster than Stuttgart's. >>=20 >> 2) For the same as before (shared exponentials) plus other reasons, = 6-31g can be less accurate. But someone told me that large ECP, as SDD = has, is not the best choice (of course small ECP for carbon means an all = electron basis set). Does someone know if this small/large basis set = issue is a general rule, a rule for transition metals, or not an = accurate rule at all? >>=20 >> 3) For the 6-31g family, it can be found everywhere dispersion and = polarization functions. For the SDD it=92s not that simple. This is a = point for Pople=92s. >>=20 >> 4) 6-31g is certainly an old basis set, optimized for the almost = obsolete HF method. I=92m sure that this is not a reason to disqualify = this basis, but I=92m also sure that in the last 40 years something = better must have appeared. This probably includes SDD, def2 and cc-pVnZ = (although the last two are way heavier). >>=20 >> 5) Accuracy of a basis set depends heavily on the method. And, as was = pointed out before, DFT is less sensitive. In my short experience, = choosing the right method (or functional) may be more important, as long = as the basis set is good enough for that method (for instance don=92t = use a double zeta basis for couple cluster). >>=20 >> Please someone with more knowledge/experience correct me or comment = on this. This issue is important for too many people on CCL. >>=20 >> Best, >>=20 >> Sebastian Kozuch >=20 >=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 > dr. Marcel Swart >=20 > ICREA Research Professor at > Institut de Qu=EDmica Computacional > Universitat de Girona >=20 > Facultat de Ci=E8ncies > Campus Montilivi > 17071 Girona > Catalunya (Spain) >=20 > tel > +34-972-418861 > fax > +34-972-418356 > e-mail > marcel.swart]=3D[icrea.cat > marcel.swart]=3D[udg.edu > web > http://www.marcelswart.eu > =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 >=20 >=20 >=20 >=20 >=20 --Apple-Mail-25-1011247218 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252 Dear = Marcel,

It would be prudent to probably not make such = sweeping statements about the accuracy of ECP-based results based solely = on your previous small basis set calculations. Were these previous = results due to the basis set or the ECP? It is not possible to tell = without expanding the basis set with the ECP. Certainly a modern = small-core ECP with a quality basis set (sorry, for example the = cc-pVnZ-PP family of sets)  is perfectly capable of reproducing = some of the best relativistic all-electron calculations, including the = spin-states of transition = metals.

-Kirk


=
On May 18, 2011, at 6:11 AM, Marcel Swart = marcel.swart=3D-=3Dicrea.cat wrote:

Dear = Sebastian,

for spin-states of transition-metals it is = indeed clear that ECPs do not give the same answer
as GTO or = STO basis sets, and is thus not accurate. At the same time, I must = stress also that
geometries and reactivities may be less = affected.

See e.g.

M. = G=FCell, J.M. Luis, M. Sol=E0 and M. Swart
"Importance of the basis = set for the spin-state energetics of iron complexes"
J. Phys. Chem. = A 2008, 112, 6384-6391

Note also that = the 6-31G* basis can be adjusted quite easily for better = performance
for spin-states (to give the s6-31G* basis = sets):

M. Swart, M. G=FCell, J.M. Luis and M. = Sol=E0
"Spin-state corrected Gaussian-type orbital basis sets"
J. = Phys. Chem. A 2010, 114, = 7191-7197

Marcel

On 18 May 2011, at 13:34, Sebastian Kozuch kozuchs*yahoo.com = wrote:

Regarding all this debate on = small basis sets, I also have some doubts and comments.

1) SDD = should be faster than 6-31g, having an ECP. But some programs can take = advantage of the fact that 6-31g has shared exponents for S and P = functions. In this case, Pople's is faster than Stuttgart's.

2) = For the same as before (shared exponentials) plus other reasons, 6-31g = can be less accurate. But someone told me that large ECP, as SDD has, is = not the best choice (of course small ECP for carbon means an all = electron basis set). Does someone know if this small/large basis set = issue is a general rule, a rule for transition metals, or not an = accurate rule at all?

3) For the 6-31g = family, it can be found everywhere dispersion and polarization = functions. For the SDD it=92s not that simple. This is a point for = Pople=92s.

4) 6-31g is certainly an old = basis set, optimized for the almost obsolete HF method. I=92m sure that = this is not a reason to disqualify this basis, but I=92m also sure that = in the last 40 years something better must have appeared. This probably = includes SDD, def2 and cc-pVnZ (although the last two are way = heavier).

5) Accuracy of a basis set = depends heavily on the method. And, as was pointed out before, DFT is = less sensitive. In my short experience, choosing the right method (or = functional) may be more important, as long as the basis set is good = enough for that method (for instance don=92t use a double zeta basis for = couple cluster).

Please someone with more = knowledge/experience correct me or comment on this. This issue is = important for too many people on CCL.

 


=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

Institut de Qu=EDmica = Computacional
Universitat de Girona

Facultat de Ci=E8ncies
Campus = Montilivi
17071 Girona
Catalunya = (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mail



= --Apple-Mail-25-1011247218-- From owner-chemistry@ccl.net Wed May 18 14:13:01 2011 From: "Jing Kong jkong:-:q-chem.com" To: CCL Subject: CCL: Workshop on Electronic Structure Calculations preceding WATOC 2011 Message-Id: <-44697-110518121240-17727-Ci8DjKVIDYduKQerNn+ZkA::server.ccl.net> X-Original-From: "Jing Kong" Content-Language: en-us Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 18 May 2011 12:12:25 -0400 MIME-Version: 1.0 Sent to CCL by: "Jing Kong" [jkong__q-chem.com] Dear colleague: Q-Chem would like to invite you to a workshop of quantum chemistry in Santiago de Compostela, Spain in the afternoon of Saturday, July 16, 2011.  It is the day before WATOC 2011 starts. The workshop will highlight some of the features in the new Q-Chem 4.0 software package.  Q-Chem 4.0 contains significant new functionality, including: * TD-DFT analytic gradient and Hessian for excited-state structure optimization;; * IRC searches for mapping complicated potential energy surfaces; * Range-separated and dispersion-corrected DFT functionals; * Faster algorithms for DFT, HF and coupled-cluster calculations; * More choices for excited-state, solvation and charge-transfer calculations; * Effective Fragment Potential and QM/MM for treating large systems; * Maximum Overlap Method for excited-state calculations of large systems; * Intracules for analysis of two-electron properties; * Shared-memory for multicore systems and implementations for GPUs; as well as many other areas. The workshop will consist of seminars and a demonstration of Q-Chem 4.0. Seminar speakers include Christian Ochsenfeld (Uni Muenchen), David Casanova (Uni Barcelona), Martin Head-Gordon (Uni California, Berkeley), Peter Gill (Australian National Uni) and Anna Krylov (Uni Southern California). The meeting will take place at the site of WATOC. The registration fee is $25 and covers coffee, tea and soft drinks. All workshop participants will receive a free six-month license for unlimited use of Q-Chem 4.0. Please register by June 16 on our website (www.q-chem.com/wsspa_regist.html). Happy Computing, Jing Kong, PhD CEO and Chief Scientist Q-Chem, Inc. From owner-chemistry@ccl.net Wed May 18 14:48:00 2011 From: "Gilles Frapper gilles.frapper!^!univ-poitiers.fr" To: CCL Subject: CCL: Evolutionary structure prediction (USPEX) + periodic DFT for beginners in France (june 2011) Message-Id: <-44698-110518112144-24701-rBOA9gHi1Cm6lbpm2wlSjQ[-]server.ccl.net> X-Original-From: Gilles Frapper Content-Type: multipart/alternative; boundary="------------050108060709000109000802" Date: Wed, 18 May 2011 17:20:25 +0200 MIME-Version: 1.0 Sent to CCL by: Gilles Frapper [gilles.frapper.:.univ-poitiers.fr] This is a multi-part message in MIME format. --------------050108060709000109000802 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit /DN-NSM 2011 : * //Periodic DFT //for beginners/ summer school (and others ;-) ): 23-25 june, Poitiers (France) /* USPEX/ workshop: 26-30 june, Poitiers (France) Dear CCL's A few places are still available in DN-NSM 2011 workshop! Deadline registration: 1 june. Prof. Artem R. Oganov and myself are organizing workshop on " /*D*iscovery of *N*ovel Nanoparticles, *S*urfaces and *B*ulk *M*aterials: evolutionary structure prediction using the *USPEX* code /", coupled with a 3-days tutorial on DFT for new users called "/periodic DFT for beginners/" using Quantum Expresso or VASP codes. The workshop will take place in June 2011 in France (Poitiers). Please see the website of the workshop at: http://dnnsm2011.conference.univ-poitiers.fr/ Special fees for PhD students: *420 EUR /8 days* workshop (23 - 30 june), including housing/meals, so-called "french cuisine" ;-) /social events: winery + Fontevraud abbey+ "bords de Loire"/ tuition. See here This workshop should be extremely useful for all new users of the USPEX code and researchers looking at novels materials, please see website for details. We have planned an excellent scientific program, there will be opportunities to meet the best experts on this topic and start collaborations. Up to now, 49 participants registered from 21 different countries. *A bientôt !* Gilles Frapper, local organisor Groupe Chimie Théorique LACCO UMR 6503 CNRS - Université de Poitiers 40 av.recteur Pineau 86022 Poitiers Cedex tél : +33 (0)5 49 45 35 74 - 06.48.13.24.13 (mobile) http://yargla.labo.univ-poitiers.fr /gilles.frapper{=}univ-poitiers.fr --------------050108060709000109000802 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit DN-NSM 2011 :
* Periodic DFT for beginners summer school  (and others ;-) ): 23-25 june, Poitiers (France)
* USPEX workshop: 26-30 june, Poitiers (France)


Dear CCL's

A few places are still available in DN-NSM 2011 workshop! Deadline registration: 1 june.

Prof. Artem R. Oganov  and myself are organizing workshop on " Discovery of Novel Nanoparticles, Surfaces and Bulk Materials: evolutionary structure prediction using the USPEX code", coupled with a 3-days tutorial on DFT for new users called "periodic DFT for beginners" using Quantum Expresso or VASP codes.

The workshop will take place in June 2011 in France (Poitiers). Please see the website of the workshop at: http://dnnsm2011.conference.univ-poitiers.fr/

Special fees for PhD students: 420 € /8 days workshop (23 - 30 june), including  housing/meals, so-called "french cuisine" ;-) /social events: winery + Fontevraud abbey+ "bords de Loire"/ tuition. See here

This workshop should be extremely useful for all new users of the USPEX code and researchers looking at novels materials, please see website for details. We have planned an excellent scientific program, there will be opportunities to meet the best experts on this topic and start collaborations.
Up to now, 49 participants registered from 21 different countries.

A bientôt !
 
Gilles Frapper, local organisor
Groupe Chimie Théorique
LACCO UMR 6503 CNRS - Université de Poitiers
40 av.recteur Pineau 86022 Poitiers Cedex
tél : +33 (0)5 49 45 35 74 - 06.48.13.24.13 (mobile) 
http://yargla.labo.univ-poitiers.fr / gilles.frapper{=}univ-poitiers.fr
--------------050108060709000109000802-- From owner-chemistry@ccl.net Wed May 18 15:23:01 2011 From: "Gerard van Westen gerard.vanwesten\a/gmail.com" To: CCL Subject: CCL: iPhone & iPad 3D Molecule Browser - iMolview Message-Id: <-44699-110518131012-10026-kQGwCfVIfGi4kzMk8bvzvg]![server.ccl.net> X-Original-From: Gerard van Westen Content-Type: multipart/alternative; boundary=00151747658c8b5fc904a38ff567 Date: Wed, 18 May 2011 19:09:31 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard van Westen [gerard.vanwesten#gmail.com] --00151747658c8b5fc904a38ff567 Content-Type: text/plain; charset=ISO-8859-1 Hi Andy, I was actually also wondering about this. As it seems that the majority of people at out department use and Android phone, this would be of tremendous help. Regards, Gerard On Wed, May 18, 2011 at 17:02, Jim Kress ccl_nospam|a|kressworks.com < owner-chemistry|a|ccl.net> wrote: > > Sent to CCL by: "Jim Kress" [ccl_nospam{=}kressworks.com] > Is this going to be done for the Android OS, too? > > Jim > > > -----Original Message----- > > From: owner-chemistry+ccl_nospam==kressworks.com%x%ccl.net [mailto: > owner- > > chemistry+ccl_nospam==kressworks.com%x%ccl.net] On Behalf Of Andrew Orry > > andy-*-molsoft.com > > Sent: Tuesday, May 17, 2011 9:29 PM > > To: Kress, Jim > > Subject: CCL: iPhone & iPad 3D Molecule Browser - iMolview > > > > > > Sent to CCL by: Andrew Orry [andy]![molsoft.com] > > On 5/7/2011 2:43 AM, Arne Dieckmann adieckma-$-googlemail.com wrote: > > > Sent to CCL by: Arne Dieckmann [adieckma],[googlemail.com] > > > Dear Andrew, > > > > > > how about loading in your own pdb files? I'd buy it if that will be > > possible. > > > > > The latest version of iMolview (v1.2) is now synced with iTunes so you > > can load in your own PDB files from there. We also fixed a graphics > > issue with older iPhone/iPod devices and introduced a number of other > > features and improvements. Please see the app page for the full release > > notes:http://www.molsoft.com/iMolview.html > > Thanks, > > Andrew > > > > -- > > Andrew Orry Ph.D. > > MolSoft LLC > > Senior Research Scientist > > 11199 Sorrento Valley Road, S209 > > San Diego > > CA 92121 > > Tel: 858-625-2000 x108 > > Fax: 828-625-2888 > > www.molsoft.com> To recover the email address of the author of the > message, please > > change> > > --00151747658c8b5fc904a38ff567 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Andy,

I was actually also wondering about this. As it= seems that the majority of people at out department use and Android phone,= this would be of tremendous help.=A0

Regards,

Gerard

On Wed, May 18= , 2011 at 17:02, Jim Kress ccl_nospam|a|k= ressworks.com <owner-chemistry|a|ccl.net> wrote:

Sent to CCL by: "Jim Kress" [ccl_nospam{=3D}kressworks.com]
Is this going to be done for the Android OS, too?

Jim

> -----Original Message-----
> From: owner-chemistry+ccl_nospam=3D=3Dkressworks.com%x%ccl.net [mailto:owner-
> chemistry+ccl_nospam=3D=3Dkressworks.com%x%c= cl.net] On Behalf Of Andrew Orry
> andy-*-molsoft.com
> Sent: Tuesday, May 17, 2011 9:29 PM
> To: Kress, Jim
> Subject: CCL: iPhone & iPad 3D Molecule Browser - iMolview
>
>
> Sent to CCL by: Andrew Orry [andy]![molsoft.com]
> On 5/7/2011 2:43 AM, Arne Dieckmann adieckma-$-googlemail.com wrote:
> > Sent to CCL by: Arne Dieckmann [adieckma],[googlemail.com]
> > Dear Andrew,
> >
> > how about loading in your own pdb files? I'd buy it if that w= ill be
> possible.
> >
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> Thanks,
> Andrew
>
> --
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> MolSoft LLC
> Senior Research Scientist
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--00151747658c8b5fc904a38ff567-- From owner-chemistry@ccl.net Wed May 18 15:58:00 2011 From: "Marcou Gilles g.marcou(a)unistra.fr" To: CCL Subject: CCL: Chemoinformatics Message-Id: <-44700-110518145225-15671-DcLZ7yM/kzDFN/rwjvF1hw(a)server.ccl.net> X-Original-From: Marcou Gilles Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 18 May 2011 21:15:00 +0200 Mime-Version: 1.0 Sent to CCL by: Marcou Gilles [g.marcou!=!unistra.fr] Dear Andras, unfortunately, in France, such survey does not exist systematicaly for master studies. However, you can contact the services of the University of Strasbourg (espace-avenir{}unistra.fr) that have such informations. Personnaly, I can tell that the students I'm still in contact with have found a job at the end of the master -during or just after their training period-, though not always in Chemoinformatics. I hope I could give you a more satisfactory answer, and I'm sure I'll be able to do so in a very near future. Gilles Marcou Le mercredi 18 mai 2011 à 09:05 +0200, Andras Borosy andras.borosy^^^givaudan.com a écrit : > Dear Mr. Marcou, > > Might you publish a salary and/or employment survey of your chemoinf > graduates? > > Many thanks, > > Andras Borosy > > > > > "Gilles MARCOU g.marcou.:.unistra.fr" > Sent by: owner-chemistry+andras.borosy==givaudan.com^ccl.net > 17.05.2011 20:45 > Please respond to > "CCL Subscribers" > > > To > "Borosy, Andras " > cc > > Subject > CCL: Chemoinformatics > > > > > > > > Sent to CCL by: "Gilles MARCOU" [g.marcou*o*unistra.fr] > Dear all, > > Chemoinformatics is young discipline with a curiculum organized around > molecular descriptors, chemical space and data mining. It is different > > from Molecular Modeling and Quantum Chemistry although it boroughs from > these disciplines. It is different also from Bioinformatics although it > has proven its usefullness mostly in the area of drug design. > > The University of Strasbourg in France, is organizing since 2000, a master > level diploma in chemoinformatics. You can find a complete description of > this master on its web site ( > http://infochimie.u-strasbg.fr/master/master_home.htm). Beside, we > organize also a 5 days short courses "Introduction to chemoinformatics ( > http://infochim.u-strasbg.fr/spip.php?rubrique123). This could also be > seen as a an example of Chemoinformatics curriculum. > > Furthermore, we organize every two year a summer school in > chemoinformatics, the last session being in 2010 > (http://infochim.u-strasbg.fr/spip.php?rubrique12) and the next session > will be in June 2012. Finaly, there exists a French Society of > Chemoinformatics (http://www.chemoinformatique.fr/) which is close to the > Internation Chemoinformatics and QSAR Society ( > http://www.chemoinformatique.fr/modules/weblinks/visit.php?lid=5). > > I hope those links will be helpful to clarify the picture of > Chemoinformatics today. > > Yours Faithfully, > Gilles Marcouhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 0026E7A3C1257894_= > Content-Type: text/html; charset="US-ASCII" > > >
Dear Mr. Marcou, >
>
Might you publish a salary and/or employment > survey of your chemoinf graduates? >
>
Many thanks, >
>
Andras Borosy >
>
>
>
> > >
"Gilles MARCOU g.marcou.:.unistra.fr" > <owner-chemistry^ccl.net> >
Sent by: owner-chemistry+andras.borosy==givaudan.com^ccl.net >

17.05.2011 20:45 > > >
>
Please respond to
> "CCL Subscribers" <chemistry^ccl.net>
>
>

> > > > >
>
To
> 		"Borosy, Andras " > <andras.borosy^givaudan.com> >
>
cc
> 		>
>
Subject
> 		CCL: Chemoinformatics
>
> > >
>
>
>
>
>

> Sent to CCL by: "Gilles  MARCOU" [g.marcou*o*unistra.fr]
> Dear all,
>
> Chemoinformatics is young discipline with a curiculum organized around > molecular descriptors, chemical space and data mining. It is different > > from Molecular Modeling and Quantum Chemistry although it boroughs from > these disciplines. It is different also from Bioinformatics although it > has proven its usefullness mostly in the area of drug design.
>
> The University of Strasbourg in France, is organizing since 2000, a master > level diploma in chemoinformatics. You can find a complete description > of this master on its web site (http://infochimie.u-strasbg.fr/master/master_home.htm). > Beside, we organize also a 5 days short courses "Introduction to chemoinformatics > (http://infochim.u-strasbg.fr/spip.php?rubrique123). This could also be > seen as a an example of Chemoinformatics curriculum.
>
> Furthermore, we organize every two year a summer school in chemoinformatics, > the last session being in 2010
> (http://infochim.u-strasbg.fr/spip.php?rubrique12) and the next session > will be in June 2012. Finaly, there exists a French Society of Chemoinformatics > (http://www.chemoinformatique.fr/) which is close to the Internation Chemoinformatics > and QSAR Society (http://www.chemoinformatique.fr/modules/weblinks/visit.php?lid=5).
>
> I hope those links will be helpful to clarify the picture of Chemoinformatics > today.
>
> Yours Faithfully,
> Gilles Marcou
>
>
> > >      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
> >      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
> >      http://www.ccl.net/chemistry/sub_unsub.shtml
> > > > >      http://www.ccl.net/spammers.txt
> >
>
> >
From owner-chemistry@ccl.net Wed May 18 16:32:01 2011 From: "Tobias Schwabe tobba_+_uni-muenster.de" To: CCL Subject: CCL: MP2 sp energy corrections to lower-level theory calcs Message-Id: <-44701-110518151837-27600-CsH4m55u+UQcb7P3ZcTjkQ]![server.ccl.net> X-Original-From: Tobias Schwabe Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 18 May 2011 21:18:27 +0200 MIME-Version: 1.0 Sent to CCL by: Tobias Schwabe [tobba]*[uni-muenster.de] Dear Angela, first some general answers: a) E(B3LYP) does not contain any of the listed corrections; the summed contributions are listed as "Sum of electronic and ...", where the electronic energy equals E(B3LYP) b) To combine energy corrections based on B3LYP and electronic energies > from MP2, just add the corrections to E(MP2) From my understanding this is only valid for optimized ground state structures, not for transition states for which the standard thermal energy corrections become somewhat meaningless. Therefore I discourage to use these terms at all in your case: only correcting the ground state is also misleading. Then, how to improve B3LYP with MP2? Well, the most obvious answer is that you just obtain the molecular structure on a lower level of theory (here: B3LYP) and the electronic structure based on a a more accurate method (here: MP2). Then the activation barrier can be assumed to be the difference in electronic energies based on MP2. If you really improve your results by this depends on how good the transition state can be described by the single-reference HF determinant which might not be the case because of elongated bonds, near-degeneracy effects and so on... In those cases DFT is often less affected. There are other ways to combine DFT and MP2 results. There is some work by Truhlar et al. which is known as multi-coefficient correlation and density functional methods. Here you add up energy terms corrected by some empirical scaling factors. Note, that these parameters might well depend on the specific combination of basis sets applied in the original study. Finally, you can perform a perturbation corrected DFT calculation, known as double-hybrid functionals (e.g. B2PLYP functional). As these calculation rely on DFT orbitals they are less prone to the break down of the SCF reference state. Look out for work of Goerigk and Grimme, who benchmark those methods intensively. In all perturbation energy calculations remember that you will need at least triple-zeta basis sets (def2-TZVP, cc-pVTZ) to get improved results. Regards, Tobias From owner-chemistry@ccl.net Wed May 18 23:56:00 2011 From: "Haibin Scopus lihb734,yahoo.com" To: CCL Subject: CCL: Workshop on Electronic Structure Calculations preceding WATOC 2011 Message-Id: <-44702-110518222616-17335-uJ3bEazzPt7Q5faL5m7DeA_._server.ccl.net> X-Original-From: Haibin Scopus Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 18 May 2011 19:26:04 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Haibin Scopus [lihb734:+:yahoo.com] Dear Dr. Kong other Qchemers,      In your releaseing note, you mentioned "TD-DFT analytic gradient and Hessian for excited-state structure optimization". So, I want to know that does it means that we can calculate the frequecy of excited states in a analytic way? Or it only calculate the gradient analytically, but the frequecy of excited states will be calculated by means of numerical difference of analytical gradient?     Looking forward to your reply!     Best wishes         Mr. Haibin Li Institute of Functional Material Chemistry, Faculty of Chemistry Northeast Normal University changchun, Jilin, 130024 PR CHINA E-mail: lihb734]![nenu.edu.cn; lihb734]![yahoo.com http://www.nenu.edu.cn ----- Original Message ----- > From: Jing Kong jkong:-:q-chem.com > To: "Li, Hai-Bin " > Cc: > Sent: Thursday, May 19, 2011 12:12 AM > Subject: CCL: Workshop on Electronic Structure Calculations preceding WATOC 2011 > > > Sent to CCL by: "Jing Kong" [jkong__q-chem.com] > Dear colleague: > > Q-Chem would like to invite you to a workshop of quantum chemistry in > Santiago de Compostela, Spain in the afternoon of Saturday, July 16, 2011.  > It is the day before WATOC 2011 starts. The workshop will highlight some of > the features in the new Q-Chem 4.0 software package.  Q-Chem 4.0 contains > significant new functionality, including: > > * TD-DFT analytic gradient and Hessian for excited-state structure > optimization;; > * IRC searches for mapping complicated potential energy surfaces; > * Range-separated and dispersion-corrected DFT functionals; > * Faster algorithms for DFT, HF and coupled-cluster calculations; > * More choices for excited-state, solvation and charge-transfer > calculations; > * Effective Fragment Potential and QM/MM for treating large systems; > * Maximum Overlap Method for excited-state calculations of large systems; > * Intracules for analysis of two-electron properties; > * Shared-memory for multicore systems and implementations for GPUs; > > as well as many other areas. > > > The workshop will consist of seminars and a demonstration of Q-Chem 4.0. > Seminar speakers include Christian Ochsenfeld (Uni Muenchen), David Casanova > (Uni Barcelona), Martin Head-Gordon (Uni California, Berkeley), Peter Gill > (Australian National Uni) and Anna Krylov (Uni Southern California). The > meeting will take place at the site of WATOC. The registration fee is $25 > and covers coffee, tea and soft drinks. > > All workshop participants will receive a free six-month license for > unlimited use of Q-Chem 4.0. > > Please register by June 16 on our website > (www.q-chem.com/wsspa_regist.html). > > > Happy Computing, > > Jing Kong, PhD > CEO and Chief Scientist > Q-Chem, Inc.>      >      >      >      >