From owner-chemistry@ccl.net Fri Jul 10 08:26:00 2009 From: "willsd{=}appstate.edu" To: CCL Subject: CCL:G: CBS-Q method in druglike molecules Message-Id: <-39734-090710075338-8966-v6lGafrV6RatJ+nivftnTA%%server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 10 Jul 2009 11:44:30 GMT MIME-Version: 1.0 Sent to CCL by: [willsd(0)appstate.edu] OK, you have a 64 bit OS running on a 64 bit machine. It is possible to run a 32 bit version of G09 on such a machine, but since the price is the same for 64 or 32 bit versions on G09, it would be bizarre to buy the 32 bit version.... I'll assume you have 64 bit version of G09. You can confirm this easily... in your G09 output files you should see something with 64 in it just after the citation. Here is what it looks like for a 64 bit version of G03: Cite this work as: Gaussian 03, Revision E.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Wallingford CT, 2004. ****************************************** Gaussian 03: EM64L-G03RevE.01 11-Sep-2007 11-Sep-2008 ****************************************** The EM64L indicates that this a 64 bit version optimized for intel em64t machines (mine has xeon processors; yours has (I think) itanium processors). Your questions: Replace QCISD(T) with QCISD? No, this is a poor idea, and difficult to do. The CBS-Q method was optimized for including QCI energies computed with perturbative triples corrections. If you remove the triples correction, the rest of the parameters in CBS-Q will no longer be the correct ones to use; the resulting energies will not be correct. It is also difficult to do this in Gxx. The Gaussian programs include CBS-Q (and related methods) as automatic options. These methods compute various energies with different methods and basis sets, then calculate differences between them (or other relatively simple extrapolation techniques); these differences are summed and added as a correction to some "fundamental" energy, and perhaps another correction is applied as well. When you request a CBS-Q calculation, Gaussian then performs ALL of the required method/basis set calculations, computes the energy differences, sums them and applies the corrections. To change how this is done (that is to replace the QCISD(T) step with QCISD) you would have to modify the source code, recompile, AND then re-calibrate your new method and find new parameters, and give it a new name (since it would no longer be CBS-Q). This would be a lot of work and would be rather far from your goal of a simple pKa estimation like you found in the literature. Different method (CBS-4M or G1)? If you want to try something other than CBS-Q, you must realize the you are giving up the calibration in the literature that tells you how accurately you can expect the CBS-Q to pKa conversion to be. There is nothing wrong with this, it just means that you will need to do more calibration work yourself, by computing more known molecules to compare your new pKa estimates with. If you are going to do this, I suggest you investigate the multi-coefficient G3 methods developed by Don Truhlar and his group (MCG3/3 is relatively inexpensive, and remarkably accurate). I do not know if these are available as automatic calculations in G09; they were not included in G03. If they are not, then the MULTILEVEL code (free from Truhlar's group) will automate the calculations for you, or you can write your own tool to compute appropriate differences and sums (I have dome this with excel). MULTILEVEL does not require commercial compilers (I have used gfortran), so it would not require buying any more software. I have used MCG3/3 on closed shell molecules and radicals. With structures and frequencies from an initial MP2(full)/6-31++G(d) calculation, this method reliably predicts adiabatic ionization energies with an error of about 0.1 eV, and I can use it for molecules where a CBS type extrapolation would be extremely slow to compute (weeks of CPU). A word of caution here: the multi-coefficient methods have more parameters than other high accuracy methods, so fooling around with the underlying calculations would cause even more problems than with CBS-Q. Truhlar's group has a lot of expertise with calibrating these methods and I am perfectly happy to simply use their results. I have also noticed that for most of my molecules, the most time consuming step is the initial MP2(full)/6-31++G(d) opt freq step; the time required for this step scales with the fifth power of the number of atoms. If you want to try MCG3/3 and you do not want to use MULTILEVEL, here is a sample input file that will give the required energies for MCG3/3 at the MP2(full) level for acetaldehyde; you would need to look at the original MCG3/3 papers to see how to combine the energies from this calculation ot get the MCG3/3 energy. You would also need the appropriate parts of the mg3s basis (also from Truhlar) for the atoms in your molecules. %chk=acet_01.chk %mem=100MW %nprocs=8 # ump2(full) 6-31++g(d) opt freq=noraman acetaldehyde geometry optimization. first try. 0 1 C -0.591726 -0.038182 -3.751955 H -1.545230 0.181729 -3.319093 H -0.226392 -0.963771 -3.358617 H -0.691928 -0.116889 -4.814342 C 0.399013 1.090748 -3.412025 H 0.496310 1.932068 -4.065946 O 1.094159 1.023790 -2.365192 --Link1-- %chk=acet_01.chk %mem=100MW %nprocs=8 # qcisd(t) 6-31g(d) guess=tcheck geom=check mcg3/3 calculation; qcisd(t) step 0 1 --Link1-- %chk=acet_01.chk %mem=100MW %nprocs=8 # mp4sdq 6-31g(2df,p) guess=tcheck geom=check mcg3/3 calculation; mp4 2df step 0 1 --Link1-- %chk=acet_01.chk %mem=100MW %nprocs=8 # mp2 Gen guess=tcheck geom=check mcg3/3 calculation; mp2/mg3s step; include appropriate portion of mg3s basis set below blank line after charge multiplicity line 0 1 -H 0 S 3 1.00 33.8650000000 0.0254938000 5.0947900000 0.1903730000 1.1587900000 0.8521610000 S 1 1.00 0.3258400000 1.0000000000 S 1 1.00 0.1027410000 1.0000000000 P 1 1.00 1.5000000000 1.0000000000 P 1 1.00 0.3750000000 1.0000000000 **** -C 0 S 6 1.00 4563.240000000 0.0019666500 682.0240000000 0.0152306000 154.9730000000 0.0761269000 44.4553000000 0.2608010000 13.0290000000 0.6164620000 1.8277300000 0.2210060000 S 3 1.00 20.9642000000 0.1146600000 4.8033100000 0.9199990000 1.4593300000 -0.0030306800 S 1 1.00 0.4834560000 1.0000000000 S 1 1.00 0.1455850000 1.0000000000 S 1 1.00 0.0438000000 1.0000000000 P 3 1.00 20.9642000000 0.0402487000 4.8033100000 0.2375940000 1.4593300000 0.8158540000 P 1 1.00 0.4834560000 1.0000000000 P 1 1.00 0.1455850000 1.0000000000 P 1 1.00 0.0438000000 1.0000000000 D 1 1.00 1.2520000000 1.0000000000 D 1 1.00 0.3130000000 1.0000000000 F 1 1.00 0.8000000000 1.0000000000 **** -O 0 S 6 1.00 8588.500000000 0.0018951500 1297.230000000 0.0143859000 299.2960000000 0.0707320000 87.3771000000 0.2400010000 25.6789000000 0.5947970000 3.7400400000 0.2808020000 S 3 1.00 42.1175000000 0.1138890000 9.6283700000 0.9208110000 2.8533200000 -0.0032744700 S 1 1.00 0.9056610000 1.0000000000 S 1 1.00 0.2556110000 1.0000000000 S 1 1.00 0.0845000000 1.0000000000 P 3 1.00 42.1175000000 0.0365114000 9.6283700000 0.2371530000 2.8533200000 0.8197020000 P 1 1.00 0.9056610000 1.0000000000 P 1 1.00 0.2556110000 1.0000000000 P 1 1.00 0.0845000000 1.0000000000 D 1 1.00 2.5840000000 1.0000000000 D 1 1.00 0.6460000000 1.0000000000 F 1 1.00 1.4000000000 1.0000000000 **** I hope this helps.... Steve Williams ----- Original Message ----- > From: "Pavle Mocilac pavle.mocilac2{}mail.dcu.ie" Date: Thursday, July 9, 2009 9:42 pm Subject: CCL:G: CBS-Q method in druglike molecules To: "Williams, Steve " > > Sent to CCL by: Pavle Mocilac [pavle.mocilac2()mail.dcu.ie] > Dear Steve, > > Thank you for this nice mail, you give me some new useful information. > As I mentioned im my previous mail, I'm using 64 bit machine and 64 > bit UNIX operating system (Silicon Graphics > Altix ICE 8200XE). I can not improve my hardware, and I'm quite sure > that the better hardware I can not get. The memory I'm allocating > is 256MW and I am using 8 processors - it is a maximum regarding the > number of processor power. > Therefore, I'm using quite awesome hardware/software performances. > > Do you think that QCISD(T) method will be possible to replace with > QCISD method? How to specify T exclusion in QCISD(T) step of CBS-Q > protocol using keywords? > Regarding the scaling the molecule, I was developing a model using the > same molecules described in reference paper, aminopyridines (13 atoms) > and for them, the calculation lasts up to 45 minutes maximum, > including in a solvent conditions. > But my drug-like molecules contain 25 atoms, but in that case, > calculation goes to more than 3 days. In fact, as I have limited time > for one job I have to say that I never finished. > In the paper I'm using as a reference G1 level was used and they > got nice correlation (pKa{calc} vs > pKa{exp}). My idea, using CBS-Q, was, in fact, to obtain even > better model... > Maybe to use CBS-4M or to try G1? Although mistakes are supposed to > be bigger... > > > Best regards, > > Pavle Mocilac > > ============================================ > Pavle Mocilac > Postgraduate Researcher > T3 - Targeted Therapeutics and Theranostics > Room X249, School of Chemistry > Dublin City University > Dublin 9, Dublin, Ireland > mobile: +353872167022 > mailto:pavle.mocilac2- -mail.dcu.ie > ============================================ > Thursday, July 9, 2009, 8:54:58 PM, you wrote: > > > > Sent to CCL by: [willsd*appstate.edu] > > Here is my $0.02... > > You would like to apply a method based on CBS-Q energies to > estimate pKa values > > for molecules with as many as 25 atoms, and the QCISD(T)/6- > 31+G(d) step is > > taking a long time. You have G09 and would like to do this > calculation with > > this software, so as to come as close as possible to reproducing > the methods > > used for similar calculations in a reference paper... > > > You have not mentioned this, but you may run into disk limitation > problems...> this is quite likely with a 32 bit version on G09, > since the 32 bit version can > > address only a limited amount of disk, and QCISD(T) will need a > lot of disk. (I > > should mention that I have not used G09... but previous versions > of Gxx had this > > limitation on the 32 bit versions, and I'd guess that 32 bit G09 > does too.) With > > the 64 bit version, running on a 64 bit machine with a 64 bit OS, > you will run > > out of physical disk long before you run out address space. So > one repliers > > comments about 32 bit vs 64 bit is quite pertinent to this > calculation. > > The CBS methods (and other high accuracy combined methods (G1, > G2, G3, > > multi-coefficient G3, ....) all try, by various methods, to get > the energy > > accuracy of a very large basis set combined with a very accurate > energy method, > > without actually doing such a calculation, since the required > computing> resources exceed what anyone has. All such methods > depend on various post-HF > > energy calculations, and these depend on computing the effects on > the energy of > > substituting electrons from occupied (in the underlying HF > wavefunction)> molecular orbitals into higher energy, unoccupied > orbitals. The SD in QCISD(T) > > means that all possible subsitutions of single electrons, and > pairs of electrons > > are included in a self-consistent manner, and the (T) means that > once the SD > > part has converged, the effect of substituting three electrons > (hence triples) > > is estimated with perturbation theory. The cost of such a > calculation is > > roughly proportional to the sixth power of the number of basis > functions (this > > is included in the G09 output), and hence proportional to the > sixth power of the > > number of atoms. The CBS method (and G1, G2....) has other steps > as well, and > > this will have other scaling behavior, so the overall scaling for > the entire > > CBS-Q method is not easy to predict. > > One replyer suggested replacing the QCISD(T) step with QCISD... > this can be made > > to give a possibly useful method, but it will not be CBS-Q, and > will not be > > comparable to your reference paper. > > > I'd suggest trying a scaled down version of your drug-like > molecule (replace > > methyl or ethyl groups with H, etc), and see if you can get the > atom count down > > to 12 or so. Do the CBS-Q calculation on this version, note the > time required, > > add a methyl or ethyl back in, repeat the CBS-Q and timing. You > can then > > estimate the scaling, and use this to estimate how long your full > 25 atom > > molecule might take. My rule of thumb is that (except in unusual > circumstances)> if it is going to take longer than a week, I will > have forgotten what I wanted > > to calculate before it is done, and I am not interested. > > > For some quite clear discussion on the calculations that lie > inside combined > > methods like CBS-Q, Frank Jensen's relatively new book > (Introduction to > > Computational Chemistry) is pretty good. (IMHO, it is an > introduction in the > > sense that he introduces nearly all of the relevant equations, > not in the sense > > of simplified. I appreciate his approach a great deal.) > > > Good luck on your hunt for pKa estimates... > > > Steve Williams > > > > ----- Original Message ----- > >> From: "Pavle Mocilac pavle.mocilac2^-^mail.dcu.ie" chemistry_._ccl.net>> Date: Thursday, July 9, 2009 10:03 am > > Subject: CCL:G: CBS-Q method in druglike molecules > > To: "Williams, Steve " > > >> > >> Sent to CCL by: Pavle Mocilac [pavle.mocilac2===mail.dcu.ie] > >> Dear Simon, > >> > >> Thank you for the information about this software, but no, I > have > >> not and will not consider any other methods beside those that > can > >> be made with Gaussian 03 or 09 and described in "CaballeroNA, > >> Melendez FJ, Munoz-Cara C, et al. Biophys. Chem 124 (2) > >> 155-160". > >> We do not have any intention to buy any new additional software > but > >> to use the one we have. Is seems to me that there are numerous > >> people on this CCL that behave as salesman and always want to > >> solve my problem by selling > >> me some additional software. > >> The reason we are using Gaussian is deeper, and for the sake of > >> consistency and comparability we do not have attention to use so > >> many different programmes that works in different way. > >> I would like to repeat that CBS-Q is my main problem and > therefore > >> I will be very happy and very grateful if there is somebody in > this > >> CCL who can help me with CBS-Q calculations in Gaussian. > >> > >> > >> Best regards, > >> > >> Pavle Mocilac > >> > >> ============================================ > >> Pavle Mocilac > >> Postgraduate Researcher > >> T3 - Targeted Therapeutics and Theranostics > >> Room X249, School of Chemistry > >> Dublin City University > >> Dublin 9, Dublin, Ireland > >> mobile: +353872167022 > >> mailto:pavle.mocilac2~!~mail.dcu.ie > >> ============================================ > >> Wednesday, July 8, 2009, 7:21:16 PM, you wrote: > >> > >> > >> > Sent to CCL by: Simon Cross [simon!=!moldiscovery.com] > >> > >> > Hi Pavle, have you considered other methods for pKa > calculation > >> of > >> > drug-like molecules? We recently published a method (Milletti, > F. > >> et al. > >> > (2007) New and Original pKa Prediction Method Using Grid > >> Molecular > >> > Interaction Fields. J. Chem. Inf. Model., 47, 2172-2181) which > is > >> used> in our software MoKa. > >> > >> > You can see more about it at www.moldiscovery.com/soft_moka.php > >> > >> > We get an RMSE of 0.4 log units for the training set of 26000 > >> data > >> > points (very close to experimental error) and external > prediction > >> error> of 0.7 log units. > >> > >> > Simon > >> > >> > Pavle Mocilac pavle.mocilac2]|[mail.dcu.ie wrote: > >> >> Sent to CCL by: "Pavle Mocilac" [pavle.mocilac2{:}mail.dcu.ie] > >> >> My dear colleagues, > >> >> > >> >> Recently I sent the question about the calculation of pKa of > >> small druglike molecules. The method asks employing high > accuracy > >> models like G1, G2, CBS-Q in order to get accurate Free Gibbs > >> energies using Gaussian 09, of course.. > >> >> Now, it seems to me that this model works OK, and fast enough > >> for very small molecules up to 10 or 12 atoms (hydrogen > included). > >> But, my molecule has 25 atoms and currently is stacked at > >> QCISD(T)/6-31+G(d') step, calculating something called "triples" > >> for more than 2 days!!!!! > >> >> I would like to emphasize that this job is being calculating > >> with Gaussian 09 (Linux version), using lots of memory () and 8 > >> processors at SGI Altix ICE 8200EX. > >> >> What is the limit of CBS-Q method regarding the number of > atoms? > >> Is 25 atoms too much? Is there any option to use some kind of > >> additional keywords to exclude "triples" calculation at > QCISD(T)/6- > >> 31+G(d') step? Will that exclusion hamper accurate result? Is it > >> better to use CBS-4M?> > >> >> > >> >> > >> > >> > >> > >> -= This is automatically added to each message by the mailing > >> script =- > >> To recover the email address of the author of the message, > please > >> changethe strange characters on the top line to the _._ sign. > You can > >> also> Conferences: > >> http://server.ccl.net/chemistry/announcements/conferences/> > Conferences:> > http://server.ccl.net/chemistry/announcements/conferences/ > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the || sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Fri Jul 10 09:00:00 2009 From: "Szabolcs Csepregi scsepregi^-^chemaxon.com" To: CCL Subject: CCL: 1. Steric hindrance 2. TS (Michael Addition) Message-Id: <-39735-090710082550-12155-d3jRwebDKMPwr3DYJMgDWQ=-=server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=UTF-8 Date: Fri, 10 Jul 2009 13:45:36 +0200 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [scsepregi**chemaxon.com] Hi Johannes,

The Geometry plugin from the Marvin calculator plugin collection can calculate atomic steric hindrance.
See: http://www.chemaxon.com/product/geometry.html

You can try it from Marvin GUI, even online from the applet: http://www.chemaxon.com/marvin/sketch/index.jsp
Alternatively, the chemaxon academic package offers free licenses for batch calculation, etc. as well.

I hope this helps.

Best regards,
Szabolcs

Szabolcs Csepregi, PhD
Dir. of Search Technologies and Markush project
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037 Hungary
http://www.chemaxon.com
Tel: +36 1 4532661 Cell: +36 20 4219863 Fax: +36 1 4532659
Skype: szabolcs.csepregi

Schwobel, Johannes J.Schwobel%x%ljmu.ac.uk wrote: 
Sent to CCL by: "Schwobel, Johannes" [J.Schwobel/./ljmu.ac.uk]
Dear CCLers,
 
I would appreciate your advice on two questions:
 
I'm calculating reactivity and transition states (TS) for the Michael addition reaction (soft nucleophiles with alpha,beta unsaturated compounds) at B3LYP level. Obviously, it seems to be very difficult to locate a TS. Does anyone have any experience with theoretical TS calculations of this type of reaction or know any further papers about that?
 
If there is a substituent in alpha-position, reactivity decreases significantly. This might have electronic or steric effects. For the latter I want to know: Is there any descriptor or parameter available to quantify the local (e.g. atom-centered) steric hindrance?
 
Thanks a lot in advance!
Johannes Schwobel
 



-=his is automatically added to each message by the mailing script =-E-mail to subscribers: CHEMISTRY^ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST^ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs 
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
From owner-chemistry@ccl.net Fri Jul 10 09:35:01 2009 From: "Huo-Lei Peng huolei.peng166(!)gmail.com" To: CCL Subject: CCL:G: Problem about calculation on the open-shell singlet in Gaussian. Message-Id: <-39736-090710013327-11742-ND5QMa9A0JucFBORaK/eFA~!~server.ccl.net> X-Original-From: Huo-Lei Peng Content-Type: multipart/alternative; boundary=001636c5a4fb6b291a046e527474 Date: Fri, 10 Jul 2009 00:32:05 -0400 MIME-Version: 1.0 Sent to CCL by: Huo-Lei Peng [huolei.peng166]=[gmail.com] --001636c5a4fb6b291a046e527474 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, Dear All: I have a question about calculation on the open-shell singlet using Gaussian. For example, nitrene species may have an open-shell and closed shell singlets. In Gaussian, how to set the calculation to get open-shell or closed-shell specifically? Thanks. Peng --001636c5a4fb6b291a046e527474 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Dear All:

I have a question about calculation on the= open-shell singlet using Gaussian. For example, nitrene species may have a= n open-shell and closed shell singlets. In Gaussian, how to set the calcula= tion to get open-shell or closed-shell specifically? Thanks.

Peng
--001636c5a4fb6b291a046e527474-- From owner-chemistry@ccl.net Fri Jul 10 10:11:01 2009 From: "huolei peng horaldraman^^gmail.com" To: CCL Subject: CCL:G: A question about open-shell singlet calculation in Gaussian. Message-Id: <-39737-090710020301-14929-x0TUxWh/hTUqmZQJGMO1GQ[*]server.ccl.net> X-Original-From: huolei peng Content-Type: multipart/alternative; boundary=001485f42318a698f4046e53b879 Date: Fri, 10 Jul 2009 02:02:45 -0400 MIME-Version: 1.0 Sent to CCL by: huolei peng [horaldraman(_)gmail.com] --001485f42318a698f4046e53b879 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, Dear All: I have a question about calculations on the open-shell singlet using Gaussian. For example, nitrene species may have an open-shell and closed shell singlets. In Gaussian, how to set the calculation to get open-shell or closed-shell specifically? Thanks. Peng --001485f42318a698f4046e53b879 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Dear All:

I have a question about calcula= tions on the open-shell singlet using Gaussian. For example, nitrene specie= s may have an open-shell and closed shell singlets. In Gaussian, how to set= the calculation to get open-shell or closed-shell specifically? Thanks.

Peng

--001485f42318a698f4046e53b879-- From owner-chemistry@ccl.net Fri Jul 10 11:22:01 2009 From: "Jose Alberto Fernandes jafernandes{:}ua.pt" To: CCL Subject: CCL:G: Problem about calculation on the open-shell singlet in Gaussian. Message-Id: <-39738-090710111405-899-Ms/PdcpmMXkvKWOQtTzA7g{}server.ccl.net> X-Original-From: "Jose Alberto Fernandes" Date: Fri, 10 Jul 2009 11:14:02 -0400 Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=-=ua.pt] Hello I don't know if I understood your problem. Lets try. Please see the following excerpt this input: # rb3lyp/3-21g guess=check The "r" before "b3lyp" means that you want a close shell calculation. If you don't want electron pairing you have to put "ub3lyp" instead of "rb3lyp". You should remember that a closed shell compound has always a spin=1, and in a open shell the spin is different from 1. In the case of nitrene (R-N ?) you can have R-N paired (spin=1) and unpaired (spin=3). So in the case of pairing you shoul input: ------------------------ # rb3lyp/3-21g guess=check comment 0 1 geometry ---------------------- If you want unpairing you should input: --------------------- # ub3lyp/3-21g guess=check comment 0 3 geometry ---------------------- If I haven't answered your question, please explain better. Best regards Jose > "Huo-Lei Peng huolei.peng166(!)gmail.com" wrote: > > Sent to CCL by: Huo-Lei Peng [huolei.peng166]=[gmail.com] > --001636c5a4fb6b291a046e527474 > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Encoding: 7bit > > Hi, Dear All: > I have a question about calculation on the open-shell singlet using > Gaussian. For example, nitrene species may have an open-shell and closed > shell singlets. In Gaussian, how to set the calculation to get open-shell or > closed-shell specifically? Thanks. > > Peng > > --001636c5a4fb6b291a046e527474 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Hi, Dear All:

I have a question about calculation on the= > open-shell singlet using Gaussian. For example, nitrene species may have a= > n open-shell and closed shell singlets. In Gaussian, how to set the calcula= > tion to get open-shell or closed-shell specifically? Thanks.
>

Peng
> > --001636c5a4fb6b291a046e527474-- > > From owner-chemistry@ccl.net Fri Jul 10 11:56:01 2009 From: "John McKelvey jmmckel]=[gmail.com" To: CCL Subject: CCL:G: CBS-Q method in druglike molecules Message-Id: <-39739-090709232029-31709-vL31YAvN8dGXH07XH4ohFg^-^server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=00163691fea5790800046e50a9e7 Date: Thu, 9 Jul 2009 22:23:46 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel#,#gmail.com] --00163691fea5790800046e50a9e7 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello, Could I suggest another approach drawn from my industrial experience? While it is always great to get absolute results one might be able to take advantage of the fact that understanding chemistry is often in "relatives?" Since your examples seem to take large amounts of time why not calibrate your problem against a set of known experimental results and use lower levels of theory? You could increase the level of theory and see how the accuracy of the calibration fit goes. I do not know if your goal is to be able to model PKa's in the absolute sense or to understand what the relative values are. My $0.02.. Cheers! John McKelvey On Thu, Jul 9, 2009 at 7:45 PM, Pavle Mocilac pavle.mocilac2{}mail.dcu.ie < owner-chemistry+*+ccl.net> wrote: > > Sent to CCL by: Pavle Mocilac [pavle.mocilac2()mail.dcu.ie] > Dear Steve, > > Thank you for this nice mail, you give me some new useful information. > As I mentioned im my previous mail, I'm using 64 bit machine and 64 bit > UNIX operating system (Silicon Graphics > Altix ICE 8200XE). I can not improve my hardware, and I'm quite sure > that the better hardware I can not get. The memory I'm allocating > is 256MW and I am using 8 processors - it is a maximum regarding the > number of processor power. > Therefore, I'm using quite awesome hardware/software performances. > > Do you think that QCISD(T) method will be possible to replace with > QCISD method? How to specify T exclusion in QCISD(T) step of CBS-Q > protocol using keywords? > Regarding the scaling the molecule, I was developing a model using the > same molecules described in reference paper, aminopyridines (13 atoms) > and for them, the calculation lasts up to 45 minutes maximum, > including in a solvent conditions. > But my drug-like molecules contain 25 atoms, but in that case, > calculation goes to more than 3 days. In fact, as I have limited time > for one job I have to say that I never finished. > In the paper I'm using as a reference G1 level was used and they got nice > correlation (pKa{calc} vs > pKa{exp}). My idea, using CBS-Q, was, in fact, to obtain even better > model... > Maybe to use CBS-4M or to try G1? Although mistakes are supposed to > be bigger... > > > Best regards, > > Pavle Mocilac > > ============================================ > Pavle Mocilac > Postgraduate Researcher > T3 - Targeted Therapeutics and Theranostics > Room X249, School of Chemistry > Dublin City University > Dublin 9, Dublin, Ireland > mobile: +353872167022 > mailto:pavle.mocilac2- -mail.dcu.ie > ============================================ > Thursday, July 9, 2009, 8:54:58 PM, you wrote: > > > > Sent to CCL by: [willsd*appstate.edu] > > Here is my $0.02... > > You would like to apply a method based on CBS-Q energies to estimate pKa > values > > for molecules with as many as 25 atoms, and the QCISD(T)/6-31+G(d) step > is > > taking a long time. You have G09 and would like to do this calculation > with > > this software, so as to come as close as possible to reproducing the > methods > > used for similar calculations in a reference paper... > > > You have not mentioned this, but you may run into disk limitation > problems... > > this is quite likely with a 32 bit version on G09, since the 32 bit > version can > > address only a limited amount of disk, and QCISD(T) will need a lot of > disk. (I > > should mention that I have not used G09... but previous versions of Gxx > had this > > limitation on the 32 bit versions, and I'd guess that 32 bit G09 does > too.) With > > the 64 bit version, running on a 64 bit machine with a 64 bit OS, you > will run > > out of physical disk long before you run out address space. So one > repliers > > comments about 32 bit vs 64 bit is quite pertinent to this calculation. > > > The CBS methods (and other high accuracy combined methods (G1, G2, G3, > > multi-coefficient G3, ....) all try, by various methods, to get the > energy > > accuracy of a very large basis set combined with a very accurate energy > method, > > without actually doing such a calculation, since the required computing > > resources exceed what anyone has. All such methods depend on various > post-HF > > energy calculations, and these depend on computing the effects on the > energy of > > substituting electrons from occupied (in the underlying HF wavefunction) > > molecular orbitals into higher energy, unoccupied orbitals. The SD in > QCISD(T) > > means that all possible subsitutions of single electrons, and pairs of > electrons > > are included in a self-consistent manner, and the (T) means that once the > SD > > part has converged, the effect of substituting three electrons (hence > triples) > > is estimated with perturbation theory. The cost of such a calculation is > > roughly proportional to the sixth power of the number of basis functions > (this > > is included in the G09 output), and hence proportional to the sixth power > of the > > number of atoms. The CBS method (and G1, G2....) has other steps as > well, and > > this will have other scaling behavior, so the overall scaling for the > entire > > CBS-Q method is not easy to predict. > > One replyer suggested replacing the QCISD(T) step with QCISD... this can > be made > > to give a possibly useful method, but it will not be CBS-Q, and will not > be > > comparable to your reference paper. > > > I'd suggest trying a scaled down version of your drug-like molecule > (replace > > methyl or ethyl groups with H, etc), and see if you can get the atom > count down > > to 12 or so. Do the CBS-Q calculation on this version, note the time > required, > > add a methyl or ethyl back in, repeat the CBS-Q and timing. You can then > > estimate the scaling, and use this to estimate how long your full 25 atom > > molecule might take. My rule of thumb is that (except in unusual > circumstances) > > if it is going to take longer than a week, I will have forgotten what I > wanted > > to calculate before it is done, and I am not interested. > > > For some quite clear discussion on the calculations that lie inside > combined > > methods like CBS-Q, Frank Jensen's relatively new book (Introduction to > > Computational Chemistry) is pretty good. (IMHO, it is an introduction in > the > > sense that he introduces nearly all of the relevant equations, not in the > sense > > of simplified. I appreciate his approach a great deal.) > > > Good luck on your hunt for pKa estimates... > > > Steve Williams > > > > ----- Original Message ----- > >> From: "Pavle Mocilac pavle.mocilac2^-^mail.dcu.ie" ccl.net> > > Date: Thursday, July 9, 2009 10:03 am > > Subject: CCL:G: CBS-Q method in druglike molecules > > To: "Williams, Steve " > > >> > >> Sent to CCL by: Pavle Mocilac [pavle.mocilac2===mail.dcu.ie] > >> Dear Simon, > >> > >> Thank you for the information about this software, but no, I have > >> not and will not consider any other methods beside those that can > >> be made with Gaussian 03 or 09 and described in "CaballeroNA, > >> Melendez FJ, Munoz-Cara C, et al. Biophys. Chem 124 (2) > >> 155-160". > >> We do not have any intention to buy any new additional software but > >> to use the one we have. Is seems to me that there are numerous > >> people on this CCL that behave as salesman and always want to > >> solve my problem by selling > >> me some additional software. > >> The reason we are using Gaussian is deeper, and for the sake of > >> consistency and comparability we do not have attention to use so > >> many different programmes that works in different way. > >> I would like to repeat that CBS-Q is my main problem and therefore > >> I will be very happy and very grateful if there is somebody in this > >> CCL who can help me with CBS-Q calculations in Gaussian. > >> > >> > >> Best regards, > >> > >> Pavle Mocilac > >> > >> ============================================ > >> Pavle Mocilac > >> Postgraduate Researcher > >> T3 - Targeted Therapeutics and Theranostics > >> Room X249, School of Chemistry > >> Dublin City University > >> Dublin 9, Dublin, Ireland > >> mobile: +353872167022 > >> mailto:pavle.mocilac2~!~mail.dcu.ie > >> ============================================ > >> Wednesday, July 8, 2009, 7:21:16 PM, you wrote: > >> > >> > >> > Sent to CCL by: Simon Cross [simon!=!moldiscovery.com] > >> > >> > Hi Pavle, have you considered other methods for pKa calculation > >> of > >> > drug-like molecules? We recently published a method (Milletti, F. > >> et al. > >> > (2007) New and Original pKa Prediction Method Using Grid > >> Molecular > >> > Interaction Fields. J. Chem. Inf. Model., 47, 2172-2181) which is > >> used> in our software MoKa. > >> > >> > You can see more about it at www.moldiscovery.com/soft_moka.php > >> > >> > We get an RMSE of 0.4 log units for the training set of 26000 > >> data > >> > points (very close to experimental error) and external prediction > >> error> of 0.7 log units. > >> > >> > Simon > >> > >> > Pavle Mocilac pavle.mocilac2]|[mail.dcu.ie wrote: > >> >> Sent to CCL by: "Pavle Mocilac" [pavle.mocilac2{:}mail.dcu.ie] > >> >> My dear colleagues, > >> >> > >> >> Recently I sent the question about the calculation of pKa of > >> small druglike molecules. The method asks employing high accuracy > >> models like G1, G2, CBS-Q in order to get accurate Free Gibbs > >> energies using Gaussian 09, of course.. > >> >> Now, it seems to me that this model works OK, and fast enough > >> for very small molecules up to 10 or 12 atoms (hydrogen included). > >> But, my molecule has 25 atoms and currently is stacked at > >> QCISD(T)/6-31+G(d') step, calculating something called "triples" > >> for more than 2 days!!!!! > >> >> I would like to emphasize that this job is being calculating > >> with Gaussian 09 (Linux version), using lots of memory () and 8 > >> processors at SGI Altix ICE 8200EX. > >> >> What is the limit of CBS-Q method regarding the number of atoms? > >> Is 25 atoms too much? Is there any option to use some kind of > >> additional keywords to exclude "triples" calculation at QCISD(T)/6- > >> 31+G(d') step? Will that exclusion hamper accurate result? Is it > >> better to use CBS-4M?> > >> >> > >> >> > >> > >> > >> > >> -= This is automatically added to each message by the mailing > >> script =- > >> To recover the email address of the author of the message, please > >> changethe strange characters on the top line to the _._ sign. You can > >> also> Conferences: > >> http://server.ccl.net/chemistry/announcements/conferences/> > Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/> > > --00163691fea5790800046e50a9e7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,

Could I suggest another approach drawn from my industrial exp= erience?=A0 While it is always great to get absolute results one might be a= ble to take advantage of the fact that understanding chemistry is often in = "relatives?"=A0 Since your examples seem to take large amounts of= time why not calibrate your problem against a set of known experimental re= sults and use lower levels of theory?=A0 You could increase the level of th= eory and see how the accuracy of the calibration fit goes.=A0

I do not know if your goal is to be able to model PKa's in the abso= lute sense or to understand what the relative values are.


My $0.= 02..

Cheers!

John McKelvey


On Thu, Jul 9, 2009 at 7:45 PM, Pavle Mocilac pavle.mocilac2{}mail.dcu.ie <owner-chemistry+*+ccl.net> wrote:

Sent to CCL by: Pavle Mocilac [pavle.mocilac2()mail.dcu.ie]
Dear Steve,

Thank you for this nice mail, you give me some new useful information.
As I mentioned im my previous mail, I'm using 64 bit machine and 64 bit= UNIX operating system (Silicon Graphics
Altix ICE 8200XE). I can not improve my hardware, and I'm quite sure that the better hardware I can not get. =A0 =A0 The memory I'm allocati= ng
is 256MW and I am using 8 processors - it is a maximum regarding the
number of processor power.
Therefore, I'm using quite awesome hardware/software performances.

Do you think that QCISD(T) method will be possible to replace with
QCISD method? How to specify T exclusion in QCISD(T) step of CBS-Q
protocol using keywords?
Regarding the scaling the molecule, I was developing a model using the
same molecules described in reference paper, aminopyridines (13 atoms)
and for them, the calculation lasts up to 45 minutes maximum,
including in a solvent conditions.
But my drug-like molecules contain 25 atoms, but in that case,
calculation goes to more than 3 days. In fact, as I have limited time
for one job I have to say that I never finished.
In the paper I'm using as a reference G1 level was used and they got ni= ce correlation (pKa{calc} vs
pKa{exp}). My idea, using CBS-Q, was, in fact, to obtain even better model.= ..
Maybe to use CBS-4M or to try G1? Although mistakes are supposed to
be bigger...


Best regards,

Pavle Mocilac

=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=3D=3D=3D=3D=3D
Pavle Mocilac
Postgraduate Researcher
T3 - Targeted Therapeutics and Theranostics
Room X249, School of Chemistry
Dublin City University
Dublin 9, Dublin, Ireland
mobile: +353872167022
mailto:pavle.mocilac2- -mail.dcu.ie
=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=3D=3D=3D=3D=3D
Thursday, July 9, 2009, 8:54:58 PM, you wrote:


> Sent to CCL by: [willsd*appstate.edu]
> Here is my $0.02...
> You would like to apply a method based on CBS-Q energies to estimate p= Ka values
> for molecules with as many as 25 atoms, and the QCISD(T)/6-31+G(d) ste= p is
> taking a long time. =A0You have G09 and would like to do this calculat= ion with
> this software, so as to come as close as possible to reproducing the m= ethods
> used for similar calculations in a reference paper...

> You have not mentioned this, but you may run into disk limitation prob= lems...
> this is quite likely with a 32 bit version on G09, since the 32 bit ve= rsion can
> address only a limited amount of disk, and QCISD(T) will need a lot of= disk. =A0(I
> should mention that I have not used G09... but previous versions of Gx= x had this
> limitation on the 32 bit versions, and I'd guess that 32 bit G09 d= oes too.) With
> the 64 bit version, running on a 64 bit machine with a 64 bit OS, you = will run
> out of physical disk long before you run out address space. =A0So one = repliers
> comments about 32 bit vs 64 bit is quite pertinent to this calculation= .

> The CBS methods (and other high accuracy combined methods (G1, G2, G3,=
> multi-coefficient G3, ....) all try, by various methods, to get the en= ergy
> accuracy of a very large basis set combined with a very accurate energ= y method,
> without actually doing such a calculation, since the required computin= g
> resources exceed what anyone has. =A0All such methods depend on variou= s post-HF
> energy calculations, and these depend on computing the effects on the = energy of
> substituting electrons from occupied (in the underlying HF wavefunctio= n)
> molecular orbitals into higher energy, unoccupied orbitals. =A0The SD = in QCISD(T)
> means that all possible subsitutions of single electrons, and pairs of= electrons
> are included in a self-consistent manner, and the (T) means that once = the SD
> part has converged, the effect of substituting three electrons (hence = triples)
> is estimated with perturbation theory. =A0The cost of such a calculati= on is
> roughly proportional to the sixth power of the number of basis functio= ns (this
> is included in the G09 output), and hence proportional to the sixth po= wer of the
> number of atoms. =A0The CBS method (and G1, G2....) has other steps as= well, and
> this will have other scaling behavior, so the overall scaling for the = entire
> CBS-Q method is not easy to predict.
> One replyer suggested replacing the QCISD(T) step with QCISD... this c= an be made
> to give a possibly useful method, but it will not be CBS-Q, and will n= ot be
> comparable to your reference paper.

> I'd suggest trying a scaled down version of your drug-like molecul= e (replace
> methyl or ethyl groups with H, etc), and see if you can get the atom c= ount down
> to 12 or so. =A0Do the CBS-Q calculation on this version, note the tim= e required,
> add a methyl or ethyl back in, repeat the CBS-Q and timing. =A0You can= then
> estimate the scaling, and use this to estimate how long your full 25 a= tom
> molecule might take. =A0My rule of thumb is that (except in unusual ci= rcumstances)
> if it is going to take longer than a week, I will have forgotten what = I wanted
> to calculate before it is done, and I am not interested.

> For some quite clear discussion on the calculations that lie inside co= mbined
> methods like CBS-Q, Frank Jensen's relatively new book (Introducti= on to
> Computational Chemistry) is pretty good. (IMHO, it is an introduction = in the
> sense that he introduces nearly all of the relevant equations, not in = the sense
> of simplified. =A0I appreciate his approach a great deal.)

> Good luck on your hunt for pKa estimates...

> Steve Williams


> ----- Original Message -----
>> From: "Pavle Mocilac pavle.mocilac2^-^mail.dcu.ie" <owner-chemistry_._ccl.net>
> Date: Thursday, July 9, 2009 10:03 am
> Subject: CCL:G: CBS-Q method in druglike molecules
> To: "Williams, Steve " <willsd_._conrad.appstate.edu>

>>
>> Sent to CCL by: Pavle Mocilac [pavle.mocilac2=3D=3D=3Dmail.dcu.ie]
>> Dear Simon,
>>
>> Thank you for the information about this software, but no, I have<= br> >> not and will not consider any other methods beside those that can<= br> >> be made with Gaussian 03 or 09 and described in "CaballeroNA,=
>> Melendez FJ, Munoz-Cara C, et al. =A0 Biophys. Chem =A0124 =A0(2)<= br> >> 155-160".
>> We do not have any intention to buy any new additional software bu= t
>> to use the one we have. Is seems to me that there are numerous
>> people on this CCL =A0that behave as salesman and always want to >> solve my problem by selling
>> me some additional software.
>> The reason we are using Gaussian is deeper, and for the sake of >> consistency and comparability we do not have attention to use so >> many different programmes that works in different way.
>> I would like to repeat that CBS-Q is my main problem and therefore=
>> I will be very happy and very grateful if there is somebody in thi= s
>> CCL who can help me with CBS-Q calculations in Gaussian.
>>
>>
>> Best regards,
>>
>> Pavle Mocilac
>>
>> =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=3D=3D=3D=3D=3D
>> Pavle Mocilac
>> Postgraduate Researcher
>> T3 - Targeted Therapeutics and Theranostics
>> Room X249, School of Chemistry
>> Dublin City University
>> Dublin 9, Dublin, Ireland
>> mobile: +353872167022
>> mailto:pavle.mocilac2~!~mail.dcu.ie
>> =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=3D=3D=3D=3D=3D
>> Wednesday, July 8, 2009, 7:21:16 PM, you wrote:
>>
>>
>> > Sent to CCL by: Simon Cross [simon!=3D!moldiscovery.com]
>>
>> > Hi Pavle, have you considered other methods for pKa calculati= on
>> of
>> > drug-like molecules? We recently published a method (Milletti= , F.
>> et al.
>> > (2007) New and Original pKa Prediction Method Using Grid
>> Molecular
>> > Interaction Fields. J. Chem. Inf. Model., 47, 2172-2181) whic= h is
>> used> in our software MoKa.
>>
>> > You can see more about it at www.moldiscovery.com/soft_moka.php<= /a>
>>
>> > We get an RMSE of 0.4 log units for the training set of 26000=
>> data
>> > points (very close to experimental error) and external predic= tion
>> error> of 0.7 log units.
>>
>> > Simon
>>
>> > Pavle Mocilac pavle.mocilac2]|[mail.dcu.ie wrote:
>> >> Sent to CCL by: "Pavle =A0Mocilac" [pavle.mocil= ac2{:}mail.dcu.ie]
>> >> My dear colleagues,
>> >>
>> >> Recently I sent the question about the calculation of pKa= of
>> small druglike molecules. The method asks employing high accuracy<= br> >> models like G1, G2, CBS-Q in order to get accurate Free Gibbs
>> energies using Gaussian 09, of course..
>> >> Now, it seems to me that this model works OK, and fast en= ough
>> for very small molecules up to 10 or 12 atoms (hydrogen included).=
>> But, my molecule has 25 atoms and currently is stacked at
>> QCISD(T)/6-31+G(d') step, calculating something called "t= riples"
>> for more than 2 days!!!!!
>> >> I would like to emphasize that this job is being calculat= ing
>> with Gaussian 09 (Linux version), using lots of memory () and 8 >> processors at SGI Altix ICE 8200EX.
>> >> What is the limit of CBS-Q method regarding the number of= atoms?
>> Is 25 atoms too much? Is there any option to use some kind of
>> additional keywords to exclude "triples" calculation at = QCISD(T)/6-
>> 31+G(d') step? Will that exclusion hamper accurate result? Is = it
>> better to use CBS-4M?>
>> >>
>> >>
>>
>>
>>
>> -=3D This is automatically added to each message by the mailing >> script =3D-
>> To recover the email address of the author of the message, please<= br> >> changethe strange characters on the top line to the _._ sign. You = can
>> also> Conferences:
>> http://server.ccl.net/chemistry/announcements/confer= ences/> Conferences:
> http://server.ccl.net/chemistry/announcements/conference= s/


-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY+*+ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST+*+ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--00163691fea5790800046e50a9e7-- From owner-chemistry@ccl.net Fri Jul 10 12:31:01 2009 From: "Hui Yang hui.yang]![utoledo.edu" To: CCL Subject: CCL:G: A question about open-shell singlet calculation in Gaussian. Message-Id: <-39740-090710121127-1559-h+Qq0spj//HnsoJ5P2AkOQ(!)server.ccl.net> X-Original-From: "Hui Yang" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_000D_01CA0152.D94A6D40" Date: Fri, 10 Jul 2009 11:37:47 -0400 MIME-Version: 1.0 Sent to CCL by: "Hui Yang" [hui.yang:-:utoledo.edu] This is a multipart message in MIME format. ------=_NextPart_000_000D_01CA0152.D94A6D40 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi Peng, Open shell and closed shell models are also referred to as unrestricted and restricted, respectively. So in Gaussian, open shell calculations use U (for unrestricted) and closed shell calculations use R. For example, RHF, UHF. Hui Yang > From: owner-chemistry+hui.yang==utoledo.edu * ccl.net [mailto:owner-chemistry+hui.yang==utoledo.edu * ccl.net] On Behalf Of huolei peng horaldraman^^gmail.com Sent: Friday, July 10, 2009 2:03 AM To: Yang, Hui Subject: CCL:G: A question about open-shell singlet calculation in Gaussian. Hi, Dear All: I have a question about calculations on the open-shell singlet using Gaussian. For example, nitrene species may have an open-shell and closed shell singlets. In Gaussian, how to set the calculation to get open-shell or closed-shell specifically? Thanks. Peng ------=_NextPart_000_000D_01CA0152.D94A6D40 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Peng,

 

Open shell and closed shell models are also referred to = as unrestricted and restricted, respectively. So in Gaussian, open shell calculations use U (for unrestricted) and closed shell calculations use = R. For example, RHF, UHF.

 

Hui Yang

 

 

From:= owner-chemistry+hui.yang=3D=3Dutoledo.edu * ccl.net = [mailto:owner-chemistry+hui.yang=3D=3Dutoledo.edu * ccl.net] On Behalf Of huolei peng horaldraman^^gmail.com
Sent: Friday, July 10, 2009 2:03 AM
To: Yang, Hui
Subject: CCL:G: A question about open-shell singlet calculation = in Gaussian.

 

Hi, Dear All:

 

I have a question about calculations on the open-shell singlet using = Gaussian. For example, nitrene species may have an open-shell and closed shell = singlets. In Gaussian, how to set the calculation to get open-shell or = closed-shell specifically? Thanks.

 

Peng

 

------=_NextPart_000_000D_01CA0152.D94A6D40-- From owner-chemistry@ccl.net Fri Jul 10 13:45:00 2009 From: "Huo-Lei Peng huolei.peng166|-|gmail.com" To: CCL Subject: CCL:G: Problem about calculation on the open-shell singlet in Gaussian. Message-Id: <-39741-090710134019-27684-qg7wiMGDx65Y0TFj817OWw-$-server.ccl.net> X-Original-From: Huo-Lei Peng Content-Type: multipart/alternative; boundary=0016e6d58f785e862f046e5d7678 Date: Fri, 10 Jul 2009 13:40:03 -0400 MIME-Version: 1.0 Sent to CCL by: Huo-Lei Peng [huolei.peng166() gmail.com] --0016e6d58f785e862f046e5d7678 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Thanks for your reply. I'd like to do calculation on the open-shell singlet (not a triplet). Open-shell(U) and restricted (R) calculations in Gaussian gave me same results. So in Gaussian, how to set input to make two electrons in two different orbitals but we still have a singlet state? Thanks. Peng On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto Fernandes jafernandes{:}ua.pt wrote: > > Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=-=ua.pt] > Hello > > I don't know if I understood your problem. Lets try. > Please see the following excerpt this input: > > # rb3lyp/3-21g guess=check > > The "r" before "b3lyp" means that you want a close shell calculation. If > you don't want electron pairing you have to put "ub3lyp" instead of > "rb3lyp". > > You should remember that a closed shell compound has always a spin=1, and > in a open shell the spin is different from 1. In the case of nitrene (R-N ?) > you can have R-N paired (spin=1) and unpaired (spin=3). > > So in the case of pairing you shoul input: > > ------------------------ > # rb3lyp/3-21g guess=check > > comment > > 0 1 > > geometry > > ---------------------- > If you want unpairing you should input: > > --------------------- > # ub3lyp/3-21g guess=check > > comment > > 0 3 > > geometry > > ---------------------- > If I haven't answered your question, please explain better. > > Best regards > > Jose > > > > > > "Huo-Lei Peng huolei.peng166(!)gmail.com" wrote: > > > > Sent to CCL by: Huo-Lei Peng [huolei.peng166]=[gmail.com] > > --001636c5a4fb6b291a046e527474 > > Content-Type: text/plain; charset=ISO-8859-1 > > Content-Transfer-Encoding: 7bit > > > > Hi, Dear All: > > I have a question about calculation on the open-shell singlet using > > Gaussian. For example, nitrene species may have an open-shell and closed > > shell singlets. In Gaussian, how to set the calculation to get open-shell > or > > closed-shell specifically? Thanks. > > > > Peng > > > > --001636c5a4fb6b291a046e527474 > > Content-Type: text/html; charset=ISO-8859-1 > > Content-Transfer-Encoding: quoted-printable > > > > Hi, Dear All:

I have a question about calculation on > the= > > open-shell singlet using Gaussian. For example, nitrene species may have > a= > > n open-shell and closed shell singlets. In Gaussian, how to set the > calcula= > > tion to get open-shell or closed-shell specifically? Thanks.
> >

Peng
> > > > --001636c5a4fb6b291a046e527474--> > > --0016e6d58f785e862f046e5d7678 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks for your reply. I'd like to do calculation on the open-shell sin= glet (not a triplet). Open-shell(U) and restricted (R) calculations in Gaus= sian gave=A0me=A0same=A0results.=A0So=A0in=A0Gaussian,=A0how=A0to=A0set=A0i= nput=A0to=A0make=A0two=A0electrons=A0in=A0two=A0different=A0orbitals=A0but= =A0we=A0still=A0have=A0a=A0singlet=A0state?

Thanks.

Peng

On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto Fernandes j= afernandes{:}ua.pt <owner-chemistry---ccl.net> wrote:

Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=3D-=3Dua.pt]
Hello

I don't know if I understood your problem. Lets try.
Please see the following excerpt this input:

# rb3lyp/3-21g guess=3Dcheck

The "r" before "b3lyp" means that you want a close shel= l calculation. If you don't want electron pairing you have to put "= ;ub3lyp" instead of "rb3lyp".

You should remember that a closed shell compound has always a spin=3D1, and= in a open shell the spin is different from 1. In the case of nitrene (R-N = ?) you can have R-N paired (spin=3D1) and unpaired (spin=3D3).

So in the case of pairing you shoul input:

------------------------
# rb3lyp/3-21g guess=3Dcheck

comment

0 1

geometry

----------------------
If you want unpairing you should input:

---------------------
# ub3lyp/3-21g guess=3Dcheck

comment

0 3

geometry

----------------------
If I haven't answered your question, please explain better.

Best regards

Jose




> "Huo-Lei Peng huolei.peng166(!)gmail.com" =A0wrote:
>
> Sent to CCL by: Huo-Lei Peng [huolei.peng166]=3D[gmail.com]
> --001636c5a4fb6b291a046e527474
> Content-Type: text/plain; charset=3DISO-8859-1
> Content-Transfer-Encoding: 7bit
>
> Hi, Dear All:
> I have a question about calculation on the open-shell singlet using > Gaussian. For example, nitrene species may have an open-shell and clos= ed
> shell singlets. In Gaussian, how to set the calculation to get open-sh= ell or
> closed-shell specifically? Thanks.
>
> Peng
>
> --001636c5a4fb6b291a046e527474
> Content-Type: text/html; charset=3DISO-8859-1
> Content-Transfer-Encoding: quoted-printable
>
> Hi, Dear All:<div><br></div><div>I have a ques= tion about calculation on the=3D
> =A0open-shell singlet using Gaussian. For example, nitrene species may= have a=3D
> n open-shell and closed shell singlets. In Gaussian, how to set the ca= lcula=3D
> tion to get open-shell or closed-shell specifically? Thanks.</div&g= t;
> <div><br></div><div>Peng</div>
>
> --001636c5a4fb6b291a046e527474--
>
>



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY---ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST---ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--0016e6d58f785e862f046e5d7678-- From owner-chemistry@ccl.net Fri Jul 10 14:56:01 2009 From: "Jose Alberto Fernandes jafernandes**ua.pt" To: CCL Subject: CCL:G: Problem about calculation on the open-shell singlet in Gaussian. Message-Id: <-39742-090710145512-28063-PkAWw4B4jCRhVRzVEDNddQ*_*server.ccl.net> X-Original-From: "Jose Alberto Fernandes" Date: Fri, 10 Jul 2009 14:55:09 -0400 Sent to CCL by: "Jose Alberto Fernandes" [jafernandes|-|ua.pt] Hello Peng This is more difficult you have to instruct Gaussian to make a singlet with two unpaired electrons. I looked in the gaussian guide and I found the test095.gjf, about the CH2 singlet. It presents the GVB command that does exactly what you want, but I cannot understand how it works. #p oss/3-21g geom=modela test force Gaussian Test Job 95 (Part 1): ch2 1-b1 using 504 0,1 c h h -o --Link1-- #p gvb(oss)/3-21g geom=modela test force Gaussian Test Job 95 (Part 2): ch2 1-b1 using 506 0,1 c h h -o Best regards Jose > "Huo-Lei Peng huolei.peng166|-|gmail.com" wrote: > > Sent to CCL by: Huo-Lei Peng [huolei.peng166() gmail.com] > --0016e6d58f785e862f046e5d7678 > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Encoding: 7bit > > Thanks for your reply. I'd like to do calculation on the open-shell singlet > (not a triplet). Open-shell(U) and restricted (R) calculations in Gaussian > gave me same results. So in Gaussian, how to set input to make two > electrons in two different orbitals but we still have a singlet state? > Thanks. > > Peng > > On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto Fernandes jafernandes{:}ua.pt > wrote: > > > > > Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=-=ua.pt] > > Hello > > > > I don't know if I understood your problem. Lets try. > > Please see the following excerpt this input: > > > > # rb3lyp/3-21g guess=check > > > > The "r" before "b3lyp" means that you want a close shell calculation. If > > you don't want electron pairing you have to put "ub3lyp" instead of > > "rb3lyp". > > > > You should remember that a closed shell compound has always a spin=1, and > > in a open shell the spin is different from 1. In the case of nitrene (R-N ?) > > you can have R-N paired (spin=1) and unpaired (spin=3). > > > > So in the case of pairing you shoul input: > > > > ------------------------ > > # rb3lyp/3-21g guess=check > > > > comment > > > > 0 1 > > > > geometry > > > > ---------------------- > > If you want unpairing you should input: > > > > --------------------- > > # ub3lyp/3-21g guess=check > > > > comment > > > > 0 3 > > > > geometry > > > > ---------------------- > > If I haven't answered your question, please explain better. > > > > Best regards > > > > Jose > > > > > > > > > > > "Huo-Lei Peng huolei.peng166(!)gmail.com" wrote: > > > > > > Sent to CCL by: Huo-Lei Peng [huolei.peng166]=[gmail.com] > > > --001636c5a4fb6b291a046e527474 > > > Content-Type: text/plain; charset=ISO-8859-1 > > > Content-Transfer-Encoding: 7bit > > > > > > Hi, Dear All: > > > I have a question about calculation on the open-shell singlet using > > > Gaussian. For example, nitrene species may have an open-shell and closed > > > shell singlets. In Gaussian, how to set the calculation to get open-shell > > or > > > closed-shell specifically? Thanks. > > > > > > Peng > > > > > > --001636c5a4fb6b291a046e527474 > > > Content-Type: text/html; charset=ISO-8859-1 > > > Content-Transfer-Encoding: quoted-printable > > > > > > Hi, Dear All:

I have a question about calculation on > > the= > > > open-shell singlet using Gaussian. For example, nitrene species may have > > a= > > > n open-shell and closed shell singlets. In Gaussian, how to set the > > calcula= > > > tion to get open-shell or closed-shell specifically? Thanks.
> > >

Peng
> > > > > > --001636c5a4fb6b291a046e527474--> > > > > > > --0016e6d58f785e862f046e5d7678 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Thanks for your reply. I'd like to do calculation on the open-shell sin= > glet (not a triplet). Open-shell(U) and restricted (R) calculations in Gaus= > sian gave=A0me=A0same=A0results.=A0So=A0in=A0Gaussian,=A0how=A0to=A0set=A0i= > nput=A0to=A0make=A0two=A0electrons=A0in=A0two=A0different=A0orbitals=A0but= > =A0we=A0still=A0have=A0a=A0singlet=A0state?
>
Thanks.

Peng

=3D"gmail_quote">On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto Fernandes j= > afernandes{:}ua.pt < ef=3D"mailto:owner-chemistry---ccl.net">owner-chemistry---ccl.net> > wrote:
>
x #ccc solid;padding-left:1ex;">
> Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=3D-=3D ef=3D"http://ua.pt" target=3D"_blank">ua.pt]
> Hello
>
> I don't know if I understood your problem. Lets try.
> Please see the following excerpt this input:
>
> # rb3lyp/3-21g guess=3Dcheck
>
> The "r" before "b3lyp" means that you want a close shel= > l calculation. If you don't want electron pairing you have to put "= > ;ub3lyp" instead of "rb3lyp".
>
> You should remember that a closed shell compound has always a spin=3D1, and= > in a open shell the spin is different from 1. In the case of nitrene (R-N = > ?) you can have R-N paired (spin=3D1) and unpaired (spin=3D3).
>
> So in the case of pairing you shoul input:
>
> ------------------------
> # rb3lyp/3-21g guess=3Dcheck
>
> comment
>
> 0 1
>
> geometry
>
> ----------------------
> If you want unpairing you should input:
>
> ---------------------
> # ub3lyp/3-21g guess=3Dcheck
>
> comment
>
> 0 3
>
> geometry
>
> ----------------------
> If I haven't answered your question, please explain better.
>
> Best regards
>
> Jose
>
>
>
>
> > "Huo-Lei Peng huolei.peng166(!) t=3D"_blank">gmail.com" =A0wrote:
> >
> > Sent to CCL by: Huo-Lei Peng [huolei.peng166]=3D[ il.com" target=3D"_blank">gmail.com]
> > --001636c5a4fb6b291a046e527474
> > Content-Type: text/plain; charset=3DISO-8859-1
> > Content-Transfer-Encoding: 7bit
>
>
> > Hi, Dear All:
> > I have a question about calculation on the open-shell singlet using > > > Gaussian. For example, nitrene species may have an open-shell and clos= > ed
> > shell singlets. In Gaussian, how to set the calculation to get open-sh= > ell or
> > closed-shell specifically? Thanks.
> >
> > Peng
> >
>
> --001636c5a4fb6b291a046e527474
> > Content-Type: text/html; charset=3DISO-8859-1
> > Content-Transfer-Encoding: quoted-printable
> >
> > Hi, Dear All:<div><br></div><div>I have a ques= > tion about calculation on the=3D
> > =A0open-shell singlet using Gaussian. For example, nitrene species may= > have a=3D
> > n open-shell and closed shell singlets. In Gaussian, how to set the ca= > lcula=3D
> > tion to get open-shell or closed-shell specifically? Thanks.</div&g= > t;
> > <div><br></div><div>Peng</div>
> >
> > --001636c5a4fb6b291a046e527474--
> >
> >
>
>
>
> -=3D This is automatically added to each message by the mailing script =3D-= > >
> E-mail to subscribers: CHEMISTRY---ccl.n= > et or use:
> =A0 =A0 =A0 get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message
>
> E-mail to administrators: CHEM= > ISTRY-REQUEST---ccl.net or use
> =A0 =A0 =A0 get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message
>
> Subscribe/Unsubscribe:
> =A0 =A0 =A0 =3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml
>
> Before posting, check wait time at: =3D"_blank">http://www.ccl.net
>
> Job: http://www.ccl.n= > et/jobs
> Conferences: rences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/co= > nferences/
>
> Search Messages: tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml a>
> > =A0 =A0 =A0h= > ttp://www.ccl.net/spammers.txt
>
> RTFI: t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/
>
>
>

> > --0016e6d58f785e862f046e5d7678-- > > From owner-chemistry@ccl.net Fri Jul 10 15:31:00 2009 From: "Matthew Clark mclark=-=pharmatrope.com" To: CCL Subject: CCL: *human* adverse event models QSAR models now available Message-Id: <-39743-090710134134-27842-ycqO2wT5vcc0PZbs5dROOQ%%server.ccl.net> X-Original-From: "Matthew Clark" Date: Fri, 10 Jul 2009 13:41:30 -0400 Sent to CCL by: "Matthew Clark" [mclark!=!pharmatrope.com] Announcing Titanium Human Adverse Event Models Pharmatrope Ltd. Announces the availability of the Titanium human adverse event models. Titanium human adverse event models help you anticipate adverse events you will encounter in clinical trials, resulting in dramatic savings for drug discovery and development programs. While many models can predict animal toxicity based on structure, Pharmatrope Titanium(TM) models are based on human data gathered by the United States Food and Drug Administration (FDA) under its Adverse Events Reporting System (AERS). The AERS is a collection of over 80 million adverse events reported over the last decade. The models are created using a fragment-based QSAR using PLS (M. Song and M. Clark, J. Chem. Inf. Model. 46 (2006), pp. 392400) go to http://pharmatrope.com for more information, and a free 3D molecule spreadsheet. email info:+:pharmatrope.com for licensing information. A demo package with three models (venous thrombosis, tendon rupture, tendonitis) is available for evaluation. Matthew Clark Pharmatrope Ltd. From owner-chemistry@ccl.net Fri Jul 10 16:06:00 2009 From: "Johannes Johansson johjo76\a/gmail.com" To: CCL Subject: CCL:G: Problem about calculation on the open-shell singlet in Gaussian. Message-Id: <-39744-090710150127-30728-QptQ5L36p/GdBmb65zYScw---server.ccl.net> X-Original-From: Johannes Johansson Content-Type: multipart/alternative; boundary=0015174c362c81aa1a046e5e98cf Date: Fri, 10 Jul 2009 21:01:11 +0200 MIME-Version: 1.0 Sent to CCL by: Johannes Johansson [johjo76!A!gmail.com] --0015174c362c81aa1a046e5e98cf Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Ping, I guess that what you are after is a scf solution in which two electrons occupies different orbitals but are antiferromagnetically coupled? In Gaussian you can first try to set the spin multiplicity to singlet but u= sing udft (or uhf) and the command guess=3Dmix or guess=3D(mix,always). If this doesnt work you can first do a SP calc (with the commands above) on the geometry of the corresponding triplet state, since this will probably b= e more similar to the geometry of the open shell singlet than to that of the closed shell singlet. (this might also work without the mix keyword) If you get an open shell singlet, which you will se in the pop analysis, you can then relax the geom by starting a geom opt in this state. Note that this open shell singlet is not an eigenfunction of the S^2 operator (it is a broken symmetry state in the single determinant formalism= ) and that it is spin contaminated by the corresponding triplet state. If the energy difference between the open shell singlet and the triplet is large you should correct the energy of the open shell singlet by using the formalism derived by Noodleman (J. Chem. Phys. 1981, 74, 5737, or Adv. Inorg. Chem. 1992, 38, 423). Good luck! /Johannes --=20 Adam Johannes Johansson Ph.D., M.Sc. Institut f=C3=BCr Organische Chemie RWTH Aachen University Landoltweg 1 52056 Aachen Germany Cell phone:0708178487 E-mail:johjo76/a\gmail.com Research web page:www.physto.se/~johjo 2009/7/10 Huo-Lei Peng huolei.peng166|-|gmail.com > Thanks for your reply. I'd like to do calculation on the open-shell singl= et > (not a triplet). Open-shell(U) and restricted (R) calculations in Gaussia= n > gave me same results. So in Gaussian, how to set input to make two electr= ons in two different orbitals but we still have a singlet state? > Thanks. > > Peng > > On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto Fernandes jafernandes{:} > ua.pt wrote: > >> >> Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=3D-=3Dua.pt] >> Hello >> >> I don't know if I understood your problem. Lets try. >> Please see the following excerpt this input: >> >> # rb3lyp/3-21g guess=3Dcheck >> >> The "r" before "b3lyp" means that you want a close shell calculation. If >> you don't want electron pairing you have to put "ub3lyp" instead of >> "rb3lyp". >> >> You should remember that a closed shell compound has always a spin=3D1, = and >> in a open shell the spin is different from 1. In the case of nitrene (R-= N ?) >> you can have R-N paired (spin=3D1) and unpaired (spin=3D3). >> >> So in the case of pairing you shoul input: >> >> ------------------------ >> # rb3lyp/3-21g guess=3Dcheck >> >> comment >> >> 0 1 >> >> geometry >> >> ---------------------- >> If you want unpairing you should input: >> >> --------------------- >> # ub3lyp/3-21g guess=3Dcheck >> >> comment >> >> 0 3 >> >> geometry >> >> ---------------------- >> If I haven't answered your question, please explain better. >> >> Best regards >> >> Jose >> >> >> >> >> > "Huo-Lei Peng huolei.peng166(!)gmail.com" wrote: >> > >> > Sent to CCL by: Huo-Lei Peng [huolei.peng166]=3D[gmail.com] >> > --001636c5a4fb6b291a046e527474 >> > Content-Type: text/plain; charset=3DISO-8859-1 >> > Content-Transfer-Encoding: 7bit >> > >> > Hi, Dear All: >> > I have a question about calculation on the open-shell singlet using >> > Gaussian. For example, nitrene species may have an open-shell and clos= ed >> > shell singlets. In Gaussian, how to set the calculation to get >> open-shell or >> > closed-shell specifically? Thanks. >> > >> > Peng >> > >> > --001636c5a4fb6b291a046e527474 >> > Content-Type: text/html; charset=3DISO-8859-1 >> > Content-Transfer-Encoding: quoted-printable >> > >> > Hi, Dear All:

I have a question about calculation o= n >> the=3D >> > open-shell singlet using Gaussian. For example, nitrene species may >> have a=3D >> > n open-shell and closed shell singlets. In Gaussian, how to set the >> calcula=3D >> > tion to get open-shell or closed-shell specifically? Thanks.
>> >

Peng
>> > >> > --001636c5a4fb6b291a046e527474-- >> > >> > >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY**ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use>> >> >> > --=20 Adam Johannes Johansson Ph.D., M.Sc. Institut f=C3=BCr Organische Chemie RWTH Aachen University Landoltweg 1 52056 Aachen Germany Cell phone:0708178487 E-mail:johjo76/a\gmail.com Research web page:www.physto.se/~johjo --0015174c362c81aa1a046e5e98cf Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Ping,=C2=A0

I guess that what you are after is a scf solution in which= two electrons occupies different orbitals but are antiferromagnetically co= upled?

In Gaussian you can first try to set the spin multiplic= ity to singlet=C2=A0but= =C2=A0using udft (or uhf) and the command guess=3Dmix or=C2=A0guess=3D(mix,= always).

If this doesnt work you can first do a SP calc (with the com= mands above) on the geometry of the corresponding triplet state, since this= will probably be more similar to the geometry of the open shell singlet th= an to that of the closed shell singlet. (this might also work without the m= ix keyword)=C2=A0If you get an open shell singlet, which you will se in the= pop analysis, you can then relax the geom by starting a geom opt in this s= tate.

Note that this open shell si= nglet is not an eigenfunction of the S^2 operator (it is a broken symmetry = state in the single determinant formalism) and that it is spin contaminated= by the corresponding triplet state. If the energy difference between the o= pen shell singlet and the triplet is large you should correct the energy of= the open shell singlet by using the formalism derived by Noodleman (J. Che= m. Phys. 1981, 74, 5737, or Adv. Inorg. Chem. 1992, 38, 423).

Good luck!

/Johannes

--=C2=A0
Adam Johannes Johansson
Ph.D., M.Sc.
Institut f= =C3=BCr Organische Chemie
RWTH Aachen University
Landoltweg 1
52056 Aachen
Germany
Cell p= hone:0708178487
E-mail:johjo76/a\gmail.com
= Research web page:www.physto.se/~johjo<= /div>





2009/7/10 Huo-Lei Peng huolei.peng166|-|gmail.com <owner-chemistry/a\ccl.net>
Thanks for your reply. I'd like to do c= alculation on the open-shell singlet (not a triplet). Open-shell(U) and res= tricted (R) calculations in Gaussian gave=C2=A0me=C2=A0same=C2=A0results.= =C2=A0So=C2=A0in=C2=A0Gaussian,=C2=A0how=C2=A0to=C2=A0set=C2=A0input=C2=A0t= o=C2=A0make=C2=A0two=C2=A0electrons=C2=A0in=C2=A0two=C2=A0different=C2=A0or= bitals=C2=A0but=C2=A0we=C2=A0still=C2=A0have=C2=A0a=C2=A0singlet=C2=A0state= ?

Thanks.

Peng

On Fri, Jul 10, 2009 at = 11:14 AM, Jose Alberto Fernandes jafernandes{:}ua.pt <owner-chemistry**ccl.net> w= rote:

Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=3D-=3Dua.pt]
Hello

I don't know if I understood your problem. Lets try.
Please see the following excerpt this input:

# rb3lyp/3-21g guess=3Dcheck

The "r" before "b3lyp" means that you want a close shel= l calculation. If you don't want electron pairing you have to put "= ;ub3lyp" instead of "rb3lyp".

You should remember that a closed shell compound has always a spin=3D1, and= in a open shell the spin is different from 1. In the case of nitrene (R-N = ?) you can have R-N paired (spin=3D1) and unpaired (spin=3D3).

So in the case of pairing you shoul input:

------------------------
# rb3lyp/3-21g guess=3Dcheck

comment

0 1

geometry

----------------------
If you want unpairing you should input:

---------------------
# ub3lyp/3-21g guess=3Dcheck

comment

0 3

geometry

----------------------
If I haven't answered your question, please explain better.

Best regards

Jose




> "Huo-Lei Peng huolei.peng166(!)gmail.com" =C2=A0wrote:
>
> Sent to CCL by: Huo-Lei Peng [huolei.peng166]=3D[gmail.com]
> --001636c5a4fb6b291a046e527474
> Content-Type: text/plain; charset=3DISO-8859-1
> Content-Transfer-Encoding: 7bit
>
> Hi, Dear All:
> I have a question about calculation on the open-shell singlet using > Gaussian. For example, nitrene species may have an open-shell and clos= ed
> shell singlets. In Gaussian, how to set the calculation to get open-sh= ell or
> closed-shell specifically? Thanks.
>
> Peng
>
> --001636c5a4fb6b291a046e527474
> Content-Type: text/html; charset=3DISO-8859-1
> Content-Transfer-Encoding: quoted-printable
>
> Hi, Dear All:<div><br></div><div>I have a ques= tion about calculation on the=3D
> =C2=A0open-shell singlet using Gaussian. For example, nitrene species = may have a=3D
> n open-shell and closed shell singlets. In Gaussian, how to set the ca= lcula=3D
> tion to get open-shell or closed-shell specifically? Thanks.</div&g= t;
> <div><br></div><div>Peng</div>
>
> --001636c5a4fb6b291a046e527474--
>
>



-=3D This is automatically added to each message by the mailing script =3D-
E-mail to subscribers: CHEMISTRY**ccl.net or use:
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/






--
Adam Johannes Johansson=
Ph.D., M.Sc.
Institut f=C3=BCr Organische Chemie
RWTH Aachen Univ= ersity
Landoltweg 1
52056 Aachen
Germany
Cell phone:0708178487<= br> E-mail:johjo76/a\gmail.com<= br>Research web page:www.physto.se/= ~johjo

--0015174c362c81aa1a046e5e98cf-- From owner-chemistry@ccl.net Fri Jul 10 16:41:01 2009 From: "Grant Hill jghill%wsu.edu" To: CCL Subject: CCL:G: Problem about calculation on the open-shell singlet in Gaussian. Message-Id: <-39745-090710153050-13775-x+qlvR4iHXLAHxW+hDs8HA|server.ccl.net> X-Original-From: Grant Hill Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 10 Jul 2009 11:25:45 -0700 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Grant Hill [jghill ~ wsu.edu] One way forward would be to specify some sort of guess wavefunction, but I'm unsure of how to do this with Gaussian. You could try Guess=Mix. This mixes the HOMO and LUMO, destroys spatial symmetry and thus tries to prevent collapse to a restricted solution. Reading the Guess entry in the Gaussian manual may provide further clues. You may also want to consider the symmetry of your wavefunction. HTH, Grant On 10 Jul 2009, at 10:40, Huo-Lei Peng huolei.peng166|-|gmail.com wrote: > Thanks for your reply. I'd like to do calculation on the open-shell > singlet (not a triplet). Open-shell(U) and restricted (R) > calculations in Gaussian gave me same results. So in Gaussian, how > to set input to make two electrons in two different orbitals but we > still have a singlet state? > > Thanks. > > Peng > > On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto Fernandes > jafernandes{:}ua.pt wrote: > > Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=-=ua.pt] > Hello > > I don't know if I understood your problem. Lets try. > Please see the following excerpt this input: > > # rb3lyp/3-21g guess=check > > The "r" before "b3lyp" means that you want a close shell > calculation. If you don't want electron pairing you have to put > "ub3lyp" instead of "rb3lyp". > > You should remember that a closed shell compound has always a > spin=1, and in a open shell the spin is different from 1. In the > case of nitrene (R-N ?) you can have R-N paired (spin=1) and > unpaired (spin=3). > > So in the case of pairing you shoul input: > > ------------------------ > # rb3lyp/3-21g guess=check > > comment > > 0 1 > > geometry > > ---------------------- > If you want unpairing you should input: > > --------------------- > # ub3lyp/3-21g guess=check > > comment > > 0 3 > > geometry > > ---------------------- > If I haven't answered your question, please explain better. > > Best regards > > Jose > > > > > > "Huo-Lei Peng huolei.peng166(!)gmail.com" wrote: > > > > Sent to CCL by: Huo-Lei Peng [huolei.peng166]=[gmail.com] > > --001636c5a4fb6b291a046e527474 > > Content-Type: text/plain; charset=ISO-8859-1 > > Content-Transfer-Encoding: 7bit > > > > Hi, Dear All: > > I have a question about calculation on the open-shell singlet using > > Gaussian. For example, nitrene species may have an open-shell and > closed > > shell singlets. In Gaussian, how to set the calculation to get > open-shell or > > closed-shell specifically? Thanks. > > > > Peng > > > > --001636c5a4fb6b291a046e527474 > > Content-Type: text/html; charset=ISO-8859-1 > > Content-Transfer-Encoding: quoted-printable > > > > Hi, Dear All:

I have a question about > calculation on the= > > open-shell singlet using Gaussian. For example, nitrene species > may have a= > > n open-shell and closed shell singlets. In Gaussian, how to set > the calcula= > > tion to get open-shell or closed-shell specifically? Thanks.
> >

Peng
> > > > --001636c5a4fb6b291a046e527474-- > > > > > > > > -= This is automatically added to each message by the mailing script > =- > > > > E-mail to subscribers: CHEMISTRY**ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > > From owner-chemistry@ccl.net Fri Jul 10 17:17:00 2009 From: "Johannes Johansson johjo76]~[gmail.com" To: CCL Subject: CCL:G: Problem about calculation on the open-shell singlet in Gaussian. Message-Id: <-39746-090710160646-12187-wVyHGiFQEfUrpTWJ8TpocA(-)server.ccl.net> X-Original-From: Johannes Johansson Content-Type: multipart/alternative; boundary=0015175114da1af58c046e5f8111 Date: Fri, 10 Jul 2009 22:06:13 +0200 MIME-Version: 1.0 Sent to CCL by: Johannes Johansson [johjo76++gmail.com] --0015175114da1af58c046e5f8111 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Ping, I guess that what you are after is a scf solution in which two electrons occupies different orbitals but are antiferromagnetically coupled? In Gaussian you can first try to set the spin multiplicity to singlet but u= sing udft (or uhf) and the command guess=3Dmix or guess=3D(mix,always). If this doesnt work you can first do a SP calc (with the commands above) on the geometry of the corresponding triplet state, since this will probably b= e more similar to the geometry of the open shell singlet than to that of the closed shell singlet. (this might also work without the mix keyword) If you get an open shell singlet, which you will se in the pop analysis, you can then relax the geom by starting a geom opt in this state. Note that this open shell singlet is not an eigenfunction of the S^2 operator (it is a broken symmetry state in the single determinant formalism= ) and that it is spin contaminated by the corresponding triplet state. If the energy difference between the open shell singlet and the triplet is large you should correct the energy of the open shell singlet by using the formalism derived by Noodleman (J. Chem. Phys. 1981, 74, 5737, or Adv. Inorg. Chem. 1992, 38, 423). If you need help with this, please feel free t= o contact me. Good luck! /Johannes --=20 Adam Johannes Johansson Ph.D., M.Sc. Institut f=C3=BCr Organische Chemie RWTH Aachen University Landoltweg 1 52056 Aachen Germany 2009/7/10 Jose Alberto Fernandes jafernandes**ua.pt > > Sent to CCL by: "Jose Alberto Fernandes" [jafernandes|-|ua.pt] > Hello Peng > > This is more difficult you have to instruct Gaussian to make a singlet wi= th > two unpaired electrons. I looked in the gaussian guide and I found the > test095.gjf, about the CH2 singlet. It presents the GVB command that does > exactly what you want, but I cannot understand how it works. > > #p oss/3-21g geom=3Dmodela test force > > Gaussian Test Job 95 (Part 1): > ch2 1-b1 using 504 > > 0,1 > c h h -o > > --Link1-- > #p gvb(oss)/3-21g geom=3Dmodela test force > > Gaussian Test Job 95 (Part 2): > ch2 1-b1 using 506 > > 0,1 > c h h -o > > Best regards > > Jose > > > "Huo-Lei Peng huolei.peng166|-|gmail.com" wrote: > > > > Sent to CCL by: Huo-Lei Peng [huolei.peng166() gmail.com] > > --0016e6d58f785e862f046e5d7678 > > Content-Type: text/plain; charset=3DISO-8859-1 > > Content-Transfer-Encoding: 7bit > > > > Thanks for your reply. I'd like to do calculation on the open-shell > singlet > > (not a triplet). Open-shell(U) and restricted (R) calculations in > Gaussian > > gave me same results. So in Gaussian, how to set input to make two > > electrons in two different orbitals but we still have a singlet state? > > Thanks. > > > > Peng > > > > On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto Fernandes jafernandes{:} > ua.pt > > wrote: > > > > > > > > Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=3D-=3Dua.pt] > > > Hello > > > > > > I don't know if I understood your problem. Lets try. > > > Please see the following excerpt this input: > > > > > > # rb3lyp/3-21g guess=3Dcheck > > > > > > The "r" before "b3lyp" means that you want a close shell calculation. > If > > > you don't want electron pairing you have to put "ub3lyp" instead of > > > "rb3lyp". > > > > > > You should remember that a closed shell compound has always a spin=3D= 1, > and > > > in a open shell the spin is different from 1. In the case of nitrene > (R-N ?) > > > you can have R-N paired (spin=3D1) and unpaired (spin=3D3). > > > > > > So in the case of pairing you shoul input: > > > > > > ------------------------ > > > # rb3lyp/3-21g guess=3Dcheck > > > > > > comment > > > > > > 0 1 > > > > > > geometry > > > > > > ---------------------- > > > If you want unpairing you should input: > > > > > > --------------------- > > > # ub3lyp/3-21g guess=3Dcheck > > > > > > comment > > > > > > 0 3 > > > > > > geometry > > > > > > ---------------------- > > > If I haven't answered your question, please explain better. > > > > > > Best regards > > > > > > Jose > > > > > > > > > > > > > > > > "Huo-Lei Peng huolei.peng166(!)gmail.com" wrote: > > > > > > > > Sent to CCL by: Huo-Lei Peng [huolei.peng166]=3D[gmail.com] > > > > --001636c5a4fb6b291a046e527474 > > > > Content-Type: text/plain; charset=3DISO-8859-1 > > > > Content-Transfer-Encoding: 7bit > > > > > > > > Hi, Dear All: > > > > I have a question about calculation on the open-shell singlet using > > > > Gaussian. For example, nitrene species may have an open-shell and > closed > > > > shell singlets. In Gaussian, how to set the calculation to get > open-shell > > > or > > > > closed-shell specifically? Thanks. > > > > > > > > Peng > > > > > > > > --001636c5a4fb6b291a046e527474 > > > > Content-Type: text/html; charset=3DISO-8859-1 > > > > Content-Transfer-Encoding: quoted-printable > > > > > > > > Hi, Dear All:

I have a question about calculatio= n > on > > > the=3D > > > > open-shell singlet using Gaussian. For example, nitrene species ma= y > have > > > a=3D > > > > n open-shell and closed shell singlets. In Gaussian, how to set the > > > calcula=3D > > > > tion to get open-shell or closed-shell specifically? Thanks.
> > > >

Peng
> > > > > > > > --001636c5a4fb6b291a046e527474--> > > > > > > > > > > --0016e6d58f785e862f046e5d7678 > > Content-Type: text/html; charset=3DISO-8859-1 > > Content-Transfer-Encoding: quoted-printable > > > > Thanks for your reply. I'd like to do calculation on the open-shell > sin=3D > > glet (not a triplet). Open-shell(U) and restricted (R) calculations in > Gaus=3D > > sian > gave=3DA0me=3DA0same=3DA0results.=3DA0So=3DA0in=3DA0Gaussian,=3DA0how=3DA= 0to=3DA0set=3DA0i=3D > > > nput=3DA0to=3DA0make=3DA0two=3DA0electrons=3DA0in=3DA0two=3DA0different= =3DA0orbitals=3DA0but=3D > > =3DA0we=3DA0still=3DA0have=3DA0a=3DA0singlet=3DA0state?
> >
Thanks.

Peng

class=3D > > =3D3D"gmail_quote">On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto Ferna= ndes > j=3D > > afernandes{:}ua.pt &= lt; hr=3D > > ef=3D3D"mailto:owner-chemistry---ccl.net">owner-chemistry---ccl.net > > > > wrote:
> >
.8ex;border-left:1p=3D > > x #ccc solid;padding-left:1ex;">
> > Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=3D3D-= =3D3D hr=3D > > ef=3D3D"http://ua.pt" target=3D3D"_blank">ua.pt]
> > Hello
> >
> > I don't know if I understood your problem. Lets try.
> > Please see the following excerpt this input:
> >
> > # rb3lyp/3-21g guess=3D3Dcheck
> >
> > The "r" before "b3lyp" means that you want a close > shel=3D > > l calculation. If you don't want electron pairing you have to put > "=3D > > ;ub3lyp" instead of "rb3lyp".
> >
> > You should remember that a closed shell compound has always a spin=3D3D= 1, > and=3D > > in a open shell the spin is different from 1. In the case of nitrene > (R-N =3D > > ?) you can have R-N paired (spin=3D3D1) and unpaired (spin=3D3D3).
> >
> > So in the case of pairing you shoul input:
> >
> > ------------------------
> > # rb3lyp/3-21g guess=3D3Dcheck
> >
> > comment
> >
> > 0 1
> >
> > geometry
> >
> > ----------------------
> > If you want unpairing you should input:
> >
> > ---------------------
> > # ub3lyp/3-21g guess=3D3Dcheck
> >
> > comment
> >
> > 0 3
> >
> > geometry
> >
> > ----------------------
> > If I haven't answered your question, please explain better.
> >
> > Best regards
> >
> > Jose
> >
> >
> >
> >
> > > "Huo-Lei Peng huolei.peng166(!) targe=3D > > t=3D3D"_blank">gmail.com" =3DA0wrote:
> > >
> > > Sent to CCL by: Huo-Lei Peng [huolei.peng166]=3D3D[ http://gma=3D > > il.com" target=3D3D"_blank">gmail.com]
> > > --001636c5a4fb6b291a046e527474
> > > Content-Type: text/plain; charset=3D3DISO-8859-1
> > > Content-Transfer-Encoding: 7bit
> >
>
> > > Hi, Dear All:
> > > I have a question about calculation on the open-shell singlet > using > > > > > Gaussian. For example, nitrene species may have an open-shell and > clos=3D > > ed
> > > shell singlets. In Gaussian, how to set the calculation to get > open-sh=3D > > ell or
> > > closed-shell specifically? Thanks.
> > >
> > > Peng
> > >
> >
> --001636c5a4fb6b291a046e527474
> > > Content-Type: text/html; charset=3D3DISO-8859-1
> > > Content-Transfer-Encoding: quoted-printable
> > >
> > > Hi, Dear All:<div><br></div><div>I have a > ques=3D > > tion about calculation on the=3D3D
> > > =3DA0open-shell singlet using Gaussian. For example, nitrene speci= es > may=3D > > have a=3D3D
> > > n open-shell and closed shell singlets. In Gaussian, how to set th= e > ca=3D > > lcula=3D3D
> > > tion to get open-shell or closed-shell specifically? > Thanks.</div&g=3D > > t;
> > > <div><br></div><div>Peng</div>
> > >
> > > --001636c5a4fb6b291a046e527474--
> > >
> > >
> >
> >
> >
> > -=3D3D This is automatically added to each message by the mailing scrip= t > =3D3D-=3D > > > >
> > E-mail to subscribers: ">CHEMISTRY---ccl.n=3D > > et or use:
> > =3DA0 =3DA0 =3DA0 tar=3D > > get=3D3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message > >
> > E-mail to administrators: ">CHEM=3D > > ISTRY-REQUEST---ccl.net or use
> > =3DA0 =3DA0 =3DA0 tar=3D > > get=3D3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message > >
> > Subscribe/Unsubscribe:
> > =3DA0 =3DA0 =3DA0 target=3D > > =3D3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml
> >
> > Before posting, check wait time at: target=3D > > =3D3D"_blank">http://www.ccl.net
> >
> > Job: > http://www.ccl.n=3D > > et/jobs
> > Conferences: http://server.ccl.net/chemistry/announcements/confe=3D > > rences/" target=3D3D"_blank"> > http://server.ccl.net/chemistry/announcements/co=3D > > nferences/
> >
> > Search Messages: http://www.ccl.net/chemistry/searchccl/index.sh=3D > > tml" target=3D3D"_blank"> > http://www.ccl.net/chemistry/searchccl/index.shtml > a>
> > > > =3DA0 =3DA0 =3DA0 target=3D3D"_blank">h=3D > > ttp://www.ccl.net/spammers.txt
> >
> > RTFI: targe=3D > > t=3D3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/<= br> > >
> >
> >

> > > > --0016e6d58f785e862f046e5d7678-- > > > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Adam Johannes Johansson Ph.D., M.Sc. Institut f=C3=BCr Organische Chemie RWTH Aachen University Landoltweg 1 52056 Aachen Germany Cell phone:0708178487 E-mail:johjo76::gmail.com Research web page:www.physto.se/~johjo --0015175114da1af58c046e5f8111 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Ping,=C2=A0
I guess that what you are after is a scf solution in which two = electrons occupies different orbitals but are antiferromagnetically coupled= ?

In Gaussian you can first try to set the spin multiplic= ity to singlet=C2=A0but= =C2=A0using udft (or uhf) and the command guess=3Dmix or=C2=A0guess=3D(mix,= always).

If this doesnt work you can first do a SP calc (with the com= mands above) on the geometry of the corresponding triplet state, since this= will probably be more similar to the geometry of the open shell singlet th= an to that of the closed shell singlet. (this might also work without the m= ix keyword)=C2=A0If you get an open shell singlet, which you will se in the= pop analysis, you can then relax the geom by starting a geom opt in this s= tate.

Note that this open shell si= nglet is not an eigenfunction of the S^2 operator (it is a broken symmetry = state in the single determinant formalism) and that it is spin contaminated= by the corresponding triplet state. If the energy difference between the o= pen shell singlet and the triplet is large you should correct the energy of= the open shell singlet by using the formalism derived by Noodleman (J. Che= m. Phys. 1981, 74, 5737, or Adv. Inorg. Chem. 1992, 38, 423). If you need h= elp with this, please feel free to contact me.

Good luck!

/Johannes

--=C2=A0
Adam Johannes Johansson
Ph.D., M.Sc.
Institut f= =C3=BCr Organische Chemie
RWTH Aachen University
Landoltweg 1
52056 Aachen
Germany



2009/7/10 Jose Alberto F= ernandes jafernandes**ua.pt = <owner-chemistry::ccl.net&= gt;

Sent to CCL by: "Jose Alberto Fernandes" [jafernandes|-|ua.pt]
Hello Peng

This is more difficult you have to instruct Gaussian to make a singlet with= two unpaired electrons. I looked in the gaussian guide and I found the tes= t095.gjf, about the CH2 singlet. It presents the GVB command that does exac= tly what you want, but I cannot understand how it works.

#p oss/3-21g geom=3Dmodela test force

Gaussian Test Job 95 (Part 1):
ch2 1-b1 using 504

0,1
c h h -o

--Link1--
#p gvb(oss)/3-21g geom=3Dmodela test force

Gaussian Test Job 95 (Part 2):
ch2 1-b1 using 506

0,1
c h h -o

Best regards

Jose

> "Huo-Lei Peng huolei.peng166|-|gmail.com" =C2=A0wrote:
>
> Sent to CCL by: Huo-Lei Peng [huolei.peng166() gmail.com]
> --0016e6d58f785e862f046e5d7678
> Content-Type: text/plain; charset=3D= ISO-8859-1
> Content-Transfer-Encoding: 7bit
>
> Thanks for your reply. I'd like to do calculation on the open-shel= l singlet
> (not a triplet). Open-shell(U) and restricted (R) calculations in Gaus= sian
> gave me same results. So in Gaussian, how to set input to make two
> electrons in two different orbitals but we still have a singlet state?=
> Thanks.
>
> Peng
>
> On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto Fernandes jafernandes{:= }ua.pt
> <own= er-chemistry---ccl.net> wrote:
>
> >
> > Sent to CCL by: "Jose Alberto Fernandes" [jafernandes= =3D-=3Dua.pt]
> > Hello
> >
> > I don't know if I understood your problem. Lets try.
> > Please see the following excerpt this input:
> >
> > # rb3lyp/3-21g guess=3Dcheck
> >
> > The "r" before "b3lyp" means that you want a = close shell calculation. If
> > you don't want electron pairing you have to put "ub3lyp&= quot; instead of
> > "rb3lyp".
> >
> > You should remember that a closed shell compound has always a spi= n=3D1, and
> > in a open shell the spin is different from 1. In the case of nitr= ene (R-N ?)
> > you can have R-N paired (spin=3D1) and unpaired (spin=3D3).
> >
> > So in the case of pairing you shoul input:
> >
> > ------------------------
> > # rb3lyp/3-21g guess=3Dcheck
> >
> > comment
> >
> > 0 1
> >
> > geometry
> >
> > ----------------------
> > If you want unpairing you should input:
> >
> > ---------------------
> > # ub3lyp/3-21g guess=3Dcheck
> >
> > comment
> >
> > 0 3
> >
> > geometry
> >
> > ----------------------
> > If I haven't answered your question, please explain better. > >
> > Best regards
> >
> > Jose
> >
> >
> >
> >
> > > "Huo-Lei Peng huolei.peng166(!)gmail.com" =C2=A0wrote:
> > >
> > > Sent to CCL by: Huo-Lei Peng [huolei.peng166]=3D[gmail.com]
> > > --001636c5a4fb6b291a046e527474
> > > Content-Type: text/plain; charset=3DISO-8859-1
> > > Content-Transfer-Encoding: 7bit
> > >
> > > Hi, Dear All:
> > > I have a question about calculation on the open-shell single= t using
> > > Gaussian. For example, nitrene species may have an open-shel= l and closed
> > > shell singlets. In Gaussian, how to set the calculation to g= et open-shell
> > or
> > > closed-shell specifically? Thanks.
> > >
> > > Peng
> > >
> > > --001636c5a4fb6b291a046e527474
> > > Content-Type: text/html; charset=3DISO-8859-1
> > > Content-Transfer-Encoding: quoted-printable
> > >
> > > Hi, Dear All:<div><br></div><div>I h= ave a question about calculation on
> > the=3D
> > > =C2=A0open-shell singlet using Gaussian. For example, nitren= e species may have
> > a=3D
> > > n open-shell and closed shell singlets. In Gaussian, how to = set the
> > calcula=3D
> > > tion to get open-shell or closed-shell specifically? Thanks.= </div>
> > > <div><br></div><div>Peng</div>=
> > >
> > > --001636c5a4fb6b291a046e527474-->
> >
> >
>
> --0016e6d58f785e862f046e5d7678
> Content-Type: text/html; charset=3DISO-8859-1
> Content-Transfer-Encoding: quoted-printable
>
> Thanks for your reply. I&#39;d like to do calculation on the= open-shell sin=3D
> glet (not a triplet). Open-shell(U) and restricted (R) calculations in= Gaus=3D
> sian gave=3DA0me=3DA0same=3DA0results.=3DA0So=3DA0in=3DA0Gaussian,=3DA= 0how=3DA0to=3DA0set=3DA0i=3D
> nput=3DA0to=3DA0make=3DA0two=3DA0electrons=3DA0in=3DA0two=3DA0differen= t=3DA0orbitals=3DA0but=3D
> =3DA0we=3DA0still=3DA0have=3DA0a=3DA0singlet=3DA0state?<div>
> <br></div><div>Thanks.</div><div><br&= gt;</div><div>Peng<br><div><br><div class= =3D
> =3D3D"gmail_quote">On Fri, Jul 10, 2009 at 11:14 AM, Jose= Alberto Fernandes j=3D
> afernandes{:}<a href=3D3D"http://ua.pt">ua.pt</a> <span dir=3D3D"ltr">&lt;<a hr= =3D
> ef=3D3D"mailto:owner= -chemistry---ccl.net">owner-chemistry---ccl.net</a>&gt;</s= pan=3D
> > wrote:<br>
> <blockquote class=3D3D"gmail_quote" style=3D3D"margi= n:0 0 0 .8ex;border-left:1p=3D
> x #ccc solid;padding-left:1ex;"><br>
> Sent to CCL by: &quot;Jose Alberto Fernandes&quot; [jafernande= s=3D3D-=3D3D<a hr=3D
> ef=3D3D"http://ua.pt" target=3D3D"_blank">ua.pt</a>]<br>
> Hello<br>
> <br>
> I don&#39;t know if I understood your problem. Lets try.<br>=
> Please see the following excerpt this input:<br>
> <br>
> # rb3lyp/3-21g guess=3D3Dcheck<br>
> <br>
> The &quot;r&quot; before &quot;b3lyp&quot; means that = you want a close shel=3D
> l calculation. If you don&#39;t want electron pairing you have to = put &quot=3D
> ;ub3lyp&quot; instead of &quot;rb3lyp&quot;.<br>
> <br>
> You should remember that a closed shell compound has always a spin=3D3= D1, and=3D
> =C2=A0in a open shell the spin is different from 1. = In the case of nitrene (R-N =3D
> ?) you can have R-N paired (spin=3D3D1) and unpaired (spin=3D3D3= ).<br>
> <br>
> So in the case of pairing you shoul input:<br>
> <br>
> ------------------------<br>
> # rb3lyp/3-21g guess=3D3Dcheck<br>
> <br>
> comment<br>
> <br>
> 0 1<br>
> <br>
> geometry<br>
> <br>
> ----------------------<br>
> If you want unpairing you should input:<br>
> <br>
> ---------------------<br>
> # ub3lyp/3-21g guess=3D3Dcheck<br>
> <br>
> comment<br>
> <br>
> 0 3<br>
> <br>
> geometry<br>
> <br>
> ----------------------<br>
> If I haven&#39;t answered your question, please explain better.<= ;br>
> <br>
> Best regards<br>
> <br>
> Jose<br>
> <br>
> <br>
> <br>
> <br>
> &gt; &quot;Huo-Lei Peng huolei.peng166(!)<a href=3D3D"= http://gmail.com" t= arge=3D
> t=3D3D"_blank">gmail.com</a>&quot; =3DA0wrote:<br>
> &gt;<br>
> &gt; Sent to CCL by: Huo-Lei Peng [huolei.peng166]=3D3D[<a href= =3D3D"http://gma=3D
> il.com" target=3D= 3D"_blank">gmai= l.com</a>]<br>
> &gt; --001636c5a4fb6b291a046e527474<br>
> &gt; Content-Type: text/plain; charset=3D3DISO-8859-1<br> > &gt; Content-Transfer-Encoding: 7bit<br>
> <div><div></div><div class=3D3D"h5">= &gt;<br>
> &gt; Hi, Dear All:<br>
> &gt; I have a question about calculation on the open-shell singlet= using<br=3D
> >
> &gt; Gaussian. For example, nitrene species may have an open-shell= and clos=3D
> ed<br>
> &gt; shell singlets. In Gaussian, how to set the calculation to ge= t open-sh=3D
> ell or<br>
> &gt; closed-shell specifically? Thanks.<br>
> &gt;<br>
> &gt; Peng<br>
> &gt;<br>
> </div></div>&gt; --001636c5a4fb6b291a046e527474<br&= gt;
> &gt; Content-Type: text/html; charset=3D3DISO-8859-1<br>
> &gt; Content-Transfer-Encoding: quoted-printable<br>
> &gt;<br>
> &gt; Hi, Dear All:&lt;div&gt;&lt;br&gt;&lt;/di= v&gt;&lt;div&gt;I have a ques=3D
> tion about calculation on the=3D3D<br>
> &gt; =3DA0open-shell singlet using Gaussian. For example, nitrene = species may=3D
> =C2=A0have a=3D3D<br>
> &gt; n open-shell and closed shell singlets. In Gaussian, how to s= et the ca=3D
> lcula=3D3D<br>
> &gt; tion to get open-shell or closed-shell specifically? Thanks.&= amp;lt;/div&g=3D
> t;<br>
> &gt; &lt;div&gt;&lt;br&gt;&lt;/div&gt;&= ;lt;div&gt;Peng&lt;/div&gt;<br>
> &gt;<br>
> &gt; --001636c5a4fb6b291a046e527474--<br>
> &gt;<br>
> &gt;<br>
> <br>
> <br>
> <br>
> -=3D3D This is automatically added to each message by the mailing scri= pt =3D3D-=3D
> <br<br=3D<br<br>
> <br>
> E-mail to subscribers: <a href=3D3D"mailto:CHEMISTRY---ccl.net">CHEMISTRY---ccl.n=3D > et</a> or use:<br>
> =C2=A0=3DA0 =3DA0 =3DA0<a href=3D3D"http://www.ccl.net/cgi-= bin/ccl/send_ccl_message" tar=3D
> get=3D3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_c= cl_message</a><br>
> <br>
> E-mail to administrators: <a href=3D3D"mailto:CHEMISTRY-REQUEST---ccl.net">CHE= M=3D
> ISTRY-REQUEST---ccl.net</a> or use<br>
> =C2=A0=3DA0 =3DA0 =3DA0<a href=3D3D"http://www.ccl.net/cgi-= bin/ccl/send_ccl_message" tar=3D
> get=3D3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_c= cl_message</a><br>
> <br>
> Subscribe/Unsubscribe:<br>
> =C2=A0=3DA0 =3DA0 =3DA0<a href=3D3D"http://www.ccl.net/chemist= ry/sub_unsub.shtml" target=3D
> =3D3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtm= l</a><br>
> <br>
> Before posting, check wait time at: <a href=3D3D"http://www.ccl.net" target=3D<= br> > =3D3D"_blank">http://www.ccl.net</a><br>
> <br>
> Job: <a href=3D3D"http://www.ccl.net/jobs" target=3D3D"_blank"= >http://www.ccl.n=3D<= br> > et/jobs</a><br>
> Conferences: <a href=3D3D"http://server.ccl.net/chem= istry/announcements/confe=3D
> rences/" target=3D3D"_blank">http://server.cc= l.net/chemistry/announcements/co=3D
> nferences/</a><br>
> <br>
> Search Messages: <a href=3D3D"http://www.ccl.net/chemist= ry/searchccl/index.sh=3D
> tml" target=3D3D"_blank">http://www.ccl.net/ch= emistry/searchccl/index.shtml</=3D
> a><br>
> <br<br>
> =C2=A0=3DA0 =3DA0 =3DA0<a href=3D3D"http://www.ccl.net/spammers.txt&quo= t; target=3D3D"_blank">h=3D
> ttp://ww= w.ccl.net/spammers.txt</a><br>
> <br>
> RTFI: <a href=3D3D"http://www.ccl.net/chemistry/aboutcc= l/instructions/" targe=3D
> t=3D3D"_blank">http://www.ccl.net/chemistry/aboutc= cl/instructions/</a><br>
> <br>
> <br>
> </blockquote></div><br></div></div>
>
> --0016e6d58f785e862f046e5d7678--
>
>



-=3D This is automatically added to each message by the mailing script =3D-=
To recover the email address of the author of the m= essage, please change
E-mail to subscribers: CHEMISTRY::ccl.net or use:
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEM= ISTRY-REQUEST::ccl.net or use
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

If your mail bounces from CCL with 5.7.1 error, che= ck:



--
Adam Johann= es Johansson
Ph.D., M.Sc.
Institut f=C3=BCr Organische Chemie
RWTH= Aachen University
Landoltweg 1
52056 Aachen
Germany
Cell phone= :0708178487
E-mail:johjo76::gmail.com<= br>Research web page:www.physto.se/= ~johjo

--0015175114da1af58c046e5f8111-- From owner-chemistry@ccl.net Fri Jul 10 17:51:01 2009 From: "Christopher Cramer cramer|-|umn.edu" To: CCL Subject: CCL:G: Problem about calculation on the open-shell singlet in Gaussian. Message-Id: <-39747-090710152339-10333-CfGba+zublF6KORP5KUetg=server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-8-509342421 Date: Fri, 10 Jul 2009 13:53:18 -0500 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Christopher Cramer [cramer(_)umn.edu] --Apple-Mail-8-509342421 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Peng, By specifying guess=mix in a udft calculation (must specify "u" in the functional name, or Gaussian will use restricted by default since it's a singlet), you can get Gaussian to make the alpha and beta HOMOs 50:50 positive and negative linear combinations of one another. This will usually converge to a so-called broken-symmetry solution having an value for the KS determinant of 1.0 more or less. One can interpret this either as the open-shell singlet energy, or project out the triplet by the Ziegler-Noodleman-Yamaguchi sort of approach. IA paper of ours from a few years back specifically addressed the different singlet states in substituted phenyl nitrenes -- see Johnson, W. T. G.; Sullivan, M. B.; Cramer, C. J. "meta and para Substitution Effects on the Electronic State Energies and Ring- Expansion Reactivities of Phenylnitrenes" Int. J. Quantum Chem. 2001, 85, 492.. Best regards, Chris On Jul 10, 2009, at 12:40 PM, Huo-Lei Peng huolei.peng166|-|gmail.com wrote: > Thanks for your reply. I'd like to do calculation on the open-shell > singlet (not a triplet). Open-shell(U) and restricted (R) > calculations in Gaussian gave me same results. So in Gaussian, how > to set input to make two electrons in two different orbitals but we > still have a singlet state? > > Thanks. > > Peng > > On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto Fernandes > jafernandes{:}ua.pt wrote: > > Sent to CCL by: "Jose Alberto Fernandes" [jafernandes=-=ua.pt] > Hello > > I don't know if I understood your problem. Lets try. > Please see the following excerpt this input: > > # rb3lyp/3-21g guess=check > > The "r" before "b3lyp" means that you want a close shell > calculation. If you don't want electron pairing you have to put > "ub3lyp" instead of "rb3lyp". > > You should remember that a closed shell compound has always a > spin=1, and in a open shell the spin is different from 1. In the > case of nitrene (R-N ?) you can have R-N paired (spin=1) and > unpaired (spin=3). > > So in the case of pairing you shoul input: > > ------------------------ > # rb3lyp/3-21g guess=check > > comment > > 0 1 > > geometry > > ---------------------- > If you want unpairing you should input: > > --------------------- > # ub3lyp/3-21g guess=check > > comment > > 0 3 > > geometry > > ---------------------- > If I haven't answered your question, please explain better. > > Best regards > > Jose > > > > > > "Huo-Lei Peng huolei.peng166(!)gmail.com" wrote: > > > > Sent to CCL by: Huo-Lei Peng [huolei.peng166]=[gmail.com] > > --001636c5a4fb6b291a046e527474 > > Content-Type: text/plain; charset=ISO-8859-1 > > Content-Transfer-Encoding: 7bit > > > > Hi, Dear All: > > I have a question about calculation on the open-shell singlet using > > Gaussian. For example, nitrene species may have an open-shell and > closed > > shell singlets. In Gaussian, how to set the calculation to get > open-shell or > > closed-shell specifically? Thanks. > > > > Peng > > > > --001636c5a4fb6b291a046e527474 > > Content-Type: text/html; charset=ISO-8859-1 > > Content-Transfer-Encoding: quoted-printable > > > > Hi, Dear All:

I have a question about > calculation on the= > > open-shell singlet using Gaussian. For example, nitrene species > may have a= > > n open-shell and closed shell singlets. In Gaussian, how to set > the calcula= > > tion to get open-shell or closed-shell specifically? Thanks.
> >

Peng
> > > > --001636c5a4fb6b291a046e527474-- > > > > > > > > -= This is automatically added to each message by the mailing script > =- > > > > E-mail to subscribers: CHEMISTRY**ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or use> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer ~ umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-8-509342421 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Peng,

  By = specifying guess=3Dmix in a udft calculation (must specify "u" in the = functional name, or Gaussian will use restricted by default since it's a = singlet), you can get Gaussian to make the alpha and beta HOMOs 50:50 = positive and negative linear combinations of one another. This will = usually converge to a so-called broken-symmetry solution having an = <S^2> value for the KS determinant of 1.0 more or less. One can = interpret this either as the open-shell singlet energy, or project out = the triplet by the Ziegler-Noodleman-Yamaguchi sort of = approach.

  IA paper of ours from a few years back = specifically addressed the different singlet states in substituted = phenyl nitrenes -- see Johnson, W. T. G.; Sullivan, M. B.; Cramer, C. J. = "meta and para Substitution Effects on the Electronic = State Energies and Ring-Expansion Reactivities of = Phenylnitrenes" Int. J. Quantum Chem. 2001, 85, = 492..

Best regards,

Chris
On Jul 10, 2009, at = 12:40 PM, Huo-Lei Peng huolei.peng166|-|gmail.com wrote:

Thanks for = your reply. I'd like to do calculation on the open-shell singlet (not a = triplet). Open-shell(U) and restricted (R) calculations in Gaussian = gave me same results. So in Gaussian, h= ow to set input to make two electrons&n= bsp;in two different orbitals but we still&n= bsp;have a singlet state?
=
Thanks.

Peng

On Fri, Jul 10, 2009 at 11:14 AM, Jose Alberto = Fernandes jafernandes{:}ua.pt <owner-chemistry**ccl.net><= /span> wrote:

Sent to CCL = by: "Jose Alberto Fernandes" [jafernandes=3D-=3Dua.pt]
Hello

I don't know if I = understood your problem. Lets try.
Please see the following excerpt = this input:

# rb3lyp/3-21g guess=3Dcheck

The "r" = before "b3lyp" means that you want a close shell calculation. If you = don't want electron pairing you have to put "ub3lyp" instead of = "rb3lyp".

You should remember that a closed shell compound has = always a spin=3D1, and in a open shell the spin is different from 1. In = the case of nitrene (R-N ?) you can have R-N paired (spin=3D1) and = unpaired (spin=3D3).

So in the case of pairing you shoul = input:

------------------------
# rb3lyp/3-21g = guess=3Dcheck

comment

0 1

geometry

= ----------------------
If you want unpairing you should input:
=
---------------------
# ub3lyp/3-21g guess=3Dcheck

= comment

0 3

geometry

= ----------------------
If I haven't answered your question, please = explain better.

Best regards

Jose



=
> "Huo-Lei Peng huolei.peng166(!)gmail.com"  wrote:
>
> Sent to = CCL by: Huo-Lei Peng [huolei.peng166]=3D[gmail.com]
> = --001636c5a4fb6b291a046e527474
> Content-Type: text/plain; = charset=3DISO-8859-1
> Content-Transfer-Encoding: 7bit
=
>
> Hi, Dear All:
> I = have a question about calculation on the open-shell singlet using
= > Gaussian. For example, nitrene species may have an open-shell and = closed
> shell singlets. In Gaussian, how to set the calculation = to get open-shell or
> closed-shell specifically? Thanks.
= >
> Peng
>
> = --001636c5a4fb6b291a046e527474
> Content-Type: text/html; = charset=3DISO-8859-1
> Content-Transfer-Encoding: = quoted-printable
>
> Hi, Dear = All:<div><br></div><div>I have a question about = calculation on the=3D
>  open-shell singlet using Gaussian. = For example, nitrene species may have a=3D
> n open-shell and = closed shell singlets. In Gaussian, how to set the calcula=3D
> = tion to get open-shell or closed-shell specifically? = Thanks.</div>
> = <div><br></div><div>Peng</div>
= >
> --001636c5a4fb6b291a046e527474--
>
>
=


-=3D This is automatically added to each message by the = mailing script =3D-



E-mail to subscribers: CHEMISTRY**ccl.net or use:
=      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=
E-mail to administrators: CHEMISTRY-REQUEST**ccl.net = or use
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=
Subscribe/Unsubscribe:
     http://www.ccl.net/chemistry/sub_unsub.shtml
=
Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conference= s/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/<= br>

=



Christopher J. Cramer

University of = Minnesota

207 Pleasant St. SE

Minneapolis, MN = 55455-0431

Phone:  (612) 624-0859 || = FAX:  (612) = 626-2006

cramer ~ umn.edu

http://pollux.chem.umn.edu/~cr= amer

    of Computational = Chemistry:  Theories and Models, = 2nd Edition")




= --Apple-Mail-8-509342421-- From owner-chemistry@ccl.net Fri Jul 10 18:26:00 2009 From: "Szabolcs Csepregi scsepregi:-:chemaxon.com" To: CCL Subject: CCL: Protonation states Message-Id: <-39748-090710175003-29563-JjU6Jq1y6KP6D0u2BCVKlg:server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=UTF-8 Date: Fri, 10 Jul 2009 23:49:17 +0200 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [scsepregi]~[chemaxon.com]
Hi Sergio,

Sorry for the late reply.
You may use the Major Microspecies plugin of Marvin:
http://www.chemaxon.com/product/maj_micro.html

You should be able to qualify for free academic licenses, and then use the cxcalc command-line tool or Instant JChem GUI for batch calculations.

I hope this helps.

Best regards,
Szabolcs

Szabolcs Csepregi, PhD
Dir. of Search Technologies and Markush project
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037 Hungary
http://www.chemaxon.com
Tel: +36 1 4532661 Cell: +36 20 4219863 Fax: +36 1 4532659
Skype: szabolcs.csepregi


Sergio Mares-Samano sergio.mares-samano,postgrad.manchester.ac.uk wrote:

Sent to CCL by: Sergio Mares-Samano [sergio.mares-samano/a\postgrad.manchester.ac.uk]
Hi,

Which software (free/open source) can I use to assign the correct ligand protonation forms? I have a database of around 5000 molecules (smile format) and used open babel to convert them into the SDF's. After performing a google search, I found that OpenBabel was a good option to get the SDF's from the smiles. Now however, I'm struggling to find a program to assign the correct charges according to a certain pH e.g. 7.

Any suggestions?

Thank you very much in advance,

Sergio Mares-Samano



E-mail to subscribers: CHEMISTRY^^ccl.net or use:
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST^^ccl.net or use
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/