From owner-chemistry@ccl.net Sun Oct 25 07:26:01 2009 From: "zoran matovic zmatovic[#]kg.ac.rs" To: CCL Subject: CCL:G: solvation energy in mopac/Comment about COSMO-RS/COSMOtherm Message-Id: <-40531-091023155041-9088-np682dmazBtaH+HZ5HzWuw|-|server.ccl.net> X-Original-From: "zoran matovic" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="ISO-8859-1"; reply-type=original Date: Fri, 23 Oct 2009 20:39:43 +0200 MIME-Version: 1.0 Sent to CCL by: "zoran matovic" [zmatovic-x-kg.ac.rs] Dear David and Andreas, Just a brief comment on this matter: In my opinion there are votes "for" and "against" premises of both of you. David probably has the right not to use commercial software or not discuss with its authors here in CCL. You realy did not mention your product in reply but may be David recall some other correspondence between you two when advertisment is in quest. Personaly I am against charging academic people for scientific soft packages and there is no excuse, whats up to me, for folks doing this. However, I fully support what you stated meaning you published cosmo-rs (not patent protected) so other similar ess might be used for free or small charge and it is of course your legitime right to charge or not what you invented. But somehow I think that a compromise must be found between use of open-source and commerciall codes especially to compute parameters for macromolecules. Finally, comparison about using pharma. or academic drugs might be seen as contraargument to charge cosmo-rs for both profit and academics or only profit companies. don't now if this help others but ... zoran and yes I am of course against advertisement here in CCL, but not to exclude ess authors from debate. ----- Original Message ----- > From: "Andreas Klamt klamt%%cosmologic.de" To: "Matovic, Zoran D " Sent: Friday, October 23, 2009 9:23 AM Subject: CCL:G: solvation energy in mopac/Comment about COSMO-RS/COSMOtherm > > Sent to CCL by: Andreas Klamt [klamt+*+cosmologic.de] > References: > <40513-091021164200-28792-kC3jADUAzy4UQ8MwUVg/HA\a/server.ccl.net> > In-Reply-To: > <40513-091021164200-28792-kC3jADUAzy4UQ8MwUVg/HA\a/server.ccl.net> > Content-Type: text/plain; charset=iso-8859-1; format=flowed > Content-Transfer-Encoding: quoted-printable > X-Spam-Status: No, score=-2.6 required=5.8 tests=BAYES_00 autolearn=ham > version=3.1.9 > X-Spam-Checker-Version: SpamAssassin 3.1.9 (2007-02-13) on server.ccl.net > > Dear David, > > I am somewhat surprised about your offense. Here is my response: > > 1) Please note that COSMO-RS is a scientifically well published method.=20 > There are at least 4 remakes of COSMO-RS, which are based on my publicati= > ons > - the COSMO-SAC remake by Lin and Sandler (available for free in a=20 > simple form from a Virginia-Tech website) > - the COSMO-RS(Ol) remake by Gensemann and Gmehling, available withn = > > the DDBST software (as far as I know at a low price) > - the re-implementation by Banerjee et al., which to my best=20 > knowledge is not distributed as software > - the re-implementation in the ADF program, which is commercial > Anyway, this proofs that I have sufficiently well published the COSMO-RS = > > method that it can be reproduced. Admittedly, in our COSMOtherm=20 > implementation of COSMO-RS we have a few parameters being not completely = > > disclosed. > 2) In my CCL entry on solvation energy in MOPAC I have only spoken about = > > the COSMO-RS method. You will not find the product name COSMOtherm in=20 > there. As developer of COSMO in MOPAC I have given the reasons why COSMO = > > in MOPAC has not been developed up to the level of quantitative=20 > prediction of dG_solv. Is there anything wrong with the fact, that I -=20 > who should know these things best - am giving this explanation in CCL? > 3) From your comment I understand that you suspect that people working=20 > commercially in Computational Chemistry cannot be considered as serious=20 > scientist. I am afraid that this is the opinion of a part of our=20 > community, but it is quite specific for it. I guess nobody would suspect = > > that the researchers in automotive industries, or in pharmaceutical=20 > companies are not doing good research. Yes, if you like you can decide=20 > to use only those drugs which have been developed at universities. But=20 > very few people do so. The difference is that these people mostly patent = > > their breakthroughs. I did not patent COSMO-RS. So I am asking the=20 > question: What is wrong with the fact that I decided to earn my income=20 > (and meanwhile that of about 6 additional scientists, 2 programmers, and = > > one secretary) based on my scientific invention? Does this make me a=20 > less honest or less serious scientist? > > If the CCL should decide to become a forum exclusive for academic=20 > computational chemists, and exclusively about public domain software,=20 > then I will stay out of it. I did not have this impression yet. By the=20 > way, then all the discussion about bugs and problems with Gaussian=20 > should also stay out there. Gaussain may be a little bit cheaper, but it = > > is commercial. Maybe the entry price for academics is lower, but I am=20 > not sure whether you are the person to decide which price is acceptable=20 > for academic licenses of comp. chem. software. The entry price for=20 > COSMOtherm is 3000 EURO for a permanent academic group license (I am not = > > sure where you take the $12 K). This price is for a permanent academic=20 > group license, including training, maintenance and updates for one year, = > > and including a graphcal user interface. If you consider this as too=20 > high, you may use a public domain remake of COSMO-RS, or other solvation = > > methods. That is your decision. > > I also encourage the organizer of the CCL (Jan) and the community to=20 > comment on this debate. If the organizer or the majority of the CCLers=20 > should share the opinion of David, I will stay out of CCL in future. > > Best regards > > Andreas > > > David A. Mannock dmannock^ualberta.ca schrieb: >> >> Sent to CCL by: "David A. Mannock" [dmannock++ualberta.ca] >> >> Andreas, we have talked before about Cosmo-RS.. You need to disclose=20 >> your financial interests in this software when answering messages and=20 >> where possible suggest alternative free DFT software where similar=20 >> solutions are available. Many of your answers in this forum seem=20 >> contain scientific solutions relative to your own product which if I=20 >> recall was $12K for a small group licence. I think I said to you at=20 >> the time that even 1/10th of the price for a single person user=20 >> licence was excessive for academic use. While I have to be realistic=20 >> about science and the modern business world, personally I understood=20 >> that this forum was for help of a scientific nature. Maybe the=20 >> moderators of this forum would care to comment on this policy. David >> >> At 12:18 AM 21/10/2009, you wrote: >> >>> Sent to CCL by: Andreas Klamt [klamt#%#cosmologic.de] >>> Dear Daniel, >>> >>> as author of COSMO in MOPAC I like to emphazise that the COSMO in=20 >>> MOPAC is not parameterized for the quantitative calculation of=20 >>> dG_solv. It is definitely good for getting the calculations closer to = > >>> solvation than just a gasphase calculation, but for two reasons I=20 >>> recommend higher levels for optimal calculation of dG_solv: >>> 1) The electrostatics of semi-empirical methods is usually not very=20 >>> accurate (because this mostly is not in the target properties of the=20 >>> parameterizations). At least in AM1, PM3, and PM5 (we did not test=20 >>> PM6) dipole moments of some functional groups can be off by one Debye = > >>> (e.g. nitro groups) and if the dipole moment is of that much the=20 >>> solvation energy will be very bad. This is the reason why I left the=20 >>> semi-empirical level for quantitative solvation calculations a few=20 >>> years after developing COSMO in MOPAC. And most likely this is also=20 >>> why the Minnesota group developed parameterized charge models based=20 >>> on semi-empirical methods in order to improve the SMx models. Since=20 >>> HF is generally overestimating polarities, this is also not extremely = > >>> reliable. The good message is that DFT is very reliable in that=20 >>> regard, and this quite independent of the special functional. From my = > >>> perspective DFT is currently the method of choice, although for=20 >>> getting the solvations energies much better than 0.3 kcal/mol one=20 >>> will need even more accurate methods than DFT. By the way, a=20 >>> semi-emirical geometry furnished with a single point DFT calculation=20 >>> can be a very good choice for calculating solvation energies. >>> 2) The second reason is that a dielectric continuum solvation model=20 >>> alone cannot give the complete solvation free energies. One needs in=20 >>> addition "non-electrostatic contributions". While in the SMx and PCM=20 >>> models these have been parameterized with many additional, solute and = > >>> solvent specific parameters and descriptors, I have never implemented = > >>> such non-electrostatic terms in MOPAC, at least not quantitatively.=20 >>> MOPAC/COSMO thus does not have these terms. Instead, I have attacked=20 >>> this question with the much more rigorous COSMO-RS approach, which=20 >>> combines COSMO with a statistical thermodynamics of interacting=20 >>> surfaces (using the COSMO polarization charges for the quantification = > >>> of the interactions) and thus describes solutes and solvents on the=20 >>> same quantum-chemical footing, gives enthalpies and entropies,=20 >>> temperature dependencies, and allows for the treatment of mixtures.=20 >>> But due to the earlier finding of 1) I have only developed COSMO-RS=20 >>> quantitatively on the DFT level. Based on a comparison on ~ 2500=20 >>> dG_solv predictions (see "On the Performance of Continuum Solvation=20 >>> Methods. A Comment on "Universal Approaches to Solvation Modeling"",=20 >>> Acc. Chem. Res., 2009, 42 (4), pp 489--492) and on the outcome of the = > >>> recent SAMPL blindtest ( publications in preparation) I dare to say=20 >>> that COSMO-RS currently is the most accurate method for the=20 >>> prediction of dG_solv. >>> >>> Andreas >>> >>> >>> >>> Daniel Glossman-Mitnik dglossman%a%gmail.com schrieb: >>>> Dear netters: >>>> >>>> How should one calculate the solvation energy of a given molecule=20 >>>> using MOPAC 2009? >>>> It is enough with doing one calculation in gas phase and another in=20 >>>> solvent and then >>>> substracting both heats of formation? >>>> Any example input related to these questions will be appreciated. >>>> >>>> Best regards, >>>> >>>> Daniel >>>> >>>> *********************************************************************= > ****************************************=20 >>>> >>>> Dr. Daniel Glossman-Mitnik: >>>> Centro de Investigaci=F3n en Materiales Avanzados, SC >>>> Grupo NANOCOSMOS - Nanotecnolog=EDa Computacional, Simulaci=F3n y=20 >>>> Modelado Molecular >>>> Miguel de Cervantes 120 - Complejo Industrial Chihuahua - Chihuahua, = > >>>> Chih 31109, Mexico >>>> Phone: +52 614 4391151 Secretary/FAX: +52 614 4394852 Lab: +52 614=20 >>>> 4394805 >>>> E-mail: daniel.glossman[A]cimav.edu.mx=20 >>>> dglossman[A]gmail.com=20 >>>> >>>> WWW: http://www.cimav.edu.mx/cv/daniel.glossman >>>> http://blogs.cimav.edu.mx/daniel.glossman >>>> *********************************************************************= > ****************************************=20 >>>> >>> >>> >>> --=20 >>> PD. Dr. Andreas Klamt >>> CEO / Gesch=E4ftsf=FChrer >>> COSMOlogic GmbH & Co. KG >>> Burscheider Strasse 515 >>> D-51381 Leverkusen, Germany >>> >>> phone +49-2171-731681 >>> fax +49-2171-731689 >>> e-mail klamt*_*cosmologic.de >>> web www.cosmologic.de >>> >>> HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt >>> Komplementaer: COSMOlogic Verwaltungs GmbH >>> HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt >>> >>> >>> >>> -http://www.ccl.net/chemistry/sub_unsub.shtmlConferences:=20 >>> http://server.ccl.net/chemistry/announcements/conferences/> >>> >> >> >> >> -=3Dhis is automatically added to each message by the mailing script =3D= > - >> To recover the email address of the author of the message, please chang= > ehttp://www.ccl.net/chemistry/sub_unsub.shtm= > lConferences:=20 >> http://server.ccl.net/chemistry/announcements/conferences/> >> >> > > > --=20 > PD. Dr. Andreas Klamt > CEO / Gesch=E4ftsf=FChrer > COSMOlogic GmbH & Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt\a/cosmologic.de > web www.cosmologic.de > > HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt> -------------------------------------------------------------------------------- No virus found in this incoming message. Checked by AVG - www.avg.com Version: 9.0.686 / Virus Database: 270.14.27/2453 - Release Date: 10/23/09 08:56:00 From owner-chemistry@ccl.net Sun Oct 25 14:51:01 2009 From: "Jim Kress ccl_nospam- -kressworks.com" To: CCL Subject: CCL: Conformational Analysis of Toxogonine, TMB-4 and HI-6 using PM6!! Message-Id: <-40532-091025144926-17105-bUOleSw15kDJCSW3uHyDEA() server.ccl.net> X-Original-From: "Jim Kress" Date: Sun, 25 Oct 2009 14:49:22 -0400 Sent to CCL by: "Jim Kress" [ccl_nospam:+:kressworks.com] Marcel, Yes, you are correct for pi stacking, as pointed out in the PCCP reference you provided. However, the basis for dispersion interactions for the X3LYP functional was limited to He and Ne dimers. However, in light of the quality of predictions of many other properties, Goddard and Xu only posited that the functional might be better for other dispersion interactions. The PCCP paper certainly calls that assumption into question. However, further development with other dispersion complexes may lead to better results. Or, one can use the other functionals you mentioned. Unfortunately, this discussion only emphasizes the chaos which currently exists in the application of DFT methodology. This is quite reminiscent of that confusion which arose (and still does) during the development and application of semi-empirical methods - although Jimmy Stewart will probably yell at me for bringing that up, given the latest methodology he has produced, MOPAC 2009 which features PM6. Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com*|*ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com*|*ccl.net] On Behalf Of Marcel Swart > marcel.swart[*]icrea.es > Sent: Friday, October 23, 2009 4:14 PM > To: Kress, Jim > Subject: CCL: Conformational Analysis of Toxogonine, TMB-4 and HI-6 using > PM6!! > > > Sent to CCL by: Marcel Swart [marcel.swart a icrea.es] > > DFT methods DO have problems with dispersion energy; see for instance > our paper in J. Mol. Model. 2007, 13, 1245-1257 how this can be handled > however: http://dx.doi.org/10.1007/s00894-007-0239-y > > Furthermore, the most popular solution is to use Grimme's dispersion > correction (J. Comput. Chem. 2006, 27, 1787-1799), as also used in the > SSB-D functional (J. Chem. Phys. 2009, 131, 094103; > http://dx.doi.org/10.1063/1.3213193). > > Your example of X3lYP is actually a bad example (I'm sorry Jim): > "The X3LYP extended density functional accurately describes H-bonding > but fails completely for stacking" by Cerny, Hobza, > http://dx.doi.org/10.1039/b502769c > > Quoting "Jim Kress ccl_nospam : kressworks.com" : > > > > > Sent to CCL by: "Jim Kress" [ccl_nospam~~kressworks.com] > >> Before getting too exited please note that the DFT methods used in the > >> validation do not describe London dispersion ... this may introduce > > > > Not totally correct. See: > > > > http://www.pnas.org/content/101/9/2673.abstract > > > > for more information. > > > > Jim Kress > > ccl_nospam.:.kressworks.com > > > > > >> -----Original Message----- > >> From: owner-chemistry+ccl_nospam==kressworks.com.:.ccl.net > >> [mailto:owner- > >> chemistry+ccl_nospam==kressworks.com.:.ccl.net] On Behalf Of Kalju Kahn > >> kalju^chem.ucsb.edu > >> Sent: Sunday, October 18, 2009 12:13 AM > >> To: Kress, Jim > >> Subject: CCL: Conformational Analysis of Toxogonine, TMB-4 and HI-6 > >> using PM6!! > >> > >> > >> Sent to CCL by: "Kalju Kahn" [kalju^chem.ucsb.edu] > >> > >> Fabio, > >> > >> Before getting too exited please note that the DFT methods used in the > >> validation do not describe London dispersion ... this may introduce > >> significant errors for larger flexible molecules where pi-stacking is > >> possible ... like the oximes in this study. > >> > >> Kalju > >> > >> > Sent to CCL by: "Fabio P. Costa" [fabioparanho=gmail.com] I'd like > >> > to performed a conformational analysis in order to investigate a > >> > chemical reaction when I've found this interesting paper: > >> > Conformational Analysis of Toxogonine, TMB-4 and HI-6 using PM6 > >> and RM1 Methods! > >> > > >> > http://jbcs.sbq.org.br/online/fpapers/09036SR.pdf > >> > Supplementary Material: > >> > :http://jbcs.sbq.org.br/online/fpapers/09036SI.pdf > >> > > >> > It shows that new semi-empirical methods are able to correctly > >> > reproduce DFT ones. It is really sound nice, I mean to able to > >> > obtain good results with a semi-empirical approach. What do you > >> think about it? > >> > > >> > > >> > Best regards. > >> > > >> > Fabio Costa> > >> > > >> > > >> > >> > >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >> Dr. Kalju Kahn > >> Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 > >> > >> > >> > >> -= This is automatically added to each message by the mailing script > >> =- To recover the email address of the author of the message, please > >> change the strange characters on the top line to the .:. sign. You can > >> also> Conferences: > >> http://server.ccl.net/chemistry/announcements/conferences/> > > > > > > > > > =================================== > dr. Marcel Swart > > ICREA Research Professor at > Institut de Qumica Computacional > Universitat de Girona > > Parc Cientfic i Tecnolgic > Edifici Jaume Casademont (despatx A-27) > Pic de Peguera 15 > 17003 Girona > Catalunya (Spain) > > tel > +34-972-183240 > fax > +34-972-183241 > e-mail > marcel.swart ~ icrea.es > marcel.swart ~ udg.edu > web > http://www.icrea.cat/Web/ScientificForm.aspx?key=372 > http://iqc.udg.edu/~marcel > =================================== > > > > -=his is automatically added to each message by the mailing script =