From owner-chemistry@ccl.net Thu Jan 13 01:50:00 2011 From: "VITORGE Pierre 094605 Pierre.VITORGE-,-cea.fr" To: CCL Subject: CCL:G: Wavefunction stability Message-Id: <-43619-110113014705-19092-if+RSbH7qB7SYBxlZB+1eQ++server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 13 Jan 2011 07:46:26 +0100 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE%a%cea.fr] Did you try scf=qc ? This usually helps to avoid changes in the electronic configuration in the course of the SCF calculation. -- Pierre Vitorge -----Message d'origine----- De : owner-chemistry+pierre.vitorge==cea.fr|-|ccl.net [mailto:owner-chemistry+pierre.vitorge==cea.fr|-|ccl.net] De la part de Peeter Burk peeter#%#chem.ut.ee Envoyé : mercredi 12 janvier 2011 17:50 À : VITORGE Pierre 094605 Objet : CCL:G: Wavefunction stability Sent to CCL by: "Peeter Burk" [peeter-$-chem.ut.ee] Dear colleagues, I seem to have both conceptually and technically troubles with wavefunction (wf) stabilities. The first solution for my system (singlet) had RHF->UHF instability. So I turned to UHF calculations, which had the internal instability. By using Stable=Opt (using Gaussian09) I was finally able to get stable UHF wf. However, the geometry optimization resulted a solution, where the wf had again a internal instability, and after Stable=Opt that geometry was no more minimum (as witnessed by combination of keywords Guess=Read Geom=Allcheck Freq). I was able to get that case solved by adding keyword Guess=(Mix,Always). So for HF I was able to get a solution. However, with MP2 I keep getting either solutions with internal instability or, when using Guess=(Mix,Always), the geometry never converges closer examination reveals in that case that the energy is oscillating between 7-8 values. Reducing the step size did not help. Does somebody have a suggestion, how to get the geometry to converge with MP2 without getting unstable wf? For comparison, I have calculated also the triplet state for my system. It converges rapidly and gives stable wf. However, the energy of that solution is higher than for the singlet (both UHF and UMP2). So what does this all tell about the studied system? Can it be studied by single determinant approach? Why do I get so much unstable solutions? Should it be studied by some multiconfigurational approach (I'm intending to study a bigger part of PES with many minima and TS-s)? Can the coupled clusters theory be the solution? But then again it will definitely be slower, especially as there are no analytical force constants (at least in Gaussian). TIA Peeter Burk University of Tartu, Estonia peeter.burk+*+ut.eehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jan 13 05:19:00 2011 From: "Kurt De Grave Kurt.DeGrave|*|cs.kuleuven.be" To: CCL Subject: CCL: PyMCS - still available? Message-Id: <-43620-110113044515-30627-nenANT4kAtlyXymNyhTSuA#%#server.ccl.net> X-Original-From: Kurt De Grave Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 13 Jan 2011 10:44:51 +0100 MIME-Version: 1.0 Sent to CCL by: Kurt De Grave [Kurt.DeGrave/a\cs.kuleuven.be] Andrew Dalke dalke * dalkescientific.com wrote: > Many years ago I announced on this list some maximum common > substructure software I wrote while working for Bioreason. The FOG program can compute maximal common subgraphs in polynomial time -- but only on outerplanar graphs. (It can tell you if one of the graphs is non-outerplanar, in which case you can fall back to another tool.) http://people.cs.kuleuven.be/~jan.ramon/fog/ Some papers where it is applied to small molecules: Schietgat, L., Costa, F., Ramon, J. and De Raedt, L.: 2010, Effective feature construction by maximum common subgraph sampling, Machine Learning pp. 1–25. De Grave, K. and Costa, F.: 2010, Molecular graph augmentation with rings and functional groups, Journal of Chemical Information and Modeling 50(9), 1660–1668. Best regards, Kurt. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Thu Jan 13 08:14:00 2011 From: "Jissy AK jissy%iisertvm.ac.in" To: CCL Subject: CCL: Charge Transfer integral calculation Message-Id: <-43621-110113054211-15583-6GyPAtpdVh9KeVurGwhHbw^server.ccl.net> X-Original-From: Jissy AK Content-Type: multipart/alternative; boundary=001636c5a81c93836c0499b7f742 Date: Thu, 13 Jan 2011 16:11:58 +0530 MIME-Version: 1.0 Sent to CCL by: Jissy AK [jissy{=}iisertvm.ac.in] --001636c5a81c93836c0499b7f742 Content-Type: text/plain; charset=ISO-8859-1 Dear colleagues, I tried out the "AT base pair: Charge transfer integrals" example given in ADF. I used exactly the same input files as given in the example. I got a NORMAL TERMINATION for the jobs, but in the output file, I did not find the overlap integral or the site energies. So. how do I get these values? Thanks in advance -- Jissy AK PhD Student IISER-TVM "It is nice to know that the computer understands the problem. But I would like to understand it too." -- Eugene P. Wigner --001636c5a81c93836c0499b7f742 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear colleagues,

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 I = tried out the "AT base pair: Charge transfer integrals" example g= iven in ADF. I used exactly the same input files as given in the example. I= got a NORMAL TERMINATION for the jobs, but in the output file, I did not f= ind the overlap integral or the site energies. So. how do I get these value= s?

Thanks in advance


--
Jissy AK
PhD Student
IISER-TVM

&q= uot;It is nice to know that the computer understands the problem. But I
would like to understand it too." -- Eugene P. Wigner
--001636c5a81c93836c0499b7f742-- From owner-chemistry@ccl.net Thu Jan 13 08:49:00 2011 From: "Peeter Burk peeter.burk^-^ut.ee" To: CCL Subject: CCL:G: Wavefunction stability Message-Id: <-43622-110113052004-14367-Au/qAxHII6T7fQd6R7/4Ng.@.server.ccl.net> X-Original-From: Peeter Burk Content-Type: multipart/mixed; boundary="------------070201040301080802080101" Date: Thu, 13 Jan 2011 12:17:47 +0200 MIME-Version: 1.0 Sent to CCL by: Peeter Burk [peeter.burk_._ut.ee] This is a multi-part message in MIME format. --------------070201040301080802080101 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Dear Pierre, Thank you for your suggestion! Yes, I tried that, but it did not help.=20 Then again, how should it? The first problem is with the stability of=20 (absolutely nonsymmetric) wavefunction... Best regards Peeter On 01/13/2011 08:46 AM, VITORGE Pierre 094605 Pierre.VITORGE-,-cea.fr wro= te: > > Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE%a%cea.fr] > Did you try scf=3Dqc ? This usually helps to avoid changes in the elect= ronic configuration in the course of the SCF calculation. > > -- > Pierre Vitorge > > -----Message d'origine----- > De : owner-chemistry+pierre.vitorge=3D=3Dcea.fr\a/ccl.net [mailto:owner= -chemistry+pierre.vitorge=3D=3Dcea.fr\a/ccl.net] De la part de Peeter Bur= k peeter#%#chem.ut.ee > Envoy=E9 : mercredi 12 janvier 2011 17:50 > =C0 : VITORGE Pierre 094605 > Objet : CCL:G: Wavefunction stability > > > Sent to CCL by: "Peeter Burk" [peeter-$-chem.ut.ee] > Dear colleagues, > > I seem to have both conceptually and technically troubles with wavefunc= tion (wf) stabilities. > > The first solution for my system (singlet) had RHF->UHF instability. So= I turned to UHF calculations, which had the internal instability. By usi= ng Stable=3DOpt (using Gaussian09) I was finally able to get stable UHF w= f. However, the geometry optimization resulted a solution, where the wf h= ad again a internal instability, and after Stable=3DOpt that geometry was= no more minimum (as witnessed by combination of keywords Guess=3DRead Ge= om=3DAllcheck Freq). I was able to get that case solved by adding keyword= Guess=3D(Mix,Always). So for HF I was able to get a solution. > > However, with MP2 I keep getting either solutions with internal instabi= lity or, when using Guess=3D(Mix,Always), the geometry never converges c= loser examination reveals in that case that the energy is oscillating bet= ween 7-8 values. Reducing the step size did not help. Does somebody have = a suggestion, how to get the geometry to converge with MP2 without gettin= g unstable wf? > > For comparison, I have calculated also the triplet state for my system.= It converges rapidly and gives stable wf. However, the energy of that so= lution is higher than for the singlet (both UHF and UMP2). > > So what does this all tell about the studied system? Can it be studied = by single determinant approach? Why do I get so much unstable solutions? = Should it be studied by some multiconfigurational approach (I'm intending= to study a bigger part of PES with many minima and TS-s)? Can the couple= d clusters theory be the solution? But then again it will definitely be s= lower, especially as there are no analytical force constants (at least in= Gaussian). > > TIA > > Peeter Burk > University of Tartu, Estonia > peeter.burk+*+ut.eehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp:= //www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > -=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 chang= e> --------------070201040301080802080101 Content-Type: text/x-vcard; charset=utf-8; name="peeter_burk.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="peeter_burk.vcf" begin:vcard fn:Peeter Burk n:Burk;Peeter email;internet:peeter.burk..ut.ee tel;work:+372 7375 258 x-mozilla-html:FALSE version:2.1 end:vcard --------------070201040301080802080101-- From owner-chemistry@ccl.net Thu Jan 13 09:23:00 2011 From: "Gerald Knizia knizia%theochem.uni-stuttgart.de" To: CCL Subject: CCL:G: Wavefunction stability Message-Id: <-43623-110113084604-5495-gaNt/bIrLhW/QgQiSOzzeQ[a]server.ccl.net> X-Original-From: Gerald Knizia Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 13 Jan 2011 14:45:49 +0100 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia-,-theochem.uni-stuttgart.de] On Wednesday 12 January 2011 17:49, Peeter Burk peeter#%#chem.ut.ee wrote: > I seem to have both conceptually and technically troubles with wavefunction > (wf) stabilities. > > The first solution for my system (singlet) had RHF->UHF instability. So I > turned to UHF calculations, which had the internal instability. By using > Stable=Opt (using Gaussian09) I was finally able to get stable UHF wf. > However, the geometry optimization resulted a solution, where the wf had > again a internal instability, [...] > > So what does this all tell about the studied system? It tells you that this is a strong multi-reference system and that you should not attempt to describe it with Hartree-Fock or DFT. > Should it be studied by some multiconfigurational approach (I'm intending > to study a bigger part of PES with many minima and TS-s)? Yes. > Can the coupled clusters theory be the solution? CCSD(T) can handle some degree of multiconfigurational character of systems. But it's rather limited in that regard. If you are not able to obtain a definite ground state Hartree-Fock solution, CCSD(T) cannot be trusted either. > But then again it will definitely be slower, especially as there are no > analytical force constants (at least in Gaussian). There are some other problems having analytical gradients for CASSCF/MCSCF and CASPT2/RS2. -- Gerald Knizia From owner-chemistry@ccl.net Thu Jan 13 09:59:00 2011 From: "Olawale Lukman Olasunkanmi waleolasunkanmi:_:gmail.com" To: CCL Subject: CCL: complexes Message-Id: <-43624-110113083114-1287-Rz2drMk34jkAowraNFWYRA*o*server.ccl.net> X-Original-From: "Olawale Lukman Olasunkanmi" Date: Thu, 13 Jan 2011 08:31:13 -0500 Sent to CCL by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi^_^gmail.com] Thank you all for your earlier contributions. I am getting there. I have got Avogadro installed and have started using it. Please, can anyone put me through how to build complexes like iron(II)phenanthroline complex with the package? There is no procedure for such molecules in the manual. Thank you. From owner-chemistry@ccl.net Thu Jan 13 10:34:00 2011 From: "Wagener, M. \(Markus\) markus.wagener- -spcorp.com" To: CCL Subject: CCL: 3rd Call for Papers: 9th International Conference on Chemical Structures (ICCS) Message-Id: <-43625-110113092127-12049-v7BNGxGL3Ap5YFxaW15iGQ]~[server.ccl.net> X-Original-From: "Wagener, M. \(Markus\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 13 Jan 2011 15:21:10 +0100 MIME-Version: 1.0 Sent to CCL by: "Wagener, M. \(Markus\)" [markus.wagener^spcorp.com] C A L L F O R P A P E R S 9th International Conference on Chemical Structures NH Leeuwenhorst Conference Hotel, Noordwijkerhout, The Netherlands 5-9 June 2011 There will again be a special issue of the Journal of Chemical Information and Modeling with contributions from the ICCS. More information can be found on the abstract submission page (www.int-conf-chem-structures.org/abstract-submission.html). For qualified PhD students there are a limited number of bursaries available. Preference will be given to those students contributing to the scientific program of the conference. Please visit the conference web site for more information: www.int-conf-chem-structures.org The 9th International Conference on Chemical Structures (ICCS) is seeking presentations of novel research and emerging technologies for the following plenary sessions: o Cheminformatics > advances in structure representation > reaction handling and electronic lab notebooks (ELNs) > molecular similarity and diversity > chemical information visualization o Structure-Activity and Structure-Property Prediction > graphical methods for SAR analysis > industrialized and large-scale model building > multi-property prediction and multi-objective optimization o Structure-Based Drug Design and Virtual Screening > new docking and scoring approaches > improved understanding of protein-ligand interactions > pharmacophore definition and search > modeling of challenging targets o Analysis of Large Chemistry Spaces > mining of chemical literature and patents > design, profiling and comparison of compound collections and screening sets > machine learning and knowledge extraction from databases o Integrated Chemical Information > advances in chemogenomics > integration of medical and biological information > semantic technologies as a driver of integration > translational informatics o Dealing with Biological Complexity > analysis and prediction of poly-pharmacology > in-silico analysis of toxicology, drug safety, and adverse events > pathways and biological networks > druggability of targets Before and after the official conference program free workshops will be offered by BioSolveIT (www.biosolveit.de), The Chemical Computing Group (www.chemcomp.com), Tripos (www.tripos.com), and Accelrys (www.accelrys.com) Joint Organizers: o Division of Chemical Information of the American Chemical Society (CINF) o Chemical Structure Association Trust (CSA Trust) o Division of Chemical Information and Computer Science of the Chemical Society of Japan (CSJ) o Chemistry-Information-Computer Division of the German Chemical Society (GDCh) o Royal Netherlands Chemical Society (KNCV) o Chemical Information Group of the Royal Society of Chemistry (RSC) o Swiss Chemical Society (SCS) We encourage the submission of papers on both applications and case studies as well as on method development and algorithmic work. The final program will be a balance of these two aspects. > From the submissions the program committee and the scientific advisory board will select about 30 papers for the plenary sessions. All submissions that cannot be included in the plenary sessions will automatically be considered for the poster session. Contributions can be submitted for any of the above and related areas, but we also welcome contributions in any aspect of the computer handling of chemical structure information, such as: o automatic structure elucidation o combinatorial chemistry, diversity analysis o web technology and its effect on chemical information o electronic publishing o MM or QM/MM simulations o practical free energy calculations o modeling of ADME properties o material sciences o analysis and prediction of crystal structures o grid and cloud computing in cheminformatics Visit the conference website at www.int-conf-chem-structures.org for more information, including details on procedures for online abstract submission and conference registration. The deadline for the submission of abstracts is 31 January 2011. We hope to see you in Noordwijkerhout. Keith T Taylor, ICCS Chair Markus Wagener, ICCS Chair This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete. From owner-chemistry@ccl.net Thu Jan 13 11:09:00 2011 From: "Marcel Swart marcel.swart,,icrea.cat" To: CCL Subject: CCL: Charge Transfer integral calculation Message-Id: <-43626-110113094230-3882-vZV5m8OWvZ4WXil7RPJhGg**server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 13 Jan 2011 15:41:55 +0100 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Marcel Swart [marcel.swart]_[icrea.cat] Hello Jissy, questions about ADF might better be asked at the ADF Forum: http://www.scm.com/forums In any case, I've just run the same example, and it gives me exactly what was to be expected, i.e. both the Overlap Integrals, and the Site Energies. I'm not sure when this TRANSFERINTEGRALS feature added, but probably it was introduced in the 2010 release. (see http://www.scm.com/News/ADF2010.html) Probably you are using an older version? Marcel On Jan 13, 2011, at 11:41 AM, Jissy AK jissy%iisertvm.ac.in wrote: > Dear colleagues, > > I tried out the "AT base pair: Charge transfer integrals" example given in ADF. I used exactly the same input files as given in the example. I got a NORMAL TERMINATION for the jobs, but in the output file, I did not find the overlap integral or the site energies. So. how do I get these values? > > Thanks in advance > > > -- > Jissy AK > PhD Student > IISER-TVM > > "It is nice to know that the computer understands the problem. But I > would like to understand it too." -- Eugene P. Wigner =================================== dr. Marcel Swart ICREA Research Professor at Institut de Química Computacional Universitat de Girona Facultat de Ciències Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart{:}icrea.cat marcel.swart{:}udg.edu web http://www.marcelswart.eu =================================== From owner-chemistry@ccl.net Thu Jan 13 11:44:00 2011 From: "Olawale Lukman Olasunkanmi waleolasunkanmi^_^gmail.com" To: CCL Subject: CCL: Gnorm in MOPAC Message-Id: <-43627-110113100120-8346-MusxCT+M0EJY1lqAFhqaWA]![server.ccl.net> X-Original-From: "Olawale Lukman Olasunkanmi" Date: Thu, 13 Jan 2011 10:01:18 -0500 Sent to CCL by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi|gmail.com] Dear all MOPAC users, Thank you for your earlier contributions. I have been able to calculate thermodynamic properties despite the error message GNORM is too large by using Let GNORM = ...statement. But what I don't know is; - will this seriously affect my thermodynamic results as contained in the error message "GNORM is too large, thermodynamic values may not be accurate". - what actually bring about the large GNORM value? Can I reduce it by any means to improve the accuracy of my calculations? Thank you all. From owner-chemistry@ccl.net Thu Jan 13 12:58:01 2011 From: "Peeter Burk peeter.burk**ut.ee" To: CCL Subject: CCL:G: Wavefunction stability Message-Id: <-43628-110113122041-28299-PQFb5la+pQw498Z44gXhmg|a|server.ccl.net> X-Original-From: "Peeter Burk" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 13 Jan 2011 19:19:32 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: "Peeter Burk" [peeter.burk__ut.ee] Dear Gerald, Thank you for suggestions, but I still have some doubts. Namely, I also suspected that the system might need multiconfigurational approach and made some CCSD(T) calculations to get the T1 diagnostic. It was quite OK (>0.01), indicating that system can be described by single determinant based methods. Or am I wrong here? Another question I have is regarding possibility of CAS type methods. As much as I understand (and that understanding is definitely very limited) one has to choose carefully the orbitals included in active space. Now, if I would like to study the bigger piece of PES, how can one assure that the "right" orbitals are chosen? Is it enough to have the same size of active space to compare the energies of different species? Best regards Peeter > > Sent to CCL by: Gerald Knizia [knizia-,-theochem.uni-stuttgart.de] > On Wednesday 12 January 2011 17:49, Peeter Burk peeter#%#chem.ut.ee wrote: >> I seem to have both conceptually and technically troubles with >> wavefunction >> (wf) stabilities. >> >> The first solution for my system (singlet) had RHF->UHF instability. So >> I >> turned to UHF calculations, which had the internal instability. By using >> Stable=Opt (using Gaussian09) I was finally able to get stable UHF wf. >> However, the geometry optimization resulted a solution, where the wf had >> again a internal instability, [...] >> >> So what does this all tell about the studied system? > > It tells you that this is a strong multi-reference system and that you > should > not attempt to describe it with Hartree-Fock or DFT. > >> Should it be studied by some multiconfigurational approach (I'm >> intending >> to study a bigger part of PES with many minima and TS-s)? > > Yes. > >> Can the coupled clusters theory be the solution? > > CCSD(T) can handle some degree of multiconfigurational character of > systems. > But it's rather limited in that regard. If you are not able to obtain a > definite ground state Hartree-Fock solution, CCSD(T) cannot be trusted > either. > >> But then again it will definitely be slower, especially as there are no >> analytical force constants (at least in Gaussian). > > There are some other problems having analytical gradients for CASSCF/MCSCF > and > CASPT2/RS2. > -- > Gerald Knizia> > From owner-chemistry@ccl.net Thu Jan 13 13:52:00 2011 From: "Victor Rosas Garcia rosas.victor##gmail.com" To: CCL Subject: CCL: complexes Message-Id: <-43629-110113103853-19082-SeJ9tFt3NUkDlIwi70iy1Q _ server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=0015174c0c3e949ea20499bc1c03 Date: Thu, 13 Jan 2011 09:38:39 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor*gmail.com] --0015174c0c3e949ea20499bc1c03 Content-Type: text/plain; charset=ISO-8859-1 Well, if you are able to sketch the structure in a piece of paper, you should be able to build the molecule in Avogadro. Building mode is the default when Avogadro starts. Personally I tick off the option of adjusting hydrogens, as I find it annoying most of the time. Of course whatever you sketch will have lots of strained bonds and angles so you will have to "clean" your structure by energy minimization (under the "Extensions" menu). You may have to resort to a different force field than the default, because the Fe(II) bonding may not be well represented by the MMFF94 forcefield. Probably UFF will work, or some semiempirical method (if you have mopac installed). That will give you a reasonable starting structure for higher level treatment. Alternatively, if you can get the XYZ coordinates from the crystal structure, Avogadro will read those and you will get a reasonable structure in one step. Hope this helps Victor 2011/1/13 Olawale Lukman Olasunkanmi waleolasunkanmi:_:gmail.com < owner-chemistry- -ccl.net> > > Sent to CCL by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi^_^gmail.com] > Thank you all for your earlier contributions. I am getting there. > I have got Avogadro installed and have started using it. > Please, can anyone put me through how to build complexes like > iron(II)phenanthroline complex with the package? There is no procedure for > such molecules in the manual. > Thank you.> > > --0015174c0c3e949ea20499bc1c03 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Well, if you are able to sketch the structure in a piece of paper, you shou= ld be able to build the molecule in Avogadro.=A0 Building mode is the defau= lt when Avogadro starts.=A0 Personally I tick off the option of adjusting h= ydrogens, as I find it annoying most of the time. Of course whatever you sk= etch will have lots of strained bonds and angles so you will have to "= clean" your structure by energy minimization (under the "Extensio= ns" menu).=A0 You may have to resort to a different force field than t= he default, because the Fe(II) bonding may not be well represented by the M= MFF94 forcefield.=A0 Probably UFF will work, or some semiempirical method (= if you have mopac installed).=A0 That will give you a reasonable starting s= tructure for higher level treatment.

Alternatively, if you can get the XYZ coordinates from the crystal stru= cture, Avogadro will read those and you will get a reasonable structure in = one step.

Hope this helps

Victor

2011/1/13 Olawale Lukman Olasunkanmi waleolasunkanmi:_:gmail.com <owner-chemistry- -ccl.net>

Sent to CCL by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi^_^<= a href=3D"http://gmail.com" target=3D"_blank">gmail.com]
Thank you all for your earlier contributions. I am getting there.
I have got Avogadro installed and have started using it.
Please, can anyone put me through how to build complexes like iron(II)phena= nthroline complex with the package? There is no procedure for such molecule= s in the manual.
Thank you.



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--0015174c0c3e949ea20499bc1c03-- From owner-chemistry@ccl.net Thu Jan 13 14:50:00 2011 From: "Henry Martinez Hmartine_-_gmail.com" To: CCL Subject: CCL: Ligand bond strength Message-Id: <-43630-110113144658-5112-bBbNVY0lrjEARmZSWNQiIQ/./server.ccl.net> X-Original-From: "Henry Martinez" Date: Thu, 13 Jan 2011 14:46:57 -0500 Sent to CCL by: "Henry Martinez" [Hmartine(-)gmail.com] Thanks for helping me out with this question. I am a beginner in this area and I have one question. I have a ligand attach to a metal. How do I calculate the bond strength ligand-metal? Thanks a lot for your help. From owner-chemistry@ccl.net Thu Jan 13 17:54:00 2011 From: "Nancy nancy5villa~!~gmail.com" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43631-110113162615-8167-pwHVnsQ1wdUfLvs+wm89Fg\a/server.ccl.net> X-Original-From: Nancy Content-Type: multipart/mixed; boundary=20cf3054a45d65a0f40499c0f525 Date: Thu, 13 Jan 2011 16:25:36 -0500 MIME-Version: 1.0 Sent to CCL by: Nancy [nancy5villa]~[gmail.com] --20cf3054a45d65a0f40499c0f525 Content-Type: multipart/alternative; boundary=20cf3054a45d65a0e50499c0f523 --20cf3054a45d65a0e50499c0f523 Content-Type: text/plain; charset=ISO-8859-1 Hi All, I happened to find a published article where molecular docking simulations of TZDs against a novel protein is detailed: "Structure-based design of a thiazolidinedione which targets the mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb 1;20(3):819-23 In this paper, the authors, using MarvinSketch v3.5.4, determined that the TZDs would exist predominantly in the enol form at pH 7.4, as opposed to the diketone form (see attached figure). It appears that the article's tautomer prediction was based only on the pH prior to docking, and had nothing to do with ligand-protein interactions. Does anyone know if the diketone or enol, or perhaps a different tautomer, would be predominant at pH 7.4? Thanks in advance. Nancy On Wed, Jan 12, 2011 at 9:53 AM, Andreas Klamt klamt-*-cosmologic.de < owner-chemistry(!)ccl.net> wrote: > > Sent to CCL by: Andreas Klamt [klamt[*]cosmologic.de] > Hi All, > > let me put my 5 cents into the game: > We have done quantum calculations for the heterocyclic ring, with just a > methyl group, since electronically the remainder of the compound should have > almost no influence on the heterocycle. > DFT/COSMO-RS calculations prove the neutral species > SMILES:CC1C(=O)[NH]C(=O)S1 of the Pioglitazone heterocycle to be favored by > 11.3 kcal/mol compared to all other neutral species of the heterocycle, > which means that there is no other relvant neutral form. > > We find with COSMOtherm that the pka of the heterocycle is 6.55, i.e. at > pH=7 it should be deprotonated with about 25%. > Since the pka of the conj. acid of the pyridine ring according to > COSMOtherm (we calculated diethylpyridine) is ~5.6 there should be ~10% in > the zwitterionic form. > > It will be hard to decide this finally, unless someone measures it, but we > are quite confident to be qualitatively right here, because the energy > differences for the tautomers should not have more than 5 kcal/mol erro, as > we learned in in the SAMPL2 tautomer contest: > see Andreas Klamt and Michael Diedenhofen, Some conclusions regarding the > predictions of tautomeric equilibria in solution based on the SAMPL2 > challenge, http://www.springerlink.com/content/l577667th758n6h1/ > > Andreas > > > > > > >> >> Hi All, >> >> Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value >> of the acidic hydrogen on the thiazolidinedione ring of pioglitazone is >> 4.57 (see attached "Figure_1.gif"). Therefore, the predominant species >> at pH 7.0 predicted by MarvinSketch is the one depicted in >> "Figure_2.gif". The different tautomeric forms predicted by MarvinSketch >> are shown in "Figure_3.gif". >> >> Can anyone explain where these predictions come from, and if they are >> correct? >> >> Thanks, >> Nancy >> >> >> On Mon, Jan 10, 2011 at 4:16 AM, Gabriele Cruciani >> gabri(0)chemiome.chm.unipg.it >> >> > wrote: >> >> >> Sent to CCL by: Gabriele Cruciani [gabri##chemiome.chm.unipg.it >> ] >> >> Nancy, >> the first form you reported is the most stable in water at pH 7.0. >> However, the fact that one form is more stable than another in water >> does not help you to understand which form will be more 'relevant' >> for docking. In protein the tautomeric equilibria may produce and >> stabilize different forms according to the complementary site. There >> are examples of tautomeric form in protein not stable in water, >> where the energy difference is more than 5 Kcal/mol. >> >> MoKa software (www.moldiscovery.com ) >> >> is fast and accurate to produce tautomer stable in water, but it can >> produce also all the (plausible) tautomeric forms. >> >> Then, a possibility is to dock them into your protein, to see if >> docking methods may differentiate their binding. >> >> Gabriele Cruciani >> >> >> >> >> Hi All, >> >> I am performing molecular docking and molecular dynamics >> simulations of the >> thiazolidinedione pioglitazone binding to the PPAR-gamma >> receptor protein >> (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous >> different >> tautomeric states; I have attached a figure depicting several of >> them. >> Which tautomer would be dominant at the physiological pH of ~7.0? >> >> Also, are there any software programs that can predict which >> tautomer would >> be correct? >> >> Thanks in advance, >> Nancy> >> >> >> E-mail to subscribers: CHEMISTRY[a]ccl.net >> or use:> >> E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net >> or useConferences: >> >> http://server.ccl.net/chemistry/announcements/conferences/> >> >> >> >> > -- > Dr. Jens Reinisch > Chemist / Customer Support > COSMOlogic GmbH & Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-363664 > mobile +49-163-7337310 > fax +49-2171-731689 > e-mail reinisch[*]cosmologic.de > web www.cosmologic.de > > HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamthttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --20cf3054a45d65a0e50499c0f523 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,

I happened to find a published article where molecular docki= ng simulations of TZDs against a novel protein is detailed:

"St= ructure-based design of a thiazolidinedione which targets the mitochondrial= protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb 1;20(3):819-23

In this paper, the authors, using MarvinSketch v3.5.4, determined that = the TZDs would exist predominantly in the enol form at pH 7.4, as opposed t= o the diketone form (see attached figure).=A0 It appears that the article&#= 39;s tautomer prediction was based only on the pH prior to docking, and had= nothing to do with ligand-protein interactions.

Does anyone know if the diketone or enol, or perhaps a different tautom= er, would be predominant at pH 7.4?

Thanks in advance.
Nancy
<= br>

On Wed, Jan 12, 2011 at 9:53 AM, Andr= eas Klamt klamt-*-cosmologic.de <owner-chemistry(!)= ccl.net> wrote:

Sent to CCL by: Andreas Klamt [klamt[*]cosmologic.de]
Hi All,

let me put my 5 cents into the game:
We have done quantum calculations for the heterocyclic ring, with just a me= thyl group, since electronically the remainder of the compound should have = almost no influence on the heterocycle.
DFT/COSMO-RS calculations prove the neutral species
SMILES:CC1C(=3DO)[NH]C(=3DO)S1 of the Pioglitazone heterocycle to be favore= d by 11.3 kcal/mol compared to all other neutral species of the heterocycle= , which means that there is no other relvant neutral form.

We find with COSMOtherm that the pka of the heterocycle is 6.55, i.e. at pH= =3D7 it should be deprotonated with about 25%.
Since the pka of the conj. acid of the pyridine ring according to COSMOther= m (we calculated diethylpyridine) is ~5.6 there should be ~10% in the zwitt= erionic form.

It will be hard to decide this finally, unless someone measures it, but we = are quite confident to be qualitatively right here, because the energy diff= erences for the tautomers should not have more than 5 kcal/mol erro, as we = learned in in the SAMPL2 tautomer contest:
see Andreas Klamt and Michael Diedenhofen, Some conclusions regarding the p= redictions of tautomeric equilibria in solution based on the SAMPL2 challen= ge, http://www.springerlink.com/content/l577667th758n6h1/

Andreas







Hi All,

Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value
of the acidic hydrogen on the thiazolidinedione ring of pioglitazone is
4.57 (see attached "Figure_1.gif"). Therefore, the predominant sp= ecies
at pH 7.0 predicted by MarvinSketch is the one depicted in
"Figure_2.gif". The different tautomeric forms predicted by Marvi= nSketch
are shown in "Figure_3.gif".

Can anyone explain where these predictions come from, and if they are
correct?

Thanks,
Nancy


On Mon, Jan 10, 2011 at 4:16 AM, Gabriele Cruciani
gabri(0)chemiome= .chm.unipg.it <http://chemiome.chm.unipg.it>

<owner-chemistry[a]ccl.net<= /a> <mailto:owner-c= hemistry[a]ccl.net>= > wrote:


=A0 =A0Sent to CCL by: Gabriele Cruciani [gabri##chemiome.chm.unipg.it
=A0 =A0<http= ://chemiome.chm.unipg.it>]

=A0 =A0Nancy,
=A0 =A0the first form you reported is the most stable in water at pH 7.0.<= br> =A0 =A0However, the fact that one form is more stable than another in wate= r
=A0 =A0does not help you to understand which form will be more 'releva= nt'
=A0 =A0for docking. In protein the tautomeric equilibria may produce and =A0 =A0stabilize different forms according to the complementary site. Ther= e
=A0 =A0are examples of tautomeric form in protein not stable in water,
=A0 =A0where the energy difference is more than 5 Kcal/mol.

=A0 =A0MoKa software (www.moldiscovery.com <http://www.moldiscovery.com>)
=A0 =A0is fast and accurate to produce tautomer stable in water, but it ca= n
=A0 =A0produce also all the (plausible) tautomeric forms.

=A0 =A0Then, a possibility is to dock them into your protein, to see if =A0 =A0docking methods may differentiate their binding.

=A0 =A0Gabriele Cruciani




=A0 =A0 =A0 =A0Hi All,

=A0 =A0 =A0 =A0I am performing molecular docking and molecular dynamics =A0 =A0 =A0 =A0simulations of the
=A0 =A0 =A0 =A0thiazolidinedione pioglitazone binding to the PPAR-gamma =A0 =A0 =A0 =A0receptor protein
=A0 =A0 =A0 =A0(PDB ID: 1ZGY). The thiazolidinedione ring can exist in num= erous
=A0 =A0 =A0 =A0different
=A0 =A0 =A0 =A0tautomeric states; I have attached a figure depicting sever= al of
=A0 =A0 =A0 =A0them.
=A0 =A0 =A0 =A0Which tautomer would be dominant at the physiological pH of= ~7.0?

=A0 =A0 =A0 =A0Also, are there any software programs that can predict whic= h
=A0 =A0 =A0 =A0tautomer would
=A0 =A0 =A0 =A0be correct?

=A0 =A0 =A0 =A0Thanks in advance,
=A0 =A0 =A0 =A0Nancy>


=A0 =A0E-mail to subscribers: CHEMISTRY[a]ccl.net
=A0 =A0<mailto:CHEMISTRY= [a]ccl.net> or use:= >
=A0 =A0E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net
=A0 =A0<mailto:C= HEMISTRY-REQUEST[a]ccl.net= > or useConferences:

=A0 =A0http://server.ccl.net/chemistry/announcements/confere= nces/>




--
Dr. Jens Reinisch
Chemist / Customer Support
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone =A0 +49-2171-363664
mobile =A0+49-163-7337310
fax =A0 =A0 +49-2171-731689
e-mail =A0reinisch[*]cos= mologic.de
web =A0 =A0 www.cosm= ologic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt




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to CCL by: Jun Zhang [coolrainbow .. yahoo.cn] Hi Burk: > Sent to CCL by: "Peeter Burk" [peeter.burk__ut.ee] > Dear Gerald, > > Thank you for suggestions, but I still have some doubts. > Namely, I also suspected that the system might need > multiconfigurational approach and made some CCSD(T) calculations to > get the T1 diagnostic. It was quite OK (>0.01), indicating that > system can be described by single determinant based methods. Or am I > wrong here? Eh, to my knowledge, as least indicated in T. J. Lee, A. P. Rendell, and P. R. Taylor,Comparison of the quadratic configuration interaction and coupled-cluster approaches to electron correlation including the effect of triple excitations,J. Phys. Chem. 94, 5463 (1990), it is when the t1 diagnostic is greater than some thresholds (0.2) that single reference method fails. However, others have pointed out that for some cases that t1 diagnostic implying a multirefernce property even MRCI cannot give considerable improvements over single method. See http://www.ccl.net/chemistry/resources/messages/2000/06/11.001-dir/index.html I think you should analyze the nature of your system to get more insight. But from the instability information you provided, it is strongly recommended a MR method since it can often eliminate instabilities. > Another question I have is regarding possibility of CAS > type methods. Yes. To give a balance description of the whole PES, you should do some benchmark calculations for points of different topologies from the PES (within the range you would study, of course)and determine the final avtive orbitals. I hope my suggestions can help you. Cheers up! Jun Zhang Nankai University coolrainbow++yahoo.cn From owner-chemistry@ccl.net Thu Jan 13 23:04:00 2011 From: "Jan Labanowski janl]_[speakeasy.net" To: CCL Subject: CCL: MOE Workshop Series 2011- San Diego/San Francisco/Cambridge/Durham - CCG Message-Id: <-43633-110113224307-17978-Jvh4dLCZ2f9MUBYQXu6POw__server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Thu, 13 Jan 2011 22:42:26 EST MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl{=}speakeasy.net] --- Forwarded to CCL by Jan Labanowski. --- Dear Colleagues and Friends, We’re happy to inform you about our MOE workshop series 2011! CCG will be hosting a series of hands-on workshops in various cities. The workshops are free of charge but pre-registration is required. Early registration is recommended as space is limited. The workshops will also be a great opportunity to chat with our scientists and learn about recent development in MOE. For more information, please visit: http://www.chemcomp.com/workshops.htm MOE overview: http://www.chemcomp.com/software.htm We look forward to meet you when we come near you! ======================================================================== SAN DIEGO area – February 22 – REGISTER: http://www.chemcomp.com/workshops-sd.htm Where: UC San Diego – 6925 Lusk Blvd., 1st floor, Computer Lab #104., San Diego, CA 92121 Time: AM session (9:00 am to 12:00 pm) Fragment Based De Novo Discovery PM session (1:00 pm to 4:00 pm) Advanced Homology and Loop Modeling ========================================================================= SAN FRANCISCO area – April 15 – REGISTER: http://www.chemcomp.com/workshops-sf.htm Where: Knowledge Development Center – 459 Seaport Ct., Redwood City, CA 94063 Time: AM session (9:00 am to 12:00 pm) Fragment Based De Novo Discovery PM session (1:00 pm to 4:00 pm) Advanced Homology and Loop Modeling ========================================================================= CAMBRIDGE area – May 12 – REGISTER: http://www.chemcomp.com/workshops-cb.htm Where: The Harvard Faculty Club – 20 Quincy Street, Cambridge, MA 02138 Time: PM session (1:30 pm to 4:30 pm) Fragment Based De Novo Discovery ========================================================================= DURHAM area – August 17 – REGISTER: http://www.chemcomp.com/workshops-dh.htm Where: North Carolina Central University – 1801 Fayetteville St., Durham, NC 27707 Time: AM session (9:00 am to 12:00 pm) Fragment Based De Novo Discovery PM session (1:00 pm to 4:00 pm) Advanced Homology and Loop Modeling ========================================================================= CAMBRIDGE area – September 22 – REGISTER: http://www.chemcomp.com/workshops-cb2.htm Where: The Harvard Faculty Club – 20 Quincy Street, Cambridge, MA 02138 Time: AM session (9:00 am to 12:00 pm) Fragment Based De Novo Discovery PM session (1:00 pm to 4:00 pm) Advanced Homology and Loop Modeling ========================================================================= Raul Alvarez Senior Marketing Manager Chemical Computing Group ralvarez---chemcomp.com www.chemcomp.com