From owner-chemistry@ccl.net Thu Oct 21 04:37:00 2010 From: "turker akcay turkerakcay%hotmail.com" To: CCL Subject: CCL: excitation state and energy gap Message-Id: <-42982-101021033203-4402-jF9ck4+qJt+0zqw789Dhog^-^server.ccl.net> X-Original-From: "turker akcay" Date: Thu, 21 Oct 2010 03:32:02 -0400 Sent to CCL by: "turker akcay" [turkerakcay(_)hotmail.com] Hi everybody; I have a question about homo-lumo transition. I studied TD-DFT (singlet) calculation for an organic compound. homo-lumo transition energy 400.21 nm. Excited State 1: Singlet-A 3.0980 eV 400.21 nm f=0.0252 114 ->115 0.70376 homo orbital energy : -0,21623 hartree lumo orbital energy : -0,09068 hartree homo-lumo energy gap :-0,12555 hartree = 3,416390784 ev = 413,75 nm what is the reason for this difference, in some calculations I meet bigger difference. is it a problem? thanks From owner-chemistry@ccl.net Thu Oct 21 05:41:01 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek(-)few.vu.nl" To: CCL Subject: CCL: excitation state and energy gap Message-Id: <-42983-101021053944-11702-qYPvde3Cql8hH/nWrZi9Rg##server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 21 Oct 2010 11:39:38 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek^-^few.vu.nl] > I have a question about homo-lumo transition. I studied TD-DFT (singlet) > calculation for an organic compound. homo-lumo transition energy 400.21 nm. > > Excited State   1:   Singlet-A      3.0980 eV  400.21 nm  f=0.0252 > homo-lumo energy gap :-0,12555 hartree = 3,416390784 ev = 413,75 nm > > what is the reason for this difference, in some calculations I meet bigger > difference. is it a problem? The excitation energy is not exactly the orbital energy difference in TDDFT, so there is no problem. This is particularly true for functionals that include HF exchange, because there you have a correction which depends on the Coulomb interaction between the hole and the excited electron. Also your excitation is probably not purely homo-lumo, even if that is the most important orbital pair. Sincerely, Ulf Ekström From owner-chemistry@ccl.net Thu Oct 21 08:04:01 2010 From: "Manoj Kumar Kesharwani manojcsmcri+/-gmail.com" To: CCL Subject: CCL:G: Installation of Gaussian 09 on CentOs Linux Message-Id: <-42984-101021074913-16845-giWUCTk6E8jPt53X4PjtiQ::server.ccl.net> X-Original-From: "Manoj Kumar Kesharwani" Date: Thu, 21 Oct 2010 07:49:10 -0400 Sent to CCL by: "Manoj Kumar Kesharwani" [manojcsmcri-$-gmail.com] I have a Intel xeon based workstation with CentOs Linux operating system. I have to procure binary code of Gaussian 09 for our system, but I am unsure about the machine type. I have checked with Gaussian support, but they are unsure about the CentOs. Can anyone suggest me which binary code of Gaussian 09 will be suitable for our machine. Importantly the machine is of 64 bit. With regards, Manoj E-mail: manojcsmcri/./gnail.com From owner-chemistry@ccl.net Thu Oct 21 09:18:00 2010 From: "Michael Boruta michael.boruta**acdlabs.com" To: CCL Subject: CCL: Assignment of IR-spectra Message-Id: <-42985-101021083133-27409-dG/zEF27l8Bvuiyl+oa6vQ[#]server.ccl.net> X-Original-From: "Michael Boruta" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 21 Oct 2010 08:20:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Michael Boruta" [michael.boruta|a|acdlabs.com] Hello Guntram, ACD/Labs has a product that would allow you to make spectra/structure assignments - however it is not automated. You need to manually make the connection from the structure to the band(s). The assignments are then stored with the spectrum. You can find out more about the product at http://www.acdlabs.com/products/adh/uvir/uvir_proc/ The software would also allow you to display both your computed and measured spectrum at the same time. The software does not compute spectra from a structure - but it can read in data from most instrument types, the generic formats like JCAMP and ASCII data. For your question about standard ways to denote the stretching or bending modes - I am not aware of any standard. I would suggest looking in the beginning of a couple of IR functional group correlation books and see how they abbreviate the various modes. Sincerely, Michael Boruta Optical Spectroscopy Product Manager Advanced Chemistry Development, Inc. (ACD/Labs) 110 Yonge Street, 14th floor Toronto ON M5C 1T4 Canada T: 215 357 8855 F: 253 540 2940 Cell phone: 267 303 3809 Toll Free 1-800-304-3988 michael.boruta-#-acdlabs.com www.acdlabs.com CONFIDENTIALITY NOTICE Unless expressly stated otherwise, this message is confidential and is intended for the addressee(s) only. If you are not an addressee, please inform the sender immediately or contact info-#-acdlabs.com. -----Original Message----- > From: owner-chemistry+michael.boruta==acdlabs.com-#-ccl.net [mailto:owner-chemistry+michael.boruta==acdlabs.com-#-ccl.net] On Behalf Of Guntram Schmidt guntram.schmidt##chemie.uni-halle.de Sent: Tuesday, October 19, 2010 6:03 PM To: Michael Boruta Subject: CCL: Assignment of IR-spectra Sent to CCL by: "Guntram Schmidt" [guntram.schmidt a chemie.uni-halle.de] Dear CCLers, I want to assign measured IR-spectra to calculated frequencies. Is there a software to do/automate this? The standard softwares seem to be only capable of displaying the computed spectra without the possibility to add another (measured) spectrum. And if not (which means, I have to use spreadsheet programs to do the assignment), is there a standard way to save those assignments? Some kind of file, where one can store both spectra and the (possible) assignment? And last but not least: Is there a way of denoting the modes in a comprehensible way? Using naming conventions like "bending mode of COOH" will become akward very fast - especially when dealing with multifunctional molecules and coupled vibrations... Thanks a lot for hints (maybe there is a paper dealing with this out there, which I missed on my search), Guntramhttp://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 Oct 21 10:35:00 2010 From: "Serdar Badoglu sbadoglu-.-gazi.edu.tr" To: CCL Subject: CCL:G: NMR peaks Message-Id: <-42986-101021103318-3324-n1MHFmEV2EcKQBGe4PDqaA=server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Thu, 21 Oct 2010 10:33:11 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu,,gazi.edu.tr] Hi CCL'ers, I am currently working on a dinuclear metal(II) complex of a benzimidazole-like molecule. While I was doing my GIAO B3LYP calculations in G03, the experimental 13C-NMR results have arrived. I'm confused. Because my calculations show only six C peaks and in the experimental spectrum there are six aromatic carbon peaks as I expected, but eight additional peaks were observed in the range of approx 40-30 ppm. I'm expertised in FTIR, not in NMR spectroscopy. So I need to know what are those extra peaks, and how I can simulate them in G03 calculations. Thanks. From owner-chemistry@ccl.net Thu Oct 21 11:09:00 2010 From: "Heribert Reis hreis=-=eie.gr" To: CCL Subject: CCL:G: Installation of Gaussian 09 on CentOs Linux Message-Id: <-42987-101021110008-17011-NqbpWkqXMbyMWorbU45NQA||server.ccl.net> X-Original-From: Heribert Reis Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Thu, 21 Oct 2010 17:59:03 +0300 Mime-Version: 1.0 Sent to CCL by: Heribert Reis [hreis(_)eie.gr] On Thu, 2010-10-21 at 07:49 -0400, Manoj Kumar Kesharwani manojcsmcri +/-gmail.com wrote: > Sent to CCL by: "Manoj Kumar Kesharwani" [manojcsmcri-$-gmail.com] > I have a Intel xeon based workstation with CentOs Linux operating system. I have to procure binary code of Gaussian 09 for our system, but I am unsure about the machine type. I have checked with Gaussian support, but they are unsure about the CentOs. Can anyone suggest me which binary code of Gaussian 09 will be suitable for our machine. Importantly the machine is of 64 bit. We are using the AMD 64 bit version of G09 (Rev A.02) on our Cluster (CentOS, Xeon X5650 processors.) Heribert > > With regards, > Manoj > E-mail: manojcsmcri^_^gnail.com> > From owner-chemistry@ccl.net Thu Oct 21 13:23:00 2010 From: "Venable, Richard (NIH/NHLBI) E venabler]~[nhlbi.nih.gov" To: CCL Subject: CCL:G: Installation of Gaussian 09 on CentOs Linux Message-Id: <-42988-101021131227-14631-b1R86r3yM/BB4IF25Za4sQ!=!server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 21 Oct 2010 13:10:48 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#nhlbi.nih.gov] CentOS is essentially a free version of RedHat Linux, without the RH packaging and support, but using the same kernel and admin paradigms. Software packaged for RH should have no issues on a CentOS system. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov > Sent to CCL by: "Manoj Kumar Kesharwani" [manojcsmcri-$-gmail.com] I have a Intel xeon based workstation with CentOs Linux operating system. I have to procure binary code of Gaussian 09 for our system, but I am unsure about the machine type. I have checked with Gaussian support, but they are unsure about the CentOs. Can anyone suggest me which binary code of Gaussian 09 will be suitable for our machine. Importantly the machine is of 64 bit. Sent to CCL by: Heribert Reis [hreis(_)eie.gr] We are using the AMD 64 bit version of G09 (Rev A.02) on our Cluster (CentOS, Xeon X5650 processors.) Heribert From owner-chemistry@ccl.net Thu Oct 21 15:19:00 2010 From: "Hamdy Saad El Sheshtawy h.elsheshtawy:jacobs-university.de" To: CCL Subject: CCL: Transition state calculations Message-Id: <-42989-101021124925-24768-e6RBGAM9hA5D4m2gjiZ2kg~!~server.ccl.net> X-Original-From: "Hamdy Saad El Sheshtawy" Date: Thu, 21 Oct 2010 12:49:16 -0400 Sent to CCL by: "Hamdy Saad El Sheshtawy" [h.elsheshtawy+*+jacobs-university.de] Dear all, I am trying to optimize the transition state for the hydrogen atom abstraction from hexamethylbenzene by cumylpyroxyl radical. It gives the error massage; Wrong number of Negative eigenvalues: Desired= 1 Actual= 0 does anyone have a clue for this problem. Hamdy From owner-chemistry@ccl.net Thu Oct 21 16:54:00 2010 From: "Jamin Krinsky jamink[]berkeley.edu" To: CCL Subject: CCL:G: Transition state calculations Message-Id: <-42990-101021165128-13785-z0CO5NnXUexk7qNFbnJZAg]=[server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 21 Oct 2010 13:51:21 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink**berkeley.edu] Dear Hamdy, In a TS search the program is looking for a structure that exhibits a set of force constants that include exactly one negative eigenvalue (the reaction coordinate). I assume you using Gaussian, and by default in that program, if more than one negative eigenvalue crops up then the program will exit, because a higher-order saddle point usually has no physical meaning. However, sometimes an "extra" negative eigenvalue will go away during the course of the optimization, so this "feature" usually does more harm than good. Also, most of the time you are just estimating the forces in a TS optimization, so something that shows up as a very small negative eigenvalue might go real values when you actually calculate the forces (for instance when you do your frequency calculation). You can disable the "number of eigenvalues" check by using the "noeigentest" option, for example opt=(ts,noeigentest). This message can also result if you do not have ANY negative eigenvalues, e.g. your structure collapsed to a minimum. You can analyze all of this by looking at force constant matrix eigenvalues, which look like this: Eigenvalues --- -0.38497 0.00256 0.00347 0.00391 0.00415 Eigenvalues --- 0.00557 0.00860 0.01032 0.01326 0.01444 Eigenvalues --- 0.01518 0.01652 0.01721 0.01793 0.01938 where any negative eigenvalues come first (note that what I show here is the first few lines of the section, for a successfully run transition state). After that output is a section titled "Eigenvectors required to have negative eigenvalues:" which shows you the elementary coordinates making up the reaction vector the run is optimizing. If there is more than one of these entries, this can help you decide which (if any) vector corresponds with what you are looking for. That is a general how-to, in your case the output tells you "Desired= 1 Actual= 0" so it looks like you fell into a minimum. Just to make it clear, if you are using DFT you may get strange behavior when trying to get a TS for a homolytic bond cleavage, I don't really fully understand why but it has something to do with multiconfigurational character between the closed and open-shell systems. Anyone feel free to correct me on this. Jamin On Thu, Oct 21, 2010 at 9:49 AM, Hamdy Saad El Sheshtawy h.elsheshtawy:jacobs-university.de wrote: > > Sent to CCL by: "Hamdy Saad El Sheshtawy" [h.elsheshtawy+*+jacobs-university.de] > Dear all, > I am trying to optimize the transition state for the hydrogen atom abstraction from hexamethylbenzene by cumylpyroxyl radical. It gives the error massage; Wrong number of Negative eigenvalues: Desired=  1 Actual=  0 > does anyone have a clue for this problem. > Hamdy>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Oct 21 19:07:01 2010 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas++chem.elte.hu" To: CCL Subject: CCL: Transition state calculations Message-Id: <-42991-101021162034-1318-YPl1HZ9oAKG4FqN3vCfB5w^server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Thu, 21 Oct 2010 22:19:58 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas/./chem.elte.hu] Hi Hamdy, Transition state optimizations always need a direction in which the optimizer serches for a maximum and for minimum in the other directions. As the optimization normally starts with a guess Hessian (second derivative matirx), it will have no negative eigenvalue and related eigenvector to be the direction to maximize for. TS optimization may start with two structures at both sides of the TS (QST2 or QST3) or if you have a good guess for the TS but no other info then you might say Opt=CalcFC to compute the second derivatives instead of using a guess or compute second derivatives numerically in some directions, covering the direction the reaction path is presumed to follow. This can be done using Opt=ModRedundant and specifying in the input the coordinates for numerical second derivative computation. If you think that your guess is good and the Hessian update will provide the necessary negative eigenvalue soon, you can simply say Opt=NoEigenTest, meaning, that the optimization won't stop with an error but this is risky, as you might miss the right direction to maximize for but still burning CPU time. I hope I could give some aid, you can write me directly if you still have problems. Best wishes, Ödön Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány Péter sétány H-1117 Budapest, Hungary Cellphone: +36-30-2553111 On Thursday 21 October 2010 18:49:16 Hamdy Saad El Sheshtawy h.elsheshtawy:jacobs-university.de wrote: > Sent to CCL by: "Hamdy Saad El Sheshtawy" > [h.elsheshtawy+*+jacobs-university.de] Dear all, > I am trying to optimize the transition state for the hydrogen atom > abstraction from hexamethylbenzene by cumylpyroxyl radical. It gives the > error massage; Wrong number of Negative eigenvalues: Desired= 1 Actual= 0 > does anyone have a clue for this problem. > Hamdy From owner-chemistry@ccl.net Thu Oct 21 22:15:00 2010 From: "David Gallagher gallagher.da-,-gmail.com" To: CCL Subject: CCL: MOPAC update: DFT accuracy; Ligand binding energies Message-Id: <-42992-101021210150-30201-AvL1uvvrFpGm3f0cBUM5GQ%server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_403828==.ALT" Date: Thu, 21 Oct 2010 18:01:28 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da#%#gmail.com] --=====================_403828==.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable MOPAC2009 update, October 2010 Accuracy has been enhanced using correction terms=20 for dispersion and H-bonding (PM6-DH2) =95 DFT accuracy "The performance of the improved correction=20 is evaluated for PM6, AM1, OM3, and SCC-DFTB=20 (enhanced by standard empirical dispersion=20 corrections) with several test sets for=20 noncovalent interactions and is shown to reach=20 the quality of current DFT-D approaches for these types of problems." (1) =95 Ligand binding energies "This rescoring method is applied to a very=20 challenging system, namely, the HIV-1 protease=20 with a set of ligands. As opposed to the=20 conventional DOCK procedure, the PM6-DH2=20 rescoring based on all of the terms distinguishes=20 between binders and nonbinders and provides a=20 reliable correlation of the theoretical and=20 experimental binding free energies. Such a=20 dramatic improvement, resulting from the PM6-DH2=20 rescoring of all the complexes, provides a=20 valuable yet inexpensive tool for rational drug=20 discovery and de novo ligand design." (2) =95 PM6 includes all 83 elements up to Bismuth,=20 and MOPAC2009 remains free to academics =95 For more information visit:=20 http://cacheresearch.com/mopac.html (1) A Transferable H-Bonding Correction for=20 Semiempirical Quantum-Chemical Methods, Martin=20 Korth, Michal Pitonak, Jan Rezac, and Pavel=20 Hobza, J. Chem. Theory Comput. 2010, 6, 344=96352 (2) A Reliable Docking/Scoring Scheme Based on=20 the Semiempirical Quantum Mechanical PM6-DH2=20 Method Accurately Covering Dispersion and=20 H-Bonding: HIV-1 Protease with 22 Ligands,=20 Jindich Fanfrlk, Agnieszka K. Bronowska, Jan=20 Rezac, Ondej Penosil, Jan Konvalinka, and Pavel=20 Hobza, J. Phys. Chem. B, 2010, 114 (39), pp 12666=9612678 --=====================_403828==.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MOPAC2009 update, October 2010

Accuracy has been enhanced using correction terms for dispersion and H-bonding (PM6-DH2)

=95 DFT accuracy 
     "The performance of the improved correction is evaluated for PM6, AM1, OM3, and SCC-DFTB (enhanced by standard empirical dispersion corrections) with several test sets for noncovalent interactions and is shown to reach the quality of current DFT-D approaches for these types of problems." (1)

=95 Ligand binding energies 
     "This rescoring method is applied to a very challenging system, namely, the HIV-1 protease with a set of ligands. As opposed to the conventional DOCK procedure, the PM6-DH2 rescoring based on all of the terms distinguishes between binders and nonbinders and provides a reliable correlation of the theoretical and experimental binding free energies. Such a dramatic improvement, resulting from the PM6-DH2 rescoring of all the complexes, provides a valuable yet inexpensive tool for rational drug discovery and de novo ligand design." (2)

=95  PM6 includes all 83 elements up to Bismuth, and MOPAC2009 remains free to academics

=95  For more information visit: http://cacheresearch.com/mopac.html


(1) A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods, Martin Korth, Michal Pitonak, Jan Rezac, and Pavel Hobza, J. Chem. Theory Comput. 2010, 6, 344=96352

(2) A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands, Jindich Fanfrlk, Agnieszka K. Bronowska, Jan Rezac, Ondej Penosil, Jan Konvalinka, and Pavel Hobza, J. Phys. Chem. B, 2010, 114 (39), pp 12666=9612678


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