From owner-chemistry@ccl.net Tue Sep 14 01:49:00 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis()borealisgroup.com" To: CCL Subject: CCL:G: Gaussian Message-Id: <-42752-100914014812-14200-FTT/jzTaM4V1Jhu/A8Neyw++server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 14 Sep 2010 07:47:57 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis(a)borealisgroup.com] Turker Hi I am not sure if this will help you but traditionally in Gaussian your checkpoint file (in your case tddft50trs.chk) holds all the information up to the point the calculation ended (well not really as it holds the information up to the point the computer last wrote on that file, but it is almost the same in your case). Therefore you can start a new calculation using the previous checkpoint file. How to do this? First make a copy of your current checkpoint file and rename it to something else let's say tddft50trs-NEW.chk. Then you can start the same calculation as before, and you can use the command guess=Read. That way the program knows to use the new checkpoint file that you need. Your command lines should look like this (the rest of the calculation command there I have no idea what they do so I just left them as it was. If they need to be changed you need to consult the Gaussian manual) %chk=C:/Users/TURKR/Desktop/tddft50trs-NEW.chk %mem=100MW %nproc=1 #p td=(singlets,nstates=50) b3lyp/6-311+g(d) guess=(save,read) geom=connectivity pop=full gfinput I hope this helps Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com*ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com*ccl.net] On Behalf Of turker akcay turkerakcay{}hotmail.com Sent: Monday, September 13, 2010 11:50 AM To: Gkourmpis, Thomas Subject: CCL:G: Gaussian Sent to CCL by: "turker akcay" [turkerakcay() hotmail.com] Hi everybody I'm new gaussian user and I use gaussian 03 for win. I am studying on TD DFT study a dinitrile compound. After 6 days processing, because of electricity cutting, my gaussian job is terminated and computer is closed. I want to resumption my job but I dont know how do it. is it possible? or should I open latest out file and restart process. My input file; %chk=C:/Users/TURKR/Desktop/tddft50trs.chk %mem=100MW %nproc=1 #p td=(singlets,nstates=50) b3lyp/6-311+g(d) guess=save geom=connectivity pop=full gfinput final part of my out file; Cannot handle 2e integral symmetry, ISym2E=1. CISAX: IP= 1 NPass= 3 NMax= 34. CISAX will form 34 AO SS matrices at one time. NMat= 34 NSing= 34. NMat= 34 NSing= 34. NMat= 32 NSing= 32. Cannot handle 2e integral symmetry, ISym2E=1. CISAX: IP= 1 NPass= 3 NMax= 34. CISAX will form 34 AO SS matrices at one time. NMat= 34 NSing= 34. NMat= 34 NSing= 34. NMat= 32 NSing= 32. Root 1 has converged. Root 2 has converged. Root 3 has converged. Root 4 has converged. Root 5 has converged. Root 6 has converged. Root 7 has converged. Root 8 has converged. Root 9 has converged. Root 10 has converged. Root 11 has converged. Root 12 has converged. Root 13 not converged, maximum delta is 0.001146383849072 Root 14 not converged, maximum delta is 0.001076901825947 Root 15 has converged. Root 16 has converged. Root 17 has converged. Root 18 has converged. Root 19 has converged. Root 20 has converged. Root 21 has converged. Root 22 has converged. Root 23 has converged. Root 24 has converged. Root 25 has converged. Root 26 has converged. Root 27 has converged. Root 28 not converged, maximum delta is 0.001298203075257 Root 29 has converged. Root 30 has converged. Root 31 has converged. Root 32 not converged, maximum delta is 0.001487599984012 Root 33 not converged, maximum delta is 0.002130187054738 Root 34 not converged, maximum delta is 0.009687228977448 Root 35 not converged, maximum delta is 0.014708674044360 Root 36 has converged. Root 37 not converged, maximum delta is 0.001056178564194 Root 38 not converged, maximum delta is 0.001307476560090 Root 39 not converged, maximum delta is 0.001281081401660 Root 40 has converged. Root 41 not converged, maximum delta is 0.001061548241041 Root 42 not converged, maximum delta is 0.001573623655971 Root 43 has converged. Root 44 has converged. Root 45 has converged. Root 46 has converged. Root 47 not converged, maximum delta is 0.001567486009780 Root 48 not converged, maximum delta is 0.005544365303514 Root 49 not converged, maximum delta is 0.015140942251070 Root 50 not converged, maximum delta is 0.016487405708613 Excitation Energies [eV] at current iteration: Root 1 : 3.097975009587616 Change is -0.000001105943253 Root 2 : 3.583514852565895 Change is -0.000007448515000 Root 3 : 3.617241820182027 Change is -0.000021813870515 Root 4 : 3.991502586858061 Change is -0.000023174927667 Root 5 : 4.138876536189863 Change is -0.000007145969739 Root 6 : 4.211283026540273 Change is -0.000007302963600 Root 7 : 4.270327709174773 Change is -0.000012531626331 Root 8 : 4.368328284874000 Change is -0.000005937553695 Root 9 : 4.445535867701103 Change is -0.000032779976579 Root 10 : 4.540640063389401 Change is -0.000002225280201 Root 11 : 4.656404960218242 Change is -0.000023209382109 Root 12 : 4.714797549284374 Change is -0.000019602079988 Root 13 : 4.754991510970658 Change is -0.00001http://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 Tue Sep 14 08:06:00 2010 From: "Frank Neese neese(0)thch.uni-bonn.de" To: CCL Subject: CCL: New ORCA Version released Message-Id: <-42753-100914071737-775-kDgDa0HPY2kbOaBmMA3mqw a server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 14 Sep 2010 13:13:11 +0200 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Frank Neese [neese{=}thch.uni-bonn.de] Dear CClers, we are happy to announce that the latest ORCA version has been uploaded to our server and is available for download. This is version 2.8.0 that has been substantially improved since the beta release earlier this year. We have conducted a concert effort to make the program more stable, more consistent, more reliable, mor efficient and to also improve parallelization. A parallel version for windows will be available soon. Concerning features, version 2.8 now supports the following: - TD-DFT analytic gradient including RIJCOSX. It is efficiently parallelized - RIJCOSX-MP2 Gradient for MP2, SCS-MP2 and double hybrid functionals. This greatly improves speed. It is also efficiently parallelized - Orbital optimized MP2 - Orbital optimized and variational CEPA methods - Brueckner orbitals for coupled cluster calculations - Improved CASSCF convergence. New converger superci_pt - Second order N-electron valence perturbation theory (NEVPT2). This is a contracted multireference perturbation theory, similar to CASPT2 (but lacks intruder states or linear dependencies in the first-order interacting space) and is very efficient. The program is parallelized and spin-orbit coupling and other magnetic properties can be calculated through quasi-degenerate perturbation theory. We hope that you will like this new version of ORCA! As always, the best way to show your appreciation is to cite our original papers when you use ORCA for your research. With our best regards, Frank Neese and Frank Wennmohs on behalf of the ORCA development team. From owner-chemistry@ccl.net Tue Sep 14 10:07:01 2010 From: "turker akcay turkerakcay-x-hotmail.com" To: CCL Subject: CCL:G: Gaussian Message-Id: <-42754-100914100525-21355-62EiRe2DRUvfAAOGsrDjPA*_*server.ccl.net> X-Original-From: "turker akcay" Date: Tue, 14 Sep 2010 10:05:24 -0400 Sent to CCL by: "turker akcay" [turkerakcay^hotmail.com] john and Thaomas, thanks so much for your reply, I have a question before I try your vauable advices. How can I know how many transitions are enough for analysis of transition study. I have a TD-DFT study including 25 transitions. But There are no peaks below 220 nm and above 400 nm so I am not sure it's suitable or not. I don't have any experimental result. "I know this relates what to do" but maybe, can you give me an advidce thanks from now... the result of out file - 25 transitions; Excitation energies and oscillator strengths: Excited state symmetry could not be determined. Excited State 1: Singlet-?Sym 3.0980 eV 400.21 nm f=0.0252 114 ->115 0.70376 This state for optimization and/or second-order correction. Total Energy, E(RPA) = -1410.34981294 Copying the excited state density for this state as the 1-particle RhoCI density. Excited state symmetry could not be determined. Excited State 2: Singlet-?Sym 3.5835 eV 345.99 nm f=0.2117 114 ->116 0.68276 114 ->117 0.11195 Excited state symmetry could not be determined. Excited State 3: Singlet-?Sym 3.6172 eV 342.77 nm f=0.4551 114 ->116 -0.13374 114 ->117 0.65556 Excited state symmetry could not be determined. Excited State 4: Singlet-?Sym 3.9914 eV 310.63 nm f=0.2250 114 ->118 0.66930 Excited state symmetry could not be determined. Excited State 5: Singlet-?Sym 4.1387 eV 299.57 nm f=0.0320 108 ->117 -0.10141 114 ->119 0.67679 Excited state symmetry could not be determined. Excited State 6: Singlet-?Sym 4.2110 eV 294.43 nm f=0.0212 114 ->120 0.67629 Excited state symmetry could not be determined. Excited State 7: Singlet-?Sym 4.2703 eV 290.34 nm f=0.0405 111 ->115 0.17959 112 ->115 -0.42348 113 ->115 0.50020 Excited state symmetry could not be determined. Excited State 8: Singlet-?Sym 4.3683 eV 283.82 nm f=0.0082 111 ->115 -0.15993 112 ->115 0.45931 113 ->115 0.49208 Excited state symmetry could not be determined. Excited State 9: Singlet-?Sym 4.4456 eV 278.89 nm f=0.0314 106 ->115 -0.16388 106 ->116 0.16317 109 ->115 -0.11910 111 ->115 0.50333 111 ->116 0.20915 112 ->115 0.30685 Excited state symmetry could not be determined. Excited State 10: Singlet-?Sym 4.5379 eV 273.22 nm f=0.0029 114 ->121 0.69157 Excited state symmetry could not be determined. Excited State 11: Singlet-?Sym 4.6563 eV 266.27 nm f=0.2465 111 ->116 0.10349 112 ->116 -0.14459 112 ->117 -0.14125 113 ->116 0.26516 113 ->117 0.55891 113 ->118 -0.10560 114 ->123 0.14093 Excited state symmetry could not be determined. Excited State 12: Singlet-?Sym 4.7147 eV 262.97 nm f=0.1339 111 ->116 -0.12838 112 ->116 0.30872 112 ->117 0.45841 112 ->118 -0.10147 113 ->117 0.19507 113 ->118 -0.10864 114 ->123 0.25613 Excited state symmetry could not be determined. Excited State 13: Singlet-?Sym 4.7551 eV 260.74 nm f=0.0117 109 ->115 -0.17425 111 ->115 -0.15031 111 ->116 0.14281 112 ->116 -0.22387 112 ->118 -0.13620 113 ->117 -0.22739 113 ->118 -0.13993 114 ->122 0.23311 114 ->123 0.41207 Excited state symmetry could not be determined. Excited State 14: Singlet-?Sym 4.7589 eV 260.53 nm f=0.0231 109 ->115 -0.24582 111 ->115 -0.16669 111 ->116 0.13041 112 ->117 0.38336 113 ->116 0.30536 113 ->118 0.14775 114 ->123 -0.26793 Excited state symmetry could not be determined. Excited State 15: Singlet-?Sym 4.8060 eV 257.98 nm f=0.0382 109 ->115 0.46473 111 ->115 0.11429 111 ->116 -0.10784 112 ->116 -0.19466 112 ->117 0.16619 113 ->116 0.32221 113 ->117 -0.16619 Excited state symmetry could not be determined. Excited State 16: Singlet-?Sym 4.8392 eV 256.21 nm f=0.0845 109 ->115 0.14950 109 ->117 0.15069 111 ->117 0.13481 113 ->117 0.11779 113 ->118 0.12757 114 ->122 0.57168 114 ->123 -0.10441 Excited state symmetry could not be determined. Excited State 17: Singlet-?Sym 4.8764 eV 254.25 nm f=0.0204 108 ->115 -0.25274 109 ->115 -0.26676 111 ->116 -0.23932 111 ->117 -0.11007 112 ->116 0.17007 112 ->117 -0.16335 113 ->116 0.41670 113 ->117 -0.13596 Excited state symmetry could not be determined. Excited State 18: Singlet-?Sym 4.8800 eV 254.07 nm f=0.0022 110 ->115 0.69466 Excited state symmetry could not be determined. Excited State 19: Singlet-?Sym 4.9087 eV 252.58 nm f=0.0077 108 ->115 0.25750 109 ->115 0.15822 111 ->116 0.24975 112 ->116 0.47401 112 ->117 -0.13729 113 ->116 0.19510 113 ->117 -0.11167 Excited state symmetry could not be determined. Excited State 20: Singlet-?Sym 4.9634 eV 249.79 nm f=0.0012 107 ->117 0.10310 108 ->115 -0.32546 111 ->116 0.12834 111 ->117 0.55430 111 ->118 0.11141 114 ->122 -0.13979 Excited state symmetry could not be determined. Excited State 21: Singlet-?Sym 5.0419 eV 245.91 nm f=0.1192 106 ->115 0.26880 108 ->115 0.44216 109 ->115 -0.14607 111 ->115 0.11671 111 ->116 -0.23735 111 ->117 0.26588 Excited state symmetry could not be determined. Excited State 22: Singlet-?Sym 5.1014 eV 243.04 nm f=0.0195 107 ->115 -0.15265 107 ->117 0.27241 108 ->117 0.14542 109 ->116 0.14769 109 ->117 0.46054 112 ->118 0.16722 113 ->118 -0.19263 Excited state symmetry could not be determined. Excited State 23: Singlet-?Sym 5.1295 eV 241.71 nm f=0.0244 109 ->120 -0.18492 110 ->116 0.15814 110 ->117 0.50145 110 ->118 -0.13012 111 ->120 -0.10270 112 ->118 0.18511 113 ->118 0.18318 114 ->125 0.12301 Excited state symmetry could not be determined. Excited State 24: Singlet-?Sym 5.1558 eV 240.47 nm f=0.0074 110 ->117 0.10719 114 ->123 -0.11136 114 ->124 0.64278 114 ->125 -0.18463 Excited state symmetry could not be determined. Excited State 25: Singlet-?Sym 5.1885 eV 238.96 nm f=0.0264 107 ->115 -0.13098 107 ->117 0.15784 108 ->117 -0.13769 109 ->116 0.10851 110 ->117 -0.21030 112 ->118 0.12327 112 ->119 0.16886 112 ->120 0.10760 112 ->123 0.10291 113 ->118 0.37355 114 ->123 0.23724 114 ->124 0.13976 Leave Link 914 at Tue Sep 07 03:26:58 2010, MaxMem= 52428800 cpu: 259882.0 (Enter C:\G03W\l601.exe) Copying SCF densities to generalized density rwf, ISCF=0 IROHF=0. From owner-chemistry@ccl.net Tue Sep 14 10:56:00 2010 From: "Maciej Haranczyk ccl^-^maciejharanczyk.info" To: CCL Subject: CCL: CFP:Cheminformatics-CombiChem Symposium, 241 ACS Meeting, Anaheim, CA Message-Id: <-42755-100914103833-22105-f/1wLbKI6HNCQJSswNteEQ~~server.ccl.net> X-Original-From: "Maciej Haranczyk" Date: Tue, 14 Sep 2010 10:38:32 -0400 Sent to CCL by: "Maciej Haranczyk" [ccl[]maciejharanczyk.info] Call for Papers: Integration of Combinatorial Chemistry with Cheminformatics: Current trends and future directions in drug discovery and material science 241th ACS National Meeting Anaheim, CA, March 27-31, 2011 CINF Division Dear Colleagues, Combinatorial and high throughput techniques have become widely used in chemistry, materials science, and drug discovery. By their nature, these techniques involve generation, storage and analysis of massive datasets. Therefore, combinatorial techniques have been stimulating the development of cheminformatic tools and approaches to handle and process such datasets. The symposium will focus on the current trends and future directions in this area of cheminformatics and the related areas of combinatorial chemistry. In particular, the organizers would like to: 1) discuss new developments in combichem/cheminformatics in bioresearch, 2) talk about challenges in emerging non-bio combinatorial chemistry. The idea is to provide a venue and exchange ideas, with the goal not only to improve bio-research but also to inspire and boost the development of cheminformatics for combinatorial materials discovery. We invite you to submit contributions to this symposium that will cover a wide range of chemical information and computational methods used to address facing the needs of combinatorial science in drugs and material discovery. Topics include, but are not limited to: - Combinatorial library design - Novel approaches in experimental (HT setups, screening in vivo) and computational screening - Data collection and storage - Visualization and data analysis Please use the new Program and Abstract Creation System (PACS) for submitting your abstract (http://abstracts.acs.org). You will need to login to PACS with your ACS portal username and password. You will find our symposium under the program of CINF division. PACS will be accepting abstracts until October 18, 2010 11:00 PM CT. Sincerely, Maciej Haranczyk Email: mharanczyk(at)lbl.gov Ph: (510) 486 7749 / Fax: (510) 486 5812 Jose Medina-Franco Email: jmedina(at)tpims.org Ph: (772) 345 4685 / Fax: (772) 345 3649 From owner-chemistry@ccl.net Tue Sep 14 11:53:00 2010 From: "Marcelo Puiatti marcelo.puiatti|*|gmail.com" To: CCL Subject: CCL: How to make an enantiomer? Message-Id: <-42756-100914114942-6971-vWVCzRXQCkhxewZ/S3X8KA---server.ccl.net> X-Original-From: Marcelo Puiatti Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 14 Sep 2010 12:49:34 -0300 MIME-Version: 1.0 Sent to CCL by: Marcelo Puiatti [marcelo.puiatti,+,gmail.com] Hi, I want to generate an enantiomer of a small molecule from its xyz coordinates. Is there any program for doing that? Thanks in advance From owner-chemistry@ccl.net Tue Sep 14 12:27:00 2010 From: "John McKelvey jmmckel,gmail.com" To: CCL Subject: CCL:G: Gaussian Message-Id: <-42757-100914115346-9852-9j6ceIANzZxtidjrpN+t2Q{}server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 14 Sep 2010 11:53:40 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel|,|gmail.com] Turker, I would guess that your calculations point out what you might expect first for the strongest experimental transitions... states 2-4,11,12,16,21 . Of course it is important to get some idea of the accuracy of the particular functional and basis set used. If you are going away for a week you could try again for 50 states to see what else shows up. John On Tue, Sep 14, 2010 at 10:05 AM, turker akcay turkerakcay-x-hotmail.com wrote: > > Sent to CCL by: "turker  akcay" [turkerakcay^hotmail.com] > john and Thaomas, thanks so much for your reply, > > I have a question before I try your vauable advices. How can I know how many > transitions are enough for analysis of transition study. I have a TD-DFT > study including 25 transitions. But There are no peaks below 220 nm and above > 400 nm so I am not sure it's suitable or not. I don't have any experimental > result. "I know this relates what to do" but maybe, can you give me an > advidce >  thanks from now... > > the result of out file - 25 transitions; > Excitation energies and oscillator strengths: > >  Excited state symmetry could not be determined. >  Excited State   1:   Singlet-?Sym    3.0980 eV  400.21 nm  f=0.0252 >     114 ->115         0.70376 >  This state for optimization and/or second-order correction. >  Total Energy, E(RPA) =  -1410.34981294 >  Copying the excited state density for this state as the 1-particle RhoCI > density. > >  Excited state symmetry could not be determined. >  Excited State   2:   Singlet-?Sym    3.5835 eV  345.99 nm  f=0.2117 >     114 ->116         0.68276 >     114 ->117         0.11195 > >  Excited state symmetry could not be determined. >  Excited State   3:   Singlet-?Sym    3.6172 eV  342.77 nm  f=0.4551 >     114 ->116        -0.13374 >     114 ->117         0.65556 > >  Excited state symmetry could not be determined. >  Excited State   4:   Singlet-?Sym    3.9914 eV  310.63 nm  f=0.2250 >     114 ->118         0.66930 > >  Excited state symmetry could not be determined. >  Excited State   5:   Singlet-?Sym    4.1387 eV  299.57 nm  f=0.0320 >     108 ->117        -0.10141 >     114 ->119         0.67679 > >  Excited state symmetry could not be determined. >  Excited State   6:   Singlet-?Sym    4.2110 eV  294.43 nm  f=0.0212 >     114 ->120         0.67629 > >  Excited state symmetry could not be determined. >  Excited State   7:   Singlet-?Sym    4.2703 eV  290.34 nm  f=0.0405 >     111 ->115         0.17959 >     112 ->115        -0.42348 >     113 ->115         0.50020 > >  Excited state symmetry could not be determined. >  Excited State   8:   Singlet-?Sym    4.3683 eV  283.82 nm  f=0.0082 >     111 ->115        -0.15993 >     112 ->115         0.45931 >     113 ->115         0.49208 > >  Excited state symmetry could not be determined. >  Excited State   9:   Singlet-?Sym    4.4456 eV  278.89 nm  f=0.0314 >     106 ->115        -0.16388 >     106 ->116         0.16317 >     109 ->115        -0.11910 >     111 ->115         0.50333 >     111 ->116         0.20915 >     112 ->115         0.30685 > >  Excited state symmetry could not be determined. >  Excited State  10:   Singlet-?Sym    4.5379 eV  273.22 nm  f=0.0029 >     114 ->121         0.69157 > >  Excited state symmetry could not be determined. >  Excited State  11:   Singlet-?Sym    4.6563 eV  266.27 nm  f=0.2465 >     111 ->116         0.10349 >     112 ->116        -0.14459 >     112 ->117        -0.14125 >     113 ->116         0.26516 >     113 ->117         0.55891 >     113 ->118        -0.10560 >     114 ->123         0.14093 > >  Excited state symmetry could not be determined. >  Excited State  12:   Singlet-?Sym    4.7147 eV  262.97 nm  f=0.1339 >     111 ->116        -0.12838 >     112 ->116         0.30872 >     112 ->117         0.45841 >     112 ->118        -0.10147 >     113 ->117         0.19507 >     113 ->118        -0.10864 >     114 ->123         0.25613 > >  Excited state symmetry could not be determined. >  Excited State  13:   Singlet-?Sym    4.7551 eV  260.74 nm  f=0.0117 >     109 ->115        -0.17425 >     111 ->115        -0.15031 >     111 ->116         0.14281 >     112 ->116        -0.22387 >     112 ->118        -0.13620 >     113 ->117        -0.22739 >     113 ->118        -0.13993 >     114 ->122         0.23311 >     114 ->123         0.41207 > >  Excited state symmetry could not be determined. >  Excited State  14:   Singlet-?Sym    4.7589 eV  260.53 nm  f=0.0231 >     109 ->115        -0.24582 >     111 ->115        -0.16669 >     111 ->116         0.13041 >     112 ->117         0.38336 >     113 ->116         0.30536 >     113 ->118         0.14775 >     114 ->123        -0.26793 > >  Excited state symmetry could not be determined. >  Excited State  15:   Singlet-?Sym    4.8060 eV  257.98 nm  f=0.0382 >     109 ->115         0.46473 >     111 ->115         0.11429 >     111 ->116        -0.10784 >     112 ->116        -0.19466 >     112 ->117         0.16619 >     113 ->116         0.32221 >     113 ->117        -0.16619 > >  Excited state symmetry could not be determined. >  Excited State  16:   Singlet-?Sym    4.8392 eV  256.21 nm  f=0.0845 >     109 ->115         0.14950 >     109 ->117         0.15069 >     111 ->117         0.13481 >     113 ->117         0.11779 >     113 ->118         0.12757 >     114 ->122         0.57168 >     114 ->123        -0.10441 > >  Excited state symmetry could not be determined. >  Excited State  17:   Singlet-?Sym    4.8764 eV  254.25 nm  f=0.0204 >     108 ->115        -0.25274 >     109 ->115        -0.26676 >     111 ->116        -0.23932 >     111 ->117        -0.11007 >     112 ->116         0.17007 >     112 ->117        -0.16335 >     113 ->116         0.41670 >     113 ->117        -0.13596 > >  Excited state symmetry could not be determined. >  Excited State  18:   Singlet-?Sym    4.8800 eV  254.07 nm  f=0.0022 >     110 ->115         0.69466 > >  Excited state symmetry could not be determined. >  Excited State  19:   Singlet-?Sym    4.9087 eV  252.58 nm  f=0.0077 >     108 ->115         0.25750 >     109 ->115         0.15822 >     111 ->116         0.24975 >     112 ->116         0.47401 >     112 ->117        -0.13729 >     113 ->116         0.19510 >     113 ->117        -0.11167 > >  Excited state symmetry could not be determined. >  Excited State  20:   Singlet-?Sym    4.9634 eV  249.79 nm  f=0.0012 >     107 ->117         0.10310 >     108 ->115        -0.32546 >     111 ->116         0.12834 >     111 ->117         0.55430 >     111 ->118         0.11141 >     114 ->122        -0.13979 > >  Excited state symmetry could not be determined. >  Excited State  21:   Singlet-?Sym    5.0419 eV  245.91 nm  f=0.1192 >     106 ->115         0.26880 >     108 ->115         0.44216 >     109 ->115        -0.14607 >     111 ->115         0.11671 >     111 ->116        -0.23735 >     111 ->117         0.26588 > >  Excited state symmetry could not be determined. >  Excited State  22:   Singlet-?Sym    5.1014 eV  243.04 nm  f=0.0195 >     107 ->115        -0.15265 >     107 ->117         0.27241 >     108 ->117         0.14542 >     109 ->116         0.14769 >     109 ->117         0.46054 >     112 ->118         0.16722 >     113 ->118        -0.19263 > >  Excited state symmetry could not be determined. >  Excited State  23:   Singlet-?Sym    5.1295 eV  241.71 nm  f=0.0244 >     109 ->120        -0.18492 >     110 ->116         0.15814 >     110 ->117         0.50145 >     110 ->118        -0.13012 >     111 ->120        -0.10270 >     112 ->118         0.18511 >     113 ->118         0.18318 >     114 ->125         0.12301 > >  Excited state symmetry could not be determined. >  Excited State  24:   Singlet-?Sym    5.1558 eV  240.47 nm  f=0.0074 >     110 ->117         0.10719 >     114 ->123        -0.11136 >     114 ->124         0.64278 >     114 ->125        -0.18463 > >  Excited state symmetry could not be determined. >  Excited State  25:   Singlet-?Sym    5.1885 eV  238.96 nm  f=0.0264 >     107 ->115        -0.13098 >     107 ->117         0.15784 >     108 ->117        -0.13769 >     109 ->116         0.10851 >     110 ->117        -0.21030 >     112 ->118         0.12327 >     112 ->119         0.16886 >     112 ->120         0.10760 >     112 ->123         0.10291 >     113 ->118         0.37355 >     114 ->123         0.23724 >     114 ->124         0.13976 >  Leave Link  914 at Tue Sep 07 03:26:58 2010, MaxMem=   52428800 cpu: > 259882.0 >  (Enter C:\G03W\l601.exe) >  Copying SCF densities to generalized density rwf, ISCF=0 IROHF=0.>      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> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel++gmail.com From owner-chemistry@ccl.net Tue Sep 14 13:41:00 2010 From: "Victor Rosas Garcia rosas.victor%gmail.com" To: CCL Subject: CCL: How to make an enantiomer? Message-Id: <-42758-100914130612-2260-k9O1BPVCf1+lObylc3KCPg++server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=0015174c1532beaf3604903b3919 Date: Tue, 14 Sep 2010 12:05:53 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor]|[gmail.com] --0015174c1532beaf3604903b3919 Content-Type: text/plain; charset=ISO-8859-1 I would just reverse the signs of all the, say, x coordinates. That is equivalent to a mirror reflection. Now if the molecule is really big, so that reversing signs by hand is impractical, I think PCMODEL can generate an enantiomer from a structure. Have a nice day! Victor 2010/9/14 Marcelo Puiatti marcelo.puiatti|*|gmail.com < owner-chemistry^-^ccl.net> > > Sent to CCL by: Marcelo Puiatti [marcelo.puiatti,+,gmail.com] > Hi, I want to generate an enantiomer of a small molecule from its xyz > coordinates. Is there any program for doing that? > > Thanks in advance > > > > --0015174c1532beaf3604903b3919 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I would just reverse the signs of all the, say, x coordinates.=A0 That is e= quivalent to a mirror reflection.=A0 Now if the molecule is really big, so = that reversing signs by hand is impractical, I think PCMODEL can generate a= n enantiomer from a structure.

Have a nice day!

Victor

2010/9= /14 Marcelo Puiatti marcelo.puiatti|*|gmail.co= m <owne= r-chemistry^-^ccl.net>

Sent to CCL by: Marcelo Puiatti [marcelo.puiatti,+,gmail.com]
Hi, I want to generate an enantiomer of a small molecule from its xyz
coordinates. Is there any program for doing that?

Thanks in advance



--0015174c1532beaf3604903b3919-- From owner-chemistry@ccl.net Tue Sep 14 14:15:00 2010 From: "Jose A. Gamez joseantonio.gamez]|[uam.es" To: CCL Subject: CCL: How to make an enantiomer? Message-Id: <-42759-100914134135-23452-M1PxjFsrfP+cd2wt04BJcw/./server.ccl.net> X-Original-From: "Jose A. Gamez" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 14 Sep 2010 19:41:56 +0200 MIME-Version: 1.0 Sent to CCL by: "Jose A. Gamez" [joseantonio.gamez:uam.es] An enantiomer is a mirror image of another molecule, so it can be obtained by reflecting a molecule into ANY mirror plane. To make things easy, let's consider the x=0 plane. A reflection of the point (x,y,z) into that plane would lead to (x, y, z) --> (-x, y, z) so it just changes the sign of the "x" coordinate. Therefore, if you just change the sign of the "x" (or "y" or "z") coordinate of all your atoms you can easily generate the enantiomer you're looking for. If your molecule is small, it will take you longer to write a program to do that rather than changing it manually. Hope this helps. Jose On Tue 14 September 2010 17:49:34 Marcelo Puiatti marcelo.puiatti|*|gmail.com wrote: > Sent to CCL by: Marcelo Puiatti [marcelo.puiatti,+,gmail.com] > Hi, I want to generate an enantiomer of a small molecule from its xyz > coordinates. Is there any program for doing that? > > Thanks in advance -- From owner-chemistry@ccl.net Tue Sep 14 17:57:00 2010 From: "Piotr Nowak piotrnowak__student.uw.edu.pl" To: CCL Subject: CCL: How to make an enantiomer? Message-Id: <-42760-100914162319-13013-MkDPyQ9HMKEyGX//ZcUjYw]*[server.ccl.net> X-Original-From: Piotr Nowak Content-Type: multipart/alternative; boundary=0022150482bb50208404903dfb66 Date: Tue, 14 Sep 2010 22:23:10 +0200 MIME-Version: 1.0 Sent to CCL by: Piotr Nowak [piotrnowak*_*student.uw.edu.pl] --0022150482bb50208404903dfb66 Content-Type: text/plain; charset=ISO-8859-1 You actually don't have to write a program or change all the signs by hand. Open Office or Excel can do the trick easily. You just have to copy your coordinates to the spreadsheet, multiply one row (or all three rows) by -1, and save the file as a csv document. Then use Emacs, Vim (or some other text editor with the column mode) to copy the coords to your input file. Good luck with stereomutation, ti would be much more difficult for experimental chemists ;-), Piotr Nowak On Tue, Sep 14, 2010 at 7:41 PM, Jose A. Gamez joseantonio.gamez]|[uam.es < owner-chemistry-.-ccl.net> wrote: > > Sent to CCL by: "Jose A. Gamez" [joseantonio.gamez:uam.es] > An enantiomer is a mirror image of another molecule, so it can be obtained > by > reflecting a molecule into ANY mirror plane. To make things easy, let's > consider the x=0 plane. A reflection of the point (x,y,z) into that plane > would lead to > (x, y, z) --> (-x, y, z) > so it just changes the sign of the "x" coordinate. Therefore, if you just > change the sign of the "x" (or "y" or "z") coordinate of all your atoms you > can easily generate the enantiomer you're looking for. If your molecule is > small, it will take you longer to write a program to do that rather than > changing it manually. > > Hope this helps. > > Jose > > On Tue 14 September 2010 17:49:34 Marcelo Puiatti marcelo.puiatti|*| > gmail.com > wrote: > > Sent to CCL by: Marcelo Puiatti [marcelo.puiatti,+,gmail.com] > > Hi, I want to generate an enantiomer of a small molecule from its xyz > > coordinates. Is there any program for doing that? > > > > Thanks in advance > --> > > -- ****** Piotr Nowak University of Warsaw Department of Chemistry Laboratory of Stereocontrolled Organic Synthesis Pasteura 1, 02-093 Warsaw, Poland http://www.google.com/profiles/omenthegreat ****** --0022150482bb50208404903dfb66 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Yo= u actually don't have to write a program or change all the signs by han= d. Open Office or Excel can do the trick easily. You just have to copy your= coordinates to the spreadsheet, multiply one row (or all three rows) by -1= , and save the file as a csv document. Then use Emacs, Vim (or some other t= ext editor with the column mode) to copy the coords to your input file.
Good luck with stereomutation, ti would be much more difficu= lt for experimental chemists ;-),

Piotr Nowak


On Tue, Sep 14, 2010 at 7:41 PM, J= ose A. Gamez joseantonio.gamez]|[uam.es <owner-chemistry= -.-ccl.net> wrote:

Sent to CCL by: "Jose A. Gamez" [joseantonio.gamez:uam.es]
An enantiomer is a mirror image of another molecule, so it can be obtained = by
reflecting a molecule into ANY mirror plane. To make things easy, let's=
consider the x=3D0 plane. A reflection of the point (x,y,z) into that plane=
would lead to
(x, y, z) --> (-x, y, z)
so it just changes the sign of the "x" coordinate. Therefore, if = you just
change the sign of the "x" (or "y" or "z") co= ordinate of all your atoms you
can easily generate the enantiomer you're looking for. If your molecule= is
small, it will take you longer to write a program to do that rather than changing it manually.

Hope this helps.

Jose

On Tue 14 September 2010 17:49:34 Marcelo Puiatti marcelo.puiatti|*|gmail.com
wrote:
> Sent to CCL by: Marcelo Puiatti [marcelo.puiatti,+,<= a href=3D"http://gmail.com" target=3D"_blank">gmail.com]
> Hi, I want to generate an enantiomer of a small molecule from its xyz<= br> > coordinates. Is there any program for doing that?
>
> Thanks in advance
--



--
******
= Piotr Nowak
University of Warsaw
Department of Chemistr= y
Laboratory of Stereocontrolled Organic Synthesis
Past= eura 1, 02-093 Warsaw, Poland
******

--0022150482bb50208404903dfb66-- From owner-chemistry@ccl.net Tue Sep 14 18:32:00 2010 From: "Jason Swails swails(~)qtp.ufl.edu" To: CCL Subject: CCL: How to make an enantiomer? Message-Id: <-42761-100914131850-11765-643ytHOW4tC3a6kk8RD7ag[-]server.ccl.net> X-Original-From: Jason Swails Content-Type: multipart/alternative; boundary=000e0cd6adc876cadf04903b67d1 Date: Tue, 14 Sep 2010 13:18:39 -0400 MIME-Version: 1.0 Sent to CCL by: Jason Swails [swails%qtp.ufl.edu] --000e0cd6adc876cadf04903b67d1 Content-Type: text/plain; charset=ISO-8859-1 Hello, If you take the additive inverse of all X-coordinates for all atoms you'll have the mirror image reflected in the Y-Z plane. If it's an enantiomer, this will be non-superimposable. You can do this quite easily with a tool of your choice -- sed, awk, or a home-brewed python/perl script. Hope this helps, Jason On Tue, Sep 14, 2010 at 11:49 AM, Marcelo Puiatti marcelo.puiatti|*| gmail.com wrote: > > Sent to CCL by: Marcelo Puiatti [marcelo.puiatti,+,gmail.com] > Hi, I want to generate an enantiomer of a small molecule from its xyz > coordinates. Is there any program for doing that? > > Thanks in advance> > > -- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 --000e0cd6adc876cadf04903b67d1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,

If you take the additive inverse of all X-coordinates for all= atoms you'll have the mirror image reflected in the Y-Z plane.=A0 If i= t's an enantiomer, this will be non-superimposable.=A0 You can do this = quite easily with a tool of your choice -- sed, awk, or a home-brewed pytho= n/perl script.

Hope this helps,
Jason

On Tue, Sep= 14, 2010 at 11:49 AM, Marcelo Puiatti marcelo.puiatti|*|gmail.com <owner-chemistry{:}ccl.net> wrote:

Sent to CCL by: Marcelo Puiatti [marcelo.puiatti,+,gmail.com]
Hi, I want to generate an enantiomer of a small molecule from its xyz
coordinates. Is there any program for doing that?

Thanks in advance



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY{:}ccl.n= et or use:
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--
Jason M. Swails
Quan= tum Theory Project,
University of Florida
Ph.D. Graduate Student
3= 52-392-4032
--000e0cd6adc876cadf04903b67d1-- From owner-chemistry@ccl.net Tue Sep 14 19:07:00 2010 From: "William F. Coleman wcoleman ~~ wellesley.edu" To: CCL Subject: CCL: How to make an enantiomer? Message-Id: <-42762-100914135644-32170-soxG48zrlzoVVHRZBmfsyw*_*server.ccl.net> X-Original-From: "William F. Coleman" Content-Type: multipart/alternative; boundary="--=_--21233d72.21233b9a.c8b567cb" Date: Tue, 14 Sep 2010 13:56:27 -0400 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman:+:wellesley.edu] This is a multi-part message in MIME format. ----=_--21233d72.21233b9a.c8b567cb Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Just change the signs of all of one of the coordinates (I usually do z, but there is no reason to do so). Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html http://www.flicksstuff.com/photos/pictures.html new galleries 9/4/2010 Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html ----=_--21233d72.21233b9a.c8b567cb Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>
Just change the signs of all of one o= f the coordinates (I usually do z, but there is no reason to do so).=

Cheers,

Flick


_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481


Editor, JCE WebWare and JCE Featured = Molecules


----=_--21233d72.21233b9a.c8b567cb-- From owner-chemistry@ccl.net Tue Sep 14 20:57:01 2010 From: "Miguel Quiliano Meza rifaximina/./gmail.com" To: CCL Subject: CCL:G: Which is the best way to work with N-OXIDES? Message-Id: <-42763-100914204336-20916-rXx/Pk5wykNsq71cWE6m9g[a]server.ccl.net> X-Original-From: Miguel Quiliano Meza Content-Type: multipart/alternative; boundary=001636920b8b5b6bc60490419eb8 Date: Tue, 14 Sep 2010 20:43:30 -0400 MIME-Version: 1.0 Sent to CCL by: Miguel Quiliano Meza [rifaximina**gmail.com] --001636920b8b5b6bc60490419eb8 Content-Type: text/plain; charset=ISO-8859-1 Hello CCL users. I am a new user of this forum so please be patient jeje. Recently, I have a problem, but basically it`s a doubt. I have performed geometrical optimization of one compound (by the way I`m not an expert using QM). It`s a derivate N-oxide. In the paper is: after Gaussian, using Gaussview I see this: o o / - \ // ---\ // I C-C / C- C I Ar I \ I I \ I I C- R I Ar I C - R I I // I I // \ C- N(+) \ C - N \ - / / ---- / // O(-) O I set a simple "# opt pm3 geom=connectivity". I want to study REDOX properties, but N(+)-O(-) seems totally different to N=O, Although you can see that nitrogen continuous with 5 bonds, I missed the N-O What do you think about this?? is correct the set of bonds between N=O? I know that partial double bond is present but is it acceptable for my objetive? If you were me, what should I do to prevent a posible mistake? What would you have done, if you have wanted a good conformation to work?? Sorry for the long message, perhaps this problem is very easy for you. I would be grateful if someone can help me or give me advices Thanks in advance. M.Q --001636920b8b5b6bc60490419eb8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 
Hello CCL users.

I am a new user of this forum so please be pat=
ient jeje.

Recently, I have a problem, but basically it`s a doubt. I=
 have performed geometrical optimization of one compound (by the way I`m no=
t an expert using QM). It`s a derivate N-oxide.


In the paper is:                 after Gaussian, using Gaussview I see =
this:

               o                                            o<=
br>      / - \   //                                   ---\    //
      I=
     C-C                                  /      C- C

      I Ar  I  \                                I       I   \
      I   =
  I   C- R                            I  Ar   I    C - R
      I     I  =
//                               I       I   //            
      \     =
C- N(+)                              \      C - N 

       \ - /  /                                   ---- /   //              =

             O(-)                                          O

I set a simple "# opt pm3 geom=3Dconnectivity". I want to study =
REDOX properties, but N(+)-O(-) seems totally different to N=3DO, Although =
you can see that nitrogen continuous with 5 bonds, I missed the N-O 


What do you think about this?? is correct the set of bonds between N=3D=
O? I know that partial double bond is present but is it acceptable for my o=
bjetive? If you were me, what should I do to prevent a posible mistake? Wha=
t would you have done, if you have wanted a good  conformation to work??
Sorry for the long message, perhaps this problem is very easy for you.
<=
br>I would be grateful if someone can help me or give me advices
Thanks =
in advance.

M.Q

--001636920b8b5b6bc60490419eb8-- From owner-chemistry@ccl.net Tue Sep 14 21:32:01 2010 From: "Miguel A. Quiliano rifaximina^gmail.com" To: CCL Subject: CCL:G: Which is the best way to work with N-OXIDES? Message-Id: <-42764-100914203751-20478-pSW5TVuO/oW7WPUf2+M8+Q**server.ccl.net> X-Original-From: "Miguel A. Quiliano" Date: Tue, 14 Sep 2010 20:37:50 -0400 Sent to CCL by: "Miguel A. Quiliano" [rifaximina a gmail.com] Hello CCL users. I am a new user of this forum so please be patient jeje. Recently, I have a problem, but basically it`s a doubt. I have performed geometrical optimization of one compound (by the way I`m not an expert using QM). It`s a derivate N-oxide. In the paper is: after Gaussian, using Gaussview I see this: o o / - \ // ---\ // I C-C / C- C I Ar I \ I I \ I I C- R I Ar I C - R I I // I I // \ C- N(+) \ C - N \ - / / ---- / // O(-) O I set a simple "# opt pm3 geom=connectivity". I want to study REDOX properties, but N(+)-O(-) seems totally different to N=O, Although you can see that nitrogen continuous with 5 bonds, I missed the N-O What do you think about this?? is correct the set of bonds between N=O? I know that partial double bond is present but is it acceptable for my objetive? If you were me, what should I do to prevent a posible mistake? What would you have done, if you have wanted a good conformation to work?? Sorry for the long message, perhaps this problem is very easy for you. I would be grateful if someone can help me or give me advices Thanks in advance. M.Q