From owner-chemistry@ccl.net Sat Nov 28 09:13:01 2009 From: "S. Bill s_bill36.^.yahoo.co.uk" To: CCL Subject: CCL:G: Energy difference Message-Id: <-40802-091128091241-12989-+By6ob9BbJYxn/Nh0GW5qw^server.ccl.net> X-Original-From: "S. Bill" Date: Sat, 28 Nov 2009 09:12:38 -0500 Sent to CCL by: "S. Bill" [s_bill36]_[yahoo.co.uk] Dear CCL users I was wondering, is 8 kcal/mol a big energy difference between two isomers? could you direct me to any articles or books concer this point? Energy differece should be in kcal/mole or kJ/mole? What is the appropraite level of calcualtion for structure optimization and energy single point for publication? If I calculated the single point energy using Gaussian03 would be equal to the single point energy for the same optimizaed stucture using Games (US)? I am a new student here. thanks S. Bill From owner-chemistry@ccl.net Sat Nov 28 13:22:00 2009 From: "Mariusz Radon mariusz.radon]_[gmail.com" To: CCL Subject: CCL: Which program to optimize the crystal structure of transition metal complex? Message-Id: <-40803-091128065016-25706-DwZQaq5Y+6ajVz7UfU567g#,#server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8 Date: Sat, 28 Nov 2009 12:43:05 +0100 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon---gmail.com] Dear Colleagues, Some time ago I have asked you which program would you recommend for periodic calculations on transition metal complex in various spin states (the spin should be under control). Characteristic for my crystal structure is rather large elementary cell and well-isolated molecules of the TM complex. Thank you very much for your answers, where you suggested many different programs, including both free and commercial software. Based on the presented arguments and (sketchy) reading of the webpages/documentation I am not able to pinpoint "best" program for our task in a fully conscious way. Our present choice is SIESTA (of course, not ruling out other free programs). Best regards, Mariusz Radon On Tue, Nov 24, 2009 at 9:40 AM, teorica.ch(~)unito.it wrote: > > Sent to CCL by: teorica.ch()unito.it > > CRYSTAL =C2=A0allows =C2=A0optimization of structures > with transition metals in different magnetic phases. > Hamiltonian: HF, DFT, and hybrids (B3LYP) > > See: > http://www.crystal.unito.it > =3D> Features > =3D> Applications > =3D> Tutorials =3D> Magnetic properties > > There is a license fee, to access executables download > > Best regards, > > Carla Roetti > Theoretical Chemistry Group - Torino >> >> >> ------------------ Messaggio originale ------------------- >> Oggetto: CCL: Which program to optimize the crystal >> structure of transition metal complex? >> Da: =C2=A0 =C2=A0 =C2=A0"Mariusz Radon mariusz.radon(0)gmail.com" >> >> Data: =C2=A0 =C2=A0Ven, 20 Novembre 2009, 7:25 pm >> A: =C2=A0 =C2=A0 =C2=A0 "Roetti, Carla " >> ---------------------------------------------------------- >> >> >> Sent to CCL by: Mariusz Radon [mariusz.radon]-[gmail.com] >> Dear Colleagues, >> >> I am looking for a program being able to optimize the >> crystal >> structure of transition metal complex (molecular structure >> and unit >> cell parameters) at DFT level. An important point is that >> I must be >> able to control the spin state of the complex, because I >> would like to >> perform such optimizations for different spin states in >> order to >> capture the influence of the spin state on the molecular >> structure and >> packing in the crystal. >> >> Could you recommend me any program capable to achieve this >> goal >> (preferably, but not necessarily free software)? Thank you >> in advance >> very much. >> >> Best regards, >> Mariusz Radon >> >> >> >> -- >> Mariusz Radon, PhD student >> Department of Theoretical Chemistry >> Jagiellonian University >> http://www.chemia.uj.edu.pl/~mradon >> mradon /at/ chemia.uj.edu.pl >> (PGP public key available on the website) >> >> >> >> -=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 change >> the strange characters on the top line to the |a| sign. You >> can also> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: >> http://www.ccl.net/chemistry/searchccl/index.shtml> >> >> > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/chemistry/sub_unsub.shtml> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt> > > --=20 Mariusz Radon, PhD student Department of Theoretical Chemistry Jagiellonian University http://www.chemia.uj.edu.pl/~mradon mradon /at/ chemia.uj.edu.pl (PGP public key available on the website) From owner-chemistry@ccl.net Sat Nov 28 14:01:02 2009 From: "Dr. Attila Bende bende!A!itim-cj.ro" To: CCL Subject: CCL:G: How to generate the band structure from Gaussian PBC calculations Message-Id: <-40804-091127090650-1014-mpnnPQq8pbjI8iPlhYI9kA]|[server.ccl.net> X-Original-From: "Dr. Attila Bende" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 27 Nov 2009 15:00:49 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: "Dr. Attila Bende" [bende/./itim-cj.ro] Dear Jun! Try, this: # PBC=NKPoint=12 IOP(5/103=10) IOP(5/98=1) IOP(5/33=1) I'm not sure that it works for two dimension, but for one dimension, Yes. You can change the NKPoint value, if you want. Best, wishes Attila > Hello CCLers, > > Recently I did some PBC calculations on Gaussian 09. I checked the > gaussian website and failed to find the procedure to generate the band > structure from PBC calculations for one or two dimensional materials. Is > is possible to do it? If yes, how? > > Any suggestion will be highly appreciated. > > Best wishes, > > Jun > -- Dr. Bende Attila (PhD) Senior Researcher III *************************************************** Molecular and Biomolecular Physics Department National Institute of R&D of Isotopic and Molecular Technologies Str. Donath nr.65-103, C.P.700 Cluj-Napoca, R-400293, Romania Phone:+40-264-584037, ext 194, Fax: +40-264-420042 e-mail: bende%a%itim-cj.ro, attlbende%a%gmail.com Web: http://www.itim-cj.ro/~bende http://www.researcherid.com/rid/A-6539-2008 *************************************************** From owner-chemistry@ccl.net Sat Nov 28 16:25:00 2009 From: "Serdar Badoglu sbadoglu|-|gazi.edu.tr" To: CCL Subject: CCL: HOMA for heterocycles Message-Id: <-40805-091128162206-18166-dooTuAfihat7FlqG4NoVUg(~)server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Sat, 28 Nov 2009 16:22:01 -0500 Sent to CCL by: "Serdar Badoglu" [sbadoglu,,gazi.edu.tr] Dear CCLers, I'm trying to learn how to calculate HOMA values of aromatic rings. For homoatomic rings everythings OK. For the heterocycles I can get the HOMA value, but I couldn't understand how to calculate EN and GEO terms. Can someone explain how to calculate EN and GEO, preferably as a step by step approach? Best regards. From owner-chemistry@ccl.net Sat Nov 28 21:24:01 2009 From: "Ronald C. Bakus rbakus{=}chem.ucsb.edu" To: CCL Subject: CCL: Problem SCF convergence(energy oscillation) in extended pi system/G03 Message-Id: <-40806-091128170522-24682-HpAarxX1s+5x3Snd3ApjBg() server.ccl.net> X-Original-From: "Ronald C. Bakus" Date: Sat, 28 Nov 2009 17:05:18 -0500 Sent to CCL by: "Ronald C. Bakus" [rbakus!=!chem.ucsb.edu] Im having some issues with a problem convergence case for a extended pi system. Without diffuse functions, convergence is fine, however, upon addition of diffuse functions the optimization will get close to completing, but on one of the last scf cycles, the energy will decrease and then oscillate around convergence. The homo-lumo gap is small, slightly less than .2H. I have already tried various combinations of the standard ways of dealing with problem scf (qc, vshift=x (x=150,300,500,1000), nodiis, novaracc, optimization+freq calc without diffuse as starting point for diffuse, etc.) with no success. I was hoping to perhaps get some input on other ways to deal with the problem. The diffuse functions will be important to later phases of the calculations. Sample Input (I have tried both syn and anti conformers of the dimethylamino groups) ------ %chk=dsb.chk %mem=20MW #p opt b3lyp/6-31+g(d,p) geom=connectivity int=ultrafine cphf=ultrafine formcheck dsb14 opt 0 1 C C 1 B1 C 2 B2 1 A1 C 3 B3 2 A2 1 D1 C 4 B4 3 A3 2 D2 C 5 B5 4 A4 3 D3 H 1 B6 2 A5 3 D4 H 2 B7 1 A6 6 D5 H 4 B8 3 A7 2 D6 H 5 B9 4 A8 3 D7 C 3 B10 2 A9 1 D8 H 11 B11 3 A10 2 D9 C 11 B12 3 A11 2 D10 H 13 B13 11 A12 3 D11 C 13 B14 11 A13 3 D12 C 15 B15 13 A14 11 D13 C 15 B16 13 A15 11 D14 C 16 B17 15 A16 13 D15 H 16 B18 15 A17 13 D16 C 17 B19 15 A18 13 D17 H 17 B20 15 A19 13 D18 C 18 B21 16 A20 15 D19 H 18 B22 16 A21 15 D20 H 20 B23 17 A22 15 D21 C 22 B24 18 A23 16 D22 H 25 B25 22 A24 18 D23 C 25 B26 22 A25 18 D24 H 27 B27 25 A26 22 D25 C 27 B28 25 A27 22 D26 C 29 B29 27 A28 25 D27 C 29 B30 27 A29 25 D28 C 30 B31 29 A30 27 D29 H 30 B32 29 A31 27 D30 C 31 B33 29 A32 27 D31 H 31 B34 29 A33 27 D32 C 32 B35 30 A34 29 D33 H 32 B36 30 A35 29 D34 H 34 B37 31 A36 29 D35 N 6 B38 5 A37 4 D36 N 36 B39 32 A38 30 D37 C 40 B40 36 A39 32 D38 H 41 B41 40 A40 36 D39 H 41 B42 40 A41 36 D40 H 41 B43 40 A42 36 D41 C 40 B44 36 A43 32 D42 H 45 B45 40 A44 36 D43 H 45 B46 40 A45 36 D44 H 45 B47 40 A46 36 D45 C 39 B48 6 A47 5 D46 H 49 B49 39 A48 6 D47 H 49 B50 39 A49 6 D48 H 49 B51 39 A50 6 D49 C 39 B52 6 A51 5 D50 H 53 B53 39 A52 6 D51 H 53 B54 39 A53 6 D52 H 53 B55 39 A54 6 D53 B1 1.38590600 B2 1.40879299 B3 1.40676154 B4 1.38827161 B5 1.41292513 B6 1.08298050 B7 1.08583864 B8 1.08754627 B9 1.08285660 B10 1.45944010 B11 1.08912863 B12 1.35168559 B13 1.08891058 B14 1.46036881 B15 1.41101301 B16 1.40955110 B17 1.38649352 B18 1.08745064 B19 1.38650055 B20 1.08563046 B21 1.40957879 B22 1.08563312 B23 1.08745466 B24 1.46038208 B25 1.08891491 B26 1.35170500 B27 1.08912993 B28 1.45944392 B29 1.40677707 B30 1.40881876 B31 1.38826824 B32 1.08755006 B33 1.38589746 B34 1.08584524 B35 1.41292195 B36 1.08285687 B37 1.08298484 B38 1.38847165 B39 1.38841623 B40 1.45260430 B41 1.09097759 B42 1.10130937 B43 1.09581331 B44 1.45285452 B45 1.09097407 B46 1.09576437 B47 1.10121929 B48 1.45286246 B49 1.09098248 B50 1.10122787 B51 1.09575774 B52 1.45262017 B53 1.09098468 B54 1.09579664 B55 1.10131866 A1 122.07360923 A2 116.25323549 A3 122.52104756 A4 120.89016562 A5 118.44193028 A6 118.09314223 A7 118.89576382 A8 118.63570829 A9 124.25260979 A10 114.09091838 A11 127.48313332 A12 118.61687356 A13 127.13426723 A14 119.07045476 A15 124.12563764 A16 122.03442793 A17 118.76061142 A18 121.16247464 A19 119.98708840 A20 121.16222854 A21 118.85028804 A22 119.20697504 A23 124.12861653 A24 114.24477657 A25 127.13686366 A26 118.42466374 A27 127.48931804 A28 119.49046853 A29 124.25717650 A30 122.52172015 A31 118.89429417 A32 122.07417140 A33 119.83267571 A34 120.89096115 A35 118.63484888 A36 118.44040512 A37 121.62197526 A38 121.62236490 A39 119.34902804 A40 109.13960300 A41 112.95155437 A42 111.01772561 A43 119.49930105 A44 109.10238405 A45 111.07362683 A46 112.96782739 A47 119.49517384 A48 109.10177009 A49 112.97116251 A50 111.06987287 A51 119.34521560 A52 109.13771153 A53 111.01169226 A54 112.95688048 D1 -0.35125191 D2 0.32638204 D3 0.40233558 D4 179.48620457 D5 -179.90506437 D6 -179.42169103 D7 -179.52106898 D8 180.00000000 D9 178.40429122 D10 -1.82780326 D11 -0.31757066 D12 179.89196744 D13 178.73985841 D14 -1.28157819 D15 -179.92043875 D16 -0.00000000 D17 179.91842635 D18 -0.19884610 D19 -0.05473033 D20 179.90530662 D21 179.97520249 D22 -179.96404995 D23 -179.65549459 D24 0.42839517 D25 0.19711844 D26 -179.94034630 D27 -179.19548240 D28 1.14931637 D29 -179.94453526 D30 -0.22485722 D31 179.95511206 D32 0.34504623 D33 -0.42074545 D34 179.50779600 D35 -179.50941383 D36 178.51739236 D37 -178.52921489 D38 171.94094710 D39 178.43928000 D40 -61.14986272 D41 60.18975765 D42 11.63000000 D43 -178.68286485 D44 -60.46741792 D45 60.95449961 D46 170.08048307 D47 178.67201365 D48 -60.96543365 D49 60.45777828 D50 9.82506217 D51 -178.40320889 D52 -60.16058276 D53 61.18077952 1 2 2.0 6 1.5 7 1.0 2 3 1.5 8 1.0 3 4 1.5 11 1.0 4 5 1.5 9 1.0 5 6 1.5 10 1.0 6 39 1.0 7 8 9 10 11 12 1.0 13 2.0 12 13 14 1.0 15 1.0 14 15 16 1.5 17 1.5 16 18 1.5 19 1.0 17 20 1.5 21 1.0 18 22 1.5 23 1.0 19 20 22 1.5 24 1.0 21 22 25 1.0 23 24 25 26 1.0 27 2.0 26 27 28 1.0 29 1.0 28 29 30 1.5 31 1.5 30 32 1.5 33 1.0 31 34 2.0 35 1.0 32 36 1.5 37 1.0 33 34 36 1.5 38 1.0 35 36 40 1.0 37 38 39 49 1.0 53 1.0 40 41 1.0 45 1.0 41 42 1.0 43 1.0 44 1.0 42 43 44 45 46 1.0 47 1.0 48 1.0 46 47 48 49 50 1.0 51 1.0 52 1.0 50 51 52 53 54 1.0 55 1.0 56 1.0 54 55 56 ----- I hope that someone far brighter than me has a suggestion, I have been fighting with this for 2 weeks. Ron Bakus rbakus _ chem.ucsb.edu UCSB