From chemistry-request@ccl.net Fri May 21 09:24:34 2004 Received: from mserv.itpa.lt (mserv.itpa.lt [193.219.53.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4LEOXrA003269 for ; Fri, 21 May 2004 09:24:33 -0500 Received: from mserv.itpa.lt (localhost [127.0.0.1]) by mserv.itpa.lt (8.12.11/8.12.6) with ESMTP id i4KFb7YI068198 for ; Thu, 20 May 2004 18:37:07 +0300 (EEST) (envelope-from tamulis/at/mserv.itpa.lt) Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.12.11/8.12.6/Submit) with ESMTP id i4KFb7r2068195 for ; Thu, 20 May 2004 18:37:07 +0300 (EEST) Date: Thu, 20 May 2004 18:37:07 +0300 (EEST) From: Arvydas Tamulis To: CHEMISTRY/at/ccl.net Subject: Re: CCL:The pi-pi stacking of hetero-aromatic ring Message-ID: <20040520183613.D65761-100000/at/mserv.itpa.lt> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Netters, Would you please to advise us the quantum chemical methods and programs that might properly calculate stacking interactions including dispersion effects in oligomeric nucleic acids (two types of interactions: in parallel planes and when planes are perpendicular). Thanking your in advance. With best regards, Arvydas Tamulis **************************************** On Fri, 14 May 2004, Tanja van Mourik wrote: > Dear Arvydas, > > > While I still am not sure for my obtained result because it was done by HF > > 6-31G. I have plans to repeat optimization using DFT PBE 6-31++G* where > > exist possibility to include fine effects of quantum mechanical dispersion > > van-der-Waals interactions. > > Please be cautious with using DFT for calculating stacking interactions. > DFT doesn't correctly describe dispersion effects, see, for example: > > Kohn, Meir and Makarov, Phys. Rev. Lett. 80, 4153 (1998) > Tuma, Boese and Handy, Phys. Chem. Chem. Phys. 1, 3939 (1999) > Hobza, Sponer and Reschel, J. Comput. Chem. 16, 1315 (1995) > Van Mourik and Gdanitz, J. Chem. Phys. 116, 9620 (2002) > > Best wishes, > > Tanja > -- > ================================================================= > Tanja van Mourik > Royal Society University Research Fellow > Chemistry Department > University College London phone: +44 (0)20-7679-4663 > 20 Gordon Street e-mail: work: T.vanMourik/at/ucl.ac.uk > London WC1H 0AJ, UK home: tanja/at/van-mourik.me.uk > > http://www.chem.ucl.ac.uk/people/vanmourik/index.html > ================================================================= > From chemistry-request@ccl.net Fri May 21 09:20:14 2004 Received: from hotmail.com (bay14-f27.bay14.hotmail.com [64.4.49.27]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4LEK9rA002975 for ; Fri, 21 May 2004 09:20:09 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 20 May 2004 15:05:25 -0700 Received: from 200.44.246.91 by by14fd.bay14.hotmail.msn.com with HTTP; Thu, 20 May 2004 22:05:24 GMT X-Originating-IP: [200.44.246.91] X-Originating-Email: [marcanocarlos(at)hotmail.com] X-Sender: marcanocarlos(at)hotmail.com From: "carlos marcano" To: chemistry(at)ccl.net Cc: chemistry-request(at)server.ccl.net Subject: We have some problems with frecuential calculaions Date: Thu, 20 May 2004 18:05:24 -0400 Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_7768_40a2_3fca" Message-ID: X-OriginalArrivalTime: 20 May 2004 22:05:25.0089 (UTC) FILETIME=[8D6C9510:01C43EB6] X-Spam-Status: No, hits=3.0 required=7.5 tests=IMPRONONCABLE_1, MIME_BOUND_NEXTPART autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_7768_40a2_3fca Content-Type: text/plain; charset=iso-8859-1; format=flowed Hi,We are a group of theoretical Chemistry in Venezuelan,we have been trying to do a frecuenciat job at the level mp2/6-31g,(169 basis functions),but I wonder why we cant do it? Problems with this type job a) Actual scratch disk usage is more large Estimated scratch disk usage b) writwa c)LINK 811(Construction molecular orbitals) We read in the web around of How does it? We intent to do create multiple files for example(8 files each one of 2GB).later of it,only complety 5 files and finally present an error with said above. We have an PC Super Power1.7GHz with 1000 MB memory and 40 GB hard disk). The operating system is WINDOWS 2000. _________________________________________________________________ MSN Amor: busca tu = naranja http://latam.msn.com/amor/ ------=_NextPart_000_7768_40a2_3fca Content-Type: text/plain; name="=?iso-8859-1?B?VFNDTE9ST2NvbmNvcnJlY2Np8242LTMxRyhkKS5vdXQ=?="; format=flowed Content-Transfer-Encoding: 8bit Content-Disposition: attachment; filename="=?iso-8859-1?B?VFNDTE9ST2NvbmNvcnJlY2Np8242LTMxRyhkKS5vdXQ=?=" Entering Link 1 = C:\G98W\l1.exe PID= -1905313. Copyright (c) 1988,1990,1992,1993,1995,1998 Gaussian, Inc. All Rights Reserved. This is part of the Gaussian(R) 98 program. It is based on the Gaussian 94(TM) system (copyright 1995 Gaussian, Inc.), the Gaussian 92(TM) system (copyright 1992 Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990 Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988 Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986 Carnegie Mellon University), and the Gaussian 82(TM) system (copyright 1983 Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license. The following legend is applicable only to US Government contracts under DFARS: RESTRICTED RIGHTS LEGEND Use, duplication or disclosure by the US Government is subject to restrictions as set forth in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFARS 252.227-7013. Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA The following legend is applicable only to US Government contracts under FAR: RESTRICTED RIGHTS LEGEND Use, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraph (c) of the Commercial Computer Software - Restricted Rights clause at FAR 52.227-19. Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA --------------------------------------------------------------- Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide assistance to any competitor of Gaussian, Inc. The licensee of this program is prohibited from giving any competitor of Gaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above. --------------------------------------------------------------- Cite this work as: Gaussian 98, Revision A.11, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, P. Salvador, J. J. Dannenberg, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 2001. ********************************************** Gaussian 98: x86-Win32-G98RevA.11 25-Sep-2001 20-May-2004 ********************************************** %chk=transcloropruebamirna %mem=18MW %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=4000MB ------------------------------------------------------------------- #P rmp2/6-31g(d) Freq=(ReadIso) nosymm guess=read geom=connectivity ------------------------------------------------------------------- 1/10=4,30=1,38=1,57=2/1,3; 2/15=1,17=6,18=5,40=1/2; 3/5=1,6=6,7=1,11=1,25=1,30=1/1,2,3; 4/5=1,7=1/1; 5/5=2/2; 8/6=3,8=1,10=1,19=11,23=2,27=524288000,30=-1/1; 9/15=3,16=-3,27=524288000/6; 11/6=1,8=1,15=11,17=12,24=-1,27=1,28=-2,29=300,31=1,32=6,42=1/1,2,10; 10/6=2,21=1,31=1/2; 8/6=4,8=1,10=1,19=11,23=2,27=524288000,30=-1/11,4; 10/5=1,20=4,31=1/2; 11/12=2,14=11,16=11,17=2,28=-2,31=1,42=1/2,10,12; 6/7=2,8=2,9=2,10=2/1; 7/8=2,10=1,12=2,25=1,30=1,44=2/1,2,3,16; 1/10=4,30=1/3; 99//99; Leave Link 1 at Thu May 20 09:36:54 2004, MaxMem= 18874368 cpu: 1.0 (Enter C:\G98W\l101.exe) ------------------------------ buscando el frecuencial del ts ------------------------------ Symbolic Z-matrix: Charge = 0 Multiplicity = 1 N C 1 B1 H 2 B2 1 A1 H 2 B3 1 A2 3 D1 0 H 2 B4 1 A3 3 D2 0 C 1 B5 2 A4 3 D3 0 H 6 B6 1 A5 2 D4 0 H 6 B7 1 A6 2 D5 0 H 6 B8 1 A7 2 D6 0 C 1 B9 2 A8 6 D7 0 O 10 B10 1 A9 2 D8 0 O 10 B11 1 A10 2 D9 0 C 12 B12 10 A11 1 D10 0 H 13 B13 12 A12 10 D11 0 C 13 B14 12 A13 10 D12 0 H 11 B15 10 A14 1 D13 0 H 15 B16 13 A15 12 D14 0 H 13 B17 12 A16 10 D15 0 C 15 B18 13 A17 12 D16 0 H 19 B19 15 A18 13 D17 0 H 19 B20 15 A19 13 D18 0 Cl 19 B21 15 A20 13 D19 0 Variables: B1 1.45276 B2 1.0875 B3 1.09455 B4 1.09617 B5 1.45149 B6 1.09621 B7 1.08753 B8 1.09473 B9 1.35869 B10 1.29445 B11 1.28875 B12 1.85593 B13 1.08709 B14 1.40709 B15 1.21414 B16 1.0896 B17 1.0853 B18 1.49986 B19 1.0923 B20 1.09262 B21 1.80558 A1 109.04907 A2 109.44099 A3 110.49852 A4 117.15548 A5 110.46315 A6 109.04963 A7 109.63822 A8 121.05615 A9 118.12021 A10 118.4409 A11 116.09458 A12 89.48242 A13 113.92518 A14 102.53238 A15 116.01133 A16 91.8087 A17 118.24346 A18 112.95266 A19 110.69481 A20 112.85216 D1 -119.8551 D2 120.48085 D3 177.62381 D4 60.64796 D5 -178.99987 D6 -59.01563 D7 172.11014 D8 3.91955 D9 -176.48023 D10 -162.14606 D11 123.19119 D12 -0.04059 D13 161.63193 D14 -112.30614 D15 -123.03125 D16 103.27139 D17 95.22375 D18 -26.68748 D19 -145.77338 Leave Link 101 at Thu May 20 09:36:55 2004, MaxMem= 18874368 cpu: 0.0 (Enter C:\G98W\l103.exe) GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. ---------------------------- ! Initial Parameters ! ! (Angstroms and Degrees) ! ---------------------- ---------------------- ! Name Value Derivative information (Atomic Units) ! ------------------------------------------------------------------------ ! B1 1.4528 calculate D2E/DX2 analytically ! ! B2 1.0875 calculate D2E/DX2 analytically ! ! B3 1.0946 calculate D2E/DX2 analytically ! ! B4 1.0962 calculate D2E/DX2 analytically ! ! B5 1.4515 calculate D2E/DX2 analytically ! ! B6 1.0962 calculate D2E/DX2 analytically ! ! B7 1.0875 calculate D2E/DX2 analytically ! ! B8 1.0947 calculate D2E/DX2 analytically ! ! B9 1.3587 calculate D2E/DX2 analytically ! ! B10 1.2944 calculate D2E/DX2 analytically ! ! B11 1.2887 calculate D2E/DX2 analytically ! ! B12 1.8559 calculate D2E/DX2 analytically ! ! B13 1.0871 calculate D2E/DX2 analytically ! ! B14 1.4071 calculate D2E/DX2 analytically ! ! B15 1.2141 calculate D2E/DX2 analytically ! ! B16 1.0896 calculate D2E/DX2 analytically ! ! B17 1.0853 calculate D2E/DX2 analytically ! ! B18 1.4999 calculate D2E/DX2 analytically ! ! B19 1.0923 calculate D2E/DX2 analytically ! ! B20 1.0926 calculate D2E/DX2 analytically ! ! B21 1.8056 calculate D2E/DX2 analytically ! ! A1 109.0491 calculate D2E/DX2 analytically ! ! A2 109.441 calculate D2E/DX2 analytically ! ! A3 110.4985 calculate D2E/DX2 analytically ! ! A4 117.1555 calculate D2E/DX2 analytically ! ! A5 110.4631 calculate D2E/DX2 analytically ! ! A6 109.0496 calculate D2E/DX2 analytically ! ! A7 109.6382 calculate D2E/DX2 analytically ! ! A8 121.0561 calculate D2E/DX2 analytically ! ! A9 118.1202 calculate D2E/DX2 analytically ! ! A10 118.4409 calculate D2E/DX2 analytically ! ! A11 116.0946 calculate D2E/DX2 analytically ! ! A12 89.4824 calculate D2E/DX2 analytically ! ! A13 113.9252 calculate D2E/DX2 analytically ! ! A14 102.5324 calculate D2E/DX2 analytically ! ! A15 116.0113 calculate D2E/DX2 analytically ! ! A16 91.8087 calculate D2E/DX2 analytically ! ! A17 118.2435 calculate D2E/DX2 analytically ! ! A18 112.9527 calculate D2E/DX2 analytically ! ! A19 110.6948 calculate D2E/DX2 analytically ! ! A20 112.8522 calculate D2E/DX2 analytically ! ! D1 -119.8551 calculate D2E/DX2 analytically ! ! D2 120.4809 calculate D2E/DX2 analytically ! ! D3 177.6238 calculate D2E/DX2 analytically ! ! D4 60.648 calculate D2E/DX2 analytically ! ! D5 -178.9999 calculate D2E/DX2 analytically ! ! D6 -59.0156 calculate D2E/DX2 analytically ! ! D7 172.1101 calculate D2E/DX2 analytically ! ! D8 3.9195 calculate D2E/DX2 analytically ! ! D9 -176.4802 calculate D2E/DX2 analytically ! ! D10 -162.1461 calculate D2E/DX2 analytically ! ! D11 123.1912 calculate D2E/DX2 analytically ! ! D12 -0.0406 calculate D2E/DX2 analytically ! ! D13 161.6319 calculate D2E/DX2 analytically ! ! D14 -112.3061 calculate D2E/DX2 analytically ! ! D15 -123.0312 calculate D2E/DX2 analytically ! ! D16 103.2714 calculate D2E/DX2 analytically ! ! D17 95.2237 calculate D2E/DX2 analytically ! ! D18 -26.6875 calculate D2E/DX2 analytically ! ! D19 -145.7734 calculate D2E/DX2 analytically ! ------------------------------------------------------------------------ Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 Number of steps in this run= 70 maximum allowed number of steps= 120. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Leave Link 103 at Thu May 20 09:36:56 2004, MaxMem= 18874368 cpu: 0.0 (Enter C:\G98W\l202.exe) ------------------------------------------------------------------------ Z-MATRIX (ANGSTROMS AND DEGREES) CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J ------------------------------------------------------------------------ 1 1 N 2 2 C 1 1.452757( 1) 3 3 H 2 1.087500( 2) 1 109.049( 22) 4 4 H 2 1.094555( 3) 1 109.441( 23) 3 -119.855( 42) 0 5 5 H 2 1.096167( 4) 1 110.499( 24) 3 120.481( 43) 0 6 6 C 1 1.451486( 5) 2 117.155( 25) 3 177.624( 44) 0 7 7 H 6 1.096208( 6) 1 110.463( 26) 2 60.648( 45) 0 8 8 H 6 1.087535( 7) 1 109.050( 27) 2 -179.000( 46) 0 9 9 H 6 1.094733( 8) 1 109.638( 28) 2 -59.016( 47) 0 10 10 C 1 1.358690( 9) 2 121.056( 29) 6 172.110( 48) 0 11 11 O 10 1.294446( 10) 1 118.120( 30) 2 3.920( 49) 0 12 12 O 10 1.288747( 11) 1 118.441( 31) 2 -176.480( 50) 0 13 13 C 12 1.855927( 12) 10 116.095( 32) 1 -162.146( 51) 0 14 14 H 13 1.087088( 13) 12 89.482( 33) 10 123.191( 52) 0 15 15 C 13 1.407089( 14) 12 113.925( 34) 10 -0.041( 53) 0 16 16 H 11 1.214144( 15) 10 102.532( 35) 1 161.632( 54) 0 17 17 H 15 1.089597( 16) 13 116.011( 36) 12 -112.306( 55) 0 18 18 H 13 1.085296( 17) 12 91.809( 37) 10 -123.031( 56) 0 19 19 C 15 1.499864( 18) 13 118.243( 38) 12 103.271( 57) 0 20 20 H 19 1.092298( 19) 15 112.953( 39) 13 95.224( 58) 0 21 21 H 19 1.092620( 20) 15 110.695( 40) 13 -26.687( 59) 0 22 22 Cl 19 1.805580( 21) 15 112.852( 41) 13 -145.773( 60) 0 ------------------------------------------------------------------------ Z-Matrix orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 7 0 0.000000 0.000000 0.000000 2 6 0 0.000000 0.000000 1.452757 3 1 0 1.027948 0.000000 1.807693 4 1 0 -0.513812 -0.895169 1.817064 5 1 0 -0.520824 0.884860 1.836616 6 6 0 -1.290380 -0.053546 -0.662468 7 1 0 -1.897767 0.817209 -0.389447 8 1 0 -1.136494 -0.065119 -1.738998 9 1 0 -1.822862 -0.960335 -0.358105 10 6 0 1.145305 0.207436 -0.700918 11 8 0 2.251665 0.328511 -0.039935 12 8 0 1.076128 0.265610 -1.986492 13 6 0 2.674286 0.034365 -2.901304 14 1 0 2.230845 -0.795092 -3.446394 15 6 0 3.785142 -0.178975 -2.064414 16 1 0 3.091593 0.122651 -0.892160 17 1 0 4.529855 0.616206 -2.046802 18 1 0 2.567456 0.992550 -3.399637 19 6 0 4.315580 -1.575568 -1.931167 20 1 0 5.145272 -1.782741 -2.610730 21 1 0 3.525647 -2.307777 -2.114726 22 17 0 4.961045 -1.926101 -0.281737 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 N 0.000000 2 C 1.452757 0.000000 3 H 2.079526 1.087500 0.000000 4 H 2.089750 1.094555 1.782818 0.000000 5 H 2.104137 1.096167 1.783958 1.780150 0.000000 6 C 1.451486 2.478331 3.388098 2.731203 2.778173 7 H 2.102622 2.768224 3.749008 3.117092 2.618379 8 H 2.078455 3.388681 4.155487 3.704362 3.750537 9 H 2.091245 2.743044 3.706756 2.539531 3.149102 10 C 1.358690 2.448074 2.519907 3.210707 3.110300 11 O 2.275853 2.721405 2.240342 3.548760 3.393768 12 O 2.274808 3.613451 3.803775 4.282797 4.189258 13 C 3.945954 5.109877 4.988614 5.769836 5.777539 14 H 4.181683 5.441555 5.448354 5.936931 6.189032 15 C 4.315221 5.170089 4.756823 5.836078 5.906870 16 H 3.220084 3.882219 3.400424 4.623289 4.590941 17 H 5.008862 5.757275 5.244063 6.530873 6.376713 18 H 4.374302 5.578774 5.520102 6.345996 6.080084 19 C 4.983578 5.705926 5.222070 6.151033 6.606111 20 H 6.038866 6.794403 6.297061 7.240053 7.681121 21 H 4.714667 5.521137 5.191310 5.811339 6.494610 22 Cl 5.329278 5.597347 4.852302 5.953305 6.514584 6 7 8 9 10 6 C 0.000000 7 H 1.096208 0.000000 8 H 1.087535 1.783066 0.000000 9 H 1.094733 1.779397 1.783082 0.000000 10 C 2.449929 3.119154 2.521607 3.207993 0.000000 11 O 3.616572 4.192704 3.810693 4.285338 1.294446 12 O 2.730432 3.420360 2.250852 3.543830 1.288747 13 C 4.553976 5.275030 3.985336 5.261334 2.685040 14 H 4.549633 5.384225 3.845392 5.098762 3.117868 15 C 5.267077 6.007773 4.933696 5.913689 2.996193 16 H 4.391525 5.062494 4.316146 5.060627 1.957499 17 H 6.019974 6.640900 5.715459 6.759748 3.665199 18 H 4.844513 5.387968 4.194715 5.686789 3.149921 19 C 5.945833 6.834322 5.660698 6.366593 3.839695 20 H 6.942871 7.829318 6.570444 7.369230 4.858799 21 H 5.512234 6.492729 5.187123 5.788597 3.740478 22 Cl 6.536951 7.387871 6.539637 6.852731 4.391761 11 12 13 14 15 11 O 0.000000 12 O 2.274846 0.000000 13 C 2.907330 1.855927 0.000000 14 H 3.587043 2.142376 1.087088 0.000000 15 C 2.589905 2.746358 1.407089 2.169172 0.000000 16 H 1.214144 2.297847 2.053924 2.847324 1.395051 17 H 3.049662 3.472000 2.124112 3.039090 1.089597 18 H 3.439225 2.179330 1.085296 1.819659 2.153613 19 C 3.385561 3.726532 2.495375 2.692800 1.499864 20 H 4.409006 4.598189 3.080922 3.188678 2.172667 21 H 3.588565 3.555123 2.613264 2.395426 2.145150 22 Cl 3.533056 4.775182 3.991845 4.329922 2.759191 16 17 18 19 20 16 H 0.000000 17 H 1.909291 0.000000 18 H 2.705344 2.413050 0.000000 19 C 2.337012 2.205257 3.436215 0.000000 20 H 3.286579 2.540020 3.869076 1.092298 0.000000 21 H 2.755005 3.092366 3.668963 1.092620 1.773378 22 Cl 2.839868 3.124853 4.895824 1.805580 2.340663 21 22 21 H 0.000000 22 Cl 2.359214 0.000000 Interatomic angles: N1-C2-H3=109.0491 N1-C2-H4=109.441 H3-C2-H4=109.578 N1-C2-H5=110.4985 H3-C2-H5=109.5617 H4-C2-H5=108.6987 C2-N1-C6=117.1555 N1-C6-H7=110.4631 N1-C6-H8=109.0496 H7-C6-H8=109.4749 N1-C6-H9=109.6382 H7-C6-H9=108.6152 H8-C6-H9=109.5861 C2-N1-C10=121.0561 C6-N1-C10=121.3033 N1-C10-O11=118.1202 N1-C10-O12=118.4409 O11-C10-O12=123.4376 C10-O12-C13=116.0946 O12-C13-H14= 89.4824 O12-C13-C15=113.9252 H14-C13-C15=120.3036 C10-O11-H16=102.5324 C13-C15-H17=116.0113 O12-C13-H18= 91.8087 H14-C13-H18=113.7818 C15-C13-H18=118.9908 C13-C15-C19=118.2435 H17-C15-C19=115.8739 C15-C19-H20=112.9527 C15-C19-H21=110.6948 H20-C19-H21=108.5139 C15-C19-Cl22=112.8522 H20-C19-Cl22=105.0687 H21-C19-Cl22=106.3688 Symmetry turned off by external request. Stoichiometry C6H12ClNO2 Framework group C1[X(C6H12ClNO2)] Deg. of freedom 60 Full point group C1 NOp 1 Rotational constants (GHZ): 1.8079226 0.5736436 0.4719325 Isotopes: N-14,C-12,H-1,H-1,H-1,C-12,H-1,H-1,H-1,C-12,O-16,O-16,C-12,H-1,C-12,H- 1,H-1,H-1,C-12,H-1,H-1,Cl-35 Leave Link 202 at Thu May 20 09:36:57 2004, MaxMem= 18874368 cpu: 1.0 (Enter C:\G98W\l301.exe) Standard basis: 6-31G(d) (6D, 7F) Integral buffers will be 262144 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned off. 178 basis functions 352 primitive gaussians 44 alpha electrons 44 beta electrons nuclear repulsion energy 640.5874148911 Hartrees. Leave Link 301 at Thu May 20 09:36:58 2004, MaxMem= 18874368 cpu: 1.0 (Enter C:\G98W\l302.exe) One-electron integrals computed using PRISM. NBasis= 178 RedAO= T NBF= 178 NBsUse= 178 1.00D-04 NBFU= 178 Leave Link 302 at Thu May 20 09:37:48 2004, MaxMem= 18874368 cpu: 50.0 (Enter C:\G98W\l303.exe) DipDrv: MaxL=1. Leave Link 303 at Thu May 20 09:37:59 2004, MaxMem= 18874368 cpu: 5.0 (Enter C:\G98W\l401.exe) Initial guess read from the checkpoint file: transcloropruebamirna.chk Guess basis functions will be translated to current atomic coordinates. Leave Link 401 at Thu May 20 09:38:12 2004, MaxMem= 18874368 cpu: 10.0 (Enter C:\G98W\l502.exe) IExCor= 0 DFT=F Ex=HF Corr=None ScaHFX= 1.0000 ScaDFX= 0.0000 0.0000 0.0000 0.0000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 Using DIIS extrapolation. Closed shell SCF: Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Two-electron integral symmetry not used. IEnd= 108745 IEndB= 108745 NGot= 18874368 MDV= 18801710 LenX= 18801710 Fock matrices will be formed incrementally for 20 cycles. Cycle 1 Pass 1 IDiag 1: Symmetry not used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. E=-0.103992411426457D+04 DIIS: error= 7.58D+00 at cycle 1. T= 3000. Gap= 0.029 NK=0 IS= 1 IE= 178 NO(<0.9)= 1 NV(>0.1)= 1 43.82e < EF 0.18e >EF Err=9.1D-11 RMSDP=1.05D+00 MaxDP=5.86D+01 Cycle 2 Pass 1 IDiag 1: RMSU= 2.97D-01 CP: 2.27D-02 E=-0.133227733400360D+04 Delta-E= -292.353219739031 DIIS: error= 4.65D-01 at cycle 2. Coeff:-0.706D-02-0.993D+00 T= 2700. Gap= 0.028 NK=0 IS= 1 IE= 178 NO(<0.9)= 1 NV(>0.1)= 1 43.84e < EF 0.16e >EF Err=8.5D-11 RMSDP=3.07D-01 MaxDP=3.30D+01 Cycle 3 Pass 1 IDiag 1: RMSU= 7.76D-02 CP: 2.34D-02 5.13D-04 E=-0.115023405980192D+04 Delta-E= 182.043274201684 DIIS: error= 8.34D-01 at cycle 3. Coeff:-0.440D-02-0.720D+00-0.275D+00 T= 2400. Gap= 0.010 NK=0 IS= 1 IE= 178 NO(<0.9)= 1 NV(>0.1)= 1 43.63e < EF 0.37e >EF Err=4.0D-11 RMSDP=8.75D-02 MaxDP=2.45D+00 Cycle 4 Pass 1 IDiag 1: RMSU= 6.72D-02 CP: 1.36D-02 8.13D-03 2.91D-01 E=-0.146708118239270D+04 Delta-E= -316.847122590779 DIIS: error= 3.46D-01 at cycle 4. Coeff:-0.214D-02-0.359D+00-0.729D-01-0.566D+00 T= 2100. Gap= 0.033 NK=0 IS= 1 IE= 178 NO(<0.9)= 0 NV(>0.1)= 0 43.90e < EF 0.10e >EF Err=8.9D-11 RMSDP=1.16D-01 MaxDP=6.12D+00 Cycle 5 Pass 1 IDiag 1: RMSU= 8.97D-02 CP: 4.82D-02 2.87D-02 -8.86D-02 1.48D-01 E=-0.148650601577206D+04 Delta-E= -19.424833379362 DIIS: error= 2.71D-01 at cycle 5. Coeff:-0.146D-02-0.223D+00-0.521D-01-0.428D+00-0.296D+00 T= 2100. Gap= 0.029 NK=2 IS= 40 IE= 51 NO(<0.9)= 0 NV(>0.1)= 1 43.66e < EF 0.34e >EF Err=1.4D-14 RMSDP=1.00D-01 MaxDP=6.80D+00 Cycle 6 Pass 1 IDiag 1: RMSU= 2.96D-02 CP: 4.55D-03 2.48D-02 1.09D-01 2.16D-01 7.36D-02 E=-0.153504395441660D+04 Delta-E= -48.537938644540 DIIS: error= 1.28D-01 at cycle 6. Coeff:-0.291D-03-0.325D-01-0.902D-02-0.127D+00-0.109D+00-0.722D+00 T= 1500. Gap= 0.044 NK=0 IS= 1 IE= 178 NO(<0.9)= 0 NV(>0.1)= 0 43.99e < EF 0.01e >EF Err=5.2D-11 RMSDP=2.23D-02 MaxDP=9.23D-01 Cycle 7 Pass 1 IDiag 1: RMSU= 1.80D-02 CP: 2.09D-03 1.73D-02 8.67D-02 1.35D-01 9.56D-02 CP: 6.18D-01 E=-0.153614250797987D+04 Delta-E= -1.098553563266 DIIS: error= 1.23D-01 at cycle 7. Coeff:-0.415D-04-0.942D-02-0.693D-02-0.180D-01 0.168D-02-0.400D+00 Coeff:-0.568D+00 T= 1500. Gap= 0.288 NK=4 IS= 36 IE= 58 NO(<0.9)= 0 NV(>0.1)= 0 44.00e < EF 0.00e >EF Err=2.8D-14 RMSDP=9.88D-03 MaxDP=2.82D-01 Cycle 8 Pass 1 IDiag 1: RMSU= 8.16D-03 CP: 1.50D-03 1.55D-02 9.41D-02 1.32D-01 8.15D-02 CP: 6.67D-01 7.14D-01 E=-0.153821497395267D+04 Delta-E= -2.072465972810 DIIS: error= 4.04D-02 at cycle 8. Coeff:-0.120D-04 0.579D-02 0.589D-03-0.132D-02 0.322D-02-0.624D-02 Coeff:-0.216D+00-0.786D+00 T= 900. Gap= 0.429 NK=0 IS= 1 IE= 178 NO(<0.9)= 0 NV(>0.1)= 0 44.00e < EF 0.00e >EF Err=0.0D+00 RMSDP=1.99D-03 MaxDP=6.24D-02 Cycle 9 Pass 1 IDiag 1: RMSU= 1.87D-03 CP: 1.35D-03 1.62D-02 9.10D-02 1.30D-01 8.09D-02 CP: 6.59D-01 7.38D-01 9.66D-01 E=-0.153832470182727D+04 Delta-E= -0.109727874597 DIIS: error= 1.87D-02 at cycle 9. Coeff: 0.127D-06 0.932D-03 0.104D-03-0.145D-02 0.656D-03 0.516D-01 Coeff:-0.575D-01-0.776D-01-0.917D+00 T= 600. Gap= 0.476 NK=0 IS= 1 IE= 178 NO(<0.9)= 0 NV(>0.1)= 0 44.00e < EF 0.00e >EF Err=0.0D+00 RMSDP=8.98D-04 MaxDP=3.08D-02 Cycle 10 Pass 1 IDiag 1: RMSU= 7.47D-04 CP: 1.36D-03 1.57D-02 9.04D-02 1.30D-01 8.17D-02 CP: 6.48D-01 7.55D-01 9.73D-01 1.04D+00 E=-0.153834577571776D+04 Delta-E= -0.021073890486 DIIS: error= 6.65D-03 at cycle 10. Coeff:-0.324D-06 0.738D-03-0.191D-03-0.585D-03-0.363D-03 0.750D-03 Coeff:-0.106D-01 0.769D-01 0.207D+00-0.127D+01 T= 300. Gap= 0.485 NK=0 IS= 1 IE= 178 NO(<0.9)= 0 NV(>0.1)= 0 44.00e < EF 0.00e >EF Err=0.0D+00 RMSDP=4.45D-04 MaxDP=1.07D-02 Cycle 11 Pass 1 IDiag 1: RMSU= 2.08D-04 CP: 1.37D-03 1.58D-02 8.98D-02 1.30D-01 8.21D-02 CP: 6.44D-01 7.63D-01 9.67D-01 1.14D+00 1.39D+00 E=-0.153834949126455D+04 Delta-E= -0.003715546797 DIIS: error= 1.74D-03 at cycle 11. Coeff:-0.160D-06 0.319D-03-0.190D-04-0.250D-03 0.113D-04-0.333D-02 Coeff: 0.145D-02 0.121D-02 0.140D+00-0.698D-01-0.107D+01 RMSDP=1.45D-04 MaxDP=3.70D-03 Cycle 12 Pass 1 IDiag 1: RMSU= 6.36D-05 CP: 1.38D-03 1.57D-02 8.97D-02 1.30D-01 8.22D-02 CP: 6.43D-01 7.65D-01 9.67D-01 1.15D+00 1.52D+00 CP: 1.28D+00 E=-0.153834979814613D+04 Delta-E= -0.000306881573 DIIS: error= 4.43D-04 at cycle 12. Coeff: 0.296D-07 0.853D-05-0.109D-04-0.107D-03 0.784D-04 0.546D-03 Coeff: 0.815D-03-0.138D-01-0.129D-01 0.708D-01 0.674D-01-0.111D+01 RMSDP=4.15D-05 MaxDP=1.21D-03 Cycle 13 Pass 1 IDiag 1: RMSU= 2.55D-05 CP: 1.38D-03 1.57D-02 8.98D-02 1.30D-01 8.22D-02 CP: 6.43D-01 7.64D-01 9.67D-01 1.13D+00 1.53D+00 CP: 1.33D+00 1.32D+00 E=-0.153834982555433D+04 Delta-E= -0.000027408205 DIIS: error= 1.47D-04 at cycle 13. Coeff: 0.453D-08-0.748D-05-0.958D-06-0.150D-04 0.207D-04 0.475D-04 Coeff: 0.404D-03-0.176D-03-0.517D-02-0.164D-01 0.117D+00-0.543D-01 Coeff:-0.104D+01 RMSDP=1.51D-05 MaxDP=3.60D-04 Cycle 14 Pass 1 IDiag 1: RMSU= 7.21D-06 CP: 1.38D-03 1.57D-02 8.98D-02 1.30D-01 8.22D-02 CP: 6.43D-01 7.64D-01 9.68D-01 1.13D+00 1.52D+00 CP: 1.34D+00 1.47D+00 1.28D+00 E=-0.153834982919234D+04 Delta-E= -0.000003638010 DIIS: error= 6.27D-05 at cycle 14. Coeff:-0.156D-07 0.187D-06 0.150D-05 0.120D-05-0.170D-05-0.256D-04 Coeff: 0.136D-03 0.114D-02 0.382D-03-0.569D-02-0.112D-01 0.114D+00 Coeff: 0.572D-01-0.116D+01 RMSDP=6.82D-06 MaxDP=1.91D-04 Cycle 15 Pass 1 IDiag 1: RMSU= 2.89D-06 CP: 1.38D-03 1.57D-02 8.98D-02 1.30D-01 8.22D-02 CP: 6.43D-01 7.64D-01 9.68D-01 1.13D+00 1.52D+00 CP: 1.33D+00 1.51D+00 1.44D+00 1.29D+00 E=-0.153834982976227D+04 Delta-E= -0.000000569930 DIIS: error= 2.40D-05 at cycle 15. Coeff:-0.136D-07 0.604D-06-0.869D-06 0.497D-05-0.502D-06-0.234D-04 Coeff: 0.290D-04 0.611D-05 0.684D-03 0.159D-02-0.139D-01 0.761D-02 Coeff: 0.116D+00 0.105D-01-0.112D+01 RMSDP=2.27D-06 MaxDP=5.15D-05 Cycle 16 Pass 1 IDiag 1: RMSU= 7.93D-07 CP: 1.38D-03 1.57D-02 8.98D-02 1.30D-01 8.22D-02 CP: 6.43D-01 7.64D-01 9.68D-01 1.13D+00 1.52D+00 CP: 1.33D+00 1.52D+00 1.48D+00 1.46D+00 1.39D+00 E=-0.153834982982640D+04 Delta-E= -0.000000064131 DIIS: error= 5.75D-06 at cycle 16. Coeff:-0.258D-08-0.559D-06 0.120D-06-0.569D-06 0.504D-06 0.159D-05 Coeff:-0.333D-05-0.171D-03-0.200D-04 0.884D-03-0.498D-03-0.122D-01 Coeff: 0.672D-02 0.139D+00-0.183D+00-0.950D+00 RMSDP=6.99D-07 MaxDP=1.99D-05 Cycle 17 Pass 1 IDiag 1: RMSU= 3.09D-07 CP: 1.38D-03 1.57D-02 8.98D-02 1.30D-01 8.22D-02 CP: 6.43D-01 7.64D-01 9.68D-01 1.13D+00 1.52D+00 CP: 1.33D+00 1.52D+00 1.49D+00 1.48D+00 1.56D+00 CP: 1.24D+00 E=-0.153834982983370D+04 Delta-E= -0.000000007301 DIIS: error= 2.60D-06 at cycle 17. Coeff: 0.192D-08-0.149D-06-0.428D-07-0.366D-06 0.208D-06-0.161D-06 Coeff:-0.206D-05 0.430D-05-0.294D-04-0.147D-03 0.129D-02-0.204D-02 Coeff:-0.897D-02 0.697D-02 0.125D+00-0.898D-01-0.103D+01 RMSDP=3.12D-07 MaxDP=6.73D-06 Cycle 18 Pass 1 IDiag 1: RMSU= 1.43D-07 CP: 1.38D-03 1.57D-02 8.98D-02 1.30D-01 8.22D-02 CP: 6.43D-01 7.64D-01 9.68D-01 1.13D+00 1.52D+00 CP: 1.33D+00 1.52D+00 1.49D+00 1.49D+00 1.63D+00 CP: 1.44D+00 1.33D+00 E=-0.153834982983514D+04 Delta-E= -0.000000001432 DIIS: error= 1.01D-06 at cycle 18. Coeff: 0.343D-09 0.334D-07-0.717D-07 0.226D-07 0.100D-06 0.171D-05 Coeff:-0.204D-05 0.221D-04-0.511D-04-0.794D-04 0.431D-03 0.163D-02 Coeff:-0.106D-02-0.209D-01 0.306D-01 0.130D+00 0.101D-01-0.115D+01 RMSDP=1.58D-07 MaxDP=4.01D-06 Cycle 19 Pass 1 IDiag 1: RMSU= 5.09D-08 CP: 1.38D-03 1.57D-02 8.98D-02 1.30D-01 8.22D-02 CP: 6.43D-01 7.64D-01 9.68D-01 1.13D+00 1.52D+00 CP: 1.33D+00 1.52D+00 1.49D+00 1.50D+00 1.64D+00 CP: 1.52D+00 1.62D+00 1.54D+00 E=-0.153834982983549D+04 Delta-E= -0.000000000349 DIIS: error= 3.86D-07 at cycle 19. Coeff:-0.486D-09 0.975D-07-0.271D-08-0.981D-07-0.181D-07 0.732D-06 Coeff: 0.910D-07 0.247D-05 0.119D-04 0.270D-05-0.131D-03 0.361D-03 Coeff: 0.126D-02-0.354D-02-0.196D-01 0.367D-01 0.133D+00-0.107D-01 Coeff:-0.114D+01 RMSDP=7.28D-08 MaxDP=1.21D-06 Cycle 20 Pass 1 IDiag 1: Restarting incremental Fock formation. E=-0.153834982983562D+04 Delta-E= -0.000000000136 DIIS: error= 2.54D-07 at cycle 1. RMSDP=2.39D-08 MaxDP=6.10D-07 Cycle 21 Pass 1 IDiag 1: RMSU= 2.39D-08 CP: 1.00D+00 E=-0.153834982983558D+04 Delta-E= 0.000000000042 DIIS: error= 1.51D-07 at cycle 2. Coeff:-0.337D+00-0.663D+00 RMSDP=8.78D-09 MaxDP=3.23D-07 SCF Done: E(RHF) = -897.762414945 A.U. after 21 cycles Convg = 0.8779D-08 -V/T = 2.0013 S**2 = 0.0000 KE= 8.965523143849D+02 PE=-3.402772737345D+03 EE= 9.678705931246D+02 Leave Link 502 at Thu May 20 10:15:36 2004, MaxMem= 18874368 cpu: 2242.0 (Enter C:\G98W\l801.exe) Range of M.O.s used for correlation: 15 178 NBasis= 178 NAE= 44 NBE= 44 NFC= 14 NFV= 0 NROrb= 164 NOA= 30 NOB= 30 NVA= 134 NVB= 134 Leave Link 801 at Thu May 20 10:15:37 2004, MaxMem= 18874368 cpu: 0.0 (Enter C:\G98W\l906.exe) Frozen-core derivative calculation, NFC= 14 NFV= 0. FulOut=F Deriv=T AODrv=T MMem= 0 MDisk= 30 MDiskD= 30 W3Min= 1394096 MinDsk= 3812475 NBas6D= 178 NBas2D= 16207 NTT= 15931 LW2= 2000000 MDV= 16691780 MDiskM= 1146 NBas2p= 15291 Disk-based method using ON**2 memory for 30 occupieds at a time. Permanent disk used for amplitudes= 43192622 words. Estimated scratch disk usage= 299688290 words. IMap= 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 IMap= 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 IMap= 41 42 43 44 Actual scratch disk usage= 289309026 words. JobTyp=1 Pass 1: I= 15 to 44. writwa ------=_NextPart_000_7768_40a2_3fca-- From chemistry-request@ccl.net Fri May 21 12:09:38 2004 Received: from av5-1-sn4.m-sp.skanova.net (av5-1-sn4.m-sp.skanova.net [81.228.10.112]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4LH9aUr012523 for ; Fri, 21 May 2004 12:09:37 -0500 Received: by av5-1-sn4.m-sp.skanova.net (Postfix, from userid 502) id C270F37E82; Fri, 21 May 2004 19:12:23 +0200 (CEST) Received: from smtp2-1-sn4.m-sp.skanova.net (smtp2-1-sn4.m-sp.skanova.net [81.228.10.183]) by av5-1-sn4.m-sp.skanova.net (Postfix) with ESMTP id B4CA237E42; Fri, 21 May 2004 19:12:23 +0200 (CEST) Received: from [192.168.0.100] (h93n1fls32o916.telia.com [213.65.165.93]) by smtp2-1-sn4.m-sp.skanova.net (Postfix) with ESMTP id 47E4D37E4F; Fri, 21 May 2004 19:12:23 +0200 (CEST) Mime-Version: 1.0 X-Sender: u42123287)at(m1.421.telia.com Message-Id: In-Reply-To: <20040520183613.D65761-100000)at(mserv.itpa.lt> References: <20040520183613.D65761-100000)at(mserv.itpa.lt> Date: Fri, 21 May 2004 19:09:08 +0200 To: Arvydas Tamulis From: Per-Ola Norrby Subject: Re: CCL:The pi-pi stacking of hetero-aromatic ring Cc: CHEMISTRY)at(ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-Spam-Status: No, hits=1.1 required=7.5 tests=FVGT_m_MULTI_ODD2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net >Would you please to advise us the quantum chemical methods and programs >that might properly calculate stacking interactions including >dispersion effects in oligomeric nucleic acids (two types of interactions: >in parallel planes and when planes are perpendicular). I don't think there is any QM method able to treat oligomeric nucleic acids which can also include accurate dispersion. DFT or HF do NOT include dispersion. The lowest level I know which does include some of the dispersion is MP2, and with any feasible basis set for this large system, the basis set deficiency error would be expected to totally swamp the dispersion. The same would be true for any correlated method. (I'll probably be flamed for this statement, but I believe it; I don't have proof though, so don't ask for it). Counterpoise correction might bring the error down, but certainly not to zero. You can get the dispersion term accurately from empirical force fields. This is a very well known term, and it has been accurately parameterized for many years. With many force fields, you will treat other non-bonded terms erroneously (like in any method that uses Lennard-Jones, where the repulsion is strongly overestimated), and the electrostatics are always a problem. I saw a JCC article a few years ago which augmented DFT with an empirical dispersion term (I don't have the reference), that seems a feasible approach. Otherwise, I'd take a force field that has proven to treat DNA well, like AMBER, it's probably superior in quality to any achievable QM. And of course it's several orders of magnitude faster... Not that I use it myself, I'm an MM3 fan, but I wouldn't advocate MM3 for oligonucleotides unless you take the electrostatics > from a QM source. Note that in DFT and HF, you always see an attractive force at something similar to the vdW distance. It's not dispersion, it's a simple basis set superposition error together with any electrostatic attraction your complex might have. Sometimes it has a similar value to the dispersion, but I wouldn't trust the predictive value of this error cancellation. If you absolutely have to have your dispersion from QM, you could probably set up some kind of extrapolation scheme, like IMOMO or ONIOM, where you use CCSD(T) with a large basis for a very small core. It will only give you accurate dispersion for a small subsystem though. You can always validate your final result by comparing to a good empirical force field... /Per-Ola -- Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ Technical University of Denmark, Department of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon)at(kemi.dtu.dk tel +45-45252123, fax +45-45933968 From chemistry-request@ccl.net Fri May 21 10:25:28 2004 Received: from axe.humboldt.edu (axe.humboldt.edu [137.150.148.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4LFPQQC007312 for ; Fri, 21 May 2004 10:25:27 -0500 Received: from zoellner (hsu5168.humboldt.edu [137.150.20.48]) by axe.humboldt.edu (8.12.6-20030924/8.12.6) with SMTP id i4LFSDuJ433295; Fri, 21 May 2004 08:28:13 -0700 (PDT) Message-Id: <3.0.1.32.20040521082531.00990430[at]axe.humboldt.edu> X-Sender: rwz7001[at]axe.humboldt.edu X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Fri, 21 May 2004 08:25:31 -0700 To: CHEMISTRY[at]ccl.net From: "Robert W. Zoellner" Subject: CCL: Gasuuian MAXCYCLE question Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Greetings All, My student and I are attempting to run a job with Gaussian that requires more optimization cycles than are allowed by the OPT(MAXCYCLE=2000) numerical limit. How can we change MAXCYCLE= to allow more than the 2000 cycle limit? (We've attempted to do this by using the input MAXCYCLE=1.0e5, for example, without success.) Thanks for the assistance. All the best, Bob Z. Robert W. Zoellner, Ph.D. Professor Department of Chemistry Humboldt State University One Harpst Street Arcata, California 95521-8299 telephone: (707)826-3244 fax: (707)826-3279 From chemistry-request@ccl.net Fri May 21 12:13:22 2004 Received: from e500-gw2.utmb.edu (mx2.utmb.edu [129.109.195.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4LHDLUr012772 for ; Fri, 21 May 2004 12:13:21 -0500 Received: from mx2.utmb.edu(129.109.195.2) by e500-gw2.utmb.edu via csmap id fa245b42_ab4a_11d8_9581_00304824a47f_29371; Fri, 21 May 2004 12:19:12 -0500 (CDT) Received: from e500-gw2.utmb.edu ([129.109.116.166]) by is1.utmb.edu (PMDF V6.1 #38124) with ESMTP id <0HY000LA4Z89WN[at]is1.utmb.edu> for chemistry[at]ccl.net; Thu, 20 May 2004 13:26:34 -0500 (CDT) Received: from unknown(129.109.116.166) by e500-gw2.utmb.edu via csmap id b418f28a_aa8b_11d8_8dd1_00304824a47f_26691; Thu, 20 May 2004 13:30:00 -0500 (CDT) Date: Thu, 20 May 2004 13:27:02 -0500 From: "Ivanciuc, Ovidiu I." Subject: CCL: The hydrophocities for 20 amino acids To: chemistry[at]ccl.net Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.0.6487.1 Content-type: text/plain; charset=Windows-1252 Thread-Topic: The hydrophocities for 20 amino acids Thread-Index: AcQ+jxriIceLI/lvRPWsAFlGba3umAACBlsh content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4LHDMUr012776 Hi, >I need the experimental results of the hydrophobicities for 20 amino >acids, could you please show me how I can get them? Any tips will be >welcome! The AAindex (Amino acid indices and similarity matrices) database, http://www.genome.ad.jp/dbget/aaindex.html contains numerical values for the major hydrophobicity scales. Another source of hydrophobicity scales for amino acids is the ProtScale from ExPASY: http://us.expasy.org/cgi-bin/protscale.pl Regards, Ovidiu Ivanciuc From chemistry-request@ccl.net Fri May 21 10:09:34 2004 Received: from web25101.mail.ukl.yahoo.com (web25101.mail.ukl.yahoo.com [217.12.10.49]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i4LF9XrA006544 for ; Fri, 21 May 2004 10:09:33 -0500 Message-ID: <20040521151220.83097.qmail[at]web25101.mail.ukl.yahoo.com> Received: from [137.158.128.106] by web25101.mail.ukl.yahoo.com via HTTP; Fri, 21 May 2004 16:12:20 BST Date: Fri, 21 May 2004 16:12:20 +0100 (BST) From: =?iso-8859-1?q?Jeff=20C?= Subject: running GAMESS using Beowulf cluster To: CHEMISTRY[at]ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Comp Chem Experts, I am new to this field so I will apologize in advance if the following question is too trivial to the skilled researchers. Currently I am trying to learn how to use gamess. The procedure is simple when comes to running gamess with single CPU. However, I am clueless when trying to run gamess on our newly built 16 nodes Beowulf cluster using MPI. I hope someone out there can give me the step-by-step guide. Much appreciated. Jeff Chen ____________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html From chemistry-request@ccl.net Fri May 21 09:49:00 2004 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4LEn0rA005307 for ; Fri, 21 May 2004 09:49:00 -0500 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Fri, 21 May 2004 14:31:24 +0100 Date: Fri, 21 May 2004 14:31:24 +0100 Message-ID: <406A6C3900051EA6~at~hawk.dcu.ie> From: "Noel O'Boyle" Subject: Summary: Gaussian MSK charges To: chemistry~at~ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4LEn0rA005313 Thanks to everyone that answered my email about choosing the correct radius for Ru in a Gaussian MSK (Merz-Singh-Kollman) atomic charge calculation. My original email is included below as well as very helpful replies from: G|nter Klatt, David Shobe, Vincent Xianlong Wang, Errol Lewars and Marcel Swart. Noel >Hello CCLers, > >I am trying to calculate Merz-Singh-Kollman charges for a ruthenium complex >using Gaussian03 and the POP=MK keyword. > >Gaussian stops with an error message because it has no Merz-Kollman radius >for Ruthenium. > >I know how to include a radius for Ruthenium (the POP=(MK,ReadRadii) keyword) >but I don't know what value I should use. Can anybody help me? > >H is 1.20 >C is 1.50 >N is 1.50 >Ru is ?? > >Are these numbers related to the van der Waal radii, or are they simply >scaling factors? > >Noel Hello Noel The radius should be the van der Waals radius of Ru in the proper oxidation state, probably somewhere around 1.7 A. Have a look at our recent paper Lienke et al., Inorg. Chem. 2001, 40, 2352-2357 and references therein (especially Bondi's and Hambley's!) Regards Guenter Noel, I had the same problem with the Breneman radii for CHELPG. I never really got an answer, either from CCL or from the journal article that introduced the method. In CHELPG at least, the atomic radii are there to create exclusion zones around each atom, and as long as you took reasonable radii that were a bit *larger* than tabulated van der Waals radii, the results were not very radius dependent. The Merz-Kollman radii appear to be similar to the CHELPG radii so probably you can do what I ended up doing, which was add 0.2 Angstroms to the van der Waals radii. But you may want to try a few values to verify that the choice of radius is not important--and then consistently use the same radius for "production" calculations. --David Shobe, Ph.D., M.L.S. Try web of elements. http://www.webelements.com/ Vincent hello, I have not done this kind of calc. with G03, but: If nothing better comes up, I suggest you plot a graph of the Merz-Kollman radii which you have (H 1.20, C 1.50, ...) against van der Waals radii; assuming you know the van der Walls radius of Ru, you should be able to get from this the Ru Merz-Kollman radius. EL See a related message from sometime ago. Although that one dealt with CHELPG instead of MSK, the same problem is present. Begin forwarded message: > From: Valentin Gogonea > Date: November 28, 2002 2:42:36 PM CET > To: chemistry~at~ccl.net > Subject: CCL:Summary: CHelpG calculation for Fe > > Dear CCLers, > > A couple of weeks ago I asked for advice for selecting the radius for > Fe(2+) for CHelpG calculations. Thank you very much to all who > answered. > > Valentin Gogonea > Cleveland State University > > Here are the replies that I received: > ----------------------------------------------------------------------- > ----------------------------------------------------------------------- > -------------------- > We never tried to go that far down in the periodic table when we > developed some > of the radii for other atoms, but I suggest that you use a > (consistent) value > that represents the van der Waals radius of the atom. The danger of > using too > large a radius is the loss of information from the other atoms in the > molecule, > and an underdetermined charge fitting model. Good luck with your > experimentation. I suggest you try several reasonable values and then > see if > the charges computed for all of the atoms are reasonably consistent. > > Curt Breneman > RPI Chemistry > > ----------------------------------------------------------------------- > ----------------------------------------------------------------------- > -------------------- > > From gromacs list: > > I did gaussian 98 calculations on Fe(III). Here are my notes > concerning the radii that I used. Hope it helps, > > Cheers, > Marc > > For iron there are several ionic radii. Let's use radii from > http://www.webelements.com/webelements/elements/text/Fe/radii.html. > > o Fe(III) 6-coordinate, octahedral 69 pm > > o Fe(III) 6-coordinate, octahedral, high spin 78.5 pm > > Note: The "efective ionic radii" quoted here assume that the ionic > radius of F- is 133 pm and that of O2- is 140 pm. The values for iron > thus correspond quite well to che tabulated Gaussian Merz-Kollman > radii, and will be scaled for Francl and Breneman, with a mean factor > for F- and O2-. Values depend upon the coordination number and for > d-block metals on the fact whether or not the metal is in a high or > low spin state. > > Atomnb AtTyp Merz-Kollman Francl Breneman > (CHELP) (CHELPG) >> ............. ............. ............. ............. ............. > 26 Fe 0.69 0.75 0.85 > 6-coordinate, > octahedral > 26 Fe 0.785 0.85 0.97 > 6-coordinate, > octahedral, > high spin > > ----------------------------------------------------------------------- > ----------------------------------------------------------------------- > -------------------- > > you could try a number of different radii and see where the charges > are approximately constant. I would guess a radius of 2.0 A. > Please, see our article, where we determine a radius for Cu2+: > E. Sigfridsson & U. Ryde (1998) "A comparison of methods for deriving > atomic charges from the electrostatic potential and moments". J. > Comp. Chem. 19, 377-395. > > Best regards, > Ulf > ----------------------------------------------------------------------- > ----------------------------------------------------------------------- > -------------------- > > We typically use Fe radius of 1.5A, sometimes even 1.3A, but the Fe(3+) > or Fe(2+) is nearly always surrounded by ligands and the whole complex > is treated by quantum calc's (DFT), so the Fe radius is not important. > Use of the bare ion alone will lead to poor properties, as we showed > in an Inorg. Chem. paper on metal cations in water in 1996. > Best Regards, > Lou Noodleman > ----------------------------------------------------------------------- > ----------------------------------------------------------------------- > -------------------- > > To read in a radius for Fe, use the option > "pop=(chelpg,ReadAtRadii)". These values are usually not the textbook > van der Waals radii, but radii that have been chosen by the authors of > a given charge scheme. The choice of a radius for an element that was > not in the original parameter set is a judgment call and depends > somewhat on the task at hand (whether the atom is ionic, for example). > Below is an example input file in which I arbitrarily chose to use the > metallic radius of Fe. > > #p rhf/sto-3g scf=tight symm=loose pop=(chelpg,readradii) test > > ferrocene example > > 0 1 > Fe -0.000000 -0.000000 0.000000 > X -0.000000 0.000000 -2.160000 > C -0.000000 1.250000 -2.160000 > C 1.188821 0.386271 -2.160000 > C -1.188821 0.386271 -2.160000 > H 0.113936 2.334029 -2.160000 > C 0.734732 -1.011271 -2.160000 > H 2.255002 0.612895 -2.160000 > C -0.734732 -1.011271 -2.160000 > H -2.184585 0.829614 -2.160000 > H 1.279732 -1.955239 -2.160000 > H -1.464084 -1.821299 -2.160000 > X 0.000000 0.000000 2.160000 > C 0.000000 1.250000 2.160000 > C -1.188821 0.386271 2.160000 > C 1.188821 0.386271 2.160000 > H -0.113936 2.334029 2.160000 > C -0.734732 -1.011271 2.160000 > H -2.255002 0.612895 2.160000 > C 0.734732 -1.011271 2.160000 > H 2.184585 0.829614 2.160000 > H -1.279732 -1.955239 2.160000 > H 1.464084 -1.821299 2.160000 > > Fe 1.24 > > > > Regards, > Jim Hess > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY~at~ccl.net -- To Everybody | CHEMISTRY-REQUEST~at~ccl.net -- To > Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl~at~ccl.net > > > > > > > ???????????????????????????????????????????? dr. Marcel Swart From chemistry-request@ccl.net Fri May 21 10:17:41 2004 Received: from server.theo.chemie.tu-muenchen.de (server.theo.chemie.tu-muenchen.de [129.187.122.133]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4LFHfrA006782 for ; Fri, 21 May 2004 10:17:41 -0500 Received: by crease.theo.chemie.tu-muenchen.de (Postfix, from userid 547) id C6682BAC2; Fri, 21 May 2004 11:37:51 +0200 (CEST) Date: Fri, 21 May 2004 11:37:51 +0200 (CEST) From: Mehdi Bounouar To: CHEMISTRY~at~ccl.net Subject: ECP gamess input Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, If someone knows why the following input in GAMESS does not work, or manages to make it run, I would really appreciate any advice. Thanks Regards ECP POTENTIALS -------------- **** ERROR READING VARIABLE NGPOT ^@ CHECK COLUMN 1 C2-ECP NONE ....V....1....V....2....V....3....V....4....V....5....V....6....V....7....V....8 *** ERROR *** AN UNEXPECTED $END WAS ENCOUNTERED IN $ECP GROUP. EVERY ATOM IN THE MOLECULE MUST BE DEFINED IN $ECP. $CONTRL SCFTYP=ROHF RUNTYP=ENERGY ECP=READ MULT=2 COORD=UNIQUE $END $SCF DIRSCF=.true. $END $SYSTEM MWORDS=120 TIMLIM=40000 $END $DATA ETHANE with QCP1: JCP 116 (2002), 9578 C1 C1 6 0.000000 0.000000 0.000000 L 1 1 0.12D0 1.00D0 1.00D0 L 1 1 0.36D0 1.00D0 1.00D0 L 1 1 1.08D0 1.00D0 1.00D0 L 1 1 3.24D0 1.00D0 1.00D0 L 1 1 9.72D0 1.00D0 1.00D0 D 1 1 0.626D0 1.00D0 C2 6 0.000000 0.000000 1.526681 N31 6 D 1 1 0.800000000 1.00000000 H 1 1.012207 0.000000 -0.392775 N31 6 P 1 1 1.10000000 1.00000000 H 1 -0.506104 -0.876597 -0.392775 N31 6 P 1 1 1.10000000 1.00000000 H 1 -0.506104 0.876597 -0.392775 N31 6 P 1 1 1.10000000 1.00000000 $END $ECP C1-ECP GEN 5 2 2 ----- POTENTIAL ----- -0.86 1 8.14 -2.60 1 1.29 3 ----- POTENTIAL ----- 5.90 0 10.16 -7.30 1 2.56 26.11 2 3.62 C2-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE $END From chemistry-request@ccl.net Fri May 21 10:00:00 2004 Received: from turmiel.ch.uj.edu.pl (turmiel.ch.uj.edu.pl [149.156.71.252]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4LExxrA006049 for ; Fri, 21 May 2004 09:59:59 -0500 Received: from turmiel.ch.uj.edu.pl (localhost.localdomain [127.0.0.1]) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8) with ESMTP id i4L75Gh0023798 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NO) for ; Fri, 21 May 2004 09:05:16 +0200 From: makowskm~at~chemia.uj.edu.pl Received: (from apache@localhost) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8/Submit) id i4L75EnX023792; Fri, 21 May 2004 09:05:14 +0200 X-Authentication-Warning: turmiel.ch.uj.edu.pl: apache set sender to makowskm~at~chemia.uj.edu.pl using -f Received: from 149.156.71.133 (SquirrelMail authenticated user makowskm) by mail.ch.uj.edu.pl with HTTP; Fri, 21 May 2004 09:05:14 +0200 (CEST) Message-ID: <38538.149.156.71.133.1085123114.squirrel~at~mail.ch.uj.edu.pl> Date: Fri, 21 May 2004 09:05:14 +0200 (CEST) Subject: CCL: dft/mrci To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new Dear CCLers, Does anybody know any software which implements DFT/MRCI method? Yours, Marcin Makowski Ph.D. student in Theoretical Chemistry Jagiellonian University From chemistry-request@ccl.net Fri May 21 16:35:42 2004 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4LLZfQF022918 for ; Fri, 21 May 2004 16:35:42 -0500 Received: by leitl.org (Postfix, from userid 500) id 7F1D73A84B6; Fri, 21 May 2004 23:38:22 +0200 (CEST) Date: Fri, 21 May 2004 23:38:22 +0200 From: Eugen Leitl To: chemistry/at/ccl.net Subject: [Beowulf] CCL:Question regarding Mac G5 performance (fwd from konstantin_kudin/at/yahoo.com) Message-ID: <20040521213822.GW16732/at/leitl.org> Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="BJXPtXU9scw8QjKC" Content-Disposition: inline User-Agent: Mutt/1.4i X-Spam-Status: No, hits=1.3 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, OFFER_URI autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --BJXPtXU9scw8QjKC Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable ----- Forwarded message from Konstantin Kudin = ----- From: Konstantin Kudin Date: Fri, 21 May 2004 14:23:48 -0700 (PDT) To: beowulf/at/beowulf.org Subject: [Beowulf] CCL:Question regarding Mac G5 performance > Again...SPEC was included, among a number of others. Would you happen > to have a cross section of code relevant to computational chemistry =20 > that might offer a fair example of platform performance? I'd enjoy a=20 > chance to get it into the labs and see how Itanuim 2 might stack up. While I can't speak for every code out there, for Gaussian03 I2 seems to work extremely well: http://www.princeton.edu/~kkudin/g03_b5_tests_1.txt Note that these are ~1 hour long jobs, which surely do not fit in cache. The interesting part is that for some real life codes I2 performance matches what SPEC numbers would predict. The cost, of course, is a different issue altogether. Konstantin =20 =09 =09 __________________________________ Do you Yahoo!? Yahoo! Domains ? Claim yours for only $14.70/year http://smallbusiness.promotions.yahoo.com/offer=20 _______________________________________________ Beowulf mailing list, Beowulf/at/beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.b= eowulf.org/mailman/listinfo/beowulf ----- End forwarded message ----- --=20 Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net --BJXPtXU9scw8QjKC Content-Type: application/pgp-signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.2-rc1-SuSE (GNU/Linux) iD8DBQFArnbOdbAkQ4sp9r4RAuJeAJ9jxykkLoEa9pRNw0mtibr0WLRozwCdEUFC frbnJQFgXiqpTeKnYxqvYWs= =NIA5 -----END PGP SIGNATURE----- --BJXPtXU9scw8QjKC-- From chemistry-request@ccl.net Fri May 21 15:52:10 2004 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4LKq9QF021784 for ; Fri, 21 May 2004 15:52:10 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HY1002020JH2R-.at.-mailserver.unimi.it> for chemistry-.at.-ccl.net; Thu, 20 May 2004 20:54:54 +0200 (MEST) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HY1002GT0JCFI-.at.-smtp.unimi.it> for chemistry-.at.-ccl.net; Thu, 20 May 2004 20:54:48 +0200 (MEST) Date: Thu, 20 May 2004 20:58:35 +0200 From: Alessandro Contini Subject: amber parameters in G03 MM To: chemistry-.at.-ccl.net Reply-to: alessandro.contini-.at.-unimi.it Message-id: <200405202058.35639.alessandro.contini-.at.-unimi.it> Organization: =?iso-8859-1?q?Universit=E0=20di?= Milano MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.4 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4LKqAQF021788 Hi, I'm triyng to set up a oniom calculation using the amber ff for the MM part. I'm using GaussView3.09 to set up the run, but I noticed that some aminoacids, in particular histidine, have missing parameters and the charge is not automatically added to the AT definition in the input file. I found this surprising as such parameters are included in the standard amber ff. Could anybody suggest me how to include those missing parameters? Thanks a lot for your help Alessandro -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini-.at.-unimi.it