From jerry@dft.chem.cuhk.hk Tue Mar 12 03:15:52 1996 Received: from iris.chem.cuhk.hk for jerry@dft.chem.cuhk.hk by www.ccl.net (8.7.1/950822.1) id DAA22119; Tue, 12 Mar 1996 03:01:59 -0500 (EST) Received: from dft.chem.cuhk.hk by iris.chem.cuhk.hk via SMTP (931110.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA09865; Tue, 12 Mar 96 16:01:16 +0800 Received: by dft (950511.SGI.8.6.12.PATCH526/930416.SGI.AUTO) id QAA13343; Tue, 12 Mar 1996 16:01:13 +0800 Date: Tue, 12 Mar 1996 16:01:13 +0800 (HKT) From: Jerry C C Chan To: chemistry@www.ccl.net Subject: Summary: Definition of diffuse function? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I would like to express my gratitude to Jan and Cory for their responds to my question. The original post is reproduced below: I am currently working with the TZV cobalt basis set developed by A. Schafer et.al. (JCP, 97 (1992) 2571.). If the TZV basis set is uncontracted from (842111/631/411) to (61121111111/3111111111/111111) and then 2 polarization p functions prepared by Wachters are added, I would like to know how I should label the new basis set? i. (61121111111/311111111111*/111111) i. (61121111111/311111111111+*/111111) ii. (61121111111/311111111111+*/111111+) In the new basis set, the smallest exponents are 0.043402 and 0.3038145779 for p and d, respectively. I think the answer depends on the definition of diffuse function. Could anybody please comment on this issue. Thank you very much. +++++++++++++++++++++++ ... Diffuse functions is even less defined. It simply means: functions which are diffuse, i.e., have small exponent. I understand, that it is usually used to s and p functions, but in principle, you may have "diffuse polarization" functions. What does it mean small exponent? Beats me... Usually exponent is considered small if it is below 0.2, and "normal" when it is above 0.7. In between, you are entering the "grey area" and it probably depends on element. For carbon 0.3 is small exponent. For heavier elements it is not necessarily small. So for cobalt, I am not sure. Also remember that term "diffuse" was really popularized in 1980's, so in papers older than that, you may find diffuse called all sorts of names. Sorry for confusing you, rather than giving straight answers, but I am afraid, some of these terms are more artistic than scientific, since construction of basis sets is a black art rather than science. Jan jkl@ccl.net +++++++++++++++++++++ I don't believe there is a systematic name for most of these basis sets, but we were faced with a similar dilemna in naming basis sets from the same paper. We wanted to use some basis sets that were included at thir ftp site which were not (explicitly) mentioned in their paper, so we had to come up with a label to describe them (See C. C. Pye et al., J. Mol. Struct. (Theochem), 307 (1994) 239 ). For the first row atoms, the SV, DZ and TZ basis sets were already defined to be a particular contraction pattern that was based on `common-sense' i.e. for carbon, of 1s2s2p minimal configuration, the 511111/411 scheme implies (LOOSELY) that there are 3 functions that describe mostly the 1s (511.../...), 3 functions that describe mostly the 2s (...111/...), and 3 that describe the 2p (....../411). What we called TQZ was when 4 functions described the 2p set, the 1s and 2s still having (loosely) 3 functions each. Since these are 'energy-optimized', the extra function is not really a diffuse or polarization function. Similarly the QPZ set (61111111/51111) has 4 functions to describe each s shell (Quadruple) and 5 functions to describe the p shell (Pentuple). If I had to describe your basis set: Co 1s2s2p3s3p3d4s (minimal) It is certainly at least TZ (in all shells). 1 missing s. The p-s are between TZ and QZ, and the d shell is hextuple-zeta, so maybe call it TsTQpHdZ or (more neatly) Ts-TQp-Hd-Z. For the extra functions you could use this as the root name and (with the Wachters functions added), call it Ts-TQp-Hd-Z(2p). In the end, WHAT you call it doesn't matter, as long as people know how you constructed the basis in order to be able to duplicate the result. -Cory ************* ***************** ! Cory C. Pye *** ** ** ** ! Graduate Student ** * **** ! Unpaid Sys Admin ** * * ! Theoretical and ** * * ! Computational Chemistry *** * * ** ! ***************** ! Les Hartree-Focks ************* ! (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Tue Mar 12 04:16:00 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id DAA22219; Tue, 12 Mar 1996 03:17:01 -0500 (EST) Received: from gate.sinica.edu.tw for ccchuang@gate.sinica.edu.tw by bedrock.ccl.net (8.7.1/950822.1) id DAA01070; Tue, 12 Mar 1996 03:16:58 -0500 (EST) Received: by gate.sinica.edu.tw (5.x/SMI-SVR4) id AA14263; Tue, 12 Mar 1996 16:15:35 +0800 Date: Tue, 12 Mar 1996 16:15:34 +0800 (CST) From: Chyh-chong Chuang To: str-nmr@net.bio.net Cc: molmodel@net.bio.net, chemistry@ccl.net Subject: coupling constant restrain of D-Amino Acid for structural refine. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: Does any one could point me some references about how to use the measured 3J-na coupling constant of a D-form amino acid as an additional restrain in nmr structural refinement. Any suggest/comment will be great appreciated. Thanks all ccchuang ============================================ Chyh-Chong Chuang Institude of Biological Chemistry, Academia Sinica,Taipei, Taiwan -------------------------------------------- Phone: 886-2-7858981 ext 7091 Fax: 886-2-7883473 E-Mail: ccchuang@gate.sinica.edu.tw ============================================ From palumbo@purple.dsfarm.UNIPD.IT Tue Mar 12 06:15:52 1996 Received: from ipdunivx.unipd.it for palumbo@purple.dsfarm.UNIPD.IT by www.ccl.net (8.7.1/950822.1) id GAA24519; Tue, 12 Mar 1996 06:06:44 -0500 (EST) From: Received: from purple.dsfarm.UNIPD.IT by IPDUNIVX.UNIPD.IT (PMDF V5.0-3 #11371) id <01I2916ALMS000039D@IPDUNIVX.UNIPD.IT> for CHEMISTRY@www.ccl.net; Tue, 12 Mar 1996 12:06:10 +0100 Received: by purple.dsfarm.UNIPD.IT (AIX 3.2/UCB 5.64/4.03) id AA19938; Tue, 12 Mar 1996 12:02:47 +0100 Date: Tue, 12 Mar 1996 12:02:47 +0100 Subject: hydrogen bond To: CHEMISTRY@www.ccl.net Cc: palumbo@purple.dsfarm.UNIPD.IT Message-id: <9603121102.AA19938@purple.dsfarm.UNIPD.IT> Content-transfer-encoding: 7BIT Dear Netters, I have a question for you: I am looking for references about hydrogen bond. In particular I need a list of tipical H-bond distances and angles relative to protein structures. Could anybody help me? Thanks in advance, Lorena Senese palumbo@purple.dsfarm.unipd.it From toukie@zui.unizh.ch Tue Mar 12 06:22:10 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.1/950822.1) id FAA24430; Tue, 12 Mar 1996 05:41:27 -0500 (EST) Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA11067; Tue, 12 Mar 96 11:41:00 +0100 X-Nupop-Charset: Swiss Date: Tue, 12 Mar 1996 12:41:50 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <45710.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Micelle structure Dear Colleagues; I am seeking published information about the structure of phospholipid miceles in aqueous solution: shape and dimensions, number of individual mole- clues per micelle, orientation of individual molecules in a micelle, etc. As an added bonus, I would like to get a structural file (PDB, Sybyl.mol2, etc.) file of a phospholipid micelle, if any one has one or _knows_ of anyone else who might have one. Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Zuerich toukie@zui.unizh.ch From herrmann@hermes.informatik.uni-stuttgart.de Tue Mar 12 08:15:54 1996 Received: from ifi.informatik.uni-stuttgart.de for herrmann@hermes.informatik.uni-stuttgart.de by www.ccl.net (8.7.1/950822.1) id HAA26147; Tue, 12 Mar 1996 07:51:12 -0500 (EST) From: Frank Herrmann Date: Tue, 12 Mar 1996 13:50:56 +0100 Message-Id: <199603121250.NAA27894@odysseus.informatik.uni-stuttgart.de> Received: by odysseus.informatik.uni-stuttgart.de; Tue, 12 Mar 1996 13:50:56 +0100 To: palumbo@purple.dsfarm.UNIPD.IT CC: CHEMISTRY@www.ccl.net In-reply-to: <9603121102.AA19938@purple.dsfarm.UNIPD.IT> (palumbo@purple.dsfarm.UNIPD.IT) Subject: Re: CCL:hydrogen bond Hello, I know 3 definitions of hydrogen bonds: - donor-acceptor distance ( e.g. 2.75 < d < 3.15 ) - donor-hydrogen-acceptor angle and hydrogen-acceptor distance ( e.g. a < 60 ; d <= 2.5 ) - energy threshold according to kabsch and sander: @article{2nd_dict, annote={confsearch,misc}, title={Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features}, author={Wolfgang Kabsch and Christian Sander}, journal= BIOPOL , volume={22}, pages={2577-2637}, year=1983} BIOPOL = biopolymers ----------------------------------------------- Frank Herrmann, Computer Scientist, PhD Student Dept. of Molecular Biophysics 0810 German Cancer Research Center Im Neuenheimer Feld 280, D-69120 Heidelberg Tel: (49) 6221-422336, FAX: (49) 6221-422333 email: Herrmann@odysseus.informatik.uni-stuttgart.de From rochus@felix.anorg.chemie.tu-muenchen.de Tue Mar 12 09:15:55 1996 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.7.1/950822.1) id IAA27140; Tue, 12 Mar 1996 08:28:58 -0500 (EST) Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id NAA11048; Tue, 12 Mar 1996 13:57:51 +0100 From: "Rochus Schmid" Message-Id: <9603121357.ZM11046@felix> Date: Tue, 12 Mar 1996 13:57:50 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: CH4/CH4 potential Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters, Can someone point me to references concerning the calculation of the potential between two methan molecules (calculated by any theoretical method)? I would also be interested in experimental results. I will summarize to the list. Thanks in advance. Greetings from Munich, Rochus -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 3209 3140 Anorganisch Chemisches Institut 1 Fax. ++49 89 3209 3473 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From owner-chemistry@ccl.net Tue Mar 12 10:15:54 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id JAA27626; Tue, 12 Mar 1996 09:37:29 -0500 (EST) Received: from earn.cvut.cz for strajbl@silicon.karlov.mff.cuni.cz by bedrock.ccl.net (8.7.1/950822.1) id JAA04915; Tue, 12 Mar 1996 09:37:17 -0500 (EST) Received: from ns.karlov.mff.cuni.cz by earn.cvut.cz (IBM VM SMTP V2R1) with TCP; Tue, 12 Mar 96 15:35:42 MET Received: from silicon.karlov.mff.cuni.cz by ns.karlov.mff.cuni.cz id aa06351; 12 Mar 96 15:27 MEZ Received: by silicon.karlov.mff.cuni.cz (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@ccl.net id NAA29715; Tue, 12 Mar 1996 13:38:37 -0800 Date: Tue, 12 Mar 1996 13:38:37 -0800 From: Marek Strajbl Message-Id: <199603122138.NAA29715@silicon.karlov.mff.cuni.cz> To: CHEMISTRY@ccl.net Subject: xmol and X-win Dear netters, I was trying to run XMol v.1.3.1 under X-windows. Program died with message: unable to connect to X11 server Other x-win programs run properly. If the XMol is run from the terminal of the computer where the program is installed (Indigo2), there are no difficulties. What's the problem? Best regards, Marek -------------------------------- Marek Strajbl Insitute of Physics, Prague e-mail: From stoutepf@carbon.dmpc.com Tue Mar 12 14:15:56 1996 Received: from gatekeeper.es.dupont.com for stoutepf@carbon.dmpc.com by www.ccl.net (8.7.1/950822.1) id NAA01278; Tue, 12 Mar 1996 13:51:22 -0500 (EST) Received: by gatekeeper.es.dupont.com; id AA21016; Tue, 12 Mar 96 13:51:17 -0500 Received: from [158.117.170.103] (esm170103.dmpc.com [158.117.170.103]) by carbon.dmpc.com (8.6.9/8.6.9) with SMTP id NAA28776 for ; Tue, 12 Mar 1996 13:49:31 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Organization: The DuPont Merck Pharmaceutical Company X-Mailer: Eudora Pro 2.1.4 for Macintosh X-Url: http://www.halcyon.com/stouten/index.html Date: Tue, 12 Mar 1996 13:47:13 -0500 To: CHEMISTRY@www.ccl.net From: stoutepf@carbon.dmpc.com (Pieter Stouten) Subject: Re: CCL:hydrogen bond At 13:50 96/03/12, Frank Herrmann wrote: >I know 3 definitions of hydrogen bonds: > >- donor-acceptor distance ( e.g. 2.75 < d < 3.15 ) >- donor-hydrogen-acceptor angle and hydrogen-acceptor distance > ( e.g. a < 60 ; d <= 2.5 ) >- energy threshold according to kabsch and sander: > One can also take the minimum after the first maximum in the O...O or H...O radial distribution functions. This criterion would be distance-based but the value actually applied would depend on the force field that is being used. The arbitrariness of the first two criteria listed above would thus be eliminated. -- Pieter Stouten || Nothing shocks me; Computer Aided Drug Design Group || The DuPont Merck Pharmaceutical Company || I am a scientist! P.O. Box 80500, Wilmington, DE 19880-0500 || Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 9090 || Internet: stoutepf@carbon.dmpc.com || Indiana Jones From dlarson@thebe.tripos.com Tue Mar 12 15:15:58 1996 Received: from gatekeeper.tripos.com for dlarson@thebe.tripos.com by www.ccl.net (8.7.1/950822.1) id OAA01887; Tue, 12 Mar 1996 14:43:23 -0500 (EST) Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id NAA20406 for ; Tue, 12 Mar 1996 13:43:18 -0600 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma020404; Tue Mar 12 13:43:12 1996 Received: from thebe.tripos (thebe.tripos.com [192.160.145.47]) by tripos.tripos.com (8.6.12/8.6.12) with SMTP id NAA05471 for ; Tue, 12 Mar 1996 13:42:06 -0600 Received: by thebe.tripos (920330.SGI/5.6) id AA12696; Tue, 12 Mar 96 13:42:05 -0600 Date: Tue, 12 Mar 1996 13:42:05 -0600 (CST) From: David Larson Subject: ACS Workshop Announcement To: CHEMISTRY@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII New Technologies and Applications in Chemical Discovery on the Personal Computer ACS, New Orleans, March 26 An ACS Workshop jointly sponsored by Tripos, Inc., MDL Information Systems, Inc. and SciVision Chemical Discovery on the Desktop --------------------------------- This workshop will present new PC-based technologies for integrated chemical discovery including molecular property calculations, molecular visualization and interactions, database searching and management, and specialized applications. Advanced applications for polymer, protein, and small molecule discovery will be highlighted. Date: Tuesday, March 26, 10 AM - Noon Location: Room 83, 3rd Floor, Convention Center New Orleans, LA A complimentary breakfast will be served. If you are interested in attending, please call us and reserve a space: 1-800-323-2960 Ext. 3242. From owner-chemistry@ccl.net Tue Mar 12 17:15:58 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id QAA03394; Tue, 12 Mar 1996 16:25:58 -0500 (EST) Received: from saturn.kent.edu for raeker@saturn.kent.edu by bedrock.ccl.net (8.7.1/950822.1) id QAA19201; Tue, 12 Mar 1996 16:25:58 -0500 (EST) Received: by saturn.kent.edu (AIX 3.2/UCB 5.64/4.03) id AA16174; Tue, 12 Mar 1996 16:25:58 -0500 Date: Tue, 12 Mar 1996 16:25:58 -0500 (EST) From: "Todd J. Raeker" To: CCL Subject: CCL: Gaussian expansion coefficients Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all A number of Quantum Chemistry texts go through a variational treatment of Hydrogen atoms using guassian function. Usually they go through the details of one function and simply present the minimum energy one would get for an expansion in gaussians. No reference is given by which one can look at the coefficients and nonllinear parameters in the expansions as a number of functions. Can some kind sole provide a reference (paper or book)? Thanks. Todd Dr. Todd J. Raeker | Department of Chemistry Theoretical Chemistry Group | Kent State University raeker@saturn.kent.edu | Kent, OH 44242-0001 Phone (216)-672-2986 | From owner-chemistry@ccl.net Tue Mar 12 22:16:00 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id VAA06212; Tue, 12 Mar 1996 21:41:31 -0500 (EST) Received: from cln.etc.bc.ca for cpalmer@etc.bc.ca by bedrock.ccl.net (8.7.1/950822.1) id VAA23451; Tue, 12 Mar 1996 21:41:22 -0500 (EST) Received: from sparky.etc.bc.ca by cln.etc.bc.ca for CHEMISTRY@ccl.net (4.1/1.39) id AA07761; Tue, 12 Mar 96 18:41:13 PST Received: from ppp211.dial.gov.bc.ca by sparky.etc.bc.ca (4.1//ident-1.0) id AA23827; Tue, 12 Mar 96 18:37:06 PST Date: Tue, 12 Mar 96 18:37:02 PST Message-Id: <9603130237.AA23827@sparky.etc.bc.ca> X-Sender: cpalmer@pop.etc.bc.ca X-Mailer: Windows Eudora Light Version 1.5.2b1 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@ccl.net From: Clancy Palmer Subject: Electroplating Lead with nickel Hi, whomever may read this. I don't know if I sent this to anyone who can or will answer but I got the address from another chemistry request. I have a business in stained glass. I have a number of small characters made of glass and lined with a lead strip. I need to electroplate this lead strip with nickel to give them a silvery shine. I can send them away to have the process done but it costs money and I would rather try and do it myself. I was wondering if anyone knew what the best way to go about it is (eg. What solution to do it in, what current/voltage to use, time to leave it in, electrodes to use, etc.). Please keep it in mind that I don't have a chemistry lab but I can get some equipment. If anyone can help or knows someone that can help, can you please send me an e-mail at cpalmer@cln.etc.bc.ca Thanks in advance, Clancy