From Platts@cardiff.ac.uk Wed Apr 30 08:39:45 1997 Received: from crane.cf.ac.uk for Platts@cardiff.ac.uk by www.ccl.net (8.8.3/950822.1) id IAA06160; Wed, 30 Apr 1997 08:27:08 -0400 (EDT) Received: from thor.cf.ac.uk by crane.cf.ac.uk with SMTP (PP); Wed, 30 Apr 1997 13:22:13 +0100 Received: from localhost (sacjap@localhost) by thor.cf.ac.uk (8.8.5/8.6.12) with SMTP id NAA23257 for ; Wed, 30 Apr 1997 13:26:34 +0100 (BST) Date: Wed, 30 Apr 1997 13:26:33 +0100 (BST) From: James Platts To: chemistry@www.ccl.net Subject: Calculation of chemical shifts Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Folks, Sorry if this is a FAQ. A colleague wants me to predict the chemical shift of a nucleus in a large-ish molecule (50+ atoms). All the literature I have seen on such calculations indicate that one needs to use a large basis set and preferably some estimate of correlation, which is out for a molecule of this size. Does anyone have any ideas how I could get a reasonable estimate of this number? Would a semi-empirical treatment be worthwhile? Many thanks, Jamie Platts From maiden@RedBrick.DCU.IE Wed Apr 30 09:08:49 1997 Received: from tolka.dcu.ie for maiden@RedBrick.DCU.IE by www.ccl.net (8.8.3/950822.1) id HAA05883; Wed, 30 Apr 1997 07:55:37 -0400 (EDT) Received: from Nurse.RedBrick.DCU.IE by tolka.dcu.ie; (5.65v3.2/1.1.8.2/14Feb96-0535PM) id AA11710; Wed, 30 Apr 1997 12:54:21 +0100 Received: from localhost (maiden@localhost) by RedBrick.DCU.IE (SomeMTA) with SMTP id MAA12789 for ; Wed, 30 Apr 1997 12:55:12 +0100 (BST) Organisation: DCU Networking Society X-Disclaimer: The DCUNS is not responsible for the content of this message Date: Wed, 30 Apr 1997 12:55:12 +0100 (BST) From: michael nolan To: chemistry@www.ccl.net Subject: mn complexes Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL HELP! I have a really bad problem and I cannot do anything about it. Here it is: I am trying to run ab-initio calculations on Mn(CO)3 and Cr(CO)3, using GAMESS-UK. I have tried the following methods (I also give if ti was succesful or not): 1) RHF/3-21G (3-21G on all atoms) for Mn(CO)3 this is successful, for Cr(CO)3 I get excessive number of iterations and an oscillation of the energy. geometry input: Caetesian coordinates, i.e geometry angstroms 0.000 0.000 0.000 metal 1.800 0.000 0.000 c .... .... 3.000 0.000 0.000 o ... ... runtype: OPTXYZ 2) RHF, 6-21G on C and O, 3-21G on Mn. for Mn(CO)3, this is successful 3) RHF with minimal basis ECP on all atoms for Mn(CO)3 and Cr(CO)3. This gives a ludicrously low energy (about -70a.u.), oscillations in the energy and excessive number of iterations I have inputted a z-matrix, cartesian coordinates from X-ray diffraction studies (using both OPTXYZ keyword and the cartesian coordinates to z-matrix conversion) and the idealised geometry above and I get the same result with them all - excessive number of iterations etc.. 4) RHF as above, but ECP-double zeta (ECPDZ) on all atoms same result 5) RHF, min. basis ECP and ECPDZ on Mn, 3-21G and 6-31G on C and O see number 4. I assume the fact that Mn(CO)3 is positively charged has nothing to do with it (it is a closed shell). I know that 3-21G and 6-31G are not good for transition metals, yet I got reasonable results using these (MOs and charge distribution). Does anyone have any ideas for how I can use ECPs (we are limited to about 1.2GB) or anything else to get these calculations to run (we do not yet have DFT). As an aside, I keep getting an error message when converting from cartesian coordinates to z-matrix. Has anyone else had this? sorry for bothering you and thank you in advance Michael Nolan Der Kobold hat gesprochen ****************************************************************************** Michael Nolan (nearly BSc.) Dublin City University (quantum chem.) 41 Woodview Chemistry + German Year 4 Lucan Co. Dublin Ireland / Republic of Ireland / ROI / Eire Email: Maiden@redbrick.dcu.ie ****************************************************************************** From howardp@syrres.com Wed Apr 30 11:40:14 1997 Received: from syrres.syrres.com for howardp@syrres.com by www.ccl.net (8.8.3/950822.1) id LAA07361; Wed, 30 Apr 1997 11:24:12 -0400 (EDT) Received: from syrres.com by syrres.syrres.com; Wed, 30 Apr 97 10:07 EST Message-Id: <3.0.32.19970430112439.006ef03c@syrres.com> X-Sender: howardp@syrres.com X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 30 Apr 1997 11:24:39 -0400 To: panc@isc.kyushu-u.ac.jp (Canping Pan), CHEMISTRY@www.ccl.net From: Phil Howard Subject: Re: CCL:help ClogP calculating Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 10:34 PM 4/28/97 +0900, Canping Pan wrote: >Hi there, > >Please help with some ClogP calculating problem. > >When I use ClogP to calculate some compounds, I missed some fragment >parameters. Now what and how can I do in order to make it usable? > >My error messages got are as follows: >---------------------------------- > >FRAGMENT | # 1 | --> ZNC(=NA)SA |MISSING | > .000 > >FRAGMENT | # 2 | --> ANC(OA)=Na |MISSING | > .000 > >FRAGMENT | # 2 | --> ZNC(=NA)OA |MISSING | > .000　 > > >(smiles for example: COc1ccccc1CNC2=NCCO2) Canping, I can't help you with the CLOGP missing fragment problem, but did calculate the Log P value with our LOGKOW program that does not have that problem. Phil Log Kow (estimated): 1.77 SMILES : COc1ccccc1CNC2=NCCO2 CHEM : MOL FOR: C11 H14 N2 O2 MOL WT : 206.25 -------+-----+--------------------------------------------+---------+-------- TYPE | NUM | LOGKOW FRAGMENT DESCRIPTION | COEFF | VALUE -------+-----+--------------------------------------------+---------+-------- Frag | 1 | -CH3 [aliphatic carbon] | 0.5473 | 0.5473 Frag | 3 | -CH2- [aliphatic carbon] | 0.4911 | 1.4733 Frag | 1 | C [aliphatic carbon - No H, not tert] | 0.9723 | 0.9723 Frag | 1 | -O- [oxygen, aliphatic attach] |-1.2566 | -1.2566 Frag | 1 | -NH- [aliphatic attach] |-1.4962 | -1.4962 Frag | 6 | Aromatic Carbon | 0.2940 | 1.7640 Frag | 1 | -O- [oxygen, one aromatic attach] |-0.4664 | -0.4664 Frag | 1 | -N=C [aliphatic attach] |-0.0010 | -0.0010 Const | | Equation Constant | | 0.2290 -------+-----+--------------------------------------------+---------+-------- Log Kow = 1.7657 Philip H. Howard, Ph.D. Phone: 315-426-3350 Environmental Sciences Center Fax: 315-426-3429 Syracuse Research Corporation Email: howardp@syrres.com Merrill Lane http://esc.syrres.com Syracuse, NY 13210 From shenkin@still3.chem.columbia.edu Wed Apr 30 18:39:52 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id RAA13717; Wed, 30 Apr 1997 17:44:24 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id RAA07971; Wed, 30 Apr 1997 17:43:00 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id RAA04597; Wed, 30 Apr 1997 17:42:50 -0400 From: "Peter Shenkin" Message-Id: <9704301742.ZM4595@still3.chem.columbia.edu> Date: Wed, 30 Apr 1997 17:42:50 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net, mmodlist@chem.iupui.edu Subject: Announcing MacroModel 6.0 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii MacroModel 6.0 has been released. Information is available at: http://www.columbia.edu/cu/chemistry/mmod/mmod.html MacroModel is a general-purpose molecular modeling package developed at Columbia University. We support several force fields and a variety of molecular-mechanics procedures. Here are a few features that are new in Version 6.0: Manuals supplied in HTML as well as PostScript and hard-copy form. HTML manuals can also be browsed at our WWW site. Support for some additional hardware options (newer 3D-graphics boards under AIX, better R10000 optimization for SGI). MacroModel (GUI): Visualization of normal modes. Interfaces to several new computational procedures. Enhancements to the atom-set language. BatchMin (computational engine): Low-mode conformational search method of Istvan Kolossvary. Fully frozen atoms. Faster GB/SA solvation calculations. Generate normal-mode movies for visualization. Xcluster (conformational cluster analysis): Average structures. Write out Average, Representative or Superimposed conformations for a single cluster (or all clusters) at any hierarchical clustering level. Some new interactive features in the visualization tools. Academic users may order using the on-line order form. Enjoy! -P. -- ************* "The past ain't what it used to be" (M. Reboul) ************* * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From ccl@www.ccl.net Tue Apr 22 00:37:53 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id XAA25355; Mon, 21 Apr 1997 23:50:49 -0400 (EDT) Received: from acheron.uwa.edu.au for mw@crystal.uwa.edu.au by bedrock.ccl.net (8.8.3/950822.1) id XAA15337; Mon, 21 Apr 1997 23:50:45 -0400 (EDT) Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by acheron.uwa.edu.au (8.8.2/8.8.0) with SMTP id LAA17425 for ; Tue, 22 Apr 1997 11:50:38 +0800 (WST) Received: from pack.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA22668; Tue, 22 Apr 1997 14:36:16 +0800 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9704220345.AA16043@pack.crystal.uwa.edu.au> Subject: H2O Geometry? To: CHEMISTRY@ccl.net Date: Tue, 22 Apr 97 11:45:19 WST Mailer: Elm [revision: 70.85] Dear Chemists, Could someone please help me with regard to isolated water geometry. I need the geometry of water molecule from gas phase electron diffraction, together with experimental errors. Also, the reference to the paper where this experiment was reported. Thank you very much. Magda Wajrak (mw@crystal.uwa.edu.au) ps. Could you please reply directly to me. From williams@bucknell.edu Tue Apr 22 20:38:04 1997 Received: from mail.bucknell.edu for williams@bucknell.edu by www.ccl.net (8.8.3/950822.1) id TAA03517; Tue, 22 Apr 1997 19:43:56 -0400 (EDT) Received: from coral.bucknell.edu by mail.bucknell.edu; (5.65v3.2/1.1.8.2/17Jul96-0109PM) id AA08262; Tue, 22 Apr 1997 19:43:45 -0400 Date: Tue, 22 Apr 1997 19:43:45 -0400 (EDT) From: Williams Brian W To: chemistry@www.ccl.net Subject: Help with an old version of AMPAC Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 501 I am using an old version of AMPAC available to me to carry out some simple calculations. I would like to try a C.I. calculation involving only singly excited configurations. The manual seems to imply that I can specify what configurations to consider using the key word "MICROS=" and specifying the configurations. The manual offers no examples using this commmand. Can anyone offer an example/explanation of how use this key word? Thanks. Brian Williams, Chemistry, Bucknell University From ccl@www.ccl.net Thu Apr 24 19:38:29 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id SAA17345; Thu, 24 Apr 1997 18:58:05 -0400 (EDT) Received: from rs6chem.chem.vill.edu for bausch@chem.vill.edu by bedrock.ccl.net (8.8.3/950822.1) id SAA16002; Thu, 24 Apr 1997 18:58:03 -0400 (EDT) Received: from [153.104.73.18] (bausch.chem.vill.edu [153.104.73.18]) by rs6chem.chem.vill.edu (8.8.5/8.8.5) with SMTP id TAA10657 for ; Thu, 24 Apr 1997 19:02:26 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 24 Apr 1997 17:58:21 -0500 To: chemistry@ccl.net From: bausch@chem.vill.edu (Joseph W. Bausch) Subject: Two questions My group has been using Gaussian 94 to optimize the geometries of a variety of polyboranes and heteroatom substituted polyboranes. We usually go up to the MP2(FULL)/6-31G* level and calculate the relative energies of isomeric systems at this level with a zero point energy correction from a HF/6-31G* level calculation. We have found a handful of systems where two tautomers exist on the potential energy surface differing only by ~ 1-3 kcal/mol. Most of these tautomeric pairs are relatively similar structurally except for the placement of a single hydrogen. Question 1: is the level of theory we are operating at accurate enough to characterize these energy differences as being significant? Question 2: if these energy differences are meaningful (or if we can do them at a level that is more reliable), is there a way to extract out from the calculations why one tautomer is more stable than the other? Thanks in advance, Joseph W. Bausch bausch@rs6chem.chem.vill.edu From ccl@www.ccl.net Fri Apr 25 10:38:39 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA20248; Fri, 25 Apr 1997 09:46:33 -0400 (EDT) Received: from kodakr.kodak.com for mckelvey@kodakr.kodak.com by bedrock.ccl.net (8.8.3/950822.1) id JAA27566; Fri, 25 Apr 1997 09:46:32 -0400 (EDT) Received: from mail.rl.kodak.com by kodakr.kodak.com with SMTP id AA14064 (5.67b/IDA-1.5 for ); Fri, 25 Apr 1997 09:44:43 -0400 Received: from mozart.rl.kodak.com by mail.rl.kodak.com (8.8.3/1.1.10.5/17Jan97-0515PM) id JAA18933; Fri, 25 Apr 1997 09:54:47 -0400 (EDT) Received: from stomper (stomper.rl.kodak.com [150.220.76.39]) by mozart.rl.kodak.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id JAA05562; Fri, 25 Apr 1997 09:46:18 -0400 Message-Id: <33606FDF.47BA@kodak.com> Date: Fri, 25 Apr 1997 09:48:31 +0100 From: John McKelvey Reply-To: mckelvey@kodakr.kodak.com Organization: Eastman Kodak Company X-Mailer: Mozilla 3.0 (WinNT; I) Mime-Version: 1.0 To: chemistry@ccl.net Cc: McKelvey@kodakr.kodak.com Subject: Pi System Valence Structures Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Netters: Does anyone have a suggestion for a code that is able to generate correct Kekule structures for extended conjugated systems that have several hetero atoms of varyious hybridisations? Will glady share the results of the inquiry. Thanks! John McKelvey McKelvey@Kodak.Com From ccl@www.ccl.net Mon Apr 28 11:59:39 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA15390; Mon, 28 Apr 1997 11:21:31 -0400 (EDT) Received: from origin.gig.usda.gov for srheller@gig.usda.gov by bedrock.ccl.net (8.8.3/950822.1) id LAA07545; Mon, 28 Apr 1997 11:21:13 -0400 (EDT) Received: by origin.gig.usda.gov (5.x/SMI-SVR4) id AA03192; Mon, 28 Apr 1997 11:14:44 -0400 Date: Mon, 28 Apr 1997 11:14:44 -0400 (EDT) From: "Stephen R. Heller" To: jcicshelp , chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu Subject: Software for review Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII April 28, 1997 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I have six (6) new software products. I am looking for some people who are willing to review these software products. In return for the review which is published in JCICS you get to keep the software or database. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. I have tried this approach for about the past four years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 30 April 1997 (Wednesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@GIG.USDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The packages I now have are: 1. The Merck Index (12 ed.) on CD-ROM (Windows version) from Chapman & Hall. (A Macintosh version should be along soon, so a second person may want to offer to review that one.) 2. Modelmaker 3.0 from Cherwell Scientific. This a simulation modeling software package for Windows 95 and Windows NT. This version includes powerful model development tools, such as sub- models and arrays of components and more model analysis capabilities, such as optimization using multiple datasets, and Simplex and Marquardt optimization. 3.AccuModel, version 1.10 for windows 95 and Windows NT, from MicroSimulations. This is a powerful desktop modeling package. 4. Alchemy 2000, version 1.1, modeling software from Tripos. The package on CD-ROM includes ChemPrint Pro, SciProtien, SciQSAR, SciPolymer, and SciLogP. 5. Kaleidagraph data analysis and graphing software from Synergy Software. This runs under Windows 95, NT and 3.11. 6. ProCite bibliographic reference manager software for Windows from RSI. Runs under Windows 3.1 or higher. Steve Heller, USDA, ARS, Plant Genome Project Bldg. 005, Room 337 Beltsville, MD 20705-2350 USA Phone: 301-504-6055 FAX: 301-504-6231 E-mail: srheller@gig.usda.gov WWW: www.hellers.com/steve