From owner-chemistry@ccl.net Tue Aug 6 06:15:48 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id FAA02529; Tue, 6 Aug 1996 05:24:39 -0400 (EDT) Received: from beba.cesnet.cz for strajbl@silicon.karlov.mff.cuni.cz by bedrock.ccl.net (8.7.5/950822.1) id FAA06162; Tue, 6 Aug 1996 05:24:36 -0400 (EDT) Received: from ns.karlov.mff.cuni.cz (ns.karlov.mff.cuni.cz [193.84.60.3]) by beba.cesnet.cz with SMTP id LAA08748 (8.6.12/IDA-1.6 for ); Tue, 6 Aug 1996 11:24:31 +0200 Received: from silicon.karlov.mff.cuni.cz by ns.karlov.mff.cuni.cz id aa19235; 6 Aug 96 11:13 MESZ Received: by silicon.karlov.mff.cuni.cz (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@ccl.net id KAA00903; Tue, 6 Aug 1996 10:59:00 -0700 Date: Tue, 6 Aug 1996 10:59:00 -0700 From: Marek Strajbl Message-Id: <199608061759.KAA00903@silicon.karlov.mff.cuni.cz> To: CHEMISTRY@ccl.net Subject: Merz-Kolman radius for K Hello all, I am looking for Merz-Kollman atomic radius for potassium (K). Does anybody help? Thanks Marek ------------------------------------ Marek Strajbl Institute of Physics, Prague, CZ e-mail: From tp@elptrs7.rug.ac.be Tue Aug 6 06:48:05 1996 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.7.5/950822.1) id FAA02537; Tue, 6 Aug 1996 05:28:03 -0400 (EDT) Received: by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA12788; Tue, 6 Aug 1996 11:29:31 +0200 Date: Tue, 6 Aug 1996 11:29:31 +0200 (DFT) From: "Park, Tae-Yun" To: Computational Chemistry List Subject: HELP!(URGENT): Serious errors in MOPAC93 & looking for solution. Message-Id: Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-1648267236-2078917053-839323771=:27164" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---1648267236-2078917053-839323771=:27164 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Previously, I have posted a bit serious errors in calculating the heat of formation(delta_Hf) for various carbenium ions in MOPAC93. So far, I've received several responses and most of them informed that, very probably, MOPAC93 is not accurate enough to calculate the heat of fomation differences between carbenium ions of same type(secondary, tertiary..) with the same number of carbon atoms. This makes me a bit panic, since I need the heat of formation data very urgently. Is it really true that MOPAC93 is not accurate enough fo delta_Hf calculation? If so, what else do I have to try ? Is there any other way in the field of computational chemistry which can produce the value of delta_Hf data as correct as possible for various gas-phase carbenium ions?? ANY suggestion/advice/information will be GREATLY appreaciated. Thanks in advance. Sincerely, Park, TAE-YUN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= State University of Ghent Laboratorium voor Petrochemische Techniek Krijgslaan 281, Blok S5 9000 Gent, Belgium TEL:+(32)-0(9)-264-4527 FAX:+(32)-0(9)-264-4999 e-mail: tp@elptrs7.rug.ac.be =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= P.S. I also attached my previous message on the errors in MOPAC. 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for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.5/950822.1) id HAA03035; Tue, 6 Aug 1996 07:48:33 -0400 (EDT) Received: from ccsc-17 (actually ccsc-17.brunel.ac.uk) by ceres.brunel.ac.uk with SMTP (PP); Tue, 6 Aug 1996 12:45:13 +0100 Date: Tue, 6 Aug 1996 12:45:10 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: carbocation reaction - response to IRC by MOPAC To: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Subject: CCL:M:Help!: IRC by mopac > I'm searching the structure of the transition state with > mopac for the reaction type, > > olefin + carbenium ion ---> (TS?) ---> carbenium ion (1) > > Actually I'm dealing with more than 100 reactions which have > the reaction type written in (1). Therefore, I tried with > other reaction, which contains more stable species, i.e., > > H > | H > H H H-C-H HCH H H H > H | H \ / H | | | | > HC-C-CH + C=C ---->(TS?)----> HC-C--C-C-C-H > H + H / \ H | | + | > H H H H H > secondary > propyl propene secondary 2-M > carbenium pentyle carbenium > > My problem is in the last step. When I do the IRC calculation > and try to look at the result structure with "molden" software, > it gives exactly same as the structure of TS I input. > > I wonder if (i) my TS is not correct, or (ii) the IRC calculation > doesn't give the molecular structure result from the calculation > so that molden only edit the structure I input. In the latter > case, however, I don't know how to edit the molecluar structure > generated by IRC calculation. > > Could anyone PLEASE help me how to confirm my TS structure by IRC? > I have tried the calculation using MOPAC93 and it works perfectly. I used my program Re_View to visualize both the negative frequency vibration of the T.S. and the final reaction profile (which was automatically generated from the MOPAC outputs using another of my programs IRC_CONV). The simulation has been added to my database of chemical simulations able to be viewed using my program Re_View. The URL for the program is: http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm and the data is on URL: http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/addreact.htm /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University From tp@elptrs7.rug.ac.be Tue Aug 6 09:15:58 1996 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.7.5/950822.1) id IAA03175; Tue, 6 Aug 1996 08:19:06 -0400 (EDT) Received: by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA23126; Tue, 6 Aug 1996 14:20:30 +0200 Date: Tue, 6 Aug 1996 14:20:30 +0200 (DFT) From: "Park, Tae-Yun" To: Computational Chemistry List Subject: (URGENT)HELP!: Serious error in MOPAC93-looking for solution Message-Id: Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-1648267236-2078917053-839323771=:27164" Content-Id: This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---1648267236-2078917053-839323771=:27164 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: ********************************************************************** I'm sending this message more than one time since my previous try to send this message to CCL was not successful and returned with the subject "Mail Failure". Please execuse me if you have received this message twice. ********************************************************************** Dear all, Previously, I have posted a bit serious errors in calculating the heat of formation(delta_Hf) for various carbenium ions in MOPAC93. So far, I've received several responses and most of them informed that, very probably, MOPAC93 is not accurate enough to calculate the heat of fomation differences between carbenium ions of same type(secondary, tertiary..) with the same number of carbon atoms. This makes me a bit panic, since I need the heat of formation data very urgently. Is it really true that MOPAC93 is not accurate enough fo delta_Hf calculation? If so, what else do I have to try ? Is there any other way in the field of computational chemistry which can produce the value of delta_Hf data as correct as possible for various gas-phase carbenium ions?? ANY suggestion/advice/information will be GREATLY appreaciated. Thanks in advance. Sincerely, Park, TAE-YUN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= State University of Ghent Laboratorium voor Petrochemische Techniek Krijgslaan 281, Blok S5 9000 Gent, Belgium TEL:+(32)-0(9)-264-4527 FAX:+(32)-0(9)-264-4999 e-mail: tp@elptrs7.rug.ac.be =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= P.S. I also attached my previous message on the errors in MOPAC. Please refer to this message if you didn't receive it previously. ====================================================================== Dear all, I've been used MOPAC93 for calculating delta_Hf(Heat of formation) for many carbenium ions in gas-phase, and I found very strange trends of these values today. Comparing the values of heat of formation for various primary, secondary, and tertiary carbenium ions, I've got a reasonable results, i.e, the heat of formation values of primary carbenium ions are greater than those of secondary carbenium ions, and the values of secondary carbenuim ions are greater than those of tertiary carbenium ions, etc. However, within secondary or tertiary carbenium ions with the same number of carbon atom, I saw the values are on opposit than I expect. Please consider the following carbenium ions: + (a) C-C-C-C-C-C [ H9C4-C(+)(CH3)2 ] | C C | + (b) C-C-C-C [ (H3C)3C-C(+)(CH3)2 ] | | C C Both are tertiary carbenium ions with carbon number of 7. According to literature, the second carbenium ion (b) should be more stable than the first one (a) due to the stablization by the branched carbon atom on the alfa-positioned carbon atom that is connected to the (+)-charged carbon atom. But the results of MOPAC calculation for heat of formation for both carbenium ions are, (a) HEAT OF FORMATION = 151.93056 KCAL (b) HEAT OF FORMATION = 160.04209 KCAL which means that the first carbenium ion is more stable than the second one! What happen?? Even I have many calculated results like this, which shows exactly the opposit trend than I expect. One of them is, + C-C-C-C-C | HEAT OF FORMATION = 160.35787 KCAL C C | C-C-C-C + | HEAT OF FORMATION = 162.62280 KCAL C The keywords I used for the calculation of heat of formation are, "SYMMETRY CHARGE=1 AM1 GEO-OK EF PRECISE". Did I make a mistake in using keywords or in somewhere else? If so, how can I get an accurate and reliable results in MOPAC?? If not, does it mean that MOPAC is not accurate enough to predict the heat of formation values within same type of carbenium ions with the same carbon number? I attached my input data files of the two carbenium ions (a) and (b) written above for MOPAC calculation. PLEASE inform me of ANY suggestions/advice on this strange values, if you have any idea on this problem. Thank you VERY MUCH in advance. -------------------------------------------------------------- Input data for carbenium ions (a) and (b) -------------------------------------------------------------- SYMMETRY CHARGE=1 AM1 GEO-OK EF PRECISE r7-8.dat C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 1.523987 1 0.000000 0 0.000000 0 1 0 0 H 1.112930 1 109.468369 1 0.000000 0 1 2 0 H 1.112946 1 109.470108 1 -119.422729 1 1 2 3 H 1.112991 1 109.470108 1 119.424484 1 1 2 3 C 1.523926 1 119.999756 1 -119.356293 1 2 1 3 C 1.523926 1 120.001495 1 61.217728 1 2 1 3 C 1.522888 1 109.475357 1 179.999634 1 7 2 1 H 1.112869 1 109.471863 1 60.070694 1 7 2 1 H 1.112946 1 109.470108 1 -60.074188 1 7 2 1 C 1.522980 1 109.499832 1 179.999634 1 8 7 2 H 1.112808 1 109.405411 1 60.088181 1 8 7 2 H 1.112869 1 109.403671 1 -60.093414 1 8 7 2 C 1.522980 1 109.499832 1 -179.999634 1 11 8 7 H 1.112991 1 109.408920 1 60.095169 1 11 8 7 H 1.112991 1 109.410660 1 -60.093414 1 11 8 7 H 1.112976 1 110.001663 1 179.999634 1 14 11 8 H 1.112976 1 109.999924 1 59.922073 1 14 11 8 H 1.112976 1 110.001663 1 -59.920319 1 14 11 8 H 1.112991 1 109.470108 1 -179.999634 1 6 2 1 H 1.112930 1 109.471863 1 60.579514 1 6 2 1 H 1.112946 1 109.473618 1 -60.577759 1 6 2 1 ----------------------------------------------------------------- SYMMETRY CHARGE=1 AM1 GEO-OK EF PRECISE r7-20.dat C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 1.524002 1 0.000000 0 0.000000 0 1 0 0 H 1.112808 1 109.464874 1 0.000000 0 1 2 0 H 1.112839 1 109.466614 1 -119.419235 1 1 2 3 H 1.112808 1 109.464874 1 119.424484 1 1 2 3 C 1.523972 1 120.001495 1 179.162949 1 2 1 3 C 1.523987 1 120.001495 1 -1.379593 1 2 1 3 C 1.522964 1 109.471863 1 -179.999634 1 7 2 1 C 1.522995 1 109.471863 1 60.000748 1 7 2 1 C 1.522995 1 109.471863 1 -59.999008 1 7 2 1 H 1.112915 1 110.006912 1 179.999634 1 8 7 2 H 1.112976 1 109.998169 1 59.918564 1 8 7 2 H 1.112976 1 109.996414 1 -59.920319 1 8 7 2 H 1.112946 1 109.470108 1 -179.999634 1 6 2 1 H 1.112946 1 109.470108 1 60.576019 1 6 2 1 H 1.112946 1 109.470108 1 -60.577759 1 6 2 1 H 1.112976 1 109.998169 1 179.999634 1 10 7 2 H 1.112976 1 109.998169 1 59.920319 1 10 7 2 H 1.112961 1 109.998169 1 -59.923813 1 10 7 2 H 1.112991 1 109.999924 1 -179.999634 1 9 7 2 H 1.112961 1 109.999924 1 59.923813 1 9 7 2 H 1.112991 1 109.999924 1 -59.922073 1 9 7 2 ---------------------------------------------------------------- ====================================================================== ---1648267236-2078917053-839323771=:27164-- From tj@eecs.uic.edu Tue Aug 6 12:15:53 1996 Received: from mail.eecs.uic.edu for tj@eecs.uic.edu by www.ccl.net (8.7.5/950822.1) id LAA04619; Tue, 6 Aug 1996 11:40:36 -0400 (EDT) Received: from bert.eecs.uic.edu (tj@bert.eecs.uic.edu [128.248.166.23]) by mail.eecs.uic.edu (8.7.5/8.7.5) with ESMTP id KAA22370 for ; Tue, 6 Aug 1996 10:40:45 -0500 (CDT) From: tj ODonnell Received: (tj@localhost) by bert.eecs.uic.edu (8.6.10/8.6.10) id KAA14163 for chemistry@www.ccl.net; Tue, 6 Aug 1996 10:40:56 -0500 Message-Id: <199608061540.KAA14163@bert.eecs.uic.edu> Subject: SMILES To: chemistry@www.ccl.net (CCL) Date: Tue, 6 Aug 1996 10:40:56 -0500 (CDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Re: Request for SMILES help I'd suggest looking at http://www.daylight.com/dayhtml/smiles/ for background, tutorial, etc. about SMILES. It comes right >from the horse's mouth, so to speak. TJ -- *---------------------------------------------------------------------* * If you need a quote: http://www.eecs.uic.edu/~tj/quotes.html * *---------------------------------------------------------------------* | Dr. TJ O'Donnell > tj@eecs.uic.edu < http://www.eecs.uic.edu/~tj/ | *---------------------------------------------------------------------* From irikura@ENH.NIST.GOV Tue Aug 6 12:24:58 1996 Received: from ENH.NIST.GOV for irikura@ENH.NIST.GOV by www.ccl.net (8.7.5/950822.1) id LAA04666; Tue, 6 Aug 1996 11:54:46 -0400 (EDT) Received: from h178075 (bratsche.nist.gov) by ENH.NIST.GOV (PMDF V5.0-5 #10952) id <01I7YDOJ6KSW00RXUY@ENH.NIST.GOV> for chemistry@www.ccl.net; Tue, 06 Aug 1996 11:56:51 -0400 (EDT) Date: Tue, 06 Aug 1996 11:55:09 -0400 From: Karl Irikura Subject: Re: CCL:M:(URGENT)HELP!: Serious error in MOPAC93-looking for solution X-Sender: irikura@enh.nist.gov To: chemistry@www.ccl.net Message-id: <01I7YDOJ86O200RXUY@ENH.NIST.GOV> MIME-version: 1.0 X-Mailer: Windows Eudora Version 2.1.1 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Try empirical estimation methods. Some are described in Lias, S. G.; Bartmess, J. E.; Liebman, J. F.; Holmes, J. L.; Levin, R. D.; Mallard, W. G. J. Phys. Chem. Ref. Data 1988, 17, Suppl. 1. "Gas-Phase Ion and Neutral Thermochemistry." See in particular section 2.5 ("Trends in the Data") and subsection 2.5.1 ("Estimation Schemes for Heats of Formation of Cations"). Section 4.4 ("Estimated Heats of Formation") may also be helpful. The book can at least provide several leads. Good luck! Karl Irikura >Is it really true that MOPAC93 is not accurate enough fo delta_Hf >calculation? If so, what else do I have to try ? Is there any other >way in the field of computational chemistry which can produce the >value of delta_Hf data as correct as possible for various gas-phase >carbenium ions?? > >ANY suggestion/advice/information will be GREATLY appreaciated. > >Thanks in advance. > > > Sincerely, > > Park, TAE-YUN >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >State University of Ghent >Laboratorium voor Petrochemische Techniek >Krijgslaan 281, Blok S5 >9000 Gent, Belgium >TEL:+(32)-0(9)-264-4527 >FAX:+(32)-0(9)-264-4999 >e-mail: tp@elptrs7.rug.ac.be >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > ---------------------------------------------- Dr. Karl K. Irikura Physical and Chemical Properties Division National Institute of Standards and Technology Gaithersburg, MD 20899 voice: 301-975-2510 fax: 301-975-3670 e-mail: irikura@enh.nist.gov ---------------------------------------------- From tp@elptrs7.rug.ac.be Tue Aug 6 13:15:55 1996 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.7.5/950822.1) id MAA04871; Tue, 6 Aug 1996 12:41:34 -0400 (EDT) Received: by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA03090; Tue, 6 Aug 1996 18:42:33 +0200 Date: Tue, 6 Aug 1996 18:42:33 +0200 (DFT) From: "Park, Tae-Yun" To: Computational Chemistry List , nae00264@niftyserve.or.jp, jstewart@fai.com Subject: Serious errors in MOPAC93 (2) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Today I found the same problem of MOPAC in calculating heat of formation(Delta_Hf) for alkanes as that for carbenium ions. I found that according to MOPAC93, the following two alkanes have the Delta_Hf values (by AM1 parameter), C-C-C-C-C-C-C-C HEAT OF FORMATION = -58.62036 KCAL C C C-C-C-C-C HEAT OF FORMATION = -46.93710 KCAL C which means that normal alkane is more stable than branched alkane; nonsense! If I didn't make any mistake in preparing input data for MOPAC, I believe the Delta_Hf data produced by MOPAC can not be used in any further calculation. Does anyone have ANY opinion on this?? Thanks in advance. Sincerely, Park, TAE-YUN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= State University of Ghent Laboratorium voor Petrochemische Techniek Krijgslaan 281, Blok S5 9000 Gent, Belgium TEL:+(32)-0(9)-264-4527 FAX:+(32)-0(9)-264-4999 e-mail: tp@elptrs7.rug.ac.be =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From gford@post.smu.edu Tue Aug 6 13:21:24 1996 Received: from post.cis.smu.edu for gford@post.smu.edu by www.ccl.net (8.7.5/950822.1) id MAA04808; Tue, 6 Aug 1996 12:26:23 -0400 (EDT) Received: by post.cis.smu.edu (/\==/\ Smail3.1.28.1 #28.3) id ; Tue, 6 Aug 96 11:26 CDT Message-Id: Date: Tue, 6 Aug 96 11:26 CDT From: "George P. Ford" Reply-To: "George P. Ford" To: CHEMISTRY@www.ccl.net Subject: Carbenium ion heats of formation. "Park, Tae-Yun" writes: > > Is it really true that MOPAC93 is not accurate enough fo delta_Hf > calculation? If so, what else do I have to try ? Is there any other > way in the field of computational chemistry which can produce the > value of delta_Hf data as correct as possible for various gas-phase > carbenium ions?? > Dear Tae-Yun: How accurate do you need? The AM1 heats of formation for the isomeric C5 carbenium ions you cite differ by ca 2 kcal/mole. The experimental difference is about the same amount in the opposite direction, i.e. a relative error of about 4 kcal/mole in the computed heats of formation. One should probably anticipate errors of at least this magnitude with any of the methods in MOPAC93. Part of the problem has to do with the fact that the relative stabilities of the isomeric carbenium ions depend on a delicate balance of intramolecular interactions. Getting these internal balances right is often the achilles' heel of the semiempirical methods. In the present context the failure of AM1 is probably related to its failure to fully account for the greater hyperconjugative ability of the more highly branched substituents. If so, it would fail to fully reproduce the tendency of this effect to offset the higher non-bonded repulsions present. As is well known properly accounting for non-bonded interactions has been one of the major stumbling blocks in the development of semiempirical theories. Perhaps less well known is the fact that these methods generally underestimate conjugative, and especially hyperconjugative, interactions. For the levels of accuracy you appear to be seeking you will have to go to more elaborate, and considerably more expensive, DFT, or ab initio methods. ============================================================================ George P. Ford | email: gford@smu.edu Department of Chemistry | web: http://www.smu.edu/~gford/ Southern Methodist University | telephone: (214)768-2479 Dallas, Texas 75275 | fax: (214)768-4089 ============================================================================