From armel@fluo.univ-lemans.fr Wed Jul 24 07:16:06 1996 Received: from fluo.univ-lemans.fr for armel@fluo.univ-lemans.fr by www.ccl.net (8.7.5/950822.1) id GAA26599; Wed, 24 Jul 1996 06:38:22 -0400 (EDT) Received: from pcb4122.univ-lemans.fr by fluo.univ-lemans.fr (AIX 3.2/UCB 5.64/4.03) id AA16332; Wed, 24 Jul 1996 11:27:09 +0200 Message-Id: <1.5.4.32.19960724103819.00665690@fluo.univ-lemans.fr> X-Sender: armel@fluo.univ-lemans.fr (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 24 Jul 1996 12:38:19 +0200 To: chemistry@www.ccl.net From: Armel Le Bail Subject: Re: CCL:Crystallographic Software Status: RO Content-Length: 834 Thanks to Oxford-Cryosystems, however the demo version seems to offer nothing about VRML. If I am not wrong, can we have an URL where to find some .wrl files produced by Crystallographica ? >Crystallographica runs on IBM PC compatible machines running Windows 3.1 = >or 95. Briefly, its main features are: ...... >* Structures may be saved in VRML format, providing stunning graphics = >on any computer with a VRML Viewer. ..... >More information, including a down-loadable demonstration version, is = >available at our Web page (http://www.demon.co.uk/oxcryo/cgraph.html). Armel Le Bail, Laboratoire des Fluorures URA CNRS 449 Faculte des Sciences, Universite du Maine, F-72017 Le Mans, France Tel: (33) 43 83 33 47 Fax: (33) 43 83 35 06 Email: armel@fluo.univ-lemans.fr Home Page: http://fluo.univ-lemans.fr:8001/ From MAILER-DAEMON@www.ccl.net Mon Jul 22 11:15:40 1996 Received: from mail-relay-BLR.ernet.in for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.7.5/950822.1) id KAA15659; Mon, 22 Jul 1996 10:21:56 -0400 (EDT) Received: from postoffice.iisc.ernet.in (twisha.ece.iisc.ernet.in [144.16.64.4]) by mail-relay-BLR.ernet.in (8.6.11/8.6.9) with ESMTP id TAA20685 for ; Mon, 22 Jul 1996 19:01:02 +0530 Received: by postoffice.iisc.ernet.in (SMI-8.6/SMI-SVR4) id TAA11580; Mon, 22 Jul 1996 19:54:20 -0500 Date: Mon, 22 Jul 1996 19:54:20 -0500 From: ipcakc@Postoffice (Dr.A.K.Chandra) Message-Id: <199607230054.TAA11580@postoffice.iisc.ernet.in> To: CHEMISTRY@www.ccl.net Subject: G94: G94/DFT/Tr.State Problem Status: RO Content-Length: 10490 Dear Netters, I found some funny problem using B3LYP/6-31G** keyword for the following transition state. It is a H-transfer process between two Cl atoms forming a symmetric transition state Cl---------H---------Cl with equal bond lengths. The Geometry optimisation leads to a perfectly symmetric structure (B3lyp/6-31G**/UHF). The system is a doublet and is a radical-molecule reaction. Now, the fun is that the eigenvalue corresponding to the imaginary frequency at the saddle point is ONLY ONE. But, if the frequencies are seen, there are 3 IMAGINARY FREQUENCIES. The Keyword I have used for optimisation of transition state is OPT=(TS,EF,CALCALL), hence frequency calculation is done along with the optimisation. The output is attached below. Can anyone help me in interpreting this result? Sincerely, V. Sreedhara Rao. -------------------------------------------- V. Sreedhara Rao Department of IPC, Indian Institute of Science, BANGALORE - 560 012. INDIA. E-mail : ipcakc@postoffice.iisc.ernet.in -------------------------------------------- ------------------------The output follows ---------------------- ********************************************** Gaussian 94: IBM-RS6000-G94RevC.2 5-Aug-1995 12-Jul-1996 ********************************************** ----------------------------------------------------------- #uhf 6-31g** opt=(ef,ts,calcall) b3lyp pop=full den=current ----------------------------------------------------------- EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF- ------------------------------------------------------------------------ Z-MATRIX (ANGSTROMS AND DEGREES) CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J ------------------------------------------------------------------------ 1 1 Cl 2 2 H 1 1.497666( 1) 3 X 2 1.000000( 2) 1 90.000( 4) 4 3 Cl 2 1.497673( 3) 3 90.000( 5) 1 180.000( 6) 0 ------------------------------------------------------------------------ SCF Done: E(UB+HF-LYP) = -920.925868655 A.U. after 13 cycles Convg = .7439D-08 -V/T = 2.0030 S**2 = .7571 Annihilation of the first spin contaminant: S**2 before annihilation .7571, after .7500 EIGENVECTOR FOLLOWING TRANSITION STATE SEARCH ANALYTICAL SECOND DERIVATIVES USED ITERATION 3 EIGENVECTORS AND EIGENVALUES 1 2 EIGENVALUES -- -.02252 .16489 1 R1 -.70710 .70711 2 R2 .70711 .70710 TS SEARCH. TAKING P-RFO STEP SEARCHING FOR LAMDA THAT MAXIMIZES ALONG THE LOWEST MODE VALUE TAKEN LAMDA= .00000000 SEARCHING FOR LAMDA THAT MINIMIZES ALONG ALL OTHER MODES VALUE TAKEN LAMDA= .00000000 STEP TAKEN. STEPSIZE IS .000014 CURRENT PARAMETER VALUES (INTERNAL COORDINATES) I X GRADIENT DISPLACEMENT NEWX 1 2.830179 -.000001 .000014 2.830193 2 2.830192 -.000001 .000001 2.830193 ITEM VALUE THRESHOLD CONVERGED? MAXIMUM FORCE .000001 .000450 YES RMS FORCE .000001 .000300 YES MAXIMUM DISPLACEMENT .000014 .001800 YES RMS DISPLACEMENT .000010 .001200 YES ************************************************* ** CONVERGENCE CRITERIA APPARENTLY SATISFIED ** ************************************************* ---------------------------- ! Optimized Parameters ! ! (Angstroms and Degrees) ! ---------------------- ---------------------- ! Name Value Derivative information (Atomic Units) ! ------------------------------------------------------------------------ ! R1 1.4977 -DE/DX = 0. ! ! R2 1.4977 -DE/DX = 0. ! ------------------------------------------------------------------------ PREDICTED CHANGE IN ENERGY .000000 EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF-EF- ------------------------------------------------------------------------ Z-MATRIX (ANGSTROMS AND DEGREES) CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J ------------------------------------------------------------------------ 1 1 Cl 2 2 H 1 1.497666( 1) 3 X 2 1.000000( 2) 1 90.000( 4) 4 3 Cl 2 1.497673( 3) 3 90.000( 5) 1 180.000( 6) 0 ------------------------------------------------------------------------ Exact polarizability: 14.928 .000 14.928 .000 .000 53.183 Approx polarizability: 15.126 .000 15.126 .000 .000 79.255 Rotating electric field derivatives to standard orientation. Rotating nuclear coordinate derivatives to standard orientation. Full mass-weighted force constant matrix: Low frequencies ----1517.7789-1517.7789-1094.5308 -.0078 -.0064 -.0064 Low frequencies --- 7.4380 7.4380 352.9932 ****** 3 imaginary frequencies (negative signs) ****** Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 PI PI SG Frequencies -- -1517.7789 -1517.7789 -1094.5308 Red. masses -- 1.0219 1.0219 1.0219 Frc consts -- 1.3870 1.3870 .7213 IR Inten -- 460.3973 460.3973 446.2129 Raman Activ -- .0000 .0000 .0000 Depolar -- .0000 .0000 .0000 Atom AN X Y Z X Y Z X Y Z 1 17 -.01 .00 .00 .00 -.01 .00 .00 .00 -.01 2 1 1.00 .00 .00 .00 1.00 .00 .00 .00 1.00 3 17 -.01 .00 .00 .00 -.01 .00 .00 .00 -.01 4 SG Frequencies -- 352.9932 Red. masses -- 34.9689 Frc consts -- 2.5672 IR Inten -- .0000 Raman Activ -- .0000 Depolar -- .0000 Atom AN X Y Z 1 17 .00 .00 .71 2 1 .00 .00 .00 3 17 .00 .00 -.71 ------------------- - Thermochemistry - ------------------- Temperature 298.150 Kelvin. Pressure 1.00000 Atm. Atom 1 has atomic number 17 and mass 34.96885 Atom 2 has atomic number 1 and mass 1.00783 Atom 3 has atomic number 17 and mass 34.96885 Molecular mass: 70.94553 amu. Principle axes and moments of inertia in atomic units: 1 2 3 EIGENVALUES -- .00000 560.19741 560.19741 X .00000 .00000 1.00000 Y .00000 1.00000 .00000 Z 1.00000 .00000 .00000 THIS MOLECULE IS A PROLATE SYMMETRIC TOP. ROTATIONAL SYMMETRY NUMBER 1. WARNING-- ASSUMPTION OF CLASSICAL BEHAVIOR FOR ROTATION MAY CAUSE SIGNIFICANT ERROR ROTATIONAL TEMPERATURE (KELVIN) .15461 ROTATIONAL CONSTANT (GHZ) 3.221616 3 IMAGINARY FREQUENCIES IGNORED. Zero-point vibrational energy 2111.4 (Joules/Mol) .50463 (Kcal/Mol) WARNING-- EXPLICIT CONSIDERATION OF 1 DEGREES OF FREEDOM AS VIBRATIONS MAY CAUSE SIGNIFICANT ERROR VIBRATIONAL TEMPERATURES: 507.88 (KELVIN) Zero-point correction= .000804 (Hartree/Particle) Thermal correction to Energy= .003523 Thermal correction to Enthalpy= .004467 Thermal correction to Gibbs Free Energy= -.023207 Sum of electronic and zero-point Energies= -920.925064 Sum of electronic and thermal Energies= -920.922346 Sum of electronic and thermal Enthalpies= -920.921402 Sum of electronic and thermal Free Energies= -920.949076 E CV S KCAL/MOL CAL/MOL-KELVIN CAL/MOL-KELVIN TOTAL 2.210 6.537 58.245 ELECTRONIC .000 .000 1.377 TRANSLATIONAL .889 2.981 38.695 ROTATIONAL .592 1.987 17.019 VIBRATIONAL .729 1.569 1.153 VIBRATION 1 .729 1.569 1.153 Q LOG10(Q) LN(Q) TOTAL BOT .472556D+11 10.674453 24.377872 TOTAL V=0 .110751D+12 11.044347 25.229583 VIB (BOT) .521657D+00 -.282615 -.650746 VIB (BOT) 1 .521657D+00 -.282615 -.650746 VIB (V=0) .122258D+01 .087278 .200965 VIB (V=0) 1 .122258D+01 .087278 .200965 ELECTRONIC .200000D+01 .301030 .693147 TRANSLATIONAL .234881D+08 7.370848 16.972005 ROTATIONAL .192837D+04 3.285191 7.564431 Internal Forces: Max .000001377 RMS .000000714 1\1\GINC-IBM580_7\Freq\UB3LYP\6-31G(d,p)\Cl2H1(2)\IPCVSR\12-Jul-1996\1 \\#UHF 6-31G** OPT=(EF,TS,CALCALL) B3LYP POP=FULL DEN=CURRENT\\clhcl-1 .6 ang.\\0,2\Cl\H,1,R1\X,2,1.,1,90.\Cl,2,R2,3,90.,1,180.,0\\R1=1.49766 611\R2=1.49767315\\Version=IBM-RS6000-G94RevC.2\State=2-SG\HF=-920.925 8687\S2=0.757\S2-1=0.\S2A=0.75\RMSD=7.439e-09\RMSF=5.912e-07\Dipole=0. ,0.,0.0000045\DipoleDeriv=-0.3424881,0.,0.,0.,-0.3424881,0.,0.,0.,0.33 71667,0.684973,0.,0.,0.,0.684973,0.,0.,0.,-0.6743387,-0.3424849,0.,0., 0.,-0.3424849,0.,0.,0.,0.3371721\Polar=14.9278148,0.,14.9278148,0.,0., 53.1825654\PG=C*V [C*(Cl1H1Cl1)]\NImag=3\\-0.02161655,0.,-0.02161655,0 .,0.,0.07118866,0.04330625,0.,0.,-0.08661238,0.,0.04330625,0.,0.,-0.08 From Annik.VanKeer@chem.kuleuven.ac.beSat Jul 27 11:24:34 1996 Date: Fri, 12 Jul 1996 17:12:21 +0100 (NFT) From: Van Keer Annik To: "Park, Tae-Yun" Subject: transition state Status: RO Content-Length: 12566 On Wed, 10 Jul 1996, Park, Tae-Yun wrote: > Dear all, > > I've received a lot of helpful messages from many CCLers, > concerning my earlier questions on how to get the structure > of transition state of the reaction, > > > > H H H H H H > | \ / | | | > H-C(+) + C=C ---->(TS?)----> H-C-C-C(+) > | / \ | | | > H H H H H H > > gas-phase gas-phase > methyl ethylene primary propyl > carbenium ion carbenium ion > > > ************************************************************** > > SADDLE DENSITY GRAPH XYZ CHARGE=1 PRECISE > Me--->p methylation activated complex > > C 0.000000 0 0.000000 0 0.000000 0 0 0 0 > C 8.471619 1 0.000000 0 0.000000 0 1 0 0 > C 1.325912 1 162.328125 1 0.000000 0 2 1 0 > H 1.108597 1 65.592545 1 -150.347214 1 1 2 3 > H 1.113968 1 120.001495 1 -151.401566 1 1 4 2 > H 1.108612 1 119.996246 1 -179.367538 1 1 4 5 > H 1.098282 1 122.722214 1 57.159393 1 2 3 1 > H 1.098328 1 122.715210 1 179.999634 1 2 3 7 > H 1.098267 1 122.715210 1 -0.316483 1 3 2 7 > H 1.098206 1 122.715210 1 -179.684021 1 3 2 7 > 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 > C .000000 0 .000000 0 .000000 0 0 0 0 > C 1.506600 1 .000000 0 .000000 0 1 0 0 > C 1.418947 1 116.688263 1 .000000 0 2 1 0 > H 1.118077 1 111.116249 1 -59.952415 1 1 2 3 > H 1.119762 1 109.783371 1 -179.449097 1 1 2 3 > H 1.118210 1 111.069687 1 61.123405 1 1 2 3 > H 1.150598 1 110.672989 1 174.990601 1 2 1 4 > H 1.150955 1 110.650314 1 64.874481 1 2 1 4 > H 1.109621 1 121.247902 1 -179.729874 1 3 2 1 > H 1.110257 1 121.556961 1 .300391 1 3 2 1 > 0 .000000 0 .000000 0 .000000 0 0 0 0 > , > > Hello Park, I donnot know if I can help you with your Mopac version because I am a Gaussian user. Firstly I do not understand why the bond between C1 and C2 is so large: 8.47 A? If you take 3 A or 3.5 A as distance between these bonds than you also have two reactants without any interaction. I guess that any change in geometry than will earlier lead to a transition state for which I guess that the initially formed CC bond is about 1.8 A. Secondly, I do not know which optimization procedure you are using, but as I see two inputs one for the reactants and another one for the products I guess your program is looking for a TS via a LST path. In this case you have to identify two identically z-matrices, with of course different parameters, which you didn't. Thirdly, it is possible that the addition of CH3(+) to C2H4 is a barrier free proces. I know that the addition of triplet CH2 to C2H4 is barrierfree. I hope that you can use my suggestions. Good luck, Annik ****************************************************************** Annik Van Keer Katholieke Universiteit Leuven Laboratorium voor Quantumchemie Celestijnenlaan 200F 3001 Heverlee, Belgium Tel:00-32-16-327384 Fax:00-32-16-327992 E-mail:annik.vankeer@chem.kuleuven.ac.be ------------------------------------------------------- PART V Subject: Help!: IRC by mopac ------------------------------------------------------- ####################(questions)######################## Dear all, I'm searching the structure of the transition state with mopac for the reaction type, olefin + carbenium ion ---> (TS?) ---> carbenium ion (1) My previous try for the reaction, H H H H H H | \ / | | | H-C(+) + C=C ---->(TS?)----> H-C-C-C(+) | / \ | | | H H H H H H gas-phase gas-phase methyl ethylene primary propyl carbenium ion carbenium ion has been found that there is no transition state, thanks to great help from many CCLers, since the gas-phase methyl carbenium ion is too unstable. 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 Searching the TS in this reaction, I followed the suggestion by many CCLers, i.e., try to get the TS structure by the following steps instead of using SADDLE calculation: 1. Try the reacion path calculation in mopac and save the structure that contains the highest energy level. 2. Refine the structure at highest energy level with key word, NLLSQ, or SIGMA, or TS. 3. FORCE calculation with the refined structure to check if there is one and only one negative frequecy value. 4. Do IRC(=1 and -1) calculation to check if the refined TS gives the reactants and product. My result is that until step 3, everything seems OK. Refinning the TS by NLLSQ/SIGMA/TS gives no significant change of the TS that obtained from step 1, probably because I used the key word PRECISE in step 1. The FORCE calculation showed that the refined structure contains only one frequency values. 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 enclosed the input/result file at the end of this message. Thank you very much in advance. Sincerely, Park, TAE-YUN Data Files for the 4 steps. Please note that the result file of step 1 is the input file for step 2... etc. ---------------------------------------------------------------- Step 1 input file: CHARGE=1 PRECISE GRAPH DENSITY r3_s-o3.dat C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 1.437805 1 0.000000 0 0.000000 0 1 0 0 C 4.501968 -1 96.018692 1 0.000000 0 1 2 0 C 1.331116 1 87.080215 1 -155.227356 1 3 1 2 C 1.476334 1 124.262665 1 -135.173477 1 4 3 1 C 1.437424 1 123.306213 1 133.821869 1 1 2 3 H 1.135651 1 110.106583 1 123.092896 1 2 1 6 H 1.120895 1 114.528610 1 0.000000 1 2 1 6 H 1.135742 1 110.066360 1 -123.042191 1 2 1 6 H 1.115219 1 118.018661 1 -56.365555 1 1 2 7 H 1.097427 1 122.281586 1 -179.999634 1 3 4 5 H 1.097809 1 122.792145 1 0.000000 1 3 4 5 H 1.103470 1 120.865265 1 0.000000 1 4 3 11 H 1.118958 1 110.075104 1 -120.477097 1 5 4 3 H 1.119080 1 110.076859 1 120.510315 1 5 4 3 H 1.117584 1 111.867340 1 0.000000 1 5 4 3 H 1.121948 1 113.719040 1 -179.999634 1 6 1 2 H 1.134903 1 110.648621 1 57.360474 1 6 1 2 H 1.134933 1 110.636383 1 -57.367462 1 6 1 2 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 4.0 3.5 3.0 2.8 2.6 2.5 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.55 ---------------------------------------------------------------- Step 2 input file(for NLLSQ): NLLSQ CHARGE=1 PRECISE DENSITY GRAPH Optimizing ts C .000000 0 .000000 0 .000000 0 0 0 0 C 1.493971 1 .000000 0 .000000 0 1 0 0 C 2.400000 1 99.829562 1 .000000 0 1 2 0 C 1.366739 1 107.774987 1 -156.603212 1 3 1 2 C 1.495494 1 127.295132 1 -95.474920 1 4 3 1 C 1.493103 1 122.565420 1 111.465448 1 1 2 3 H 1.108922 1 112.541937 1 169.169618 1 2 1 6 H 1.109391 1 113.333661 1 45.130877 1 2 1 6 H 1.118316 1 107.399773 1 -73.220364 1 2 1 6 H 1.098555 1 116.705711 1 -32.527608 1 1 2 7 H 1.092716 1 119.490590 1 165.857707 1 3 4 5 H 1.091757 1 122.354434 1 9.374023 1 3 4 5 H 1.098702 1 118.584661 1 -13.736600 1 4 3 11 H 1.111796 1 109.120250 1 -115.208112 1 5 4 3 H 1.110446 1 110.429073 1 126.570168 1 5 4 3 H 1.107787 1 113.319142 1 4.958871 1 5 4 3 H 1.108134 1 112.416348 1 -172.721816 1 6 1 2 H 1.118042 1 107.755456 1 69.492728 1 6 1 2 H 1.109678 1 113.288218 1 -48.800221 1 6 1 2 ---------------------------------------------------------------- Step 3 input file (for NLLSQ): FORCE CHARGE=1 DENSITY GRAPH ISOTOPE TS checking by FORCE calculation C .000000 0 .000000 0 .000000 0 0 0 0 C 1.494700 1 .000000 0 .000000 0 1 0 0 C 1.493679 1 122.365784 1 .000000 0 2 1 0 C 2.380560 1 102.504395 1 110.467232 1 2 3 1 C 1.368080 1 107.971291 1 74.388344 1 4 2 3 C 1.495277 1 127.264130 1 -95.821228 1 5 4 2 H 1.108898 1 112.496826 1 169.901352 1 1 2 3 H 1.109529 1 113.296120 1 46.004711 1 1 2 3 H 1.117890 1 107.496994 1 -72.487534 1 1 2 3 H 1.098734 1 86.146576 1 -42.602459 1 2 4 5 H 1.092931 1 119.365471 1 165.091675 1 4 5 6 H 1.092000 1 122.211273 1 9.421019 1 4 5 6 H 1.098602 1 118.611084 1 84.593826 1 5 4 2 H 1.111888 1 109.074448 1 -114.666496 1 6 5 4 H 1.110686 1 110.417656 1 127.198174 1 6 5 4 H 1.107639 1 113.346970 1 5.549870 1 6 5 4 H 1.108230 1 112.441048 1 -172.787689 1 3 2 1 H 1.117836 1 107.759140 1 69.464531 1 3 2 1 H 1.109580 1 113.282127 1 -48.948452 1 3 2 1 ----------------------------------------------------------------- Step 4 input file (for NLLSQ and for backward reaction, i.e, IRC=-1) This step is restarted immediately after the step 3. IRC=-1 RESTART CHARGE=1 DENSITY GRAPH ISOTOPE TS checking by IRC calculation C .000000 0 .000000 0 .000000 0 0 0 0 C 1.494700 1 .000000 0 .000000 0 1 0 0 C 1.493679 1 122.365784 1 .000000 0 2 1 0 C 2.380560 1 102.504395 1 110.467232 1 2 3 1 C 1.368080 1 107.971291 1 74.388344 1 4 2 3 C 1.495277 1 127.264130 1 -95.821228 1 5 4 2 H 1.108898 1 112.496826 1 169.901352 1 1 2 3 H 1.109529 1 113.296120 1 46.004711 1 1 2 3 H 1.117890 1 107.496994 1 -72.487534 1 1 2 3 H 1.098734 1 86.146576 1 -42.602459 1 2 4 5 H 1.092931 1 119.365471 1 165.091675 1 4 5 6 H 1.092000 1 122.211273 1 9.421019 1 4 5 6 H 1.098602 1 118.611084 1 84.593826 1 5 4 2 H 1.111888 1 109.074448 1 -114.666496 1 6 5 4 H 1.110686 1 110.417656 1 127.198174 1 6 5 4 H 1.107639 1 113.346970 1 5.549870 1 6 5 4 H 1.108230 1 112.441048 1 -172.787689 1 3 2 1 H 1.117836 1 107.759140 1 69.464531 1 3 2 1 H 1.109580 1 113.282127 1 -48.948452 1 3 2 1 ------------------------------------------------------------------ ####################(Answers)######################## From MAILER-DAEMON@www.ccl.net Tue Jul 16 02:39 EDT 1996 Received: from irene for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.7.5/950822.1) id CAA07999; Tue, 16 Jul 1996 02:39:47 -0400 (EDT) Received: by irene (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id BAA14162; Tue, 16 Jul 1996 01:39:48 -0500 Date: Tue, 16 Jul 1996 01:39:48 -0500 From: christin@irene (Christine Byrd) Message-Id: <199607160639.BAA14162@irene> To: chemistry@www.ccl.net Subject: MOPAC output files Content-Type: text Content-Length: 1136 Status: RO I have a few questions regarding Mopac .out and .syb files. My observation: I've noticed that .syb files are created after running a MOPAC, despite failure of a compound to pass one of the gradient tests (Herbert's or Peter's). On the other hand, .syb files are not generated when MOPAC "abandons" a calculation for a specific compound. I was hoping if perhaps someone would explain: (1) The criteria according to which MOPAC chooses to submit a compound to either "Peter's Test" or "Herbert's Test." (2) Which consequences not passing one of the gradient tests has on the resulting MOPAC calculation. I need to run MOPAC calculations on a rather large database and would like to run them using SPL Macros, for the sake of time and accuracy. Should the failure to pass one of the tests mentioned above have consequences on the MOPAC calculation and thus on the .syb file, is there a clever way to check for compliance with the tests utilizing a Macro? I would appreciate any advice. Cheers, Christine Byrd Christine Byr e-mail: christin@irene.uams.edu From ccl@www.ccl.net Mon Jul 22 20:15:46 1996 Received: for ccl@www.ccl.net by www.ccl.net (8.7.5/950822.1) id UAA19080; Mon, 22 Jul 1996 20:04:00 -0400 (EDT) From: Computational Chemistry Message-Id: <199607230004.UAA19080@www.ccl.net> Subject: UFF To: chemistry@www.ccl.net Date: Mon, 22 Jul 1996 20:04:00 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Status: RO Content-Length: 2532 > >From schlecmf@esvax.dnet.dupont.com Mon Jul 22 10:15:41 1996 > Received: from gatekeeper.es.dupont.com for schlecmf@esvax.dnet.dupont.com > by www.ccl.net (8.7.5/950822.1) id JAA15439; Mon, 22 Jul 1996 09:20:08 -0400 (EDT) > From: > Received: by gatekeeper.es.dupont.com; id JAA02231; Mon, 22 Jul 1996 09:20:09 -0400 > Received: by esds01.es.dupont.com; id AA21661; Mon, 22 Jul 96 09:20:00 -0400 > Message-Id: <9607221320.AA21661@esds01.es.dupont.com> > Received: from esvax.dnet; by esds01.dnet; Mon, 22 Jul 96 09:20:08 EDT > Date: Mon, 22 Jul 96 09:20:08 EDT > To: chemistry@www.ccl.net > Apparently-To: chemistry@www.ccl.net > Subject: CCL: Re: UFF > > > Peter: > > I just got notification from the automated current awareness WWWeb utility > at Amazon Books (http://www.amazon.com/) about a soon-to-publish book by Rappe > and Casewit which is very likely concerned to some extent with Rappe's > Universal Force Field: > ---------------------------------------------- > "Molecular Mechanics Across Chemistry," by Anthony K. Rappe , Carla J. Casewit > > Hardcover > Price information not available. > Published by Univ Science Books > Publication date: August 1996 > ISBN: 0935702776 > > Not Yet Available: > ---------------------------------------------- > This information (and capability of ordering) is found at: > > http://www.amazon.com/exec/obidos/ISBN=0935702776 > > I've seen Rappe give talks on the subject at some recent ACS meetings. > Some authors are referring to Halgren's new Merck Molecular Force Field > (MMFF94) as a/the UFF. There are also references to UFF which concern the > "Universality of Free Fall" in the study of interplanetary matter, and to > Urea-Formaldehyde Fertilizer, both of which are probably of little interest. > Following are a few recent references which I believe are specifically > concerned with Rappe's UFF. > > Anal. Sci. Technol. (1995), 8(4), 519-27. [Chem. Abstr. 124:305980] > Macromolecules (1995), 28(22), 7370-5. [Chem. Abstr. 123 229465] > J. Am. Chem. Soc. (1995), 117(23), 6194-8. [Chem. Abstr. 123 55409] > J. Mol. Struct. (1994), 323(1-3), 93-101. [Chem. Abstr. 121 120549] > Inorg. Chim. Acta (1993), 213(1-2), 319-24. [Chem. Abstr. 120 4998] > Inorg. Chem. (1993), 32(16), 3438-50. [Chem. Abstr. 119 80553] > > Hope this helps. > > Matthew F. Schlecht > DuPont Agricultural Products > Newark, DE 19714-0030 USA > schlecmf@esvax.dnet.dupont.com > From cramer@maroon.tc.umn.eduSat Jul 27 11:20:14 1996 Date: Wed, 10 Jul 1996 09:48:28 -0500 (CDT) From: Christopher J Cramer To: tp@elptrs7.rug.ac.be Subject: Re: CCL:M:Searching transition state with MOPAC; part2 Status: RO Content-Length: 4564 Park, Tae-Yun > > > > H H H H H H > | \ / | | | > H-C(+) + C=C ---->(TS?)----> H-C-C-C(+) > | / \ | | | > H H H H H H > > gas-phase gas-phase > methyl ethylene primary propyl > carbenium ion carbenium ion > > What makes you think there IS a transition state structure? In the gas phase, I would expect this reaction to have a good chance of being barrierless. Rather than attempt to locate a TS structure a priori, you might simply do constrained optimizations pulling off the methyl group by 0.1 angstrom increments (for instance). If you generate a reaction path without a barrier, you will know that it is fruitless to look for a TS. On the other hand, if you do find a barrier, you will know where to start your TS optimization. CJC -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-7541 cramer@maroon.tc.umn.edu http://pollux.chem.umn.edu/~cramer ------------------------------------------------------- PART IV Subject: Searching transition state with MOPAC; part2 ------------------------------------------------------- ####################(questions)######################## Dear all, I've received a lot of helpful messages from many CCLers, concerning my earlier questions on how to get the structure of transition state of the reaction, H H H H H H | \ / | | | H-C(+) + C=C ---->(TS?)----> H-C-C-C(+) | / \ | | | H H H H H H gas-phase gas-phase methyl ethylene primary propyl carbenium ion carbenium ion Thanks a lot! I greatly appreciate all the messages concerning this problem. Most of the messages pointed out that I made a mistake to prepare the input file for SADDLE calculation; all the atom should be in the same order between reactants and product z-matrix field. I made second try with a corrected input file as follows; ************************************************************** SADDLE DENSITY GRAPH XYZ CHARGE=1 PRECISE Me--->p methylation activated complex C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 8.471619 1 0.000000 0 0.000000 0 1 0 0 C 1.325912 1 162.328125 1 0.000000 0 2 1 0 H 1.108597 1 65.592545 1 -150.347214 1 1 2 3 H 1.113968 1 120.001495 1 -151.401566 1 1 4 2 H 1.108612 1 119.996246 1 -179.367538 1 1 4 5 H 1.098282 1 122.722214 1 57.159393 1 2 3 1 H 1.098328 1 122.715210 1 179.999634 1 2 3 7 H 1.098267 1 122.715210 1 -0.316483 1 3 2 7 H 1.098206 1 122.715210 1 -179.684021 1 3 2 7 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 C .000000 0 .000000 0 .000000 0 0 0 0 C 1.506600 1 .000000 0 .000000 0 1 0 0 C 1.418947 1 116.688263 1 .000000 0 2 1 0 H 1.118077 1 111.116249 1 -59.952415 1 1 2 3 H 1.119762 1 109.783371 1 -179.449097 1 1 2 3 H 1.118210 1 111.069687 1 61.123405 1 1 2 3 H 1.150598 1 110.672989 1 174.990601 1 2 1 4 H 1.150955 1 110.650314 1 64.874481 1 2 1 4 H 1.109621 1 121.247902 1 -179.729874 1 3 2 1 H 1.110257 1 121.556961 1 .300391 1 3 2 1 0 .000000 0 .000000 0 .000000 0 0 0 0 ************************************************************** This time MOPAC produced a structure of transition state which is almost the same as that of reactants, that is, there was almost no change between reactants and transition state. I've tried to refine the transition state with the key words, "TS", "SIGMA", and "NLLSQ" separately, which gives no change either. Why is the result like this? Could anyone PLEASE tell me how can I go further to obtain a reliable structure of the transition state?? Thank you VERY MUCH in advance. ####################(Answers)######################## From steve@bellatrix.pcl.ox.ac.uk Fri Jul 12 09:13:34 1996 Received: from oxmail3.ox.ac.uk for steve@bellatrix.pcl.ox.ac.uk by www.ccl.net (8.7.5/950822.1) id IAA17483; Fri, 12 Jul 1996 08:49:59 -0400 (EDT) Received: from joule.pcl.ox.ac.uk by oxmail3 with SMTP (PP) with ESMTP; Fri, 12 Jul 1996 10:35:08 +0100 Received: from bellatrix (bellatrix.pcl.ox.ac.uk [163.1.21.231]) by joule.pcl.ox.ac.uk (8.6.10/8.6.5) with ESMTP id KAA13032 for <@joule.pcl:chemistry@www.ccl.net>; Fri, 12 Jul 1996 10:34:44 +0100 Received: by bellatrix (940816.SGI.8.6.9/940406.SGI.AUTO) id KAA27057; Fri, 12 Jul 1996 10:33:06 GMT Date: Fri, 12 Jul 1996 10:33:05 +0000 (GMT) From: Steve Doughty To: chemistry@www.ccl.net Subject: MGMS EC-1 Announcement Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII FIRST ELECTRONIC MOLECULAR GRAPHICS AND MODELLING SOCIETY CONFERENCE ******************************************************************** The First Electronic Molecular Graphics and Modelling Society Conference (MGMS EC-1) will be held on the Internet (the Net) and World Wide Web (the Web) from Oct 7-18, 1996. The conference is sponsored by Elsevier and the Molecular Graphics and Modelling Society and will be co-organized by Graham Richards, Art Olson, Rod Hubbard and Barry Hardy. MGMS EC-1 will be a fully international event open to all members of the scientific community and will cover a broad range of disciplines related to molecular modelling, graphics and simulation methods and applications. Conference subject areas are: Protein Structure; Membranes and Membrane Proteins; Bioinformatics; Computational Nanotechnology; Protein Folding; Modelling of In Vivo Activity; Knowledge-based Library Design; Surface Science; Host-guest interactions; Carbohydrates; Enzyme Mechanisms; Conformational Analysis; Nucleic Acids; Quantum Chemistry; Car-Parrinello Methods and Applications; Structure-based Design; Visualization; and Perspectives. Each subject area has a section convener who will screen abstracts sent by authors for suitability. Authors can opt to submit a non-permanent presentation like a normal conference poster or a presentation which will be refereed and considered for publication in the Journal of Molecular Graphics. Referees will be appointed by the section conveners. Presentations must be prepared in Hypertext Markup Language (HTML), graphics (GIF,JPEG) and other web-compatible formats (VRML,Java,PDF) so that participants can view the papers via the World Wide Web. Aid and consultation will be provided to participants in the weeks prior to the event to help them with their presentation (Email:mgmsorg@bellatrix.pcl.ox.ac.uk). Further details will be given in the authors' guide accessible via the URL: http://bellatrix.pcl.ox.ac.uk/mgms/ During the conference discussions will take place via the Internet in real-time using a virtual conference centre based on a MOO (multiple-user domain, object oriented) and via Internet-accessible electronic mailing lists. Trial sessions for those not familiar with MOOs will be held before the conference. Before the conference, a timetable for MOO discussion sessions of each section will be posted. Since these realtime discussions are an integral part of the conference, authors will be expected to attend one for their subject; the right is reserved not to referee submissions by authors who do not attend one of these sessions. The Conference will feature a Virtual Trade Center where commercial vendors, software and hardware developers, consultants, and contractors will be able to display their goods and services and provide software demonstrations in return for exhibition fees to support conference activities. Any potential exhibitors should contact Barry Hardy at barry@bellatrix.pcl.ox.ac.uk ******************* DEADLINES AND DATES 1) DO NOW - The MGMS mailing list Conference-related news and announcements will be posted regularly to the MGMS mailing list (http://bellatrix.pcl.ox.ac.uk/hypermail/mgms/). If you wish to subscribe to the MGMS list send the following one line message to majordomo@bellatrix.pcl.ox.ac.uk: subscribe mgms@bellatrix.pcl.ox.ac.uk your_email@address your_name 2) DO NOW - Registration The deadline for registration is Sept 15th 1996. Early registration is strongly encouraged to aid the efficient operation of the conference including the establishment of timely access to the conference. If you intend to participate in MGMS EC-1 please use the registration form accessible via http://bellatrix.pcl.ox.ac.uk/mgms/ which is available for electronic registration. The registration will be used to construct a registrant database for the conference which will generate the conference mailing list and handle assignment of userids and passwords. In addition it is necessary to pay for registration via ordinary means: The conference fee will be 35 pounds sterling (50 US dollars) with a special rate for students of 20 pounds sterling (30 US dollars). A copy of a suitable student identification or a letter from the supervisor will be required to be charged at the lower rate. Registration payments can be accepted by credit card, direct bank transfer, cheque or bank draft. Regardless of method of payment we ask you to supply accompanying correspondence with your complete name, address, fax and phone number, and email address which should be mailed directly to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK Payment Instructions: a) Credit Card We can currently accept Visa, Mastercard, Switch or JCB. We cannot yet accept American Express as our application with them has still to be processed. Please send your credit card type, number and expiration date via regular mail to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK b) Bank Transfer Your payment can be made in sterling by direct bank transfer into the folowing account: Account Number: 20-6518 50772712 Account Name: Greenlea Communications Bank: Barclays Bank, Oxford City Centre Branch, P.O. Box 333, Oxford, OX1 3HS, UK --Please ensure your full name is listed with the transfer details. --You are responsible for any bank charges associated with the transfer from your bank. --Please notify us directly of your transfer payment. 3) Cheque/Bank Draft Cheques or bank orders (in pounds or dollars) should be made out to Greenlea Communications and mailed to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK Acknowledgement of Registration and Payment: When you first register at the conference site you should receive an acknowledgement email with a password and userid. After receipt of your registration fee you will receive a further acknowledgement and your userid and password will be validated to allow access to the conference site (when it opens). (Note: Registration payments received during the period July 23- August 14 will not be immediately processed and acknowledged. They will be processed as soon after August 14 as possible.) Academic registrants from economically-disadvantaged countries can write to Barry Hardy requesting an exemption to the registration fee. Exemptions will be made on a discretionary basis taking into account the reasons given for the request and will be dependent on suitable funds being available. We will consider economically disadvantaged countries to include those of Eastern Europe, Africa, Central and South America, Indian sub-continent, etc. 3) DEADLINE for receipt of ABSTRACT. The deadline for receipt of presentation abstracts is August 1. Email your abstract directly to the appropriate section convener listed below. Fuller details of the scope of each section will be given in the authors' guide accessible via http://bellatrix.pcl.ox.ac.uk/mgms/ Your abstract should be no longer than 300 words. And remember to state which category of presentation (non-permanent poster or refereed paper) you wish. If you are unsure as to which section your abstract is suitable for, please email a possible section convener or Barry Hardy (barry@bellatrix.pcl.ox.ac.uk). Section conveners do have the discretion to reject abstracts, ask for revisions to an abstract or to send the abstract to the convener of a more suitable section. 4) DEADLINE for receipt of PRESENTATION The deadline for receipt of papers and posters is Sept 15th. You must deposit your text and graphics files at the conference ftp site for presentation at the conference. Ftp instructions will be provided at the conference site. Hard copies of final refereed papers following the format of the Journal of Molecular Graphics should be sent by Dec 1 to: Graham Richards, Journal of Molecular Graphics, Physical & Theoretical Chemistry Lab, Sth Parks Rd, University of Oxford, Oxford, OX1 3QZ, UK. Journal guidelines are posted at http://bellatrix.pcl.ox.ac.uk/mgms/ Although there is no limit to the graphics authors choose to display in their conference presentation, the editor reserves the right to limit the number of free colour figures in each printed journal article. 5) Refereeing Period The refereeing period will commence upon completion of the conference. If you have a presentation at MGMS EC-1 you may be requested to contribute a refereeing evaluation on another conference presentation. Referee reports will be due November 15. ******************* SECTIONS AND SECTION CONVENERS (Please email section conveners with questions related to your particular section and presentation. Details on the sections are accessible via http://bellatrix.pcl.ox.ac.uk/mgms/) Any general emails (such as registration queries, maillist queries, HTML queries, password queries, timetable queries, general technical advice on browsers and graphics, MOO queries, etc.) should be sent to: mgmsorg@bellatrix.pcl.ox.ac.uk 1. Protein Structure Rod Hubbard University of York, UK Email:rod@yorvic.york.ac.uk 2. Nucleic Acids David Beveridge and Dennis Sprous Wesleyan University, USA Email:bever@rose.chem.wesleyan.edu,dsprous@rose.chem.wesleyan.edu 3. Membranes and Membrane Proteins Alan Robinson University of Oxford, UK Email:alan@bellatrix.pcl.ox.ac.uk and Terry Stouch Bristol-Myers Squibb, USA Email:stouch@dino.bms.com 4. Bioinformatics Steve Gardner Oxford Molecular, UK Email:sgardner@oxmol.co.uk 5. Computational Nanotechnology Al Globus NASA-Ames, USA Email:globus@nas.nasa.gov 6. Protein Folding Jeffrey Skolnick Scripps Institute, USA Email:skolnick@scripps.edu 7. Modelling of In Vivo Activity Edward Hodgkin Wyeth-Ayerst Research, USA Email:hodgkie@war.wyeth.com 8. Knowledge-based Library Design Mike Hann GlaxoWellcome, UK Email:mmh1203@ggr.co.uk 9. Surface Science Donald Brenner North Carolina State, USA Email:dwb@ripley.mte.ncsu.edu 10. Host-Guest interactions Jon Essex Southampton University, UK Email:J.W.Essex@soton.ac.uk 11. Carbohydrates and Protein-Carbohydrate Interactions Anne Imberty CNRS, France Email:imberty@nantes.inra.fr 12. Enzyme Mechanisms Guy Grant University College Dublin, Ireland Email:ggrant@macollamh.ucd.ie 13. Stochastic Methods for Conformational Sampling Robert Topper The Cooper Union, USA Email:topper@cooper.edu 14. Quantum Chemistry Tim Clark University of Erlangen, Germany Email:clark@organik.uni-erlangen.de 15. Structure-based Design David Winkler CSIRO, Australia Email:D.Winkler@chem.csiro.au 16. Car-Parrinello Methods and Applications Michele Parrinello Max-Planck Institute, Germany Email:prr@prr.mpi-stuttgart.mpg.de 17. Visualization Art Olson Scripps Institute, USA Email:olson@scripps.edu 18. Perspectives in Molecular Modelling Graham Richards University of Oxford, UK Email:gr@vax.ox.ac.uk ------------------------------------------------------------------ // || \\ // Stephen Doughty || "The best and most \\ // Physical & Theoretical Chemistry Lab.||beautiful things in \\ // Oxford University, ||this world cannot be \\ // South Parks Road, OXFORD, OX1 3QZ, UK||seen or even touched.\\ // ||They must be felt \\ // Tel: +44 1865 275475 ||with the heart." \\ //--------------------------------------------------------------\\ // Email : steve@bellatrix.pcl.ox.ac.uk \\ // WWW : http://bellatrix.pcl.ox.ac.uk/people/steve/ \\ ------------------------------------------------------------------ From echamot@xnet.comSat Jul 27 10:23:18 1996 Date: Thu, 27 Jun 96 14:25:24 EDT From: Ernest Chamot To: "Park, Tae-Yun" Subject: Re: CCL:M:HELP!(urgent):theoretical discrimication & software Status: RO Content-Length: 13280 Hi TAE-YUN, I'm sure you realize you are taking on quite a task for your research: >I'm a ph.D. student of State University of Ghent, Belgium. >I'm working with zeolite HZSM-5. The goal of my work is >to develop a detailed kinetic model for hydrocarbon >transformation process over HZSM-5 catalyst. A tremendous amount of research has gone into working out the kinetics for the strictly thermal processes of cracking hydrocarbons to olefins. The catalytic process is, of course, more complicated. And zeolites in particular have been subject to a great deal of study, both theoretically and experimentally, just to understand the nature of their catalysis, not to mention working out the detailed kinetics that result as a consequence. I have done some work in both areas, so I offer the following observations in addition to some specific responses to your query. 1) The mechanism that leads to the formation of olefins (among other products) from hydrocarbons is very complicated. The beta scission reaction to eliminate an olefin from a free radical is the dominant process in the thermal reaction of light hydrocarbons. This cascade takes place in competition with an array of rearangement reactions and cyclizations (which lead to aromatics and ultimately to coke). I am attaching a .gif file of part of the mechanism showing this cascade and a few of the rearrangement reactions. (I had a more complete mechanism, showing the steps leading to various cyclics and aromatics and coke precursors, but I can't lay my hand on it at the moment.) 2) The same mechanism applies to the carbenium ion process (initiated by "acid" catalysis), except the relative rates will be different. The rearrangement and cyclization reactions are known to be much faster, relative to the beta-scission. (The major reason a cracking catalyst for hydrocarbons to light olefins has never been commercialized is due to the fact that zeolites and other acid catalysts all coke virtually instantaneously at temperatures at which olefins are favored thermodynamically over paraffins.) 3) One way zeolite catalysts exhibit selectivity is by imposing geometrical constraints upon the "activated complex" of the reactant and the catalytic site, as you propose studying. More commonly, observed selectivities are due to geometric constraints on either the ingress of reactants or the egress of products: all possible products can form within the pores, but only the ones that can fit through the pores to get out are observed. Other products stay inside and continue to reversibly interconvert back to reactants and forward to the mix of potential products. Hence, the energetics of the "activated complex" as affected by the geometric constraints about the acidic site inside a zeolite pore will only be relavent for reactions with both reactants and products small enough to pass completely unhindered into and out of the zeolite pores. So far as your specific questions: >I have some urgent questions for my ph.D. work, which have >been discussed with many people who were in the field of >chemical engineering/organic chemistry/electrical chemistry >in my university or in the internet. > >So far, I could not get reliable solutions, which have stuck >me for relatively long time. During searching for the solutions, >I realized that the best people who can give me an advice are >in the field of computational chemistry. > >Please take some time to read the following questions >and give me some informaion/advice if it doesn't bother >you too much. > > >*** About the structure of surface carbenium ions and symmetry number *** > >First thing I have to calculate is the symmetry number >of surface carbenium ions on the zeolite surface, which >is formed by protonation of various olefins. > >1. How can we describe the bonding of carbenuim > ions to the surface? Is the bonding more > ionic or covalent? I know the proton is surely > covalently bound, but it is less clear for the > case of hydrocarbons(more exactly olefins) adsorbed > on zeolite. If you really mean to model the "surface" of the zeolite, you will have to consider a combination of sites, all contributing to an overall reaction. There are several sites within a zeolite that can be acidic, depending on where the trivalent atom (Al, B, etc.) substitutes for the tetravalent atom (Si), forcing the adjacent oxygen to be capped with an acidic hydrogen: O O O O O O | H+ | | | | | - Si - O - Al(-) - O - Si - vs. - Si - O - Si - O - Si - | | | | | | O O O O O O These are referred to as "T sites" based on the labeling of the definitive XRD data: T1, T2, T3, ... T8 for the MFI class of zeolites (ZSM-5) for instance. A great deal of computational studies have gone into trying to determine which sites are the catalytically active ones, but although several claim to have determined the preferred sites or the active sites, none are without serious questions. The only calculations (in my opinion) that aren't seriously flawed by either unrealistic assumptions about the geometry or by electronically unrealistic choice of model compounds (to make the calculations tractable) are those by Tony Hess's group, and the most recent work of van Santen's group: Teunissen, Jansen, and R. A. van Santen, J. Phys. Chem., 99, 1873-9 (1995) (and references therein to A. Hess). "Surface" sites will be constructed from each of these T-sites with one or more connections missing. Here again, there is a continuing argument as to what you end up with. Some have assumed everything ends up with hydroxyl caps. Others are convinced that there are extra bridging oxygens, etc. H H+ H / / / O O O O O | | | / \ / \ - Si - O - Al(-) - O - Si - vs. -Si- O -Si- O -Si- O -Si- | | | | | | | O O O O O O O There is also continuing discussion of whether the "acidic" site is a Bronsted acid (H+) or a Lewis acid (RO3Al), usually depending on whether the reaction conditions are such that elimination of water would be expected. Basically, although there is plenty of opinion, there is no consensus on either where "the" active acid site is in a zeolite, or what that site looks like. You will need to pick what you believe is most reasonable and either prove it, or at least be consistent with it when you associate an olefin with the site, or create an ion pair by protonation of the olefin next to the site. >2. What is the symmetry number for such surface carbenium > ions comparing with corresponding gas phase carbenium > ions? In most cases, I believe, the symmetry number > of surface ions are identical with those in gas phase, > if there is no 2-fold axes. As there is not a consensus on the structure of the acidic site, the structure of the activated complexes which incorporate the site is not known. Much modeling has assumed there is symmetry (at least a plane of symmetry, and sometimes 2 planes of symmetry), but this is definitely not correct. In a zeolite the different T sites each occupy unique assymetric centers. The only way there could be any element of symmetry in an absolute sense would be for every unit cell of the zeolite to also have a similarly bonded activated complex at the same time. This is not a reasonable expectation. Local symmetry may be more important than absolute symmetry, however. For this, you would have to consider each of the T sites in the zeolite you are interested in, and decide how locally you want to define the system. Then there may be a few sites with a local plane of symmetry, but for the most part these won't be symmetric either. Calculations I had done on the T2 site in MFI zeolites showed that you will have to include at least 2 layers of silicon-oxygen bonds away from the acidic site to even directionally calculate the relative acidities of aluminosilicates and borosilicates. E. Chamot, Modeling Acid Sites in MFI Zeolites with Realistic Geometric Constraints," Preprints Division of Petroleum Chemistry, Inc. Vol 37, No. 2, ACS San Francisco Meeting, March, 1992. I assume the symmetry "number" you are asking about is defined by the engineering software or method you are planning on using to predict energies (CHETAH? Benson?) Chemically, the symmetry group would be C1: no elements of symmetry, unless by coincidence one of the sites nearly has 2-fold symmetry when considered locally. (Orienting the carbenium ion next to the active site will not increase the symmetry, obviously, only decrease the symmetry.) > >**** About the structure of activated complex ****** > >Next problem that I have to solve is concerning the structure >of activated complex in transition state for beta-scission. > >That is, an elementary step representing beta-scission, > > R1 ---> (Transition State) ----> R2 + O > >where R1 and R2 are the reactant and product carbenium ion, >respectively, and O is the product olefin. > >What I want to know is the structure of the activated complex >in the transition state, as detailed as possible in a certain >theoretical way; how many bonds are related, which bonds are to >be broken, which bond will be formed, and what does the activated >complex look like(is it more like carbenium ion or more like >olefin?), etc. > >Is there any reference/software to describe the structure >of activated complex for this reaction in a theoretical way? This is something that would be quite amenable to computation, once one determined the appropriate structure of the catalytic site to use when building the activated complex. A Quantum Mechanical method would have no problem determining where bonds actually existed, what the atom-atom distances and angles were, or how the electronics would reorganize to distribute partial charges and bonds. The software is certainly there, but again, I am not aware of any consensus on the correct system to model, however. >**** About heat of formation for gas phase carbenium ions *** > >My final question is about the calculation of thermodynamic data, >more exactly, the heat of formation of gas-phase carbenium ions. . . . >The only solution I found recently is using a certain quantum >chemistry package such as "MOPAC". My question is that is this >a suitable package (accurate enough) to calculate the heat of >formation data I need? Yes, this would be an entirely appropriate use of computational chemistry: calculating a thermodynamic value or series of thermodynamic values that are difficult to come by experimentally. MOPAC will do this quite easily, and should be able to handle molecules and ions large enough for your purposes (up to 70-100 atoms with reasonable compute power.) Moreover, although one normally thinks of zeolites as inorganic, the zeolite structure turns out to be very covalent in nature and MOPAC (which contains parameters for Si and Al) works very well for modeling the system when compared to high level ab initio calculations (see Hess's work). As you point out, you need to consider the accuracy of the calculation. Ab initio methods can always be made more accurate, but you rapidly become limited by how large a molecule you can handle: you may be limited to C6 and less (especially if you are to consider all isomers.) Heats of formation have been calculated with MOPAC using the AM1 parameterization and in the case of a series of cations the calculations reproduced the experimentally available data to within 4.7 kcal on the average: Dewar, Zoebisch, Healy, and Stewart, J. Amer. Chem. Soc., 13, 3901 (1985). Not too exciting, but if you can use RELATIVE energies (especially between "isodesmic" reactions) you can probably do a lot better. > If so, how can I obtain a copy of this >package? If not, is there any other software in the field of >computational chemistry to calculate these data? MOPAC is available in several forms. I believe some version of it is still available from the QCPE for a nominal charge. It is sold as part of the CAChe worksystem (which includes a very easy to use interface, and standard procedures already built for using MOPAC), and by MSI/Biosym. The parameters themselves (AM1 and PM3) are part of both Spartan and HyperChem. The URL's I have for these organizations are: CAChe http://www.oxmol.com/ MSI/Biosym http://www.msi.com/ Spartan http://wavefun.com/ HyperChem http://www.hyper.com/ Good luck. And as a final piece of advice, make sure you carve out a piece of this problem that is doable. EC --- Ernest Chamot Consultant in Computational Chemistry Applications Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 (708) 637-1559 (Voice & Fax) echamot@xnet.com http://www.xnet.com/~chamotlb Enclosure: RxnScheme.GIF [14,877 bytes] (I cut off this scheme due to its large size. If someone needs this image, please contact me or Mr. Ernest Chamot) From echamot@xnet.comSat Jul 27 11:01:35 1996 Date: Sun, 7 Jul 96 20:18:00 EDT From: Ernest Chamot To: "Park, Tae-Yun" Subject: Re: CCL:M:Heat of formation calculation using MOPAC. Status: RO Content-Length: 5636 Hi TAE-YUN, I haven't seen a head-to-head comparison of AM1 to PM3 specifically for carbenium ion heats of formation, though there have been several published comparisons of the two methods. I am not surprised, however, that you are finding: >AM1 is much closer to those experimental >data than the case of PM3 when the molecule >contains the cabon atoms up to 5. Even though: >According to the manual of MOAPC, however, >PM3 is more improved parameter than AM1! The main difference, relevant to your use, is that the AM1 parameterization was developed to be theoretically consistent, whereas the PM3 parameterization was developed to most closely reproduce known experimental data. That means that more molecules were used to develop the PM3 parameters than the AM1 parameters (something like 657 vs. 100), but most experimental data is on stable, ground state molecules, so it isn't necessarily as good for species not readily observed: transition states, intermediates, etc. I would expect carbenium ions to be among those difficult to observe species that are not well represented in the parameterizations. An old reference I have shows AM1 coming within 4.7 kcal rms error for a series of cations. Is this comparable to the numbers you are getting? If so, then yes, I would expect that: >the AM1 would also produce >better result if the molecule becomes larger >(upto C8)? EC --- Ernest Chamot Consultant in Computational Chemistry Applications Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 (708) 637-1559 (Voice & Fax) echamot@xnet.com http://www.xnet.com/~chamotlb (Concluding Remarks for part II) I concluded that AM1 is slightly better than PM3 for the calculation of heat of formation for various carbenium ions. ------------------------------------------------------- PART III Subject: Transition state search using MOPAC. ------------------------------------------------------- ####################(questions)######################## Dear all, I need some help from people who uses MOPAC frequently, as I'm a real beginner of using MOPAC. I want to search the transition state(TS) of the following reaction with MOPAC93: H H H H H H | \ / | | | H-C(+) + C=C ---->(TS?)----> H-C-C-C(+) | / \ | | | H H H H H H gas-phase gas-phase methyl ethylene primary propyl carbenium ion carbenium ion After reading the session of transition state location(SADDLE) in MOPAC manual, I have prepared the following input data for MOPAC: *************************************************************** UHF SADDLE DENSITY GRAPH XYZ CHARGE=1 BAR=0.03 Me--->p methylation activated complex C .000000 0 .000000 0 .000000 0 0 0 0 H 1.113983 1 .000000 0 .000000 0 1 0 0 H 1.113983 1 120.001495 1 .000000 0 1 2 0 H 1.113968 1 119.999756 1 -179.453217 1 1 2 3 C 5.210007 1 129.371857 1 -179.367538 1 1 2 3 C 1.336975 1 114.626526 1 -2.741700 1 5 1 2 H 1.099976 1 120.501572 1 -179.999634 1 5 6 1 H 1.100006 1 119.749710 1 -179.453217 1 5 6 7 H 1.099976 1 120.499832 1 179.999634 1 6 5 7 H 1.099976 1 119.749710 1 .547287 1 6 5 7 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 C .000000 0 .000000 0 .000000 0 0 0 0 C 1.506600 1 .000000 0 .000000 0 1 0 0 C 1.418946 1 116.679237 1 .000000 0 2 1 0 H 1.118213 1 111.091591 1 -60.563965 1 1 2 3 H 1.119848 1 109.781792 1 179.985870 1 1 2 3 H 1.118203 1 111.102783 1 60.532600 1 1 2 3 H 1.150792 1 110.664017 1 174.500137 1 2 1 4 H 1.150722 1 110.665337 1 64.389313 1 2 1 4 H 1.109605 1 121.234596 1 179.993790 1 3 2 1 H 1.110235 1 121.565987 1 -.003556 1 3 2 1 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 **************************************************************** The result with this input data was terrible; in the transition state, H2 and H were separated! The data were prepared as follows: 1. I've drawn two reactants using CS Chem 3D Pro and save as MOPAC input. I could not optimize the geometry of these two molecules in MOPAC simulatneously, since there are two molecules exist. 2. The data for the product carbenuim ions was prepared with CS Chem3D Pro again, and the geometry of this molecule was minimized with MOPAC keywards, "SYMMETRY CHARGE=1 AM1 GEO-OK EF PRECISE" and then saved as an optimezed data for the product carbenium ion. 3. Then I combined these two files and modified according to the decription in the MOPAC manual for SADDLE calculation. 4. And I've got the terrible result. What's wrong with my input data for the SADDLE calculation? Is it really possible to get the optimized geometry of transition state for the reaction I mentioned above by using MOPAC? If so, could anyone PLEASE tell me how I can get a reliable structure of the transition state theoretically? ANY suggestion/advice will be GREATLY APPRECIATED! Thank you very much in advence. ####################(Answers)######################## From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.deSat Jul 27 11:07:03 1996 Date: Tue, 9 Jul 1996 21:32:47 -0600 From: Emadeddin Tajkhorshid Status: RO Reply to: E.tajkhorshid@dkfz-heidelberg.de To: "Park, Tae-Yun" Subject: Re: CCL:M:Transition state search using MOPAC. Hi Tae-Yun As far as I exprienced MOPAC, you should use the same order of atoms in your input file for the geometry of reactants and products. Otherwise you will find a nonsense result. Because MOPAC tries to reconstruct the reaction coordinate toward saddle point via considering the satrting and ending geometry of each atom and is not able to automatically find the right counterpart in the second strusture. On the other hand it is recommended to use XYZ key word even if you use internal coordinate. This can prevent some kind of special errors which may occur in this routine Good luck Emad -- E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2339 Dept. Molecular Biophysics (0810) FAX: +49 6221 42 2333 P.O.Box 101949 Email: E.Tajkhorshid@dkfz-heidelberg.de 69009 Heidelberg, FRG ********************************************************************** * It is nice to be important, but it is more important to be nice! * ********************************************************************** From wallenborn@phys.chem.ethz.chSat Jul 27 11:15:38 1996 Date: Wed, 10 Jul 1996 11:14:33 +0200 From: Ernst Wallenborn To: tp@elptrs7.rug.ac.be Subject: Re: Transition state search using MOPAC. Status: RO Content-Length: 2567 Hi tere, i guess your MOPAC input is corrupt. See: UHF SADDLE DENSITY GRAPH XYZ CHARGE=1 BAR=0.03 Me--->p methylation activated complex C .000000 0 .000000 0 .000000 0 0 0 0 ^^^^^ a zero here means "do not optimize this coordinate". This is what you want for 6 coords (since you have 3N-6 degrees of freedom), but not more. Here's already three of them. H 1.113983 1 .000000 0 .000000 0 1 0 0 H 1.113983 1 120.001495 1 .000000 0 1 2 0 six zeroes so far, including this one. Now the spatial position of your complex is fixed. Any more zeroes will distort the result. H 1.113968 1 119.999756 1 -179.453217 1 1 2 3 C 5.210007 1 129.371857 1 -179.367538 1 1 2 3 C 1.336975 1 114.626526 1 -2.741700 1 5 1 2 H 1.099976 1 120.501572 1 -179.999634 1 5 6 1 H 1.100006 1 119.749710 1 -179.453217 1 5 6 7 H 1.099976 1 120.499832 1 179.999634 1 6 5 7 H 1.099976 1 119.749710 1 .547287 1 6 5 7 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 First of all, what's Oxygen doing here in the first place. You gave it a bond distance of 0.00 not to be optimized, to atom 0. This cannot lead to any sensical results. C .000000 0 .000000 0 .000000 0 0 0 0 This is even worse. Now you have two atoms, on a non-defined position in space, which do not belong there anyway, and which cannot be moved! C 1.506600 1 .000000 0 .000000 0 1 0 0 C 1.418946 1 116.679237 1 .000000 0 2 1 0 H 1.118213 1 111.091591 1 -60.563965 1 1 2 3 H 1.119848 1 109.781792 1 179.985870 1 1 2 3 H 1.118203 1 111.102783 1 60.532600 1 1 2 3 H 1.150792 1 110.664017 1 174.500137 1 2 1 4 H 1.150722 1 110.665337 1 64.389313 1 2 1 4 H 1.109605 1 121.234596 1 179.993790 1 3 2 1 H 1.110235 1 121.565987 1 -.003556 1 3 2 1 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 I guess you mistake was using Chem3D as z-matrix generator. Try to save as xyz file and read this into mopac (you'll have to manually edit the input file, naturally). Or settle for a different z-matrix editor altogether (i use molden, cause it's unix, free and gives good control over the actual variables) Hope this helps. -- -ernst wallenborn. i'm not a bug. i'm an undocumented feature. From gford@post.cis.smu.eduSat Jul 27 11:24:16 1996 Date: Wed, 10 Jul 96 12:29 CDT From: "George P. Ford" To: tp@elptrs7.rug.ac.be Subject: Re: CCL:M:Searching transition state with MOPAC; part2 Status: RO Content-Length: 3229 "Park, Tae-Yun" writes: > Dear all, > > I've received a lot of helpful messages from many CCLers, > concerning my earlier questions on how to get the structure > of transition state of the reaction, > > > > H H H H H H > | \ / | | | > H-C(+) + C=C ---->(TS?)----> H-C-C-C(+) > | / \ | | | > H H H H H H > > gas-phase gas-phase > methyl ethylene primary propyl > carbenium ion carbenium ion > > > > Thanks a lot! I greatly appreciate all the messages concerning > this problem. > > Most of the messages pointed out that I made a mistake to prepare > the input file for SADDLE calculation; all the atom should be in > the same order between reactants and product z-matrix field. > Dear Pack: I have a couple of comments on your study that might be useful. One refers specifically to the transition state problem, the other relates to the philosophy of your study. The use of saddle is best reserved for complex situations were several bonds are being made and broken at the same time. Reactions like yours, where the transition vector can be anticipated to involve essentially the formation of a single bond, are almost always best studied by following a simple reaction coordinate for the reverse reaction. (This might be a bit less clear-cut if you were not using a Z-matrix-based geometry definition). This also has the advantage of immediately identifying those reactions where there is no transition state per se, i.e. the energy simply falls monotonically from reactants to products. A quick look at your system at the AM1 level shows it to be a reaction of this kind. There is no t.s. - the energy rises to a plateau corresponding to the dissociation energy. A saddle calculation should end up at some arbitrary point on that plateau which it apparently did. While this exercise has hopefully illustrated something about locating transition states it probably isnUt the way to study the chemistry of carbenium ions. The trouble is that the potential surfaces given by AM1, and MNDO (I assume also PM3) are completely wrong. The relative ordering, and even the nature (minimum vs t.s.) of most of the stationary points is incorrect. For example, corner protonated cyclopropane which is probably an intermediate on the true reaction path you are seeking is incorreclty predicted by these methods to be a saddle point. Conversely, the primary propyl cation, predicted to be a minimum at the semiempirical level, is actually a saddle point. Hope this helps, George P. Ford ============================================================================ 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 ============================================================================ From lldmpc::mrgate::a1::moralega@lldmpc.dnet.dupont.comSat Jul 27 11:07:45 1996 Date: Tue, 9 Jul 96 16:18:10 EDT From: "lldmpc::mrgate::a1::moralega"@lldmpc.dnet.dupont.com To: tp@elptrs7.rug.ac.be Subject: RE: CCL:M:Transition state search using MOPAC. Status: RO Content-Length: 2297 From: NAME: GUILLERMO A. MORALES FUNC: Research and Development TEL: 695-1053 To: NAME: tp@elptrs7.rug.ac.be <"tp@elptrs7.rug.ac.be"@ESDS01@MRGATE@LLDMPC> Hi Tae-Yun, I've located transition states for Diels-Alder reactions using CS Chem 3D Pro and MOPAC. I haven't done any work with carbocations, though. Anyways, this is the method I used. Check it out and compare it with yours. 1) Using CS Chem 3D Pro build first the expected product and minimize it. 2) Check that the atom numbers are continuous (1,2,3,etc.). If for some reason one is skipped then renumber ALL the atoms manually (check the manual on how to do this). 3) Save the molecule in MOPAC format. 4) Now with the pointer selec the CH3 unit on the far left (like when you do cut/paste in windows), drag it to the left side of the screen and delete the C-C bond. This is going to be your CH3+ ion. 5) The rest of the molecule is going to be converted automatically into CH3-CH3 Make it manually CH2=CH2 6) I think if you select the CH2=CH2 with the pointer you can minimiza ONLY that molucule EVEN THOUGH the CH3+ is present. I'm not really sure of this. 7) BEFORE you save this window as a MOPAC file MAKE SURE the atom numbers ARE THE SAME. In other words, if in the CH3+ the C is atom 1, then the other H are 2,3,4 MAKE SURE in the expected product the carbon on the left is atom 1 and it's corresponding Hs ae 2,3 and 4. Same fopr the CH2=CH2 unit. This step is CRUCIAL for the saddle calculation since the connectivity in starting materials MUST BE the same as in final products. 8) Now combine both MOPAC files the way you did it before, include the appropriate keywords and run the calculations. 9) Even if the final geometry is not the real transition state (thing I doubt), then take the generated final geometry and refine it. This should do the trick. If you have any more questions just let me know, OK? Good luck. Guillermo. ------------------------------------------------------------------------------- Guillermo A. Morales, Ph.D. Postdoctoral Fellow The DuPont-Merck Pharmaceuticals Co. ------------------------------------------------------------------------------- Note: The ideas/comments herein expressed are mine only. From gwaltney@qtp.ufl.edu Fri Jul 5 12:44 EDT 1996 Received: from qtp.ufl.edu for gwaltney@qtp.ufl.edu by www.ccl.net (8.7.5/950822.1) id MAA19290; Fri, 5 Jul 1996 12:44:41 -0400 (EDT) Received: from red5.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/4.11) id LAA24020; Fri, 5 Jul 1996 11:44:31 -0500 Received: by red5.qtp.ufl.edu (SMI-8.6/4.11) id LAA20439; Fri, 5 Jul 1996 11:43:44 -0500 From: "Steve Gwaltney" Date: Fri, 5 Jul 1996 11:43:44 -0500 Message-Id: <199607051643.LAA20439@red5.qtp.ufl.edu> To: chemistry@www.ccl.net Subject: Re: CCL:MCSCF freq. + scaling factors Cc: muguet@poly.polytechnique.fr Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-MD5: jkxo4rPvdNWiF4B5b5LYew== Content-Type: text/plain; charset=us-ascii Content-Length: 2949 Status: RO > Dear CCL Netters CHEMISTRY@www.ccl.net > > Ref: CAS vs HF frequencies, vibration scaling factors, > > I would like to add my grain of salt to these 2 threads. > > 1/ I would tend to think that MCSCF ( and then CAS ) frequencie are > much better than HF and ALSO MP2. > In the case, where static correlation is important, no doubt MCSCF > is better. It has been argued (in the CCL discussion) > than MP2 might be better to describe dynamic correlation, why ? > In fact, I begun to be suspicious of MP2 schemes, when I realized > that most MP2 energy is coming from the highest virtual MOs, which > feature extremely bizarre contours ( plot them !) and also > very large MO coefficients. > > 2/ For frequencies computed within the harmonic approximation, > scaling factors might correct both for > lack of proper correlation treatment,and > lack of anharmonicity. > > It is safer, whenever possible, to try to separate these 2 issues. > In fact MP2 frequencies, often seem better than MCSCF frequencies > but this might come from a compensation of error with anharmonicity. > Most of the MP2 energy does not come from the highest virtual MO's. The MP2 energy formula is 2 (2) 1 || E = _ sum(ijab) ___________ 4 e +e -e -e i j a b where e and e are the energies of the occupied (spin) orbitals, i j and e and e are the energies of the virtual orbitals. What this a b shows is that when you are exciting out of very low lying occupied orbitals or you are exciting into very high lying virutal orbitals, the denominator is large, and therefore that term contributes very little to the total energy correction. The large energy corrections come when you are exciting from high lying occupied orbitals into low lying virtual orbitals. As to the quality of MP2 vibrational frequencies: in R.J. Bartlett and J.F. Stanton, _Reviews_in_Computational_Chemistry_ Vol. 5, K.B. Lipkowitz and D.B. Boyd, eds. (VCH, New York) 1994, the authors give the following figures. For eight small molecules for which experimental harmonic vibrational frequencies are known, here are the average percent errors for various methods using a DZP basis: SCF 8.7 CISD 3.7 MBPT(2) (also known as MP2) 3.2 SDQ-MBPT(4) 2.5 CCSD 2.2 MBPT(4) 3.1 CCSD(T) 2.4 By the time we get to CCSD(T), the basis set error is probably larger than the method error. No MCSCF values were given, so it is not possible to directly compare the quality of MP2 and MCSCF frequencies. However, it is clear that the quality of MP2 frequencies does not come from a cancellation of method and anharmonicity errors. Steve Steven Gwaltney gwaltney@qtp.ufl.edu Quantum Theory Project University of Florida From Alan.Shusterman@directory.Reed.EDUSat Jul 27 11:34:58 1996 Date: 17 Jul 96 12:53:57 PDT From: Alan Shusterman To: tp@elptrs7.rug.ac.be Subject: Re: CCL:M:Help!: IRC by mopac Status: RO Content-Length: 2377 --- You wrote: I'm searching the structure of the transition state with mopac for the reaction type, olefin + carbenium ion ---> (TS?) ---> carbenium ion (1) --- end of quoted material --- Dear Dr. Park, I believe that you will find it very difficult to get transition states for the electrophilic additions that you are interested in. There are two problems here: 1) the reactions are usually very exothermic and 2) a transition state probably does not exist in the gas phase I have done a few AM1 calculations that illustrate each point (I used SPARTAN version 4.1). First, I examined the addition of 2-propyl cation, Me2CH, to propene, H2C=CHMe, to give 4-methyl-2-pentyl cation, Me2CHCH2CHMe. This reaction converts a secondary cation into another secondary cation and might be expected to be thermoneutral. It is not. The reaction is very exothermic. The AM1 reaction energy is about -28 kcal/mol for propene (7) + 2-propyl cation (192) -> product cation (171) (AM1 heats of formation given in parentheses). An exothermic reaction is actually expected in this case partly because a weak CC pi bond is replaced by a strong CC sigma bond. Next, I tried to find a transition state for the addition. I constrained the length of the forming CC bond in the product cation to be 1.85 angstroms and optimized the geometry of the constrained product. The resulting molecule had an AM1 energy of 182.5 kcal/mol and one large imaginary vibrational frequency corresponding to stretching of the forming CC bond. In other words, the structure and vibration data make this look like a possible transition state. Unfortunately, the energy of this molecule (182) lies in between the energies of the reactants (199) and product (171). It does not correspond to an energy maximum. Thus, when I tried to use this molecule and its Hessian to find an AM1 transition state I was unsuccessful. The energy of the molecule steadily climbed towards 199 and the molecule dissociated into propene and 2-propyl cation. If you think about this type of reaction from a theoretical point of view, say using the curve-crossing model of Shaik and Pross, it seems to me that you would also predict that a transition state might not exist in the gas phase. So these results could be fairly general. Alan Shusterman Department of Chemistry Reed College Portland, OR, 97202 USA From lim@rani.chem.yale.eduSat Jul 27 11:34:45 1996 Date: Wed, 17 Jul 96 12:51:20 EDT From: Dongchul Lim To: Park Tae-Yun Subject: Re: CCL:M:Help!: IRC by mopac Status: RO Content-Length: 2122 > Searching the TS in this reaction, I followed the suggestion > by many CCLers, i.e., try to get the TS structure by the > following steps instead of using SADDLE calculation: > > 1. Try the reacion path calculation in mopac and save the > structure that contains the highest energy level. > > 2. Refine the structure at highest energy level with key > word, NLLSQ, or SIGMA, or TS. > > 3. FORCE calculation with the refined structure to check > if there is one and only one negative frequecy value. > > 4. Do IRC(=1 and -1) calculation to check if the refined > TS gives the reactants and product. > > My result is that until step 3, everything seems OK. Refinning > the TS by NLLSQ/SIGMA/TS gives no significant change of the TS > that obtained from step 1, probably because I used the key word > PRECISE in step 1. The FORCE calculation showed that the refined > structure contains only one frequency values. > > 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? > Hello, I've never used MOLDEN for any purpose, I guess it reads only the first structure from your output, always giving the initial TS geometry. As you may know, an output from IRC calculation contains more than one geometry, i.e., geometries on the reaction coordinate from the TS leading to either the reactants or the product. Therefore, if a MOPAC job has been terminated normally, the last structure in the ouput should correspond to the reactants or the product. Cut the final Z-matrix (or the Cartesian coordinates) from the output and view it with a common molecule viewer program. Good luck! -Dongchul Lim From ccl@www.ccl.net Tue Jul 30 17:17:26 1996 Received: for ccl@www.ccl.net by www.ccl.net (8.7.5/950822.1) id QAA29747; Tue, 30 Jul 1996 16:51:09 -0400 (EDT) From: Computational Chemistry Message-Id: <199607302051.QAA29747@www.ccl.net> Subject: Conference To: chemistry@www.ccl.net Date: Tue, 30 Jul 1996 16:51:09 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Status: RO Content-Length: 1971 Forwarded message: From owner-chemistry@ccl.net Sun Jul 28 20:35 EDT 1996 From: Date: Mon, 29 Jul 1996 10:29:52 +1000 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Apparently-To: Apparently-To: Apparently-To: Apparently-To: Content-Type: text/plain; charset="us-ascii" Content-Length: 1477 Australian Science - Australia's Future Date: Mon, 29 Jul 1996 10:32:29 +1000 To: anchodd@postoffice.utas.edu.au, aschin-list@nuscc.nus.sg, chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net From: D.Winkler@chem.csiro.au (Dr. Dave Winkler) Subject: Structure-Based Design at E-MGMS (October 1996) The First Electronic Molecular Graphics and Modelling Society Conference (MGMS EC-1) will be held on the Internet (the Net) and World Wide Web (the Web) from Oct 7-18, 1996. The conference is sponsored by Elsevier and the Molecular Graphics and Modelling Society and will be co-organized by Graham Richards, Art Olson, Rod Hubbard and Barry Hardy. MGMS EC-1 will be a fully international event open to all members of the scientific community and will cover a broad range of disciplines related to molecular modelling, graphics and simulation methods and applications. I would like to encourage any final subsmissions of papers for the STRUCTURE-BASED DESIGN section of the conference. Please submit abstracts to me as soon as possible. Details can be found at the following URL: http://bellatrix.pcl.ox.ac.uk/mgms/ Cheers, Dave Dr. David A. Winkler Voice: 61-3-9542-2477 Principal Research Scientist Fax: 61-3-9543-8160 CSIRO Division of Chemicals and Polymers http://www.csiro.au Private Bag 10,Clayton South MDC, http://www.wark.csiro.au Clayton 3169, Australia From schaft@caos.kun.nlSat Jul 27 11:34:17 1996 Date: Wed, 17 Jul 1996 17:31:30 +0200 (MDT) From: Gijs Schaftenaar To: tp@elptrs7.rug.ac.be Subject: Re: IRC & Molden Status: RO Content-Length: 699 Dear TAE-YUN Park, Concerning the IRC calculation, try the same calculation with keywords LARGE and X-PRIO, so that the coordinates of the intermediate steps along the reaction coordinate are written to the output file. Then have a look with molden. Regards, Gijs -- +----------------------------+-----------------------------------+ Gijs Schaftenaar, Drs. | CAOS/CAMM Center Email: schaft@caos.kun.nl | University of Nijmegen URL : http://www.caos.kun.nl/staff/schaft.html Tel. : +31 24 3653369 | Toernooiveld 1 Fax : +31 24 3652977 | 6525 ED Nijmegen, The Netherlands +-------- CAOS/CAMM is the Dutch National Node in EMBnet --------+ From borkent@caos.kun.nlSat Jul 27 11:15:07 1996 Date: Wed, 10 Jul 1996 09:40:09 +0200 (MDT) From: Hens Borkent To: tp@elptrs7.rug.ac.be Subject: mopac ts calc. Status: RO Content-Length: 834 Dear Tae-Yun Park, Your question is a rather frequent one these days, so at our site we have developed a tutorial on this subject: http://www.caos.kun.nl/~borkent/compcourse/comp.html You can also have a look at the Re-view pages for more suggestions: http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/ In your case it boils down to drawing the product, then increase the reaction bond length gradually, in which you should observe a maximum, optimize this conformation using the keyword TS, check frequencies with FORCE. I'll give it a try as well. Sincerely, -- ***** J.H. (Hens) Borkent, CAOS/CAMM Center, *CAOS * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CAMM* e-mail: borkent@caos.kun.nl ***** http://www.caos.kun.nl/staff/borkent.html From ZUILHOF@rulgca.LeidenUniv.nlSat Jul 27 10:59:16 1996 Date: Sat, 06 Jul 1996 00:55:02 +0100 (MET) From: Han Zuilhof To: tp@elptrs7.rug.ac.be Subject: carbenium ions Status: RO Content-Length: 1814 Dear Park, Several years ago I've computed the stability of a variety of alkyl and vinyl cations using AM1, PM3, and several ab initio methods. A preliminary report on this was published: Tetrahedron Lett. 1994, 35, 265. In my experinece AM1 is somewhat better than PM3. It makes no sense to go to ab initio methods when one does not include correlation energy corrections. MP2/6-31G*//6-31G* did best (even better than the MP3 equivalent) of the methods we looked at (AM1, PM3, HF/6-31G*, MP2/6-31G*//6-31G* and MP3/6-31G*//6-31G*). A full report on this issue should be published soon. A copy of the chapter of my Ph. D. thesis -which deals in part with this issue- can be obtained from: dr. Gerrit Lodder; Dept. of Chemistry, Gorlaeus Laboratoria; Rijksuniversiteit Leiden; Postbus 9500; 2300 RA Leiden; Nederland. I hope this will help you. If I can assist you in any other way, please let me know. With best regards, Han Zuilhof ****************************************************************************** ** Dr. Han Zuilhof ** e-mail: ZUILHOF@chem.chem.rochester.edu ** ** Department of Chemistry ** (optional: ZUILHOF@rulgca.leidenuniv.nl) ** ** University of Rochester ** ** ** Rochester, NY, 14627 ** Fax: (716) 473-6889 ** ** USA ** Voice: (716) 275-2219 ** ****************************************************************************** ** ** ** "Excite a photochemist!" ** ** ** ****************************************************************************** From borkent@caos.kun.nlSat Jul 27 11:18:10 1996 Date: Wed, 10 Jul 1996 14:38:10 +0200 (MDT) From: Hens Borkent To: tp@elptrs7.rug.ac.be Subject: M:Searching transition state Status: RO Content-Length: 1020 Dear T-Y Park, As promised I had a look at your molecule and found that there is a complication in the form of a cyclic intermediate, which is more stable than the product. Furthermore it is possible that you find no TS, because in vacuum the methyl cation is high in energy and the energy is falling if it approaches the ethylene, continuously. So in fact you have to explore the pot.energy surface by varying the C-C distance and the C-C-C bond angle. There is probably a TS between the bridged intermediate (CH3 symmetrical above the ethylene) and the propyl cation. This is in fact a corner-protonated cyclopropane. This system must have been studied in the literature, using ab initio methods as well. (Von Schleyer, JACS, early 80's). Best regards, -- ***** J.H. (Hens) Borkent, CAOS/CAMM Center, *CAOS * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CAMM* e-mail: borkent@caos.kun.nl ***** http://www.caos.kun.nl/staff/borkent.html From owner-chemistry@ccl.net Tue Jul 23 16:15:58 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id PAA23382; Tue, 23 Jul 1996 15:42:43 -0400 (EDT) Received: from theory.tc.cornell.edu for jeanne@tc.cornell.edu by bedrock.ccl.net (8.7.5/950822.1) id PAA10282; Tue, 23 Jul 1996 15:42:31 -0400 (EDT) Received: from [128.84.181.75] (JEANNE.TC.CORNELL.EDU [128.84.181.75]) by theory.tc.cornell.edu (8.6.9/8.6.6) with SMTP id PAA65581; Tue, 23 Jul 1996 15:31:03 -0400 Date: Tue, 23 Jul 1996 15:31:03 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: (Recipient list suppressed) From: jeanne@TC.Cornell.EDU (Jeanne C. Butler) Subject: Experiences in System Administration of the IBM RS/6000 SP Status: RO Content-Length: 1796 Cornell Theory Center Workshop Experiences in System Adminstration of the IBM RS/6000 SP Thursday, October 10 - Friday, October 11, 1996 Cornell Theory Center Cornell University Ithaca, NY Registration deadline: Friday, September 6, 1996 ------------- OVERVIEW ------------- The Cornell Theory Center (CTC), a nationally funded high performance computing center, is offering a 1.5 day workshop dealing with experiences in system administration of the IBM SP. The workshop will consist mainly of a series of panel sessions on different topics, given by representatives of CTC and several other SP sites. Each panel session will feature short presentations by panel members followed by time for discussion and questions from the audience. IBM will give a presentation on and demonstration of graphical tools being developed for system management. Ample time will be provided for informal discussions. CTC's SP, which consists of 512 RISC processors connected by a high performance switch, is the largest of its kind in the world. Resource scheduling is handled by EASY-LoadLeveler. Details may be found on the Web at http://www.tc.cornell.edu/Resources/. -------------------- PREREQUISITES -------------------- This workshop is intended for system administrators who already have experience in managing an SP system. Therefore, we will assume participants are already familiar with the basics of managing an SP system, and have had experience in doing so. Sessions will focus on sharing experiences, and will not be tutorials. There will not be any hands-on sessions. ------------------------------------ REGISTRATION INFORMATION ------------------------------------ To register for this workshop, and for additional information, go to: http://www.tc.cornell.edu/Edu/Upcoming/sysadm.html From newhoir@duc.auburn.eduSat Jul 27 11:24:06 1996 Date: Wed, 10 Jul 1996 11:47:12 -0500 From: Irene Newhouse To: tp@elptrs7.rug.ac.be Subject: Re: CCL:M:Searching transition state with MOPAC; part2 Status: RO Content-Length: 840 Try your latest structure in a frequency computation & see if there is indeed 1 & only 1 'negative' frequency [it's really imaginary, but is reported as negative by the program]. I've found transition states to be very nonintuitive. Not surprising, since so little experimental work can be done! The 'obvious' choices for TSs, I've found, are often plain wrong!!! If this is not indeed a very reactant-like TS, & you still haven't located it, look at the literature & see if you can find a similar computation somewhere. Use that as a model, no matter how strange it looks, & see where it gets you. For example, see Foresman & Frisch's book on using Gaussian for the Formal- dehyde decomp/formation rxn from CO & H2. I'd not have guessed that TS struc- ture in a month of Sundays, yet that's what it is! Good luck! Irene Newhouse From jig@qorg.unizar.esSat Jul 27 11:14:17 1996 Date: Wed, 10 Jul 96 9:22:32 METDST From: Jose Ignacio Garcia To: tp@elptrs7.rug.ac.be Subject: SADDLE calculation Status: RO Content-Length: 1906 My guess for your problem is that the "terrible" result you get is mainly due to the fact that you are trying to calculate an ion-molecule reaction IN THE GAS PHASE. As ions are VERY unstable in the gas phase, its reactivity can be also very different that that observed in solution, where the ion is comfortably solvated. Thus, in general, in an isolated system calculation as yours, an ion always will tend to be "solvated" by the neutral molecule, through a polarisability mechanism, and will approach to its hydrogen atoms. Often, this approach ends with a hydrogen abstraction reaction, as you observed. I have not experience with cation reactions, but this is exactly what happens with the paradigmatic SN2 reaction between chloride ion and methyl chloride. If one wants to correctly describe the SN2 attack, one must be careful in designing the chloride approach trajectory. Maybe the inclusion of solvation effects through a continuum model would help to fix this problem. I hope this helps you. Best regards. Jose I. Garcia -- -------------------------------------------------------------------------------- Dr. Jose Ignacio Garcia-Laureiro Phone : 34-(9)76-762077 Departamento de Quimica Organica 761210 Instituto de Ciencia de Materiales de Aragon Fax : 34-(9)76-761159 C.S.I.C.-Universidad de Zaragoza e-mail: jig@qorg.unizar.es E-50009 ZARAGOZA (SPAIN) jig@msf.unizar.es jig@posta.unizar.es -------------------------------------------------------------------------------- "And all this science I don't understand it's just my job five days a week..." ELTON JOHN - Rocket man -------------------------------------------------------------------------------- From jig@qorg.unizar.esSat Jul 27 11:16:34 1996 Date: Wed, 10 Jul 96 14:14:42 METDST From: Jose Ignacio Garcia To: tp@elptrs7.rug.ac.be Subject: SADDLE calculation Status: RO Content-Length: 1491 Hello! It's me again. Have you tried to use an alternative method to SADDLE? For instance, a reaction coordinate can be estimated by starting from the product and breaking the C-C bond. As the C-C distance increases, the total energy will change, and a maximum will probably appear. The structure corresponding to this maximum can be then used as an starting point for a TS or NLLSQ calculation. By the way, I am still concerned with solvation. It is sure that in the approach of the cation to the neutral molecule, an energy minimum corresponding to an ion-molecule pair will be observed. Best regards. Jose I. Garcia -- -------------------------------------------------------------------------------- Dr. Jose Ignacio Garcia-Laureiro Phone : 34-(9)76-762077 Departamento de Quimica Organica 761210 Instituto de Ciencia de Materiales de Aragon Fax : 34-(9)76-761159 C.S.I.C.-Universidad de Zaragoza e-mail: jig@qorg.unizar.es E-50009 ZARAGOZA (SPAIN) jig@msf.unizar.es jig@posta.unizar.es -------------------------------------------------------------------------------- "And all this science I don't understand it's just my job five days a week..." ELTON JOHN - Rocket man -------------------------------------------------------------------------------- From owner-chemistry@ccl.net Sat Jul 13 05:29 EDT 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id FAA22413; Sat, 13 Jul 1996 05:29:10 -0400 (EDT) Received: from po8.andrew.cmu.edu for ar1z+@andrew.cmu.edu by bedrock.ccl.net (8.7.5/950822.1) id FAA23424; Sat, 13 Jul 1996 05:29:10 -0400 (EDT) Received: (from postman@localhost) by po8.andrew.cmu.edu (8.7.5/8.7.3) id FAA17792; Sat, 13 Jul 1996 05:29:01 -0400 Received: via switchmail; Sat, 13 Jul 1996 05:29:00 -0400 (EDT) Received: from po6.andrew.cmu.edu via qmail ID ; Sat, 13 Jul 1996 05:28:17 -0400 (EDT) Received: from unix14.andrew.cmu.edu via qmail ID ; Fri, 12 Jul 1996 13:45:46 -0400 (EDT) Received: from mms.4.60.Jun.27.1996.03.02.53.sun4.51.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix14.andrew.cmu.edu.sun4m.54 via MS.5.6.unix14.andrew.cmu.edu.sun4_51; Fri, 12 Jul 1996 13:45:46 -0400 (EDT) Message-ID: <8ltcx_K00YUq0EM1E0@andrew.cmu.edu> Date: Fri, 12 Jul 1996 13:45:46 -0400 (EDT) From: Alexander J Ropelewski To: chemistry@www.ccl.net Subject: CCL:biomedical workshop announcement BIOMEDICAL WORKSHOPS PITTSBURGH SUPERCOMPUTING CENTER August 25-28, 1996 The Pittsburgh Supercomputing Center is offering an "ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS" workshop. The workshop is open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have previous experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for what is commonly referred to as "homology modeling", specifically the methods known as threading techniques. This involves fitting the sequences of proteins whose structure is not known to the known three-dimensional structure of another protein. The workshop will feature the threading techniques developed by Dr. Stephen H. Bryant of the Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine. Dr. Bryant's work focuses on empirical energy functions that measure the complementarity of sequence and folding motif and on algorithms for rapid threading. His group is also developing computer programs for automatically creating homology models derived from core structural motifs identified by other sequence analysis techniques. Instructors are: Dr. Stephen H. Bryant, National Center for Biotechnology Information, National Library of Medicine Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. APPLICATION DEADLINE: July 17, 1996. For additional information, please refer to http://www.psc.edu/biomed/workshops.html CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant, (412)268-4960, blankens@psc.edu ********** PITTSBURGH SUPERCOMPUTING CENTER ADVANCED SEQUENCE ANALYSIS WORKSHOP APPLICATION Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From jrg@chem.duke.edu Tue Jul 23 11:15:54 1996 Received: from chem.duke.edu for jrg@chem.duke.edu by www.ccl.net (8.7.5/950822.1) id KAA21552; Tue, 23 Jul 1996 10:25:12 -0400 (EDT) Received: from pauling.chem.duke.edu (pauling.chem.duke.edu [152.3.169.110]) by chem.duke.edu (8.7.4/Duke-1.1) with ESMTP id KAA09240; Tue, 23 Jul 1996 10:23:35 -0400 (EDT) Received: (jrg@localhost) by pauling.chem.duke.edu (8.7.4/Duke-1.1) id KAA20498; Tue, 23 Jul 1996 10:23:34 -0400 (EDT) Date: Tue, 23 Jul 1996 10:23:31 -0400 (EDT) From: Juvencio Robles X-Sender: jrg@pauling To: "'Computational Chemistry'" cc: robles juvencio , cancun 1997 organizers -- pruitt chris , garritz andoni , eubanks dwaine , juaristi eusebio , duke yang weitao , cancun 1997 speakers -- alvarado-swaisgood aileen , bader richard , "biosym (julie)" , gazquez joseluis , cisneros gerardo , parr robert unc , sosa plinio , "spartan (carmen y Hehre)" , uncch tropsha alex , uami vela alberto , Scott Zimmermann , bartolotti lee 1 Subject: final program for CANCUN 97 symposium on Comp chem --> education Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 4628 Dear CCL'ers Here is the final program and description of the Symposium 544: "New Trends in Atomic and Molecular Structure Teaching" which is to be held during the Fifth Chemical Congress of North America We hope many of you would be interested to attend and to send contributions. > ************************************** > > Fifth Chemical Congress of North America. > > Cancun, MEXICO. (November 11-15, 1997) > > Symposium 544: "New Trends in Atomic and Molecular Structure Teaching" > > Organizers: Juvencio Robles (University of Guanajuato) and Weitao > Yang (Duke University). > > ************************************** > > Description and Justification: > > Visualization of atomic and molecular structures, along with > associated structure-reactivity relationships and the microscopic para- > meters that describe them are important topics of modern research, but > could be incorporated to some extent in both undergraduate and graduate > chemistry curricula. Recent developments in theory, hardware and > molecular modelling software enable students to acquire clearer understan- > ding of relationships between conformation, structure, energetics, and > many other aspects of modern chemistry education. > This symposium attempts to make a bridge between important recent > research developments in this field and potential opportunities to > improve teaching of some difficult subject areas in chemistry. > > SCOPE: > > The scope of this symposium will cover these areas: > > 1) Computational Chemistry and related software/hardware for atomic > and molecular structure education. > > 2) New theoretical concepts that provide insight in the teaching of > this field. This includes quantum chemistry and Density functional theory > related concepts (such as electronegativities, HSAB principle, hardness, > fukui functions, action principle), molecular electrostatic > potentials, etc. > > 3) Models and analogies useful to teach difficult concepts in this field. > > > CONFIRMED SPEAKERS AND THEIR TENTATIVE TOPICS > > The following speakers, from the three countries, have accepted our > invitation to participate at this symposium > > > USA: > > 1) Scott Zimmermann (Brigham Young University) "Molecular modelling in > Biochemistry". > > 2) Alex Tropsha (UNC-Chapel Hill) "Integration of formal training and > research in molecular modelling curriculum". > > 3) Warren Hehre (Wavefunction, Inc.) "Practical electronic structure > methods". > > 4) Chengteh Lee (Cray Research) "Molecular design of water structure". > > 5) Aileen Alvarado-Swaisgood (Biosym/MSI) "Recent successes in the > integration of computational chemistry software into the curriculum > of academic institutions worldwide". 6) Lee Bartolotti (North Carolina Super Computing Center) "Density-Functional Theory: A Tool for Researchers and Educators." > MEXICO: > 7) J.L. Gazquez (Univ. Autonoma Metropolitana) "Hard and Soft Acids > and Bases". > > 8) Alberto Vela (Univ. Autonoma Metropolitana) "Symbolic Mathematics in > the quantum chemistry classroom: The UAM-I experience". > > 9) Plinio Sosa (Univ. Nac. Autonoma de Mexico) "Atomic and Molecular > structure teaching at the high school level". > > 10) Gerardo Cisneros (Cray Research de Mexico) "Symmetry eigenfunction > tools for research and training". > > > CANADA: > > 11) Richard Bader (McMaster University) "Relating chemistry to > quantum mechanics using the electron and current densities and the > action principle". > > ******************************************* > > Sessions chairmen: > > 1) Robert G. Parr (University of North Carolina -Chapel Hill) > 2) Weitao Yang (Duke Uiversity) > 3) Juvencio Robles (University of Guanajuato). > Temporary address until July 31,1996: ---------------------------------------------------------------- Juvencio Robles TEL: (919)660-1529 Visiting Professor FAX: (919)660-1605 Department of Chemistry EMAIL: jrg@chem.duke.edu Duke University Box 90346 Durham, North Carolina 27708-0346 USA ---------------------------------------------------------------- Permanent address: **************************************************************** Dr. Juvencio Robles |e-mail: roblesj@quijote.ugto.mx Profesor de Quimica | Facultad de Quimica, | Universidad de Guanajuato, |phone: +(52-473) 26885 Noria Alta s/n | Guanajuato, Gto. 36050 |fax: +(52-473) 24250 MEXICO. | **************************************************************** From olsonl@darwin.pprd.abbott.comSat Jul 27 11:24:00 1996 Date: Wed, 10 Jul 1996 10:56:02 -0500 From: "Leif P. Olson" To: tp@elptrs7.rug.ac.be Subject: mopac ts Status: RO Content-Length: 2320 Hi Tae-Yun, I would suggest taking a different approach altogether, breaking up the problem into several parts: 1) get an approximate transition state for the reaction. Forget about SADDLE and so forth; just do a trajectory calculation where you start with your 1-n-propyl cation and stretch the bond in small increments (say, 0.1 angstroms) from the starting point to about 4 or 5 angstroms. Remember, by microscopic reversibility, the ts for the reverse reaction is precisely the same as the forward reaction. Also, by starting with one molecule rather than two, you can be pretty sure that the program will not get confused about how to assign the electrons in the orbitals, at least in the early stages of the reaction. 2) take the highest point in the trajectory and see if it seems like some reasonable structure. If so, change the coordinate system from internal coordinates (used in the trajectory calculation) to xyz coordinates. Searches using the TS keyword, in my experience, almost always benefit from being done in Cartesian coordinates (despite what the manual says regarding the use of this in only difficult cases). The eigenvector-following algorithm works pretty well (TS keyword). 3) Once you have a refined TS structure, you may want to refine it a bit further; i.e., if you are quite close to a symmetric structure, you may want to go back to internal coordinates and make 179.8 degree dihedrals to 180.000, for example. This must be done judiciously, but can in some cases overcome rounding errors that creep in. Now try another TS calculation (or NLLSQ or SIGMA) using tighter optimization criteria. 4) Do a FORCE calculation to see if you are at a true transition state 5) Do an IRC run to make sure that the transition state you have actually goes to reactants and products (actually this requires two IRC runs). If you used the PRECISE keyword in step 2, you can generally skip step 3 entirely. But the general pattern has proven successful for me in the past. The two most important points seem to be (i) having a good guess at an approximate transition state; and (ii) using the combination of XYZ and TS. As a separate issue: why not do good-quality ab initio calculations instead? You only have three heavy atoms. Leif Olson olsonl@darwin.pprd.abbott.com From kcousins@wiley.csusb.eduSat Jul 27 11:24:24 1996 Date: Wed, 10 Jul 1996 13:11:17 -0700 (PDT) From: Kimberley Cousins To: tp@elptrs7.rug.ac.be Subject: TS location Status: RO Content-Length: 689 Hi. I've had limited luck with Saddle, and usually use the "reaction coordinate" approach. Your first Z matrix is set up to do just that. Instead of "1" for C1-C2 bond length opt, use "-1" and list a series of decreasing bond lenghths following a blank line following the Z matrices (like 7.1, 6.1, 5.1 . . .) and look for the highest energy structure generated that doesn't otherwise fly apart. This should (might) be your approx TS structure that you can optimize further using NLLSQ or the like. Kimberley Cousins Department of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@wiley.csusb.edu From milet@quantix.u-strasbg.fr Thu Jul 11 06:30 EDT 1996 Received: from quantix.u-strasbg.fr for milet@quantix.u-strasbg.fr by www.ccl.net (8.7.5/950822.1) id GAA08404; Thu, 11 Jul 1996 06:30:16 -0400 (EDT) Received: by quantix.u-strasbg.fr (AIX 3.2/UCB 5.64/4.03) id AA38252; Thu, 11 Jul 1996 12:30:28 +0200 From: Date: Thu, 11 Jul 1996 12:30:28 +0200 Message-Id: <9607111030.AA38252@quantix.u-strasbg.fr> To: chemistry@www.ccl.net Subject: CCL: random stops in G94 Content-Type: text Content-Length: 1042 Status: RO Dear All, We have a strange and random problem : we are running Gaussian 94 on a IBM 43P (Power PC) under AIX4.1.4 with 128 Meg of memory and 284 Meg of pagingspace. Gaussian 94 was compiled with IBM Fortran 3.2. We run Gaussian with : nohup 'script-in-csh' and it stops mysteriously with no error message (nor in the output file nor in the errlog), no core dump...just stops (the scratch files are not removed by Gaussian). Sometimes after a re-start of the script it goes to the end and sometimes it stops again after one or more optimisation steps. It happens after writing the energy on the output file. There is enough temporary scratch space available. Does anyone have had the same problem ? or have an idea what it could be and/or what to do ? Thanks in advance Anne Milet =========================================================== Anne Milet Laboratoire de Chimie quantique UPR 139 4, rue Blaise Pascal 67000 Strasbourg e-mail : milet@quantix.u-strasbg.fr =========================================================== From luo96@cyberramp.net Thu Jul 18 02:16:17 1996 Received: from mailhost.cyberramp.net for luo96@cyberramp.net by www.ccl.net (8.7.5/950822.1) id BAA22131; Thu, 18 Jul 1996 01:41:43 -0400 (EDT) Received: from ramp1-12.cyberramp.net (ramp1-12.cyberramp.net [206.42.4.61]) by mailhost.cyberramp.net (8.7.1/8.7.1/$Revision: 1.2 $) with SMTP id AAA24329 for ; Thu, 18 Jul 1996 00:41:08 -0500 (CDT) Date: Thu, 18 Jul 1996 00:41:08 -0500 (CDT) Message-Id: <199607180541.AAA24329@mailhost.cyberramp.net> X-Sender: luo96@cyberramp.net (Unverified) X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: luo96@cyberramp.net (Yu-Ran Luo) Subject: Which Company Would Consider A Novel Proposal? Status: RO Content-Length: 3022 Which Company Would Consider A Novel Proposal? >Hi, Neters, > > Are you interested to predict BOND DISSOCIATION ENERGIES (BDEs) >in large organic species ? > > You know, the BDEs are considered to be fundamental to chemistry and >biochemistry. However, about thousands of the experimental BDEs values in >organic species are available today although several hundreds of research >groups measured for sixty years. > > We thus need theory to help enlarge our knowledge. Here I would share a >good news with you. > > I found a reliable and simple method for predicting BDEs during the past >nine years. It is most powerful to large organic, organometallic and >biologically active species. Now the values of trillions of BDEs can be >estimated easily by my approach and a calculator (not computer so far!). The >large-size species include biologically active species (eg., Vitamins A, C, D, >E, K), drugs (nicotine, hormones), toxicant, explosives/energetic materials >(eg., TNT, RDX, NTO), fuels/coals and so on. Once an organic molecular >structure is drawn, I can quickly point out where the weakest bond is, how >large this BDE is, what the stability and reactivity of this molecule are, and >which position in this molecule will react first (active site or reaction >center). These predictions will save a lot of money and time for scientists >and engineers, and very useful for the computer-aided molecular design. > > You may give me a test. Which molecules you are interested? Please show >me and draw the structures. I would give you the answers ASAP. > > I hope my research will be a new and powerful tool for chemistry, >chemical engineering, energy science, molecular biology, medicinal chemistry, >protein/enzyme chemistry. Why is the human visual system sensitive only to >light of wavelengths from about 760 to 380 nm? Why is "super-vitamin E" >possible? Which structure is a super-vitamin E? I can give quantitative >answers now. The main reason is that I can describe the species energetics and >its change/transfer. > > My method is different from MO theory, FDT, MM and the group additivity. >But my results can compare with the FDT calculations based new Gaussian >package and supercomputer. > > My method is a key to open the unknown door of molecular energetics. >Some scientists thus advised me to make an electronic version of my method and >link it with a good software available so that you only play a mouse and >keyboard when predicting the BDEs. This is a good suggestion. You know, there >are so many chemical/biochemical software companies. Unfortunately, they have >not known my method. > > Which company would consider this project and make this link? Please >tell me. My proposal is > > My Method For BDEs + A Best Structure Software ---> A New Program > > Thank you for your attention. > > Yu-Ran Luo, Ph. D. > (3100 Verbena Drive, Plano, TX 75075, Phone and Fax 214-509-2075, > E-Mail: luo96@cyberramp.net) From Y0H8797@ACS.TAMU.EDUSat Jul 27 10:55:40 1996 Date: Fri, 5 Jul 1996 12:06:02 -0500 (CDT) From: YONG HUANG To: TP@elptrs7.rug.ac.be Subject: From CCL archive ---------Yong (Texas A&M) Status: RO Content-Length: 17524 From: SMTP%"pitsel@chemul.uni.lodz.pl" 2-NOV-1995 06:52:30.77 To: Y0H8797 CC: Subj: CCL:G:summary AM1 vs PM3 Return-Path: Received: from www.ccl.net by VMS2.TAMU.EDU with SMTP; Thu, 2 Nov 1995 6:52:28 -0600 (CST) Received: for chemistry-request@www.ccl.net by www.ccl.net (8.6.10/950822.1) id DAA27298; Thu, 2 Nov 1995 03:34:28 -0500 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id DAA27135; Thu, 2 Nov 1995 03:20:05 -0500 Received: from chemul.uni.lodz.pl for pitsel@chemul.uni.lodz.pl by bedrock.ccl.net (8.7.1/950822.1) id DAA09331; Thu, 2 Nov 1995 03:19:26 -0500 (EST) Received: by chemul.uni.lodz.pl (5.65/25-eef) id AA18481; Thu, 2 Nov 95 08:19:12 +0100 Message-Id: <9511020719.AA18481@chemul.uni.lodz.pl> From: pitsel@chemul.uni.lodz.pl (Piotr Seliger) X-Mailer: SCO System V Mail (version 3.2) To: chemistry@ccl.net, jlye@tx.ncsu.edu, m.t.cronin@livjm.ac.uk, moralega%a1@lldmpc Subject: CCL:G:summary AM1 vs PM3 Date: Thu, 2 Nov 95 8:19:11 MEZ Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk This is the summary of the responses I got to my request about AM1 vs PM3 references. Thanks for help. ---------------- ***************************************************************************** Dear Dr. Seliger, Following is a note that I sent to the next over a year ago. Perhaps it will be informative. Our SAM1 papers also extensively documented PMs vs AM1 as well as SAM1. The references for these are: 1. Dewar, M. J. S.; Jie, C.; Yu, G. Tetrahedron 1993, 23, 5003. 2. Holder, A. J.; Dennington, R. D.; Jie, C. Tetrahedron 1994, 50, 627. 3. Holder, A. J.; Evleth, E. M. in Modeling the Hydrogen Bond; Smith, D. A.; American Chemical Society, Washington, DC, 1994; pp 113. Please let me know if I can be of further assistance Regards, Andy Holder -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- UUUU UUU MMM MMKK KKKK CCCC | ANDREW J. HOLDER UU U MM MMK K CC CC | Assoc. Prof. of Comp./Org. Chemistry UU U MMM M MK KK CCC | Dept. of Chemistry UU U M MM MK KK CC CC | University of Missouri-Kansas City UUUUU MMM M MMKK KK CCCC | Kansas City, MO 64110 KK | aholder@cctr.umkc.edu K | (816) 235-2293, FAX (816) 235-5502 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Netters, A few weeks ago, Jeffrey Nauss asked about a comparison between the AM1 and PM3 semiempirical methods. Both of these semiempirical methods are included in most programs that support semiempirical calculations (AMPAC, MOPAC, etc.). Please note that the following discussion is MY OPINION and a compendium of MY EXPERIENCES. I hope you find it somewhat useful. The lead references to each method follows: AM1: Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902. PM3: Stewart, J. J. P. J. Comput. Chem. 1989, 10, 209. AM1 stands for "Austin Model 1" and PM3 stands for "Parameterization Method 3". Both methods implement the same basic NDDO theory pioneered by Michael Dewar while at the University of Texas at Austin. The differ- erence is in how the parameters that the semiempirical methods utilize to replace portions of the full ab initio implementation of Hartree-Fock theory. Perhaps the most important difference between AM1 and PM3 is the involvement of the researcher in the parameterization process. PM3 was developed using a largely undirected mathematical optimization process with greatly reduced guidance from chemical knowledge or intuition, an addition that the Dewar methods consider essential. The human researcher knows for which molecules it is necessary to obtain the best fit. For instance, it is useless to obtain parameters for carbon and hydrogen that describe the properties of cubane correctly if the results for benzene are significantly different from experiment. An attentive and knowledgeable chemist can also guide the search into areas of the parameter hypersurface that make sense as far as the absolute magnitude of the parameters themselves are concerned. As with many chemical properties, the parameter values should vary periodically. While this should not unduly constrain the final values, parameters should follow well-defined general trends for proper interaction with other elements. In terms of the actual NDDO model, the actual parameters allowed to vary in the two methods are quite different. In AM1, a large number of values we used from spectroscopy for some of the one-center terms and the other parameters derived with these values fixed. (This is possible only for the lighter elements in the Main Group.) PM3 allowed ALL of these values to float, resulting in substantially more parameters. AM1 also had a quite different concept as to the application of the Guassian functions introduced with AM1 to adjust the core-electron/core- electron repulsion function. Workers in the Dewar group and subsequently in my group see Gaussian functions as PATCHES to the theory, not integral parts. All models fail at some point and the Gaussians were introduced to help with some of the systematic errors in MNDO. Traditionally, these patches were applied to adjust for difficult molecular systems AFTER semiempirical parameters were stabilized. PM3 includes these Gaussian functions (two for each element) FROM THE BEGINNING. Our experience indicates that in such a situtaion, the chemistry os the element will very likely be very strongly effected by the presence of these functions and the importance of the "real", "chemical" parameters will be reduced and swallowed up bu the Gaussians. In short, Gaussians should only be used where absolutely needed, and then viewed with askance. The essence of the difference between the two philosophies is evident: the theoretical basis for the method is either accepted or denied. Significant approximations are made to gain the speed advantage that semiempirical methods enjoy over their ab initio quantum mechanical brethren. But both the ab initio and semiempirical models are based on the Hartree-Fock set of ideas. These ideas possess theoretical rigor as regards solution of the Schrodinger Equation. If one simply views the semiempirical parameters as adjustables within a curve-fit scheme rather than as components of a theoretical model, little faith or importance resides in the meaning of their final values. Simply put, the method of parameterization described above and used so successfully with AM1 and MNDO (and now SAM1) expresses confidence in the theory. With a firmer footing in chemical reality, AM1 parameters are more likely to yield useful results for situations not specifically included in the molecular basis set for parameterization (MBSP). Some Practical Considerations ----------------------------- The differences in errors between the two methods as published are minimal, but that does not relate the real story of how the methods perform differently. Some key points: - PM3 is clearly better for NO2 compounds as a larger number of these were included in the MBSP. - PM3 is usually a little better for geometries, as these were also heavily weighted. - The molecular orbital picture with PM3 is usually different from that expected or that predicted by other methods. This is a direct consequence of the lack of attention paid to the absolute values of Uss and Upp. It can be seen in the lack of performance in ionization potentials. - PM3 charges are usually unreliable, again a result of the rather strange values that some of the parameters take on, even when other experimental data such as heats of formation and geometries are acceptable. This makes PM3 essentially useless for the derivation of molecular m echanics force fields. Perhaps the best known example of this is the case of formamide. The partial charges for the atoms in the molecules are listed below. The lack of any appreciable charge on N has led to a reversal of the actual bond dipole between C and N in this molecule! Atom AM1 PM3 HF/6-31G* --------------------------------------------- O -0.3706 -0.3692 -0.5541 C 0.2575 0.2141 0.5079 N -0.4483 -0.0311 -0.8835 O // H-C \ NH2 - Several papers have been published describing the performance of AM1 vs. PM3: Dewar, M. J. S.; Healy, E. F.; Yuan, Y.-C.; Holder, A. J. J. Comput. Chem. 1990, 11, 541. Smith, D.A. J. Fluor. Chem. 1990, 50, 427 Smith, D.A.; Ulmer, C.W.; Gilbert, M.J. J. Comput. Chem. 1992, 13, 640. - Most reserachers in my experience have stopped using PM3 and have returned to AM1. An Example of Parameterization Values for Aluminum -------------------------------------------------- Parameter AM1 MNDO PM3 Uss, eV -24.353585 -23.807097 -24.845404 Upp, eV -18.363645 -17.519878 -22.264159 zetas, au 1.516593 1.70288 } 1.444161 zetap, au 1.306347 1.073269 betas, eV -3.866822 -0.594301 } -2.670284 betap, eV -2.317146 -0.956550 alpha 1.976586 1.868839 1.521073 Gaussians: Intensity #1, eV 0.090000 - -0.473090 Width #1 12.392443 - 1.915825 Position #1 2.050394 - 1.451728 Intensity #2, eV - - -0.154051 Width #2 - - 6.005086 Position #2 - - 2.51997 The point on the potential surface located by PM3 is significantly different than that located by AM1. This is immediately apparent from the large discrepancy between the Upp values. These are the important one- electron energy values and they have strong influence on the parameter hypersurface. Also, the difference between Uss and Upp for both MNDO and AM1 is about 6 eV. This has been reduced to 2.5 eV in PM3. The real difficulty, however, is in the Beta values. These parameters are the two-center/one- electron resonance terms and are responsible for bonding interactions between atoms. The PM3 values are almost zero, resulting in the conclusion that there is very little bonding between atoms involving aluminum! (Note that the AM1 values for betas and betap spread out around the single MNDO value for beta. This suggests that the MNDO values were reasonable and AM1 adds greater flexibility.) PM3 regains the bonding interactions lost in the low beta values with two strongly attractive Gaussians spanning the bonding region. ******************************************************************************* We did a short note on rotational barriers in branched alkenes: L. A. Burke et al. J. Physical Organic Chem vol 5,614-616(1992). We were surprised at the time that no one else seemed to have published such results. Luke Anthony Burke tel:609-225-6158 Department of Chemistry fax:609-225-6506 Rutgers University e-mail: Camden, NJ 08102 burke@camden.rutgers.edu USA ****************************************************************************** The comparison of AM1 against PM3 has been quite recently discussed on this list. You may try to search trough archives. My three pens to that discuss may be that AM1 absolutely incorrectly describes interaction in small water clusters; while it was known that it gives not correct hydrogen bond geometry for dimers - I found that it also fails for geometry of larger systems: tetramers, octamers etc. The geometry is absolutely different from what we expect for such clusters (as known from ab-initio and MD studies). In the same time PM3 reproduces these geometries acceptably good - difference in oxygen position between PM3 and HF/6-31G* is ~ 0.1 A for octamers. This is a reason that I am now using PM3 in my Molecular Dynamics studies that use semi-empirical energy surface to derive forces (kind of "quantum" dynamics). Mirek --------------------------------------------------------------- dr Miroslaw Sopek MAKO-LAB Computer Graphics Laboratory ul. Piotrkowska 102a 90-026 LODZ, POLAND tel. (48)(42)332946,322346 fax. (48)(42)332937 e-mail: mako@pdi.lodz.pl, sopekmir@mitr.p.lodz.pl --------------------------------------------------------------- ******************************************************************************* 1995 Oct 28 Recently the NET was asked for refs to (1) AM1 compared to PM3, and (2) Sigma-aromaticity. Here are some refs: AM1 cf. PM3 1) Extensive comparison: J Computer-Aided Molecular Design, 4 (1990) Issue 1 (Special issue) ; discusses PM3, AM1 and MNDO 2) W. Thiel, Tetrahedron, 44 (1988) 7393 3) J. J. P. Stewart, J Comp Chem 11 (1990) 543 10 (1989) 209 10 (1989) 221 12 (1991) 320 4) Dewar et al J Comp Chem 11 (1990) 541 5) Smith et al J Comp Chem 13 (1992) 640 6) In a letter to the Net (1995), Andy Holder (SemiChem) said: PM3 is better than AM1 for NO2 compounds and usually a little better for geom's. It is not as good for MO's and is unreliable for charges. Sigma-aromaticity 1) M. J. S. Dewar "Chemical Implications of Sigma Conjugation" J Am Chem Soc 106 (1984) 669 2) Inagaki et al JACS 116 (1994) 5954 3) Ichikawa et al J Phys Chem 99 (1995) 2307 4) Hiberty et al JACS 117 (1995) 7760 =========== Errol Lewars Chem Dept Trent U, Peterborough Ontario Canada ===== *****************************************************************************8 Piotr- We have a paper in press with Spectrochimica Acta comparing AM1 and PM3 for the prediction of carboxylate stretches. Briefly, PM3 is much closer in absolute terms, but AM1 represents differences between compounds more reliably. This is a very limited specific application, of course, and probably only useful to spectroscopists. I would be interested in hearing what others have to say about more general comparisons. Regards, Steve Cabaniss ****************************************************************************** If you mean comparison of conformational energies you might want to have a look at our paper in J.Comp:Chem. 12, 200 (1991). Kind Regards * Klaus Gundertofte * Head, Department of Computational Chemistry * H.Lundbeck A/S * Ottiliavej 9 * DK-2500 Valby - Denmark Fax +45 3630 1385 * Phone +45 3644 2425-3206 * E-mail kgu@lundbeck.dk *************************************************************************** Hi Piotr, The performance of this methods in relation to which property ? If you are interested in heats of formation both are OK with about the same results. For minimum energy conformations PM3 has lots of problems. I performed many calculations with PM3, AM1 and ab initio and PM3 is qualitatively wrong in most cases. For electronic properties I didn't tried PM3. Best regards, Edgardo Garcia Cristol Chem & Biochem University of Colorado BOULDER CO USA **************************************************************************** Note: %0 Journal Article %A Gano, J.E. %A Jacob, E.J. %A Roesner, R. %D 1991 %T Evaluation of PM3, AM1, and MNDO for Calculation of Higher Energy Ionization Potentials %B J. Computat. Chem. %V 12 %P 127-134 James E. Gano, Director Instrumentation Center in Arts and Sciences University of Toledo Toledo, Ohio 43606 Instrumentation Center : http://www.icenter.utoledo.edu Department of Chemistry: http://www.chem.utoledo.edu 419-530-7847 419-530-4033 (FAX) ****************************** THE END ********************************* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Piotr Seliger PPP I TTT SSS EEE L Department of General P P I T S E L and Inorganic Chemistry, PPP I T SSS EE L University of Lodz, P I T S E L Narutowicza 68, P I T SSS EEE LLL 90-136 Lodz, POLAND "The right to knowledge is like E-mail: pitsel@chemul.uni.lodz.pl the right to life" (G.B.Shaw) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From csilmt12@area.BA.CNR.IT Wed Jul 10 05:40 EDT 1996 Received: from icnucevx.cnuce.cnr.it for csilmt12@area.BA.CNR.IT by www.ccl.net (8.7.5/950822.1) id FAA00975; Wed, 10 Jul 1996 05:40:07 -0400 (EDT) Received: from area.ba.cnr.it by mailsrv.cnuce.cnr.it (PMDF V5.0-6 #9955) id <01I6WN70C15CAC2VQH@mailsrv.cnuce.cnr.it> for CHEMISTRY@www.ccl.net; Wed, 10 Jul 1996 11:38:58 +0100 (MET) Received: by area.ba.cnr.it; (5.65/1.1.8.2/27Mar96-1138AM) id AA25733; Wed, 10 Jul 1996 11:38:52 +0200 Date: Wed, 10 Jul 1996 11:38:52 +0200 (MET DST) From: Massimo Trotta Subject: basic fluorescence information To: CHEMISTRY@www.ccl.net Message-id: <9607100938.AA25733@area.ba.cnr.it> MIME-version: 1.0 X-Mailer: ELM [version 2.4 PL24 PGP3 *ALPHA*] Content-transfer-encoding: 7bit Content-Type: text/plain; charset=US-ASCII Content-Length: 929 Status: RO Dear All, this is probably not exactly a question for a computational chemistry list, but it is possible that some of you have experience in basic fluorescence spectroscopy: I am looking for literature or any suggestion regarding the fluorescenze of substituted benzoquinones: Should they fluoresce or not? Also indication on Electronic Lists on fluorescence related topics. thank you in advances massimo trotta -- !==============================================================! ! Massimo Trotta ! ! Centro Studi Chimico Fisici sull'Interazione Luce Materia ! ! c/o Dept. of Chemistry ! ! V. Orabona, 4 I-70126 Italy ! ! e-mail: csilmt12@area.ba.cnr.it ! ! http://www.ba.cnr.it/~csilmt12 !==============================================================! From rino@ibc.wustl.edu Wed Jul 10 10:26 EDT 1996 Received: from wugate.wustl.edu for rino@ibc.wustl.edu by www.ccl.net (8.7.5/950822.1) id KAA02918; Wed, 10 Jul 1996 10:26:39 -0400 (EDT) Received: from ibc.wustl.edu by wugate.wustl.edu (8.7.5/8.6.11) with SMTP id JAA15455 for ; Wed, 10 Jul 1996 09:26:41 -0500 Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id JAA25619; Wed, 10 Jul 1996 09:26:36 -0500 Date: Wed, 10 Jul 1996 09:26:36 -0500 (CDT) From: Rino Ragno To: chemistry@www.ccl.net Subject: Conf. space & RBs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1326 Status: RO Dear Netters, any of you out there knows if there is any program/routine that is able to compute both the number of rotatable bonds and the number of geometrically possible number of conformers of a given molecules? Thank in advance to every one is going to answer. Rino Ragno ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: rino@wucmd.wustl.edu || || Institute for Biomedical Computing or: rino@ibc.wustl.edu || || Center for Molecular Design Phone : 314-362-2273 || || Box 8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || || || ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ From rino@ibc.wustl.edu Wed Jul 24 13:16:18 1996 Received: from wugate.wustl.edu for rino@ibc.wustl.edu by www.ccl.net (8.7.5/950822.1) id MAA28022; Wed, 24 Jul 1996 12:18:52 -0400 (EDT) Received: from ibc.wustl.edu (ibc.wustl.edu [128.252.122.174]) by wugate.wustl.edu (8.7.5/8.7.3) with SMTP id LAA01067 for ; Wed, 24 Jul 1996 11:19:33 -0500 test-header: [rino@ibc.wustl.edu] Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id LAA17075; Wed, 24 Jul 1996 11:19:59 -0500 Date: Wed, 24 Jul 1996 11:19:59 -0500 (CDT) From: Rino Ragno To: chemistry@www.ccl.net Subject: Re: CCL:Conf. space & RBs In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 4257 On Wed, 10 Jul 1996, I wrote the following: > Dear Netters, > > any of you out there knows if there is any program/routine that is able > to compute both the number of rotatable bonds and the number of > geometrically possible number of conformers of a given molecules? > > Thank in advance to every one is going to answer. > > Rino Ragno > Here are the summary of the replies I got: From: Arthur Wang Subject: Re: CCL:Conf. space & RBs I believe that the Systematic Search Module in SYBYL can do this. Arthur ******************** From: brandau@ccgatewy.vchgroup.de Subject: Re: CCL:Conf. space & RBs Dear Rino, have a look at MOLGEN, a structure generator which - if I understand you correctly - should produce just what you want, i.e from a given molecular formula all possible isomers (i.e. connectivities). you can also enter contraints. I can send you brochures if you wish but you might also ask Thomas Wieland at wieland@btm2d1.mat.uni-bayreuth.de, one of the developers, they also have a web page of which I dont't have the address at hand. Sincerely Stefan ******************** From: "Dr. Neil E. Hoare" Dear Rino, Firstly I think most packages e.g. Sybyl, will allow you to do the type of conformational search you require. The program can assign rotatable bonds or you can define the ones you want. I think you have asked a very intresting question about calculating the possible number of conformations. This type of approach requires a criteria for 'when are conformations different ?'. Are you going to consider geometric & torsional rotations only. If so what techniques can you use as a measure of similarity (distance and similarity matrices ?) Example : If we consider a rotation of 30 degrees to be significant enough to cause a change in conformation, for butane (3 rotatable bonds) we have 12^3 = 1728 conformers. I have been studying systems containing 7 rotatable so the above hypothesis leads to 3.6 * 10^7 conformers ! I would like to see a summary of replies if this is available. I hope this is of use, please contact me if you want. Best wishes, Neil -- Neil Hoare PhD CChem MRSC hoaren@sisko.sci.port.ac.uk Tel : (+44) 1705 843623 Centre for Molecular Design Fax : (+44) 1705 843722 University of Portsmouth U.K. ******************** From: Soaring Bear Subject: CCL:Conf. space & RBs The Apex QSAR module from Biosym/MSI has a conformer generator that does this, but you still have to give it parameters of how you want to distinguish conformers by angles, energies, distances. It is pretty easy but expensive. What will your use be? bear _____ ____ bear@ellington.pharm.arizona.edu * ___) * _ \ http://ellington.pharm.arizona.edu/~bear : (___ : |_) : Cyber-Chemist: cancer drug design topo-O O-topo \___ \ | _ < Molecular & Nutritional Biochemist 5'. : : .*** ___) : | |_) : Herbs, Nutrition, Natural Dentistry |'*. .*'| | (_____/oaring |____/ear, UA New Pharmacy 404, Tucson 85721 | | *.,* | | | 3'*,DNA helix| *' Thanks a lot to every one RR ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: rino@wucmd.wustl.edu || || Institute for Biomedical Computing or: rino@ibc.wustl.edu || || Center for Molecular Design Phone : 314-362-2273 || || Box 8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ From ipcakc@Postoffice.ncst.ernet.in Mon Jul 15 23:44 EDT 1996 Received: from sangam.ncst.ernet.in for ipcakc@Postoffice.ncst.ernet.in by www.ccl.net (8.7.5/950822.1) id XAA07479; Mon, 15 Jul 1996 23:44:20 -0400 (EDT) Received: from postoffice.iisc.ernet.in (twisha.ece.iisc.ernet.in [144.16.64.4]) by sangam.ncst.ernet.in (8.6.12/8.6.6) with ESMTP id JAA19048 for ; Tue, 16 Jul 1996 09:13:10 +0530 Received: by postoffice.iisc.ernet.in (SMI-8.6/SMI-SVR4) id JAA08392; Tue, 16 Jul 1996 09:00:03 -0500 Date: Tue, 16 Jul 1996 09:00:03 -0500 From: ipcakc@Postoffice.ncst.ernet.in (Dr.A.K.Chandra) Message-Id: <199607161400.JAA08392@postoffice.iisc.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Norrish Content-Type: text Content-Length: 511 Status: RO Dear netters, Does anybody have an idea of NORRISH TYPE II (Intramolecular gamma-Hydrogen abstraction processes) in ORGANO-THIO (C=S) compounds in ground or excited states? If so, please send me a reference/s. Thanks in advance, V.SREEDHARA RAO **************************************** V. SREEDHARA RAO Department of Inorganic and Physical Chemistry Indian Institute of Science (I.I.Sc) BANGALORE - 560 012. India. E-mail : ipcakc@postoffice.iisc.ernet.in (or) akc@hamsadvani.serc.iisc.ernet.in From KIRBYR@biochem-pharma.com Thu Jul 25 09:16:24 1996 Received: from internet.biochem-pharma.com for KIRBYR@biochem-pharma.com by www.ccl.net (8.7.5/950822.1) id IAA02756; Thu, 25 Jul 1996 08:41:30 -0400 (EDT) Received: from post.biochem-pharma.com (post.biochem-pharma.com [192.168.169.250]) by internet with SMTP (DuhMail/2.0) id IAA06879; Thu, 25 Jul 1996 08:34:13 -0400 Received: by post.biochem-pharma.com with Microsoft Mail id <31F795EE@post.biochem-pharma.com>; Thu, 25 Jul 96 08:42:38 PDT From: "Kirby, Robert" To: "'chemistry@www.ccl.net'" Subject: Free Energy Pert Scripts in CHARMM Date: Thu, 25 Jul 96 08:41:00 PDT Message-ID: <31F795EE@post.biochem-pharma.com> Return-Receipt-To: Encoding: 17 TEXT X-Mailer: Microsoft Mail V3.0 Status: RO Content-Length: 574 CCL, I am looking for example scripts which do Free Energy Perturbation Calculations using CHARMM. I have a couple of short ones from MSI but they do not cover the real situation of a molecule inside a protein generated in QUANTA and submitted to a CHARMM FEP calculation by a CHARMM script. If anyone has one of these lying around could I get a copy of it at your convenience. Thank-you Robert A. Kirby BioChem Therapeutiques Inc. 275 Armand-Frappier Blvd. Laval, Quebec, H7V 4A7 #514-978-7914 fax 514-978-7777 kirbyr@biochem-pharma.com From Steve.Bowlus@sandoz.comSat Jul 27 11:13:31 1996 Date: Wed, 10 Jul 1996 01:21:48 +0200 From: Steve.Bowlus@sandoz.com To: tp@elptrs7.rug.ac.be Subject: M: SADDLE Status: RO Content-Length: 1385 First, the SADDLE command does not give an optimized geometry of the TS -- only an approximate geometry. The "best" TS approximation must be refined using the TS keyword, or NLLSQ, or some combination (perhaps in several steps), followed by a FORCE calculation to assure you are at a TS (one -ve root to the Hessian), and ideally followed by reaction coordinate calculations (IRC=1 and IRC=-1) to generate the product and starting material. Only through all this work can you assure you have a TS for the reaction you are interested in. This applies to all TS, incidentally, whether you generate them by the SADDLE command or by guessing. Since your results are so spectacularly strange, it seems most likely that your starting geometry for the separate pieces is indigestible. I would do some minimization in Mopac on the starting side before trying the saddle calculation. I expect there are several "reasonable" geometries for this, and you might have to try several before you get it right. Given a "reasonable" starting geometry, you might try running the calculation in AMPAC, if you have access to the program. I believe the algorithm for locating TS is different from that used in Mopac, but the two programs should give otherwise very similar results (with minor modification, the AMPAC output can be transferred to Mopac as well). I think the keyword is CHAIN. sb From rino@ibc.wustl.edu Wed Jul 24 13:16:13 1996 Received: from wugate.wustl.edu for rino@ibc.wustl.edu by www.ccl.net (8.7.5/950822.1) id MAA28082; Wed, 24 Jul 1996 12:25:38 -0400 (EDT) Received: from ibc.wustl.edu (ibc.wustl.edu [128.252.122.174]) by wugate.wustl.edu (8.7.5/8.7.3) with SMTP id LAA01378 for ; Wed, 24 Jul 1996 11:26:18 -0500 test-header: [rino@ibc.wustl.edu] Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id LAA17124; Wed, 24 Jul 1996 11:26:45 -0500 Date: Wed, 24 Jul 1996 11:26:45 -0500 (CDT) From: Rino Ragno To: Computational Chemistry List Subject: Zn MM parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 1262 Dear CCL'ers: I am looking for zinc (Zn++) molecular mechanic parameters. Does anybody developed zinc parameters to use in macromodel? All the replies will be summarized. Thank to every one is going to answer. RR ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: rino@wucmd.wustl.edu || || Institute for Biomedical Computing or: rino@ibc.wustl.edu || || Center for Molecular Design Phone : 314-362-2273 || || Box 8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || || || ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ From Steve.Bowlus@sandoz.comSat Jul 27 11:20:04 1996 Date: Wed, 10 Jul 1996 16:51:24 +0200 From: Steve.Bowlus@sandoz.com To: tp@elptrs7.rug.ac.be Subject: Mopac ts Status: RO Content-Length: 416 I would try moving the starting structures closer together, so that the reactants "look" more like a ts. The c-c bond length in the ts is (at a guess) on the order of 1.8 - 2.0 A -- try 2.2 - 2.4 A. You may also have to simply guess the ts structure, and then refine using TS, NLLSQ, etc. it will be _crucial_ in this case that you do the IRC calculations to assure you have a ts for the desired reaction. sb From oldziej@IRO.UMontreal.CASat Jul 27 11:11:41 1996 Date: Tue, 9 Jul 1996 16:45:36 -0400 (EDT) From: Stanislaw Oldziej To: tp@elptrs7.rug.ac.be Subject: Transition state: Status: RO Content-Length: 1792 Hi, 1. You should remember that order of atoms in substrate compex and in products should be identical. If you see in substrate atom 2 it is hydrogen in products it is carbon ect. 2. Why you using UHF ? With best regards Stanislaw Oldziej From laidig@pg.comSat Jul 27 11:12:46 1996 Date: Tue, 9 Jul 1996 17:30:25 -0400 From: Bill Laidig To: "Park, Tae-Yun" Subject: Re: CCL:M:Transition state search using MOPAC. Tae-Yun, I would do this calculation as follows since I do not know what the TS will look like in advance. I would optimize the geometry of the product ion first. Next, I would do a series of constrained minimizations in which the CH3-C2H4+ r(C-C) was systematically stretched (i.e. the first calculation has r(C-C) at the equilibrium distance (re), next fixed at re+0.1, next fixed at re+0.2... After a maximum along the stretching coordinate was located, I would next use this geometry unconstrained in a TS calculation. Bill -- ****************************************************************************** * "Like jewels in a crown, the precious stones glittered in the queen's * * round metal hat." - Jack Handey * * * * Bill Laidig * * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * * Miami Valley Laboratories laidig@pg.com (preferred) * * P.O. Box 538707 wd_laidig@pg.com * * Cincinnati, OH 45253-8707 laidig@qtp.ufl.edu * ****************************************************************************** From owner-chemistry@ccl.net Thu Jul 25 17:16:24 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id QAA05294; Thu, 25 Jul 1996 16:28:38 -0400 (EDT) Received: from gig.usda.gov for srheller@origin.gig.usda.gov by bedrock.ccl.net (8.7.5/950822.1) id QAA18926; Thu, 25 Jul 1996 16:28:36 -0400 (EDT) Received: by gig.usda.gov (5.x/SMI-SVR4) id AA23371; Thu, 25 Jul 1996 16:09:01 -0400 Date: Thu, 25 Jul 1996 16:09:00 -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 Status: RO Content-Length: 2744 25 July, 1996 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 three (3) new software/database products. I am looking for 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 six 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 27 July 1996 (Saturday), 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. Accord for Microsoft Excel (PC Edition), version 2.0 from Synopsys in Leeds, UK. Allows one to manage and analyze chemical data within the Excel spreadsheet program. Works with Excel version 5.0. Requires Excel. 2. Gower Chemical Reference Series of five databases consisting of five CD-ROM's from Ashgate Publishing. The company has requested that just ONE person review all six products to give a comprehensive review of all of the data available in these reference series. The six are: a. Cosmetics & Personal Care b. Food Additives c. Plastic & Rubber Additives d. Pharmaceutical Additives e. Industrial Surfactants f. Gardner's Chemical Synonyms & Tradenames 3. Cognos, version 1.3 for the Macintosh. Cognos is a reaction retrieval system from InfoChem in Munich, Germany. The system comes on a CD-ROM. 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 From JDA03546@niftyserve.or.jpSat Jul 27 10:42:37 1996 Date: Tue, 25 Jun 1996 13:24:00 +0900 From: "JDA03546@niftyse" To: "Park, Tae-Yun" Subject: RE:CCL:M:HELP!(urgent):theoretical discr Status: RO Content-Length: 1537 Hi Park, I'm studying zeolite by means of coputational techniques. Regarding to your post, there are millions of literatures about the computational simulations on zeolites, both by MD and MO. So why don't you search the literature first? Anyway, for the mechanism of the hydrocarbon cracking over zeolite, you may start from the report by R. A. Santen, et. al. appeared on Cat. Lett., 27, p345, 1994, and ibid. 28, p211, 1994. Good luck. --- Teraish Kazuo TEL:0492-66-8375 FAX:0492-66-8359 E-MAIL:JDA03546@niftyserve.or.jp ------------------------------------------------------- PART II Subject: Heat of formation calculation using MOPAC. ------------------------------------------------------- ####################(questions)######################## Hi! I have a question on the parameters in MOPAC. I'm tring to calculate the heat of formation for more or less 100 different gas-phase carbenium ions. Which parameter would be suitable for this calculation? PM3? AM1? I tried to compare the results obtained from MOPAC with a few experimental data available in the literature, and found that AM1 is much closer to those experimental data than the case of PM3 when the molecule contains the cabon atoms up to 5. According to the manual of MOAPC, however, PM3 is more improved parameter than AM1! My question is that the AM1 would also produce better result if the molecule becomes larger (upto C8)? Any suggestion would be greatly appreciated. #####################(answers)########################## From oldziej@IRO.UMontreal.CASat Jul 27 11:24:11 1996 Date: Wed, 10 Jul 1996 12:49:16 -0400 (EDT) From: Stanislaw Oldziej To: tp@elptrs7.rug.ac.be Subject: Transition state Status: RO Content-Length: 1637 Hi 1. In my opinion you substrates and product are to "far" one to each anothera. Try to optimize substrate compex and products. You should expect that substrates are formed pi-complex stabilized by interaction between empty p-orbital of the carbocation and pi-orbitals of ethylene. I thing that distans carbon-carbon should be in range 3-2.2 A but not 8 (see your input). If you have optimized complexes than run SADDLE. 2. If you not find TS using procedure from point 1. Try PATH option with changing distance between two atoms your input schould look like: CHARGE=1 PRECISE Me--->p methylation activated complex C .000000 0 .000000 0 .000000 0 0 0 0 C 1.500000 -1 .000000 0 .000000 0 1 0 0 C 1.418947 1 116.688263 1 .000000 0 2 1 0 H 1.118077 1 111.116249 1 -59.952415 1 1 2 3 H 1.119762 1 109.783371 1 -179.449097 1 1 2 3 H 1.118210 1 111.069687 1 61.123405 1 1 2 3 H 1.150598 1 110.672989 1 174.990601 1 2 1 4 H 1.150955 1 110.650314 1 64.874481 1 2 1 4 H 1.109621 1 121.247902 1 -179.729874 1 3 2 1 H 1.110257 1 121.556961 1 .300391 1 3 2 1 0 .000000 0 .000000 0 .000000 0 0 0 0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 You can start from product to substrates (like in example) or in reversed direction. After this you should select structure with the highest energy and try to optimized it by NLLSQ and/or TS. 3. You should done calculation using another methods AM1, PM3 Stanislaw Oldziej P.S. Sorry for my still bad English From tp@elptrs7.rug.ac.be Sat Jul 27 06:16:41 1996 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.7.5/950822.1) id FAA12836; Sat, 27 Jul 1996 05:53:23 -0400 (EDT) Received: by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA23346; Sat, 27 Jul 1996 11:54:47 +0200 Date: Sat, 27 Jul 1996 11:54:46 +0200 (DFT) From: "Park, Tae-Yun" To: Computational Chemistry List Cc: YONG HUANG , Nancy Mills Subject: Summary of my earlier questions & Thanks Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 5795 Dear all, During last a few weeks, I posted several questions on my Ph.D. work to CCL, which is related to comput- ataional chemistry field. Hereby, I summerized my questions and answers from many CCLers, which gave me a great help. I have decided to post this summary since there are other CCLers who want to know what I have got from this e-mail communication. Let me express my deep thanks to all the CCL members who are interested in my questions and sending me impressive and helpful answers. Especially, I'd like to express my sincere thanks to Mr. Ernest Chamot who sent me a detailed and valuable message which give me a great help and encoregement. What I'm afraid now is that this summary would be too long to send by e-mail so that it occupies too much disk space. Please execuse me if this message creates any disk space problem on your mail box. 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 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ------------------------------------------------------- PART I subject: HELP!(urgent):theoretical discrimication & software ------------------------------------------------------- ####################(questions)######################## *** About the structure of surface carbenium ions and symmetry number *** First thing I have to calculate is the symmetry number of surface carbenium ions on the zeolite surface, which is formed by protonation of various olefins. 1. How can we describe the bonding of carbenuim ions to the surface? Is the bonding more ionic or covalent? I know the proton is surely covalently bound, but it is less clear for the case of hydrocarbons(more exactly olefins) adsorbed on zeolite. 2. What is the symmetry number for such surface carbenium ions comparing with corresponding gas phase carbenium ions? In most cases, I believe, the symmetry number of surface ions are identical with those in gas phase, if there is no 2-fold axes. Consider the following examples. C \ C-C+-C (secondary ion in gas phase) / C symmetry number=3*3*3=27 C \ C-C-C (secondary ion on the surface) / | C | --(+)-- symmetry number=3*3*3=27 If there is two-fold axes, however, C \ 2-fold axes.....C+-C-C (tertiary ion in gas phase) / C symmetry number=(3*3*3)*2=54 C \ Not a 2-fold axes(?)...C+-C-C (tertiary on the surface) /| C | --(+)-- symmetry number=3*3*3=27 I think the surface ion loose its 2-fold axes due to the bonding to the catalyst surface. I just want to know whether those approach to calculate the symmetry number of surface carbenium ions is theoretically correct. To check this point, I think, the bonding of carbenium ions to the surface should be defined first, in a certain way of theoretical approach. **** About the structure of activated complex ****** Next problem that I have to solve is concerning the structure of activated complex in transition state for beta-scission. That is, an elementary step representing beta-scission, R1 ---> (Transition State) ----> R2 + O where R1 and R2 are the reactant and product carbenium ion, respectively, and O is the product olefin. What I want to know is the structure of the activated complex in the transition state, as detailed as possible in a certain theoretical way; how many bonds are related, which bonds are to be broken, which bond will be formed, and what does the activated complex look like(is it more like carbenium ion or more like olefin?), etc. **** About heat of formation for gas phase carbenium ions *** My final question is about the calculation of thermodynamic data, more exactly, the heat of formation of gas-phase carbenium ions. Recently, a solution to solve the problem associated with the large number of the parameters has been considered, i.e, by applying the "Polanyi relation". This relation needs only relative differences in heat of reactions in each elementary steps. This means that the heat of formation for the surface carbenium ions are not necessary, but, at least, heat of formation of gas-phase carbenium ions appearing in the reaction network should be given. Unfortunately, only limited amount of data can be found in the literature, so that some analytical method to calculate the heat of formation is necessary. Benson's group contribution method has been known as one of the most approprate way to calculate the thermodydamic properties. The group contribution value of positively-charged carbon atom involved in the carbenium ions is, however, not available at the moment. The only solution I found recently is using a certain quantum chemistry package such as "MOPAC". My question is that is this a suitable package (accurate enough) to calculate the heat of formation data I need? If so, how can I obtain a copy of this package? If not, is there any other software in the field of computational chemistry to calculate these data? *************** End of my questions ************************* #####################(answers)########################## From kallies@serv.chem.uni-potsdam.de Thu Jul 4 14:15 EDT 1996 Received: from mail-buffer.sbu.ac.uk for kallies@serv.chem.uni-potsdam.de by www.ccl.net (8.7.5/950822.1) id OAA13950; Thu, 4 Jul 1996 14:15:38 -0400 (EDT) Received: from psb.sbu.ac.uk (psb.sbu.ac.uk [136.148.1.5]) by mail-buffer.sbu.ac.uk (8.7.4/8.7.3) with SMTP id TAA14255; Thu, 4 Jul 1996 19:08:41 +0100 (BST) Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Thu, 04 Jul 1996 19:15:26 BST Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.2 VAX) with SMTP; Tue, 28 May 1996 12:09:31 BST Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.5/950822.1) id GAA15261; Tue, 28 May 1996 06:47:50 -0400 (EDT) Received: from hp.rz.uni-potsdam.de for kallies@serv.chem.uni-potsdam.de by www.ccl.net (8.7.5/950822.1) id GAA15248; Tue, 28 May 1996 06:47:11 -0400 (EDT) Received: from serv.chem.uni-potsdam.de by hp.rz.uni-potsdam.de with SMTP (1.37.109.10G/16.2) id AA147940342; Tue, 28 May 1996 09:59:02 +0200 Received: from pch10.chem.uni-potsdam.de by serv.chem.uni-potsdam.de (AIX 3.2/UCB 5.64/4.03) id AA19368; Tue, 28 May 1996 10:00:24 +0100 Date: Tue, 28 May 1996 10:00:24 +0100 Message-ID: <9605280900.AA19368@serv.chem.uni-potsdam.de> To: csilmt12@area.ba.cnr.it From: "B. Kallies" Subject: CCL:autoprotolysis constant of alcohols CC: chemistry@www.ccl.net Content-Type: text Content-Length: 1381 Status: RO Dear Dr. Trotta, Christian Reichardt collected some pK(auto) for amphiprotic solvents in "Solvents and Solvent Effects in Organic Chemistry" 2nd. ed., VCH 1990, p. 431 ff. There will be found for 2 ROH =3D R(OH)2(+) + RO(-) Solvent R pK(auto) at 25=B0C ----------------------------------------- Methanol CH3 17.20 Ethanol C2H5 18.88 1-Propanol C3H7 19.43 1-Butanol C4H9 21.56 1-Pentanol C5H11 20.65 and some others. Original references and some other original literature citations are given, too. Yours sincerely B. Kallies --------------------------------------------------- DC Bernd Kallies Institut fuer Physikalische und Theoretische Chemie Universitaet Potsdam Am Neuen Palais 10 14469 Potsdam GERMANY e-mail: kallies@serv.chem.uni-potsdam.de Fax: ++49 / 0331 977 1315 --------------------------------------------------- -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: kallies@serv.chem.uni-potsdam.de -- Original Sender From: Address: kallies@serv.chem.uni-potsdam.de CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From MAILER-DAEMON@www.ccl.net Tue Jul 23 18:15:58 1996 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.7.5/950822.1) id RAA24102; Tue, 23 Jul 1996 17:45:16 -0400 (EDT) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) for chemistry@www.ccl.net id XAA05332; Tue, 23 Jul 1996 23:42:23 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9607232342.ZM5330@schiele> Date: Tue, 23 Jul 1996 23:42:18 -0600 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@www.ccl.net Subject: ANNOUNCE: WWW chemical structures database Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit Status: RO Content-Length: 1662 At last, it is publicily accessible: The first WWW chemical structures database with molecules taken (and reconstructed) from chemical MIME files scattered all around the world on the WWW. A spider collected this information automatically. The database contains more than 2250 entries. All normal chemical database search operations are supported (fullstructure, substructure, weight, formula etc), and we give you the complete link environment, i.e. you can easily select and view the (hopefully interesting) HTML pages which refer to the structures. In contrast to the CambridgeSoft ChemFinder database we take all structure information directly from the net and reconstruct a common, searchable, vb-oriented representation (the really hard part). We think this is the first example of an automatically generated database with Web information which is non-textual. Access to the database is free. No registration is necessary. One mode of access is by means of an WWW forms-based interface which presents the query results via dynamically generated HTML pages. Its URL is http://schiele.organik.uni-erlangen.de/services/webmol.html Please mail us your comments. P.S.: Have a look at our other chemical WWW services: http://schiele.organik.uni-erlangen.de/services/ -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From csilmt12@area.ba.cnr.it Thu Aug 8 04:22:42 1996 Received: from area.ba.cnr.it for csilmt12@area.ba.cnr.it by www.ccl.net (8.7.5/950822.1) id DAA23748; Thu, 8 Aug 1996 03:37:11 -0400 (EDT) Received: by area.ba.cnr.it; (5.65/1.1.8.2/16Jul96-0442PM) id AA32566; Fri, 2 Aug 1996 11:37:30 +0200 From: Massimo Trotta Message-Id: <9608020937.AA32566@area.ba.cnr.it> Subject: dipolar mements To: chemistry@www.ccl.net Date: Fri, 2 Aug 1996 11:37:30 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL24 PGP3 *ALPHA*] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Status: RO Content-Length: 1503 Dear all, I'm studying the dipolar moments of some organic molecules in the ground and first excited states using semi-empirical calculations (on Hyperchem 4.0) and I have a couple of question regarding those calculations: a) I decided to use ZINDO/1 as semiempirical method (available methods are CNDO, INDO, MINDO3, MNDO, AM1, PM3, ZINDO/1 and ZINDO/s), but the choice was not made on how appropriate is the method for evaluating dipolar moment. Am I doing right? is there any reason for choosing this or that SE method for the dipolar moment calculations? b) In evaluating the dipole moment in the excited state I select the option _Next Lowest_ in the SE option dialog box. Should I work with _Unrestricted Hartree Fox_ to get more accurate number or _Restrictes HF_ gives the same accuracy as well?. c) How can I display, in hyperchem or with some other software (freeware) the dipolar moments as spacial vectors overlapped on the molecules? Any indication is welcome. will summarize. massimo -- !==============================================================! ! Massimo Trotta ! ! Centro Studi Chimico Fisici sull'Interazione Luce Materia ! ! c/o Dept. of Chemistry ! ! V. Orabona, 4 I-70126 Italy ! ! e-mail: csilmt12@area.ba.cnr.it ! ! http://www.ba.cnr.it/~csilmt12 !==============================================================! From chemistry-request@www.ccl.net Fri Aug 9 23:16 EDT 1996 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.5/950822.1) id XAA05680; Fri, 9 Aug 1996 23:16:34 -0400 (EDT) Date: Fri, 9 Aug 1996 23:16:34 -0400 (EDT) Message-Id: <199608100316.XAA05680@www.ccl.net> From: Mail Delivery Subsystem for chemistry Subject: EQS4WIN To: ccl@www.ccl.net Content-Type: text Content-Length: 2494 Status: RO We are pleased to announce the availability of EQS4WIN, a PC-Windows software package which calculates equilibrium compositions for a wide range of problem types, ranging from ionic system speciation to combustion flame temperatures. It accomplishes this via a unique state-of-the-art computational engine and unified theoretical approach based on the research of Smith and Missen. The free Lite version of EQS4WIN is ideally suited for student use, and the Standard Version carries substantial educational and network discounts. The Lite version of EQS4WIN is available from http://www.mathtrek.com This version is fully-functional apart from limitations of input/output and problem size. It also includes example template problem files illustrating its application to problems from many areas, including analytical chemistry, aquatic chemistry, biochemistry, chemical vapor deposition, combustion, environmental chemistry, geochemistry, and metallurgy. **************************************************************** Best Regards Mathtrek Systems 3-340 Stone Road West, Suite 165 W. R. Smith, PhD, P. Eng. Guelph, Ontario CANADA N1G 4W4 Senior Scientist Tel: 519-763-1356 FAX: 519-763-4525 EMail: support@mathtrek.com http://www.mathtrek.com ****************************************************************