From chemistry-request@server.ccl.net Wed Sep 19 07:52:28 2001 Received: from firewall.theory.ki.ku.dk ([192.38.103.130]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8JBqN315776 for ; Wed, 19 Sep 2001 07:52:27 -0400 Received: (from gproxy@localhost) by firewall.theory.ki.ku.dk (980427.SGI.8.8.8/970903.SGI.AUTOCF) id NAA29045 for ; Wed, 19 Sep 2001 13:53:20 +0200 (MDT) Received: from marcus.theory.ki.ku.dk(192.168.100.9) by firewall via smap (3.2) id xma029043; Wed, 19 Sep 01 13:53:12 +0200 Received: from localhost (tl@localhost) by marcus.theory.ki.ku.dk (8.9.0/8.9.0) with ESMTP id NAA13659 for ; Wed, 19 Sep 2001 13:46:34 +0200 Date: Wed, 19 Sep 2001 13:46:34 +0200 (CEST) From: Thomas Lorenzen To: chemistry@ccl.net Subject: Where is the optimized structure after a gaussian optimization Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi' During geometry optimizations in g94 I am suddenly in doubt, as to which of the following formates, which are representing the optimized structure. Below I give excerpts of the last parts of a log file. ############################################################ Item Value Threshold Converged? Maximum Force 0.000019 0.000450 YES RMS Force 0.000004 0.000300 YES Maximum Displacement 0.004086 0.001800 NO RMS Displacement 0.000941 0.001200 YES GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad .................... Standard orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 1 0.958118 -1.418822 3.726503 2 1 2.094953 -2.735917 3.385061 3 1 0.677686 -2.500992 2.346957 4 6 1.454782 -1.975008 2.920429 5 6 2.239670 -1.068567 2.010995 6 8 3.387405 -1.304349 1.641304 7 7 1.621646 0.152407 1.621215 8 1 0.623630 0.092445 1.603471 9 6 2.158440 0.882667 0.459892 10 1 2.332826 0.230720 -0.418428 11 1 1.437751 1.662654 0.162356 12 1 3.116196 1.356455 0.731118 13 8 0.781001 -2.406763 -0.814605 14 1 0.057654 -1.772807 -0.777901 15 7 -1.285947 -0.384760 -0.512264 16 6 -2.610741 -0.706823 -0.451525 17 1 -3.031906 -1.715876 -0.500590 18 6 -1.177188 0.997822 -0.413214 19 1 -0.209494 1.504903 -0.438038 20 6 -2.454213 1.535533 -0.289764 21 7 -3.343729 0.451394 -0.314386 22 1 -4.373883 0.521365 -0.252768 23 8 -5.945650 -1.439914 -0.171635 24 8 -6.061101 0.735805 -0.181767 25 6 -6.636299 -0.398144 -0.146375 26 1 4.781233 0.110735 -0.927721 27 1 6.134143 -0.482254 -1.684979 28 7 5.720598 0.291331 -1.212849 29 6 6.526190 0.891953 -0.217003 30 8 7.737551 0.709096 -0.274038 31 6 1.655300 -1.980402 -1.827606 32 1 1.141262 -2.017986 -2.807953 33 1 1.959407 -0.920403 -1.658880 34 6 2.869542 -2.917593 -1.840510 35 1 2.547273 -3.961635 -1.638019 36 1 3.317425 -2.925997 -2.854345 37 7 3.944584 -2.471611 -0.922256 38 1 3.562974 -2.071027 -0.075448 39 1 4.502727 -3.262496 -0.676723 40 6 -2.859870 2.951406 -0.141046 41 1 -3.380583 3.088443 0.828408 42 1 -1.945078 3.574095 -0.086276 43 6 -3.748099 3.420875 -1.274616 44 1 -3.254122 3.313060 -2.248637 45 1 -4.009529 4.480126 -1.154511 46 1 -4.688002 2.851523 -1.315224 47 6 -8.169199 -0.461118 -0.078904 48 1 -8.606417 0.395522 -0.626119 49 1 -8.530867 -1.370312 -0.595745 50 6 -8.641471 -0.456743 1.355598 51 1 -8.244134 -1.314846 1.913189 52 1 -9.736948 -0.502959 1.420814 53 1 -8.320374 0.451133 1.882606 54 6 5.860664 1.807396 0.792250 55 1 4.801983 1.505681 0.970281 56 1 6.368558 1.697396 1.770435 57 6 5.919620 3.247245 0.332295 58 1 5.379832 3.395992 -0.612077 59 1 5.465956 3.914097 1.076902 60 1 6.953278 3.582661 0.176603 ---------------------------------------------------------- .................... Item Value Threshold Converged? Maximum Force 0.000029 0.000450 YES RMS Force 0.000005 0.000300 YES Maximum Displacement 0.001658 0.001800 YES RMS Displacement 0.000430 0.001200 YES Optimization completed. -- Stationary point found. .................... Test job not archived. 1\1\GINC-TEOSGI\FOpt\RPM3\ZDO\C16H34N5O5(1-)\TL\20-Jan-1998\0\\#T PM3 OPT=(MAXCYCLE=360,ADDREDUN) SCF=DIRECT TEST\\PM3 optimize - Acyl01 - d ist(O-C)=3.45 fixed - dist(H-N)=1.95 fixed\\-1,1\H,0.9606732195,-1.409 183882,3.7295009063\H,2.0975810511,-2.7268998469,3.3907048391\H,0.6796 358433,-2.494900999,2.3528682967\C,1.4569678018,-1.9673046107,2.924536 1299\C,2.2411134781,-1.0630026201,2.0123356863\O,3.3886737452,-1.29947 81633,1.6425478608\N,1.6225946048,0.1568509509,1.6198412014\H,0.624580 7189,0.0966344419,1.6028540779\C,2.1585311466,0.8842823845,0.456349102 2\H,2.3325236427,0.2301511806,-0.420423353\H,1.4374965551,1.6633616676 ,0.1572769998\H,3.1163507905,1.3589564451,0.7257949853\O,0.7810179706, -2.4086524697,-0.8089844999\H,0.0575587635,-1.7747578305,-0.7734464147 \N,-1.2861752262,-0.3863259473,-0.5105094062\C,-2.6108641608,-0.708512 8317,-0.4481531054\H,-3.031844975,-1.7177754281,-0.4944093444\C,-1.177 6489549,0.9965251886,-0.4150252966\H,-0.2100778367,1.5037456667,-0.441 7184326\C,-2.4547132823,1.5342787719,-0.2921625812\N,-3.3440147101,0.4 498935709,-0.3135016458\H,-4.3741454547,0.5198029572,-0.2514374173\O,- 5.9454478955,-1.4415950876,-0.1643886522\O,-6.0613657828,0.7340669423, -0.179957369\C,-6.6363015268,-0.399909362,-0.1413470087\H,4.7806472633 ,0.1093923842,-0.9308943252\H,6.1332247177,-0.4852266921,-1.6874681064 \N,5.7198008594,0.2894638785,-1.2170469651\C,6.5258678464,0.8927742754 ,-0.2232121241\O,7.7372332095,0.7100283731,-0.2805178699\C,1.654612999 9,-1.9846733078,-1.8235906652\H,1.1399900098,-2.0248465132,-2.80352720 58\H,1.9585973118,-0.9241864562,-1.6577321949\C,2.8690462371,-2.921638 2889,-1.8348579836\H,2.5471205217,-3.9652324205,-1.6295303118\H,3.3163 171752,-2.9325132964,-2.8489396185\N,3.9445493513,-2.4731069373,-0.918 3865186\H,3.5633669942,-2.0704612171,-0.0723642\H,4.5030081596,-3.2632 508632,-0.6711914904\C,-2.86058047,2.9504379315,-0.1467822688\H,-3.380 7352424,3.0898187948,0.8226363621\H,-1.945887752,3.5734563335,-0.09414 29995\C,-3.7495949828,3.4168497664,-1.2809985742\H,-3.2561838989,3.306 6735352,-2.2550434342\H,-4.0111767941,4.4763459583,-1.1634169129\H,-4. 6894011208,2.847198543,-1.3195967006\C,-8.1691476754,-0.463034776,-0.0 72789078\H,-8.6068774959,0.3921253387,-0.6219045643\H,-8.5309357578,-1 .3736105596,-0.5871074273\C,-8.6405517705,-0.4551291409,1.3619829965\H ,-8.2426954984,-1.311734261,1.9215036916\H,-9.7359795419,-0.5014096804 ,1.4279798666\H,-8.3193290516,0.4541462128,1.8864978587\C,5.8607590646 ,1.8106281861,0.7841233528\H,4.8022497299,1.5091426291,0.9635581423\H, 6.369268656,1.7032115542,1.7622755988\C,5.9191313778,3.2493214676,0.32 04901868\H,5.378741012,3.3955641037,-0.6239278579\H,5.4657769388,3.917 959507,1.0636817716\H,6.9526244417,3.5845591212,0.1633238837\\Version= SGI-G94RevE.2\HF=-0.493957\RMSD=0.000e+00\RMSF=8.316e-04\Dipole=4.1168 757,1.1388895,0.8043294\PG=C01 [X(C16H34N5O5)]\\@ ############################################################ I notice, that the coordinates in the "Stanard orientation" section are a little different from the coordinates in the "Test job not archived" section, so my question is thus, which of these represent the optimized structure. Best Regards. Thomas. ---------------------------------------------------------------------- Cand. Scient. Thomas Lorenzen Phone : (+ 45) 35 32 02 50 Department of Chemistry Fax : (+ 45) 35 32 02 59 University of Copenhagen Mail : tl@theory.ki.ku.dk DK, 2100 Copenhagen, Denmark Homepage : http://theochem.ki.ku.dk/~tl ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Sep 19 01:11:41 2001 Received: from hotmail.com ([64.4.17.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8J5Bf322107 for ; Wed, 19 Sep 2001 01:11:41 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 18 Sep 2001 22:11:35 -0700 Received: from 211.23.84.2 by lw11fd.law11.hotmail.msn.com with HTTP; Wed, 19 Sep 2001 05:11:35 GMT X-Originating-IP: [211.23.84.2] From: "=?big5?B?v+Agqvenuw==?=" To: chemistry@server.ccl.net Subject: I nedd your help, please give me your hand. Date: Wed, 19 Sep 2001 13:11:35 +0800 Mime-Version: 1.0 Content-Type: text/plain; charset=big5; format=flowed Message-ID: X-OriginalArrivalTime: 19 Sep 2001 05:11:35.0343 (UTC) FILETIME=[8DB973F0:01C140C9] Dear all: Using Gaussian, I use UB3LYP and ROHF to calculate the MO of HSiO, how do I empty the unpaired electron into £k-type orbital not into £m-type orbital, except the command "alter". It seems unuseful for this case. If anyone have any suggestion, please e-mail to chlai54@hotmail.com. Thanks a lot in advances. Chin-Hung Lai 2001.9.19 _________________________________________________________________ ¦b http://explorer.msn.com.tw/intl.asp §K¶O¤U¸ü MSN Explorer From chemistry-request@server.ccl.net Wed Sep 19 05:12:46 2001 Received: from jivdhan.unipune.ernet.in ([196.1.114.31]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8J9Cj331505 for ; Wed, 19 Sep 2001 05:12:45 -0400 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.11.1/8.11.1) with ESMTP id f8JEoTr17737 for ; Wed, 19 Sep 2001 20:20:29 +0530 Received: from localhost (quanta@localhost) by chem.unipune.ernet.in (8.9.3/8.8.7) with ESMTP id OAA19767 for ; Wed, 19 Sep 2001 14:43:07 +0530 Date: Wed, 19 Sep 2001 14:43:07 +0530 (IST) From: QUANTA To: CCL Subject: Reference needed Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Sirs/Madams: Could someone please give me refrences on the largest molecular systems studied by ab intio/semi empirical/ MM/MD-MC methods. Thanks in advance. ANANT KULKARNI From chemistry-request@server.ccl.net Wed Sep 19 01:54:21 2001 Received: from server.mldnet.com (root@[212.56.192.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8J5sI323227 for ; Wed, 19 Sep 2001 01:54:18 -0400 Received: from ppp-212.56.193.66.mldnet.com (ppp-212.56.193.66.mldnet.com [212.56.193.66]) by server.mldnet.com (8.9.3/8.9.3) with ESMTP id IAA21393; Wed, 19 Sep 2001 08:54:07 +0300 Date: Wed, 19 Sep 2001 08:59:12 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.53d) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <663593681.20010919085912@yahoo.com> To: CHEMISTRY@ccl.net CC: "ch" , =?koi8-r?B?RnJhbmNpc2NvIE110296?= ((UIB)) Subject: Summary: Calculated Spectra and Oscillator Strength Questions MIME-Version: 1.0 Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 8bit ::: Calculated Spectra and Oscillator Strength Questions Summary :::::::::::: (as of 19-Sep-2001) :: Original questions ::::::::::::::::::::::::::::::::::::::::::::::::::::::: > I have one (may be dummy question) on calculated UV/Vis spectra. > I use ArgsuLab 2.0.0. for calculation of spectra. As a result I get smth > like that > (see below). Here are my questions: > * How could I compare Oscillator Strength data with lg e values > from experiment? > * Where could I find description of length, velocity and Hansen > Oscilator Strength? > * Could anybody point me references on TDA and RPA excited state analysis? > [...ArgusLab output skipped...] :...........................................................................: :: Summary :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: * No direct comparison between osc. str. and lg e values could be made. This is treated as a rough guide--large numbers indicate intense peaks. * Length, velocity and Hansen oscilator strength are described in John McKelvey's messge below. * Excelent source of information is Q-Chem reference manual which covers CIS, RPA, TDDFT and approximate (TDA) TDDFT :...........................................................................: :: Original answers ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ............................................................................. From: jmmckel@attglobal.net Date: Saturday, September 08, 2001, 9:59:43 AM ............................................................................. Mike , Good questions; empirical answers. After 20+ years of running Zindo on dyes I can only tell you that computed oscillater strengths [f] of ~1 or larger tend to correlate with log(e)'s of 4-5. It is necessary to calibrate the f's against log(e)'s or e's themselves. The length OS is computed simply using the transition density with the already available dipole moment matrix elements over basis set. This is very cheap and easy. Sum(i,j) TD(i,j). TD is computed using the MO's and the CI coefficients for configurations. F is proportionsl the this quantity**2* Excitation energy. The velocity form is TD*. Fis proportional to this squared * the inverse of the transition energy. This is more complicated, but still not expensive. The Hansen [I think] is proportional to the product of the two above [before sqaring], and the transition energy cancels out. For large systems the Hansen result often lies between the two from which it is derived. The velocity form is probably the most reliable, but again, do some plotting against experiment... Hope this helps.. There is a discussion comparing the length and velocity forms in the QM book by Eyring, Waletr, and Kimball. For a complete basis set and a complete CI, i.e. an exact calculation, the two forms are supposed to give exactly the same result. But being in INDO space, etc.... Calibrate. Regards John McKelvey ............................................................................. From: Geoff Hutchison Date: Wednesday, August 22, 2001, 5:29:28 AM ............................................................................. >* How could I compare Oscillator Strength data with lg e values > from experiment? Don't. In a very approximate sense, osc. str. is roughly proportional to the intensity of the peaks. Even for very accurate electronic structure methods, this is treated as a rough guide--large numbers indicate intense peaks, etc. >* Could anybody point me references on TDA and RPA excited state analysis? TDA is roughly the same as CIS as far as ab-initio methods go. Basically it would be RPA, but you only treat single excitations rather than both excitations and de-excitations as you do in RPA. How detailed a reference are you looking for? Do you want descriptions of the equations-of-motion and the derivations, or do you want a reference manual? ............................................................................. From: elewars Date: Friday, August 17, 2001, 8:34:20 PM ............................................................................. To compare oscillator strength with exp, do calculations on some compounds for which you have exp epsilon values, and cf. the calc and exp values. EL ............................................................................. From: jmmckel@attglobal.net Date: Friday, August 17, 2001, 10:45:49 AM ............................................................................. Mike, Some partial answers: The mapping of theory onto experiment in the semi-empirical world, like in ARGUS [basically Zerner's INDO/S], depends in a significant part on SE theory giving results "that make sense," i.e., getting large oscillator strengths about where one finds large extinction coefficients, etc. It is hard to hope/expect more. The basis set is limited, the CI usually much too small, and the methods are calibrated to behave in a certain molecular size space. [ I know of one code, Roos' MOLCAS-5, that nails things so well, including vibronic effects, that it is shocking, but it is ab initio.... ] Oscillator strengths come basically in two "pure" flavors, and also in a mixed flavor. Dipole: f = constant*hv***2 Velocity f = constant*1/hv***2 Mixed f = constant **.. I 've seen fairly good results from TDDFT; from SE RPA the results can be _quite_ dependent on parameterization, but can't provide any references. I hope you will post the results of your query. Regards, John McKelvey ............................................................................. From: Geoff Hutchison Date: Wednesday, August 22, 2001, 6:15:12 PM ............................................................................. > Reference manual would be OK, but I am not sure if I could find it > here in Moldova. Of cource if reference manual available from Internet > it would be great. Also, I would like to have a reference on original > articles of this methods or review of this methods. I'd probably recommend part of the Q-Chem reference manual: which covers CIS, RPA, TDDFT and approximate (TDA) TDDFT. It includes references as needed. See chapter 6 (p. 135-162). -Geoff ............................................................................. From: Stefan Grimme Date: Tuesday, March 14, 2000, 1:24:25 PM ............................................................................. Dear Mike, a rough estimate is epsilon(l/mol cm-1)=f*2.5x10^8/delta with delta the band half-width in cm-1 (e.g. 5000). Stefan ___________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet Corrensstrasse 40 D-48149 Muenster Tel (+49)-251-83 36512/33241 Fax (+49)-251-83 36515 Email:grimmes@uni-muenster.de ___________________________________________ ............................................................................. From: Deepak Singh Date: Tuesday, March 14, 2000, 12:07:21 AM ............................................................................. Oscillator strengths are traditionally always in the same dimensionless units, so a value of 1 would indicate a high transition probability and one as low as yours would argue against a transition. Unfortunately with CIS you cannot look at forbidden transitions. Regards Deepak ............................................................................. From: jmmckel@attglobal.net Date: Monday, March 13, 2000, 6:47:36 PM ............................................................................. Mike, First, in general, the calculated oscillator strengths, are about the only fingerprint one has to identify in the calculation what might correspond to experiment... That's probably what you are doing. The oscilator strength calculated corresponds in name to the extinction coefficient multiplied by the band width at half-height, in 1/cm space, times a constant...i.e. the area under the absorbtion band. If all 1/2 heights are assumed to be the same then there may be a rather reasonable comparicon, as you are concerned about. With log(E) ~ 4, it is usually safe to use "f" to identify what corresponds to experimental bands. I diod this for ~20 years at Kodak, and it ~always worked... John McKelvey :...........................................................................: