From owner-chemistry@ccl.net Sat Aug 8 09:49:01 2009 From: "John M Simmie john.simmie(-)nuigalway.ie" To: CCL Subject: CCL: How to compute bond energy Message-Id: <-39957-090808094714-21132-eXeb3Gw0lzi/L5RyWD4DFw^server.ccl.net> X-Original-From: "John M Simmie" Date: Sat, 8 Aug 2009 09:47:10 -0400 Sent to CCL by: "John M Simmie" [john.simmie ~ nuigalway.ie] Errol Lewars' answer to this query does not need amplification except that the most accurate and up-to-date database for enthalpies of formation of smallish-sized organic molecules and radicals can be found in the Burcat & Ruscic online "Third Millennium Thermodynamic Database for Combustion and Air-Pollution Use with updates from Active Thermochemical Tables". In a similar vein the most comprehensive collection of chemical bond energies is to be found in Yu-Ran Luo's book "Comprehensive Handbook of Chemical Bond Energies". As regards his suggestion for a computational chemistry textbook he is too modest not to have mentioned his own text "Computational Chemistry" which is an excellent introduction to the field and covers the practical aspects of computing bond energies extremely well. Prof. John Simmie, Combustion Chemistry Centre National University of Ireland, Galway john.simmie at nuigalway.ie -----Original Message----- > From: owner-chemistry+john.simmie==nuigalway.ie++ccl.net [mailto:owner-chemistry+john.simmie==nuigalway.ie++ccl.net] On Behalf Of errol lewars elewars]![trentu.ca Sent: 06 August 2009 20:32 To: Simmie, John Subject: CCL: How to calculate a bond energy Sent to CCL by: errol lewars [elewars=-=trentu.ca] 2009 Aug 06 Hello, The usual bond energies are 298 K enthalpy differences deltaH between fragments and reactants, e.g. C-C BE for CH3-CH3: deltaH(C-C) = 2H(CH3) - H(CH3CH3) This can be calculated directly, if your molecule is not too big (see below) by a high-accuracy multistep method. I give a few examples. A CBS-4M CH3 CBS-4 Enthalpy= -39.756477, CH3-CH3 CBS-4 Enthalpy= -79.658510 deltaH = 2 H(CH3) - H(CH3CH3) = 2(-39.756477) - (-79.658510) = 0.145556 = 382.2 kJ mol-1 B G3MP2 CH3 G3MP2 Enthalpy= -39.752870, CH3-CH3 G3MP2 Enthalpy= -79.646717 deltaH = 2 H(CH3) - H(CH3CH3) = 2(-39.752870) - (-79.646717) = 0.140977 = 370.2 kJ mol-1 C CBS-QB3 CH3 CBS-QB3 Enthalpy= -39.740778, CH3-CH3 CBS-QB3 Enthalpy= -79.626122 deltaH = 2 H(CH3) - H(CH3CH3) = 2(-39.740778) - (-79.626122) = 0.144566 = 379.6 kJ mol-1 D CBS-APNO CH3 CBS-APNO Enthalpy= -39.740778, CH3-CH3 CBS-APNO Enthalpy= -79.626122 deltaH = 2 H(CH3) - H(CH3CH3) = 2(-39.799535) - (-79.743561) = 0.144491 = 379.4 kJ mol-1 I convertes hartree to JkJ mol-1 by mult by 2626 (as if 2625.5 makes any difference). The exp C-C bond enthalpy for CH3CH3 is said to be 377.0 kJ mol-1 (90.1 kcal mol-1; E. V. Anslyn, D. A. Dougherty, "Modern Physical Organic Chemisty", University Science Books, Sausalito, CA, 2006; p 72. The CBS-APNO value may be better than the exp. CBS-4M is the least, CBS-APNO the most, accurate; G3MP2 and CBS-QB3 are comparable. The approximate size limits and times for these methods are (number of heavy atoms/hours for that number): CBS-4m, 19/3h; G3MP2, 13/12h; CBS-QB3, 10/9h; CBS-APNO, 5/2.4 Using energies at the SCF (Hartreee-Fock) level your bond E will not be good; even DFT or MP2 will probably be significantly inferior to these methods. If your molecule is too big for a high-accuracy multistep method, you could use an isodesmic reaction incorporated into a thermodynamic cycle. You can check these methods in a book on computational chemistry. Good luck. E. Lewars === Eduardo Lemos de Sa edulsa*o*quimica.ufpr.br wrote: > Sent to CCL by: "Eduardo Lemos de Sa" [edulsa#%#quimica.ufpr.br] Sirs > and Ladies > > I have a silly questions: how can I calculate a energy rising from a > bond between two atoms in a organic molecule? I guess that the answer can be: > calculate the SCF energy for the whole molecule, for two radicals > originated from the dissociation. Thus, bound energy would be: sum > (SCF energy for radicals) - SCF energy for the complete molecule. Am I right? > > Thank you in advance > > Yours > > Eduardo From owner-chemistry@ccl.net Sat Aug 8 15:51:00 2009 From: "Thomas P Stockfisch t.stockfisch(_)cox.net" To: CCL Subject: CCL: xalloc "C" routine in Zerner's ZINDO Message-Id: <-39958-090808152332-22177-Gbv8AaAYXW+jrp71wHM5NQ**server.ccl.net> X-Original-From: "Thomas P Stockfisch" Date: Sat, 8 Aug 2009 15:23:28 -0400 Sent to CCL by: "Thomas P Stockfisch" [t.stockfisch,,cox.net] John - I have a lot of experience porting to linux (millions of lines of code) and might be interested in volunteering. Could you point me towards the source so I could have a look? Tom Stockfisch t.stockfisch*_*cox.net http://www.tstockfisch.com From owner-chemistry@ccl.net Sat Aug 8 21:43:01 2009 From: "John McKelvey jmmckel=-=gmail.com" To: CCL Subject: CCL: ZINDO Code compilation Message-Id: <-39959-090808213855-7122-9BGHuwkY1fveVVdk5+YRjQ[*]server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=0014853c0d6856bb1f0470ab6c17 Date: Sat, 8 Aug 2009 21:31:06 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel~~gmail.com] --0014853c0d6856bb1f0470ab6c17 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Folks, Thank all of you very much who have helped locate documentation for ZINDO. That is great. And thanks to all who volunteered information and even volunteered to help with the code! It turns out that the g77+gcc compile problems and memory allocation problems seem to have gone away on using gfortran+gcc, thanks Kevin Gilbert at Serena Software.. We are not 100% out of the woods, but a very large part of stuff is running OK. John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel * gmail.com --0014853c0d6856bb1f0470ab6c17 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Folks,

Thank all of you very much who have helped locate docume= ntation for ZINDO.=A0 That is great.

And thanks to all who volunteer= ed information and even volunteered to help with the code!
It turns out = that the g77+gcc compile problems and memory allocation problems seem to ha= ve gone away on using gfortran+gcc, thanks Kevin Gilbert at Serena Software= ..=A0 We are not 100% out of the woods, but a very large part of stuff is r= unning OK.

John

--
John McKelvey
10819 Middleford PlFt Wayne, IN 46818
260-489-2160