From Jonathan.Connor@mailhost.mcc.ac.uk Mon Dec 11 07:27:50 1995 Received: from nessie.mcc.ac.uk for Jonathan.Connor@mailhost.mcc.ac.uk by www.ccl.net (8.6.10/950822.1) id HAA20159; Mon, 11 Dec 1995 07:21:36 -0500 Message-Id: <199512111221.HAA20159@www.ccl.net> Received: from mailhost.mcc.ac.uk by mailhost.mcc.ac.uk id <11868-0@mailhost.mcc.ac.uk>; Mon, 11 Dec 1995 12:20:13 +0000 Subject: calorie conversion To: chemistry@www.ccl.net Date: Mon, 11 Dec 1995 12:20:07 +0100 (MET) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2866 From: Jonathan Connor Sender: Jonathan.Connor@mailhost.mcc.ac.uk The conversion factor 1 calorie = 4.1868 joule (exactly) refers to the international calorie, which is not usually used in electronic structure calculations, thermochemistry or reaction kinetics. In these subjects, the thermochemical calorie is the relevant one, for which 1 calorie = 4.184 joule (exactly). There is also the 15 degree centrigrade calorie for which 1 calorie = 4.1855 joule (approximately). The moral is "avoid calories"! Forwarded message: > Delivery-Date: Sun, 10 Dec 1995 08:07:22 +0000 > From: schlecmf > Message-Id: <9512072038.AA16252@esds01.es.dupont.com> > Date: Thu, 7 Dec 95 15:38:10 EST > To: chemistry@www.ccl.net > Subject: CCL:Units Conversion > Sender: chemistry-request@www.ccl.net > Errors-To: jkl@ccl.net > Precedence: bulk > > > Regarding the recent inquiry on units conversion, > > Could anyone come up with reasonable accuracy (at least 6 significant > > figures) for > > > > Hartrees to Joules > > Calories to Joules > > Bohr to Angstrom > > > > Non of my texts even have the definition of a Hartree. > > > > Thanks in advance > > > > Alex > > > > +--------------------------------------------------+ > > |Alternate E-mail A.J.Turner@Bath.ac.uk | > > |www home @ http://www.bath.ac.uk/~chpajt/home.html| > > +--------------------------------------------------+ > I can recommend a WWWeb site which will carry out such > conversions interactively: > > http://www.chemie.fu-berlin.de/chemistry/general/units.html > > Instructions are given in English and German, but it is > simple to use. Submitting the requested conversion queries to > this resource gave the following answers. > > 1 hartree = 4.359748e-18 joule > 1 calorie = 4.1868 joule (fewer than the requested six > significant figures) > 1 bohrradius = 0.5291772 angstrom > > This server is often busy, so reference to a manual will > often provide the answer quicker. > > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 > --- > -- ****************************************************************************** Professor J.N.L. Connor, Phone(direct line): 0161-275-4693 (national) Department of Chemistry, :+44-161-275-4693 (international) University of Manchester, Manchester M13 9PL, Phone(secretary): 0161-275-4686 or 4600 England. Fax: 0161-275-4734 or 4598 ****************************************************************************** From owner-chemistry@ccl.net Mon Dec 11 09:42:52 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA22239; Mon, 11 Dec 1995 09:35:54 -0500 Received: from astro.ocis.temple.edu for xiaopeng@astro.ocis.temple.edu by bedrock.ccl.net (8.7.1/950822.1) id JAA17996; Mon, 11 Dec 1995 09:35:42 -0500 (EST) Received: (from xiaopeng@localhost) by astro.ocis.temple.edu (8.7.1/8.7.1) id JAA17139; Mon, 11 Dec 1995 09:35:42 -0500 (EST) Date: Mon, 11 Dec 1995 09:35:41 -0500 (EST) From: Peking To: chemistry@ccl.net Subject: PM3(tm) Spartan can not do it. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I found that although Spartan claim it can do PM3(tm) calculation. It turns out if you do submit this kind of job,it can not do it. I try to use it for optimizing the geometry of a 35 atoms system including a Ti, When I submit the job, the computer told me that PS-GVB basis function has not installed! Does anyone know which software can do this calculation? furthur if I want to do the "transition structure" geometry optimization, which one can do? Thanks in advance! xiaopeng ======================================================= 215-2047149(office) 215-5357188(home) xiaopeng@astro.ocis.temple.edu ====================================================== From yu@infiniti.wavefun.com Mon Dec 11 11:27:53 1995 Received: from volvo.wavefun.com for yu@infiniti.wavefun.com by www.ccl.net (8.6.10/950822.1) id LAA23918; Mon, 11 Dec 1995 11:25:36 -0500 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA17212; Mon, 11 Dec 95 08:24:45 -0800 Received: from infinity.wavefun.com(198.147.95.8) by volvo.wavefun.com via smap (V1.3) id sma017208; Mon Dec 11 08:24:30 1995 Received: by infiniti.wavefun.com (931110.SGI/930416.SGI.AUTO) for @volvo.wavefun.com:Darren.Andrews@man.ac.uk id AA22896; Mon, 11 Dec 95 08:24:02 -0800 From: "Jianguo Yu" Message-Id: <9512110823.ZM22894@infiniti.wavefun.com> Date: Mon, 11 Dec 1995 08:23:56 -0800 Reply-To: yu@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Parameters for Magnesium Cc: Darren.Andrews@man.ac.uk, huang@wavefun.com Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Dec 10, 3:47pm, Darren Andrews wrote: > Subject: CCL:AM1 Parameters for Magnesium > Can anyone provide good Semi-Empirical parameters for Magnesium, > preferrably for AM1 calculations. > > Darren.Andrews@man.ac.uk > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: Darren.Andrews@man.ac.uk > -- Original Sender From: Address: Darren.Andrews@man.ac.uk > 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 > >-- End of excerpt from Darren Andrews PM3 and MNDO have parameters for magnesium (PM3: James J.P. Steward, J.Compt.Chem: MNDO: A.A.Voityuk, Zh. Strukt. Khim., 29, 926(1988)). SPARTAN can perform the calculations of Mg compounds by MNDO and PM3. If you want to know more details, please contact support@wavefun.com Jianguo Yu -- +-----------------------+------------------+-------------------------+ |Jianguo Yu, Ph.D. | ______________ | E-Mail: yu@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | "The doctrines observe | |Suite 370 | \ \\/ | nature" | |Irvine, CA 92715 | \/ | Lao-tzu (604-531 B.C.)| +-----------------------+------------------+-------------------------+ From owner-chemistry@ccl.net Mon Dec 11 11:38:47 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA23762; Mon, 11 Dec 1995 11:13:44 -0500 Received: from nessie.mcc.ac.uk for Jonathan.Connor@mailhost.mcc.ac.uk by bedrock.ccl.net (8.7.1/950822.1) id LAA19712; Mon, 11 Dec 1995 11:11:54 -0500 (EST) Message-Id: <199512111611.LAA19712@bedrock.ccl.net> Received: from mailhost.mcc.ac.uk by mailhost.mcc.ac.uk id <23719-0@mailhost.mcc.ac.uk>; Mon, 11 Dec 1995 16:11:26 +0000 Subject: calorie conversion To: chemistry@ccl.net Date: Mon, 11 Dec 1995 16:11:16 +0100 (MET) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit From: Jonathan Connor Sender: Jonathan.Connor@mailhost.mcc.ac.uk Forwarded message: The conversion factor 1 calorie = 4.1868 joule (exactly) refers to the international calorie, which is not usually used in electronic structure calculations, thermochemistry or reaction kinetics. In these subjects, the thermochemical calorie is the relevant one, for which 1 calorie = 4.184 joule (exactly). There is also the 15 degree centrigrade calorie for which 1 calorie = 4.1855 joule (approximately). The moral is "avoid calories"! > Forwarded message: > > Delivery-Date: Sun, 10 Dec 1995 08:07:22 +0000 > > From: schlecmf > > Message-Id: <9512072038.AA16252@esds01.es.dupont.com> > > Date: Thu, 7 Dec 95 15:38:10 EST > > To: chemistry@www.ccl.net > > Subject: CCL:Units Conversion > > Sender: chemistry-request@www.ccl.net > > Errors-To: jkl@ccl.net > > Precedence: bulk > > > > > > Regarding the recent inquiry on units conversion, > > > Could anyone come up with reasonable accuracy (at least 6 significant > > > figures) for > > > > > > Hartrees to Joules > > > Calories to Joules > > > Bohr to Angstrom > > > > > > Non of my texts even have the definition of a Hartree. > > > > > > Thanks in advance > > > > > > Alex > > > > > > +--------------------------------------------------+ > > > |Alternate E-mail A.J.Turner@Bath.ac.uk | > > > |www home @ http://www.bath.ac.uk/~chpajt/home.html| > > > +--------------------------------------------------+ > > I can recommend a WWWeb site which will carry out such > > conversions interactively: > > > > http://www.chemie.fu-berlin.de/chemistry/general/units.html > > > > Instructions are given in English and German, but it is > > simple to use. Submitting the requested conversion queries to > > this resource gave the following answers. > > > > 1 hartree = 4.359748e-18 joule > > 1 calorie = 4.1868 joule (fewer than the requested six > > significant figures) > > 1 bohrradius = 0.5291772 angstrom > > > > This server is often busy, so reference to a manual will > > often provide the answer quicker. > > > > > > --- > > Administrivia: This message is automatically appended by the mail exploder: > > 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 > > --- > > > > -- > ****************************************************************************** > Professor J.N.L. Connor, Phone(direct line): 0161-275-4693 (national) > Department of Chemistry, :+44-161-275-4693 (international) > University of Manchester, > Manchester M13 9PL, Phone(secretary): 0161-275-4686 or 4600 > England. Fax: 0161-275-4734 or 4598 > ****************************************************************************** > -- ****************************************************************************** Professor J.N.L. Connor, Phone(direct line): 0161-275-4693 (national) Department of Chemistry, :+44-161-275-4693 (international) University of Manchester, Manchester M13 9PL, Phone(secretary): 0161-275-4686 or 4600 England. Fax: 0161-275-4734 or 4598 ****************************************************************************** From owner-chemistry@ccl.net Mon Dec 11 11:42:54 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA23991; Mon, 11 Dec 1995 11:28:07 -0500 Received: from myriad.cis.pitt.edu for SATYAM@vms.cis.pitt.edu by bedrock.ccl.net (8.7.1/950822.1) id LAA19989; Mon, 11 Dec 1995 11:28:00 -0500 (EST) From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.3-10 #10002) id <01HYOGUEXYOG9YK2CE@vms.cis.pitt.edu>; Mon, 11 Dec 1995 11:27:14 -0400 (EDT) Date: Mon, 11 Dec 1995 11:27:14 -0400 (EDT) Subject: How different <2s/X/2Px> give same 14.674 factor in Dipole Moment? To: chemistry@ccl.net Message-id: <01HYOGUEYYGY9YK2CE@vms.cis.pitt.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Quantum Chemists :: While going thru the calculation of the dipole moment..using the CNDO method..in few references we looked thru..we found different expressions for the <2s_A|X|2px_A> and mu_X in Debyes.. How does one get same value of 14.674 from these different factors involved here ? Are we missing something in understanding these equations or are there any typographical mistakes in these equations ? Any help will be useful.. The General Expression is : mu_X (2s, 2px) = 2.* {Sum_over_A} [ P(2s_A, 2px_A) <2s_A|X|2px_A>] A : Stands for nucleus X, x : X-components a_0 : bohr radius Zeta_A : Orbital Exponent of atom A Zeff_A : 2*Zeta_A All Should give in Units of Debyes :: ____________________________________________________________________ (1) Ref: Pople & Beveridge p. 87 (Book) :: mu_X (2s, 2px) = - 14.674 {Sum_over_A} [ P(2s_A, 2px_A) / Zeta_A ] ___________________________________________________________________ (2) Ref: Sadlej and Cooper p 147 (Book) :: mu_X (2s, 2px) = - 14.6740 {Sum_over_A} [ P(2s_A, 2px_A) / Zeff_A ] >>>>>>> NOTE :: Zeff_A = 2.* Zeta_A (as in book) where <2s_A|X|2px_A> = 5 Sqrt(3) /6 Zeta_A ____________________________________________________________________ (3) Ref: Ellis and Jaffe p 72 in Book by Sega <2s_A|X|2px_A> = 5 a_0 / 2 Sqrt(3 Zeta_A) ____________________________________________________________________ (4) Ref: Maksic and Bloor JPC Vol 77 p.1520 & 1521 (1973) <2s_A|X|2px_A> = 5 Sqrt(3) a_0 / 3 * Zeta_A ____________________________________________________________________ Thanks in Advance. Satyam (satyam@vms.cis.pitt.edu) From topper@cooper.edu Mon Dec 11 12:27:54 1995 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.6.10/950822.1) id MAA25236; Mon, 11 Dec 1995 12:25:05 -0500 Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA12900 (5.65c/IDA-1.4.4 for ); Mon, 11 Dec 1995 12:27:36 -0500 Received: by zeus.cooper.edu id AA25274 (5.67b/IDA-1.5); Mon, 11 Dec 1995 12:20:37 -0500 From: TOPPER ROBERT Message-Id: <199512111720.AA25274@zeus.cooper.edu> Subject: CCL:Units Conversion To: chemistry@www.ccl.net Date: Mon, 11 Dec 1995 12:20:37 -0500 (EST) Cc: topper@cooper.edu X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2386 In 1986, CODATA, the Committee on Data for Science and Technology of the International Council of Scientific Unions, published a set of self-consistent values for the basic constants and conversion constants derived from a least-squares fit to over 200 different measurements. They are reported every year in Physics Today and are summarized by E. Richard Cohen and Barry N. Taylor. One can find pretty much all of the conversion factors needed for molecular modeling in this report, which always comes out in the August issue. Notably, there is no conversion factor for calories in that table. Prof. Connor's warning about calories is important; one should always be careful when quoting numbers in calories. The CODATA tables don't contain a conversion factor to calories for precisely this reason. If you have a look at the CRC Handbook of Chemistry and Physics you will also see other definitions of the calorie; there is a 20 degree Celsius calorie, for example (equal to 4.18190 Joule). By the way. there are also some other definitions of the Joule floating around; 1 Joule (Int.) = 1.000165 Joule (abs), 1 Joule (abs) = 10-7 ergs (exactly). The Joule (abs) is the usual SI definition of the Joule, which CODATA uses. The CODATA table contains interesting minutiae, or "fun facts." For example, in the section entitles "X-ray standards," the standard "crystallographic Angstrom," indicated by A*, is 1.000 014 81 * 10^-10 meters. and I always thought 1 A = 10^-10 meters, exactly! Silly me... hope this helps someone rqt ************************************************************************ Robert Q. Topper email: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html ************************************************************************ The Cooper Union for the Advancement of Science and Art, founded in 1859, is a private institution of higher learning where all students receive full-tuition scholarships to study engineering, architecture and art. ************************************************************************ From owner-chemistry@ccl.net Mon Dec 11 12:42:54 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA25380; Mon, 11 Dec 1995 12:36:52 -0500 Received: from UMSLVMA.UMSL.EDU for wwelsh@jinx.umsl.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA21066; Mon, 11 Dec 1995 12:36:49 -0500 (EST) Received: from admiral.umsl.edu by UMSLVMA.UMSL.EDU (IBM VM SMTP V2R2) with TCP; Mon, 11 Dec 95 11:38:22 CST Received: from [134.124.76.179] by admiral.umsl.edu (5.4R3.10) id AA26158; Mon, 11 Dec 1995 11:36:40 -0600 Message-Id: <9512111736.AA26158@admiral.umsl.edu> X-Sender: wwelsh@jinx.umsl.edu X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 11 Dec 1995 11:36:08 -0600 To: chemistry@ccl.net From: wwelsh@jinx.umsl.edu (William Welsh) Subject: correct citation for Mopac 6.0 Fellow Netters, I need the correct citation to use for Mopac 6.0 when referencing it in an article. Thanks. At present, I'm using Mopac, Edition 6.0, J. J. P. Stewart, Frank J. Seiler Research Laboratory, U. S. Air Force Academy, Colorado Springs, Co 80840. Thanks ... Bill Welsh From bonvoisi@cemes.cemes.fr Mon Dec 11 12:45:40 1995 Received: from oceane.cict.fr for bonvoisi@cemes.cemes.fr by www.ccl.net (8.6.10/950822.1) id MAA25317; Mon, 11 Dec 1995 12:30:47 -0500 Received: from cemes.cemes.fr (cemes.cemes.fr [192.93.13.1]) by oceane.cict.fr (8.6.9/8.6.9) with SMTP id SAA12288 for ; Mon, 11 Dec 1995 18:29:59 +0100 Received: by cemes.cemes.fr; Mon, 11 Dec 95 18:28:22 EST From: bonvoisi@cemes.cemes.fr (Bonvoisin Jacques) Message-Id: <9512111728.AA00620@cemes.cemes.fr> Subject: Mo parameters for EHMO calculation To: chemistry@www.ccl.net Date: Mon, 11 Dec 1995 18:28:20 +0100 (GMT+0100) Cc: bonvoisi@cemes (Jacques Bonvoisin) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 576 Hi CCL'ers Can someone tell me where I can find the Charge Iteration Parameters for Molybdenum in order to perform Extended Huckel cal- culations ? Thanks to everyone. -- +----------------------------------------------------------------+ | Jacques BONVOISIN | | CNRS/CEMES-LOE Tel : +33 62 25 78 52 | | 29 , rue Jeanne Marvig Fax : +33 62 25 79 99 | | F-31055 Toulouse Cedex Email: bonvoisi@cemes.fr | +----------------------------------------------------------------+ From jxh@ibm12.biosym.com Mon Dec 11 14:12:55 1995 Received: from bioc1.biosym.com for jxh@ibm12.biosym.com by www.ccl.net (8.6.10/950822.1) id OAA26865; Mon, 11 Dec 1995 14:06:53 -0500 Received: from ibm12.biosym.com by bioc1.biosym.com (5.64/0.0) id AA25807; Mon, 11 Dec 95 11:09:41 -0800 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA17052; Mon, 11 Dec 1995 11:06:31 -0800 Received: from Messages.8.5.N.CUILIB.3.45.SNAP.NOT.LINKED.ibm12.biosym.com.rs.aix3 via MS.5.6.ibm12.biosym.com.rs_aix3; Mon, 11 Dec 1995 11:06:30 -0800 (PST) Message-Id: Date: Mon, 11 Dec 1995 11:06:30 -0800 (PST) From: Joerg Hill To: CHEMISTRY@www.ccl.net Subject: Re: CCL:Units Conversion References: <9512072038.AA16252@esds01.es.dupont.com> > Could anyone come up with reasonable accuracy (at least 6 significant > figures) for > > Hartrees to Joules > Calories to Joules > Bohr to Angstrom > > Non of my texts even have the definition of a Hartree. Hartrees and Bohrs (and all other so-called atomic units) are a system of units in which all fundamental physical constants have the value 1 (which makes computations all lot simpler). To put it another way, you can write atomic units using fundamental physical constants, e. g.: 1 Bohr = 1 a_0 = 4 pi epsilon_0 hbar^2 / (m_e e^2) 1 Hartree = e^2 / (4 pi epsilon_0 a_0) where epsilon_0 is the permittivity of vacuum (4 pi epsilon_0 = 1e7/c^2), hbar is the Planck constant divided by 2 pi, m_e is the mass of an electron, and e is the elementary charge. The latest refinement of the fundamental physical constants can be found under: http://physics.nist.gov/PhysRefData/codata86/codata86.html. The conversion between calories and Joules actually depends on which calories you have (as someone else already pointed out). Joerg-R. Hill From owner-chemistry@ccl.net Mon Dec 11 14:27:56 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA26983; Mon, 11 Dec 1995 14:15:00 -0500 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by bedrock.ccl.net (8.7.1/950822.1) id OAA22223; Mon, 11 Dec 1995 14:14:55 -0500 (EST) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA17855; Mon, 11 Dec 95 11:15:17 -0800 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma017853; Mon Dec 11 11:15:07 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA24115; Mon, 11 Dec 95 11:14:40 -0800 Date: Mon, 11 Dec 95 11:14:40 -0800 From: hcj@mazda.wavefun.com (Harry C. Johnson IV) Message-Id: <9512111914.AA24115@mazda.wavefun.com> To: xiaopeng@astro.ocis.temple.edu Cc: chemistry@ccl.net In-Reply-To: (message from Peking on Mon, 11 Dec 1995 09:35:41 -0500 (EST)) Subject: Re: CCL:PM3(tm) Spartan can not do it. Reply-To: hcj@wavefun.com >>>>> "xiaopeng" == Peking writes: xiaopeng> Dear netters, I found that although Spartan claim it can xiaopeng> do PM3(tm) calculation. It turns out if you do submit xiaopeng> this kind of job,it can not do it. I try to use it for xiaopeng> optimizing the geometry of a 35 atoms system including a xiaopeng> Ti, When I submit the job, the computer told me that xiaopeng> PS-GVB basis function has not installed! Hmmm... Spartan version 4.0 with PM3(tm) and Ti parameters has been out for quite some time and many of our users, including myself, have done calculations on Ti complexes, as well as several other transition metals without trouble. The problem you have encountered is that you have attempted to run PM3(tm) _with_ the solvation model. The two are not compatible at this time. If you look in your output file you will see a message to that effect. The error message which shows up in the graphics dialog is actually incorrect, and will be changed in the future. Your calculation should run correctly if you specify no solvent. xiaopeng> Does anyone know which software can do this xiaopeng> calculation? furthur if I want to do the "transition xiaopeng> structure" geometry optimization, which one can do? Spartan is the only software package of which I am aware that can perform PM3(tm) calculations, however, there may be others that can perform semi-empirical calculations on Ti, using ZINDO for instance. Spartan can perform the transition structure optimization in which you are interested as well as several other types of calculations. However, the current solvent models do not support d-orbital contributions. Hope this helps! -Harry +-----------------------+------------------+-------------------------+ |Harry C. Johnson IV | ______________ | E-Mail: hcj@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | | |Suite 370 | \ \\/ | "Seems to me its all | |Irvine, CA 92715 | \/ | just chemistry" - RUSH | +-----------------------+------------------+-------------------------+ From jkl@ccl.net Mon Dec 11 17:13:02 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id RAA00675; Mon, 11 Dec 1995 17:06:29 -0500 Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.7.1/950822.1) id RAA24128; Mon, 11 Dec 1995 17:06:25 -0500 (EST) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id RAA04358; Mon, 11 Dec 1995 17:06:25 -0500 Date: Mon, 11 Dec 1995 17:06:25 -0500 Message-Id: <199512112206.RAA04358@krakow.ccl.net> To: chemistry@www.ccl.net Subject: The Internet Censors in US Congress are back Cc: jkl@ccl.net Sorry -- this is not CC, but the coordinator feels it is important. Please get involved and study the issue, react if you feel so... More info on this issue can be had at http://www.cdt.org/ ========================================================================== CAMPAIGN TO STOP THE NET CENSORSHIP LEGISLATION IN CONGRESS On Tuesday December 12, 1995, Join With Hundreds of Thousands Of Your Fellow Internet Users In A NATIONAL INTERNET DAY OF PROTEST PLEASE WIDELY REDISTRIBUTE THIS DOCUMENT WITH THIS BANNER INTACT REDISTRIBUTE ONLY UNTIL December 20, 1995 --------------------------------------- Outrageous proposals to censor the Internet demand that the Internet Community take swift and immediate action. We must stand up and let Congress know that we will not tolerate their attempts to destroy this medium! Please join hundreds of thousands of your fellow citizens in a National Day of Protest on Tuesday December 12, 1995. A vote on this issue is exected to occur Tuesday 12/12. House Speaker Newt Gingrich (R-GA), who opposed the Original Exon/Coats CDA, along with Rep. Rick White (R-WA), are working to narrow the current proposals in an effort to protect freedom of speech and the viability of the Internet as a means of education and commerce. They and the rest of their colleagues in Congress need to hear from concerned citizens and the net.community before it is too late. On Tuesday December 12, CDT, VTW, EFF, EPIC, the ACLU, and other activist groups are urging you to join us in a National Day of Protest. The goal is to flood key members of the House and Senate with phone calls, faxes and email with the message that the Internet community WILL NOT TOLERATE Congressional attempts to destroy the Internet, limit our freedoms, and trample on our rights. ========================================================== Cut and forwarded by Jan Labanowski jkl@ccl.net From owner-chemistry@ccl.net Mon Dec 11 18:28:00 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA01787; Mon, 11 Dec 1995 18:21:22 -0500 Received: from auric.chem.csiro.au for D.Winkler@chem.csiro.au by bedrock.ccl.net (8.7.1/950822.1) id SAA24992; Mon, 11 Dec 1995 18:21:16 -0500 (EST) Received: from [138.194.40.190] (mac-40190.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA24090 (5.67b/IDA-1.5 for chemistry@ccl.net); Tue, 12 Dec 1995 10:17:57 +1100 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 12 Dec 1995 10:19:45 +1000 To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net, anchodd@tasman.cc.utas.edu.au From: D.Winkler@chem.csiro.au (Dr. Dave Winkler) Subject: Suprcomputing in Life Sciences meeting Following our successful first ever Australian Symposium , CSIRO Supercomputing Support Group is organising the Second CSIRO Symposium on "COMPUTATIONAL CHALLENGES IN LIFE SCIENCES" 5-7 February 1996 Melbourne, Australia Aim of the Symposium: -------------------- To bring together CSIRO and other researchers in the life sciences to hear about and discuss current trends in computational approaches to complex biological problems. Expected Outcome: ----------------- Attendees wiil gain a better understanding of the capabilities and current applicability of advanced computational systems to life sciences research. Venue: ------ Theatres 1 & 2 SEECS Building Melbourne University 221 Bouverie Street Carlton, Victoria 3053 Australia Symposium Topics: ----------------- 1. Nervous system modelling and simulation 2. Organ and organism modelling: virtual plants, visible man 3. Bioinformatics 4. Drug design, biochemistry, molecular biology 5. Imaging methods and interpretation techniques: x-ray, NMR, MR imaging, etc; 3D and 4D visualisation Full details and registration form is available at: http://www.mel.dit.csiro.au/LifeSci/cfp.html Cheers, Dave Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers CSIRO: http://www.csiro.au Private Bag 10,Rosebank MDC, Clayton, Australia http://www.chem.csiro.au From ng570@andechs.pnl.gov Mon Dec 11 18:30:47 1995 Received: from andechs.pnl.gov for ng570@andechs.pnl.gov by www.ccl.net (8.6.10/950822.1) id SAA01808; Mon, 11 Dec 1995 18:23:01 -0500 Received: by andechs.pnl.gov (AIX 3.2/UCB 5.64/4.03) id AA09678; Mon, 11 Dec 1995 15:22:31 -0800 From: ng570@andechs.pnl.gov (Kirk Peterson) Message-Id: <9512112322.AA09678@andechs.pnl.gov> Subject: Workshop announcement To: chemistry@www.ccl.net (Computational Chemistry List) Date: Mon, 11 Dec 1995 15:22:31 -0800 (PST) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1834 ANNOUNCEMENT: Workshop in Relativistic Quantum Mechanics by Dr. Ken Dyall (NASA Ames Research Center) January 15 - 19, 1996 at the Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland, WA Sponsered by : Theory, Modeling, and Simulation Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory The workshop/short course will consist of a total of 16 lectures over a period of 5 days. An equal number of tutorials for discussion and problem solving are also scheduled during this time. The goals of the course are to provide the theoretical ground work necessary for research involving relativistic quantum mechanics. The course was originally taught last spring in Denmark at the graduate level ("Introduction to Relativistic Quantum Chemistry"). Topics to be covered include: "Classical" relativity, E&M, and quantization Relativistic quantum mechanics with the Dirac equation Four-component wave functions Quantum Electrodynamics Symmetry and double groups Dirac Hartree Fock and electron correlation Two-component wave functions Douglas-Kroll transformation Spin and spin-orbit coupling Perturbation theory Effective core potentials (ECPs) Further information, including registration materials, can be accessed via the Web at http://w3.pnl.gov:2080/quantum/index.html/ Specific questions can be directed to Kirk Peterson at ka_peterson@pnl.gov Pacific Northwest National Laboratory is a multiprogram national laboratory operated by Battelle Memorial Institute, under Contract No. DE-AC06-76RLO 1830. From arthur_j@chem.usyd.edu.au Mon Dec 11 20:13:00 1995 Received: from lars.chem.su.oz.au for arthur_j@chem.usyd.edu.au by www.ccl.net (8.6.10/950822.1) id UAA02780; Mon, 11 Dec 1995 20:07:44 -0500 Received: (from arthur_j@localhost) by lars.chem.su.oz.au (8.6.9/8.6.9) id MAA16095; Tue, 12 Dec 1995 12:07:47 +1100 Date: Tue, 12 Dec 1995 12:07:45 +1100 (EDT) From: Jonathan Arthur Subject: Fortran debugger To: chemistry@www.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everyone, Does anyone know of a good (and free!) utility to assist in debugging Fortran programs? (For UNIX) And if so where can I get it from? Thanks in advance, Jonathan _______________________________________________________________ Jonathan Arthur Theoretical Chemistry e-mail: arthur_j@chem.usyd.edu.au School of Chemistry (F11) telephone: +61-2-351-4416 The University of Sydney fax: +61-2-351-3329 NSW 2006 AUSTRALIA URL: http://www.usyd.edu.au/~jarthur/jono.html _______________________________________________________________ From owner-chemistry@ccl.net Mon Dec 11 06:33:22 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA19709; Mon, 11 Dec 1995 06:33:21 -0500 Received: from rulway.leidenuniv.nl for frits@chemde4.leidenuniv.nl by bedrock.ccl.net (8.7.1/950822.1) id GAA16814; Mon, 11 Dec 1995 06:33:17 -0500 (EST) Received: from chemde4.LeidenUniv.nl by rulway.leidenuniv.nl with SMTP id AA26345 (5.67b/IDA-1.5 for <@RULWAY.LEIDENUNIV.NL:chemistry@ccl.net>); Mon, 11 Dec 1995 12:33:15 +0100 Received: by chemde4.leidenuniv.nl (920330.SGI/920502.SGI) for @RULWAY.LEIDENUNIV.NL:elewars@alchemy.chem.utoronto.ca id AA16614; Mon, 11 Dec 95 12:38:20 +0100 Date: Mon, 11 Dec 95 12:38:20 +0100 From: frits@chemde4.leidenuniv.nl (Frits Daalmans) Message-Id: <9512111138.AA16614@chemde4.leidenuniv.nl> To: "E. Lewars" Subject: Re: CCL:MATRIX ALGEBRA PROGRAM Cc: chemistry@ccl.net There are probably umpteen packages that can do that... what you could do is, grab a numerical library (say, lapack), and make a couple of wrapper functions (input of a matrix, output to screen/file, etc.) and make a "toolkit" of programs that use these routines. That's what I did (including the library itself :-( reinventing the wheel) but I am NOT sorry, because it is very convenient to be able to work with matrices just from the UNIX shell (with these tools) instead of writing programs for each case: i.e. (imaginary UNIX session) do some calculations, obtain some numerical results, use a tiny self-written tool to extract data from e.g. GAMESS or G94 output, mat_mult > C mat_eigval > Ceigval look at the eigenvalues, continue work,... If you are smart, you don't go this way but compile well-known freeware toolkits (I don't know of any though... if there are *really* *none* available I'll put mine under GPL and "publish" 'em). Good luck, Frits Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@chemde4.leidenuniv.nl Tel: [+31] (0)71-5274505 From tamasgunda@tigris.klte.hu Mon Dec 11 06:45:03 1995 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.6.10/950822.1) id GAA19792; Mon, 11 Dec 1995 06:44:58 -0500 Message-Id: <199512111144.GAA19792@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Mon, 11 Dec 1995 09:28:06 EST From: tamasgunda@tigris.klte.hu To: chemistry@www.ccl.net Date: Mon, 11 Dec 1995 09:28:07 +1 Subject: Sybyl aromatic bonds Dear Netters, > > Have you ever used SYBYL? During the last few days, I was astonished to > find SYBYL does have problem in reading PDB files. Let me elaborate now. > [troubles with aromatic atoms deleted] The converison program Mol2mol can handle such a problems, as it uses a quite sophisticated algorithm to perceive the chemical surrounding of atoms, when reassigning of atom and bond types is necessary. Moreover, when converting to SYBYL or similar molecule file formats with extended atom types, the user can interfere and choose whether aromatic or single/double bond and atom types should be used in the output file. The program is available from Cherwell Scientific Publ., http://cherwell.com/cherwell, or info@cherwell.com Tamas E. Gunda ************************************************************************ Tamas E. Gunda, Ph.D. phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From Y0H8797@ACS.TAMU.EDU Sat Dec 9 17:57:19 1995 Received: from VMS1.TAMU.EDU for Y0H8797@ACS.TAMU.EDU by www.ccl.net (8.6.10/950822.1) id RAA29380; Sat, 9 Dec 1995 17:51:02 -0500 Date: Sat, 9 Dec 1995 16:50:59 -0600 (CST) From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <951209165059.2246bdad@ACS.TAMU.EDU> Subject: Summary: Koopmans' Theorem and Neglect of Bond in CAChe MOPAC Input A week ago I asked 2 questions about Koopmans' Theorem and CAChe MOPAC. Many thanks to Drs. J.-M.Sichel, R.Fournier, B.Duke, M.J.Ondrechen, I.Mayer, Jack ?, E.Chamot, R.P.Mattie, J.Pollard, D.Lichtenberger, J.Schulte, R.Winchester and Matt. The follwoing is a summary. Words in [] are mine. I asked Drs. J.-M.Sichel and R. Fournier more questions which are attached to the end. Lines preceeded by > are mine. My questions are: (1) Can anyone tell me whether ionization potential calculated based on Koopman's Theorem is just the IP for vertical ionization? I suspect so because I think what Koopman's Theorem misses is just the vibrational relaxation in the ionic state after the electron is gone. Please correct me if I'm wrong. (2) I use CAChe MOAPC to calculate the distances and bond orders between the 3 hydrogens of a NH3 right above the pai ring of ferulic acid (4-OH-3-OCH3- cinnamic acid). After geometry optimization, NH3 shifts to the edge of the pai-ring. I did this calculation in 3 ways: 1) no bonding is specified between H's of NH3 and pai-ring; 2) 1 H of NH3 hydrogen-bonded to carbons #1,3,5 (if the 6 C's are numbered 1 to 6); 3) 3 H's of NH3 hydrogen-bonded to C's #1,3,5, respectively. My question is: Does the calculation take into account whether I specified the bonding at all? It seems it doesn't. The results always show small bond order between H's of NH3 and substituents of the ring AND EVEN SMALLER bond order between those H's of NH3 and C's of the ring, regardless of whether I draw hydrogen bond lines in the CAChe Editor (Graphic Interface for MOPAC). Seems MOPAC Input doesn't have bond information. I guess specifying bonds in Editor doesn't do anything at all. Can someone clarify this for me? Thank you very much. I'll summarize. Yong y0h8797@acs.tamu.edu From: SMTP%"sichelj@Umoncton.CA" 2-DEC-1995 15:29:38.31 [to 1st question] There are also contributions due to: 1. Relaxation of the orbitals in the ion after the electron is gone; and 2. Difference in correlation energy between molecule and ion; and (3. Difference in relativistic correction, but this is very small for molecules with only light atoms). John-M. Sichel From: SMTP%"fournier@mail.physics.unlv.edu" 2-DEC-1995 15:55:52.48 [to the 1st question] Koopmans' theorem approximates the vertical IP because, as you said, it does not take into account nuclei relaxation. But what's more, it does not take into account ELECTRON relaxation either! It assumes orbitals stay the same before and after ionization, only orbital occupation numbers change. That's a serious approximation and the results would be very bad if it was not partly cancelled by the neglect of correlation which introduces an error of opposite sign --- the stabilizing correlation energy is larger in the N-electron system than in the (N-1) electron system. This can be schematically represented with energy levels for the N-electron and (N-1)-electron systems calculated in 3 ways, (the "error cancellation effect" is exaggerated): Koopmans' theorem with relaxation of with correlation orbitals in the (N-1) state in both states ("exact" result) N-1 ------- ^ \ | \ | - - - - - N-1 ------- | ^ \ - - - - - - - N-1 ------- | | ^ | | | | | | N ------- - - - - - - N ------- | \ | \ | - - - - - - - - N ------- Sincerely, Rene Fournier. P.S. It is Koopmans' (not Koopman's) theorem because it is due to Koopmans (not Koopman). [This embarrassed me.] From: SMTP%"b_duke@lacebark.ntu.edu.au" 2-DEC-1995 19:08:29.84 [to the 1st question] Koopman's theorem states that IP = -e sub i for vertical ionisation >from the i'th MO if MO theory is correct and the same orbitals fit the ion as fit the parent molecule. In other words it ignors orbital relaxation - the change in the MOs on removing an electron - and it ignors electron correlation - the error in MO theory. See our article in J Chem Ed in the July issue, I think (I do not have the reference with me). [to the 2nd question] MOPAC does not use bond information. It converts the Z-matrix to cartesians and calculates the energy and orbitals for that geometry. Cheers, Brian. [Cheers, Brian. Thank you.] From: SMTP%"MARYJO@neu.edu" 3-DEC-1995 22:43:33.84 Regarding Koopmans' Theorem: It misses two things- 1) Electronic relaxation, which is the reajustment of the N-1 electrons upon lost of the first electron, and 2) Nuclear relaxation. Koopmans' "Theorem" is not really a theorem, as it is not rigorous, however it works in Hartree-Fock because the error due to electron correlation is usually equal and opposite of the error due to electron relaxation. In cases where correlation is unusually small, the relaxation correction can be significant. One is always better off with some sort of transition operator method. Good luck with your project, Mary Jo Ondrechen From: SMTP%"ccl@cric.chemres.hu" 4-DEC-1995 07:09:29.59 1. Koopmans theorem is only an approximation even to vertical ionization potential because: a) it is pertinent to the SCF wave function, so no electron correlation is accounted for; b) the "relaxation" of the one-electron orbitals taking place during the ionization is also neglected. Effects a) and b) are often of opposite sign and partly compensate each other. 2. A quantum chemical program like MOPAC is devoted to determine where the bonds are, not to utilize this knowledge. Regards, Prof. Istvan Mayer From: SMTP%"jas@medinah.atc.ucarb.com" 4-DEC-1995 07:24:14.99 [to the 1st question] Koopmans' theorem basically says that the MO energy approximates the vertical IP by ignoring ELECTRONIC relaxation in the ionic state. The correction for this electronic relaxation is to perform two separate total energy calculations for the neutral and ionics states and subtract (usually called 'delta SCF'). This still ignores any vibrational structure due to zero-point vibrations in both states as well the vibrational fine structure due to Frank Condon overlaps between the vibrational amplitudes of the two states. It also ignores any nuclear (geometric) relaxation of the ionic state. To do it correctly, you need to fully characterize the PE's for both the neutral and ionic states, use total energy differences, add zero-point corrections, solve the vibrational (nuclear) problem for each state, and compute Frank Condon overlaps. You could also compute the dipole moment derivatives to get the relative IR intensities (and polarizabilities for Raman intensities). [to the 2nd question] MOPAC is a quantum mechanical (albeit semi-empirical) method and could care less about the bonds, atom types, atomic charges, etc, used to construct the molecule in the Editor. Only the atomic coordinates and total (net) charge of the molecule are used by any QM method. The bond and atom types are used by the Editor's beautifier and MM2 calculations only. - Jack From: SMTP%"echamot@xnet.com" 4-DEC-1995 07:41:48.83 [to the 1st question] Yes, you are basically correct. In your second question: [about the 2nd question] Your observation [MOPAC doesn't care about bonding in the input file] is also correct. You have to remember, however, that drawing bonds (on paper or on the computer) is really an artifact to help us chemists envision in our own mind the more complicated (but more accurate) description of molecules, by thinking of them simply as atoms held together by discrete bonds: the ball and spring model. Quantum Mechanical methods (including semi-empirical methods such as the method in Mopac) use principles from physics to model the system more accurately as a set of positive nuclei surrounded by a cloud of electrons, using wavefunctions to describe the orbitals. When you model a compound semi-empirically, then, the program optimizes the electron distribution as well as the molecular geometry to try to find the way that the molecule really wants to exist. After the calculations converge, Mopac calculates the bond orders you are interested in, but this reflects the (valence) electron density between each pair of atoms. Drawing bonds in the Editor is still useful, though. For one thing, these bonds are used by the classical, Molecular Mechanics calculations, which do stick with the bonding scheme that you specify. If you run a Mechanics optimization on your system first, with each of the bonding schemes you're interested in, you will get a good set of starting points for the various geometries you are trying to investigate. Then use Mopac (or another Quantum Mechanical method) to refine the structure, and see which (if any) are the preferred geometries. Another reason to draw the bonds, at least with CAChe Mopac, is that the calculated bond orders (that otherwise only appear in Mopac's text output file) will be included in the molecule file for each of the bonds shown in the molecule. If you hadn't specified a particular bond when building the molecule, and the atoms didn't get close enough for CAChe Mopac to suggest a bond, then that calculated bond order for that atom pair will not show up in the visualization. Ernest Chamot From: SMTP%"rpmattie@voicenet.com" 4-DEC-1995 10:04:29.71 The Koopmans Theorem for IP is just the orbital energy of the ionized electron. Depending on how you look at it, there are a number of types of relaxation that are neglected. Do not rely upon the Koopmans Theorem! It does not get the ionization energies in the proper order. You cannot use it to interpret ionization spectra. When you are looking at experimental IP energies, make sure the authors have specified whether these are adiabatic or vertical ionizations. Renee Peloquin Mattie From: SMTP%"jpollard@U.Arizona.EDU" 4-DEC-1995 10:11:40.83 You are correct about your thoughts on Koopman's theorem. This is why computational chemists had such a hard time assigning the photoelectron spectrum of dinitrogen and ferrocene (relaxation energy) JRP, UofA From: SMTP%"DLICHTEN@XRAY0.CHEM.ARIZONA.EDU" 4-DEC-1995 10:53:25.98 In regard to your recent question, Koopmans' (note where apostrophe is) Theorem refers to the vertical ionization because no nuclear relaxation is included. This is the correct assumption for vertical ips measured by electron spectroscopy. Koopmans' Theorem is still an approximation to ips because, most importantly, it does not take into account electron relaxation energies (a theoretical consequence of the frozen orbital assumption implicit in the theory) and electron correlation (a consequence of the Hartree-Fock approximation). You have an expert on this at TAMU, Mike Hall in chemistry. He will be able to explain this very clearly to you. [Thanks Dr. Lichtenberger] Dennis Lichtenberger From: SMTP%"schulte@ws09.pc.chemie.th-darmstadt.de" 4-DEC-1995 12:32:53.06 Dear Dr. Huang [should be "Dear Pre-dr. Huang"] According to Koopman's theorem the measured IP for a certain state corresponds to the orbital energy of the ionized electron. But for quite a lot of molecules this relation is only a rather crude approximation, because several electronic relaxation and correlation processes remain unconsidered in Koopmans theorem. 1. SCF-relaxation energy After the electron has been removed, the remaining electrons of the cation reorganize. This relaxation energy is a pure electronic effect. Theoretically you can describe this effect by a Delta SCF calculation: one calculation for the neutral state and one calculation for the cationic state. Then you obtain the difference in the total energies of both systems, which corresponds to the IP corrected by those relaxation effects which are described in the SCF picture. Very often this is sufficient, if Koopmans theorem itself fails. 2. correlation effects These effects can be considered in a perturbational Greens function approach, which can be extended to different orders. a. If you go from the N-electron- to the N-1-electron system you also have a loss in ground-state correlation energy. In second order it is called ''pair removal energy'' b. Due to the reorganization of the electrons in the cationic state also the correlation energy changes. This energy is called ''pair relaxation energy'' All the calculations listed in 1 and 2 are done within the Born-Oppenheimer approximation, which states that the nuclear coordinates do not change during electronic processes. Vibrational effects therefore still are unconsidered in this picture. I think MOPAC 7 contains a GF package written by D. Danovich. Since I use another GF package I cannot tell you much about its functionality. Here in Darmstadt we have an INDO program written by M.C. Boehm, which is capable of the above listed calculations. Sincerely Yours, Joachim Schulte From: SMTP%"randy_winchester@msmtp.iddw.saci.org" 4-DEC-1995 08:31:23.37 I'm not too sure about the answer to your question about Koopman's theorem, but I think you are right. Your conclusions about MOPAC are also correct. There is (as far as I know) no transfer of information from the editor to the program MOPAC about bond order or even prescence of bonds. This is usually a plus, since the calculation is not biased by your expectations. I hope this is helpful. Randy Winchester From: SMTP%"/G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com" 5-DEC-1995 06:30:58.83 [to the 2nd question] One of the big flaws of a graphical interface is the thinking that the graphics themselves have meaning. This is especially true for semiempirical and ab-initio schemes. Unless you do something to lock a particular conformation, risking locking it into a non-minimum conformation, all the atoms are 'free' to do whatever they want in a minimization. There's no such thing as a bond, especially a hydrogen bond, outside of the 'bonding state' generated by a particular agreeable overlap of orbitals. Try drawing a molecule with every atom bonded to every other atom, and you'll get the same result as bonding no atoms to any other atom in the graphical interface for MOPAC. Molecular mechanics, on the other hand, is a whole different story. matt [I asked Dr. Sichel more questions who kindly answered in the following] From: SMTP%"sichelj@Umoncton.CA" 6-DEC-1995 09:30:50.50 On Wed, 6 Dec 1995, YONG HUANG wrote: > 1. How big is the orbital relaxation in the ion compared to atomic vibrational > relaxation? I assume your "orbital relaxation" means electron relaxation. Its' > time scale should femtosec while atomix relaxation is picosec., right? Electronic (or orbital) relaxation is often 1-2 eV and occurs on the timescale of photoelectron spectroscopy, so it shifts the peaks to lower ionization energies. Vibrational relaxation would indeed be slower, but vibrational transitions may accompany photoionization and lead to splitting of an orbital peak into a vibrational multiplet. This is important for bonding and antibonding electrons, but much less so for nonbonding electrons whose removal does not affect bond length. > 2. I'm not very clear about your difference in correlation energy between a > molecule and an ion. To be honest, I'm not a calculation guy. Correlation energy is the correction to the Hartree-Fock energy due to the tendency of electrons to avoid each other by correlating their motions. It is negative (stabilizing) and the most important contribution is due to correlation of pairs of electrons in the same MO. For a closed-shell molecule, ionization removes (one electron of) one pair so the ion will have less correlation energy. This effect increases the ionization energy and may roughly cancel the orbital relaxation effect, but of course the cancellation is not guaranteed. An early article which explains all these points was by W Graham Richards in the late 60's or early 70's, possibly in Journal of Mass Spec + Ion Physics. John-M. Sichel [Also to Dr. Fournier who kindly answered as follows] From: SMTP%"fournier@mail.physics.unlv.edu" 6-DEC-1995 14:39:12.33 >What's the energy of electron relaxation approximately compared to atomic >vibrational relaxation energy? I don't know exactly, but for ionization of a valence orbital I would guess that the electron relaxation energy is on the order of 1 eV, but it could be 2 or 3 eV, maybe more, in some cases. The difference in correlation energy between the N-electron and (N-1)-electron systems is also on the order of 1 eV, but of opposite sign: for atoms Li to K, it varies between 0.1 eV (Li) and 1.7 eV (Ne) ["Density functional theory of atoms and molecules", R. G. Parr and W. Yang, Oxford University Press, 1989; table 8.1 on page 178]. Generally speaking, the vertical transition corresponds to the peak maximum of an electronic transition (excitation or ionization) and I suppose that what you mean by "vibrational relaxation" is the difference between peak maximum and peak origin (0-->0 transition). This difference (the vibrational relaxation energy) depends very much on the type of system and transition, but just to give an example it is roughly 0.1 eV, 0.5 eV and 0.5 eV for the 3 lowest ionization potentials of formaldehyde. Roughly speaking, it is a small number (say, between 0 and 5) times the frequency of the vibrational mode most directly affected by the ionization. I guess it should be on the order of 0.2 eV or less for non-bonding or delocalized orbitals because there is little change in bond orders and bond lengths, the most intense transition would be the 0-->0, and the only change are small distortions in all bond lengths and angles. In an extreme case, H_2 --> H_2+ + electron, the vibrational relaxation energy is about 1.0 eV and I guess this is one of the largest value. In general the effect of electron relaxation and electron correlation on calculated IPs are larger (sometimes much larger) than the vibrational relaxation energy. >Also, I don't quite understand the correlation (means relaxation? I just meant the usual definition of correlation energy. The difference between the exact energy of a system "E(exact)" and the limit Hartree-Fock calculation, or in other words, any error remaining in a Hartree-Fock calculation with a complete (infinite) basis set: E(corr.) = E(exact) - E(HF) < 0 see for instance Parr and Yang (reference above) page 13-14. Sincerely, Rene Fournier. From: SMTP%"sichelj@Umoncton.CA" 6-DEC-1995 15:23:40.86 > Is there any way to calculate vertical ionization potential which takes into > account all electron effects (orbital relaxation and electron correlation) but > not atomic vibrational relaxation? I talked to my boss about a new idea which Many methods include correlation, e.g. CI etc. etc. To exclude nuclear (vibrational) relaxation, just calculate the ion energy at the geometry found for the neutral molecule, without re-optimizing geometry. > modifies the traditional energy diagram (E vs. Rxn Coord). I want to add one > more dimension to it---electron coord. In this new 3-D diagram, "vertical" This would be invalid. It means calculating the energy for fixed values of an electron co-ordinate. But an electron cannot be fixed according to the quantum-mechanical uncertainty principle; you must consider it as a wave with a probability distribution. Note that the Born-Oppenheimer approximation does allow one to fix nuclei because they are heavy. But this does not work for electrons, which is why their co-ordinates are never included in a potential surface. John-M. Sichel From owner-chemistry@ccl.net Mon Dec 11 22:28:02 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id WAA04667; Mon, 11 Dec 1995 22:19:49 -0500 Received: from auric.chem.csiro.au for D.Winkler@chem.csiro.au by bedrock.ccl.net (8.7.1/950822.1) id WAA26541; Mon, 11 Dec 1995 22:19:33 -0500 (EST) Received: from [138.194.40.190] (mac-40190.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA25363 (5.67b/IDA-1.5 for chemistry@ccl.net); Tue, 12 Dec 1995 14:17:28 +1100 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 12 Dec 1995 14:19:16 +1000 To: anchodd@tasman.cc.utas.edu.au, chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net From: D.Winkler@chem.csiro.au (Dr. Dave Winkler) Subject: Computational Challenges in Life Sciences (2nd Circular) >Date: Tue, 12 Dec 95 11:59:44 EST >From: Marek.T.Michalewicz@mel.dit.csiro.au >To: LS_list@mel.dit.csiro.au > >Second CSIRO Symposium on "COMPUTATIONAL CHALLENGES IN LIFE SCIENCES" >5-7 February 1996 >Melbourne, Victoria, AUSTRALIA > >*********************************** >Second Circular and Call for Papers >*********************************** > >Visit Melbourne for three days during the Southern Summer and hear reports >of some of the most fascinating research in computational biology, medicine, >neurophysiology, agronomy... Life Sciences in general. >Or tell others about your research! > >Have you seen "The Visible Man"? How can it be used to simulate deformation of >the body to simulate obesity, musclebuilding, infection and trauma? >How is Visible Human used in a surgical simulation? > >Can the human brain be thought of as a computer or a dynamical system? >Can computation help us understand the functioning of a nervous system - >from a neuron to the whole system? > >... and lots more in protein biology, plant modelling, drug design, etc. > > >The (continually updated) information on the 2nd CSIRO SYMPOSIUM ON >"COMPUTATIONAL CHALLENGES IN LIFE SCIENCES", 5-7 FEBRUARY 1996, MELBOURNE > >is available on WWW. For general information, list of invited speakers, >titles of talks and abstracts, call for papers, >ELECTRONIC REGISTRATION (as easy as a mouse click), >and other items please browse through: > >========================================================== >http://www.mel.dit.csiro.au/LifeSci/cfp.html >========================================================== > >Programme > >Invited speakers: > >Day 1: Monday 5-Feb-1996: - Computational Neurosciences Symposium > >Professor Max Bennett > University of Sydney, NSW, AUSTRALIA > Modelling the synapse >Professor Steve Redman, > Australian National University, ACT, AUSTRALIA > Modelling individual neurons >Dr Joel Bornstein > University of Melbourne, Victoria, AUSTRALIA > Large scale computational reconstruction of enteric nerve circuits >Professor James Wright > Mental Health Research Institute of Victoria, AUSTRALIA > Models of cerebral dynamics >Dr Timothy van Gelder > University of Melbourne, Victoria, AUSTRALIA > Computation and dynamics in Cognitive Science: An Overview > >Day 2: Tuesday 6-Feb-1996 : - Virtual Plants, Agronomy > >Professor Przemyslaw Prusinkiewicz > University of Calgary, Alberta, CANADA > L-systems: from the theory to plant modeling methodology >Dr Jim Hanan > CSIRO Division of Entomology, Plant Insect Group, Queensland, AUSTRALIA > Practical aspects of virtual plant research >Professor W R Remphrey > University of Manitoba, Manitoba, CANADA > Architectural modelling of trees: A question of detail and complexity >Professor David Green > Charles Sturt University, NSW, AUSTRALIA > Modelling plants in landscapes >Dr Art Diggle > University of Western Australia, WA, AUSTRALIA > Examples of agronomic processes represented with collections > of interacting objects > >Day 3: Wednesday 7-Feb-1996 : - Visible Human, Biomolecular Engineering, >Biochemistry, Bioinformatics > >Professor V Spitzer > University of Colorado, Colorado, USA > The Visible Human Project - Male and Female >Professor Carmay Lim > Academia Sinica, TAIWAN > Protein Dynamics: Correlation between NMR Spectroscopy, X-ray > Crystallography and Molecular Dynamics Simulations >Dr Geoffrey J. Barton > Laboratory of Molecular Biophysics, University of Oxford, UNITED KINGDOM > Protein Structure Prediction: Meeting the challenge of genome projects >Dr Tim Littlejohn > Australian National Genomic Information Service (ANGIS), AUSTRALIA > Delivering the goods: putting solutions to computational problems > into the hands of biologists >Dr Jill E. Gready > Australian National University, AUSTRALIA > Reaction mechanisms in enzyme active sites using a "divide and conquer" > approach: mixed quantum and molecular mechanics (qm/MM) >Dr Georg F. Weiller > Australian National University, ACT, AUSTRALIA > Graphical Representations in Sequence Analysis >Professor Benoit Roux > Universite de Montreal, CANADA > Molecular Dynamics simulations of membrane proteins >Professor Matthew Witten > University of Michigan at Ann Arbor, Michigan, USA > Recent Advances In Computational Medicine: The Man In The Machine Revisited > >Hoping to meet you at the Symposium! > >Sincerely, > > >Dr Marek Michalewicz, >Organising and Program Committees Secretary, >CSIRO Supercomputing Support Group, >Division of Information Technology, >723 Swanston Street, Carlton, >Vic. 3053, Australia >phone: +61 3 9282 2621; fax: +61 3 9282 2600 >e-mail: marek@mel.dit.csiro.au > Cheers, Dave Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers CSIRO: http://www.csiro.au Private Bag 10,Rosebank MDC, Clayton, Australia http://www.chem.csiro.au