From awhit@dir.mcc.ac.uk Thu May 25 06:57:41 1995 Received: from ib.rl.ac.uk for awhit@dir.mcc.ac.uk by www.ccl.net (8.6.10/930601.1506) id GAA06033; Thu, 25 May 1995 06:55:26 -0400 From: Received: from letterbox.rl.ac.uk by ib.rl.ac.uk (IBM VM SMTP V2R2) with TCP; Thu, 25 May 95 11:54:59 BST Via: uk.ac.mcc.dir; Thu, 25 May 1995 11:53:10 +0100 Date: Thu, 25 May 95 11:54:31 BST Message-Id: <25000.9505251054@dir.mcc.ac.uk> To: chemistry Subject: 2nd Int. Conf. for Chemical Information Users. UNIVERSITY OF MANCHESTER UMIST MANCHESTER COMPUTING CENTRE *********************************************** * * * * * 2nd INTERNATIONAL CONFERENCE * * * * for * * * * CHEMICAL INFORMATION USERS * * * * * *********************************************** Tuesday 14th and Wednesday 15th November 1994 MANCHESTER, UK The purpose of the Conference is to address the needs of users of chemical information from both the academic and industrial sectors. 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END OF MESSAGE From ivarm@boc.ic.ee Thu May 25 08:57:42 1995 Received: from argus.chemnet.ee for ivarm@boc.ic.ee by www.ccl.net (8.6.10/930601.1506) id IAA07178; Thu, 25 May 1995 08:51:57 -0400 Received: from boc.ic.ee (boc.ic.ee [193.40.63.200]) by argus.chemnet.ee (8.6.9/8.6.9) with SMTP id PAA04445 for ; Thu, 25 May 1995 15:32:47 +0300 Received: from argus.chemnet.ee by boc.ic.ee id aa10540; Thu, 25 May 95 16:45:11 estonia From: "Ivar Martin" Date: Thu, 25 May 95 15:42:40 EST Message-Id: <567.ivarm@boc.ic.ee_POPMail/PC_3.2.2> Reply-To: X-POPmail-Charset: English To: chemistry@ccl.net Subject: Summary: Imaginary freq. and rate constant Dear CCL people, to those of you who responded to my question about rate constant calculation based on transition state vibrational properties, I am very grateful for sharing your knowledge! I would like to send my thanks to the following people for their valuable coments: Ryan Bettens Joe Durant Frank Jensen Istvan Mayer Arvi Rauk John Rupley Robert Q. Topper Dom Zichi My original question was: As it is expected, MOPAC calculates one imaginary vibrational frequency at TS. Is it correct to use this frequency as pre-exponent factor (frequency factor) in Arrhenius rate constant equation? The unanimous answer was: NO, IT IS NOT CORRECT! RATIONALE: ------------------------------------- From: Arvi Rauk The imaginary frequency only measures the curvature of the reaction coordinate at the transition state. It may be used in the Bell formula for a quantum mechanical tunnelling correction to the classical rate which would only be a funcion of the barrier height. ------------------------------------- From: Frank Jensen The A*exp(-E/RT) expression is equivalent to the TS expression kT/h * exp(deltaS/R) * exp(-deltaH/RT). Delta S and H may be calculated from S and H of the reactant and TS. S and H for a given structure may be calculated by means of stat. mech. from properties of the individual molecules, i.e. moments of inertia and vibrational frequencies. The important feature here is that there are 3N-6 vibrational contributions to the reactant, but only 3N-7 for the TS, i.e. the imaginary frequency is NOT involved. In TS theory it is assumed that the motion along the reaction coordinate (the imaginary frequency at the TS) is treated classically. Only if e.g. tunneling is considered does the imaginary frequency enter, for example by means of a Bell correction etc. So, to answer your question, no the imag. freq. has nothing to do with A in the A*exp(-E/RT) expression. A is essentially related to deltaS for the reaction. --------------------------------------- From: Joe Durant No, the negative frequency associated with the reaction coordinate is not used in the calculation of the sum of states for the transition state! I suggest a careful reading of Robinson and Holbrook "Unimolecular Reactions", or the kinetics texts by Johnston or Benson. I quote from Robinson and Holbrook, pg 12 "Q(double dagger) is the partition function for all the degrees of freedom of the activated complex except the reaction coordinate." The translational degree of freedom gives rise to the kT/h term in the rate constant expression. The negative frequency is related to the barrier shape, and can be used in tunneling calculations. A closely related point is that the negative frequency does not contribute to the zero point energy of the transition state. ------------------------------------------ From: John Rupley Transition State Theory assumes in its model free flight at the barrier top, i.e., a flat barrier top (corresponding to a zero frequency!). The frequency factor is the frequency of attempt at barrier crossing, and can be taken as the frequency defining the shape of the reactant _well_ in the direction of the reaction coordinate. This frequency is built into the deltaS# part of the deltaG# of the Arrhenius expression. The imaginary frequency and the curvature of the potential surface at the barrier top also enter into the Kramers and related classical models, for reaction in a dense medium. ----------------------------------------------- From: Dom Zichi The correct frequency to be used in the transition state theory rate expression, kTST, is that of the reactant well, not the frequency describing the curvature at the barrier top. This is easily seen from the following. A simple TST rate assumes that every trajectory at the transition barrier q# which has a forward flux toward products will always end up as product. This leads to the following expression for kTST, / / . . kTST= | dq | dp e(-H/kBT) q theta(q) delta(q#) / Qrct / / where theta is a step function which equals one for positive flux toward products and 0 for negative flux, delta(q#) is a delta function of position along the reaction coordinate q at the barrier top and Qrct is the partition function for the reactant well, / / Qrct= | dq | dp e(-Hr/kBT) / / 2 2 2 For Hr = m w q /2 + p /2 valid to q#, i.e. H(q)= Hr(q) qq# one can easily obtain kTST = (w/2*pi) exp(-H(q#)/kBT). The frequency term counts the number of times a forward reaction is attempted while the exponential term counts the number of trajectories that make it to the barrier top relative to the reactant well. ----------------------------------------------- From: Istvan Mayer The existence of an "imaginary frequency" at the TS is a reformulation of the fact, that the enrgy has a maximum (and not a minimum) along a given (normal) coordinate. Although it is expressed in frequency units, it is really a measure of the curvature of that point only, and has nothing to do directly with any reaction rate. The "quasi-thermodynamic" formulation of Eyring's "absolute reaction rate" or "transitiuon state" theory was a great-scale misunderstanding, which caused very much harm to science. 20 years ago I wrote: "The activated complexes are not true chemical species, do not fulfil the conditions defining a canonic ensemble, and therefore cannot be considered as independent subjects of the canonic distribution." (J. Chem. Phys. 60, 2564, 1974). This also means that there is no meaning to attribute any thermodynamic quantities to the TS. This does not mean that there can be no modern variants of transition state theory, which are free of the deffects of the old one. ----------------------------------------------- From: Ryan Bettens Assuming that the rate constant, k, is given by, k = A exp{-E_a/(k_b T)} for all T. E_a is the barrier height and k_b is Boltzmann's constant. From RRKM theory A is given by, A = (alpha/h) f_{inf} G^*(E - E_a)/N(E - E_a). Where, alpha is the reaction path degeneracy, h is planks constant, f_{inf} high-pressure centrifugal correction factor, E the internal excitation energy, G^*(E - E_a) total number of states between 0 and (E - E_a) for the transition state (hereafter TS), N(E - E_a) the number of states per unit energy range at (E - E_a) for the reactant. To get a nice interpretation for what A actually is we (a) ignore alpha, (b) ignore rotation (this cannot be done if the reactant is linear and the TS is non-linear and visa versa), (c) assume an harmonic oscillator and the approximation of Whitteen and Rabinovitch (1). A then becomes, A = {(E - E_a + a^* (E_z)^*)/(E - E_a + a E_z)}^(s - 1) x {Prod(i = 1 to s) nu_i}/{Prod(i = 1 to s - 1) (nu_i)^*}. Where, s is the number of degrees of vibrational freedom of the reactant, a is an empirical correction factor from ref. (1), E_z is the zero-point energy ^* refer to the TS with one less degree of vibrational freedom. Approximating the first term, which is taken to the power of (s - 1), as unity, A finally becomes the ratio of the product of harmonic frequencies of the reactant to the product of the harmonic frequencies of the TS. Note that there is (s - 1) frequencies in the TS (the "missing" degree of freedom is the mode responsible for the chemical change, i.e., the mode with the negative force constant) compared with the reactant's s frequencies. Furthermore, if we make the assumption that the TS's frequencies are not much different from the reactant's frequencies, except for the "missing" frequency, we find, A = nu_i where nu_i is the mode in the reactant which when energized is responsible for the chemical change. Thus for a C-C single bond dissociating A ~ 900 cm^{-1} = 2.7 x 10^{13} s^{-1}. All of the above expressions come from Forst (2), which I suggest you take a look at if you really want a good understanding of the approximations made etc. Ref.'s (1) G. Z. Whitten and B. S. Rabinovitch, J. Chem. Phys., V38 (1963) 2466. (2) W. Forst, Theory of Unimolecular Reactions, 1973, Academic Press, New York. --------------------------------------- From: Robert Topper May I suggest that you have a look at some of the recent papers by Donald Truhlar (Minnesota) and his group! They have developed two codes for the calculation of reaction rate constants. One of these, called MORATE, interfaces with MOPAC to carry out transition-state theory calculations for polyatomic systems. At its highest level of theory, MORATE includes corrections for multidimensional tunneling and zero-point motion. However, this would entail getting information about the potential energy all along the reaction coordinate and not just at the transition state. However, MORATE can also carry out calculations using only the transition-state properties. With the experience you have gained using MOPAC you could probably use MORATE with ease. It is extremely well-documented and is available from QCPE and the CPC library... and the methods are also described in a number of articles. They have been extensively benchmarked (where possible) against "exact" quantum scattering theory treatments and against experiment. Overall, the methods work quite well for absolute rate constants and do a terrific job of getting at kinetic isotope effects. Truhlar's group is constantly developing the technology and improving the user-friendliness of the code... and they have been doing so for a number of years now. It is written almost entirely in machine-portable FORTRAN and is available for a number of platforms. That said, you must realize that the absolute, accurate calculation of reaction rate constants can occasionally be frought with difficulties. For example; transition-state theory makes some assumptions about the nature of reactive motion. In particular, TST is only "rigorously" correct when no back-reaction is possible (i.e., when a molecule goes from reactants to products it never re-forms into reactants. See "Chemical Kinetics and Dynamics" by Steinfeld, Francisco and Hase for a nice introductory discussion of this). This is sort of a tough situation to achieve experimentally. However, in my own weird, brief experience in studying these effects I have never seen a case where the correction was larger than an order of magnitude...which is considered to be pretty good for rate constants. And that order of magnitude was in pretty extreme cases. There are other possibilities... the presence of "dynamical bottlenecks" to reaction can slow things down (this is a nonlinear effect). Overall though, TST can be a very accurate and useful approximation. One case in which you are pretty much guaranteed that TST will work is when the time scale of reaction is much much faster than the time scale of back-reaction... this can happen when the products' phase space is very much larger than that of the transition state. Also, any reaction that involves dissociation is a good candidate. ----------------------------------- THANK YOU ALL AGAIN! _______________________________ Dr. Ivar Martin Department of Bioorganic Chemistry tel: +372 2 526510 Institute of Chemistry fax: +372 2 536371 Akadeemia tee 15 EE0026 e-mail: ivarm@boc.ic.ee Tallinn, ESTONIA From elewars@alchemy.chem.utoronto.ca Thu May 25 10:57:44 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/930601.1506) id KAA09110; Thu, 25 May 1995 10:53:28 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.10/8.6.10) id KAA18989 for chemistry@ccl.net; Thu, 25 May 1995 10:53:20 -0400 Date: Thu, 25 May 1995 10:53:20 -0400 From: "E. Lewars" Message-Id: <199505251453.KAA18989@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: SOME SAMPLE ZMATRICES 1995 May 25 T. Koch asked for examples of Z-matrices which constrain molecules to some particular symmetry, about a week ago. Although Z-matrices may be on the way out (Warren J. Hehre *Practical Strategies for Electronic Structure Calculations*, pp 20, 21), here are some (the art of writing Z-mat's is discussed in *A Handbook of Computational Chemistry* by Tim Clark, ca. 1984, and in *Exploring Chemistry with Electronic Structure Methods* by J. B. Foresman and A. Frisch): -------------------- # Fopt=(CalcHFFC) mp2 6-31G* scf=direct MP2/6-31G* opt on CO2 cyclic dimer; input: HF/6-31G* geom (D2h) 0 1 X1 X2 X1 1. X3 X2 X3X2 X1 90. X4 X2 X3X2 X1 90. X3 180. C5 X1 X3X2 X2 90. X3 0. O6 X1 O6X1 X2 90. X3 -90. C7 X1 X3X2 X2 90. X3 180. O8 X1 O6X1 X2 90. X3 90. O9 C5 O9C5 X3 90. X2 180. O10 C7 O9C5 X4 90. X2 180. X3X2 0.9369 O6X1 0.9880 O9C5 1.1525 ================================ # Fopt=(CalcHFFC) mp2 6-31G* scf=direct MP2/6-31G* opt on H2CO3; input: HF/3-21G (sic, 3-21G) geom (C2v) 0 1 O1 C2 O1 C2O1 O3 C2 O3C2 O1 A321 O4 C2 O3C2 O1 A321 O3 180. H5 O4 H5O4 C2 A542 O1 0. H6 O3 H5O4 C2 A542 O1 0. C2O1 1.202 O3C2 1.332 H5O4 0.966 A321 125.4 A542 111.8 ================================= # mp4 6-31+G* scf=direct MP4/6-31+G* single-p on CO2; MP2/6-31G* geom (Dih) 0 1 O1 C2 O1 C2O1 X3 C2 1. O1 90. O4 C2 C2O1 X3 90. O1 180. C2O1 1.1797 ============================== # 3-21G Fopt scf=direct PROPANE. Doubly eclipsed conformation (C2v). Input params from MM (Sybyl) 0 1 C1 C2 C1 C2C1 NOTE THAT HERE, AND IN BUTANE, C3 C2 C2C1 C1 A321 BELOW, AFTER THE DIHEDRAL FOR H4 C3 H4C3 C2 A432 C1 0. THE 1ST H OF A CH3 IS DEFINED H5 C3 H5C3 C2 A532 H4 D5324 (e.g. 0., FOR D4321) THE DIHED H6 C3 H5C3 C2 A532 H4 -D5324 FOR THE OTHER OTHER TWO CH3 H'S H7 C1 H4C3 C2 A432 C3 0. IS REFERRED BACK TO THE 1ST H H8 C1 H5C3 C2 A532 H7 D5324 (e.g. D5324, NOT D5321); THIS H9 C1 H5C3 C2 A532 H7 -D5324 MAY SOMETIMES SPEED UP H1O C2 H10C2 C1 A1021 C3 D10213 OPTIMIZATION BY ALLOWING A H11 C2 H10C2 C1 A1021 C3 -D10213 CH3 TO BE ROTATED AS A UNIT C2C1 1.562 H4C3 1.099 H5C3 1.102 H10C2 1.109 A321 115.0 A432 113.3 A532 110.6 A1021 108.8 D5324 120.6 D10213 122.3 ================= # am1 Scan Nosym PES scan on butane. C2C1 (central CC) from 1.510-->1.520 in 21 steps of 0.001 D4123 from 0-->360 in 37 steps of 10. All other params frozen. 38X22=836 points [D4123 = 180. represents the staggered conf.] 0 1 C1 C2 C1 C2C1 C3 C2 1.508 C1 113. C4 C1 1.508 C2 113. C3 D4123 H5 C3 1.117 C2 111. C1 180. H6 C3 1.117 C2 111. H5 120. H7 C3 1.117 C2 111. H5 -120. H8 C4 1.117 C1 111. C2 180. H9 C4 1.117 C1 111. H8 120. H1O C4 1.117 C1 111. H8 -120. H11 C2 1.123 C1 109. C3 122. H12 C2 1.123 C1 109. H11 117. H13 C1 1.123 C4 109. H9 178. H14 C1 1.123 C4 109. H9 62. C2C1 1.510 21 0.001 D4123 0. 37 10. ==================== # 6-31G* scf=direct 2-PROPENOL. The Cs conformer with H-O/C=C eclipsed; C-H of Me/C=C eclipsed. Single-point job. 0 1 C1 C2 C1 1.340 O3 C2 1.386 C1 120.5 H4 O3 0.967 C2 107.5 C1 0. C5 C2 1.484 O3 114.2 C1 180. H6 C5 1.118 C2 110.4 C1 0. H7 C5 1.118 C2 110.3 H6 -120.5 H8 C5 1.118 C2 110.3 H6 120.5 H9 C1 1.095 C2 121.5 O3 180. H1O C1 1.096 C2 122.3 O3 0. ======================= WATER, C2v 0 1 H1 O2 H1 O2H1 H3 O2 O2H1 H1 A321 [then give O2H1 etc] ====================== WATER, C2v [here a dummy atom is used to position the molecule nice and symmetrically in the coord. system; this may make it easier to interpret the results] 0 1 O1 X2 O1 1. H3 O1 H3O1 X2 A312 H4 O1 H3O1 X2 A312 ============================= =============================== Errol Lewars ======================= ================= From schatz@copper.chem.nwu.edu Thu May 25 11:06:35 1995 Received: from casbah.acns.nwu.edu for schatz@copper.chem.nwu.edu by www.ccl.net (8.6.10/930601.1506) id KAA08973; Thu, 25 May 1995 10:48:27 -0400 Received: from copper.chem.nwu.edu by casbah.acns.nwu.edu with ESMTP (1.37.109.16/20.3) id AA163753301; Thu, 25 May 1995 09:48:21 -0500 Received: by copper.chem.nwu.edu (950221.405.SGI.8.6.10/930119.SGI.jml) for chemistry@ccl.net id JAA06935; Thu, 25 May 1995 09:48:00 -0500 Date: Thu, 25 May 1995 09:48:00 -0500 From: schatz@copper.chem.nwu.edu (George C. Schatz) Message-Id: <199505251448.JAA06935@copper.chem.nwu.edu> To: chemistry@ccl.net Subject: awards announcement To: Computational Chemistry Community From: George C. Schatz Chair, Theoretical Chemistry Subdivision Physical Division, American Chemical Society Date: May 25, 1995 Below are the announcements for two Awards in Computational Chemistry that are open to current graduate students. These awards are administered by the Theoretical Chemistry Subdivision of the Physical Division of the ACS. They replace the Cray Award that has been given by the Subdivision for the past several years. We are grateful to DEC, IBM, the Pittsburgh Supercomputer Center, and the Cornell Supercomputer Center for their support of these awards. The competition is open to any graduate student (regardless of citizenship) who is an ACS member (or whose advisor is an ACS member). These awards are designed to encourage graduate work in computational chemistry, to recognize research accomplishments, and to stimulate interest in the Subdivision of Theoretical Chemistry and the Physical Division of the ACS. Applicants can apply for one or both of the awards. A single Awards Committee will consider all the applicants. Note that the deadline for applications is July 1, and the awards applications should be sent to James Skinner at the University of Wisconsin. Selection of the award winners will take place at the ACS meeting this August in Chicago. I encourage graduate students in any area of computational chemistry to apply. If you have any questions, contact me at schatz@chem.nwu.edu or James Skinner at skinner@bert.chem.wisc.edu. Digital Equipment Corporation/Pittsburgh Supercomputing Center Graduate Student Award in Computational Chemistry The ACS division of Physical Chemistry and the Subdivision of Theoretical Chemistry, seek applicants for the Digital Equipment Corporation/Pittsburgh Supercomputing Center Graduate Student Award in Computational Chemistry. Supported by Digital and the Pittsburgh Supercomputing Center, this award will provide a one-time cash stipend of $2500 as a supplement to normal financial aid to a doctoral candidate in the research-dissertation stage in the 1995-1996 academic year. The Pittsburgh Supercomputing Center (PSC) will provide up to 1000 Alpha CPU-hours on its Alpha Cluster for the awardee to actually carry out a portion of the awarded research. PSC will also provide telephone or e-mail access to a staff user consultant for help in troubleshooting problems with use of the Cluster. A place in PSC's November, 1995 PVM Workshop will be reserved for the awardee. Awardee selection will be made on a competitive basis. Applicants should be working on new and innovative computational chemistry methods or applications in theoretical chemistry. In particular, the use of high performance parallel computing environments such as High Performance Fortran, PVM, or other parallel software constructs on workstation farms or SMP multiprocessor systems is required. Applicants should prepare a written description of the computational chemistry research project that requires high performance computing as can be provided by Alpha systems, with an explanation of the scientific importance of the project. Proposals need to include an estimate of the computing resources required in Alpha cpu-hours. Applicants should explain how they plan to use the grant funds. Two letters of recommendation, including one from the student's advisor, along with a vita and transcript are required. In addition, a PI (other than the applicant) responsible for the applicant's use of the Alpha systems resources arranged by Digital or the PSC, needs to be stipulated. Forward applications by July 1, 1995 to Prof. James L. Skinner, Department of Chemistry, 1101 University Ave., University of Wisconsin, Madison, WI 53706. The awardee will be chosen and announced at the Fall 1995 ACS National Meeting. Alpha is a registered trademark of Digital Equipment Corporation. IBM/Cornell Theory Center Graduate Student Award in Computational Chemistry The ACS division of Physical Chemistry and the Subdivision of Theoretical Chemistry seek applicants for the IBM/Cornell Theory Center Graduate Student Award in Computational Chemistry. Supported by IBM and the Cornell Theory Center, this award will provide a one-time cash stipend of $2500 as a supplement to normal financial aid to a doctoral candidate in the research-dissertation stage in the 1995-1996 academic year. The Theory Center will provide up to 1000 service units on its SP2 parallel computer for the awardee to actually carry out a portion of the awarded research. The awardee will have access to the consulting services of the Theory Center normally available to all users. Awardee selection will be made on a competitive basis. Applicants should be working on new and innovative computational chemistry methods or applications in theoretical chemistry. Applicants should prepare a written description of a computational chemistry research project that requires high performance computing, with an explanation of the scientific importance of the project. Proposals need to include an estimate of the computing resources required in SP2 cpu-hours. Applicants should explain how they plan to use the grant funds. Two letters of recommendation, including one from the student's advisor, along with a vita and transcript, are required. In addition, a PI (other than the applicant) responsible for the applicant's use of the Cornell Center resources must be identified. Forward applications by July 1, 1995 to Prof. James L. Skinner, Department of Chemistry, 1101 University Ave., University of Wisconsin, Madison, WI 53706. The awardee will be chosen and announced at the Fall 1995 ACS National Meeting. From ramon@ce.ifisicam.unam.mx Thu May 25 22:12:53 1995 Received: from ce.ifisicam.unam.mx.ifisicam.unam.mx for ramon@ce.ifisicam.unam.mx by www.ccl.net (8.6.10/930601.1506) id WAA20320; Thu, 25 May 1995 22:11:09 -0400 Message-Id: <199505260211.WAA20320@www.ccl.net> Received: by ce.ifisicam.unam.mx (1.38.193.3/16.2) id AA17581; Thu, 25 May 95 20:09:05 -0500 From: Ramon Garduno Subject: Where is SETOR? To: chemistry@ccl.net (POST MSG's) Date: Thu, 25 May 95 20:09:05 CDT Mailer: Elm [revision: 70.85] Dear netters: I take a few minutes of your valuable time to ask your help in locating the source of SETOR: a program for 3D solid model representations of macromolecules; J. Mol. Graphics (1993) v11, pp135. Many thanks to those that will respond. Cheers, -- ____________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA | EMAIL: ramon@ce.ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | rgard@redvax1.dgsca.unam.mx Laboratorio de Cuernavaca | VOICE: (73)175388 Apdo. Postal 139-B | (73)111611 62191 Cuernavaca, Morelos | FAX: (73)111603 MEXICO | (73)173077 ___________________________________ EOF _____________________________________