From states@wucs1.wustl.edu Tue Oct 13 18:16:01 1992 Date: Tue, 13 Oct 92 23:16:01 -0500 To: Helmut Grubmueller From: states@wucs1.wustl.edu Subject: Re: On the use of Cut-off Schemes in MD >Arne Elofsson writes: > In recent years, a whole bunch of methods have been developed > to speed up the simulations of multi-body systems considerably > *without* any significant loss (i.e. significant in the course > of MD-simulations) of accuracy.... > b) Multiple time step (MTS) methods employing distance classes: > This method, (which is not to be confused with *variable* time > step methods), has also been successfully employed for MD-simulations > (see refs below) and turns out to yield speed ups comparable > to the FMM. The MTS method can be regarded as a generalization > of the cut-off method in that intaractions of atom pairs separated > by a large distance are not completely neglected (as it is the case > for the cut-off method); instead, these interactions (forces) are > computed less frequently and are approximated by extrapolation. For completeness, you should add to your list of citations: Brooks, BR, Brucolerri, RE, Olafson, BD, States, DJ, Swaminathan, S, and Karplus, M (1983) J. Comp. Chem 4:187 This is the original description of the CHARMM modeling program and includes a discussion of a multiple time step algorithm implemented in CHARMM (see the "Extended Electrostatics" section) David States Institute for Biomedical Computing / Washington University in St. Louis From yam@crystal.pc.uec.ac.jp Wed Oct 14 03:48:56 1992 Date: Wed, 14 Oct 92 16:21:17 JST From: yam@crystal.pc.uec.ac.jp (Norimasa Yamazaki) To: chemistry@ccl.net Subject: ORTEP To whom concerned, Dear Sir, I've heard Dr. Gary Newton is looking for ORTEP. Has he already got it? I have two kinds of ORTEP, one for SUN SPARC station, the other for Macintosh. Features of those are as follows, ORTEP for SUN 1) It runs on OpenWindows of SPARC station 2. 2) It has a editor window and a picture window. You can edit instructions and see the result at once. 3) It can create a PostScript file. 4) After drawn on the picture window, you can change symbol positions by dragging them with a mouse. It's for symbols only, not for lines. ORTEP for Macintosh 1) It runs on Macintosh equipped with 68020(30) and FPU. 2) It can create PICT format files. So if you own "MacDraw II", you can edit the picture. You can add or delete any words, any lines and so on. If you like it, I'll send these programs. Best regards, Norimasa Yamazaki University of Electro-Communications, Tokyo, Japan e-mail: yam@crystal.pc.uec.ac.jp From DSMITH@uoft02.utoledo.edu Sun Oct 14 05:19:33 1992 Date: 14 Oct 1992 09:19:33 -0400 (EDT) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Spin density calculations for benzene To: chemistry@ccl.net I saw this on the SCI.CHEM Usenet newsgroup but not on our mail exploder. I thought that it would be appropriate to ask this question on the net. Please respond not only to the net, but directly to Jussi Eloranta (not me, I am just a conduit). Thanks. Doug Smith +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ X-News: uoft02 sci.chem:7457 From: eloranta@jyu.fi (Jussi Eloranta) Subject:Spin density calculations for benzene Date: Sun, 11 Oct 1992 13:02:24 GMT Message-ID:<1992Oct11.130224.20749@jyu.fi> We just received gaussian 92 and I tried to calculate spin densities for benzene anion. The results were (using HF): Total atomic spin densities: 1 1 C -0.434526 2 C 0.493475 3 C 0.494552 4 C -0.434527 5 C 0.493482 6 C 0.494592 7 H -0.040585 8 H 0.027736 9 H -0.040687 10 H -0.040576 11 H 0.027740 12 H -0.040677 Sum of Mulliken spin densities= 1.00000 This result is not symmetrical (obviously it should be..). Does anyone know why? The only reason that I can think of is that benzene has orbitals nearly with the same energy and the electron is jumping from one level to another. This would mean that I had to take mean value of the spin densities for these orbitals. If I do this then I get nearly the correct value (= measured value with EPR spectrometer). If this is true then this would mean lots of troubles for more compilcated molecules... :-( Gaussian also reports the following values: Fermi contact analysis (atomic units). 1 1 C -0.158284 2 C 0.134964 3 C 0.135348 4 C -0.158284 5 C 0.134970 6 C 0.135350 7 H -0.020671 8 H 0.013269 9 H -0.020724 10 H -0.020667 11 H 0.013271 12 H -0.020718 How are these calculated are what are they? From "Fermi contact analysis" I could think that it is hyperfine coupling constant calculated using Fermi's equation (ie. constant * psi(at nucleus)**2)? Jussi Eloranta University of Jyvaskyla, Dept. of physical chemistry. -- ============================================================================ Jussi Eloranta Internet(/Bitnet): ! The ultimate trip is University of Jyvaskyla, Jussi.Eloranta@jyu.fi ! death. Finland [130.234.0.1] ! -- Jim Morrison From MAALOUF@RISVAX.ROWLAND.ORG Wed Oct 14 06:52:43 1992 Date: Wed, 14 Oct 1992 10:52:43 -0400 (EDT) From: MAALOUF@RISVAX.ROWLAND.ORG Subject: xterm for the RS6000 To: CHEMISTRY@ccl.net Dear Netters, Does anyone have an `xterm' binary for the IBM RS6000? I am using AIXTERM on my 320h and it is not very pleasant. I'm trying to avoid compiling that portion of the X11 distribution if someone out there has a binary that they are willing to share. Thanks is advance. George Maalouf Harvard University and The Rowland Institute maalouf@proline.rowland.org From RWOODS@biop.ox.ac.uk Wed Oct 14 18:45:00 1992 Date: Wed, 14 Oct 92 18:45 GMT From: RWOODS%VAX.MOLECULAR-BIOPHYSICS.OXFORD.AC.UK@OHSTVMA.ACS.OHIO-STATE.EDU To: CHEMISTRY@ccl.net Subject: Spin density calculations for benzene In reply to Jussi Eloranta's question, I seem to recall that benzene ANION is a classic example of a species that exhibits a Jahn-Teller effect. Thus, the spin densities calculated within the Born-Oppenheimer approximation would be expected have symmetry lower thn C6v. Robert J. Woods Glycobiology Institute University of Oxford Oxford OX1 3QU From DSMITH@uoft02.utoledo.edu Sun Oct 14 12:06:20 1992 Date: 14 Oct 1992 16:06:20 -0400 (EDT) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: cations with Jahn-Teller distortion To: chemistry@ccl.net My recent posting (for someone else) about the benzene anion and the responses generated, and the recent sentiments expressed by many on this mail exploder about getting back to chemistry, especially chemistry which is more than questions, problems, and software, leads me to the following: We have been investigating nitrenium ions (six electron, positively charged nitrogen species) based on the azepine ring system at the RHF, UHF, and CASSCF levels. The 3-21G basis set was used, and calculations were run using Gaussian 90 and 92. Azepine is a seven membered ring, C6H7N, with three carbon carbon double bonds. If (conceptually) one removes a hydride from the nitrogen, the cation formed has six pi electrons in a ring, with an empty p orbital on nitrogen involved in making the entire system aromatic. The spin multiplicity of the system can be a singlet, with both nitrogen electrons paired and the p orbital empty, or a triplet, with the two electrons unpaired. The former leads to aromaticity, the latter to a seven p-pi cyclic electron system. The singlet behaves as one might expect, i.e. it is aromatic and planar at both the RHF and CAS(6,7) levels, where six pi electrons are distributed amongst the three pi orbitals, three pi* orbitals and the empty nitrogen p(z) orbital. The CAS calculations indicate that the ground state configuration is approximately 88% of the total wavefunction. The geometry is of C2v symmetry. The triplet behaves abnormally, or at least not as I would have expected. It is planar, despite the seventh electron in conjugation. And the system apparently is undergoing a Jahn-Teller distortion from C2v symmetry. (All this is at the UHF level. We were unable to get CAS optimizations to converge, although CAS single points at the UHF optimized geometry did.) We think that we have located a low lying normal mode vibration which clearly shows this distortion. This leads me to wonder: is J-T distortion common for organic cations? Is this the first example (which I doubt)? Can anyone tell me about other examples? We have submitted this work to the Journal of Organic Chemistry, and are just now sending out the revised manuscript. Therefore I am not sure that I am at liberty to share more of the results right now. However, any interested party is invited to ask for more (direct email, not via the mail exploder) or for a preprint/reprint. Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From cramer@chemsun.chem.umn.edu Sun Oct 14 10:32:31 1992 Date: 14 Oct 1992 15:32:31 -0500 (CDT) From: Christopher Cramer Subject: Spin density calculations for benzene (fwd) To: chemistry@ccl.net, eloranta@jyu.fi In reply to: > > X-News: uoft02 sci.chem:7457 > From: eloranta@jyu.fi (Jussi Eloranta) > Subject:Spin density calculations for benzene > Date: Sun, 11 Oct 1992 13:02:24 GMT > Message-ID:<1992Oct11.130224.20749@jyu.fi> > > > We just received gaussian 92 and I tried to calculate spin densities for > benzene anion. [Stuff about asymmetry and Fermi Contact values] > Since benzene has two degenerate LUMO's, the wavefunction for the radical anion should undergo a Jahn-Teller distortion (even if the geometry is prevented from doing so by calculational fiat) to lift the degeneracy at the expense of the empty orbital. Mike Frisch may weigh in to tell us how the resultant wavefunction from G92 may be other than D6h if that symmetry is imposed from the start, but this is one of those cases where symmetry would clearly produce an unstable wavefunction in any case. People with more expertise than I have discussed Hartree-Fock doublet instability at length, it is perhaps most notorious in the allyl radical. With respect to Fermi contact values (.rho.(X) where X is the nucleus in question), .rho.(X) = SUM {P * phi(mu,r[X]) * phi(nu,r[X])} where the SUM runs over mu and nu, the basis function indices, P is the one particle spin density matrix, i.e. P(.alpha. - .beta.,.mu..nu.), and the basis functions phi are evaluated at the coordinates of the nucleus X. Isotropic hyperfine coupling constants are derivable therefrom by the relation hfc = (8.pi./3) * g * g(X) * beta * beta(X) * .rho.(X) where g and beta are the g-value and Bohr magneton for the unpaired electron and g(X) and beta(X) are the corresponding values for the magnetic nucleus. While I've done some work in this area, the real experts are probably Ernie Davidson and David Feller -- they have numerous papers on the adequacy of various methods to calculate both isotropic and anisotropic coupling constants via similar methodologies. (Apologies to other workers in the area who I don't have space to mention.) Their program MELDF is particularly well equipped to handle such calculations. Finally, since the poster seems to be implying the observed ESR spectrum is symmetric (sorry, I'm not equipped with an immediately handy reference to tell), it is important to note that in a typical isotropic system, averaging of the lowest energy microstate over all of the atoms in benzene might be expected to dynamically give rise to a symmetric spectrum, depending on the energy barrier for interconversion. Chris -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 From SHAUN%JASON.DECNET@relay.the.net Sun Oct 14 11:54:00 1992 Date: 14 Oct 1992 17:54:00 -0600 (CST) From: "Shaun D. Black" Subject: Fortran to C converters To: chemistry@ccl.net Dear Comp.Chem-ers, About a year ago there was a significant amount of discussion on Fortran to C converter programs. I wonder, does anyone know of such a piece of code that will convert IBM mainframe Fortran77 to C? Thanks in advance for your help. Cheers. -Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = University of Texas | Bitnet: shaun%jason.decnet@thenic.bitnet = = Health Center at Tyler | Phone: (903)877-2806 FAX: (903)877-7558 = - Tyler, TX 75710-2003 | 8-) (Start every day with a smile...) = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From bernhold@qtp.ufl.edu Wed Oct 14 17:09:49 1992 Date: Wed, 14 Oct 92 21:09:49 EDT From: bernhold@qtp.ufl.edu To: Christopher Cramer , chemistry@ccl.net, Subject: Re: Spin density calculations for benzene (fwd) On Oct 14 3:32pm, Christopher Cramer wrote: > expense of the empty orbital. Mike Frisch may weigh in to tell us how the > resultant wavefunction from G92 may be other than D6h if that symmetry is > imposed from the start, but this is one of those cases where symmetry would > clearly produce an unstable wavefunction in any case. I'm not Mike Frisch, but I probably weigh more :-) Gaussian, and most other quantum chemistry codes are limited to abelian point groups for practical reasons. The largest abelian subgroup of D6h is D2h, so that's what the calculation would have been done in. The HF wavefunction is forced to maintain the symmetry imposed by the _calculation_, but in this case it is not the symmetry of the nuclear framework. Therefore, the wavefunction (and hence the spin densities) will satisfy D2h symmetry, but not necessarily D6h. Some codes (I don't remember of Gaussian does or not) will analyze the symmetry of the wavefunction after an SCF calculation and compare it to the symmetry of the nuclear framework. This can be a very useful thing to check if you're in the habit of studying "challenging" systems. When studying Jahn-Teller systems, be careful about which potential surface you're on too. -- David Bernholdt bernhold@qtp.ufl.edu Quantum Theory Project bernhold@ufpine.bitnet University of Florida Gainesville, FL 32611 904/392 6365 From gawboy@sodium.mps.ohio-state.edu Wed Oct 14 16:58:40 1992 Date: Wed, 14 Oct 92 20:58:40 EDT From: Galen Gawboy To: CHEMISTRY@ccl.net Subject: spin densities in C6H6- Jussi Eloranta wrote: > We just received gaussian 92 and I tried to calculate spin densities for >benzene anion. The results were (using HF): > > Total atomic spin densities: > 1 > 1 C -0.434526 > 2 C 0.493475 > 3 C 0.494552 > 4 C -0.434527 > 5 C 0.493482 > 6 C 0.494592 > 7 H -0.040585 > 8 H 0.027736 > 9 H -0.040687 > 10 H -0.040576 > 11 H 0.027740 > 12 H -0.040677 > Sum of Mulliken spin densities= 1.00000 R. J. Woods has correctly pointed out that C6H6- is a classic example of a species which exhibits a Jahn-Teller distortion. However he did not bring up the important fact that species such as C6H6- and C5H5 also are prone to artifactual symmetry breaking. A loose definition of artifactual symmetry breaking is that the electronic wave function does not reflect the symmetry of the nuclear framework. For the cases of C5H5 and C6H6-, non-dynamical correlation effects are quite important in achieving a qualitatively correct description of the wave function, meaning that a single reference description of the wave function is not likely to give a reliable description of the Jahn- Teller distortion. This issue is less important for cases such as C6H6-, when a researcher can tell by looking at the wave function whether or not symmetry breaking is an issue. This issue becomes more serious when hetero- atoms are substituted on the the ring, (such as in the case of the pyrolyl radical). In this case a single reference wave function could now exhibit the full symmetry of the nuclear framework, even if the wave function is experiencing artifactual symmetry breaking! This could lead to a gross over estimation of the distortion of the 5 membered ring, and unreliable predictions for the spin density. It would appear to me that the UHF wave function is experiencing artifactual symmetry breaking. This can be overcome by performing a pi CAS MCSCF calculation on the anion. Artifactual symmetry breaking of HF wave functions has recieved a considerable amount of attention over the years. Here are just a few of the references available on the topic. If you do not have sufficient resources to do the CAS MCSCF calculation, a Restricted Active Space MCSCF calculation can also solve your problem. Unfortunately you would have to use another quantum chemistry package. An incomplete list of possibilities would be COLUMBUS,(available by anonymous ftp from ftp.tcg.anl.gov), SWEDEN, MESA, I also recall hearing that GAMESS can do RAS MCSCF calculations, I am sure that there are also many other fine RAS MCSCF codes out in netland. P. O. Lowdin, Rev. Mod. Phys., 35, 496, (1963). P. O. Lowdin, Adv. Chem. Phys., 14, 283, (1969). J. Cizek, and J. Paldus, J. Chem. Phys., 47, 3976 (1967). J. Cizek, and J. Paldus, Phys. Rev. A3, 525 (1971). J. McKelvey, and W. J. Hehre, Mol. Phys., 25, 983 (1975). J. McKelvey and J. Berthier, Chem. Phys. Lett., 41, 476 (1976). C. F. Jackels and E. R. Davidson, J. Chem. Phys., 64, 2908 (1976). R. Seeger and J. A. Pople, J. Chem. Phys., 66, 3045 (1977). J. Paldus and A. Veillard, Mol. Phys., 35, 445 (1978). L. Englebrecht and B. Liu, J. Chem. Phys., 78, 3097 (1983). E. R. Davidson and W. T. Borden, J. Phys. Chem., 87, 4783 (1983). D. Feller, E. R. Davidson, and W.T. Borden, J. Am. Chem. Soc., 106, 2513 1984 A. D. McLean, B. H. Lengsfield III, J. Pacansky, and Y. Ellinger, J. Chem. Phys., 83, 3567 (1985). P. G. Szalay, A. G. Csaszar, G. Foragasi, A. Karpfen, and H. Lischka, J. Chem. Phys., 93, 1246 (1990). G. P. Blahouse III, B. F. Yates, Y. Xie, and H. F. Schaefer III, J. Chem. Phys. , 93, 8105 (1990). J. E. Del Bene, K. Kim, and I. Shavitt, Can. J. Chem., 69, 246 (1991). Hope this helps. -regards Galen F. Gawboy