From mrigank@imtech.ernet.in Fri Apr 29 04:32:31 1994 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.4/930601.1506) id DAA05286; Fri, 29 Apr 1994 03:58:09 -0400 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id NAA03971 for chemistry@ccl.net; Fri, 29 Apr 1994 13:27:50 +0530 Received: from imtech.UUCP by ern.doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA01685; Fri, 29 Apr 94 13:24:26+0530 Message-Id: <9404290754.AA01685@ern.doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Fri, 29 Apr 94 13:19:16 +0530 Date: Fri, 29 Apr 94 13:19:16 +0530 From: "Dr. Mrigank" To: chemistry@ccl.net Subject: Homology modelling ? X-Vms-Mail-To: CHEM,MRIGANK Hi Can some one tell how to get COMPOSER,COMPARER or PROMD for homology modelling. Or any other PD software for the same. Mrigank ---- Dr. Mrigank \/Phone +91 172 45004 x216, +91 172 44252 Institute of Microbial Technology /\Email: mrigank@imtech.ernet.in P O Box 1304, Sector 39A \/UUCP:...!uunet!sangam!vikram!imtech!mrigank Chandigarh 160 014 India. /\Fax +91 172 40985 or +91 172 603903 ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+ -- Various phillosphers have interpreted the world in varios ways. The point, however, is to change it. From Patrick.Bultinck@rug.ac.be Fri Apr 29 05:32:26 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.4/930601.1506) id EAA05465; Fri, 29 Apr 1994 04:40:21 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA08202 (5.67b/IDA-1.5 for ); Fri, 29 Apr 1994 10:39:45 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA04728; Fri, 29 Apr 94 10:36:53 +0200 Date: Fri, 29 Apr 1994 10:36:52 +0200 (MET DST) From: Patrick Bultinck Sender: Patrick Bultinck Reply-To: Patrick Bultinck Subject: Summary on symmetry (what a rhyme) To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 46972 Hello netters, Seems I started something... I am sending you this summary, since people have pointed out to me that the subjct is possibly interesting for a whole lot of CCL-subscribers... It seems to me that the discussion will remain open for quite some time, since both pro and contra messages to my opinion have reached my address or the CCl. It seems to me that there are two more or less basic approaches : - Do not use symmetry, and if you reach a minimum energy structure that is only a little apart from a certain point-group, you may want to do a symmetry calculation to see if the deviation of the symmetry is relevant or not. (so you need a frequency analysis...) - Use symmetry, and do a frequency analysis after you reached a stationary point. If the F.A. prooves that you have reached a minimum, cheer... Otherwise you need another calculation in which you lower the symmetry, and repeat the above... The prime matter you need to consider is (my opinion) what will be the time for the calculation of the minimum, and if it is at all possible to define (guess) a symmetry for the minimum. Off course the lower you take the symmetry, the higher the time for the calculation, but the lower the risk you will need to do the calculations for a lower symmetry group... So in short (still my opinion after what I read, learned ...) : Symmetry No Symmetry CPU time depending high on the start Symmetry group (the higher the symmetry, the higher the risk of having to do more calculations) a good choice will make substantial lower- ings of the CPU time Integral eval. Relatively cheap Expensive (also determines CPU time, off c(o)urse) Number of Often higher than One required one F.A. calc. It is not clear to me if one can a priori state for a certain molecule (unless you have certitude of a certain symmetry point group, from experiment) what will be the most CPU-time friendly way of calculating stuff. I hope this was, and is, a useful topic for the CCl, and would very much appreciate if futher comments are sent to my E-mail address, if there would be messages I find very useful, or if I would have received about five more, I will send them to CCl as a sort of appendix to this summary. Off course, you can continue the discussion on CCl, I would enjoy the discussion, since it illustrates that there is still quite something left to say on a routine matter like optimising geometries..... THANKS EVERYBODY WHO REACTED, AND GAVE HIS COMMENT TO ME !!!!!!! Original message : Netters, I have just sent a reply to a question concerning the use of a Z-matrix for a calculation on ethylene, using GAMESS (US). As a direct consequence I rembered something that I am not very comfortable with... In section 4 of the GAMESS manual, I find under a title : ***The role of symmetry*** that it is best to use symmetry during an optimisation. However GAMESS never lowers the symmetry during an optimisation. It is a well known fact that sometimes a minimal energy structure differs (a lot) >from the symmetry you might expect. Isn't it then safer to always do unconstrained optimisations, and if you think that the result differs so little from a certain symmetry point group, you can always do a symmetry-optimisation starting from the geometry with that symmetry, and compare energies... The most important disadvantage is off course that it often takes a lot of time to reach a certain symmetry point group, when you start from zero-symmery. Any thoughts on this... Those interested in a summary of some sort should send me a note, if enough interest exists, I send one to CCL. Thanks, |-----------------------------------------------------------------------| | C-C Patrick Bultinck | | / \ Dept. Physical & Inorganic Chemistry | | C-O O-C Section Quantum Chemistry | | | | University of Ghent | | C-O O-C Krijgslaan 281 (S-3) | | \ / 9000 Gent | | C-C Belgium | | Tel. Int'l code/32/9/264.44.44 | | Macrocycles Fax. Int'l code/32/9/264.49.83 | | Quantum Chemical E-mail : Patrick.Bultinck@rug.ac.be | | Calculations | |-----------------------------------------------------------------------| Replies : > Isn't it then safer to always do > unconstrained optimisations, and if you think that the result differs so > little from a certain symmetry point group, you can always do a > symmetry-optimisation starting from the geometry with that symmetry, and > compare energies... If you start with a high symmetry geometry, this structure is always a stationary point with respect to any symmetry-breaking directions. No gradient can ever (except for numerical reasons, of course) lead to a lower-symmetry structure. Therefore, if you are not sure whether your choice of symmetry is correct for the desired minimum, you could start the optimisation with a C1 geometry. > The most important disadvantage is off course that it often takes a lot > of time to reach a certain symmetry point group, when you start from > zero-symmery. Even worse, the calculation of the wave function needs much more time in C1 than in any other point group. If the minimum has symmetry, you waste a lot of time optimizing it in C1. I prefer the optimisation in high symmetry with subsequent calculation of harmonic frequencies. If one force constant gets negative, then I know (more or less) precisely which symmetry reduction leads to the minimum. If the minimum is "nearly symmetric", restarting the optimizer will be relatively cheap. Frequencies are, however, quite costly. Just my thoughts. Greetings, Gernot | Gernot Katzer How does a system manager change a light bulb? | katzer@bkfug.kfunigraz.ac.at | katzer@balu.kfunigraz.ac.at He doesn't. He just denies access to everyone to | the area served by the light bulb in question. | NEVER make me sysmgr! | > > Netters, > > I have just sent a reply to a question concerning the use of a Z-matrix > for a calculation on ethylene, using GAMESS (US). > > As a direct consequence I rembered something that I am not very > comfortable with... > > In section 4 of the GAMESS manual, I find under a title : ***The role of > symmetry*** that it is best to use symmetry during an optimisation. > However GAMESS never lowers the symmetry during an optimisation. It is a > well known fact that sometimes a minimal energy structure differs (a lot) > from the symmetry you might expect. Isn't it then safer to always do > unconstrained optimisations, and if you think that the result differs so > little from a certain symmetry point group, you can always do a > symmetry-optimisation starting from the geometry with that symmetry, and > compare energies... > > The most important disadvantage is off course that it often takes a lot > of time to reach a certain symmetry point group, when you start from > zero-symmery. > > Any thoughts on this... > > Those interested in a summary of some sort should send me a note, if > enough interest exists, I send one to CCL. > Patrick, You are essentially right, but if you do a constrained optimisation and then do a frequency calculation, you you will find out whether you have a local minimum or not. If you do not, that is the time to lower the symmetry. Hope this helps. Cheers, Brian, -- Associate Professor Brian Salter-Duke (Brian Duke) School of Chemistry and Earth Sciences, Northern Territory University, Box 40146, Casuarina, NT 0811, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@uncl04.ntu.edu.au Dear Patrick: It has been our experience that Nature does tend to favor high symmetry conformations, so much in fact that it is interesting to find cases where this is not the case. So that is a "philosophical" reason to optimize with symmetry (this assumes of course that one calculates and diagonalizes a Hessian to verify the nature of the stationary point). You mentioned the the most pratical reason yourself: geometry convergence is greatly accelerated by using symmetry. Should your molecule be C1, it it still an efficient way to refine your guess at the structure. Best regards, Jan Jensen Iowa State University In reply to Patrick Bultinck's question about symmetry: > > In section 4 of the GAMESS manual, I find under a title : ***The role of > symmetry*** that it is best to use symmetry during an optimisation. > However GAMESS never lowers the symmetry during an optimisation. It is a > well known fact that sometimes a minimal energy structure differs (a lot) > from the symmetry you might expect. Isn't it then safer to always do > unconstrained optimisations, and if you think that the result differs so > little from a certain symmetry point group, you can always do a > symmetry-optimisation starting from the geometry with that symmetry, and > compare energies... > > The most important disadvantage is off course that it often takes a lot > of time to reach a certain symmetry point group, when you start from > zero-symmery. > Several quantum chemistry codes do not lower symmetry during an optimization. As a matter of fact, if the gradient does not reflect the full symmetry of the point group used, there is a symmetrization problem. Concerning using point group symmetry or not: If a molecule has a possibility of a higher point group symmetry than C1, it is a good idea to exploit it. Integrals, optimizations, etc. can run faster if the program is able to use symmetry information. While the molecule with symmetry may not be the global minimum on the surface it is certainly some sort of stationary point on the surface. (Note that it might be a transition state or "higher order transition state". If the stationary point is a transition state, it is possible to follow the imaginary frequency leading to a minimum. You would also have found an important point on the reaction surface!) Even if you find a non-symmetric minimum that is lower than the symmetric molecule, you are not guaranteed that it is the global minimum. Only in fairly small molecules is it "easy" to verify that the global minimum has been found. As was pointed out, it can take time to "find" symmetry if you don't start out with it. On the other hand, if you have a symmetric molecule, it is possible to distort it into lower symmetry and search for a lower symmetry molecule. My point is that even if it is not necessarily the lowest energy isomer on the surface, a molecule with symmetry may tell you something about the surface and it is a good starting point. Of course, "forcing" a molecule into higher symmetry than is practical is not necessarily a good idea either. Hope this helps, Theresa Windus Department of Chemistry e-mail: windus@chem.nwu.edu Northwestern University Patrick Bultinck writes..... >Netters, > >I have just sent a reply to a question concerning the use of a Z-matrix >for a calculation on ethylene, using GAMESS (US). > >As a direct consequence I rembered something that I am not very >comfortable with... > >In section 4 of the GAMESS manual, I find under a title : ***The role of >symmetry*** that it is best to use symmetry during an optimisation. >However GAMESS never lowers the symmetry during an optimisation. It is a >well known fact that sometimes a minimal energy structure differs (a lot) >from the symmetry you might expect. Isn't it then safer to always do >unconstrained optimisations, and if you think that the result differs so >little from a certain symmetry point group, you can always do a >symmetry-optimisation starting from the geometry with that symmetry, and >compare energies... > >The most important disadvantage is off course that it often takes a lot >of time to reach a certain symmetry point group, when you start from >zero-symmery. > >Any thoughts on this... Yes, I would like to see a discussion on this subject opened up. I would especially be interested in comments from some of the more experienced computation chemists. Also, those persons who did calculations long enough ago when the lack of computer power necessitated the use of symmetry could, I am sure, have some interesting input on this subject. Up to this point, I thought that the use of symmetry in calculations was a big NO-NO because you are arbitrarily constraining the system and "garbage in is garbage out". But I just ran across a time when we had to use symmetry: We are investigating a complexation between a small organic molecule and a fragment containing several metal centers. The whole point is to match the metal orbitals with those calculated for the organic fragment and determine why one fragment reacts one way and other fragments react anther way. The only way that we can make sense out of the orbitals in the organic fragment is to constrain the system to some point group - must get orbital symmetries. So, the questions is: If this works, is it by some stroke of luck or does this reaction ONLY occure if the organic fragment (considering free rotation) reaches d3h symmetry while in the proximity of the metal centers? (I am being facetious to some degree). Don't we, as scientists, have to keep all constraints and limitations of our model in mind when looking at systems and use our chemical intuition as a guide? Isn't the use of symmetry just one more constraint to keep in mind or does the use of symmetry *invalidate* any scientific findings? Of course, the symmetry argument (to use or not to use) probably goes along with the "bigger is better" argument and I will probably still stay away >from symmetry as much as possible and run with the largest basis set and highest level of theory that disk allows, provided OSC permits. Chuck -- Charles W. Ulmer, II Graduate Student Senior Scientist D.A.Smith Group DASGroup, Inc. University of Toledo 3807 Elmhurst Road Toledo, OH, 43606 Toledo, OH 43613 phone: (419)537-4028 culmer@uoft02.utoledo.edu fax: (419)537-4033 WE ARE PERHAPS NOT FAR REMOVED FROM THE TIME WHEN WE SHALL BE ABLE TO SUBMIT THE BULK OF CHEMICAL PHENOMENA TO CALCULATION. -- JOSEPH LOUIS GAY-LUSSAC MEMOIRES DE LA SOCIETE D'ARCUEIL, 2, 207 (1808) To add a few remarks to Theresa Windus's comments, which are basically all correct. It is true that symmetry is handled differently by different programs. "Gaussian" finds symmetry present in the input nuclear coordinates and applies it unless you explicitly switch it off. But geometry optimizations will typically, irritatingly, quit as soon as a change in point group occurs. It is actually easier to deal with symmetry in programs like "cadpac" where you just input the symmetry-unique atoms and/or specify internal coordinates which are constrained to be related to one another by symmetry. The gradient of the energy w.r.t. nuclear displacements should transform as the totally symmetric 'irrep' in whatever point group you happen to be in. For 'closed-shell' systems (no electronic degeneracies) this means in practice that 'symmetric' structures are usually stationary points. The only distortions to which the energy gradient could be non-zero are totally symmetric. Thus one should be cautious with, say, van der Waals clusters, in which a totally- symmetric distortion which corresponds to dissociation might be favourable if the high-symmetry structure contains repulsions. The matter in 'open-shell' systems is more complicated. Imposing high symmetry on a Jahn-Teller system, for example, will obviously lead to problems. In other systems in which the electronic state does not transform as the totally symmetric irrep, one should be careful. Finally, also in open-shell systems, the use of symmetry in UHF-type calculations contains many 'hidden' pitfalls, most of which are documented. It is critical to examine the wavefunction of whatever state you converge to. One can carry out the calculation in a symmetric nuclear configuration both with and without the constraining the symmetry of the wavefunction. This can lead to massive energetic differences, and totally different behaviour w.r.t. spin-contamination, etc. All results are sensitive to starting guess, etc., and the "solution" can change during the course of an optimization. Advice: examine your *whole* computer output very thoroughly! The belief that 'transition states' are high-symmetry species is all-but totally dispelled at this time. Basically, for minima, anything goes, but there is no guarantee that "nature" favours symmetric structures over their lower-symmetry counterparts. (One only has to look at van der Waals molecules to see evidence of that.) For transition states, all that the supposedly-useful symmetry theorems tell you is an upper-limit on the point group symmetry but even that is almost always a lower symmetry than either of the pertinant minima. In general, surfaces are sufficiently complicated that transition states end up having little symmetry at all. If you somehow converged to one during a _minimization_ then you either made a shrewd guess or were very lucky. Finally, there is an unfortunate tendency, which is widespread, to refer to stationary points at which more than one Hessian eigenvalue is negative as "higher _order_ saddles". This nomenclature is incorrect. The 'order' of a stationary point specifies the lowest non-vanishing term in a locally- expanded Taylor series. Thus almost all stationary points that we, as "chemists" meet, are second-order points, because they have non-vanishing second derivatives. Third order points have zero-second derivatives, and are characterised by cubic terms in the potential, e.g., "monkey-saddles". As has been discussed many times, these points are extremely rare and, to my knowledge, a 'real' one has yet to be conclusively identified on a molecular PES. The characterisation of second-order stationary points is achieved by stating the Hessian "index" - the number of negative eigenvalues. Thus a transition state has a Hessian index of 1. Structures with indexes>1 are 'maxima' in a subspace. The term "rank" also has a distinct meaning - it is the number of non-zero Hessian eigenvalues - and rarely finds application in chemistry. All these terms are described more fully in P.G.Mezey's book, "Potential Energy Hypersurfaces", Elsevier. This point might seem to be pedantic, but there are a number of terms to be used, and each has a specific and DISTINCT meaning: 'order', 'index', 'rank' and also 'signature'. (For the meaning of the last of these, see R.F.W. Bader, "The Theory of Atoms in Molecules", OUP.) Richard Bone ================================================================================ R. G. A. Bone. Molecular Research Institute, 845 Page Mill Road, Palo Alto, CA 94304-1011, U.S.A. Tel. +1 (415) 424 9924 x110 FAX +1 (415) 424 9501 E-mail rgab@purisima.molres.org Hi, Just a few more remarks regarding Richard Bone's comments: > "Gaussian" finds symmetry present in the input nuclear coordinates and > applies it unless you explicitly switch it off. But geometry optimizations > will typically, irritatingly, quit as soon as a change in point group occurs. If you wish to force the symmetry, this can be averted by using the same variable name for the symmetric lengths and angles, thus there is no possibility of a change in point group. > The gradient of the energy w.r.t. nuclear displacements should transform as > the totally symmetric 'irrep' in whatever point group you happen to be in. >For 'closed-shell' systems (no electronic degeneracies) this means in practice > that 'symmetric' structures are usually stationary points. The only There are actually a number of cases where this is indeed not the case. Amides, for instance, tend not to be planar but are slightly puckered at the N. It often doesn't take much energy to force it to be planar, but non-planar is the minimum at any levels of theory that I've seen. Also, quite bulky molecules often avoid a symmetric form in favor of spreading out the steric interactions. The only way to be sure anything is really a minimum or a transition state is to perform a frequency calculation at the end, whether or not one uses symmetry in the calculation. I had started the methyl groups in DMA in one orientation and they stayed put, even though I did not invoke symmetry. The frequency calculation showed it to be a transition state, and further optimizations using those forces lead to the minimum structure. The use of symmetry is still quite useful in speeding computations, and the freq. calc. will tell you whether you were correct or incorrect in assuming the particular level of symmetry. (Use individual variables for each bond and angle if you want to optimize further, though!) Dan Severance (APLS - Association for Prevention of Long Sigs) dan@omega.chem.yale.edu Regarding the use of symmetry in quantum calculations. Most of the stuff I've looked at never was more than C1 to start with so it's not been a problem. By tinkering with the Z-matrix and enforcing certain types of symmetry (like requiring selected C-H bonds to have the same length), I've seen between 10 and 300% differences in speed for test systems I've worked with. For example, in dimethyl terephthalate, I can require all of the aromatic C-H bonds to be of the same length, and I can require certain other bonds (e.g. both carbonyls) to be the same length. Any time I'm really interested in the most accurate, quantitative results, I'll do a symmetry disallowed optimization, or at least a symmetry disallowed frequency calculation, to see how far from a true minimum I happen to be. My opinion (worth what you paid for it ;-) ): Symmetry can be used to advantage, particularly less restrictive symmetry than full point group symmetry, but you take a risk of getting a misleading answer when you do that. The classic one (and one that a student of mine got tripped up on this fall) was keeping the symmetry and getting a planar biphenyl. If I'm really concerned, I've been known to run the starting geometry through a few femtoseconds of dynamics to completely ruin any symmetry/stationary points I've happened to introduce in constructing the molecule. Bruce Wilson (bewilson@emn.com) Yes, I agree it is safer never to use symmetry. But sometimes it is worth the risk. I am willing to use symmetry in the optimization of, e.g., benzene and ethylene. Sometimes you get burned. Once I used symmetry to optimize the geometry of sulfuric acid (C2v according to the JANNAF Tables), and missed the opportunity of discovering that it should have been C2. Symmetry can also give lower energies than not using symmetry. Thus, in benzene the only `error' can be in the two bond lengths, if symmetry is used. If symmetry is NOT used, errors due to unequal bond lengths and due to angles differing from 120 degrees will cause the energy to rise. Jimmy Stewart Patrick Bultinck started a discussion about whether or not symmetry constraints should be used in calculations. When we do a geometry optimization we're seeking a stationary point (which almost alwars means a relative minimum or a transition state). Since it's sound practice to characterize any stationary point you have found by calculating its freqs, it is probably a good idea to routinely impose symmetry (for esthetic reasons and to save time) and let the number of imaginary vibrations tell you when to relax it to go from a transition state to a minimum. Theresa Windus says "while the molece with symmetry may not be the global minimum...it is certainly some sort of stationary point..." Does anybody know of a formal theorem that says non-C1 structures are always stationary points, or some place where this is explicitly stated? It's just that it would be nice to see some sort of proof; it's not quite obvious that it MUST be so, altho' I do see that it looks reasonable. Thanks. === E. Lewars wrote: > [ ... ] > Theresa Windus says "while the molece with symmetry may not be the global > minimum...it is certainly some sort of stationary point..." Does anybody > know of a formal theorem that says non-C1 structures are always stationary ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > points, or some place where this is explicitly stated? It's just that it ^^^^^^ If you OPTIMIZE your molecule under the restriction of a specific point group and you find a point where all force vanish you have found a stationary point (that's how stationary points are defined). So it doesn't matter whether the molecule possesses symmetry or not at this point of its potential surface. > would be nice to see some sort of proof; it's not quite obvious that it > MUST be so, altho' I do see that it looks reasonable. But the probability that you have found a MINIMUM is very small. In most cases you will found one or even more imaginary frequencies and you have to optimize further using a subgroup of your current point group (C1 is a always a subgroup) and starting with a distortion of your current geometry (preferably along a normal mode with an imaginary frequency), since otherwise you stay at your current stationary point of the potential surface (there are no force your optimizer can minimize). Using symmetry makes sense if you know from experiment that your molecule belongs to a special point group or your chemical intuition tells you that symmetry may play a role. Use of symmetry for speeding up or making calculations possible has always to be considered as giving you wrong answers (no minima). If your molecules are models for larger systems and the imaginary frequencies affect only parts of the molecule which are not present in your larger system, you may use symmetry, too. Joerg-R. Hill In reply to Dan Severence's comments: i) Gaussian calculations. >> "Gaussian" finds symmetry present in the input nuclear coordinates and >> applies it unless you explicitly switch it off. But geometry optimizations >> will typically, irritatingly, quit as soon as a change in point group occurs. > > If you wish to force the symmetry, this can be averted by using the >same variable name for the symmetric lengths and angles, thus there is >no possibility of a change in point group. > Yes, Dan is correct, provided that you can do it. Constraining the internal coordinates in the Z-matrix is the way out. But I had one fiendish example once (in "C_i" symmetry) where it was not possible to do this: two related angles could not be specified by the same internal coordinate and the optimization failed as soon as these angles became slightly inequivalent. ii) I was very careful in my comment about the gradient. >> The gradient of the energy w.r.t. nuclear displacements should transform as >> the totally symmetric 'irrep' in whatever point group you happen to be in. >>For 'closed-shell' systems (no electronic degeneracies) this means in practice >> that 'symmetric' structures are usually stationary points. The only > > There are actually a number of cases where this is indeed not the > case. Amides, for instance, tend not to be planar but are slightly > puckered at the N. It often doesn't take much energy to force it to > be planar, but non-planar is the minimum at any levels of theory that > I've seen. Also, quite bulky molecules often avoid a symmetric > form in favor of spreading out the steric interactions. > Note that I said that symmetric structures are usually STATIONARY POINTS, not 'MINIMA'. Nothing I said contradicted the example of a non-planar amide. But, symmetry can not be interpreted to be 'local' either. I was about to venture that the configuration in which the bonds about the N-atom are planar would probably be a 'transition state' but of course such a structure may not be a stationary point at all if there are other 'out-of-plane' atoms in the molecule which are not related to one another by reflection in the plane. (Remember those non-bonded interactions ...). If the _whole_ molecule is planar or has a plane of symmetry then (if closed-shell, and in the absence of totally symmetric distortions) it will be a stationary point but I couldn't tell you, a priori, what sort. N.B., Just because symmetric structures are usually stationary, does not mean the converse, either, viz: stationary points do not have to be 'symmetric'. There are clearly a number of pitfalls and potential confusions in the discussion of symmetry. I will shortly post a useful reference-list to CCL which not only provides background to my own comments but should hopefully be a useful almanac to anybody with an interest in this field. Watch this space ......... Richard Bone ================================================================================ R. G. A. Bone. Molecular Research Institute, 845 Page Mill Road, Palo Alto, CA 94304-1011, U.S.A. Tel. +1 (415) 424 9924 x110 FAX +1 (415) 424 9501 E-mail rgab@purisima.molres.org Dear netters Here's my two ore contribution to the symmetry discussion. The goal of a calculation is to get a physically relevant result. Therefore the use of absolute symmetry restrictions should be scientifically motivated. Of course, it is usually a good approach to start with a high symmetry and then step by step relax the restrictions. This will economize resources and may at the same time give meaningful information about saddle points. Frequency calculations in principle involve quite a lot - something like n*(n-1)/2 for n degrees of freedom - of lower symmetry calculations, involving all possible pairs of displacements of individual atoms. That may be too much effort, since a check for saddle points requires only n such calculations - or less if bond stretching is avoided. Thanks for your bandwidth ... In view of the current comments on the philosophy of the use of symmetry in the computation of molecular potential energy surfaces, I thought it would be useful to put out a compendium of 'primary' references in this field. I revisited my (1992) PhD thesis and culled the following. It is worth restating, though, that there is no theorem which allows you claim that a minimum-energy structure (in fact, any stationary point) must have any point group symmetry at all, in the absence of other information, e.g., a force law. (The converse is open to serious discussion, nevertheless: - does a structure of given symmetry have to be a stationary point?) Symmetry can be used somewhat heuristically, however, with caution. And, as has also, already been stated, once one has located a stationary point (confirmed by checking all gradient components), the only sure way of testing whether or not it is a local minimum, is to calculate the Hessian. A general discussion of all basic features of PESs can be found in; ------------------ P.G.Mezey, Studies in Physical and Theoretical Chemistry, 53, "Potential Energy Hypersurfaces", Elsevier, (1987). Symmetry at Stationary Points ----------------------------- If one is looking for a 'proof' that the energy must be stationary w.r.t. all non-totally symmetric distortions (i.e., the oft-desired result that "symmetric structures are (frequently) stationary points") then there are two papers which address the issue (for a non-degenerate electronic state): D. J. Wales, J. Am. Chem. Soc., 112, 7908, (1990) - a paper which considers the balance of forces on the atoms at various points in a given structure. H. Metiu, J. Ross, R. Silbey and T. F. George, J. Chem. Phys.,61, 3200, (1974) This paper observes that the discussion is linked closely with the notion of expanding the local potential surface in normal coordinates (and their derivatives, etc.). [Because, of course, normal coordinates are guaranteed to transform as irreducible representations of the point group.] This, in turn, leads on to discussions of reaction paths, etc. and an understanding of how the gradient vector transforms under symmetry operations, a subject which has been addressed by many authors. Symmetry of the gradient. ------------------------- The first of these papers contains a straightforward and rigorous formal proof. J. W. McIver, Jr. and A. Komornicki, Chem. Phys. Lett., 10, 303, (1971) The papers by Pearson describe a perturbation-theory approach. R. G. Pearson, J. Am. Chem. Soc., 91, 1252, (1969) R. G. Pearson, J. Am. Chem. Soc., 91, 4947, (1969) R. G. Pearson, Theor. Chim. Acta., 16, 107, (1970) R. G. Pearson, J. Chem. Phys., 52, 2167, (1970) R. G. Pearson, Pure Appl. Chem., 27, 45, (1971) R. G. Pearson, Acc. Chem. Res., 4, 152, (1971) R. G. Pearson, Symmetry Rules for Chemical Reactions, Wiley Interscience, (1976) Rodger and Schipper have a formalism based upon normal-mode expansions. A. Rodger and P. E. Schipper, Chem. Phys., 107, 329, (1986) A *landmark* paper by Pechukas describes the properties of steepest-descent paths and leads to cornerstone statements of transition state symmetries. P. Pechukas, J. Chem. Phys., 64, 1516, (1976) Transition State Symmetry Rules ------------------------------- The believed limitations on the symmetries of transition states have lead to many analyses, beginning with Stanton and McIver: J. W. McIver, Jr. and R. E. Stanton, J. Am. Chem. Soc., 94, 8618, (1972) R. E. Stanton and J. W. McIver, Jr., J. Am. Chem. Soc., 97, 3632, (1975) J. W. McIver, Jr., Acc. Chem. Res., 7, 72, (1974) A. Rodger and P. E. Schipper, Chem. Phys., 107, 329, (1986) A. Rodger and P. E. Schipper, Inorg. Chem., 27, 458, (1988) A. Rodger and P. E. Schipper, J. Phys. Chem., 91, 189, (1987) R. G. A. Bone, Chem. Phys. Lett., 193, 557, (1992) Exceptions and Pitfalls ----------------------- The application of symmetry and many assumptions about the form of a PES can lead to problems if unusual features are present. The oft-cited example is that of a (putative) monkey-saddle (3rd order 'degenerate' critical point), but except where symmetry itself may impose severe restrictions on the form of the potential function, it is safe to assume that there will always be minor perturbations which lift the degeneracy. Near 4th-order critical points can arise on exceptionally flat surfaces and when symmetry demands that 3rd order terms in the potential must vanish. Far more frequent are bifur- cations. Strictly a "bifurcation" is a feature of a path. Valtazanos and Ruedenberg demonstrated their association with "valley-ridge inflection points" on a PES: P. Valtazanos and K. Ruedenberg, Theor. Chim. Acta., 69, 281, (1986) Bifurcations are legion. For description of one on a very simple and surpris- ing surface, see: R. G. A. Bone, Chem. Phys., 178, 255, (1993). Other more exotic examples, include: J. F. Stanton, J. Gauss, R. J. Bartlett, T. Helgaker, P. Jorgensen, H. J. Aa. Jensen and P. R. Taylor, J. Chem. Phys., 97, 1211, (1992). T. Taketsugu and T. Hirano, J. Chem. Phys., 99, 9806, (1993) The main significance of bifurcations in the context oif symmetry is that they are points at which, symmetry may be 'broken'. For a qualitative discussion of the plethora of forms of PES and the influence of point group symmetry, see: R. G. A. Bone, T. W. Rowlands, N. C. Handy and A. J. Stone, Molec. Phys., 72, 33, (1991) And, a paper which describes concepts useful for characterisation the local symmetry of potential energy surfaces in Jahn-Teller systems. A. Ceulemans, D. Beyens and L. G. Vanquickenbourne, J. Am. Chem. Soc., 106, 5824, (1984) Symmetry-breaking in Open-Shell Systems --------------------------------------- This subject has a long history, so I will be selective here: General considerations/review: E. R. Davidson, J. Phys. Chem., 87, 4783, (1983) UHF calculations: L. Farnell, J. A. Pople and L. Radom, J. Phys. Chem., 87, 79, (1983) D. B. Cook, Int. J. Quant. Chem., 43, 197, (1992) D. B. Cook, in "The Self-Consistent Field Approximation", Ed. R. Carbo D. B. Cook, J. Chem. Soc. Far. Trans. 2, 82, 187, (1986) P. O. Lowdin, Rev. Mod. Phys., 35, 496, (1963)( W. D. Allen and H. F. Schaefer, III, Chem. Phys., 133, 11, (1989) Calculations with MC-SCF/CAS-SCF P. Pulay and T. P. Hamilton, J. Chem. Phys., 88, 4926, (1988) J. M. Bofill and P. Pulay, J. Chem. Phys., 90, 3637, (1989) Calculations with a Coupled-Cluster Wavefunction J. D. Watts and R. J. Bartlett, J. Chem. Phys., 95, (1991) Final Comments: There is no definitive answer to the question of what role symmetry should play in a given molecular problem. There will always be a compromise between (computational) resources available and thoroughness of analysis. Sometimes it makes sense to start in high symmetry, sometimes not. Sometimes it is only possible to use symmetry - because of the difference it makes to the size of the calculation. In calculating a reaction path, it's probably a good idea to use as little symmetry as possible. When optimizing a geometry, symmetry will help you get to a stationary point (probably) but only a frequency calculation can tell you what it is. When searching for saddle-points, the theorems tell you that you'll only increase in symmetry (at the T.S.) if you're finding a T.S. for a 'degenerate' rearrangement. Otherwise, your transition state cannot be searched for by minimizing in a symmetry-constraint. This means that the majority of T.S.'s don't have any useful distinguishing symmetries. Sad, but true. Despite the zeal with which chemists have pursued those symmetric 'beauties', the Fullerenes, Nature more often displays low-symmetry than high-symmetry, but a bit of thought shows that two low-symmetry structures are often related to one another by a symmetry operation in a higher-symmetry 'midpoint' so symmetry of the PES is always conserved. Richard Bone ================================================================================ R. G. A. Bone. Molecular Research Institute, 845 Page Mill Road, Palo Alto, CA 94304-1011, U.S.A. Tel. +1 (415) 424 9924 x110 FAX +1 (415) 424 9501 E-mail rgab@purisima.molres.org Dear Netters, I have some comments concerning the discussion about symmetry. R.G.A.Bone wrote: >The gradient of the energy w.r.t. nuclear displacements should transform >as the totally symmetric 'irrep' in whatever point group you happen to be >in. For 'closed-shell' systems (no electronic degeneracies) this means in >practice that 'symmetric' structures are usually stationary points. E.Lewars wrote: >Does anybody know of a formal theorem that says non-C1 structures are >always stationary points? Yes, I do. There is the rigorous theorem that states that any symmetrical structure is a stationary point with respect to NOT totally symmetric nuc- lear displacements. I know some references to this statement but only in Russian textbooks (sorry). This is a purely geometrical statement and does not depend upon the symmetry of electronic state and whether or not the system has closed shells only. The molecules with Jahn-Teller effect are not exclusions. Their symmetric structures are also stationary points, but not minima. But the term "stationary point" is defined as a point where all partial derivatives (consequently, gradient) is equal to zero. It need not be a maximum or a minimum, but can be a saddle point. If one optimizes geometry within symmetry constraints, it guarantees that the found stricture is a minimum with respect to totally symmetric nuclear displacements and hence a stationary point with respect to all possible displacements. Note that one starts optimizing a structure from a symmetrical geometry, it is impossible to come to a structure with a lower symmetry, no matter this symmetry is imposed explicitly (using variables with the same names in Z-matrix) or simply actually present in the starting geometry. This is due to the fact that "the gradient of the energy w.r.t. nuclear displacements should transform" as R.Bone writes. (however, not "should transform" but "does transform"). The error messages such as GAUSSIAN's "change of point group or standard orientation" arises either from numerical errors in transforming Cartesian coordinates into internal or from "false" Z-matrix (in which some parameters are denoted by the same variables though they are not symmetrically equivalent). Sergei F.Vyboishchikov Universitaet Marburg, Germany E-Mail: sergei@ps1515.chemie.uni-marburg.de On Apr 27, 11:27pm, R.G.A. Bone wrote: > Subject: CCL:Symmetry: Definitive References > It is worth restating, though, that there is no theorem which > allows you claim that a minimum-energy structure (in fact, any > stationary point) must have any point group symmetry at all, in > the absence of other information, e.g., a force law. (The > converse is open to serious discussion, nevertheless: - does a > structure of given symmetry have to be a stationary point?) Excuse me; I'm not an expert on this sort of thing, so I may be missing something, but consider ethane in the staggered conformation. This conformation is an energetic minimum, and has point-group symmetry. If I simply stretch or compress the C-C bond, I do not change the point-group, but I am no longer at a minimum, nor at any other stationary point. Doesn't this demonstrate that symmetric structures need not be stationary points? -P. -- ********************** "So much for global warming...." ********************* Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ***************************************************************************** Peter Shenkin wites: "...consider ethane in the staggered conformation. This conf is an energetic minimum, and point-group symmetry. If I simply stretch or compress the C-C bond, I do not change the point group, but I am no longer at a minimum, nor at any other stationary point. Doesn't this demonstrate that symmetric structures need not be stationary points?" Yes, but wer're not really asking if a symmetric structure of *arbitrary* geometry is a stationary point, but rather if such a structure, optimized within the limits of its symmetry (keeping the Sch:/nfliess point group, e.g. C2v, Cs, etc) must go to a stationary point. === Ok, I'll make this my last statement on this subject: Peter Shenkin writes in reply to my latest... >> It is worth restating, though, that there is no theorem which >> allows you claim that a minimum-energy structure (in fact, any >> stationary point) must have any point group symmetry at all, in >> the absence of other information, e.g., a force law. (The >> converse is open to serious discussion, nevertheless: - does a >> structure of given symmetry have to be a stationary point?) > > Excuse me; I'm not an expert on this sort of thing, so I may > be missing something, but consider ethane in the staggered > conformation. This conformation is an energetic minimum, and > has point-group symmetry. If I simply stretch or compress the > C-C bond, I do not change the point-group, but I am no longer > at a minimum, nor at any other stationary point. > > Doesn't this demonstrate that symmetric structures need not > be stationary points? > > -P. > Yes, he is right, I was being a little sloppy; in my first posting on this subject, I amplified the same point ... > ... this means in practice > that 'symmetric' structures are usually stationary points.The only distortions > to which the energy gradient could be non-zero are totally symmetric. Thus one > should be cautious with, say, van der Waals clusters, in which a totally- > symmetric distortion which corresponds to dissociation might be favourable if > the high-symmetry structure contains repulsions. The distortion that Shenkin mentions is, of course, totally symmetric (A_1g in D3d point group). I guess I shouldn't have made the unqualified statement, assuming that people would remember a detail of an earlier posting. The remaining missing qualifier from the basic statement is that one assumes that one's "symmetric structure" has been energy-minimized. Perhaps one can remove potential confusion by stating that: if one has a structure of given symmetry, then one can probably find a stationary point by energy-minimization, constraining that symmetry. The energy has changed only w.r.t. totally-symmetric distortions of the initial structure. This is not the same as suggesting that symmetric structures are often stationary- points, which I accept is rather a bold statement, given that any structure can be subjected to an infinitesimal distortion. The main point of practicality is that the energy of a symmetric structure will be stationary w.r.t. non- totally-symmetric distortions; in most instances a 'guessed' structure of a given symmetry (particularly high symmetry) will be close to a stationary point (requiring small changes only in the totally symmetric degrees of freedom to minimize to it). And in that sense one may loosely state that symmetric structures commonly turn out to be stationary points. As we can all see - symmetry is a complicated subject and one which is difficult to write about. Apologies if I clouded the issue. Till the next 'virtual interaction' ... Richard Bone ================================================================================ R. G. A. Bone. Molecular Research Institute, 845 Page Mill Road, Palo Alto, CA 94304-1011, U.S.A. Tel. +1 (415) 424 9924 x110 FAX +1 (415) 424 9501 E-mail rgab@purisima.molres.org That's all folks, at least upto now. As mentionned, future mailings will still be very welcome, and I hope that CCl will be considering this matter for the next few days (weeks) to come. Greetings, from Belgium Patrick (E-mail address, address, fax, ... in the original message (see above)). From lohrenz@sg1506.chemie.uni-marburg.de Fri Apr 29 07:32:27 1994 Received: from sg1506.chemie.uni-marburg.de for lohrenz@sg1506.chemie.uni-marburg.de by www.ccl.net (8.6.4/930601.1506) id HAA06048; Fri, 29 Apr 1994 07:19:48 -0400 Received: by sg1506.chemie.uni-marburg.de (931110.SGI/931108.SGI.ANONFTP) for CHEMISTRY@ccl.net id AA24382; Fri, 29 Apr 94 13:21:00 +0200 From: lohrenz@sg1506.chemie.uni-marburg.de (John Lohrenz) Message-Id: <9404291121.AA24382@sg1506.chemie.uni-marburg.de> Subject: Summary: Problems with G92-DFT To: CHEMISTRY@ccl.net Date: Fri, 29 Apr 94 13:20:58 MDT Cc: jonas@sg1506.chemie.uni-marburg.de (Volker Jonas) X-Mailer: ELM [version 2.3 PL11] Some days ago I posted a query to the net about problems with G92-DFT. I was asked to summerize the answers what I want to do with this mail. The most important information was that GAUSSIAN is working on this problem and that a new release will be presented (hopefully soon). A good hint was to combine a finer grid with SCF=NoVarAcc (N.v.Eikema Hommes) which worked at least in my "problem cases". Special thanks for this detailed answer. Following are the explicit answers (I had to translate the one by Nico, hopefully you get the message). Thanks again for all answers, John ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ The original question was: >Dear netters, > >not too long ago I started to carry out DFT calculations using >G92. Quite frequently my calculations run into the following >problem: > Warning! Spurious integrated density > >I encountered this error in many different calculations using the >BLYP or the SVWN functionals with the 3-21G(d) or the 6-31G(d) basis >set. Both singlet and triplet calculations gave similar mistakes. Some= >times it helped to use guess=always, but I think there should be better >and faster possibilities... >Can someone out there tell me what this means and even more important >how can I prevent my calculations to run into this error. > ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Nico van Eikema Hommes writes (in short): Possible solutions are: 1. simply comment the call in link1e. The calculation continues and one realizes that: 2. the problem disappears completely or becomes remarkably less grave when the convergence criterium is fulfilled. Consequently the reason is the initial guess (projected INDO or Ae), which is quite bad. (Let me state at this point, that from time to time my calculations got through only when I used the INDO guess, they failed with a guess read from the read-write file. How can we understand this?) 3. With INT=FINEGRID and SCF=NOVARACC (SCF=(NOVARACC,TIGHT) for single point calculations) the problem arises only with extended basis sets like 6-311+G* etc. Therefore these keyword have to be used here in Erlangen. The default grid is far too rough! 4. Interestingly convergence problems seem to be less grave with this option. However it is better to carry out a HF-single-point calculation than the SCF=QC (suggested by GAUSSIAN inc.) if convergence is still a problem (unless you have plenty of computer time). Finally one has to realize that frequency jobs are very slow. However G92/DFT is a very nice extension and usage is easier than ADF or DGauss. ------------------------------------------------------------------------------ the original message follows: From hommes@organik.uni-erlangen.de Tue Apr 26 11:37:52 1994 From: Nico van Eikema Hommes Subject: Re: CCL:Problems with G92dft Date: Tue, 26 Apr 94 11:35:41 METDST Hallo John, Das war also einer der ersten Dinge, worueber ich mich aufgeregt habe als wir G92/dft bekommen hatten. Es kommt eigentlich fast immer! Natuerlich habe ich sofort eine Loesung ausge"hack"t: 1. der lnk1e call wird unprotokollarisch auskommentiert. Damit laeuft der Rechnung weiter. (Ich muesste schauen wo das auch wieder genau war). Dann stellt man erstaunt fest: 2. das Problem verschwindet ganz oder wird weitaus weniger gravierend, wenn das Konvergenzkriterium erreicht wird. Es liegt also am Initial Guess (projected Indo o.Ae), der ziemlich hundsmiserabel ist. 3. Mit den Keywords INT=FINEGRID und SCF=NOVARACC (SCF=(NOVARACC,TIGHT) fuer Single Points!) tritt es nur noch bei extended Basis Sets auf, also 6-311+G* etc. Deshalb sind diese Keywords hier in Erlangen zum Pflicht erhoben worden. Das default Grid ist viel zu grob! 4. Konvergenzschwierigkeiten sind damit interessanterweise auch schon weniger schlimm, allerdings ist ein HF Single Point am Anfang viel besser als SCF=QC (von Gaussian, Inc. empfohlen), sollte es immer noch nicht klappen. (es sei denn, der Rechner soll einfach fuer drei wochen blockiert sein). Und wenn endlich alles laeuft, muss man feststellen, dass Frequenzen unlaublich laaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaange brauchen mit DFT. Aber sonst ist es eine schoene Erweiterung, und viel angenehmer als ADF oder DGauss zu benutzen. Viele Gruesse, Nico -- Dr. N.J.R. van Eikema Hommes Computer-Chemie-Centrum hommes@organik.uni-erlangen.de Universitaet Erlangen-Nuernberg Phone: +49-(0)9131-856532 Naegelsbachstr. 25 FAX: +49-(0)9131-856566 D-91052 Erlangen, F.R.G. ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ From dobbskd@esvax.dnet.dupont.com Thu Apr 21 14:02:29 1994 Date: Thu, 21 Apr 94 08:00:09 EDT To: lohrenz Subject: RE: CCL:Problems with G92dft Status: RO Try using a finer grid and/or turn off symmetry (NOSYM). These are quick fixes for now. Gaussian, Inc. is working on better solutions; try talking to them. Kerwin ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ From mckelvey@Kodak.COM Thu Apr 21 18:38:43 1994 Date: Thu, 21 Apr 94 06:22:34 -0400 From: mckelvey@Kodak.COM To: "lohrenz@sg1506.chemie.uni-marburg.de"@Kodak.COM Subject: RE: CCL:Problems with G92dft Status: RO There is a bug...I had it also. It went away when I went from Rev F to Rev G. Contact Gaussian... John McKelvey Eastman Kodak ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ From chemistry-request@ccl.net Thu Apr 21 12:05:20 1994 Date: Thu, 21 Apr 1994 10:18:45 +0100 From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: CCL:Problems with G92dft Status: RO Many have had this problem. Speaking to Doug Fox of Gaussian about 1 month ago, I am given to understand that a patch release will be coming out soon that will address this problem. Doug, over to you?? Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.02, Tel:+44 71 225 8339, Fax:+44 71 589 3869. >From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ John Lohrenz Ak Prof. G. Boche Fachbereich Chemie der Philipps-Universitaet Marburg D-35032 Marburg From d.baghurst@ic.ac.uk Fri Apr 29 09:32:31 1994 Received: from punch.ic.ac.uk for d.baghurst@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id IAA07055; Fri, 29 Apr 1994 08:59:57 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <01397-0@punch.ic.ac.uk>; Fri, 29 Apr 1994 13:59:29 +0100 Received: from mingos-c.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA23563; Fri, 29 Apr 94 13:59:58 +0100 Message-Id: <9404291259.AA23563@cscmgb.cc.ic.ac.uk> X-Sender: drb01@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 29 Apr 1994 13:56:39 +0100 To: CHEMISTRY@ccl.net From: d.baghurst@ic.ac.uk (D.Baghurst) Subject: Help with Forticon X-Mailer: Does anybody know where I can get a manual/help for the Forticon program? It doesn't seem to be with the sources on kekule and archie didn't help. ---------------------------------------------------------------------- Dr. David Baghurst,Department of Chemistry,Imperial College, South Kensington,London. SW7 2AY. Tel: 071-589-5111 ext. 4642. Fax: 071-589-3869. E-mail: drb01@ic.ac.uk From marty@ionchannel.med.harvard.edu Fri Apr 29 11:32:48 1994 Received: from harvard.harvard.edu for marty@ionchannel.med.harvard.edu by www.ccl.net (8.6.4/930601.1506) id KAA08314; Fri, 29 Apr 1994 10:52:28 -0400 Received: by harvard.harvard.edu (5.54/a0.25) (for chemistry@ccl.net) id AA05271; Fri, 29 Apr 94 10:52:48 EDT Received: from ionchannel.med.harvard.edu by heimdall.med.harvard.edu.med.harvard.edu (4.1/SMI-4.1) id AA17543; Fri, 29 Apr 94 10:48:48 EDT Received: from [134.174.159.129] by ionchannel.med.harvard.edu via SMTP (931110.SGI/920502.SGI) for @heimdall.med.harvard.edu:chemistry@ccl.net id AA16149; Fri, 29 Apr 94 10:52:09 -0700 Message-Id: <9404291752.AA16149@ionchannel.med.harvard.edu> X-Sender: marty@ionchannel.med.harvard.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 29 Apr 1994 09:52:23 -0400 To: chemistry@ccl.net From: marty@ionchannel.med.harvard.edu (Marty Gallagher) Subject: Biosym with X-windows -- The conclusion X-Mailer: Hello. Thanks to all who responded to my quesiton of running biosym on a PC with a X-windows emulator. The conclusion of everyone who responded (including Biosym's tech service) was the same so I won't waste bandwith by including everyone's response and will just give you the straight dope. Yes you can run Biosym with an X-windows emulator *iF* You have version 2.3 *and* you purchase a separate Biosym module called "Axxess." For people who were interested, you can get a demo (the licensed program is *not* free) of Xwin from gopher.rz.uni-wuerzburg.de Thanks again to all! -- Marty ========================================================================= Martin J. Gallagher phone: (617) 432-1729 Dept. of Neurobiology fax: (617) 734-7557 Harvard Medical School E-mail: marty@ionchannel.med.harvard.edu 220 Longwood Ave Boston, MA 02115 =========================================================================== From TANG@Kitten.Chem.uh.edu Fri Apr 29 13:32:37 1994 Received: from Kitten.Chem.uh.edu for TANG@Kitten.Chem.uh.edu by www.ccl.net (8.6.4/930601.1506) id NAA10316; Fri, 29 Apr 1994 13:12:43 -0400 Date: Fri, 29 Apr 1994 12:12:44 -0500 (CDT) From: "Tang, Huang (UH-Chem)" To: chemistry@ccl.net Message-Id: <940429121244.27c00c88@Kitten.Chem.uh.edu> Subject: one more symmetry argument , 29-APR-1994 Dear Netters, We have seen lots of symmetry related messages. It seems to me there are some confusions regarding using symmetry in calcualtions. IMHO, to use symmetry or not is totally intuitively-based decision. There is no a priori reason to prove that symmetric or asymmetric geometry should be minimum or not. But chemical sense (VSEPR rules based) always favors to start from symmetric geom. Take TiCl4 (or simply CH4) as an example, it makes little sense to start from C1 symmetry, though you'll get to Td geom eventually and costly. As molecules are bigger and more complicated, using symmetry is always a good starting point. Though high symmetry geom might not be minimum, it also gives us certain info anout the structure. The example is MoH6 which is not Oh structure! For some multi-well potential surfaces, even you start from C1 symmetry, there is no guarrantee you'll reach a global minimum. Therefore using lower symmetry is not a good starting point, unless your intuition tells you to do so (how from the beginning? I don't know :-) There are some confusions about minimum (saddle point) and stationary point. We all refer these terms to OPTIMIZED structure, not randomly drawn structure. Using any symmetry constraint, you can always get to a stationary point (counter-examples? I'd like to hear one :-), meaning you can always optimize it to a point where all gradients vanish (within a given threshold). But the stationary point may not be a minimum. At times you have to break or lower symmetry to reach a minimum (after you are sure >from a freq. calcn.) All in all, computational chemistry is still chemistry. Do whatever makes chemical sense. Happy computing... -------- _ Tang, Huang _| ~- Chem. Dept, U. of Houston \, _} Houston, Texas 77204-5641 \( e-mail: tang@kitten.chem.uh.edu phone: (O) (713) 743-3269 From axh14@cac.psu.edu Fri Apr 29 15:32:38 1994 Received: from milkman.cac.psu.edu for axh14@cac.psu.edu by www.ccl.net (8.6.4/930601.1506) id OAA11777; Fri, 29 Apr 1994 14:55:33 -0400 Received: from wilbur.cac.psu.edu by milkman.cac.psu.edu with SMTP id AA05822 (5.65c/IDA-1.4.4 for ); Fri, 29 Apr 1994 14:55:28 -0400 From: ARTHUR HOAG Received: by wilbur.cac.psu.edu id ; Fri, 29 Apr 1994 14:55:28 -0400 Date: Fri, 29 Apr 1994 14:55:28 -0400 Message-Id: <199404291855.AA12829@wilbur.cac.psu.edu> To: chemistry@ccl.net Subject: printing chem output I am looking for a program to manipulate and print spartan and gaussian output. I also would like to be able to add text and have it work on a pc not a mac ( I am probably asking to much :) ). I have used xmol but it does not meet my needs. Any suggestions????? I can make my files pdb files or probably a couple other formats. I would just like to print with size consistency (this is the main problem with xmol) and label atoms, angles, and bond lengths. **Please send any responses to axh14@wilbur.cac.psu.edu since I dont read the list much** THANKS!!! Arthur Hoag axh14@wilbur.cac.psu.edu ph 814-863-7980 From cmartin@rainbow.uchicago.edu Fri Apr 29 16:21:25 1994 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.4/930601.1506) id PAA12298; Fri, 29 Apr 1994 15:34:04 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Fri, 29 Apr 94 14:34:02 CDT Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA02645; Fri, 29 Apr 94 14:46:20 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9404291946.AA02645@rainbow.uchicago.edu> Subject: The Reality Behind Semiempirical Parameters To: chemistry@ccl.net Date: Fri, 29 Apr 1994 14:46:20 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 5259 More on Semi-empirical methods... I would like to expand on a point made by E. G. Zoebisch in her detailed description of the development of AM1. Specifically, she claims that it is not possible for semiempirical parameters to be ``wrong.'' Lets consider why this may or may not be true, in the context of effective Hamiltonian theory. I hope this sparks some discussion about how to improve the current semiempirical models. First, most semiempirical methods are constructed using the Hartree Fock (HF) Hamiltonian as a base, or, at best, using the valence shell subblock of the full CI Hamiltonians. These valence shell equations, however, do not reproduce experiment to chemical accuracy, and thus semiempirical methods employ empirical data to compensate for the lack of accuracy of the valence shell CI equations. (Additionally, semiempirical methods include data on heats of formation, a property which can not be described by the full CI Hamiltonian. This poses additional theoretical difficulties I will not discuss here) If, however, one does not employ the HF model as the base for semiempirical methods, but rather employs an exact, valence only theory, then it would be possible to make some factual statements about the semiempirical parameters. It is, in fact, possible to derive an exact effective valence shell Hamiltonian (Hv) which (as shown by Freed): (1) can be derived from the full CI equations and, in principle, reproduces the full CI state energies exactly for the valence-like states of a molecule. (2) produces, in practice (via ab initio perturbation theory), very accurate energies for all valence-like states (3) contains parameters which are ab initio analogs of the standard semi-empirical model effective valence-shell Hamiltonians. (4) We may write Hv as a sum of many-electron operators: Hv = Ec + U(1) + V(1,2) + W(1,2,3) + X(1,2,3,4) + ... Where U(1) is an effective 1 electron operator, V(1,2) is an effective 2 electron operator, etc. The additional 3, 4, etc. electron operators take into account correlation effects (orbital polarization, core-valence correlations, etc.) which are neglected in the HF model, but which are in the full CI equations. If we consider Hv as the proper (or at least a better) starting place for understanding semiempirical methods, then we can make some factual statements about semiempirical parameters: (1) For small systems, such as atoms and diatomics, it is possible to evaluate the Hv parameters from experimental data. In other words, some Hv parameters are observables. For example, it is possible to obtain the most of the semiempirical pi-electron parameters directly from experimental data. For larger molecules, linear combinations of Hv parameters are observables. Note that the above arguments do not hold for the Hartree Fock(HF) model. The HF model is not equivalent to the full Schr\"odinger equation--the Hv equations are! (2) Generally for a given molecule, there are more Hv parameters than experimental data points, and thus the Hv equations lead to an overdetermined set of equations. (3) Most semiempirical models are cast in terms of the ZDO approximation, the NDO, etc. In fact, the true Hv contains additional 3- and 4-electron parameters which are either (a) neglected or (b) averaged into the semiempirical 1- and 2-electron terms (4) For pi-electron systems, the 3- and 4-electron parameters are only a few tenths of an eV, whereas for all-valence-electron methods, these non-classical parameters are several eV in magnitude. (5) The HF matrix elements are, of course, transferable between molecules. The true 1- and 2-electron Hv parameters display remarkable transferability for pi-electron systems as well (to within a few tenths of an eV or less) Thus, for pi-electron systems, it is meaningful to ask what are the ab initio values of the pi-electron (or PPP) parameters, if one keeps in mind that (a) you are neglecting the 3- and 4-electron terms (which is not bad for large pi-electron systems), as well as the other (b) you understand the size of the parameters you are neglecting and how they will affect the properties you are attempting to describe. For example, we have only examined spectra so far, which is what PPP methods are generally used for. (c) you consider the whole valence shell CI, and not just single excitations. By reducing the size of the valence shell CI, the true parameters might have to be ``renormalized'' for that subspace as well. A variety of other workers have considered this problem. (d) it is noted that the standard PPP values are in fact somewhat different from the true values (beta is about 0.5 to 1 eV off, gamma is also, etc.) We are currently investigating this. For all-valence-electron models, however, the situation is far more complex than the PPP model might lead on to expect! The standard semiempirical methods (MNDO, INDO, etc.) use parameters which appear to contain the true 3- and 4-electron parameters in an average sense. Since this averaging is somewhat arbitrary, this can help explain why different parameterization are needed for different properties. The theory of all-valence-electron methods is still a wide open and very complex problem. Chuck Martin From cmartin@rainbow.uchicago.edu Fri Apr 29 18:21:16 1994 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.4/930601.1506) id RAA13731; Fri, 29 Apr 1994 17:23:55 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Fri, 29 Apr 94 16:23:46 CDT Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA05874; Fri, 29 Apr 94 16:36:14 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9404292136.AA05874@rainbow.uchicago.edu> Subject: Clarifying The Reality Behind Semiempirical Methods To: chemistry@ccl.net Date: Fri, 29 Apr 1994 16:36:14 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 758 With regard to the last message, When I am spekaing about pi-electron systems, I meant to say (if it was not clear) that some of the PPP parameters for ethylene are observables, while the other observables are simple linear combinations on 2 or 3 PPP parameters. This may not have been clear prevous posting Chuck ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu US Mail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-5863 ================================================================== From burkhart@goodyear.com Fri Apr 29 18:27:00 1994 Received: from goodyear.com for burkhart@goodyear.com by www.ccl.net (8.6.4/930601.1506) id RAA13887; Fri, 29 Apr 1994 17:44:49 -0400 Received: from rdsrv2 by goodyear.com (4.1/SMI-4.1) id AA04201; Fri, 29 Apr 94 17:44:48 EDT Received: from rds325 by rdsrv2 (4.1/SMI-4.1) id AA08134; Fri, 29 Apr 94 17:44:47 EDT Received: by rds325 (940406.SGI/931108.SGI.AUTO.ANONFTP) for chemistry@ccl.net id AA00956; Fri, 29 Apr 94 17:44:46 -0400 Date: Fri, 29 Apr 94 17:44:46 -0400 From: burkhart@goodyear.com (Craig W. Burkhart) Message-Id: <9404292144.AA00956@rds325> To: chemistry@ccl.net Subject: Brideshead (er, SE) Revisited... I have read with interest the comments of Zoebisch and Martin on the different approaches one might take in developing a new method. This is the kind of commentary I had hoped would have occurred earlier. As a user of quantum chemical methods, and not a method developer, I have some questions I would like to pose regarding the Pariser-Pople-Parr (PPP) methods: 1) If my memory is correct, PPP methods use fairly sparse matrices, which, depending on your method of matrix storage, can lead to inefficient use of memory/disk or poor compute performance. Is this in fact true? 2) In an all-valence-electron PPP model, what do you use for a description of the core electrons? 3) Can you obtain reasonable geometries and relative energies for those geometries? 4) Can you obtain torsion functions that correspond to experiment? Thanks for reactivating the discussion... -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D. Senior Research Chemist E-mail: cburkhart@goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.3163 Research Center Fax: 216.796.3304 142 Goodyear Boulevard Akron, OH 44305 -------------------------------------------------------------------------- It is also a good rule not to put too much confidence into experimental results until they have been confirmed by theory - Eddington -------------------------------------------------------------------------- From cmartin@rainbow.uchicago.edu Fri Apr 29 22:21:17 1994 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.4/930601.1506) id WAA15482; Fri, 29 Apr 1994 22:10:58 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Fri, 29 Apr 94 21:10:58 CDT Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA09324; Fri, 29 Apr 94 21:24:05 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9404300224.AA09324@rainbow.uchicago.edu> Subject: Questions about the PPP semiempirical method To: chemistry@ccl.net Date: Fri, 29 Apr 1994 21:24:04 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 3191 I'll try to answer some of Craig Burkhart's questions. I am very interested to hear what other people have to say. Alkso, I am now just starting to reparameterize the PPP model using our Hv theory and I am extremely curious as to what the kinds of features a new PPP would be popular. Onto the questions: >1) If my memory is correct, PPP methods use fairly sparse >matrices, which, depending on your method of matrix >storage, can lead to inefficient use of memory/disk >or poor compute performance. Is this in fact true? The PPP valence shell matrix is very sparse, but there are known methods for generating solutions to sparse eigenvaluu problems. For example, the full CI matrix is also quite sparse, and I would suspect that methods that work for the full CI problem (Davidson's CI method, etc.) would work nicely for PPP. I have a real stupid CI program I wrote that does the job for me, but I would also be interetse in finding out what else is available. >2) In an all-valence-electron PPP model, what do you use >for a description of the core electrons? Do you mean a CNDO method? Isn't that the standard generalization of PPP to the all valence case? It seems to me that a complete description of the core electrons is a tricky method in any semiempirical method. For example, it may be possible to parameterize the HF equations, but I would guess that performing extensive CI that contains core excitations would not work so well. For example, in Zerner's Review in the books "Review's in Computation Chemistry," Vol 2, he states that standard semiempirical methods can employ CI with singles and doubles, but not triples. I think I can come up with a back-of-the-envelope explanation for this, and if someone can find some specific examples, I could try to mimic the problems using Hv calculations. >3) Can you obtain reasonable geometries and relative > energies for those geometries? For PPP? Does anyone use PPP for geometries? I am in the process now of reparameterizing PPP for spectra. I am specifically avoiding geometries because (a) only main group atoms functions appear in the Hamiltonian (b) the spectra can be described well even though I neglect numerous large Hv parameters (0.05 to 0.2 eV) I believe that because there are so many ``large'' Hv parameters I can obtain a nice cancellation of errors. Note that the ``large'' Hv parameters are both of the kind neglected by the ZDO approximation (2-electron, 3-center, etc.), and non-classical (3,4-electron). >4) Can you obtain torsion functions that correspond > to experiment? We hope to begin studying some twisted polyenes, but it is clear that the PPP approximation will break down when as the molecule loses conjugation. Chuck ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu US Mail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-5863 ==================================================================