From chemistry-request@ccl.net Tue Jan 7 20:26:02 1992 Date: Wed, 08 Jan 92 08:32:11 SST From: Ms Chin W S Subject: Imaginary frequency from AMPAC To: Computational Chemistry List Status: R Hi, friends, I am using some procedures in AMPAC 2 to do transition state calculations. It has always been said that a TRUE transition state should be characterised by (1) one and only one negative force constant and (2) one and only one imaginary frequency. I have a few problems here : (1) What is actually an imaginary frequency ? ( Any reference recommended ?) How do we check this ? Does it mean a negative vibrational frequency given in the AMPAC output using FORCE procedure ? (2) If I obtain two negative force constants, one of them is very small, about -0.01 to -0.02, is this acceptable for a true transition state ? I am thinking of doing the same calculations using ab initio method, any commend will be most gratefully appreciated. Thanking in advance, Chin W S From chemistry-request@ccl.net Tue Jan 7 22:04:09 1992 Date: Wed, 8 Jan 92 13:45:11 EST From: Dr. G. Paul Savage Subject: IUPAC naming program? To: CHEMISTRY@ccl.net Status: R Does anyone know of a program that takes graphic structures and generates the correct IUPAC name? I recall having heard of one being developed but I don't know if was ever finished or released. This would be particularly useful for complex organic molecules. Paul Savage scientia est potentia ============================================================================= From jpj@lotus.medicine.rochester.edu Wed Jan 8 09:18:47 1992 Date: Wed, 8 Jan 92 14:18:37 GMT From: jpj@lotus.medicine.rochester.edu (Jeffrey P. Jones) To: chem@ccl.net Subject: Imaginary Freq. Status: R >Hi, friends, >I am using some procedures in AMPAC 2 to do transition state calculations. >It has always been said that a TRUE transition state should be >characterised by (1) one and only one negative force constant and (2) one >and only one imaginary frequency. I have a few problems here : >(1) What is actually an imaginary frequency ? ( Any reference recommended ?) > How do we check this ? Does it mean a negative vibrational frequency > given in the AMPAC output using FORCE procedure ? >(2) If I obtain two negative force constants, one of them is very small, > about -0.01 to -0.02, is this acceptable for a true transition state ? >I am thinking of doing the same calculations using ab initio method, any >commend will be most gratefully appreciated. >Thanking in advance, >Chin W S An imaginary frequency is the vibrational frequency for decomposition of the transition state to reactants or products. This is characteristic of a saddle point. You should only have one negative vibrational frequency if you are at a transition state. If you get a second small negative frequency you probably have a problem with rotation around the bond that is involved in the reaction. (This assumes you are looking at an intermolecular bond breaking reaction.) Inspection of the geometry will usually indicate what should be rotated. See "Reaction Rates of Isotopic Molecules" , Melander and Saunders For a comparison of different computational methods in transition state calculations see, J. Comp. Chem. 1991, 12, 1134 (It never hurts to advertise.) In the second reference, rotation from a D2d to a D2h geometry in the transition state gives a small negative vibrational frequency of about 30 cm-1 using AM1. ############################################################################## Jeffrey P. Jones U. of Rochester Department of Pharmacology 601 Elmwood Ave. Rochester, NY 14642 internet jpj@lotus.medicine.rochester.edu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From chemistry-request@ccl.net Wed Jan 8 09:44:24 1992 Date: Wed, 8 Jan 1992 07:27 CST From: Andy Holder Subject: TRANSITION STATE LOCATION To: CHEMISTRY@ccl.net Status: R On the subject of transition states, ONE negative frequency indicates a transition state. (Since the frequencies are computed directly from the force constants, it is not neccessary to check them as well.) If you have more than one, a true transition state has not been reached. If there are two, you are on a "ridgeline". You must analyze the motion of the smaller value and "goose" the geometry along this motion and re-optimize. (Yes, I know, incredibly ted- ious.) Very small negative frequencies usually correspond to things like methyl rotations. I don't know the exact structure you are working with, but that is likely. If you have more than two negative frequencies, this can be a problem. People doing reactions spend the majority of their time stomping out spurious negative frequencies. As if that wasn't enough, you must make sure that your TS corresponds to the one for the reaction you are examining. To do this, examine the motions associated with the ONE negative frequency and again "goose" the geometry along these coordinates. If you end up with product, that's good. You can also goose it backwards and hopefully end up with reactant. I have mentioned twice "analyze the motion". You can do this is several ways. After doing a FORCE calculation, the cartesian components of motion for each atom are printed under the force constant listing. Making sure that the molecule is oriented the way the force calculation has indicated (its in there) just look at what the atoms with large components actually do for a partic- ular vibration. The second method (the one I use) is to perform an LTRD calculation. This will give you the components of nega- tive frequencies in internal coordinates. This is usually much easier to interpret. Again figure out which components are large and count optimizable geometric parameters to match them up. Hope this abbreviated version helps. Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 502 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-1717 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Wed Jan 8 12:45:52 1992 Date: Wed, 08 Jan 92 17:18 CET To: chemistry@ccl.net From: "J.O." Subject: LCAO and LMTO codes needed Status: R Hi there, I am looking for: 1 - LCAO code (general enough to be useful in solid state calculations) 2 - LMTO code (e.g. from H.L.Skriver's "The LMTO Method") 3 - any interest group for electronic structure calculations of solids 4 - any band structure code (e.g. from Papaconstantopoulos' "Band Structure of Elemental Solids"). I want to excuse for interference loosely related to computational chemistry but my 3-month explorations were vain, so this is last chance. Thanks in advance for any help and information. Janusz Oleniacz, JANOLEN@PLWATU21.BITNET Warsaw, POLAND From chemistry-request@ccl.net Wed Jan 8 13:13:10 1992 Date: Wed, 08 Jan 1992 09:59:33 PST From: "W. Todd Wipke" To: chemistry@ccl.net Subject: IUPAC naming program Status: R >>X-MX-Warning: Warning -- Invalid "From" header. >>From: Dr. G. Paul Savage >>To: CHEMISTRY@ccl.net >> >>Does anyone know of a program that takes graphic structures and generates the >>correct IUPAC name? I recall having heard of one being developed but I don't >>know if was ever finished or released. This would be particularly useful for >>complex organic molecules. >> >>Paul Savage scientia est potentia >>============================================================================= Beilstein has a name generating program, and one has been developed at Toyohashi University, a contact there is Prof. S. Sasaki. From results I have seen, the names produced are reasonable, but may not follow every preference rule, so the ordering of substituents, or choice of base skeleton may differ. -Todd Wipke Molecular Engineering Laboratory University of California Santa Cruz, CA 95064 wipke@chemistry.ucsc.edu From chemistry-request@ccl.net Wed Jan 8 13:15:58 1992 Date: Wed, 8 Jan 92 17:47:49 GMT From: jpj@lotus.medicine.rochester.edu (Jeffrey P. Jones) To: chemistry@ccl.net Subject: Imaginary Freq. Status: R >Hi, friends, >I am using some procedures in AMPAC 2 to do transition state calculations. >It has always been said that a TRUE transition state should be >characterised by (1) one and only one negative force constant and (2) one >and only one imaginary frequency. I have a few problems here : >(1) What is actually an imaginary frequency ? ( Any reference recommended ?) > How do we check this ? Does it mean a negative vibrational frequency > given in the AMPAC output using FORCE procedure ? >(2) If I obtain two negative force constants, one of them is very small, > about -0.01 to -0.02, is this acceptable for a true transition state ? >I am thinking of doing the same calculations using ab initio method, any >commend will be most gratefully appreciated. >Thanking in advance, >Chin W S An imaginary frequency is the vibrational frequency for decomposition of the transition state to reactants or products. This is characteristic of a saddle point. You should only have one negative vibrational frequency if you are at a transition state. If you get a second small negative frequency you probably have a problem with rotation around the bond that is involved in the reaction. (This assumes you are looking at an intermolecular bond breaking reaction.) Inspection of the geometry and common sense will usually indicate what should be rotated. See "Reaction Rates of Isotopic Molecules" , Melander and Saunders For a comparison of different computational methods in transition state calculations see, J. Comp. Chem. 1991, 12, 1134 (It never hurts to advertise.) In the second reference, rotation from a D2d to a D2h geometry in the transition state gives a small negative vibrational frequency of about 30 cm-1 using AM1. ############################################################################## Jeffrey P. Jones U. of Rochester Department of Pharmacology 601 Elmwood Ave. Rochester, NY 14642 internet jpj@lotus.medicine.rochester.edu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From chemistry-request@ccl.net Wed Jan 8 14:39:37 1992 Date: Wed, 8 Jan 92 14:30:13 -0500 From: Florian Von Trentini To: chemistry@ccl.net Subject: EH program with addtl. features Status: R Hi: I am currently looking for an extended Huckel program which has (at least some of) the following features: - Allows for transition metals - Models repulsive interactions between the cores - Optimizes geometries - Calculates vibrational frequencies - Handles, optionally, periodic boundary conditions in two dimensions. Any suggestions are wellcome. Thanks, Florian vonTrentini Address: engelhrd@flyer.ncsc.org From chemistry-request@ccl.net Wed Jan 8 15:27:25 1992 Date: Wed, 8 Jan 1992 14:06 CDT From: Dianna Laakso Subject: G90 Normal Mode Analysis To: chemistry@ccl.net Status: R I am looking for a program to run on a PC that will display the normal mode analysis from a Gaussian90 output (ie, the displacements in cartesian coordinates from the equilibrium geometry corresponding to each normal mode) as a graphic, to aid in identifying the modes. Any suggestions will be greatly appreciated. -- Dianna Laakso Research Assistant drl@vaxb.acs.unt.edu Department of Chemistry drl@sol.acs.unt.edu University of North Texas