From moret@far.ruu.nl Sat May 15 06:47:43 1993 Message-Id: <199305151006.AA22679@accucx.cc.ruu.nl> From: Ed Moret Subject: semi.QM energy of electron/proton?? To: chemistry@ruucmc.far.ruu.nl Date: Sat, 15 May 93 12:04:27 METDST Dear Netters, We need some help with interpretation of the results of a study on the energies of species of 2,5-bis-aziridinyl-1,4-benzoquinone. This highly cytostatic compound is depicted below. Its reactiveness permits reduction with 1 or 2 electrons, protonation with 1 or 2 protons on both the oxygens and the nitrogens. This renders 27 different species, not counting the two options of protonating 1 oxygen and 1 nitrogen differently. Optimising all species with Mopac 6.0/Ampac 1 (the radical species were AM1 optimised with UHF and DOUBLET keywords, followed by a 1SCF RHF calculation for comparison with the non-radical species), we obtained the total energies. In order to comment on the likeliness of some step, we have to account for the fact that we had an electron or a proton as extra reagent in the reaction: A + e- --> B or A + H+ --> B. The question is: what is the energy of this electron or proton? Given the definition of Total Energy used in Mopac, they would be 0? What it amounts to is this: if giving a proton to the compound below decreases total energy with 6 eV and giving an electron to the compound decreases total energy with 3 eV, may we conclude that protonation is most likely to occur first in vacuo? We are aware of the important effects of the surroundings (in fact several enzymes do the reduction in vitro) but would hate to admit that no conclusions at all can be made after such a quantum chemical investigation. O || C C /\ / \ C--N--C C || || C C--N--C \ / \/ C C || O Besides welcoming wise lessons on the energy of electrons/protons in quantum theory, we would like some answer to the explicit question of the comparison of difference in total energies upon protonation or reduction as stated above. Responses will be summarised to this list, if the responder does not object. Thanks and regards Ed Moret (moret@far.ruu.nl) ------------------------------------------------------------------------- E.E. Moret (@more@) moret@far.ruu.nl Computational Medicinal Chemistry/Department of Pharmaceutical Chemistry Faculty of Pharmacy/Utrecht University/the Netherlands Telephone (31-30)536979/536958 Facsimile (31-30)516674 ------------------------------------------------------------------------- From milan@helix.nih.gov Sat May 15 09:55:11 1993 Date: Sat, 15 May 93 13:55:11 -0400 From: milan@helix.nih.gov (Milan Hodoscek) Message-Id: <9305151755.AA19403@helix.nih.gov> To: Ed Moret Subject: semi.QM energy of electron/proton?? > Optimising all species with Mopac 6.0/Ampac 1 (the radical species were AM1 > optimised with UHF and DOUBLET keywords, followed by a 1SCF RHF calculation > for comparison with the non-radical species), we obtained the total energies. > In order to comment on the likeliness of some step, we have to account > for the fact that we had an electron or a proton as extra reagent in the > reaction: A + e- --> B or A + H+ --> B. > > The question is: what is the energy of this electron or proton? > Given the definition of Total Energy used in Mopac, they would be 0? It can't be zero! You should write reactions like A +e- -> B- = A- ; A + H+ -> B+ = A+. Or A(something for radical). So the MOPAC energy for proton affinity can be calculated by: Etot(A)-Etot(A+) and for electron affinity Etot(A) - Etot(A-) That means you have to use CHARGE keyword in mopac6.0 input. Milan Hodoscek From raman@bioc01.uthscsa.edu Sat May 15 10:28:34 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9305152028.AA13816@bioc01.uthscsa.edu> Subject: Xpdb To: chemistry@ccl.net Date: Sat, 15 May 1993 15:28:34 -0500 (CDT) Dear Netters This is a follow-up on the thread that I initiated regarding a program called Xpdb, which resembled Xmol. I have had numerous discussions with the author and from what I can gather, he would rather have all the enquiries mailed directly to him. Although, MSC has now informed us of the availability of Xmol, free of a time-bomb, it would be nice to have a n alternative in case of policy changes! So, here is the email address for the author of Xpdb and all those who are interested in this program should contact him for the same: Mr. Vinod T. Nair Centre for High Performance Computing University of Texas Austin, TX email: vtn@almach.chpc.utexas.edu I aplogise for the delay in supplying this information. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ******************************************************************************