From owner-chemistry@ccl.net Wed Jun 7 02:19:00 2006 From: "Fuji Yama yamafuji6],[yahoo.com" To: CCL Subject: CCL:G: Photoinduced electron transfer (PET) and gaussian03 Message-Id: <-31910-060607021540-6081-LDiCxc5tLExStP5g7nfXCQ a server.ccl.net> X-Original-From: "Fuji Yama" Date: Wed, 7 Jun 2006 02:15:36 -0400 Sent to CCL by: "Fuji Yama" [yamafuji6- -yahoo.com] Dear members, 1) Is it possible to study the Excited state electron transfer (Photoinduced electron transfer-PET) from a nucleobase to an intercalator, using gaussian03? 2) I did a simple TD-DFT calculation (using g03) with an intercalator alone and the same intercalator flanking with two nucleobases (same as the system described by J.M.Jean and K.B.Hall in Biochemistry 2002, 41, 13152-13161). With the flanking bases, I have observed an additional excitation peak (with reasonable oscillator strength of 0.0206) in the higher wavelength region which corresponds to the experimentally observed Eo-o of the intercalator. The excitation is basically form HOMO to LUMO, and HOMO is mainly populated on the nucleobases, LUMO is mainly populated on the intercalator. So is this excitation peak corresponds to the PET from nucleobase to the intercalator? 3) Can you please suggest me some useful references and readings? Thank you very much. From owner-chemistry@ccl.net Wed Jun 7 08:56:01 2006 From: "Telkuni telkuni+/-venus.dti.ne.jp" To: CCL Subject: CCL: Software for ArgusLab4.0 Message-Id: <-31911-060607080013-16227-g+bOJAsHUFZje39bJoPcpg##server.ccl.net> X-Original-From: "Telkuni" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="Windows-1252" Date: Wed, 7 Jun 2006 20:13:15 +0900 MIME-Version: 1.0 Sent to CCL by: "Telkuni" [telkuni(0)venus.dti.ne.jp] Hello, CCLers. I've developed a software for ArgusLab outputs(ver_4.0 or less). Its name is "OutputEditor for ArgusLab4.0 -P01". It takes Flash-Movie GUI style. The software which is coded by Flash ActionScript gives extracted and reconstructed output data for Windows csv style. One can apply this style outputs to Windows Excel, so he can analyze these outputs as table format. You can download this software as Windows ".exe" file style from http://www.venus.dti.ne.jp/~telkuni/mol-tech The size of this software is 1,015KB. Zip file which includes instruction and sample-outputs have been uploaded at same site. And you can get other FlashMovies. ** Proposal of this software has already been notified Mark Thompson. Supplement for the instruction(PDF): You must place text-format outputs on same directory of this software. Caution: I tried the operation under the Windows environment only. Sincerely yours, ---------------------------------------------------- Telkuni Tsuru mol-tech.1[a]wind.dti2.ne.jp Bunshi Gijyutu (Vice E-mail: telkuni[a]venus.dti.ne.jp ) From owner-chemistry@ccl.net Wed Jun 7 23:20:01 2006 From: "Gustavo A Mercier gamercier[a]yahoo.com" To: CCL Subject: CCL: B Matrix in GAMESS-US - Bug? Message-Id: <-31912-060607231521-31673-qJrEoFBxocpog82paPG/BQ=-=server.ccl.net> X-Original-From: "Gustavo A Mercier" Date: Wed, 7 Jun 2006 23:15:19 -0400 Sent to CCL by: "Gustavo A Mercier" [gamercier(-)yahoo.com] Hi! I might have found a bug in GAMESS-US... but before I make any claims I would like a second opinion. I am encoding the B matrix the converts infinitesimal cartesian displacements to internal coordinate displacements. This matrix is used in the theory of molecular vibrations and the generation of delocalized coordinates, etc. To check my code I've compared the output from GAMESS-US subroutines in zmatrx.src. However, there are differences in the B matrices I compute and the one computed with the GAMESS-US code.These are associated with the torsion angle terms. After looking at the code in GAMESS-US and the formulae in Molecular Vibrations by Wilson, Decius, and Cross, pub. Dover 1980, I find the following discrepancy: In computing the matrix elements for the torsion angles 1,2,3,4, ie. the angle between the planes 123 and 234 with the atoms 1 and 4 at the ends, and 2 and 3 along the line of sight with 2 closest to the viewer 1 1 \ bend | \ angle 1 | \ | torsion angle 2 -------- 3 23 \ \ bend angle 2 \ \ \ 4 4 i = 1, j = 2, k = 3, l = 4 > From Wilson's book: Cos(angle_1) = Dot(2--1>,2-->3) where i-->j is a unit vector from i to j Cos(angle_2) = Dot(3-->2,3-->4) and Dot is the cartesian dot product However in GAMESS-US the code (subroutine BTORS in zmatrx.src) computes Cos(angle_1) = Dot(1-->2,2-->3) Cos(angle_2) = Dot(2-->3,3-->4) There is a reversal in the orientation of the first unit vector associated with the first bond that makes the angle. The end result is that there is a sign reversal in the Cos terms between the two programs. I don't see this "corrected" in the remainder of the code. Anyone who can shed any light on this discrepancy, beyond stating that there is a bug in the GAMESS-US code or a typographical error in the 1980 edition of Wilson's book? (I am familiar with Wilson's definition, so I favor an error in GAMESS-US. However, before I make any claims I would appreciate a second opinion!) Neither one of the codes generates B matrices that reproduce the delocalized coordinates for the fluoroethylene example in Baker's et al J. Chem. Phys. 105(1) 192-212 (1996). Thanks! Gustavo Mercier