From tp@elptrs7.rug.ac.be Sat Aug 3 10:15:11 1996 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.7.5/950822.1) id KAA16218; Sat, 3 Aug 1996 10:06:56 -0400 (EDT) Received: by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA19700; Sat, 3 Aug 1996 16:08:30 +0200 Date: Sat, 3 Aug 1996 16:08:30 +0200 (DFT) From: "Park, Tae-Yun" To: Computational Chemistry List Subject: Help!: How to visualize the (+)-charged carbon atom? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, This message is to ask some help how I can visualize/describe the positively-charaged carbon atom in a transition molecule by using molecular/electronic density plot with a suitable graphical software. Please execuse me if this message is concerning too basic or not suitable for people in the field of comutational chemistry, as I'm not a quantum chemist although I need some knowledge in this field for my Ph.D. work. ================================================================== My question is the following: ================================================================== I'm using MOPAC93 for various semiempirical calculations and Molden/Chem 3D Pro to visualize the results obtained from MOPAC93. I'm mainly interested in the description of a molecule contains (+)-charged carbon atom. Please consider the following simple situation. To get the optimized geometry and heat of formation of secondary propyl carbenium ion,C-C(+)-C, I executed the the MOPAC93 with the keywords, "CHARGE=1 AM1 GEO-OK EF PRECISE DENSITY GRAPH". With this running of MOPAC93, I've got several result files, such as "*.arc, *.den, *.gpt, and *.out". The optimized geometry and final heat of formaiton is available in the file "*.out" If I edit the final/optimized geometry using molden/Chem3D Pro, however, all I can see is the 3-dimensional molecule structure of the optimized secondary propyl carbenium ion, and there is no information of the (+)-charged carbon atom in this figure; if someone who doesn't know chemistry well look at this 3D structure, he never knows which carbon atom is (+)-charged. In order to visualize the characteristic of the (+)-charged carbon atom, I believe I have to draw molecular/density plot for the secondary propyl carbenium ion, right?? My problem is starting from here. The molden software is the only thing I have which is able to draw some molecular density. By input one of the result files, "*.gpt" into molden, I can draw various molecular density plots, such as HOMO(Highest Occupied Molecular Orbitals), LUMO(Lowest Unoccupied Molecular Orbitals), Norm. Density, Bond, Orbitals, etc... More exactly there are about 23 different plots availabe in molden. (19 Orbitals + HOMO + LUMO + Norm. Density + Bond). But what are these? Which one is suitable for visualizing the (+)-charged carbon atom and why?? Am I standing in the correct way? Or is there any other methods/softwares to this?? The manual of molden software gave me almost no help, very probably due to my lack of knowledge of quantum chemistry. Is it possible to characterize the (+)-charged carbon atom with mopac output and some graphical software?? Of course, my question written above is not the final goal I want to reach. The reason of the question will be explained below. ================================================================== The reason of my question is the following: ================================================================== Thanks to the great help from the members of CCL, I was able to find out the structure of the transition state in the reaction, H | H H H H-C-H HCH H H H H | H \ / H | | | | HC-C-CH + C=C ----->(TS)----> HC-C--C-C-C-H H + H / \ H | | + | H H H H H secondary propyl propene secondary 2-M carbenium pentyle carbenium ion ion The transition state(TS) was edited by molden/Chem3D Pro and shows that (i) the double bond in the propene still exist, and (ii) the TS is more close to reactants. But I want to know more about this transition state as followins. 1. Does the double bond in the TS has the same strength as in the reactant(propene)? Isn't it partially broken? If so, how can I visulaize/describe this partially broken double bond?? 2. What about the (+)-charged carbon atom in TS? Is it also almost no difference from the (+)-charged carbom atom of the reactant carbenium ion(secondary propyl carbenium ion)?? 3. What about the new bond formed between two reactants in TS? Isn't it partially formed? If so, again, how can I visulaize/describe this partially formed bond?? All these questions are not possibly answered by just editing the TS in 3-dimensional molecular structure. But is it possible to get some answers of these questions by using molecular/electronic density plots? It would be GREATLY APPRECIATED if you could let me know ANY information/advice on my questions written above. I also attached my TS structure in MOPAC fomat at the end of this message Thank you VERY MUCH in advance. Sincerely, Park, TAE-YUN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= State University of Ghent Laboratorium voor Petrochemische Techniek Krijgslaan 281, Blok S5 9000 Gent, Belgium TEL:+(32)-0(9)-264-4527 FAX:+(32)-0(9)-264-4999 e-mail: tp@elptrs7.rug.ac.be =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= ---------------------------------------------------------------- TS structure(refined by NLLSQ): ---------------------------------------------------------------- C .000000 0 .000000 0 .000000 0 0 0 0 C 1.494700 1 .000000 0 .000000 0 1 0 0 C 1.493679 1 122.365784 1 .000000 0 2 1 0 C 2.380560 1 102.504395 1 110.467232 1 2 3 1 C 1.368080 1 107.971291 1 74.388344 1 4 2 3 C 1.495277 1 127.264130 1 -95.821228 1 5 4 2 H 1.108898 1 112.496826 1 169.901352 1 1 2 3 H 1.109529 1 113.296120 1 46.004711 1 1 2 3 H 1.117890 1 107.496994 1 -72.487534 1 1 2 3 H 1.098734 1 86.146576 1 -42.602459 1 2 4 5 H 1.092931 1 119.365471 1 165.091675 1 4 5 6 H 1.092000 1 122.211273 1 9.421019 1 4 5 6 H 1.098602 1 118.611084 1 84.593826 1 5 4 2 H 1.111888 1 109.074448 1 -114.666496 1 6 5 4 H 1.110686 1 110.417656 1 127.198174 1 6 5 4 H 1.107639 1 113.346970 1 5.549870 1 6 5 4 H 1.108230 1 112.441048 1 -172.787689 1 3 2 1 H 1.117836 1 107.759140 1 69.464531 1 3 2 1 H 1.109580 1 113.282127 1 -48.948452 1 3 2 1 ----------------------------------------------------------------