The program offers transition state optimization but in the case of e.g. (By the way here is my first question: at the semiempirical level the program offers the heat of formation in kcal/mol, while at ab initio level energy in Hartree.I do not know, whether the latter is electronic energy only or total energy, but even using the proportionality factor between kcal/mol and Hartree too large difference is observed).
The calculation of the reaction heat is relatively straightforward: I calculate the optimized energy of the methyl radical ethyene and subtract the sum of these two energies from the energy of the propyl radical obtained. Let us assume a very simple reaction: methyl radical + ethylene and try to determine the activation energy. I am looking for the advice of ChemBio 3D Ultra users.
Analize stoichiometry chemdraw ultra 12 how to#
Please help me how to get the desired atom numbering. Attached herewith is the 2D structure of one of the compounds with atom numbering obtained from research papers. In short visualization tools label the carbon atoms differently from what I found in literature.
For example my focus is carbon atom 11 but it is labelled as say C-16 in 3D structure. I know which atom number I want to focus on but it is difficult for me to manually search that atom number for multiple compounds. I editted thoes atom serial numbers in chemDraw and ChemBio3D Ultra and saved it in pdb format but when I viewed this pdb file in pymol, it displayed different atom numbers. So I manually drew the structures using ChemDraw but it also assigns different atom numbers to carbon. I downloaded those compounds from pubchem but the carbon atom numbering is different from what I found from literature and previous research (when viewed from different visualization tools). Hello everyone I have to analyze interactions of some compounds with particular focus on some specific atoms.
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