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Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases
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dataset
posted on 2016-10-12, 18:33 authored by Pedro SilvaPedro SilvaFirefly inputs and outputs for the paper "Refining the reaction mechanism of O2
towards its substrate in cofactor-free dioxygenases", to be submitted to PeerJ on or around 16 Jun 2016.
Four files are NOT inputs/outputs of quantum chemical computations:
- docking.tar, which contains the results of AutoDock VINA docking computations, as performed by YASARA. The files with .sce or .yob extensions may be viewed with YASARA.
-HODMe_grid.txt and HODnBu_grid.txt, which contain the data used to generate the 2D potential energy surfaces depicted in Figure 4.In these files, 1st column is C3-C4 distance (in angstrom); 2nd column is O-O distance (alson in angstrom; 3rd column is relative energy (in kcal/mol).
-BSSE.xls contains the energies for the evaluation of the effect of BSSE on the differences between the energies of radical-pairs at 80 angstrom distance and the values obtained by summing the energies of separate substrates. The gas-phase data clearly show that no BSSE error exists. The difference in solution energies is likewise independent of the SCF energy, and comes about simply due to the way the PCM model treats a system with two separated cavities: the final column ("total interaction") shows that in the radical pair the difference of solvation energy (vs. independent substrates) is almost exactly equal to the difference of total energy. I am still trying to understand why such difference is only apparent in the radical pair system, and not in the HODMe:O2 system.
Four files are NOT inputs/outputs of quantum chemical computations:
- docking.tar, which contains the results of AutoDock VINA docking computations, as performed by YASARA. The files with .sce or .yob extensions may be viewed with YASARA.
-HODMe_grid.txt and HODnBu_grid.txt, which contain the data used to generate the 2D potential energy surfaces depicted in Figure 4.In these files, 1st column is C3-C4 distance (in angstrom); 2nd column is O-O distance (alson in angstrom; 3rd column is relative energy (in kcal/mol).
-BSSE.xls contains the energies for the evaluation of the effect of BSSE on the differences between the energies of radical-pairs at 80 angstrom distance and the values obtained by summing the energies of separate substrates. The gas-phase data clearly show that no BSSE error exists. The difference in solution energies is likewise independent of the SCF energy, and comes about simply due to the way the PCM model treats a system with two separated cavities: the final column ("total interaction") shows that in the radical pair the difference of solvation energy (vs. independent substrates) is almost exactly equal to the difference of total energy. I am still trying to understand why such difference is only apparent in the radical pair system, and not in the HODMe:O2 system.
