6
$\begingroup$

I wish to investigate the antioxidant properties of several hydrocarbon compounds, which are each mono- or polyhydroxylated, specifically at the phenyl ring. I wish to gain insight into my workflow for deciding which conformers to utilize in these calculations. At the moment, I am most concerned that I am developing the correct algorithm for narrowing down the compounds to be calculated in a fairly-accurate manner. Once I have these compounds, I may then decide how to approach the radical forms (i.e., compound-OH vs. radical form, or compound-O*).

The main subject of this question is choosing which conformers to keep- and thus compute at higher levels of theory- by the use of Boltzmann weights. I am getting these weights from Spartan, automatically, calculated by what I assume is: $$\frac{N_i}{N_j}=e^{-(\epsilon_i-\epsilon_j)/kT}$$ This formula is what I intend to use for calculating the weights after GAMESS and Gaussian calculations, as I have only reached the last set of Spartan calculations, albeit for only some molecules. Without any further explanation, here is my intended workflow (I will add any edits to the bottom of this original post- thank you for your help):

  1. Spartan

    • a. Conformer Distribution
      • i. MMFF level of theory
      • ii. (Monte Carlo algorithm applied)
      • iii. Max conformers examined=10,000
      • iv. Keep 100% of conformers
    • b. Energy- Semi-empirical
      • i. PM3 Level of theory
      • ii. Calculated at both gas and water (PCM)
    • c. Energy- Hartree-Fock
      • i. 3-21+G* level of theory
      • ii. Calculated for both gas and water (PCM)
          1. Only calculated for conformers showing SE PM3 Boltzmann weight of ≥.001
    • d. Energy- Density Functional
      • i. ωB97X-V/3-21++G** level of theory
      • ii. Calculated for both gas and water (PCM)
          1. Only calculated for conformers showing HF 3-21+G*Boltzmann weight of ≥.01
  2. GAMESS

    • a. Equilibrium Geometry- Density Functional
      • i. Only calculated for conformers showing ωB97X-V/3-21++G** Boltzmann weight of ≥.05
      • ii. Three separate methods for both gas and water (PCM)
          1. B3LYP/6-31+G* level
          1. ωB97X-D/6-31+G* level
          1. PBE0 (PBE1PBE)/6-31+G* level
    • b. Equilibrium Geometry- Density Functional
      • i. Only calculated for conformers showing (B3LYP, ωB97X-D, & PBE0)/6-31+G* Boltzmann weight of ≥.05
      • ii. Three separate methods for both gas and water (PCM)
          1. B3LYP/6-311++G** level
          1. ωB97X-D/6-311++G** level
          1. PBE0/6-311++G** level
  3. Gaussian

    • a. Equilibrium Geometry- Density Functional
      • i. Only calculated for conformers showing (B3LYP, ωB97X-D, & PBE0)/6-311++G** Boltzmann weight of ≥.10
      • ii. One method used in Gaussian, for both gas and water (IEF-PCM), for the corresponding results from the previous GAMESS calculations, or six separate files (i.e, B3LYP H2O and gas, ωB97X-D water and gas, & PBE0 water and gas). To each of these 6 files, a radical form was generated (i.e. RO*), thus 12 separate files are created- 6(ROH) and 6(RO*).
          1. Zero point energy M06-2X/6-311++G(3df,3dp) level
            • a. Used to calculate energies of corresponding compounds and their radical counterparts (compound-OH and compound-O*)

edit(19.Sept'16): typos

$\endgroup$
3
  • $\begingroup$ It would be very useful if you tell us exactly what will you do with them. $\endgroup$ – user1420303 Sep 20 '16 at 2:46
  • $\begingroup$ Sorry, maybe I'm not understanding you correctly? This is exactly what I will do with the molecules, in trying to understand some of the correlations between bond dissociation energies in homolytic cleavage of the hydroxyl groups. These are mainly biological compounds which will likely never see the light of day, but to understand their properties further is of large interest to my academic pursuits. $\endgroup$ – Jacob Nowatzke Sep 20 '16 at 3:13
  • 1
    $\begingroup$ In such case, I would only retain one conformer. Differences in bond energies among the conformers will be small enough compeared with the accuracy of DFT. $\endgroup$ – user1420303 Sep 20 '16 at 3:22

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.