Abstract:

    Jaguar was used to perform computational activities on the porphyrin ring system.  This molecule is one of the most prevalent bioinorganic molecules.  Jaguar performed very well in the presence of a transition metal.  A Becke 3:P86 density functional theory with a LAV1S* basis set was used for the calculation.  Jaguar performed very well with an effective core potential and a symmetry limitation.  An oxygen molecule was added to the iron atom to examine the physical properties of the ring with the bound oxygen.  The molecular orbitals, density, and electrostatic potential were all calculated, plotted  and viewed in gOpenMol.

Introduction:

    The porphyrin ring system has long been an interest to bioinorganic chemists because of the iron center.  This is the functional aspect of the heme group.  This interesting system is found in many different proteins in the body.  This iron center contributes the electron chain tranport by the oxidation and reduction of the iron center.  When the the iron is in the +2 oxidation state,it is firmly bound the ring system.  When the iron is in the +3 oxidation state, it is out of the ring as a free ion that is capable of being reduced and bound back into the ring system.  This project was to study the properties of the ring system and later add bound molecules (carbon monoxide, oxygen, and cyanide) to study the physical properties of the system with the different molecules bound.  The project initially started out on Gaussian, according to an article obtained from the Journal of Computational Chemistry, to perform an ONIOM multi-layer calculation (5).  The project eventually moved to another computational program, Jaguar.  The whole ring system was geometry optimized using a LAV1S* basis set.  The density functional method was recommended by an article obtained from Chemical Reviews (7).  The density and the electostatic potential was calculated and plotted.  The molecular orbitals were calculated and displayed using gOpenMol.

Method:

HyperChem (3)

All of the necessary molecules were built in HyperChem and converted to to readable files for Gaussian and Jaguar.

Gaussian (1)

A multi-layer ONIOM calculation was used with a molecular mechanics calculations on the ring system and a STO-3G basis set on the Fe-N bonds.  This was attempted many times, but the process similar parameters that were successful in Jaguar (LANL2DZ basis set), and it still failed in Gaussian.  Gaussian seemed to fail ever time a transition metal was introduced.  This problem was alleviated when Jaguar was introduced.

Jaguar (4)

This program was introduced into the chemstry department in October 2000.  The first transition metal that was calculated using Jaguar was a hexacyanoferrate(II) ion.  It ran very smoothly and the structure was even optimized.  The biggest test of all was to run the porphyrin ring.  The problem with Jaguar was that it did not calculate different layers, it calculated the whole molecule using whatever basis set chosen.  I chose Becke3:P86, this is Perdew's density funtional that has a gradient correction along with Becke's three parameters (exact Hartree-Fock wavefunction, Slater local exchange functional, and Becke's 1988 non-local gradient correction).  I was interested in the gradient correction for the faster convergence.  The system was optimized using a LAV1S* because of the effective core potential.  The effective core potential was chosen because of the number of electrons.  This particular method would only optimize the valence electrons of the iron and a total analytic optimization on the rest of the structure with a STO-3G basis set.  100 iterations were chosen for the optimization with an initial guess using ligand field theory.  A GVB-DIIS convergence was recommended for faster convergence so that was also using in the calculation (6).  The energy convergence was loosened to 1E-03.  An oxygen molecule was added to the porphyrin ring system to study inspect the different physical properties that occurred.  It is suspected that the iron atom comes out of the plane when it is not bount, but it is planar when it is bound to the oxygen.  I was not able to answer that question because in order to calculate the original porphyrin ring, I had to restrict the symmetry.  This ran and eventually converged to an optimized structure.  Using the *.in files that were generated after each run, the potential and the density and the molecular orbitals were calculated.

gOpenMol (2)

gOpenMol is able use the out file generated from Jaguar to create visual plots of the electrostatic potential, the density, and the molecular orbitals.  The coordinates were imported from Jaguar and converted to readable coordinates for gOpenMol.  The *.plt files were made into readable gom files.  These were plotted on a contour map with red for the positive wavefunction and blue for the negative wavefunction.

Results and Conclusions:

Molecular Orbitals of the Porphyrin Ring

Figure 1:  81                                                                             Figure 2:  82 Figure 3: 83                                                                             Figure 4:  84(HOMO) Figure 5:  85 (LUMO)                                                             Figure 6:  86 Figure 7:  Density plot                                                              Figure 8:  Electrostatic potential

Molecular Orbitals of the Porphyrin Ring Bound to an Oxygen Molecule
 
 

Figure 9:  89                                                                            Figure 10: 90 Figure 11: 91                                                                           Figure 12: 92 (HOMO) Figure 13:  93 (LUMO)                                                           Figure 14:  94

In conclusion, I found that the Jaguar program handled transition metal complexes very well.  It is a useful program for rigorous calculations such as the porphyrin ring.  In Gaussian, I found that it did not handle transition metal complexes very well and I was never able to optimize the structure without the link dying.  Future research would involve the attachment of the carbon monoxide and the cyanide.  This would be interesting to compare the physical properties of the porphyrin and how it changes with the addition of certain molecules.  The tightest bound molecule should be the cyanide group because of the maximum amount of p electrons to donate.

(1) Gaussian 98W.  Gaussian, Inc.  1998.  http://www.gaussian.com

(2) gOpenMol. Leif Laakonson <CSC> 2000.

(3) HyperChem 6.0 Pro for Windows. 2000. Hypercube, Gainesville, FL.

(4) Jaguar 4.0.  Schrodinger, Inc.  1998.  http://www.schrodinger.com.

(5) Marechal et al.  Journal of Computational Chemistry. vol. 21, no. 4, 282-294 (2000)

(6) Siegbahn, Per E. and Margareta R. A. Blomberg.  Annual Reviews of Physical Chemsitry.  1999.

(7) Siegbahn, Per E. and Margareta R. A. Blomberg.  Chemical Reviews.  vol. 100, 421-437.  2000.