Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results

Abstract

The semiempirical PM5 method has been used to calculate fully optimized structures of magnesium-bacteriochlorin, magnesium-chlorin, magnesium-porphin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), and d, and bacteriochlorophylls a, b, c, d, e, f, g, and h with all homologous structures. Hartree-Fock/6-31G* ab initio and density functional B3LYP/6-31G* methods were used to optimize structures of methyl chlorophyllide a, chlorophyll c(1), and methyl bacteriochlorophyllides a and c for comparison. Spectroscopic transition energies of the chromophores and their 1:1 or 1:2 solvent complexes were calculated with the Zindo/S CIS method. The self-consistent reaction field model was used to estimate solvent shifts. The PM5 calculations predict planar structure of the porphyrin ring and central position of the four coordinated magnesium atoms in all pigments studied, in accord with the experimental, ab initio, and density functional results, a significant improvement as compared to the older semiempirical PM3 approach. Only small differences in PM5 and B3LYP/6-31G* or Hartree-Fock/6-31G* minimum energy geometries of the reference molecules were observed. Calculations show that in 1:1 solvent complexes, where the magnesium atom is five coordinated, the magnesium atom is shifted out of the plane of the porphyrin ring towards the solvent molecule, while the hexa coordinated 1:2 complexes are again planar. The PM5 method gives atomic charges that are comparable with those obtained from the Hartree-Fock/6-31G* and B3LYP/6-31G* calculations. The single point ZINDO/S CIS calculations with PM5 minimum energy structure gave excellent correlations between calculated and experimental transition energies of the chlorophylls and bacteriochlorophylls studied. Such correlations may be used for prediction of transition energies of the chromophores in protein binding sites. Calculations also predict existence of dark electronic states below the main Soret absorption band in all chromophores studied. The results suggest that the semiempirical PM5 method is a fairly reliable and computationally efficient method in predicting molecular parameters of porphyrin-like molecules.

Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes

“…Compared to the former, the latter method overestimates by a factor of 2-3 both the excitation energies and the broadening of the energy spectrum. Just like in several previous studies, 19,20,45,46 we have found that the ZINDO/S method repeatedly yields results in good agreement with existing experimental data.…”

“…43,44 Because it is much faster and more accurate than most of the computationally affordable ab initio QC methods ͓e.g., the Hartree-Fock ͑HF͒ CIS method with the minimal STO-3G * basis set͔, ZINDO/S CIS has been extensively used in the literature to compute low lying optically allowed excited states of pigment molecules. 19,20,45,46 In cases like ours, where thousands of QC calculations are required, the proper balancing between speed and accuracy is absolutely essential. To further increase the computational speed, the active orbital space for the CIS calculations was restricted to the ten highest occupied molecular orbitals ͑HOMOs͒ and the ten lowest unoccupied molecular orbitals ͑LUMOs͒.…”

Conformational control of cofactors in nature – the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

“…57 In general, exceptionally good performance of the PM5//ZINDO/S scheme (i.e., PM5 geometry optimization followed by a ZINDO/S single-point energy calculation) is found for the Mg complexes of unsubstituted porphyrin, chlorin and bacteriochlorin as well as Chls and BChls. 56 The PM5 optimized structures of unligated and 6-coordinate complexes predicts a planar porphyrin with the Mg in the 4N-plane, whilst 5-coordinate species show a substantial out-of-plane displacement of the Mg atom, in line with both B3LYP and HF/6-31g*. Additionally, all methods correctly predict that the Mg-N bond(s) to the reduced rings are longer than those from non-reduced rings.…”

“…Partial atomic charges were also found to be consistent amongst the semiempirical, HF and DFT methods. 56 Overall, the best transition energies were obtained using the B3LYP/6-31g*//ZINDO/S scheme. However, PM5//ZINDO/S was also considered to perform well and was recommended for use in large calculations where the more accurate and expensive B3LYP/6-31g* optimizations are impractical.…”

Quantum Chemical Description of Absorption Properties and Excited‐State Processes in Photosynthetic Systems

“…For Chl and BChl a and c it was shown that the HF method results in larger bond-length alternation than DFT/B3LYP. The maximal difference in CÀC bond length within the porphyrin ring lies between 0.011 for Chl c 1 and 0.044 for BChl c. [92] These structures lead to higher excitation energies than those optimized with DFT. [92] Another striking optimization effect was found for the native Chl pigments.…”