A New Method for Evaluating the Conformations and Normal Modes of Macromolecule Vibrations with a Reduced Force Field. 2. Application to Nonplanar Distorted Metal Porphyrins

Abstract

We have developed a novel method for molecular mechanics calculations and normal-mode analysis. It is based on symmetry of local units that constitutes the given molecule. Compared with general valence force field calculations, the number of free parameters is reduced by 40-80% in our procedure. It was found to reproduce very well the vibrational frequencies and mode compositions of aromatic compounds and porphyrins, as shown by comparison with DFT calculations. A slightly altered force field obtained from Ni(II) porphin was then used to calculate the structure and the normal modes of several meso-substituted Ni(II) porphyrins which are known to be subject to significant ruffling and/or saddling distortions. This method satisfactorily reproduces their nonplanar structure and Raman band frequencies in the natural abundance and isotopic derivative spectra. The polarization properties of bands from out-of-plane modes are in accordance with the predicted nonplanar distortions. Moreover, we found that some of the modes below 800 cm -1 which appear intense in the Raman spectra contain considerable contributions from both in-plane and out-of-plane vibrations, so that the conventional mode assignments become questionable. We also demonstrate that the intensity and polarization of some low-frequency Raman bands can be used as a (quantitative) marker to elucidate type and magnitude of out-of-plane distortions. These were recently shown to affect heme groups of hemoglobin, myoglobin, and, in particular, of cytochrome c.

Polarized resonance Raman dispersion spectroscopy on metalporphyrins

“…[24] support this view. It is further corroborated by the fact, that the low frequency Raman spectrum taken with Soret excitation exhibits considerably strong polarized bands from B 2u -type modes, while B 1u -modes are barely detectable [29]. Both become FC-active via distortions of the same symmetry (cf.…”

“…3 depicts the eigenvectors of four Raman active normal modes of A 1g , A 2g , B 1g and B 2g symmetry of the model substance Ni(II)porphin (NiP). They were calculated by Unger et al [29], who used a recently developed molecular mechanics force field. A 1g -modes are totally symmetric and preserve the molecule's symmetry.…”

“…However, it is not that much dominated by the classical A 1g -modes n 7 and n 8 , as was obtained for planar porphyrins and also for the spectra of some heme proteins. This results from, in part, heavy vibrational mixing between out-of-plane and in-plane components, which allows the out-of-plane modes to steal intensity from the planar ones [29]. In fact, for some modes the normal mode composition no longer allows discrimination between in-plane and out-of-plane modes.…”

Non‐planar heme deformations and excited state displacements in horseradish peroxidase detected by Raman spectroscopy at Soret excitation

“…26 NiTiPrP, for example, is predominantly ruffled and as a consequence, the B 1u -type modes 10 , 12 become Raman active and appear relatively intense in the lowwavenumber Raman spectrum. 26 In NiOETPP, saddling is the dominant oop deformation, thus the 15 , 16 and 17 26 Shelnutt co-workers have investigated nonplanar porphyrins in solution and in heme proteins by means of their NSD analysis. 12,36 -38 Table 2 lists the oop deformations of hemes in resting (wild-type) HRP C, met and deoxyMb obtained by using the NSD program provided by Shelnutt's group.…”

“…Low-wavenumber spectra of the saddled Ni(II) octaethyltetraphenylporphyrin and the ruffled Ni(II) meso-tetra(tert-butyl)porphyrin do indeed exhibit Raman bands assignable to lower wavenumber B 2u and B 1u modes, respectively. 26 Finally, we used the above-obtained vibronic coupling values to estimate the heme oop displacements for the low spin state of HRP C detected at alkaline pH. We assumed that the vibronic coupling properties are not significantly changed by the change of the iron spin state.…”