Normal Structural Decomposition Research Articles

Crystal structure of [5-n-butyl-10-(2,5-di-meth-oxy-phen-yl)-2,3,7,8,13,12,17,18-octa-ethyl-porphyrin-ato]nickel(II).

The asymmetric unit of the title nickel(II) porphyrin, [Ni(C48H60N4O2)], contains one independent mol-ecule. The average Ni-N bond length is 1.917 (13) Å. The mol-ecules are arranged in a closely spaced lattice structure in which neighbouring porphyrins are oriented in inversion-related dimers. The nickel(II) porphyrin is characterized by a significant degree of a ruffled (B 1u ) conformation with small contributions from saddle (B 2u ) and wave (y) [Eg (y)], as determined using normal structural decomposition. Disorder in the 2,5-di--meth-oxy-phenyl substituent was modelled over two positions with a 60% occupancy for the major moiety. One of the ethyl groups is also disordered over two positions and was modelled with the major moiety being present in 51.3% occupancy.

Resonance Raman spectroscopic examination of ferrochelatase-induced porphyrin distortion

Ferrochelatase, the terminal enzyme of the heme biosynthetic pathway, catalyzes the insertion of ferrous iron into protoporphyrin IX to give heme. Resonance Raman spectroscopy has been instrumental in defining the distortion (mode and extent) of the porphyrin substrate, which is a critical step in the catalytic mechanism of ferrochelatase. Saddling is the predominant porphyrin out-of-plane deformation induced upon binding to ferrochelatase. Our analysis demonstrated that the intensity of the γ(15) line, which is assigned to an out-of-plane porphyrin vibration, in resonance Raman spectra obtained for wild-type- and variant ferrochelatase-bound porphyrin, correlates with the saddling deformation undergone by the porphyrin substrate. Further analysis of the three dimensional X-ray structures of bacterial, human and yeast ferrochelatases and the type and extent of distortion of the protein-bound porphyrin substrate and inhibitors using normal structure decomposition, support the view that ferrochelatase catalysis involves binding of a distorted porphyrin substrate and releasing of a flatter, metalated porphyrin.

Theoretical Study of the Inner Hydrogen Migration in the β-Substituted 5,10,15,20-Tetraphenylporphyrins

In order to investigate the mechanism of the N-H migration in asymmetrical metal-free porphyrins, four porphyrins of electron-withdrawing or electron-donating substituent at the β-position were studied theoretically. For porphyrin 2 (R = OMe), 3 (R = Me), and 4 (R = NO(2)), four different asynchronous N-H migration pathways exist due to symmetry reasons. The corresponding trans-, cis-, and transition state geometries were analyzed using a normal structure decomposition method. Our data show that the hydrogen migration of porphyrin 2, 3, and 4 in clockwise (A, B) are much more preferred than counterclockwise (C, D) direction.

Influence of the Core Conformation on the NH-Tautomerism in Porphyrins: A Study of meso-(1,3-Dithian-2-yl)porphyrins

In order to investigate the mechanism of the NH-tautomerism in porphyrins, three meso-dithianyl-substituted porphyrins of different substitution pattern were studied theoretically. The corresponding trans-, cis- and saddle-point geometries were optimized with DFT methods, and the macrocyclic conformations obtained were analyzed using normal-structure-decomposition (NSD) analysis. Special attention was given to the influence of the participating out-of-plane and in-plane conformations on the NH-tautomerism, and the interplay of substituents, core conformations and energies of the transition-state structures was critically evaluated. The calculated energy barriers of the preferred pathways are compared with experimental activation enthalpies determined by variable-temperature (VT) NMR spectroscopy.

The importance of vibronic perturbations in ferrocytochrome c spectra: A reevaluation of spectral properties based on low-temperature optical absorption, resonance Raman, and molecular-dynamics simulations

We have measured and analyzed the low-temperature (T=10 K) absorption spectrum of reduced horse heart and yeast cytochrome c. Both spectra show split and asymmetric Q(0) and Q(upsilon) bands. The spectra were first decomposed into the individual split vibronic sidebands assignable to B(1g) (nu15) and A(2g) (nu19, nu21, and nu22) Herzberg-Teller active modes due to their strong intensity in resonance Raman spectra acquired with Q(0) and Q(upsilon) excitations. The measured band splittings and asymmetries cannot be rationalized solely in terms of electronic perturbations of the heme macrocycle. On the contrary, they clearly point to the importance of considering not only electronic perturbations but vibronic perturbations as well. The former are most likely due to the heterogeneity of the electric field produced by charged side chains in the protein environment, whereas the latter reflect a perturbation potential due to multiple heme-protein interactions, which deform the heme structure in the ground and excited states. Additional information about vibronic perturbations and the associated ground-state deformations are inferred from the depolarization ratios of resonance Raman bands. The results of our analysis indicate that the heme group in yeast cytochrome c is more nonplanar and more distorted along a B(2g) coordinate than in horse heart cytochrome c. This conclusion is supported by normal structural decomposition calculations performed on the heme extracted from molecular-dynamic simulations of the two investigated proteins. Interestingly, the latter are somewhat different from the respective deformations obtained from the x-ray structures.

The charge transfer band in horseradish peroxidase correlates with heme in-plane distortions induced by calcium removal.

Horseradish peroxidase C (HRPC) is a class III peroxidase whose structure is stabilized by the presence of two endogenous calcium atoms. Calcium removal has been shown to decrease the enzymatic activity of the enzyme. The spin state of the iron, a mixture of high spin (HS) and mixed quantum spin state (QS) consisting of intermediate spin (IS) 3/2 + (HS) 5/2, is also significantly affected by calcium removal, going from a predominant QS component to a predominant HS component upon removal of one calcium. Removal of both calcium ions, however, results in the appearance of a significant LS contribution, easily monitored in the charge transfer (CT) band region by low-T absorption. Normal structural decomposition (NSD) calculations of the in-plane (ip) modes of the heme extracted from HRPC native and Ca(2+)-depleted models show that removal of the proximal calcium is associated with perturbed E(u) and increased A(1g) ip distortions of the heme. The effect of complete or distal calcium removal on the heme also results in increased A(1g) ip distortions, but in significantly decreased E(u) distortions. The overall effect is to decrease the nonplanarity of the heme: the total ip distortion of the native HRPC heme is 0.200 and 0.134 A for the Ca(2+)-depleted species. Our NSD results corroborate the role proposed for the protein matrix, namely to fine-tune the active site by inducing subtle changes in heme planarity and spin state of the iron.

Structural Characterization of Synthetic and Protein-Bound Porphyrins in Terms of the Lowest-Frequency Normal Coordinates of the Macrocycle

The X-ray crystal structures of synthetic and protein-bound metalloporphyrins are analyzed using a new normal structural decomposition method for classifying and quantifying their out-of-plane and in-plane distortions. These distortions are characterized in terms of equivalent displacements along the normal coordinates of the D4h-symmetric porphyrin macrocycle (normal deformations) by using a computational procedure developed for this purpose. Often it turns out that the macrocyclic structure is, even in highly distorted porphyrins, accurately represented by displacements along only the lowest-frequency normal coordinates. Accordingly, the macrocyclic structure obtained from just the out-of-plane normal deformations of the saddling (sad, B2u)-, ruffling (ruf, B1u)-, doming (dom, A2u)-, waving [wav(x), wav(y); Eg]-, and propellering (pro, A1u)-type essentially simulates the out-of-plane distortion of the X-ray crystal structure. Similarly, the observed in-plane distortions are decomposed into in-plane norm...