Normal-coordinate Structural Decomposition Research Articles

Inducing ring distortions in unsubstituted metallophthalocyanines using axial N-heterocyclic carbenes.

A series of metallophthalocyanine (PcM) complexes with axial N-heterocyclic carbene ligands (NHC; 1,3-diisopropylimidazol-2-ylidene (DIP) and 1,3-dimethylbenzimidazol-2-ylidene (DMB)) were prepared and structurally characterized. PcCoII(DIP), PcZnII(DIP), and PcZnII(DMB) are five-coordinate complexes with mild dome-type Pc-ring distortions, while PcFeII(DIP)2 is six-coordinate and has a very large ruffle-type ring-distortion with respect to typical PcM(L)2 systems. The distortion is induced by the highly steric axial DIP ligands. The distortions were quantified and classified by their bond lengths and torsion angles, and according to the normal-coordinate structural decomposition (NSD) analysis. Upon ligation of the NHC, the insoluble PcM materials were solublized in common organic solvents, with typical UV-visible Q-band maxima observable between 658 and 677 nm; the increased solubility is rationalized in terms of the reduced solid-state aggregation of the complexes, attributable to the axial ligation.

Molecular Interactions Identified by Two-Dimensional Analysis-Detailed Insight into the Molecular Interactions of the Antimalarial Artesunate with the Target Structure β-Hematin by Means of 2D Raman Correlation Spectroscopy.

A thorough understanding of the interaction of endoperoxide antimalarial agents with their biological target structures is of utmost importance for the tailored design of future efficient antimalarials. Detailed insights into molecular interactions between artesunate and β-hematin were derived with a combination of resonance Raman spectroscopy, two-dimensional correlation analysis, and density functional theory calculations. Resonance Raman spectroscopy with three distinct laser wavelengths enabled the specific excitation of different chromophore parts of β-hematin. The resonance Raman spectra of the artesunate-β-hematin complexes were thoroughly analyzed with the help of high-resolution and highly sensitive two-dimensional correlation spectroscopy. Spectral changes in the peak properties were found with increasing artesunate concentration. Changes in the low-frequency, morphology-sensitive Raman bands indicated a loss in crystallinity of the drug-target complexes. Differences in the high-wavenumber region were assigned to increased distortions of the planarity of the structure of the target molecule due to the appearance of various coexisting alkylation species. Evidence for the appearance of high-valent ferryl-oxo species could be observed with the help of differences in the peak properties of oxidation-state sensitive Raman modes. To support those findings, the relaxed ground-state structures of ten possible covalent mono- and di-meso(Cm)-alkylated hematin-dihydroartemisinyl complexes were calculated using density functional theory. A very good agreement with the experimental peak properties was achieved, and the out-of-plane displacements along the lowest-frequency normal coordinates were investigated by normal coordinate structural decomposition analysis. The strongest changes in all data were observed in vibrations with a high participation of Cm-parts of β-hematin.

Structural effects of meso-halogenation on porphyrins.

The use of halogens in the crystal engineering of supramolecular porphyrin assemblies has been a topic of strong interest over the past decades. With this in mind we have characterized a series of direct meso-halogenated porphyrins using single crystal X-ray crystallography. This is accompanied by a detailed conformational analysis of all deposited meso-halogenated porphyrins in the CSD. In this study we have used the Hirshfeld fingerprint plots together with normal-coordinate structural decomposition and determined crystal structures to elucidate the conformation, present intermolecular interactions, and compare respective contacts within the crystalline architectures. Additionally, we have used density functional theory calculations to determine the structure of several halogenated porphyrins. This contrasts conformational analysis with existing X-ray structures and gives a method to characterize samples that are difficult to crystallize. By using the methods outlined above we were able to deduce the impact a meso halogen has on a porphyrin, for example, meso-halogenation is dependent on the type of alternate substituents present when forming supramolecular assemblies. Furthermore, we have designed a method to predict the conformation of halogenated porphyrins, without need of crystallization, using DFT calculations with a high degree of accuracy.

Use of low frequency Raman bands to identify non-planar deformation of Ni(II) meso-tetraphenylporphyrin induced by axial ligands

It is important to identify non-planar deformations of porphyrin macrocycle in metallo-porphyrin proteins due to their functional relevance. The relationship between non-planar deformations of porphyrin macrocycle and low frequency Raman spectral bands of Ni(II) meso-tetraphenyl porphyrin (NiTPP), with different coordination numbers, was studied by density functional theory (DFT), normal coordinate structural decomposition method and Raman experiments. The results show that the crystal of four-coordinate NiTPP has two major kinds of non-planar deformations: ruffling and saddling. The non-planar deformations of ruffling and saddling for NiTPP are 1.473 Å and 0.493 Å determined by DFT calculation. The ruffling and saddling deformations can be identified by using the low frequency Raman characteristic peaks (γ12, γ13) and (γ16, γ17), respectively. When four-coordinate NiTPP is transformed to the six-coordinate bis(pyrrolidine) NiTPP (NiTPP(Pyr)2), the large non-planar distortion of the porphyrin macrocycle almost disappears, with the non-planar deformation of saddling only about 0.213 Å estimated by DFT calculation. Experimentally, we can make use of the characteristic peaks of low frequency Raman spectra to identify the saddling deformation beyond 0.25 Å.

Weak Interactions and Conformational Changes in Core-Protonated A2- and Ax-Type Porphyrin Dications.

Individual chemical motifs are known to introduce structural distortions to the porphyrin macrocycle, be it in the core or at the periphery of the macrocycle. The interplay when introducing two or more of these known structural motifs has been scarcely explored and is not necessarily simply additive; these structural distortions have a chance to compound or negate to introduce new structural types. To this end, a series of compounds with complementary peripheral (5,15-disubstitution) and core (acidification) substitution patterns were investigated. The single-crystal X-ray structures of 18 5,15-diphenylporphyrin, 5,15-diphenylporphyrindi-ium diacid, and related compounds are reported, including the first example of a 5,15-dialkylporphyrindi-ium. Normal-coordinate structural decomposition (NSD) analysis is used for a detailed analysis of the conformation of the porphyrin subunit within the crystal structures. An elongation of porphyrin macrocycles along the C5,C15- axis (B2g symmetry) is observed in all of the free base porphyrins and porphyrin dications; distance across the core is around 0.3 Å in the free base and diacid compounds, and more than doubled in 5,15-dipentylporphyrin and 5,15-dipentylporphyrindi-ium diacid. While the free base porphyrins are largely planar, a large out-of-plane distortion can be observed in 5,15-diphenylporphyrin diacids, with the expected “projective saddle” shape characteristic for such systems. The combination of these two distortions (B2u and B2g) from regular porphyrin structure results in a macrocycle best characterized in the chiral point-group D2. A rare structural type of a cis-hydrogen bond chelate is observed for 5,15-dipentylporphyrindi-ium diacid, which adopts an achiral C2v symmetry. Crystallographic data indicate that the protonated porphyrin core forms hydrogen bonding chelates (N-H⋯X⋯H-N) to counter-anions. Weaker interactions, such as induced intramolecular C-H⋯O interactions from the porphyrin periphery are described, with distances characteristic of charge-assisted interactions. This paper offers a conceptual framework for accessing porphyrin macrocycles with designable distortion and symmetry, useful for the selective perturbation of electronic states and a design-for-application approach to solid state porphyrin materials.

Tin(IV) Porphyrins Containing β‐Substituted Bromines: Synthesis, Conformations, Electrochemistry and Photophysical Evaluation

Tin(IV) porphyrins containing bromine atoms at 2,3,12,13 β‐pyrrole positions are synthesised using four different bisaxial ligands; namely, chloro 2, hydroxo 3, phenolato 4 and 4‐nitrophenolato 5. The compounds are characterised using 1H NMR spectroscopy, ESI‐MS and elemental analysis. Despite steric loading at the β‐pyrrole positions, the X‐ray diffraction crystal structure analysis of 4 reveals a planar macrocyclic conformation. However, the structure of 5 shows a nonplanar conformation, with a predominant out‐of‐plane wave distortion mode. Normal‐coordinate structural decomposition (NSD) analysis, as well as analysis of the Sn–N distances, shows that the relief of steric strain in 4 is through in‐plane core elongation, while in 5, both in‐plane and out‐of‐plane distortions are evident. The effect of the highly charged central metal ion, SnIV, together with β‐bromine atoms and different axial ligands on the photophysical and electrochemical redox properties of the porphyrin π‐ring system, is studied with UV/Vis, fluorescence and transient‐absorption spectroscopy. Photophysical studies disclose redshifted absorption bands and reduced fluorescence quantum yield, as a result of the presence of bromine atoms. Cyclic voltammetric measurements indicate that the porphyrin π system becomes much easier to reduce. Preliminary experiments on the singlet‐oxygen‐generation efficiency reveal the role of the axial ligands in tuning such properties.

Crystal structures of unsymmetrically mixed β-pyrrole substituted nickel(II)-meso-tetraphenylporphyrins

Crystal structures of solvated unsymmetrically substituted meso-tetraphenylporphyrins, 2,3,12,13,17-pentachloro-5,7,8,10,15,18,20-hepta-phenylporphyrin, H2TPP(Ph)3(Cl)5, 1 and its nickel(II), NiTPP(Ph)3(Cl)5, 2 were determined by single crystal XRD analysis. In addition, a new unsymmetrically substituted porphyrin, 2,3,12,13,17-pentacyano-5,7,8,10,15,18,20-heptaphenyl-porphinato nickel(II) complex, NiTPP(Ph)3(CN)5, 3 complex was synthesized and its solvated structure was examined by crystallography. These porphyrins exhibited dramatic nonplanar conformation of the macrocycle as evidenced from the average displacement of the β-pyrrole carbon (±ΔC β) from the mean plane of the porphyrin ring and the trend in nonplanarity varies in the order: 2 (1.189(5) Å) > 1 (1.036(6) Å) > 3 (0.895(6) Å). The normal-coordinate structural decomposition analysis of these structures revealed mainly saddle distortion of the macrocycle combined with small degree of ruffled or domed distortions. The Hirshfeld surface analysis of structures 1-3 revealed solvate dependent intermolecular contacts with varying degree of H …H (43–49%), C …H (17–19%), H …Cl (25–30%) and N …H (∼19%) contact contributions. Crystal structures of solvated 2,3,12,13,17-penta(chloro or cyano)-5,7,8,10,15,18,20-heptaphenylporphyrin H2TPP(Ph)3(Cl)5, and their Ni(II) complexes, NiTPP(Ph)3(Cl)5 and NiTPP(Ph)3(CN)5 were determined by single crystal XRD. They revealed nonplanar conformation of the macrocycle (ΔCb > ± 0.9 Å). The structures were examined by normal-coordinate structural decomposition and Hirshfeld surface analyses.

Synthesis of antipodal β-trisubstituted meso-tetraphenylporphyrins and the crystal structure of hexaphenylporphinatozinc(II) bispyridinate complex

A series of antipodal β-trisubstituted meso-tetraphenylporphyrins, H2TPP(R)3 (R = CH3, Ph, PE, and 2′-thienyl) derivatives and their metal (Cu(II) and Zn(II)) complexes were synthesised and characterised by electronic absorption, 1H NMR spectroscopy and mass spectrometry. The magnitude of the red-shift in absorption bands in these free-base porphyrins depend on the nature of the substituent and follow the general trend: PE >2′-thienyl > Br > Ph > CH3. Synthesis, characterisation and crystal structure of 2,5,10,12,15,20-hexaphenylporphinato zinc(II) bispyridinate, ZnTPP(Ph)2(Py)2 complex is also reported. It shows planar geometry of the porphyrin ring with two β-phenyls located at the antipodal 2,12-pyrrole positions. The two axially coordinated pyridine ring planes are oriented almost parallel to each other and they are in staggered conformation relative to opposite pyrrolic nitrogens. The normal-coordinate structural decomposition analysis of the ZnTPP(Ph)2(Py)2 complex revealed slight wave distortion of the macrocycle. We report the synthesis of a family of antipodal β-tri-substituted meso-tetraphenylporphyrins (MTPP(R)3; M = 2H, Cu(II) and Zn(II); R = CH3, Ph, 2-thienyl and PE). Further, synthesis and crystal structure of an antipodal β-pyrrole diphenylated, 2,5,10,12,15,20-hexaphenylporphinatozinc(II) bispyridinate, ZnTPP(Ph)2(Py)2 complex is also reported.

Structural elucidation of a few electron-deficient porphyrin/fullerene cocrystallates: Effect of fullerene on the porphyrin ring conformation

A series of electron-deficient porphyrin/fullerene solvated cocrystallates, β-tetracyano/tetrabromo-meso-tetraphenylporphyrin/Cn (n=60 or 70) [(H2TPP(CN)4)3·C60, 1; (CuTPP(CN)4)3·C60, 2; (H2TPP(CN)4)·C70, 3; (H2TPPBr4)·(C60)2, 4] were examined by single crystal XRD analysis. Cocrystallates 1 and 2 showed hexagonal honeycomb layer-like structure while 3 and 4 revealed one-dimensional linear/zigzag chain structure. Porphyrin ring in the cocrystallates, 1–3 revealed enhanced distortion (r.m.s.>0.245(6)Å) than that of a nearly planar parent H2TPP(CN)4 (0.046(3)Å) structure. The supramolecular interactions in the cocrystallates, 1–4 revealed shortest (por)C…C(C70)=3.165Å, (C60)C…Npor=3.034Å and (C60)C…C(C60)=2.992Å close contact distances. The normal-coordinate structural decomposition analysis of the macrocycle in 1–3 revealed mainly saddling (∼71%) with minimal domed (10–15%) distortions. The nonplanar distortion in these cocrystallates has been ascribed to intermolecular interactions/crystal packing forces.

Mixed β-pyrrole substituted meso-tetraphenylporphyrins and their metal complexes: Synthesis, structures and electrochemical redox properties

Synthesis of two new classes of mixed β-pyrrole substituted tetraphenylporphyrins, H2TPP(Ph)4(R)4 (R=2-thienyl and phenylethynyl, PE) and H2TPP(CH3)4(R)4 (R=2-thienyl and PE) and their metal complexes have been reported. These porphyrins showed dramatic red-shift in electronic absorption bands relative to their corresponding MTPP(R)4 derivatives. Crystal structures of H2TPP(R)4(2-thienyl)4 (R=Ph and CH3) and MTPP(CH3)4(PE)4 (M=Zn(II) and Cu(II)) derivatives are highly nonplanar as evidenced from the mean displacement of β-pyrrole carbon (ΔCb) in the range ±(0.33–1.07)Å. Normal-coordinate structural decomposition analysis of the 24-atom core in these crystal structures revealed largely saddle (73–93%) combined with different degree of ruffled, domed and wave distortions. Electrochemical redox properties of these porphyrins exhibited interesting trend in redox potentials relative to their corresponding H2TPP(R)4s. The tunable trend in redox potentials and electronic absorption bands of mixed substituted porphyrins suggests the role of nonplanarity of macrocycle and electronic effects of the substituents.

Investigations of the low frequency modes of ferric cytochrome c using vibrational coherence spectroscopy.

Femtosecond vibrational coherence spectroscopy is used to investigate the low frequency vibrational dynamics of the electron transfer heme protein, cytochrome c (cyt c). The vibrational coherence spectra of ferric cyt c have been measured as a function of excitation wavelength within the Soret band. Vibrational coherence spectra obtained with excitation between 412 and 421 nm display a strong mode at ∼44 cm–1 that has been assigned to have a significant contribution from heme ruffling motion in the electronic ground state. This assignment is based partially on the presence of a large heme ruffling distortion in the normal coordinate structural decomposition (NSD) analysis of the X-ray crystal structures. When the excitation wavelength is moved into the ∼421–435 nm region, the transient absorption increases along with the relative intensity of two modes near ∼55 and 30 cm–1. The intensity of the mode near 44 cm–1 appears to minimize in this region and then recover (but with an opposite phase compared to the blue excitation) when the laser is tuned to 443 nm. These observations are consistent with the superposition of both ground and excited state coherence in the 421–435 nm region due to the excitation of a weak porphyrin-to-iron charge transfer (CT) state, which has a lifetime long enough to observe vibrational coherence. The mode near 55 cm–1 is suggested to arise from ruffling in a transient CT state that has a less ruffled heme due to its iron d6 configuration.

Comparison of different theory models and basis sets for the calculation of FbC-M10Iso-Bn geometry and geometries of chlorin-imide and chlorin-isoimide isomeric pairs

Various density functional theory (DFT) methods with different basis sets to predict the molecular geometry of FbC-M10Iso-Bn macrocycle, a chlorin-isoimide, are compared in this study. DFT methods, including M06-2X, B3LYP, LSDA, B3PW91, PBEPBE, and BPV86, are examined. Different basis sets, such as 6-31G*, 6-31+G (d, p), 6-311+G (d, p), 6-311++G (d, p), cc-PVDZ, cc-PVTZ, and cc-PVQZ are also considered. The examined hybrid DFT methods are in agreement with the geometry of X-ray crystallography available for comparison. B3LYP/cc-PVDZ level is particularly consistent with available X-ray crystallography in terms of predicting the geometries of FbC-M10Iso-Bn. Geometries of chlorin-imide and chlorin-isoimide isomeric pairs are described through B3LYP/cc-PVDZ method. The bond lengths of chlorin-isoimide, specifically C13–C14, C14–C15, and C2–C3, increase as bond overlap index decreases because of charge transfer. β-β bond lengths (C2–C3 bond lengths) with a three-substituent benzylcarbamoyl group also increase as bond overlap index decreases compared with other molecules. The bond lengths of chlorin-imide are smaller than those of chlorin-isoimide. Angles with β-β bond lengths, specifically C2–C3–C4 in ring A, also decrease with a three-substituent benzylcarbamoyl group; however, the angles in C1–C2–C3 increase. Potential energy on the surfaces of the chlorin-imide and chlorin-isoimide isomeric pairs is optimized by calculating the total and relative energies at B3LYP/cc-PVDZ level. Results indicate that chlorin-imides are more stable than chlorin-isoimides. Normal-coordinate structural decomposition shows that chlorin-imides exhibit greater deformation than chlorin-isoimides except for FbC-M10Iso-Ph.

Inactivation of the Heme Degrading Enzyme IsdI by an Active Site Substitution That Diminishes Heme Ruffling

IsdG and IsdI are paralogous heme degrading enzymes from the bacterium Staphylococcus aureus. Heme bound by these enzymes is extensively ruffled such that the meso-carbons at the sites of oxidation are distorted toward bound oxygen. In contrast, the canonical heme oxygenase family degrades heme that is bound with minimal distortion. Trp-66 is a conserved heme pocket residue in IsdI implicated in heme ruffling. IsdI variants with Trp-66 replaced with residues having less bulky aromatic and alkyl side chains were characterized with respect to catalytic activity, heme ruffling, and electrochemical properties. The heme degradation activity of the W66Y and W66F variants was approximately half that of the wild-type enzyme, whereas the W66L and W66A variants were inactive. A crystal structure and NMR spectroscopic analysis of the W66Y variant reveals that heme binds to this enzyme with less heme ruffling than observed for wild-type IsdI. The reduction potential of this variant (-96 ± 7 mV versus standard hydrogen electrode) is similar to that of wild-type IsdI (-89 ± 7 mV), so we attribute the diminished activity of this variant to the diminished heme ruffling observed for heme bound to this enzyme and conclude that Trp-66 is required for optimal catalytic activity.

Deformation of Chlorin Rings in the Photosystem II Crystal Structure

The crystal structure of Photosystem II (PSII) analyzed at a resolution of 1.9 Å revealed deformations of chlorin rings in the chlorophylls for the first time. We investigated the degrees of chlorin ring deformation and factors that contributed to them in the PSII crystal structure, using a normal-coordinate structural decomposition procedure. The out-of-plane distortion of the P(D1) chlorin ring can be described predominantly by a large "doming mode" arising from the axial ligand, D1-His198, as well as the chlorophyll side chains and PSII protein environment. In contrast, the deformation of P(D2) was caused by a "saddling mode" arising from the D2-Trp191 ring and the doming mode arising from D2-His197. Large ruffling modes, which were reported to lower the redox potential in heme proteins, were observed in P(D1) and Chl(D1), but not in P(D2) and Chl(D2). Furthermore, as P(D1) possessed the largest doming mode among the reaction center chlorophylls, the corresponding bacteriochlorophyll P(L) possessed the largest doming mode in bacterial photosynthetic reaction centers. However, the majority of the redox potential shift in the protein environment was determined by the electrostatic environment. The difference in the chlorin ring deformation appears to directly refer to the difference in "the local steric protein environment" rather than the redox potential value in PSII.

Investigation of the Low Frequency Dynamics of Heme Proteins: Native and Mutant Cytochrome P450cam and Redox Partner Complexes

Vibrational coherence spectroscopy (VCS) is used to investigate the low-frequency dynamics of camphor-free and camphor-bound cytochrome P450(cam) (CYP 101) and its L358P mutant. The low-frequency heme vibrations are found to be perturbed upon binding to the electron transfer partner putidaredoxin (Pdx). A strong correlation between the "detuned" vibrational coherence spectrum, which monitors frequencies between 100 and 400 cm(-1), and the lower frequency part of the Raman spectrum is also demonstrated. The very low frequency region ≤200 cm(-1), uniquely accessed by open-band VCS measurements, reveals a mode near 103 cm(-1) in P450(cam) when camphor is not present in the distal pocket. This reflects the presence of a specific heme distortion, such as saddling or ruffling, in the substrate-free state where water is coordinated to the low-spin iron atom. Such distortions are likely to retard the rate of electron transfer to the substrate-free protein. The presence of strong mode near ∼33 cm(-1) in the camphor-bound form suggests a significant heme-doming distortion, which is supported by analysis using normal coordinate structural decomposition. Pdx also displays a strong coherent vibration near 30 cm(-1) that in principle could be involved in vibrational resonance with its electron transfer target. A splitting of the 33 cm(-1) feature and intensification of a mode near 78 cm(-1) appear when the P450(cam)/Pdx complex is formed. These observations are consistent with vibrational mixing and heme geometric distortions upon Pdx binding that are coincident with the increased thiolate electron donation to the heme. The appearance of a mode near 65 cm(-1) in the coherence spectra of the L358P mutant is comparable to the mode at 78 cm(-1) seen in the P450(cam)/Pdx complex and is consistent with the view that the heme and its environment in the L358P mutant are similar to the Pdx-bound native protein. Resonance Raman spectra are presented for both P450(cam) and the L358P mutant and the changes are correlated with an increased amount of thiolate electron donation to the heme in the mutant sample.

Structural and electrochemical properties of β-tetrabromo-mesotetrakis(4-alkyloxyphenyl)porphyrins and their metal complexes

Crystal structure of 2,3,12,13-tetrabromo-5,10,15,20-tetrakis(4-butyloxy phenyl)porphinato copper(II) tetrahydrofuran solvate was examined and it features enhanced non-planar distortion of the porphyrin ring. The normal coordinate structural decomposition (NSD) analysis for the out-of-plane displacement of atoms of the macrocyclic ring in CuT(4-CnP)PBr4 (n = 4, 6) indicates mainly saddled distortion combined with small contribution from wave conformation. The electrochemical studies on MT (4-CnP)PBr4 (M = 2H, Cu(II), Zn(II)) revealed cathodic shift in redox potentials in contrast to the corresponding brominated porphyrins, MTPPBr4. This is perhaps due to non-planarity of the porphyrin ring and the positive inductive effect of the alkyloxy groups.

Investigations of Low-Frequency Vibrational Dynamics and Ligand Binding Kinetics of Cystathionine β-Synthase

Vibrational coherence spectroscopy is used to study the low frequency dynamics of the truncated dimer of human cystathionine beta-synthase (CBS). CBS is a pyridoxal-5'-phosphate-dependent heme enzyme with cysteine and histidine axial ligands that catalyzes the condensation of serine and homocysteine to form cystathionine. A strong correlation between the "detuned" coherence spectrum (which probes higher frequencies) and the Raman spectrum is demonstrated, and a rich pattern of modes below 200 cm(-1) is revealed. Normal coordinate structural decomposition (NSD) of the ferric CBS crystal structure predicts the enhancement of normal modes with significant heme "doming", "ruffling", and "saddling" content, and they are observed in the coherence spectra near approximately 40, approximately 60, and approximately 90 cm(-1). When pH is varied, the relative intensities and frequencies of the low frequency heme modes indicate the presence of a unique protein-induced heme structural perturbation near pH 7 that differs from what is observed at higher or lower pH. For ferric CBS, we observe a new mode near approximately 25 cm(-1), possibly involving the response of the protein, which exhibits a phase jump of approximately pi for excitation on the blue and red side of the Soret band maximum. The low frequency vibrational coherence spectrum of ferrous CBS is also presented, along with our efforts to probe its NO-bound complex. The CO geminate rebinding kinetics of CBS are similar to the CO-bound form of the gene activator protein CooA, but with the appearance of a significant additional kinetic inhomogeneity. Analysis of this inhomogeneity suggests that it arises from the two subunits of CBS and leads to a factor of approximately 20 for the ratio of the average CO geminate rebinding rates of the two subunits.

Consistent force field for metalloporphyrins

Molecular mechanics (MM) calculations to analyze the puckering of metalloporphyrins isolated and adsorpted on a graphite layer (0001) as a function of metal ion size and the peripheral substitution are presented. The Consistent Force Field (CFF) program was used with new parameters for metalloporphyrins, which included an out-of-plane bending function. Normal-coordinate Structural Decomposition (NSD) analysis was performed on the equilibrium structures obtained by MM calculations. The conformers were also stereochemically characterized and compared with available experimental data and with conformers obtained in a previous MM study.

XAFS Debye-Waller factors for deformed hemes and metal substituted hemes

We present an efficient and accurate method for calculating XAFS Debye-Waller factors for deformed active sites of hemoproteins and metal substituted hemes. Based on the Normal Coordinate Structural Decomposition scheme, the deformation of the porphyrin macrocycle is expressed as a linear combination of the normal modes of the planar species. In our approach, we identify the modes that contribute most to the deformation. Small metal-porphyrin structures which match the macrocycle structural deformation of the deformed hemoprotein site are used to calculate the Debye-Waller parameters at sample's temperature. The Debye-Waller factors are directly obtained by calculating the normal mode spectrum of the corresponding metal-porphyrin structure using Density Functional Theory. Our method is tested on Ni-tetraadamantyl porphyrin and cytochrome c structures with more than 500 available scattering paths.

Trafficking of heme and porphyrins in metazoa.

Trafficking of heme and porphyrins in metazoa.