https://zenodo.org/record/1258475/files/article.pdf

Electron transfers in chemistry and biology

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

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Cell biology and molecular basis of denitrification.

ion phase that leads to an alkyl radical coordinated to the iron-hydroxo complex by a weak OH---C hydrogen bond, labeled as CI; (ii) an alkyl (or OH) rotation phase whereby the alkyl group achieves a favorable orientation for rebound; and (iii) a rebound phase that leads to C-O bond making and the ferric-alcohol complexes, 4,2P. The two profiles remain close in energy throughout the first two phases and then bifurcate. Whereas the HS state exhibits a significant barrier and a genuine TS for rebound, in the LS state, once the right orientation of the alkyl group is achieved, the LS rebound proceeds in a virtually barrier-free fashion to the alcohol. As such, alkane hydroxylation proceeds by TSR,70-72,120 in which the HS mechanism is truly stepwise with a finite lifetime for the radical intermediate, whereas the LS mechanism is effectively concerted with an ultrashort lifetime for the radical intermediate. Subsequent studies of ethane and camphor hydroxylation by the Yoshizawa group117,181-183 arrived at basically the same conclusion, that the mechanism is typified by TSR. The differences between the results of Shaik et al.130,173,177-180 and Yoshizawa et al.117,181-183 were rationalized recently71,72 and shown to arise owing to technical problems and the choice of the mercaptide ligand,117,181-183 which is a powerful electron donor and is too far from the representation of cysteine in the protein environment. The most recent study of camphor hydroxylation, which was done at a higher quality,117 converged to the picture reported by Shaik et al.130,173,177-180 and shows a stepwise HS process with a barrier of more than 3 kcal/mol for C-O bond formation by rebound of the camphoryl radical vis-à-vis an effectively concerted LS process for which this barrier is 0.7 kcal mol-1 and is the rotational barrier for reaching the rebound position. By referring to Figure 21, it is possible to rationalize the clock data of Newcomb in a simple manner. The apparent lifetimes are based on the assumption that there is a single state that leads to the reaction, such that the radical lifetime can be quantitated from the rate constant of free radical rearrangement and the ratio of rearranged to unrearranged alcohol product. However, in TSR, the rearranged (R) product is formed only/mainly on the HS surface, while the unrearranged (U) product is formed mainly on Figure 20. Formal descriptions of iron(III)-peroxo, iron(III)-hydroperoxo, and iron(V)-oxo species with indication of the negative charges. The roles “electrophile” or “nucleophile” are assigned according to the charge type. Reprinted with permission from ref 7. Copyright 2000 Springer-Verlag Heidelberg. 3964 Chemical Reviews, 2004, Vol. 104, No. 9 Meunier et al.

Mechanism of oxidation reactions catalyzed by cytochrome p450 enzymes.

J-aggregates are of significant interest for organic materials conceived by supramolecular approaches. Their discovery in the 1930s represents one of the most important milestones in dye chemistry as well as the germination of supramolecular chemistry. The intriguing optical properties of J-aggregates (in particular, very narrow red-shifted absorption bands with respect to those of the monomer and their ability to delocalize and migrate excitons) as well as their prospect for applications have motivated scientists to become involved in this field, and numerous contributions have been published. This Review provides an overview on the J-aggregates of a broad variety of dyes (including cyanines, porphyrins, phthalocyanines, and perylene bisimides) created by using supramolecular construction principles, and discusses their optical and photophysical properties as well as their potential applications. Thus, this Review is intended to be of interest to the supramolecular, photochemistry, and materials science communities.

J-aggregates: from serendipitous discovery to supramolecular engineering of functional dye materials.

It is well-known that time-dependent density functional theory (TDDFT) yields substantial errors for the excitation energies of charge-transfer (CT) excited states, when approximate standard exchange-correlation (xc) functionals are used, for example, SVWN, BLYP, or B3LYP. Also, the correct 1/R asymptotic behavior of CT states with respect to a distance coordinate R between the separated charges of the CT state is not reproduced by TDDFT employing these xc-functionals. Here, we demonstrate by analysis of the TDDFT equations that the first failure is due to the self-interaction error in the orbital energies from the ground-state DFT calculation, while the latter is a similar self-interaction error in TDDFT arising through the electron transfer in the CT state. Possible correction schemes, such as inclusion of exact Hartree−Fock or exact Kohn−Sham exchange, as well as aspects of the exact xc-functional are discussed in this context. Furthermore, a practical approach is proposed which combines the benefits o...

Failure of time-dependent density functional theory for long-range charge-transfer excited states: the zincbacteriochlorin-bacteriochlorin and bacteriochlorophyll-spheroidene complexes.

Zinc tetraphenylporphyrin (ZnTPP) and magnesium octaethylporphyrin (MgOEP) undergo reversible oneand two-electron oxidations. Removal of the first electron by controlled potential electrolysis or by oxidation with xenon difluoride or bromine results in cation radicals whose esr spectra clearly indicate electron abstraction from the porphyrin ring. The observed hyperfine structure is assigned, with the help of deuterium labeling, to interaction of the unpaired electron with the meso protons of MgOEP+ and with the protons on the phenyl groups of ZnTPP+. Electronic absorption spectra of the radicals, dications, and of a dimer of MgOEP+ which exists at low temperatures are presented. The results of an SCF-MO study are compared with the experimental esr and optical data. These calculations suggest that a radical may occupy either of two close-lying ground states. We conclude that the ground-state symmetries of ZnTPP+ and MgOEP+ are, respectively, 2AZu and 2A1u of the D4h point group. C steps in photosynthetic and metabolic processes involve metalloporphyrin redox properties. Prior studies of heme function have stressed the redox characteristics of the central metal; s, 4 in contradistinction, primary photosynthetic events involving (I) Aspects of this work were previously presented: (a) J. Fajer. D. C. Borg. D. Dolphin. and R. H. Felton. Abstracts. 157th National Meeting of the American Chemical Society. Minneapolis, Minn .• April 1969. p 130; (b) R. H. Felton. D. Dolphin. D. C. Borg. and J. Fajer. J. A mer. Chern. Soc .• 91. 196 (1969). (2) (a) Department of Applied Science, Brookhaven National Laboratory; (b) Medical Department. Brookhaven ::-.lational Laboratory; (cl Harvard University; (d) Georgia Institute of Technology. (3) J. E. Falk, \"Porphyrins and Metalloporphyrins,\" Elsevier Publishing Co., New York, N. Y., 1964. (4) B. Chance, R. W. Estabrook. and T. Yonetani, Ed .• \"Hemes and Hemoproteins.\" Academic Press, New York, N. Y .• 1966. chlorophyll appear to depend upon ring redox properties.o· 6 A striking feature of the porphyrin ring is its ability to undergo facile reduction and oxidation. Reductions of chlorophylF and metalloporphyrins,8 dissolved in apr otic solvents. have been accomplished byelectrochemical and chemical techniques, and the results (5) B. Kok, Biochirn. Biophys. Acta, 48. 527 (1961). (6) J. Weikard, A. Muller. and H. T. Witt. Z. Natur/orsch .• 18b. 139 (1963). (7) R. H. Felton, G. W. Sherman, and H. Linschitz. Nature, 203, 631 (1964). (8) G. L. Closs and L. E. Closs. J. Arner. Chem. Soc., 85, 818 (1963); N. Hush and J. Dodd. J. Chern. Soc .• 4601 (1964); D. Clack and N. Hush. J. Amer. Chern. Soc., 87, 4238 (1965); R. H. Felton and H. Linschitz, ibid., 88, 1113 (1966). Fajer, Borg, Forman, Dolphin, Felton / Dications of Metalloporphyrins

pi-Cation radicals and dications of metalloporphyrins.

Two-electron oxidation of cobaltous octaethylporphyrin [Co(II)(Et)8P] yields a stable π-cation radical [Co(III)(Et)8P]2+., the optical spectrum of which exhibits spectral changes dependent upon the nature of the counterion. Comparison of these spectra with those of Compounds I of horseradish peroxidase and catalase leads us to propose that these Compounds I contain a π-cation radical of the heme prosthetic group. This proposal explains the oxidation level, optical spectra, and stability of the primary compounds without recourse to properties such as stoichiometric mixtures of special porphyrins, stable Fe(V) porphyrins, or unique conformers of heme porphyrins. Explanations are advanced to account for the missing electron spin resonance signal of Compound I of horseradish peroxidase.

https://www.pnas.org/content/pnas/68/3/614.full.pdf

Compounds I of Catalase and Horse Radish Peroxidase: π-Cation Radicals

Nonplanar porphyrins. X-ray structures of (2,3,7,8,12,13,17,18-octaethyl- and -octamethyl-5,10,15,20-tetraphenylporphinato)zinc(II)

Bacteriopheophytin, the magnesium-free base of bacteriochlorophyll, undergoes reversible one-electron reduction in organic solvents to yield an anionic free radical with characteristic optical and electron spin resonance spectra. The reduction potential of bacteriopheophytin, E1/2 approximately --0.55 V against a normal hydrogen electrode, compared to E1/2 approximately --0.85 V for bacteriochlorophyll, renders it a likely electron acceptor in the primary charge separation of photosynthesis. Comparison of these data with picosecond optical changes recently observed upon pulsed laser excitation of bacterial reaction centers leads us to propose that bacteriopheophytin is indeed a transient electron acceptor and that the primary charge separation of bacterial photosynthesis occurs between the bacteriochlorophyll complex P870 and bacteriopheophytin to yield the radicals of the oxidized chlorophyll dimer cation and reduced pheophytin anion.

https://www.pnas.org/content/pnas/72/12/4956.full.pdf

Primary charge separation in bacterial photosynthesis: oxidized chlorophylls and reduced pheophytin.

Time-resolved and steady-state optical data are presented for a series of substituted free-base porphyrins. The porphyrins are grouped into [open quotes]normal[close quotes] and [open quotes]perturbed[close quotes] categories based on observed photophysical behavior, and the distinctions between the two classes correlate well with the conformations of the molecules. Normal porphyrins qualitatively and quantitatively follow the deactivation pathways traditionally reported for planar metal-free porphyrins. In contrast, the out-of-plane distortion in a series of sterically-crowded porphyrins results in unusual optical properties and enhanced radiationless decay of the [sup 1]([pi],[pi]*) excited state. In particular, macrocycle distortions increase the rates of both the internal conversion and intersystem crossing decay pathways. Enhanced internal conversion of [sup 1]([pi],[pi]*) to the ground state in the perturbed porphyrins is interpreted as arising from an enhanced Franck-Condon factor associated with a structural reorganization in the excited state. Enhanced intersystem crossing from [sup 1]([pi],[pi]*) most likely arises from increased spin-orbit coupling caused by the nonplanarity of the macrocycle. 39 refs., 6 figs., 2 tabs.

Photophysical properties of conformationally distorted metal-free porphyrins. Investigation into the deactivation mechanisms of the lowest excited singlet state

Jack Fajer

Papers

pi-Cation radicals and dications of metalloporphyrins.

Compounds I of Catalase and Horse Radish Peroxidase: π-Cation Radicals

Nonplanar porphyrins. X-ray structures of (2,3,7,8,12,13,17,18-octaethyl- and -octamethyl-5,10,15,20-tetraphenylporphinato)zinc(II)

Primary charge separation in bacterial photosynthesis: oxidized chlorophylls and reduced pheophytin.

Photophysical properties of conformationally distorted metal-free porphyrins. Investigation into the deactivation mechanisms of the lowest excited singlet state