Proton-coupled hole hopping in nucleosomal and free DNA initiated by site-specific hole injection

Nucleosomes were reconstituted from recombinant histones and a 147-mer DNA sequence containing the damage reporter sequence 5'-…d([2AP]T[GGG](1)TT[GGG](2)TTT[GGG](3)TAT)… with 2-aminopurine (2AP) at position 27 from the dyad axis. Footprinting studies with ˙OH radicals reflect the usual effects of "in" and "out" rotational settings, while, interestingly, the guanine oxidizing one-electron oxidant CO(3)(˙-) radical does not. Site-specific hole injection was achieved by 308 nm excimer laser pulses to produce 2AP(˙+) cations, and superoxide via the trapping of hydrated electrons. Rapid deprotonation (~100 ns) and proton coupled electron transfer generates neutral guanine radicals, G(-H)˙ and hole hopping between the three groups of [GGG] on micro- to millisecond time scales. Hole transfer competes with hole trapping that involves the combination of O(2)(˙-) with G(-H)˙ radicals to yield predominantly 2,5-diamino-4H-imidazolone (Iz) and minor 8-oxo-7,8-dihydroguanine (8-oxoG) end-products in free DNA (Misiaszek et al., J. Biol. Chem. 2004, 279, 32106). Hole migration is less efficient in nucleosomal than in the identical protein-free DNA by a factor of 1.2-1.5. The Fpg/piperidine strand cleavage ratio is ~1.0 in free DNA at all three GGG sequences and at the "in" rotational settings [GGG](1,3) facing the histone core, and ~2.3 at the "out" setting at [GGG](2) facing away from the histone core. These results are interpreted in terms of competitive reaction pathways of O(2)(˙-) with G(-H)˙ radicals at the C5 (yielding Iz) and C8 (yielding 8-oxoG) positions. These differences in product distributions are attributed to variations in the local nucleosomal B-DNA base pair structural parameters that are a function of surrounding sequence context and rotational setting.     

Theoretical rate constants of super-exchange hole transfer and thermally induced hopping in DNA

Recently, the electronic properties of DNA have been extensively studied, because its conductivity is important not only to the study of fundamental biological problems, but also in the development of molecular-sized electronics and biosensors. We have studied theoretically the reorganization energies, the activation energies, the electronic coupling matrix elements, and the rate constants of hole transfer in B-form double-helix DNA in water. To accommodate the effects of DNA nuclear motions, a subset of reaction coordinates for hole transfer was extracted from classical molecular dynamics (MD) trajectories of DNA in water and then used for ab initio quantum chemical calculations of electron coupling constants based on the generalized Mulliken-Hush model. A molecular mechanics (MM) method was used to determine the nuclear Franck-Condon factor. The rate constants for two types of mechanisms of hole transfer-the thermally induced hopping (TIH) and the super-exchange mechanisms-were determined based on Marcus theory. We found that the calculated matrix elements are strongly dependent on the conformations of the nucleobase pairs of hole-transferable DNA and extend over a wide range of values for the "rise" base-step parameter but cluster around a particular value for the "twist" parameter. The calculated activation energies are in good agreement with experimental results. Whereas the rate constant for the TIH mechanism is not dependent on the number of A-T nucleobase pairs that act as a bridge, the rate constant for the super-exchange process rapidly decreases when the length of the bridge increases. These characteristic trends in the calculated rate constants effectively reproduce those in the experimental data of Giese et al. [Nature 2001, 412, 318]. The calculated rate constants were also compared with the experimental results of Lewis et al. [Nature 2000, 406, 51].     

The significance of proton migration during hole hopping through DNA

Hole transfer through DNA is coupled with proton transfer processes.     

Toroidal hopping of a single hole through the circularly-arrayed naphthyl groups in hexanaphthylbenzene cation radical

Synthesis of a dendritic (soluble) hexanaphthylbenzene derivative is described in which the six naphthyl groups are connected to the central benzene ring in a propeller-shaped arrangement. Observation of multiple oxidation waves in its cyclic voltammogram as well as an intense charge-resonance transition (extending beyond 1600 nm) in its cation radical, generated by laser-flash photolysis using photoexcited chloranil as an oxidant, suggests that a single hole is mobilized via electron transfer (or hopping) over six identical (circularly arrayed) redox centers.     

Bioinspired catalyst design and artificial metalloenzymes

Many bioinspired transition-metal catalysts have been developed over the recent years. In this review the progress in the design and application of ligand systems based on peptides and DNA and the development of artificial metalloenzymes are reviewed with a particular emphasis on the combination of phosphane ligands with powerful molecular recognition and shape selectivity of biomolecules. The various approaches for the assembly of these catalytic systems will be highlighted, and the possibilities that the use of the building blocks of Nature provide for catalyst optimisation strategies are discussed.     

Oxidations by copper metalloenzymes and some biomimetic approaches

This paper illustrates the various aspects of the reactivity of the Cu(II)–Cu(I) system in biological systems, with one example of an enzymatic reaction in which Cu(II) alone is oxidizing enough to carry out the reaction (superoxide dismutase), one example in which a Cu(II)-bound peroxo intermediate is the active species (tyrosinase) and the examples of galactose oxidase and copper amine oxidases in which Cu(II) is associated with a redox active organic cofactor. In some cases, we will show some illustrations of biomimetic approaches developed in our laboratories, aimed at a better understanding of reaction mechanisms and at an original design of new catalysts with potential applications in synthetic chemistry. Some comments are given concerning the respective features of copper and iron.     

The scanning probe microscopy of metalloproteins and metalloenzymes

In recent years, the concept of microscopy and the ability to study processes at a truly molecular level have been revolutionised by the development of a family of instruments based on acquiring data through the scanning of a proximal probe across a surface. Scanning Probe Microscopes (SPMs) enable surface-confined structures to be resolved at ?ngstrom-resolution, in real time, and under a variety of controllable conditions. Despite initial difficulties, much progress has been in the application of this technology to the high-resolution analysis of biological systems; these have varied from complex cellular systems to molecular biopolymers. Studying the interactions of protein with surfaces has been intrinsic to the development of our understanding of blood coagulation, fibrinolysis, thrombus formation and the synthesis of biocompatible materials. The specific interactions of metalloproteins and enzymes with electrode surfaces remains central to the understanding of the bioelectrochemical processes and to the development of biosensing devices. Though ellipsometry, Raman, microcalorimetry, surface plasmon resonance, and other spectroscopic methods, can provide much information on these interfaces, the acquired data are averaged over a large number of molecular species with a low spatial resolution. Proximal probe methods have much to offer in this regard and have revolutionized our ability to monitor such interactions.     

Spin-driven activation of dioxygen in various metalloenzymes and their inspired models

Although potentially powerful, molecular oxygen is an inert oxidant due to the triplet nature of its ground state. Therefore, many enzymesse various metal cations (M) to produce singlet active species M(n) O(2) . In this communication we investigate the topology of the Electron Localization Function (ELF) within five biomimetic complexes which are representative of the strategies followed by metalloenzymes to activate O(2) . Thanks to its coupling to the constrained DFT methods the ELF analysis reveals the tight connection between the spin state of the adduct and the spatial organization of the oxygen lone pairs. We suggest that enzymes could resort to spin state control to tune the regioselectivity of substrate oxidations.     

Charge hopping in DNA.

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G(+) with water. In addition, it has been assumed that the presence of units with several adjacent stacked G bases on the same strand leads to the additional vibronic relaxation process (G(+)G...G) --> (GG...G)(+). The latter may also compete with the hole transfer from (G(+)G...G) to a single G site, depending on the relative positions of energy levels for G(+) and (G(+)G...G). A hopping model is proposed to take the competition of these three rate steps into account. It is shown that the model includes two important limits. One corresponds to the situation where the charge relaxation inside a multiple guanine unit is faster than hopping. In this case hopping is terminated by several adjacent G bases located on the same strand, as has been observed for the GGG triple. In the opposite, slow relaxation limit the GG...G unit allows a hole to migrate further in accord with experiments on strand cleavage exploiting GG pairs. We demonstrate that for base pair sequences with only the GGG triple, the fast relaxation limit of our model yields practically the same sequence- and distance dependencies as measurements, without invoking adjustable parameters. For sequences with a certain number of repeating adenine:thymine pairs between neighboring G bases, our analysis predicts that the hole transfer efficiency varies in inverse proportion to the sequence length for short sequences, with change to slow exponential decay for longer sequences. Calculations performed within the slow relaxation limit enable us to specify parameters that provide a reasonable fit of our numerical results to the hole migration efficiency deduced from experiments with sequences containing GG pairs. The relation of the results obtained to other theoretical and experimental studies of charge transfer in DNA is discussed. We propose experiments to gain a deeper insight into complicated kinetics of charge-transfer hopping in DNA.     

Concerted reactions of polynuclear metalloenzymes and their functional chemical models

The mechanisms of the many-electron oxidation of water by a chemical model of the manganese oxidase cofactor in photosynthesis photosystem II (manganese(IV) clusters) and nitrogen reduction in chemical models of nitrogenase cofactor (vanadium(II) and molybdenum(III) clusters) were considered. The hypothesis was suggested according to which polynuclear enzyme cofactors and their functional chemical models performed two important functions, catalyzed noncomplementary processes and effected many-substrate concerted reactions with decreased activation energies.     

Engineered and artificial metalloenzymes for selective C–H functionalization

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Including quantum decoherence in surface hopping

In this paper we set up a method called overlap decoherence correction (ODC) to take into account the quantum decoherence effect in a surface hopping framework. While keeping the standard surface hopping approach based on independent trajectories, our method allows to account for quantum decoherence by evaluating the overlap between frozen Gaussian wavepackets, the time evolution of which is obtained in an approximate way. The ODC scheme mainly depends on the parameter σ, which is the Gaussian width of the wavepackets. The performance of the ODC method is tested versus full quantum calculations on three model systems, and by comparison with full multiple spawning (FMS) results for the S(1)→S(0) decay in the azobenzene molecule.     

Electronic effects of electron-donating and -withdrawing groups in model complexes for iron-tyrosine-containing metalloenzymes

Three new iron(III) complexes with the ligand N,N'-bis(2-hydroxybenzyl)-N,N'-bis(pyridin-2-ylmethyl)ethylenediamine, H2bbpen, containing electron-donating and -withdrawing groups (Me, Br, NO2) in the 5-position of the phenol rings were synthesized and fully characterized by IR spectroscopy, ESI mass spectrometry, and CHN elemental analyses. X-ray structures of the iron(III) complexes containing NO2 and Me groups were determined. The effects of the substituents on the electronic properties of the complexes were detected by UV-visible spectroscopy, cyclic voltammetry, and X-ray crystallography. Linear correlations between the Hammett parameter for the substituents (sigma(p)) and the Fe(III)/Fe(II) redox potentials or ligand-metal charge-transfer (LMCT) processes of the complexes were obtained. A theoretical study using DFT is presented and shows good agreement between the experimental and calculated data.     

Fewest-switches surface hopping and decoherence in multiple dimensions

In a recent article (Subotnik, J. E.; Shenvi, N. J. Chem. Phys.2011, 134, 24105), we introduced a new approach for incorporating decoherence into the fewest-switches surface-hopping (FSSH) algorithm, titled augmented FSSH (A-FSSH). The A-FSSH algorithm was designed to correct the well-known overcoherence problem in traditional FSSH, and thus allow wave packets on different surfaces to separate naturally subject to different forces. As presented earlier, however, the A-FSSH algorithm was restricted to two electronic states. We now extend the method to more than two electronic states and present several new model problems with multiple electronic and nuclear dimensions. Lastly, starting with the quantum Liouville equation, we rederive and implement the new phase correction suggested by Shenvi (Shenvi, N.; Subotnik, J. E.; Yang, W. J. Chem. Phys.2011, 135, 24101) and co-workers for propagating the electronic amplitude along a specified nuclear trajectory and find much improved results in certain cases.     

金属组学：Wood—Ljungdahl通路中的金属蛋白／金属酶

本文概述了厌氧微生物的Wood-Ljungdahl通路及通路中的一组金属蛋白／金属酶,主要介绍该通路的来源、过程及通路中的四种金属蛋白,金属酶：甲酸脱氢酶、钻铁硫蛋白、乙酰辅酶A合成酶和CO脱氢酶．甲酸脱氢酶催化CO2和甲酸的可逆氧化还原,是CO2转化为甲酸进而转化为甲基四氢叶酸的关键金属酶;钴铁硫蛋白是该通路中的甲基转换器,接受甲基四氢叶酸的甲基之后再传递给乙酰辅酶A合成酶;CO脱氢酶催化CO2与CO之间的可逆氧化还原;乙酰辅酶A合成酶通过浓缩甲基、CO和辅酶A而催化乙酰辅酶A的合成．本文重点对这四种金属蛋白／金属酶的结构、性质、功能及催化机理的研究进展进行了综述．     

Metalloproteins/metalloenzymes for the synthesis of acetyl-CoA in the Wood-Ljungdahl pathway

This paper focuses on the group of metalloproteins/metalloenzymes in the acetyl-coenzyme A synthesis pathway of anaerobic microbes called Wood-Ljungdahl pathway, including formate dehydrogenase (FDH), corrinoid iron sulfur protein (CoFeSP), acetyl-CoA synthase (ACS) and CO dehydrogenase (CODH). FDH, a key metalloenzyme involved in the conversion of carbon dioxide to methyltetrahydrofolate, catalyzes the reversible oxidation of formate to carbon dioxide. CoFeSP, as a methyl group transformer, accepts the methyl group from CH₃-H₄ folate and then transfers it to ACS. CODH reversibly catalyzes the reduction of CO₂ to CO and ACS functions for acetyl-coenzyme A synthesis through condensation of the methyl group, CO and coenzyme A, to finish the whole pathway. This paper introduces the structure, function and reaction mechanisms of these enzymes.     

Artificial metalloenzymes: The powerful alliance between protein scaffolds and organometallic catalysts

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Charge separation in DNA via consecutive adenine hopping

Charge transfer in DNA is of current interest because of the involvement of charge transfer in oxidative DNA damage and electronic molecular devices. We have investigated the charge separation process via the consecutive adenine (A)-hopping mechanism using laser flash photolysis of DNA conjugated with naphthaldiimide (NDI) as an electron acceptor and phenothiazine (PTZ) as a donor. Upon the 355-nm laser flash excitation of NDI, the charge separation and recombination process between NDI and PTZ was observed. The yields of the charge separation via the consecutive A-hopping were slightly dependent upon the number of A bases between the two chromophores, while the charge recombination rate was strongly dependent upon the distance. The charge-separated state persisted over 300 micros when NDI was separated from PTZ by eight A bases. Furthermore, the rate constant of the A-hopping process was determined to be 2 x 10(10) s(-1) from an analysis of the yield of the charge separation depending on the number of A-hopping steps.