Distribution of the cationic state over the chlorophyll pair of the photosystem II reaction center

The reaction center chlorophylls a (Chla) of photosystem II (PSII) are composed of six Chla molecules including the special pair Chla P(D1)/P(D2) harbored by the D1/D2 heterodimer. They serve as the ultimate electron abstractors for water oxidation in the oxygen-evolving Mn(4)CaO(5) cluster. Using the PSII crystal structure analyzed at 1.9 ? resolution, the redox potentials of P(D1)/P(D2) for one-electron oxidation (E(m)) were calculated by considering all PSII subunits and the protonation pattern of all titratable residues. The E(m)(Chla) values were calculated to be 1015-1132 mV for P(D1) and 1141-1201 mV for P(D2), depending on the protonation state of the Mn(4)CaO(5) cluster. The results showed that E(m)(P(D1)) was lower than E(m)(P(D2)), favoring localization of the charge of the cationic state more on P(D1). The P(D1)(?+)/P(D2)(?+) charge ratio determined by the large-scale QM/MM calculations with the explicit PSII protein environment yielded a P(D1)(?+)/P(D2)(?+) ratio of ~80/~20, which was found to be due to the asymmetry in electrostatic characters of several conserved D1/D2 residue pairs that cause the E(m)(P(D1))/E(m)(P(D2)) difference, e.g., D1-Asn181/D2-Arg180, D1-Asn298/D2-Arg294, D1-Asp61/D2-His61, D1-Glu189/D2-Phe188, and D1-Asp170/D2-Phe169. The larger P(D1)(?+) population than P(D2)(?+) appears to be an inevitable fate of the intact PSII that possesses water oxidation activity.     

Photostability via sloped conical intersections: a computational study of the excited states of the naphthalene radical cation

On the basis of an extensive ab initio electronic structure study of the ground and excited-state potential energy surfaces of the naphthalene radical cation (N*+), we propose a mechanism for its ultrafast nonradiative relaxation from the second excited state (D2) down to the ground state (D0), which could explain the experimentally observed photostability [Zhao, L.; Lian, R.; Shkrob I. A.; Crowell, R. A.; Pommeret, S.; Chronister, E. L.; Liu, A. D.; Trifunac, A. D. J. Phys. Chem. A., 2004, 108, 25]. The proposed photophysical relaxation pathway involves internal conversion from the D2 state down to the D0 state via two consecutive, accessible, sloped conical intersections (CIs). The two crossings, D0/D1 and D1/D2, are characterized at the complete active space self-consistent field (CASSCF) level. At this level of theory, the D0/D1 crossing is energetically readily accessible, while the D1/D2 CI appears too high in energy to be involved in internal conversion. However, the inclusion of dynamic correlation effects, via single point CASPT2 calculations including excitations out of the valence pi- and sigma-orbitals, lowers the D0 and D2 state energies with respect to D1. Extrapolations at the CASPT2 level predict that the D1/D2 crossing is then significantly lower in energy than with CASSCF indicating that with a higher-level treatment of dynamic correlation it may be energetically accessible following vertical excitation to D2. N*+ is proposed as one of the species contributing to a series of diffuse infrared absorption bands originating from interstellar clouds. Understanding the mechanism for photostability in the gas phase, therefore, has important consequences for astrophysics.     

Remarkable reactivities of the xanthone ketyl radical in the excited state compared with that in the ground state

The properties and reactivities of the xanthone (Xn) ketyl radical (XnH*) in the doublet excited state (XnH*(D1)) were examined by using two-color two-laser flash photolysis. The absorption and fluorescence of XnH*(D1) were observed for the first time. Several factors governing the deactivation processes of XnH*(D1) such as interaction and reaction with solvent molecules were discussed. The remarkable change of reactivity of XnH*(D1) compared with that in the ground state (XnH*(D0)) was indicated from the experimental results. The rapid halogen abstraction of XnH*(D1) from some halogen donors such as carbon tetrachloride (CCl4) was found to occur. The halogen abstraction occurred more efficiently in the polar solvents than in the nonpolar solvents. It is suggested that the polar solvents promote the spin distribution of XnH*(D1) of the phenyl ring favorable to the halogen abstraction.     

重水中固氮酶催化还原乙炔产物的^1H NMR研究

用^1HNMR研究了固氮酶在重水中催化还原乙炔的反应产物氘代乙烯.种用群对称性对^1HNMR谱图进行了归属,计算了几种可能的C`2H~2D~2结构以及C~2H~3D结构的NMR谱线频和强度,得出了理论谱.通过理论谱与实验谱的比较,表明固氮酶在重水中催化还原乙炔的产物主要以顺式结构C~2H~2D~2为主,并含有较多的单氘代烯.单氘代乙烯相对乙烯的化学位移往高场移动约4.0Hz,而双氘代乙烯向高场的位移大约是单氘代乙烯的2倍左右。     

The effect of the order of the autocatalysis on the transverse stability of reaction fronts

A linear stability analysis of planar reaction fronts to transverse perturbations is considered for a system based on an autocatalytic reaction of general order p. Dispersion curves, plots of the growth rate sigma against a transverse wavenumber k, are obtained for a range of values of p and D, where D is the ratio of the diffusion coefficients of autocatalyst and substrate. A value D(0) of D, dependent on p, is found at which sigma(max), the maximum value of sigma in the unstable regime, is largest, with D(0) increasing as p is increased. An asymptotic analysis for small wavenumbers is derived, which enables the region in the (p, D) parameter space for instability to be determined. An analysis for D small is undertaken, which leads to upper bounds on the wavenumber for a possible instability.     

C40异构体的结构和稳定性的理论研究

利用Gaussian98程序,采用密度泛函(DFT)方法中的B3LYP,选用6-31G基组对富勒烯(Fullerene)C40的6种异构体[D5d,Td,D2h,C3v,D2(Ⅰ),D2(Ⅱ)]进行了几何构型优化,其中,对于Td对称性的C40由于易发生Jahn-Teller畸变,则降低其对称性为D2d,再进行优化.对它们的平衡几何和电子结构进行了比较具体的分析,同时,根据计算得到的总能量推断出这6种异构体的稳定性顺序是D2(Ⅰ)>D5d>Td>C3v>D2h>D2(Ⅱ).     

Ab initio and DFT studies of the spin-orbit and spin-spin contributions to the zero-field splitting tensors of triplet nitrenes with aryl scaffolds

Spin-orbit and spin-spin contributions to the zero-field splitting (ZFS) tensors (D tensors) of spin-triplet phenyl-, naphthyl-, and anthryl-nitrenes in their ground state are investigated by quantum chemical calculations, focusing on the effects of the ring size and substituted position of nitrene on the D tensor. A hybrid CASSCF/MRMP2 approach to the spin-orbit term of the D tensor (D(SO) tensor), which was recently proposed by us, has shown that the spin-orbit contribution to the entire D value, termed the ZFS parameter or fine-structure constant, is about 10% in all the arylnitrenes under study and less depends on the size and connectivity of the aryl groups. Order of the absolute values for D(SO) can be explained by the perturbation on the energy level and spatial distributions of π-SOMO through the orbital interaction between SOMO of the nitrene moiety and frontier orbitals of the aryl scaffolds. Spin-spin contribution to the D tensor (D(SS) tensor) has been calculated in terms of the McWeeny-Mizuno equation with the DFT/EPR-II spin densities. The D(SS) value calculated with the RO-B3LYP spin density agrees well with the D(Exptl) -D(SO) reference value in phenylnitrene, but agreement with the reference value gradually becomes worse as the D value decreases. Exchange-correlation functional dependence on the D(SS) tensor has been explored with standard 23 exchange-correlation functionals in both RO- and U-DFT methodologies, and the RO-HCTH/407 method gives the best agreement with the D(Exptl) -D(SO) reference value. Significant exchange-correlation functional dependence is observed in spin-delocalized systems such as 9-anthrylnitrene (6). By employing the hybrid CASSCF/MRMP2 approach and the McWeeny-Mizuno equation combined with the RO-HCTH/407/EPR-II//U-HCTH/407/6-31G* spin densities for D(SO) and D(SS), respectively, a quantitative agreement with the experiment is achieved with errors less than 10% in all the arylnitrenes under study. Guidelines to the putative approaches to D(SS) tensor calculations are given.     

Solvent effect on the deactivation processes of benzophenone ketyl radicals in the excited state

The solvent effects on ketyl radicals of benzophenone derivatives (BPD) in the excited state (BPDH*(D1)) were investigated. Absorption and fluorescence spectra of BPDH*(D1) in various solvents were measured using nanosecond-picosecond two-color two-laser flash photolysis. The fluorescence peaks from BPDH*(D1) showed a shift due to the dipole-dipole interaction with the solvent molecules. The dipole moments (mu(e)) of BPDH*(D1) were estimated to be 7-10 D, indicating that BPDH*(D1) are highly polarized. It was revealed that the fluorescence lifetime (tau(f)) depends on mu(e) in acetonitrile because the stabilization by solvent molecules affects the tau(f) value in polar solvents, predominantly. On the contrary, the conformation of BPDH*(D1) plays an important role in cyclohexane because the efficiency of the unimolecular reaction from BPDH*(D1) depends on the conformation. The substituent effect on the electron transfer from BPDH*(D1) to their parent molecules was also discussed.     

Formation of the diphenyl molecule in the crossed beam reaction of phenyl radicals with benzene

The chemical dynamics to form the D5-diphenyl molecule, C6H5C6D5, via the neutral-neutral reaction of phenyl radicals (C6H5) with D6-benzene (C6D6), was investigated in a crossed molecular beams experiment at a collision energy of 185 kJ mol(-1). The laboratory angular distribution and time-of-flight spectra of the C6H5C6D5 product were recorded at mass to charge mz of 159. Forward-convolution fitting of our data reveals that the reaction dynamics are governed by an initial addition of the phenyl radical to the pi electron density of the D6-benzene molecule yielding a short-lived C6H5C6D6 collision complex. The latter undergoes atomic deuterium elimination via a tight exit transition state located about 30 kJ mol(-1) above the separated reactants; the overall reaction to form D5-diphenyl from phenyl and D6-benzene was found to be weakly exoergic. The explicit identification of the D5-biphenyl molecules suggests that in high temperature combustion flames, a diphenyl molecule can be formed via a single collision event between a phenyl radical and a benzene molecule.     

The kinetic role of carboxylate residues in the proximity of the trinuclear centre in the O2 reactivity of CotA-laccase

Multicopper oxidases catalyze the four-electron reduction of dioxygen to water without the release of any reactive oxygen intermediate species. The role of carboxylate residue Asp116 located at the exit channel for water molecules of CotA-laccase has been investigated by site-saturation mutagenesis. A total of 300 clones was picked and screened for activity. Five variant enzymes, D116E, D116A, D116N, D116T and D116L, were selected for further characterisation. Spectroscopic analysis revealed only small perturbations in the geometry of the catalytic Cu sites of variants. However, a severe drop in turnover numbers (k(cat)) and downshifts by approximately 1-2 units of the optimal pH were observed for the oxidation of substrates, as compared with the wild type. The kinetics of formation and decay of peroxide intermediate (PI) was studied in type 1 depleted (T1D) CotA-laccase and in T1D-D116 or T1D-E498 mutants, previously shown to be involved in the mechanism of dioxygen reduction. It is noteworthy that CotA shows 10 times lower rates of PI formation and 10(3) higher PI decay rates as compared with other studied multicopper oxidases. The generation of PI is pH independent and mostly unaffected by the D116 or E498 mutations. In contrast, the decay of PI is markedly compromised by the replacement of D116 or E498 with non-carboxylate residues. The E498 residue appears to be the main protonable species for acceleration of PI decay at low pH. The D116 residue seems to be essential in the modulation of E498 protonation and in assisting protons to hydroxyl groups bound to the T2 Cu.     

Unveiling the Layer‐Dependent Catalytic Activity of PtSe2 Atomic Crystals for the Hydrogen Evolution Reaction

Two‐dimensional (2D) PtSe₂ shows the most prominent layer‐dependent electrical properties among various 2D materials and high catalytic activity for hydrogen evolution reaction (HER), and therefore, it is an ideal material for exploring the structure–activity correlations in 2D systems. Here, starting with the synthesis of single‐crystalline 2D PtSe₂ with a controlled number of layers and probing the HER catalytic activity of individual flakes in micro electrochemical cells, we investigated the layer‐dependent HER catalytic activity of 2D PtSe₂ from both theoretical and experimental perspectives. We clearly demonstrated how the number of layers affects the number of active sites, the electronic structures, and electrical properties of 2D PtSe₂ flakes and thus alters their catalytic performance for HER. Our results also highlight the importance of efficient electron transfer in achieving optimum activity for ultrathin electrocatalysts. Our studies greatly enrich our understanding of the structure–activity correlations for 2D catalysts and provide new insight for the design and synthesis of ultrathin catalysts with high activity.     

Selective ion binding by protein probed with the statistical mechanical integral equation theory

Selective ion binding by human lysozyme and its mutants is probed with the three-dimensional interaction site model theory which is the statistical mechanical integral equation theory. Preliminary and partial results of the study have been already published (Yoshida, N. et al. J. Am. Chem. Soc. 2006, 128, 12042-12043). The calculation was carried out for aqueous solutions of three different electrolytes, CaCl2, NaCl, and KCl, and for four different mutants of the human lysozyme: wild type, Q86D, A92D, and Q86D/A92D, which have been studied experimentally. The discussion of this article focuses on the cleft that consists of amino acid residues from Q86 to A92. For the wild type of protein in the aqueous solutions of all the electrolytes studied, there are no distributions observed for the ions inside the cleft. The Q86D mutant shows essentially the same behavior with that of the wild type. The A92D mutant shows strong binding ability to Na+ in the recognition site, which is in accord with the experimental results. There are two isomers of the Q86D/A92D mutant, e.g., apo-Q86D/A92D and holo-Q86D/A92D. Although both isomers exhibit the binding ability to the Na+ and Ca2+ ions, the holo isomer shows much greater affinity compared with the apo isomer. Regarding the selective ion binding of the holo-Q86D/A92D mutant, it shows greater affinity to Ca2+ than to Na+, which is also consistent with the experimental observation.     

Energy disposal during desorption of D2 from the surface and subsurface region of Ni(111)

The recombination of surface and subsurface D atoms on Ni(111) has been studied using resonance-enhanced multiphoton ionisation (REMPI) to measure the internal state and translational energy distributions of the desorbing product. By detecting D2 formed during temperature-programmed desorption we were able to examine the reaction between subsurface and surface D atoms, and the recombination of two D atoms chemisorbed on the surface. Translational energy distributions for D2 formed by recombination of surface D are very sensitive to coverage. Desorption from a low coverage surface produced a translational energy release of 2.6 kT, but a thermal rotational distribution, reflecting an entrance channel barrier to dissociative chemisorption on the clean Ni(111) surface. Sticking probabilities predicted from detailed balance are consistent with molecular beam adsorption measurements. Desorption from D coverages above 0.5 ML resulted in a sub-thermal energy release, desorption being mediated by a molecular precursor state with D2 dissociation occurring via a non-activated, trapping-dissociation channel. In contrast, the reaction of subsurface D produces translationally hot D2, with a mean energy approaching 8 kTs at 180 K. This is consistent with the energetics for direct recombination of a chemisorbed D atom with a metastable subsurface D atom, which overcomes an activation barrier to resurface of between 0.35 and 0.47 eV depending on D concentration. The energy release decreases at higher temperature, probably as a result of a reduction in the energy of resurfacing D as the subsurface D concentration drops. This low energy component is attributed to accommodation of resurfacing D which is unable to react directly, followed by slow thermal desorption via the high coverage, surface D recombination channel. No internal rotational or vibration excitation was found in D2 formed by reaction of subsurface D.     

N-（O,O-二异丙基）磷酰化丝氨酸成肽反应的立体效应研究

研究了N－（O,O－二异丙基）磷酰化－L－（或D－）丝氨酸和L－（或D－）组氨酸在水溶液中的反应及其与L－（或D－）组氨酸甲酯在DMSO中的反应,用SDS作对离子试剂,采用离子对反相高效液相色谱方法及反应产物进行分析。结果表明,所有反应体系中均有丝组二肽生成,而L－L和D－D型丝组二肽的生成量约是L－D和D－L型产物的4倍。     

Anomalous fluorescence from the azaxanthone ketyl radical in the excited state

The time-resolved absorption and fluorescence spectra of the azaxanthone (AX) ketyl radical (AXH.) in the excited state (AXH.(Dn) (n = 1 or 2)) were observed during the nanosecond-picosecond two-color two-laser flash photolysis. AXH. showed dual fluorescence peaks at 460 and 645 nm, which were assigned to the D2 --> D0 and D1 --> D0 transitions, respectively. It was found that the lifetime of the D2 --> D0 fluorescence (1.0 ns) was longer than that of the D1 --> D0 fluorescence (0.4 ns). The fluorescent quantum yields of the D1 --> D0 and D2 --> D0 fluorescence were estimated to be 0.0008 +/- 0.0002 and 0.05 +/- 0.02, respectively. These anomalous emitting properties can be attributed to the pyridine ring in AX. AXH. is a new example of a neutral radical which violates Kasha's rule.     

Porous Carbon Fibers Containing Pores with Sizes Controlled at the Ångstrom Level by the Cavity Size of Pillar[6]arene

We report a new synthesis method of fibrous carbon material with pores sizes that are precisely controlled at the Ångstrom level, by carbonization of two dimensional (2D) porous sheets of pillar[6]arenes. The 2D porous sheets were prepared by 2D supramolecular polymerization induced by oxidation of hydroquinone units of pillar[6]arenes. Owing to the hexagonal structure of pillar[6]arene, the assembly induced by 2D supramolecular polymerization gave hexagonal 2D porous sheets, and the highly ordered structure of the 2D porous sheets formed regular fibrous structures. Then, carbonization of the 2D porous sheets afforded fibrous carbon materials with micropores. The micropore size of the fibrous porous carbon prepared from pillar[6]arene was the same size as that of the starting material pillar[6]arene assembly.     

Studies of translational diffusion in the smectic A phase of a Gay-Berne mesogen using molecular dynamics computer simulation

Molecular dynamics computer simulations are used to determine the self-diffusion coefficients for a Gay-Berne model mesogen GB (4.4,20,1,1) in the isotropic, nematic and smectic A phases along two isobars. The values of the parallel and perpendicular diffusion coefficients, D(parallel) and D(perpendicular), are calculated and compared in the different phases. For the phase sequence isotropic-smectic A, D(perpendicular)*> or =D(parallel)* over the whole smectic A range with the ratio D(parallel)*/D(perpendicular)* decreasing with decreasing temperature. At a higher pressure, a nematic phase is observed between these two phases and we find that D(parallel)*>D(perpendicular)* throughout the nematic region and the inequality D(parallel)*>D(perpendicular)* remains on entering the smectic A phase. However, the ratio D(parallel)*/D(perpendicular)* decreases with decreasing temperature within the smectic A range and eventually this ratio inverts such that D(perpendicular)*>D(parallel)* at low temperatures. The temperature dependence of the parallel diffusion coefficient in the smectic A phase for this model mesogen is compared to that predicted by a theoretical model for diffusion subject to a cosine potential.     

Exclusive interaction of the 15.5 kD protein with the terminal box C/D motif of a methylation guide snoRNP

Box C/D small nucleolar RNAs (snoRNAs) direct site-specific methylation of ribose 2'-hydroxyls in ribosomal and spliceosomal RNAs. To identify snoRNA functional groups contributing to assembly of an active box C/D snoRNP in Xenopus oocytes, we developed an in vivo nucleotide analog interference mapping procedure. Deleterious substitutions consistent with requirements for binding the 15.5 kD protein clustered within the terminal box C/D motif only. In vitro analyses confirmed a single interaction site for recombinant 15.5 kD protein and identified the exocyclic amine of A89 in box D as essential for binding. Our results argue that the 15.5 kD protein interacts asymmetrically with the two sets of conserved box C/D elements and that its binding is primarily responsible for the stability of box C/D snoRNAs in vivo.     

Determination of the internal state distribution of the SD product from the S(1D)+D2 reaction

The S(1D)+D2-->SD+D reaction has been studied through a photolysis-probe experiment in a cell. S(1D) reagent was prepared by 193 nm photolysis of CS2, and the SD(X 2Pi) product was detected by laser fluorescence excitation. The nascent rotational/fine-structure state distribution of the SD(X 2Pi) product was determined. This reaction, previously studied theoretically and in a crossed molecular beam experiment, is known to proceed through formation and decay of a long-lived collision complex involving the deep well in the H2S ground electronic state. The determined SD rotational state distribution in the v=0 vibrational level was found to be approximately statistical, with a small preference for formation of the F1 (Omega=3/2) fine-structure manifold over F2 (Omega=1/2). The branching into the Lambda doublet levels was also investigated, and essentially equal populations of levels of A' and A" symmetry were found. The present results are compared with previous investigations of this reaction and the analogous O(1D)+D2 reaction.