Directed evolution of ATP binding proteins from a zinc finger domain by using mRNA display

Antibodies have traditionally been used for isolating affinity reagents to new molecular targets, but alternative protein scaffolds are increasingly being used for the directed evolution of proteins with novel molecular recognition properties. We have designed a combinatorial library based on the DNA binding domain of the human retinoid-X-receptor (hRXRalpha). We chose this domain because of its small size, stable fold, and two closely juxtaposed recognition loops. We replaced the two loops with segments of random amino acids, and used mRNA display to isolate variants that specifically recognize adenosine triphosphate (ATP), demonstrating a significant alteration of the function of this protein domain from DNA binding to ATP recognition. Many novel independent sequences were recovered with moderate affinity and high specificity for ATP, validating this scaffold for the generation of functional molecules.     

Infrared spectra and density functional calculations of CH2 = MHX and CH[triple bond]MH2X complexes prepared in reactions of methyl halides with Mo and W atoms

The simple methylidene and methylidyne complexes (CH2=MHX and CH[triple bond]MH2X; X = F, Cl, Br, and I) are prepared in reactions of laser-ablated Mo and W atoms with the methyl halides and investigated by matrix infrared spectroscopy and density functional theory calculations. These complex structures are photoreversible: visible irradiation converts the methylidene complex to the methylidyne complex, and UV irradiation reverses this effect via alpha-hydrogen migration. While the higher oxidation state complexes are readily formed regardless of halogen size, the Mo methylidyne complex is relatively less favored with increasing halogen size, and the W complex shows the opposite tendency. The group 6 metal methylidenes are predicted to have the most agostically distorted structures among the early transition-metal methylidenes. The computed carbon-metal bond shortens with increasing halogen size for both the methylidene and methylidyne complexes. Harmonic and anharmonic frequencies computed by DFT converge on the experimental values and thus provide support for the identification of these new Mo and W complexes.     

Transannular distance dependence of stabilization energy of the intramolecular dimer radical cation of cyclophanes

The intramolecular dimer radical cation and charge-transfer complex of various cyclophanes were investigated by using pulse radiolysis measurements. The charge resonance band due to the dimer radical cation of cyclophanes appeared in the near-IR region, which showed a blue-shift as the distance between the two benzene rings of cyclophane decreased. The stabilization energy of the dimer radical cation, which was estimated from the peak position of the charge resonance band, was explained by the exchange interaction, while the substituent effect was small. The absorption peak of the charge-transfer complex with chlorine atom also showed the shift in accordance with the oxidation potential of cyclophanes.     

Synthesis and electrochemical properties of nonstoichiometric LiAlxMn2−xO4−δ as cathode materials for rechargeable lithium ion battery

Nonstoichiometric spinel oxides, LiAl_xMn_2−xO_4−δ (x=0.1,0.2), were synthesized under controlled partial pressure of oxygen, and their elecrochemical performances were investigated. As an Al content increases, solubility limit of the oxygen nonstoichiometry, δ, increased, while partial molar enthalpy of the formation of oxygen nonstoichiometry decreased.Cycle performance of LiAl_xMn_2−xO₄ showed significant improvement comparing with that of LiMn₂O₄ cathode. However, the decrease of theoretical capacity was accompanied with Al doping. Nonstoichiometric LiAl_xMn_2−xO_4−δ showed the increase in capacity with keeping good cycle performances as well as stoichiometric LiAl_xMn_2−xO₄. Although the introduction of oxygen nonstoichiometry leads to the increase of Mn³⁺ which is known as Jahn-Teller ion, DSC curves for LiAl_xMn_2−xO_4−δ showed no exothermic peak due to phase transition arising from Jahn-Teller distortion around room temperature.     

Intramolecular and intermolecular energy transfers in donor-acceptor linear porphyrin arrays

We present highly time-resolved spontaneous fluorescence spectra of a porphyrin array system that consists of an energy donor and an acceptor linked by a phenyl group. The donors are meso-meso directly linked zinc(II) porphyrin arrays and the acceptor is a zinc(II) 5,15-di(phenylethynyl)porphyrin. The spectra over the entire Q (S1) emission band following the excitation of the donor B (S2) state have been measured directly without the conventional spectral reconstruction method. The time-resolved fluorescence spectra revealed detailed energy relaxation processes within the donor and subsequent energy transfer to the acceptor. The observed energy transfer rates to the acceptor are consistent with the Forster energy transfer rates calculated on the assumption that the energy is localized in the Q state of each porphyrin unit of the donor prior to the energy transfer. The passage of the energy deposited initially on one porphyrin unit of the donor to the acceptor illustrates a sequence of energy delocalization and localization processes before it finally reaches the acceptor.     

Cross sections for electron trapping by DNA and its component subunits I: Condensed tetrahydrofuran deposited on Kr

We report cross sections for electron capture processes occurring in condensed tetrahydrofuran (THF) for incident electron energies in the range of 0-9 eV. The charge trapping cross section for 6-9 eV electrons is very small, and an upper limit of 4 x 10(-19) cm2 is estimated from our results. This latter is thus also an upper bound for the cross section for dissociative electron attachment process that is known to occur at these energies for condensed THF. At energies close to zero eV electron trapping proceeds via intermolecular stabilization. The cross section for this process is strongly dependent on the quantity of deposited THF. Since THF may model the furyl ring found in deoxyribose, these measurements indicate that this ring likely plays little role in either initiating or enhancing strand break damage via the attachment of the low energy secondary electrons produced when DNA is exposed to ionizing radiation.     

Metal ion sensing novel calix[4]crown fluoroionophore with a two-photon absorption property

1,3-Alternate calix[4]arene-based fluorescent chemosensors bearing two-photon absorbing chromophores have been synthesized, and their sensing behaviors toward metal ions were investigated via absorption band shifts as well as one- and two-photon fluorescence changes. Free ligands absorb the light at 461 nm and weakly emit their fluorescence at 600 nm when excited by UV-vis radiation at 461 nm, but no two-photon excited fluorescence is emitted by excitation at 780 nm. Addition of an Al(3+) or Pb(2+) ion to a solution of the ligand causes a blue-shifted absorption and enhanced fluorescence due to a declined resonance energy transfer (RET) upon excitation by one- and two-photon processes. Addition of a Pb(2+) ion to a solution of 1.K(+) results in a higher fluorescence intensity than the original 1.Pb(2+) complex regardless of one- or two-photon excitation, due to the allosteric effect induced by the complexation of K(+) with a crown loop.     

Formation of insoluble perylenetetracarboxylic diimide films by electro- or photo-crosslinking of pyrrole units

Perylenetetracarboxylic diimide derivatives bearing 2- or 4-peripheral pyrrole pendants could be efficiently crosslinked to form an insoluble film either by electropolymerization or visible light induced oxidative photopolymerization of the pyrrole units.     

Inverted sapphyrin: a new family of doubly N-confused expanded porphyrins

The synthesis of an inverted, methoxylated sapphyrin derivative is described. This system, wherein inversion of pyrrolic nitrogen atoms is configurationally enforced via the use of a 3,3'-bipyrrolic precursor, displays what is best described as "weak aromaticity" as judged from its spectroscopic features and supporting theoretical calculations.