Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling

The C‐terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non‐neutralized. Because of the flexibility of the unbound CTD, a free‐energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized. The fragments were expressed by an all‐atom model and were immersed in an explicit solvent. The acetylation and charge‐neutralization varied FEL greatly, which might be convenient to exert a hub property. The acetylation slightly enhanced alpha‐helix structures that are more compact than sheet/loop conformations. The charge‐neutralization produced hairpins. Additionally, circular dichroism experiments confirmed the computational results. We propose possible binding mechanisms of CTD to partners by investigating FEL. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Synthesis of Angularly Substituted trans‐Fused Decalins through a Metallacycle‐Mediated Annulative Cross‐Coupling Cascade

A convergent coupling reaction is described that enables the stereoselective construction of angularly substituted trans‐fused decalins from acyclic precursors. The process builds on our alkoxide‐directed titanium‐mediated alkyne–alkyne coupling and employs a 1,7‐enyne coupling partner. Overall, the reaction is thought to proceed through initial formation of a tetrasusbstituted metallacyclopentadiene, stereoselective intramolecular [4+2] cycloaddition, elimination, isomerization, and regio‐ and stereoselective protonation. Distinct from our early studies directed at the synthesis of trans‐fused hydrindanes, the current annulative coupling reveals an important effect of TMSCl in controlling the final protonation—the event that establishes the stereochemistry of the ring fusion.     

Graphs corresponding to reference polynomial or to circuit characteristic polynomial

A vertex-weighted graphG ^* is studied which is obtained by deleting edgee _rs in a circuit of a graphG and giving two vertices _r and _s weightsh _r = 1 andh _s = -1, respectively. It is shown that if subgraphG - _r is identical with subgraphG - _s, then the reference polynomial ofG ^* is identical with that ofG and the characteristic polynomial ofG ^* contains the contributions due to only a certain part of the circuits found in the original graphG. This result gives a simple way to find a graph whose characteristic polynomial is equal to the reference polynomial in the topological resonance energy theory or to the circuit characteristic polynomial in the circuit resonance energy theory. This approach can be applied not only to Hilckel graphs but also to Möbius graphs, provided that they satisfy a certain condition. The significances of this new type of reference graph thus obtained are pointed out.     

The Structure of the Aggregate Form of Bacteriochlorophyll c Showing the Qy Absorption above 740 nm as Determined by the Ring-current Effects on 1H and 13C Nuclei and by 1H–1H Intermolecular NOE Correlations

¹³C-enriched bacteriochlorophyll c (S[I, E] BChl c _F) was suspended in a 1:3 mixture of methylene chloride and carbon tetrachloride to form an aggregate showing the Q_y absorption above 740 nm; changes in the ¹³C chemical shifts were traced when methanol was titrated to dissolve the aggregate, and then, the changes were correlated to the ring-current effects due to the neighboring macrocycles in the aggregate. A pair of aggregate structures has been proposed based on the ring-current effects on both ¹H and ¹³C nuclei; the monomeric units are stacked together to form an inclined column with different sliding directions, in which the y-axis of the molecule is parallel to the long axis of the column. In order to confirm this pair of models, the ring-current effects on the ¹H and ¹³C nuclei were calculated based on both the magnetic-dipole and the loop-current approximations. Further, an application of three-dimensional F1 ¹³C-edited F3 ¹³C-filtered heteronuclear single-quantum correlation-nuclear Overhauser effect spectroscopy to the above aggregate consisting of a 1:1 mixture of ¹³C-labeled and unlabeled BChl c succeeded in detecting selectively the ¹H–¹H intermolecular nuclear Overhauser effect correlations, which established the coexistence of the above pair of stacked structures in the aggregate.     

Time-dependent changes in the carotenoid composition and preferential binding of spirilloxanthin to the reaction center and anhydrorhodovibrin to the LH1 antenna complex in Rhodobium marinum

Carotenoids were isolated from the cells of Rhodobium marinum, and their structures were determined by mass spectrometry and 1H nuclear magnetic resonance spectroscopy; the carotenoids include lycopene, rhodopin, anhydrorhodovibrin, rhodovibrin and spirilloxanthin. Time-dependent changes in the carotenoid composition in the reaction center (RC) and the light-harvesting complex 1 (LH1) were traced by high-performance liquid chromatography analysis of the extracts. The carotenoid composition changed according to the spirilloxanthin biosynthetic pathway. However, spirilloxanthin having the longest conjugated chain was always preferentially bound to the RC, and anhydrorhodovibrin and other precursors to the LH1.     

Optical control of two-photon excitation efficiency of alpha-perylene crystal by pulse shaping

Optimized pulse shaping experiments were carried out on the control of two-photon excitation efficiency of an alpha-perylene crystal in the temperature region from 30 to 290 K. It was found that a pulse train with a pulse interval of 90 fs and an alternately reversing phase relation increased the excitation efficiency by a factor of 2 for the whole temperature region. The pulse shape characteristic for effective efficiency increase was reduced by double pulse experiments in which the dependence of the emission intensity on the pulse interval and relative phase between pulses were measured. The mechanism of the efficiency increase is briefly discussed using a sliding-window Fourier transform of the pulse shape.     

Strong near-infrared luminescence in BaSnO3

Powdered samples of the perovskite BaSnO(3) exhibit strong near-infrared (NIR) luminescence at room temperature, following band-gap excitation at 380 nm (3.26 eV). The emission spectrum is characterized by a broad band centered at 905 nm (1.4 eV), tailing on the high-energy side to approximately 760 nm. The Stokes shift is 1.9 eV, and measured lifetimes in the range 7-18 ms depend on preparative conditions. These extraordinary long values indicate that the luminescence involves a defect state(s). At low temperatures, both a sharp peak and a broad band appear in the visible portion of the luminescence spectrum at approximately 595 nm. Upon cooling, the intensity of the NIR emission decreases, while the integrated intensities of the visible emission features increase to approximately 40% of the NIR intensity at 77 K. Room-temperature photoluminescence (PL) is observed across the Ba(1-x)Sr(x)SnO(3) series. As the strontium content increases, the excitation maximum and band gap shift further into the UV, while the intensity of the NIR emission peak decreases and shifts further into the infrared. This combination leads to an unexpectedly large increase in the Stokes shift. The unusual NIR PL in BaSnO(3) may originate from recombination of a photogenerated valence-band hole and an occupied donor level, probably associated with a Sn(2+) ion situated roughly 1.4 eV above the valence-band edge.     

Synthesis, stabilities, and redox behavior of Di(1-azulenyl)(6-azulenyl)methylium hexafluorophosphates. Generation of a donor-acceptor-substituted neutral radical by azulenes

Several di(1-azulenyl)(6-azulenyl)methanes and 1,3-bis[(1-azulenyl)(6-azulenyl)methyl]azulenes were prepared by the condensation reaction of azulenes with diethyl 6-formylazulene-1,3-dicarboxylate under acidic conditions. The products were converted into di(1-azulenyl)(6-azulenyl)methylium hexafluorophosphates and azulene-1,3-diylbis[(1-azulenyl)(6-azulenyl)methylium] bis(hexafluorophosphate)s via hydride abstraction reaction with DDQ following the exchange of counterions. These mono- and dications exhibited high stability with large pK(R)(+) values (5.6-10.1), despite the captodative substitution of azulenes. The electrochemical reduction of the monocations upon cyclic voltammetry (CV) exhibited a reversible two-step, one-electron reduction wave with a small difference between the first reduction potential (E(1)(red)) and the second one (E(2)(red)), which exhibited the generation of highly amphoteric neutral radicals in solution. The electrochemical reduction of dications showed voltammograms, which were characterized by subsequent two single-electron waves and a two-electron transfer upon CV attributable to the formation of a radical cation, a diradical (or twitter ionic structure), and a dianionic species, respectively. Formation of a persistent neutral radical from a monocation was revealed by ESR and UV-vis spectroscopies and theoretical calculations. The ESR spectra of the neutral radical gave two hyperfine coupling constants: a(H) = 0.083 (6H) and 0.166 mT (9H) (g = 2.0024), indicating that an unpaired electron delocalizes over all three of the azulene rings. The stable monoanion, which shows the localization of the charge on the 6-azulenyl substituent, was also successfully generated from the di(1-azulenyl)(6-azulenyl)methane derivative.