Conformational changes of non-B DNA

In contrast to B-DNA that has a right-handed double helical structure with Watson-Crick base pairing under the ordinary physiological conditions, repetitive DNA sequences under certain conditions have the potential to fold into non-B DNA structures such as hairpin, triplex, cruciform, left-handed Z-form, tetraplex, A-motif, etc. Since the non-B DNA-forming sequences induce the genetic instability and consequently can cause human diseases, the molecular mechanism for their genetic instability has been extensively investigated. On the contrary, non-B DNA can be widely used for application in biotechnology because many DNA breakage hotspots are mapped in or near the sequences that have the potential to adopt non-B DNA structures. In addition, they are regarded as a fascinating material for the nanotechnology using non-B DNAs because they do not produce any toxic byproducts and are robust enough for the repetitive working cycle. This being the case, an understanding on the mechanism and dynamics of their structural changes is important. In this critical review, we describe the latest studies on the conformational dynamics of non-B DNAs, with a focus on G-quadruplex, i-motif, Z-DNA, A-motif, hairpin and triplex (189 references).     

Norharmane: old yet highly selective dual channel ratiometric fluoride and hydrogen sulfate ion sensor

Norharmane provides a simple unexplored class of anion receptor, that allows for the ratiometric selective detection of F(-) and HSO(4)(-) ions. The presence of a strong base can easily form hydrogen bonds with the acidic hydrogen bond donor moiety and the relatively strong acid can easily protonate the basic hydrogen bond acceptor moiety, which can modulate the optical response and can detect the anions efficiently with high selectivity. In view of that, it is promising to conceive the use of these systems in various sensing applications as well as in other situations, such as anion transport and purification, where the availability of cheap and easy-to-make anion receptors, would be advantageous.     

Reorganization energy of supramolecular donor–acceptor dyad of octaethylporphyrin isomers and axial-coordinated acceptor: Experimental and computational study

The internal reorganization energy (λ_V) of photoinduced electron transfer (ET) in the supramolecular donor–acceptor dyads of 2,3,7,8,12,13,17,18-octaethylporphinatozinc(II) (ZnOEP) and electron acceptor ligands was compared with those of structural isomers, 2,3,7,8,11,12,17,18-octaethylhemiporphycenatozinc(II) (ZnHPc) and 2,3,6,7,12,13,16,17-octaethylporphycenatozinc(II) (ZnPcn). First, ET process of the supramolecular donor–acceptor dyads of ZnOEP was investigated by means of the transient absorption spectroscopy mainly. The formation of supramolecular dyads was confirmed by absorption spectral change, from which the association constant was estimated. The ET process was confirmed by the observation of radical cation of ZnOEP during the laser flash photolysis. The ET rates of these dyads are in the order of ZnOEP > ZnHPc > ZnPcn, when the driving forces for ET are similar to each other. From the free energy dependence of ET rates, the λ_V values of OEP and its isomers were estimated. The estimated λ_V value was in the order of ZnOEP < ZnHPc < ZnPcn. This tendency was reproduced by calculation at B3LYP/6-31G(d) and BHandHLYP/6-31G(d) levels. The origin of this tendency was discussed on the basis of the structural change during the ET process.     

Microbial conversion of curcumin into colorless hydroderivatives by the endophytic fungus Diaporthe sp. associated with Curcuma longa

We investigated the microbial conversion of curcumin (1) using endophytic fungi associated with the rhizome of Curcuma longa (Zingiberaceae). We found that Diaporthe sp., an endophytic filamentous fungus, converts curcumin (1) into four colorless derivatives, namely (3R,5R)-tetrahydrocurcumin (2), a novel (3R,5S)-hexahydrocurcumin (3) named neohexahydrocurcumin, (3S,5S)-octahydrocurcumin (4) and meso-octahydrocurcumin (5).     

Prediction error criterion for selecting variables in a linear regression model

Several criteria, such as CV, C _p , AIC, CAIC, and MAIC, are used for selecting variables in linear regression models. It might be noted that C _p has been proposed as an estimator of the expected standardized prediction error, although the target risk function of CV might be regarded as the expected prediction error R _PE. On the other hand, the target risk function of AIC, CAIC, and MAIC is the expected log-predictive likelihood. In this paper, we propose a prediction error criterion, PE, which is an estimator of the expected prediction error R _PE. Consequently, it is also a competitor of CV. Results of this study show that PE is an unbiased estimator when the true model is contained in the full model. The property is shown without the assumption of normality. In fact, PE is demonstrated as more faithful for its risk function than CV. The prediction error criterion PE is extended to the multivariate case. Furthermore, using simulations, we examine some peculiarities of all these criteria.     

Heterometallic d8–d10 Coupling of Rh(I) and M(0) (M=Pd,Pt) in a Sandwich Framework of π-Conjugated Ligands

A heterometallic M−M′ bond formation is a key to construct atomically precise bimetallic clusters and materials. However, it is sometimes not straightforward to construct a heterometallic M−M′ bond through conventional methods including redox condensation. Here, we found that a sandwich framework of π-conjugated unsaturated hydrocarbon ligands provides a unique coordination environment that facilitates unusual coupling of d⁸ Rh^I and d¹⁰ M⁰ (M=Pd, Pt). The molecular orbital analysis showed that the electron-accepting ability of the sandwich framework through back-donation allows the formation of a dσ-type Rh−Pd bond in a (d–d)¹⁸ electron system.     

Expansion of Photostable Luminescent Radicals by Meta-Substitution

Polychlorinated pyridyldiphenylmethyl radicals having substituents meta to the position bearing the carbon-centered radical (α-carbon) are synthesized. All of them are stable in ambient conditions in solutions and fluorescent in cyclohexane. The fluorescence of the radicals with bromo, phenyl, 4-chlorophenyl, or 2-pyridyl substituents are enhanced in chloroform, while the emission of the radicals with 2-thienyl or 2-furyl substituents are quenched in chloroform. DFT and TD-DFT calculations indicate that the first doublet excited states of the former are locally excited, while the first doublet excited states of the latter are charge transfer states from the π-electron-donating substituent to the accepting radical. The latter also show much higher photostability under 370-nm light irradiation compared with the first reported photostable fluorescent radical, (3,5-dichloro-4-pyridyl)bis(2,4,6-trichlorophenyl)methyl radical (PyBTM), with pronounced bathochromic shifts of the fluorescence.     

C-O-bond cleavage of esters with a naphthyl group in the higher triplet excited state during two-color two-laser flash photolysis

A C-O-bond cleavage of esters having a naphthyl group, NpCO-OR and RCO-ONp (Np=alpha- and beta-naphthyl ((alpha)Np and (beta)Np, respectively), R=Ph and Me), was found during the two-color two-laser flash photolysis in acetonitrile. The C-O-bond cleavage occurred when NpCO-OR and RCO-ONp were excited to the singlet excited states (S1). On the other hand, no reaction occurred from the lowest triplet excited states (T1). When NpCO-OR(T1) and RCO-ONp(T1) were excited to the higher triplet excited states (Tn) using the second laser during the two-color two-laser flash photolysis, the C-O-bond cleavage occurred. The C-O-bond cleavage quantum yield (Phi) was estimated from the plots of the T1-state esters disappeared within a laser flash versus the second laser intensities. The C-O-bond cleavage in (beta)NpCO-OPh(Tn) occurred more efficiently than in (alpha)NpCO-OPh(Tn) and that in PhCO-O(beta)Np(Tn) occurred more efficiently than in PhCO-O(alpha)Np(Tn). The Phi value for ester with Ph and beta-Np groups was larger than that for ester with Ph and alpha-Np groups. The Phi value for MeCO-O(alpha)Np(Tn) was similar to those for PhCO-ONp(Tn), while that for MeCO-O(beta)Np(Tn) was much smaller than those for PhCO-ONp(Tn) and MeCO-O(alpha)Np(Tn). On the other hand, no C-O-bond cleavage was observed in NpCO-OMe(Tn). The Phi value depended on the characters of the groups (Np, Ph, and Me) on the ester. Whether R is Ph or Me with or without pi electron, respectively, is important for the C-O-bond cleavage. In other words, electronic delocalization of the T(n) state including Np and ester groups is necessary for the occurrence of the C-O-bond cleavage in NpCO-OR(Tn) and RCO-ONp(Tn).     

Lifetime regulation of the charge-separated state in DNA by modulating the oxidation potential of guanine in DNA through hydrogen bonding

A series of naphthalimide (NI)- and 5-bromocytosine ((br)C)-modified oligodeoxynucleotides (ODNs) were prepared, and their lifetimes of the charge-separated states during the photosensitized one-electron oxidation of DNA were measured. Various lifetimes of the charge-separated states were observed depending on the sequence and the incorporation sites of (br)C, and the oxidation potential of G in the (br)C:G base-pair relative to that of G in the C:G base-pair and in the GGG sequence was determined by comparing the lifetimes of the charge-separated states. The change in the cytosine C5 hydrogen to bromine resulted in a 24 mV increase in the oxidation potential of G in the (br)C:G base-pair as compared to that of G in the C:G base-pair, the value of which is comparable to a 58 mV decrease in the oxidation potential of G in the GGG sequence. These results clearly demonstrate that hole transfer in DNA can be controlled through hydrogen bonding by introducing a substituent on the cytosine.     

Reflection spectra of silicate glasses in the vacuum ultraviolet region

Reflection spectra of silicate glasses were measured in the spectral region 2–13 eV. The bands due to bridging oxygen were found at 11.6 and 10.4–9.5 eV. The bands for non-bridging oxygens were found in the region 8.8–4.9 eV. They shift to lower energy with increasing ionic radius for the low valency cations while they shift to higher energy with increasing ionic radius for the high valency cations. The correlation between the measured bands and the absorption wavelength calculated from Drude-Voigt dispersion formula is discussed.