Vibrational dynamics of DNA. II. Deuterium exchange effects and simulated IR absorption spectra

In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm(-1). However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D(2)O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the (18)O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.     

Copper-catalyzed beta-Boration of alpha,beta-unsaturated carbonyl compounds: rate acceleration by alcohol additives

[reaction: see text] The efficient addition of bis(pinacolato)diboron to alpha,beta-unsaturated carbonyl compounds with a copper-diphosphine catalyst has been carried out. A dramatic rate acceleration of the reaction was realized by adding alcohol additives. With use of this procedure, a variety of alpha,beta-unsaturated carbonyl compounds including conjugated substrates at the acid oxidation level such as esters and nitriles were reacted to give to the corresponding beta-boryl carbonyl compounds in high yields.     

Expression of hepatitis C virus nonstructural 4B in transgenic mice

Hepatitis C virus (HCV) is a pathogen that is of great medical significance in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma worldwide. Although the HCV proteins have been intensively investigated over the past decade, the biochemical functions of the NS4B protein are still largely unknown. To investigate NS4B as a potential causative agent of liver disease, transgenic mice expressing the NS4B protein in liver tissue were produced. The transgenic animals were phenotypically similar to their normal littermates for up to 18 months of age. Our results suggest that the HCV NS4B protein is not directly cytopathic or oncogenic in our transgenic mice model.     

Angular distributions of H-induced HD and D2 desorptions from the Si(100) surfaces

We measured angular distributions of HD and D2 molecules desorbed via the reactions H+DSi(100)-->HD [abstraction (ABS)] and H+DSi(100)-->D2 [adsorption-induced-desorption (AID)], respectively. It was found that the angular distribution of HD molecules desorbed along ABS is broader than that of D2 molecules desorbed along AID, i.e., the former could be fit with cos(2.0+/-0.2) theta, while the latter with cos(5.0+/-0.5) theta. This difference of the angular distributions between the two reaction paths suggests that their dynamic mechanisms are different. The observed cos2 theta distribution for the ABS reaction was reproduced by the classical trajectory calculations over the London-Eyring-Polanyi-Sato potential-energy surfaces. The simulation suggests that the HD desorption along the ABS path takes place along the direction of Si-D bonds, but the apparent angular distribution is comprised of multiple components reflecting the different orientations of D-occupied Si dimers in the (2 x 1) and (1 x 2) double domain structures.     

Physicochemical characterization of self-assembled poly(∈-caprolactone) grafted dextran nanoparticles

Amphiphilic graft copolymer composed of poly(∈-caprolactone) and dextran was synthesized by ring opening polymerization of ∈-caprolactone initiated through the hydroxyl end of dextran in the presence of stannous 2-ethylhexanoate [Sn (oct)₂] as a catalyst. It has been widely characterized by Fourier transform infrared spectroscopy, ¹H NMR, and thermogravimetric analysis. Nanoparticles were prepared in aqueous medium by co-solvent evaporation technique at room temperature (25 °C). Hydrodynamic diameter and particle size were measured by dynamic light scattering spectroscopy and atomic force microscopy, respectively. Core-shell geometry of polymeric nanoparticle was characterized by fluorescence spectrophotometer using pyrene as a probe. Critical micelle concentration of polymer in triple distilled water decreased from 6.9 × 10⁻⁴ to 8.9 × 10⁻⁴ g/l with increasing hydrophobic moiety. Further, the physiological stability of the nanoparticles in phosphate buffer saline of pH 7.4 at 37 °C was evaluated, which showed promising in drug delivery system.     

Oxidation of guanine in G, GG, and GGG sequence contexts by aromatic pyrenyl radical cations and carbonate radical anions: relationship between kinetics and distribution of alkali-labile lesions

Oxidatively generated DNA damage induced by the aromatic radical cation of the pyrene derivative 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), and by carbonate radicals anions, was monitored from the initial one-electron transfer, or hole injection step, to the formation of hot alkali-labile chemical end-products monitored by gel electrophoresis. The fractions of BPT molecules bound to double-stranded 20-35-mer oligonucleotides with noncontiguous guanines G and grouped as contiguous GG and GGG sequences were determined by a fluorescence quenching method. Utilizing intense nanosecond 355 nm Nd:YAG laser pulses, the DNA-bound BPT molecules were photoionized to BPT*+ radicals by a consecutive two-photon ionization mechanism. The BPT*+ radicals thus generated within the duplexes selectively oxidize guanine by intraduplex electron-transfer reactions, and the rate constants of these reactions follow the trend 5'-..GGG.. > 5'-..GG.. > 5'-..G... In the case of CO3*- radicals, the oxidation of guanine occurs by intermolecular collision pathways, and the bimolecular rate constants are independent of base sequence context. However, the distributions of the end-products generated by CO3*- radicals, as well as by BPT*+, are base sequence context-dependent and are greater than those in isolated guanines at the 5'-G in 5'-...GG... sequences, and the first two 5'- guanines in the 5'-..GGG sequences. These results help to clarify the conditions that lead to a similar or different base sequence dependence of the initial hole injection step and the final distribution of oxidized, alkali-labile guanine products. In the case of the intermolecular one-electron oxidant CO3*-, the rate constant of hole injection is similar for contiguous and isolated guanines, but the subsequent equilibration of holes by hopping favors trapping and product formation at contiguous guanines, and the sequence dependence of these two phenomena are not correlated. In contrast, in the case of the DNA-bound oxidant BPT*+, the hole injection rate constants, as well as hole equilibration, exhibit a similar dependence on base sequence context, and are thus correlated to one another.     

Novel single-crystal-to-single-crystal anion exchange and self-assembly of luminescent d(10) metal (Cd(II), Zn(II), and Cu(I)) complexes containing C(3)-symmetrical ligands

Ligands L1 and L2' (L1=N,N',N'-tris(4-pyridyl)trimesic amide, L2'=N,N',N'-tris(3-pyridinyl)-1,3,5-benzenetricarboxamide) belonging to an interesting family of tripyridyltriamides with C(3)-symmetry have been utilized to construct 3D porous or hydrogen-bonded frameworks. Through a novel single-crystal-to-single-crystal anion-exchange process, [Cd(L1)(2)(ClO(4))(2)](n) (1c) can be obtained from [Cd(L1)(2)Cl(2)](n) (1b) in the presence of ClO(4)(-) anions. This anion-exchange process is highly selective and only the substitution of Cl(-) by ClO(4)(-) or PF(6)(-) could be realized; Cl(-) was found not to be substituted by BPh(4)(-). This demonstrates that the exchange process depends on the size of the anions in relation to the size of the cavities in the host material (ca. 7.5 A). In addition, the anion-exchange properties of 1 b have also been investigated by means of powder X-ray diffraction (PXRD), elemental analysis (EA), and infrared absorption spectroscopy (IR). Structurally, [Zn(L1)(NO(3))(2)](n)(2) consists of a 2D coordination network with five-coordinate Zn(II) ions. Surprisingly, different trigonal-bipyramidal Zn(II) ions propagate to form distinct respective sheet structures, A and B, which are packed in an A-B-A-B manner in the crystal lattice, and these are hydrogen-bonded to give a 3D extended framework. The molecular structure of [CuI(L2')](n)(3) shows that the Cu(I) ion adopts a distorted tetrahedral geometry, and 3 also forms a 2D coordination network. Significantly, this 2D coordination network is further assembled into a remarkable 3D homochiral framework through triple hydrogen bonding and pi...pi interactions. All of these 3D coordination polymers and/or hydrogen-bonded frameworks are luminescent in the solid state, and their solid-state luminescent properties have been investigated at room temperature and/or at 77 K.     

Comparative study of pesticide multi-residue extraction in tobacco for gas chromatography-triple quadrupole mass spectrometry

Coacervates made of surfactant aggregates, namely aqueous and reverse micelles and vesicles, were firstly used as solvents in single-drop microextraction (SDME) and proposed for the extraction and concentration of chlorophenols prior to liquid chromatography. The formation of coacervate drops in the needle tip of conventional microsyringes depended on the type of intermolecular forces established between the surfactant headgroups making up the supramolecular aggregates; hydrogen bond interactions were strong enough to permit the formation of spherical drops. Stability of 1-50 microL coacervate drops was achieved by introducing the microsyringe needle tip in a PTFE rod, the end of which had been machined out with a heated flanging-tool to get circular flanges (diameters in the range 3.5-6 mm). The parameters affecting the efficiency of single-drop coacervative microextraction (SDCME) were investigated using vesicular coacervates as a solvent and 2-chlorophenol (CP), 2,4-dichlorophenol (DCP), 2,4,6-trichlorophenol (TCP) and pentachlorophenol (PCP) as model analytes. Coacervative microextraction dynamics fit to the general rate equation of liquid-liquid extraction. The effect of variables such as extraction time, drop volume, stirring rate, pH and temperature, on the extraction of chlorophenols was similar to that described for organic solvent drops. Electrolyte concentrations above 0.1 M caused drop instability. Under the optimum conditions, detection limits were in the range 0.1-0.3 microg L(-1). The relative standard deviation was between 4.3 and 5.6 at 20 microg L(-1) spiked level. The method was applied to the determination of the four chlorophenols in wastewater, superficial water from a reservoir and groundwater and the recoveries were in the range 79 and 106% at 5-20 microg L(-1) spiked level.     

Detection and spectral analysis of trifluoromethyl groups at a surface by sum frequency generation vibrational spectroscopy

Sum frequency generation (SFG) vibrational spectroscopy was used to detect the presence of trifluoromethyl groups on the surface of 4-(trifluoromethyl)benzyl alcohol (TFMBA) in air. Supplementary data from infrared and Raman spectra were correlated to ab initio calculations by use of density functional theory (DFT) for TFMBA and three related compounds to reliably assign vibrational modes to the spectra. It was shown that strongly ordered CF3 groups dominate the surface of the TFMBA, and the vibrational modes of this functional group are strongly coupled to the benzene ring of the benzyl alcohol. This coupling, along with the SFG activity of the CF3 group, is removed with the insertion of an oxygen atom between the CF3 group and the benzene ring.     

Porphyrins bearing stable meso-alkylidenyl double bonds. A new family of nonplanar porphyrinoids

[Structure: see text] Unique core-modified porphyrinoids, such as oxabenziporphyrins, oxapyriporphyrins, and thiapyriporphyrins, bearing exocyclic C-C double bonds at meso-positions, have been synthesized and characterized. The synthesis was accomplished by utilizing typical "3+1"-type condensation. Two different stable tautomeric forms were isolated, and the two tautomeric forms can be interconvertible upon treatment with base. In contrast, only the structure bearing an exocyclic double bond was isolated in the case of oxapyriporphyrin and oxabenziporphyrin.