In this work{,} we report infrared spectra of large neutral and protonated methanol clusters{,} (MeOH)n and H+(MeOH)n{,} in the CH and OH stretching vibrational region in the size range of n = 10-50. The infrared-ultraviolet double resonance scheme combined with mass spectrometry was employed to achieve moderate size selection of the neutral clusters with the addition of a phenol molecule as a chromophore. Infrared dissociation spectroscopy was performed on the protonated methanol clusters by using a tandem quadrupole mass spectrometer to enable the precise size selection of the clusters. While the neutral clusters showed essentially the same spectra in all the observed size range{,} the protonated clusters showed remarkable narrowing of the H-bonded OH stretch band with increasing n. In n [greater-than-or-equal] [similar]30{,} the spectra of the neutral and protonated clusters become almost identical. These spectral features demonstrate that hydrogen bond networks of methanol prefer simple cyclic structures (or {"}bicyclic{"} structures in protonated methanol) and branching of the hydrogen bond networks (side-chain formation) is almost negligible. Implications of the spectra of the clusters are also discussed by comparison with spectra of bulk phases.

Three binary molecule conjugates were designed and synthesized by conjugating a chromophore (3, 6-bis-(1-methyl-4-vinylpyridinium)-carbazole diiodide, BMVC) to mono-, bis- and trishydroxyl photosensitizers, respectively. BMVC plays the role of cancer cells recognizer; AIEE (aggregation-induced emission enhancement) generator and FRET (Fluorescence Resonance Energy Transfer) donor. The self assembling properties of these binary conjugates result in different degrees of AIEE and then achieve the formations of FONs (fluorescent organic nanoparticles), which present efficient FRET and singlet oxygen generations. Biologically, FONs-photosensitizers from these compounds were much more phototoxicities to cancer cell than to normal cell without significant dark toxicity. In addition, their intracellular fluorescent colors switching upon photo-excitation are expected to be used for further cell death biomarker applications. This improved photodynamic activity might be due to the aggregation of compounds in the cell that form FONs which can promote PDT (photodynamic therapy) and are observed in cancer cell but not normal cell.

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The challenge of G-quadruplexes is that the G-rich sequences can adopt various G4 structures and possibly interconvert among them, particularly under the change of environmental conditions. Both NMR and circular dichroism (CD) show the spectral conversion of d[AG3(T2AG3)3] (HT22) from Na-form to K-form after Na+/K+ ion exchange. No appreciable change on the induced CD spectra of BMVC molecule and the single molecule tethered particle motion of HT22 in Na+ solution upon K+ titration suggests that the spectral conversion is unlikely due to the structural conversion via fully unfolded intermediate. Although a number of mechanisms were proposed for the spectral change induced by the Na+/K+ ion exchange, determining the precise structures of HT22 in K+ solution may be essential to unravel the mechanism of the structural conversion. Thus, development of a new method for separating different structures is of critical importance for further individual verification. In the second part of this review, we describe a new approach based on "micelle-enhanced ultrafiltration" method for DNA structural separation. The BMVC, a G-quadruplex ligand, is first modified and then forms a large size of emulsion after ultrasonic emulsification, together with its different binding affinities to various DNA structures; for the first time, we are able to separate different DNA structures after membrane filtration. Verification of the possible structural conversion and investigation of structural diversity among various G4 structures are essential for exploring their potential biological roles and for developing new anticancer drugs.

The magic number behavior of ((CH3)3N)n–H+–H2O clusters at n = 3 is investigated by applying infrared spectroscopy to the clusters of n = 1–3. Structures of these clusters are determined in conjunction with density functional theory calculations. Dissociation channels upon infrared excitation are also measured, and their correlation with the cluster structures is examined. It is demonstrated that the magic number cluster has a closed-shell structure, in which the water moiety is surrounded by three (CH3)3N molecules. The ion core (protonated site) of the clusters is found to be (CH3)3NH+ for n = 1–3, but coexistence of an isomer of the H3O+ ion core cannot be ruled out for n = 3. Large rearrangement of the cluster structures of n = 2 and 3 before dissociation, which has been suggested in the mass spectrometric studies, is confirmed on the basis of the structure determination by infrared spectroscopy.

The gel assay, circular dichroism, and differential scanning calorimetry results all demonstrate that a major monomer component of bcl2mid exists at low [K(+)] and an additional dimer component appears at high [K(+)]. This implies that bcl2mid is a good candidate for elucidating the mechanisms of structural conversion between different G-quadruplexes. We further discovered that the conversion between the monomer and dimer forms of bcl2mid does not occur at room temperature but is detected when heated above the melting point. In addition, the use of the lithium cation to keep the same ionic strength in a K(+) solution favors the formation of the bcl2mid dimer. We also found that the bcl2mid dimer is more stable than the monomer. However, after the bcl2mid monomer is formed in a K(+) solution, there is no appreciable structural conversion from the monomer to the dimer detected with addition of Li(+) at room temperature. Furthermore, the spectral changes of bcl2mid when transitioning from sodium form to potassium form take place upon K(+) titration. The absence of the dimer form for bcl2mid after the direct addition of 150 mM [K(+)] at room temperature suggests that the spectral changes are not due to rapid unfolding and refolding. In addition, this work reveals the conditions that would be useful for NMR studies of G-quadruplexes.

It has been demonstrated that replacing Li(2)NH with the mixed imide Li(2)Mg(NH)(2) improves the reaction conditions for the hydrogen-storage system Li(2)NH + H(2) <-> LiNH(2) + LiH, at the expense of reducing the gravitational hydrogen capacity from 6.5% to 5.6%. In this article, we report from first-principles calculations a possible mixed imide Li(6)Mg(NH)(4) that has less Mg concentration and higher gravimetric capacity for hydrogen storage than Li(2)Mg(NH)(2). We find that Li(6)Mg(NH)(4) is thermodynamically more stable than the phase-separated mixture of Li(2)Mg(NH)(2) and Li(2)NH over a large temperature range. The reaction LiH + 1/4Mg(NH(2))(2) + 1/2LiNH(2) <-> 1/4Li(6)Mg(NH)(4) + H(2) can be completed via two steps and releases 6.0 wt % hydrogen in total, at a temperature about 40 degrees C lower than that for the cycling between LiNH(2) and Li(2)NH.

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The structural and dynamic properties of water on the GaN(0001) polar surface are investigated via classical molecular dynamics simulations. The interfacial molecules are observed to have enhanced structural ordering and slowed-down dynamics compared to the liquid bulk; these unique properties are evidenced in the slower reorientational relaxation, smaller diffusion constant, and longer residence lifetime for water located at the surface region up to ∼7 Å from the substrate. Further analysis of the vibrational spectra at low frequencies shows that both the hydrogen bond network bending and the hydrogen bond stretching bands at the interface shift to the blue compared to those in the bulk, due to the strong coupling between the O atom of water and the Ga sites. The distinct spectral features along with the anisotropy of the hydrogen bond distributions of the interfacial water are complex results determined by both the substrate–water and water–water interactions.

The nature of water networks exposed to ionizing radiation is important in various radiation-related chemistry and biology. To understand structural evolution of ionized water networks at the molecular level{,} we report here infrared spectra of water cluster radical cations (H2O)n+ (n = 3 - 11) in the gas phase. Spectral features of free OH stretch modes are quite similar to those of protonated water clusters H+(H2O)n{,} of which the hydrogen-bond network structures have been revealed. In addition{,} we observed an extra band attributed to the stretch of an OH radical in (H2O)n+. These results indicate that nominal (H2O)n+ should be regarded as H+(H2O)n-1(OH) motifs having similar network shapes to those of H+(H2O)n. We also analyzed hydrogen-bonded OH stretch bands and found that hydrogen-bond strength is a key factor to determine the position of the OH radical relative to the protonated site (H3O+/H5O2+). Because an OH radical is a weaker hydrogen bond acceptor than water{,} the first solvation shell of the protonated site is preferentially filled with water. As a result{,} the OH radical is separated from the protonated (charged) site by at least one water molecule in n [greater-than-or-equal] 5 clusters. This result shows the instability of the H3O+-OH ion-radical contact pair in water networks{,} and implies the higher mobility of the OH radical due to its release from the charged site. Observed structural preferences are confirmed both in cold and warm cluster ion sources.

Human telomere contains guanine-rich (G-rich) tandem repeats of single-stranded DNA sequences at its 3' tail. The G-rich sequences can be folded into various secondary structures, termed G-quadruplexes (G4s), by Hoogsteen basepairing in the presence of monovalent cations (such as Na(+) and K(+)). We developed a single-molecule tethered particle motion (TPM) method to investigate the unfolding process of G4s in the human telomeric sequence AGGG(TTAGGG)3 in real time. The TPM method monitors the DNA tether length change caused by formation of the G4, thus allowing the unfolding process and structural conversion to be monitored at the single-molecule level. In the presence of its antisense sequence, the folded G4 structure can be disrupted and converted to the unfolded conformation, with apparent unfolding time constants of 82 s and 3152 s. We also observed that the stability of the G4 is greatly affected by different monovalent cations. The folding equilibrium constant of G4 is strongly dependent on the salt concentration, ranging from 1.75 at 5 mM Na(+) to 3.40 at 15 mM Na(+). Earlier spectral studies of Na(+)- and K(+)-folded states suggested that the spectral conversion between these two different folded structures may go through a structurally unfolded intermediate state. However, our single-molecule TPM experiments did not detect any totally unfolded intermediate within our experimental resolution when sodium-folded G4 DNA molecules were titrated with high-concentration, excess potassium ions. This observation suggests that a totally unfolding pathway is likely not the major pathway for spectral conversion on the timescale of minutes, and that interconversion among folded states can be achieved by the loop rearrangement. This study also demonstrates that TPM experiments can be used to study conformational changes in single-stranded DNA molecules.

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