Protonated Water Dimer on Benzene: Standing Eigen or Crouching Zundel?

Protonated water clusters that are hydrogen-bonded to a neutral benzene molecule are a reductionist model for protons at hydrophobic surfaces, which are of fundamental importance in biological energy transduction processes. Of particular interest is the protonated water dimer (“Zundel ion”) on benzene, whose gas-phase messenger IR spectrum has been previously interpreted in terms of an asymmetric binding of the protonated water dimer to the benzene ring through a single water molecule. This “standing Eigen” isomer has a hydronium core. We have found an alternative “crouching Zundel” isomer, which attaches to the benzene ring symmetrically via both of its water molecules. When Ar-tagged, it has an IR spectrum in much better agreement with experiment than the standing Eigen isomer, particularly at the lower frequencies. These conclusions are based on static harmonic (and anharmonic) normal-mode analysis using density functional theory with various (dispersion corrected) functionals and particularly on dynamic anharmonic spectra obtained from the dipole autocorrelation functions from classical ab initio molecular dynamics with the BLYP, PBE, and B3LYP functionals. Possible implications to protons on water/organic-phase interfaces are discussed

Additional file 1 of Impacts of grandparenting on older Chinese adults’ mental health: a cross-sectional study

Supplementary Material

Reinvestigation of the Infrared Spectrum of the Gas-Phase Protonated Water Tetramer

Gas-phase H₉O₄⁺ has been considered an archetypal Eigen cation, H₃O⁺(H₂O)₃. Yet <i>ab initio</i> molecular dynamics (AIMD) suggested that its infrared spectrum is explained by a linear-chain Zundel isomer, alone or in a mixture with the Eigen cation. Recently, hole-burning experiments suggested a single isomer, with a second-order vibrational perturbation theory (VPT2) spectrum agreeing with the Eigen cation. To resolve this discrepancy, we have extended both calculations to more advanced DFT functionals, better basis sets, and dispersion correction. For Zundel-isomers, we find VPT2 anharmonic frequencies for four low-frequency modes involving the excess proton unreliable, including the 1750 cm^–1 band that is pivotal for differentiating between Zundel and Eigen isomers. Because the analogous bands of the H₅O₂⁺ cation show little effect of anharmonicity, we utilize the harmonic frequencies for these modes. With this caveat, both AIMD and VPT2 agree on the spectrum as originating from a Zundel isomer. VPT2 also shows that both isomers have the <i>s</i>ame spectrum in the high frequency region, so that the hole burning experiments should be extended to lower frequencies

Complete Assignment of the Infrared Spectrum of the Gas-Phase Protonated Ammonia Dimer

The infrared (IR) spectrum of the ammoniated ammonium dimer is more complex than those of the larger protonated ammonia clusters due to close-lying fundamental and combination bands and possible Fermi resonances (FR). To date, the only theoretical analysis involved partial dimensionality quantum nuclear dynamic simulations, assuming a symmetric structure (<i>D</i>_3<i>d</i>) with the proton midway between the two nitrogen atoms. Here we report an extensive study of the less symmetric (<i>C</i>_3<i>v</i>) dimer, utilizing both second order vibrational perturbation theory (VPT2) and <i>ab initio</i> molecular dynamics (AIMD), from which we calculated the Fourier transform (FT) of the dipole-moment autocorrelation function (DACF). The resultant IR spectrum was assigned using FTed velocity autocorrelation functions (VACFs) of several interatomic distances and angles. At 50 K, we have been able to assign all 21 AIMD fundamentals, in reasonable agreement with MP2-based VPT2, about 30 AIMD combination bands, and a difference band. The combinations involve a wag or the NN stretch as one of the components, and appear to follow symmetry selection rules. On this basis, we suggest possible assignments of the experimental spectrum. The VACF-analysis revealed two possible FR bands, one of which is the strongest peak in the computed spectrum. Raising the temperature to 180 K eliminated the “proton transfer mode” (PTM) fundamental, and reduced the number of observed combination bands and FRs. With increasing temperature, fundamentals red-shift, and the doubly degenerate wags exhibit larger anharmonic splittings in their VACF bending spectra. We have repeated the analysis for the H₃ND⁺NH₃ isotopologue, finding that it has a simplified spectrum, with all the strong peaks being fundamentals. Experimental study of this isotopologue may thus provide a good starting point for disentangling the N₂H₇⁺ spectrum

Additional file 1 of Psychometric evaluation of the Chinese version of advance care planning self-efficacy scale among clinical nurses

Additional file 1

Genistein Affects Histone Modifications on Dickkopf-Related Protein 1 (DKK1) Gene in SW480 Human Colon Cancer Cell Line

<div><p>Genistein (GEN) is a plant-derived isoflavone and can block uncontrolled cell growth in colon cancer by inhibiting the WNT signaling pathway. This study aimed to test the hypothesis that the enhanced gene expression of the WNT signaling pathway antagonist, DKK1 by genistein treatment is associated with epigenetic modifications of the gene in colon cancer cells. Genistein treatment induced a concentration-dependent G2 phase arrest in the human colon cancer cell line SW480 and reduced cell proliferation. Results from several other human colon cancer cell lines confirmed the growth inhibitory effects of genistein. Overexpression of DKK1 confirmed its involvement in growth inhibition. Knockdown of DKK1 expression by siRNA slightly induced cell growth. DKK1 gene expression was increased by genistein in SW480 and HCT15 cells. DNA methylation at the DKK1 promoter was not affected by genistein treatment in all the cell lines tested. On the other hand, genistein induced histone H3 acetylation of the DKK1 promoter region in SW480 and HCT15 cells. This indicates that increased histone acetylation is associated with the genistein-induced DKK1 expression. The association between histone acetylation and DKK1 gene expression is confirmed by the histone deacetylase inhibitor trichostatin A (TSA) treatment. In conclusion, genistein treatment decreases cell growth and proliferation in colon cancer cell lines. The effect is associated with the increased DKK1 expression through the induction of histone acetylation at the DKK1 promoter region.</p> </div

ChIP analysis of chromatin modifications.

<p><b>A</b>) A schematic drawing of the <i>DKK1</i> gene. Black arrowheads represent primers used for PCR to test three regions in the ChIP assay: promoter, coding and 5′ upstream control. Filled boxes represent exons of the <i>DKK1</i> gene, while the open box represents the <i>DKK1</i> promoter. Black lines represent introns. <b>B</b>) ChIP analysis of the relative protein abundance within different regions of the <i>DKK1</i> gene in SW480 and DLD-1 cells. Immunoprecipitated DNA was analyzed by real time PCR. Specific antibodies used for immunoprecipitation are labeled on the x-axis. A nonspecific rabbit IgG was used as the negative control. Data were plotted as the ratio to the value from 25% of input DNA. Three independent experiments were analyzed and presented as the mean ± SEM. Asterisks (*) indicate statistical significance compared with the Control using the same antibody within the cell line (p<0.05).</p

Color space distribution and quantization.

<p>(<b>A</b>) Input image <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112475#pone.0112475-Liu1" target="_blank">[20]</a>. (<b>B</b>) Original color distribution of <b>A</b> in the RGB color space. (<b>C</b>) Color distribution of uniform quantization. (<b>D</b>) Color distribution of minimum variance quantization.</p

Uniform quantization vs. minimum variance quantization.

<p>(<b>A</b>) Precision-Recall curves. (<b>B</b>) Precision-Recall bars. (<b>C</b>) F-measure curves.</p

Replacement for low frequent colors with minimum variance quantization.

<p>(<b>A</b>) Minimum variance quantized <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112475#pone-0112475-g002" target="_blank">Fig. 2</a><b>A</b>. (<b>B</b>) Color histogram of the image in <b>A</b>. (<b>C</b>) Full resolution output image resulting from the retained high frequent colors. (<b>D</b>) Color histogram of <b>C</b>.</p