385 research outputs found
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
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><sub>3<i>d</i></sub>) with the proton midway between the two nitrogen atoms. Here we
report an extensive study of the less symmetric (<i>C</i><sub>3<i>v</i></sub>) 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
H<sub>3</sub>ND<sup>+</sup>NH<sub>3</sub> 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 N<sub>2</sub>H<sub>7</sub><sup>+</sup> 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
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
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
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