sj-pdf-1-imr-10.1177_03000605221121968 - Supplemental material for Ectopic papillary thyroid carcinoma mimicking distant metastatic tissue

Supplemental material, sj-pdf-1-imr-10.1177_03000605221121968 for Ectopic papillary thyroid carcinoma mimicking distant metastatic tissue by Yingsong Qi, Jianwei Liu, Ya Liu, Zhihua Shen and Na Hu in Journal of International Medical Research</p

Molecular Dynamics Simulations of Hydrogen Bond Dynamics and Far-Infrared Spectra of Hydration Water Molecules around the Mixed Monolayer-Protected Au Nanoparticle

Molecular dynamics simulations have been performed to systematically investigate the structure and dynamics properties, hydrogen bond (HB) dynamics, and far-infrared (far-IR) spectra of hydration water molecules around the mixed monolayer-protected Au nanoparticles (MPANs) with different ligand compositions and length. Our simulation results demonstrate that the translational and rotational motions of hydration water molecules in the proximity of charged terminal NH₃⁺ and COO^– groups are suppressed significantly with respect to the bulk water. Compared to the bulk water, meanwhile, longer structural relaxation times of hydration H₂O–H₂O HBs indicate enhanced strength of H₂O–H₂O HBs at the interface of mixed MPANs. Accordingly, these hydration water molecules around the charged terminal groups can exhibit a considerable blue-shift in far-IR spectra for all ligand compositions and length studied here. A series of detailed HB analyses manifest that above restricted behavior of hydration water molecules can be attributed to the stronger H₂O–NH₃⁺ and H₂O–COO^– HBs and the corresponding structural relaxation times are much greater than those of hydration H₂O–H₂O HBs. Furthermore, we find that increasing ligand length can affect much the morphology of self-assemble monolayers in water owing to enhanced hydrophobic interactions between alkane chains and water molecules and favor the translational mobility of hydration water molecules owing to weaken electrostatic interactions. Unlike the translational motions, our comparison results among different ligand lengths clearly confirm that the rotational relaxation of hydration water molecules should be dominated by the local and directional HBs at the interfaces, rather than the previous explanation of the ratio between hydrophobic/hydrophilic exposed regions. More importantly, our simulations reveal at a molecular level that the ligand composition has a little influence on the structure, dynamics, HBs, and far-IR spectra of hydration water molecules around the mixed MPANs mainly due to the comparable strength between H₂O–NH₃⁺ and H₂O–COO^– HBs

Additional file 1 of Chloroplast genome analyses of Caragana arborescens and Caragana opulens

Additional file 1: Table S1. Statistical table of sequencing data

Kinetics Study of the Ketalization Reaction of Cyclohexanone with Glycol Using Brønsted Acidic Ionic Liquids as Catalysts

It is remarkable that Brønsted acidic ionic liquids (BAILs) have several unique advantages in the acid-catalysis reaction, which avoids the technical issues raised from mineral acids. The kinetics for the ketalization of cyclohexanone with glycol using BAILs as catalysts was therefore studied for the first time. The effects of various parameters such as kind of BAILs, temperature, catalyst loading, and molar ratio of the reactants on the conversion of cyclohexanone were examined in detail, and a pseudohomogeneous (PH) kinetic model was used successfully to correlate the experimental data in the temperature range from 313.15 to 343.15 K. The kinetic parameters such as reaction rate constant, activation energy, and chemical equilibrium constant then were proposed and utilized to interpret the catalytic activities of the BAILs catalysts. It was also validated from the comparison of catalytic performance among the BAILs, H₂SO₄, and solid resin that the BAILs were considered to be environmentally friendly and high efficient catalysts, and were suggested to replace mineral and solid acids in the synthesis of ketal

Comparison of cpDNA isolation from the three plant species among different extraction methods.

<p>Three methods, including A) modified protocol, B) DNAse I treatment and C) sucrose gradient centrifugation, were separately employed to isolate cpDNAs from a) <i>O. brachyantha</i>, b) <i>L. japonica</i>, and c) <i>P. utihis</i>. For each plant species, 20 g fresh leaves were used. The DNA bands were shown on a 0.8% agarose gel. M indicates 1 kbp DNA ladder.</p

Additional file 1 of Chloroplast genomes of Caragana tibetica and Caragana turkestanica: structures and comparative analysis

Additional file 1: Table S1. Types and numbers of Repeats in chloroplast genome of 9 Caragana spices. Table S2. Types and numbers of SSR in chloroplast genome of 9 Caragana spices. Table S3. Distribution of SSRs in cp genome of C. tibetica and C.turkestanica. Table S4. Analysis of coding ability and codon preference of chloroplast genome of C. tibetica and C.turkestanica

Flowchart showing the major steps for the isolation of cpDNAs using the modified high salt method.

<p>Flowchart showing the major steps for the isolation of cpDNAs using the modified high salt method.</p

Reference guided chloroplast genome assembly.

<p>A) <i>O. brachyantha</i> (consensus) sequence reads were aligned to <i>O. nivara</i>; B) <i>L. japonica</i> (consensus) sequence reads were aligned to <i>O. nivara</i>; and C) <i>P. utihis</i> (consensus) sequence reads were aligned to <i>Prunus persica</i>. The genome coverage is shown as green peaks and arrows indicate regions of high coverage.</p

Summary of total sequenced data and aligned reads of three plant species.

<p>Summary of total sequenced data and aligned reads of three plant species.</p

Molecular-Level Understanding of Solvation Structures and Vibrational Spectra of an Ethylammonium Nitrate Ionic Liquid around Single-Walled Carbon Nanotubes

Molecular dynamics simulations have been performed to explore the solvation structures and vibrational spectra of an ethylammonium nitrate (EAN) ionic liquid (IL) around various single-walled carbon nanotubes (SWNTs). Our simulation results demonstrate that both cations and anions show a cylindrical double-shell solvation structure around the SWNTs regardless of the nanotube diameter. In the first solvation shell, the CH₃ groups of cations are found to be closer to the SWNT surface than the NH₃⁺ groups because of the solvophobic nature of the CH₃ groups, while the NO₃^– anions tend to lean on the nanotube surface, with three O atoms facing the bulk EAN. On the other hand, the intensities of both C–H (the CH₃ group of the cation) and N–O (anion) asymmetric stretching bands at the EAN/SWNT interface are found to be slightly higher than the corresponding bulk values owing to the accumulation and orientation of cations and anions in the first solvation shell. More interestingly, the N–O stretching band exhibits a red shift of around 10 cm^–1 with respect to the bulk value, which is quite contrary to the blue shift of the O–H stretching band of water molecules at the hydrophobic interfaces. Such a red shift of the N–O stretching mode can be attributed to the enhanced hydrogen bonds (HBs) of the NO₃^– anions in the first solvation shell. Our simulation results provide a molecular-level understanding of the interfacial vibrational spectra of an EAN IL on the SWNT surface and their connection with the relevant solvation structures and interfacial HBs