Miracle-dz/UniFAR-FTUs huggingface dataset:
New Strategy of Mass Spectrum Simulation Based on Reduced and Concentrated Knowledge Databases

Abstract A new strategy for mass spectrum simulation is proposed based on the analysis of different reported techniques and developed software packages. This new strategy consists of using four pivot knowledge databases: functional groups, fragmentation pathways, end‐point and pseudo end‐point fragments, and peak‐intensity relationships. The key database is the cleavage mode database, which was constructed by data mining of large mass spectra databases. An important advantage of this concentrated database is its rich information but largely reduced size compared with the databases used in other reported systems. Based on this new strategy, a mass spectrum simulation system, MASSIS, was developed, and the performance was evaluated by comparing the simulated spectra with experimental data for a large population of molecules. The results show that this system possesses high performance. The average ratio of simulated spectra with respect to experimental ones is superior to 90% for all compounds taken together. The reported mass spectral simulation system in this paper could be the first general software for organic chemistry use. This paper was invited as a contribution to a special issue of the journal concerning Chemical Spectroscopy in China. It was presented at Sichuan University, Chengdu China, August 1–7, 2004; the 4th Conference for Worldwide Young Chinese Chemists.
Thickness Dependent Ordering in Laterally Confined Monolayers of Spherical-Domain Block Copolymers

Monolayers of spherical-domain block copolymer, exhibiting hexagonal symmetry with a (10) periodicity of 25 nm, are laterally confined in hexagonal wells 12 μm wide and 26 nm deep that span the entire area of a two-inch diameter silicon wafer. The structure is characterized with grazing-incidence small-angle X-ray diffraction, which provides a quantitative measure of the positional and orientational order over macroscopic areas. Results are interpreted within the KTNHY framework for 2D phase behavior. At T = 210 °C, films that are 41 nm thick (monolayer plus brush) form oriented single crystals where the close-packed rows of the lattice are aligned with the edges of the wells. Translational order is determined to decay algebraically with a correlation function of the form gT(r) ∼ r-0.25, consistent with a KTNHY 2D crystal having a shear modulus μ = 1.7 × 10-4 N/m. Orientational order is long-range, with a full width at half-maximum of 1.1°. Decreasing the film thickness by 1 nm results in hexatic ordering.
Dye Attached Nanoparticles for Lysozyme Adsorption

In this work, Reactive Blue 15 dye functionalized poly(HEMA) nanoparticles were synthesized for reversible adsorption of lysozyme from its aqueous solution. For this, nano-sized poly(HEMA) nanoparticles were synthesized by the surfactant free emulsion polymerization. Reactive Blue 15 dye then covalently attached to the polymeric structure. These novel dye attached poly(HEMA) nanoparticles were used for the adsorption of lysozyme. Characterization of dye attached nanoparticles was carried out by using FTIR, AFM, and elemental analysis. Incorporation of the dye onto the polymeric structure was demonstrated by FTIR and elemental analysis, while the size and the shape of the nanoparticles were shown by AFM. The incorporated amount of the dye was found to be 70.3 μmol/g nanoparticle with sulphur stoichiometry and it was found that the prepared nanoparticles were in a spherical form and were about 100 nm diameter. Lysozyme adsorption studies were carried out with different conditions (pH, lysozyme concentration, temperature, and ionic strength) and maximum lysozyme adsorption was found to be 630.7 mg/g nanoparticle at pH 7.0 in 25°C medium temperature. Adsorbed lysozyme was desorbed by 1.0 M of NaCl with 96% recovery and synthesized dye-attached nanoparticles were used 10 times without any decrease in their adsorption capacity.
Alkylation of Position C‐5 of Triacetic Acid Lactone by [2,3] Sigmatropic Rearrangement of Sulphonium Ylides

Reactions of the 4-methoxy-6-(phenylthiomethyl)-2H-pyran-2-ones 4 with three different diazo compounds under copper or rhodium catalysis give the corresponding sulphonium ylides, which through [2,3] sigmatropic rearrangement and further prototropy afford the pyrones 6, functionalized at the difficutly accessible position C-5. Desulphurations of products 6 with deactivated Raney nickel give the pyrones 17–19. The influence of the experimental conditions on the competition between [2,3] sigmatropic and Stevens rearrangement has been studied for the reaction of 4-methoxy-6-(phenylthiomethyl)-2H-pyran-2-one (4a) and dimethyl diazomalonate. Several products (9, 10, and 11) arising from sulphonium ylides equilibration and radical recombination have been found in addition to the [2,3] sigmatropic and the Stevens rearrangement products 6d and 8. Alkylierung der 5-Stellung von Triessigsaurelacton durch [2,3]-sigmatrope Umlagerung von Sulfonium-Yliden Die Reaktionen von 4-Methoxy-6-(phenylthiomethyl)-2H-pyran-2-onen 4 mit drei verschiedenen Diazoverbindungen unter Kupfer- oder Rhodium-Katalyse liefern entsprechende Sulfonium-Ylide, die durch [2,3]-sigmatrope Umlagerung und nachfolgende Prototropie die Pyrone 6, die an der schwer zuganglichen 5-Stellung funktionalisiert sind, ergeben. Entschwefelung von 6 mit desaktiviertem Raney-Nickel ergibt die Pyrone 17–19. Der Einflus der experimentellen Bedingungen auf die Konkurrenz von [2,3]-sigmatroper und Stevens-Umlagerung wurde bei der Reaktion von 4-Methoxy-6-(phenylthiomethyl)-2H-pyran-2-on (4a) mit Diazomalonsaure-dimethylester studiert. Zusammen mit den aus [2,3]-sigmatroper und Stevens-Umlagerungen abgeleiteten Verbindungen 6d und 8 wurden noch andere Produkte (9, 10 und 11), die uber Sulfonium-Ylid-Gleichgewichtseinstellung und Radikalverknupfung entstehen, isoliert.
Insolubilization of sodium chondroitin sulfate by forming a semi‐interpenetrating polymer network with acrylic acid: A potential carrier for colon‐specific drug delivery

To reduce the highly hydrophilic property of chondroitin sulfate (ChS), a semi-interpenetrating polymer network (semi-IPN) of chondroitin sulfate/polyacrylic acid (PAA) was prepared as a drug carrier by crosslinking acrylic acid with diethyleneglycol diacrylate. The swelling properties of the semi-IPNs with different concentrations of crosslinking agent were correlated. The moisture sorption profiles were evaluated using differential thermal analysis. Ketoprofen was used as a drug probe to evaluate the performance of the drug released from the semi-IPN matrices. The prepared semi-IPNs demonstrated significant swelling reduction properties with both gastric and intestinal fluids compared with those of both the pure ChS and the ChSAA blend without the crosslinking agent. The amount of accumulated drug released from the semi-IPNs was less than 30 wt % at pH 1.2 and up to 80 wt % at pH 7.4. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 85: 114–122, 2002
Spectroscopic and Equilibrium Dialysis Studies of the Poly(acrylic acid)–Cu(II) Complex in the pH Range 3.5–7

The complex formation between poly(acrylic acid), poly(Acr), and Cu2+ ion was studied in 150 mM NaCl solutions at 25 °C and at the mixing ratios of Acr residues-to-Cu2+, R, of 32, 16 and 8, in the pH range of 3.5–7 by the spectroscopic and equilibrium dialysis methods. The dialysis results showed that more than 90% of the Cu2+ ions remain bound to the polymer at pH’s higher than 4.5, but the bound Cu(II) begins to dissociate at lower pH values. The data also revealed that the true absorption spectra of poly (Acr)–Cu(II) complexes varied with pH and R in a complicated manner. The analysis of the bound Cu(II) spectra disclosed the presence of three different kinds of Cu(II)–Acr complexes over the entire pH range. It is the relative amounts of these three complexes that vary with pH and R. With a newly devised plot of the dialysis data, the stability constant for each Cu(II)–Acr complex was determined. In the poly(Acr)–Cu(II) macrocomplex, each Cu(II) was estimated to bind to two or four carboxylato ligands.
Facile method for preparation of superfine copper nanoparticles with high concentration of copper chloride through photoreduction

Superfine copper nanoparticles were synthesized through direct photoreduction of a high concentration of copper ions in an ethanol solution with a photoinitiator at room temperature in the presence of polyethylene imine (PEI). This synthetic method was very effective in decreasing the effect of copper ion concentration on copper particle size. The reaction process was monitored using UV-vis spectroscopy, and the obtained copper nanoparticles were investigated using transmission electron microscopy. The results show that PEI acted not only as a coordinating agent to the copper ion, but also as a polymer cage that reduced the chance of copper nanoparticle aggregation.
Digital Image Processing and Development of Machine Learning Models for the Discrimination of Corneal Pathology: An Experimental Model

Machine learning (ML) has an impressive capacity to learn and analyze a large volume of data. This study aimed to train different algorithms to discriminate between healthy and pathologic corneal images by evaluating digitally processed spectral-domain optical coherence tomography (SD-OCT) corneal images. A set of 22 SD-OCT images belonging to a random set of corneal pathologies was compared to 71 healthy corneas (control group). A binary classification method was applied where three approaches of ML were explored. Once all images were analyzed, representative areas from every digital image were also extracted, processed and analyzed for a statistical feature comparison between healthy and pathologic corneas. The best performance was obtained from transfer learning—support vector machine (TL-SVM) (AUC = 0.94, SPE 88%, SEN 100%) and transfer learning—random forest (TL- RF) method (AUC = 0.92, SPE 84%, SEN 100%), followed by convolutional neural network (CNN) (AUC = 0.84, SPE 77%, SEN 91%) and random forest (AUC = 0.77, SPE 60%, SEN 95%). The highest diagnostic accuracy in classifying corneal images was achieved with the TL-SVM and the TL-RF models. In image classification, CNN was a strong predictor. This pilot experimental study developed a systematic mechanized system to discern pathologic from healthy corneas using a small sample.
Identification of substance in complicated mixture of simulants under the action of THz radiation on the base of SDA (spectral dynamics analysis) method

The SDA (Spectral Dynamics Analysis) - method (method of THz spectrum dynamics analysis in THz range of frequencies) is used for the detection and identification of substances with similar THz Fourier spectra (such substances are named usually as the simulants) in the two- or three-component medium. This method allows us to obtain the unique 2D THz signature of the substance - the spectrogram- and to analyze the dynamics of many spectral lines of the THz signal, passed through or reflected from substance, by one set of its integral measurements simultaneously; even measurements are made on short-term intervals (less than 20 ps). For long-term intervals (100 ps and more) the SDA method gives an opportunity to define the relaxation time for excited energy levels of molecules. This information gives new opportunity to identify the substance because the relaxation time is different for molecules of different substances. The restoration of the signal by its integral values is made on the base of SVD - Single Value Decomposition - technique. We consider three examples for PTFE mixed with small content of the L-Tartaric Acid and the Sucrose in pellets. A concentration of these substances is about 5%-10%. Our investigations show that the spectrograms and dynamics of spectral lines of THz pulse passed through the pure PTFE differ from the spectrograms of the compound medium containing PTFE and the L-Tartaric Acid or the Sucrose or both these substances together. So, it is possible to detect the presence of a small amount of the additional substances in the sample even their THz Fourier spectra are practically identical. Therefore, the SDA method can be very effective for the defense and security applications and for quality control in pharmaceutical industry. We also show that in the case of substances-simulants the use of auto- and correlation functions has much worse resolvability in a comparison with the SDA method.
Recovery of high surface area alumina from aluminium dross tailings

Aluminium dross tailings (ADT), a chemical waste from a factory producing aluminium in Egypt, was used for the recovery of the aluminium content in the form of alumina (Al 2 O 3 ). Extraction of the aluminium was carried out via atmospheric- and high-pressure leaching with caustic soda. Then, it was separated from the sodium aluminate solutions thus obtained, using six different precipitation methods (via H 2 O 2 , via carbonation, via ammonium carbonate, via ammonium bicarbonate, via ammonium aluminium sulfate, via addition of active seeds). The precipitates were filtered, washed, dried and calcined at 600°C to produce the test aluminas. The precipitates and the calcination products were analysed for their chemical and crystalline phase compositions. The calcination products (aluminas) were subjected to sorpometry for surface area determination, and to particle sizing. The results indicated that highly pure (SiO 2 200 m 2 /g) and uniform small crystallite sizes (60-70A) could be efficiently recovered from ADT. Optimal recovery conditions were examined and determined.
Optical properties of thiophene-containing liquid crystalline and hybrid liquid crystalline materials

We report new mesogens made of thiophene and stilbene moieties as main building blocks that exhibit nematic and/or smectic phases. The liquid crystalline properties of their thiophene/azobenzene analogues have been found to be strongly suppressed compared to their thiophene/stilbene analogues. In twinned “bent-core” thiophene/azobenzene compound relatively strong fluorescence was found. A new hybrid material built of AuNPs coated with a thiophene-containing mesogenic ligand that forms a smectic phase is shown. In solutions of thiophene-mesogen coated AuNPs an unusual decrease of the ligand fluorescence decay rate was observed. Fluorescence lifetime increase is ascribed to two-point anchoring of ligand molecules resulting in molecule orientation tangential to the AuNP surface. UV-Visible absorption and fluorescence data of all synthesised compounds are presented.
Lignin Structural Modifications Resulting from Ethanol Organosolv Treatment of Loblolly Pine

Milled wood lignin samples from untreated Loblolly pine, post-ethanol organosolv pretreatment, and ethanol organosolv dissolved lignin were isolated and characterized by quantitative 13C and 31P nuclear magnetic resonance (NMR) spectroscopy. β-O-4 linkages are the predominant substructures present in lignin from the starting material, as well as after the pretreatment. During organosolv treatment of Loblolly pine, acid-catalyzed cleavage of β-O-4 linkages and ester bonds were the major mechanisms of lignin cleavage. This degradative pathway results in the formation of a dissolved ethanol organosolv lignin, which is more condensed and has a lower molecular weight than the starting lignin. The residual lignin isolated from the solid pretreated residue was also more condensed. Results from quantitative 13C and 31P NMR show that the residual and dissolved lignin fractions after pretreatment have a higher abundance of phenols and carboxylic acids and lower aliphatic carbon content and may be suitable as antiox.
Synthesis, formation mechanism and photoelectric properties of GeS nanosheets and nanowires

Single-crystalline GeS nanosheets and nanowires have been selectively synthesized by simply varying the reaction conditions via a convenient wet chemical approach. The formation mechanism of the nanosheets and nanowires has been proposed. The results from time-dependent reactions proved that the GeS nanowires were formed by a rolling-up mechanism. Films made of as-synthesized GeS nanosheets and nanowires were found to have an outstanding photoelectric response, suggesting their potential in solar energy applications. The structure, morphology, composition and optical absorption properties of the as-prepared samples were characterized using X-ray powder diffraction, transmission electron microscopy, energy-dispersive X-ray spectrometry and scanning electron microscopy.
Synthesis and characterization of the new high pressure phases ACu3 V4O12(A=Gd, Tb, Er)

New ACu3V4O12 (A=Gd, Tb, Er) phases have been prepared at high pressure and high-temperature conditions (P∼8–9 GPa, T∼1000°C) in a toroid-type high pressure cell. These compounds crystallize in the cubic symmetry with a perovskite-like structure. At ambient pressure, they are paramagnetic and have activation-type conductivity. The effect of high pressure (10–50 GPa) on the electrical properties of the materials was analyzed in the temperature range from 78 to 300 K. Pressure ranges of the transition from activation type to metallic conductivity have been determined. The crystal structure of ACu3V4O12 (A=Gd, Tb, Er) was found to be stable up to 50 GPa.
Application of infrared spectrometry to the study of tautomeric equilibria and hydrogen bonding basicity of medical and biochemical agents: N,N′-disubstituted amidines

The hydrogen bonding basicity of 20 N,N′-disubstituted formamidines, acetamidines and benzamidines containing the same or different groups at the amino and imino nitrogen atoms was measured by means of the formation constant KHB of their complexes with 4-fluorophenol in carbon tetrachloride. A method for the prediction of tautomeric equilibrium constants is proposed and was applied to unsymmetrically N,N′-disubstituted amidines. The results obtained were compared with those found on the basis of pKa measurements in azeotropic ethanol.
Rapid determination of methylmercury in biological materials by GC-MIP-AES or GC-ICP-MS following simultaneous ultrasonic-assisted in situ ethylation and solvent extraction

A simple and rapid sample pre-treatment procedure was developed for the determination of methylmercury in biological materials. The procedure is based on acid leaching (5 min) of sample materials followed by simultaneous in situ derivatisation and extraction (40 min) in the presence of sodium tetraethylborate and nonane, buffered at pH 7.0, in an ultrasonic field. The nonane phase with an overall average recovery of methylmercury higher than 90% was analysed by gas chromatography (GC) coupled to microwave induced plasma atomic emission spectrometry (MIP-AES) or inductively coupled plasma mass spectrometry (ICP-MS). Detection limits (as Hg), based on three times the standard deviation of a standard solution, were 4.4 ng g−1 for GC-MIP-AES and 2.6 ng g−1 for GC-ICP-MS. No artefact formation of methylmercury during sample pre-treatment was observed following the addition of a 201Hg2+ isotope standard. The method was validated by the analysis of three biological certified reference materials and applied to the determination of methylmercury in a fish sample.
Molecular Dynamics Simulation of a GM3 Ganglioside Bilayer

A first molecular dynamics simulation of a fully hydrated GM3 ganglioside bilayer is presented. Several properties characterizing the membrane structure and surrounding water are evaluated and compared to known data related to phospholipids. Our results are in good agreement with experimental small-angle X-ray scattering data. Overall, the simulated bilayer shows very long relaxation times such that a full equilibration is attained in about 30 ns. The long equilibration time is due to the slow relaxation of the torsional angle at the level of the galactose−sialic acid linkage. Once equilibrated, GM3 exhibits a good packing of the hydrophilic moieties, due to preferential alignment of its longitudinal axis along the bilayer normal, and a high degree of disorder in the tail region. The ionic nature of the hydrophilic heads manifests itself in a slow decay of the water orientational order parameter.
A new definition of cavities for the computation of solvation free energies by the polarizable continuum model

A set of rules for determining the atomic radii of spheres used to build the molecular cavities in continuum solvation models are presented. The procedure is applied to compute the hydration free energy for molecules containing H, C, N, O, F, P, S, Cl, Br, and I at a computational level (Hartree–Fock with a medium size basis set) allowing the study of relatively large systems. The optimized radii reduce the mean error with respect to the experimental solvation energies below 0.20 kcal/mol for a set of 43 neutral solutes and around 1 kcal/mol for 27 ions. Moreover the correct trends are observed for the solvation energies of homolog series, like the series ammonia–trimethylamine, that are not correctly reproduced by usual solvation models.
Excluded volume effects for branched polymers: Monte Carlo results

As a simple model of randomly branched polymers, we consider the different ways that N‐bond trees may be self‐avoidingly embedded on a lattice. A general Monte Carlo approach is developed and applied. The mean square radii of gyration of the conformations with a given N are found to vary with N as Nν, where ν? 1.23 and ν? 0.92 in two and three dimensions. The critical importance of volume exclusion for branched structures is discussed.
Critical evaluation of anharmonic corrections to the equilibrium isotope effect for methyl cation transfer from vacuum to dielectric continuum

Harmonic and anharmonic vibrational frequencies are computed for isotopologues of methyl cation in vacuum and in a polarised continuum model (PCM) dielectric continuum (ϵ = 80) within Gaussian09. Comparison of results in vacuum for two methods (B3LYP and second-order Møller–Plesset perturbation theory) and three basis sets (6-31+G(d), cc-aug-PVDZ, cc-aug-PVQZ) with published anharmonic frequencies obtained from an accurate vibrational configuration interaction (VCI) method shows the smallest root mean square error in the frequencies from B3LYP/6-31+G(d) with anharmonic corrections. Using this method to calculate isotopic partition function ratios (IPFRs) for all six pairs of CH3+, CH2D+, CHD2+ and CD3+ gives better results for anharmonic frequencies than for unscaled harmonic frequencies, but scaled harmonic frequencies give even better results for less cost. The scaling factor is simply the ratio of the sum of the anharmonic VCI frequencies to the sum of the harmonic B3LYP/6-31+G(d) frequencies, which corresponds to the dominance of zero-point energy changes in determining the IPFRs. Both the scaled and unscaled harmonic frequencies provide reasonable estimates for the equilibrium isotope effects (EIEs) upon transfer of methyl cation from vacuum to PCM ‘water’, but the anharmonic PCM calculations give erratic results. The use of scaled B3LYP/6-31+G(d) harmonic frequencies is recommended for the estimations of EIEs rather than expensive anharmonic corrections.