Force-field parametrization based on radial and energy distribution functions

We propose a novel force-field-parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher-level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Role of hydrolytic degradation of polylactide drug carriers in developing micro- and nanoscale polylactide-based drug dosage forms

The present analytical survey explores different aspects of hydrolytic degradation of drug dosage forms (DF) based on polylactides, homopolymers of lactic acid (PLA) and copolymers of lactic and glycolic acids (PLGA). The study includes various scientific data from multiple sources describing the effect of the PLGA nanocarrier hydrolytic degradation rate on the profile of drug release from the DFs intended for intravenous and intramuscular administration, including micro- and nanoparticles, and implants. The following aspects are explored in the review: design of experiments aimed at studying the hydrolytic degradation kinetics of PLGA carriers; commonly employed analytical methods; interpretation of the mechanism of PLGA-based DF hydrolytic degradation; factors that influence the hydrolytic degradation rate of PLGA drug carriers as part of DFs; interrelation between the processes of polymer carrier hydrolytic degradation and drug substance release from the PLGA-based DFs.

     

Thermal conductivity of high strength polyethylene fiber in low temperature

High strength polyethylene fiber (Toyobo, Dyneema® fiber, hereinafter abbreviated to DF) used as reinforcement of fiber‐reinforced plastics for cryogenic use has a high thermal conductivity. To understand the thermal conductivity of DF, the relation between fiber structure and thermal conductivity of several kinds of polyethylene fibers having different modulus from 15 to 134 GPa (hereinafter abbreviated to DFs) was investigated. The mechanical series‐parallel model composed of crystal and amorphous was applied to DFs for thermal conductivity. This mechanical model was obtained by crystallinity and crystal orientation angle measured by solid state NMR and X‐ray. Thermal conductivity of DF in fiber direction was dominated by that of the continuous crystal region. The thermal conductivity of the continuous crystal part estimated by the mechanical model increases from 16 to 900 mw/cmK by the increasing temperature from 10 to 150K, and thermal diffusivity of the continuous crystal part was estimated to about 100 mm²/s, which is almost temperature independent. The phonon mean free path of the continuous crystal region of DF obtained by thermal diffusivity is almost temperature independent and its value about 200 Å. With the aforementioned, the mechanical series‐parallel model composed of crystal and amorphous regions could be applied to DFs for thermal conductivity. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1495–1503, 2005     

Dioxins in Soil and Fish Samples from a Waste Pentachlorophenol Manufacturing Plant

A method to analyze polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/DFs, dioxins) and coplanar polychlorinated biphenyls in environmental samples is developed and used to determine the levels of PCDD/DFs in 13 soil and 4 fish samples collected around a waste pentachlorophenol manufacturing plant. The 2,3,7,8-tetrachlorodioxin toxic equivalents (TEQ) values range from 0.239 ng-TEQ/g to 1357 ng-TEQ/g in soil samples and 0.041 ng-TEQ/g to 0.247 ng-TEQ/g in fish samples. A broader survey of PCDD/DF contamination in the vicinity around the manufacturing plant is strongly recommended.     

A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen‐Dependent Oxidation

Metalloproteins utilize O₂ as an oxidant, and they often achieve a 4‐electron reduction without H₂O₂ or oxygen radical release. Several proteins have been designed to catalyze one or two‐electron oxidative chemistry, but the de novo design of a protein that catalyzes the net 4‐electron reduction of O₂ has not been reported yet. We report the construction of a diiron‐binding four‐helix bundle, made up of two different covalently linked α₂ monomers, through click chemistry. Surprisingly, the prototype protein, DF‐C1, showed a large divergence in its reactivity from earlier DFs (DF: due ferri, two iron). DFs release the quinone imine and free H₂O₂ in the oxidation of 4‐aminophenol in the presence of O₂, whereas Fe^III‐DF‐C1 sequesters the quinone imine into the active site, and catalyzes inside the scaffold an oxidative coupling between oxidized and reduced 4‐aminophenol. The asymmetry of the scaffold allowed a fine‐engineering of the substrate binding pocket, that ensures selectivity.     

Centrifugo-pneumatic valving utilizing dissolvable films

In this article we introduce a novel technology that utilizes specialized water dissolvable thin films for valving in centrifugal microfluidic systems. In previous work (William Meathrel and Cathy Moritz, IVD Technologies, 2007), dissolvable films (DFs) have been assembled in laminar flow devices to form efficient sacrificial valves where DFs simply open by direct contact with liquid. Here, we build on the original DF valving scheme to leverage sophisticated, merely rotationally actuated vapour barriers and flow control for enabling comprehensive assay integration with low-complexity instrumentation on "lab-on-a-disc" platforms. The advanced sacrificial valving function is achieved by creating an inverted gas-liquid stack upstream of the DF during priming of the system. At low rotational speeds, a pocket of trapped air prevents a surface-tension stabilized liquid plug from wetting the DF membrane. However, high-speed rotation disrupts the metastable gas/liquid interface to wet the DF and thus opens the valve. By judicious choice of the radial position and geometry of the valve, the burst frequency can be tuned over a wide range of rotational speeds nearly 10 times greater than those attained by common capillary burst valves based on hydrophobic constrictions. The broad range of reproducible burst frequencies of the DF valves bears the potential for full integration and automation of comprehensive, multi-step biochemical assay protocols. In this report we demonstrate DF valving, discuss the biocompatibility of using the films, and show a potential sequential valving system including the on-demand release of on-board stored liquid reagents, fast centrifugal sedimentation and vigorous mixing; thus providing a viable basis for use in lab-on-a-disc platforms for point-of-care diagnostics and other life science applications.     

Azo polymer colloidal spheres containing different amounts of functional groups and their photoinduced deformation behavior

In this work, colloidal spheres composed of azo polymers with different chromophore loading densities were prepared, and their photoinduced deformation behavior was studied. The colloids were constructed by using a series of amphiphilic epoxy-based random copolymers containing 4-carboxylazobenzene functional groups with different degrees of functionalization (DFs). The colloidal spheres were fabricated through gradual hydrophobic aggregation of the polymeric chains in tetrahydrofuran-H2O dispersion media, which was induced by gradually adding water into the systems. The colloidal spheres were characterized by using transmission electron microscopy and dynamic light scattering. The photoinduced deformation behavior was studied by irradiating the colloidal spheres with a linearly polarized Ar+ laser beam. Results showed that the critical water content (CWC) for the colloid formation is related to the DF of the polymers, and CWC increases with the increase of DF. The hydrodynamic diameter of the colloidal spheres is also related to the DF of the polymers. When the DF of the polymers increases, the average size of the colloids gradually decreases. The hydrodynamic diameter of the colloidal spheres increases as the water dropping rate decreases. When the dropping rate is below 20 microL/s, the size of the colloidal spheres increases abruptly as the dropping rate further decreases. Upon the linearly polarized Ar+ laser beam irradiation, the colloids composed of polymers with different DFs can all be elongated along the polarization direction of the laser beam. As DF increases, the deformation degree characterized by the axial ratio (l/d) almost linearly increases. These observations can give some insight into the photoinduced deformation mechanism and can be used to construct colloids with different sizes and photoresponsive ability.     

Exploring Weak Ligand–Protein Interactions by Long‐Lived NMR States: Improved Contrast in Fragment‐Based Drug Screening

Ligands that have an affinity for protein targets can be screened very effectively by exploiting favorable properties of long‐lived states (LLS) in NMR spectroscopy. In this work, we describe the use of LLS for competitive binding experiments to measure accurate dissociation constants of fragments that bind weakly to the ATP binding site of the N‐terminal ATPase domain of heat shock protein 90 (Hsp90), a therapeutic target for cancer treatment. The LLS approach allows one to characterize ligands with an exceptionally wide range of affinities, since it can be used for ligand concentrations [L] that are several orders of magnitude smaller than the dissociation constants K_D. This property makes the LLS method particularly attractive for the initial steps of fragment‐based drug screening, where small molecular fragments that bind weakly to a target protein must be identified, which is a difficult task for many other biophysical methods.     

Assessing the validity of DLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions

The domain-based local pair natural orbital coupled-cluster with single, double, and perturbative triples excitation (DLPNO-CCSD(T)) method was employed to portray the activation and reaction energies of four ubiquitous enzymatic reactions, and its performance was confronted to CCSD(T)/complete basis set (CBS) to assess its accuracy and robustness in this specific field. The DLPNO-CCSD(T) results were also confronted to those of a set of density functionals (DFs) to understand the benefit of implementing this technique in enzymatic quantum mechanics/molecular mechanics (QM/MM) calculations as a second QM component, which is often treated with DF theory (DFT). On average, the DLPNO-CCSD(T)/aug-cc-pVTZ results were 0.51 kcal·mol⁻¹ apart from the canonic CCSD(T)/CBS, without noticeable biases toward any of the reactions under study. All DFs fell short to the DLPNO-CCSD(T), both in terms of accuracy and robustness, which suggests that this method is advantageous to characterize enzymatic reactions and that its use in QM/MM calculations, either alone or in conjugation with DFT, in a two-region QM layer (DLPNO-CCSD(T):DFT), should enhance the quality and faithfulness of the results.     

Semiorganic nonlinear optical l-lysine sulphate growth and characterization

l-Lysine sulphate (LLS), a semiorganic nonlinear optical (NLO) material useful for frequency doubling in the IR region, has been synthesized. The solubility studies have been carried out in the temperature range 30–50 °C. Single crystals have been grown by slow evaporation method from an aqueous acetone solution of l-lysine and sulphuric acid. The grown crystals were bulk, bright and transparent. These crystals were characterized by X-ray and FTIR studies. Powder X-ray pattern indicates that LLS crystallizes in orthorhombic space group P2₁2₁2₁ with four unit cells. FTIR spectral studies were performed for the conformation of the l-lysine molecule and hydrogen bonds. The optical transmission spectra of the grown crystal are tested by UV–vis spectrophotometer and found that the crystal was transparent over entire visible region. The second harmonic generation test of the LLS revealed the nonlinear nature of the crystal.     

iMatch: a retention index tool for analysis of gas chromatography-mass spectrometry data

A method was developed to employ National Institute of Standards and Technology (NIST) 2008 retention index database information for molecular retention matching via constructing a set of empirical distribution functions (DFs) of the absolute retention index deviation to its mean value. The effects of different experimental parameters on the molecules' retention indices were first assessed. The column class, the column type, and the data type have significant effects on the retention index values acquired on capillary columns. However, the normal alkane retention index (I(norm)) with the ramp condition is similar to the linear retention index (I(T)), while the I(norm) with the isothermal condition is similar to the Kováts retention index (I). As for the I(norm) with the complex condition, these data should be treated as an additional group, because the mean I(norm) value of the polar column is significantly different from the I(T). Based on this analysis, nine DFs were generated from the grouped retention index data. The DF information was further implemented into a software program called iMatch. The performance of iMatch was evaluated using experimental data of a mixture of standards and metabolite extract of rat plasma with spiked-in standards. About 19% of the molecules identified by ChromaTOF were filtered out by iMatch from the identification list of electron ionization (EI) mass spectral matching, while all of the spiked-in standards were preserved. The analysis results demonstrate that using the retention index values, via constructing a set of DFs, can improve the spectral matching-based identifications by reducing a significant portion of false-positives.     

LIGHT-SCATTERING STUDY OF POLYELECTROLYTE HOLLOW CAPSULES

Silver halide (AgX) microcrystal was used as template to synthesize hollow polyelectrolyte capsules. These hollow capsules were characterized by laser light scattering (LLS) used to measure the size of the capsules in solution. The ratio of hydrodynamic radius (Rh) from dynamic LLS to the radius of gyration (Rg) from static LLS is almost unity, revealing that the entities are hollow in solution. The results suggest that the LLS method can be regarded as a good complement to the confocal laser scanning microscopy (CLSM) method for the characterization of small hollow capsules, and it possesses the advantage of not needing fluorescence labeling.     

Spectroscopy of HF and HF-containing clusters in solid parahydrogen

We report measurements of FT-IR absorption spectroscopy of HF, DF, and their clusters in solid parahydrogen (pH(2)). The observed spectra contain many absorption lines which were assigned to HF monomers, HF polymers, and clusters with other species, such as N(2), O(2), orthohydrogen (oH(2)), etc. The rotational constants of HF and DF monomers were determined from the cooperative transitions of the vibration of solid pH(2) and the rotation of HF and DF. Small reduction of the rotational constants indicates that HF and DF are nearly free rotors in solid pH(2). Time dependence of the spectra suggests that HF and DF monomers migrate in solid pH(2) and form larger polymers, probably via tunneling reactions through high energy barriers on inserting another monomer to the polymers. The line width of HF monomers in solid pH(2) was found to be 4 cm(-1), which is larger than that of other hydrogen halides in solid pH(2). This broad line width is explained by rapid rotational relaxation due to the accidental coincidence between the rotational energy of HF and the phonon energy with maximum density of states of solid pH(2) and the rotational-translational coupling in a trapping site.     

Removal of nickel and strontium from simulated radioactive wastewater via a pellet coprecipitation-microfiltration process

In order to increase the decontamination factor (DF) and concentration factor (CF) for the treatment of radioactive wastewater, a pellet coprecipitation microfiltration process which aimed at removing the neutron activation product ⁶³Ni and fission product ⁹⁰Sr was studied. In this study average DFs were (4.60 ± 0.42) × 10³ for nickel and 559 ± 24 for strontium, respectively. When about 1.8 m³ wastewater was treated, the sludge volume was significantly minimised after 24 h settling and CF reached over 1 × 10³. DFs and CF values were improved by 1–2 orders of magnitude in this study compared with those achieved by conventional methods.     

Computational study of the oxidation and decomposition of dibenzofuran under atmospheric conditions

The atmospheric degradation of dibenzofuran (DF) initiated by OH addition has been studied by using density functional theory (B3LYP method). Site C1 in DF is predicted to be the favored site for OH addition, with a branching ratio of 0.61 to produce a DF-OH(1) adduct. The calculated reaction rate constant for OH addition to DF has been used to predict the atmospheric lifetime of DF to be 0.45 day. Three different modes of attack of O2 ((3)Sigma(g)) on DF-OH(1) have been examined. Abstraction of hydrogen gem to OH in DF-OH(1) by O2 ((3)Sigma(g)) (producing 1-dibenzofuranol I) and dioxygen addition in the three radical sites in cis and trans orientation (relative to the ispo-added OH) of the pi-delocalized electron system of DF-OH(1) are feasible under atmospheric conditions. The free energy of activation (at 298.15 K) for the formation of 1-dibenzofuranol is 15.1 kcal/mol with a free energy change of -36.3 kcal/mol, while the formation of DF-OH(1)-O2 adducts are endergonic by 9.2-21.8 kcal/mol with a 16.3-23.6 kcal/mol free energy of activation. On the basis of the calculated reaction rate constants, the formation of 1-dibenzofuranol is more important than the formation of DF-OH-O2 adducts. The results presented here are a first attempt to gain a better understanding of the atmospheric oxidation of dioxin-like compounds on a precise molecular basis.     

Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

In recent years, there has been an increased interest in understanding the enzymatic mechanism of glycosidases resorting mostly to DFT and DFT/MM calculations. However, the performance of density functionals (DFs) is well known to be system and property dependent. Trends drawn from general studies, despite important to evaluate the quality of the DFs and to pave the way for the development of new DFs, may be misleading when applied to a single specific system/property. To overcome this issue, we carried out a benchmarking study of 40 DFs applied to the geometry optimization and to the electronic barrier height (E _Barrier) and electronic energy of reaction (E _R) of prototypical glycosidase‐catalyzed reactions. Additionally, we report calculations with SCC‐DFTB and four semiempirical MO methods applied to the same problem. We have used a universal molecular model for retaining glycosidases, comprising only a 22‐atoms system that mimics the active site and substrate. High accuracy reference geometries and energies were calculated at the CCSD(T)/CBS//MP2/aug‐cc‐pVTZ level of theory. Most DFs reproduce the reference geometries extremely well, with mean unsigned errors (MUE) smaller than 0.05 Å for bond lengths and 3° for bond angles. Among the DFs, wB97X‐D, CAM‐B3LYP, B3P86, and PBE1PBE have the best performance in geometry optimizations (MUE = 0.02 Å). Conversely, semiempirical MO and SCC‐DFTB methods yielded less accurate geometries (MUE between 0.09 and 0.17 Å). The inclusion of D3 correction has a small, but still relevant, influence in the geometry predicted by some DFs. Regarding E _Barrier, 11 DFs (MPW1B95, CAM‐B3LYP, M06 ‐ 2X, PBE1PBE, wB97X ‐ D, B1B95, BMK, MN12 – SX, M05, M06, and M11) presented errors below 1 kcal.mol^?1, in relation to the reference energy. Most of these functionals belong to the family of hybrid functionals (H‐GGA, HH‐GGA, and HM‐GGA), which shows a positive influence of HF exchange in the determination of E _Barrier. The inclusion of D3 correction has not affected significantly the E _Barrier and E _R. The use of geometries at the accurate but expensive MP2/aug‐cc‐pVTZ level of theory has a small, albeit not insignificant, influence in the E _Barrier when compared with energies calculated with geometries determined with the DFs (usually a few tenths of kcal.mol^?1, with exceptions). In general, semiempirical MO methods and DFTB are associated with larger errors in the determination of E _Barrier, with unsigned errors from 6.9 to 24.7 kcal.mol^?1.     

Conventional and unconventional infrared spectrometry and their quantitative interpretation

In condensed matter, optical properties can be described by a dielectric function (DF), and the structures observed in spectra are then related to the poles and zeros of the DF. As an example, model functions are calculated by a fit to measured spectroscopic data for polystyrene and silica. The first material shows weak, narrow bands and the latter strong, broad bands and a negative real part of the DF.Based on these model DFs, spectra are simulated which are expected to be obtained by “conventional” methods such as transmittance or reflectance measurements, or by “unconventional” methods such as reflectance at oblique incidence, diffuse reflectance, photoacoustic spectroscopy and attenuated total reflectance. A variety of simulated, typical spectra are plotted as a small “atlas”. Conditions are discussed that allow a straightforward procedure for interpreting the spectra quantitatively, i.e., the evaluation of the resonance frequency and the concentration of the oscillators under consideration.It is shown that for systems characterized by weak, narrow oscillator lines, mostly an intuitive interpretation is possible, looking only at the position and strength of “lines” in the spectra. Materials showing strong polar vibrations, however, require more sophisticated procedures for interpreting the spectra.     

Nanofiber formation of hydroxylpropylcellulose (HPC)

The aggregative behaviors of hydroxypropylcellulose (HPC) molecules in aqueous solution and on substrates have been observed by employing laser light scattering (LLS) and, after deposition on a mica surface, atomic force microscopy (AFM). LLS studies showed that the HPC molecules formed large aggregates through self-association when the concentration of the solution was above the critical concentration c(t). AFM measurements revealed that when a dilute aqueous solution of HPC molecules was deposited onto a mica substrate at a temperature below its lower critical solution temperature (LCST) thin nanofibers were formed with a height of 0.9 nm, whereas thick nanofibers were formed when an aqueous solution of HPC molecules was deposited onto a substrate above its LCST. Furthermore, the growth of nanofibers led to the formation of fan structures.     

Advances on photosystem II investigation by measurement of delayed chlorophyll fluorescence by a phosphoroscopic methods

A method for data acquisition based on recording of light signal from a conventional phophoroscope fluorometer with high-speed digitalization is proposed to extract more information from a delayed chlorophyll a fluorescence (DF) signal. During the signal processing from all points registered by the fluorometer, we obtain simultaneously a large number of induction curves of DF decaying at different time ranges. In addition, it is possible to register a series of dark relaxation kinetics of DF, recorded at different moments during the induction period or at different temperatures. This allows the evaluation of the contribution of DF kinetic components during the induction period or at different temperatures and the comparison between DF signals registered with different phophoroscopes. With the phosphoroscope system used in this study, we have shown that the contribution of the millisecond components (with lifetimes 0.6 and 2-4 ms) predominates during the first second of the induction period. After 1 s of illumination, the amplitudes of the 0.6 ms and 2-4 ms components and of the slower one (with lifetime more than 10 ms) become approximately equal. The change in lifetime of the different components during the induction and during gradual heating is also observed. It is shown that all registered DF kinetic components have different temperature dependences.