Application of error-ranked singular value decomposition for the determination of potential-derived atomic-centered point charges

The present work provides a detailed investigation on the use of singular value decomposition (SVD) to solve the linear least-squares problem (LLS) for the purposes of obtaining potential-derived atom-centered point charges (PD charges) from the ab initio molecular electrostatic potential (V(QM)). Given the SVD of any PD charge calculation LLS problem, it was concluded that (1) all singular vectors are not necessary to obtain the optimal set of PD charges and (2) the most effective set of singular vectors do not necessarily correspond to those with the largest singular values. It is shown that the efficient use of singular vectors can provide statistically well-defined PD charges when compared with conventional PD charge calculation methods without sacrificing the agreement with V(QM). As can be expected, the methodology outlined here is independent of the algorithm for sampling V(QM) as well as the basis set used to calculate V(QM). An algorithm is provided to select the best set of singular vectors used for optimal PD charge calculations. To minimize the subjective comparisons of different PD charge sets, we also provide an objective criterion for determining if two sets of PD charges are significantly different from one another.     

pH and temperature responsiveness in AgNPs stabilized by a new poly(vinylidene fluoride) random graft copolymer

Poly(vinylidene fluoride)(PVDF)‐graft‐random copolymers(PD) of diethyleneglycol methylether methacrylate(MeO₂MA) and dimethylaminoethyl methacrylate(DMAEMA) are synthesized by a combined atom transfer radical coupling and atom transfer radical polymerization technique at three different co‐monomer compositions. The molar ratio of MeO₂MA to DMAEMA in PD are measured to be 1:5.8, 1:1.3, and 1:0.5 for PD1, PD2, and PD3 graft copolymers. In PD2 the feed ratio and mole ratio are same indicating an azeotropic composition causing highest yield (89%) and highest molecular weight (9.29 × 10⁵). The grafted chains of PD are temperature and pH responsive and in basic pH they show a sudden increase in size above certain temperature for LCST‐type phase transition, however, this is not observed at pH 4 and 7. PD can generate AgNPs under UV irradiation and morphology of PD at 30 °C varies with pH from vesicle to nanosphere. The AgNPs lie on the surface of the vesicles or assemble with the PD chains forming nanosphere morphology. At different pH, PD samples exhibit plasmon peaks at different wavelengths attributed to various size, shapes and cluster formation. The UV–vis spectra of AgNPs stabilized by PD1 and PD2 samples exhibits similar LCST‐type phase transition as observed above, but that of PD3 does not show any such transition. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 960–970     

Fabrication of Defined Polydopamine Nanostructures by DNA Origami‐Templated Polymerization

A versatile, bottom‐up approach allows the controlled fabrication of polydopamine (PD) nanostructures on DNA origami. PD is a biosynthetic polymer that has been investigated as an adhesive and promising surface coating material. However, the control of dopamine polymerization is challenged by the multistage‐mediated reaction mechanism and diverse chemical structures in PD. DNA origami decorated with multiple horseradish peroxidase‐mimicking DNAzyme motifs was used to control the shape and size of PD formation with nanometer resolution. These fabricated PD nanostructures can serve as “supramolecular glue” for controlling DNA origami conformations. Facile liberation of the PD nanostructures from the DNA origami templates has been achieved in acidic medium. This presented DNA origami‐controlled polymerization of a highly crosslinked polymer provides a unique access towards anisotropic PD architectures with distinct shapes that were retained even in the absence of the DNA origami template.     

Potential-Derived point-charge model study of electrostatic interaction energies in some hydrogen-bonded systems

Mulliken's atomic charges (MC ) and potential derived (PD ) point charges obtained from STO -3G wave functions are used to study the electrostatic interaction energies for a series of representative hydrogenbonded complexes. The results of the above-mentioned models are compared with the more accurate results of segmental multipole moment (SMM ) expansion, and it is shown that the PD model is superior to the Mc model. The results of PD model are shown to be well correlated with the results of SMM expansion technique. Results of our calculations using 6-31G and 6-31G** PD charges are also reported here. Electrostatic interaction energies obtained using 6-31G** PD charges are compared with the 6-31G** SCF interaction energies available for the nine hydrogen-bonded dimers of ammonia, water, and hydrogen fluoride and a good con-elation between the two is shown. The interrelationship between the results of different basis sets are also examined for the PD point-charge model. The electrostatic interaction energies obtained using STO -3G PD model are shown to be well correlated to the results of 6-31G and 6-31G** PD models.     

杜氏盐藻多糖的高效体积排阻色谱的保留特性及其分析方法的研究

通过对从杜氏盐藻中提取出的不同多糖级分在高效体积排阻色谱柱(Waters Ultrahydragel Linear,7.8 mm i.d.×300 mm,2根串联)上的保留特性的考察及其分离分析条件的优化,建立了高效体积排阻色谱分析盐藻多糖平均相对分子质量及其分布的方法。结果表明:流动相中盐的种类及其浓度、pH值对3种酸性多糖级分(特别是硫酸化多糖级分PD4a)的保留行为有显著影响;在柱温为45 ℃,流速为0.9 mL/min条件下,使用0.1 mol/L的NaAc水溶液作流动相基本上能消除非特异性吸附作用及分子间缔合等因素的干扰,使各多糖级分基本以非缔合状态按立体排除机制保留和分离。在优化的色谱条件下,测得的盐藻多糖5个级分的重均相对分子质量(Mw)分别为1548000,33000,67000,424000,10000;测得的硫酸化多糖级分PD4a的Mw和峰面积的相对标准偏差分别为1.7%和 0.88%(n=5)。     

Immune Checkpoint PD‐1/PD‐L1: Is There Life Beyond Antibodies?

The PD‐1/PD‐L1 interaction has emerged as a significant target in cancer immunotherapy. Current medications include monoclonal antibodies, which have shown impressive clinical results in the treatment of several types of tumors. The cocrystal structure of human PD‐1 and PD‐L1 is expected to be a valuable starting point for the design of novel inhibitors, along with the recent crystal structures with monoclonal antibodies, small molecules, and macrocycles.     

Homogeneous,Low‐volume,Efficient, and Sensitive Quantitation of Circulating Exosomal PD‐L1 for Cancer Diagnosis and Immunotherapy Response Prediction

Immunotherapy has revolutionized cancer treatment, but its efficacy is severely hindered by the lack of effective predictors. Herein, we developed a homogeneous, low‐volume, efficient, and sensitive exosomal programmed death‐ligand 1 (PD‐L1, a type of transmembrane protein) quantitation method for cancer diagnosis and immunotherapy response prediction (HOLMES‐Exo_PD‐L1). The method combines a newly evolved aptamer that efficiently binds to PD‐L1 with less hindrance by antigen glycosylation than antibody, and homogeneous thermophoresis with a rapid binding kinetic. As a result, HOLMES‐Exo_PD‐L1 is higher in sensitivity, more rapid in reaction time, and easier to operate than existing enzyme‐linked immunosorbent assay (ELISA)‐based methods. As a consequence of an outstanding improvement of sensitivity, the level of circulating exosomal PD‐L1 detected by HOLMES‐Exo_PD‐L1 can effectively distinguish cancer patients from healthy volunteers, and for the first time was found to correlate positively with the metastasis of adenocarcinoma. Overall, HOLMES‐Exo_PD‐L1 brings a fresh approach to exosomal PD‐L1 quantitation, offering unprecedented potential for early cancer diagnosis and immunotherapy response prediction.     

Polymethine dyes as spectral-fluorescent probes for biomacromolecules

It is known that polymethine dyes (PD) can form complexes with biomacromolecules, in which, as a rule, fluorescence buildup is observed. In addition, PD possess a unique property to form ordered aggregates of different types (dimers, H- and J-aggregates) both in the free state and on biomacromolecules as templates. This creates a basis for application of PD as spectral-fluorescent probes for biomacromolecules, which is a matter of this review. Besides, the review is devoted to studies of noncovalent interactions of PD with biomacromolecules: nucleic acids, proteins, and some others.     

Feasibility of light-emitting diode uses for annular reactor inner-coated with TiO2 or nitrogen-doped TiO2 for control of dimethyl sulfide

Limited environmental pollutants have only been investigated for the feasibility of light‐emitting diodes (LED) uses in photocatalytic decomposition (PD). The present study investigated the applicability of LEDs for annular photocatalytic reactors by comparing PD efficiencies of dimethyl sulfide (DMS), which has not been investigated with any LED‐PD system, between photocatalytic systems utilizing conventional and various LED lamps with different wavelengths. A conventional 8 W UV/TiO₂ system exhibited a higher DMS PD efficiency as compared with UV‐LED/TiO₂ system. Similarly, a conventional 8 W visible‐lamp/N‐enhanced TiO₂ (NET) system exhibited a higher PD efficiency as compared with six visible‐LED/NET systems. However, the ratios of PD efficiency to the electric power consumption were rather high for the photocatalytic systems using UV‐ or visible‐LED lamps, except for two LED lamps (yellow‐ and red‐LED lamps), compared to the photocatalytic systems using conventional lamps. For the photocatalytic systems using LEDs, lower flow rates and input concentrations and shorter hydraulic diameters exhibited higher DMS PD efficiencies. An Fourier‐transformation infrared analysis suggested no significant absorption of byproducts on the catalyst surface. Consequently, it was suggested that LEDs can still be energy‐efficiently utilized as alternative light sources for the PD of DMS, under the operational conditions used in this study.     

Redox potential inversion by ionic hydrogen bonding between phenylenediamines and pyridines

In electrochemical oxidations, the second oxidation potential of phenylenediamines (PD) varies because of hydrogen-bonding formation for PD(+?) with pyridines. A linear relationship was obtained for the potential shift as a function of pK(a) of the protonated pyridines and potential inversion could be observed. The oxidized PD(+?) could also form hydrogen bonding with alcohols and the shift of potential exhibits a different pattern.     

Novel charge-transfer complexes of 4-hexylamino-1,8-naphthalimide-labelled PAMAM dendrimer with some acceptors: a spectrophotometric study

Poly(amidoamine) dendrimers are very interesting macromolecules with highly branched structures and globular-shaped branched polymeric architectures. They are widely used for drug and gene delivery applications. In order to provide important insight into the interactions of poly(amidoamine) dendrimers with some organic acceptors, the binding of small molecules to 4-hexylamino-1,8-naphthalimide-labelled PAMAM dendrimer (PD) have been studied by spectrophotomeric method. The acceptors used in this research include chloranilic acid (CLA), p-chloranil (CHL), 2,6-dichloroquinone-4-chloroimide (DCQ), 2,6-dibromoquinone-4-chloroimide (DBQ), 7,7?,8,8?-tetracyanoquinodimethane (TCNQ), picric acid (PA), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) and iodine monobromide (IBr). The spectrophotometric measurements proved that all the charge-transfer (CT) complexes are formed via a stoichiometry (PD: acceptor) of 1:2 (except for IBr acceptor). Accordingly the obtained complexes could be formulated as [(PD)(CLA)₂], [(PD)(DCQ)₂], [(PD)(DBQ)₂], [(PD)(TCNQ)₂], [(PD)(PA)₂], [(PD)(CHL)₂], [(PD)(DDQ)₂] and [(PD)(IBr)₄]. Benesi–Hildebrand and its modification methods were applied to estimate the spectroscopic and physical data.     

3-Deoxygalactosone, a new glucose degradation product in peritoneal dialysis fluids: Identification, quantification by HPLC/DAD/MSMS and its pathway of formation

Heat sterilization of peritoneal dialysis (PD) fluids leads to the formation of glucose degradation products (GDPs), which considerably impair long-term application of PD. Knowledge of the exact composition of GDPs present in a PD fluid is important to improve the biocompatibility of dialysis solutions. The present study conducted a targeted screening for novel GDPs with α-dicarbonyl structure in PD fluids. Thus, 3-deoxygalactosone (3-DGal) was identified for the first time in PD fluids. Quantification of 3-DGal was achieved by high-performance liquid chromatography (HPLC)/DAD/MSMS after derivatization with o-phenylendiamine to yield the quinoxaline derivative. Baseline separation of all α-dicarbonyl GDPs, particularly of the diastereomers 3-deoxyglucosone (3-DG) and 3-DGal, required the application of a polar, phenyl-based RP column for HPLC and additional pH-gradient elution. Concentrations of 3-DGal ranged between 55.8 and 136.9 μM in single-chamber PD fluids, and between 2.5 and 12.4 μM in double-chamber PD fluids. In solutions containing glucose, 3-DGal is formed from 3-DG via the intermediate 3,4-dideoxyglucosone-3-ene (3,4-DGE). Further studies are now required to determine the (patho-)physiological properties of 3-DGal.     

Aptamer-functionalized Ti3C2-MXene Nanosheets with One-step Potentiometric Detection of Programmed Death-ligand 1

This communication describes a simple sensitive one-step potentiometric aptasensing method for quantitative detection of a referenced therapeutic biomarker (programmed death-ligand 1, PD−L1). The aptasensor is constructed by modifying PD−L1-specific aptamer on Ti₃C₂-MXene nanosheets-functionalized electrode. Introduction of PD−L1 induces the specific reaction between PD−L1 and aptamer, thereby resulting in the change of spatial structures. The surface electric potential of modified electrode is shifted upon addition of PD−L1 proteins before and after the reaction of aptamer with the analyte. Interestingly, potentiometric aptamer with Ti₃C₂-MXene nanosheets can achieve a higher sensitivity and a lower detection limit toward target PD−L1 relative to aptamer-modified electrode. Experimental results indicated that the linear range and detection limit of using Ti₃C₂-MXene nanosheets were 0.01–100 ng mL⁻¹ and 7.8 pg mL⁻¹ PD−L1, respectively. Meanwhile, the specificity, reproducibility, storing stability and accuracy of potentiometric aptasensor are acceptable for the screening of PD−L1 in human serum samples.     

Identification of RFLP G6PD mutations by using microcapillary electrophoretic chips (Experion)

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is one of the most well-known human genetic defects, identified in more than 400 million individuals in the world. To date, no commercial kits are available for the mutation screening of this disease. Seventy G6PD-deficient Italian individuals admitted to the Laboratory of Clinical Molecular Biology of Hospital "Agostino Gemelli" of Rome were screened for the most frequent Italian mutations, by means of allele-specific PCR, followed by restriction fragment length electrophoresis. The present study compares two techniques for the identification of restriction patterns: agarose gel electrophoresis versus Experion system. When the first screening was negative, the entire G6PD gene was sequenced using the ABI 3100 Avant Instrumentation. The G6PD variants identified and their frequencies were the following: G6PD Mediterranean (75.7%), G6PD Seattle (7.1%), G6PD A(-) 202 + 376 (7.1%), and G6PD Cassano (2.8%). In addition, we identified by direct sequencing two new mutations, namely Buenos Aires and Rignano. With the Experion method, the size band determination was more accurate than that obtained by gel electrophoresis. The Experion system resulted as a valid, easy, and reproducible diagnostic method for the screening of G6PD mutation as compared with the agarose electrophoretic analysis.     

具有不同取代基的吡唑啉衍生物的光致发光和电致发光

在合成两种具有不同取代基的吡唑啉衍生物PD1和PD2的基础上,研究了不同取代基效应对其光致发光和电致发光性质的影响.结果表明甲氧基取代的化合物PD2较N,N-二甲氨基取代的化合物PD1具有更高的荧光量子产率.而在作为有机电致发光器件的掺杂染料,当其器件结构为ITO/TPD/TPBI:2% PD/TP-BI/Mg:Ag时,PD1掺杂染料却有着较PD2更高的电致发光效率.当器件的电流密度为420 mA/cm²时,掺杂染料为PD1的器件在487 nm处发射蓝光,其发光亮度为1224 cd/m².     

Solvation dynamics of electron produced by two-photon ionization of liquid polyols. II. Propanediols

Temporal evolution of transient absorption spectra of electrons produced by two-photon ionization of two isomers, propane-1,2-diol (12PD) and propane-1,3-diol (13PD), with 263 nm femtosecond laser pulses has been studied on picosecond time scale. The two-photon absorption coefficients of 12PD and 13PD at 263 nm were determined to be beta = (2.0 +/- 0.3) x 10(-11) and (2.4 +/- 0.3) x 10(-11) m W(-1), respectively. Time-resolved absorption spectra ranging from 440 to 720 nm have been measured, showing a blue shift for the first tens of picoseconds for both solvents. However, the observed solvation dynamics of electron appears faster in 13PD than in 12PD. The transient signals of electron solvation have then been reconstructed with different models (stepwise mechanism or continuous relaxation model) using a Bayesian data analysis method. Results are discussed, compared with those previously obtained in ethylene glycol (J. Phys. Chem. A 2006, 110, 1705) and corroborate the interpretation, according to which the solvation of electrons is mainly governed by continuous solvent molecular motions.     

Blocking of the PD‐1/PD‐L1 Interaction by a D‐Peptide Antagonist for Cancer Immunotherapy

Blockade of the protein–protein interaction between the transmembrane protein programmed cell death protein 1 (PD‐1) and its ligand PD‐L1 has emerged as a promising immunotherapy for treating cancers. Using the technology of mirror‐image phage display, we developed the first hydrolysis‐resistant D ‐peptide antagonists to target the PD‐1/PD‐L1 pathway. The optimized compound ^DPPA‐1 could bind PD‐L1 at an affinity of 0.51 μM in vitro. A blockade assay at the cellular level and tumor‐bearing mice experiments indicated that ^DPPA‐1 could also effectively disrupt the PD‐1/PD‐L1 interaction in vivo. Thus D ‐peptide antagonists may provide novel low‐molecular‐weight drug candidates for cancer immunotherapy.     

Neuroprotective effects of tanshinone IIA in experimental model of Parkinson disease in rats

Neurodegenerative diseases including Parkinson's disease (PD) cause many problems for the patient. Treatment options include the administration of chemical drugs, which are associated with many side effects. Therefore, the current study was aimed to investigate tanshinone IIA effects on the experimental model of PD in rats and to study the neuroprotective mechanisms of this natural product. After preparation of rats and induction of PD by 6-hydroxypopamine (6-OHDA), different concentrations of tanshinone IIA were administered to the rats for 10 days. Apomorphine-induced rotation and muscle rigidity behavioral tests were used to evaluate PD induction and to study the effects of tanshinone IIA. After separation of the hippocampus, biochemical parameters such as lipid peroxidation, protein oxidation, succinic dehydrogenase (SDH), super oxide dismutase (SOD), reactive oxygen species (ROS), malate dehydrogenase (MDH), catalase (CAT), reduced glutathione (GSH), lactate dehydrogenase (LDH), IL-1β, TNF-α, INF-γ, IL-10 cytokines and NF-?B protein expression were measured. The results showed that PD rats receiving tanshinone IIA improved their performance in behavioral tests. Decreased oxidative stress indices and increased antioxidant capacity were observed in the hippocampal tissue of PD rats receiving tanshinone IIA. Also, administration of tanshinone IIA to PD rats downregulated inflammatory cytokines TNF-α. IL-1β and INF-γ and decreased NF-?B protein expression. Tanshinone IIA has therapeutic effects in PD condition as results of antioxidant and anti-inflammatory properties. Therefore, this natural product is recommended in PD treatment.     

Photodissociation tandem mass spectrometry at 266 nm of an aliphatic peptide derivatized with phenyl isothiocyanate and 4-sulfophenyl isothiocyanate

Photodissociation (PD) tandem mass spectra have been obtained at 266 nm for the protonated molecules of a tryptic peptide, ASHLGLAR, and of its phenyl isothiocyanate and 4-sulfophenyl isothiocyanate derivatives, generated by matrix-assisted laser desorption/ionization. Derivatization with the aromatic chromophores greatly reduced the intensity of the laser required for efficient PD. Major fragment ions observed in the three spectra are quite similar. General features of the PD tandem mass spectra and their potential utility for analytical purposes are discussed.