Open Ring Structure Research Articles

Two-dimensional correlation and codistribution spectroscopy (2DCOS and 2DCDS) analyses of time-dependent ATR IR spectra of d-glucose anomers undergoing mutarotation process in water

Two cyclic diastereoisomeric structures, known as α- and β-anomers of d-glucose with different configurations around C1 with OH groups in axial or equitroial positions, undergo the mutarotation conversion to each other in water. Two-dimensional correlation and codistribution spectroscopy (2DCOS and 2DCDS) analyses were applied to the time-dependent ATR IR spectra of aqueous solutions of α- and β-d-glucose undergoing such mutarotation conversion. 2DCOS analysis reveals that the increase and decrease in the IR intensities after the dissolution of α- or β-d-glucose are not fully synchronized, suggesting the mutarotation of d-glucose in water is not a simple binary conversion process but a multi-step reaction involving an intermediate species with a finite and observable concentration level and lifetime. 2DCDS analysis of the time-dependent ATR IR spectra clearly demonstrated the presence of intermediate species contributing to the band positions overlapped close to bands for α- and β-d-glucose. The fact that band positions identified for the intermediate species for α- to β-d-glucose conversion are the same for the reverse reaction suggests that they arise from the same species, most likely the open-ring structure produced by the hydrolysis.

Very Small-Size Uniplanar Printed Monopole Antenna for Dual-Band WLAN Laptop Computer Applications

This paper presents a very small-size uniplanar printed monopole antenna design with an overall size of only 8.7 mm $\times 5.4$ mm $\times 0.8$ mm. It is comprised of an open-ring structure and a hook-shaped radiating element that is extended within this open-ring structure. The proposed antenna can excite two resonance modes with broad 10-dB impedance bandwidths of 6.4% (2.35–2.51 GHz) and 19.5% (4.90–6 GHz), and this dual-band operation can cover the entire WLAN 2.4/5.2/5.8-GHz bands. Furthermore, a good gain of 3.34–5.38 dBi and desirable radiation efficiencies of 52%–87% were also measured across the two bands of interest.

The Architecture of the Anbu Complex Reflects an Evolutionary Intermediate at the Origin of the Proteasome System

SummaryProteasomes are self-compartmentalizing proteases that function at the core of the cellular protein degradation machinery in eukaryotes, archaea, and some bacteria. Although their evolutionary history is under debate, it is thought to be linked to that of the bacterial protease HslV and the hypothetical bacterial protease Anbu (ancestral beta subunit). Here, together with an extensive bioinformatic analysis, we present the first biophysical characterization of Anbu. Anbu forms a dodecameric complex with a unique architecture that was only accessible through the combination of X-ray crystallography and small-angle X-ray scattering. While forming continuous helices in crystals and electron microscopy preparations, refinement of sections from the crystal structure against the scattering data revealed a helical open-ring structure in solution, contrasting the ring-shaped structures of proteasome and HslV. Based on this primordial architecture and exhaustive sequence comparisons, we propose that Anbu represents an ancestral precursor at the origin of self-compartmentalization.

Computational study of the competitive binding of valproic acid glucuronide and carbapenem antibiotics to acylpeptide hydrolase

The efficacy of the antiepileptic drug VPA is decreased by co-administered carbapenems (CBPMs). The mechanism of CBPM selective inhibition of acylpeptide hydrolase (APEH) hydrolysis of VPA-glucuronide (VPA-G) to VPA is unclear due to the lack of APEH structural information. Here we performed homology modeling of the three-dimensional structure of APEH and subsequent docking simulations with a modeled structure to understand this mechanism. Docking simulations indicated that four groups of binding structures were involved in the binding of VPA-G, panipenem, and meropenem to APEH, but only one or two binding structures were involved in the binding of meropenem with an open β-lactam ring structure and other antibiotics involving ampicillin. One of the four VPA-G binding structures was close enough to the APEH catalytic triad to facilitate VPA-G hydrolysis. This binding structure was also the most stable binding structure for panipenem, suggesting potential inhibition of VPA-G hydrolysis by panipenem. Fragment molecular orbital calculations of interaction energies of amino acid residues of APEH with VPA-G, panipenem, and meropenem indicated that the binding structure for panipenem closest to the catalytic triad is stabilized upon APEH interaction. These data suggest that APEH binding characteristics with CBPMs may help explain the selective inhibition of APEH by CBPMs.

Time-dependent density functional theory study on direction-dependent electron and hole transfer processes in molecular systems.

We report on real-time time-dependent density functional theory calculations on direction-dependent electron and hole transfer processes in molecular systems. As a model system, we focus on α-sulfur. It is shown that time scale of the electron transfer process from a negatively charged S8 molecule to a neighboring neutral monomer is comparable to that of a strong infrared-active molecular vibrations of the dimer with one negatively charged monomer. This results in a strong coupling between the electrons and the nuclei motion which eventually leads to S8 ring opening before the electron transfer process is completed. The open-ring structure is found to be stable. The similar infrared-active peak in the case of hole transfer, however, is shown to be very weak and hence no significant scattering by the nuclei is possible. The presented approach to study the charge transfer processes in sulfur has direct applications in the increasingly growing research field of charge transport in molecular systems. © 2017 Wiley Periodicals, Inc.

Structure and properties of conducting poly(o-phenylenediamine) synthesized in different inorganic acid medium

Poly(o-phenylenediamine) was chemically synthesized from the monomer o-phenylenediamine in various inorganic acid medium, viz., hydrochloric (HCl), sulphuric (H2SO4) and phosphoric acid (H3PO4) to investigate the differences in structures and properties of the synthesized polymers. From the various characterizations, it was confirmed that the ladder type polymer with some open ring structure was formed in HCl medium while open ring type amine derivative of polyaniline structure was obtained in H2SO4 medium and the ladder type dimer was formed in H3PO4 medium. The structural differences of the polymers were correlated with the polymerization mechanism in different acid medium. Thus, the polymer synthesized in H2SO4 was well soluble in polar organic solvent like dimethyl sulfoxide (DMSO), N,N-dimethyl formamide, tetrahydrofuran etc. and casting of freestanding film was possible from DMSO solution. The highest average DC conductivity of H2SO4 doped polymer synthesized in H2SO4 medium was observed as 7.14×10−4 S/cm. The conductivity and doping properties of the polymer were explained here from the proper characterizations.

Synthesis of processable conducting poly(m-aminophenol) having structure like keto derivative of polyaniline

Poly(m-aminophenol) was synthesized chemically from m-aminophenol in aqueous hydrochloric acid using ammonium persulfate as an oxidizing agent. To get processable poly(m-aminophenol) the polymerization condition was optimized by varying HCl concentration and temperature. The synthesized polymers at lower HCl concentration were insoluble in organic solvents, but synthesized polymers at higher acid concentration were found to be soluble in aqueous sodium hydroxide, dimethyl formamide, dimethyl sulfoxide. The polymers were characterized by ultraviolet visible, proton magnetic resonance and Fourier transform infrared spectroscopy. X-ray diffraction analysis and elemental analysis of the synthesized polymers were also performed. DC electrical conductivity of the acid doped polymers was measured by Four-probe method. The spectral evidences clearly indicated that the ladder structure was formed in lower aqueous HCl concentration while open ring keto derivative of polyaniline was formed at higher HCl concentration. The polymer with open ring structure was better processabe and higher conductive in doped state than that of the other one. Difference of their properties like solubility, conductivity of the polymers synthesized at different condition was due to their structural difference.

Influence of pH of the Reaction Medium on the Structure and Property of Conducting Poly(o-Phenylenediamine)

Poly(o-phenylenediamine) (PoPD) was synthesized from o-phenylenediamine (oPD) using ammonium persulfate (APS) as an oxidizing agent in varying pH of reaction medium. The polymers were characterized by UV-VIS, 1HNMR and FTIR spectroscopy, thermogravimetric and elemental (CHNS) analyses. Solubility tests for the synthesized polymers were performed in various solvents and it was found that the polymer synthesized in lower pH medium was insoluble. The difference in their solubility is due to their structural difference, which can be supported by the proposed mechanisms of polymerizations. The spectral results clearly indicated that the ladder structure was formed in lower pH medium while open ring structure (with some ladder unit) or dimer was formed at higher pH. Fourprobe DC electrical conductivity of the synthesized polymers was also measured. The average DC conductivity of the polymer doped with hydrochloric acid was observed 8.8 x 10-5 S/cm for the synthesized open ring polymer while it was only 1.7 x 10-7 S/cm for the synthesized ladder polymer.

The Contamination Mechanism and Behavior of Amide Bond Containing Organic Contaminant on PEMFC

This paper presents a study of the effects of an organic contaminant containing an amide bond (-CONH-), ɛ-caprolactam, on polymer electrolyte membrane fuel cells (PEMFCs). The ɛ-caprolactam has been detected in leachates from polyphthalamide materials that are being considered for use as balance-of-plant structural materials for PEMFCs. Contamination effects from ɛ-caprolactam in Nafion membranes are shown to be controlled by temperature. A possible explanation of the temperature effect is the endothermic ring-opening reaction of the amide bond (-NHCO-) of the cyclic ɛ-caprolactam. UV-vis and ATR-IR spectroscopy studies confirmed the presence of open ring structure of ɛ-caprolactam in membranes. The ECSA and kinetic current for the ORR of the Pt/C catalyst were also investigated and were observed to decrease upon contamination by the ɛ-caprolactam. By comparison of the CVs of ammonia and acetic acid, we confirmed the adsorption of carboxylic acid (-COOH) or carboxylate anion (-COO-) onto the surface of the Pt. Finally, a comparison of in situ voltage losses at 80°C and 50°C also revealed temperature effects, especially in the membrane, as a result of the dramatic increase in the HFR.

Mechanical properties of films made from dialcohol cellulose prepared by homogeneous periodate oxidation

2,3-Dialdehyde celluloses were prepared by homogeneous periodate oxidation in an aqueous solution of methylol cellulose. Since methylol cellulose stays dissolved in water for a certain time before decomposing gradually into regenerated cellulose, the oxidation reaction progressed homogeneously throughout the period. The resulting dialdehyde cellulose achieved an oxidation level of over 90 % in as little as 12 h. Reducing the dialdehyde celluloses with NaBH4 resulted in water-soluble dialcohol celluloses, which have an open-ring structure at the C2–C3 position. The dialcohol celluloses were characterized using nuclear magnetic resonance spectrometry, Fourier transform infrared spectroscopy, and differential scanning calorimetry. The Tg of the products decreased with increasing oxidation levels. The products might be processable, and unique tensile properties were obtained by cutting the C2–C3 bonds in the glucopyranose rings. The dialcohol celluloses prepared using a cast method yielded clear and transparent films which showed unique mechanical properties by tensile tests depending on the values of oxidation level.

The 1.8-Å Crystal Structure of the N-Terminal Domain of an Archaeal MCM as a Right-Handed Filament

Mini-chromosome maintenance (MCM) proteins are the replicative helicase necessary for DNA replication in both eukarya and archaea. Most of archaea only have one MCM gene. Here, we report a 1.8-Å crystal structure of the N-terminal MCM from the archaeon Thermoplasma acidophilum (tapMCM). In the structure, the MCM N-terminus forms a right-handed filament that contains six subunits in each turn, with a diameter of 25Å of the central channel opening. The inner surface is highly positively charged, indicating DNA binding. This filament structure with six subunits per turn may also suggests a potential role for an open-ring structure for hexameric MCM and dynamic conformational changes in initiation and elongation stages of DNA replication.

Towards the understanding of the photochemical ring opening and closing mechanisms for spiropyrans using 2H-pyran and the maximum overlap method

A first principle study on 2H-pyran has been carried out to elucidate the photochemical ring opening and closing mechanism of spiropyrans. A systematic study on relative energies using Hartree-Fock, density functional and post-Hartree-Fock methods was carried out to determine an appropriate level of theory for these systems. Second order Moller-Plesset perturbation theory (MP2) shows good agreement with the CCSD calculations, converges at the 6–31 + G(2df, p) basis set level and predicts the closed ring structure as the most stable. The maximum overlap method (MOM) was used to calculate the excited states of both 2H-pyan and the open ring structure 2,4-pentadienal. Excitation of the planar form of 2H-pyran at 189 nm leads to direct photochemical ring opening. Excitation of the open-ring structure at 283 nm causes the reverse process, ring closing, to occur. Our excited state calculations indicate that thermal conversion of the more stable puckered structure of 2H pyran into the planer form needs to take place before the photochemical ring opening can occur.

Genetic Manipulation of the Fusarium fujikuroi Fusarin Gene Cluster Yields Insight into the Complex Regulation and Fusarin Biosynthetic Pathway

In this work, the biosynthesis and regulation of the polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS)-derived mutagenic mycotoxin fusarin C was studied in the fungus Fusarium fujikuroi. The fusarin gene cluster consists of nine genes (fus1-fus9) that are coexpressed under high-nitrogen and acidic pH conditions. Chromatin immunoprecipitation revealed a correlation between high expression and enrichment of activating H3K9-acetylation marks under inducing conditions. We provide evidence that only four genes are sufficient for the biosynthesis. The combination of genetic engineering with nuclear magnetic resonance and mass-spectrometry-based structure elucidation allowed the discovery of the putative fusarin biosynthetic pathway. Surprisingly, we indicate that PKS/NRPS releases its product with an open ring structure, probably as an alcohol. Our data indicate that 2-pyrrolidone ring closure, oxidation at C-20, and, finally, methylation at C-20 are catalyzed by Fus2, Fus8, and Fus9, respectively.

False-positive penicillin immunoassay: An unnoticed common problem

False-positive penicillin immunoassay: An unnoticed common problem

ATP-dependent conformational dynamics underlie the functional asymmetry of the replicative helicase from a minimalist eukaryote

The heterohexameric minichromosome maintenance (MCM2-7) complex is an ATPase that serves as the central replicative helicase in eukaryotes. During initiation, the ring-shaped MCM2-7 particle is thought to open to facilitate loading onto DNA. The conformational state accessed during ring opening, the interplay between ATP binding and MCM2-7 architecture, and the use of these events in the regulation of DNA unwinding are poorly understood. To address these issues in isolation from the regulatory complexity of existing eukaryotic model systems, we investigated the structure/function relationships of a naturally minimized MCM2-7 complex from the microsporidian parasite Encephalitozoon cuniculi. Electron microscopy and small-angle X-ray scattering studies show that, in the absence of ATP, MCM2-7 spontaneously adopts a left-handed, open-ring structure. Nucleotide binding does not promote ring closure but does cause the particle to constrict in a two-step process that correlates with the filling of high- and low-affinity ATPase sites. Our findings support the idea that an open ring forms the default conformational state of the isolated MCM2-7 complex, and they provide a structural framework for understanding the multiphasic ATPase kinetics observed in different MCM2-7 systems.

First-Principles Study of the Initial Reaction of OH- and O-Terminated β-Si3N4 Surfaces with Hydrogen Fluoride

Density functional theory has been applied to the reaction of molecular HF with several different bonds found on the closed- and open-ring (1010) surfaces of β-Si3N4 that have been terminated in O and OH so as to model a native oxide. The only energetically favorable primary reaction is HF + Si–OH → Si–F + H2O. This is moderately exothermic, but the activation energy is somewhat higher than for the same reaction on the SiC (0001) surface, which is consistent with experiments in which Si–OH is detected under steady-state conditions for β-Si3N4 undergoing exposure to dilute aqueous HF solutions. Removal of the native oxide depends in detail on the surface structure. Si–O–Si bridges on the closed-ring surface are less reactive than those on the open-ring structure, and in the former case, the reaction 2 HF + Si–O–Si → 2 Si–F + H2O is significantly endothermic. For the open-ring surface, the same reaction is moderately exothermic, although the first step, which forms Si–F + HO-Si, is moderately endothermic. ...

Mechanism of degradation of poly(p‐phenylene benzobisoxazole) under hydrolytic conditions

AbstractPoly(p‐phenylene benzobisoxazole) (PBO) fiber has received great interest because of its excellent mechanical properties and good thermal stability. The objective of this study was to expose degradation mechanism of PBO under neutral and acidic conditions by molecular mass and Fourier transform infrared (FTIR) spectroscopy. Results were not consistent with the classic degradation mechanism, which indicates that degradation should occur through the ring opening and chain scission of the benzoxazole ring. The FTIR absorption spectra of PBO suggested that the o‐hydroxy amide linkage (the open ring structure) was present in the PBO molecule chain to some extent because of the incomplete polymerization. Further investigation showed that hydrolysis might occur in the open ring section during hydrolytic degradation. Based on the experimental data, a new degradation mechanism was proposed. It suggests that, in the early and middle stages, hydrolysis occurred primarily in the o‐hydroxy amide linkage of the open ring. The concentration of the o‐hydroxy amide structure determined the speed of degradation of PBO. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011

Excess and deviation properties of {(glycylglycine + ZnCl 2) in aqueous methanol} mixtures

The excess molar volumes ( V E), viscosity deviations (Δ η), deviations in isentropic compressibility (Δ κ S) and excess molar refractivity (Δ R m E ) for {(glycylglycine + ZnCl 2) in aqueous methanol} mixture have been calculated from the experimental values. The bridging water molecules bend the chains into stable open ring structures together with intermolecular hydrogen bonding and interstitial accommodation leading to negative V E values. The positive Δ η values indicate a structure breaking effect of aqueous glycylglycine–ZnCl 2 upon contact with methanol molecules. It is also noted that chelation of zinc to glycylglycinate is through carboxylic group and not the amino group. The negative Δ κ S values suggest the formation of an open ring structure lowering the entropy of the solution. Due to weak interaction between solute and solvent, the molecular structure of individual molecule does not change significantly and leads to negative Δ R m E values. Finally, the results have lead to a good understanding of the thermodynamics properties of the studied liquid mixture.

On the photocatalytic degradation of phenol and dichloroacetate by BiVO 4: The need of a sacrificial electron acceptor

The photodegradation of phenol and dichloroacetic acid (DCAA) by BiVO 4 was studied in the absence as well as presence of selected electron scavengers. The experiments were performed under the visible (vis) irradiation of aqueous solutions over a wide pH range (1–13). Phenol was photocatalytically degraded by BiVO 4 into p-benzoquinone below pH 3 and into an open-ring structure at pH 13. Methylene blue (MB) accelerated the reaction below the isoelectric point of BiVO 4 and did not undergo significant degradation. In presence of H 2O 2, phenol was rapidly degraded up to pH 9. The degradation rates are two orders of magnitude higher than in absence of electron scavenger. The degradation of dichloroacetic acid was only possible in presence of H 2O 2. High initial concentrations of H 2O 2 inhibit the reaction and its consumption is very fast. Sequential additions of this sacrificial electron acceptor (SEA) enables the total degradation of a 1 mM DCAA solution.

Oscillatory persistent currents in quantum rings: Semiconductors versus superconductors

Persistent currents are a hallmark of superconductivity in metals. To observe those dissipationless currents in a non-superconducting ring, the circumference of the ring must be short enough so that the phase coherence of the electronic wave functions is preserved around the loop. Recent progress in the fabrication of self-assembled semiconductor quantum rings (SAQRs), which can be filled with only a few (1–2) electrons, has offered the unique possibility to study the magnetic-field-induced oscillations in the persistent current carried by a single electron. In this paper, we discuss similarities and distinctions between the behavior of persistent currents in semiconductor and superconductor samples and give an overview of the recent results for oscillatory persistent currents in SAQRs. Although the real SAQR shape differs strongly from an idealized circular-symmetric open ring structure, the Aharonov–Bohm oscillations of the magnetization survive, as observed in low temperature magnetization measurements on In x Ga 1− x As/GaAs SAQRs.