A generalized fortress problem using k-consecutive vertex guards

The fortress problemwas posed independently by Joseph Malkelvitch and Derick Wood to determine the number of guards sufficient to cover the exterior of an n-vertex polygon. O'Rourke and Wood showed that vertex guards are sometimes necessary and always sufficient. Yiu and Choi considered a variation of the problem by allowing each guard to patrol an edge (called an edge guard) of the polygon and obtained a tight bound of edge guards for general polygons. In this paper, we unify and generalize both results by considering the number of k-consecutive vertex guards that are required to solve the fortress problem. A tight bound of is obtained. Received 21 July 1999; revised 23 March 2000.     

Assessment of bone calcium and phosphorus content using micro X‐ray fluorescence spectrometry (μ‐EDXRF): effects of long‐term cadmium poisoning

This study assesses whether the concentrations of biologically important elements in bones are altered by long‐term consumption of cadmium (Cd)‐contaminated water. Heavy metal poisoning has significant impact on humans, and pollutants such as Cd are often found at high concentrations in waterways. Twelve Sprague Dawley rats consumed water with 50 p.p.m. Cd (Cd group), and another 12 consumed normal water (control group). Six subjects from each group were sacrificed after 2 weeks and the others after 4 weeks. Spectra were acquired from the femur by using the EDAX Eagle III micro‐XRF setup, and quantitative calculations were performed by using the fundamental parameter method to determine the concentrations of elements. A bone calcium/phosphorus concentration ratio (Ca/P) of 2.07 ± 0.001 is observed in the spectra from control subjects after 2 weeks and 2.07 ± 0.001 after 4 weeks. In Cd subjects, Ca/P after 2 weeks is 2.04 ± 0.001 and after 4 weeks is 1.97 ± 0.003. Statistically significant differences are obtained when comparing controls with Cd subjects at both time points and when comparing Cd subjects at both time points. Cadmium poisoning significantly affects bone Ca and P concentrations, increasing the likelihood of osteoporosis and other bone diseases. Copyright © 2016 John Wiley & Sons, Ltd.     

Key Word Index for Volume 11

Other Index

Key Word Index for Volume 11     

Functionalized Alkynylplatinum(II) Polypyridyl Complexes for Use as Sensitizers in Dye‐Sensitized Solar Cells

A series of platinum(II) alkynyl‐based sensitizers has been synthesized and found to show light‐to‐electricity conversion properties. These dyes were developed as sensitizers for the application in nanocrystalline TiO₂ dye‐sensitized solar cells (DSSCs). Their photophysical and electrochemical properties were studied. The excited‐state property was probed using nanosecond transient absorption spectroscopy, which showed the formation of a charge‐separated state that arises from the intramolecular photoinduced charge transfer from the platinum(II) alkynylbithienylbenzothiadiazole moiety (donor) to the polypyridyl ligand (acceptor). A lifetime of 3.4 μs was observed for the charge‐separated state. A dye‐sensitized solar cell based on one of the complexes showed a short‐circuit photocurrent of 7.12 mA cm^?2, an open circuit voltage of 780 mV, and a fill factor of 0.65, thus giving an overall power conversion efficiency of 3.6 %.     

A Time‐Resolved Spectroscopic Study of the Bichromophoric Phototrigger 3′,5′‐Dimethoxybenzoin Diethyl Phosphate: Interaction Between the Two Chromophores Determines the Reaction Pathway

3′,5′‐Dimethoxybenzoin (DMB) is a bichromophoric system that has widespread application as a highly efficient photoremovable protecting group (PRPG) for the release of diverse functional groups. The photodeprotection of DMB phototriggers is remarkably clean, and is accompanied by the formation of a biologically benign cyclization product, 3′,5′‐dimethoxybenzofuran (DMBF). The underlying mechanism of the DMB deprotection and cyclization has, however, until now remained unclear. Femtosecond transient absorption (fs‐TA) spectroscopy and nanosecond time‐resolved resonance Raman (ns‐TR³) spectroscopy were employed to detect the transient species directly, and examine the dynamic transformations involved in the primary photoreactions for DMB diethyl phosphate (DMBDP) in acetonitrile (CH₃CN). To assess the electronic character and the role played by the individual sub‐chromophore, that is, the benzoyl, and the di‐meta‐methoxybenzylic moieties, for the DMBDP deprotection, comparative fs‐TA measurements were also carried out for the reference compounds diethyl phosphate acetophenone (DPAP), and 3′,5′‐dimethoxybenzylic diethyl phosphate (DMBnDP) in the same solvent. Comparison of the fs‐TA spectra reveals that the photoexcited DMBDP exhibits distinctly different spectral character and dynamic evolution from those of the reference compounds. This fact, combined with the related steady‐state spectral and density functional theoretical results, strongly suggests the presence in DMBDP of a significant interaction between the two sub‐chromophores, and that this interaction plays a governing role in determining the nature of the photoexcitation and the reaction channel of the subsequent photophysical and photochemical transformations. The ns‐TR³ results and their correlation with the fs‐TA spectra and dynamics provide evidence for a novel concerted deprotection–cyclization mechanism for DMBDP in CH₃CN. By monitoring the direct generation of the transient DMBF product, the cyclization time constant was determined unequivocally to be ≈1 ns. This indicates that there is little relevance for the long‐lived intermediates (>10 ns) in giving the DMBF product, and excludes the stepwise mechanism proposed in the literature as the major pathway for the DMB cyclization reaction. This work provides important new insights into the origin of the 3′,5′‐dimethoxy substitution effect for the DMB photodeprotection. It also helps to clarify the many different views presented in previous mechanistic studies of the DMB PRPGs. In addition to this, our fs‐TA results on the reference compound DMBnDP in CH₃CN provide the first direct observation (to the best of our knowledge) showing the predominance of a prompt (≈2 ps) heterolytic bond cleavage after photoexcitation of meta‐methoxybenzylic compounds. This provides insight into the long‐term controversies about the photoinitiated dissociation mode of related substituted benzylic compounds.     

Biofuel cell controlled by enzyme logic network — Approaching physiologically regulated devices

A “smart” biofuel cell switchable ON and OFF upon application of several chemical signals processed by an enzyme logic network was designed. The biocomputing system performing logic operations on the input signals was composed of four enzymes: alcohol dehydrogenase (ADH), amyloglucosidase (AGS), invertase (INV) and glucose dehydrogenase (GDH). These enzymes were activated by different combinations of chemical input signals: NADH, acetaldehyde, maltose and sucrose. The sequence of biochemical reactions catalyzed by the enzymes models a logic network composed of concatenated AND/OR gates. Upon application of specific “successful” patterns of the chemical input signals, the cascade of biochemical reactions resulted in the formation of gluconic acid, thus producing acidic pH in the solution. This resulted in the activation of a pH-sensitive redox-polymer-modified cathode in the biofuel cell, thus, switching ON the entire cell and dramatically increasing its power output. Application of another chemical signal (urea in the presence of urease) resulted in the return to the initial neutral pH value, when the O₂-reducing cathode and the entire cell are in the mute state. The reversible activation–inactivation of the biofuel cell was controlled by the enzymatic reactions logically processing a number of chemical input signals applied in different combinations. The studied biofuel cell exemplifies a new kind of bioelectronic device where the bioelectronic function is controlled by a biocomputing system. Such devices will provide a new dimension in bioelectronics and biocomputing benefiting from the integration of both concepts.     

Thermal and mass spectrometric fragmentation of esters of deuterated long chain carboxylic acids

A method combining thermal fragmentation and mass spectrometry for the determination of the position of double bonds in an unsaturated ester is presented. The thermal fragmentation of methyl esters of deuterated long chain carboxylic acids yields a homologous series of olefins plus a homologous series of unsaturated esters. The positions of the deuterium atoms in the original ester are revealed by the deuterium content of its fragments as determined by mass spectrometry. Therefore, the positions of double bonds of a polyunsaturated acid can be determined by pyrolysis after saturation by deuterium. The structures of the unsaturated fragments are ascertained by mass spectrometric method, and the formation of the ion [M – 32] in the mass spectrometric fragmentation of unsaturated methyl esters is studied by means of deuterium labeling.     

Applying Direct Yellow 11 to a modified Simons’ staining assay

For quantification of overall fiber accessibility of lignocellulosic substrates, Direct Yellow 11 (C.I. 40000) is a suitable alternative to the discontinued Pylam Products’ dye Direct Orange 15 (C.I. 40002/40003). In this study we present a side-by-side comparison between the two azo-stilbene dyes. We characterize individual dye fractions and provide equations to determine individual concentrations. We present a modified Simons’ staining protocol incorporating the high molecular weight fraction of Direct Yellow 11. We perform tests on lignin, cellulosic, and lignocellulosic materials. In all tests, the two dyes perform similarly and satisfy many accessibility measurement criteria. We demonstrate that the adsorption of Direct Yellow 11 onto a substrate correlates with that substrate’s propensity for enzymatic hydrolysis. We confirm this correlation on a series of organic solvent pretreatments and on a series of lignocellulosic substrates. Finally, we outline the inherent limitations of performing adsorption experiments with Direct Yellow 11 and other high molecular weight dyes.     

Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate‐controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition‐state structure and bonding optimally requires the use of theoretical models. In this work, we apply density‐functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2′‐O‐transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well‐studied series of phosphate and phosphorothioate mono‐, di‐ and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non‐enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate–KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.