Models of macromolecular chains based on Classical and Quantum Mechanics: comparison with Gaussian models

Different approaches to the study of open linear freely‐jointed (unhindered) threedimensional macromolecular chains at thermal equilibrium, based upon either Classical Hamiltonian Dynamics with constraints (namely, a formulation equivalent to Kramers' one) or Quantum Mechanics (with stiff harmonic springs), are reviewed and discussed in detail. Results from those approaches are compared to those arising from the standard Gaussian model. Fraenkel's approach, based upon Classical Mechanics (with stiff harmonic springs) and its comparison with the Gaussian model are also treated. It is argued that the quantum formulation is required in order that the treatment of the high‐frequency vibrations be consistent. The role of the uncertainty principle is discussed, in support of the quantum‐mechanical approach. At a later stage, internal rotations can be treated through Classical Statistical mechanics, under certain conditions. The quantum‐Mechanics‐based model appears to be consistent with the Gaussian model, while the one based upon constrained Hamiltonian Dynamics yields certain discrepancies with the latter. Classical and quantum‐mechanical approaches to open linear freely‐rotating (hindered) threedimensional macromolecular chains are also treated: the consistency of the quantum‐mechanics‐based model is displayed by deriving approximately the existence of a persistence length. It is argued that the possible advantages of the quantum‐mechanical formulation should be expected not at large scales but at shorter ones. The specific topics to be treated are described in the summary of contents given below.     

Moment expansion analysis for time-domain asymptotics

We apply our recently developed distributional technique [2, 3] to study time-domain asymptotics. This enables us to present a rigorous mathematical discussion and extensions of the results given by Chapman [1] and subsequent workers in this field. The present analysis is facilitated by defining functions which are distributionally small at infinity. We find that one of the advantages of using this technique is that multidimensional extensions can be derived very easily. © 1998 B. G. Teubner Stuttgart–John Wiley & Sons Ltd.     

A mild oxidative method for the preparation of γ-hydroxy-α-nitroolefins from α,β-epoxyketoximes using IBX

An efficient method for the preparation of γ-hydroxy-α-nitroolefins from α,β-epoxyketoximes has been developed using IBX. The reaction occurs at room temperature without the formation of over-oxidation products and also has an easy work-up procedure.     

Recent Advances in the Chemistry and Biology of Naturally Occurring Antibiotics

Ever since the world‐shaping discovery of penicillin, nature's molecular diversity has been extensively screened for new medications and lead compounds in drug discovery. The search for agents intended to combat infectious diseases has been of particular interest and has enjoyed a high degree of success. Indeed, the history of antibiotics is marked with impressive discoveries and drug‐development stories, the overwhelming majority of which have their origin in natural products. Chemistry, and in particular chemical synthesis, has played a major role in bringing naturally occurring antibiotics and their derivatives to the clinic, and no doubt these disciplines will continue to be key enabling technologies. In this review article, we highlight a number of recent discoveries and advances in the chemistry, biology, and medicine of naturally occurring antibiotics, with particular emphasis on total synthesis, analogue design, and biological evaluation of molecules with novel mechanisms of action.     

On the accurate measurement of amide one-bond 15N-1H couplings in proteins: effects of cross-correlated relaxation, selective pulses and dynamic frequency shifts

Amide one-bond 15N-1H scalar couplings of 15N- and [15N,2H]-isotopically enriched ubiquitin have been measured with the Quantitative J approach by monitoring NMR signal intensity modulation. Scalar couplings of the non-deuterated protein are in average approximately 0.6 Hz larger than values of deuterated ubiquitin. This deviation is 30 times the error derived from experiment reproducibility. Refocusing dipole/dipole cross-correlated relaxation decreases the discrepancy to approximately 0.1 Hz, suggesting that it likely originates from relaxation interference. Alternatively, the subtraction of J values obtained at different magnetic fields largely reduces the relaxation effects. In contrast, the dynamic frequency shift whose main contribution to 1J(15N-1H) arises from 15N chemical shielding anisotropy/NH dipole cross-correlation, is not eliminated by refocusing spin evolution under this interaction. Furthermore, the average difference of 1J(15N-1H) values at two magnetic fields closely agrees with the theoretical expected difference in the dynamic frequency shift.     

Metabolomic Profiling of Fresh Goji (Lycium barbarum L.) Berries from Two Cultivars Grown in Central Italy: A Multi-Methodological Approach

The metabolite profile of fresh Goji berries from two cultivars, namely Big Lifeberry (BL) and Sweet Lifeberry (SL), grown in the Lazio region (Central Italy) and harvested at two different periods, August and October, corresponding at the beginning and the end of the maturation, was characterized by means of nuclear magnetic resonance (NMR) and electrospray ionization Fourier transform ion cyclotron resonance (ESI FT-ICR MS) methodologies. Several classes of compounds such as sugars, amino acids, organic acids, fatty acids, polyphenols, and terpenes were identified and quantified in hydroalcoholic and organic Bligh-Dyer extracts. Sweet Lifeberry extracts were characterized by a higher content of sucrose with respect to the Big Lifeberry ones and high levels of amino acids (glycine, betaine, proline) were observed in SL berries harvested in October. Spectrophotometric analysis of chlorophylls and total carotenoids was also carried out, showing a decrease of carotenoids during the time. These results can be useful not only to valorize local products but also to suggest the best harvesting period to obtain a product with a chemical composition suitable for specific industrial use. Finally, preliminary studies regarding both the chemical characterization of Goji leaves generally considered a waste product, and the biological activity of Big Lifeberry berries extracts was also investigated. Goji leaves showed a chemical profile rich in healthy compounds (polyphenols, flavonoids, etc.) confirming their promising use in the supplements/nutraceutical/cosmetic field. MG63 cells treated with Big Lifeberry berries extracts showed a decrease of iNOS, COX-2, IL-6, and IL-8 expression indicating their significant biological activity.     

Pesticides and degradation products in groundwaters from a vineyard region: Optimization of a multiresidue method based on SPE and GC‐MS

A reliable multiresidue method based on solid phase extraction was developed using GC–MS to determine and quantify 34 pesticides, including herbicides, fungicides, insecticides, and some of their degradation products, in groundwater in a vineyard region of La Rioja (northern Spain). Different parameters were optimized and good recoveries (65–108% range) and precisions (12–19% range) were achieved with spiked water samples for a concentration of 0.1 μg/L. The experimental results showed an excellent linearity (r² > 0.99) over the 0.1–1.5 μg/L range. The detection limits of the proposed method were 1–37 ng/L for most of the compounds studied. The methodology has been successfully applied to the analysis of groundwater samples from vineyard areas in La Rioja and the presence of pesticides, especially fungicides and herbicides, at several concentration levels was revealed. Terbuthylazine, its metabolite desethyl‐terbuthylazine, and fluometuron were the pesticides most frequently detected in higher concentrations. Overall and taking into consideration the European Union maximum residue limit of pesticides in groundwater, 16 of the 34 compounds included in this study were detected in concentrations over that limit in at least one of the samples analyzed.     

An electrochemical immunosensor for ochratoxin A determination in wines based on a monoclonal antibody and paramagnetic microbeads

We report a direct competitive immunosensor for the rapid determination of ochratoxin A (OTA) in wine samples. Magnetic beads (1 ± 0.5 μm diameter) covered with streptavidin were functionalized with a monoclonal antibody against OTA, and then left to incubate in a solution of tracer (ochratoxin conjugated to the enzyme peroxidase) and a range of OTA concentrations (10(-4) to 1,000 ng mL(-1)). After washing and separation steps helped with a magnetic field, a volume of the dispersion was put on screen-printed electrodes under a magnet, and after adding the substrate the p-benzoquinone generated enzymatically was detected by differential-pulse voltammetry. Wine samples (2 mL) were easily prepared simply by adjusting to pH = 7.5 with diluted NaOH and by adding polyvinylpyrrolidone for complexing polyphenols, without any other clean-up or preconcentration steps. The limit of detection for detecting OTA in wines was of 0.11 ± 0.01 ng L(-1), well below the permitted content of the mycotoxin by the European Union (<2 ng mL(-1)). Spiked wines were subjected to immunosensor calibrations to study the matrix effects. OTA concentrations measured with the immunosensor were compared with those obtained by high-performance liquid chromatography coupled to fluorescence detection (AOAC official method 2001.01). The OTA levels from two red wines of "Campo de Borja", Spain, ranged from about 0.027 to 0.033 ng mL(-1) of OTA.     

Autocorrelation measures for the quadratic assignment problem

In this article we provide an exact expression for computing the autocorrelation coefficient ξ and the autocorrelation length ? of any arbitrary instance of the Quadratic Assignment Problem (QAP) in polynomial time using its elementary landscape decomposition. We also provide empirical evidence of the autocorrelation length conjecture in QAP and compute the parameters ξ and ? for the 137 instances of the QAPLIB. Our goal is to better characterize the difficulty of this important class of problems to ease the future definition of new optimization methods. Also, the advance that this represents helps to consolidate QAP as an interesting and now better understood problem.