The pattern of distribution of amino groups modulates the structure and dynamics of natural aminoglycosides: implications for RNA recognition

Aminoglycosides are clinically relevant antibiotics that participate in a large variety of molecular recognition processes involving different RNA and protein receptors. The 3-D structures of these policationic oligosaccharides play a key role in RNA binding and therefore determine their biological activity. Herein, we show that the particular NH2/NH3(+)/OH distribution within the antibiotic scaffold modulates the oligosaccharide conformation and flexibility. In particular, those polar groups flanking the glycosidic linkages have a significant influence on the antibiotic structure. A careful NMR/theoretical analysis of different natural aminoglycosides, their fragments, and synthetic derivatives proves that both hydrogen bonding and charge-charge repulsive interactions are at the origin of this effect. Current strategies to obtain new aminoglycoside derivatives are mainly focused on the optimization of the direct ligand/receptor contacts. Our results strongly suggest that the particular location of the NH2/NH3(+)/OH groups within the antibiotics can also modulate their RNA binding properties by affecting the conformational preferences and inherent flexibility of these drugs. This fact should also be carefully considered in the design of new antibiotics with improved activity.     

Ligand adsorption on an activated carbon for the removal of chromate ions from aqueous solutions

The results presented in this work are related to the design of a guideline to develop specific properties at the surface of an activated carbon (AC). For this, two model aromatic compounds have been synthesized and their electrolytic behavior in aqueous solutions was studied by a potentiometric method. The textural characteristics of the activated carbon were determined by porosimetry methods. The nature of oxygen-carrying functions and the acid-base behavior of the AC surface were characterized by TPD and potentiometric titration methods, respectively. The adsorption and desorption equilibria of the aromatic compounds on activated carbon were measured in aqueous solutions, and the hysteresis between adsorption and desorption, which reveals irreversible adsorption, was discussed on the basis of the frontier orbital theory. HOMO and LUMO orbitals of the adsorbent and adsorbates were calculated, and irreversible adsorption was attributed to the small energy difference between HOMO and LUMO of the aromatic adsorbates and the adsorbent. Adsorption equilibria of K2CrO4 in aqueous solution on the AC alone and on the AC-aromatic ligand adsorbents, respectively, prove the efficient development of specific chemical functions at the carbon surface provided by the adsorbed aromatic compounds.     

Enhancement by polydispersity of the biaxial nematic phase in a mixture of hard rods and plates

The phase diagram of a polydisperse mixture of uniaxial rodlike and platelike hard parallelepipeds is determined for aspect ratios kappa=5 and 15. All particles have equal volume, and polydispersity is introduced in a highly symmetric way. The corresponding binary mixture is known to have a biaxial phase for kappa=15, but to be unstable against demixing into two uniaxial nematics for kappa=5. The phase diagram for kappa=15 is qualitatively similar to that of the binary mixture, regardless of the amount of polydispersity, while for kappa=5 a sufficient amount of polydispersity stabilizes the biaxial phase. This provides clues for designing an experiment to observe this long searched biaxial phase.     

Overcomplete Free Energy Functional for D = 1 Particle Systems with Next Neighbor Interactions

We deduce an overcomplete free energy functional for D=1 particle systems with next neighbor interactions, where the set of redundant variables are the local block densities _i of i interacting particles. The idea is to analyze the decomposition of a given pure system into blocks of i interacting particles by means of a mapping onto a hard rod mixture. This mapping uses the local activity of component i of the mixture to control the local association of i particles of the pure system. Thus it identifies the local particle density of component i of the mixture with the local block density _i of the given system. Consequently, our overcomplete free energy functional takes on the hard rod mixture form with the set of block densities _i representing the sequence of partition functions of the local aggregates of particle numbers i. The system of equations for the local particle density of the original system is closed via a subsidiary condition for the block densities in terms of . Analoguous to the uniform isothermal-isobaric technique, all our results are expressible in terms of effective pressures. We illustrate the theory with two standard examples, the adhesive interaction and the square-well potential. For the uniform case, our proof of such an overcomplete format is based on the exponential boundedness of the number of partitions of a positive integer (Hardy-Ramanujan formula) and on Varadhan's theorem on the asymptotics of a class of integrals.     

Monitoring powder blending by NIR spectroscopy

A strategy is proposed for the monitoring of powder blending. Samples are taken throughout the blender vessel and scanned by diffuse reflectance spectroscopy in the NIR range. The NIR spectra are first subjected to the Standard Normal Variate transformation (SNV). The first approach consists of overlaying the transformed spectra taken from different locations at each time. To quantify the differences between the spectra, the standard deviation spectrum at each time is calculated and the mean standard deviation value is plotted as a function of time. This plot indicates the time at which the blend is most homogeneous. Each individual spectrum can be compared with the mixture spectrum, which is an approximation of the spectrum of a true homogeneous sample. For that purpose several approaches, i.e. determination of the dissimilarity, Principal Component Analysis, are proposed. As an alternative approach to monitoring the blending the use of SIMPLISMA is recommended.Dedicated to Professor Dr. h.c. mult. J.F.K. Huber on the occasion of his 70th birthday     

Theoretical study on the structures and electronic spectra of TCNE2-.

Investigations into the charge-separated states and electron-transfer transitions in tetracyanoethylene (TCNE) complexes have recently generated much interest. In this work we present theoretical calculations showing that the most stable structure of the dianion TCNE2- has D2d symmetry in vacuum as well as in the solvents dichloromethane and acetonitrile. By means of the coupled cluster linear response, we compute the vertical electronic spectrum in both the gas phase and solution. The theoretical results are compared to the experimental data and good agreement is achieved.     

Magnetic–fluorescent Langmuir–Blodgett films of fluorophore-labeled ferritin nanoparticles

We have covalently coupled fluorophore 4-(2-hydroxyethoxy)-7-nitro-2,1,3-benzoxadiazole (NBD) to the external ferritin shell through lysine residues. An increase in the luminescence quantum yield of the fluorescent ferritin particles and a blue shift in its emission peak compared to individual fluorophore were observed. The study of the particles by transmission electron microscopy showed that the native iron core ferritin is intact and that no degradation occurs during chemical functionalization of the protein shell. The NBD-labeled ferritin particles are water soluble, which allowed their controlled deposition by the Langmuir–Blodgett (LB) technique. Superparamagnetic and fluorescent properties of the particles are preserved within the LB film.     

Struggle for space: viral extinction through competition for cells

The design of protocols to suppress the propagation of viral infections is an enduring enterprise, especially hindered by limited knowledge of the mechanisms leading to viral extinction. Here we report on infection extinction due to intraspecific competition to infect susceptible hosts. Beneficial mutations increase the production of viral progeny, while the host cell may develop defenses against infection. For an unlimited number of host cells, a feedback runaway coevolution between host resistance and progeny production occurs. However, physical space limits the advantage that the virus obtains from increasing offspring numbers; thus, infection clearance may result from an increase in host defenses beyond a finite threshold. Our results might be relevant to devise improved control strategies in environments with mobility constraints or different geometrical properties.     

Runge–Kutta convolution quadrature methods for well-posed equations with memory

Runge–Kutta based convolution quadrature methods for abstract, well-posed, linear, and homogeneous Volterra equations, non necessarily of sectorial type, are developed. A general representation of the numerical solution in terms of the continuous one is given. The error and stability analysis is based on this representation, which, for the particular case of the backward Euler method, also shows that the numerical solution inherits some interesting qualitative properties, such as positivity, of the exact solution. Numerical illustrations are provided.