Proton dynamics in the strong chelate hydrogen bond of crystalline picolinic acid N-oxide. A new computational approach and infrared, raman and INS study

Infrared, Raman and INS spectra of picolinic acid N-oxide (PANO) were recorded and examined for the location of the hydronic modes, particularly O-H stretching and COH bending. PANO is representative of strong chelate hydrogen bonds (H-bonds) with its short O...O distance (2.425 A). H-bonding is possibly well-characterized by diffraction, NMR and NQR data and calculated potential energy functions. The analysis of the spectra is assisted by DFT frequency calculations both in the gas phase and in the solid state. The Car-Parrinello quantum mechanical solid-state method is also used for the proton dynamics simulation; it shows the hydron to be located about 99% of time in the energy minimum near the carboxylic oxygen; jumps to the N-O acceptor are rare. The infrared spectrum excels by an extended absorption (Zundel's continuum) interrupted by numerous Evans transmissions. The model proton potential functions on which the theories of continuum formation are based do not correspond to the experimental and computed characteristics of the hydrogen bond in PANO, therefore a novel approach has been developed; it is based on crystal dynamics driven hydronium potential fluctuation. The envelope of one hundred 0 --> 1 OH stretching transitions generated by molecular dynamics simulation exhibits a maximum at 1400 cm-1 and a minor hump at approximately 1600 cm-1. These positions square well with ones predicted for the COH bending and OH stretching frequencies derived from various one- and two-dimensional model potentials. The coincidences with experimental features have to be considered with caution because the CPMD transition envelope is based solely on the OH stretching coordinate while the observed infrared bands correspond to heavily mixed modes as was previously shown by the normal coordinate analysis of the IR spectrum of argon matrix isolated PANO, the present CPMD frequency calculation and the empirical analysis of spectra. The experimental infrared spectra show some unusual characteristics such as large temperature effects on the intensity of some bands, thus presenting a challenge for theoretical band shape treatments. Our calculations clearly show that the present system is characterized by an asymmetric single well potential with no large amplitudes in the hydronium motion, which extends the existence of Zundel-type spectra beyond the established set of hydrogen bonds with large hydronic vibrational amplitudes.     

Comprehensive study of the parameters influencing the detection of organotin compounds by a pulsed flame photometric detector in sewage sludge

An investigation of the operating conditions of a pulsed flame photometric detection (PFPD) system for the determination of organotin compounds (OTCs) in sewage sludge is reported. During the analyses, some spectral interferences were observed. For their elimination detector parameters such as gate delay and gate width were investigated. In addition, the applicability of three different internal standards was evaluated. Under optimised analytical conditions (gate delay 3 ms, gate width 2 ms, tripropyltin as internal standard) limits of detection (LOD) were determined. The LOD for butyltins ranged between 8 and 16 ng Sn g(-1), for phenyltins around 8 ng Sn g(-1) and for octyltins between 5 and 10 ng Sn g(-1). Since there is no certified reference material (CRM) available for sewage sludge, the accuracy of the analytical procedure was checked by the analysis of CRM PACS-2 (marine sediment) and a spiked sludge sample. Good agreement between determined and certified values was obtained. Sewage sludge from a local wastewater treatment plant was analysed and the results compared with data from the literature.     

Natural convection in porous media ‐ a meshless solution of the Brinkman extended Darcy model

A numerical study is performed on steady natural convection inside a differentially heated square cavity. The cavity is filled with porous media which exhibits the Brinkman extended Darcy behavior. The solution procedure for coupled mass, momentum, and energy equations is based on primitive variables and RBF collocation method with r⁷ function. Numerical examples include calculations at filtration with Rayleigh number 100, and Darcy numbers 10^–3 and 10^–5. The solution is compared with reference results of the fine‐grid finite volume method.     

Simultaneous integration of mixed quantum-classical systems by density matrix evolution equations using interaction representation and adaptive time step integrator

A density matrix evolution method [H. J. C. Berendsen and J. Mavri, J. Phys. Chem., 97, 13464 (1993)] to simulate the dynamics of quantum systems embedded in a classical environment is applied to study the inelastic collisions of a classical particle with a five-level quantum harmonic oscillator. We improved the numerical performance by rewriting the Liouville–von Neumann equation in the interaction representation and so eliminated the frequencies of the unperturbed oscillator. Furthermore, replacement of the fixed time step fourth-order Runge–Kutta integrator with an adaptive step size control fourth-order Runge–Kutta resulted in significantly lower computational effort at the same desired accuracy. © 1996 by John Wiley & Sons, Inc.     

Energetic Basis of AGCGA‐Rich DNA Folding into a Tetrahelical Structure

It was recently discovered that, besides well‐known G‐quadruplexes and i‐motifs, DNA may adopt another type of noncanonical structure called AGCGA‐quadruplexes. Here, the folding of the VK2 fragment from the regulatory region of the PLEKHG3 gene is studied and, for the first time, the energetic contributions that stabilize this unique fold are described. Similarly to the B‐DNA, it is stabilized by hydrophobic desolvation and, in contrast to G‐quadruplexes, also by specific binding of water molecules. Compared to B‐DNA, VK2 folding is enthalpically less favorable due to poorer base‐stacking interactions, resulting in substantial conformational flexibility. This entropically favorable conformational “breathing” stabilizes the AGCGA‐quadruplexes. In conclusion, AGCGA‐quadruplexes have a distinguishing thermodynamic fingerprint and the corresponding driving forces enabling their folding are consistent with the observed structural features.     

On sufficient properties of sufficient matrices

Central European Journal of Operations Research - In this paper we study sufficient matrices, which play an important role in theoretical analysis of interior-point methods for linear...     

29Si and 27Al MAS NMR assessment of the C-(A-) S–H nanomolecular structure of Ultra-High-Performance Concrete (UHPC) modified with pyrogenic oxides

Ultra-High Performance Concrete (UHPC) that contains pyrogenic oxides (Pox) and has been heat-cured with microwave energy reaches as high as 420 MPa after 1 day. The influence of microwave curing on the strength gain is much more pronounced in UHPC than in normal concrete. ²⁹Si and ²⁷Al MAS NMR nanomolecular structure investigation of Ultra-High-Performance Concrete (UHPC) modified with nanoscale pozzolans (pyrogenic oxides) reveals significant differences from other concrete types that may explain such high early strength. There is an increase in polymerization degree of C-(A) S–H (C–S–H containing Al) phase of the UHPC modified with pyrogenic oxides, followed by a trend of substitution of silicon atoms on the Q? sites of C–S–H (calcium-silicate-hydrates) through aluminum atoms. The mean chain length (MCL) and degree of connectivity (Dc) are the highest for pyrogenic oxides containing UHPC that have been cured with microwave energy. The increase of polymerization degree is more pronounced for alumina-based pyrogenic oxide containing UHPC.     

Protein-protein binding site prediction by local structural alignment

Generalization of an earlier algorithm has led to the development of new local structural alignment algorithms for prediction of protein-protein binding sites. The algorithms use maximum cliques on protein graphs to define structurally similar protein regions. The search for structural neighbors in the new algorithms has been extended to all the proteins in the PDB and the query protein is compared to more than 60,000 proteins or over 300,000 single-chain structures. The resulting structural similarities are combined and used to predict the protein binding sites. This study shows that the location of protein binding sites can be predicted by comparing only local structural similarities irrespective of general protein folds.     

N NQR in the tetrazole family

¹⁴N NQR frequencies and spin–lattice relaxation times were measured in technologically important 5-aminotetrazole and 5-aminotetrazole monohydrate at different temperatures between 77 K and 300 K. Five NQR triplets ν₊, ν₋ and ν₀ were found for the five inequivalent nitrogen atoms in each compound between 0.7 MHz and 4 MHz. Carr-Purcell based multipulse sequences were used to accumulate quadrupole echo signals before the FFT analysis. Assignment of the frequencies to atomic positions was made and the results are analysed in relation to the molecular chemical bonds and possible H-bonds in the crystal structures. The new NQR frequencies are reasonably related to the previously published NQR spectrum of the third family member, 1H-tetrazole.     

Influence of ultrasonic processing on the macromolecular properties of poly (d,l-lactide-co-glycolide) alone and in its biocomposite with hydroxyapatite

In this work poly(d,l-lactide-co-glycolide) (PLGA) and a poly(d,l-lactide-co-glycolide)/hydroxyapatite (PLGA/HAp) composite processed in an ultrasonic field at higher (25 °C) and lower (8 °C) temperatures were studied with respect to the molecular properties of the obtained materials. The processing of the PLGA and the PLGA/HAp composite in an ultrasonic field resulted in a change of molar mass averages of the polymer/polymeric part of these materials, while an amorphous structure and a 50:50 lactide-to-glycolide co-monomer ratio were preserved without the formation of crystalline oligomers. However, mobility of polymeric chains obtained after ultrasonic processing was lower indicating ordering the structure of polymeric chains as a result of processing. Additionally, it was observed that the mobility of the PLGA macromolecules was lower within the composite in comparison with the mobility of the chains within the PLGA alone in the case when both were obtained after ultrasonic processing. This was a consequence of the structure formation through the interactions between the PLGA and the HAp. Based on these results different degradation rate of PLGA in composite can be expected, which is important in the application of this material for the controlled drug delivery of medicaments.