3-Nitrophenol-4,4 '-bipyridyl N,N '-dioxide (2/1): a DFT study and CSD analysis of DPNO molecular complexes

The title 2:1 complex of 3-nitrophenol (MNP) and 4,4'-bipyridyl N, N'-dioxide (DPNO), 2C(6)H(5)NO(3)center dot C(10)H(8)N(2)O(2) or 2MNP center dot DPNO, crystallizes as a centrosymmetric three-component adduct with a dihedral angle of 59.40 (8)degrees between the planes of the benzene rings of MNP and DPNO (the DPNO moiety lies across a crystallographic inversion centre located at the mid-point of the C-C bond linking its aromatic rings). The complex owes its formation to O-H center dot center dot center dot O hydrogen bonds [O center dot center dot center dot O = 2.605 (3) angstrom]. Molecules are linked by intermolecular C-H center dot center dot center dot O and C-H center dot center dot center dot N interactions forming R(2)(1) (6) and R(2)(2) (10) rings, and R(6)(6) (34) and R(4)(4) (26) macro-rings, all of which are aligned along the [(1) over bar 01] direction, and R(2)(2) (10) and R(2)(1) (7) rings aligned along the [010] direction. The combination of chains of rings along the [(1) over bar 01] and [010] directions generates the three-dimensional structure. A total of 27 systems containing the DNPO molecule and forming molecular complexes of an organic nature were analysed and compared with the structural characteristics of the dioxide reported here. The N-O distance [1.325 (2) angstrom] depends not only on the interactions involving the O atom at the N-O group, but also on the structural ordering and additional three-dimensional interactions in the crystal structure. A density functional theory (DFT) optimized structure at the B3LYP/6-311G(d,p) level is compared with the molecular structure in the solid state.

Spin gaps and spin-flip energies in density-functional theory

Energy gaps are crucial aspects of the electronic structure of finite and extended systems. Whereas much is known about how to define and calculate charge gaps in density-functional theory (DFT), and about the relation between these gaps and derivative discontinuities of the exchange-correlation functional, much less is known about spin gaps. In this paper we give density-functional definitions of spin-conserving gaps, spin-flip gaps and the spin stiffness in terms of many-body energies and in terms of single-particle (Kohn-Sham) energies. Our definitions are as analogous as possible to those commonly made in the charge case, but important differences between spin and charge gaps emerge already on the single-particle level because unlike the fundamental charge gap spin gaps involve excited-state energies. Kohn-Sham and many-body spin gaps are predicted to differ, and the difference is related to derivative discontinuities that are similar to, but distinct from, those usually considered in the case of charge gaps. Both ensemble DFT and time-dependent DFT (TDDFT) can be used to calculate these spin discontinuities from a suitable functional. We illustrate our findings by evaluating our definitions for the Lithium atom, for which we calculate spin gaps and spin discontinuities by making use of near-exact Kohn-Sham eigenvalues and, independently, from the single-pole approximation to TDDFT. The many-body corrections to the Kohn-Sham spin gaps are found to be negative, i.e., single-particle calculations tend to overestimate spin gaps while they underestimate charge gaps.

Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni

Schistosomes are unable to synthesize purines de novo and depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds to Schistosoma mansoni PNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are used to propose a structural explanation for the selective binding of adenosine to some LMW PNPs but not to others. The results indicate that transition-state analogues based on adenosine or other 6-amino nucleosides should not be discounted as potential starting points for alternative inhibitors.

Density functional theory investigation of 3d, 4d, and 5d 13-atom metal clusters

The knowledge of the atomic structure of clusters composed by few atoms is a basic prerequisite to obtain insights into the mechanisms that determine their chemical and physical properties as a function of diameter, shape, surface termination, as well as to understand the mechanism of bulk formation. Due to the wide use of metal systems in our modern life, the accurate determination of the properties of 3d, 4d, and 5d metal clusters poses a huge problem for nanoscience. In this work, we report a density functional theory study of the atomic structure, binding energies, effective coordination numbers, average bond lengths, and magnetic properties of the 3d, 4d, and 5d metal (30 elements) clusters containing 13 atoms, M(13). First, a set of lowest-energy local minimum structures (as supported by vibrational analysis) were obtained by combining high-temperature first- principles molecular-dynamics simulation, structure crossover, and the selection of five well-known M(13) structures. Several new lower energy configurations were identified, e. g., Pd(13), W(13), Pt(13), etc., and previous known structures were confirmed by our calculations. Furthermore, the following trends were identified: (i) compact icosahedral-like forms at the beginning of each metal series, more opened structures such as hexagonal bilayerlike and double simple-cubic layers at the middle of each metal series, and structures with an increasing effective coordination number occur for large d states occupation. (ii) For Au(13), we found that spin-orbit coupling favors the three-dimensional (3D) structures, i.e., a 3D structure is about 0.10 eV lower in energy than the lowest energy known two-dimensional configuration. (iii) The magnetic exchange interactions play an important role for particular systems such as Fe, Cr, and Mn. (iv) The analysis of the binding energy and average bond lengths show a paraboliclike shape as a function of the occupation of the d states and hence, most of the properties can be explained by the chemistry picture of occupation of the bonding and antibonding states.

Density functional theory and ab initio molecular dynamics study of NO adsorption on Pd(111) and Pt(111) surfaces

The origin of the unique geometry for nitric oxide (NO) adsorption on Pd(111) and Pt(111) surfaces as well as the effect of temperature were studied by density functional theory calculations and ab initio molecular dynamics at finite temperature. We found that at low coverage, the adsorption geometry is determined by electronic interactions, depending sensitively on the adsorption sites and coverages, and the effect of temperature on geometries is significant. At coverage of 0.25 monolayer (ML), adsorbed NO at hollow sites prefer an upright configuration, while NO adsorbed at top sites prefer a tilting configuration. With increase in the coverage up to 0.50 ML, the enhanced steric repulsion lead to the tilting of hollow NO. We found that the tilting was enhanced by the thermal effects. At coverage of 0.75 ML with p(2 x 2)-3NO(fcc+hcp+top) structure, we found that there was no preferential orientation for tilted top NO. The interplay of the orbital hybridization, thermal effects, steric repulsion, and their effects on the adsorption geometries were highlighted at the end.

Theory of nitride oxide adsorption on transition metal (111) surfaces: a first-principles investigation

In this work, we report a density functional theory study of nitric oxide (NO) adsorption on close-packed transition metal (TM) Rh(111), Ir(111), Pd(111) and Pt(111) surfaces in terms of adsorption sites, binding mechanism and charge transfer at a coverage of Theta(NO) = 0.25, 0.50, 0.75 monolayer (ML). Based on our study, an unified picture for the interaction between NO and TM(111) and site preference is established, and valuable insights are obtained. At low coverage (0.25 ML), we find that the interaction of NO/TM(111) is determined by an electron donation and back-donation process via the interplay between NO 5 sigma/2 pi* and TM d-bands. The extent of the donation and back-donation depends critically on the coordination number (adsorption sites) and TM d-band filling, and plays an essential role for NO adsorption on TM surfaces. DFT calculations shows that for TMs with high d-band filling such as Pd and Pt, hollow-site NO is energetically the most favorable, and top-site NO prefers to tilt away from the normal direction. While for TMs with low d-band filling (Rh and Ir), top-site NO perpendicular to the surfaces is energetically most favorable. Electronic structure analysis show that irrespective of the TM and adsorption site, there is a net charge transfer from the substrate to the adsorbate due to overwhelming back-donation from the TM substrate to the adsorbed NO molecules. The adsorption-induced change of the work function with respect to bare surfaces and dipole moment is however site dependent, and the work function increases for hollow-site NO, but decreases for top-site NO, because of differences in the charge redistribution. The interplay between the energetics, lateral interaction and charge transfer, which is element dependent, rationalizes the structural evolution of NO adsorption on TM(111) surfaces in the submonolayer regime.

A HARD AND VARIABLE X-RAY EMISSION FROM THE MASSIVE EMISSION-LINE STAR HD 157832

We report the discovery with XMM-Newton of a hard-thermal (T similar to 130 MK) and variable X-ray emission from the Be star HD 157832, a new member of the puzzling class of gamma-Cas-like Be/X-ray systems. Recent optical spectroscopy reveals the presence of a large/dense circumstellar disk seen at intermediate/high inclination. With a B1.5V spectral type, HD 157832 is the coolest gamma-Cas analog known. In addition, its non-detection in the ROSAT all-sky survey shows that its average soft X-ray luminosity varied by a factor larger than similar to 3 over a time interval of 14 yr. These two remarkable features, ""low"" effective temperature, and likely high X-ray variability turn HD 157832 into a promising object for understanding the origin of the unusually high-temperature X-ray emission in these systems.

Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.

Random perturbations of stochastic processes with unbounded variable length memory

We consider binary infinite order stochastic chains perturbed by a random noise. This means that at each time step, the value assumed by the chain can be randomly and independently flipped with a small fixed probability. We show that the transition probabilities of the perturbed chain are uniformly close to the corresponding transition probabilities of the original chain. As a consequence, in the case of stochastic chains with unbounded but otherwise finite variable length memory, we show that it is possible to recover the context tree of the original chain, using a suitable version of the algorithm Context, provided that the noise is small enough.

Polymer matrix sensitizing effect on photoluminescence properties of Eu(3+)-beta-diketonate complex doped into poly-beta-hydroxybutyrate (PHB) in film form

In this work is reported the sensitization effect by polymer matrices on the photoluminescence properties of diaquatris(thenoyltrifluoroacetonate)europium(III), [Eu(tta)(3)(H(2)O)(2)], doped into poly-beta-hydroxybutyrate (PHB) with doping percentage at 1, 3, 5, 7 and 10% (mass) in film form. TGA results indicated that the Eu(3+) complex precursor was immobilized in the polymer matrix by the interaction between the Eu(3+) complex and the oxygen atoms of the PHB polymer when the rare earth complex was incorporated in the polymeric host. The thermal behaviour of these luminescent systems is similar to that of the undoped polymer, however, the T(onset) temperature of decomposition decreases with increase of the complex doping concentration. The emission spectra of the Eu(3+) complex doped PHB films recorded at 298 K exhibited the five characteristic bands arising from the (5)D(0) -> (7)F(J) intraconfigurational transitions (J = 0-4). The fact that the quantum efficiencies eta of the doped film increased significantly revealed that the polymer matrix acts as an efficient co-sensitizer for Eu(3+) luminescent centres and therefore enhances the quantum efficiency of the emitter (5)D(0) level. The luminescence intensity decreases, however, with increasing precursor concentration in the doped polymer to greater than 5% where a saturation effect is observed at this specific doping percentage, indicating that changes in the polymeric matrix improve the absorption property of the film, consequently quenching the luminescent effect.

Structure, stability, depolarized light scattering, and vibrational spectra of fullerenols from all-electron density-functional-theory calculations

We have investigated the stability, electronic properties, Rayleigh (elastic), and Raman (inelastic) depolarization ratios, infrared and Raman absorption vibrational spectra of fullerenols [C(60)(OH)(n)] with different degrees of hydroxylation by using all-electron density-functional-theory (DFT) methods. Stable arrangements of these molecules were found by means of full geometry optimizations using Becke's three-parameter exchange functional with the Lee, Yang, and Parr correlation functional. This DFT level has been combined with the 6-31G(d,p) Gaussian-type basis set, as a compromise between accuracy and capability to treat highly hydroxylated fullerenes, e.g., C(60)(OH)(36). Thus, the molecular properties of fullerenols were systematically analyzed for structures with n=1, 2, 3, 4, 8, 10, 16, 18, 24, 32, and 36. From the electronic structure analysis of these molecules, we have evidenced an important effect related to the weak chemical reactivity of a possible C(60)(OH)(24) isomer. To investigate Raman scattering and the vibrational spectra of the different fullerenols, frequency calculations are carried out within the harmonic approximation. In this case a systematic study is only performed for n=1-4, 8, 10, 16, 18, and 24. Our results give good agreements with the expected changes in the spectral absorptions due to the hydroxylation of fullerenes.

Complex kinetics, high frequency oscillations and temperature compensation in the electro-oxidation of ethylene glycol on platinum

Despite the fact that the majority of the catalytic electro-oxidation of small organic molecules presents oscillatory kinetics under certain conditions, there are few systematic studies concerning the influence of experimental parameters on the oscillatory dynamics. Of the studies available, most are devoted to C1 molecules and just some scattered data are available for C2 molecules. We present in this work a comprehensive study of the electro-oxidation of ethylene glycol on polycrystalline platinum surfaces and in alkaline media. The system was studied by means of electrochemical impedance spectroscopy, cyclic voltammetry, and chronoamperometry, and the impact of parameters such as applied current, ethylene glycol concentration, and temperature were investigated. As in the case of other parent systems, the instabilities in this system were associated with a hidden negative differential resistance, as identified by impedance data. Very rich and robust dynamics were observed, including the presence of harmonic and mixed mode oscillations and chaotic states, in some parameter region. Oscillation frequencies of about 16 Hz characterized the fastest oscillations ever reported for the electro-oxidation of small organic molecules. Those high frequencies were strongly influenced by the electrolyte pH and far less affected by the EG concentration. The system was regularly dependent on temperature under voltammetric conditions but rather independent within the oscillatory regime.

Complex Oscillatory Response of a PEM Fuel Cell Fed with H(2)/CO and Oxygen

Oscillatory kinetics is commonly observed in the electrocatalytic oxidation of most species that can be used in fuel cell devices. Examples include formic acid, methanol, ethanol, ethylene glycol, and hydrogen/carbon monoxide mixtures, and most papers refer to half-cell experiments. We report in this paper the experimental investigation of the oscillatory dynamics in a proton exchange membrane (PEM) fuel cell at 30 degrees C. The system consists of a Pt/C cathode fed with oxygen and a PtRu (1:1)/C anode fed with H(2) mixed with 100 ppm of CO, and was studied at different cell currents and anode flow rates. Many different states including periodic and nonperiodic series were observed as a function of the cell current and the H(2)/CO flow rate. In general, aperiodic/chaotic states were favored at high currents and low flow rates. The dynamics was further characterized in terms of the relationship between the oscillation amplitude and the subsequent time required for the anode to get poisoned by carbon monoxide. Results are discussed in terms of the mechanistic aspects of the carbon monoxide adsorption and oxidation. (C) 2010 The Electrochemical Society. [DOI: 10.1149/1.3463725] All rights reserved.

Tidal-amplitude rhythms of larval release: variable departure from presumed optimal timing among populations of the mottled shore crab

It is widely assumed that optimal timing of larval release is of major importance to offspring survival, but the extent to which environmental factors entrain synchronous reproductive rhythms in natural populations is not well known. We sampled the broods of ovigerous females of the common shore crab Pachygrapsus transversus at both sheltered and exposed rocky shores interspersed along a so-km coastline, during four different periods, to better assess inter-population differences of larval release timing and to test for the effect of wave action. Shore-specific patterns were consistent through time. Maximum release fell within 1 day around syzygies on all shores, which matched dates of maximum tidal amplitude. Within this very narrow range, populations at exposed shores anticipated hatching compared to those at sheltered areas, possibly due to mechanical stimulation by wave action. Average departures from syzygial release ranged consistently among shores from 2.4 to 3.3 days, but in this case we found no evidence for the effect of wave exposure. Therefore, processes varying at the scale of a few kilometres affect the precision of semilunar timing and may produce differences in the survival of recently hatched larvae. Understanding the underlying mechanisms causing departures from presumed optimal release timing is thus important for a more comprehensive evaluation of reproductive success of invertebrate populations.