Adaptive steered molecular dynamics: validation of the selection criterion and benchmarking energetics in vacuum

The potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] in a landmark article demonstrating the efficacy of combining steered molecular dynamics and Jarzynski's nonequilibrium relation. In this study, the recently developed adaptive steered molecular dynamics (ASMD) algorithm [G. Ozer, E. Valeev, S. Quirk, and R. Hernandez, J. Chem. Theory Comput. 6, 3026 (2010)] is used to reproduce the PMF of the unraveling of decaalanine in vacuum by averaging over fewer nonequilibrium trajectories. The efficiency and accuracy of the method are demonstrated through the agreement with the earlier work by Park and Schulten, a series of convergence checks compared to alternate SMD pulling strategies, and an analytical proof. The nonequilibrium trajectories obtained through ASMD have also been used to analyze the intrapeptide hydrogen bonds along the stretching coordinate. As the decaalanine helix is stretched, the initially stabilized i → i + 4 contacts (α-helix) is replaced by i → i + 3 contacts (3(10)-helix). No significant formation of i → i + 5 hydrogen bonds (π-helix) is observed.     

Dynamical simulation of dipolar Janus colloids: Equilibrium structure and thermodynamics

The static microstructures and thermodynamics of a colloidal dispersion of dipolar Janus (DJ) particles-that is, dipolar spheres in which each hemisphere is specified by a different charge interaction-have been investigated through simulation. DJ particles are modeled at a high level of detail with pairwise potentials represented as a sum of a spherically symmetric soft repulsion and an orientation-dependent electrostatic component using continuous potentials. The latter is important because it allows for the use of conventional molecular dynamics simulations, and is in contrast to the patch model and dipolar hard sphere model, which are discontinuous and therefore do not. The electrostatics are represented through a rigorous pointwise (PW) covering of two different hemispheres filled by points of corresponding charge. An isotropic coarse-graining (CG) of the PW models serves as a limit of the structure wherein the orientations of the DJ particles can be pairwise averaged. Over the range of volume fractions and DJ charge densities studied-consistent with reversible structures absent of long-range correlations-the CG model agrees well with the PW model with respect to equilibrium structure (isotropic pair correlation) and ensemble free energy. Time-dependent relaxation simulations of the PW model suggest that chain structures are not expected in liquid phases in contrast to that which has been observed for point dipole models of simple polar fluids.     

13C-Nmr Spectroscopy of β-Nitrostyrenes. II. Mono-, Bi- and Tri-Methoxy Phenyl-Substitutions and Long Distance Electronic Effects

By means of ¹³C-NMR spectroscopy and AM1 molecular orbital calculations of mono-, bi- and tri-methoxy-β-nitrostyrenes at the meta and para positions, we have characterized a long distance electronic charge transfer pattern on the ethylenic bridge (CH=CH) and on the aromatic ring (Ph) carbon centers, determined by the electron-donor nature of the methoxy-substituent groups.

After a complete spectral assignment of the ¹³C-NMR signals, we have found a functional dependence of the chemical shifts on the C₁ and C_β centers respect to the C₄ and C₃ methoxy subtitution sites on the aromatic ring, while in the same molecular series C_alfa-chemical shifts are practically constants. on the other hand, the ¹³C-NMR chemical shifts of the C₃ and C₄ centers plus the analysis of the AM1 electronic charge density have permitted us determine the long distance charge transfer effect induced by the C₄ methoxy substitutions as well as the attenuation of this effect due to the C₃ methoxy substitutions.     

A Spectroscopic Model for the Study of Preferential in the Ground and Excited Electronic States.

The preferential solvation of a solute molecule in mixed solvents is analysed in terms of the spectral solvent shifts. A spectroscopic model is developed in order to know the preferential solvation degree in the ground electronic state as well as in the first excited electronic state by measuring the absorption and fluorescence spectra respec tively.

Triphenylene was found to be a good model probe molecule in n-butanol/carbon tetrachloride mixtures for both electronic states. Furthermore Tryphenylene in its ground electronic state was studied in chloroform/methanol mixtures.     

Multipumping Nitrite Determination in Exhaled Breath Condensate

Abstract

A flow system based on multicommutation is proposed for the rapid, clean, and inexpensive determination of nitrites in small volumes of breath condensates. The procedure exploits the colorimetric detection of nitrite with the Griess reagent [0.03% naphthylethylene diamine dihydrochloride (NED), 0.5% sulpfhanilamide, and 3.0% phosphoric acid] in acidic medium at 540 nm correcting the variations of the baseline with measurements at 424 nm. The flow system was designed with a set of solenoid micropumps to minimize sample and reagent consumption and waste generation. The detection limit was estimated as 3.8 ng mL^?1 (99.7% confidence level) with a linear response ranging up to 500 ng mL^?1. The coefficient of variation was estimated as 0.7% for a solution containing 300 ng mL^?1 nitrite (n=9). Approximately 144 determinations can be carried out per hour, consuming only 678.4 µg Griess reagent and generating 1.184 mL of effluent per determination, thus providing an environmentally friendly alternative and a nonexpensive method. The procedure was successfully applied to determine nitrite in breath condensates.     

An electrostatic correction for improved crystal density predictions of energetic ionic compounds

In recent years, there has been considerable interest in predicting the crystal densities of both molecular and ionic energetic compounds using the computed volumes V_m of the isolated gas phase molecules or ions. The surfaces enclosing the volumes are taken to be the 0.001 au (electrons/bohr³) contours of the molecules’ and ions’ electronic densities. For molecular solids, it is known that the ratio M/V_m (M = molecular mass) gives densities that are overall reasonably good, although they can be markedly improved by introduction of an electrostatic interaction correction term. For ionic solids, the subject of this paper, the ratio M/V_m (M = formula unit mass) is not nearly as effective; V_m tends to be significantly larger than the effective volumes of the ions in the crystal, leading to underestimated densities, with an average absolute error of 0.089 g/cm³. The correction term that improves molecular crystal densities is not applicable in the case of ionic solids; however we show, for a database of 25 compounds plus five test cases, that an average absolute error of 0.033 g/cm³ can be achieved by combining M/V_m with terms involving the average positive and negative potentials and areas on the cationic and anionic surfaces. The root-mean-square error is 0.040 g/cm³.     

Learning temporal nodes Bayesian networks

Temporal Nodes Bayesian Networks (TNBNs) are an alternative to Dynamic Bayesian Networks for temporal reasoning with much simpler and efficient models in some domains. TNBNs are composed of temporal nodes, temporal intervals, and probabilistic dependencies. However, methods for learning this type of models from data have not yet been developed. In this paper, we propose a learning algorithm to obtain the structure and temporal intervals for TNBNs from data. The method consists of three phases: (i) obtain an initial approximation of the intervals, (ii) obtain a structure using a standard algorithm and (iii) refine the intervals for each temporal node based on a clustering algorithm. We evaluated the method with synthetic data from three different TNBNs of different sizes. Our method obtains the best score using a combined measure of interval quality and prediction accuracy, and a competitive structural quality with lower running times, compared to other related algorithms. We also present a real world application of the algorithm with data obtained from a combined cycle power plant in order to diagnose temporal faults.     

Error estimation properties of Gaussian process models in stochastic simulations

The theoretical relationship between the prediction variance of a Gaussian process model (GPM) and its mean square prediction error is well known. This relationship has been studied for the case when deterministic simulations are used in GPM, with application to design of computer experiments and metamodeling optimization. This article analyzes the error estimation of Gaussian process models when the simulated data observations contain measurement noise. In particular, this work focuses on the correlation between the GPM prediction variance and the distribution of prediction errors over multiple experimental designs, as a function of location in the input space. The results show that the error estimation properties of a Gaussian process model using stochastic simulations are preserved when the signal-to-noise ratio in the data is larger than 10, regardless of the number of training points used in the metamodel. Also, this article concludes that the distribution of prediction errors approaches a normal distribution with a variance equal to the GPM prediction variance, even in the presence of significant bias in the GPM predictions.     

Experimental assessment of the phonon confinement in TiO2 anatase nanocrystallites by Raman spectroscopy

TiO₂ aerogels prepared by sol‐gel method and followed by supercritical drying have been annealed at temperatures ranging between 400 and 550 °C. The obtained TiO₂ anatase crystallites with the mean size between 6.4 and 13.9 nm, as obtained from transmission electron microscopy measurements, have been further investigated by Raman spectroscopy. It was found that the peak position and full width at half maximum (FWHM) of the TiO₂ anatase Raman bands located around 144, 398, and 638 cm⁻¹ are influenced by crystallite dimension. These spectral changes can be assigned to the combined action of several nanosize effects such as phonon confinement, phonon coupling, strain, and stoichiometry defects. Surprisingly, the best discrimination of the FWHM change with the nanocrystallite mean size was achieved for the 638 cm⁻¹ band, whereas the best discrimination for the peak position was found for the 398 cm⁻¹ band. The critical size values obtained from the peak position and FWHM evaluation were between 12.7 and 13.1 nm. Taking into consideration that only the phonon confinement and inhomogeneous strain can induce an asymmetric broadening of the Raman signal, the bands asymmetry was evaluated, and the critical size values of the nanocrystallites were determined to be between 10 and 11 nm. For a symmetric size distribution of TiO₂ anatase crystallites with dimensions between 6.4 and 13.9 nm, the obtained result indicates that the phonon confinement contribution to the overall size effects is more than 75%. No evidence about the influence of the phonon coupling and vacancies on the Raman features was observed. The comparison of the data derived from the experimental analysis with those obtained by applying the theoretical phonon confinement model indicates the necessity of developing an improved phonon confinement model. The asymmetry approach can be applied for a great variety of nanostructures, as a measure of the confinement effect. Copyright © 2011 John Wiley & Sons, Ltd.