Development of non‐bonded interaction parameters between graphene and water using particle swarm optimization

New Lennard‐Jones parameters have been developed to describe the interactions between atomistic model of graphene, represented by REBO potential, and five commonly used all‐atom water models, namely SPC, SPC/E, SPC/Fw, SPC/Fd, and TIP3P/Fs by employing particle swarm optimization (PSO) method. These new parameters were optimized to reproduce the macroscopic contact angle of water on a graphene sheet. The calculated line tension was in the order of 10⁻¹¹ J/m for the droplets of all water models. Our molecular dynamics simulations indicate the preferential orientation of water molecules near graphene–water interface with one O H bond pointing toward the graphene surface. Detailed analysis of simulation trajectories reveals the presence of water molecules with ≤∼1, ∼2, and ∼4 hydrogen bonds at the surface of air–water interface, graphene–water interface, and bulk region of the water droplet, respectively. Presence of water molecules with ≤∼1 and ∼2 hydrogen bonds suggest the existence of water clusters of different sizes at these interfaces. The trends observed in the libration, bending, and stretching bands of the vibrational spectra are closely associated with these structural features of water. The inhomogeneity in hydrogen bond network of water at the air–water and graphene–water interface is manifested by broadening of the peaks in the libration band for water present at these interfaces. The stretching band for the molecules in water droplet shows a blue shift as compared to the pure bulk water, which conjecture the presence of weaker hydrogen bond network in a droplet. © 2017 Wiley Periodicals, Inc.     

Accurate Calculation of Equilibrium Reduced Density Matrix for the System-Bath Model: a Multilayer Multiconfiguration Time-Dependent Hartree Approach and its Comparison to a Multi-Electronic-State Path Integral Molecular Dynamics Approach?

An efficient and accurate method for computing the equilibrium reduced density matrix is presented for treating open quantum systems characterized by the system-bath model. The method employs the multilayer multiconfiguration time-dependent Hartree theory for imaginary time propagation and an importance sampling procedure for calculating the quantum mechanical trace. The method is applied to the spin-boson Hamiltonian, which leads to accurate results in agreement with those produced by the multi-electronic-state path integral molecular dynamics method.     

Evaluation and improvement of QSAR predictions of skin sensitization for pesticides

In vivo skin sensitization assays have to be provided by applicants to the competent authorities in the European Union for the approval of active substances (AS) in pesticides. This study aimed to test the practicability of in silico predictions for AS by freely available (Q)SAR tools to evaluate their use as a time- and cost-effective alternative to animal testing in the context of the 3R concept. Predictions of skin sensitization for 48 selected sensitizing and non-sensitizing AS by the software programs CAESAR, Toxtree, OECD (Q)SAR Toolbox, CASE Ultra, Leadscope and SciQSAR were collected and compared. Different data evaluation methodologies (score definition, mean, weighted mean, threshold score definition) were applied to optimize the predictions. The calculation methods were internally cross-validated and further validated with an additional validation set of 80 AS. Although the presented calculation methodologies are not suitable as a stand-alone method, this study has shown weaknesses and strengths of some prominent (Q)SAR programs and diverse combinatorial options in the prediction of skin sensitization by pesticidal AS. The present study will help to foster discussions on in silico alternatives to animal testing in the pesticide area.     

Recursive condition for positivity of the angle for multivariate stationary sequences

In this note a recursive type condition for positivity of the angle between past and future for -variate stationary sequences is provided. In the case it gives a simple different proof of a result due to Solev and Tserkhtsvadze on basicity of bivariate stationary sequences.

     

Varying weights for orthogonal polynomials with monotonically varying recurrence coefficients

We consider orthogonal polynomials , where n is the degree of the polynomial and N is a discrete parameter. These polynomials are orthogonal with respect to a varying weight W_N which depends on the parameter N and they satisfy a recurrence relation with varying recurrence coefficients which we assume to be varying monotonically as N tends to infinity. We establish the existence of the limit and link this limit to an external field for an equilibrium problem in logarithmic potential theory.     

Aperture-Angle and Hausdorff-Approximation of Convex Figures

The aperture angle α(x,Q) of a point x ∉ Q in the plane with respect to a convex polygon Q is the angle of the smallest cone with apex x that contains Q. The aperture angle approximation error of a compact convex set C in the plane with respect to an inscribed convex polygon Q⊂C is the minimum aperture angle of any x∈C∖Q with respect to Q. We show that for any compact convex set C in the plane and any k>2, there is an inscribed convex k-gon Q⊂C with aperture angle approximation error . This bound is optimal, and settles a conjecture by Fekete from the early 1990s. The same proof technique can be used to prove a conjecture by Brass: If a polygon P admits no approximation by a sub-k-gon (the convex hull of k vertices of P) with Hausdorff distance σ, but all subpolygons of P (the convex hull of some vertices of P) admit such an approximation, then P is a (k+1)-gon. This implies the following result: For any k>2 and any convex polygon P of perimeter at most 1 there is a sub-k-gon Q of P such that the Hausdorff-distance of P and Q is at most  . This research was supported by the Korea Research Foundation Grant funded by the Korean Government (MOEHRD) (KRF-2006-311-D00763). NICTA is funded through the Australian Government’s Backing Australia’s Ability initiative, in part through the Australian Research Council.     

New cut angle quartz crystal microbalance with low frequency-temperature coefficients in an aqueous phase

In a traditional quartz crystal microbalance (QCM), an AT-cut (cut angle φ = 35.25° in yxl orientation) quartz wafer is employed because it has low frequency–temperature coefficients (dF/dT) at room temperature region. But when a QCM is in contact with a liquid phase, its frequency is also related to the properties of the liquid, which are temperature dependent. The value of dF/dT is about 20 Hz/°C for a 9 MHz AT-cut QCM with one side facing water. In this work, a group of QCMs in new cut angles were prepared. The influence of the cut angle on the frequency–temperature characteristic, response sensitivities to surface mass loading and viscodensity of liquid were investigated. An intrinsically temperature-compensated QCM sensor that possesses low dF/dT values in aqueous solution was reported. When a 9 MHz QCM with φ = 35.65° was contacted with water with one side, its dF/dT value is close to zero at ca. 25 °C and its averaged value of |dF/dT| is only 0.6 Hz/°C in the temperature range of 23–27 °C. The frequency responses to surface mass loading and viscodensity of liquid phase are very close among the QCMs with the cut angles in the range of 35.15–35.7°. The intrinsically temperature-compensated QCM was applied to investigate the alternate adsorption processes of cationic polyelectrolyte and silica nanoparticle.     

Development of algorithms for automated spectrophotometric titrations

A versatile method for evaluation of equilibrium constants from automated spectrophotometric titrations is described. General algorithms were derived for normalized titration curves of reactions having various stoichiometric ratios. Normalization of data involve converting it from absorption versus time to product formed (0 to 1) versus equivalents of titrant added. Relevance of derived algorithms was assessed by the quality of their fit to real data. The demonstration system chosen for this investigation was the 1:3 complexation reaction of Fe(II) and 1,10-phenantroline (o-Phen). Titrations were performed at three distinct infusion rates under controlled pH of 5.0 and at 25.0 °C, with sets produced using both Fe(II) and o-Phen as the titrant. Direct fitting of titration curves yielded values for overall equilibrium constants. Furthermore, resulting curves revealed reproducible initial deviation, consistent with step-wise reaction, when titrating Fe(II) with o-Phen. No unusual deviations were evident anywhere in the titration curves when Fe(II) was the titrant. Overall, our approach facilitates adoption of automated titrimetry and data analysis methodologies for the determination of stoichiometries and equilibrium constants of many UV/Vis active reactions.     

Force field parameters for rotation around chi torsion axis in nucleic acids

To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids.     

Gas hydrate equilibrium dissociation conditions in porous media using two thermodynamic approaches

We employ two thermodynamic approaches, based on the equal fugacities and the equal activities, to predict the gas hydrate equilibrium dissociation conditions in the porous media. The predictions are made for the hydrate systems, CH₄/H₂O, C₂H₆/H₂O, C₃H₈/H₂O, CO₂/H₂O, CH₄/CO₂/H₂O, C₃H₈/CH₄/C₂H₆/H₂O, and CH₄/CH₃OH/H₂O. For the non-hydrate phase, we used the Trebble–Bishnoi equation in the fugacity approach and the Soave–Redlich–Kwong equation in the activity approach. For the hydrate phase, the van der Waals–Platteeuw model incorporated with the capillary model of Llamedo et al. [M. Llamedo, R. Anderson, B. Tohidi, Am. Mineral. 89 (2004) 1264–1270] was used in the two approaches. The predictions are found to be in satisfactory to good agreement with the experimental data. The predictive ability of the fugacity approach is better than that of the activity approach.