Computational Study of Cage Like (ZnO)12 Cluster Using Hybrid and Hybrid Meta Functionals

Density Functional Theory employing hybrid and M06 functionals in combination with three different basis sets is used to calculate the ground state of a cage like (ZnO)₁₂ nanocluster which has been consistently reported as the more stable cluster for its particular size. B3LYP and B3PW91 hybrid functionals combined with 6‐31+G*, Lanl2dz and SDD basis sets are employed to treat the ZnO molecular system. Alternatively, three M06 functionals in combination with three basis sets are employed in the nanostructure calculations. Results obtained by treating ZnO sodalite cage nanocluster with M06 functionals demonstrated comparable quality to results obtained with hybrid functionals. Within this study, efficient theoretical DFT methods with the widely known hybrid and the recently created M06 meta‐hybrid functionals are employed to study nanostructured ZnO. Our resulting parameters provide a fresh approach performance wise on the different theoretical methods to treat transition metal nanostructures, particularly, ZnO nanoclusters geometry and electronic structure.     

Calculations of dynamic dipole polarizabilities of Li and Na atoms in debye plasma using the model potential technique

The effects of Debye plasma on the frequency‐dependent polarizabilities of Li and Na atoms are investigated using symplectic algorithm within the framework of the pseudostate summation technique. Dynamic dipole polarizabilities of Li (2s ²S) and Na(3s ²S) as functions of scaled number density of the plasma electrons for arbitrary plasma temperature are presented. Screening effects on the resonance frequencies are also presented. In free‐atomic cases, our calculated results are comparable with the reported theoretical and experimental predictions. © 2012 Wiley Periodicals, Inc.     

Solubility of novel open-chain crown ether bridged diphosphates in supercritical carbon dioxide

The solubility of newly synthesized chelating agents, i.e., tetraethylene glycol bis (2-ethylhexyl) dimethyl diphosphate (EG4EH), tetraethylene glycol bis (n-octyl) dimethyl diphosphate (EG4Oct), and tetraethylene glycol bis (2-butoxyethyl) dimethyl diphosphate (EG4BOE) in supercritical carbon dioxide (scCO₂) were determined at temperatures ranging from (318.15 to 333.15) K and pressures ranging from (12 to 21) MPa. Solubility increases in the order of EG4Oct (MW = 606.33) < EG4BOE (MW = 582.26) < EG4EH (MW = 606.33), indicating that branched side chains of the ligands play an important part in increasing solubility in scCO₂. Semi empirical density-based models proposed by Bartle and Chrastil were used to correlate the experimental data, and AARD values were calculated to be (1.2 to 2.9)% and (0.40 to 0.93)% for Bartle and Chrastil model, respectively. Additionally, the partial molar volumes of those compounds were estimated following the theory developed by Kumar and Johnston.     

Volumetric behaviour of the (2,2,4-trimethylpentane + methylbenzene + butan-1-ol) ternary system and its binary sub-systems within the temperature range (298.15–328.15) K

Densities and speeds of sound of the (2,2,4-trimethylpentane + methylbenzene + butan-1-ol) ternary system as well as all its binary sub-systems were measured at four temperatures, namely 298.15 K, 308.15 K, 318.15 K, and 328.15 K at atmospheric pressure by a vibrating-tube densimeter DSA 5000. The binary (isooctane + toluene) system was studied previously. Excess quantities (molar volume, adiabatic compressibility, and isobaric thermal expansivity) of the mixtures studied were calculated from the experimental densities and speed of sounds. The excess molar volume data were correlated using the Redlich–Kister equation. Both the positive and S-shaped excess molar volume curves were found for the systems studied. The excess molar volumes versus concentration of binary systems differed in the shape and temperature dependence. The experimental binary data were compared with literature data. The experimental excess molar volumes were analyzed by means of the Extended Real Associated Solution (ERAS) model. The experimental data and the ERAS model can help to estimate real behaviour of the systems studied.     

Thermodynamic modeling for clathrate hydrates of ozone

We report a theoretical study to predict the phase-equilibrium properties of ozone-containing clathrate hydrates based on the statistical thermodynamics model developed by van der Waals and Platteeuw. The Patel–Teja–Valderrama equation of state is employed for an accurate estimation of the properties of gas phase ozone. We determined the three parameters of the Kihara intermolecular potential for ozone as a = 6.815 · 10⁻² nm, σ = 2.9909 · 10⁻¹ nm, and ε · k_B⁻¹ = 184.00 K. An infinite set of ε–σ parameters for ozone were determined, reproducing the experimental phase equilibrium pressure–temperature data of the (O₃ + O₂ + CO₂) clathrate hydrate. A unique parameter pair was chosen based on the experimental ozone storage capacity data for the (O₃ + O₂ + CCl₄) hydrate that we reported previously. The prediction with the developed model showed good agreement with the experimental phase equilibrium data within ±2% of the average deviation of the pressure. The Kihara parameters of ozone showed slightly better suitability for the structure-I hydrate than CO₂, which was used as a help guest. Our model suggests the possibility of increasing the ozone storage capacity of clathrate hydrates (∼7% on a mass basis) from the previously reported experimental capacity (∼1%).     

Experimental shift allowance in the deconvolution of SIMS depth profiles

We study the deconvolution of the secondary ion mass spectrometry (SIMS) depth profiles of silicon and gallium arsenide structures with doped thin layers. Special attention is paid to allowance for the instrumental shift of experimental SIMS depth profiles. This effect is taken into account by using Hofmann's mixing‐roughness‐information depth model to determine the depth resolution function. The ill‐posed inverse problem is solved in the Fourier space using the Tikhonov regularization method. The proposed deconvolution algorithm has been tested on various simulated and real structures. It is shown that the algorithm can improve the SIMS depth profiling relevancy and depth resolution. The implemented shift allowance method avoids significant systematic errors of determination of the near‐surface delta‐doped layer position. Copyright © 2013 John Wiley & Sons, Ltd.     

Application of XPS imaging analysis in understanding interfacial delamination and X‐ray radiation degradation of PMMA

The recent development of X‐ray Photoelectron Spectroscopy (XPS) instrumentation with spatial resolution down to several microns has advanced the capability of elemental and chemical state imaging. XPS imaging analysis has been applied in understanding the delamination problems of siloxane coatings on polymethyl‐methacrylate (PMMA) polymer. It was found that delamination occurred by interfacial failure, and the coating suffered complete delamination from a PMMA substrate. This example offered an opportunity for the investigation of X‐ray damage on polymers encountered in XPS imaging analysis. This paper also demonstrated how to construct a constrained peak model with the aid of chemical knowledge and supporting evidence of the sample. Monte Carlo error analysis was used to determine the validity of the peak fit models used. Copyright © 2013 John Wiley & Sons, Ltd.     

XPS of oxygen atoms on Ag(111) and Ag(110) surfaces: Accurate study with SAC/SAC‐CI combined with dipped adcluster model

O1s core‐electron binding energies (CEBE) of the atomic oxygens on different Ag surfaces were investigated by the symmetry adapted cluster‐configuration interaction (SAC‐CI) method combined with the dipped adcluster model, in which the electron exchange between bulk metal and adsorbate is taken into account properly. Electrophilic and nucleophilic oxygens (O_elec and O_nuc) that might be important for olefin epoxidation in a low‐oxygen coverage condition were focused here. We consider the O1s CEBE as a key property to distinguish the surface oxygen states, and series of calculation was carried out by the Hartree–Fock, Density functional theory, and SAC/SAC‐CI methods. The experimental information and our SAC/SAC‐CI results indicate that O_elec is the atomic oxygen adsorbed on the fcc site of Ag(111) and that O_nuc is the one on the reconstructed added‐row site of Ag(110) and that one‐ and two‐electron transfers occur, respectively, to the O_elec and O_nuc adclusters from the silver surface. © 2013 Wiley Periodicals, Inc.     

High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/ . © 2013 Wiley Periodicals, Inc.     

Water PMF for predicting the properties of water molecules in protein binding site

Water is an important component in living systems and deserves better understanding in chemistry and biology. However, due to the difficulty of investigating the water functions in protein structures, it is usually ignored in computational modeling, especially in the field of computer‐aided drug design. Here, using the potential of mean forces (PMFs) approach, we constructed a water PMF (wPMF) based on 3946 non‐redundant high resolution crystal structures. The extracted wPMF potential was first used to investigate the structure pattern of water and analyze the residue hydrophilicity. Then, the relationship between wPMF score and the B factor value of crystal waters was studied. It was found that wPMF agrees well with some previously reported experimental observations. In addition, the wPMF score was also tested in parallel with 3D‐RISM to measure the ability of retrieving experimentally observed waters, and showed comparable performance but with much less computational cost. In the end, we proposed a grid‐based clustering scheme together with a distance weighted wPMF score to further extend wPMF to predict the potential hydration sites of protein structure. From the test, this approach can predict the hydration site at the accuracy about 80% when the calculated score lower than ?4.0. It also allows the assessment of whether or not a given water molecule should be targeted for displacement in ligand design. Overall, the wPMF presented here provides an optional solution to many water related computational modeling problems, some of which can be highly valuable as part of a rational drug design strategy. © 2012 Wiley Periodicals, Inc.