Wetting on nanoporous alumina surface: transition between Wenzel and Cassie states controlled by surface structure

This paper reports a systematic study on the relationship between surface structure and wetting state of ordered nanoporous alumina surface. The wettability of the porous alumina is dramatically changed from hydrophilicity to hydrophobicity by increasing the hole diameter, while maintaining the hole interval and depth. This phenomenon is attributed to the gradual transition between Wenzel and Cassie states which was proved experimentally by comparing the wetting behavior on these porous alumina surfaces. Furthermore, the relationship between surface wettability and hole depth at a fixed hole interval and diameter was investigated. For those porous alumina with relatively larger holes in diameter, transition between Wenzel and Cassie states was also achieved with increasing hole depth. A capillary-pressure balance model was proposed to elucidate the unique structure-induced transition, and the criteria for the design and construction of a Cassie wetting surface was discussed. These structure-induced transitions between Wenzel and Cassie states could provide further insight into the wetting mechanism of roughness-induced wettability and practical guides for the design of variable surfaces with controllable wettability.     

Density of configurational states from first-principles calculations: the phase diagram of Al-Na surface alloys.

The structural phases of Al(x)Na(1-x) surface alloys have been investigated theoretically and experimentally. We describe the system using a lattice-gas Hamiltonian, determined from density functional theory, together with Monte Carlo (MC) calculations. The obtained phase diagram reproduces the experiment on a quantitative level. From calculation of the (configurational) density of states by the recently introduced Wang-Landau MC algorithm, we derive thermodynamic quantities, such as the free energy and entropy, which are not directly accessible from conventional MC simulations. We accurately reproduce the stoichiometry, as well as the temperature at which an order-disorder phase transition occurs, and demonstrate the crucial role, and magnitude, of the configurational entropy.     

Rationalization of the behavior of solid-liquid surface free energy of water in Cassie and Wenzel wetting states on rugged solid surfaces at the nanometer scale

The present work aims to contribute to the understanding at a molecular level of the origin of the hydrophobic nature of surfaces exhibiting roughness at the nanometer scale. Graphite-based smooth and model surfaces whose roughness dimension stretches from a few angstroms to a few nanometers were used in order to generate Cassie and Wenzel wetting states of water. The corresponding solid-liquid surface free energies were computed by means of molecular dynamics simulations. The solid-liquid surface free energy of water-smooth graphite was found to be -12.7 ± 3.3 mJ/m(2), which is in reasonable agreement with a value estimated from experiments and fully consistent with the features of the employed model. All the rugged surfaces yielded higher surface free energy. In both Cassie and Wenzel states, the maximum variation of the surface free energy with respect to the smooth surface was observed to represent up to 50% of the water model surface tension. The solid-liquid surface free energy of Cassie states could be well predicted from the Cassie-Baxter equation where the surface free energies replace contact angles. The origin of the hydrophobic nature of surfaces yielding Cassie states was therefore found to be the reduction of the number of interactions between water and the solid surface where atomic defects were implemented. Wenzel's theory was found to fail to predict even qualitatively the variation of the solid-liquid surface free energy with respect to the roughness pattern. While graphite was found to be slightly hydrophilic, Wenzel states were found to be dominated by an unfavorable effect that overcame the favorable enthalpic effect induced by the implementation of roughness. From the quantitative point of view, the solid-liquid surface free energy of Wenzel states was found to vary linearly with the roughness contour length.     

The benzene+OH potential energy surface: intermediates and transition states

The potential energy surface for the interaction between benzene and hydroxyl radical is studied in detail using quantum mechanical methods, with a particular focus on the hydrogen abstraction pathway. Geometric parameters are optimized using a variety of density functional methods as well as perturbation theory. Energies are refined using coupled cluster singles and doubles with perturbative triples [CCSD(T)] extrapolated to the complete basis set limit. At our most reliable level of theory, complexation energies are found to be (with zero-point corrected energies in parentheses) 3.7 (2.8) kcal/mol for the benzene-hydroxyl radical complex and 2.9 (-1.7) kcal/mol for the phenyl radical-water complex. The barrier to H abstraction lies 6.5 (4.2) kcal/mol above the infinitely separated benzene and hydroxyl radical monomers.     

Temperature-induced phase transition in h-MoO3: Stability loss mechanism uncovered by Raman spectroscopy and DFT calculations

This paper reports the study of the metastable hexagonal molybdenum oxide (h-MoO₃) rods by looking at the vibrational, structural and morphological properties. The MoO₃ as-synthesized rods were prepared by the precipitation method and characterized by X-ray diffraction, Raman spectroscopy and scanning electron microscopy, revealing a hexagonal phase and submicrometric size of the MoO₃. The vibrational modes of the h-MoO₃ were calculated by density-functional perturbation theory (DFPT) and used by first time to do the signature of the experimentally observed Raman modes, filling a gap in this field. Experimental temperature-dependent Raman spectroscopy study was carried out on h-MoO₃ rods and pointed out to a phase transition in the 675-690 K temperature range. This phase transition was confirmed by scanning electron microscopy that was used to analyze the morphological changes in the MoO₃ samples during the heating cycle. Temperature-dependent Raman data analysis combined with DFT calculations allowed us to confirm the mechanism that underlies the stability loss of the hexagonal phase at the critical temperature and to correlate the wavenumber difference of two specific Raman bands with the real temperature of the sample.     

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations

An efficient method for the calculation of minimum free energy pathways and free energy profiles for conformational transitions is presented. Short restricted perturbation-targeted molecular dynamics trajectories are used to generate an approximate free energy surface. Approximate reaction pathways for the conformational change are constructed from one-dimensional line segments on this surface using a Monte Carlo optimization. Accurate free energy profiles are then determined along the pathways by means of one-dimensional adaptive umbrella sampling simulations. The method is illustrated by its application to the alanine "dipeptide." Due to the low computational cost and memory demands, the method is expected to be useful for the treatment of large biomolecular systems.     

Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations

Polyglutamine (polyQ) diseases, including Huntington’s disease (HD), are caused by expansion of polyQ-encoding repeats within otherwise unrelated gene products. The aggregation mechanism of polyQ diseases, the inhibition mechanism of Congo red, and the alleviation mechanism of trehalose were proposed here based on quantum chemical calculations and molecular dynamics simulations. The calculations and simulations revealed the following. The effective molecular bonding is between glutamine (Gln) and Gln (Gln + Gln), between Gln and Congo red (Gln + Congo red), and between Gln and trehalose (Gln + trehalose). The bonding strength is −13.1 kcal/mol for Gln + Gln, −24.4 kcal/mol for Gln + Congo red, and −12.0 kcal/mol for Gln + trehalose. In the polyQ region, both the number of intermolecular Gln + Gln formations and the total calories generated by the Gln + Gln formation are proportional to the number of repetitions of Gln. We propose an aggregation mechanism whose heat generated by the intermolecular Gln + Gln formation causes the pathogeny of polyQ disease. In our aggregation mechanism, this generated heat collapses the host protein and promotes fibrillogenesis. Without contradiction, our mechanism can explain all the experimental results reported to date. Our mechanism can also explain the inhibition mechanism by Congo red as an inhibitor of polyglutamine-induced protein aggregation and the alleviation mechanism by trehalose as an alleviator of that aggregation. The inhibition mechanism by Congo red is explained by the strong interaction with Gln and by the characteristic structure of Congo red.     

Optimizing the structures of minimum and transition state on the free energy surface

Presented here is the application of a scheme for optimizing the structures of minima and transition states on the free energy surface (FES) for a path along a fixed reaction coordinate with the aid of ab initio molecular dynamics (AIMD) simulation. In the direction of the reaction coordinate, the values corresponding to the stationary points were optimized using the quasi-Newton method, in which the gradient of the free energy along the reaction coordinate was obtained by a constraint AIMD method, and the Bofill Hessian update scheme was used. The equilibrium values for the other directions were taken as the corresponding averages in the dynamic simulation. This scheme was applied to several elementary bimolecular addition reactions: (A) BH(3) + H(2)O --> H(2)O.BH(3); (B) BF(3) + NH(3) --> FB(3).NH(3); (C) SO(3) + NH(3) --> O(3)S.NH(3); (D) C(2)H(4) + CCl(2) --> H(4)C(2).CCl(2); (E) Ni(NH(2))(2) + PH(3) --> (NH(2))(2)Ni.PH(3); (F) W(CO)(5) + CO --> W(CO)(6). For reactions A, B, C, and F, no transition state (TS) exists on the potential energy surface (PES). However there is a TS on the FES. This stems from the curvature difference of the PES and -TDeltaS as a function of the reaction coordinate. For all reactions, it is found that the TS shifts toward the complexation product with increasing temperature because of the curvature increase of -TDeltaS. The equilibrium bond distances for the inactive coordinates perpendicular to the reaction coordinate always increase with temperature, which is due to the thermal excitation and anharmonicity of the PES.     

Binding free energy, energy and entropy calculations using simple model systems

Free energy differences are calculated for a set of two model host molecules, binding acetone and methanol. Two active sites of different characteristics were constructed based on an artificially extended C60 fullerene molecule, possibly functionalised to include polar interactions in an otherwise apolar, spherical cavity. The model host systems minimise the necessary sampling of conformational space while still capturing key aspects of ligand binding. The estimates of the free energies are split up into energetic and entropic contributions, using three different approaches investigating the convergence behaviour. For these systems, a direct calculation of the total energy and entropy is more efficient than calculating the entropy from the temperature dependence of the free energy or from a direct thermodynamic integration formulation. Furthermore, the compensating surrounding–surrounding energies and entropies are split off by calculating reduced ligand-surrounding energies and entropies. These converge much more readily and lead to properties that are more straightforwardly interpreted in terms of molecular interactions and configurations. Even though not experimentally accessible, the reduced thermodynamic properties may prove highly relevant for computational drug design, as they may give direct insights into possibilities to further optimise ligand binding while optimisation in the surrounding–surrounding energy or entropy will exactly cancel and not lead to improved affinity.     

Surface structure and phase transition of K adsorption on Au(111): by ab initio atomistic thermodynamics

We studied the interactions between atomic potassium (K) and Au(111) at a range of coverage (i.e., Θ(K) = 0.11-0.5 monolayer (ML)) by ab initio atomic thermodynamics. For K on-surface adsorption, we found that K energetically favors the three-fold hollow sites (fcc or hcp), while the most significant surface rumpling was obtained at the atop sites. The incorporation of gold atoms in the adsorbate layer gradually becomes energetically favorable with increasing K coverage. We proposed a possible model with a stoichiometry of K(2)Au for the (2 × 2)-0.5 ML phase observed in lower energy electron diffraction (LEED): one K at atop site and the other K as well as one Au adatom at the second-nearest fcc/hcp and hcp/fcc, respectively. Clear theoretical evidences were given for the ionic interaction of K on Au surface. Additionally, phase transitions were predicted based on chemical potential equilibrium of K, largely in line with the earlier reported LEED observations: the clean surface → (√3 × √3)R30° → (2 × 2), and (2 × 2) → (√3 × √3)R30° reversely at an elevated temperature.     

Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations

We propose a new approach for the umbrella sampling method in molecular dynamics simulations of complex systems. An accelerated sampling of the slow degrees of freedom is achieved by generating a single self-adaptive trajectory that tends to span uniformly the reaction coordinate using a time dependent bias potential derived from the preceding history of the system. To show the convergent behavior and the efficiency of the method, we present the free energy surface of alanine dipeptide in water as a function of the backbone dihedral angles.     

Polyethylene glycol adsorption on silica: from bulk phase behavior to surface phase diagram

A characterization of the bulk-phase diagram from literature data and new NMR and DSC measurements provided us with valuable elements that are helpful for gaining, from aqueous solution, better insight into the surface behavior of polyethylene glycol on Aerosil 200. Adsorption isotherms built further to measurements by a depletion method showed a strong and temperature-dependent variation of the isotherm shape in agreement with the variations of interactions already evidenced in the bulk. In temperature-concentration areas, where water is behaving as a helix-promoting solvent, the finding of positive PEG adsorptions and stairlike isotherms agrees with observations reported in the literature. We identified some of the vertical parts as corresponding to the formation of monolayers of helix-shaped PEG molecules. In poor-solvent zones, adsorptions were null or negative, and the isotherms exhibited oscillations suggesting very different surface behavior. Our data analysis evidenced the presence of a much greater amount of water than in the previous surface states; however, the similar analysis of PEG behavior remains relevant. Indeed, the occurrence of first-order transitions in the surface layer implies some water reorganization, permitting the PEG molecules to move closer to the surface and become helix-shaped to rearrange in a monolayer. The surface phase diagram confirmed this analysis in a very satisfying way.     

First-principles calculations of AlN nanowires and nanotubes: atomic structures, energetics, and surface states

We explore the atomic and electronic structures of single-crystalline aluminum nitride nanowires (AlNNWs) and thick-walled aluminum nitride nanotubes (AlNNTs) with the diameters ranging from 0.7 to 2.2 nm by using first-principles calculations and molecular dynamics simulations based on density functional theory (DFT). We find that the preferable lateral facets of AlNNWs and thick-walled AlNNTs are {1010} surfaces, giving rise to hexagonal cross sections. Quite different from the cylindrical network of hexagons revealed in single-walled AlNNTs, the wall of thick-walled AlNNTs displays a wurtzite structure. The strain energies per atom in AlNNWs are proportional to the inverse of the wire diameter, whereas those in thick-walled AlNNTs are independent of tube diameter but proportional to the inverse of the wall thickness. Thick-walled AlNNTs are energetically comparable to AlNNWs of similar diameter, and both of them are energetically more favorable than single-walled AlNNTs. Both AlNNWs and AlNNTs are wide band gap semiconductors accompanied with surface states located in the band gap of bulk wurtzite AlN.     

The molecular mechanism studies of chirality effect of PHA-739358 on Aurora kinase A by molecular dynamics simulation and free energy calculations

Aurora kinase family is one of the emerging targets in oncology drug discovery and several small molecules targeting aurora kinases have been discovered and evaluated under early phase I/II trials. Among them, PHA-739358 (compound 1r) is a 3-aminopyrazole derivative with strong activity against Aurora A under early phase II trial. Inhibitory potency of compound 1r (the benzylic substituent at the pro-R position) is 30 times over that of compound 1s (the benzylic substituent at the pro-S position). In present study, the mechanism of how different configurations influence the binding affinity was investigated using molecular dynamics (MD) simulations, free energy calculations and free energy decomposition analysis. The predicted binding free energies of these two complexes are consistent with the experimental data. The analysis of the individual energy terms indicates that although the van der Waals contribution is important for distinguishing the binding affinities of these two inhibitors, the electrostatic contribution plays a more crucial role in that. Moreover, it is observed that different configurations of the benzylic substituent could form different binding patterns with protein, thus leading to variant inhibitory potency of compounds 1r and 1s. The combination of different molecular modeling techniques is an efficient way to interpret the chirality effects of inhibitors and our work gives valuable information for the chiral drug design in the near future.     

Nucleoside free energy perturbation calculations: Mutation of purine-to-pyrimidine and pyrimidine-to-purine nucleosides

Free energy perturbation calculations were conducted on the mutations of pyrimidine-to-pyrimidine, purine-to-purine, purine-to-pyrimidine, and pyrimidine-to-purine nucleosides. The parameters and technique required for these perturbations is presented. Each of the four nucleosides in DNA were mutated into the other three nucleosides, and the calculated change in free energy for each of the 12 mutations is reported.     

Chirality, surface anchoring, and the cholesteric-smectic A phase transition

Magnetic Freedericksz transition measurements were performed on samples of chiral and racemic mixtures in the cholesteric/nematic phase. We found that the quantity Ф, which is defined as the threshold field H_th times the cell thickness, is larger for the chiral than for the racemic mixtures. This result is inconsistent with chiral contributions to the anchoring strength potential. Instead, the data support a model by Lubensky wherein the transition temperature to the smectic A phase is suppressed in a chiral liquid crystal.     

Low temperature nanostructured lithium titanates: controlling the phase composition, crystal structure and surface area

Low temperature lithium titanate compounds (i.e., Li₄Ti₅O₁₂ and Li₂TiO₃) with nanocrystalline and mesoporous structure were prepared by a straightforward aqueous particulate sol–gel route. The effect of Li:Ti molar ratio was studied on crystallisation behaviour of lithium titanates. X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) revealed that the powders were crystallised at the low temperature of 500 °C and the short annealing time of 1 h. Moreover, it was found that Li:Ti molar ratio and annealing temperature influence the preferable orientation growth of the lithium titanate compounds. Transmission electron microscope (TEM) images showed that the average crystallite size of the powders annealed at 400 °C was in the range 2–4 nm and a gradual increase occurred up to 10 nm by heat treatment at 800 °C. Field emission scanning electron microscope (FE-SEM) analysis revealed that the deposited thin films had mesoporous and nanocrystalline structure with the average grain size of 21–28 nm at 600 °C and 49–62 nm at 800 °C depending upon the Li:Ti molar ratio. Moreover, atomic force microscope (AFM) images confirmed that the lithium titanate films had columnar like morphology at 600 °C, whereas they showed hill-valley like morphology at 800 °C. Based on Brunauer–Emmett–Taylor (BET) analysis, the synthesized powders showed mesoporous structure containing pores with needle and plate shapes. The surface area of the powders was enhanced by increasing Li:Ti molar ratio and reached as high as 77 m²/g for the ratio of Li:Ti = 75:25 at 500 °C. This is one of the smallest crystallite size and the highest surface areas reported in the literature, and the materials could be used in many applications such as rechargeable lithium batteries and tritium breeding materials.     

Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions

Thermodynamic integration is a widely used method to calculate and analyze the effect of a chemical modification on the free energy of a chemical or biochemical process, for example, the impact of an amino acid substitution on protein association. Numerical fluctuations can introduce large uncertainties, limiting the domain of application of the method. The parametric energy function describing the chemical modification in the thermodynamic integration, the "Alchemical path," determines the amplitudes of the fluctuations. In the present work, I propose a measure of the fluctuations in the thermodynamic integration and an approach to search for a parametric energy path minimizing that measure. The optimal path derived with this approach is very close to the theoretical minimum of the measure, but produces nonergodic sampling. Nevertheless, this path is used to guide the design of a practical and efficient path producing correct sampling. The convergence with this practical path is evaluated on test cases, and compares favorably with that of other methods such as power or polynomial path, soft-core van der Waals, and some other approaches presented in the literature.     

INDO-Type calculations on the ground state and various ionic states of transition metal tricarbonyls

By means of the ΔSCF and transition operator (TO) methods based on a recently developed INDO extension to the first transition metal series, the first ionization potentials of benzene—chromium tricarbonyl ( I ), cyclopentadienyl manganese tricarbonyl ( II ), the iron—tricarbonyl complexes with trimethylenemethane ( III ), and cyclobutadiene ( IV ) have been calculated and compared with experimental data. It is shown that the electronic structure of I to IV can be rationalized by Hoffmann's fragment approach in both the ground state and the cationic hole states. Within the series I—IV there are remarkable energy differences in the ground state for MOs derived from the 1a₁ and 1e orbitals of the M(CO)₃ fragment. The observation that only one band is associated with the ionization events from MOs predominantly localized at the metal site is traced back to large relaxation effects. In the cationic hole states the split of the M(CO)₃ fragment orbitals 1a₁ and 1e is minute in all four compounds.