Computational study of the Stone-Wales transformation in C36

The transition of the D6h neutral and charged isomers to D2d isomers of C36 via Stone-Wales transformation has been studied by means of the hybrid density functional method (B3LYP). The results show that the transition state (TS) and reaction pathway could be identified for the rearrangement from C36-D6h to C36-D2d on the potential energy surface. We found that the neutral and charged transition states all have C2 molecular point group symmetry with the two migrating carbon atoms remaining close to the fullerene surface. The other kind of possible TS with a carbene-like structure along the stepwise reaction path does not exist as a stationary point with the density functionals utilized here. The classical barriers are 6.23 eV through the neutral TS, 6.37 eV through the anionic TS, and 6.29 eV through the cationic TS at the B3LYP/6-31G level of theory.     

Pervaporation of water-ethanol mixtures through symmetric and asymmetric TPX membranes

In this work, the pervaporation performance and mechanism of water-ethanol mixtures through symmetric and asymmetric TPX [poly(4-methyl-1-pentene)] membranes were investigated. The results show that TPX is a highly water permselective material although it is strongly hydrophobic. It was found that, for a symmetric dense TPX membrane, the feed solution vaporizes first and then permeates through the membrane. The water selectivity stems from the huge difference in diffusivity between water and ethanol vapors. To improve the permeation flux, asymmetric TPX membranes were prepared by a wet inversion method. However, due to the swelling effect of ethanol on TPX, small pores occur when the dense skin contacts the feed solution, resulting in a loss of water selectivity. Stain experiments were carried out to verify this mechanism. In addition, it was found that a parallel model can describe the mechanism quite accurately. Good agreement between the theoretical calculation and experimental measurement has been obtained. Furthermore, we also found that the loss of selectivity can be avoided by turning the asymmetric membrane over; that is, let the dense skin face the permeate.     

Butatrienes as extended alkenes: barriers to internal rotation and substitution effects on the stabilities of the ground states and transition states

The barriers to internal rotation of methylated, ethynylated, and vinylated butatrienes and alkenes were calculated at the CASPT2/6-31G(d)//B3LYP/6-31G(d) level. Calculated butatriene rotational barriers are lower than those of analogous alkenes, but there is a larger variance in rotational barrier for alkenes than for butatrienes. The barriers to rotation were analyzed by isodesmic equations designed to estimate the substituent effects in the ground (GS) and transition (TS) states individually. The GSs of both series are stabilized to roughly the same extent. In contrast, the TSs of butatrienes are more stabilized overall than those of alkenes. Much of the stabilization in the TS of butatrienes comes from the internal triple bond and not from the substituent. Estimation of the substituent stabilization alone reveals the TSs of ethylenes to be more stabilized by substitution than butatrienes.     

Testing the TPSS meta-generalized-gradient-approximation exchange-correlation functional in calculations of transition states and reaction barriers

We have studied the performance of local and semilocal exchange-correlation functionals [meta-generalized-gradient-approximation (GGA)-TPSS, GGA-Perdew-Burke-Ernzerhof (PBE), and local density approximation (LDA)] in the calculation of transition states, reaction energies, and barriers for several molecular and one surface reaction, using the plane-wave pseudopotential approach. For molecular reactions, these results have been compared to all-electron Gaussian calculations using the B3LYP hybrid functional, as well as to experiment and high level quantum chemistry calculations, when available. We have found that the transition state structures are accurately identified irrespective of the level of the exchange-correlation functional, with the exception of a qualitatively incorrect LDA prediction for the H-transfer reaction in the hydrogen bonded complex between a water molecule and a OH radical. Both the meta-GGA-TPSS and the GGA-PBE functionals improve significantly the calculated LDA barrier heights. The meta-GGA-TPSS further improves systematically, albeit not always sufficiently, the GGA-PBE barriers. We have also found that, on the Si(001) surface, the meta-GGA-TPSS barriers for hydrogen adsorption agree significantly better than the corresponding GGA-PBE barriers with quantum Monte Carlo cluster results and experimental estimates.     

Electrostatic surface interactions in mixtures of symmetric and asymmetric electrolytes: a Monte Carlo study

Canonical Monte Carlo simulations of the interaction between a uniformly charged spherical particle and a discretely charged planar surface in solutions of symmetric and asymmetric electrolytes were performed. To assess the nature of the interactions, the force exerted on the colloidal particle perpendicular to the planar surface was calculated. Attractive minima in the interaction force between the similarly charged surfaces reveal the occurrence of two phenomena: long-range attraction of electrostatic origin and short-range attraction due to depletion effects. The degree of electrostatic coupling determines the magnitude and range of like-charge attraction between the two surfaces.     

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.     

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.     

Microwave-assisted synthesis of symmetric and asymmetric viologens

Viologens are generally synthesized by N-alkylating 4,4′-bipyridine with alkyl halides. Under conventional heating conditions, however, their synthesis suffers from long reaction times and, often, low yields. In this work, symmetric and asymmetric viologens were synthesized under the assistance of microwave irradiation in good to excellent yields and in short reaction times.     

Graphene nucleation on transition metal surface: structure transformation and role of the metal step edge

The nucleation of graphene on a transition metal surface, either on a terrace or near a step edge, is systematically explored using density functional theory calculations and applying the two-dimensional (2D) crystal nucleation theory. Careful optimization of the supported carbon clusters, C(N) (with size N ranging from 1 to 24), on the Ni(111) surface indicates a ground state structure transformation from a one-dimensional C chain to a 2D sp(2) C network at N ≈ 10-12. Furthermore, the crucial parameters controlling graphene growth on the metal surface, nucleation barrier, nucleus size, and nucleation rate on a terrace or near a step edge are calculated. In agreement with numerous experimental observations, our analysis shows that graphene nucleation near a metal step edge is superior to that on a terrace. On the basis of our analysis, we propose the use of graphene seeds to synthesize high-quality graphene in large area.     

Stereochemistry of transition states and mechanisms of chemical reactions on silica surface

The activation energy of substitution and bond cleavage reactions of siloxane derivatives on silica surfaces is discussed considering the stereochemistry of the transition state. General concepts are developed and utilized in predicting reactivity trends for reactions occurring on the silica surface.     

Pressure induced transition between superhydrophobic states: configuration diagrams and effect of surface feature size

The stability of wetting states, namely the Cassie state (partial wetting) and the Wenzel state (complete wetting) of surfaces with protrusions, is determined by comparing the total free energy of a liquid drop in terms of their apparent contact angles for different protrusion features. It is found that when the area fraction of the topographical features and the intrinsic contact angle for a flat surface are large, the Cassie state is favored, but it can be either the metastable or stable state. It is shown that the transition from the Cassie state to the Wenzel state requires the application of a pressure to the meniscus between the surface protrusions. The critical transition pressure increases not only with increasing area fraction and intrinsic contact angle, but also with decreasing protrusion size. During the transition, a high-pressure gas can be trapped around the protrusions that can cause the Cassie state to be recovered after the release of the applied pressure. The analysis shows that a droplet can 'hang' upside-down when the protrusion size is very small; namely, the protrusions can pin the meniscus. These results are discussed relative to the advancing and receding contact angle.     

An algorithm for the location of transition states

An algorithm for locating transition states designed for use in the ab initio program package GAUSSIAN 82 is presented. It is capable of locating transition states even if started in the wrong region of the energy surface, and, by incorporating the ideas on hessian mode following due to Cerjan and Miller, can locate transition states for alternative rearrangement/dissociation reactions from the same initial starting point. It can also be used to locate minima.     

Scratching the (cell) surface: cytokine engineering for improved ligand/receptor trafficking dynamics

Cytokines can be engineered for greater potency in stimulating cellular functions. An obvious test criterion for an improved cytokine is receptor-binding affinity, but this does not always correlate with improved biological response. By combining protein-engineering techniques with studies of receptor trafficking and signaling, it might be possible to identify the ligand receptor-binding properties that should be sought.     

Symmetry calculation for molecules and transition states

The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three‐dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label‐stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules. © 2014 Wiley Periodicals, Inc.     

Generalized Stone-Wales transformation as the possible origin of ferromagnetism in polymeric C60: a density-functional theory study

Recently, there has been a proposal [Y.-H. Kim et al., Phys. Rev. B 68, 125420 (2003)] suggesting that ferromagnetic interactions in compressed and heated polymeric-C(60) solids could be due to the existence of triplet open cages resulting from successive generalized Stone-Wales transformations within the C(60) cage. Here, by performing B3LYP3-21G and B3LYP6-31G(d) optimizations, we carried out a systematic investigation of the thermodynamics and kinetics of the mechanism of generation of these open cages in their closed-shell singlet, open-shell singlet, and triplet states. We also computed the magnetic interactions induced by the open cages presenting a triplet ground state. Our results indicate that this mechanism is not appropriate to explain the ferromagnetism found in compressed and heated polymeric C(60) for the following reasons: (a) the formation of the only open cage presenting a triplet ground state requires overpassing a highest energy point of 318 kcal/mol, well above other competitive mechanisms reported in the literature; the triplet open cages formed are not stable against their transformation into a diamagnetic intermediate; (c) the magnetic interactions between two adjacent triplet open cages are antiferromagnetic.     

Quantifying growth of symmetric and asymmetric lipid bilayer domains

Here, we examine by atomic force microscopy (AFM) the kinetics and morphology of lipid domain growth during lipid phase separation by rapid thermal cooling of fully mixed two-component supported lipid bilayers. At the undercooled temperatures chosen, symmetric 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC)-rich domains favored slower reaction-limited growth whereas asymmetric galactosylceramide (GalCer)-rich domains favored faster diffusion-limited growth, indicated by shape factors and kinetic exponents. Because kinetically limited conditions could be accessed, we were able to estimate the activation energy barrier (approximately 16kT) and lateral diffusion coefficient (approximately 0.20 microm2/s) of lipid molecular addition to a growing domain. We discuss these results with respect to transition states, obstructed diffusion, and the necessity for coordinating growth in both leaflets in a symmetric lipid domain.     

One-pot synthesis of new symmetric and asymmetric xanthene dyes

Symmetric and asymmetric xanthene dyes have been prepared by a convenient one-step procedure from aldehyde and diol or m-aminophenol precursors using concentrated phosphoric acid as a solvent. This protocol provides access to water-soluble dyes with large Stoke’s shifts and far-red fluorescence emission. These compounds are envisioned as components of fluorescence-based sensors for a variety of imaging applications.     

An improved method for the evaluation of transition states

A simple but efficient coupled iteration procedure is proposed for searching saddle points and extrema along the line of constrained minimum energy paths by (analytical) calculation of the derivatives, i.e., the reduced forces and reduced force constants. The advantage of the method is shown with analytical potentials as well as a calculation of HCH? HNC rearrangement, as working examples.     

Kinetic barriers and ordering of non-covalently bound states

Binding of a dimer of a glycopeptide antibiotic to two molecules of a ligand that are bound to a membrane surface (by a hydrocarbon anchor) has been investigated. This binding on a surface is cooperatively enhanced (surface enhancement) relative to the binding in solution, because the former occurs intramolecularly on a template. Previously a correlation between surface enhancement and thermodynamic stability of the dimer in free solution (Kdimsol) was hypothesised. However, we found that two weakly dimerising antibiotics (vancomycin and ristocetin A) with similar Kdimsol give very different surface enhancements. We propose a model to explain the data correlating surface enhancement to the kinetic barrier to dissociation of the dimer. The surface enhancement of binding can be expected to increase with increasing tightness of the non-covalent interactions formed at the dimer interface. The effect should be found in general where cooperativity is exercised within an organised template (e.g., DNA duplexes and proteins).     

On the calculation of transition states

An algorithm has been developed to calculate transition state geometries directly in the framework of ab initio single-determinant molecular orbital theory. As an example, the procedure is applied to the rearrangement of ethenylidene to acetylene.