Adiabatic and non-adiabatic electrochemical electron transfer in terms of Green’s function theory

We present a model Hamiltonian for electrochemical electron transfer, and use Green’s functions as the starting point for three different approaches to the calculation of rate constants: first order perturbation theory, which is equivalent to the Levich and Dogonadze theory, the calculation of adiabatic free energy surfaces, and propagation in time. We discuss the similarities and differences between these methods.     

β-Technetium trichloride: formation, structure, and first-principles calculations

A second polymorph of technetium trichloride, β-TcCl(3), has been identified from the reaction between Tc metal and Cl(2) gas. The structure of β-TcCl(3) consists of infinite layers of edge-sharing octahedra, similar to its MoCl(3) and RuCl(3) analogues. The Tc-Tc distance [2.861(3) ?] between adjacent octahedra is indicative of metal-metal bonding. Earlier theoretical work predicted that β-TcCl(3) is less stable than α-TcCl(3). In agreement with the prediction, β-TcCl(3) slowly transforms into α-TcCl(3) (Tc(3)Cl(9)) over 16 days at 280 °C.     

Electronic structure and energy decomposition of binuclear transition metal complexes containing β-diketiminate and imido ligands: spin state and metal’s nature effects

DFT calculations with full geometry optimization using BP86-D and OPBE functionals have been performed on series of [(BDI)M(NH)]₂(Bz) and [(BDI)M(NH)]₂(Tol) (M = Ti, V, Nb, Cr, Mn, Fe, Co, and Ni; BDI = β-diketiminate; NH = imido group; Bz = benzene; and Tol = toluene) of various spin states (singlet S = 0, triplet S = 1, quintet S = 2, and singlet S = 0 of broken symmetry method). Depending on the metal nature and its electron count and the spin state, the six-membered ring in [(BDI)M(NH)]₂(Bz) and [(BDI)M(NH)]₂(Tol) adopts various hapticities that involve full or partial coordination, giving rise to a flat or a distorted ring, respectively. The NH^2? imido group is linear or bent with respect to its sp or sp² hybridization acting as a six- or a four-electron donor, respectively. The (BDI)^? anion is a bidentate ligand as a six-electron donor. The optimized geometries do not show direct metal-metal bonding and correspond to long separations. The optimized structures for Nb metal are comparable to the available experimental ones. The Ziegler-Rauk energy decomposition analysis scheme was employed to characterize the geometry distortion, the steric interaction (electrostatic and Pauli), and the orbital interaction terms in the total bonding energy. The results showed that the interaction terms in all the studied complexes are governed by one third covalent and two thirds ionic characters, which are in agreement with the ΔE_elstat (electrostatic) and ΔE_orb (orbital) contributions, respectively, into the total attractive interaction (ΔE_elstat + ΔE_orb).     

Linear augmented cylindrical wave Green’s function method for perfect nanotubes and nanotubes with regular and point impurities

Nanotubes are giant cage molecules looking like closed hollow cylindrical shells. This review deals with basic principles of the linear augmented cylindrical Green’s function method and its applications to calculation of the electronic structure of perfect nanotubes and those containing substitutional impurities. A major argument for using cylindrical waves to describe nanotubes is that such a choice of the basis set makes it possible to explicitly consider the actual cylindrical geometry of nanotubes, which, in particular, ensures rapid convergence of iterative procedures. A computation technique has been described and the results of calculations of the band structure and densities of states of carbon and boron nitride nanotubes have been reported. Special attention has been paid to the changes in the electronic properties of nanotubes induced by the substitution of nitrogen, boron, or oxygen for C atoms in the carbon nanotubes, as well as to the isoelectronic substitution of P, Sb, or As for the nitrogen and of Al, In, or Ga for the boron in boron nitride nanotubes.     

Cassis and Green Tea: Spontaneous Release of Natural Aroma Compounds from β-Alkylthioalkanones

In depth headspace analysis of the slow degradation of β-alkylthioalkanones in ambient air led to the discovery of a novel δ-cleavage pathway, by which β-mercaptoketones are released. Since β-mercaptoketones are potent natural aroma compounds occurring in many fruits, herbs and flowers, the discovery of an enzyme-independent molecular precursor for this class of high-impact molecules is of practical importance. Moreover, the formation of β-diketones and aldehydes by concomitant oxidation at the α-sulfur-position enhances the versatility of this class of aroma precursors. A mechanistic model is proposed which suggests that the oxidative degradation occurs through a novel Pummerer-type rearrangement of initially formed persulfoxides.     

A mathematical approach to chemical equilibrium theory for gaseous systems—II: extensions and applications

Straightforward mathematical techniques are used innovatively to form a coherent theoretical system to deal with chemical equilibrium problems. For a systematic theory it is necessary to establish a system to connect different concepts. This paper shows the usefulness and consistence of the system by applications of the theorems introduced previously. Some theorems are shown somewhat unexpectedly to be mathematically correlated and relationships are obtained in a coherent manner. It has been shown that theorem 1 plays an important part in interconnecting most of the theorems. The usefulness of theorem 2 is illustrated by proving it to be consistent with theorem 3. A set of uniform mathematical expressions are associated with theorem 3. A variety of mathematical techniques based on theorems 1–3 are shown to establish the direction of equilibrium shift. The equilibrium properties expressed in initial and equilibrium conditions are shown to be connected via theorem 5. Theorem 6 is connected with theorem 4 through the mathematical representation of theorem 1.     

Wilhelm Ostwald’s energetics 3: energetic theory and applications,part II

This is the third of a series of essays on the development and reception of Wilhelm Ostwald’s energetics. The first essay described the chemical origins of Ostwald’s interest in the energy concept and his motivations for seeking a comprehensive science of energy. The second essay and the present one discuss his various attempts, beginning in 1891 and extending over almost 3 years, to develop a consistent and coherent energetic theory. A final essay will consider reactions to this work and Ostwald’s replies, and will also seek to evaluate his program of research. Ostwald’s project—to reconstruct physics and chemistry “as a pure energetics”—is worth attending to for several reasons: first, because Ostwald did ground-breaking work in chemistry (he was awarded a Nobel Prize in 1909 for his studies in catalysis and rates of reaction); second, because an important school of physical chemistry formed around him at Leipzig, a school that promoted his ideas; and, finally, because he was a prominent and vigorous participant in debates at the end of the nineteenth century concerning the proper course of physical theory.

Demystifying the pH dependent conformational changes of human heparanase pertaining to structure–function relationships: an in silico approach

Heparanase (HPSE) is an endo-β-d-glucuronidase that has diverse functions in mammals which includes cell survival, cell adhesion and cell migration. HPSE features both enzymatic and non-enzymatic functionalities in a pH dependent manner. Hence, in this study, an extensive molecular dynamics simulation, molecular docking, protein Angular dispersion analysis were performed for apo form and holo forms to understand its conformational changes at varied pH conditions. On comparative conformational analysis of apo and holo forms, it was inferred that the HSPE has undergone pH dependent structural changes, thereby affecting the binding of Heparan sulfate proteoglycan (HSPG). Moreover, HPSE also showed favourable structural changes for optimal binding of HSPG at pH 5.0 and 6.0, as inferred from functional flap displacements within HPSE. Thus, this study provides significant insights on optimal pH for HPSE to exhibit its enzymatic activity. The outcome of this study shall aid in ideal lead generation for targeting HPSE mediated disease conditions.     

Effects of fabrication conditions on the structure and function of membranes formed from poly(acrylonitrile–vinylchloride)

Phase-inversion membranes formed from poly(acrylonitril–co-vinylchloride) (PAN–PVC) have been utilized for encapsulating living cells for transplantation; however, a detailed analysis of the structure and function of the integral skin layer has not been reported. PAN–PVC membranes fabricated under different precipitation conditions were analyzed using microscopic techniques and several functional tests. Structural analysis with scanning atomic force microscopy (AFM) revealed the presence of nodular elements in the skin layer which changed as a function of precipitation conditions. In addition, membrane hydraulic permeabilities, sieving coefficients, and diffusive permeabilities also varied with precipitation conditions. Furthermore, changes in the functional properties could be related to the size of the nodular elements and their accompanying interstitial space. The results provide insight into the fundamental interrelationships that exist between membrane fabrication, the fine surface morphology of the skin layer, and membrane performance.     

Graphane/fluorographene bilayer: considerable C-H···F-C hydrogen bonding and effective band structure engineering

Systematic density functional theory (DFT) computations revealed the existence of considerable C-H···F-C bonding between the experimentally realized graphane and fluorographene layers. The unique C-H···F-C bonds define the conformation of graphane/fluorographene (G/FG) bilayer and contribute to its stability. Interestingly, G/FG bilayer has an energy gap (0.5 eV) much lower than those of individual graphane and fluorographene. The binding strength of G/FG bilayer can be significantly enhanced by applying appropriate external electric field (E-field). Especially, changing the direction and strength of E-field can effectively modulate the energy gap of G/FG bilayer, and correspondingly causes a semiconductor-metal transition. These findings open new opportunities in fabricating new electronics and opto-electronics devices based on G/FG bilayer, and call for more efforts in using weak interactions for band structure engineering.     

Fourth-order nematic elasticity and modulated nematic phases: a poor man’s approach

We propose an extension of Frank-Oseen’s elastic energy for bulk nematic liquid crystals which is based on the hypothesis that the fundamental deformations allowed in nematic liquid crystals are splay, twist and bend. The extended elastic energy is a fourth-order form in the fundamental deformations. The existence of bulk spontaneous modulated or deformed nematic liquid crystal ground states is investigated. The analysis is limited to bulk nematic liquid crystals in the absence of limiting surfaces and/or external fields. The non deformed ground state is stable only when Frank-Oseen’s elastic constants are positive. In case where at least one of them is negative, the ground state becomes deformed. The analysis of the stability of the deformed states in the space of the elastic parameters allows to characterise different types of deformed nematic phases. Some of them are new nematic phases, for instance a twist – splay nematic phase is predicted. Inequalities between second-order elastic constants which govern the stability of the twist–bend, splay–bend, and splay–twist states are obtained. Their stability in respect to triple splay–bend–twist deformations is investigated.     

Density functional theory study on quasi-three-dimensional oxidized platinum surface: phase transition between ��-PtO2-like and ��-PtO2-like structures

We investigate the oxidation process of a platinum surface by using the density functional theory approach under the periodic boundary condition. This oxidation process has received much attention because it is an initial step in the dissolution of platinum catalysts in polymer electrolyte fuel cells. In this research, we determine the optimized structure of ?? -PtO₂-like and ??-PtO₂-like oxidized platinum surfaces, which have recently been proposed on the basis of in situ X-ray diffraction analysis, at the Kohn Sham density functional theory (KS-DFT) generalized gradient approximation (GGA) level of theory. We discuss the phase transition from the ??-PtO₂-like surface to the ??-PtO₂-like surface, including the place-exchange reaction between oxygen and platinum atoms. We propose an intermediate structure in the phase transition, and show that the ??-PtO₂-like structure can be formed directly from this intermediate structure.     

Mössbauer quadrupole splittings and electronic structure in heme proteins and model systems: a density functional theory investigation

We report the results of a series of density functional theory (DFT) calculations aimed at predicting the (57)Fe M?ssbauer electric field gradient (EFG) tensors (quadrupole splittings and asymmetry parameters) and their orientations in S = 0, (1)/(2), 1, (3)/(2), 2, and (5)/(2) metalloproteins and/or model systems. Excellent results were found by using a Wachter's all electron basis set for iron, 6-311G for other heavy atoms, and 6-31G for hydrogen atoms, BPW91 and B3LYP exchange-correlation functionals, and spin-unrestricted methods for the paramagnetic systems. For the theory versus experiment correlation, we found R(2) = 0.975, slope = 0.99, intercept = -0.08 mm sec(-)(1), rmsd = 0.30 mm sec(-)(1) (N = 23 points) covering a DeltaE(Q) range of 5.63 mm s(-)(1) when using the BPW91 functional and R(2) = 0.978, slope = 1.12, intercept = -0.26 mm sec(-)(1), rmsd = 0.31 mm sec(-)(1) when using the B3LYP functional. DeltaE(Q) values in the following systems were successfully predicted: (1) ferric low-spin (S = (1)/(2)) systems, including one iron porphyrin with the usual (d(xy))(2)(d(xz)d(yz))(3) electronic configuration and two iron porphyrins with the more unusual (d(xz)d(yz))(4)(d(xy))(1) electronic configuration; (2) ferrous NO-heme model compounds (S = (1)/(2)); (3) ferrous intermediate spin (S = 1) tetraphenylporphinato iron(II); (4) a ferric intermediate spin (S = (3)/(2)) iron porphyrin; (5) ferrous high-spin (S = 2) deoxymyoglobin and deoxyhemoglobin; and (6) ferric high spin (S = (5)/(2)) metmyoglobin plus two five-coordinate and one six-coordinate iron porphyrins. In addition, seven diamagnetic (S = 0, d(6) and d(8)) systems studied previously were reinvestigated using the same functionals and basis set scheme as used for the paramagnetic systems. All computed asymmetry parameters were found to be in good agreement with the available experimental data as were the electric field gradient tensor orientations. In addition, we investigated the electronic structures of several systems, including the (d(xy))(2)(d(xz),d(yz))(3) and (d(xz),d(yz))(4)(d(xy))(1) [Fe(III)/porphyrinate](+) cations as well as the NO adduct of Fe(II)(octaethylporphinate), where interesting information on the spin density distributions can be readily obtained from the computed wave functions.     

Electronic structure and stability of anionic AuGen (n = 1–20) clusters and assemblies: a density functional modeling

Structural Chemistry - In the present study electronic structure and stabilities of cationic gold-doped germanium clusters, AuGen (n?=?1 to 20), and their assemblies have been...     

Composites based on polyurethane–urea and ground rubber from car tyres: relation between structure and properties

The basis of this work is an investigation of multicomponent systems containing a reactive polyurethane–urea matrix, recycled rubber filler, and porosity. Rubber crumb with varying particle sizes obtained from used car tyres was used as the filler. As a matrix, water-curable isocyanate pre-polymer was used. Porosity was caused by the inability of the matrix to fully fill space between rubber particles, combined with foaming from matrix curing. We report on dependences of PUU/rubber system mechanical properties on the composition and structural parameters. Mechanical property values were obtained via tensile loading of prepared rectangular slabs. We found that mechanical behaviour exhibits strong correlation with a structural parameter called interspace filling, which expresses how much the matrix fills space between filler particles. Interspace filling is dependent on the degree of porosity and the volume fraction of the PUU matrix in a hypothetical nonporous material. Therefore, this work offers a simple characterization of complex materials, of which the studied porous composite is an example. Our results could contribute to the development of applications for large volumes of recycled rubber in materials used in rapid repair of roads and pavements.     

Use of γ-irradiation to produce films from whey,casein and soya proteins: structure and functionals characteristics

γ-irradiation and thermal treatments have been used to produce sterilized cross-linked films. Formulations containing variable concentrations of calcium caseinate and whey proteins (whey protein isolate (WPI) and commercial whey protein concentrate) or mixture of soya protein isolate (SPI) with WPI was investigated on the physico-chemical properties of these films. Results showed that the mechanical properties of cross-linked films improved significantly the puncture strength for all types of films. Size-exclusion chromatography showed for no cross-linked proteins, a molecular mass of around 40 kDa. The soluble fractions of the cross-linked proteins molecular distributions were between 600 and 3800 kDa. γ-irradiation seems to modify to a certain extent the conformation of proteins which will adopt structures more ordered and more stable, as suggested by X-ray diffraction analysis. Microstructure observations showed that the mechanical characteristics of these films are closely related to their microscopic structure. Water vapor permeability of films based on SPI was also significantly decreased when irradiated. Microbial resistance was also evaluated for cross-linked films. Results showed that the level of biodegradation of cross-linked films was 36% after 60 d of fermentation in the presence of Pseudomonas aeruginosa.     

Why are time-dependent density functional theory excitations in solids equal to band structure energy gaps for semilocal functionals, and how does nonlocal Hartree-Fock-type exchange introduce excitonic effects?

We examine the time-dependent density functional theory (TD-DFT) equations for calculating excitation energies in solids with Gaussian orbitals and analytically show that for semilocal functionals, their lowest eigenvalue collapses to the minimum band orbital energy difference. With the introduction of nonlocal Hartree-Fock-type exchange (as in hybrid functionals), this result is no longer valid, and the lowest TD-DFT eigenvalue reflects the appearance of excitonic effects. Previously reported "charge-transfer" problems with semilocal TD-DFT excitations in molecules can be deduced from our analysis by taking the limit to infinite lattice constant.     

Directing the secondary structure of polypeptides at will: from helices to amyloids and back again?

An ageing society faces an increasing number of neurodegenerative diseases such as Alzheimer's, Parkinson's, and Creutzfeld-Jacob disease. The deposition of amyloid fibrils is a pathogenic factor causing the destruction of neuronal tissue. Amyloid-forming proteins are mainly alpha-helical in their native conformation, but undergo an alpha-helix to beta-strand conversion before or during fibril formation. Partially unfolded or misfolded beta-sheet fragments are discussed as direct precursors of amyloids. To potentially cure neurodegenerative diseases we need to understand the complex folding mechanisms that shift the equilibrium from the functional to the pathological isoform of the proteins involved. This paper describes a novel approach that allows us to study the interplay between peptide primary structure and environmental conditions for peptide and protein folding in its whole complexity on a molecular level. This de novo designed peptide system may achieve selective inhibition of fibril formation.     

Multi-technique surface characterization of bio-based films from sisal cellulose and its esters: a FE-SEM, μ-XPS and ToF-SIMS approach

Bio-based films were prepared from LiCl/DMAc solutions containing sisal cellulose esters (acetates, butyrates and hexanoates) with different degrees of substitution (DS 0.7–1.8) and solutions prepared with the cellulose esters and 20 wt% sisal cellulose. A novel approach for characterizing the surface morphology utilized field emission scanning electron microscopy (FE-SEM), X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS) and contact angle analysis. XPS and ToF-SIMS were a powerful combination while investigating both the ester group distribution on the surface and effects of cellulose content on the film. The surface coverage by ester aliphatic chains was estimated using XPS measurements. Fibrous structures were observed in the FE-SEM images of the cellulose and bio-based films, most likely because the sisal cellulose chains aggregated during dissolution in LiCl/DMAc. Therefore, the cellulose aggregates remained after the formation of the films and removal of the solvent. The XPS results indicated that the cellulose loading on the longer chain cellulose esters films (DS 1.8) increased the surface coverage by ester aliphatic chains (8.2 % for butyrate and 45 % for hexanoate). However, for the shortest ester chains, the surface coverage decreased (acetate, 42 %). The ToF-SIMS analyses of cellulose acetate and cellulose hexanoate films (DS 1.8) revealed that the cellulose ester groups were evenly distributed across the surface of the films.