First principles study of the structure, electronic state and stability of cations

Structural and electronic properties of semiconductor binary microclusters cations have been investigated using the B3LYP-DFT method in the ranges of n=1, 2 and m=1–7. Full structural optimization, adiabatic ionization potentials calculation and frequency analysis are performed with the basis of 6-311+G(d). The charged-induced structural changes in these cations have been discussed. The strong As–As bond is also favored over Al–As bonds in the cations in comparison with corresponding neutral cluster. With As_m forming the base, adding Al atom(s) in different positions would find the stable structures of cations quickly and correctly. , , and are predicted to be species with high stabilities and possible to be produced experimentally.     

Photoinduced multi-mode quantum dynamics of pyrrole at the – conical intersections

The photoinduced dynamics of pyrrole at the – S₀ and – S₀ conical intersections has been investigated by multi-mode time-dependent quantum wave-packet calculations. Diabatic potential-energy surfaces have been constructed for both conical intersection using accurate multi-reference ab initio electronic-structure calculations. In addition to the NH stretching coordinate, the three (four) symmetry-allowed coupling modes of A₂ (B₁) symmetry have been considered for the – S₀ (– S₀) conical intersections. Wave-packet dynamics calculations have been performed for three-dimensional models, taking account of the two dominant coupling modes of each conical intersection. The electronic population-transfer processes at the conical intersections, the branching ratio for the dissociation to the ground and excited states of the pyrrolyl radical, and their dependence on the initial preparation of the system have been investigated. It is shown that the excitation of the NH stretching mode strongly enhances the photodissociation rate, while the excitation of the strongest coupling mode has a pronounced effect on the branching ratio of the photodissociation process. Although the inclusion of the second (weaker) coupling mode has little effect on the electronic population dynamics, it leads to interesting changes of the nodal pattern of the wave packet at the conical intersections. The calculations provide insight into the effect of the multiple coupling modes on the process of direct photodissociation through a conical intersection.     

DFT study of the structure of hydroxybenzoic acids and their reactions with OH and radicals

B3LYP/6-31++G(d) method was used for the structural study of 3,4,5-trihydroxybenzoic acid (3,4,5-THBA), 3,4-dihydroxybenzoic acid (3,4-DHBA), and 4-hydroxybenzoic acid (4-HBA). Calculated structures agree with available X-ray experimental data within 2%. The phenolic OH bond dissociation enthalpy (BDE) of all sites in each benzoic acid were determined and compared with those of phenol (for 4-HBA) and catechol (for 3,4-DHBA). The consistency between the calculated values and experimental ones are within 5.4% and 9.2%, respectively, for 4-HBA and 3,4-DHBA. The reactions of benzoic acids with and OH radicals were studied and it turns out that benzoic acids react differently with both radicals. We have shown that the reaction of hydroxybenzoic acids with the hydroxyl radical was governed by a phenolic hydrogen (H⁺ + e⁻) transfer from the acid to the radical, while for the superoxide radical, the reaction is governed by a proton (H⁺) transfer from the acid to the radical. The first reaction is evidenced by the delocalization of the radical on the entire quinone moiety, and the second reaction is evidenced by the negative NBO charge on the phenoxide moiety as well as the localization of the radical on the hydroperoxy (O₂H) moiety.     

A DFT study of the hydration of monophosphate complexes of iron (III),

A systematic theoretical DFT study of the bonding between the cation Fe³⁺ and the anion was carried out. The role of water ligands is presented. Several isomers with tetrahedral, bipyramidal and octahedral environments around the iron ion were investigated. 5-fold coordination of the Fe³⁺ cation is found when 5 and 6 water molecules are included. Calculated infrared spectra are also presented.     

DFT study and IR spectra of hexaphenoxycyclotriphosphazene generation phosphorus dendrimer

The infrared (150–3500 cm⁻¹) spectra have been recorded for hexaphenoxycyclotriphosphazene [NP(OPh)₂]₃ and all-D isotope specie. These compounds include a cyclotriphosphazene core and terminal phenoxy groups of elementoorganic dendrimers. The structural optimization and normal mode analysis are performed for elementoorganic dendrimer on the basis of the ab initio density functional theory. It is found that the dendrimer exists in a single stable conformation with slightly non-planar cyclotriphosphazene core. Relying on DFT calculations a complete vibrational assignment is proposed for different parts of the studied dendrimers. The softness of sulphur atom in the thiophosphoryl core to nucleophilic attack is higher than the softness of the atoms of the cyclotriphosphazene core. The reactivity of the core is less than that of terminal groups.     

Unique charge ordering of manganese in a new mixed valent phosphate

A new mixed-valent manganese phosphate, , has been synthesized using hydrothermal method. Its monoclinic C2/c structure (a=12.5506(16) Å, b=10.4816(18) Å, c=13.6723(10) Å, β=103.758(11)°) forms a 3D framework of MnO₆ octahedra, MnO₅ trigonal bipyramids, PO₄ and PO₃OH tetrahedra. The main structural feature of this phosphate deals with its [Mn₄O₁₆]_∞ chains running along , which are interconnected through PO₄ and PO₃OH tetrahedra, forming intersecting tunnels running along [110], and [001]. The geometry of the [Mn₄O₁₆]_∞ chains and the charge ordering of manganese in the latter are unique: they consist of trimeric units of divalent manganese “” alternating with single trivalent Mn^IIIO₆ octahedra along . In each “” unit one central Mn^IIO₆ octahedron shares two opposite edges with two Mn^IIO₅ trigonal bipyramids. Along , one Mn(II) octahedron alternates with one Mn(III) octahedron by sharing one corner. The relationships between the structure of this unique charge ordered phosphate and other manganese phosphates are discussed.     

Electroreduction of anions on chemically etched and electrochemically polished Bi(1 1 1) electrode

Electroreduction kinetics of to anions at chemically etched (CHE) and electrochemically polished (EP) Bi(1 1 1) electrodes has been studied using rotating disc electrode method. The surface nanostructure of CHE Bi(1 1 1) and EP Bi(1 1 1) electrodes has been studied by in situ STM and the very different values of root mean squared roughness (Rms) have been obtained (1000 times higher for CHE Bi(1 1 1) (Rms  143 nm) than for EP Bi(1 1 1) (Rms  0.145 nm)). The influence of the nanoroughness of CHE Bi(1 1 1) on the current density, heterogeneous reaction rate constant and corrected Tafel plots (cTp) has been demonstrated. For CHE Bi(1 1 1) the more pronounced inhibition of electroreduction reaction at moderate negative surface charge density has been observed in comparison with EP Bi(1 1 1), caused by the differences in surface charge density and also in diffuse layer ψ₀ potential drop values at crystallographically different homogeneous regions (planes) exposed at the surface of the macroheterogeneous polycrystalline CHE Bi(1 1 1) surface. The very low apparent transfer coefficient α_app obtained indicates the nearly activationless charge transfer mechanism for electroreduction at the CHE Bi(1 1 1) electrode similarly to EP Bi(1 1 1). However, α_app only very weakly depends on Rms for the Bi electrodes at high negative surface charge densities where the values of ψ₀ potential are nearly equal for different planes at fixed electrode potential. At very high negative surface charge densities the cationic catalysis through the adsorbed ion pairs is possible.     

Fluorinated stannanes : Part 1. The stereospecific synthesis of fluorinated stannanes via a novel transmetalation of fluorinated zinc and cadmium reagents

Fluorinated stannanes are versatile synthetic intermediates. Reaction of fluorinated vinyl, alkyl and aryl zinc or cadmium reagents with tri-n-butyltin chloride at room temperature yielded the corresponding tri-n-butyl stannanes in moderate to excellent yields. The zinc or cadmium reagents also reacted efficiently with other trialkyl and triaryl chlorostannanes. These zinc and cadmium reagents were prepared in excellent yields by stirring the fluorinated halides with activated zinc or cadmium metal.     

Novel synthesis of 5-thio-hexopyranoside: preparation of 5-thio-d- and l-glucose and 1,6-anhydro-5-thio-l- and d-altrose

Asymmetric synthesis of both d- and l-isomers of 5-thioglucose and 1,6-anhydro-5-thioaltrose are described. The key intermediates, l- and d-threose diethylacetal derivatives, were derived by chemical transformation from d-xylose or d-arabinose and by Sharpless asymmetric dihydroxylation from γ-hydroxycrotylaldehyde diethylacetal. They transformed to γ-thiiranyl diethylacetal via trans-2,3-epoxy alcohol in seven steps. Acetic acid-promoted cyclization of γ-thiiranyl diethylacetal gave 5-thiopyranoside. Removal of the protected groups under the acidic conditions afforded 5-thio-d- and l-glucose and 1,6-anhydro-5-thio-l- and d-altrose, respectively.     

Racemization behavior of l,l-lactide during heating

To control the depolymerization process of poly(l-lactic acid) into l,l-lactide for feedstock recycling, the racemization of l,l-lactide as a post-depolymerization reaction was investigated. In the absence of a catalyst, the conversion to meso-lactide increased with increase in the heating temperature and time at a higher rate than the conversion into oligomers. The resulting high composition of meso-lactide suggests that the direct racemization of l,l-lactide had occurred in addition to the known racemization mechanism that occurs on the oligomer chains. In the presence of MgO, the oligomerization rapidly proceeded to reach an equilibrium state between monomers and oligomers. The equilibrium among l,l-, meso-, and d,d-lactides was found to be a convergent composition ratio l,l-:meso-:d,d-lactides = 1:1.22:0.99 (wt/wt/wt) after 120 min at 300 °C. This composition ratio also indicates that in addition to the known racemization reaction on the oligomer chains, direct racemization among the lactides is also a frequent occurrence.     

Improved synthesis of 6-amino-6-deoxy-d-galactono-1,6-lactam and d-mannono-1,6-lactam from corresponding unprotected d-hexono-1,4-lactones

Regioselective bromination of unprotected d-galactono-1,4-lactone and d-mannono-1,4-lactone with PPh₃/CBr₄ led to 6-bromo-6-deoxy derivatives. These intermediates were treated with LiN₃ and hydrogenated to give 6-amino-6-deoxy-d-galactono-1,6-lactam (8) and 6-amino-6-deoxy-d-mannono-1,6-lactam (13) in 74 and 67% overall yield, respectively.     

New building blocks for peptide and depsipeptide synthesis: hexafluoroacetone protected l-homoisoserine and d,l-homoisocysteine derivatives

Efficient syntheses of l-homoisoserine and d,l-homoisocysteine derivatives starting from l-malic and d,l-thiomalic acid using hexafluoroacetone as protecting and activating agent are described. The new compounds are interesting building blocks for the preparation of non-natural peptides and depsipeptides as well as for the construction of new GABA derivatives.     

One-pot inversion of d-mannono-1,4-lactone for the practical synthesis of l-ribose

l-Ribose was synthesized in a concise manner from d-mannono-1,4-lactone using one-pot inversion conditions. Treatment of d-mannono-1,4-lactone with piperidine, followed by mesylation-induced S_N2-type O-alkylation, afforded the desired one-pot inversion in an optimum yield, and the following straightforward transformations provided l-ribose in good yields.     

Amperometric simultaneous sensing system for d-glucose and l-lactate based on enzyme-modified bilayer electrodes

An amperometric biosensor system which uses screen-printed electrodes to simultaneously detect d-glucose and l-lactate has been developed and applied for simple and rapid determination of d-glucose and l-lactate levels in lactic fermenting beverages. The system was constructed from three-dimensionally layered electrodes. Taking into consideration the effects of easily oxidized substances contained in the samples, ferricyanide ions, which are electrochemically oxidized at a lower voltage, were chosen as a mediator. A linear relationship between steady-state current and concentration was found over a range of 1-100 mM (d-glucose) and 1-50 mM (l-lactate); the variation coefficients were 1.43% (n = 10) and 3.50% (n = 10) for the d-glucose and l-lactate sensors, respectively. When applied to lactic fermenting beverages, there was good agreement between the results obtained by the proposed sensing system and those obtained by the HPLC method. Using the proposed method, assays were completed within 5 min.     

Crystallization in ultra-thin polymer films: Morphogenesis and thermodynamical aspects

We present a computer model for polymer crystallization in ultra-thin films where chains are considered as dynamical units. In our model chains can change their internal state of order by cooperative motions to improve thermodynamic stability. The interplay between reorganization, enthalpic interactions and the morphology of crystals enables us to explain many properties of growth, morphogenesis and melting of polymer lamellae. We emphasize the relation between the thermodynamic stability of non-equilibrium crystals and morphological features which are beyond the average thickness of the lamellae. In particular, we show that melting of polymers is preceded by reorganization processes and the stability of polymer crystals is not necessarily related to the structure formed at the crystallization point. The simulations allow for the determination of some non-equilibrium properties such as the internal energy and the non-equilibrium heat capacity. We show that multiple-peak melting endotherms result from morphological transformations. The results of our computer simulations are compared with AFM observations in ultra-thin polyethyleneoxide films.     

Selection of synthetic receptors capable of sensing the difference in binding of d-Ala-d-Ala or d-Ala-d-Lac ligands by screening of a combinatorial CTV-based library

Screening of a combinatorial CTV-based artificial, synthetic receptor library 1 {1-13, 1-13, 1-13} for binding of a variety d-Ala-d-Ala and d-Ala-d-Lac containing ligands (6-11) was carried out in phosphate buffer (0.1 N, pH=7.0). After screening and Edman sequencing, synthetic receptors were found containing amino acid sequences, which are either characteristic for binding dye labeled d-Ala-d-Ala or d-Ala-d-Lac containing ligands. For example, receptors capable of binding d-Ala-d-Ala containing ligands 6, 7, 9 and 11 contained—almost in all cases—at least one basic amino acid residue—predominantly Lys—in their arms. This was really a striking difference with the arms of the receptors capable of binding d-Ala-d-Lac containing ligands 8 and 10, which usually contained a significant number of polar amino acids (Gln and Ser), especially in ligand 8, but hardly any basic amino acids. Use of different (fluorescent) dye labels showed that the label has a profound, albeit not decisive, influence on the binding by the receptor. A hit from the screening of the CTV-library with FITC-peptidoglycan (6) was selected for resynthesis and validation.     

beta-Barrel transmembrane proteins: Geometric modelling, detection of transmembrane region, and structural properties

The location of the membrane lipid bilayer relative to a transmembrane protein structure is important in protein engineering. Since it is not present on the determined structures, it is essential to automatically define the membrane embedded protein region in order to test mutation effects or to design potential drugs. beta-Barrel transmembrane proteins, present in nature as outer membrane proteins (OMPs), comprise one of the two transmembrane protein fold classes. Lately, the number of their determined structures has increased and this enables the implementation and evaluation of structure-based annotation methods and their more comprehensive study. In this paper, we propose two new algorithms for (i) the geometric modelling of beta-barrels and (ii) the detection of the transmembrane region of a beta-barrel transmembrane protein. The geometric modelling algorithm combines a non-linear least square minimization method and a genetic algorithm in order to find the characteristics (axis, radius) of a shape with axial symmetry which best models a beta-barrel. The transmembrane region is detected by profiling the external residues of the beta-barrel along its axis in terms of hydrophobicity and existence of aromatic and charged residues. TbB-Tool implements these algorithms and is available in . A non-redundant set of 22 OMPs is used in order to evaluate the algorithms implemented and the results are very satisfying. In addition, we quantify the abundance of all amino acids and the average hydrophobicity for external and internal beta-stranded residues along the axis of beta-barrel, thus confirming and extending other researchers' results.