Self-diffusion rates in Al from combined first-principles and model-potential calculations

Monovacancy diffusion alone dominates over diffusion due to divacancies and interstitials in Al for all temperatures up to the melting point. Deviations from a single Arrhenius dependence are due to anharmonicity. The conclusion is based on a combination of theoretical methods, from density functional theory to thermodynamic integration, without fitting to experimental data. The calculated diffusion rate agrees with experimental data over 11 orders of magnitude.     

REACTIVITY AND STEREOSELECTIVITY IN THE DIELS-ALDER REACTIONS BETWEEN CYCLOPENTADIENE AND SOME α, β-UNSATURATED THIOESTERS

Abstract

Some new norbornene thioester derivatives of endo configuration are sinthesized. Proofs are provided that thioester group has more preference for endo configuration than the ester group.     

Selective Sulfenylative Desulfonylation or Decarbalkoxylation of α-Sulfonyl Malonates with DABCO or Bu3N: Reactivity and Conformational Analysis

The study on reactivity of several α-substituted α-sulfonyl malonates toward 1,4-diazabicyclo[2.2.2]octane (DABCO) and Bu₃N is described. The reactivity with DABCO revealed the possible competition between decarbalkoxylation and unexpected desulfonylation, depending on the α-substituent, because of sterical hindrance around the electrophilic centers (SO₂ and CO₂R). The derivatives with crowded α-substituents suffer selective desulfonylation, and a novel and efficient desulfonylation method can be proposed. The dependence of the reactivity of α-sulfonyl malonates on the sterical hindrance around the electrophilic centers is confirmed by conformational analysis (Macromodel/MM2? and Mopac/MP3). The carbanionic mechanism is proved because the corresponding protonated, deuterated, and sulfenylated products were obtained by addition of the corresponding electrophilic agents. Bu₃N showed itself to be a novel selective decarbalkoxylation agent for any α-substituted α-sulfonyl malonate.     

Metadynamics in essential coordinates: free energy simulation of conformational changes

We propose an approach that combines an extraction of collective motions of a molecular system with a sampling of its free energy surface. A recently introduced method of metadynamics allows exploration of the free energy surface of a molecular system by means of coarse-grained dynamics with flooding of free energy minima. This free energy surface is defined as a function of a set of collective variables (e.g., interatomic distances, angles, torsions, and others). In this study, essential coordinates determined by essential dynamics (principle component analysis) were used as collective variables in metadynamics. First, dynamics of the model system (explicitly solvated alanine dipeptide, Ace-Ala-Nme) was simulated by a classical molecular dynamics simulation. The trajectory (1 ns) was then analyzed by essential dynamics to obtain essential coordinates. The free energy surface as a function of the first and second essential coordinates was then explored by metadynamics. The resulting free energy surface is in agreement with other studies of this system. We propose that a combination of these two methods (metadynamics and essential dynamics) has great potential in studies of conformational changes in peptides and proteins.     

Determination of hydroxycamptothecin affinities to albumin and membranes by steady-state fluorescence anisotropy measurements

Camptothecin (CPT) and its hydroxycamptothecin analogs are fluorescent compounds exhibiting strong anticancer properties. They exist in two forms: active lactone and inactive carboxylate. The deactivation proceeds via hydrolysis in neutral and base solutions. A serious limitation to the clinical application of CPT is the strong affinity of its carboxylate form to human serum albumin (HSA) which destabilizes its active lactone form. However, binding to membranes in blood improves the stability of the lactone form of CPT and its analogs. A high-throughput screening assay based on the steady-state fluorescence anisotropy method was used to determine the protein- and membrane-binding properties of 10 hydroxycamptothecin (10-OH-CPT), 7-ethyl-10-hydroxycamptothecin (SN-38) and 7-tert-butyldimethylsil-10-hydroxycamptothecin (DB-67). The relative affinities of hydroxycamptothecins to HSA and model membranes in the form of DMPC liposomes were determined, and DB-67 exhibited the most desirable properties including the highest affinity to membranes in its lactone form and low affinity to HSA in its carboxylate form.     

Comparison of SERRS and RRS excitation profiles of [Fe(tpy)2]2+ (tpy = 2,2':6',2'‐terpyridine) supported by DFT calculations: effect of the electrostatic bonding to chloride‐modified Ag nanoparticles on its vibrational and electronic structure

Nonresonance (or normal) Raman scattering (NRS), resonance Raman scattering (RRS), surface‐enhanced Raman scattering (SERS), and surface‐enhanced RRS (SERRS) spectra of [Fe(tpy)₂]²⁺ complex dication (tpy = 2,2':6',2''‐terpyridine) are reported. The comparison of RRS/NRS and SERRS/SERS excitation profiles of [Fe(tpy)₂]²⁺ spectral bands in the range of 445–780 nm is supported by density functional theory (DFT) calculations, Raman depolarization measurements, comparison of the solid [Fe(tpy)₂](SO₄)₂ and solution RRS spectra, and characterization of the Ag nanoparticle (NP) hydrosol/[Fe(tpy)₂]²⁺ SERS/SERRS active system by surface plasmon extinction spectrum and transmission electron microscopy image of the fractal aggregates (D = 1.82). By DFT calculations, both the Raman active modes and the electronic states of the complex have been assigned to the symmetry species of the D_2d point group. It has been demonstrated that upon the electrostatic bonding of the complex dication to the chloride‐modified Ag NPs, the geometric and ground state electronic structure of the complex and the identity of the three different metal‐to‐ligand charge transfer (¹MLCT) electronic transitions remain preserved. On the other hand, the effect of ion pairing manifests itself by a slight change in localization of one of the electronic transitions (with max. at 552 nm) as well as by promotion of the Herzberg–Teller activation of E modes resulting from coupling of E and B₂ excited electronic states. Finally, the very low, 1 × 10⁻¹¹ M SERRS spectral detection limit of [Fe(tpy)₂]²⁺ at 532‐nm excitation is attributed to a concerted action of the electromagnetic and molecular resonance mechanism, in conjunction to the electrostatic bonding of the complex dication to the chloride‐modified Ag NP surface. Copyright © 2014 John Wiley & Sons, Ltd.     

Effect of Two Different UVA Doses on the Rabbit Cornea and Lens

The aim of the present paper was to examine the irradiation effect of two doses of UVA rays (365 nm) on the rabbit cornea and lens. Corneas of anesthetized adult albino rabbits were irradiated with UVA rays for 5 days (daily dose 1.01 J cm⁻² in one group of rabbits and daily dose 2.02 J cm⁻² in the second group of animals). The third day after the last irradiation, the rabbits were killed, and their eyes were employed for spectrophotometrical, biochemical and immunohistochemical investigations. Normal eyes served as controls. Absorption spectra of the whole corneal centers were recorded over the UV–VIS (visible) spectral range. Levels of antioxidant and prooxidant enzymes, nitric oxide synthases and nitric oxide (indirectly measured as nitrate concentration) were investigated in the cornea. Malondialdehyde, a byproduct of lipid peroxidation, was examined in the cornea and lens. The results show that the staining for endothelial nitric oxide synthase was more pronounced in corneas irradiated with the higher UVA dose. Otherwise, UVA rays at either dose did not significantly change corneal light absorption properties and did not cause statistically significant metabolic changes in the cornea or lens. In conclusion, UVA rays at the employed doses did not evoke harmful effects in the cornea or lens.     

Identification of volatile aroma compounds in processed cheese analogues based on different types of fat

The simple and rapid solid-phase micro-extraction method using gas chromatography was used for the identification and quantification of volatile aroma compounds in various types of processed cheese analogues produced from different types of fat (butter, butter oil, coconut oil, palm oil, and sunflower oil). In total, 31 organic compounds belonging to five chemical groups were identified, with the alcohols and fatty acids quantitatively predominant. The contents of the aroma compounds (the so-called aroma profiles) of the analogues and corresponding fats used as raw materials were compared. Significant differences (p < 0.05) were found between samples. The highest total content of aroma compounds was found in coconut oil analogue ((547.30 ± 9.82) mg kg^?1), the lowest in palm oil analogue ((372.01 ± 16.16) mg kg^?1). The concentrations of aroma compounds in fats were substantially lower (p < 0.05) than in analogues. Hence, the largest number of aroma analogues came from Edam cheese used for production as a protein source.