Experimental and theoretical studies on the reactions of 1-amino-5-benzoyl-4-phenyl-1<Emphasis Type="Italic">H</Emphasis>-pyrimidine-2-one/-thione compounds with ethyl acetoacetate

The reaction of 1-amino-5-(4-methylbenzoyl)-4-(4-methylphenyl)pyrimidin-2(1H)-one/-thione (1a,b) with ethyl acetoacetate (EA) afforded moderate to good yields (59–63%) of ethyl 2-methyl-4-(4-methylbenzoyl)-5-(4-methylphenyl)-7-oxo/-thioxo-3,3a-dihydropyrazolo[1,5-c]pyrimidine-3-carboxylate (2a,b). The newly synthesized compounds were characterized by elemental analyses, IR, ¹H and ¹³C NMR spectral data. All were compared with their previous analogues. The reaction mechanism of 1 with EA was studied by means of the B3LYP/6-31G(d,p) method. In addition, for reactants Fukui functions were performed using the data calculated with the Becke3–Lee–Yang–Parr (B3LYP) hybrid function.     

Coupling between lysozyme and trehalose dynamics: microscopic insights from molecular-dynamics simulations

We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems.     

Molecular Simulation of Fibronectin Adsorption onto Polyurethane Surfaces

Poly(ethylene glycol)-based polyurethanes have been widely used in biomedical applications; however, they are prone to swelling. A natural polyol, castor oil, can be incorporated into these polyurethanes to control the degree of the swelling, which alters mechanical properties and protein adsorption characteristic of the polymers. In this work, we modeled poly(ethylene glycol) and castor oil copolymers of hexamethylene diisocyanate-based polyurethanes (PEG-HDI and CO-HDI, respectively) and compared their mechanisms for fibronectin adsorption using molecular mechanics and molecular dynamics simulations. Results showed that the interplay between the hydrophobic residues concentrated at the N-terminal end of the protein, the surface roughness, and the hydrophilicity of the polymer surface determine the overall protein adsorption affinity. Incorporating explicit water molecules in the simulations results in higher affinity for fibronectin adsorption to more hydrophobic surface of CO-HDI surfaces, emphasizing the role that water molecules play during adsorption. We also observed that the strain energies that are indicative of flexibility and consequently entropy are significantly affected by the changes in the patterns of β-sheet formation/breaking. Our study lends supports to the view that while castor oil controls the degree of swelling, it increases the adsorption of fibronectin to a limited extent due to the interplay between its hydrophobicity and its surface roughness, which needs to be taken into account during the design of polyurethane-based biomaterials.     

Frustrated magnetic interactions,giant magneto–elastic coupling,and magnetic phonons in iron–pnictides

We present a detailed first-principles study of Fe-pnictides with particular emphasis on competing magnetic interactions, structural phase transition, giant magneto–elastic coupling and its effect on phonons. The exchange interactions J_i,j(R) are calculated up to ≈12 Å from two different approaches based on direct spin-flip and infinitesimal spin-rotation. We find that J_i,j(R) has an oscillatory character with an envelop decaying as 1/R³ along the stripe-direction while it is very short range along the diagonal direction and antiferromagnetic. A brief discussion of the neutron scattering determination of these exchange constants from a single crystal sample with orthorhombic-twinning is given. The lattice parameter dependence of the exchange constants, dJ_i,j/da are calculated for a simple spin-Peierls like model to explain the fine details of the tetragonal–orthorhombic phase transition. We then discuss giant magneto–elastic effects in these systems. We show that when the Fe-spin is turned off the optimized c-values are shorter than experimental values by 1.4 Å for CaFe₂As₂, by 0.4 Å for BaFe₂As₂, and by 0.13 Å for LaOFeAs. We explain this strange behavior by unraveling surprisingly strong interactions between arsenic ions, the strength of which is controlled by the Fe-spin state through Fe–As hybridization. Reducing the Fe-magnetic moment, weakens the Fe–As bonding, and in turn, increases As–As interactions, causing a giant reduction in the c-axis. These findings also explain why the Fe-moment is so tightly coupled to the As-z position. Finally, we show that Fe-spin is also required to obtain the right phonon energies, in particular As c-polarized and Fe–Fe in-plane modes that have been recently observed by inelastic X-ray and neutron scattering but cannot be explained based on non-magnetic phonon calculations. Since treating iron as magnetic ion always gives much better results than non-magnetic ones and since there is no large c-axis reduction during the normal to superconducting phase transition, the iron magnetic moment should be present in Fe-pnictides at all times. We discuss the implications of our results on the mechanism of superconductivity in these fascinating Fe-pnictide systems.     

DFT, FT-Raman and FT-IR investigations of 5-o-tolyl-2-pentene

FT-IR and Raman spectra of 5-o-tolyl-2-pentene (OTP) have been experimentally reported in the region of 4000-10 cm(-1) and 4000-100 cm(-1), respectively. The optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of cis and trans isomers of OTP (C12H16) have been theoretically examined by means of B3LYP hybrid density functional theory (DFT) method together with 6-31G(d) and 6-31++G(d,p) basis sets. Furthermore, reliable vibrational assignments have made on the basis of potential energy distribution (PED) calculated. Comparison between the experimental and theoretical results indicates that density functional B3LYP method is able to provide satisfactory results for predicting vibrational wavenumbers and trans isomer is supposed to be the most stable form of OTP molecule.     

Synthesis, electrochemical and structural characterization of novel azacrown ether containing macrocyclic redox-active vic-dioxime ligand and its mononuclear transition metal complexes: Application of DEPT, HSQC, HMBC-NMR and cyclic voltammetry

This paper presents a new azacrown containing vic-dioxime; anti-N-(4-aminophenyl)aza-15-crown-5-glyoxime (LH₂), and its mononuclear nickel(II), copper(II), cobalt(II), cadmium(II) and zinc(II) complexes. The azacrown moieties appended at the periphery of the oxime provide solubility for the vic-dioxime ligand and complexes in common organic solvents. The mononuclear M(LH)₂ (M = Ni and Cu), M(LH)₂(H₂O)₂ (M = Co) and [M(LH)(H₂O)(Cl)] (M = Cd and Zn) complexes have been obtained with the metal:ligand ratios of 1:2 and 1:1. The structure of the ligand is confirmed by elemental analysis, Fourier transform infrared (FT-IR), ultraviolet-visible (UV-Vis), mass spectrometry (MS), one-dimensional (1D) ¹H, ¹³C NMR, distortionless enhancement by polarization transfer (DEPT) and two-dimensional (2D) heteronuclear single quantum coherence (HSQC) and heteronuclear multiple bond correlation (HMBC) techniques. The structures of the complexes are confirmed by elemental analyses, MS, UV-Vis, FT-IR and ¹H, ¹³C NMR techniques. Redox behaviors of the ligand and its complexes have been investigated by cyclic voltammetry at the glassy carbon electrode in 0.1 M TBATFB in DMSO. The antibacterial activity was studied against Staphylococcus aureus ATCC 29213, Streptococcus mutans RSHM 676, Enterococcus faecalis ATCC 29212, Lactobacillus acidophilus RSHM 06029, Escherichia coli ATCC 25922, Pseudomonasaeruginosa ATCC 27853. The antimicrobial test results indicate that all the complexes have low levels of antibacterial activity against both Gram negative and Gram positive bacterial species.     

Measurement of the reaction 2H(e,e') at 180 degrees close to the deuteron breakup threshold

Inclusive inelastic electron scattering off the deuteron under 180 degrees has been studied at the S-DALINAC close to the breakup threshold at momentum transfers q=0.27 fm;{-1} and 0.74 fm;{-1} with good energy resolution sufficient to map in detail the spin flip M1 response, which governs the starting reaction pn-->dgamma of big-bang nucleosynthesis over most of the relevant temperature region. Results from potential model calculations and (for q=0.27 fm;{-1}) from pionless nuclear effective field theory are in excellent agreement with the data.