The Effects of Charged Amino Acid Side-Chain Length on Diagonal Cross-Strand Interactions between Carboxylate- and Ammonium-Containing Residues in a β-Hairpin

The β-sheet is one of the common protein secondary structures, and the aberrant aggregation of β-sheets is implicated in various neurodegenerative diseases. Cross-strand interactions are an important determinant of β-sheet stability. Accordingly, both diagonal and lateral cross-strand interactions have been studied. Surprisingly, diagonal cross-strand ion-pairing interactions have yet to be investigated. Herein, we present a systematic study on the effects of charged amino acid side-chain length on a diagonal ion-pairing interaction between carboxylate- and ammonium-containing residues in a β-hairpin. To this end, 2D-NMR was used to investigate the conformation of the peptides. The fraction folded population and the folding free energy were derived from the chemical shift data. The fraction folded population for these peptides with potential diagonal ion pairs was mostly lower compared to the corresponding peptide with a potential lateral ion pair. The diagonal ion-pairing interaction energy was derived using double mutant cycle analysis. The Asp2-Dab9 (Asp: one methylene; Dab: two methylenes) interaction was the most stabilizing (−0.79 ± 0.14 kcal/mol), most likely representing an optimal balance between the entropic penalty to enable the ion-pairing interaction and the number of side-chain conformations that can accommodate the interaction. These results should be useful for designing β-sheet containing molecular entities for various applications.     

DNA Interaction,DNA Photocleavage,Photocytotoxicity In Vitro,and Molecular Docking of Naphthyl-Appended Ruthenium Complexes

With the development of metal-based drugs, Ru(II) compounds present potential applications of PDT (photodynamic therapy) and anticancer reagents. We herein synthesized two naphthyl-appended ruthenium complexes by the combination of the ligand with naphthyl and bipyridyl. The DNA affinities, photocleavage abilities, and photocytotoxicity were studied by various spectral methods, viscosity measurement, theoretical computation method, gel electrophoresis, and MTT method. Two complexes exhibited strong interaction with calf thymus DNA by intercalation. Production of singlet oxygen (¹O₂) led to obvious DNA photocleavage activities of two complexes under 365 nm light. Furthermore, two complexes displayed obvious photocytotoxicity and low dark cytotoxicity towards Hela, A549, and A375 cells.     

Nonlinear Modeling Study of Aerodynamic Characteristics of an X38-like Vehicle at Strong Viscous Interaction Regions

Strong viscous interaction and multiple flow regimes exist when vehicles fly at high altitude and high Mach number conditions. The Navier–Stokes(NS) solver is no longer applicable in the above situation. Instead, the direct simulation Monte Carlo (DSMC) method or Boltzmann model equation solvers are usually needed. However, they are computationally more expensive than the NS solver. Therefore, it is of great engineering value to establish the aerodynamic prediction model of vehicles at high altitude and high Mach number conditions. In this paper, the hypersonic aerodynamic characteristics of an X38-like vehicle in typical conditions from 70 km to 110 km are simulated using the unified gas kinetic scheme (UGKS), which is applicable for all flow regimes. The contributions of pressure and viscous stress on the force coefficients are analyzed. The viscous interaction parameters, Mach number, and angle of attack are used as independent variables, and the difference between the force coefficients calculated by UGKS and the Euler solver is used as a dependent variable to establish a nonlinear viscous interaction model between them in the range of 70–110 km. The evaluation of the model is completed using the correlation coefficient and the relative orthogonal distance. The conventional viscous interaction effect and rarefied effect are both taken into account in the model. The model can be used to quickly obtain the hypersonic aerodynamic characteristics of X38-like vehicle in a wide range, which is meaningful for engineering design.     

Effect of Coconut Protein and Xanthan Gum,Soybean Polysaccharide and Gelatin Interactions in Oil-Water Interface

We report on our study of the interactions between coconut protein extracted from coconut meat and three hydrocolloids (gelatin, xanthan gum, and soybean polysaccharide) and their interfacial adsorption and emulsification properties. We used Zeta potential, fluorescence spectroscopy scanning and ITC to investigate the interactions between a fixed concentration (1%) of coconut protein and varying concentrations of hydrocolloid. Through the interfacial tension and interfacial viscoelasticity, the interfacial properties of the hydrocolloid and coconut protein composite solution were explored. The physical stability of the corresponding emulsion is predicted through microstructure and stability analysis. Xanthan gum forms a flocculent complex with coconut protein under acidic conditions. Soy polysaccharides specifically bind to coconut protein. Under acidic conditions, this complex is stabilized through the steric hindrance of soy polysaccharides. Due to gelatin-coconut protein interactions, the isoelectric point of this complex changes. The interfacial tension results show that as time increases, the interfacial tensions of the three composite solutions decrease. The increase in the concentration of xanthan gum makes the interfacial tension decrease first and then increase. The addition of soybean polysaccharides reduces the interfacial tension of coconut protein. The addition of xanthan gum forms a stronger elastic interface film. Emulsion characterization showed that the gelatin-added system showed better stability. However, the addition of xanthan gum caused stratification quickly, and the addition of soybean polysaccharides also led to instability because the addition of polysaccharides led to a decrease in thermodynamic compatibility. This research lays the foundation for future research into coconut milk production technology.     

Spectroscopy of light nuclei with skyrme-type interactions

Deformed Hartree-Fock calculations are performed for some light nuclei in a large configuration space consisting of first four major shells. The interaction employed is the modified Skyrme interaction in which the deformed density is replaced by the band averaged scalar density that makes the Hamiltonian rotationally invariant rendering the spectroscopic calculations feasible. It is shown that the introduction of density dependence spreads out the energy spectra and that the Skyrme variant SIV which has a weak density dependence gives best overall agreement for energy spectra and the available data for the electromagnetic properties of the nuclei studied. It is found that the maximum contribution to the energy of any state in the low lying spectrum comes from thes-state attractive ands-state repulsive parts of the Skyrme interaction. It is also shown that when two-body density dependent version of Skyrme interaction is used, the Koopmans theorem no longer holds.     

Effects of Organic Acids on the Release of Fruity Esters in Water: An Insight at the Molecular Level

It is well known that organic acids (OAs) could affect the flavour of fruit juices and beverages. However, the molecular mechanism of aroma release is still unclear. In this study, the effects of citric acid (CA), L-(-)-malic acid (MA) and L-lactic acid (LA) on the release of six selected esters and their sensory perception were investigated by means of HS-GC-MS analyses and odour detection threshold determination, respectively. Meanwhile, the density functional theory (DFT) calculation was employed to explore the interaction modes between esters and OAs. HS-GC-MS analyses showed that the concentration and the type of OAs regulated the release of esters. The results were basically consistent with the detection threshold change of those esters. The DFT calculation suggested that the main intermolecular interaction was hydrogen bonds, and several esters could form a ternary ring structure with OAs through hydrogen bonds. The interactions can induce the different release behaviours of esters in OAs water solution. The number of carboxyl functional groups in OAs and the spatial conformation of esters appeared to influence the magnitude of the interaction. The above results demonstrated the mechanism of OAs affecting the release of esters and indicated a possible flavour control way by using different OAs and OA concentrations.     

A Shortcut Application of a Flory‐Like Model to Asphaltene Precipitation

A model, previously developed to determine the asphaltene precipitation onset, considered that asphaltene separation is ruled by the solvent quality of the surrounding media. Here, it is shown that it is equivalent to Flory‐Huggins model, when it is hypothesized that the asphaltene concentration is always in the instability range. With this, the controversy on the use of a concentration‐dependent model to describe a phenomenon that is practically independent of concentration is by‐passed. Moreover, improvements of the model are presented, together with sensitivity analysis with respect to its parameters. Two field case applications are reported, showing that the model gives a reasonable fit.     

The electronic origin of unusually large nJFN coupling constants in some fluoroximes

SOPPA(CCSD) calculations show that the FC term is the most important contribution to the through‐space transmission of J_FN coupling constants for the fluoroximes studied in this work. Because of the well‐known behavior of FC term, a new rationalization for the experimental ^TSJ_FN SSCC is presented. It is mainly based on the overlap matrix (S_ij) between fluorine and nitrogen lone pairs obtained from NBO analyses. An expression is proposed to take into account the influence of the electronic density (D_ij) between coupled nuclei as well as the s% character at the site of the coupling nuclei of bonds and non‐bonding electron pairs involved in D_ij. In using this approach, a linear correlation between ^TSJ_FN versus D_ij is obtained. The most important aspect of this rationalization is related to the facility for understanding the behavior of some unusual experimental coupling constants. It is shown that, at least in this case, the electronic origin of the so‐called through‐space coupling is transmitted through to the overlap of orbitals on the coupled atoms, suggesting that, at least for these compounds, instead of through‐space coupling, it should better be dubbed as ‘through overlapping orbital coupling’. Copyright © 2013 John Wiley & Sons, Ltd.     

PbII 4,4,4-trifluoro-1-naphthyl-1,3-butanedione complexes of 1,10-phenanthroline and 2,2′-bipyridine ligands

Lead(II) 4,4,4-trifluoro-1-naphthyl-1,3-butanedione (Htfnb) complexes of 1,10-phenanthroline (phen) and 2,2′-bipyridine (bpy), [Pb₂(bpy)₂(tfnb)₂] (1) and [Pb₂(phen)₂(tfnb)₂] (2), have been synthesized and characterized by elemental analysis, IR, spectroscopy and X-ray crystallography. The self-assembly of 1 and 2 is likely to be caused by C–H ··· F–C, C–H ··· O and π–π stacking interactions.     

A moving mesh algorithm for aero‐thermo‐mechanical modelling in turbomachinery

This paper describes the development of a mesh deformation method used for aero‐thermo‐mechanical coupling of turbo‐engine components. The method is based on the nonlinear solution of an elastic medium analogy, solved using finite element discretisation and modified to let the boundary nodes be free to slide over the deflected surfaces. This sliding technique relies on a B‐spline reconstruction of the moving boundary and increases the robustness of the method in situations where the boundary deflection field presents significant gradients or large relative motion between two distinct boundaries. The performance of the method is illustrated with the application to an interstage cavity of a turbine assembly, subjected to the deformations computed by a coupled thermo‐mechanical analysis of the engine component. Copyright © 2011 John Wiley & Sons, Ltd.