First-principles calculations of the electronic and geometrical structures of neutral [Sc,O,H] molecules and the monocations, ScOH(0,+) and HScO(0,+)

Using multireference configuration interaction and coupled-cluster methodologies, with quadruple-ζ basis sets, we explored the potential energy surfaces of the ground and excited states of the neutral and cationic triatomics [Sc,O,H](0,+). In its ground state, the neutral species is trapped into either a linear ScOH or a bent HScO conformation; these two minima are approximately equal in energy and separated by a barrier of 40 kcal/mol. The linear ScOH structure is preferred by the excited states of the neutral species and by all of the electronic states of the charged molecular systems that we studied in this work. Both ScOH and ScOH(+) present ionic characters, Sc(+)OH(-) and Sc(2+)OH(-), similar to those found for the isovalent ScF(0,+) species. The HScO(0,+) structures are obtained by covalent or dative interaction of hydrogen and ScO(0,+). For most of the minima located in this work, we calculated geometries, vibrational frequencies, binding energies, excitation energies, and dipole moments. Our numerical results agree well with existing experimental data.     

Atomistic simulation of lipid and DiI dynamics in membrane bilayers under tension

Membrane tension modulates cellular processes by initiating changes in the dynamics of its molecular constituents. To quantify the precise relationship between tension, structural properties of the membrane, and the dynamics of lipids and a lipophilic reporter dye, we performed atomistic molecular dynamics (MD) simulations of DiI-labeled dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under physiological lateral tensions ranging from -2.6 mN m(-1) to 15.9 mN m(-1). Simulations showed that the bilayer thickness decreased linearly with tension consistent with volume-incompressibility, and this thinning was facilitated by a significant increase in acyl chain interdigitation at the bilayer midplane and spreading of the acyl chains. Tension caused a significant drop in the bilayer's peak electrostatic potential, which correlated with the strong reordering of water and lipid dipoles. For the low tension regime, the DPPC lateral diffusion coefficient increased with increasing tension in accordance with free-area theory. For larger tensions, free area theory broke down due to tension-induced changes in molecular shape and friction. Simulated DiI rotational and lateral diffusion coefficients were lower than those of DPPC but increased with tension in a manner similar to DPPC. Direct correlation of membrane order and viscosity near the DiI chromophore, which was just under the DPPC headgroup, indicated that measured DiI fluorescence lifetime, which is reported to decrease with decreasing lipid order, is likely to be a good reporter of tension-induced decreases in lipid headgroup viscosity. Together, these results offer new molecular-level insights into membrane tension-related mechanotransduction and into the utility of DiI in characterizing tension-induced changes in lipid packing.     

TiO2-ZrO2 affinity chromatography polymeric microchip for phosphopeptide enrichment and separation

We fabricated a TiO(2)-ZrO(2) affinity chromatography micro-column on 2 mm PMMA plates, and demonstrated the enrichment and separation of (a) a standard mono- and tetra-phosphopeptide, and (b) phosphopeptides contained in a tryptic digest of β-Casein. The chromatography column consisted of 32 parallel microchannels with common input and output ports and was fabricated by lithography directly on the polymeric substrate followed by plasma etching (i.e. standard MEMS processing) and sealed with lamination. The liquid deposited TiO(2)-ZrO(2) stationary phase was characterized by X-ray diffraction and was found to be mostly TiO(2) and ZrO(2) in crystalline phases. Off-chip UV detection and MALDI MS identification of the separated effluents were used. The chip had a capacity of >1.4 μg (0.7 nmol) of a prototype mono-phosphopeptide and a recovery of 94 ± 3%, and can be used with small samples (less than 0.1 μL depending on the syringe pump used). The chip design allows an expansion of its capacity by means of increasing the number of parallel microchannels at a constant sample volume. Our approach provided an alternative to off-line extraction tips (with typical capacities of 1-2 μg and sample volumes of 1-10 μL), and to on-chip efforts based on packed bed and frit formats.     

Heart Failure and PAHs,OHPAHs, and Trace Elements Levels in Human Serum: Results from a Preliminary Pilot Study in Greek Population and the Possible Impact of Air Pollution

Cardiovascular diseases (CVDs) have been associated with environmental pollutants. The scope of this study is to assess any potential relation of polycyclic aromatic hydrocarbons (PAHs), their hydroxylated derivatives, and trace elements with heart failure via their direct determination in human serum of Greek citizens residing in different areas. Therefore, we analyzed 131 samples including cases (heart failure patients) and controls (healthy donors), and the respective demographic data were collected. Significantly higher concentrations (p < 0.05) were observed in cases’ serum regarding most of the examined PAHs and their derivatives with phenanthrene, fluorene, and fluoranthene being the most abundant (median of >50 μg L⁻¹). Among the examined trace elements, As, Cd, Cu, Hg, Ni, and Pb were measured at statistically higher concentrations (p < 0.05) in cases’ samples, with only Cr being significantly higher in controls. The potential impact of environmental factors such as smoking and area of residence has been evaluated. Specific PAHs and trace elements could be possibly related with heart failure development. Atmospheric degradation and smoking habit appeared to have a significant impact on the analytes’ serum concentrations. PCA–logistic regression analysis could possibly reveal common mechanisms among the analytes enhancing the hypothesis that they may pose a significant risk for CVD development.     

Monte Carlo simulations of a coarse grained model for an athermal all-polystyrene nanocomposite system

The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as random walks and the system is described through a coarse grained Hamiltonian. This approach is related to self-consistent-field theory but does not invoke a saddle point approximation and is suitable for treating large three-dimensional systems. The local structure of the polymer matrix in the vicinity of the nanoparticles is found to be different in many ways from that of the corresponding bulk, both at the segment and the chain level. The local polymer density profile near to the particle displays a maximum and the bonds develop considerable orientation parallel to the nanoparticle surface. The depletion layer thickness is also analyzed. The chains orient with their longest dimension parallel to the surface of the particles. Their intrinsic shape, as characterized by spans and principal moments of inertia, is found to be a strong function of position relative to the interface. The dispersion of many nanoparticles in the polymeric matrix leads to extension of the chains when their size is similar to the radius of the dispersed particles.     

Using quaternions to calculate RMSD

A widely used way to compare the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the root-mean-square deviation (RMSD). We present a simple derivation, based on quaternions, for the optimal solid body transformation (rotation-translation) that minimizes the RMSD between two sets of vectors. We prove that the quaternion method is equivalent to the well-known formula due to Kabsch. We analyze the various cases that may arise, and give a complete enumeration of the special cases in terms of the arrangement of the eigenvalues of a traceless, 4 x 4 symmetric matrix. A key result here is an expression for the gradient of the RMSD as a function of model parameters. This can be useful, for example, in finding the minimum energy path of a reaction using the elastic band methods or in optimizing model parameters to best fit a target structure.     

Interaction-induced dipoles of hydrogen molecules colliding with helium atoms: a new ab initio dipole surface for high-temperature applications

We report new ab initio results for the interaction-induced dipole moments Δμ of hydrogen molecules colliding with helium atoms. These results are needed in order to calculate collision-induced absorption spectra at high temperatures; applications include modeling the radiative profiles of very cool white dwarf stars, with temperatures from 3500 K to 9000 K. We have evaluated the dipoles based on finite-field calculations, with coupled cluster methods in MOLPRO 2006 and aug-cc-pV5Z (spdfg) basis sets for both the H and He centers. We have obtained values of Δμ for eight H(2) bond lengths ranging from 0.942 a.u. to 2.801 a.u., for 15 intermolecular separations R ranging from 2.0 a.u. to 10.0 a.u., and for 19 different relative orientations. In general, our values agree well with earlier ab initio results, for the geometrical configurations that are treated in common, but we have determined more points on the collision-induced dipole surface by an order of magnitude. These results make it possible to calculate transition probabilities for molecules in excited vibrational states, overtones, and rotational transitions with ΔJ > 4. We have cast our results in the symmetry-adapted form needed for absorption line shape calculations, by expressing Δμ as a series in the spherical harmonics of the orientation angles of the intermolecular vector and of a unit vector along the H(2) bond axis. The expansion coefficients depend on the H(2) bond length and the intermolecular distance R. For large separations R, we show that the ab initio values of the leading coefficients converge to the predictions from perturbation theory, including both classical multipole polarization and dispersion effects.     

Rotational superposition and least squares: the SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller

We clarify once again that Kabsch's method and the Quaternion method are mathematically equivalent methods, that is, that they contain identical information and, when properly understood and applied, lead to identical answers to any questions regarding least-squares rotational superposition, either by proper rotations or by rotation-reflections. We also provide the correct bounds for the eigenvalue spectrum.     

Computational studies of (HIO3) isomers and the HO2 + IO reaction pathways

The geometries, harmonic vibrational frequencies, relative energetics, and enthalpies of formation of (HIO3) isomers have been examined using quantum mechanical methods. At all levels of theory employed, MP2, B3LYP, and CCSD(T), the lowest energy structure is found to be the HOIO2 form, which shows particular stability. The two isomers HOOOI and HOOIO are closely located at the CCSD(T) level of theory. The higher energy structure is HIO3. The interisomerization transition states have been determined, along with the transition states involved in the various pathways of the reaction HO2 + IO.