Normal mode analysis of molecular motions in curvilinear coordinates on a non-Eckart body-frame: an application to protein torsion dynamics

Normal mode analysis (NMA) was introduced in 1930s as a framework to understand the structure of the observed vibration-rotation spectrum of several small molecules. During the past three decades NMA has also become a popular alternative to figuring out the large-scale motion of proteins and other macromolecules. However, the “standard” NMA is based on approximations, which sometimes are unphysical. Especially problematic is the assumption that atoms move only “infinitesimally”, which, of course, is an oxymoron when large amplitude motions are concerned. The “infinitesimal” approximation has the further unfortunate side effect of masking the physical importance of the coupling between vibrational and rotational degrees of freedom. Here, we present a novel formulation of the NMA, which is applied for finite motions in non-Eckart body-frame. Contrary to standard normal mode theory, our approach starts by assuming a harmonic potential in generalized coordinates, and tries to avoid the linearization of the coordinates. It also takes explicitly into account the Coriolis terms, which couple vibrations and rotations, and the terms involving Christoffel symbols, which are ignored by default in the standard NMA. We also computationally explore the effect of various terms to the solutions of the NMA equation of motions.     

Intensely luminescent homoleptic alkynyl decanuclear gold(I) clusters and their cationic octanuclear phosphine derivatives

Treatment of Au(SC(4)H(8))Cl with a stoichiometric amount of hydroxyaliphatic alkyne in the presence of NEt(3) results in high-yield self-assembly of homoleptic clusters (AuC(2)R)(10) (R = 9-fluorenol (1), diphenylmethanol (2), 2,6-dimethyl-4-heptanol (3), 3-methyl-2-butanol (4), 4-methyl-2-pentanol (4), 1-cyclohexanol (6), 2-borneol (7)). The molecular compounds contain an unprecedented catenane metal core with two interlocked 5-membered rings. Reactions of the decanuclear clusters 1-7 with gold-diphosphine complex [Au(2)(1,4-PPh(2)-C(6)H(4)-PPh(2))(2)](2+) lead to octanuclear cationic derivatives [Au(8)(C(2)R)(6)(PPh(2)-C(6)H(4)-PPh(2))(2)](2+) (8-14), which consist of planar tetranuclear units {Au(4)(C(2)R)(4)} coupled with two fragments [AuPPh(2)-C(6)H(4)-PPh(2)(AuC(2)R)](+). The titled complexes were characterized by NMR and ESI-MS spectroscopy, and the structures of 1, 13, and 14 were determined by single-crystal X-ray diffraction analysis. The luminescence behavior of both Au(I)(10) and Au(I)(8) families has been studied, revealing efficient room-temperature phosphorescence in solution and in the solid state, with the maximum quantum yield approaching 100% (2 in solution). DFT computational studies showed that in both Au(I)(10) and Au(I)(8) clusters metal-centered Au → Au charge transfer transitions mixed with some π-alkynyl MLCT character play a dominant role in the observed phosphorescence.     

Functional Columnar Liquid Crystalline Phases From Ionic Complexes of Dendronized Polymers and Sulfate Alkyl Tails

We describe how cationic dendronized polymers of generations 1, and 2 and anionic monoalkyl tails can be combined by supramolecular ionic complexation into comb-like liquid crystalline polymers. The final structures in bulk of these supramolecular complexes were studied by differential scanning calorimetry (DSC), cross-polarized optical microscopy (CPOM), small angle x-rays scattering (SAXS) and transmission electron microscopy (TEM). The combination of these techniques allowed elucidating (i) that these complexes exhibit thermotropic behaviour, (ii) that various liquid crystalline structures in the 3–5 nm length scale can be obtained such as columnar rectangular, columnar tetragonal, columnar hexagonal and lamellar, depending both on alkyl tail length and polymer generation, (iii) that although the alkyl tails represent the majority phase in the columnar phases, they form the cylindric domains, and the dendronized polymers occupy the continuous domains. Therefore, upon selective cleavage of the alkyl tails in the columnar phases, the present self-assembly approach may constitute an efficient strategy towards the formation of porous organic matrices with ultra-dense pore size in the range of 2 to 4 nm.     

Comparison of Experimental Strategies to Study l-Type Amino Acid Transporter 1 (LAT1) Utilization by Ligands

l-Type amino acid transporter 1 (LAT1), expressed abundantly in the brain and placenta and overexpressed in several cancer cell types, has gained a lot of interest in drug research and development, as it can be utilized for brain-targeted drug delivery, as well as inhibiting the essential amino acid supply to cancer cells. The structure of LAT1 is today very well-known and the interactions of ligands at the binding site of LAT1 can be modeled and explained. However, less is known of LAT1′s life cycle within the cells. Moreover, the functionality of LAT1 can be measured by several different methods, which may vary between the laboratories and make the comparison of the results challenging. In the present study, the usefulness of indirect cis-inhibition methods and direct cellular uptake methods and their variations to interpret the interactions of LAT1-ligands were evaluated. Moreover, this study also highlights the importance of understanding the intracellular kinetics of LAT1-ligands, and how they can affect the regular function of LAT1 in critical tissues, such as the brain. Hence, it is discussed herein how the selected methodology influences the outcome and created knowledge of LAT1-utilizing compounds.     

On functions with derivatives in a Lorentz space

We establish a sharp integrability condition on the partial derivatives of a Sobolev mapping to guarantee that sets of measure zero get mapped to sets of measure zero. This condition is sharp also for continuity and differentiability almost everywhere. Received: 6 January 1999 / Revised version: 5 May 1999     

Inner functions in weak Besov spaces

It is shown that inner functions in weak Besov spaces are precisely the exponential Blaschke products.     

Surface characterization of unbleached kraft pulps by means of ESCA

The effect of digestion conditions (amount of effective alkali, digestion time) on the surface compositions of unbleached softwood (Pinus sylvestris) kraft pulp has been investigated by electron spectroscopy for chemical analysis (ESCA). The quantities monitored were the angular dependence of the total O/C ratio, the relative amounts of carbons in different states of oxidation and the adsorption of Al and Ca ions to the carboxyl groups in the surface. Examination of the angular dependence of ESCA intensities shows that the concentration of alkyl carbon is high in a very thin surface layer and that it decreases linearly with decreasing kappa number. The concentration of alkyl carbon is decreased by extraction of the fibres with dichloromethane, but the amount remaining in the surface after extraction still decreases linearly with decreasing kappa number (i.e. it decreases with increasing digestion time). It is suggested that the observed enrichment of alkyl carbon in the outermost surface layers most probably is due to reprecipitation of lignin. In pulp that has not been extracted, there is also strong enrichment of extractives in the surface. This amount increases with increasing effective alkali but is relatively independent of digestion time. ESCA analysis of the Al and Ca bound to the carboxyl groups shows that the amount depends on digestion time; the results are consistent with the notion that the reprecipitated lignin contains carboxyl groups.     

A lab-on-a-chip compatible bioaffinity assay method for human alpha-fetoprotein

A new lab-on-a-chip compatible binding assay platform is introduced. The platform combines dry-chemistry bioaffinity reagents and the recently introduced ArcDia TPX binding assay technique. The technique employs polymer microspheres as a solid phase reaction carrier, fluorescently labeled antibody conjugates, and detection of fluorescence emission from the surface of individual microspheres by two-photon excitation fluorescence. Signal response of the technique is independent of the reaction volume, thus the technique is particularly well suited for detection of bioaffinity reactions from miniature volumes. Performance of the new assay platform is studied by means of an immunometric assay of human alpha-fetoprotein (hAFP) in 384-plate format, and the results are compared to those of a corresponding wet-chemistry assay method. The results show that the ArcDia TPX detection technique can be combined with dry-chemistry reagents without compromises in assay performance. The microchip field has so far been characterized with a lack of microchip-compatible detection platforms which would allow cost-effective microchip design and sensitive bioaffinity detection. The presented detection technique is expected to provide a solution for this shortage.     

Morphology of dry lignins and size and shape of dissolved kraft lignin particles by X-ray scattering

Lignin is a highly branched polymer consisting of phenylpropane units, and it is one of the ingredients of the supporting matrix in plant cell walls. The morphology of several lignins extracted from plant cell walls using different methods was studied by small-angle and ultra-small-angle X-ray scattering. A power-law type intensity was observed for the dry lignins, but on the basis of the power-law exponent the fractal approach often applied to lignins is not fully justified. However, the intensity of kraft lignin did show a power law with surface fractal dimension D(s) = 2.7 +/- 0.1. The specific surface area of the lignins ranged from about 0.5 to 60 m(2)/g with 20% relative accuracy. The radius of gyration was determined from small-angle X-ray scattering data for aqueous solutions of kraft lignin. The shape of the particles in NaCl and NaOH solutions was found to be elongated. The particles were about 1-3 nm thick, while the length (5-9 nm) depended on the solvent and on the lignin concentration. The size of these primary particles was approximately the same as the size of the pores in the fractal aggregates of the dry kraft lignin. Their size was determined to be about 3.5 nm.