How do rotameric conformations influence the time-resolved fluorescence of tryptophan in proteins? A perspective based on molecular modeling and quantum chemistry

We discuss the dynamics of tryptophan rotamers in the context of the non-exponential fluorescence decay in proteins. The central question is: how does the ground-state conformational heterogeneity influence the time evolution of tryptophan fluorescence? This problem is examined here from the theoretical perspective. Three methods at different levels of theory, and with different scopes and computational requirements are reviewed. The Dead-end elimination method is limited to side-chain dynamics and provides an efficient way to detect the stable tryptophan rotamers in a protein. Its application to the study of heterogeneous emission characteristics is illustrated. Molecular dynamics is aimed at the full phase space of the macromolecule in solution, but must rely on classical force fields and laws of evolution. We examine to what extent the molecular mechanics paradigm yields sufficiently accurate thermodynamic results, and what are the possible kinetic implications. Finally Quantum Chemistry is the only theoretical method that allows a direct assessment of the excited states. It is necessarily restricted to small molecular systems, and thus must be used in a hybrid combination with classical methods and electrostatic models. So far understanding of the emitting state has greatly progressed as a result of these calculations, but the actual treatment of the photophysical decay processes at the quantum level has not yet really started.     

Quantitative analysis of urinary glycerol levels for doping control purposes using gas chromatography-mass spectrometry

The administration of glycerol to endurance athletes results in an increased fluid retention and improved performance, particularly under hot and humid conditions. Consequently, glycerol is considered relevant for sports drug testing and methods for its detection in urine specimens are required. A major issue in this regard is the natural occurrence of trace amounts of glycerol in human urine, which necessitates a quantitative analysis and the determination of normal urinary glycerol levels under various sporting conditions. A quantitative method was established using a gas chromatography/isotope-dilution mass spectrometry-based approach that was validated with regard to lower limit of detection (0.3 microg mL(-1)), lower limit of quantification (0.9 microg mL(-1)), specificity, linearity (1.0-98.0 microg mL(-1)), intraday and interday precision (<20% at 2.4, 24.1 and 48.2 microg mL(-1)) as well as accuracy (92-110%). Sample aliquots of 20 microL were enriched with five-fold deuterated glycerol, dried and derivatised using N-methyl-trimethylsilyltrifluoroacetamide (MSTFA) before analysis. The established method was applied to a total of 1039 doping control samples covering various sport disciplines (349 endurance samples, 286 strength sport samples, 325 game sport samples and 79 other samples) in- and out-of-competition, which provided quantitative information about the glycerol content commonly observed in elite athletes' urine samples. About 85% of all specimens yielded glycerol concentrations < 20.0 microg mL(-1) and few reached values up to 132.6 microg mL(-1). One further sample, however, was found to contain 2690 microg mL(-1), which might indicate the misuse of glycerol, but no threshold for urinary glycerol concentrations has been established yet due to the lack of substantial data. Based on the results obtained from the studied reference population, a threshold for glycerol levels in urine set at 200 microg mL(-1) is suggested, which provides a tool to doping control laboratories to test for the misuse of this agent in elite and amateur sport.     

Structure-transport analysis for particulate packings in trapezoidal microchip separation channels

This article investigates the efficiency of particulate beds confined in quadrilateral microchannels by analyzing the three-dimensional fluid flow velocity field and accompanying hydrodynamic dispersion with quantitative numerical simulation methods. Random-close packings of uniform, solid (impermeable), spherical particles of diameter d(p) were generated by a modified Jodrey-Tory algorithm in eighteen different conduits with quadratic, rectangular, or trapezoidal cross-section at an average bed porosity (interparticle void fraction) of epsilon = 0.48. Velocity fields were calculated by the lattice Boltzmann method, and axial hydrodynamic dispersion of an inert tracer was simulated at Péclet numbers Pe = u(av)d(p)/D(m) (where u(av) is the average fluid flow velocity through a packing and D(m) the bulk molecular diffusion coefficient) from Pe = 5 to Pe = 30 by a Lagrangian particle-tracking method. All conduits had a cross-sectional area of 100d(p)(2) and a length of 1200d(p), translating to around 10(5) particles per packing. We present lateral porosity distribution functions and analyze fluid flow profiles and velocity distribution functions with respect to the base angle and the aspect ratio of the lateral dimensions of the different conduits. We demonstrate significant differences between the top and bottom parts of trapezoidal packings in their lateral porosity and velocity distribution functions, and show that these differences increase with decreasing base angle and increasing base-aspect ratio of a trapezoidal conduit, i.e., with increasing deviation from regular rectangular geometry. Efficiencies are investigated in terms of the axial hydrodynamic dispersion coefficients as a function of the base angle and base-aspect ratio of the conduits. The presented data support the conclusion that the efficiency of particulate beds in trapezoidal microchannels strongly depends on the lateral dimensions of the conduit and that cross-sectional designs based on large side-aspect-ratio rectangles with limited deviations from orthogonality are favorable.     

Microkinetic simulations of the oxidation of CO on Pd based nanocatalysis: a model including co-dependent support interactions

The catalysed oxidation of CO using mass-selected Pd(13) clusters supported on thin MgO films was modelled using a microkinetic simulation of the reaction. The model of the system includes reverse spill-over calculations which were intrinsically incorporated into the formulation of the kinetics. The spill-over model is based on a capture-zone approach including a co-dependence on the variables of the kinetic equations. The experimental values were determined using dual pulsed-molecular beam measurements and recorded at a range of temperatures. The experiment allowed the turn-over frequency and reaction probability to be determined as a function of mole fraction. Comparison of the kinetic model with the experimental data gives excellent agreement and strongly highlights the importance of substrate effects. In particular, the origin of the low temperature catalysis of the Pd clusters is elucidated. The model allows the mole fraction and temperature dependent values such as the sticking coefficients for these clusters to be predicted.     

Systematische Studie zu den Koordinationseigenschaften des Guanidin‐Liganden N1,N2‐Bis(1,3‐dimethylimidazolidin‐2‐yliden)‐ethan‐1,2‐diamin mit den Metallen Mn,Co, Ni,Ag und Cu

A Systematic Study on the Coordination Properties of the Guanidine Ligand N¹,N²‐Bis(1,3‐dimethylimidazolidin‐2‐ylidene)‐ethane‐1,2‐diamine with the Metals Mn, Co, Ni, Ag and Cu The syntheses and characterization of the compounds [Mn(DMEG₂e)Cl₂] ( 1 ), [Co(DMEG₂e)Cl₂] ( 2 ), [Ni(DMEG₂e)₂]I₂ ( 3 ), [Cu(DMEG₂e)I] ( 4 ) and {[Ag(DMEG₂e)]BF₄}_n ( 5 ) with the bisguanidine ligand N¹,N²‐bis(1,3‐dimethylimidazolidin‐2‐ylidene)ethane‐1,2‐diamine (DMEG₂e) are described. All complexes are synthesized by the reaction of the corresponding metal salt with the DMEG₂e ligand in MeCN or THF. The coordination of the metal atoms vary from a distorted tetrahedron in 1 and 2 , a distorted trigonal planar coordination in 4 to linear coordination in 5 . Contrasting to the compounds 1 , 2 , 4 and 5 which exhibit a 1:1 ratio of metal to ligand, two DMEG₂e ligands are bound to the Ni atom in the case of 3 resulting in a coordination polyhedron which represents the stage exactly in the middle between the square‐planar and the tetrahedral geometry. Whereas crystals of 1 , 2 , 3 and 4 contain discrete molecules, in 5 the Ag atoms are alternately linked by two different DMEG₂e ligands to form a chain structure. The comparative discussion of several DMEG₂e containing complexes with the compounds reported herein supplements this systematic study.