Calculated chemical shifts as a fine tool of conformational analysis: an unambiguous solution for haouamine alkaloids

In this study, for the first time, conformational analysis by calculated chemical shifts (CCS) deals with a real conformational problem of a large biomolecule. This new methodology is applied to haouamine A, which is much more stereodynamically puzzled than the small models used to validate previous CCS-based conformational studies. Thorough NMR experiments by Zubia et al. on this exotic polyfunctional paracyclophane alkaloid could not determine which experimentally detected interconversion of this compound occurs in solution, rotation or N-inversion. The present study uses CCS to locate the lowest energy conformers and thus to identify the observed stereodynamic process. Molecular mechanics calculations were used to explore the conformational space of this polycyclic system, and then the geometry of located conformers was refined by ab initio calculations at the B3LYP/6-31G(d,p) level; an implicit model for acetone solution was employed. Calculated relative energies are considered too inaccurate to identify the lowest energy (i.e., those detectable by NMR) conformers. Instead, rational regression analysis of CCS for carbon atoms using B3LYP/6-31+G(d)//GIAO-based calculations singled out two conformers from a large set of alternative low energy structures, although solvation shell was not explicitly included in the model. For only these two conformers, the differences in CCS (Delta delta) for selected pairs of carbons are very similar to the experimental Delta delta values. Thus, the conformers monitored by NMR have now been identified; their piperideine ring is of (1)Sf and Sf 1 (sofa-shaped) geometry. This azacycle appears to be flexible despite the presence of the ethylenebiphenylene bridge in haouamines. Interconversion between the conformers probably occurs via a concerted process of inversion of the piperideine ring, N-inversion coupled with rotation around the C-N bond, and rotation around two C-C bonds in the ethylenebiphenylene bridge. This CCS method of conformational analysis is sufficiently simple and reliable that if chemical shifts for a pair of the same carbons are sufficiently different in routine (13)C NMR spectra of stereoisomers (ca. > or = 2 ppm), the "resolving power" of the CCS technique may rival that of NMR techniques.     

Spatial fluctuations affect the dynamics of motor proteins

Motor proteins are active biological molecules that perform their functions by converting chemical energy into mechanical work. They move unidirectionally along rigid protein filaments or DNA and RNA molecules in discrete steps by hydrolyzing ATP (adenosine triphsophate) or related energy-rich compounds. Recent single-molecule experiments have shown that motor proteins experience significant spatial fluctuations during its motion, leading to broad step-size distributions. The effect of these spatial fluctuations is analyzed explicitly by considering discrete-state stochastic models that allow us to compute exactly all dynamic properties. It is shown that for symmetric spatial fluctuations there is no change in mean velocities for weak external forces, while dispersions and stall forces are strongly affected at all conditions. These results are illustrated by several simple examples. Our method is also applied to analyze the effect of step-size fluctuations on dynamics of myosin V motor proteins. It is argued that spatial fluctuations might be used to control and regulate the dynamics of motor proteins.     

How to accelerate protein search on DNA: location and dissociation

One of the most important features of biological systems that controls their functioning is the ability of protein molecules to find and recognize quickly specific target sites on DNA. Although these phenomena have been studied extensively, detailed mechanisms of protein-DNA interactions during the search are still not well understood. Experiments suggest that proteins typically find their targets fast by combining three-dimensional and one-dimensional motions, and most of the searching time proteins are non-specifically bound to DNA. However these observations are surprising since proteins diffuse very slowly on DNA, and it seems that the observed fast search cannot be achieved under these conditions for single proteins. Here we propose two simple mechanisms that might explain some of these controversial observations. Using first-passage time analysis, it is shown explicitly that the search can be accelerated by changing the location of the target and by effectively irreversible dissociations of proteins. Our theoretical predictions are supported by Monte Carlo computer simulations.     

Condensation of N interacting bosons: a hybrid approach to condensate fluctuations

We present a new method of calculating the distribution function and fluctuations for a Bose-Einstein condensate (BEC) of N interacting atoms. The present formulation combines our previous master equation and canonical ensemble quasiparticle techniques. It is applicable both for ideal and interacting Bogoliubov BEC and yields remarkable accuracy at all temperatures. For the interacting gas of 200 bosons in a box we plot the temperature dependence of the first four central moments of the condensate particle number and compare the results with the ideal gas. For the interacting mesoscopic BEC, as with the ideal gas, we find a smooth transition for the condensate particle number as we pass through the critical temperature.     

Characterization of palladium nanoparticles by using X-ray reflectivity, EXAFS, and electron microscopy

We compared the characteristics of dodecanethiolate palladium nanoparticles synthesized by two different techniques, a one-phase method and a two-phase method. From transmission electron microscopy (TEM), we determined that the particle sizes were 46 +/- 10 angstroms and 20 +/- 5 angstroms for the one- and two-phase particles, respectively. Electron diffraction confirmed that their structure was face-centered cubic (fcc). The lattice constant a0 was 3.98 +/- 0.01 angstroms and 3.90 +/- 0.01 angstroms for the one- and two-phase particles, respectively. High-resolution TEM (HRTEM) showed that the one-phase particles had an ordered core surrounded by a disordered shell structure, while the two-phase particles appeared to be crystalline throughout. The particles were also analyzed with extended X-ray absorption fine structure (EXAFS). A cuboctahedral fcc model was used to fit the data, which implied particle sizes of less than 10 angstroms for both the one- and two-phase particles. The discrepancy between the two techniques was attributed to the presence of a disordered phase, which we presumed was composed of Pd-S compounds. Compared with the bulk palladium, lattice expansion was observed in both one- and two-phase particles by electron diffraction, HRTEM, and EXAFS. At the air/water interface, a uniform film that produced surface pressure/area isotherms could only be obtained from the two-phase particles. The one-phase particles did not wet the water surface. X-ray reflectivity data indicated that the Langmuir monolayer of the two-phase particles was only 13 angstroms thick. TEM revealed the diameter of the particles in this layer to be 23 angstroms; hence the particles assumed an oblate structure after spreading. EXAFS examination of a stack of 750 Langmuir monolayers indicated far fewer Pd-S compounds, which may have dissolved in the water. The data were consistent with a model of a monolayer of truncated cuboctahedron Pd particles that were 7 angstroms thick and 19 angstroms in diameter.     

Comparison of decanethiolate gold nanoparticles synthesized by one-phase and two-phase methods

We investigated the differences between the decanethiolate gold nanoparticles synthesized by two different routes: one-phase and two-phase methods. Their properties were compared in bulk and at the air-water interface by transmission electron microscopy (TEM), X-ray reflectivity (XR), extended X-ray absorption fine structure (EXAFS) spectroscopy, X-ray powder diffraction (XRD), thermal gravimetric analysis (TGA), time-of-flight secondary-ion mass spectrometry (TOF-SIMS), electron paramagnetic resonance (EPR), and Langmuir-Blodgett technique. The mean nanoparticles sizes obtained by EXAFS and XRD were found to be smaller than those by the TEM measurements. We explained these differences by the structural disorder and multiple twinning in the nanoparticles. The one-phase particles were found by EXAFS to be smaller and had a higher grafting density of thiol chains than the two-phase particles. We attributed these differences to the enhanced disorder of the one-phase particles. At the air-water interface, the one-phase particles did not spread, while the two-phase particles spread and formed Langmuir films. TEM and XR results revealed that the close-packed monolayer of the two-phase particles collapsed and folded into multilayer films upon further compression.     

Effect of high-frequency modes and hot transitions on free energy gap dependence of charge recombination rate

The charge recombination (CR) dynamics of geminate ion pairs formed by excitation of the ground-state donor-acceptor complexes in polar solvent have been investigated within the framework of stochastic approach. It is shown that for low exergonic reactions these dynamics critically depend on the reorganization energy of intramolecular high-frequency mode. Even moderate reorganization energies (0.1-0.2 eV) significantly accelerate the excited-state population decay making it nearly exponential. In the solvent-controlled regime, the majority of the excited donor-acceptor complexes recombine at nonthermal (hot) stage when the nonequilibrium initial wave packet passes through a number of term crossings corresponding to the transitions with creation of several vibrational quanta. Analysis of this mechanism allows to conclude (i) the CR in viscous solvents proceeds much faster than the diffusive relaxation of solvent, (ii) under certain conditions, the CR rate becomes practically independent of the diffusive component of solvent relaxation which is determined by solvent viscosity, (iii) in contrast to predictions of Marcus theory, the CR rate decreases monotonically with the rise of reaction exergonicity even at small free energy gaps, in accordance with experimental results. Two semiquantitative approaches providing rather simple analytical expressions for the hot charge recombination dynamics are suggested. These approximations give a good reproduction of the excited-state decay in the wide area of model parameters.     

The first metal-based paullone derivative with high antiproliferative activity in vitro

9-Bromo-7,12-dihydroindolo[3,2-d][1]benzazepin-6(5H)-one, kenpaullone, which displays similarities in the activity profile to flavopiridol, was modified by chemical transformations at the lactam unit to provide a peripheral binding site able to accommodate metal ions. The first metal-based paullone has been prepared and characterized by single-crystal X-ray diffraction methods, solid-state cross-polarization magic angle spinning 13C NMR spectroscopy, electrospray ionization mass spectra, and electronic spectra. The gallium complex [GaL2]Cl.2.5H2O, the metal-free ligand (HL), and the starting compound used for the preparation of HL were assessed in vitro for their cytotoxicity in a panel of human tumor cell lines. The gallium complex was found to be 1.5-18-fold more cytotoxic than HL, with an average IC50 value of 2.0 microM.     

Plasmon beams interaction at interface between metal and dielectric with saturable Kerr nonlinearity

We present a novel theory of surface plasmon polariton interaction on the surface of dielectric with saturable Kerr nonlinearity. The effect of the total internal reflection of a weak signal plasmon beam from a high-power reference beam is discussed. Both ray and wave theories are used to describe signal propagation. The effect of the signal tunneling through the narrow inhomogeneity induced by the reference beam is considered.