Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium

The B-form of DNA can populate two different backbone conformations: BI and BII, defined by the difference between the torsion angles ε and ζ (BI = ε-ζ < 0 and BII = ε-ζ > 0). BI is the most populated state, but the population of the BII state, which is sequence dependent, is significant and accumulating evidence shows that BII affects the overall structure of DNA, and thus influences protein-DNA recognition. This work presents a reparametrization of the CHARMM27 additive nucleic acid force field to increase the sampling of the BII form in MD simulations of DNA. In addition, minor modifications of sugar puckering were introduced to facilitate sampling of the A form of DNA under the appropriate environmental conditions. Parameter optimization was guided by quantum mechanical data on model compounds, followed by calculations on several DNA duplexes in the condensed phase. The selected optimized parameters were then validated against a number of DNA duplexes, with the most extensive tests performed on the EcoRI dodecamer, including comparative calculations using the Amber Parm99bsc0 force field. The new CHARMM model better reproduces experimentally observed sampling of the BII conformation, including sampling as a function of sequence. In addition, the model reproduces the A form of the 1ZF1 duplex in 75 % ethanol, and yields a stable Z-DNA conformation of duplex (GTACGTAC) in its crystal environment. The resulting model, in combination with a recent reoptimization of the CHARMM27 force field for RNA, will be referred to as CHARMM36.     

On the analyses of fluorescence depolarisation data in the presence of electronic energy migration. Part I: Theory and general description

A new and general procedure is described for a detailed analysis of time-resolved fluorescence depolarisation data in the presence of electronic energy migration. An isotropic ensemble of bifluorophoric molecules (D(1)-R-D(2)) has been studied to demonstrate its utility. Intramolecular donor-donor energy migration occurs between the two donor groups (D), which are covalently connected to a rigid linker group (R). These groups undergo restricted reorientational motions with respect to the R group. The analysis of depolarisation data basically involves the search for best-fit parameters which describe the local reorientational motions, the intermolecular D(1)-D(2) distance, as well as the mutual orientations of the donors. For this, the analysis is partly performed on the Fourier domain and the best-fit parameters are determined by using an approach based on a Genetic Algorithm. The energy migration process has been described by using Monte Carlo simulations and an extended F?rster theory (EFT). It is found that the EFT provides the least time-consuming computational method. Since one-photon and two-photon excited fluorescence experiments can be applied for energy migration studies, a general and unified theoretical formulation is given.     

Electronic Structure of an [FeFe] Hydrogenase Model Complex in Solution Revealed by X-ray Absorption Spectroscopy Using Narrow-Band Emission Detection

High-resolution X-ray absorption spectroscopy with narrow-band X-ray emission detection, supported by density functional theory calculations (XAES-DFT), was used to study a model complex, ([Fe(2)(μ-adt)(CO)(4)(PMe(3))(2)] (1, adt = S-CH(2)-(NCH(2)Ph)-CH(2)-S), of the [FeFe] hydrogenase active site. For 1 in powder material (1(powder)), in MeCN solution (1'), and in its three protonated states (1H, 1Hy, 1HHy; H denotes protonation at the adt-N and Hy protonation of the Fe-Fe bond to form a bridging metal hydride), relations between the molecular structures and the electronic configurations were determined. EXAFS analysis and DFT geometry optimization suggested prevailing rotational isomers in MeCN, which were similar to the crystal structure or exhibited rotation of the (CO) ligands at Fe1 (1(CO), 1Hy(CO)) and in addition of the phenyl ring (1H(CO,Ph), 1HHy(CO,Ph)), leading to an elongated solvent-exposed Fe-Fe bond. Isomer formation, adt-N protonation, and hydride binding caused spectral changes of core-to-valence (pre-edge of the Fe K-shell absorption) and of valence-to-core (K?(2,5) emission) electronic transitions, and of Kα RIXS data, which were quantitatively reproduced by DFT. The study reveals (1) the composition of molecular orbitals, for example, with dominant Fe-d character, showing variations in symmetry and apparent oxidation state at the two Fe ions and a drop in MO energies by ～1 eV upon each protonation step, (2) the HOMO-LUMO energy gaps, of ～2.3 eV for 1(powder) and ～2.0 eV for 1', and (3) the splitting between iron d(z(2)) and d(x(2)-y(2)) levels of ～0.5 eV for the nonhydride and ～0.9 eV for the hydride states. Good correlations of reduction potentials to LUMO energies and oxidation potentials to HOMO energies were obtained. Two routes of facilitated bridging hydride binding thereby are suggested, involving ligand rotation at Fe1 for 1Hy(CO) or adt-N protonation for 1HHy(CO,Ph). XAES-DFT thus enables verification of the effects of ligand substitutions in solution for guided improvement of [FeFe] catalysts.     

A practical electromediated ipso-hydroxylation of aryl and alkyl boronic acids under an air atmosphere

An efficient electromediated aerobic ipso-hydroxylation reaction of aryl and alkyl boronic acids has been developed. Furthermore, mechanistic insight into the role of superoxide anions in this reaction has also been provided based on electrochemical studies and experimental results.     

Sparsity of the average curvature information matrix

We present a theorem regarding the average curvature properties of partially separable functions which need not be differentiable or continuous. This has implications for derivative-free optimization methods which make use of average curvature information to select the set of search directions. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Effects of the physicochemical properties of titanium dioxide nanoparticles, commonly used as sun protection agents, on microvascular endothelial cells

Until now, the potential effects of titanium dioxide (TiO₂) nanoparticles on endothelial cells are not well understood, despite their already wide usage. Therefore, the present work characterizes six TiO₂ nanoparticle samples in the size range of 19 × 17 to 87 × 13 nm, which are commonly present in sun protection agents with respect to their physicochemical properties (size, shape, ζ-potential, agglomeration, sedimentation, surface coating, and surface area), their interactions with serum proteins and biological impact on human microvascular endothelial cells (relative cellular dehydrogenase activity, adenosine triphosphate content, and monocyte chemoattractant protein-1 release). We observed no association of nanoparticle morphology with the agglomeration and sedimentation behavior and no variations of the ζ-potential (?14 to ?19 mV) in dependence on the surface coating. In general, the impact on endothelial cells was low and only detectable at concentrations of 100 μg/ml. Particles containing a rutile core and having rod-like shape had a stronger effect on cell metabolism than those with anatase core and elliptical shape (relative cellular dehydrogenase activity after 72 h: 60 vs. 90 %). Besides the morphology, the nanoparticle shell constitution was found to influence the metabolic activity of the cells. Upon cellular uptake, the nanoparticles were localized perinuclearly. Considering that in the in vivo situation endothelial cells would come in contact with considerably lower nanoparticle amounts than the lowest-observable adverse effects level (100 μg/ml), TiO₂ nanoparticles can be considered as rather harmless to humans under the investigated conditions.     

Quantitative Medium-Resolution NMR Spectroscopy Under Non-Equilibrium Conditions,Studied on the Example of an Esterification Reaction

Medium-resolution nuclear magnetic resonance spectroscopy is a promising tool for the monitoring of liquid reactions. For process analytical applications, the requirements of robustness and insensitivity of the spectrometer in relation to high temperatures and pressures are challenging. Within this study, a flow probe using a glass dewar is presented. Temperatures of flowing samples up to 130 °C and pressures up to 40 bar were successfully applied, and the corresponding temperature loss of the flowing sample at 2 ml min^?1 was <2.4 °C at 130 °C. Furthermore, if the process requires a measurement in a non-equilibrium state of magnetization, a comprehensive data treatment is given. For this purpose, the influences of the flow and T ₁ of the substances under investigation are studied in detail on the example of a homogeneously catalyzed esterification. In addition, data analysis schemes were designed such that the experiments directly revealed mole fractions from the spectra. Limited spectral resolutions and low signal-to-noise ratio still did not obstruct quantitative interpretation of the experiments.     

Aggregation and the estimation of equation systems

Simulations based on two sets of data are used to assess the impact of combining equations on the accuracy of parameter estimates and their asymptotic standard errors.     

Polarized fluorescence and absorption spectroscopy of 1,32-dihydroxy-dotriacontane-bis-rhodamine 101 ester. A new and lipid bilayer-spanning probe

We report on the properties of 1,32-dihydroxy-dotriacontane-bis-rhodamine 101 ester (Rh101C₃₂Rh101) in lipid bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and in liquid solvents. The results are compared with those of rhodamine 101 octadecanyl ester (Rh101C₁₈). Both molecules are solubilized in the lipid bilayer and the Rh101 moieties are anchored in the lipid-water interface, so that the electronic transition dipole moments (S ₀ S ₁) are oriented preferentially in the plane of the bilayer. At low concentrations of the dyes in lipid bilayers of DOPC, the fluorescence relaxation is single exponential with a lifetime of =4.9±0.2 ns. The relative fluorescence quantum yield of _C32/_C18 0.95 in DOPC vesicles. These results strongly suggest that only a small fraction of the Rh101C₃₂Rh101 molecules are quenched, by, for example, intra- or intermolecular dimers in the ground state at mole fractions of less than 0.1% in the lipid bilayers. For Rh101C₃₂Rh101 in lipid vesicles, the steady-state and time-resolved fluorescence anisotropies are compatible with efficient intramolecular electronic energy transfer. It is concluded that nearly every Rh101C₃₂Rh101 molecule is spanning across the lipid bilayer of DOPC.