A Semigroup Approach to Stochastic Delay Equations in Spaces of Continuous Functions

We present a semigroup approach to stochastic delay equations of the form

Comparison of a two-dimensional liquid chromatography/mass spectrometry approach with a chip-based nanoelectrospray device for structural elucidation of metabolites in a human ADME study using a quadrupole time-of-flight mass spectrometer

The study of the metabolic fate of drugs is essential for the safety assessment of new compounds in the drug development process. However, the characterization and structural elucidation of metabolites from in vivo experiments is still a very challenging task. In this paper, we compare a two-dimensional liquid chromatography/mass spectrometry (LC/MS) approach using either a capillary LC/MS system or the recently introduced chip-based nanoelectrospray/MS system (Nanomate) as the second dimension for structural elucidation of metabolites by MS. More than 30 radioactive fractions of a chromatographic separation from a human urine sample were analyzed and 54 metabolites could be identified. The long persisting and stable nanoelectrospray enabled the search for unknown metabolites by precursor-ion scanning experiments followed by product-ion scanning experiments of potential metabolites using a quadrupole time-of-flight (qTOF) mass spectrometer. The number of fragments produced by nanoelectrospray with product-ion scanning was significantly higher compared to LC/MS experiments with in-source fragmentation. Therefore, the assignment of possible modifications in metabolites to certain moieties of the drug could be investigated with higher accuracy. The capillary LC/MS system for the second dimension was more sensitive in the case of low abundant metabolites. These metabolites could not be detected by direct nanoelectrospray infusion, which limits the application of the Nanomate for trace metabolites.     

First-principles thermochemistry for the production of TiO2 from TiCl4

Despite the industrial importance of the process, the detailed chemistry of the high-temperature oxidation of titanium tetrachloride (TiCl4) to produce titania (TiO2) nanoparticles remains unknown, partly due to a lack of thermochemical data. This work presents the thermochemistry of many of the intermediates in the early stages of the mechanism, computed using quantum chemistry. The enthalpies of formation and thermochemical data for TiOCl, TiOCl2, TiOCl3, TiO2Cl2, TiO2Cl3, Ti2O2Cl3, Ti2O2Cl4, Ti2O3Cl2, Ti2O3Cl3, Ti3O4Cl4, and Ti5O6Cl8 were calculated using density functional theory (DFT). The use of isodesmic and isogyric reactions was shown to be important for determining standard enthlapy of formation (Delta(f)H(degree)(298K)) values for these transition metal oxychloride species. TiOCl2, of particular importance in this mechanism, was also studied with CCSD(T) and found to have Delta(f)H(degree)(298K) = -598 +/- 20 kJ/mol. Finally, equilibrium calculations were performed to identify which intermediates are likely to be most prevalent in the high temperature industrial process, and as a first attempt to identify the size of the critical nucleus.     

Translational diffusion constants of the amino acids: measurement by NMR and their use in modeling the transport of peptides

In this work, the translational self-diffusion constants, DT's, of 12 amino acids (Ala, Arg, Asn, Asp, Cys, Glu, His, Ile, Lys, Met, Phe, and Ser) are measured by field gradient NMR and extrapolated to infinite dilution. The experiments were carried out in D2O at 298 K at pD approximately =3.5 in 50 mM sodium phosphate buffer. Of these 12 amino acids, 6 are being reported for the first time (Asp, Cys, Glu, His, Lys, and Met) and the remaining 6 (Ala, Arg, Asn, Ile, Phe, and Ser) are compared with DT's from the literature. When corrected for differences in solvent viscosity and temperature, the discrepancy between DT's measured in the present work and those reported previously is always <8%, which is reasonable given the range of values reported previously by different groups. With the present work, DT's for all of the amino acids are now available. These diffusion constants are then used in modeling studies of the diffusion and free solution electrophoretic mobility, mu, of several model peptides. For this set of peptides, it is shown that modeling using revised input parameters results in improved agreement between model and experimental mobilities.     

Supramolecular self-assembly initiated by solid-solid wetting

We present a preparation method for self-assembled supra-molecular monolayers of unsubstituted organic semiconductors and pigments on a solid substrate, applicable under ambient conditions. The deposition is based on a solid-solid wetting phenomenon, whereas the subsequent layer growth proceeds according to standard models. Molecular adsorption results from direct contact of the compound in a nanocrystalline state with the solid surface. Based on complementary force field calculations, we propose that molecules disintegrate from the crystalline state and adsorb on the surface because of a gain in binding energy. The preparation method is exemplified by means of a linear hydrogen-bonded system, namely quinacridone (QAC) on graphite. In addition, the chosen system allows us to actively guide the self-assembly after deliberate removal of molecules from a predefined area.     

Heavy Grignard reagents: challenges and possibilities of aryl alkaline earth metal compounds

Compounds of the type aryl--M--X, with M=Ca, Sr, Ba and X as any kind of ligand (such as halide, phosphanide, amide, aryl), are presented. The low reactivity of the heavy alkaline earth metals calcium, strontium, and barium enforces an activation prior to use for the direct synthesis. The insertion of these metals into C--I bonds of aryl iodides (direct synthesis) yields aryl metal iodides and has to be performed at low temperatures and in THF. Aryl alkaline-earth-metal compounds show some characteristics: 1) the ease of ether cleavage enforces low reaction temperatures, 2) for Sr and Ba the Schlenk equilibrium is shifted towards homoleptic MI2 and MPh2, 3) high solubility of diaryl alkaline-earth-metal derivatives in THF even at low temperatures initiated quantum chemical investigations on the aggregation behavior, and 4) a strong low field shift of the 13C resonances of the ipso carbon atoms in NMR spectra was observed. First results from quantum chemical calculations on diaryl dicalcium(I) suggest a long Ca--Ca bond with a considerable Ca--Ca bond dissociation energy. Initial results on a selection of applications such as metallation, metathesis, and addition reactions of aryl calcium compounds are presented as well.     

Solubilizing sodium fluoride in acetonitrile: synthesis, molecular structure, and complexation behavior of bis(organostannyl)methyl-substituted crown ethers

The synthesis of the crown-ether-substituted bis(organostannyl)methanes Ph(3)SnCH(2)Sn(Ph(2))-CH(2)-[16]crown-5 (1) and Ph(2)ISnCH(2)Sn(I)(Ph)-CH(2)-[16]crown-5 (2) is reported. Both compounds have been characterized by elemental analyses, (1)H, (13)C, (19)F, and (119)Sn NMR spectroscopy, and in the case of compound 2 also by electrospray ionization mass spectrometry. Single-crystal X-ray diffraction analysis revealed for the aqua complex 2.H(2)O trigonal-bipyramidal-configured tin atoms with intramolecular Sn(1)-O(1) and Sn(2)-O(1W) distances of 2.555(2) and 2.440(3) A, respectively. The water molecule is trapped in a sandwich-like fashion between the crown ether oxygen atoms O(2) and O(4) and the Sn(2) atom. NMR spectroscopy unambiguously proved the ability of compound 2 in acetonitrile to overcome the high lattice energy of sodium fluoride and to complex the latter under charge separation.     

Diffusive dynamics on multidimensional rough free energy surfaces

The dynamics of processes relevant to chemistry and biophysics on rough free energy landscapes is investigated using a recently developed algorithm to solve the Smoluchowski equation. Two different processes are considered: ligand rebinding in MbCO and protein folding. For the rebinding dynamics of carbon monoxide (CO) to native myoglobin (Mb) from locations around the active site, the two-dimensional free energy surface (FES) is constructed using extensive molecular dynamics simulations. The surface describes the minima in the A state (bound MbCO), CO in the distal pocket and in the Xe4 pocket, and the transitions between these states and allows to study the diffusion of CO in detail. For the folding dynamics of protein G, a previously determined two-dimensional FES was available. To follow the diffusive dynamics on these rough free energy surfaces, the Smoluchowski equation is solved using the recently developed hierarchical discrete approximation method. From the relaxation of the initial nonequilibrium distribution, experimentally accessible quantities such as the rebinding time for CO or the folding time for protein G can be calculated. It is found that the free energy barrier for CO in the Xe4 pocket and in the distal pocket (B state) closer to the heme iron is approximately 6 kcal/mol which is considerably larger than the inner barrier which separates the bound state and the B state. For the folding of protein G, a barrier of approximately 10 kcal/mol between the unfolded and the folded state is consistent with folding times of the order of milliseconds.     

Decomposition of density matrix renormalization group states into a Slater determinant basis

The quantum chemical density matrix renormalization group (DMRG) algorithm is difficult to analyze because of the many numerical transformation steps involved. In particular, a decomposition of the intermediate and the converged DMRG states in terms of Slater determinants has not been accomplished yet. This, however, would allow one to better understand the convergence of the algorithm in terms of a configuration interaction expansion of the states. In this work, the authors fill this gap and provide a determinantal analysis of DMRG states upon convergence to the final states. The authors show that upon convergence, DMRG provides the same complete-active-space expansion for a given set of active orbitals as obtained from a corresponding configuration interaction calculation. Additional insight into DMRG convergence is provided, which cannot be obtained from the inspection of the total electronic energy alone. Indeed, we will show that the total energy can be misleading as a decrease of this observable during DMRG microiteration steps may not necessarily be taken as an indication for the pickup of essential configurations in the configuration interaction expansion. One result of this work is that a fine balance can be shown to exist between the chosen orbital ordering, the guess for the environment operators, and the choice of the number of renormalized states. This balance can be well understood in terms of the decomposition of total and system states in terms of Slater determinants.     

Conventional sample enrichment strategies combined with high-performance liquid chromatography-solid phase extraction-nuclear magnetic resonance analysis allows analyte identification from a single minuscule Corydalis solida plant tuber

Identification of putative biomarker molecules within the genus Corydalis (Papaveraceae) was pursued by combining conventional off-line sample enrichment with high-performance liquid chromatography-solid phase extraction-nuclear magnetic resonance (HPLC-SPE-NMR) based structure elucidation. Off-line reversed phase solid phase extraction (SPE) was used to enrich the desired analytes from a methanolic extract (93 mg dry weight) of a miniscule single tuber (233 mg dry weight) of C. solida. An aliquot of the SPE fraction (2.1 mg) was subjected to separation in the HPLC-SPE-NMR hyphenation. Chromatographic peaks bearing the metabolites under investigation were trapped in the SPE device in a single experiment and transferred to a 600 MHz NMR spectrometer equipped with a 30 microl cryofit insert fed into a 3 mm cryoprobe. Recorded homo- and heteronuclear 1D and 2D NMR data allowed the identification of the three analytes under investigation as protopine, allocryptopine, and N-methyl-laudanidinium acetate. The latter is a rare alkaloid, which has been isolated only once before.