Structure determination in a new type of amorphous molecular solids with different nonlinear optical properties: a comparative structural analysis.

The microscopic structures of two amorphous molecular solids with extremely nonlinear optical properties have been studied. They consist of organotetrel chalcogenide clusters with the chemical formula [(RSn)4S6]. The basic molecular building blocks are adamantane-like {Sn4S6} cores with organic ligands R attached to the Sn atoms. While the material equipped with R=naphthyl generates frequency doubling upon irradiation with a simple infrared laser diode, the material decorated with R=phenyl responds by emitting brilliant white light. The structural differences were investigated using x-ray scattering and extended x-ray absorption fine structure combined with molecular Reverse Monte Carlo. Transmission electron microscopy and scanning precession electron diffraction were used to examine structural differences from mesoscopic down to microscopic scales. Characteristic differences were found on all scales. While close core-to-core distances between {Sn4S6} cluster cores and molecular distortions are found in the white light emitting material, undistorted molecules and significantly larger core distances characterize the material showing frequency doubling. Here however, results of scanning precession electron diffraction reveal the formation of nanocrystalline structures in the amorphous matrix, which we identify as cause for the suppression of white light emission.

Structural origins of the unusual thermal stability of amorphous CuxGe50-xTe50(0⩽x⩽33.3).

We have investigated the local atomic structures of several compositions of the amorphous phase of the system CuxGe50-xTe50(0⩽x⩽33.3), based on extended x-ray absorption fine-structure as well as anomalous x-ray scattering experiments, and discuss the unusual trend regarding their thermal stability as a function of the Cu content. At low concentrations (x⩽15), Cu atoms tend to agglomerate in flat nanoclusters reminiscent of the crystalline phase of metallic Cu, leading to a more and more Ge-deficient Ge-Te host network structure with growing Cu content and an increasing thermal stability. At higher Cu concentrations (x⩾25), Cu is incorporated into the network, leading to an overall weaker bonding situation which is associated with a decreasing thermal stability.

Calculation of the static and dynamical correlation energy of pseudo-one-dimensional beryllium systems via a many-body expansion.

Due to the importance of both static and dynamical correlation in the bond formation, low-dimensional beryllium systems constitute interesting case studies to test correlation methods. Aiming to describe the whole dissociation curve of extended Be systems we chose to apply the method of increments (MoI) in its multireference (MR) formalism. To gain insight into the main characteristics of the wave function, we started by focusing on the description of small Be chains using standard quantum chemical methods. In a next step we applied the MoI to larger beryllium systems, starting from the Be6 ring. The complete active space formalism was employed and the results were used as reference for local MR calculations of the whole dissociation curve. Although this is a well-established approach for systems with limited multireference character, its application regarding the description of whole dissociation curves requires further testing. Subsequent to the discussion of the role of the basis set, the method was finally applied to larger rings and extrapolated to an infinite chain.

On the calculation of complete dissociation curves of closed-shell pseudo-onedimensional systems via the complete active space method of increments.

The method of increments (MoI) has been employed using the complete active space formalism in order to calculate the dissociation curve of beryllium ring-shaped clusters Be(n) of different sizes. Benchmarks obtained through different quantum chemical methods including the ab initio density matrix renormalization group were used to verify the validity of the MoI truncation which showed a reliable behavior for the whole dissociation curve. Moreover we investigated the size dependence of the correlation energy at different interatomic distances in order to extrapolate the values for the periodic chain and to discuss the transition from a metal-like to an insulator-like behavior of the wave function through quantum chemical considerations.

Specific many-electron effects in X-ray spectra of simple metals and graphene.

In this work the influence of many-electron effects on the shape of characteristic X-ray emission bands of the simple metals Mg and Al is examined by means of ab initio calculations and semi-empirical models. These approaches are also used for the analysis of C K-emission and absorption spectra of graphene. Both the dynamical screening of the core vacancy and the Auger-effect in the valence band (VB) have been taken into account. Dynamical screening of the core vacancy by valence electrons (the so-called MND effect) is considered ab initio in the framework of density functional theory. The Auger effect in the VB was taken into account within a semi-empirical method, approximating the quadratic dependence of the VB hole level width on the difference between the level energy and the Fermi energy. All theoretical spectra are in very good agreement with available experimental data.

Computation of the electronic flux density in the Born-Oppenheimer approximation.

A molecule in the electronic ground state described in the Born­Oppenheimer approximation (BOA) by the wave function ΨBO = Φ0χ0 (where Φ0 is the time-independent electronic energy eigenfunction and χ0 is a time-dependent nuclear wave packet) exhibits a nonzero nuclear flux density, whereas it always displays zero electronic flux density (EFD), because the electrons are in a stationary state. A hierarchical approach to the computation of the EFD within the context of the BOA, which utilizes only standard techniques of quantum chemistry (to obtain Φ0) and quantum dynamics (to describe the evolution of χ0 on the ground-state potential energy surface), provides a resolution of this puzzling, nonintuitive result. The procedure is applied to H2(+) oriented parallel with the z-axis and vibrating in the ground state (2)Σg(+). First, Φ0 and χ0 are combined by the coupled-channels technique to give the normally dominant z-component of the EFD. Imposition of the constraints of electronic continuity, cylindrical symmetry of Φ0 and two boundary conditions on the EFD through a scaling procedure yields an improved z-component, which is then used to compute the complementary orthogonal ρ-component. The resulting EFD agrees with its highly accurate counterpart furnished by a non-BOA treatment of the system.

Coupled-channels quantum theory of electronic flux density in electronically adiabatic processes: application to the hydrogen molecule ion.

This article presents the results of the first quantum simulations of the electronic flux density (j(e)) by the "coupled-channels" (CC) theory, the fundamentals of which are presented in the previous article [Diestler, D. J. J. Phys. Chem. A 2012, DOI: 10.1021/jp207843z]. The principal advantage of the CC scheme is that it employs exclusively standard methods of quantum chemistry and quantum dynamics within the framework of the Born-Oppenheimer approximation (BOA). The CC theory goes beyond the BOA in that it yields a nonzero j(e) for electronically adiabatic processes, in contradistinction to the BOA itself, which always gives j(e) = 0. The CC is applied to oriented H(2)(+) vibrating in the electronic ground state ((2)Σ(g)(+)), for which the nuclear and electronic flux densities evolve on a common time scale of about 22 fs per vibrational period. The system is chosen as a touchstone for the CC theory, because it is the only one for which highly accurate flux densities have been calculated numerically without invoking the BOA [Barth et al, Chem. Phys. Lett. 2009, 481, 118]. Good agreement between CC and accurate results supports the CC approach, another advantage of which is that it allows a transparent interpretation of the temporal and spatial properties of j(e).

High prevalence of Mycoplasma pneumoniae in intestinal mucosal biopsies from patients with inflammatory bowel disease and controls.

Intestinal microflora are believed to play an important role in the pathogenesis of inflammatory bowel disease (IBD). Mycoplasma have been suggested previously as organisms of ubiquitous distribution with the potential to cause inflammatory diseases, including IBD in susceptible individuals. The aim of this study was to determine the frequency of the presence of M. pneumoniae DNA in intestinal biopsies from patients with IBD and non-IBD controls using a microplate polymerase chain reaction-hybridization assay (PCR-ELISA). A total of 260 endoscopic biopsies (49 from 19 patients with Crohn's disease, 76 from 27 patients with ulcerative colitis, and 135 from 43 non-IBD controls) were used in this study. Overall, M. pneumoniae-specific DNA was detected in 100 endoscopic biopsy samples (38.5%). Among them, the detection rate of M. pneumoniae DNA was significantly higher in biopsies from patients with CD (59.2%) than in those from patients with UC (26.3%) or non-IBD controls (37.7%) (chi2 = 13.65, P < or = 0.001). The high prevalence of M. pneumoniae in both IBD patients and controls suggest this organism is ubiquitous and may persist in the intestinal mucosa. Epidemiological studies in IBD suggest acquisition of some agents early in life probably during epidemics in temperate latitudes. M. pneumoniae could be one of the ubiquitous agents implicated in the pathogenesis of IBD.

Increased serum levels of eotaxin in patients with inflammatory bowel disease.

BACKGROUND: The CC-chemokines eotaxin and eotaxin-2, produced by epithelial and phagocytic cells, are potent and selective chemoattractants for eosinophils and basophils. The eosinophil is a potent inflammatory cell thought to play an important role in the pathogenesis of inflammatory bowel disease (IBD). In this study we investigated the serum concentrations of eotaxin and eotaxin-2 in patients with Crohn disease and ulcerative colitis. METHODS: Thirty-one patients with Crohn disease, 35 patients with ulcerative colitis and 41 control patients were studied. Eotaxin and eotaxin-2 serum levels were measured with solid phase sandwich enzyme-linked immunosorbent assays. RESULTS: Significantly increased serum eotaxin levels were observed in both patients with Crohn disease (289.4+/-591.5 pg/ml) and ulcerative colitis (207.0+/-243.4 pg/ml) when compared with controls (138.0+/-107.8 pg/ml) (P < 0.01). Moreover, patients with active Crohn disease and ulcerative colitis showed significantly higher serum eotaxin levels than patients with quiescent disease (434.0+/-776.8 pg/ml versus 113.8+/-65.4 pg/ml in Crohn disease and 295.7+/-337.1 versus 121.2+/-91.9 pg/ml in ulcerative colitis, P < 0.05). In contrast, there was no significant difference in eotaxin-2 serum levels among patients with Crohn disease (863.5+/-448.2 pg/ml), ulcerative colitis (1028.3+/-431.4 pg/ml) and controls (981.4+/-539.4 pg/ml). CONCLUSIONS: Eotaxin is significantly increased in serum of patients with active Crohn disease and ulcerative colitis, suggesting that this cytokine may play a role in the pathogenesis of IBD.

Detection of Listeria monocytogenes by polymerase chain reaction in intestinal mucosal biopsies from patients with inflammatory bowel disease and controls.

BACKGROUND AND AIMS: Components of the intestinal microflora are believed to play an important role in the pathogenesis of inflammatory bowel disease (IBD) in genetically susceptible hosts acting either as a non-specific antigenic stimulus or as a specific pathogen. Listeria monocytogenes has been suggested as an organism with the potential to cause IBD. The objective of the present study was to investigate the prevalence of L. monocytogenes DNA in intestinal biopsies from patients with IBD and from non-IBD controls by using nested polymerase chain reaction (PCR). METHODS: The DNA was extracted from 274 colonoscopic biopsies, which were obtained from 23 patients with Crohn's disease (CD), 28 with ulcerative colitis (UC) and 39 non-IBD control patients. Nested PCR amplification was used to detect the presence of the L. monocytogenes listeriolysin O (hly) gene. The sequences of positive PCR products were determined and compared with databases. RESULTS: The sensitivity of our nested PCR was 10 fg L. monocytogenes DNA. Overall, L. monocytogenes DNA was detected in 13.0% patients with CD, 17.9% patients with UC and 25.6% non-IBD control patients or in 29 of 274 (10.6%) endoscopic biopsies. Among them, L. monocytogenes DNA was detected in four of 67 (6%) biopsies from patients with CD, five of 94 (5.3%) biopsies from patients with UC and 20 of 113 biopsies (17.7%) from non-IBD control patients. Sequence analysis of positive PCR products demonstrated more than 95% similarity to the hly gene sequence of L. monocytogenes, confirming the authenticity of our PCR products. CONCLUSION: Listeria monocytogenes DNA was detected in the intestine of both patients with IBD and in non-IBD control patients, probably reflecting the widespread presence of this organism in the environment. The low yield of positive biopsies in our IBD patients (5-6%) and the fact that the detection rate of L. monocytogenes DNA was similar in endoscopic biopsies from IBD patients and non-IBD controls does not support a direct role for L. monocytogenes in the pathogenesis of IBD, at least in New Zealand patients.

Concepts for the syntheses of biotinylated steroids. Part II: 17beta-estradiol derivatives as immunochemical probes.

Biotinylated 17beta-estradiol (E2) derivatives are helpful probes for a better understanding of biospecific E2 interactions with steroid-binding proteins such as the estrogen receptor and anti-steroid antibodies. We describe synthetic strategies for the biotinylation of E2 toward the 3, 6alpha, and 7alpha positions using biotinyl-N-hydroxysuccinimide esters with different spacers, varying in structure and chain length. Key reaction for biotinylation at the 3 position is the regioselective ether formation of the phenolate E2 anion with a linker mesylate without protecting the 17beta-hydroxyl group. The 6alpha position is accessible via a 3,17beta protected 6alpha-hydroxy E2, prepared by stereospecific sodium borohydride reduction of 6-oxo E2. Direct cyanoethylation of the alcohol followed by reduction to the amine allows the biotinylation to 6alpha-O-coupled cyanoethyloxy linker E2 derivatives. Alternatively, 6alpha-O-coupled cyanoalkyloxy polyether linker E2 probes are obtained by a Williamson ether synthesis of the alcohol precursor with omega-t-butyl-dimethylsilyloxy-5-oxa-nonylmesylate. Cyanoethylation of the desilylated compound and further reduction of the nitrile led to the terminal amine. Reductive amination of the 3, 17beta acetylated 6-oxo E2 compound with 6-cyanoethyloxyhexyl ammonium acetate yields in a mixture of 6alpha/beta-N-alkylated E2 nitriles. The epimers are separated by reversed-phase HPLC and the 6alpha-compound subsequently reduced to the terminal amine. The 7alpha-biotinylated E2 compound is derived from 7alpha-(11'-undecyl-N-methyl-N-butylamide) E2, which is already known from literature. Subsequently, the 3 and 17beta positions are protected, and the amide is reduced to the 7alpha-(11'-undecanol) compound. Further cyanoethylation and reduction led to the 11'-amino-ethyloxyundecyl E2. Using (1)H NMR analysis, it could be shown that the biotin moiety of the biotinylated 6alpha- and 7alpha-E2 derivatives has an axial position which results in a vertical orientation of the substituent toward the alpha-face of the planar tetracyclic backbone. Thus, a negligible alteration of the original structure of the upper beta-face offers the feasibility of applying the 6alpha- and 7alpha-derivatives as optimal tracers in competitive immunoassays.

Concepts for the syntheses of biotinylated steroids. Part I: testosterone derivatives as immunochemical probes.

We describe synthetic strategies for the biotinylation of testosterone (T) at positions 3, 7alpha, 17alpha, and 19. These T probes are able to mimic ligand binding and may provide for a better understanding of the biospecific interaction with steroid-binding proteins such as the androgen receptor, anti-steroid antibodies, or steroid-binding serum globulins. For the 7alpha- and 17alpha-derivatives, biotinyl-N-hydroxy-succinimide esters with different types of spacer chains were used. The 3-biotin hydrazone derivative was produced using N-(epsilon-biotinyl)-caproyl hydrazide, whereas for the 19-biotinylation, a biotinyl-1-N-diamino-3, 6-dioxaoctane-amide was applied. Key reaction for the biotinylation at position 3 is the oximation of the 3-oxo function. The 17alpha-position is accessible by the reaction of the 3-protected 4-androsten-17-epoxide with oxygen in the beta-position, followed by nucleophilic ring opening with cyanide which provides the 17alpha-cyanomethyl derivative. The key step is the regioselective ketal protection of the 3-oxo function of androst-4-ene-3,17-dione using a stannoxane catalyst. An alternative pathway for the insertion of biotin at the 19-position was established by the synthesis of 17beta-hydroxy-androst-4-en-3-one-19-yl carboxymethyl ether. After activation by the carbodiimide method, the compound reacts with aminoterminal biotin derivatives. The copper(I)-catalyzed 1,6 Michael addition of 17-acetoxy-6,7-dehydro-T leads to 7alpha-derivatives by use of omega-silyl protected hydroxylalkyl-modified Grignard reagents. A functional group interconversion using the Staudinger reaction transforms the azide function into a primary omega-amino group. The absolute configurations of the different biotinylated derivatives were investigated by (1)H NMR studies. For the 7alpha-biotinylated T series, additionally, an X-ray analysis proved the axial position of the spacer group. This results in a vertical orientation of the biotin moiety toward the alpha-face of the planar tetracyclic backbone. Thus, a negligible alteration of the original structure of the upper beta-face offers the feasibility of applying the 7alpha-derivatives as optimal immunochemical tracers in competitive immunoassays. Biotinylated T derivatives should be also suitable for ligand-binding studies to the androgen receptor or to sex hormone-binding globulin.

Time-dependent inhibition of recA protein-catalyzed ATP hydrolysis by ATPgammaS: evidence for a rate-determining isomerization of the recA-ssDNA complex.

The ATP analog ATPgammaS is a competitive inhibitor of the recA protein-catalyzed ssDNA-dependent ATP hydrolysis reaction. The degree of inhibition by ATPgammaS, however, changes in a time-dependent manner and is consistent with a two step binding mechanism. In the first step, ATPgammaS binds to the recA-ssDNA complex in a rapid equilibrium step (KD = 50 microM). This initial binding step is followed by an isomerization of the recA-ssDNA-ATPgammaS complex to a new conformational state in which ATPgammaS is bound with a significantly higher affinity (overall K(D) = 0.3 microM). This isomerization is followed by the slow hydrolysis of ATPgammaS to ADP and thiophosphate (0.01 min(-1)). The first-order rate constant for the ATPgammaS-mediated isomerization step (20 min(-1)), although significantly greater than the rate of ATPgammaS hydrolysis, is identical to the steady-state rate constant for the recA protein-catalyzed ATP hydrolysis reaction. These results are consistent with a kinetic model in which an ATP-mediated isomerization of the recA-ssDNA complex represents the rate-determining step on the recA protein-catalyzed ssDNA-dependent ATP hydrolysis reaction pathway.

7 alpha-Biotinylated testosterone derivatives as tracers for a competitive chemiluminescence immunoassay of testosterone in serum.

Ring core-biotinylated testosterone tracers were synthesized with bridges of three different lengths connecting the biotin moiety to the steroid core (7 alpha-Cn-Bio-T, n = 3, 6, or 11). Together with a position 7-specific polyclonal anti-testosterone antibody, we used the 7 alpha-C11-Bio-T tracer to develop a novel, labeled-hapten competitive immunoassay for total testosterone in serum. (The C3 and C6 tracers proved to be not suitable for analogous immunoassays.) Enhanced chemiluminescence signal was generated by use of a second immobilized antibody and a streptavidin-horseradish peroxidase conjugate. The measuring range of the assay is 0.2-20.0 nmol/L, linearity of serial dilutions can be demonstrated, the lower detection limit is 0.125 nmol/L, and the interassay imprecisions are 13-16%. Accuracy determinations in mass spectrometry-controlled reference specimens showed a mean recovery of 95%. In addition, the assay shows low cross-reactivities, demonstrating the favorable specificity of the combination of a "nearly native" tracer with a position analog antibody. The optimized steric structure and the long spacer arm of the biotinylated testosterone tracer make this chemiluminescence assay well-suited for measuring total testosterone concentration in serum.

Interactions of human replication protein A with oligonucleotides.

Replication protein A (RPA) is a heterotrimeric, single-stranded DNA binding protein that is essential for eukaryotic DNA replication. In order to gain a better understanding of the interactions between RPA and DNA, we have examined the interactions of human RPA with single-stranded oligonucleotides. Our analysis of RPA.DNA complexes demonstrated that RPA binds as a heterotrimer. Stoichiometric binding reactions monitored by fluorescence quenching indicated that the binding site size of human RPA is 30 nucleotides and that between 20-30 nucleotides of DNA directly interact with RPA. The binding of RPA to DNA of different lengths was systematically examined using deoxythymidine-containing oligonucleotides. We found that the binding affinity of RPA for short oligonucleotides was length dependent. The apparent association constant of RPA varied over 200-fold from approximately 7 x 10(7) M-1 for oligo(dT)10 to approximately 1.5 x 10(10) M-1 for oligo(dT)50. Human RPA binds to oligonucleotides with low cooperativity; the cooperativity parameter (omega) for RPA binding was estimated to be approximately 15.