Elasticity reconstruction: Beyond the assumption of local homogeneity

Elasticity imaging is a novel domain which is currently gaining significant interest in the medical field. Most inversion techniques are based on the homogeneity assumption, i.e. the local spatial derivatives of the complex-shear modulus are ignored. This analysis presents an analytic approach in order to overcome this limitation, i.e. first order spatial derivatives of the real-part of the complex-shear modulus are taken into account. Resulting distributions in a gauged breast lesion phantom agree very well with the theoretical expectations. An in-vivo example of a cholangiocarcinoma demonstrates that the new approach provides maps of the viscoelastic properties which agree much better with expectations from anatomy.     

Determination of protein-ligand affinity constants from direct migration time in capillary electrophoresis

A simple method to calculate dissociation constants for protein-ligand interactions by partial-filling capillary electrophoresis is demonstrated. The method uses raw migration time data for the ligand and needs only additional information about capillary inner radius and the absolute amount of protein loaded. A theoretical study supported by experimental data also demonstrates that the retention of analyte in affinity capillary electrophoresis (ACE) using the partial-filling technique depends linearly on the absolute amount of selector added but is independent of both selector zone length and selector mobility. Factors such as field strength and electroosmotic flow are also cancelled out if they are kept constant. The theory is confirmed and the usefulness of the method is demonstrated by enantioseparations using alpha-acid glycoprotein (AGP) and cellulase (Cel 7A) as chiral selectors.     

Further development of reduced graphs for identifying bioactive compounds

Reduced graphs provide summary representations of chemical structures. Here, a variety of different types of reduced graphs are compared in similarity searches. The reduced graphs are found to give comparable performance to Daylight fingerprints in terms of the number of active compounds retrieved. However, no one type of reduced graph is found to be consistently superior across a variety of different data sets. Consequently, a representative set of reduced graphs was chosen and used together with Daylight fingerprints in data fusion experiments. The results show improved performance in 10 out of 11 data sets compared to using Daylight fingerprints alone. Finally, the potential of using reduced graphs to build SAR models is demonstrated using recursive partitioning. An SAR model consistent with a published model is found following just two splits in the decision tree.     

A study of the formation, purification and application as a SWNT growth catalyst of the nanocluster [HxPMo12O40[subset]H4Mo72Fe30(O2CMe)15O254(H2O)98

The synthetic conditions for the isolation of the iron-molybdenum nanocluster FeMoC [HxPMo12O40 [subset]H4Mo72Fe30(O2CMe)15O254(H2O)98], along with its application as a catalyst precursor for VLS growth of SWNTs have been studied. As-prepared FeMoC is contaminated with the Keplerate cage [H4Mo72Fe30(O2CMe)15O254(H2O)98] without the Keggin [HxPMo12O40]n- template, however, isolation of pure FeMoC may be accomplished by Soxhlet extraction with EtOH. The resulting EtOH solvate is consistent with the replacement of the water ligands coordinated to Fe being substituted by EtOH. FeMoC-EtOH has been characterized by IR, UV-vis spectroscopy, MS, XPS and 31P NMR. The solid-state 31P NMR spectrum for FeMoC-EtOH (delta-5.3 ppm) suggests little effect of the paramagnetic Fe3+ centers in the Keplerate cage on the Keggin ion's phosphorous. The high chemical shift anisotropy, and calculated T1 (35 ms) and T2 (8 ms) values are consistent with a weak magnetic interaction between the Keggin ion's phosphorus symmetrically located within the Keplerate cage. Increasing the FeCl2 concentration and decreasing the pH of the reaction mixture optimizes the yield of FeMoC. The solubility and stability of FeMoC in H2O and MeOH-H2O is investigated. The TGA of FeMoC-EtOH under air, Ar and H2 (in combination with XPS) shows that upon thermolysis the resulting Fe : Mo ratio is highly dependent on the reaction atmosphere: thermolysis in air results in significant loss of volatile molybdenum components. Pure FeMoC-EtOH is found to be essentially inactive as a pre-catalyst for the VLS growth of single-walled carbon nanotubes (SWNTs) irrespective of the substrate or reaction conditions. However, reaction of FeMoC with pyrazine (pyz) results in the formation of aggregates that are found to be active catalysts for the growth of SWNTs. Activation of FeMoC may also be accomplished by the addition of excess iron. The observation of prior work's reported growth of SWNTs from FeMoC is discussed with respect to these results.     

Electrochemical impedance spectroscopy and surface plasmon resonance studies of DNA hybridization on gold/SiOx interfaces

The use of Au/SiO(x) interfaces for the investigation of DNA hybridization using electrochemical impedance spectroscopy (EIS) and surface plasmon resonance (SPR) simultaneously is demonstrated. Standard glass chemistry was used to link single-stranded DNA (ss-DNA) on aldehyde-terminated Au/SiO(x) interfaces. The layer thickness and amount of grafted oligonucleotides (ODNs) were calculated from SPR on the basis of a multilayer system of glass/Ti/Au/SiO(x)/grafted molecule. Capacitance and resistance values of the modified interface before and after hybridization were calculated from EIS data using an equivalent circuit and allowed the affinity rate constant, K(A) = 4.07 x 10(5) M(-1), to be determined. The EIS results were comparable to those obtained by SPR hybridization kinetics recorded in parallel.     

Evolving interpretable structure-activity relationship models. 2. Using multiobjective optimization to derive multiple models

A multiobjective evolutionary algorithm (MOEA) is described for evolving multiple structure-activity relationships (SARs). The SARs are encoded in easy-to-interpret reduced graph queries which describe features that are preferentially present in active compounds compared to inactives. The MOEA addresses a limitation associated with many machine learning methods; that is, the inherent tradeoff that exists in recall and precision which is usually handled by combining the two objectives into a single measure with a consequent loss of control. By simultaneously optimizing recall and precision, the MOEA generates a family of SARs that lie on the precision-recall (PR) curve. The user is then able to select a query with an appropriate balance in the two objectives: for example, a low recall-high precision query may be preferred when establishing the SAR, whereas a high recall-low precision query may be more appropriate in a virtual screening context. Each query on the PR curve aims at capturing the structure-activity information into a single representation, and each can be considered as an alternative (equally valid) solution. We then investigate combining individual queries into teams with the aim of capturing multiple SARs that may exist in a data set, for example, as is commonly seen in high-throughput screening data sets. Team formation is carried out iteratively as a postprocessing step following the evolution of the individual queries. The inclusion of uniqueness as a third objective within the MOEA provides an effective way of ensuring the queries are complementary in the active compounds they describe. Substantial improvements in both recall and precision are seen for some data sets. Furthermore, the resulting queries provide more detailed structure-activity information than is present in a single query.     

Rhodium(II)-catalyzed enantioselective C-H functionalization of indoles

A catalytic, enantioselective method for the C-H functionalization of indoles by diazo compounds has been achieved. With catalytic amounts of Rh(2)(S-NTTL)(4), the putative Rh-carbene intermediates from α-alkyl-α-diazoesters react with indoles at C(3) to provide α-alkyl-α-indolylacetates in high yield and enantioselectivity. From DFT calculations, a mechanism is proposed that involves a Rh-ylide intermediate with oxocarbenium character.     

SPROUT: A program for structure generation

Summary SPROUT is a new computer program for constrained structure generation that is designed to generate molecules for a range of applications in molecular recognition. It uses artificial intelligence techniques to moderate the combinatorial explosion that is inherent in structure generation. The program is presented here for the design of enzyme inhibitors. Structure generation is divided into two phases: (i) primary structure generation to produce molecular graphs to fit the steric constraints; and (ii) secondary structure generation which is the process of introducing appropriate functionality to the graphs to produce molecules that satisfy the secondary constraints, e.g., electrostatics and hydrophobicity. Primary structure generation has been tested on two enzyme receptor sites; the p-amidino-phenyl-pyruvate binding site of trypsin and the acetyl pepstatin binding site of HIV-1 protease. The program successfully generates structures that resemble known substrates and, more importantly, the predictive power of the program has been demonstrated by its ability to suggest novel structures.     

Evidence of neutral radical induced analyte ion transformations in APPI and Near-VUV APLI

We report on the reactions of neutral radical species [OH, Cl, O(³P), H], generated in a typical atmospheric pressure ionization (API) source upon irradiation of the sample gases with either 193 nm laser radiation or 124 nm VUV light, the latter commonly used in atmospheric pressure photoionization (APPI). The present investigations focus on the polycyclic aromatic hydrocarbon pyrene as representative of the aromatic compound class. Experimental results are supported by computational methods: simple kinetic models are used to estimate the temporal evolution of the concentrations of reactants, intermediates, and final products, whereas density functional theory (DFT) energy calculations are carried out to further elucidate the proposed reaction pathways. The neutral radicals are generated upon photolysis of background water and oxygen always present in appreciable mixing ratios in typical API sources. Substantial amounts of oxygenated analyte product ions are observed using both techniques. In contrast, upon atmospheric pressure laser ionization (APLI) with 248 nm radiation, oxygenated products are virtually absent. In addition, kinetic data evaluation yielded a bimolecular rate constant of k=(1.9±0.9)×10⁻⁹ cm³ molecule⁻¹ s⁻¹ for the reaction of the pyrene radical cation with OH radicals.