Photochemical and thermal rearrangements of a benzoylnaphthobarrelene-like system

8-Benzoyl-9-deuterionaphtho[de-2.3.4]bicyclo[3.2.2]nona-2,6,8-triene (12a)rearranges in a photochemical di-π-methane-type process to the l-benzoylatho[de-[2.3.4]tricyclo[4.3.0.0^2,9]nona-3,7-dienes 14a-c.The dihydro derivate 13a and the hydroxypheoylmethyl analogs 21a and 22a undergo similarly regioselective rearrangements to 15a+c, 23a-c, and 24a, respectively. At 298 K the primary photoreaction directly occus from the S₁(n,π^*) and T₂(n,π^*) states, and it proceeds from T₁(π,π^*) and from S₂(π,π^*) either directly or via T₂. At lower temperature on direct irradiation. S₁→T intersystem crossing and triplet reaction compete with reaction from the singlet. The rearrangement 12a→14a-c proceeds along three reaction paths evolving from the two primary photochemical processes of naphthyl-vinyl and vinyl-vinyl bonding in β-position to the CO (12→25+29). Two ground-state triplet diradical intermediates such as 25 and 27 have been shown to intervene consecutively—for the first time in di-π-methane photochemistry. Each has been characterized by ESR and IR, and the second one additionally by fluorescence and fluorescence excitation, and by laser flash photolysis.The failure of products 14a-c to interconvert photochemically is ascribed to efficient energy dissipation through thermally reversible pbotocleavage of the 3-membered ring.Compounds 12 and 14 thermally interconvert in the dark which constitutes the first example of a ground-state counterpart of a di-π-methane photorearrangement. The thermal reaction includes a path with highly regioselective (and possibly concerted) product formation competing with a stepwise process causing positional scrambling. The sequence 12→14 (photochemically; Φ = 1.0 at 366 nm and 298 K) and an electrophile-catalyzed reversal 14→12 in the dark is a model of a chemical light energy storage cycle which can be conducted without loss of reactants.     

Synthetic, Structural, Spectroscopic, and Theoretical Studies of Structural Isomers of the Cluster Pt(3)(&mgr;-PPh(2))(3)Ph(PPh(3))(2). A Unique Example of Core Isomerism in Phosphine Phosphido-Rich Clusters

Two isomers of the phosphido-bridged platinum cluster Pt(3)(&mgr;-PPh(2))(3)Ph(PPh(3))(2) (2 and 3) have been isolated, and their structures have been solved by single-crystal X-ray diffraction. Compound 2 crystallizes in the orthorhombic space group Cmc2(1) with a = 22.192(10) ?, b = 17.650(9) ?, c = 18.182(8) ?, and Z = 4. Compound 3 crystallizes with 2 molecules of dichloromethane in the monoclinic space group C2/c with a = 21.390(10) ?, b = 18.471(9) ?, c = 19.021(11) ?, beta = 105.27(5) degrees, and Z = 4. The two isomers differ essentially in their metal-metal distances and Pt-(&mgr;-PPh(2))-Pt angles. Thus 2, having an imposed C(s) symmetry, contains a bent chain of metal atoms with two short Pt-Pt distances of 2.758(3) ? and a long separation of 3.586(2) ?. In 3, which has an imposed C(2) symmetry, the metal atoms form an isosceles triangle with two Pt-Pt distances of 2.956(3) ? and one of 3.074(4) ?. These isomers can be smoothly interconverted by changing the crystallization solvents. Solution and solid-state (31)P NMR studies have been performed in order to assign the resonances of the different P nuclei and relate their chemical shifts with their structural environments. Raman spectroscopy was used to assign the nu(Pt-Pt) modes of the two structural isomers. Theoretical studies based on extended Hückel calculations and using the fragment molecular orbital approach show that the isomer with the three medium Pt-Pt distances is slightly more stable, in agreement with earlier theoretical predictions. Cluster core isomerism remains a rare phenomenon, and the present example emphasizes the role and the importance of flexible phosphido bridges in stabilizing clusters as well as the unprecedented features which can be observed in phosphine phosphido-rich metal clusters.     

Finite element error bounds for a curve shrinking with prescribed normal contact to a fixed boundary

We approximate the evolution of a curve subject to motion bycurvature by linear finite elements. The curve evolves insidea given domain and meets orthogonally. We derive optimal boundsfor the error with respect to the L²- and H¹-norms and presentsome computed examples.     

Heated nontronite: Possible relations to the magnetic phase in the Martian soil

We have modified the iron-containing layer silicate nontronite into a magnetic sample by heat treatment at 900 C for 5 minutes and studied the properties of the sample by Mössbauer spectroscopy, X-ray powder diffraction and infrared spectroscopy. Mössbauer spectra obtained in applied magnetic fields show that the majority of the iron is situated in a ferrimagnetic phase, related to maghemite.     

Cyclopropanecarboxylic acid esters as potential prodrugs with enhanced hydrolytic stability

Esters of cyclopropanecarboxylic acid demonstrate a substantial increase in stability under both acid- and base-catalyzed hydrolytic conditions. Comparison of the stability of valacyclovir 13 with the cyclopropane analogue 14 shows that at 40 degrees C and pH 6 the half-life of 14 is >300 h while the value for 13 is 69.7 h. CBS-QB3 calculations on isodesmic reactions for transfer of groups from an alkane to an ester show that a cyclopropyl group provides hyperconjugative stabilization.     

Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds

We investigate the classification performance of circular fingerprints in combination with the Naive Bayes Classifier (MP2D), Inductive Logic Programming (ILP) and Support Vector Inductive Logic Programming (SVILP) on a standard molecular benchmark dataset comprising 11 activity classes and about 102,000 structures. The Naive Bayes Classifier treats features independently while ILP combines structural fragments, and then creates new features with higher predictive power. SVILP is a very recently presented method which adds a support vector machine after common ILP procedures. The performance of the methods is evaluated via a number of statistical measures, namely recall, specificity, precision, F-measure, Matthews Correlation Coefficient, area under the Receiver Operating Characteristic (ROC) curve and enrichment factor (EF). According to the F-measure, which takes both recall and precision into account, SVILP is for seven out of the 11 classes the superior method. The results show that the Bayes Classifier gives the best recall performance for eight of the 11 targets, but has a much lower precision, specificity and F-measure. The SVILP model on the other hand has the highest recall for only three of the 11 classes, but generally far superior specificity and precision. To evaluate the statistical significance of the SVILP superiority, we employ McNemar's test which shows that SVILP performs significantly (p < 5%) better than both other methods for six out of 11 activity classes, while being superior with less significance for three of the remaining classes. While previously the Bayes Classifier was shown to perform very well in molecular classification studies, these results suggest that SVILP is able to extract additional knowledge from the data, thus improving classification results further.     

De novo design of a single-chain diphenylporphyrin metalloprotein

We describe the computational design of a single-chain four-helix bundle that noncovalently self-assembles with fully synthetic non-natural porphyrin cofactors. With this strategy, both the electronic structure of the cofactor as well as its protein environment may be varied to explore and modulate the functional and photophysical properties of the assembly. Solution characterization (NMR, UV-vis) of the protein showed that it bound with high specificity to the desired cofactors, suggesting that a uniquely structured protein and well-defined site had indeed been created. This provides a genetically expressed single-chain protein scaffold that will allow highly facile, flexible, and asymmetric variations to enable selective incorporation of different cofactors, surface-immobilization, and introduction of spectroscopic probes.     

Understanding false positives in reporter gene assays: in silico chemogenomics approaches to prioritize cell-based HTS data

High throughput screening (HTS) data is often noisy, containing both false positives and negatives. Thus, careful triaging and prioritization of the primary hit list can save time and money by identifying potential false positives before incurring the expense of followup. Of particular concern are cell-based reporter gene assays (RGAs) where the number of hits may be prohibitively high to be scrutinized manually for weeding out erroneous data. Based on statistical models built from chemical structures of 650 000 compounds tested in RGAs, we created "frequent hitter" models that make it possible to prioritize potential false positives. Furthermore, we followed up the frequent hitter evaluation with chemical structure based in silico target predictions to hypothesize a mechanism for the observed "off target" response. It was observed that the predicted cellular targets for the frequent hitters were known to be associated with undesirable effects such as cytotoxicity. More specifically, the most frequently predicted targets relate to apoptosis and cell differentiation, including kinases, topoisomerases, and protein phosphatases. The mechanism-based frequent hitter hypothesis was tested using 160 additional druglike compounds predicted by the model to be nonspecific actives in RGAs. This validation was successful (showing a 50% hit rate compared to a normal hit rate as low as 2%), and it demonstrates the power of computational models toward understanding complex relations between chemical structure and biological function.