Applications of maximum likelihood principal component analysis: incomplete data sets and calibration transfer

The application of a new method to the multivariate analysis of incomplete data sets is described. The new method, called maximum likelihood principal component analysis (MLPCA), is analogous to conventional principal component analysis (PCA), but incorporates measurement error variance information in the decomposition of multivariate data. Missing measurements can be handled in a reliable and simple manner by assigning large measurement uncertainties to them. The problem of missing data is pervasive in chemistry, and MLPCA is applied to three sets of experimental data to illustrate its utility. For exploratory data analysis, a data set from the analysis of archeological artifacts is used to show that the principal components extracted by MLPCA retain much of the original information even when a significant number of measurements are missing. Maximum likelihood projections of censored data can often preserve original clusters among the samples and can, through the propagation of error, indicate which samples are likely to be projected erroneously. To demonstrate its utility in modeling applications, MLPCA is also applied in the development of a model for chromatographic retention based on a data set which is only 80% complete. MLPCA can predict missing values and assign error estimates to these points. Finally, the problem of calibration transfer between instruments can be regarded as a missing data problem in which entire spectra are missing on the ‘slave’ instrument. Using NIR spectra obtained from two instruments, it is shown that spectra on the slave instrument can be predicted from a small subset of calibration transfer samples even if a different wavelength range is employed. Concentration prediction errors obtained by this approach were comparable to cross-validation errors obtained for the slave instrument when all spectra were available.     

Effect of molecular oxygen on the variable-temperature 29Si MAS NMR spectra of zeolite-sorbate complexes

Structure determinations of siliceous zeolite-sorbate host-guest complexes by solid-state NMR require highly resolved 29Si MAS NMR spectra. As the temperature is lowered, the 29Si MAS NMR spectra of many zeolite-sorbate complexes become broadened such that the resolution of the individual 29Si peaks is lost, limiting the application of solid-state NMR for structure determination. It is shown that the 29Si peak widths are related to the 29Si T2 relaxation times and that the source of the 29Si relaxation and the line broadening is paramagnetic molecular oxygen in the channels of the zeolite. Removal of the oxygen by purging the sample with nitrogen gas leads to a dramatic increase in the resolution of the 29Si MAS NMR spectrum of the p-dibromobenzene/ZSM-5 complex. An analysis of the individual 29Si T1 relaxation times reveals that the oxygen molecules are localized mainly in the zigzag channels of ZSM-5, suggesting that the p-dibromobenzene molecules are located in the channel intersections.     

Rapid synthesis of pomalidomide-conjugates for the development of protein degrader libraries

Current methods for the preparation of heterobifunctional pomalidomide-conjugates rely on methods that are often low yielding and produce intractable byproducts. Herein we describe our strategy for the reliable and succinct preparation of pomalidomide-linkers which is essential to the formation of these conjugates. We present the preparation of 18 pomalidomide-linkers in high yield compared to current literature methods. Our findings show that secondary amines consistently afford greater yields than their primary counterparts, a trend that we were able to exploit in the synthesis of several new pomalidomide homo-dimers in enhanced yields compared to similar literature syntheses. This trend was further utilised to develop the first one-pot synthesis of JQ1-pomalidomide conjugates in yields up to 62%, providing a method that is suited to rapid preparation of conjugate libraries as is frequently required for the development of new protein degraders.

Current methods for the preparation of heterobifunctional pomalidomide-conjugates rely on methods that are often low yielding and produce intractable byproducts. Herein we describe our strategy for the succinct preparation of pomalidomide-linkers.     

Crystal Structure, Electrical Transport, and Magnetic Properties of Niobium Monophosphide

Large single crystals of NbP have been prepared. A single-crystal X-ray diffraction study shows that it crystallizes in tetragonal symmetry with space group I4(1)md (No. 109) and lattice parameters a = 3.3324(2) ?, c = 11.3705(7) ?, and Z = 4. A full matrix least-squares refinement based on a unique data set of 285 reflections (I> 2sigma(I)) yielded R(F) = 0.017 and R(w)(F(2)) = 0.046 for nine variables. The unit cell consists of one unique Nb and one P, each in trigonal prismatic coordination with the other element. There are two short and four long bond distances of Nb-P. The Nb-Nb bond distances are significantly shorter than R(c) = 4.09 ?, the critical distance required for good Nb-Nb 4d orbital overlap for niobium metal-metal bonds. NbP shows metallic behavior with rho = 4.5 x 10(-)(5) Omega cm at room temperature. Magnetic susceptibility measurements on a collection of randomly oriented single crystals indicate very weak Pauli paramagnetism ( approximately 10(-)(5) emu/mol). A discussion of the structure as well as the physical properties of NbP compared with those of previous results are presented. The band structure of NbP based on the extended Hückel (tight-binding) calculations is presented along with an analysis that reveals that the valence band is built up from three center bonds localized within Nb(3) triangles.     

A total synthesis of tarchonanthuslactone exploiting N-pyrrole carbinols as efficient stereocontrolling elements

[reaction: see text] A short stereoselective total synthesis of the polyketide natural product, tarchonanthuslactone, has been achieved. The key sequence involves the first reported catalytic enantioselective reduction of an N-acyl pyrrole and subsequent use of this stereocenter in a diastereoselective reductive cascade. This proceeded with unprecedentedly high stereocontrol and offered an elegant method of generating the desired syn stereochemistry present in the final target in one step.     

Evaluation and validation of the ABI 3700, ABI 3100, and the MegaBACE 1000 capillary array electrophoresis instruments for use with short tandem repeat microsatellite typing in a forensic environment

The demand for high-throughput DNA profiling has increased with the introduction of national DNA databases and has led to the development of automated methods of short tandem repeat (STR) profile production; however, a potential bottleneck still exists at the gel electrophoresis stage. Capillary electrophoresis sequencers capable of processing 96 samples with considerably reduced manual intervention are now available. In this paper, we compare the ABI Prism 377 slab-gel sequencer currently used by the Forensic Science Service with three leading capillary array electrophoresis instruments: the ABI Prism 3700, the Amersham MegaBACE 1000 and the 16-capillary ABI Prism 3100. We describe the experiments used to evaluate and validate these platforms for forensic use with the STR multiplex Ampf/STR SGMplus [1, 2], along with comparative data from the ABI Prism 377 sequencer.     

Asymmetric synthesis of β-substituted Baylis-Hillman products via lithium amide conjugate addition

A three-step protocol for the asymmetric synthesis of a range of β-substituted Baylis-Hillman products has been developed. This procedure involves the diastereoselective conjugate addition of lithium (R)-N-methyl-N-(α-methylbenzyl)amide to an α,β-unsaturated ester to generate an N-protected β-amino ester in high de. Subsequent asymmetric aldol reaction via deprotonation with LDA, transmetallation with B(OMe)₃ and addition of an aldehyde gives a range of syn-aldol products in moderate to high de. Purification of the syn-aldol products to homogeneity followed by tandem N-oxidation and Cope elimination gives the desired β-substituted Baylis-Hillman products in good yield and high de and ee.     

Total synthesis of the polyenoyltetramic acid polycephalin C

The total synthesis of the polyenoyltetramic acid polycephalin C is described. Key steps of the synthesis include a double Swern oxidation, double Takai reaction and a double Stille reaction. In addition, the absolute stereochemistry of the ring junction has been determined by synthesis of both isomers and comparison of their CD spectra with natural polycephalin C.     

Selective addition to iridium of aryl C-H bonds ortho to coordinating groups. Not chelation-assisted

Precursors of the pincer-ligated iridium species, (PCP)Ir, react with nitrobenzene or acetophenone at ambient temperature to give O,C-chelated complexes resulting from addition of an aryl C-H bond and coordination of a nitro or acetyl oxygen. The C-H additions appear to be completely regioselective for the position ortho to the functional group; however, structural characterization and low-temperature NMR studies demonstrate that the reaction does not proceed via coordination of the functional group followed by C-H addition. In the case of nitrobenzene, kinetic preference for the para and meta positions is demonstrated at low temperature. Addition occurs more slowly at the ortho position, without assistance by the functional group; the ortho-C-H addition product is then trapped by chelation.