An automated instrument for human STR identification: design, characterization, and experimental validation

The microfluidic integration of an entire DNA analysis workflow on a fully integrated miniaturized instrument is reported using lab‐on‐a‐chip automation to perform DNA fingerprinting compatible with CODIS standard relevant to the forensic community. The instrument aims to improve the cost, duration, and ease of use to perform a “sample‐to‐profile” analysis with no need for human intervention. The present publication describes the operation of the three major components of the system: the electronic control components, the microfluidic cartridge and CE microchip, and the optical excitation/detection module. Experimental details are given to characterize the level of performance, stability, reliability, accuracy, and sensitivity of the prototype system. A typical temperature profile from a PCR amplification process and an electropherogram of a commercial size standard (GeneScan 500?, Applied Biosystems) separation are shown to assess the relevance of the instrument to forensic applications. Finally, we present a profile from an automated integrated run where lysed cells from a buccal swab were introduced in the system and no further human intervention was required to complete the analysis.     

Cu(II) coordination polymers incorporating 3-aminopyridine and flexible aliphatic dicarboxylate ligands: Synthesis,structure and magnetic properties

The synthesis, structural chemistry and magnetic properties of a series of new Cu(II) polymers with α,ω-dicarboxylic acids (sebacic (H₂seb), suberic (H₂sub), succinic (H₂suc) and adipic (H₂adip)) and 3-aminopyridine (3-apy) are described: [Cu(Hsub)₂(3-apy)₂·2CH₃OH]_n (1); [Cu(Hseb)₂(3-apy)₂·4CH₃OH]_n (2); [Cu(Hsuc)₂(3-apy)₂]_n (3); [Cu(adip)(3-apy)₂]_n·n(H₂adip) (4). All four compounds feature a bis-monodentate bridging mode of the coordinated dicarboxylate moiety. Compounds 1 and 2 exhibit linear chains, whereas compound 3 shows two-dimensional structure. The 3-apy ligand acts as terminal ligand in 1–3. Compound 4 contains a doubly deprotonated adipate (adip²⁻) that connects Cu centers into linear chains. Additionally, 3-apy acts as a bridge in 4, resulting in the formation of parallel two-dimensional layers distant enough to host neutral molecules of adipic acid. Magnetic susceptibility measurements of compounds 1 and 3 show Curie law behavior indicating that the S = 1/2 Cu(II) spin carriers are magnetically well isolated by the dicarboxylate ligands.     

Chemistry of vinylidene complexes. XVIII. Synthesis and molecular structure of the novel trinuclear μ3-vinylidene complex CpReFePt(μ3-CCHPh)(CO)6(PPh3)

The interaction between Cp(CO)₂RePt(μ-CCHPh)(PPh₃)₂ (1) and Fe₂(CO)₉ afforded the new heterometallic μ₃-vinylidene cluster CpReFePt(μ₃-CCHPh)(CO)₆(PPh₃) (2). An X-ray diffraction study shows the complex 2 possesses a trimetallic Re-Fe-Pt chain core. The bond lengths are Re-Fe 2.8221(8), Fe-Pt 2.5813(8) Å; the Re?Pt distance is 3.3523(7) Å; the bond angle Re-Fe-Pt is 76.55(3)°. The μ₃-CCHPh ligand is η¹-bound to the Re and Pt atoms and η²-coordinated to the Fe atom. The CC bond length is 1.412(4) Å. The Pt atom is coordinated by the PPh₃ and CO groups. Complex 2 is characterized by the IR and ¹H, ¹³C and ³¹P NMR spectra.     

Cover Picture: Photoprogrammable Organic Light‐Emitting Diodes (Angew. Chem. Int. Ed. 22/2009)

Programmable organic light‐emitting diodes: UV irradiation converts an oxetane‐functionalized dithienylethene derivative from its colorless open form into a dark blue closed form, while visible light reverses the reaction. In the Communication on page 4038 ff., K. Meerholz and co‐workers describe a reversibly switchable organic light‐emitting diode based on this principle.

     

Theoretical analysis of the porphyrin-porphyrin exciton interaction in circular dichroism spectra of dimeric tetraarylporphyrins

Chiral bis-porphyrins are currently the subject of intense interest as chiral receptors and as probes in the determination of structure and stereochemistry. To provide an improved framework for interpreting the circular dichroism (CD) spectra of bis-porphyrins, we have calculated the CD spectra of chiral bis-porphyrins from three classes: I, where porphyrins can adopt a relatively wide range of orientations relative to each other; II, porphyrins have a fixed relative orientation; III, porphyrins undergo pi-stacking. The calculations primarily utilized the classical polarizability theory of DeVoe, but were supplemented by the quantum mechanical matrix method. Class I was represented by three isomers of the diester of 5alpha-cholestane-3,17-diol with 5-(4'-carboxyphenyl)-10,15,20-triphenylporphin (2-alphabeta, 2-betaalpha, 2-betabeta). Careful analysis of the torsional degrees of freedom led to two to four minimum-energy conformers for each isomer, in each of which the phenyl-porphyrin bonds had torsional angles near 90 degrees. Libration about these bonds is relatively unrestricted over a range of +/-45 degrees. CD spectra in the Soret region were calculated as Boltzmann-weighted averages over the low-energy conformers for each isomer. Three models were used: the effective transition moment model, in which only one of the degenerate Soret components is considered, along the 5-15 direction; the circular oscillator model, in which both Soret components are given equal weight; and the hybrid model, in which the 10-20 oscillator is given half the weight of the 5-15 oscillator, to mimic the effect of extensive librational averaging about the 5-15 direction. All three models predict Soret exciton couplets with signs in agreement with experiment. Quantitatively, the best results are given by the hybrid and circular oscillator models. These results validate the widely used effective transition moment model for qualitative assignments of bis-porphyrin chirality and thus permit application of the exciton chirality model. However, for quantitative studies, the circular oscillator or hybrid models should be used. The simplified effective transition moment and hybrid models are justified by the librational averaging in the class I bis-porphyrins and should only be used with such systems. Two class II bis-porphyrins were also studied by DeVoe method calculations in the circular oscillator model, which yielded good agreement with experiment. Class III bis-porphyrins were represented by 2-alphaalpha, for which the calculations gave qualitative agreement. However, limitations in the conformational analysis with the close contacts and dynamic effects in these pi-stacked systems preclude quantitative results.     

DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the “classical” B conformation (BI‐form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence‐dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII‐like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2548–2559, 2010     

CuII Coordination Chemistry of Patellamide Derivatives: Possible Biological Functions of Cyclic Pseudopeptides

Two synthetic derivatives of the naturally occurring cyclic pseudooctapeptides patellamide A–F and ascidiacyclamide, that is, H₄pat², H₄pat³, as well as their Cu^II complexes are described. These cyclic peptide derivatives differ from the naturally occurring macrocycles by the variation of the incorporated heterocyclic donor groups and the configuration of the amino acids connecting the heterocycles. The exchange of the oxazoline and thiazole groups by dimethylimidazoles or methyloxazoles leads to more rigid macrocycles, and the changes in the configuration of the side chains leads to significant differences in the folding of the cyclic peptides. These variations allow a detailed study of the various possible structural changes on the chemistry of the Cu^II complexes formed. The coordination of Cu^II with these macrocyclic species was monitored by high‐resolution electrospray mass spectrometry (ESI‐MS), spectrophotometric (UV/Vis) and circular dichroic (CD) titrations, and electron paramagnetic resonance (EPR) spectroscopy. Density functional theory (DFT) calculations and molecular mechanics (MM) simulations have been used to model the structures of the Cu^II complexes and provide a detailed understanding of their geometric preferences and conformational flexibility. This is related to the Cu^II coordination chemistry and the reactivity of the dinuclear Cu^II complexes towards CO₂ fixation. The variation observed between the natural and various synthetic peptide systems enables conclusions about structure–reactivity correlations, and our results also provide information on why nature might have chosen oxazolines and thiazoles as incorporated heterocycles.     

From an Icosahedron to a Plane: Flattening Dodecaiodo‐dodecaborate by Successive Stripping of Iodine

It has been shown by electrospray ionization–ion‐trap mass spectrometry that B₁₂I₁₂^2? converts to an intact B₁₂ cluster as a result of successive stripping of single iodine radicals or ions. Herein, the structure and stability of all intermediate B₁₂I_n^? species (n=11 to 1) determined by means of first‐principles calculations are reported. The initial predominant loss of an iodine radical occurs most probably via the triplet state of B₁₂I₁₂^2?, and the reaction path for loss of an iodide ion from the singlet state crosses that from the triplet state. Experimentally, the boron clusters resulting from B₁₂I₁₂^2? through loss of either iodide or iodine occur at the same excitation energy in the ion trap. It is shown that the icosahedral B₁₂ unit commonly observed in dodecaborate compounds is destabilized while losing iodine. The boron framework opens to nonicosahedral structures with five to seven iodine atoms left. The temperature of the ions has a considerable influence on the relative stability near the opening of the clusters. The most stable structures with five to seven iodine atoms are neither planar nor icosahedral.