A New Insight into the Stereoelectronic Control of the Pd0-Catalyzed Allylic Substitution: Application for the Synthesis of Multisubstituted Pyran-2-ones via an Unusual 1,3-Transposition

Pyran-2-ones 3 undergo a novel Pd⁰-catalyzed 1,3-rearrangement to afford isomers 6 . The reaction proceeds via an η²-Pd complex, the pyramidalization of which (confirmed by quantum chemistry calculations) offers a favorable antiperiplanar alignment of the Pd−C and allylic C−O bonds ( C ), thus allowing the formation of an η³-Pd intermediate. Subsequent rotation and rate-limiting recombination with the carboxylate arm then gives isomeric pyran-2-ones 6 . The calculated free energies reproduce the observed kinetics semi-quantitatively.     

Program for analyzing knots represented by polygonal paths

Knots can occur in real and model biological macromolecules. We describe a program for determining whether or not any knots are present in model structures and for classifying those knots that do occur. The program computes the Alexander polynomial, Δ(t), for any model. This polynomial characterizes the knot in the sense that if two knots have different Alexander polynomials, then the knots are topologically distinct. The Alexander polynomial of the circle, or trivial knot, is Δ(t)≡1. If the computed Alexander polynomial is not identically equal to unity, then the structure is nontrivially knotted, and the program will then determine a lower bound on the minimum number of path crossings. The program is entirely general, and may be used to analyze any closed polygonal path. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 813–818, 1999     

High-frequency and -field EPR investigation of a manganese(III) N-confused porphyrin complex, [Mn(NCTPP)(py)2

We report the first high-frequency and -field electron paramagnetic resonance (HFEPR) study of a Mn(III) N-confused porphyrin (NCP) complex (NCP is also known as inverted porphyrin or 2-aza-21-carbaporphyrin). We have found a striking variation in the electronic properties of the S = 2 Mn(III) ion coordinated by NCP compared to other Mn(III) porphyrinoid complexes. Thus, inversion of a single pyrrole ring greatly changes the equatorial ligand field exerted and leads to large magnitudes of both the axial and rhombic zero-field splitting [respectively, D = -3.084(3) cm(-1), E = -0.608(3) cm(-1)], which are unprecedented in other Mn(III) porphyrinoids.     

Raman spectroscopy in combination with background near-infrared autofluorescence enhances the in vivo assessment of malignant tissues

The diagnostic ability of optical spectroscopy techniques, including near-infrared (NIR) Raman spectroscopy, NIR autofluorescence spectroscopy and the composite Raman and NIR autofluorescence spectroscopy, for in vivo detection of malignant tumors was evaluated in this study. A murine tumor model, in which BALB/c mice were implanted with Meth-A fibrosarcoma cells into the subcutaneous region of the lower back, was used for this purpose. A rapid-acquisition dispersive-type NIR Raman system was employed for tissue Raman and NIR autofluorescence spectroscopic measurements at 785-nm laser excitation. High-quality in vivo NIR Raman spectra associated with an autofluorescence background from mouse skin and tumor tissue were acquired in 5 s. Multivariate statistical techniques, including principal component analysis (PCA) and linear discriminant analysis (LDA), were used to develop diagnostic algorithms for differentiating tumors from normal tissue based on their spectral features. Spectral classification of tumor tissue was tested using a leave-one-out, cross-validation method, and the receiver operating characteristic (ROC) curves were used to further evaluate the performance of diagnostic algorithms derived. Thirty-two in vivo Raman, NIR fluorescence and composite Raman and NIR fluorescence spectra were analyzed (16 normal, 16 tumors). Classification results obtained from cross-validation of the LDA model based on the three spectral data sets showed diagnostic sensitivities of 81.3%, 93.8% and 93.8%; specificities of 100%, 87.5% and 100%; and overall diagnostic accuracies of 90.6%, 90.6% and 96.9% respectively, for tumor identification. ROC curves showed that the most effective diagnostic algorithms were from the composite Raman and NIR autofluorescence techniques.     

The Role of Multiple Teaching Strategies in Promoting Active Learning in Organic Chemistry

We have introduced four alternative teaching strategies into our yearlong organic chemistry course and have assessed changes in student performance relative to the same course taught by the same instructors using a more traditional lecture format. These strategies, which include reading worksheets, dialogues, in-class worksheets, and role-playing, allow the professor to move through a learning cycle that may effectively accommodate the students needs and multiple learning styles. The reading worksheets guide students through the concept phase and dialogues help students identify the importance of the concepts as they articulate these ideas for themselves. Group worksheets and role-playing provide opportunities for peer-interaction, application of knowledge, creativity, and self-expression. Others have shown that active learning strategies neither enhance nor diminish a students ability to retain factual information, a finding that is supported by our study. Our data from this one study show, however, that students taught by a more traditional approach demonstrate a greater variation in final exam performance between first and second semesters than those taught using a combination of techniques. This result reflects a shift in emphasis from the professor as an information source to the actively engaged student taking responsibility for his or her own learning. This study suggests that these methods, when used in a consistent fashion in conjunction with interactive lecturing, provide a broad base to facilitate student learning and aid in the development of higher order thinking skills.     

The Mechanism of Biochemical NO-Sensing: Insights from Computational Chemistry

The binding of small gas molecules such as NO and CO plays a major role in the signaling routes of the human body. The sole NO-receptor in humans is soluble guanylyl cyclase (sGC) – a histidine-ligated heme protein, which, upon NO binding, activates a downstream signaling cascade. Impairment of NO-signaling is linked, among others, to cardiovascular and inflammatory diseases. In the present work, we use a combination of theoretical tools such as MD simulations, high-level quantum chemical calculations and hybrid QM/MM methods to address various aspects of NO binding and to elucidate the most likely reaction paths and the potential intermediates of the reaction. As a model system, the H-NOX protein from Shewanella oneidensis (So H-NOX) homologous to the NO-binding domain of sGC is used. The signaling route is predicted to involve NO binding to form a six-coordinate intermediate heme-NO complex, followed by relatively facile His decoordination yielding a five-coordinate adduct with NO on the distal side with possible isomerization to the proximal side through binding of a second NO and release of the first one. MD simulations show that the His sidechain can quite easily rotate outward into solvent, with this motion being accompanied in our simulations by shifts in helix positions that are consistent with this decoordination leading to significant conformational change in the protein.     

Travelling‐wave ion mobility mass spectrometry and negative ion fragmentation of hybrid and complex N‐glycans

Nitrogen collisional cross sections (CCSs) of hybrid and complex glycans released from the glycoproteins IgG, gp120 (from human immunodeficiency virus), ovalbumin, α1‐acid glycoprotein and thyroglobulin were measured with a travelling‐wave ion mobility mass spectrometer using dextran as the calibrant. The utility of this instrument for isomer separation was also investigated. Some isomers, such as Man₃GlcNAc₃ from chicken ovalbumin and Man₃GlcNAc₃Fuc₁ from thyroglobulin could be partially resolved and identified by their negative ion fragmentation spectra obtained by collision‐induced decomposition (CID). Several other larger glycans, however, although existing as isomers, produced only asymmetric rather than separated arrival time distributions (ATDs). Nevertheless, in these cases, isomers could often be detected by plotting extracted fragment ATDs of diagnostic fragment ions from the negative ion CID spectra obtained in the transfer cell of the Waters Synapt mass spectrometer. Coincidence in the drift times of all fragment ions with an asymmetric ATD profile in this work, and in the related earlier paper on high‐mannose glycans, usually suggested that separations were because of conformers or anomers, whereas symmetrical ATDs of fragments showing differences in drift times indicated isomer separation. Although some significant differences in CCSs were found for the smaller isomeric glycans, the differences found for the larger compounds were usually too small to be analytically useful. Possible correlations between CCSs and structural types were also investigated, and it was found that complex glycans tended to have slightly smaller CCSs than high‐mannose glycans of comparable molecular weight. In addition, biantennary glycans containing a core fucose and/or a bisecting GlcNAc residue fell on different mobility‐m/z trend lines to those glycans not so substituted with both of these substituents contributing to larger CCSs. Copyright © 2016 John Wiley & Sons, Ltd.     

Insights into polyether biosynthesis from analysis of the nigericin biosynthetic gene cluster in Streptomyces sp. DSM4137

Nigericin was among the first polyether ionophores to be discovered, but its biosynthesis remains obscure. The biosynthetic gene cluster for nigericin has been serendipitously cloned from Streptomyces sp. DSM4137, and deletion of this gene cluster abolished the production of both nigericin and the closely related metabolite abierixin. Detailed comparison of the nigericin biosynthetic genes with their counterparts in the biosynthetic clusters for other polyketides has prompted a significant revision of the proposed common pathway for polyether biosynthesis. In particular, we present evidence that in nigericin, nanchangmycin, and monensin, an unusual ketosynthase-like protein, KSX, transfers the initially formed linear polyketide chain to a discrete acyl carrier protein, ACPX, for oxidative cyclization. Consistent with this, deletion of either monACPX or monKSX from the monensin gene cluster effectively abolished monensin A biosynthesis.     

The effect of electrolyte on the encapsulation efficiency of vesicles formed by the nonionic surfactant, 2C18E12

Encapsulation efficiencies of vesicles formed by the nonionic surfactant 1,2-dioctadecyl-rac-glycerol-3-omega-methoxydodecylethylene glycol (abbreviated as 2C18E12) and its phospholipid counterpart, distearoylphosphatidylcholine (DSPC) at 298 K, were determined by the entrapment of the water-soluble dye, carboxyfluorescein (CF) to be 0.045+/-0.001 and 0.03+/-0.04 L mol(-1) for 2C18E12 vesicles prepared using low osmolarity (270 m Osm) Krebs-Henseleit (K-H) buffer and a modified 'high salt' (1600 m Osm) variant of K-H buffer, respectively, and 0.64+/-0.01 and 0.31+/-0.04 Lmol(-1) for DSPC vesicles prepared under the same conditions and in the same buffers. Freeze fracture electron microscopy studies confirmed the presence of vesicles when 2C18E12 and DSPC were dispersed in water and both buffer solutions. Small angle neutron scattering (SANS) studies, using D2O in place of H2O, showed that when 2C18E12 vesicles were prepared in the 'high salt' variant of K-H buffer as opposed to K-H buffer or water, a higher proportion of multilamellar vesicles (MLV) were formed. Furthermore when prepared in the 'high salt' variant of K-H buffer, the 2C18E12 bilayers were thinner, and when present in the form of MLV exhibited a smaller layer of water separating the bilayers. However, even in the absence of electrolyte, 2C18E12 formed surprisingly thin bilayers due to the penetration of the polyoxyethylene chains into the hydrophobic chain region of the bilayer. Due to the dehydrating effect of the high concentration of electrolyte present in the 'high salt' variant of K-H, the polyoxyethylene head groups penetrated further into the hydrophobic region of the bilayer making the bilayer even thinner. In the case of the DSPC vesicles, although the SANS study showed an increase in the relative proportion of multilamellar to unilamellar vesicles when samples were prepared in the 'high salt' variant of K-H buffer, no differences were observed in the thickness and the d-spacing of the vesicle bilayers. Variable temperature turbidity measurements of 2C18E12, and DSPC vesicles prepared in water indicated phase changes at 320+/-0.5 and 327+/-0.5 K, respectively, and were unchanged when the 'high salt' variant of K-H buffer was used as hydrating medium. Taken together, these results suggest that a low phase transition temperature was not the reason for the poor entrapment efficiency of 2C18E12 vesicles but rather the very 'thin' hydrophobic barrier formed by the penetration of the polyoxyethylene chains into the hydrophobic region of the bilayer.     

The Dynamics of the Reaction of FeO+ and H2: A Model for Inorganic Oxidation

Extensive density functional theory (DFT) calculations using the B3LYP functional were used to explore the sextet and quartet energy potential energy surfaces (PESs) of the title reaction, and as a basis to fit global analytical reactive PESs. Surface-hopping dynamics on these PESs reproduce the experimentally observed reactivity and confirm that hydrogen activation rather than spin-state change is rate-limiting at low reaction energy, where the main products are Fe⁺ and H₂O. A change in spin state is inefficient in the product region so that excited-state ⁴Fe⁺ is the dominant product. At higher energies, spin-allowed hydrogen atom abstraction to form FeOH⁺ predominates. At intermediate energy, a previously unexpected rebound mechanism contributes significantly to the reactivity.