FT Raman and DFT Study on a Series of All- anti Oligothienoacenes End-Capped with Triisopropylsilyl Groups

Herein, we study the Π-conjugational properties of a homologous series of all -anti oligothienoacenes containing four to eight fused thiophene rings by means of FT Raman spectroscopy and DFT calculations. The theoretical analysis of the spectroscopic data provides evidence that selective enhancement of a very limited number of Raman scatterings is related to the occurrence in these oligothienoacenes of strong vibronic coupling between collective Ν(C[bouble bond]C) stretching modes in the 1600–1300 cm −1 region and the HOMO/LUMO frontier orbitals (HOMO=highest occupied molecular orbital; LUMO=lowest unoccupied molecular orbital). The correlation of the Raman spectroscopic data and theoretical results for these all -anti oligothienoacenes with those previously collected for a number of all -syn oligothienohelicenes gives further support to the expectation that cross-conjugation is dominant in heterohelicenes. Fully planar all -anti oligothienoacenes display linear Π conjugation which seemingly does not reach saturation with increasing number of annulated thiophene rings in the oligomeric chain at least up to the octamer.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64547/1/3069_ftp.pd

Structure of HrcQ(B)-C, a conserved component of the bacterial type III secretion systems

Type III secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum of diseases including bacteremia, septicemia, typhoid fever, and bubonic plague in mammals, and localized lesions, systemic wilting, and blights in plants. In addition, type III secretion systems are also required for biogenesis of the bacterial flagellum. The HrcQ(B) protein, a component of the secretion apparatus of Pseudomonas syringae with homologues in all type III systems, has a variable N-terminal and a conserved C-terminal domain (HrcQ(B)-C). Here, we report the crystal structure of HrcQ(B)-C and show that this domain retains the ability of the full-length protein to interact with other type III components. A 3D analysis of sequence conservation patterns reveals two clusters of residues potentially involved in protein–protein interactions. Based on the analogies between HrcQ(B) and its flagellum homologues, we propose that HrcQ(B)-C participates in the formation of a C-ring-like assembly

Analysis of systems hardware flown on LDEF. Results of the systems special investigation group

The Long Duration Exposure Facility (LDEF) was retrieved after spending 69 months in low Earth orbit (LEO). LDEF carried a remarkable variety of mechanical, electrical, thermal, and optical systems, subsystems, and components. The Systems Special Investigation Group (Systems SIG) was formed to investigate the effects of the long duration exposure to LEO on systems related hardware and to coordinate and collate all systems analysis of LDEF hardware. Discussed here is the status of the LDEF Systems SIG investigation through the end of 1991

Synthesis, crystal structure and spectroscopic studies of a new silver complex derived from [1-(3-pyridinyl) ethanone]

In this work, a new silver (I) complex, [Ag(3-pye)2(H2O)](NO3) where 3-pye=1-(3-pyridinyl) ethanone, has been synthesized and characterized by elemental analyses, FT-IR, fluorescence spectroscopy, and single X-ray crystallography. The X-ray diffraction analysis revealed that the Ag(I) complex crystallized in the monoclinic system with the C2/c space group. Computational studies were performed using DFT approache on the present complex to get insight into the structural parameters, spectral characteristics and electronic properties. The characterization results were found to be consistent with the proposed structure of the complex, and the DFT approach supported the experimental results. Also, Hirshfeld surface analysis was used to identify the non-covalent interactions within the crystal structure as well as to visualize the conformity of the crystal structure

Mechanisms of Porphyrinoid and Carotenoid Spectral Tuning Revealed with Quantum Chemistry

Continued advances in a myriad of biomedical and technological fields require the rational design of molecules or supramolecular architectures with specific photophysical properties. Central to this endeavor is a mechanistic understanding of optical property modulation as a function of molecular structure, conformation, and environment. Natural pigments and protein-pigment complexes constitute a ‘solutions manual’ to challenges in electronic (optical) engineering that has been refined over a few billion years of evolution, and from which design principles can be deduced. In this thesis, unique mechanisms for modulating the optical properties of natural or synthetic porphyrinoid and carotenoid pigments are elucidated with quantum chemical methods. Our investigations add a new conformational mechanism, as well as design principles for regioisomer-dependent electronic substituent effects to the cannon of structural tools for regulating the optical properties of pyrrole-modified porphyrins. The lessons learned provide insight into analogous spectral tuning mechanisms found in nature. We also delineate the molecular factors optimally regulating light harvesting in a natural photosynthetic antenna complex. These discoveries have advanced the fundamental understanding and practical utilization of structure-optical property modulation mechanisms, and may aid the design of next-generation photonic-based technologies

Extraction of chemical structures and reactions from the literature

The ever increasing quantity of chemical literature necessitates the creation of automated techniques for extracting relevant information. This work focuses on two aspects: the conversion of chemical names to computer readable structure representations and the extraction of chemical reactions from text. Chemical names are a common way of communicating chemical structure information. OPSIN (Open Parser for Systematic IUPAC Nomenclature), an open source, freely available algorithm for converting chemical names to structures was developed. OPSIN employs a regular grammar to direct tokenisation and parsing leading to the generation of an XML parse tree. Nomenclature operations are applied successively to the tree with many requiring the manipulation of an in-memory connection table representation of the structure under construction. Areas of nomenclature supported are described with attention being drawn to difficulties that may be encountered in name to structure conversion. Results on sets of generated names and names extracted from patents are presented. On generated names, recall of between 96.2% and 99.0% was achieved with a lower bound of 97.9% on precision with all results either being comparable or superior to the tested commercial solutions. On the patent names OPSIN s recall was 2-10% higher than the tested solutions when the patent names were processed as found in the patents. The uses of OPSIN as a web service and as a tool for identifying chemical names in text are shown to demonstrate the direct utility of this algorithm. A software system for extracting chemical reactions from the text of chemical patents was developed. The system relies on the output of ChemicalTagger, a tool for tagging words and identifying phrases of importance in experimental chemistry text. Improvements to this tool required to facilitate this task are documented. The structure of chemical entities are where possible determined using OPSIN in conjunction with a dictionary of name to structure relationships. Extracted reactions are atom mapped to confirm that they are chemically consistent. 424,621 atom mapped reactions were extracted from 65,034 organic chemistry USPTO patents. On a sample of 100 of these extracted reactions chemical entities were identified with 96.4% recall and 88.9% precision. Quantities could be associated with reagents in 98.8% of cases and 64.9% of cases for products whilst the correct role was assigned to chemical entities in 91.8% of cases. Qualitatively the system captured the essence of the reaction in 95% of cases. This system is expected to be useful in the creation of searchable databases of reactions from chemical patents and in facilitating analysis of the properties of large populations of reactions

Chiral Auxiliaries and Chirogenesis

This Reprint Book highlights and overviews the most important and novel aspects of chiral auxiliary and chirogenesis in different natural/physical sciences and in modern technologies. In particular, some newly emerging classes of molecules used for these purposes are described. This book consists of four review articles and one research paper and is of interest for general chemistry readership, including graduate and postgraduate students, and for researchers specializing in the fields of chirality and stereochemistr

Electronic Structure Evaluation of Competing Pathways in the Gold(III)-Catalyzed Ohloff-Rautenstrauch Cyclosimerization Converting Propargylic Acetates to Carene-like Natural Products

Propargylic acetates can lead to complex transformations upon exposure to a gold catalyst. Gold catalyzed transformations also allow for simple synthesis of a number of natural products. Gold (III)-cycloisomerization of a 5-acetoxy-1,6-enyne is reported to proceed through two pathways that differ in the order of major events: cyclization followed by ester migration (“cyclization first”) or the reverse (“migration first”). Both pathways could theoretically proceed in either order. This rearrangement is called the Ohloff-Rautenstrauch rearrangement and has high regio- and stereocontrol affording a bicylo[4.1.0]heptane carbon substructure. This rearrangement allows for the synthesis of the carene class of natural products. Computational modeling determining the mechanism and preference for the pathways in the gas- and solvent-phase (dichloroethane, IEFPCM) are described herein. Structures for the pathways are found using the B2PLYP/6-31G(d)-LANL2DZ model chemistry while energies are found at the B2PLYP-D3/def2TZVP//B2PLYP/6-31G(d)-LANL2DZ level. Both pathways feature multiple steps with low energy barriers. Highest-energy structures for both pathways are close in energy (ΔΔE‡ = 2.8 kcal/mol for solvent phase). Turnover frequency for each pathway are calculated suggesting that the cyclization first pathway may dominate