Structure generation by reduction: a new strategy for computer-assisted structure elucidation

A problem common to computer programs for structure elucidation is the efficient and prospective use of the input information to constrain the structure generation process. The input may consist of potentially overlapping substructure requirements and alternative substructure interpretations of spectral data. Other useful information may be structural features that must not be present in the output structures. All of these may interact in a complex manner that is impossible to determine by use of a bond-by-bond structure assembly algorithm. A new method is described called structure reduction. In contrast to structure assembly, this method begins with a set of all bonds and removes inconsistent bonds as structure generation progresses. This results in a more efficient use of the input information and the ability to use potentially overlapping required substructures. Several examples illustrate the application of our computer program COCOA, which uses this method to solve real-world structure elucidation problems.     

From crystal to micelle: A new approach to the micellar structure

The structure of sodium and rubidium deoxycholate micellar aggregates in aqueous solutions was found to be helical and to be stabilized mainly by polar interactions. Astonishingly, the lateral surface of the helix is covered by nonpolar groups and the interior part is filled with cations surrounded by water molecules, as in the case of an inverted micelle. This helical model was inferred from the crystal structures of sodium and rubidium deoxycholates and proved by spectroscopic and diffractometric experimental data. The strategy of the approach to the determination of the micellar structure and the comparison with another model, previously proposed for the bile salt micelles, are reported. On the basis of some results obtained for sodium tauro- and glyco-deoxycholates, micellar models are suggested which could account for the biological function of these important conjugated bile salts.     

Phytochrome structure: A new methodological approach

Higher plants use the protein phytochrome as a photosensor. In physiological temperatures phytochrome exists in two forms: Pr and Pfr. The chromophore of phytochrome is an open-chain tetrapyrrole. On the pathway from Pr to Pfr four intermediates (Lumi-R, Meta-Ra, Meta-Rb, and Meta-Rc) can be distinguished, while only two (Lumi-F and Meta-F) can be seen on the way back from Pfr to Pr. We have used the x-ray structure of the C-Phycocyanin protein Fremyella diplosiphon bacteria as a template to build a model (∼200 atoms) that includes only the chromophore and five amino acids of the phytochrome (Arg316–Cys321–His322–Leu323–Gln324) around it. Using the existing experimental evidences, we have proposed a three-dimensional (3D) structure for Pr, Pfr, and intermediates and a mechanism for the photoisomerization as well. Structures were fully optimized using AM1 (Unichem package on a Cray J90-NACAD). Using the INDO/S method of Zerner and co-workers, we calculated the absorption spectra of the model compounds and compared them with the experimental data. The oscillator strength ratio is an indicator of the chomophore conformation in biliproteins. The calculated spectra reproduces well the spectra of the phytochrome (Pr, Pfr, and intermediates) except for the lower energy band. This result is attributed to the small number of amino acids in the models. The calculated ratios (f_VIS/f_UV−f_osc of visible band over f_osc of UV band and f₂/f₁−f_osc of second absorption band over f_osc of first absorption band) for the models match very well the experimental ratios obtained for the phytochrome (Pr, Pfr, and intermediates). This supports the proposed mechanism for the photoisomerization process. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1145–1157, 1998     

High-performance bioreactors: a new generation

Compact loop bioreactors with a total volume of 4 l were equipped with electrically controllable valves and pumps, most of the currently available on-line sensors, direct digital control systems and a process minicomputer; complete automatic operation was thus achieved. These reactors perform excellently: the mixing time is <1 s, oxygen transfer is not a limiting factor and the precision of control of more than 10 process variables is much better than so far reported on other systems. Such high-performance bioreactors were used in investigating the stable synchronous oscillations of Saccharomyces-type yeasts and the reduction of slightly soluble organic compounds with biocatalysts. The inherent advantages of on-line measurement (and control) are discussed.     

溴氯卡宾产生新方法及其机理的讨论

本文报道以卤仿和某些多卤代烃组成的混合试剂在超声辐射下产生溴氯卡宾的新方法,并讨论了反应机理。     

Microprinting – a new approach to study competitive structure formation on surfaces

A new approach to the experimental investigation of heterogeneous crystallization on surfaces with molecularly defined structures is demonstrated. Crystallization and competitive dewetting processes of polyethylene on heterogeneous micropatterned surfaces were studied using molecular imprinting techniques for structured chemical modification of surfaces on micrometer scale in laterally defined areas. Examination of spherulitic textures by low‐voltage SEM and AFM shows remarkable differences in spherulite sizes due to surface chemical influences. The results are discussed in terms of a diffusion limited aggregation process which causes the dendritic and spherulitic structures and which is influenced by the dewetting process.     

Fuzzy structure generation: a new efficient tool for Computer-Aided Structure Elucidation (CASE)

Contemporary Computer-Aided Structure Elucidation (CASE) systems are heavily based on the utilization of 2D NMR spectra. The utilization of HMBC/GHMBC and COSY/GCOSY correlations generally assumes that these correlations result from (2-3)JCH and (2-3)JHH spin-spin couplings, respectively, and consequently these values are used as the default setting in these systems. Our previous studies1,2 have shown that about half of the problems studied actually contain some correlations of 4-6 bonds, so-called "nonstandard" correlations. In such cases the initial 2D NMR data are contradictory, and the correct solution is therefore not directly attainable. Unfortunately nonstandard correlations and the number of intervening bonds usually cannot be identified experimentally. In this work we suggest a new approach that we term Fuzzy Structure Generation. This allows the solution of structural problems whose 2D NMR data contain an unknown number of nonstandard correlations having different and unknown lengths. Suggested methods for the application of Fuzzy Structure Generation are described, and their application is illustrated by a series of real-world examples. We conclude that Fuzzy Structure Generation is efficient, and there is no real alternative at present in terms of a universal practical method for the structure elucidation of organic molecules from 2D NMR data.     

HPLC-SEC: a new approach to characterise complex wastewater effluents

This work investigates the use of HPLC-SEC to characterise dissolved organic matter (DOM) of complex wastewater effluents. A silica-based column, sodium acetate eluent and multiple detections were employed: UV-254 absorbance for humictype, and tryptophan-like (Ex/Em = 270/355) and tyrosine-like (Ex/Em = 270/310) fluorescence for protein type compounds. Effects of eluent pH, eluent ionic strength and injection volume on separation efficiency were tested. Humic-type and protein-type fractions were clearly differentiated and eluted within and out of calibration range. Eluent ionic strength had the greatest influence on global resolution; the lowest eluent concentration of 0.01 M produced the best separation for all wastewater effluents tested at any detection. UV-254 absorbance was higher at neutral and basic eluent pH while tryptophan-like fluorescence depended on the sample composition rather than on the eluent pH or ionic strength. Tyrosine-like fluorescence decreased significantly with the increase of eluent ionic strength. Accurate molecular weight measurements could not be done, the separation being influenced by secondary interactions, but could be approximated using separate calibrations with sodium salts of polystyrene-sulfonates and protein standards. The results show that this method is suitable for determining DOM in wastewater at low eluent concentrations (up to 0.03 M), at neutral or slightly basic pH.     

Electrotelluration: a new approach to tri- and tetrasubstituted alkenes

A novel electrotelluration process is described in which a Michael addition of an alkyl or aryl tellurolate anion occurs onto an activated alkyne with subsequent trapping of a vinyl anion with electrophiles (aldehydes and ketones) other than a proton. This process provides an efficient regio- and stereospecific route to tri- and tetrasubstituted alkenes. Methodologically significant examples of this chemistry were studied in which aryl and alkyl tellurolate anions were added to omega-keto alkynyl esters in a Michael reaction, and the incipient vinyl anions were trapped intramolecularly by the internal aldehydes. The reactive centers were tethered by different lengths of alkyl chains to form highly functionalized five-, six-, seven-, and eight-membered rings in modest to good yields.     

Single-molecule magnets: a new approach to investigate the electronic structure of Mn12 molecules by scanning tunneling spectroscopy

A new approach to the deposition of Mn12 single-molecule magnet monolayers on the functionalized Au(111) surface optimized for the investigation by means of scanning tunneling spectroscopy was developed. To demonstrate this method, the new Mn12 complex [Mn12O12(O2CC6H4F)16(EtOH)4].4.4CHCl3 was synthesized and characterized. In MALDI-TOF mass spectra the isotopic distribution of the molecular ion peak of the latter complex was revealed. The complex was grafted to Au(111) surfaces via two different short conducting linker molecules. The Mn12 molecules deposited on the functionalized surface were characterized by means of scanning tunneling microscopy showing homogeneous monolayers of highest quality. Scanning tunneling spectroscopy measurements over a wider energy range compared with previous results could be performed because of the optimized Au(111) surface functionalization. Furthermore, the results substantiate the general suitability of short acidic linker molecules for the preparation of Mn12 monolayers via ligand exchange and represent a crucial step toward addressing the magnetic properties of individual Mn12 single-molecule magnets.     

Anisotropic island growth: a new approach to thin film electrocrystallization

The electrochemical deposition of metals onto foreign substrates usually occurs through Volmer-Weber island growth, and hence the structure and properties of thin films are critically dependent on the mechanism of nucleation and growth. For example, high nucleus densities are essential for achieving island coalescence at small thickness. Here we demonstrate a new approach to controlling thin film microstructure through the control of island geometry. By promoting anisotropic island growth, film coalescence can be achieved at smaller thickness and with lower island densities.     

Wrinkle engineering: a new approach to massive graphene nanoribbon arrays

Wrinkles are often formed on CVD-graphene in an uncontrollable way. By designing the surface morphology of growth substrate together with a suitable transfer technique, we are able to engineer the dimension, density, and orientation of wrinkles on transferred CVD-graphene. Such kind of wrinkle engineering is employed to fabricate highly aligned graphene nanoribbon (GNR) arrays by self-masked plasma-etching. Strictly consistent with the designed wrinkles, the density of GNR arrays varied from ～0.5 to 5 GNRs/μm, and over 88% GNRs are less than 10 nm in width. Electrical transport measurements of these GNR-based FETs exhibit an on/off ratio of ～30, suggesting an opened bandgap. Our wrinkle engineering approach allows very easily for a massive production of GNR arrays with bandgap-required widths, which opens a practical pathway for large-scale integrated graphene devices.     

Transient infrared spectroscopy: a new approach to investigate valence tautomerism

In this work we present, to our knowledge for the first time, the results of a transient infrared spectroscopic study of the photoinduced valence tautomerism process in cobalt-dioxolene complexes with sub-picosecond time resolution. The molecular systems investigated were [Co(tpa)(diox)]PF(6) (1) and [Co(Me(3)tpa)(diox)]PF(6) (2), where diox = 3,5-di-tert-butyl-1,2-dioxolene; tpa = tris(2-pyridylmethyl)amine and Me(3)tpa its 6-methylated analogue. Complex (1) is present in solution as ls-Co(III)(catecholate) (1-CAT), while (2) as hs-Co(II)(semiquinonate) (2-SQ). DFT calculation of the harmonic frequencies for (1) and (2) allowed us to identify the vibrational markers of catecholate and semiquinonate redox isomers. Irradiation with 405 and 810 nm pulses (~35 fs) of (1-CAT) induces the formation of an intermediate excited species from which the ground state population is recovered with a time constant of 1.5 ± 0.3 ns. Comparing the 1 ns transient infrared spectrum with the experimental difference spectrum FTIR(2-SQ)-FTIR(1-CAT) and with the calculated difference spectrum IR(c)(1-SQ)-IR(c)(1-CAT) we are able to unequivocally identify the long lived species as the semiquinonate redox isomer of (1). On the other hand, no evidence of photoconversion is observed upon irradiation of (2) with 405 nm. Temporal evolution of transient spectra was analyzed with the combined approach consisting of singular values decomposition and global fitting (global analysis). After 405 and 810 nm excitation of (1-CAT), the semiquinonate excited species is formed on an ultrafast time scale (<200 fs) and cools down within the first 50 ps. Excitation of (2-SQ) with 405 nm wavelength produces a short lived excited state in which the semiquinonate nature of dioxolene is preserved and the ground state recovery is completed within 30 ps.     

Single-atom electrocatalysis: a new approach to in vivo electrochemical biosensing

Science China Chemistry - Modulation of interfacial electron transfer has been proven to pave a new approach to in vivo electrochemical monitoring of brain chemistry; however, designing and...     

Electrophile-induced ether transfer: a new approach to polyketide structural units

[Structure: see text] A strategically novel approach to the formation of syn-1,3-diol mono- and diethers through electrophilic activation of homoallylic alkoxymethyl ethers has been developed. The resulting polyketide-like synthetic fragments are generated in good yield and with excellent stereocontrol. A chairlike transition state is proposed to account for the high stereoselectivity. Varying the conditions of the reaction workup results in the efficient generation of mono- and diether containing structural units common to polyketide natural products.     

Circulating miRNAs: a new generation of anti-doping biomarkers

MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. Cell-free miRNAs detected in blood plasma are used as specific and sensitive markers of physiological processes and some diseases. Circulating miRNAs are highly stable in body fluids, for example plasma. Therefore, profiles of circulating miRNAs have been investigated for potential use as novel, non-invasive anti-doping biomarkers. This review describes the biological mechanisms underlying the variation of circulating miRNAs, revealing that they have great potential as a new class of biomarker for detection of doping substances. The latest developments in extraction and profiling technology, and the technical design of experiments useful for anti-doping, are also discussed. Longitudinal measurements of circulating miRNAs in the context of the athlete biological passport are proposed as an efficient strategy for the use of these new markers. The review also emphasizes potential challenges for the translation of circulating miRNAs from research into practical anti-doping applications.     

The Bogorol family of antibiotics: template-based structure elucidation and a new approach to positioning enantiomeric pairs of amino acids

The sequence positions of d and l Leu and Lys residues in bogorol A (1) have been defined by a simple and novel approach that utilizes small amounts of sample and focuses on detecting the order in which amino acids are liberated from the parent peptide during acid-catalyzed hydrolysis. This technique builds on a previously established relationship between the steric and electronic features of amino acids and their predilection for acidic liberation from polypeptides via dipeptides. The results, which complete the structure of bogorol A, have been confirmed by traditional degradation experiments. Utilizing the knowledge of the structure of bogorol A (1) as a template, we rapidly elucidated the structures of bogorols B-E (2-5) via analysis of ESI-MS and ESI-MS/MS data and GC analysis of degradation products. The bogorol cationic peptide antibiotics contain a number of unusual structural features, which include the reduction of the C-terminal residue to valinol, an N-terminal residue of 2-hydroxy-3-methylpentanoic acid, the incorporation of four d amino acids, and the presence of a dehydroamino acid. Bogorols show selective and relatively potent activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus spp., as well as moderate activity against Escherichia coli.