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Search for "parallel" in Full Text gives 447 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial
Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5
- (LD) is another type of polarization spectroscopy which does not require a chiral sample but rather an oriented one. It is based on the differential absorption of light polarized either parallel or perpendicular to a certain axis of orientation. This is also applicable to biomacromolecules such as
- ) competition experiments between two ligands aiming for the same binding site would require a specific design; and so on. 3.1. Practical information Cuvettes: quartz, preferably high-quality manufactured with precisely parallel walls (e.g., fluorimetric cuvettes) and minimal residual strain. Cylindrical cells
- conditions). End: maximum absorption of sample + 50 nm (the additional wavelength range is required to monitor if the baseline beyond the absorption region of the sample is flat after spectrum subtraction). It is compulsory to monitor in parallel the two channels corresponding to ECD and HT (related to
The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands
Beilstein J. Org. Chem. 2017, 13, 2842–2853, doi:10.3762/bjoc.13.276
- drugs contain fluorine atoms or fluoroalkyl groups, representing 150 fluorinated molecules, and this trend is expected to increase to about 30% in the early future as a new generation of fluorinated compounds is currently in Phase II−III clinical trials [1]. In parallel, pharmaceutical peptides are
The photodecarboxylative addition of carboxylates to phthalimides as a key-step in the synthesis of biologically active 3-arylmethylene-2,3-dihydro-1H-isoindolin-1-ones
Beilstein J. Org. Chem. 2017, 13, 2833–2841, doi:10.3762/bjoc.13.275
- . Sulfuric acid-catalyzed dehydrations of the benzylated hydroxyphthalimidines 3a–q in dichloromethane at room temperature resulted in the corresponding olefins 7a–q in good to excellent yields of 66–95% (Scheme 5 and Table 3). The simple reaction protocol enabled parallel operations in a Radleys Carousel 6
Metal-mediated base pairs in parallel-stranded DNA
Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265
- applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the
- glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine–Ag(I)–cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated
- base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes. Keywords: DNA; metal-mediated base pairs; nucleic acids; Introduction
A concise flow synthesis of indole-3-carboxylic ester and its derivatisation to an auxin mimic
Beilstein J. Org. Chem. 2017, 13, 2549–2560, doi:10.3762/bjoc.13.251
- off from the first separator into a second equivalent unit or by simply splitting the original quenched flow over two parallel separators. Although functional these approaches were not the optimum in design or utilisation of the separator components. We therefore also investigated the replacement of
Syntheses, structures, and stabilities of aliphatic and aromatic fluorous iodine(I) and iodine(III) compounds: the role of iodine Lewis basicity
Beilstein J. Org. Chem. 2017, 13, 2486–2501, doi:10.3762/bjoc.13.246
- "spacers" that electronically insulate the arene ring from the perfluoroalkyl groups, have been previously isolated [17]. As described below, the pursuit of the preceding objectives has met with both success and some unanticipated speed bumps, for which parallel computational studies have provided valuable
- fluorophilicity (extraction of a CH3CN solution with perfluorohexane). An analogous procedure with Rf10I gave the higher homolog 1,3-Rf10C6H4I in 50% yield [9], and a lesser amount of what was presumed to be the dialkylation product. The analogous para diiodide 1,4-C6H4I2 gave parallel chemistry, as illustrated
Sulfation and amidinohydrolysis in the biosynthesis of giant linear polyenes
Beilstein J. Org. Chem. 2017, 13, 2408–2415, doi:10.3762/bjoc.13.238
- (SMALA_2697) was added to the reaction mixture together with PAPS. As shown in Figure 3D, 1d was efficiently converted into 1c under these conditions. Therefore parallel pathways do exist (Scheme 3) for the formation of mediomycin A (1c) from desulfoclethramycin (1b), which is the full-length initial product
- biosynthetic gene clusters for mediomycin (med) from Streptomyces mediocidicus and clethramycin (cle) from S. malaysiensis DSM4137. The numbers refer to the position of each orf in the genome sequence. The parallel pathways for the biosynthesis of mediomycin A. Supporting Information Supporting Information
Homologated amino acids with three vicinal fluorines positioned along the backbone: development of a stereoselective synthesis
Beilstein J. Org. Chem. 2017, 13, 2316–2325, doi:10.3762/bjoc.13.228
- being investigated in parallel [5][6]. At this stage, it was clear that O’Hagan’s method [34] (Scheme 3) was the most promising strategy that had been examined so far. But four major obstacles remained: first, the starting material 27 was volatile and difficult to stockpile; second, the purification of
- unfavourable parallel alignment of the Cα–F and Cγ–F bonds. The extended conformer of 6b may be a minor contributor only. Conclusion Full details have been presented of the efforts that were required to identify and optimise a synthetic route towards the δ-amino acids 6a and 6b, molecules which contain three
Peptide synthesis: ball-milling, in solution, or on solid support, what is the best strategy?
Beilstein J. Org. Chem. 2017, 13, 2087–2093, doi:10.3762/bjoc.13.206
- ) [24]. Overall, the Boc-VVIA-OBn peptide was obtained in 5 steps with 59% yield and 88% purity (Scheme 1). Synthesis in solution In parallel, the Boc-VVIA-OBn tetrapeptide was produced using the conventional synthesis in solution. For this, the amino ester salts (p-toluenesulfonate or hydrochloride
Remarkable functions of sn-3 hydroxy and phosphocholine groups in 1,2-diacyl-sn-glycerolipids to induce clockwise (+)-helicity around the 1,2-diacyl moiety: Evidence from conformation analysis by 1H NMR spectroscopy
Beilstein J. Org. Chem. 2017, 13, 1999–2009, doi:10.3762/bjoc.13.196
- (+) and gg(−) conformations around the 1,2-diacyl moiety (Figure 1). From X-ray crystallography data, a common structure in which the 1,2-diacyl chains are aligned in parallel is observed, which adopts either the gt(+) or gg(−) conformer [7][10][12]. An analogous conformation has been reportedly observed
- % compared to those by Equation 2. The current study applies both Equation 1 and Equation 2 in parallel while the main discussion utilizes the results by Equation 2 as the advanced equation. Definition of ‘helicity index’, ‘helical disparity (%)’ and ‘helical volume (%)’ The ‘helicity index’ [18] comprises
Enzymatic synthesis of glycosides: from natural O- and N-glycosides to rare C- and S-glycosides
Beilstein J. Org. Chem. 2017, 13, 1857–1865, doi:10.3762/bjoc.13.180
- substrates can also be envisioned. In parallel, our knowledge of the enzymatic mechanisms has allowed us to modify and improve the original activities through reasoned site-directed mutagenesis. However, despite major advances, all the rules that finely tune the biocatalysts are still poorly understood and
Mechanochemical synthesis of thioureas, ureas and guanidines
Beilstein J. Org. Chem. 2017, 13, 1828–1849, doi:10.3762/bjoc.13.178
- subdivided into two structural families. The chains in the family I are stacked in a parallel fashion with a width of the supramolecular stack corresponding to the Bragg diffraction angle range 5–7° and the (200) reflection, intensity of which is a result of diffraction from the sulfur atoms in neighbouring
A recursive microfluidic platform to explore the emergence of chemical evolution
Beilstein J. Org. Chem. 2017, 13, 1702–1709, doi:10.3762/bjoc.13.164
- emergence of adaptive evolution. Differential fitness can then be induced in droplets when they are forced to compete for the same feedstocks [23]. Successive increases in the rate of droplet growth could be indicative of evolutionary processes in response to the continuous selection pressure. In parallel
The chemistry and biology of mycolactones
Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159
Molecular recognition of N-acetyltryptophan enantiomers by β-cyclodextrin
Beilstein J. Org. Chem. 2017, 13, 1572–1582, doi:10.3762/bjoc.13.157
- , exhibits more freedom: the carboxylic and acetylamino groups of guests D and F inside β-CD B are close and parallel, whereas in β-CD monomer A the acetylamino moiety of the major guest C is close to the carboxyl group of minor guest E, their respective carboxyl and acetylamino groups pointing to opposite
Chemical systems, chemical contiguity and the emergence of life
Beilstein J. Org. Chem. 2017, 13, 1551–1563, doi:10.3762/bjoc.13.155
- alternative approaches in relation to the emergence of specific biomolecules and biochemical assemblies. The pursuance of such, normally parallel, approaches has led to the development of hypotheses either called by their chemical embodiment, such the lipid- [5], PAH- (polycyclic aromatic hydrocarbons) [6
BODIPY-based fluorescent liposomes with sesquiterpene lactone trilobolide
Beilstein J. Org. Chem. 2017, 13, 1316–1324, doi:10.3762/bjoc.13.128
- low concentration of an immunostimulator (LPS, 100 pg·mL−1) was used. In the presence of LPS, the dose-dependent curve for NO production was running higher and it was in parallel with the curve of non-stimulated cells. The synergistic effect of construct 6 with LPS on increased NO production was
Synthesis of alkynyl-substituted camphor derivatives and their use in the preparation of paclitaxel-related compounds
Beilstein J. Org. Chem. 2017, 13, 1230–1238, doi:10.3762/bjoc.13.122
- signals. Upon reaction with catalytic amounts of PtCl2(PhCN)2, compound 21b converts into two products, apparently in a parallel reaction, and these were separated by chromatography. One product is the expected 22b, whose structure is analogous to 22a described above. The other one, 23, has undergone
- into the functional group it next reacts with. The intermediate D can be regarded as the common precursor for the parallel formation of the observed products, 23 by dissociation from the Pt catalyst and proton migration from the sulfonamide to the alcoholate, and 22 by a cascade of electron movements
Towards open-ended evolution in self-replicating molecular systems
Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118
- requires experiments to be run under conditions where replication and replicator destruction occur in parallel. Such conditions were employed in only a small subset of the work on self-replicating molecules where the emphasis has mostly been on replication in the absence of destruction. Which replicators
- macrocycles of different sizes as depicted in Figure 12b. The design of the peptide chains is such that self-assembly of the chains into parallel β-sheets is promoted, which in turn leads to the formation of stacks of macrocycles as shown in Figure 12c. Growth of these stacks occurs exclusively via the ends
Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience
Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114
- three to six anti-parallel β-strands. As a large proportion of crystal structures are complexed with carbohydrates (from monosaccharides to oligosaccharides), three CBM types have been classified based on their sugar recognition modes: surface binders, ”endo-type” binders and “exo-type” binders [44
- parallel arrangement of parallel-stranded left-handed double helices [86][87]. A second look at the crystal structure of the A-polymorph became possible when microcrystals were grown from short chains of synthetic starch and diffraction data collected using a micron-sized beam at a synchrotron source
From chemical metabolism to life: the origin of the genetic coding process
Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111
- must still be compatible with the OS. Naturally, of course, there is still another feature that is absent in the fiction: creation of a progeny. Yet, this is, as everybody will accept, a core function of life. The key role of coding In parallel with a remarkably prescient vision of cardinal features of
- . The RNA-metabolism world The reproduction of progressively more efficient metabolic pathways preceded the replication of nucleic acids (perhaps in parallel with the replication of proteins, as we saw with the centriole example). A key question is now to understand how both processes could be linked
- tRNA has been proposed recently [61]. With ribozymes involved in the catalysis of peptide-bond formation, and primal tRNAs as handles carrying amino acids used in the process, an alternative or complement to the swinging-arm peptide synthesis would have evolved in parallel, with RNA-dependent peptide
G-Protein coupled receptors: answers from simulations
Beilstein J. Org. Chem. 2017, 13, 1071–1078, doi:10.3762/bjoc.13.106
- variations of metadynamics allow very effective use of massively parallel supercomputers in order to investigate ligand binding and unbinding and transitions between active and inactive receptor conformations. Indeed, the power of modern simulations is such that we must revisit the relationship between
- specialized hardware such as Anton [25] but are less effective on more conventional massively parallel supercomputers because the simulations only scale up to a relatively limited number of CPUs or GPUs [35]. Luckily, of the many enhanced-sampling techniques [35], modern variations of metadynamics [27] can
- make very effective use of massively parallel hardware. Briefly, metadynamics enhances the sampling in MD simulations by adding small Gaussian destabilizing potentials at positions that the simulations has already visited enough. “Positions” need to be defined in terms of a small number of geometrical
Aggregation behaviour of a single-chain, phenylene-modified bolalipid and its miscibility with classical phospholipids
Beilstein J. Org. Chem. 2017, 13, 995–1007, doi:10.3762/bjoc.13.99
- round shaped and they are oriented either parallel (black arrow head) or perpendicular to the grid surface (white arrow head). EM images of a bolalipid/phospholipid = 1:5 mixture show the existence of disk-like aggregates of comparable size for all three different phospholipids (Figure 6D–F). However
Automating multistep flow synthesis: approach and challenges in integrating chemistry, machines and logic
Beilstein J. Org. Chem. 2017, 13, 960–987, doi:10.3762/bjoc.13.97
- kinetics parameters of a series-parallel substitution reaction [38]. Reizman et al. have studied Suzuki–Miyaura cross-coupling optimization using a DoE-based algorithm and feedback system [45]. The authors studied both continuous and discrete variables for optimization. Recently Fitzpatrick and Ley have
- (±)-oxomaritidine (gas–liquid–solid reaction) Baxendale et al. have developed a multistep synthesis for (±)-oxomaritidine, a cytotoxic alkaloid of the amaryllidaceae family of natural products [9] (Scheme 4). The process involved seven reaction steps out of which the first two reactions were carried out in parallel
- resin will get consumed after some time and the corresponding section needs to be activated or recycled in order to maintain continuous production. In such cases, it is possible to have two parallel reactors containing a packing of azide exchange resin, which can be operated in a cyclic manner to
Opportunities and challenges for the sustainable production of structurally complex diterpenoids in recombinant microbial systems
Beilstein J. Org. Chem. 2017, 13, 845–854, doi:10.3762/bjoc.13.85
- ]. Eponymous intermediate of this pathway is the product of the second enzymatic step where 1-deoxy-D-xylulose-5-phosphate (DXP) is reduced to 2-C-methyl-D-erythritol-4-phosphate (see Scheme 1). Parallel occurrence of both pathways in higher plants is regulated through compartmentalization [30] with
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