Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• more precise control of the position and orientation of the label than the former, and therefore should be more sensitive to local environment changes than the former, which indirectly and non-specifically senses the global formation of duplex or base stack. PNA probes with tethered labels One of the

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• complemented with among others the adenine analogue FRET pair, qAN1–qAnitro, increasing the flexibility of the methodology. Here we present the design, synthesis, photophysical characterization and use of such base analogues. They enable a higher control of the FRET orientation factor, κ2, have a different

• ][6]. FRET is a process that depends on the radiationless energy transfer between a donor and an acceptor molecule [7]. The reason that it can be used as a structure and dynamics technique is that it depends heavily on the distance and relative orientation between the donor and acceptor. Typical

• , Equation 3). This factor takes the relative orientation of the transition dipole moments of the donor and acceptor into account and, thus, introduces an orientation dependence to R0 and consequently also to the energy transfer efficiency, E. The orientation factor, which ranges between 0 and 4, is governed

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

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

• (ECD) will be discussed first as the most common technique with the least pitfalls. Thus it is most often appropriate for the characterization of the systems of interest. Then, LD follows as a complementary method used to reveal the mutual orientation of the ligand chromophore with respect to the DNA

• significant structural information based on electric and magnetic transition moments of adjacent chromophores and their mutual orientation. This is especially true in the presence of strong chromophores interacting through the coupled oscillator mechanism mentioned above. Consequently, based on the

Photocatalytic formation of carbon–sulfur bonds

• Alexander Wimmer and
• Burkhard König

Beilstein J. Org. Chem. 2018, 14, 54–83, doi:10.3762/bjoc.14.4

• explained by the decomposition of the organic photocatalyst during the H2 evolution process. Increasing amounts of the photocatalyst increased the yield of product and H2. Very recently, the same group reported a regioselective photoredox-catalyzed preparation of vinyl sulfones in Markovnikov orientation

• Eosin Y as photoredox catalyst generates both, the sulfur-centred radical of the sulfinic acid as well as the α-vinyl carbon-centred radical. Radical/radical cross-coupling leads to the desired vinyl sulfone in Markovnikov orientation. The reaction is applicable to diverse functionalized terminal

• year before (Scheme 47) [84]. They propose that either a hydroxide anion, derived from cleaved TBHP, or a water molecule (solvent) attacks nucleophilic on the cationic intermediate in anti-Markovnikov orientation. The resulting β-hydroxysulfone is then further oxidized to the respective β-ketosulfone

Aminosugar-based immunomodulator lipid A: synthetic approaches

• Alla Zamyatina

Beilstein J. Org. Chem. 2018, 14, 25–53, doi:10.3762/bjoc.14.3

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• m7G, yielding mRNA with the cap in reverse orientation (Figure 3). Up to one half of the mRNA can contain the cap in its reverse orientation and will not be translated [47]. This problem was solved by developing anti-reverse cap analogues (ARCA) that are methylated or deoxygenated at the 3′-OH of the

• N7-methylguanosine ribose (m27,3′-OGpppG or m7,3′-dGpppG). This prevents elongation at the “wrong” 3′-OH and hence ARCA caps are exclusively incorporated in the correct orientation [48][49]. Interestingly, modifications at the 2′-position of m7G also prevented reverse incorporation of the cap

• analogue [50]. The problem of orientation is circumvented when GpppA cap analogues are used in combination with the T7 class II promotor phi2.5 which allows initiating RNA synthesis with ATP. Hence, GpppA- or m7GpppA-capped RNAs can be produced [51]. When the common GTP-initiating T7 class III promoter

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

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

• strands. Review Parallel-stranded DNA In canonical DNA duplexes, the complementary oligonucleotide strands are oriented in an antiparallel fashion. From a geometrical point of view, this correlates with a cisoid orientation of the glycosidic bonds in Watson–Crick base pairs. A parallel-stranded

• orientation of oligonucleotide strands may also occur in nature, albeit in more complex topologies such as triple helices or quadruplexes [31][32]. Nonetheless, the formation of parallel-stranded DNA duplexes can be induced in various ways, leading to a variety of non-canonical DNA duplex topologies that

Synthesis and supramolecular properties of regioisomers of mononaphthylallyl derivatives of γ-cyclodextrin

• Markéta Bláhová,
• Sergey K. Filippov,
• Lubomír Kováčik,
• Jiří Horský,
• Simona Hybelbauerová,
• Zdenka Syrová,
• Tomáš Křížek and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2017, 13, 2509–2520, doi:10.3762/bjoc.13.248

• complexation of the alkylation agent to the CD cavity and orientation of the agent´s reactive center towards the 3-OH group [11][12][13]. Here, we report the preparation of regioisomers of novel mononaphthylallyl γ-CD (NA-CD), i.e., 3-(naphthalene-2-yl)prop-2-en-1-yl γ-CD, which is interesting for several

A permutation approach to the assignment of the configuration to diastereomeric tetrads by comparison of experimental and ab initio calculated differences in NMR data

• Przemysław J. Boratyński

Beilstein J. Org. Chem. 2017, 13, 2478–2485, doi:10.3762/bjoc.13.245

• initial 6–9 geometries corresponded to rotation along major degrees of freedom, i.e., C4’–C9 and C9–C8 bonds and orientation of the pendant ring. Conformers of up to 3 kcal/mol higher in energy were considered in the calculation and their contribution was included in the Boltzmann-weighted average

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241

• ) counterpart due to the conformational contribution of the terminal fluorinated moiety. Both predictions clearly contradict the experimentally observed tendencies. A possible problem with the existing models is that they assume a defined orientation for the fluorine-bearing moiety. However, this moiety may be

• orientation, respectively [79][80]. This conformational equilibrium manifests in the χ angles, which is reflected by the J-coupling observed between the α-CH and β-CH2 groups in the 1H NMR spectra (Jαβ) [81][82]. A recent analysis of the Jαβ values by Braga et al. was used to quantify the pucker equilibrium

One-pot syntheses of blue-luminescent 4-aryl-1H-benzo[f]isoindole-1,3(2H)-diones by T3P^® activation of 3-arylpropiolic acids

• Melanie Denißen,
• Alexander Kraus,
• Guido J. Reiss and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2017, 13, 2340–2351, doi:10.3762/bjoc.13.231

• shoulder. This appearance might result from the free rotation of the N-phenyl substituents, furnishing emissive conformers that arise from a coplanar (λmax,em at 468.0 nm as a shoulder for compound 4a) and torsional orientation (λmax,em at 408.5 nm as a maximum for compound 4a) of the N-phenyl substituent

Synthesis of ergostane-type brassinosteroids with modifications in ring A

• Vladimir N. Zhabinskii,
• Darya A. Osiyuk,
• Yuri V. Ermolovich,
• Natalia M. Chaschina,
• Tatsiana S. Dalidovich,
• Miroslav Strnad and
• Vladimir A. Khripach

Beilstein J. Org. Chem. 2017, 13, 2326–2331, doi:10.3762/bjoc.13.229

• the contrary, no correlation was observed between the corresponding protons in compound 22, which is consistent with the α-orientation of the epoxide ring. 2β,3β-, 2β,3α- and 2α,3β-diols of type 6–8 Experiments on the identification of steroidal phytohormones in immature seeds of Phaseolus vulgaris

Synthesis and application of trifluoroethoxy-substituted phthalocyanines and subphthalocyanines

• Satoru Mori and
• Norio Shibata

Beilstein J. Org. Chem. 2017, 13, 2273–2296, doi:10.3762/bjoc.13.224

• , it is considered that the performance of solar cells that use per(trifluoroethoxy)phthalocyanine, which exhibits a strong repulsion effect, will be low. It is expected that phthalocyanine will be put to practical use within solar cells by improving the orientation control in thin films. Development

Dialkyl dicyanofumarates and dicyanomaleates as versatile building blocks for synthetic organic chemistry and mechanistic studies

• Grzegorz Mlostoń and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2017, 13, 2235–2251, doi:10.3762/bjoc.13.221

• first one is the ring closure leading to 9, and the second one involves the addition of a second carbene followed by ring closure to yield 8. The reaction with Z-1b led to the same set of products with trans-orientation of the substituents in 8 indicating the appearance of an intermediate zwitterion 11

• the homogeneous products are trans-configured. This assumption is supported by the results obtained with cyclopentadiene and both E- and Z-1b [32]. Whereas the reaction with E-1b led to only one stereoisomer, in the case of Z-1b, exo- and endo-isomers with preserved cis-orientation of the CN and CO2Me

Intramolecular glycosylation

• Xiao G. Jia and
• Alexei V. Demchenko

Beilstein J. Org. Chem. 2017, 13, 2028–2048, doi:10.3762/bjoc.13.201

• arming participating group [112][113]. These glycosylations provided complete 1,2-trans stereoselectivity, anti with respect to the orientation of the picolinyl group. When the picolinyl ether or picoloyl ester group was placed at remote positions, glycosylations occurred syn with respect to the

• orientation of the picolinyl/picoloyl group [114]. The stereoselectivity was explained by the occurrence of the hydrogen bonding between the hydroxy group of glycosyl acceptor (NuH) and the nitrogen atom of the picolinyl/picoloyl group. Subsequently, the glycosyl acceptor is delivered towards the oxacarbenium

Are boat transition states likely to occur in Cope rearrangements? A DFT study of the biogenesis of germacranes

• José Enrique Barquera-Lozada and
• Gabriel Cuevas

Beilstein J. Org. Chem. 2017, 13, 1969–1976, doi:10.3762/bjoc.13.192

• epimer 3’ from 1 is not thermodynamically highly favored. Therefore, the hemiacetal formation with the right orientation is fundamental to produce an elemanolide more stable than the (Z,E)-germacranolide. It has been proposed that the configuration of an elemane depends on the most stable conformation of

Conformational impact of structural modifications in 2-fluorocyclohexanone

• Francisco A. Martins,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2017, 13, 1781–1787, doi:10.3762/bjoc.13.172

• such hyperconjugative interactions and therefore often give way to the C–H bond in occupying the antiperiplanar orientation relative to the C–F bond [2][3][4][5][6]. The electrostatic fluorine gauche effect has also been introduced in cases where the partially negative fluorine interacts with a

• study [19], the introduction of an endocyclic oxygen in 2-fluorocyclohexanone to give the 3-fluorodihydro-2H-pyran-4(3H)-one was expected to favor the axial orientation of the fluorine substituent because of the prospective gauche arrangement with the endocyclic oxygen, giving rise to the fluorine

• organofluorine heterocycles [21][22][23][24]. Thus, this computational study has multi-focus objectives, namely exploring the effect of replacing the carbonyl oxygen and the methylene group at position 4 by other groups in order to induce conformational changes (relative to the fluorine orientation), as well as

18-Hydroxydolabella-3,7-diene synthase – a diterpene synthase from Chitinophaga pinensis

• Jeroen S. Dickschat,
• Jan Rinkel,
• Patrick Rabe,
• Arman Beyraghdar Kashkooli and
• Harro J. Bouwmeester

Beilstein J. Org. Chem. 2017, 13, 1770–1780, doi:10.3762/bjoc.13.171

• conversion of stereoselectively deuterated terpene precursors, because the problem of determining the absolute configuration of the terpene under investigation is simplified to a problem of delineating the relative orientation of its stereocentres to the known absolute configuration at the deuterated carbon

Theoretical simulation of the infrared signature of mechanically stressed polymer solids

• Matthew S. Sammon,
• Milan Ončák and
• Martin K. Beyer

Beilstein J. Org. Chem. 2017, 13, 1710–1716, doi:10.3762/bjoc.13.165

• property of the applied force, the change of the vibrational modes with increasing force depends on the orientation of the normal mode displacement of each atom relative to the force vector. To illustrate the molecular origin of the changes in the calculated infrared spectrum due to force, the four

Molecular recognition of N-acetyltryptophan enantiomers by β-cyclodextrin

• Spyros D. Chatziefthimiou,
• Mario Inclán,
• Petros Giastas,
• Athanasios Papakyriakou,
• Konstantina Yannakopoulou and
• Irene M. Mavridis

Beilstein J. Org. Chem. 2017, 13, 1572–1582, doi:10.3762/bjoc.13.157

• were tried. In aqueous solution, the orientation of the guest in both complexes is different than in the β-CD–L-NAcTrp complex in the crystal. Overall, the study shows that subtle differences observed between the β-CD–L,D-NAcTrp complexes in aqueous solution are magnified at the onset of

• guest molecules of L-NAcTrp are enclosed in a head-to-head fashion (host:guest ratio, 1:1). The pair of L-NAcTrp molecules inside the dimer are found in orientational disorder, i.e., the guest exhibits a major orientation, molecules C and D (occupancy 65%), and a co-existing minor orientation (molecules

• , compared to the conformation observed in the crystal. In addition, both complexes are in contact with a second β-CD molecule suggesting presence of higher stoichiometries and possibility of different inclusion modes at low concentration. Overall, the orientation of both enantiomeric guests with respect to

Chemical systems, chemical contiguity and the emergence of life

• Terrence P. Kee and
• Pierre-Alain Monnard

Beilstein J. Org. Chem. 2017, 13, 1551–1563, doi:10.3762/bjoc.13.155

• . The correct orientation of the various compounds was easily determined chemically, e.g., by derivatization of the triad photo-sensitizer with a charged group that defined which side of the molecule could insert into the hydrophobic core of the membranes [92]. However, a correct addition sequence

A speedy route to sterically encumbered, benzene-fused derivatives of privileged, naturally occurring hexahydropyrrolo[1,2-b]isoquinoline

• Olga Bakulina,
• Alexander Ivanov,
• Vitalii Suslonov,
• Dmitry Dar’in and
• Mikhail Krasavin

Beilstein J. Org. Chem. 2017, 13, 1413–1424, doi:10.3762/bjoc.13.138

• major diastereomer was shown to possess the (RS,RS)-configuration (vide infra) and is referred to as ‘anti‘ throughout this article (considering orientation of carboxylic group relative to C11a–C12 bond of the five-membered ring); the minor, (RS,SR)-configured diastereomer is referred to as ‘syn

Synthesis of novel 13α-estrone derivatives by Sonogashira coupling as potential 17β-HSD1 inhibitors

• Ildikó Bacsa,
• Rebeka Jójárt,
• János Wölfling,
• Gyula Schneider,
• Bianka Edina Herman,
• Mihály Szécsi and
• Erzsébet Mernyák

Beilstein J. Org. Chem. 2017, 13, 1303–1309, doi:10.3762/bjoc.13.126

• hydrogenations of the two regioisomers presumably arose from the steric hindrance caused by the vicinity of ring B in the case of compound 15. The cis or trans orientation of the resulting geometric isomers was deduced from the vicinal coupling constants according to the literature data, because cis and trans

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• µm on a wood section of 10 µm thick and oriented perpendicular to the incident beam [89]. As depicted in Figure 19, a complete distribution map of the orientation of the axes of the cellulose microfibril, of a specimen of 52 × 42 µm, was established through a series of 546 diffraction patterns. These

• -focus X-ray diffraction from synchrotron radiation offered the possibility to explore the arrangements of the crystalline domains which are at the origin of the birefringence of the starch granule. Using a 2 μm wide X-ray beam, a complete cartography of the relative orientation on a single granule could

• be drawn. Two-dimensional fiber diffraction patterns were collected for each domain on a grid of 4 × 4 μm. Information about the nature of the crystalline structure (for allomorphs A, B and C) was obtained confirming the orientation of amylopectin double helices in the crystalline lamellae as well as

From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

• , the processes that allow aged organisms to construct young ones are of key interest. These processes, in turn, give a direction to the very process of “life and evolution” via accumulation of information, in a ratchet-like manner. Combining “action” with “orientation” will help us to understand the