Isolation and structure determination of a tetrameric sulfonyl dilithio methandiide in solution based on crystal structure analysis and ⁶Li/¹³C NMR spectroscopic data

• Jürgen Vollhardt,
• Hans Jörg Lindner and
• Hans-Joachim Gais

Beilstein J. Org. Chem. 2020, 16, 2057–2063, doi:10.3762/bjoc.16.172

• and dynamics in solution [1][2][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43]. The main obstacles at characterizing dilithio methandiides in terms of aggregate size, C–Li connectivity, Li coordination of the dianionic C atoms, and

• ][36][37][38][39][40][41][42][43]. They generally showed intricate aggregates with complex C–Li and C–Li–heteroatom chains, containing doubly lithiated C atoms. However, as much as there is now knowledge of the structure of dilithio methandiides in the crystal, as little is known about the structure

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• ][21][22][23]. More specifically, we investigate how core α(1-3)-linked fucose (Fuc) and β(1-2)-linked xylose (Xyl) affect the structure and dynamics of plants N-glycoforms [23] and of hybrid constructs with mammalian N-glycoforms [24]. At first glance plants protein N-glycosylation [23] is quite

• GlcNAc and results in the occurrence of Lewis A (LeA) instead of Lewis X (LeX) terminal motifs on the arms [23][26]. In a previous study, we characterized through extensive sampling the structure and dynamics of complex biantennary N-glycans commonly found in the human IgGs Fc region [24]. The results of

• differences in terms of molecular recognition [19][27] and dangerous immunogenic responses [20][21][22]. In this work we have analysed the effects on the N-glycans structure and dynamics of two motifs in particular, namely β(1-2)-Xyl and core α(1-3)-Fuc, common in plants [23] and invertebrates [30], but

The phenyl vinyl ether–methanol complex: a model system for quantum chemistry benchmarking

• Dominic Bernhard,
• Fabian Dietrich,
• Mariyam Fatima,
• Cristóbal Pérez,
• Hannes C. Gottschalk,
• Axel Wuttke,
• Ricardo A. Mata,
• Martin A. Suhm,
• Melanie Schnell and
• Markus Gerhards

Beilstein J. Org. Chem. 2018, 14, 1642–1654, doi:10.3762/bjoc.14.140

• , Germany Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 6, D-37077

Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA

• Timo Weinrich,
• Eva A. Jaumann,
• Ute M. Scheffer,
• Thomas F. Prisner and
• Michael W. Göbel

Beilstein J. Org. Chem. 2018, 14, 1563–1569, doi:10.3762/bjoc.14.133

• ; Introduction EPR spectroscopy is well established to study the structure and dynamics of nucleic acids [1][2][3][4][5][6][7][8]. Although the information attainable by EPR is less detailed when compared to NMR, it is often complementary. While local conformations are normally obtained from NMR data, EPR can

Fluorogenic PNA probes

• Tirayut Vilaivan

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

• dT in the DNA strand with comparable affinity to that for A, and the base pairing resulted in fluorescence quenching. While the quenching of 2-AP can be useful for probing the structure and dynamics of the PNA and its DNA/RNA hybrids, the quenching effect is small and not highly specific as quenching

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

• acid bases inside the base-stack, base analogue donor and acceptor molecules complement external fluorophores like the Cy-, Alexa- and ATTO-dyes and enable detailed investigations of structure and dynamics of nucleic acid containing systems. The first base–base FRET pair, tCO–tCnitro, has recently been

• . Base–base FRET has been around for less than a decade, only in 2017 expanded beyond one FRET pair, and represents a highly promising structure and dynamics methodology for the field of nucleic acids. Here we bring up its advantages as well as disadvantages and touch upon potential future applications

• . Keywords: B-to-Z-DNA transition; fluorescent base analogues; FRET; netropsin; nucleic acid structure and dynamics; quadracyclic adenines; tricyclic cytosines; Z-DNA; Review Introduction The importance of nucleic acid structure and dynamics in the understanding of vital processes in living organisms has

Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

• Nattawut Yotapan,
• Chayan Charoenpakdee,
• Pawinee Wathanathavorn,
• Boonsong Ditmangklo,
• Hans-Achim Wagenknecht and
• Tirayut Vilaivan

Beilstein J. Org. Chem. 2014, 10, 2166–2174, doi:10.3762/bjoc.10.224

• Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany 10.3762/bjoc.10.224 Abstract DNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work

• insertion are suggestive of different interactions between the Nile red label and the duplexes. Keywords: click chemistry; deoxyribonucleic acid; DNA bulge; fluorescence; nucleic acids; solvatochromism; Introduction Fluorescent labels are important tools for investigating the structure and dynamics of

Formation of smectic phases in binary liquid crystal mixtures with a huge length ratio

• Nadia Kapernaum,
• Friederike Knecht,
• C. Scott Hartley,
• Jeffrey C. Roberts,
• Robert P. Lemieux and
• Frank Giesselmann

Beilstein J. Org. Chem. 2012, 8, 1118–1125, doi:10.3762/bjoc.8.124

• phase of the longer mesogen was identified as a smectic F phase. Keywords: bidispersity; liquid crystals; phase diagrams; smectic phases; smectic F phase; structure and dynamics; Introduction The mixing of different liquid crystals is a common technique to tailor their properties for specific

Chemical aminoacylation of tRNAs with fluorinated amino acids for in vitro protein mutagenesis

• Shijie Ye,
• Allison Ann Berger,
• Dominique Petzold,
• Oliver Reimann,
• Benjamin Matt and
• Beate Koksch

Beilstein J. Org. Chem. 2010, 6, No. 40, doi:10.3762/bjoc.6.40

• atoms within the peptide chain [17][18][19]. Finally, due to the high NMR sensitivity of fluorine, the incorporation of fluorinated amino acid analogues into proteins provides the opportunity for probing the structure and dynamics that play a role in protein–protein and protein–ligand interaction, and

Molecular length distribution and the formation of smectic phases

• Nadia Kapernaum,
• C. Scott Hartley,
• Jeffrey C. Roberts,
• Robert P. Lemieux and
• Frank Giesselmann

Beilstein J. Org. Chem. 2009, 5, No. 65, doi:10.3762/bjoc.5.65

• transition. Thus smectic A seems to be the most stable phase to accommodate mesogenic molecules of substantially different length. These surprising results are of general interest for the understanding of the structure and dynamics of smectic phases, as the structure of these bidisperse smectics is signified

• by extensive out-of-layer fluctuations. Keywords: bidispersity; liquid crystals; phase diagrams; smectic phases; structure and dynamics; Introduction The classical (and highly successful) approach to systematically tailor liquid crystal materials for specific applications is the formulation of

• phase transition to SmA. These quite counterintuitive results are of general interest for the understanding of the structure and dynamics of smectic phases. Several theoretical approaches have been made to predict the behaviour of bidisperse mixtures [14][15][16][17][18]. They analyzed the stability of