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

• Yoshihiro Nishida,
• Mengfei Yuan,
• Kazuo Fukuda,
• Kaito Fujisawa,
• Hirofumi Dohi and
• Hirotaka Uzawa

Beilstein J. Org. Chem. 2017, 13, 1999–2009, doi:10.3762/bjoc.13.196

• > 3JH1proS,H2 Hz). This rule is maintained among 1,2-diacetyl-, 1,2-dipalmitoyl-, and 1,2-dibenzoyl-sn-glycerols and substituents at the sn-3 position. The validity of this rule is confirmed in a comparative analysis using circular dichroism (CD) spectroscopy [17][18]. The current study applies these

2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

• Julia Kinzel,
• Daniel F. Sauer,
• Marco Bocola,
• Marcus Arlt,
• Tayebeh Mirzaei Garakani,
• Andreas Thiel,
• Klaus Beckerle,
• Tino Polen,
• Jun Okuda and
• Ulrich Schwaneberg

Beilstein J. Org. Chem. 2017, 13, 1498–1506, doi:10.3762/bjoc.13.148

• protein FhuA ΔCVFtev. The theoretical calculations are in line with the experimental findings, that FhuA ΔCVFtev is properly folded using refolding buffer with 50 mM MPD, which was confirmed by CD spectroscopy (Figure S1, Supporting Information File 1). 2-Methyl-2,4-pentanediol stabilizes FhuA ΔCVFtev up

• FhuA ΔCVFtev (see MD simulation results, Figure 2C and D), ensuring the long-term stability of the protein (Figure S1, Supporting Information File 1). The aforementioned features are consistent with results from circular dichroism (CD) spectroscopy (Figure S1, Supporting Information File 1), showing

• block copolymer PE–PEG and amphiphilic MPD are used, respectively. Refolding is achieved by dialysis of the protein in a solution containing the particular refolding agents. The structural integrity of FhuA ΔCVFtev was confirmed with CD spectroscopy (Figure 3). When either PE–PEG or MPD is applied, the

Inhibition of peptide aggregation by means of enzymatic phosphorylation

• Kristin Folmert,
• Malgorzata Broncel,
• Hans v. Berlepsch,
• Christopher H. Ullrich,
• Mary-Ann Siegert and
• Beate Koksch

Beilstein J. Org. Chem. 2016, 12, 2462–2470, doi:10.3762/bjoc.12.240

• and normalized to the starting value at t = 5 min of one. The shown plots represent an average of three independent measurements. Transmission electron microscopy Peptides, prepared as for CD spectroscopy measurements, were examined after 24 hours. Aliquots (6 µL) of the corresponding solution were

Determination of the absolute stereostructure of a cyclic azobenzene from the crystal structure of the precursor containing a heavy element

• Reji Thomas and
• Nobuyuki Tamaoki

Beilstein J. Org. Chem. 2016, 12, 2211–2215, doi:10.3762/bjoc.12.212

• substitution (S-(−)-(E)-1). A reductive debromination of S-(−)-(E)-1 results in formation of one of the enantiomers of (E)-2. Using a combination of HPLC and CD spectroscopy we could safely assign the stereostructure of one of the enantiomers of (E)-2, the reduced product R-(−)-(E)-1. Keywords: azobenzene

Artificial Diels–Alderase based on the transmembrane protein FhuA

• Hassan Osseili,
• Daniel F. Sauer,
• Klaus Beckerle,
• Marcus Arlt,
• Tomoki Himiyama,
• Tino Polen,
• Akira Onoda,
• Ulrich Schwaneberg,
• Takashi Hayashi and
• Jun Okuda

Beilstein J. Org. Chem. 2016, 12, 1314–1321, doi:10.3762/bjoc.12.124

• proteins [15]. Conclusion Herein, we report the synthesis of Cu(I) NHC and Cu(II) terpyridyl complexes equipped with a maleimide moiety which underwent covalent conjugation at the cysteine residue 545 of the transmembrane protein FhuAΔCVFtev. These biohybrid conjugates were analyzed by CD spectroscopy

• fluorescence titration, and correct refolding was determined by CD spectroscopy, as previously reported [17][18]. Digestion of the proteins was performed as previously reported [17]. General procedure: Diels–Alder reaction To the corresponding catalyst (1 mol %) in 2 mL of buffer solution (0.125 mM PE-PEG

Self and directed assembly: people and molecules

• Tony D. James

Beilstein J. Org. Chem. 2016, 12, 391–405, doi:10.3762/bjoc.12.42

• electrochemistry [77]. The system has also been used with Eric Anslyn (University of Texas at Austin) to determine the ee of amines using circular dichroism (CD) spectroscopy [78]. The system was more recently used to measure the ee of amines using fluorescence [79]. The UK Office of Science and Innovation (OSI

Bromotyrosine-derived alkaloids from the Caribbean sponge Aplysina lacunosa

• Qun Göthel,
• Thanchanok Sirirak and
• Matthias Köck

Beilstein J. Org. Chem. 2015, 11, 2334–2342, doi:10.3762/bjoc.11.254

• same side of the molecule. The absolute configuration of compound 1 was investigated by CD spectroscopy. The CD spectrum of 1 showed positive Cotton effects (λmax 248, Δε +5.16, λmax 285, Δε +4.58) with the same sign and magnitude as observed for (+)-aerothionin (11) [25][34][35]. Thus, the absolute

Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• included in this study by adding one, two, or three heptad repeats containing alanine in their f-positions (R2A3, R2A4 and R2A5); these were based on the sequence of R2A2 (Figure 1). Secondary and quaternary structure of the model peptides Circular dichroism (CD) spectroscopy and analytical

• approximately 3 nm (Figure 2C). As expected from CD spectroscopy, R1A3 forms α-helical assemblies at pH 9 with an average size of approximately 1 µm but appears to adopt a soluble coiled-coil structure at pH 11 because the particle size decreases to 3 nm. Surprisingly, all other VW05 variants form α-helical

• even after three days the value is only half of those measured for R2A3 and R2A4. It is known that gold nanoparticles may affect the secondary structure of a peptide or protein [33]. To investigate the effect of Au/MUA nanoparticles on the secondary structure of the peptides included in this study, CD

DNA display of glycoconjugates to emulate oligomeric interactions of glycans

• Alexandre Novoa and
• Nicolas Winssinger

Beilstein J. Org. Chem. 2015, 11, 707–719, doi:10.3762/bjoc.11.81

• resulted in acetylation of the glycan thus blocking the glycan’s hydroxy groups. The generality of this method was illustrated with the synthesis of 16 different DNA conjugates containing one or two glycan units. Analysis of glycan-modified duplexes by CD spectroscopy indicated minimal perturbation of the

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks

• Boris Schmidtgall,
• Claudia Höbartner and
• Christian Ducho

Beilstein J. Org. Chem. 2015, 11, 50–60, doi:10.3762/bjoc.11.8

• was observed (particularly for DNA/RNA duplexes). Further experiments with native counterstrands bearing one nucleobase mismatch were performed, and duplex structures were studied by CD spectroscopy. Overall, we found that NAA-modified DNA oligonucleotides (i) formed stable duplexes with complementary

A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR)

• Darinka Dzubiel,
• Heiko Ihmels,
• Mohamed M. A. Mahmoud and
• Laura Thomas

Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

• -b′′′]tetraquinolizinium (5) and thiazole orange (6) were studied. It is demonstrated with absorption, fluorescence and CD spectroscopy that all investigated ligands bind with relatively high affinity to the ILPR-quadruplex DNA a2 (0.2–5.5 × 106 M−1) and that in most cases the binding parameters of

• interactions The interactions of the ligands 1d, 1e, 2, 4–6 with ILPR-DNA a2 were analyzed by CD spectroscopy (Figure 8, Figure S7 in Supporting Information File 1). In most cases, the weak CD signal at 265 nm decreases and the CD signal at 295 nm increases slightly when the ligands were added. Upon addition

• absorption range of compounds 4–6. Discussion Generally, it is possible to distinguish between different G-quadruplex DNA forms with the aid of CD spectroscopy [32]. Hence, in agreement with literature data [9][10], the characteristic bands at 235, 265 and 295 nm (Figure 2) show that the employed ILPR-DNA a2

Homochiral BINOL-based macrocycles with π-electron-rich, electron-withdrawing or extended spacing units as receptors for C₆₀

• Marco Caricato,
• Silvia Díez González,
• Idoia Arandia Ariño and
• Dario Pasini

Beilstein J. Org. Chem. 2014, 10, 1308–1316, doi:10.3762/bjoc.10.132

• ’-binaphthyl scaffolds, which incorporate either π-electron rich, π-electron deficient or π-extended spacing units. The cyclic adducts are obtained in an acceptable yield in a one-pot synthetic procedure, and easily purified by flash column chromatography. NMR and CD spectroscopy give an insight into the

• ). CD spectroscopy was performed with a spectropolarimeter; spectra were recorded at 25 °C at a scanning speed of 50 nm min−1 and were background corrected. The reported spectra are the instrument-averaged results of four consecutive scans. General procedure for the preparation of macrocycles 3 and 4

Synthesis of a sucrose dimer with enone tether; a study on its functionalization

• Zbigniew Pakulski,
• Norbert Gajda,
• Magdalena Jawiczuk,
• Jadwiga Frelek,
• Piotr Cmoch and
• Sławomir Jarosz

Beilstein J. Org. Chem. 2014, 10, 1246–1254, doi:10.3762/bjoc.10.124

• oxidized with osmium tetroxide to a diol. Absolute configurations of the allylic alcohol as well as the diol were determined by circular dichroism (CD) spectroscopy using the in situ dimolybdenum methodology. Keywords: CD-spectroscopy; Cotton effect; multivalent glycosystems; osmylation; stereoselective

• surprising. The assignment of the configuration of this diol was further confirmed also by the CD methodology; this is discussed in the next chapter. Determination of the absolute configuration of 11 and 13 It is widely acceptable that the circular dichroism (CD) spectroscopy utilizing the in situ

• glucose-rings were connected via an enone linker. The dimer was then converted into a (partially protected) triol via a stereoselective reduction of the carbonyl group and highly selective cis-dihydroxylation of the double bond. The configuration at each new stereogenic center was determined by CD

A new building block for DNA network formation by self-assembly and polymerase chain reaction

• Holger Bußkamp,
• Sascha Keller,
• Marta Robotta,
• Malte Drescher and
• Andreas Marx

Beilstein J. Org. Chem. 2014, 10, 1037–1046, doi:10.3762/bjoc.10.104

• by ESI–IT–MS (see Supporting Information File 1). Characterization of bDNA by thermal denaturation studies and CD spectroscopy. Formation of stable duplexes with complementary DNA strands is a prerequisite for the employment of the bDNA ODN I and ODN II in PCR experiments. Thus, we investigated

• circular dichroism (CD) spectroscopy. The CD spectra of Y-shaped bDNA ODN I bound to oligonucleotides 8–11, respectively, show dichroic peaks similar to those of unmodified DNA duplexes, indicating that bDNA maintain the B-DNA form (see Supporting Information File 1). As the Y-shaped bDNA is able to

Molecular architecture with carbohydrate functionalized β-peptides adopting 3₁₄-helical conformation

• Nitin J. Pawar,
• Navdeep S. Sidhu,
• George M. Sheldrick,
• Dilip D. Dhavale and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2014, 10, 948–955, doi:10.3762/bjoc.10.93

• oligomers varying the sugar (glucose, galactose, xylose) and sugar protecting groups. The influence of sugar units and the configuration of sugar-β-amino acids on β-peptide secondary structure were investigated by CD spectroscopy. Keywords: carbohydrate recognition; conformation; glycopeptide; β-peptide

• was chosen as C-terminal amino acid. Further the C-glycosidic attachment of the sugar units at the peptide backbone was varied with respect to the configuration. As evident from CD spectroscopy, out of eight β-glycopeptides 1–8 (Figure 2), the five β-glycopeptides 2–6 were shown to adopt a 314-helix

• TFA/water (4:1) [58] provided D-galactose and D-xylose derived β-glycopeptides 4 and 6. The structural integrity of β-peptides 1–8 was ensured by high resolution ESI mass spectrometry. Conformational studies: carbohydrate influence on helical content β-Peptides can be characterized by CD spectroscopy

Synthesis of enantiomerically pure (2S,3S)-5,5,5-trifluoroisoleucine and (2R,3S)-5,5,5-trifluoro-allo-isoleucine

• Holger Erdbrink,
• Elisabeth K. Nyakatura,
• Susanne Huhmann,
• Ulla I. M. Gerling,
• Dieter Lentz,
• Beate Koksch and
• Constantin Czekelius

Beilstein J. Org. Chem. 2013, 9, 2009–2014, doi:10.3762/bjoc.9.236

• propensity of 5-F3Ile is significantly lower than Ile, but surprisingly high when compared with 4’-F3Ile. Keywords: amino acids; CD-spectroscopy; fluorine; helix propensity; organo-fluorine; trifluoroisoleucine; Introduction Due to the unique physicochemical properties of fluorine, namely its small size

• peptide (KX), its α-helix propensity can be calculated from circular dichroism (CD) spectroscopy [8][9]. Therefore, 5-F3Ile was converted into its Fmoc analogue and subsequently used in solid-phase synthesis of K-5-F3Ile applying standard Fmoc-based chemistry (see Supporting Information File 1) [30]. The

Multivalent display of the antimicrobial peptides BP100 and BP143

• Imma Güell,
• Rafael Ferre,
• Kasper K. Sørensen,
• Esther Badosa,
• Iteng Ng-Choi,
• Emilio Montesinos,
• Eduard Bardají,
• Lidia Feliu,
• Knud J. Jensen and
• Marta Planas

Beilstein J. Org. Chem. 2012, 8, 2106–2117, doi:10.3762/bjoc.8.237

• formation by CD. As shown by CD spectroscopy, the preassembly of BP100 did not result in a more organized structure, especially for carbopeptide 3, which suggests that the high hemolysis observed for carbopeptides cannot be attributed to a higher degree of secondary-structure formation. A likely explanation

Antifreeze glycopeptide diastereomers

• Lilly Nagel,
• Carsten Budke,
• Axel Dreyer,
• Thomas Koop and
• Norbert Sewald

Beilstein J. Org. Chem. 2012, 8, 1657–1667, doi:10.3762/bjoc.8.190

• 5, the retro-inverso AFGP analogue 7, and their corresponding aglycons 6 and 8 (Scheme 2) were analyzed be CD spectroscopy in water at room temperature and additionally at temperatures between −10 and +80 °C. The allo-L-threonine containing glycopeptide 5 shows a CD signature typical of a PPII-like

• analogues [41][42]. Conclusion A GalNAc-substituted AFGP analogue [AA-allo-T(GalNAc)]4AA (5) and a retro-inverso AFGP analogue [aat(GalNAc)]4aa (7) with GalNAc-D-Thr and D-Ala building blocks were synthesized. The conformations of these glycopeptides and their corresponding aglycons were investigated by CD

• spectroscopy. According to these data, both peptides adopt polyproline II helical conformations, albeit with reduced propensity (5) or opposite helicity (7). The structure of the glycopeptides was correlated with their ability to inhibit ice growth in microphysical recrystallization assays. Both AFGP analogues

Design of a novel tryptophan-rich membrane-active antimicrobial peptide from the membrane-proximal region of the HIV glycoprotein, gp41

• Evan F. Haney,
• Leonard T. Nguyen,
• David J. Schibli and
• Hans J. Vogel

Beilstein J. Org. Chem. 2012, 8, 1172–1184, doi:10.3762/bjoc.8.130

• observed antimicrobial effects. Circular dichroism spectroscopy The backbone conformations of all of the gp41 peptide derivatives were examined by using far-UV circular dichroism (CD) spectroscopy. The resulting CD spectra of the peptides in buffer, SDS, DPC and 50% trifluoroethanol (TFE) are shown in

• overlap almost perfectly with each other suggests that this peptide adopts equivalent structures in all three environments. The conformations of the gp41w derivatives in the presence of LUVs of varying composition were also examined with CD spectroscopy (Figure 6). In the presence of zwitterionic ePC:ePE

Toward unidirectional switches: 2-(2-Hydroxyphenyl)pyridine and 2-(2-methoxyphenyl)pyridine derivatives as pH-triggered pivots

• Christina Tepper and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2012, 8, 977–985, doi:10.3762/bjoc.8.110

• unidirectionally at the molecular level. If a 2-(2-methoxyphenyl)pyridine derivative is fixed to a chiral cyclopeptidic scaffold, a unidirectional progress of the rotation is achieved macroscopically. Keywords: CD spectroscopy; chirality; molecular modeling; molecular switches; unidirectional movements

• switches adopt a preferred conformation in solution is through the use of CD spectroscopy. For this purpose, the CD spectrum of 13 in dichloromethane as the solvent was recorded (Figure 6a). Additionally, the CD spectra of (M)-13 and (P)-13 were simulated with the time-dependent density functional theory

Synthesis and anion recognition properties of shape-persistent binaphthyl-containing chiral macrocyclic amides

• Marco Caricato,
• Nerea Jordana Leza,
• Claudia Gargiulli,
• Giuseppe Gattuso,
• Daniele Dondi and
• Dario Pasini

Beilstein J. Org. Chem. 2012, 8, 967–976, doi:10.3762/bjoc.8.109

• spectrophotometers. Mass spectra were recorded by using an electrospray ionization instrument. Optical rotations were measured on a polarimeter with a sodium lamp (λ = 589 nm) and are reported as follows: [α]Drt (c = g (100 mL solution)−1). CD spectroscopy was performed by using a spectropolarimeter; spectra were

Diarylethene-modified nucleotides for switching optical properties in DNA

• Sebastian Barrois and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2012, 8, 905–914, doi:10.3762/bjoc.8.103

• by CD spectroscopy, but not in the case of the spiropyran form. Attempts to attach spiropyrans covalently to DNA are rare [26][27] and include our recent approaches to incorporate synthetically the spiropyran chromophore [28], by either DNA building block 1 [29] or by DNA base modifications 2 and 3

Investigation of the network of preferred interactions in an artificial coiled-coil association using the peptide array technique

• Raheleh Rezaei Araghi,
• Carsten C. Mahrenholz,
• Rudolf Volkmer and
• Beate Koksch

Beilstein J. Org. Chem. 2012, 8, 640–649, doi:10.3762/bjoc.8.71

• on a C-8 column (Phenomenex® Luna C8, 10 μM, 250 mm × 21.2 mm). The identities of peptides were confirmed using an ESI–TOF instrument. Circular-dichroism (CD) spectroscopy [18]: Peptide samples were analyzed in 10 mM phosphate buffer (pH 7.4). Far-ultraviolet circular-dichroism spectra and GndHCl

Conserved and species-specific oxylipin pathways in the wound-activated chemical defense of the noninvasive red alga Gracilaria chilensis and the invasive Gracilaria vermiculophylla

• Martin Rempt,
• Florian Weinberger,
• Katharina Grosser and
• Georg Pohnert

Beilstein J. Org. Chem. 2012, 8, 283–289, doi:10.3762/bjoc.8.30

• comparison of the obtained NMR and MS spectra by co-injection with authentic standards [3]. Stereochemistry of PGE2 was verified with CD spectroscopy in comparison with an authentic standard. Spectroscopic data of 5. 5-((1E,3E,5E,7Z,10Z)-hexadeca-1,3,5,7,10-pentaenyl)dihydrofuran-2(3H)-one (5) was obtained

Gelation or molecular recognition; is the bis-(α,β-dihydroxy ester)s motif an omnigelator?

• Peter C. Griffiths,
• David W. Knight,
• Ian R. Morgan,
• Amy Ford,
• James Brown,
• Ben Davies,
• Richard K. Heenan,
• Stephen M. King,
• Robert M. Dalgliesh,
• John Tomkinson,
• Stuart Prescott,
• Ralf Schweins and
• Alison Paul

Beilstein J. Org. Chem. 2010, 6, 1079–1088, doi:10.3762/bjoc.6.123

• , m = 4, indicating a rather rigid structure, with a Gaussian cross-section of 25–40 Å depending on gelator concentration and structure. The rodlike segments were typically hundreds of Å in length, suggesting a stacked geometry that was later confirmed with CD spectroscopy. With an increase in