Organophosphorus chemistry: from model to application

• György Keglevich

Beilstein J. Org. Chem. 2023, 19, 89–90, doi:10.3762/bjoc.19.8

• studied by single-crystal X-ray diffraction by Khrizanforov et al., and the preferred conformations were substantiated by DFT calculations [6]. Finally, Hersh and Chan presented a method to improve the accuracy of 31P NMR chemical shift calculations by use of scaling methods [7]. György Keglevich Budapest

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• recommendations by Tantillo and co-workers [3] for cases involving multiple conformations, and in addition here the presence of lone pairs on third-row atoms provides additional reason to use a higher level basis set than the usual 6-31G(d) [3]. As pointed out by van Wüllen [18], the energy-optimized structure

• by Krivdin [24], a partially experimental absolute shielding for 85% H3PO4 in water was used (σ(85% H3PO4) = 351.6 ppm), derived from the experimental chemical shift of PH3 referenced to 85% H3PO4 [53]. The use of this value has the virtue of eliminating all theoretical complications of conformations

• conformations in our hands that especially for (H2P)2PH affected the calculated chemical shifts, and (e) while we did not check all chemical shifts, the citation in reference [37] for CH2=C(H)PF2, the furthest downfield point (and hence a critical value) is wrong, although the value of 219.5 ppm is correct [60

Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements

• Alexios I. Vicatos,
• Zakiena Hoossen and
• Mino R. Caira

Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184

• per cell and again reveal the similarity in the conservation of water molecule sites in the two isostructural complexes. The detailed host conformations are defined by numerous, relevant geometrical parameters that include measures of the angular tilts of the individual glucose rings relative to the

Comparison of crystal structure and DFT calculations of triferrocenyl trithiophosphite’s conformance

• Ruslan P. Shekurov,
• Mikhail N. Khrizanforov,
• Ilya A. Bezkishko,
• Tatiana P. Gerasimova,
• Almaz A. Zagidullin,
• Daut R. Islamov and
• Vasili A. Miluykov

Beilstein J. Org. Chem. 2022, 18, 1499–1504, doi:10.3762/bjoc.18.157

• orientations towards the phosphorus lone electron pair (LEP). A comparison of DFT calculations and X-ray diffraction data is presented, herein we show which conformations are preferred for a given ligand. Keywords: DFT calculations; multi-ferrocenyl compounds; phosphorus thioesters; trithiophosphite; X-ray

• –S bonds, and three Fe–cyclopentadienyl axes. The rotation around the P–S bonds results in a totally unsymmetrical structure with three ferrocenylthio groups exhibiting different orientations towards the phosphorus lone electron pair (Figure 1). Several possible conformations of triferrocenyl

• value is predicted for one of the gauche S–Fc bonds in the tgg conformer (−60°), whereas the second one is almost parallel to LEP (8°). The energy difference between the considered conformations is quite small, suggesting other factors playing a significant role. The highest energy predicted for the ggg

Synthesis and electrochemical properties of 3,4,5-tris(chlorophenyl)-1,2-diphosphaferrocenes

• Almaz A. Zagidullin,
• Farida F. Akhmatkhanova,
• Mikhail N. Khrizanforov,
• Robert R. Fayzullin,
• Tatiana P. Gerasimova,
• Ilya A. Bezkishko and
• Vasili A. Miluykov

Beilstein J. Org. Chem. 2022, 18, 1338–1345, doi:10.3762/bjoc.18.139

• chemically, two possible conformations of 8b were considered, 8b-I and 8b-II (Figure 2). Similar to a previous report on 8c [37], both 8b-I and 8b-II adopted an almost eclipsed conformation during optimization. Computations predicted slightly lower energy (1 kcal⋅mol−1) for conformation 8b-I, with Cl

• ), P1–C1 1.837(3) for 6c. Deposition numbers 2176393 for 5c and 2176394 for 6c contain the supplementary crystallographic data for this paper [41]. Considered conformations of 8b-I and 8b-II. Top: experimental UV–vis spectra of 8с (black) and 8b (red). Bottom: broadened calculated UV–vis spectra of 8c

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• of the omega in the case without C-Raf; thirdly, above the pore between the two binding grooves of the omega in the presence of C-Raf. Overall, the clustering and the pattern of energies reflect the C2 symmetry of the 14-3-3ζ dimer. Minimum energy conformations Closer inspection of energies reveals

• center of the ω where the AIE moieties hover above the central pore (Figure 6c and d). In these two conformations, at least one of the lysine groups lies at the minimum energy position of the lysine affinity map (more information about the affinity map is given in the “Energy grids” section). Both GCP

• groups locate in the two minimum energy positions of the GCP affinity map as well. In both minimum energy conformations of the ligand, at least one GCP or Lys group is found near one of the phosphorylated serine (pSer) residues of the C-Raf peptides (Figure 6d). This is consistent with a strong

Vicinal ketoesters – key intermediates in the total synthesis of natural products

• Marc Paul Beller and
• Ulrich Koert

Beilstein J. Org. Chem. 2022, 18, 1236–1248, doi:10.3762/bjoc.18.129

• stabilization of reactive conformations by chelation or dipole control. Keywords: aldol addition; ketoesters; natural products; total synthesis; Introduction Vicinal ketoesters contain a carbonyl group adjacent to an ester group. One keto group results in α-ketoesters 1 and two vicinal keto groups lead to α,β

• bearing an electrophilic keto group as reactive site. The vicinal arrangement of carbonyl groups allows the stabilization of reactive conformations by chelation or dipole control. Suitable key reactions are e.g., aldol additions, carbonyl ene reactions, Mannich reactions, and additions of organometallic

Electrochemical and spectroscopic properties of twisted dibenzo[g,p]chrysene derivatives

• Tomoya Imai,
• Ryuhei Akasaka,
• Naruhiro Yoshida,
• Toru Amaya and
• Tetsuo Iwasawa

Beilstein J. Org. Chem. 2022, 18, 963–971, doi:10.3762/bjoc.18.96

• . Optimizations of DBC-H(56°)-1 and DBC-H(56°)-2 based on DFT calculations were performed by fixing the atoms, as described above [56]. The conformations of the MeO group in DBC-H(56°)-1 and DBC-H(56°)-2 are nearly perpendicular (98.3°) to and parallel (179.8°) to the benzene ring, respectively (Figure 3 and

First series of N-alkylamino peptoid homooligomers: solution phase synthesis and conformational investigation

• Maxime Pypec,
• Laurent Jouffret,
• Claude Taillefumier and
• Olivier Roy

Beilstein J. Org. Chem. 2022, 18, 845–854, doi:10.3762/bjoc.18.85

• observed for Xaa–Pro amide bonds and polyproline chains can adopt either the all-trans type II (PPII) or the all-cis type I (PPI) helical conformations, the latter being only observed in alcohol-type solvents [14]. In contrast to the prolyl-amide bond in acyclic peptides (≈5% of cis-Pro) [15], the cis

• form a unique sheet-like secondary structure, whereas molecular modeling showed that N-aryl peptoid oligomers composed of monomers in the same conformation (as observed in the crystal of dimer 2) might adopt right or left-handed helical conformations that resemble the polyproline type II helix. The χ1

• molecule are in the same conformation with either two positive values of the φ angle (conformation B) or two negative values for the mirror image conformation A. These two local conformations could exist at each monomer position, leading to a potential mixture of secondary structures. We therefore

Synthesis and HDAC inhibitory activity of pyrimidine-based hydroxamic acids

• Virginija Jakubkiene,
• Gabrielius Ernis Valiulis,
• Markus Schweipert,
• Asta Zubriene,
• Daumantas Matulis,
• Franz-Josef Meyer-Almes and
• Sigitas Tumkevicius

Beilstein J. Org. Chem. 2022, 18, 837–844, doi:10.3762/bjoc.18.84

• tend to adopt the more stable keto-E and keto-Z conformations [36]. In the 1H NMR spectra of the synthesized hydroxamic acids 12–18 and 25–31 two sets of proton signals from the NH and OH groups of the hydroxamic acid residue are observed. Following data [36], we assigned the more intense peaks to the

Thiophene/selenophene-based S-shaped double helicenes: regioselective synthesis and structures

• Mengjie Wang,
• Lanping Dang,
• Wan Xu,
• Zhiying Ma,
• Liuliu Shao,
• Guangxia Wang,
• Chunli Li and
• Hua Wang

Beilstein J. Org. Chem. 2022, 18, 809–817, doi:10.3762/bjoc.18.81

• photocyclization reaction sites of 5 were predicted by the orbital-weighted Fukui function in Multiwfn using Gaussian 09 [31][32] at the B3LYP/6-31G** [33] level of theory to verify the reaction-site selectivity of oxidative photocyclization further. Results showed that the conformations of 5a are varied, but the

Structural basis for endoperoxide-forming oxygenases

• Takahiro Mori and
• Ikuro Abe

Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71

• . Structure of NvfI In the structural analysis of NvfI, three different active site conformations (open, partially closed, and closed) were observed (PDB IDs: 7DE2, 7EMZ, and 7ENB) (Figure 4A–C) [28]. The conformations of the loop regions between Ser122-Gly128 and Trp199-Pro209 were altered by soaking with

BINOL as a chiral element in mechanically interlocked molecules

• Matthias Krajnc and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2022, 18, 508–523, doi:10.3762/bjoc.18.53

• polyacetylene, with a special focus on the different possible co-conformations of the rotaxane (see Figure 7) [54]. The synthesis of the acetylene monomers 31, containing a chiral rotaxane side-chain, was achieved by tributylphosphane-catalyzed esterification. Two different macrocycles having either one BINOL

Comparative study of thermally activated delayed fluorescent properties of donor–acceptor and donor–acceptor–donor architectures based on phenoxazine and dibenzo[a,j]phenazine

• Saika Izumi,
• Prasannamani Govindharaj,
• Anna Drewniak,
• Paola Zimmermann Crocomo,
• Satoshi Minakata,
• Leonardo Evaristo de Sousa,
• Piotr de Silva,
• Przemyslaw Data and
• Youhei Takeda

Beilstein J. Org. Chem. 2022, 18, 459–468, doi:10.3762/bjoc.18.48

• internal conversion. In this sense, it is important to look into the energy gaps between triplet states of both molecules. Considering the average gaps taken from all the conformations sampled in the nuclear ensemble from the T1 state geometry, we obtain T1 to T2 gaps of approximately 0.4 eV for both

Site-selective reactions mediated by molecular containers

• Rui Wang and
• Yang Yu

Beilstein J. Org. Chem. 2022, 18, 309–324, doi:10.3762/bjoc.18.35

• cavitand hosts were also modified with imidazolium cationic or carboxylic anionic feet [29]. Before the reaction, NMR analysis of the host–guest complex indicated that the bound guest was in yo-yo motions time-averaged between unsymmetrical J-shaped conformations and symmetrical U-shaped ones. Treatment of

• -organize them with certain confined conformations. In this case, the linear diterpenoid substrate 29 possessed a folded U-shaped conformation within the cavity, with the terminal trisubstituted olefin exposed to the solution while the other three internal ones were protected by the cage host. The structure

• . Contemporaneously, the Rebek group illustrated another interesting site-selective monoepoxidation of α,ω-dienes mediated by the water-soluble cavitand host E (Figure 10) [71]. The α,ω-dienes were determined to adopt a yo-yo motion between two J-shaped conformations or the rapid tumbling of a coiled conformation

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• permeability [1][2][3]. Hence, peptide-based drugs became of high interest because of their high selectivity combined with low toxicity. Cross-linking of side chain residues results in constrained conformations and can be used to stabilise α-helical secondary structures. This technique is called peptide

• portion of the macrocycle and is similar to c1, with the Trp’s indole group pointing in the other direction. In the trans isomer, both conformations are also found, however, with different populations and order. Conformation c2 of P5 trans is helical and resembles c3 of P5 cis, yet with a significantly

• accurate values would be obtained with methods better adapted for kinetics, such as Markov models (for a general overview see reference [94]). Yet, such low barriers are not sufficient to trap the SMC peptide in conformations that can be separated experimentally at ambient conditions [95] and the analysis

Biological properties and conformational studies of amphiphilic Pd(II) and Ni(II) complexes bearing functionalized aroylaminocarbo-N-thioylpyrrolinate units

• Samet Poyraz,
• Samet Belveren,
• Sabriye Aydınoğlu,
• Mahmut Ulger,
• Abel de Cózar,
• Maria de Gracia Retamosa,
• Jose M. Sansano and
• H. Ali Döndaş

Beilstein J. Org. Chem. 2021, 17, 2812–2821, doi:10.3762/bjoc.17.192

• conformations analyzed by the 1H NMR spectra of nickel and palladium complexes, presumably correlated with their activity. According to the previous activities of derivatives of this nature [15][16] the cis-complex was identified as the therapeutic arrow. We initially tried to determine the driving force

• the metal atom considered, only one of the ligand conformations were energetically accessible (energetic difference of +14.6 and +5.7 kcal·mol−1, for nickel and palladium conformers, respectively, Figure 2). In these cases, the energetic difference between conformers A and B lies in the existence of

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• are ideal probes to study polysaccharides at the molecular level and identify structure–property correlations. Access to synthetic polysaccharides facilitated the correlation of chemical structure with molecular conformations [5][6], intermolecular interactions [7][8], and biological response [9

Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

• Mathias B. Danielsen and
• Jesper Wengel

Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125

• moieties attached to the sugar scaffold The sugar moiety of ONs has been extensively studied with respect to the significance of structure and configurations of substituents, and the resulting conformations of the furanose ring, on the properties of ONs (including ASOs). The great variation at which

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• negative charge on PNA’s backbone. Electrostatic repulsion of the negatively charged phosphates dominates the conformational properties and structure of nucleic acids. In contrast to proteins that prefer to fold in compact structures, DNA and RNA inherently prefer extended conformations that minimize the

• resembled the B- and A-form conformations of natural nucleic acids. The PNA–RNA duplex adopted a conformation very close to the standard A-form helix [40]. In contrast, the PNA–DNA duplex adopted an intermediate structure where positioning of the base pairs was A-like, while the backbone curvature, sugar

• -form helix" by the study authors [41]. Despite the much larger displacement of the bases from the helix axis, the base stacking in the P-form helix resembles that of an A-form DNA duplex. The sugars of a DNA strand adopt C3′-endo conformations with an average interphosphate distance of ≈6 Å, which is

Breaking paracyclophane: the unexpected formation of non-symmetric disubstituted nitro[2.2]metaparacyclophanes

• Suraj Patel,
• Tyson N. Dais,
• Paul G. Plieger and
• Gareth J. Rowlands

Beilstein J. Org. Chem. 2021, 17, 1518–1526, doi:10.3762/bjoc.17.109

• chains at non-adjacent carbon positions. Their constrained three-dimensional shapes enforce unusual conformations and interactions between the aromatic decks, all of which results in their unique properties [2][3][4][5]. The most studied cyclophane is [2.2]paracyclophane (1, Figure 1). Not only is it the

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• data in the supporting information for completion. However, we were able to extract atom coordinates and NSD data which can be compared to the existing crystal structures (Supporting Information File 1, Figures S72–S74 and S75–S129) [28][45]. Series 1 In series 1 (Figure 22) the conformations of the

Synthesis of multiply fluorinated N-acetyl-D-glucosamine and D-galactosamine analogs via the corresponding deoxyfluorinated glucosazide and galactosazide phenyl thioglycosides

• Vojtěch Hamala,
• Lucie Červenková Šťastná,
• Martin Kurfiřt,
• Petra Cuřínová,
• Martin Dračínský and
• Jindřich Karban

Beilstein J. Org. Chem. 2021, 17, 1086–1095, doi:10.3762/bjoc.17.85

• exocyclic C5‒C6 bond in solution (3JH5-F6 = 24.6–27.1 Hz), whereas the corresponding ᴅ-galacto-configured analogs 60, 67, 69, and 72 adopted gauche,trans (gt) or trans,gauche (tg) conformations to a significant degree (3JH5-F6 = 12.7–14.6 Hz). These findings were in accordance with the previous reports by

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• ][105][106][107]. GNA duplexes possess only one large groove which corresponds to the canonical minor groove, the canonical major groove is a convex surface. Furthermore, the glycol backbone adopts two conformations alternating between gauche and anti conformations such that each base pair contains one

Menthyl esterification allows chiral resolution for the synthesis of artificial glutamate analogs

• Kenji Morokuma,
• Shuntaro Tsukamoto,
• Kyosuke Mori,
• Kei Miyako,
• Ryuichi Sakai,
• Raku Irie and
• Masato Oikawa

Beilstein J. Org. Chem. 2021, 17, 540–550, doi:10.3762/bjoc.17.48

• supported by taking into account the steric interactions between the heterotricycle and the menthyl ring, as follows. There are no major differences in the conformations of the heterotricycle and the menthyl rings in 10, 10*, 21, and 21*. It is reasonably speculated that 1) the four bonds between the rings

• Corporation), employing initial conformations generated by MM2 (ChemBio3D Ultra, Version 14.0.0.117). The calculations were basically independent from the initial conformations. A same set of conformers was obtained after CONFLEX calculations, starting with different conformers employed as initial conformers