[1,3]/[1,4]-Sulfur atom migration in β-hydroxyalkylphosphine sulfides

• Katarzyna Włodarczyk,
• Piotr Borowski and
• Marek Stankevič

Beilstein J. Org. Chem. 2020, 16, 88–105, doi:10.3762/bjoc.16.11

• pseudorotation. This, in turn, should have led to a remarkable deterioration of the enantiomeric excess of the product. The same might be postulated for the rearrangement of alkenylphosphine sulfide 65, which should form a pentavalent intermediate equally well. In the next step, the enantiomerically enriched β

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• pseudorotation phase angle P adopting values of 175° (6a) and 181° (6b), respectively. The maximum puckering amplitude νmax was 43° (6a) and 40° (6b). Furthermore, the nucleobase displayed an anti orientation. The carbocyclic ring adopted a chair conformation. As a consequence, the angle γ was aligned in the

• ones of the bc4,3-T, indicating that at least on the nucleoside level the fluorine atoms seemed to have a minor effect on the overall structure. To further study the preferred sugar pucker of the 6’-diF-bc4,3-T nucleoside, a potential energy profile versus pseudorotation phase angle of nucleoside 7 was

• (left) and 6b (right). a) Potential energy profile versus pseudorotation phase angle of nucleoside 7 and b) its minimal energy conformer. CD spectra of ON1–4 with complementary a) DNA, and b) RNA. Total strand conc. 2 μM in 10 mM NaH2PO4, 150 mM NaCl, pH 7.0. Hydrolysis products of the RNase H

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• structure, giving evidence of mixed A/B-type helices. Molecular modeling To gain more information on the structural features of the 6’F-bc4,3 modification, we performed molecular dynamics simulations of the modified duplexes. We first calculated the potential energy profile versus pseudorotation phase angle

• variation of the pseudorotation phase angle P at the range of the maximum puckering amplitude νmax and was visualized in the pseudorotation wheel (Figure 3a). The two low energy regions appeared in the Southern hemisphere. The lowest energy conformer was associated with the furanose unit in a C2’-endo

• if paired to DNA or RNA. The preferred sugar arrangement was found in a narrow range in the Southern area of the pseudorotation wheel (C1’-exo, C2’-endo, Figure 5a and b), indicating that this modification is a DNA mimic. This finding is in agreement with the observed Tm values and also reflects the

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• structural change known as Berry pseudorotation [20]: one of the equatorial ligands remains equatorial, while the rest turn apical and the apical ligands equatorial. Several alternative models for isomerization of trigonal-bipyramidal pentacoordinate compounds have been presented [21], but Berry

• pseudorotation has almost exclusively used in mechanistic discussion of RNA cleavage. The stability of the phosphorane intermediate largely depends on its state of protonation. The first pKa value of the acyclic tetraalkoxy monohydroxy phosphorane has been estimated to be 8.6 for an equatorial hydroxy group and

• obtained by the attack of 2´-OH on the phosphorus atom with concomitant transfer of the proton to the non-bridging oxygen [46][47], is able to pseudorotate at physiological pH. It is not quite clear whether the pseudorotation takes place through the monoanionic species or kinetically invisible protonation

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• terminal hydroxy group of the primer has to attack the activated 5'-phosphate of the primer, most likely producing a pentavalent intermediate. Unless the leaving group finds itself in the proper apical position of the intermediate, this is followed by pseudorotation and then the release of the leaving

• extension occurs as expected, most probably via addition/elimination, including a pentavalent intermediate and possibly by a pseudorotation to place the ethylimidazole leaving group in an apical position. Since either of the two alcohols of the terminal diol of the primer can attack, a mixture of 3',5'- and

On the mechanism of imine elimination from Fischer tungsten carbene complexes

• Philipp Veit,
• Christoph Förster and
• Katja Heinze

Beilstein J. Org. Chem. 2016, 12, 1322–1333, doi:10.3762/bjoc.12.125

• dissociation, followed by an oxidative addition/pseudorotation/reductive elimination pathway with short-lived, elusive seven-coordinate hydrido tungsten(II) intermediates cis(N,H)-W(CO)4(H)(Z-15) and cis(C,H)-W(CO)4(H)(Z-15). Keywords: carbene complexes; ferrocene; imine; mechanism; tungsten; Introduction

• (pathway 3a and 3b, Scheme 4) giving W(CO)4(E-3) or W(CO)4(Z-3), respectively. Furthermore, the free coordination site in W(CO)4(E-2) or W(CO)4(Z-2) offers an oxidative addition/pseudorotation/reductive elimination pathway via the hydrido tungsten(II) complexes W(CO)4(H)(Z-15) with the formally anionic

• addition has been proposed in the literature for the iron (aminophenyl)phenylcarbene complex [Cp(CO)(S(SiEt3))Fe(4)] leading to an intermediate hydrido species followed by the elimination of E-1,2-diphenylimine E-5 [73]. Pseudorotation of cis(N,H)-W(CO)4(H)(Z-15) to the isoenergetic rotamer cis(C,H)-W(CO)4

Synthesis of γ-hydroxypropyl P-chirogenic (±)-phosphorus oxide derivatives by regioselective ring-opening of oxaphospholane 2-oxide precursors

• Iris Binyamin,
• Shoval Meidan-Shani and
• Nissan Ashkenazi

Beilstein J. Org. Chem. 2015, 11, 1332–1339, doi:10.3762/bjoc.11.143

• apical position produces β-hydroxyethylphosphate (Scheme 1A). Dioxaphospholane 1 contains two identical oxygen atoms that can be cleaved with no preference due to fast pseudorotation between two practically energetically equivalent phosphorane intermediates, in which these two oxygen centers interconvert

• was found to be completely regioselective [20], since the P–C bond occupies the equatorial position according to the preference rules [33]. Therefore, fast pseudorotations (PR), either Berry’s pseudorotation or Turnstile rotation [34], which form identical TBP intermediates, are suppressed (Scheme 1B

• TBP phosphorane intermediate is formed, which could not undergo pseudorotation due to a high energetic barrier. The endocyclic P–O bond is cleaved almost exclusively (Scheme 4) to form the respective phosphinates and phosphine oxides in high yields. Propargyl organophosphorus compounds present a

Pyrrolidine nucleotide analogs with a tunable conformation

• Lenka Poštová Slavětínská,
• Dominik Rejman and
• Radek Pohl

Beilstein J. Org. Chem. 2014, 10, 1967–1980, doi:10.3762/bjoc.10.205

• of a conformational analysis show that the alkylation/acylation can be effectively used for tuning the pyrrolidine conformation over the whole pseudorotation cycle. Keywords: conformation; NMR; nucleic acids; nucleotide analog; phosphonic acid; pseudorotation; pyrrolidine; Introduction Nucleotides

• relationship [8]. Exocyclic dihedral angles are in turn in direct relation with endocyclic dihedral angles between ring atoms defining the conformation of the five-membered ring based on the pseudorotation concept [9]. This straightforward approach is complicated by the presence of more than one rapidly

• equilibrium of conformers. The output of the PSEUROT provides pseudorotation parameters: phase angles (P), the maximum puckering amplitudes (Φmax) and the relative amounts of individual conformers. The original PSEUROT program was later complemented with the program MULDER [11]. Recently, the Matlab

Fifty years of oxacalix[3]arenes: A review

• Kevin Cottet,
• Paula M. Marcos and
• Peter J. Cragg

Beilstein J. Org. Chem. 2012, 8, 201–226, doi:10.3762/bjoc.8.22

• the macrocycle, but upon cooling an asymmetric Cs symmetry emerged. It was proposed that rapid interconversion between isomers occurred by a “turnstile” or Berry-pseudorotation mechanism. A subsequent paper from the group reported the crystal structure of the titanium(IV) isopropoxide (Ti(iPrO)4