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

• computational methods [11][12][13][14]. Still, experimental studies with small molecular model compounds play an essential role in mechanistic studies of the enzymatic cleavage of nucleic acids. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding

• occurrence of the proton transfer as part of the rate limiting step may be evaluated by altering the acidity of the proton donor (or acceptor). Plotting of log k against the pKa of the proton donor (or acceptor) gives the Brönsted α (β for the acceptor) that refers to the extent of proton transfer in the

• state start to play a role. That is why both normal and inverse effects are possible. The kinetic solvent isotope effect (KSIE) is another mechanistic tool frequently used to distinguish between alternative mechanisms. KSIE is an indication of a kinetically significant proton transfer that takes place

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• electric fields generated by ions and molecules in solution. This property along the ESIPT process (excited state intramolecular proton transfer) [35] makes them ideal for ratiometric environment-sensitive probes and sensors [36][37][38][39][40][41][42][43]. Among them the 4’-dimethylamino derivative (DMHF

• different concentrations are shown in Figure 3. Upon addition of ATP, a new band appears at 440 nm in the excitation spectra. This feature can be attributed to the specific intermolecular proton transfer from the hydroxy group of the flavone to the phosphate moiety of the ATP [34]. The fluorescence

• -based probes exploit the ESIPT nature of these fluorophores to generate multiple emission bands [39][41][42][43]. In this case, however, a new fluorescence band appears in the excitation spectra due to an intermolecular proton transfer from the flavone to the phosphate chain of the nucleotide. Therefore

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

• be increased. To overcome this limitation, anilines were used as redox mediators, which are first oxidized by the photocatalyst and subsequently activate the aliphatic thiol via direct hydrogen abstraction or sequential electron- and proton-transfer steps. With this concept they were now able to

• the alkene moiety of the 1,7-enyne, two consecutive cyclizations lead to the final sulfonylated benzo[α]fluoren-5-one. Electron and proton transfer and subsequent formation of dihydrogen close the catalytic cycle and regenerate the photocatalyst. Sulfinamides Formation of sulfoxides A new method for

Vinylphosphonium and 2-aminovinylphosphonium salts – preparation and applications in organic synthesis

• Anna Kuźnik,
• Roman Mazurkiewicz and
• Beata Fryczkowska

Beilstein J. Org. Chem. 2017, 13, 2710–2738, doi:10.3762/bjoc.13.269

• subsequent 1,2-proton transfer followed by the elimination of triphenylphosphine and ring closure via formation of the new C–N bond gave the final γ-lactam derivatives 80 (Scheme 50) [66]. In 2013 Mohebat et al. used 6-amino-N,N'-dimethyluracil as an NH-acid and precursor of the carbon nucleophile in the

Rh(II)-mediated domino [4 + 1]-annulation of α-cyanothioacetamides using diazoesters: A new entry for the synthesis of multisubstituted thiophenes

• Jury J. Medvedev,
• Ilya V. Efimov,
• Yuri M. Shafran,
• Vitaliy V. Suslonov,
• Vasiliy A. Bakulev and
• Valerij A. Nikolaev

Beilstein J. Org. Chem. 2017, 13, 2569–2576, doi:10.3762/bjoc.13.253

• catalyst, proton transfer and, finally, 1,3-shift of alkoxycarbonyl group in the intermediate imine D to produce thiophenes 3 and 5. However, this pathway seems to be less probable, since intramolecular cyclization B → C should have lower activation energy relative to intermolecular interaction of C=S

Intramolecular glycosylation

• Xiao G. Jia and
• Alexei V. Demchenko

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

• post-glycosylational modifications are also required. As a result, glycosylation that is already a four-step process (activation, dissociation, nucleophilic attack, proton transfer, Scheme 1a) has to be supplemented with additional manipulations that could lead to the decrease in over-all efficiency

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

• SeO2 [8][69][70][71]. The only remaining route for the thermal transformation of 1 into 3 is path O. In this path, the hemiacetalization is the first step. We used a water molecule to facilitate the proton transfer in this stage. In the experiment, a hydroxylic group of other proximate germacranolide

• including a water molecule to facilitate the proton transfer. Schematic representations of the calculated C5 epimeric structures of 2 and 3. Relative electronic energies in kcal/mol. The energies are relative to 1a. Reaction paths of the Cope rearrangements of closed (dark blue and orange) and open (red and

N-Propargylamines: versatile building blocks in the construction of thiazole cores

• S. Arshadi,
• E. Vessally,
• L. Edjlali,
• R. Hosseinzadeh-Khanmiri and
• E. Ghorbani-Kalhor

Beilstein J. Org. Chem. 2017, 13, 625–638, doi:10.3762/bjoc.13.61

• regioselective 5-exo-dig cyclization–proton transfer–isomerization sequential process. They found that the easily available N-(propargylcarbamothioyl)amides 53 in the presence of 1,4-diazabicyclo[2.2.2]octane (DABCO) as the base in refluxing ethanol, rapidly cyclized and produced the corresponding dihydrothiazol

The reductive decyanation reaction: an overview and recent developments

• Jean-Marc R. Mattalia

Beilstein J. Org. Chem. 2017, 13, 267–284, doi:10.3762/bjoc.13.30

• iminyl anion intermediate 27. The latter easily isomerizes to its isomer 28 where a sodium cation–π-interaction occurs. The last step involves a C–C bond cleavage and proton transfer with elimination of NaCN (Scheme 12). This proton transfer occurs with retention of configuration as experimentally

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• 492 nm, respectively, and are represented in Figure 3 and Figure 4. The hydrogen-bond interaction between the OH group in R1 and the guest anion is assisted through an intermolecular proton transfer (IPT) suggesting a proton abstraction from a OH group and introduction of a negative charge on the

• F− and AcO− ions to receptor R2, the absorption band at 459 nm red shifted to 560 nm indicative of the strong influence of –R and the −I effect of the NO2 substituent on the intermolecular proton-transfer process. A substantial enhancement of the ICT in R2 in comparison with R1 indicates a more

Interactions between photoacidic 3-hydroxynaphtho[1,2-b]quinolizinium and cucurbit[7]uril: Influence on acidity in the ground and excited state

• Jonas Becher,
• Daria V. Berdnikova,
• Darinka Dzubiel,
• Heiko Ihmels and
• Phil M. Pithan

Beilstein J. Org. Chem. 2017, 13, 203–212, doi:10.3762/bjoc.13.23

• observed for the excited-state proton transfer (ESPT) of so-called photoacids. The latter are weak acids in the ground state, whereas their acidity in the excited state increases significantly [25][26][27]. As the activity of photoacids is triggered by light, they have a great potential to be employed as

Catalytic Wittig and aza-Wittig reactions

• Zhiqi Lao and
• Patrick H. Toy

Beilstein J. Org. Chem. 2016, 12, 2577–2587, doi:10.3762/bjoc.12.253

• products 32 catalyzed by tributylphosphine (33, 0.05 equivalents) (Scheme 9) [26]. In these transformations the initial reaction between 31 and 33 generated zwitterion 34, that underwent internal proton transfer to generate ylide 35. This in turn reacted with aldehyde 6 to form 32 and phenylsilane was used

Thiazol-4-one derivatives from the reaction of monosubstituted thioureas with maleimides: structures and factors determining the selectivity and tautomeric equilibrium in solution

• Alena S. Pankova,
• Pavel R. Golubev,
• Alexander F. Khlebnikov,
• Alexander Yu. Ivanov and
• Mikhail A. Kuznetsov

Beilstein J. Org. Chem. 2016, 12, 2563–2569, doi:10.3762/bjoc.12.251

• for this transformation was postulated. It includes a nucleophilic attack of the thiourea sulfur atom on the C=C bond of the maleimide followed by a proton transfer and nucleophilic attack of the thiourea nitrogen atom on one of the two carbonyl groups; the latter step is considered rate determining

• the nature of the dynamic process observed in solutions of 2-aminothiazolidines. This phenomenon was first detected by UV spectroscopy [19] and believed to be caused by a proton transfer between nitrogen atoms (amino–imino tautomerism), however, contradictory information on the equilibrium ratio of

• tautomerization process of thiazolidine 3g in solution led to a very strong broadening of its signals in the 1H NMR spectrum at 23 °C (Figure 2). Decreasing the temperature to −20 °C slowed down the proton transfer and the two sets of signals could be clearly seen and were fully assigned to the two forms of 3g as

Facile synthesis of a 3-deazaadenosine phosphoramidite for RNA solid-phase synthesis

• Elisabeth Mairhofer,
• Elisabeth Fuchs and
• Ronald Micura

Beilstein J. Org. Chem. 2016, 12, 2556–2562, doi:10.3762/bjoc.12.250

• -N3 is associated with the catalysis during ribosomal peptide bond formation, a proposal about its role in proton transfer has been disputed heavily since the first ribosome crystal structures up to very recent investigations [8][9][10]. The involvement of N3, and not N1, is surprising with respect to

A detailed view on 1,8-cineol biosynthesis by Streptomyces clavuligerus

• Jan Rinkel,
• Patrick Rabe,
• Laura zur Horst and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2016, 12, 2317–2324, doi:10.3762/bjoc.12.225

• generated by plant enzymes [24][37][38]. Both enzymes from Salvia officinalis and from Streptomyces clavuligerus share the syn addition in the final cyclisation step which can be rationalised by a direct intramolecular proton transfer, circumventing the need of a low-energy neutral intermediate such as α

• -terpineol. However, in case of the sesquiterpene ethers corvol ethers A (19) and B (18) a reprotonation step was shown to proceed from the opposite face than the preceeding attack of water, thus excluding a direct proton transfer from oxygen to the neighbouring carbon (reactions from 12 to 14 in Scheme 2

• to 13C-labelled carbons. B) Intramolecular proton transfer from the protonated hydroxy function in (S)-7 to C-2. Cyclisation of GPP to 1 via the (R)-terpinyl cation ((R)-6, left) or the (S)-terpinyl cation ((S)-6, right). Mechanism for the cyclisation of FPP to corvol ethers A (19) and B (18). WMR

Enantioconvergent catalysis

• Justin T. Mohr,
• Jared T. Moore and
• Brian M. Stoltz

Beilstein J. Org. Chem. 2016, 12, 2038–2045, doi:10.3762/bjoc.12.192

• . The resulting intermediate undergoes proton transfer and elimination of the phosphonium moiety, resulting in product 30 and regeneration of the catalyst. This exceptional demonstration of stereocontrol requires that the catalysts precisely organize both the electrophilic and nucleophilic reactants to

Unusual reactions of diazocarbonyl compounds with α,β-unsaturated δ-amino esters: Rh(II)-catalyzed Wolff rearrangement and oxidative cleavage of N–H-insertion products

• Valerij A. Nikolaev,
• Jury J. Medvedev,
• Olesia S. Galkina,
• Ksenia V. Azarova and
• Christoph Schneider

Beilstein J. Org. Chem. 2016, 12, 1904–1910, doi:10.3762/bjoc.12.180

• appearance of the amides 4 and 7 during the processes studied (Scheme 3). At first, upon catalytic decomposition of diazocarbonyl compounds 2a–c and 3c, N-ylide E is generated, stabilization of which by proton transfer produces an ordinary N–H-insertion product, α-ketoamine F. Similar reactions are well

The hydrolysis of geminal ethers: a kinetic appraisal of orthoesters and ketals

• Sonia L. Repetto,
• James F. Costello,
• Craig P. Butts,
• Joseph K. W. Lam and
• Norman M. Ratcliffe

Beilstein J. Org. Chem. 2016, 12, 1467–1475, doi:10.3762/bjoc.12.143

• body of data for our purposes, as potential FDII will operate under non-buffered, relatively apolar conditions. Though easily stated, the mechanism for the formation of a charged intermediate [5][7][8][9][10][11] followed by attack of water, cleavage of RO–C bonds, and several proton-transfer reactions

Development of chiral metal amides as highly reactive catalysts for asymmetric [3 + 2] cycloadditions

• Yasuhiro Yamashita,
• Susumu Yoshimoto,
• Mark J. Dutton and
• Shū Kobayashi

Beilstein J. Org. Chem. 2016, 12, 1447–1452, doi:10.3762/bjoc.12.140

• biologically active compounds are particularly important. Chiral Lewis acid/Brønsted base-catalyzed carbon–carbon bond-forming reactions are one of the most efficient methods from the viewpoint of atom economy because only proton transfer occurs between starting materials and target products [2]. Several kinds

The EIMS fragmentation mechanisms of the sesquiterpenes corvol ethers A and B, epi-cubebol and isodauc-8-en-11-ol

• Patrick Rabe and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2016, 12, 1380–1394, doi:10.3762/bjoc.12.132

• (Scheme 2B). Furthermore, the high resolution GC–QTOF MS2 analysis of m/z = 179 reveals that the base peak ion is a direct precursor of m/z = 161 by the loss of water (Figure S1, Supporting Information File 1). Starting from cation A1+, a ring opening reaction with a proton transfer to the oxygen may

• opening of A2+ to C2+ followed by a ring expansion to D2+, a proton transfer to E2+ and loss of water to F2+. The fragment ion F2+ is structurally the same as F1+ suggested above for m/z = 161 of 1. This structural identity of F1+ and F2+ is also reflected by the highly similar MS2 spectra of m/z = 161

Reactivity studies of pincer bis-protic N-heterocyclic carbene complexes of platinum and palladium under basic conditions

• David C. Marelius,
• Curtis E. Moore,
• Arnold L. Rheingold and
• Douglas B. Grotjahn

Beilstein J. Org. Chem. 2016, 12, 1334–1339, doi:10.3762/bjoc.12.126

• pyridine was 3.57 pKa units more basic than pyridine [9][10]. Considering reactions other than simple proton transfer, imidazol-2-yl complexes have recently been used to bind to a second transition metal [11]. Additionally, Cp*Ir complexes from our group [12] demonstrated heterolysis of the H–H bond of H2

Conjugate addition–enantioselective protonation reactions

• James P. Phelan and
• Jonathan A. Ellman

Beilstein J. Org. Chem. 2016, 12, 1203–1228, doi:10.3762/bjoc.12.116

• introduction of a proton, the smallest element in the periodic table, presents its own unique challenges. Significant racemic background reactions can compete with the desired enantioselective protonation because proton transfer is among the fastest of all processes. The α-electron withdrawing group, needed to

• intramolecular proton transfer was the stereodetermining step. Alternatively, Sunoj and co-workers performed DFT calculations on the mechanism of the enantioselective Stetter reaction between p-chlorobenzaldehyde and N-acetylamido acrylate and proposed that tert-butyl alcohol plays a key role as the proton

1H-Imidazol-4(5H)-ones and thiazol-4(5H)-ones as emerging pronucleophiles in asymmetric catalysis

• Antonia Mielgo and
• Claudio Palomo

Beilstein J. Org. Chem. 2016, 12, 918–936, doi:10.3762/bjoc.12.90

• ][10][11][12][13]. Regarding reactions which involve proton transfer events, soft enolization [14][15][16] constitutes an efficient tool for the deprotonation of some carbonyl compounds [17][18]. In these cases, a relatively weak amine is generally used to reversibly deprotonate a relatively acidic

Strecker degradation of amino acids promoted by a camphor-derived sulfonamide

• M. Fernanda N. N. Carvalho,
• M. João Ferreira,
• Ana S. O. Knittel,
• Maria da Conceição Oliveira,
• João Costa Pessoa,
• Rudolf Herrmann and
• Gabriele Wagner

Beilstein J. Org. Chem. 2016, 12, 732–744, doi:10.3762/bjoc.12.73

• below for proton transfer. The situation is different in the second mechanism via an eight-membered ring shown in Figure 8 (bottom). There is no need for the carboxylic group to approach the camphor moiety so closely, and the transfer occurs rather in the periphery of the molecule. Consequently, the

• of water is necessary for this step. 2. The fastest tautomerization in the reaction mixture occurs between 7a and 8 (the ene-sulfonamide). The low barriers (8.4 and 10.6 kcal/mol) should allow the equilibrium to be established rapidly. On the other hand, there is no possibility of proton transfer

• compounds as well as carboxylate anions. This is different in the ninhydrin reaction where the corresponding anions lose CO2 upon attempted geometry optimization. Decarboxylation of the imines of the oxoimine 1 only occurs when a zwitterion is formed by proton transfer to one of the two nitrogen atoms. This

Recent advances in N-heterocyclic carbene (NHC)-catalysed benzoin reactions

• Rajeev S. Menon,
• Akkattu T. Biju and
• Vijay Nair

Beilstein J. Org. Chem. 2016, 12, 444–461, doi:10.3762/bjoc.12.47

• anion equivalent 3 is known as the "Breslow intermediate". Its reaction with another molecule of aldehyde leads to the formation of an alkoxide intermediate 4. Proton transfer and subsequent release of thiazolylidene 1 affords the final product, the α-hydroxy ketone 5. Breslow demonstrated that