Complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives

• Leonid S. Kikot',
• Catherine Yu. Kulygina,
• Alexander Yu. Lyapunov,
• Svetlana V. Shishkina,
• Roman I. Zubatyuk,
• Tatiana Yu. Bogaschenko and
• Tatiana I. Kirichenko

Beilstein J. Org. Chem. 2017, 13, 2056–2067, doi:10.3762/bjoc.13.203

• in the crystals. Meanwhile the hydrogen bond between one hydroxy group of cation 82+ and an oxygen atom of the polyether chain of clip 3 has been observed. The inclusion complexes of clips 2 and 3 with cations 82+ and 92+ have 1:1 composition in the crystal phase (Figure 8 and Figure 9). Similar to

• capability of additional stabilization of the complexes of the clips with paraquat derivatives due to the formation of the hydrogen bonds. Indeed, such an hydrogen bond is observed between one hydroxy group of cation 82+ and the polyether oxygen atom of clip 3 (О–H···O, O···O, О–H···O, 2.14, 2.97 Å, 170.2

• °). But a similar hydrogen bond is absent in the complex 2@8. One hydrogen bond is formed by the hydroxy group of 9 and the carbonyl oxygen atom of the diphenylglycoluril fragment of the clip (О–H···O, O···O, О–H···O, 2.02, 2.85 Å, 170.1° for 2 and 2.06, 2.86 Å, 161.3° for 3) in the complexes 2@9 and 3@9

Conformational impact of structural modifications in 2-fluorocyclohexanone

• Francisco A. Martins,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2017, 13, 1781–1787, doi:10.3762/bjoc.13.172

• hydrogen bond F···HN (e.g., dF···HN = 2.21 Å and F···H–N angle = 110.0°, when X/Y = CH2/NHZ), despite similar interactions hardly ever appear in organofluorine compounds when forming 5-membered rings [25][26]. In addition, it is also quite intuitive that fluorine tends to occupy the axial orientation in

• as Y, which exhibit intramolecular hydrogen bond with the equatorial fluorine) show axial prevalence. On the other hand, the equatorial conformer is preferred when X = S and NHeq (except for Y = NHE). While the axial preference for compounds with X = NHax can be determined by an electrostatic

• , dipolar relaxation F···HaxN (since an intramolecular hydrogen bond has not been clearly demonstrated in 3-fluoropiperidine [7][8][9][10][11][12][13]), such behavior for compounds with X = CH2 seems to be dependent on the C=Y bond, since X = CH2 is not a good proton donor. In this case, the axial

Synthesis and metal binding properties of N-alkylcarboxyspiropyrans

• Alexis Perry and
• Christina J. Kousseff

Beilstein J. Org. Chem. 2017, 13, 1542–1550, doi:10.3762/bjoc.13.154

• similar tether do not. To probe involvement of the carboxylate/carboxylic acid moiety (e.g., in forming inter- or intramolecular hydrogen bonds) we prepared C6 ester derivative 10 (Figure 7) as a direct point of comparison with C6SP. In the absence of a hydrogen bond donor group, the concentration of 10MC

• stabilisation and that only beyond a threshold distance does hydrogen bond donation of the carboxylic acid become important. This is a key point in designing functional materials based on N-alkylcarboxyspiropyrans. Conclusion In summary, we have developed a high-yielding, two-step synthesis of N

Bifunctional organocatalysts for the asymmetric synthesis of axially chiral benzamides

• Ryota Miyaji,
• Yuuki Wada,
• Akira Matsumoto,
• Keisuke Asano and
• Seijiro Matsubara

Beilstein J. Org. Chem. 2017, 13, 1518–1523, doi:10.3762/bjoc.13.151

• -hydroxybenzamide substrates comprise both amide and phenolic moieties. These can interact with a hydrogen-bond donor and a hydrogen-bond acceptor, respectively. Such interactions are expected to recognize a specific conformation of the substrate molecule to realize the enantioselective construction of axially

Syntheses of 3,4- and 1,4-dihydroquinazolines from 2-aminobenzylamine

• Jimena E. Díaz,
• Silvia Ranieri,
• Nadia Gruber and
• Liliana R. Orelli

Beilstein J. Org. Chem. 2017, 13, 1470–1477, doi:10.3762/bjoc.13.145

• different nucleophilicity of both amino groups, the predictable formation of a hydrogen bond between the aromatic amino group (hydrogen bond donor) and the aliphatic NHR (hydrogen bond acceptor) could increase the nucleophilicity of the former and decrease the reactivity of the latter, favoring the chance

Switchable highly regioselective synthesis of 3,4-dihydroquinoxalin-2(1H)ones from o-phenylenediamines and aroylpyruvates

• Juraj Dobiaš,
• Marek Ondruš,
• Gabriela Addová and
• Andrej Boháč

Beilstein J. Org. Chem. 2017, 13, 1350–1360, doi:10.3762/bjoc.13.132

• of the studied derivatives [4][5]. In this case, their tautomeric equilibrium is shifted to enamines 3 that have been stabilized by an intramolecular hydrogen bond (Scheme 1). A new pseudo-ring is formed via the hydrogen bond in 3, which further spreads the planarity of the 3,4-dihydroquinoxalin-2(1H

• crystallisation from DMSO, pure 16d (SYN) was isolated. We elucidated its structure in similar manner as for the 17d (ANTI) isomer (Figure 2) and confirmed that the 1H NMR (DMSO-d6) higher shifted signal for the H-N(4) group is the one that forms a intramolecular hydrogen bond with the carbonyl group from a side

• -dihydroquinoxaline-2(1H)-ones. Their ANTI (17) or SYN (16) structures were assigned by complex 2D NMR techniques (HSQC, NOESY and HMBC) or by a proposed simplified method (NOE interaction between higher 1H NMR (DMSO-d6) shifted H-N(4), bonded by intramolecular hydrogen bond, and H-C(5) or interaction of lower

A strategic approach to [6,6]-bicyclic lactones: application towards the CD fragment of DHβE

• Tue Heesgaard Jepsen,
• Emil Glibstrup,
• François Crestey,
• Anders A. Jensen and
• Jesper Langgaard Kristensen

Beilstein J. Org. Chem. 2017, 13, 988–994, doi:10.3762/bjoc.13.98

• ring and the B–C ring, which contrasts a mutational-computational study by Bermudez and co-workers suggesting that the lactone carbonyl is a hydrogen bond acceptor and hence locating the key pharmacophores in the C and D rings [9]. In order to weigh these hypotheses against one another, we have

Synthesis of tetrasubstituted pyrazoles containing pyridinyl substituents

• Josef Jansa,
• Ramona Schmidt,
• Ashenafi Damtew Mamuye,
• Laura Castoldi,
• Alexander Roller,
• Vittorio Pace and
• Wolfgang Holzer

Beilstein J. Org. Chem. 2017, 13, 895–902, doi:10.3762/bjoc.13.90

• 2a,b, 3a,b and 4a,b) strongly hints to the involvement of the former into an intramolecular hydrogen bond as indicated in Scheme 3. Cross-coupling reactions Initial attempts to react 4-bromopyrazole 5 – obtained from reaction of 2a with N-bromosuccinimide – with phenylboronic acid (or 3

Derivatives of the triaminoguanidinium ion, 5. Acylation of triaminoguanidines leading to symmetrical tris(acylamino)guanidines and mesoionic 1,2,4-triazolium-3-aminides

• Jan Szabo,
• Julian Greiner and
• Gerhard Maas

Beilstein J. Org. Chem. 2017, 13, 579–588, doi:10.3762/bjoc.13.57

• of 1,2,4-triazolium triflate 9b in the solid state (Figure 3) is similar to that of 8b. However, the uptake of one water molecule per formula unit has resulted in different hydrogen bond patterns. A centrosymmetric hydrogen-bonded dimer (CF3SO3·H2O)2 is present which is connected to two cations

Decarboxylative and dehydrative coupling of dienoic acids and pentadienyl alcohols to form 1,3,6,8-tetraenes

• Ghina’a I. Abu Deiab,
• Mohammed H. Al-Huniti,
• I. F. Dempsey Hyatt,
• Emma E. Nagy,
• Kristen E. Gettys,
• Sommayah S. Sayed,
• Christine M. Joliat,
• Paige E. Daniel,
• Rupa M. Vummalaneni,
• Andrew T. Morehead Jr,
• Andrew L. Sargent and
• Mitchell P. Croatt

Beilstein J. Org. Chem. 2017, 13, 384–392, doi:10.3762/bjoc.13.41

• . Pathway B involves a Morita–Baylis–Hillman type process. The role of water would be to hydrogen bond to the carboxylate to make the system more electrophilic (B). This would accelerate the addition of the phosphine to generate zwitterion C [58]. Preliminary modeling for this ion indicates that both the

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

• and R2 with varied positional substitution of a cyano and nitro signaling unit having a hydroxy functionality as the hydrogen bond donor site have been designed, synthesized and characterized by FTIR, 1H NMR spectroscopy and mass spectrometry. The receptors R1 and R2 exhibit prominent visual response

• receptors for anions have been developed based on various modes of interactions such as hydrogen bond and electrostatic interactions which rely on directionality and distance-dependent nature, respectively. Hydrogen bond formation is further tuned by the acidity of protons by virtue of the presence of

• −, F− and AcO− ions through hydrogen bond interaction followed by a deprotonation process [27][28][29]. The design of molecular logic gates with chemical and biological molecules has been at the forefront creating a new avenue to advanced diagnostics and therapeutics through molecular computers. As an

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

• Monica Ferro,
• Franca Castiglione,
• Nadia Pastori,
• Carlo Punta,
• Lucio Melone,
• Walter Panzeri,
• Barbara Rossi,
• Francesco Trotta and
• Andrea Mele

Beilstein J. Org. Chem. 2017, 13, 182–194, doi:10.3762/bjoc.13.21

• involved in hydrogen bonds. The presence of such a signal provides evidence for two remarkable facts: i) the drug entrapped in the nanosponge is in the acidic form, and ii) the ibuprofen molecules hosted in the CDNS are fully involved in a hydrogen-bond network. This point is worth of a comment: racemic

• the 13C CP-MAS NMR chemical shift of encapsulated IbuH match those of pure, crystalline IbuH provide useful, additional information to spot on the nature of the hydrogen bond network introduced in the previous section. As significant IbuH···CDNS interactions are not detected, the hydrogen bond

A novel method for heterocyclic amide–thioamide transformations

• Walid Fathalla,
• Ibrahim A. I. Ali and
• Pavel Pazdera

Beilstein J. Org. Chem. 2017, 13, 174–181, doi:10.3762/bjoc.13.20

• ) gave a broad singlet and a singlet signal at δ 13.71 and 3.87 ppm, associated with NH and OCH3 groups, respectively. The significant downfield shift of the NH proton is probably due to intermolecular hydrogen bond interactions of the type NH···S=C. All the isolated thioureas C1–13 exhibited similar 1H

A new class of organogelators based on triphenylmethyl derivatives of primary alcohols: hydrophobic interactions alone can mediate gelation

• Wangkhem P. Singh and
• Rajkumar S. Singh

Beilstein J. Org. Chem. 2017, 13, 138–149, doi:10.3762/bjoc.13.17

• carried out the FTIR analysis of TPM-G12 in solution (CHCl3, non-self-assembled state) and xerogel (KBr, self-assembled state) and compared their differences. Since there is no structural component capable of forming relatively strong intermolecular non-covalent interactions in TPM-G12 (e.g., hydrogen

• bond, ionic bond), we did not expect much difference between the two IR spectra. Indeed, this is the case as shown in Figure 6. Aromatic ring peaks for C–H str (3019 cm−1), out-of-plane C–H def (768 cm−1) and C=C str (1402 cm–1, 1448 cm–1 and 1490 cm–1) are seen in the solution state. Except for out-of

The synthesis of α-aryl-α-aminophosphonates and α-aryl-α-aminophosphine oxides by the microwave-assisted Pudovik reaction

• Erika Bálint,
• Ádám Tajti,
• Anna Ádám,
• István Csontos,
• Konstantin Karaghiosoff,
• Mátyás Czugler,
• Péter Ábrányi-Balogh and
• György Keglevich

Beilstein J. Org. Chem. 2017, 13, 76–86, doi:10.3762/bjoc.13.10

• -assisted addition of >P(O)H reagents to N-benzylideneaniline (1c). MW-assisted addition of dialkyl phosphites to N-chlorobenzylidene(butyl)amines 1d–f. Characteristic IR absorptions of the reaction components. IR absorptions measured and obtained from the 3D diagram after deconvolution (in cm−1). Hydrogen

• bond dimensions (Å, Deg) for compounds 5b and 5d.a Relative enthalpies, free energies and entropies for the tautomeric forms in case of methoxy and phenyl substituents. Relative enthalpies, free energies and entropies for the addition reaction of >P(O)H species to imines. Supporting Information

Synthesis of structurally diverse 3,4-dihydropyrimidin-2(1H)-ones via sequential Biginelli and Passerini reactions

• Andreas C. Boukis,
• Baptiste Monney and
• Michael A. R. Meier

Beilstein J. Org. Chem. 2017, 13, 54–62, doi:10.3762/bjoc.13.7

• 9 and an isocyanide 11 [21]. The Passerini reaction works best in non-polar solvents like dichloromethane. The mechanism of the Passerini reaction (Scheme 1b) is proposed to proceed via the formation of a hydrogen bond (H-bond) adduct between carboxylic acid 8 and carbonyl component 9, resulting in

New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

• Pavel Nagorny and
• Zhankui Sun

Beilstein J. Org. Chem. 2016, 12, 2834–2848, doi:10.3762/bjoc.12.283

• Pavel Nagorny Zhankui Sun Chemistry Department, University of Michigan, Ann Arbor, MI 48109, USA School of Pharmacy, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai 200240, P. R. China 10.3762/bjoc.12.283 Abstract Hydrogen bond donor catalysis represents a rapidly growing subfield

• of organocatalysis. While traditional hydrogen bond donors containing N–H and O–H moieties have been effectively used for electrophile activation, activation based on other types of non-covalent interactions is less common. This mini review highlights recent progress in developing and exploring new

• organic catalysts for electrophile activation through the formation of C–H hydrogen bonds and C–X halogen bonds. Keywords: C–H hydrogen bond; counteranion activation; electrophile activation; halogen bond donor; hydrogen bond donor; organocatalysis; Review Introduction Over the past century chemists

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• [123]. Here the binding energy of a target–ligand complex is solely estimated by a hydrogen bond term and a dehydration energy term. ChemScore [122] and SCORE [124] are two other scoring functions that are also empirical. Consensus-based scoring functions Current scoring functions are not perfect and

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

• Vladimir A. Stepchenko,
• Anatoly I. Miroshnikov,
• Frank Seela and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2016, 12, 2588–2601, doi:10.3762/bjoc.12.254

• group of the Glu166 side-chain forms an additional hydrogen bond with a water molecule, which, in turn, takes a part in hydrogen bonding to the 4C(=O) oxo function of uracil and to the adjacent guanidinium group of Arg223 [40]. In addition, the side-chain of Arg168 is directly hydrogen-bonded to the 4C

• to the direct 2C(=O)/His85 hydrogen bonding of thymine (product of reaction) in a closed form [3] (cf. [52][55]). This uncertainty does not allow identifying the most important type of hydrogen bond and analyzing its impact on the N-1 sp3 → sp2 transformation of the substrate. The enzymatic synthesis

Sydnone C-4 heteroarylation with an indolizine ring via Chichibabin indolizine synthesis

• Florin Albota,
• Mino R. Caira,
• Constantin Draghici,
• Florea Dumitrascu and
• Denisa E. Dumitrescu

Beilstein J. Org. Chem. 2016, 12, 2503–2510, doi:10.3762/bjoc.12.245

• sydnone-ring environment in the crystal of 12c differs significantly from that in 9d. The dipolar alignment of the sydnone moieties observed in 9d does not occur in 12c. The exocyclic atom O6 engages as an acceptor in an intermolecular C–H···O hydrogen bond. Further stabilizing interactions in the crystal

Construction of bis-, tris- and tetrahydrazones by addition of azoalkenes to amines and ammonia

• Artem N. Semakin,
• Aleksandr O. Kokuev,
• Yulia V. Nelyubina,
• Alexey Yu. Sukhorukov,
• Petr A. Zhmurov,
• Sema L. Ioffe and
• Vladimir A. Tartakovsky

Beilstein J. Org. Chem. 2016, 12, 2471–2477, doi:10.3762/bjoc.12.241

• modulation of the molecular geometry, for example through coordination with metal cations, hydrogen bond formation or irradiation. These unique structural features of the hydrazone fragment have been successfully exploited in the design of various molecular switches, fluorophores and machines. Bis- and

Diels–Alder reactions in confined spaces: the influence of catalyst structure and the nature of active sites for the retro-Diels–Alder reaction

• Ángel Cantín,
• M. Victoria Gomez and
• Antonio de la Hoz

Beilstein J. Org. Chem. 2016, 12, 2181–2188, doi:10.3762/bjoc.12.208

• showed a retro-DAR enhancing reactivity, even Al, the best hydrogen-bond-donating agent. This result implies that the competitive retro-DAR takes place not only due to the capability to act as Brønsted sites of metallic centers, but also due to the structure of MCM-41 and ITQ-2. This effect can be used

Diastereoselective synthesis of 3,4-dihydro-2H-pyran-4-carboxamides through an unusual regiospecific quasi-hydrolysis of a cyano group

• Mikhail Yu. Ievlev,
• Oleg V. Ershov,
• Mikhail Yu. Belikov,
• Angelina G. Milovidova,
• Viktor A. Tafeenko and
• Oleg E. Nasakin

Beilstein J. Org. Chem. 2016, 12, 2093–2098, doi:10.3762/bjoc.12.198

• structure of pyrans 2 as well as the trans configuration of the substituents at the asymmetric atoms C2 and C4 were established by X-ray diffraction (Figure 1) [25]. The conformation of the six-membered heterocyclic ring is stabilized by an intermolecular hydrogen bond C2–H2···O2. The distance O2···H2 is

Synthesis and characterization of fluorinated azadipyrromethene complexes as acceptors for organic photovoltaics

• Forrest S. Etheridge,
• Roshan J. Fernando,
• Sandra Pejić,
• Matthias Zeller and
• Geneviève Sauvé

Beilstein J. Org. Chem. 2016, 12, 1925–1938, doi:10.3762/bjoc.12.182

• with all reflections using Shelxl 2014 [43] using the graphical interface Shelxle [44]. H atoms attached to carbon atoms were positioned geometrically and constrained to ride on their parent atoms, with carbon hydrogen bond distances of 0.95 Å for aromatic C–H and 0.99 Å for CH2 moieties, respectively

Ionic liquids as transesterification catalysts: applications for the synthesis of linear and cyclic organic carbonates

• Maurizio Selva,
• Alvise Perosa,
• Sandro Guidi and
• Lisa Cattelan

Beilstein J. Org. Chem. 2016, 12, 1911–1924, doi:10.3762/bjoc.12.181

• cycles where the DPC yield still exceeded 70%. The proposed reaction mechanism consisted in the activation of the carbonyl group of DMC by the hydrogen-bond interaction with the cation of the IL catalyst followed by a nucleophilic attack of 1-pentanol (Scheme 16). A similar transesterification reaction