cis–trans-Amide isomerism of the 3,4-dehydroproline residue, the ‘unpuckered’ proline

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2016, 12, 589–593, doi:10.3762/bjoc.12.57

• analogues which possess a 3,4-double bond: 3,4-dehydroproline and 4-trifluoromethyl-3,4-dehydroproline. Both indicate a flat pyrroline ring in their crystal structures, in agreement with previous theoretical calculations. In solution, the peptide mimics exhibit an almost unchanged equilibrium of the trans

Mechanism, kinetics and selectivity of selenocyclization of 5-alkenylhydantoins: an experimental and computational study

• Biljana M. Šmit,
• Radoslav Z. Pavlović,
• Dejan A. Milenković and
• Zoran S. Marković

Beilstein J. Org. Chem. 2015, 11, 1865–1875, doi:10.3762/bjoc.11.200

• theory (DFT) methods. The pathways of the reaction are investigated in detail. There are two regioselective pathways related to 5-exo and 6-endo products. Theoretical calculations and the monitoring of the cyclization reaction using 1H NMR spectroscopy are in a good agreement with the proposed mechanism

• sustains the statement about existing of such an intermediate. Theoretical calculations of the 1H chemical shifts for intermediate (S,R/S,S)-INT1 are in agreement with the observed values (Table 1, Figure 1). Starting 5-alkenylhydantoin 1 was synthesized from 6-methyl-hepten-2-on [24] by Bucherer–Bergs

• regio- and stereoisomerism of all intermediates and products were done on the basis of excellent correlation of experimental and calculated 1H chemical shifts as well as relative free energies. Theoretical calculations are in good agreement with our experimental results. Experimental All commercials

Tetrathiafulvalene-based azine ligands for anion and metal cation coordination

• Awatef Ayadi,
• Aziz El Alamy,
• Olivier Alévêque,
• Magali Allain,
• Nabil Zouari,
• Mohammed Bouachrine and
• Abdelkrim El-Ghayoury

Beilstein J. Org. Chem. 2015, 11, 1379–1391, doi:10.3762/bjoc.11.149

• that occurs in ligand L2 leading to a resonance structure that involves the C=N hydrazone bond as it can be seen in (Figure S2, Supporting Information File 1). Theoretical calculations Theoretical calculations based on density functional theory (DFT) methods have been performed with the Gaussian 09

Surprisingly facile CO₂ insertion into cobalt alkoxide bonds: A theoretical investigation

• Willem K. Offermans,
• Claudia Bizzarri,
• Walter Leitner and
• Thomas E. Müller

Beilstein J. Org. Chem. 2015, 11, 1340–1351, doi:10.3762/bjoc.11.144

• of zinc succinate. This was used to explain the activity of the former three and the inactivity of the latter. Theoretical calculations revealed a decrease in the activation barrier for the homopolymerisation as well as the copolymerisation step with increasing metal–metal distance. Moreover, the

Thiazole-induced rigidification in substituted dithieno-tetrathiafulvalene: the effect of planarisation on charge transport properties

• Rupert G. D. Taylor,
• Joseph Cameron,
• Iain A. Wright,
• Neil Thomson,
• Olena Avramchenko,
• Alexander L. Kanibolotsky,
• Anto R. Inigo,
• Tell Tuttle and
• Peter J. Skabara

Beilstein J. Org. Chem. 2015, 11, 1148–1154, doi:10.3762/bjoc.11.129

• charge transfer (CT) from the TTF to the electron-deficient thiazole units, facilitated due to their planarity. The structural properties of each compound will be expanded upon in the theoretical calculations section. Solution-state cyclic voltammetry was employed to determine the highest occupied

• , resulting in donation from the nitrogen lone pair to the sulfur atoms of the TTF unit increasing the electron density on the TTF unit and destabilising the HOMO. Theoretical calculations DFT calculations were carried out using the CAM-B3LYP [17] functional and TZVP [18] basis set in dichloromethane with the

New tris- and pentakis-fused donors containing extended tetrathiafulvalenes: New positive electrode materials for rechargeable batteries

• Shintaro Iwamoto,
• Yuu Inatomi,
• Daisuke Ogi,
• Satoshi Shibayama,
• Yukiko Murakami,
• Minami Kato,
• Kazuyuki Takahashi,
• Kazuyoshi Tanaka,
• Nobuhiko Hojo and
• Yohji Misaki

Beilstein J. Org. Chem. 2015, 11, 1136–1147, doi:10.3762/bjoc.11.128

• obtained as stable solids. Theoretical calculations We performed theoretical calculations of 5A, 6Aa and 7Aa by using the Gaussian 09 program based on the density functional theory (DFT) at the B3LYP/6-31G(d) level [27]. Their HOMO and HOMO–n (n = 1–2 and 1–4) of the trans isomers of 5a, 6a and 8a are

Single-molecule conductance of a chemically modified, π-extended tetrathiafulvalene and its charge-transfer complex with F₄TCNQ

• Raúl García,
• M. Ángeles Herranz,
• Edmund Leary,
• M. Teresa González,
• Gabino Rubio Bollinger,
• Marius Bürkle,
• Linda A. Zotti,
• Yoshihiro Asai,
• Fabian Pauly,
• Juan Carlos Cuevas,
• Nicolás Agraït and
• Nazario Martín

Beilstein J. Org. Chem. 2015, 11, 1068–1078, doi:10.3762/bjoc.11.120

• theoretical calculations. To the best of our knowledge, these are the first reported single-molecule conductance measurements on a molecular charge-transfer species. Keywords: break junction measurements; charge-transfer complex; DFT-based transport; molecular electronics; tetrathiafulvalene; Introduction

• experimental resolution, based on the value we measure for the CT complex. Ab initio calculations To gain insight into the conduction mechanism of compound 5, we performed theoretical calculations based on a combination of density functional theory (DFT) and Green’s functions techniques within the framework of

• functionalized with two (p-acetylthio)phenylethynyl substituents at positions 2 and 6 of the anthracene central core. We then describe single-molecule conductance measurements on this new derivative, along with measurements of the charge-transfer complex formed with F4TCNQ. Finally, we present theoretical

Glycoluril–tetrathiafulvalene molecular clips: on the influence of electronic and spatial properties for binding neutral accepting guests

• Yoann Cotelle,
• Marie Hardouin-Lerouge,
• Stéphanie Legoupy,
• Olivier Alévêque,
• Eric Levillain and
• Piétrick Hudhomme

Beilstein J. Org. Chem. 2015, 11, 1023–1036, doi:10.3762/bjoc.11.115

• central double bond of each TTF moiety, the intramolecular wall-to-wall distance was determined to be equal to 8.25 Å and 7.41 Å for clip 2 and 3, respectively (Figure 2) [18]. Then the corresponding wall-to-wall distance between the two TTF units was determined by theoretical calculations using the semi

• . Structures of molecular clips 1–4. Intramolecular distances between TTF moieties from X-ray analysis for clips 2 and 3 and theoretical calculations for clip 4. Cyclic voltammograms of molecular clips 1, 2, 3, 4 and F4-TCNQ at 10−3 M in 0.1 M TBAPF6/CH2Cl2/CH3CN 3:1 on a glassy carbon electrode at 100 mV·s−1

Trifluoromethyl-substituted tetrathiafulvalenes

• Olivier Jeannin,
• Frédéric Barrière and
• Marc Fourmigué

Beilstein J. Org. Chem. 2015, 11, 647–658, doi:10.3762/bjoc.11.73

• introduced on the dithiole ring upon substitution with the CN and CO2Me (−M) EWG are not offset by the competing CF3 group, confirming its much weaker mesomeric effect on the conjugated dithiole core. Optical properties and theoretical calculations have shown that the HOMO–LUMO gap is not much modified in

Enhancing the reactivity of 1,2-diphospholes in cycloaddition reactions

• Almaz Zagidullin,
• Vasili Miluykov,
• Elena Oshchepkova,
• Artem Tufatullin,
• Olga Kataeva and
• Oleg Sinyashin

Beilstein J. Org. Chem. 2015, 11, 169–173, doi:10.3762/bjoc.11.17

• theoretical calculations and experimental work [7][8]. At the same time both the presence of the P=C bond in phospholes as well as the transient 2H-phospholes [3] increase the cycloaddition reactivity. It was previously demonstrated that 1-alkyl-1,2-diphospholes combine the properties of both 1H-phospholes

Solution processable diketopyrrolopyrrole (DPP) cored small molecules with BODIPY end groups as novel donors for organic solar cells

• Diego Cortizo-Lacalle,
• Calvyn T. Howells,
• Upendra K. Pandey,
• Joseph Cameron,
• Neil J. Findlay,
• Anto Regis Inigo,
• Tell Tuttle,
• Peter J. Skabara and
• Ifor D. W. Samuel

Beilstein J. Org. Chem. 2014, 10, 2683–2695, doi:10.3762/bjoc.10.283

• as the conjugation increases (95 and 97 nm), with compound 10 giving two peaks at 607 and 645 nm. Theoretical calculations support the assignment of these absorption bands to the π–π* transition which is localised on the DPP core (vide infra). Optical HOMO–LUMO gaps in solution were calculated from

• –LUMO gap to the same extent. The aggregation of 9 in the solid state results in a decrease of the energy gap making it appear similar to 10, even if the conjugation length is shorter [49]. Theoretical calculations DFT optimisations were carried out for compounds 9 and 10, with the optimised structures

• microscopy (AFM). Theoretical calculations DFT optimisations were carried out in TURBOMOLE 6.3.1 [57] using B97-D [58] functional with def2-TZVP [59] basis set in dichloromethane using COSMO [60] solvent model. RI-J [61] approximation was implemented for these optimisations. TDDFT [62] and CHelpG [51

Synthesis and biological evaluation of novel N-α-haloacylated homoserine lactones as quorum sensing modulators

• Michail Syrpas,
• Ewout Ruysbergh,
• Christian V. Stevens,
• Norbert De Kimpe and
• Sven Mangelinckx

Beilstein J. Org. Chem. 2014, 10, 2539–2549, doi:10.3762/bjoc.10.265

• of these possible conformational effects, combined with the electron-withdrawing effect of the halogens, will be subject of future theoretical calculations. Due to the presence of the halogen as an electrophilic moiety, it could be possible that the reduced activity of the novel halogenated analogues

Towards the sequence-specific multivalent molecular recognition of cyclodextrin oligomers

• Michael Kurlemann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 2428–2440, doi:10.3762/bjoc.10.253

• result in different steric environments during the interactions, but the exact effects cannot be predicted and have to be solved by theoretical calculations and simulations. In the last step the interactions of the trivalent guest strands 11, 12, 13 and 14 with complementary and non-complementary

Chiral phosphines in nucleophilic organocatalysis

• Yumei Xiao,
• Zhanhu Sun,
• Hongchao Guo and
• Ohyun Kwon

Beilstein J. Org. Chem. 2014, 10, 2089–2121, doi:10.3762/bjoc.10.218

Stereocontrolled synthesis of 5-azaspiro[2.3]hexane derivatives as conformationally “frozen” analogues of L-glutamic acid

• Beatrice Bechi,
• David Amantini,
• Cristina Tintori,
• Maurizio Botta and
• Romano di Fabio

Beilstein J. Org. Chem. 2014, 10, 1114–1120, doi:10.3762/bjoc.10.110

• partial facial selectivity was observed in favor of the Si face attack (ratio 20a:20c = 1.5:1). To explain the results, the relative stability of the four diastereoisomers 20a–d was assessed by theoretical calculations. 10000 conformations were generated for each molecule by using the mixed torsional/low

• acetate. The cyclopropanation reaction occurred with trans selectivity preferentially affording the two trans cyclopropane products. Theoretical calculations on the stability of the four possible diastereoisomers were in agreement with both literature and experimental data observed. The final constrained

Conformational analysis of 2,2-difluoroethylamine hydrochloride: double gauche effect

• Josué M. Silla,
• Claudimar J. Duarte,
• Rodrigo A. Cormanich,
• Roberto Rittner and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2014, 10, 877–882, doi:10.3762/bjoc.10.84

• phase and in implicit water through theoretical calculations. Despite the presence of σCH→σ*CF and σCH→σ*CN interactions, which usually rule the hyperconjugative gauche effect in 1,2-disubstituted ethanes, the most important forces leading to the double gauche effect (+NH3 in the gauche relationship

• a 2-substituted ethylamine fragment [1][2][3][4][5]. According to theoretical calculations, such conformational preference takes place in the gas phase and persists in water solution, where most biochemical processes occur. We have recently shown that, in water solution, the axial preference of 3

• through theoretical calculations and infrared spectroscopy [11]. No significant double gauche effect has been found in 1, since conformers possessing two fluorine atoms in the gauche relationship with the amino group (gauche-gauche, gg) are estimated to be similarly populated to those conformers with only

Staudinger ligation towards cyclodextrin dimers in aqueous/organic media. Synthesis, conformations and guest-encapsulation ability

• Malamatenia D. Manouilidou,
• Yannis G. Lazarou,
• Irene M. Mavridis and
• Konstantina Yannakopoulou

Beilstein J. Org. Chem. 2014, 10, 774–783, doi:10.3762/bjoc.10.73

• titration experiments: the binding constant with 1-adamantylamine was similar to that of natural β-CD. Theoretical calculations for isolated molecules (PM3 level of theory) and in the presence of solvent [water, PM3(COSMO)] as well as DFT calculations suggested that the compounds prefer to adopt

• characterization combined with theoretical calculations, revealed the full capacity of the cavities for molecular inclusion despite the dynamic equilibria between closed and open conformations of the products in water. Results and Discussion Synthesis – The Staudinger ligation via linker 2 (Scheme 2) was initially

• formation in one step. Despite the well verified formation of intra- as well as intermolecular inclusion complexes, the compounds proved to be effective in encapsulating a suitable external guest in each cavity. The data were fully supported by theoretical calculations that confirmed the energetic

Use of activated enol ethers in the synthesis of pyrazoles: reactions with hydrazine and a study of pyrazole tautomerism

• Denisa Tarabová,
• Stanislava Šoralová,
• Martin Breza,
• Marek Fronc,
• Wolfgang Holzer and
• Viktor Milata

Beilstein J. Org. Chem. 2014, 10, 752–760, doi:10.3762/bjoc.10.70

• obtained from theoretical calculations at 293.15 K. However, the calculated proportion of tautomers does not include the effects of the reaction conditions and kinetics factors on the final proportion of individual tautomers in solution. Total electronic IEFPCM-B3LYP/6-311++G** energies with zero-point

Thermodynamically stable [4 + 2] cycloadducts of lanthanum-encapsulated endohedral metallofullerenes

• Yuta Takano,
• Yuki Nagashima,
• M. Ángeles Herranz,
• Nazario Martín and
• Takeshi Akasaka

Beilstein J. Org. Chem. 2014, 10, 714–721, doi:10.3762/bjoc.10.65

• . Although the structure of 5b was not elucidated using X-ray crystallographic analysis, synthetic precedents with absorption spectral data and theoretical calculations [16] strongly suggest that the most feasible addition site of the addend is that indicated in Scheme 2. The thermodynamic stability of 5b

New hydrogen-bonding organocatalysts: Chiral cyclophosphazanes and phosphorus amides as catalysts for asymmetric Michael additions

• Helge Klare,
• Jörg M. Neudörfl and
• Bernd Goldfuss

Beilstein J. Org. Chem. 2014, 10, 224–236, doi:10.3762/bjoc.10.18

• supplementary crystallographic data for this compound. Computational details All theoretical calculations were performed with the program package TURBOMOLE-6.3 [48]. The employed density functionals was the nonempirical TPSS-functional developed by Tao, Perdew, Scuseria and Staroverov [49], combined with the

3-Pyridinols and 5-pyrimidinols: Tailor-made for use in synergistic radical-trapping co-antioxidant systems

• Luca Valgimigli,
• Daniele Bartolomei,
• Riccardo Amorati,
• Evan Haidasz,
• Jason J. Hanthorn,
• Susheel J. Nara,
• Johan Brinkhorst and
• Derek A. Pratt

Beilstein J. Org. Chem. 2013, 9, 2781–2792, doi:10.3762/bjoc.9.313

• 4-position relative to the reactive hydroxyl moiety. Due to steric interactions between the adjacent ring methyl, the dimethylamino substituent in 4c is rotated out of the plane of the aromatic ring [17]. On the basis of theoretical calculations, H-atom transfer between phenol and the phenoxyl

• slow the analogous reaction between the radical derived from 4c and 11 relative to the other reaction couples. However, it should be pointed out that theoretical calculations on the phenol/phenoxyl H-atom transfer reaction do not include substituents in the ortho positions relative to the phenolic

New developments in gold-catalyzed manipulation of inactivated alkenes

• Michel Chiarucci and
• Marco Bandini

Beilstein J. Org. Chem. 2013, 9, 2586–2614, doi:10.3762/bjoc.9.294

• the key role of intramolecular hydrogen bond (H-bond) interactions for both reactivity and stereoselectivity [65]. Theoretical calculations and experimental evidences ruled out the SN1 reaction mechanism via allylic carbocation. Experiments with stereodefined hydroxy allylic alcohols revealed that the

Gold(I)-catalyzed enantioselective cycloaddition reactions

• Fernando López and
• José L. Mascareñas

Beilstein J. Org. Chem. 2013, 9, 2250–2264, doi:10.3762/bjoc.9.264

• experimental data as well as theoretical calculations suggested that both cycloadducts, 14 and 15, arise from the same intermediate, the cycloheptanyl metal–carbene species VIII, which might evolve through a 1,2-hydrogen shift to give the seven-membered carbocycles 14 (Scheme 8, a), or by a ring-contraction

Flow synthesis of phenylserine using threonine aldolase immobilized on Eupergit support

• Jagdish D. Tibhe,
• Hui Fu,
• Timothy Noël,
• Qi Wang,
• Jan Meuldijk and
• Volker Hessel

Beilstein J. Org. Chem. 2013, 9, 2168–2179, doi:10.3762/bjoc.9.254

• microreactor. Analysis of the four isomers of phenylserine on a chiral column. Phenylserine synthesis. Synthesis of chiral α-aminoalcohol by telescoping aldolase reaction with decarboxylation. Comparison of direct and indirect method. Comparison of productivity between the theoretical calculations and

Structure of 1,5-benzodiazepinones in the solid state and in solution: Effect of the fluorination in the six-membered ring

• Marta Pérez-Torralba,
• Rosa M. Claramunt,
• M. Ángeles García,
• Concepción López,
• M. Carmen Torralba,
• M. Rosario Torres,
• Ibon Alkorta and
• José Elguero

Beilstein J. Org. Chem. 2013, 9, 2156–2167, doi:10.3762/bjoc.9.253

• -033; email: deposit@ccdc.cam.ac.uk). Theoretical calculations. The geometry of the molecules has been fully optimized with the hybrid HF/DFT B3LYP [29][30][31] computational method and the 6-31G(d) basis set [32]. Frequency calculations have been carried out at the same computational level to verify