Unusual traits of cis and trans-2,3-dibromo-1,1-dimethylindane on the way from 1,1-dimethylindene to 2-bromo-, 3-bromo-, and 2,3-dibromo-1,1-dimethylindene

• Rudolf Knorr,
• David S. Stephenson,
• Ernst Lattke,
• Petra Böhrer and
• Jakob Ruhdorfer

Beilstein J. Org. Chem. 2016, 12, 1178–1184, doi:10.3762/bjoc.12.113

• angles in either one of the two cis-1 conformations are of similar sizes and do not permit a conformational differentiation. On the other hand, the close to 90° torsional angle between 3-H and 2-H in the 2eq-H,3eq-H conformation of trans-1 would imply an almost vanishing 3JH,H value, in contrast with the

• -dimethylindene (2) and their envelope conformations: ax = pseudoaxial, eq = pseudoequatorial; Me = methyl. The ways to 2-bromo- (4), 3-bromo- (3), and 2,3-dibromo-1,1-dimethylindene (7); SuIm = succinimide, NBS = N-bromosuccinimide, Me = methyl. Unsolvated 2-bromo-3-lithio-1,1-dimethylindene (10) precipitated

Efficient syntheses of climate relevant isoprene nitrates and (1R,5S)-(−)-myrtenol nitrate

• Sean P. Bew,
• Glyn D. Hiatt-Gipson,
• Graham P. Mills and
• Claire E. Reeves

Beilstein J. Org. Chem. 2016, 12, 1081–1095, doi:10.3762/bjoc.12.103

• -chlorobut-2-en-1-ol ((E)-60) and (Z)-3-methyl-4-chlorobut-2-en-1-ol ((Z)-61). Using NOESY interactions to establish the conformations of the C=C bonds within (E)-10 and (Z)-9. Synthesis of isoprene nitrates (E)-11 and (Z)-12 from ketone 63. Attempted synthesis of rac-8 from O-mesylate rac-71. Synthesis of O

The synthesis of functionalized bridged polycycles via C–H bond insertion

• Jiun-Le Shih,
• Po-An Chen and
• Jeremy A. May

Beilstein J. Org. Chem. 2016, 12, 985–999, doi:10.3762/bjoc.12.97

• rigid structures restrict molecular conformations for binding to multiple biological entities. Given the natural scarcity of most of these compounds, few have been extensively screened for biological activity, and some have not been tested at all. Unsurprisingly, many synthetic strategies for the

A cross-metathesis approach to novel pantothenamide derivatives

• Jinming Guan,
• Matthew Hachey,
• Lekha Puri,
• Vanessa Howieson,
• Kevin J. Saliba and
• Karine Auclair

Beilstein J. Org. Chem. 2016, 12, 963–968, doi:10.3762/bjoc.12.95

• expected to present type II and III behavior, respectively. Acrylic acid (10a) is known to react well in metathesis with catalyst 3 and therefore was used to test the suitability of compounds 8 and 9 in metathesis at 40 °C overnight [21]. As expected based on its large number of accessible conformations

A convenient route to symmetrically and unsymmetrically substituted 3,5-diaryl-2,4,6-trimethylpyridines via Suzuki–Miyaura cross-coupling reaction

• Dariusz Błachut,
• Joanna Szawkało and
• Zbigniew Czarnocki

Beilstein J. Org. Chem. 2016, 12, 835–845, doi:10.3762/bjoc.12.82

• the corresponding enentiomeric conformations, stable at least in the NMR time scale. Indeed, the presence of enantiomeric forms of 47 and 69 was confirmed by 1H NMR recorded in the presence of (+)-butylphenylphosphinothioic acid [80] as a chiral solvating agent. Recently, we have employed a similar

Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics

• Maria C. Guimarães,
• Mariene H. Duarte,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76

• have been made to attenuate the drawback of using a conformation that is possibly wrong, e.g., by using average conformations, ensemble and multidimensional methods [5][6][7][8], but the risk of chemical–biological misinterpretation remains. Receptor-dependent QSAR methods have also been developed [9

• high level calculations (in a receptor-free environment) in QSAR modelling was evaluated using a comparative study of the optimized and bioactive conformations of the fluorinated anesthetic isoflurane, which binds to a 4-helix bundle protein (apoferritin) [12] and to the integrin LFA1 enzyme [13

• ]. Results and Discussion Conformational analysis 2-Chloro-2-(difluoromethoxy)-1,1,1-trifluoroethane (isoflurane) undergoes rotational isomerization around two dihedral angles (Cl–C–O–C and C–O–C–H) and, considering three limit orientations for each of them (gauche, gauche' and anti), nine conformations are

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

• decarboxylation. Since the parent zwitterions 5 and 6 cannot be calculated as energy minima, there is no chance to understand, e.g., which conformations of 5 will lead preferentially to 7a and 7b, respectively. Since it was found experimentally that the amine 12 is the key intermediate for the formation of

From steroids to aqueous supramolecular chemistry: an autobiographical career review

• Bruce C. Gibb

Beilstein J. Org. Chem. 2016, 12, 684–701, doi:10.3762/bjoc.12.69

• type II photoreactions. NMR analysis revealed that, depending on the size of the R group, the guests adopted one of three principle packing motifs (Figure 10a). In essence, the host acts as an external template to promote the formation of distinct guest conformations. As a result of their packing motif

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

• Pro structural analogues, azetidine-2-carboxylic acid (norproline) and pipecolic acid (homoproline) [4], it appears that the high isomerization barrier is a feature associated with the 5-membered pyrrolidine ring of Pro [5]. The pyrrolidine ring of Pro can be found in several conformations, designated

• the carbamate groups as C(=O)–O–H···O=C(–Ot-Bu)–N. The same has been recently reported in particular in the cases of N-Boc-2-methylproline [41] and N-Boc 4,5-difluoromethanoproline [42]. In the crystal structure the ring conformations were found to be: twisted endo-pucker for 5, exo-pucker for 7, and

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• pocket for the oxazolidinone ring is characterized by universally conserved 23S-rRNA nucleotides, leading to very similar ligand-bound conformations in different bacterial ribosomes [23]. From a theoretical point of view, the simulation of recognition processes employing nucleotide-based receptors is

• plot for all sampled conformers shows that the AMBER force field produces a homogeneous distribution of the low energy conformations, while the OPLS-AA low-RMSD structures are clustered in confined areas with a 10 kJ/mol wide conformer gap between 25–35 kJ/mol. We finally evaluated our force fields

• protocol calculating the various conformations of linezolid inside the ribosome, applying the OPLS-AA force field. Indeed both, the lowest energy minimum and the 10 following conformations are characterized by a side chain, which is oriented pseudoequatorial with respect to the plane of the molecule

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• solvolysis of syn- and anti-norborn-2-en-7-ylmethyl-X diastereomers (Is and Ia, Figure 6; X is a leaving group) both led to the same two products, but in different ratios, despite sharing a common intermediate (in different conformations; V, Figure 6) [59]. The major product generated from the solvolysis of

Versatile deprotonated NHC: C,N-bridged dinuclear iridium and rhodium complexes

• Albert Poater

Beilstein J. Org. Chem. 2016, 12, 117–124, doi:10.3762/bjoc.12.13

• isomers of complex [M(cod){µ-C3H2N2(Mes)-κC2,κN3}]2). The latter two isomers display conformations head-to-head (H-H) and head-to-tail (H-T) of CS and C2 symmetry, respectively. The isomerization from the H-H to the H-T conformation is feasible, whereas next substitutions of the cod ligand by CO first

Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies

• Giuseppina Raffaini,
• Fabio Ganazzoli and
• Antonino Mazzaglia

Beilstein J. Org. Chem. 2016, 12, 73–80, doi:10.3762/bjoc.12.8

• ± sign refers to the value calculated from the standard deviations of the average potential energy values due to the thermal fluctuations. However, the very large stability of each aggregate within the MD run indicates that both are very robust conformations that may form at least for kinetic reasons and

Determination of formation constants and structural characterization of cyclodextrin inclusion complexes with two phenolic isomers: carvacrol and thymol

• Miriana Kfoury,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2016, 12, 29–42, doi:10.3762/bjoc.12.5

• : the methyl group of both guests is oriented toward the narrower rim of the CD cavity whereas the isopropyl moiety points to the wider rim. Molecular modeling A molecular modeling study was performed to rationalize the NMR results, find out the most probable conformations of the inclusion complexes in

• conformations was carried out by a conformational Monte Carlo research method using the MMFFs force field in the presence of water (GB/SA implicit model) with the generation of 5000 conformations (FMNR conjugate gradient minimization convergence fixed to 0.01 kJ Å−1 mol−1). Prior to docking and simulations, the

Inclusion complexes of 2-methoxyestradiol with dimethylated and permethylated β-cyclodextrins: models for cyclodextrin–steroid interaction

• Mino R. Caira,
• Susan A. Bourne,
• Halima Samsodien and
• Vincent J. Smith

Beilstein J. Org. Chem. 2015, 11, 2616–2630, doi:10.3762/bjoc.11.281

• 2ME, namely 2-methoxyestradiol-3,17-di,O-bis-sulfamate [9], the A-ring being planar (aromatic), the B-, C- and D-rings being a half-chair, a chair and a twist form (twisted on C13–C14) respectively. Thus, no significant distortions of the host or guest conformations are evident as a result of

• host and guest during complexation [1]. Complex units A and B of TRIMEB·2ME, related by a pseudo-translation of ≈b/2, have nearly identical structural features, namely common TRIMEB host conformations and lack of host disorder, apparent twofold disorder of the 2ME methylene group at C6 (site-occupancy

• host molecules have significantly different conformations. The steroid molecules included in the respective complex units A–D are shown in Figure 6 where each is overlayed on the steroid nucleus taken from the crystal structure of 2ME alone [9], the comparison being based on maximum overlap of the A

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

• Giuseppina Raffaini,
• Antonino Mazzaglia and
• Fabio Ganazzoli

Beilstein J. Org. Chem. 2015, 11, 2459–2473, doi:10.3762/bjoc.11.267

• of the molecules in solution, and then we perform MD runs of these geometries until equilibrium, monitored inter alia through the system energy and its components, and through the intermolecular separations, is achieved. Eventually, we carry out final optimizations of different conformations saved

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• the orientation and stability of the binary α-MGS/β-CD inclusion complex at the atomic level. Two conformations of inclusion complexes in water (complexes I and II in Figure S1, Supporting Information File 1) were generated, and subjected to MD simulation for 20 ns. The results implied that the

Self-assemblies of γ-CDs with pentablock copolymers PMA-PPO-PEO-PPO-PMA and endcapping via atom transfer radical polymerization of 2-methacryloyloxyethyl phosphorylcholine

• Jing Lin,
• Tao Kong,
• Lin Ye,
• Ai-ying Zhang and
• Zeng-guo Feng

Beilstein J. Org. Chem. 2015, 11, 2267–2277, doi:10.3762/bjoc.11.247

• /MAS NMR and 2D NOESY NMR testing Figure 5 shows the solid-state 13C CP/MAS NMR spectra of the PEP100M15CD PPR sample and γ-CDs. In line with previous research [20], the less symmetric, cyclic conformations of γ-CDs in the uncomplexed crystalline state bring about its spectrum with multiple, clear C1

2-Hetaryl-1,3-tropolones based on five-membered nitrogen heterocycles: synthesis, structure and properties

• Yury A. Sayapin,
• Inna O. Tupaeva,
• Alexandra A. Kolodina,
• Eugeny A. Gusakov,
• Vitaly N. Komissarov,
• Igor V. Dorogan,
• Nadezhda I. Makarova,
• Anatoly V. Metelitsa,
• Valery V. Tkachev,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2015, 11, 2179–2188, doi:10.3762/bjoc.11.236

• ). The geometric features of compounds 5g and 6e are similar to those of their 2-quinolyl congeners, 2-(2-quinolyl)-5,6,7-trichloro-1,3-tropolones and 2-(2-quinolyl)-4,5,6,7-tetrachloro-1,3-tropolones [23]. In all these compounds, the seven-membered rings are acoplanar and have bath conformations folded

Conformational equilibrium in supramolecular chemistry: Dibutyltriuret case

• Karina Mroczyńska,
• Małgorzata Kaczorowska,
• Erkki Kolehmainen,
• Ireneusz Grubecki,
• Marek Pietrzak and
• Borys Ośmiałowski

Beilstein J. Org. Chem. 2015, 11, 2105–2116, doi:10.3762/bjoc.11.227

• to exist in linear form without any intramolecular HBs and stabilized by four intermolecular ones. In general the dibutyltriuret molecule carrying four hydrogen bond donors (D, red, Figure 2) and three hydrogen bond acceptors (A, blue) can exist in various conformations stabilized by one or two

• intramolecular hydrogen bonds and destabilized by electronic repulsions (black dot) in some of them [50]. The conformations of 1 correspond to the following hydrogen-bonding patterns: 1a DDDD, 1b DDA, 1c DDDA, 1d DDA, and 1e ADDA. This means that the subjected compound may associate by quadruple (in 1a, 1c and

• 1e), triple (in 1b and 1d) and double (all forms) hydrogen bonding with suitable counterparts. For example, DDDD pattern in 1a should be able to interact with AAAA of 10. On the other hand all conformations can associate with 2–9 by interaction with a DD part of listed patterns. The principal

Supramolecular chemistry: from aromatic foldamers to solution-phase supramolecular organic frameworks

• Zhan-Ting Li

Beilstein J. Org. Chem. 2015, 11, 2057–2071, doi:10.3762/bjoc.11.222

• Technology, reported the formation of straight conformations by oligomers 13a,b and 14, which was driven by successive intramolecular hydrogen bonding [31] (Scheme 7), whereas Jiang Zhu, who is currently an associate professor at North Sichuan Medical College, described the zigzag conformation of oligomers

• backbones of hydrogen-bonded foldamers and thus prepared oligomers 24a–c [57] (Scheme 13). The octoxy groups provided solubility in common solvents such as chloroform. These and the methoxy groups formed successive hydrogen bonds to induce the backbones to form folded conformations, which have a cavity of

• -triazole foldamers. In 2008, several groups independently described that the intermolecular C–H····Cl− hydrogen bonding could induce benzene-linked 1,2,3-triazole oligomers to form folded or helical conformations [61][62][63]. Currently, this family of foldamers have found wide applications in anion

Investigation of the role of stereoelectronic effects in the conformation of piperidones by NMR spectroscopy and X-ray diffraction

• Cesar Garcias-Morales,
• David Ortegón-Reyna and
• Armando Ariza-Castolo

Beilstein J. Org. Chem. 2015, 11, 1973–1984, doi:10.3762/bjoc.11.213

• .11.213 Abstract This paper reports the synthesis of a series of piperidones 1–8 by the Mannich reaction and analysis of their structures and conformations in solution by NMR and mass spectrometry. The six-membered rings in 2,4,6,8-tetraphenyl-3,7-diazabicyclo[3.3.1]nonan-9-ones, compounds 1 and 2, adopt

• terms of delocalization interactions from electron hyperconjugation. This study describes the synthesis of a series of 2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9-one compounds (Figure 4) with restricted conformations. The complete analysis of the chemical shifts and the indirect coupling constants gives

• , and C2, respectively. A signal corresponding to the carbonyl carbon is located at 211.66 ppm. Figure 5a shows the conformations of 1, determined by the t-ROESY experiment. In solution, one of the six-membered rings is in the chair conformation, while the second is in the boat conformation to prevent

[2.2]Paracyclophane derivatives containing tetrathiafulvalene moieties

• Laura G. Sarbu,
• Lucian G. Bahrin,
• Peter G. Jones,
• Lucian M. Birsa and
• Henning Hopf

Beilstein J. Org. Chem. 2015, 11, 1917–1921, doi:10.3762/bjoc.11.207

• ., lengthened bridge bonds and widened bridge angles, flattened boat conformations for the rings). The moieties C3/4/5/17/18/O1 and C19/20/21/S1/S2/N1 are to a good approximation planar and subtend an interplanar angle of 80°. Short intramolecular contacts H13···S2 2.83 Å and H2B···O1 2.29 Å are observed. CCDC

A comprehensive study of olefin metathesis catalyzed by Ru-based catalysts

• Albert Poater and
• Luigi Cavallo

Beilstein J. Org. Chem. 2015, 11, 1767–1780, doi:10.3762/bjoc.11.192

• , Piers and co-workers demonstrated the bottom-bound geometry for a Ru-cyclobutane model compound by NMR data [46]. However, Grubbs and co-workers supported the side-bound pathway [47]. And this sort of discrepancy is displayed in Scheme 3, where the same catalyst shows two conformations, a and b, bottom

SmI₂-mediated dimerization of indolylbutenones and synthesis of the myxobacterial natural product indiacen B

• Nils Marsch,
• Peter G. Jones and
• Thomas Lindel

Beilstein J. Org. Chem. 2015, 11, 1700–1706, doi:10.3762/bjoc.11.184

• assignment of the relative configuration of compounds 6–8 was possible on the basis of NOESY spectra. The relative configuration of flexible compound 9 could not be determined. Since NOESY cross peaks may result from different conformations in equilibrium, we first identified positions which were likely to