The effect of cyclodextrin complexation on the solubility and photostability of nerolidol as pure compound and as main constituent of cabreuva essential oil

• Joyce Azzi,
• Pierre-Edouard Danjou,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2017, 13, 835–844, doi:10.3762/bjoc.13.84

• narrow side of CD. Molecular modelling The theoretical molecular modelling is useful to illustrate the most energetically favorable three-dimensional structure of the inclusion complex in solution. The inclusion complex conformer that presents the weakest relative binding energies (ΔE) (i.e., the most

• stable conformer) is represented in Figure 4b. The results showed that the formation of the β-CD/trans-Ner inclusion complex is an energetically favorable process and that the inclusion mode is coherent with the experimental NMR results. Photodegradation studies of Ner To the best of our knowledge, no

• diagrams of CD/trans-Ner inclusion complexes. Phase solubility profile of cabreuva EO obtained by the TOC method. a) 2D ROESY spectrum of β-CD/trans-Ner inclusion complex in D2O and b) representation of the most stable inclusion complex conformer. Photodegradation kinetics of cis-Ner (a), trans-Ner (b

Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

• Franca Castiglione,
• Fabio Ganazzoli,
• Luciana Malpezzi,
• Andrea Mele,
• Walter Panzeri and
• Giuseppina Raffaini

Beilstein J. Org. Chem. 2017, 13, 714–719, doi:10.3762/bjoc.13.70

• comparison of the X-ray structure and the MD simulations in water of 2/β-CD complex showed that 2 is present as single conformer in the crystal and in two conformations in the solution state. Materials and Methods X-ray diffraction Single crystals of 1/β-CD and 2/β-CD were obtained after many attempts by

Dimerization reactions of aryl selenophen-2-yl-substituted thiocarbonyl S-methanides as diradical processes: a computational study

• Michael L. McKee,
• Grzegorz Mlostoń,
• Katarzyna Urbaniak and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2017, 13, 410–416, doi:10.3762/bjoc.13.44

• computational methods. The preferred formation of the unusual macroheterocycle, competitive with the 1,3-ring closure leading to a thiirane and the head-to-head dimerization yielding a 1,4-dithiane derivative, respectively, was explained based on the analysis of the structure of the favored conformer of the

• a 1.2 kcal/mol activation barrier (TS2) forming a C–C bond to give the intermediate, delocalized diradical 12 in a spontaneous reaction (∆G = −50.5 kcal/mol, Figure 3). This diradical can adopt a number of conformations. While the conformer surface was not fully explored, five conformers were

• density at the two corresponding C atoms and the strain required to reach the transition state. The spin densities of the two C atoms in conformer 12F, which is the precursor of the final product 9, is 0.25 e–, which is smaller than that of the two C atoms that do not form a new C–C bond (0.55 e−, Figure

Synthesis and optical properties of new 5'-aryl-substituted 2,5-bis(3-decyl-2,2'-bithiophen-5-yl)-1,3,4-oxadiazoles

• Anastasia S. Kostyuchenko,
• Tatyana Yu. Zheleznova,
• Anton J. Stasyuk,
• Aleksandra Kurowska,
• Wojciech Domagala,
• Adam Pron and
• Alexander S. Fisyuk

Beilstein J. Org. Chem. 2017, 13, 313–322, doi:10.3762/bjoc.13.34

• applied. Figure 3 shows a general representation of the compounds studied in this work. At the initial stage, a systematic conformational analysis of the series of substituted 1,3,4-oxadiazoles was conducted with the goal to determine the lowest-energy conformer(s). It has been found that 15c and 15d can

• exist only as a single conformer of planar structure. An increasing conformational variety has been observed for derivatives with substituents of increasing size. Thus, 15e can exist in two conformations with different orientation of the terminal substituents with respect to the central core. At the

• of 5'-aryl-substituted 2,5-bis(3-decyl-2,2'-bithiophen-5-yl)-1,3,4-oxadiazoles 15b–g in DCM. Selected geometrical parameters (bond lengths, B and dihedral angles, D) for all found conformers of the studied compoundsa, as well as relative energies, Erel, for each conformer in the ground state obtained

Silyl-protective groups influencing the reactivity and selectivity in glycosylations

• Mikael Bols and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2017, 13, 93–105, doi:10.3762/bjoc.13.12

• also cause an enhancing effect by favoring conformational inversion to the stereoelectronically more stable conformer in the transition state. The reactivity of TBS-protected thioglycosides was further investigated by Scanlan and co-workers who made the fucosyl donor 34 (Scheme 6) [28]. Interestingly

Biomimetic synthesis and HPLC–ECD analysis of the isomers of dracocephins A and B

• Viktor Ilkei,
• András Spaits,
• Anita Prechl,
• Áron Szigetvári,
• Zoltán Béni,
• Miklós Dékány,
• Csaba Szántay Jr,
• Judit Müller,
• Árpád Könczöl,
• Ádám Szappanos,
• Attila Mándi,
• Sándor Antus,
• Ana Martins,
• Attila Hunyadi,
• György Tibor Balogh,
• György Kalaus (†),
• Hedvig Bölcskei,
• László Hazai and
• Tibor Kurtán

Beilstein J. Org. Chem. 2016, 12, 2523–2534, doi:10.3762/bjoc.12.247

• - and 4’-OH protons and the condensed hetero ring had M helicity with envelope conformation and C-2 pointing out of the plane (ωC-8a,O-1,C-2,C-3 = −51.6°, ωC-8a,C-4a,C-4,C-3 = 0.4° for the lowest-energy conformer). The C-2 aryl group was nearly coplanar with the C-2–H-2 bond and the ωH-2,C-2,C-1’,C-2

Synthesis, dynamic NMR characterization and XRD studies of novel N,N’-substituted piperazines for bioorthogonal labeling

• Constantin Mamat,
• Marc Pretze,
• Matthew Gott and
• Martin Köckerling

Beilstein J. Org. Chem. 2016, 12, 2478–2489, doi:10.3762/bjoc.12.242

• second conformer). Radio-TLC (eluent: ethanol) of [18F]5b (Rf = 0.50; reaction mixture). (Radio)HPLC of 5a (tR = 7.7 min, UV trace, red), 5b (tR = 6.7 min, UV trace: blue) and [18F]5b (tR = 7.1 min, γ-trace, green). The differences in the retention times of 5b and [18F]5b occurs due to the setup of UV

Useful access to enantiomerically pure protected inositols from carbohydrates: the aldohexos-5-uloses route

• Felicia D’Andrea,
• Giorgio Catelani,
• Lorenzo Guazzelli and
• Venerando Pistarà

Beilstein J. Org. Chem. 2016, 12, 2343–2350, doi:10.3762/bjoc.12.227

• and 2.3 Hz) agree with four substituents in the equatorial position for the preferred conformer. A comparable example of intramolecular aldol condensation of a 1,5-dicarbonyl derivative has been reported by Tadano et al. [39]. Almost a sole aldol product was obtained in a good yield and was

Experimental and theoretical investigations into the stability of cyclic aminals

• Edgar Sawatzky,
• Antonios Drakopoulos,
• Martin Rölz,
• Christoph Sotriffer,
• Bernd Engels and
• Michael Decker

Beilstein J. Org. Chem. 2016, 12, 2280–2292, doi:10.3762/bjoc.12.221

• ’–c’), shared the same minimum energy conformer in which the phenyl ring in position 2 and the N-3 side group are in anti-axial orientation (exemplarily shown for compound 8a in Figure 7a) while the other compounds (neutral form: 8d,f, 9b,c; protonated form: 8f’, 9b’,c’) adhere to a conformer of

• : 177049 [46], 717617 [49], 778079 [50], 722943 [51], 820149 [52]; and for equatorial motif: 177050, 177052 [46]). Interestingly, the least stable compound 13b and the significantly more stable compound 8e were found to share the same anti-axial conformer in the neutral and in the N-3 protonated form

• using Molecular Mechanics (MM). For this purpose, the conformer of minimal energy for compounds 9b and 13b,c was kept frozen, while the N-side groups were changed into a methyl residue. The resulting structures were therefore identical with compound 8a, thus differences in potential energy are

Thiophene-forming one-pot synthesis of three thienyl-bridged oligophenothiazines and their electronic properties

• Dominik Urselmann,
• Konstantin Deilhof,
• Bernhard Mayer and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2016, 12, 2055–2064, doi:10.3762/bjoc.12.194

• = 298 K). DFT-calculated minimum conformer of the 2,5-bis(terphenothiazinyl)thiophene 3c (calculated with the B3LYP functional and the 6-311G(d,p) basis set). Relevant Kohn–Sham FMOs contributing to the S1 states that are assigned to the longest wavelengths absorption bands of thienyl-bridged

Varioloid A, a new indolyl-6,10b-dihydro-5aH-[1]benzofuro[2,3-b]indole derivative from the marine alga-derived endophytic fungus Paecilomyces variotii EN-291

• Peng Zhang,
• Xiao-Ming Li,
• Xin-Xin Mao,
• Attila Mándi,
• Tibor Kurtán and
• Bin-Gui Wang

Beilstein J. Org. Chem. 2016, 12, 2012–2018, doi:10.3762/bjoc.12.188

• Cotton effects (CEs) had the same sign for conformer A and B, while the lower-wavelength (<250 nm) CEs were significantly different. The hindered rotation along the biaryl linkage may have implied an additional stereogenic element, which would have enabled atropodiastereomers with axial chirality. In

• order to explore the possibility of axial chirality, torsional angle scans were performed on the lowest-energy M (conformer A) and P (conformer B) helicity gas-phase conformers or atropodiastereomers. Rotational energy barriers between the two isomers were estimated to be ca. 35–42 kJ/mol for TS1 (ωC12

• compound 1. Structure and population of the low-energy B3LYP/6-31G(d) conformers (>2%) of (2R,3R)-1. Experimental ECD spectrum of 1 in MeCN compared with the computed PBE0/TZVP spectra of the lowest-energy M (ωC12−C13−C3’−C9’ = –46.1°, conformer A) and P (ωC12−C13−C3’−C9’ = 133.4°, conformer B) helicity

Rearrangements of organic peroxides and related processes

• Ivan A. Yaremenko,
• Vera A. Vil’,
• Dmitry V. Demchuk and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2016, 12, 1647–1748, doi:10.3762/bjoc.12.162

Experimental and theoretical insights in the alkene–arene intramolecular π-stacking interaction

• Valeria Corne,
• Ariel M. Sarotti,
• Carmen Ramirez de Arellano,
• Rolando A. Spanevello and
• Alejandra G. Suárez

Beilstein J. Org. Chem. 2016, 12, 1616–1623, doi:10.3762/bjoc.12.158

• approximately a 9:1 ratio, according to the relative area of the signals. Some authors have claimed that this effect could be due to a conformational equilibrium of s-cis and s-trans species that is shifted toward the s-trans conformer at lower temperatures [18][19][20][21]. Similar studies were carried out for

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

• ) ≈ 13:4. The antiperiplanar lone pair hypothesis (ALPH) proposes that the axial anomer of 4 constitutes the major conformer in solution [28], perhaps affording some stereoelectronic advantage to an early transition state which appears operative in the case of such acid-catalysed processes [29]. The

• structures (see Experimental section). The half-chair (C2) arrangement was found to be the only stable conformer for the 1,3-dioxolane ring with all other conformers being rotamers about the C(2)–CH2R and C(2)–OMe bonds [where R = H (5) or t-Bu (16)]. The orientation of the C(2)O–Me group is ignored from

• enthalpy. No such flattened conformer exists for 5. The calculations are consistent with the model presented earlier in Figure 4. The increasing steric demand of substituent R [i.e., R = H (5); → Et (9); → iPr (12) → t-Bu (16)] leads to transannular clashing with axial C(3)/(4)–H atoms and subsequent

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

• conformer holds a pseudodiaxial, vicinal Br/H anti relationship and hence is (presumably) able to react somewhat faster. We abstained from separating trans-1 and cis-1 since the availability of two different mixtures facilitated the NMR assignments and because any cis-1/trans-1 mixture or the ensuing 3/4

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

• energies. These correspond to conformers 1, 2 and 3 of Table 1, the most stable ones in the gas phase and implicit solution. It is worth mentioning that, according to our calculations, the solvent has a little effect on the conformer populations, such as in enflurane [16], suggesting that intramolecular

• bonding is not a decisive interaction for the conformational equilibrium of isoflurane. Using a solvation model with explicit water, where specific solute–solvent interactions take place, conformer 1 is again the most stable form, suggesting that implicit solvation describes satisfactorily the actual

• differences in the Cl–C–O–C and C–O–C–H dihedral angles (±8° and 17°, respectively), the isoflurane structure bound to apoferritin (PDB code: 1XZ3 [9]) does not match any optimized conformer (Figure 1). So, does it make sense to use enzyme-free optimized conformations to obtain biochemical insights from 3D

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

• energy the 3,4-double bond increased the relative stability of the s-trans conformer by 0.2–0.3 kJ/mol, whereas the 4-CF3-group demonstrated an opposite effect of about 0.3 kJ/mol (standard error ±0.1 kJ/mol). Despite both effects being rather marginal, this indicates that the increase of the

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

• on the following assumption: in order to avoid an enthalpic penalty, the conformer of a drug-like molecule in the unbound state has to be similar to the bioactive conformational state. The result of our MC scans is shown in Figure 2. An overall number of ca. 450 low energy (40kJ/mol window

• 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

• intensified our scan at this point in order to make sure that we will not produce false positive hits for the linezolid analogues. An initial phase with 5000 steps produced a low energy conformer very similar to the conformation of linezolid in the crystal structure. After another 5000 steps (starting from

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

• (specifically, those derived from the conformer of the bisabolyl cation that most readily formed the cedryl cation in the dynamics simulations) into the crystallographically-determined structure of epi-isozizaene synthase revealed that some carbocations along the reaction coordinate were bound more strongly

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

• present as two conformers in the ratio 0.61:0.39. One consequence of this is that there are two distinct positions for the O19–H phenolic group, each conformer forming a hydrogen bond with a different TRIMEB acceptor oxygen atom. Further details of this disorder and its implications are given below

Recent highlights in biosynthesis research using stable isotopes

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2015, 11, 2493–2508, doi:10.3762/bjoc.11.271

•  8) that prevented a full assignment of NMR data by conventional methods. To correlate a conformational signal set, (U-13C15)FPP was synthesized and 13C,13C-COSY showed the connected carbon skeleton for each conformer. The 15 obtained labeled natural products also allowed a detailed analysis of the

Fe(II)/Et₃N-Relay-catalyzed domino reaction of isoxazoles with imidazolium salts in the synthesis of methyl 4-imidazolylpyrrole-2-carboxylates, its ylide and betaine derivatives

• Ekaterina E. Galenko,
• Olesya A. Tomashenko,
• Alexander F. Khlebnikov,
• Mikhail S. Novikov and
• Taras L. Panikorovskii

Beilstein J. Org. Chem. 2015, 11, 1732–1740, doi:10.3762/bjoc.11.189

• corresponding solvent at 298 K. Calculated data are based on the most stable conformer of 2−6. Supporting Information Supporting Information File 246: Detailed experimental procedures including characterization data for all synthesized compounds, 1H and 13C NMR spectra for all new compounds. Computational

Structure and conformational analysis of spiroketals from 6-O-methyl-9(E)-hydroxyiminoerythronolide A

• Ana Čikoš,
• Irena Ćaleta,
• Dinko Žiher,
• Mark B. Vine,
• Ivaylo J. Elenkov,
• Marko Dukši,
• Dubravka Gembarovski,
• Marina Ilijaš,
• Snježana Dragojević,
• Ivica Malnar and
• Sulejman Alihodžić

Beilstein J. Org. Chem. 2015, 11, 1447–1457, doi:10.3762/bjoc.11.157

• Determining the structure of the thermodynamically stable product 4 proved to be more challenging. Our initial hypothesis was that it was an anomerically stabilised 8C5 conformer of 3 with the 6-methoxy group in the more stable equatorial position. Molecular mechanics calculations, however, showed that such a

Articulated rods – a novel class of molecular rods based on oligospiroketals (OSK)

• Pablo Wessig,
• Roswitha Merkel and
• Peter Müller

Beilstein J. Org. Chem. 2015, 11, 74–84, doi:10.3762/bjoc.11.11

• cooling to 0 °C the IM/IEX ratio is increased to 100:30 (Figure 4, green curve) and at 77 K in a solid EPA [25] matrix the excimer emission completely disappears (Figure 4, blue curve). This behavior underlines the above-mentioned dynamic character of the excimer and suggests that the conformer 32a-STR is

Molecular cleft or tweezer compounds derived from trioxabicyclo[3.3.1]nonadiene diisocyanate and diacid dichloride

• Gert Kollenz,
• Ralf Smounig,
• Ferdinand Belaj,
• David Kvaskoff and
• Curt Wentrup

Beilstein J. Org. Chem. 2015, 11, 1–8, doi:10.3762/bjoc.11.1

• of 4 and 5 (see Figure S2 and Figure S3, Supporting Information File 1), the lowest-energy conformers shown in Figure 6 and Figure 7 are in very good agreement with the X-ray structures. The nearly parallel dangling chains in the lowest-energy conformer of 4 are particularly noteworthy (Figure 6). As