Accuracy in determining interproton distances using Nuclear Overhauser Effect data from a flexible molecule

• Catharine R. Jones,
• Craig P. Butts and
• Jeremy N. Harvey

Beilstein J. Org. Chem. 2011, 7, 145–150, doi:10.3762/bjoc.7.20

• obtained in a rigid organic molecule, it seems sensible to examine whether this approach can be extended more generally to multi-conformational systems with similar accuracy. Further, it is likely that the accurate interproton distance-assessments from NOE will allow accurate modelling of conformer

• populations in solution with fewer NOE constraints, or indeed improvements in the accuracy of modelling with the same number of NOE constraints. If flexible systems exhibiting multiple conformations in solution are interconverting rapidly on the NMR time-scale, then conformational exchange will lead to

• molecules when compared to their time-averaged computationally-derived distances in the alkyl chain of a small molecule – 4-propylaniline. These NOE-derived distances can thus be applied to modelling the populations (and hence energy differences) of the conformers, again with good accuracy when compared to

Catalysis: transition-state molecular recognition?

• Ian H. Williams

Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117

• objectives, such as the design of TS analogues as potential drugs, or the design of synthetic catalysts (including catalytic antibodies), require prior knowledge of the TS structure to be mimicked. Examples, both old and new, of computational modelling studies are discussed, which illustrate this fundamental

• . In March 1991, at a workshop held under the auspices of the Science and Engineering Research Council’s Molecular Recognition Initiative, I presented a paper on theoretical modelling of transition states for biochemical processes, which included a computational model for carbonyl reduction catalysed

Kinetic studies and predictions on the hydrolysis and aminolysis of esters of 2-S-phosphorylacetates

• Milena Trmčić and
• David R. W. Hodgson

Beilstein J. Org. Chem. 2010, 6, 732–741, doi:10.3762/bjoc.6.87

• homogeneous solutions that are amenable to simple kinetic modelling. Our predictive analyses were performed ~pH 7.4 based on King’s approach for predicting the optimal reaction pH for reactions between nucleophiles and reactive electrophiles [9]. The results from this exercise are plotted below (Figure 3 and

New amphiphilic glycopolymers by click functionalization of random copolymers – application to the colloidal stabilisation of polymer nanoparticles and their interaction with concanavalin A lectin

• Otman Otman,
• Paul Boullanger,
• Eric Drockenmuller and
• Thierry Hamaide

Beilstein J. Org. Chem. 2010, 6, No. 58, doi:10.3762/bjoc.6.58

• [1] whilst mannose units can be used for nerve cells targeting [2]. Besides naturally occurring polysaccharides, macromolecular engineering allows quite interesting possibilities for modelling of synthetic glycopolymers [3]. The hydrophobic component can be introduced by any convenient polymer moiety

The C–F bond as a conformational tool in organic and biological chemistry

• Luke Hunter

Beilstein J. Org. Chem. 2010, 6, No. 38, doi:10.3762/bjoc.6.38

• in these systems. Hyperconjugation effects Consider the well-studied molecule 1,2-difluoroethane (11, Figure 1c). There are two possible staggered conformers, with the fluorine atoms either gauche or anti. NMR and molecular modelling studies have shown that the gauche conformer is lower in energy

• molecular conformation as well as the molecular dipole moment. The difluoro compound 60 (Figure 15) can be viewed as a conceptual progression from the axially fluorinated liquid crystal 58. NMR and modelling data show that the fluoroalkyl chain of 60 adopts a zigzag conformation in which the two C–F bonds

(Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties

• José L. Jiménez Blanco,
• Fernando Ortega-Caballero,
• Carmen Ortiz Mellet and
• José M. García Fernández

Beilstein J. Org. Chem. 2010, 6, No. 20, doi:10.3762/bjoc.6.20

• ] that were found to form rigid secondary structures predetermined by the linkage position as evidenced from CD and NMR measurements. Moreover, conformational analysis by molecular modelling calculation on the β(1→2)-linked decamer 9 supported a helical arrangement, stabilised by a intramolecular

• acid. Following the same objective, Xie’s group prepared orthogonally protected cyclic homo-oligomers with two to four SAA units that can be selectively or fully deprotected to afford macrocycles that can undergo further functionalisation (Figure 11) [55]. Conformational analysis by molecular modelling

• (Figure 19). Molecular modelling predicts the existence of a flexible, relatively hydrophobic cavity suited for molecular inclusion of non-polar guests [79][88]. NMR supports this fact and confirms the high symmetry of these hosts, where all glucopyranosyl units are magnetically equivalent as in the case

Molecular length distribution and the formation of smectic phases

• Nadia Kapernaum,
• C. Scott Hartley,
• Jeffrey C. Roberts,
• Robert P. Lemieux and
• Frank Giesselmann

Beilstein J. Org. Chem. 2009, 5, No. 65, doi:10.3762/bjoc.5.65

• extrapolated value of 46.4 Å corresponds quite well to the value of 45.5 Å we obtained for the extended length of the PhP14 molecule from molecular modelling studies (see Figure 2). For 2PhP the experimental d-value from SAXS (25.9 Å) also agrees very well with the extended length of the molecule (25.6 Å

• PhP14, 6PhPz and 2PhP differing in molecular lengths by a factor of approximately two. The molecular lengths were determined from the most extended conformers, after optimizing their energy using molecular modelling with MOPAC/AM1. Phase diagram of the system 2PhP/PhP14. Over a broad temperature and

• concentration range only the SmA phase is stable. The layer spacing in the SmA phase at T = Tc vs mole fraction for the system 2PhP/PhP14 (filled triangles) and calculated value of the molecular length for pure PhP14 from molecular modelling (open square). Reduced layer spacing for the mixtures which exhibit

Influence of spacer chain lengths and polar terminal groups on the mesomorphic properties of tethered 5-phenylpyrimidines

• Gundula F. Starkulla,
• Elisabeth Kapatsina,
• Angelika Baro,
• Frank Giesselmann,
• Stefan Tussetschläger,
• Martin Kaller and
• Sabine Laschat

Beilstein J. Org. Chem. 2009, 5, No. 63, doi:10.3762/bjoc.5.63

• values obtained from the X-ray experiments fit with the molecular lengths derived from simple molecular modelling (Chem3D) [13]. For example, the XRD pattern of the azide derivative 6c results in a layer distance of 25.5 Å, whereas the calculated length of the molecule for the most elongated conformation

Coaxial electrospinning of liquid crystal-containing poly(vinylpyrrolidone) microfibres

• Eva Enz,
• Ute Baumeister and
• Jan Lagerwall

Beilstein J. Org. Chem. 2009, 5, No. 58, doi:10.3762/bjoc.5.58

• been predicted by numerical modelling of the coaxial electrospinning process [15]. Depending on the exact spinning conditions either a bubbly slug or annular flow pattern may result. On the other hand there are still many parts of the fibre samples where no LC seems to be present at all. When

Saddle-shaped tetraphenylenes with peripheral gallic esters displaying columnar mesophases

• Eugen Wuckert,
• Constanze Hägele,
• Frank Giesselmann,
• Angelika Baro and
• Sabine Laschat

Beilstein J. Org. Chem. 2009, 5, No. 57, doi:10.3762/bjoc.5.57

• mesophases with increasing chain lengths has been also observed in other columnar systems [32][33] and has been attributed to the enhanced core–core interaction necessary for the formation of the Colr phases [34]. According to molecular modelling [35] and comparison with the XRD data each disk within the

• /cooling rate 5 K/min). Texture of 2h under the POM at 25 °C upon cooling from the isotropic liquid (heating/cooling rate 5 K/min; magnification 100×). Molecular modelling of the saddle-shaped tetraphenylene (octakis)acyl core unit of 2 [35]. Clearing temperatures Tcl [°C] of tetraphenylenes 2e–l as a

Chiral amplification in a cyanobiphenyl nematic liquid crystal doped with helicene-like derivatives

• Alberta Ferrarini,
• Silvia Pieraccini,
• Stefano Masiero and
• Gian Piero Spada

Beilstein J. Org. Chem. 2009, 5, No. 50, doi:10.3762/bjoc.5.50

• detailed modelling of all intermolecular interactions. The SC method is particularly suitable for dopants with relatively high HTP, whose behavior is dominated by short-range interactions with the host. In general, low Q values may not be in agreement with measured HTPs. Another possible reason for this

A stable enol from a 6-substituted benzanthrone and its unexpected behaviour under acidic conditions

• Marc Debeaux,
• Kai Brandhorst,
• Peter G. Jones,
• Henning Hopf,
• Jörg Grunenberg,
• Wolfgang Kowalsky and
• Hans-Hermann Johannes

Beilstein J. Org. Chem. 2009, 5, No. 31, doi:10.3762/bjoc.5.31

• the reaction products is proposed and supported by DFT calculations. Keywords: consecutive reactions; intramolecular cyclization; molecular modelling; spiro compounds; X-ray structural analysis; Introduction Compounds for optoelectronic applications with electroluminescent (e.g. organic light

The vicinal difluoro motif: The synthesis and conformation of erythro- and threo- diastereoisomers of 1,2-difluorodiphenylethanes, 2,3-difluorosuccinic acids and their derivatives

• David O'Hagan,
• Henry S. Rzepa,
• Martin Schüler and
• Alexandra M. Z. Slawin

Beilstein J. Org. Chem. 2006, 2, No. 19, doi:10.1186/1860-5397-2-19

• isomer has three distinct staggered conformations; c, d and e. Computationally, this requires modelling the subtle balance between the correlation effects due to gauche fluorine atoms and those due to gauche phenyl rings. In the gas phase (entropy and zero energy corrected) conformers c and d are iso

Methods for the synthesis of polyhydroxylated piperidines by diastereoselective dihydroxylation: Exploitation in the two-directional synthesis of aza-C-linked disaccharide derivatives

• Andrew Kennedy,
• Adam Nelson and
• Alexis Perry

Beilstein J. Org. Chem. 2005, 1, No. 2, doi:10.1186/1860-5397-1-2

• conformations of the piperidines 20-22 were determined using a combination of three approaches: (a) analysis of the magnitude of vicinal coupling constants (see Table 2); (b) the observation of through-space nOe correlations; and (c) molecular modelling using the MMFF force field. The determination of the