Space filling of β-cyclodextrin and β-cyclodextrin derivatives by volatile hydrophobic guests

• Sophie Fourmentin,
• Anca Ciobanu,
• David Landy and
• Gerhard Wenz

Beilstein J. Org. Chem. 2013, 9, 1185–1191, doi:10.3762/bjoc.9.133

• positions of β-CD. Our binding data are well described by the space filling of the cavity, as defined either by the number of carbons n, the molecular volume of the guest VG or by molecular modeling. Experimental Materials Benzene and cyclohexane derivatives were purchased from Aldrich, β-CD and

The diketopiperazine-fused tetrahydro-β-carboline scaffold as a model peptidomimetic with an unusual α-turn secondary structure

• Francesco Airaghi,
• Andrea Fiorati,
• Giordano Lesma,
• Manuele Musolino,
• Alessandro Sacchetti and
• Alessandra Silvani

Beilstein J. Org. Chem. 2013, 9, 147–154, doi:10.3762/bjoc.9.17

• constrained α-turn mimetics has received little attention until now. We report here the synthesis and conformational evaluation of the THBC-DKP-based peptidomimetic 1a (Figure 2), for which molecular modeling allowed us to envisage a 13-membered hydrogen-bond-stabilized α-turn conformation. Results and

• molecular modeling and these experimental results, for 1a we can presume the presence in solution of conformers bearing a 13-membered intramolecular hydrogen bond involving the NHMe proton and the Cbz carbonyl group, as visualized in the perspective view of the low energy conformer of 1a. Conclusion In

A bisazobenzene crosslinker that isomerizes with visible light

• Subhas Samanta,
• Harris I. Qureshi and
• G. Andrew Woolley

Beilstein J. Org. Chem. 2012, 8, 2184–2190, doi:10.3762/bjoc.8.246

• of a new crosslinker in which a central piperazine unit links two azobenzene chromophores. Molecular modeling indicates that this crosslinker can undergo a large change in end-to-end distance upon trans,trans to cis,cis isomerization. Photochemical characterization indicates that it does isomerize

• solution of 2 in DMSO-d6 containing a known concentration of 1,2-dichloroethane (DCE) as an internal reference was recorded. The NMR solution was later diluted in DMSO and the UV–vis spectrum was recorded to calculate the molar extinction coefficient. Molecular modeling: Models of trans,trans, trans,cis

Asymmetric desymmetrization of meso-diols by C₂-symmetric chiral 4-pyrrolidinopyridines

• Hartmut Schedel,
• Keizo Kan,
• Yoshihiro Ueda,
• Kenji Mishiro,
• Keisuke Yoshida,
• Takumi Furuta and
• Takeo Kawabata

Beilstein J. Org. Chem. 2012, 8, 1778–1787, doi:10.3762/bjoc.8.203

• ring, catalyst 3 was found to be most effective for the asymmetric desymmetrization (Scheme 1). However, the enantioselectivity of the asymmetric desymmetrization was far from being sufficient. Molecular modeling of the related catalysts indicated that a C2-symmetric PPY catalyst with functional side

• responsible for the asymmetric acylation. The most stable conformer A of the acylpyridinium ion was generated by a molecular modeling search (AMBER* force field with the GB/SA solvation model for chloroform using MacroModel V 9.0 (50,000 steps MCMM)) and shown in Figure 2a and Figure 2b. Since the amide

• molecular modeling study. It is also anticipated that an axial-OH may be the better hydrogen-bond donor than an equatorial-OH, according to the reported higher acidity of the axial hydroxy groups of cyclohexane derivatives [39]. An alternative model for the transition-state assembly is shown in Figure 3

Toward unidirectional switches: 2-(2-Hydroxyphenyl)pyridine and 2-(2-methoxyphenyl)pyridine derivatives as pH-triggered pivots

• Christina Tepper and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2012, 8, 977–985, doi:10.3762/bjoc.8.110

• unidirectionally at the molecular level. If a 2-(2-methoxyphenyl)pyridine derivative is fixed to a chiral cyclopeptidic scaffold, a unidirectional progress of the rotation is achieved macroscopically. Keywords: CD spectroscopy; chirality; molecular modeling; molecular switches; unidirectional movements

Synthesis and anion recognition properties of shape-persistent binaphthyl-containing chiral macrocyclic amides

• Marco Caricato,
• Nerea Jordana Leza,
• Claudia Gargiulli,
• Giuseppe Gattuso,
• Daniele Dondi and
• Dario Pasini

Beilstein J. Org. Chem. 2012, 8, 967–976, doi:10.3762/bjoc.8.109

• , centered at 320 nm (quite different from (R,R)-10). The CD spectra (in EtOH) show activity associated with all active UV chromophores and more marked activity for the macrocycle (R,R)-10, with exciton couplet signals greater in intensity than the ones of the other macrocycles. Molecular modeling Molecular

• slightly in the case of the more distorted (R,R)-10 (70.8 and 72.6°) and (R,R)-12 (85.9 and 85.6°). Molecular modeling does not give clear hints as to why macrocycle (R,R)-13 could not be obtained. The shortest distances between the symmetry-related NH groups, shown in Figure 3, are compatible with the

• suited than glutarate to fit into the cavity of 12 by interacting simultaneously with two different NH groups placed on the same binaphthyl residue (see above, molecular modeling), possibly in a cooperative fashion [39]. Similar titrations were carried out on (R,R)-10 and (R,R)-11, bearing acetoxy

Unprecedented deoxygenation at C-7 of the ansamitocin core during mutasynthetic biotransformations

• Tobias Knobloch,
• Gerald Dräger,
• Wera Collisi,
• Florenz Sasse and
• Andreas Kirschning

Beilstein J. Org. Chem. 2012, 8, 861–869, doi:10.3762/bjoc.8.96

• exchange of the tertiary carbinol at C-7 on phase-sensitive 1H–13C-correlation NMR spectra (HSQC). It needs to be noted that NOE-analysis combined with molecular modeling did not allow elucidation of the absolute configuration at C-14 for the new derivatives 13a and 13b, as it did not allow for the

High-affinity multivalent wheat germ agglutinin ligands by one-pot click reaction

• Henning S. G. Beckmann,
• Heiko M. Möller and
• Valentin Wittmann

Beilstein J. Org. Chem. 2012, 8, 819–826, doi:10.3762/bjoc.8.91

• divalent ligands and 2800 for a trivalent WGA ligand, compared to N,N’-diacetylchitobiose as the corresponding monovalent ligand, were observed. Molecular modeling studies, in which the chitobiose moieties were fitted into crystallographically determined binding sites of WGA, correlate the binding

• binding enhancement would have been expected comparable to the several-hundred-fold increase observed when moving from mono- to divalent ligand structures. Molecular modeling To provide a structure-based rationalization for the determined binding potencies of C2–C6, we performed molecular modeling studies

• GlcNAc residues kept in their optimal positions. Our molecular modeling studies revealed that the para-disubstituted aromatic linker of C3 cannot adopt a low-energy conformation if the chitobiose residues are kept in their ideal positions in the binding sites of WGA, resulting in significant ring strain

Perhydroazulene-based liquid-crystalline materials with smectic phases

• Zakir Hussain,
• Henning Hopf and
• S. Holger Eichhorn

Beilstein J. Org. Chem. 2012, 8, 403–410, doi:10.3762/bjoc.8.44

• molecular design of new liquid crystals, electro-optical properties can now be predicted quite precisely based on molecular modeling [1][2]. However, full evaluation of the value of a new structure is still only possible after synthesis. In the past few years many attempts have been made to improve the

Dependency of the regio- and stereoselectivity of intramolecular, ring-closing glycosylations upon the ring size

• Patrick Claude,
• Christian Lehmann and
• Thomas Ziegler

Beilstein J. Org. Chem. 2011, 7, 1609–1619, doi:10.3762/bjoc.7.189

• in ratios depending upon the ring size formed during glycosylation. No β(1→2) linked disaccharides were formed. Molecular modeling of saccharides 6–8 revealed that a strong aromatic stacking interaction between the aromatic parts of the benzyl and benzylidene protecting groups in the galactosyl and

• glucosyl moieties was mainly responsible for the observed regioselectivity and anomeric selectivity of the ring-closing glycosylation step. Keywords: intramolecular glycosylation; molecular modeling; prearranged glycosides; Introduction Intramolecular O-glycosidic bond formation of tethered glycosyl

• for the observed regio- and stereochemistry of the reaction, we also performed a molecular modeling study, applying a force-field that was developed for general use in organic and pharmaceutical chemistry [28][29][30]. Results and Discussion For the preparation of the prearranged glycosides 5, we

Photoinduced homolytic C–H activation in N-(4-homoadamantyl)phthalimide

• Nikola Cindro,
• Margareta Horvat,
• Kata Mlinarić-Majerski,
• Axel G. Griesbeck and
• Nikola Basarić

Beilstein J. Org. Chem. 2011, 7, 270–277, doi:10.3762/bjoc.7.36

• availability of H-atoms in the homoadamantane skeleton for the abstraction by the phthalimide, molecular modeling was performed. The geometry of 5 was optimized by DFT B3LYP/6-31G method (Figure 1) [61]. Investigation of the distances between the carbonyl groups of the phthalimide moiety and the H-atoms of the

Oxalyl retro-peptide gelators. Synthesis, gelation properties and stereochemical effects

• Janja Makarević,
• Milan Jokić,
• Leo Frkanec,
• Vesna Čaplar,
• Nataša Šijaković Vujičić and
• Mladen Žinić

Beilstein J. Org. Chem. 2010, 6, 945–959, doi:10.3762/bjoc.6.106

• were identified as the most likely motifs appearing in the gel aggregates. Molecular modeling studies of (S,S)-1a/(S,R)-1a and (S,S)-1b/(S,R)-1b diasteroisomeric pairs revealed a decisive stereochemical influence yielding distinctly different low energy conformations: those of (S,R)-diastereoisomers

• gelation [24][25][26][27][28][29][30][31][58][59][60]. Herein, we provide experimental and molecular modeling evidence that the oxalamide retro-peptides indeed tend to form unidirectional hydrogen bonded assemblies of gelator molecules that adopt fully extended conformations. We also present the evidence

• temperature regime the downfield shifts of the same protons indicate the breaking of intermolecular hydrogen bonds. This conclusion is supported by molecular modeling (see the respective paragraph) which showed that the low energy conformation of (S,R)-1b is similar to those found for bis(amino acid

Synthesis, electronic properties and self-assembly on Au{111} of thiolated (oligo)phenothiazines

• Adam W. Franz,
• Svetlana Stoycheva,
• Michael Himmelhaus and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2010, 6, No. 72, doi:10.3762/bjoc.6.72

• , contact angle measurements, X-ray photoelectron spectroscopy, and infrared reflection absorption spectroscopy (IRRAS) [39], we applied ellipsometry in combination with molecular modeling at the force field and DFT levels of theory for the characterization of SAMs of in situ liberated (oligo)phenothiazinyl

• . Supporting Information Supporting Information File 112: Molecular modeling coordinates of 2a, 2c, 2d, 2e, and 4, cyclic voltammograms of 2a, 2b, 2c, 2d, 2e, and 4, and absorption and emission spectra of 2d and 2e. Acknowledgements The financial support of this work by the Deutsche Forschungsgemeinschaft

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32

• + = 146) was also observed. The formation of a pseudocavity by intramolecular hydrogen bonding in 14 and contribution to the binding of the host’s oxyimino part were suggested by molecular modeling of the ammonium complex. In ammonium ions, where hydrogen atoms arereplaced by organic residues, the

Recognition properties of receptors consisting of imidazole and indole recognition units towards carbohydrates

• Monika Mazik and
• André Hartmann

Beilstein J. Org. Chem. 2010, 6, No. 9, doi:10.3762/bjoc.6.9

• glycosides. It has been shown that both hydrogen bonding and interactions of the carbohydrate CH units with the aromatic rings of the receptors contribute to the stabilization of the receptor–carbohydrate complexes. The molecular modeling calculations, synthesis and binding properties of 4 and 5 towards

• with mono- and disaccharide substrates. Herein, we describe the synthesis, molecular modeling calculations and the binding properties of the compounds 4 and 5. To compare the binding properties of the new compounds with those of the previously published receptors, octyl β-D-glucopyranoside (6a), methyl

• –1. Molecular modeling The formation of hydrogen bonds and CH···π interactions between the binding partners was also suggested by molecular modeling calculations. For example, molecular modeling suggested that all OH groups and the ring oxygen atom of the bound β-galactoside 8b in the complex 4•8b

Synthesis and binding studies of two new macrocyclic receptors for the stereoselective recognition of dipeptides

• Ana Maria Castilla,
• M. Morgan Conn and
• Pablo Ballester

Beilstein J. Org. Chem. 2010, 6, No. 5, doi:10.3762/bjoc.6.5

• introduction of two linkers connecting the two peptide strands affording, a macrocyclic structure. In doing so, we expect that the molecular recognition properties of the designed receptor will also benefit from the macrocyclic effect [17][18][19][20]. Simple molecular modeling studies [21] revealed that a

• explained below. The exploration of the conformational space of both macrocycles, using molecular modeling, indicated the existence of a built-in cavity. These studies also suggested that the reduced conformational flexibility of the receptors avoids the complete collapse of the cavity through the formation

• receptors toward n-C6H13-L-Phe-L-Phe-NH2, with the aim of gaining some information about the geometry of the complex. Molecular modeling suggested that although the formation of an endo-complex in which n-C6H13-L-Phe-L-Phe-NH2 is threaded through the macrocyclic ring of the receptor is plausible, the steric

Ring-alkyl connecting group effect on mesogenic properties of p-carborane derivatives and their hydrocarbon analogues

• Aleksandra Jankowiak,
• Piotr Kaszynski,
• William R. Tilford,
• Kiminori Ohta,
• Adam Januszko,
• Takashi Nagamine and
• Yasuyuki Endo

Beilstein J. Org. Chem. 2009, 5, No. 83, doi:10.3762/bjoc.5.83

• an isostructural series of diesters 16[6] and 18B, and also tetraesters 19 and 20, and a detailed comparative analysis focusing on the impact of the connecting group on mesogenic properties. The analysis is aided by molecular modeling of the pertinent molecular fragments. In addition, we report two

• . Consistent with our previous analysis, the effect is much stronger for p-carboranes (>90 K) than for carbocycles (<80 K) with the typical order: D, C < A < B. Molecular Modeling For a better understanding of the terminal substituent’s impact on the conformational ground state of the molecules, four benzene

An enantiomerically pure siderophore type ligand for the diastereoselective 1 : 1 complexation of lanthanide(III) ions

• Markus Albrecht,
• Olga Osetska,
• Thomas Abel,
• Gebhard Haberhauer and
• Eva Ziegler

Beilstein J. Org. Chem. 2009, 5, No. 78, doi:10.3762/bjoc.5.78

• should be prototypes for further lanthanide(III) complexes with an enterobactine analogue binding situation. Keywords: CD spectroscopy; enterobactin; lanthanide; macrocycles; molecular modeling; Introduction The availability of metal ions for biological systems is essential for growth and function

[3.3]Dithia-bridged cyclophanes featuring a thienothiophene ring: synthesis, structures and conformational analysis

• Sabir H. Mashraqui,
• Yogesh Sanghvikar,
• Shailesh Ghadhigaonkar,
• Sukeerthi Kumar,
• Auke Meetsma and
• Elise Trân Huu Dâu

Beilstein J. Org. Chem. 2009, 5, No. 74, doi:10.3762/bjoc.5.74

• -bridges in 11 as well as other cyclophanes described in the preceding section could be inhibited if the transition state structures have free energies of activation >100 kJ/mol [5]. This aspect is currently being examined using molecular modeling approach. Conclusion In conclusion, we have reported the

Dipyridodiazepinone derivatives; synthesis and anti HIV-1 activity

• Nisachon Khunnawutmanotham,
• Nitirat Chimnoi,
• Arunee Thitithanyanont,
• Patchreenart Saparpakorn,
• Kiattawee Choowongkomon,
• Pornpan Pungpo,
• Supa Hannongbua and
• Supanna Techasakul

Beilstein J. Org. Chem. 2009, 5, No. 36, doi:10.3762/bjoc.5.36

• ][5][6][7][8]. On the basis of molecular modeling analysis on the wild-type (WT) and Y181C HIV-1 RT, it was found that the dipyridodiazepinone derivatives containing an unsubstituted lactam nitrogen and a 2-chloro-8-arylthiomethyl moiety, when compared with 9 [4] (Figure 2) as reference, are effective