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

• development of an enzymatic bioreaction and found that the dynamics of a biochemical reaction can be studied in a few seconds [35]. Although many promising routes have been developed for the synthesis of chiral α-amino alcohols, these often depend on the use of toxic and expensive chiral ligands coupled to

Structure elucidation of β-cyclodextrin–xylazine complex by a combination of quantitative ¹H–¹H ROESY and molecular dynamics studies

• Syed Mashhood Ali,
• Kehkeshan Fatma and
• Snehal Dhokale

Beilstein J. Org. Chem. 2013, 9, 1917–1924, doi:10.3762/bjoc.9.226

• , could be obtained. We calculated the peak intensity ratio from the inter-proton distances for the most stable conformations obtained by molecular dynamics studies in vacuum. The results show that highly accurate structural information can be deduced efficiently by the combined use of quantitative ROESY

• and molecular dynamics analysis. On the other hand, a ROESY spectrum with no spin diffusion can only compliment an averaged ensemble conformation obtained by molecular dynamics which is generally considered ambiguous. Keywords: β-cyclodextrin; inclusion complex; ROESY; simulation studies; xylazine

• here the study of the complexation of β-CD with xylazine (XZ) (Figure 1) in aqueous medium by NMR spectroscopy and molecular dynamics. Xylazine has two rings, one substituted benzene ring which can only partially penetrate the CD cavity due to the presence of two methyl groups and a heterocyclic ring

True and masked three-coordinate T-shaped platinum(II) intermediates

• Manuel A. Ortuño,
• Salvador Conejero and
• Agustí Lledós

Beilstein J. Org. Chem. 2013, 9, 1352–1382, doi:10.3762/bjoc.9.153

• at work in solution. Recently, ab initio molecular dynamics (AIMD) simulations of some representative T-shaped Pt(II) complexes (T5b, A2b and A11a), performed in explicit dichloromethane solvent, have provided a detailed description of the mechanism by which the equivalence of signals takes place

• [106]. Simulations showed that the dynamics of the agostic interaction in solution strongly depends on the complex. Contingent upon the strength of the agostic interaction and the flexibility of the ligand, several events related with the occupation of the fourth coordination site by an agostic bond

Photoionisation of the tropyl radical

• Kathrin H. Fischer,
• Patrick Hemberger,
• Andras Bodi and
• Ingo Fischer

Beilstein J. Org. Chem. 2013, 9, 681–688, doi:10.3762/bjoc.9.77

• Kathrin H. Fischer Patrick Hemberger Andras Bodi Ingo Fischer Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland Süd, 97074 Würzburg, Germany Molecular Dynamics Group, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland 10.3762/bjoc.9.77 Abstract We present a

A computational study of base-catalyzed reactions of cyclic 1,2-diones: cyclobutane-1,2-dione

• Nargis Sultana and
• Walter M. F. Fabian

Beilstein J. Org. Chem. 2013, 9, 594–601, doi:10.3762/bjoc.9.64

• rearrangements of biacetyl and benzil [11]. Car–Parrinello molecular dynamics simulations of the hydrolysis of formamide in basic solution indicated that the traditional view of attack by hydroxide anion rather than a first-solvation-shell water molecule is more likely; however, the more powerful electrophile

A new intermediate in the Prins reaction

• Shinichi Yamabe,
• Takeshi Fukuda and
• Shoko Yamazaki

Beilstein J. Org. Chem. 2013, 9, 476–485, doi:10.3762/bjoc.9.51

• . Dynamical calculations of a classical trajectory using the atom-centered density matrix propagation molecular dynamics model on the four TSs were carried out, and results of IRC calculations were confirmed by them. Keywords: DFT calculations; hemiacetal intermediate; hydrogen bond; Prins reaction

• to confirm the obtained TS characters, dynamical calculations of a classical trajectory calculation using the atom-centered density matrix propagation molecular dynamics (ADMP) model [35][36][37] on TSs were carried out. Geometries of the TSs at 2000 steps of 0.1 femtoseconds (10−15 seconds) were

New GABA amides activating GABA_A-receptors

• Peter Raster,
• Andreas Späth,
• Svetlana Bultakova,
• Pau Gorostiza,
• Burkhard König and
• Piotr Bregestovski

Beilstein J. Org. Chem. 2013, 9, 406–410, doi:10.3762/bjoc.9.42

• Peter Raster Andreas Spath Svetlana Bultakova Pau Gorostiza Burkhard Konig Piotr Bregestovski Institute of Organic Chemistry, University of Regensburg, D-93040 Regensburg, Germany Inserm-U1106, Brain Dynamics Institute, Mediterranean University, 13005 Marseille, France Institute for Bioengineering

Spin state switching in iron coordination compounds

• Philipp Gütlich,
• Ana B. Gaspar and
• Yann Garcia

Beilstein J. Org. Chem. 2013, 9, 342–391, doi:10.3762/bjoc.9.39

• [135][136]. The possibility of investigating spin fluctuation rates was established with the classical iron(II) complex [Fe(phen)2(NCS)2], polymorph I [135][136]. In another case, fast dynamics have been revealed in the HS regime of the ST coordination polymer [Fe(NH2trz)3](NO3)2 (NH2trz = 4-amino

A new synthetic protocol for coumarin amino acid

• Xinyi Xu,
• Xiaosong Hu and
• Jiangyun Wang

Beilstein J. Org. Chem. 2013, 9, 254–259, doi:10.3762/bjoc.9.30

• the dye BODIPY-Fl to study the dynamics of protein–protein interactions [2]. Wang and co-workers genetically incorporated 1a to a position near to amino acids, which can be phosphorylated to investigate how phosphorylation affects the fluorescence properties of 1a, and the variation in the

Presence or absence of a novel charge-transfer complex in the base-catalyzed hydrolysis of N-ethylbenzamide or ethyl benzoate

• Shinichi Yamabe,
• Wei Guan and
• Shigeyoshi Sakaki

Beilstein J. Org. Chem. 2013, 9, 185–196, doi:10.3762/bjoc.9.22

• -centered density-matrix-propagation molecular dynamics (ADMP) model [57][58][59] were also conducted. Relative energies (ΔEs) and Gibbs free ones (ΔGs) were obtained by single-point calculations of RB3LYP/6-311++G(d,p) {SCRF = PCM, solvent = water} on the RB3LYP/6-31(+)G(d) geometries and their ZPVE and

• . The trajectory calculation may give a different result, if the potential surface at the OH− addition step is shallow. In order to check this point, the ADMP molecular dynamics calculation was made starting from TS1(es) of the ester n = 16. After 800 femtoseconds, the resultant geometry is shown in the

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

• Jutta Erika Helga Köhler and
• Nicole Grczelschak-Mick

Beilstein J. Org. Chem. 2013, 9, 118–134, doi:10.3762/bjoc.9.15

• investigated by three different theoretical methods: classical quantum mechanics (QM) on AM1 and on the BP/TZVP-DISP3 level of approximation, and thirdly by classical molecular dynamics simulations (MD) at different temperatures (120 K and 273 to 300 K). The hydrogen bonds at the larger O2/O3 rim of empty β

• certainly no longer displayed the highly ordered hydrogen bonds of β-CD and benzene occupied many different positions inside the cavity, before it left the β-CD finally at its O2/O3 side. Keywords: AM1; benzene; COSMO-RS; cyclodextrin; hydrogen bonds; inclusion complex; molecular dynamics; quantum

• ). The β-CD dimers are connected with hydrogen bonds on their O2/O3 sides (Figure 1). Investigations of such “flat energy hypersurfaces” due to hydrogen bonds and noncovalent interactions demand several theoretical methods to capture the entire network of forces on which they rely. Molecular dynamics

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

• residues [24]. The end-to-end distance changes expected upon photoisomerization of the resulting crosslink were estimated by molecular dynamics methods. Figure 1 shows models of compound 2 in trans,trans, trans,cis, and cis,cis-isomeric states. These simulations indicate that the trans,trans and cis,cis

• -isomers (force constant 16). Molecular dynamics runs were performed in vacuo, essentially as described previously [36], with a distance-dependent dielectric constant, and 1–4 scale factors of 0.833 for electrostatic and 0.5 for van der Waals interactions, a step size of 1 fs and 300 K as the simulation

Hydrophobic analogues of rhodamine B and rhodamine 101: potent fluorescent probes of mitochondria in living C. elegans

• Laurie F. Mottram,
• Safiyyah Forbes,
• Brian D. Ackley and
• Blake R. Peterson

Beilstein J. Org. Chem. 2012, 8, 2156–2165, doi:10.3762/bjoc.8.243

• of mitochondria in vivo, including visualization of the dynamics of fusion and fission of these organelles in the germline of living animals. Results and Discussion Synthesis of fluorophores As shown in Scheme 1, the triarylmethane scaffolds of HRB 9 and HR101 10 were synthesized by condensation of

• here is the ability to examine mitochondrial fusion and fission dynamics in the germline of living C. elegans after acute treatment with the hydrophobic rhodamine analogues HRB 9 and HR101 10. In this tissue, genetically encoded proteins are unsuitable for imaging of mitochondria, because transgenes

• of the HRB 9 and HR101 10 fluorophores. Partition constants of fluorophores. Supporting Information Supporting Information File 336: Supplementary time-lapse confocal microscopy video showing dynamics of mitochondrial fusion and fission in a living adult C. elegans animal imaged after treatment with

Chemical modification allows phallotoxins and amatoxins to be used as tools in cell biology

• Jan Anderl,
• Hartmut Echner and
• Heinz Faulstich

Beilstein J. Org. Chem. 2012, 8, 2072–2084, doi:10.3762/bjoc.8.233

• .8.233 Abstract Phallotoxins inhibit the dynamics of microfilaments in cells and lead to apoptosis. Due to poor cellular uptake these effects cannot be studied in live cells, even at millimolar toxin concentrations, nor can phalloidin be used for the elimination of tumor cells. Uptake is greatly enhanced

• still under investigation, may explain the continuing interest in these two kinds of specific inhibitors. Phalloidin has been used to study actin dynamics in vitro [1], and in microscopic studies after microinjection into single cells [4]. Beside such experiments phalloidin conjugated to fluorescent

Peptides presenting the binding site of human CD4 for the HIV-1 envelope glycoprotein gp120

• Julia Meier,
• Kristin Kassler,
• Heinrich Sticht and
• Jutta Eichler

Beilstein J. Org. Chem. 2012, 8, 1858–1866, doi:10.3762/bjoc.8.214

• through cyclization, as evidenced by binding assays, as well as through molecular-dynamics simulations of peptide–gp120 complexes. The specificity of the peptide–gp120 interaction was demonstrated by using peptide variants, in which key residues for the interaction with gp120 were replaced by alanine or D

• binding properties of CD4-M1 and CD4-M2, molecular dynamics (MD) simulations of the peptides in complex with gp120 were carried out and compared to a simulation of the CD4–gp120 complex. Analysis confirmed that the linear peptide CD4-M1 is more flexible than the respective region in CD4 (Figure 5A

• site of gp120. Conclusion The binding behaviour of synthetic CD4 mimetic peptides was shown to be strongly related to their conformational flexibility, as demonstrated by binding assays in conjunction with molecular-dynamics simulations. These results illustrate the utility of peptide mimics of protein

Synthesis of 5-oxyquinoline derivatives for reversal of multidrug resistance

• Torsten Dittrich,
• Nils Hanekop,
• Nacera Infed,
• Lutz Schmitt and
• Manfred Braun

Beilstein J. Org. Chem. 2012, 8, 1700–1704, doi:10.3762/bjoc.8.193

• . Acknowledgements We are grateful to the Volkswagenstiftung for generous support of the project “Conformational dynamics of the multidrug resistance ABC-transporter LmrA modulated by substrates and inhibitors”.

Molecular solubilization of fullerene C₆₀ in water by γ-cyclodextrin thioethers

• Hai Ming Wang and
• Gerhard Wenz

Beilstein J. Org. Chem. 2012, 8, 1644–1651, doi:10.3762/bjoc.8.188

• still greater van der Waals diameter of 1.0 nm [2]. Molecular dynamics studies strongly favour a sandwich-like structure of the complex, in which two γ-CD molecules tightly interact through hydrogen bonds between their secondary rims and in which C60 is situated in the middle at the widest sites of both

Impact of cyclodextrins on the behavior of amphiphilic ligands in aqueous organometallic catalysis

• Hervé Bricout,
• Estelle Léonard,
• Christophe Len,
• David Landy,
• Frédéric Hapiot and
• Eric Monflier

Beilstein J. Org. Chem. 2012, 8, 1479–1484, doi:10.3762/bjoc.8.167

• helped explain the catalytic results. The presence of RAME-β-CD in the aqueous compartment improved the phosphane-based aggregate dynamics. The exchanges between the hydrophobic substrate-containing aggregate core and the catalyst-containing aqueous phase were then greatly favored, resulting in an

• structure was slightly altered because of the interaction of RAME-β-CD with the micelle constituents, especially the inclusion process (Figure 4). As the micelle dynamics was improved, the exchanges between the hydrophobic substrate-containing micelle core and the catalyst-containing aqueous solution were

• values over 200 000 M−1 were measured. With the RAME-β-CD/interaction being strong, the aggregate dynamics was greatly favored at a CD/phosphane ratio of around 1:1 (high TOF). In that case, the intensity of the aggregate destructuring process was stronger at a higher CD/phosphane ratio (low TOF) as a

Partial thioamide scan on the lipopeptaibiotic trichogin GA IV. Effects on folding and bioactivity

• Marta De Zotti,
• Barbara Biondi,
• Cristina Peggion,
• Matteo De Poli,
• Haleh Fathi,
• Simona Oancea,
• Claudio Toniolo and
• Fernando Formaggio

Beilstein J. Org. Chem. 2012, 8, 1161–1171, doi:10.3762/bjoc.8.129

• -range connectivities, diagnostic of the presence of mixed 310-/α-helical conformations. The conformational properties of ψ[CS-NH]9 were further investigated by simulated annealing (SA) and restrained molecular dynamics (MD) calculations. A total of 69 interproton distance restraints, derived from the

• was used. The MD calculations involved a minimization stage of 100 cycles, followed by SA and refinement stages. The SA consisted of 30 ps of dynamics at 1,500 K (10,000 cycles, in 3 fs steps) and of 30 ps of cooling from 1,500 to 100 K in 50 K decrements (15,000 cycles, in 2 fs steps). The SA

Formation of smectic phases in binary liquid crystal mixtures with a huge length ratio

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

Beilstein J. Org. Chem. 2012, 8, 1118–1125, doi:10.3762/bjoc.8.124

• phase of the longer mesogen was identified as a smectic F phase. Keywords: bidispersity; liquid crystals; phase diagrams; smectic phases; smectic F phase; structure and dynamics; Introduction The mixing of different liquid crystals is a common technique to tailor their properties for specific

Control over molecular motion using the cis–trans photoisomerization of the azo group

• Estíbaliz Merino and
• María Ribagorda

Beilstein J. Org. Chem. 2012, 8, 1071–1090, doi:10.3762/bjoc.8.119

• that distances the porphyrin units, causing a mechanical spin rotation in the bis-isoquinoline molecule similar to a pedal. This device is effective if the porphyrin–Zn and bis-isoquinoline units remain associated during the photoisomerization, i.e., the dynamics of dissociation between these units is

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

• subjected to molecular dynamics cycles and subsequent reoptimization [28]. The most stable minimized structures of the macrocycles are shown in Figure 3, in which the distances between the four hydrogen atoms of the NH amide groups within each macrocycle are reported (in angstroms). The two macrocycles

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

Beilstein J. Org. Chem. 2012, 8, 915–929, doi:10.3762/bjoc.8.104

• adopt several conformations with different populations. The conformational space of a glycan can be analyzed by molecular dynamics (MD) simulations (see in the following) [100]. For this purpose the models generated by the GLYCAM Biomolecules Builder are convenient, as this tool already provides 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

• were determined by an enzyme-linked lectin assay (ELLA), resulting in IC50 values in the low-micromolar/high-nanomolar range. A trivalent ligand has a remarkable IC50 value of 220 nM. Molecular dynamics calculations based on published X-ray crystal structures of WGA-ligand complexes provide an

An easily accessible sulfated saccharide mimetic inhibits in vitro human tumor cell adhesion and angiogenesis of vascular endothelial cells

• Grazia Marano,
• Claas Gronewold,
• Martin Frank,
• Anette Merling,
• Christian Kliem,
• Sandra Sauer,
• Manfred Wiessler,
• Eva Frei and
• Reinhard Schwartz-Albiez

Beilstein J. Org. Chem. 2012, 8, 787–803, doi:10.3762/bjoc.8.89

• [17]. Molecular dynamics simulations have shown that furans with two saccharides bound to hydroxymethyl groups show a nearly perfect alignment with each of the three terminal saccharides in Lewisy [15], another member of the Lewis histo blood group family, which is involved in tumor cell adhesion [18

• interference with the adhesion of melanoma (Figure 2) and endothelial cells (Figure 7) to the extracellular matrix protein. In order to investigate the molecular interactions of GSF in the RGD binding site of the integrin molecule in more detail we performed molecular dynamics (MD) simulation in explicit water

• , 2H, CH2OSO3), 7.65 (s, 1H, H5), 7.68 (s, 1H, H2); 13C NMR (63 MHz, DMSO-d6) δ 58.4, 60.5, 60.6 (CH2OSO3, CH2OGal, C6´), 68.2, 70.6, 73.4, 75.2 (C2´, C3´, C4´, C5´), 102.6 (C1´), 121.3, 121.7 (C3, C4), 141.49, 141.52 (C2, C5). In silico blind-docking and molecular dynamics simulations A flexible