Antibiotics from predatory bacteria

• Juliane Korp,
• María S. Vela Gurovic and
• Markus Nett

Beilstein J. Org. Chem. 2016, 12, 594–607, doi:10.3762/bjoc.12.58

• is among the ecological forces, which drive the diversity and dynamics of microbial consortia [1][2][3]. While protozoa and nematodes are widely known as bacterivores [4][5], the existence of predatory prokaryotes is often neglected despite the abundance of the latter and their early occurrence in

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

• transformations. Cautions for analyzing both experimental and theoretical data on carbocation rearrangements are included throughout. Keywords: carbocation; density functional theory; dynamics; mechanism; terpene; Review Introduction to terpene forming carbocation rearrangements Terpene natural products display

• [31][32][33][34]. To acquire evidence for non-statistical dynamic effects, molecular dynamics (MD) simulations are run for a statistically relevant number of trajectories (typically on the order of hundreds or thousands, depending on the system and the starting point for trajectories) [35][36]. The

• most common modern technique for computing dynamics trajectories for organic reactions is the method of direct dynamics. With direct dynamics, instead of solving for a PES analytically, each point along a trajectory is calculated numerically “as needed” or “on-the-fly”. A quantum chemical program

Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

• Eric V. Anslyn

Beilstein J. Org. Chem. 2016, 12, 362–376, doi:10.3762/bjoc.12.40

• medical school, research was one of my pursuits from freshman year throughout my undergraduate career. The project entailed the use of variable-temperature NMR to measure the dynamics of ligand migration in trimetallic osmium clusters [22][23]. Dr. Rosenberg was an inspirational figure, and his pursuit

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

• have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations

• nanoaggregates even in apolar solvents. Keywords: aggregation; amphiphilic cyclodextrins; molecular dynamics; nanoparticles; self-assembly; simulations; Introduction Amphiphilic cyclodextrins (aCD) are a class of molecules highly investigated for their self-assembly properties and inherent potential

• shown in Scheme 1b (n = 1), dissolved in an apolar solvent and an atomistic Molecular Dynamics study of a model compound (n = 0 in Scheme 1) carried out in vacuo. In particular, the latter approach aims to model the bottom-up aggregation of the model aCD molecules, an approach that was started in [11

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 2D DOSY spectra was processed by means of the Bruker Dynamics Center software (version 2.1.9). The diffusion constants were calculated by exponential fitting of the data belonging to individual columns of the 2D matrix. The software gave the mean value of the diffusion coefficient. The Kf values

Polydisperse methyl β-cyclodextrin–epichlorohydrin polymers: variable contact time ¹³C CP-MAS solid-state NMR characterization

• Isabelle Mallard,
• Davy Baudelet,
• Franca Castiglione,
• Monica Ferro,
• Walter Panzeri,
• Enzio Ragg and
• Andrea Mele

Beilstein J. Org. Chem. 2015, 11, 2785–2794, doi:10.3762/bjoc.11.299

• recognition sites for the template molecule. As a matter of fact, high-resolution solid-state NMR is a powerful tool to characterize the structure of polymers [23][24] and to study their dynamics [25][26]. Crini has reported previously a solid-state NMR spectroscopy study [27][28] of β-cyclodextrin polymers

• different amounts of imprinting agent, as in the present case. We herein propose an approach based on solid-state 13C NMR techniques such as variable contact time cross-polarization magic angle spinning with dipolar decoupling (VCP-MAS) to describe these new materials. The dynamics of cross-polarization can

• of the two experimental spectra reveals that no chemical shift variations are observed. Consequently, no relevant structural modification occurs on the β-CD moiety during the polymerization process. Dynamics of cross polarization – theoretical description Important features of the dynamic behavior of

Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin

• Waratchada Sangpheak,
• Jintawee Kicuntod,
• Roswitha Schuster,
• Thanyada Rungrotmongkol,
• Peter Wolschann,
• Nawee Kungwan,
• Helmut Viernstein,
• Monika Mueller and
• Piamsook Pongsawasdi

Beilstein J. Org. Chem. 2015, 11, 2763–2773, doi:10.3762/bjoc.11.297

• hesperetin with cyclodextrins (β-CD and DM-β-CD) were theoretically investigated by molecular dynamics simulation. The free energy values obtained suggested a more stable inclusion complex with DM-β-CD. The vdW force is the main guest–host interaction when hesperetin binds with CDs. The phase solubility

• physical properties and biological activities of hesperetin and naringenin through complexation with cyclodextrins. Computational tools (molecular dynamics simulation) were adopted to first predict the stability of flavanones/CDs inclusion complexes. Consequently, the experimental phase solubility and

• values showed the same trend with values from molecular dynamics simulation that complexing with DM-β-CD was more effective than with β-CD, and the values obtained were in good agreement with the previous report [42]. These results suggested that both flavanones bind to and interact with DM-β-CD stronger

Smart molecules for imaging, sensing and health (SMITH)

• Bradley D. Smith

Beilstein J. Org. Chem. 2015, 11, 2540–2548, doi:10.3762/bjoc.11.274

• was vital for efficient rotaxane formation. The interlocked molecule retained its salt binding ability and association of the ions modulated the rotaxane structural dynamics [33][34]. Squaraine rotaxanes The interests in molecular imaging and rotaxane structures merged in 2005 with the discovery and

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

• report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics

• correlating their structures with the pharmaceutical properties. Keywords: aggregation; amphiphilic cyclodextrins; micelles; molecular dynamics simulations; nanoparticles; self-assembly; Introduction Inclusion complexes with supramolecular structures formed by native or modified cyclodextrins (CDs) are

• supramolecular aggregates was seldom, if ever, considered, apart from the above-mentioned reference [35]. To improve our understanding of the factors driving the formation of aCD molecular assemblies, we describe in this paper an atomistic molecular dynamics investigation of a model compound of a non-ionic aCD

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

• anion affinity and selectivity of a neutral anion receptor, bis(cyclopeptide) [17]. Molecular dynamics (MD) simulations can give important insights into the energetics of structural interactions. The hydrated structure of β-CD in aqueous solution [18] and those showing host–guest interactions between

• given in Table 1. Details of molecular dynamics simulations In the present study, all MD simulations were performed using the SANDER module of the Amber10 software package in accordance with the recently reported MD simulations of flavonoid/β-CD inclusion complexes in water [34][35]. The particle-mesh

• then heated to 300 K within the 500 steps of relaxation time using the Canonical Ensemble (NVT) algorithm at constant volume up to 1 g/mL of water density. Finally, the MD simulations were performed at 1 atm and 300 K for 20 ns. The structural dynamics over simulation time were monitored by root mean

The marine sponge Agelas citrina as a source of the new pyrrole–imidazole alkaloids citrinamines A–D and N-methylagelongine

• Christine Cychon,
• Ellen Lichte and
• Matthias Köck

Beilstein J. Org. Chem. 2015, 11, 2029–2037, doi:10.3762/bjoc.11.220

• Museum, University of Amsterdam (The Netherlands). Sponge identification was kindly conducted by W. H. de Weerdt and Dr. R. W. M. van Soest, Institute for Biodiversity and Ecosystem Dynamics, Zoölogical Museum, University of Amsterdam, The Netherlands (new address of RWMvS: Netherlands Centre for

Asymmetric 1,4-bis(ethynyl)bicyclo[2.2.2]octane rotators via monocarbinol functionalization. Ready access to polyrotors

• Cyprien Lemouchi and
• Patrick Batail

Beilstein J. Org. Chem. 2015, 11, 1881–1885, doi:10.3762/bjoc.11.202

• )bicyclo[2.2.2]octane rotators. The good yields allow the large amounts required for self-assembly and subsequent investigations of the dynamics of the rotors in the solid state to be readily prepare. The chemistry, physical chemistry and materials chemistry and physics of asymmetric rotors and their

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

• bond of C2H4 is nearly perpendicular to the Ru–methylidene bond, whereas in the bigger substrate the tether forces the coordinated C=C bond to be almost aligned with the Ru–alkylidene bond. However, the molecular dynamics simulations (vide infra) clearly indicate that in the trans geometries the C2H4

Donor–acceptor type co-crystals of arylthio-substituted tetrathiafulvalenes and fullerenes

• Xiaofeng Lu,
• Jibin Sun,
• Shangxi Zhang,
• Longfei Ma,
• Lei Liu,
• Hui Qi,
• Yongliang Shao and
• Xiangfeng Shao

Beilstein J. Org. Chem. 2015, 11, 1043–1051, doi:10.3762/bjoc.11.117

• thought to be the cooperative consequence of the molecular geometry of Ar-S-TTF, the shape and size of the fullerene molecule, the solvent adduct, and the crystallization dynamics. The donor–acceptor interaction mode and the packing motif of the fullerenes largely depend on the composition of the co

Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands

• Katharina Koschek,
• Vedat Durmaz,
• Oxana Krylova,
• Marek Wieczorek,
• Shilpi Gupta,
• Martin Richter,
• Alexander Bujotzek,
• Christina Fischer,
• Rainer Haag,
• Christian Freund,
• Marcus Weber and
• Jörg Rademann

Beilstein J. Org. Chem. 2015, 11, 837–847, doi:10.3762/bjoc.11.93

• precipitation. Experimental results were compared with parameters obtained from molecular dynamics simulations in order to understand the observed differences between the three carrier materials. In summary, the more rigid and condensed peptide–polymer conjugates based on the dextran scaffold seem to be

• understanding of structure–activity relationships of polymeric ligands. For this purpose, the thermodynamics and the stoichiometry of protein binding events were determined experimentally for all multivalent ligands. Finally, atomistic molecular dynamics simulations were conducted in order to rationalize the

• bivalent binding mode for the complex of Dex-2 and tandem-WW-FBP21, which is supported also by the solubility of the non-crosslinked peptide-polymer–protein complex. Molecular dynamics simulations of multivalent ligands In order to better understand our experimental observations regarding binding

Adsorption mechanism and valency of catechol-functionalized hyperbranched polyglycerols

• Stefanie Krysiak,
• Qiang Wei,
• Klaus Rischka,
• Andreas Hartwig,
• Rainer Haag and
• Thorsten Hugel

Beilstein J. Org. Chem. 2015, 11, 828–836, doi:10.3762/bjoc.11.92

• possible and allows for good cohesion between the layers of this material. Here we investigated the molecular details, valency and dynamics on how molecules with multiple DOPA groups adhere to surfaces. Results and Discussion The publication by Lee et al. [11] sparked considerable interest and since then

Synthesis of carbohydrate-scaffolded thymine glycoconjugates to organize multivalency

• Anna K. Ciuk and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2015, 11, 668–674, doi:10.3762/bjoc.11.75

• [6]. This work is based on the idea that changes of ligand orientation as well as changes of their conformational availability are regulating parameters in carbohydrate recognition, in particular on the cell surface. Indeed, we have formerly shown that the molecular dynamics of glycodendrimers

• galectin-mediated organization of cell surface glycoconjugates influences glycan dynamics and essential biological processes like signaling [8]. Therefore, in order to advance our understanding of carbohydrate-mediated biological response, we are seeking further molecular architectures that allow us

• organizing the multivalency of sugar ligands. We planned for a divalent system to start with, in which the dynamics of two at first flexible branches can be controlled by an intramolecular [2 + 2] cycloaddition reaction (Figure 1A). In order to control the [2 + 2] cycloaddition process, it was planned to

TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy

• Dnyaneshwar B. Gophane and
• Snorri Th. Sigurdsson

Beilstein J. Org. Chem. 2015, 11, 219–227, doi:10.3762/bjoc.11.24

• labels; structure-dependent dynamics; Introduction The knowledge about structures and conformational dynamics of nucleic acids, as well as other biomolecules, is essential to understand their biological functions, including interactions with other molecules. The exact atom-to-atom structural information

• ][41][42], non-native base-pairing properties of nucleobases [43][44][45][46] and their dynamics [42][47][48]. Fluorescence spectroscopy, using environmentally sensitive fluorescent nucleosides has been used for detection of local structural perturbations [49][50][51][52][53][54][55][56][57], including

• the investigation of single-base mismatches [51][54][56][58][59], abasic sites [60] as well as nick sites in duplex DNA [61], and ligand-induced folding of riboswitches [62][63]. Continuous wave (CW) EPR spectroscopy can be used for the determination of structure-dependent dynamics based on the line

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

• equilibrium of articulated rods The fundamental feature of articulated rods is the restricted conformational space with two dominating species: a stretched and a folded conformation. This feature was concluded from Molecular Dynamics (MD) simulation revealing a bimodal distribution of the end-to-end distance

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• . The obtained results [92][93][94] stress the importance of DNA-basepair dynamics for the electronic transfer processes in DNA-stacks. The efficiency of transfer is rather more controlled by motions of chromophores involved in aromatic stacking of DNA-reporter complex than with rigid aryl-stacking

Synthesis and characterization of a new photoinduced switchable β-cyclodextrin dimer

• Florian Hamon,
• Claire Blaszkiewicz,
• Marie Buchotte,
• Estelle Banaszak-Léonard,
• Hervé Bricout,
• Sébastien Tilloy,
• Eric Monflier,
• Christine Cézard,
• Laurent Bouteiller,
• Christophe Len and
• Florence Djedaini-Pilard

Beilstein J. Org. Chem. 2014, 10, 2874–2885, doi:10.3762/bjoc.10.304

• calculations, the geometrical force field parameters needed for molecular dynamics simulations were derived. Molecular dynamics simulations performed on the two configurations of AZO-CDim 1 highlighted the rigidity of the linker, which governs the relative position of the two CD cavities. The trajectories

• objects in solution. The experimental data strongly suggests that AZO-CDim 1 is a switchable host which forms two different inclusion complexes with this ditopic guest. The structural analyses of the molecular dynamics trajectories of the two configurations of the AZO-CDim 1 systems enable us to draw some

• moiety as the linker [36]. At this stage, based on the molecular dynamics study, at least two supramolecular polymers can be considered: the first is linear, as often described in the literature [43][44] (Figure 8b), and the second is cyclic (Figure 8c). Furthermore, it is possible that such linear or

Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

• Bodee Nutho,
• Wasinee Khuntawee,
• Chompoonut Rungnim,
• Piamsook Pongsawasdi,
• Peter Wolschann,
• Alfred Karpfen,
• Nawee Kungwan and
• Thanyada Rungrotmongkol

Beilstein J. Org. Chem. 2014, 10, 2789–2799, doi:10.3762/bjoc.10.296

• to investigate the preferential binding mode and encapsulation of the flavonoid fisetin in the nano-pore of β-cyclodextrin (β-CD) at the molecular level using various theoretical approaches: molecular docking, molecular dynamics (MD) simulations and binding free energy calculations. The molecular

• complexes. In addition, the quantum mechanics calculations with M06-2X/6-31G(d,p) clearly showed that both solvation effect and BSSE correction cannot be neglected for the energy determination of the chosen system. Keywords: cyclodextrin; fisetin; flavonoid; MM-PBSA; molecular dynamics simulation; QM-PBSA

• stability against exposure to strong UV light and high temperatures [24][25]. In recent years, computational approaches have played a significant role in monitoring inclusion complexation between cyclodextrin and guest molecules [26][27] at the molecular level [28][29]. Molecular dynamics (MD) simulations

Anomalous diffusion of Ibuprofen in cyclodextrin nanosponge hydrogels: an HRMAS NMR study

• Monica Ferro,
• Franca Castiglione,
• Carlo Punta,
• Lucio Melone,
• Walter Panzeri,
• Barbara Rossi,
• Francesco Trotta and
• Andrea Mele

Beilstein J. Org. Chem. 2014, 10, 2715–2723, doi:10.3762/bjoc.10.286

• used to investigate transport phenomena in heterogeneous systems endowed with liquid-like dynamics by applying pulsed field gradient spin echo (PGSE) methodologies under magic-angle spinning conditions [23]. This point is of great interest in the field of controlled release of active pharmaceutical

• fitting procedures were done by Dynamics Center software (2.1.8 version) (Bruker). The experimental error is between 2 and 3%. TEM Images were recorded on a Transmission Electron Microscope Philips CM200 FEG at 200 kV electron accelerating potential. CDNSEDTA 1:4 and CDNSEDTA 1:8 were swollen with a

Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• values of ≈5 × 104 kHz. Further experiments concerning a multiple compartment chamber with a common aqueous sub-phase, as well as a thermostated device for a suppression of nonspecific base pairing are underway [15]. Moreover, ab initio molecular-dynamics- (AIMD)- and ab initio Monte-Carlo- (AIMC

Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support

• Alejandro Gimenez Molina,
• Amit M. Jabgunde,
• Pasi Virta and
• Harri Lönnberg

Beilstein J. Org. Chem. 2014, 10, 2279–2285, doi:10.3762/bjoc.10.237

• , dynamics of chain invasion and recognition by small molecular entities [6][7][8][9][10]. The quantities of short RNA sequences required for such studies are often larger than what can easily be obtained by lab-scale solid phase synthesis. In other words, there seems to be a need for a straightforward