Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• [69][70][71]. Moya and co-workers deeply studied the intracellular dynamics and aggregation of glucose-AuNPs by employing fluorescence correlation spectroscopy (FCS) [12]. They demonstrated that GAuNPs were ubiquitous distributed inside the cell as single NP or small aggregates, suggesting a strong

Continuous-flow processes for the catalytic partial hydrogenation reaction of alkynes

• Carmen Moreno-Marrodan,
• Francesca Liguori and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2017, 13, 734–754, doi:10.3762/bjoc.13.73

• catalysis [103][104]. Monolithic reactors may surpass most drawbacks typical of packed-bed systems, including high pressure drops, low contacting efficiency, large distribution of residence times, formation of hot-spots or stagnation zones, which results in poorly controlled fluid dynamics, hence in low

• selectivity trend was explained in terms of both adsorption mode on and relative accessibility to Pd active sites, depending on surface potentials and hindrance of modifiers, on the basis of density functional theory and molecular dynamics calculations. The rationale was summarized in the so-called

Membrane properties of hydroxycholesterols related to the brain cholesterol metabolism

• Malte Hilsch,
• Ivan Haralampiev,
• Peter Müller,
• Daniel Huster and
• Holger A. Scheidt

Beilstein J. Org. Chem. 2017, 13, 720–727, doi:10.3762/bjoc.13.71

• fluorescence techniques [21]. Also, a decreased but still significant effect of the hydroxysterols on lipid condensation compared to native cholesterol was found in molecular dynamics simulations, which is probably caused by an increased tilt angle of the sterols to the membrane normal [8][21]. However, using

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

• /β-CD and 2/β-CD complexes, with the aromatic ring system entering the cavity from the large rim of the cyclodextrin and the alkylammonium chain protruding out of the cavity and facing the secondary OH rim. These features matched those found in the molecular dynamics (MD) simulations in solution and

• . Keywords: amitriptyline; β-cyclodextrin; crystal structure; cyclobenzaprine; molecular dynamics simulations; NOE; Introduction The present paper reports on a multidisciplinary approach [1][2] based on single crystal X-ray diffraction, solution NMR spectroscopy and molecular dynamics (MD) simulations with

• : 2K points acquired in the F2 domain, 512 increments and subsequent zero-filling to 1K to process data. Molecular dynamics simulations The simulations employed InsightII/Discover [15] with the CVFF force field [16]. The structure of molecules 1 and 2 were first subjected to an MD run in vacuo and

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

• Addy Pross and
• Robert Pascal

Beilstein J. Org. Chem. 2017, 13, 665–674, doi:10.3762/bjoc.13.66

• (Figure 1B). These structures therefore result from dissipative self-assembly for which fascinating examples have been provided in the recent literature [19][20][21]. In biology, one of the most typical examples of this kind of assembly processes can be found in the dynamics of the cytoskeleton. However

• above which Raleigh–Bénard instability is observed (Figure 5). The result of convection is, of course, an increase of energy dissipation by the resulting non-linear process, though its emergence depends on the action of gravity and the laws of fluid dynamics. Regarding the origin of life, we suggested

Contribution of microreactor technology and flow chemistry to the development of green and sustainable synthesis

• Flavio Fanelli,
• Giovanna Parisi,
• Leonardo Degennaro and
• Renzo Luisi

Beilstein J. Org. Chem. 2017, 13, 520–542, doi:10.3762/bjoc.13.51

• the basis of computational fluids dynamics (CFD). The simulation results showed that serpentine 3D-structured channels (Figure 2), possessing five turns after each mixing point in a total length of 1 mm, was able to deliver the highest mixing efficiency. The inner volume for the reactor was of 25 μL

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

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

Beilstein J. Org. Chem. 2017, 13, 182–194, doi:10.3762/bjoc.13.21

• . As detailed in the Discussion, this technique is quite rarely used. The results of the 1H Fast MAS NMR experiments provided further structural details of the state of the drug molecule loaded in the CDNS materials. Theoretical Aspects The CP-MAS experiment and CP dynamics Cross-polarization (CP) is a

• nuclei and B1 is the so-called spin-lock field generated by the spectrometer acquisition hardware. The efficiency of the CP process strongly depends on the structural and dynamic properties of the system, in particular molecular conformational changes, rotational dynamics and internuclear distances in

• detected via 1H NMR and discussed in the previous section is likely to involve two IbuH units in the formation of dimers. Dynamics of cross polarization We applied variable contact time (VCT) 1H-13C CP-MAS NMR techniques to study the CP kinetics of both the CDNS polymers. As an example, the array of 13C CP

Benzothiadiazole oligoene fatty acids: fluorescent dyes with large Stokes shifts

• Lukas J. Patalag and
• Daniel B. Werz

Beilstein J. Org. Chem. 2016, 12, 2739–2747, doi:10.3762/bjoc.12.270

• sufficient to understand membrane dynamics and function. Often membrane domains are formed in which certain lipids, glycolipids or proteins are enriched [2][3][4]. Such domains – also called lipid rafts – do not only differ in their chemical composition, but also show different physical properties (e.g

• -dipyrromethene) [11][12], BOIMPY- (bis(borondifluoride)-8-imidazodipyrromethene) [13] and pyrene-labeled fatty acids [14]. Of course, all these alterations might also affect the membrane structure and its dynamics. While the NBD-fluorophore suffers from unsuitable polarity, a pyrene motif disrupts the unpolar

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• , agonists, inhibitors, etc. of a target) design. Molecular dynamics (MD) simulations are frequently used in SBDD to give insights into not only how ligands bind with target proteins but also the pathways of interaction and to account for target flexibility. This is especially important when drug targets are

• AMBER [120] (Assisted Model Building and Energy Refinement) which have been built mainly for molecular dynamics simulations. The molecular docking program DOCK [121] uses force-field based scoring functions derived from molecular dynamics force-field AMBER. Empirical scoring functions Empirical scoring

• , these fragments can be joined to obtain a possible new drug molecule. In the SILCS (site identification by ligand competitive saturation) method, molecular dynamics simulations are used to identify fragments that bind to a target [161][162]. SILCS uses explicit molecular dynamics simulations where the

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• cells. Unfortunately, only few papers have studied the dynamics of this process on cells. For instance, the kinetics of cholesterol efflux have been examined in different cell lines such as fibroblasts [117], human erythrocytes [122], rat cerebellar neurons [123], differentiated human neurons and

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

• Doctoral Program “Receptor Dynamics”.

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

• conformational dynamics, we further carried out a detailed computational study at the M06-2X level of theory [22] for the three acrylates 6a–c. This meta-GGA functional, developed by Truhlar [23] has been shown to be one of the approaches of choice to model noncovalent interactions [9]. After a complete

• -stacking interactions. To the best of our knowledge this is the first report that provides experimental and computational evidences to understand the effect of such intramolecular interactions in the conformational dynamics of the system. This equilibrium, that involves a fast s-cis/s-trans exchange and a

Synthesis and fluorosolvatochromism of 3-arylnaphtho[1,2-b]quinolizinium derivatives

• Phil M. Pithan,
• David Decker,
• Manlio Sutero Sardo,
• Giampietro Viola and
• Heiko Ihmels

Beilstein J. Org. Chem. 2016, 12, 854–862, doi:10.3762/bjoc.12.84

• -methylquinolinium have a strong emphasis on the dynamics and the charge separation in the excited state. Therefore, the work presented here may initiate investigations along these lines to further understand and fully explore the useful solvatochromic properties of this class of compounds. Conclusion In summary, we

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