The effect of milling frequency on a mechanochemical organic reaction monitored by in situ Raman spectroscopy

• Patrick A. Julien,
• Ivani Malvestiti and
• Tomislav Friščić

Beilstein J. Org. Chem. 2017, 13, 2160–2168, doi:10.3762/bjoc.13.216

• of reactive encounters between the particles. In contrast, ex situ gas chromatography studies of the Knoevenagel condensation between vanillin and barbituric acid in a planetary mill revealed a sigmoidal dependence of reaction yield with time [22]. Similarly, sigmoidal dynamics were detected by in

Remarkable functions of sn-3 hydroxy and phosphocholine groups in 1,2-diacyl-sn-glycerolipids to induce clockwise (+)-helicity around the 1,2-diacyl moiety: Evidence from conformation analysis by ¹H NMR spectroscopy

• Yoshihiro Nishida,
• Mengfei Yuan,
• Kazuo Fukuda,
• Kaito Fujisawa,
• Hirofumi Dohi and
• Hirotaka Uzawa

Beilstein J. Org. Chem. 2017, 13, 1999–2009, doi:10.3762/bjoc.13.196

• the 1,3-isomer marginally affects the 1H NMR signals of 3. As shown in Table 1, entries 2 and 3, the solvents marginally affect the 1H NMR signals of 2. Clearly, sn-3 OH plays an essential role in the conformational dynamics, as shown above. The dynamic change is probably caused by solvation by

• hydration occurring around the carbonyl groups in the 1,2-diacyl moiety triggers the dynamics of the molecular alignments in liposomes. Probably, an analogous phenomenon related to the solvation around sn-3 OH was observed. Thus, solvation is thought to play a key role in the dynamic conformation change

Enzymatic synthesis of glycosides: from natural O- and N-glycosides to rare C- and S-glycosides

• Jihen Ati,
• Pierre Lafite and
• Richard Daniellou

Beilstein J. Org. Chem. 2017, 13, 1857–1865, doi:10.3762/bjoc.13.180

• still not well understood and controlling this ratio remains a challenge that still need to be solved, even if the use of artificial donors [10], the bioengineering of these biocatalysts [61] and the study of internal water dynamics [62] for examples have permitted important progresses. Consequently

Correction: Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2017, 13, 1669–1669, doi:10.3762/bjoc.13.161

• Stephanie R. Hare Dean J. Tantillo Department of Chemistry, University of California–Davis, 1 Shields Avenue, Davis, CA 95616, USA 10.3762/bjoc.13.161 Keywords: carbocation; density functional theory; dynamics; mechanism; terpene; The originally published Figure 6 had several mis-drawn

2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

• Julia Kinzel,
• Daniel F. Sauer,
• Marco Bocola,
• Marcus Arlt,
• Tayebeh Mirzaei Garakani,
• Andreas Thiel,
• Klaus Beckerle,
• Tino Polen,
• Jun Okuda and
• Ulrich Schwaneberg

Beilstein J. Org. Chem. 2017, 13, 1498–1506, doi:10.3762/bjoc.13.148

• rhodium-based biohybrid catalyst. Unlike commonly used detergents such as sodium dodecyl sulfate or polyethylene polyethyleneglycol, MPD does not form micelles in solution. Molecular dynamics simulations revealed the effect and position of stabilizing MPD molecules. The advantage of the amphiphilic MPD

• carried out, reaching higher molecular weights and yields compared to catalysis with the micelle-forming refolding reagent PE–PEG. Minimum of MPD molecules was analyzed by molecular dynamics studies to enable refolding of SDS-denatured transmembrane protein FhuA ΔCVFtev [29]. This report aims to

•  1). Molecular dynamics (MD) simulations reveal an optimal minimum number of ≈200 MPD molecules for shielding the hydrophobic transmembrane region of FhuA ΔCVFtev MD simulations of FhuA ΔCVFtev were performed in a box with varying numbers of MPD molecules from 126 MPD, 189 MPD, 252 MPD to 378 MPD

Grip on complexity in chemical reaction networks

• Albert S. Y. Wong and
• Wilhelm T. S. Huck

Beilstein J. Org. Chem. 2017, 13, 1486–1497, doi:10.3762/bjoc.13.147

• the predictability and perhaps the possibility to influence the dynamics of change, but science has yet to find an answer to this complexity [15]. One of the ultimate aims for systems like a living cell, is to understand how the interplay between molecular level events and network topology determines

• true when those changes induce systems beyond a critical value, where the resulting abrupt shifts or phase transitions become unpredictable [20][21][22]. The analysis of the structure and the dynamics of a complex web of intricate interactions is a risk in removing the link between molecular structure

• dissipative self-assembling structures, creating new forms of smart materials [31][32][33][34][35]. Yet, we are severely limited by too few examples of systems which are both extensive enough to exhibit dynamics, and at the same time, simple enough to be tunable [36]. In this perspective, we will attempt to

Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research

• Ben Shirt-Ediss,
• Sara Murillo-Sánchez and
• Kepa Ruiz-Mirazo

Beilstein J. Org. Chem. 2017, 13, 1388–1395, doi:10.3762/bjoc.13.135

• experimental challenges aimed at constructing protocell systems made of a diversity of functionally coupled components and, thereby, at characterizing more precisely the type of prebiotic evolutionary dynamics that such protocells could engage in. Keywords: functional integration; origins of life; prebiotic

• be grown and multiplied under lab conditions [31]; their rich inherent dynamics [32]; and the competition–selection experiments they make possible, if mixed with different liposome populations [33][34][35][36]. Thus, the interest of working with these model systems stems from the fact that they

• move the field of origins of life forward would be to couple simple chemistry to prebiotic vesicle dynamics: chemical reactions provide the power for endogenous synthesis and vesicles the adequate scaffolding for the functional integration of what is synthesized. We will proceed briefly with the issue

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

• needed. Spectroscopic studies on structure, dynamics and recognition of ONs by other biopolymers, small molecules or metal complexes, for example, may consume ONs in amounts that cannot be conveniently reached by lab-scale solid-phase synthesizers. In addition to synthesis on a soluble support

Aqueous semisynthesis of C-glycoside glycamines from agarose

• Juliana C. Cunico Dallagnol,
• Alexandre Orsato,
• Diogo R. B. Ducatti,
• Miguel D. Noseda,
• Maria Eugênia R. Duarte and
• Alan G. Gonçalves

Beilstein J. Org. Chem. 2017, 13, 1222–1229, doi:10.3762/bjoc.13.121

• aminomonosaccharides 9 and 13 are interesting moieties, regarding their resemblance with the bioactive (+)-muscarine 14 (Figure 2). Indeed, ongoing docking and molecular dynamics experiments revealed the amino-AnGal moiety as a promising platform to launch the design of new mAChR modulators [11]. The differences in

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

• to biology, it does not directly explain the emergence of the RNA and DNA dominated world as we know it, which would probably have required open-ended evolution. 3 Evolutionary dynamics of replicators 3.1 Enzyme mediated replication Iconic early experiments aiming to achieve Darwinian type evolution

• strands by creating heat gradients in pores that act as a thermal trap [38]. The thermal traps selectively retain longer DNA sequences, thereby effectively overcoming the inherent advantage of the replication of short sequences. 3.2 Dynamics of self-replicators Ashkenasy recently reported a peptide based

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• dynamics, plasticity of GTs and conformation changes that allow for substrate recognition and catalysis [37]. In plants, GTs are also involved in the biosynthesis of hemicellulose. Xyloglucan is one of the main hemicellulose components in the cell walls of dicots. Its biosynthesis involves different GTs

• manner is creating an opportunity to investigate the microstructure and non-equilibrium dynamics of soft matter on a length scale from a few angtroms to micrometers and on a timescale descending to the millisecond. Grazing incidence X-ray reflectometry Glycolipids: Despite their importance in the

• constitution and dynamics of plasma membranes, the structural and physicochemical features of gangliosides have been somehow neglected presumably because of the lack of appropriate experimental techniques. X-ray reflectometry is a surface-sensitive analytical technique based on the measure of the intensity of

G-Protein coupled receptors: answers from simulations

• Timothy Clark

Beilstein J. Org. Chem. 2017, 13, 1071–1078, doi:10.3762/bjoc.13.106

• Timothy Clark Computer-Chemie-Centrum, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany 10.3762/bjoc.13.106 Abstract Molecular-dynamics (MD) simulations are playing an increasingly important role in research into

• ; molecular dynamics; Introduction Evolution is a unique optimization mechanism. Firstly, it stops optimizing as soon as an acceptable solution is reached. There is no evolutionary pressure for elegance, simplicity or even effectiveness above the critical threshold. Secondly, because evolution always starts

• experimental findings [29] suggest that both an agonist ligand and a bound G-protein are necessary in order to activate GPCRs. It is therefore significant that the first molecular dynamics (MD) simulations of a ternary GPCR complex were reported only four years ago [30]. Such simulations are now commonplace

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