Effects of solvent additive on “s-shaped” curves in solution-processed small molecule solar cells

• John A. Love,
• Shu-Hua Chou,
• Ye Huang,
• Guilllermo C. Bazan and
• Thuc-Quyen Nguyen

Beilstein J. Org. Chem. 2016, 12, 2543–2555, doi:10.3762/bjoc.12.249

• , reduced surface recombination, and interfacial defects leading to traps; device simulations have shown that all of these could indeed result in the s-shape behavior [23][24][25][26][27][28][29][30]. Herein we describe the development of a novel small molecule system with nearly ideal optoelectronic

Inhibition of peptide aggregation by means of enzymatic phosphorylation

• Kristin Folmert,
• Malgorzata Broncel,
• Hans v. Berlepsch,
• Christopher H. Ullrich,
• Mary-Ann Siegert and
• Beate Koksch

Beilstein J. Org. Chem. 2016, 12, 2462–2470, doi:10.3762/bjoc.12.240

• , resulting in the suppression of the β-aggregation propensity. This is in accordance with simulations carried out by Rousseau et al. who proposed that charged amino acid residues flanking aggregating peptide segments could act as gatekeeper residues that reduce the aggregation propensity of the peptide [61

Efficient syntheses of climate relevant isoprene nitrates and (1R,5S)-(−)-myrtenol nitrate

• Sean P. Bew,
• Glyn D. Hiatt-Gipson,
• Graham P. Mills and
• Claire E. Reeves

Beilstein J. Org. Chem. 2016, 12, 1081–1095, doi:10.3762/bjoc.12.103

• and high NO concentration. They compared their results with field observations, collected during the Southern oxidant and Aerosol Study (SOAS) campaign conducted in 2013, and model simulations. These studies identified NO as the limiting factor in IPN production [11]. Schwantes et al. reported a

Correction: Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 608–610, doi:10.3762/bjoc.12.59

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• and promising antibacterial agents for the treatment of serious Gram-positive infections. Our predictions rely on force field simulations, supervised by first principle calculations and available experimental data. Different force fields were tested in order to reproduce linezolid's conformational

• ) virtual screenings [28][29][30] of large molecular databases to B) sophisticated simulations of the state equations [31][32]. Nevertheless, both strategies have their own advantages and disadvantages when it comes to the reliable prediction of new drug candidates. While fast virtual screening methods

• flexibility of the U2620 (U2585 in Escherichia coli) moiety has already been discussed elsewhere [20]. Nevertheless, due to our simulation, there is no hydrogen bond between this nucleobase and the morpholine ring. The absence of a second hydrogen bond in our simulations (which is indeed observed for

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

• [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

• questions. MD simulations have been employed to answer two different questions about the chemical reactions discussed below: (1) what mechanism(s) is energetically viable? and (2) do (non-statistical) dynamic effects exert control over product distributions? While trajectories can be started from anywhere

• still not standard practice, but the potential for the utility of dynamics simulations in a variety of systems has certainly been demonstrated. The studies detailed below primarily highlight situations where molecular dynamics simulations were used to quantify “non-IRC” behavior, but the value of

My maize and blue brick road to physical organic chemistry in materials

• Anne J. McNeil

Beilstein J. Org. Chem. 2016, 12, 229–238, doi:10.3762/bjoc.12.24

• simulations with mentorship from my colleague Professor Charles L. Brooks III [36]. Our goal was to model the solid-state interactions as well as the solvent interactions. We wanted to avoid starting the simulation with a crystal structure, knowing that this criterion would ultimately limit the structural

A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy

• Steven C. Zimmerman

Beilstein J. Org. Chem. 2016, 12, 125–138, doi:10.3762/bjoc.12.14

• capability. However, Monte Carlo simulations by Blake and Jorgensen indicate that the cleft of 9 is actually a good host for chloroform and that the carboxylic acid is solvated by more than one chloroform molecule [21]. Another possibility is that the aromatic cleft might somehow decrease the acidity of the

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

• of the initial aggregation stage could easily take place. In particular, these simulations carried out with relatively small systems comprising a few molecules allowed us to assess that the driving force for aggregation was due to a synergy of different contributions. In particular, we found that the

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

• conformations was carried out by a conformational Monte Carlo research method using the MMFFs force field in the presence of water (GB/SA implicit model) with the generation of 5000 conformations (FMNR conjugate gradient minimization convergence fixed to 0.01 kJ Å−1 mol−1). Prior to docking and simulations, the

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

• free energy of inclusion complexes Root mean square displacements (RMSDs) for all atoms of the complex, cyclodextrin and hesperetin in respect with those of initial structures (Figure S1, Supporting Information File 1) suggested that the three independent simulations of β-CD (A1–A3) and DM-β-CD (B1–B3

• Molecular dynamics (MD) simulations with periodic boundary condition were performed on the three best docked structures of the hesperetin/CDs complexes (Figure 7) similar to our previous studies on naringenin/CDs complexes [40][60] using the Amber 12 software package [61]. Note that the docked structures

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

• 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

• portion of a whole vesicle [37]. Otherwise, coarse-grained Monte Carlo simulations in two dimensions modelled the self-assembly of aCD [38]. It should be underlined, however, that in the atomistic simulations a manually pre-assembled system was generally assumed, while the spontaneous formation of

• = OH), simply denoted in the following as the model aCD. The simulations used molecular mechanics (MM) and molecular dynamics (MD) methods, and were carried out both in vacuo, to mimic a non-polar and weakly interacting solvent, and in explicit water, using a box of water molecules with periodic

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

• the β-CD structure and guest molecules in its inclusion compounds have been reported [19][20][21]. Moreover, MD simulations of β-CD in water and ethanol mixtures have been performed to investigate the orientation of the co-solvent in the hydrophobic cavity of the β-CD [22]. Recently, Biedermann et al

• simulations are therefore a useful technique providing details of the molecular interactions of structural components in different environments (e.g., water or water/co-solvent mixtures) which are often encountered in formulations. In our previous work [24], the preliminary results of phase solidities of the

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

Structure and conformational analysis of spiroketals from 6-O-methyl-9(E)-hydroxyiminoerythronolide A

• Ana Čikoš,
• Irena Ćaleta,
• Dinko Žiher,
• Mark B. Vine,
• Ivaylo J. Elenkov,
• Marko Dukši,
• Dubravka Gembarovski,
• Marina Ilijaš,
• Snježana Dragojević,
• Ivica Malnar and
• Sulejman Alihodžić

Beilstein J. Org. Chem. 2015, 11, 1447–1457, doi:10.3762/bjoc.11.157

• -dimensional structure and avoid time-consuming molecular dynamic simulations, the starting model of 2 was created from the X-ray single crystal structure of tricyclic spiroketal (CSD entry: ERYTHR) [55], with replacement of the 6-hydroxy group by 6-methoxy. A two-step minimization process consisted of adding

The synthesis of active pharmaceutical ingredients (APIs) using continuous flow chemistry

• Marcus Baumann and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2015, 11, 1194–1219, doi:10.3762/bjoc.11.134

• results with the devised simulations. More recently, scientists at Novartis (Switzerland) extended this study by developing a semi-continuous flow approach for the synthesis of the oral antidiabetic vildagliptine (77) using in situ generated Vilsmeier reagent (Scheme 13) [74]. Neat streams of DMF and

Cathodic hydrodimerization of nitroolefins

• Michael Weßling and
• Hans J. Schäfer

Beilstein J. Org. Chem. 2015, 11, 1163–1174, doi:10.3762/bjoc.11.131

• experiments they can be clearly assigned to be phenyl protons. Comparable results, as shown for 2, were found for the mixtures of diastereomers of the other hydrodimers. Besides decoupling experiments also 1H NMR simulations give valuable support to assign the complex coupling pattern. This is shown for 18b

Glycoluril–tetrathiafulvalene molecular clips: on the influence of electronic and spatial properties for binding neutral accepting guests

• Yoann Cotelle,
• Marie Hardouin-Lerouge,
• Stéphanie Legoupy,
• Olivier Alévêque,
• Eric Levillain and
• Piétrick Hudhomme

Beilstein J. Org. Chem. 2015, 11, 1023–1036, doi:10.3762/bjoc.11.115

• . The stepwise oxidation of each molecular clip involves an electrochemical mechanism with three one-electron processes and two charge-coupled chemical reactions, a scheme which is supported by electrochemical simulations. The fine-tunable π-donating ability of the TTF units and the cavity size allow to

• measurements demonstrated that the mixed-valence state in these fused glycoluril-TTF molecular clips seems to originate from intermolecular TTF interactions, according to measurements at various concentrations and to cyclic voltammogram simulations. Spatial and electrochemical properties were shown to be

• . (middle) 3D representation: x-axis = wavelength, y-axis = time and z-axis = absorbance. (bottom) concentration-time profiles of each simulated species in the thin layer (50 µm) calculated from electrochemical simulations of Figure 4 (E1 = 0.090 V, E2 = 0.165 V, E3 = 0.435 mV, KMV = 11400 M−1, KDIM = 680 M

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

First principle investigation of the linker length effects on the thermodynamics of divalent pseudorotaxanes

• Andreas J. Achazi,
• Doreen Mollenhauer and
• Beate Paulus

Beilstein J. Org. Chem. 2015, 11, 687–692, doi:10.3762/bjoc.11.78

• contributions, enthalpic and entropic temperature effects as well as solvent effects are included in our simulations in order to compare to experimentally obtained Gibbs energy of association. Results and Discussion In order to investigate the cooperativity effects of the binding between divalent host molecules

• ]. This procedure yields very good results for the Gibbs energy of association in the case of the crown-6/ammonium complex in comparison with experiment [25]. For the simulations of the crown-8/ammonium systems the same solvent as in the experiment [16] is used, namely a 2.2:1 mixture of chloroform

• pseudorotaxanes the absolute agreement between the calculated and the experimentally determined Gibbs energies is not as good as in the case of monovalent binding, but the same trends are observed in the simulations as in experiment. The divalent pseudorotaxane with the n0 linker shows a significantly stronger

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

• can rotate and move around the azobenzene axis. Throughout the simulations, the C4–C4’ distances and the C–N=N–C dihedral angles did not fluctuate much. The C–C average value was 8.9 ± 0.1 and 5.8 ± 0.3 Å and the C–N=N–C dihedral angle was 175.1 ± 4.8 and −6.3 ± 5.4° for the trans and cis

• parameterized according to the strategy previously developed using the RED program [47] along with the RED server [48]. Molecular dynamics (MD) simulations were performed using the SANDER module of the AMBER10 program suite to perform MD simulations on the aforementioned complexes [49]. The systems were

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

• 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

• were used to describe the molecular mechanisms of inclusion complexation between the flavonoids quercetin/myricetin and cyclodextrin in comparison with the experimental results from 1H NMR spectroscopy [30]. Choi and coworkers [31] also reported a theoretical study based on MD simulations in order to

Improving ITC studies of cyclodextrin inclusion compounds by global analysis of conventional and non-conventional experiments

• Eléonore Bertaut and
• David Landy

Beilstein J. Org. Chem. 2014, 10, 2630–2641, doi:10.3762/bjoc.10.275

• to cover the range of stability generally observed in cyclodextrin chemistry, our simulations have been realized for four formation constants ranging from 102 M−1 to 105 M−1 (for a guest solubility equal to 2 mM). Results are presented in Table 1. Numerous experiments lead to uncertainties superior

• ) multiplied by the student t factor (1.96). Simulations of the accuracy were carried out for both the real systems studied in this work and hypothetical systems. In the latter case, corresponding binding isotherms were simulated by the postulation of thermodynamic parameters and experimental conditions and by

Towards the sequence-specific multivalent molecular recognition of cyclodextrin oligomers

• Michael Kurlemann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 2428–2440, doi:10.3762/bjoc.10.253

• result in different steric environments during the interactions, but the exact effects cannot be predicted and have to be solved by theoretical calculations and simulations. In the last step the interactions of the trivalent guest strands 11, 12, 13 and 14 with complementary and non-complementary

Effect of cyclodextrin complexation on phenylpropanoids’ solubility and antioxidant activity

• Miriana Kfoury,
• David Landy,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2014, 10, 2322–2331, doi:10.3762/bjoc.10.241

• constructed manually and minimized, prior to inclusion simulations. The docking of each PP inside CD was realized by means of conformational Monte Carlo searches, with the generation of 5000 conformations (FMNR conjugate gradient minimization, convergence fixed to 0.01 kJ Å−1 mol−1). During the search, CD was