Copper(II)-salt-promoted oxidative ring-opening reactions of bicyclic cyclopropanol derivatives via radical pathways

• Eietsu Hasegawa,
• Minami Tateyama,
• Ryosuke Nagumo,
• Eiji Tayama and
• Hajime Iwamoto

Beilstein J. Org. Chem. 2013, 9, 1397–1406, doi:10.3762/bjoc.9.156

• this prediction, cyclopropanols 1, prepared by SmI2-promoted intramolecular Barbier reaction of the corresponding α-bromomethyl cycloalkanones 6 [28], were subjected to reactions promoted by various copper(II) salts, CuX2 (Scheme 5). The results of the reaction of 1b with Cu(OAc)2 (Scheme 6) are

Host–guest complexes of mixed glycol-bipyridine cryptands: prediction of ion selectivity by quantum chemical calculations, part V

• Svetlana Begel,
• Ralph Puchta and
• Rudi van Eldik

Beilstein J. Org. Chem. 2013, 9, 1252–1268, doi:10.3762/bjoc.9.142

• presented work was initiated with the objective to systematically study the selective complexation of alkali, alkaline-earth and earth metal cations by [2.2.bpy] and [2.bpy.bpy] cryptands. In general, the prediction of a favorable complexation can be made based on two characteristics, viz., bond distances

• systems, the examination of the energy of a model reaction, depicted in Scheme 1, provides valuable results, important for the prediction of the cryptand’s selectivity. All cations were calculated in the six-fold coordination environment, to maintain equal conditions for all studied systems. For the

Spectroscopic characterization of photoaccumulated radical anions: a litmus test to evaluate the efficiency of photoinduced electron transfer (PET) processes

• Maurizio Fagnoni,
• Stefano Protti,
• Davide Ravelli and
• Angelo Albini

Beilstein J. Org. Chem. 2013, 9, 800–808, doi:10.3762/bjoc.9.91

•  3d), reversible with air. These were attributed to the corresponding radical anions, not previously characterized, but fitting with a computational prediction of 559 nm for the radical anion of the unsubstituted N-methylphthalimide [43]. Finally, with both of the aromatic esters investigated, the

Utilizing the σ-complex stability for quantifying reactivity in nucleophilic substitution of aromatic fluorides

• Magnus Liljenberg,
• Tore Brinck,
• Tobias Rein and
• Mats Svensson

Beilstein J. Org. Chem. 2013, 9, 791–799, doi:10.3762/bjoc.9.90

• synthetic routes to a target molecule, e.g., a candidate drug. To this end, efficient models that enable the prediction of product selectivity and relative reaction rates in a quantitative or semiquantitative way would be highly valuable. As a complement to experimental work, the use of such tools can help

• attack of anionic nucleophiles to aromatic fluorides for a great many examples. They found that an approach using F− as model nucleophile without solvent calculations was sufficient to give a good qualitative prediction of the main site of nucleophilic attack. The σ-complex approach failed when the

• preserving an accuracy that in many cases is sufficient for an, at least semiquantitative, prediction of reactivity. Results The performance of the SS concept was examined on the basis of correlations with experimentally determined reaction rate constants (k) of three series of reactions (series A, B and C

NHC-catalysed highly selective aerobic oxidation of nonactivated aldehydes

• Lennart Möhlmann,
• Stefan Ludwig and
• Siegfried Blechert

Beilstein J. Org. Chem. 2013, 9, 602–607, doi:10.3762/bjoc.9.65

• 83% of the desired ester were achieved. Following path a, a hydroperoxyl anion is formed as a side product. In our experiments we could not detect this anion. We therefore assume that it acts as an additional oxidation agent under formation of water. To fortify this prediction, a test experiment with

Inclusion of the insecticide fenitrothion in dimethylated-β-cyclodextrin: unusual guest disorder in the solid state and efficient retardation of the hydrolysis rate of the complexed guest in alkaline solution

• Dyanne L. Cruickshank,
• Natalia M. Rougier,
• Raquel V. Vico,
• Susan A. Bourne,
• Elba I. Buján,
• Mino R. Caira and
• Rita H. de Rossi

Beilstein J. Org. Chem. 2013, 9, 106–117, doi:10.3762/bjoc.9.14

• be consistent with this prediction. This pseudo-translational symmetry was indeed a feature of the structural solution and is illustrated in Figure 3, where it relates the two complex units A and B in the crystal asymmetric unit of DIMEB·1. While the gross structures of the independent complex units

Dipyrazolo[1,5-a:4',3'-c]pyridines – a new heterocyclic system accessed via multicomponent reaction

• Wolfgang Holzer,
• Gytė Vilkauskaitė,
• Eglė Arbačiauskienė and
• Algirdas Šačkus

Beilstein J. Org. Chem. 2012, 8, 2223–2229, doi:10.3762/bjoc.8.251

• reliable, unambiguously assigned chemical shift data is important as reference material for NMR prediction programs, such as CSEARCH/NMRPREDICT [34][35] or ACD/C+H predictor [36]. Such programs have become more and more popular in the past few years, particularly for the prediction of 13C NMR chemical

The chemistry of bisallenes

• Henning Hopf and
• Georgios Markopoulos

Beilstein J. Org. Chem. 2012, 8, 1936–1998, doi:10.3762/bjoc.8.225

Design of a novel tryptophan-rich membrane-active antimicrobial peptide from the membrane-proximal region of the HIV glycoprotein, gp41

• Evan F. Haney,
• Leonard T. Nguyen,
• David J. Schibli and
• Hans J. Vogel

Beilstein J. Org. Chem. 2012, 8, 1172–1184, doi:10.3762/bjoc.8.130

• . Additionally, they would have to disassociate into monomers before they could insert themselves into the bacterial membrane. Recent artificial-neural-network prediction models of antimicrobial peptides have found that peptide aggregation in solution indeed contributes to a low antimicrobial activity [27

Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics

• Workalemahu M. Berhanu,
• Mohamed A. Ibrahim,
• Girinath G. Pillai,
• Alexander A. Oliferenko,
• Levan Khelashvili,
• Farukh Jabeen,
• Bushra Mirza,
• Farzana Latif Ansari,
• Ihsan ul-Haq,
• Said A. El-Feky and
• Alan R. Katritzky

Beilstein J. Org. Chem. 2012, 8, 1146–1160, doi:10.3762/bjoc.8.128

• [38]. Clustering of the structures in such a multidimensional space is the natural choice for similarity analysis. Clustering Clustering is a widely used technique that has found application in the selection of compounds for screening, analysis of substructure search output, and the prediction of

Synthesis and in silico screening of a library of β-carboline-containing compounds

• Kay M. Brummond,
• John R. Goodell,
• Matthew G. LaPorte,
• Lirong Wang and
• Xiang-Qun Xie

Beilstein J. Org. Chem. 2012, 8, 1048–1058, doi:10.3762/bjoc.8.117

• predict potential targets of the newly synthesized library of β-carboline-containing compounds. High-throughput docking studies for protein-target prediction of newly synthesized compounds Molecular docking studies were performed with the 34 newly synthesized compounds, represented by scaffolds 1, 2, 3

• pyrazole group of 6{10}. Ligand-based strategy for target prediction Ligand-based target prediction algorithms have been developed based upon an established medicinal chemistry principle that structurally similar compounds, with comparable physical properties, should convey related biological properties

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

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

• templates in vaccine development [67][68][69][70], and glycomimetics that block specific enzymes or lectins can be used for therapeutic purposes [71][72][73][74][75][76][77]. The Glycan Pathway Prediction (GPP) tool of the RINGS portal [78] can be used to predict glycans that can be obtained with a given

• protein databases. Tools to input, convert, or analyze glycan structures. Tools for prediction and analysis of carbohydrate/glycoprotein 3D structures. Prediction and analysis of glycosylation sites. Tools to support experimental analysis of glycans.

Investigation of the network of preferred interactions in an artificial coiled-coil association using the peptide array technique

• Raheleh Rezaei Araghi,
• Carsten C. Mahrenholz,
• Rudolf Volkmer and
• Beate Koksch

Beilstein J. Org. Chem. 2012, 8, 640–649, doi:10.3762/bjoc.8.71

• the increasing number of helical assemblies made of peptidic foldamers, the combination of artificial oligomers with natural peptides remains a challenge. The main difficulties arise in the prediction of a suitable side-chain composition and the geometry of the foldameric binding groove that interacts

Synthesis, solid-state fluorescence properties, and computational analysis of novel 2-aminobenzo[4,5]thieno[3,2-d]pyrimidine 5,5-dioxides

• Kenichirou Yokota,
• Masayori Hagimori,
• Naoko Mizuyama,
• Yasuhisa Nishimura,
• Hiroshi Fujito,
• Yasuhiro Shigemitsu and
• Yoshinori Tominaga

Beilstein J. Org. Chem. 2012, 8, 266–274, doi:10.3762/bjoc.8.28

• of trustworthy quality. The CASSCF peak, in contrast, overshoots the experimental peak. The best prediction was obtained by using the most elaborate method, MS-CASPT2, which can take the majority of the electronic correlations into account. The MS-CASPT2 result indicates that the excitation character

The interplay of configuration and conformation in helical perylenequinones: Insights from chirality induction in liquid crystals and calculations

• Elisa Frezza,
• Silvia Pieraccini,
• Stefania Mazzini,
• Alberta Ferrarini and
• Gian Piero Spada

Beilstein J. Org. Chem. 2012, 8, 155–163, doi:10.3762/bjoc.8.16

• ) was investigated by integrating measurements of helical twisting power with a conformational analysis by DFT calculations and with the prediction of their twisting ability by the surface-chirality method. The two quasi-enantiomeric derivatives induce oppositely handed cholesteric phases when

• ) calculations, and with the prediction of the twisting ability of conformers, by the surface chirality (SC) method [29]. Results and Discussion HTP measurement The propensity of a dopant to induce a helical organization in the liquid-crystalline matrix is measured by its helical twisting power, which is defined

• data are available. However, the prediction that χ1 ~ χ2 ~ 30° appears reasonable for 2, considering that the narrower χ1 angle in cercosporin is a consequence of the constraints imposed by the bridge in the “6,7-bay region”. In view of their higher stability, only conformers in the propeller form were

Natural product biosyntheses in cyanobacteria: A treasure trove of unique enzymes

• Jan-Christoph Kehr,
• Douglas Gatte Picchi and
• Elke Dittmann

Beilstein J. Org. Chem. 2011, 7, 1622–1635, doi:10.3762/bjoc.7.191

• . Conclusion Genome sequencing projects of cyanobacteria have revealed a far greater potential of cyanobacteria to produce natural products than expected. It can thus be anticipated that genomic mining techniques that start with the theoretical prediction of structures from genomic data will be of increasing

Predicting the UV–vis spectra of oxazine dyes

• Scott Fleming,
• Andrew Mills and
• Tell Tuttle

Beilstein J. Org. Chem. 2011, 7, 432–441, doi:10.3762/bjoc.7.56

• predict the absorption spectra of a series of oxazine dyes and the effect of solvent on the accuracy of these predictions. Based on the results of this study, it is clear that for the series of oxazine dyes an accurate prediction of the excitation energy requires the inclusion of solvent. Implicit solvent

• the prediction of the λmax value of 1 (M06-L error: 69 nm; −0.30 eV). Surprisingly, the gas-phase calculated value of λmax for 1 is relatively accurate. The gas-phase B3LYP calculation of 1 underestimates the value of λmax by only 16 nm (0.08 eV), although this appears to be a fortuitous error

• have investigated the ability of TD-DFT to predict the absorption spectra of a series of oxazine dyes and the effect of solvent on the accuracy of these predictions. Based on the results of this study, it is clear that for the series of oxazine dyes and accurate prediction of the excitation energy

Accuracy in determining interproton distances using Nuclear Overhauser Effect data from a flexible molecule

• Catharine R. Jones,
• Craig P. Butts and
• Jeremy N. Harvey

Beilstein J. Org. Chem. 2011, 7, 145–150, doi:10.3762/bjoc.7.20

• Catharine R. Jones Craig P. Butts Jeremy N. Harvey Department of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom 10.3762/bjoc.7.20 Abstract The determination of accurate NOE-derived interproton distances and confirmation/prediction of relative populations in

Organic gelators and hydrogelators

• Jean-Pierre Desvergne

Beilstein J. Org. Chem. 2010, 6, 846–847, doi:10.3762/bjoc.6.99

• . However, despite numerous efforts to establish a structure-property relationship for the development of low molecular weight gelling agents, prediction of the gelling ability of a compound is not straightforward. A major challenge today is the rational design of small size molecular gelators coupled with

Kinetic studies and predictions on the hydrolysis and aminolysis of esters of 2-S-phosphorylacetates

• Milena Trmčić and
• David R. W. Hodgson

Beilstein J. Org. Chem. 2010, 6, 732–741, doi:10.3762/bjoc.6.87

• features a PDF document presenting details of studies using the bromoacetyl-OBt system 1 (R = Bt) and bromoacetyl-NHS system 1 (R = NHS), and associated experimental details, as well as Excel™ spreadsheets for the prediction of product outcomes and the optimisation of leaving group pKaH values of 2-S

• -thiophosphate esters with reference to controlling aminolysis over hydrolysis. Supporting Information File 129: Synthesis and application of bromoacetyl-OBt and NHS systems Supporting Information File 130: Prediction of product distribution using p-nitrophenyl ester 7 (R = pNP) Supporting Information File 131

• : Prediction of product distribution using m-nitrophenyl ester 7 (R = mNP) Supporting Information File 132: Optimisation of leaving group pKaH values of 2-S-thiophosphate esters Acknowledgements We thank the Department of Chemistry, Durham University for support in the form of a studentship (MT), and the

Recognition properties of receptors consisting of imidazole and indole recognition units towards carbohydrates

• Monika Mazik and
• André Hartmann

Beilstein J. Org. Chem. 2010, 6, No. 9, doi:10.3762/bjoc.6.9

• building blocks for the acyclic structures, effective carbohydrate receptors with different binding selectivities could be obtained. However, the exact prediction of the binding selectivity still represents an unsolved problem. Binding studies in homogeneous solution The interactions of the receptors and

• into the acyclic receptor structure, effective carbohydrate receptors with different binding preferences can be generated. However, the exact prediction of the binding preference still represents an unsolved problem and remains an important goal for future research. Experimental section Analytical TLC

Prediction of reduction potentials from calculated electron affinities for metal-salen compounds

• Sarah B. Bateni,
• Kellie R. England,
• Anthony T. Galatti,
• Handeep Kaur,
• Victor A. Mendiola,
• Alexander R. Mitchell,
• Michael H. Vu,
• Benjamin F. Gherman and
• James A. Miranda

Beilstein J. Org. Chem. 2009, 5, No. 82, doi:10.3762/bjoc.5.82

• predicted from computed EAs using the linear correlation derived from the training set. In addition, Fry has also recently published an account of a similar procedure in the prediction of oxidation potentials of substituted triphenylamines using density functional theory [8]. In that work, Fry explored

Inversion symmetry and local vs. dispersive interactions in the nucleation of hydrogen bonded cyclic n-mer and tape of imidazolecarboxamidines

• Sihui Long,
• Venkatraj Muthusamy,
• Peter G. Willis,
• Sean Parkin and
• Arthur Cammers

Beilstein J. Org. Chem. 2008, 4, No. 23, doi:10.3762/bjoc.4.23

• minimization and their level of accuracy, especially in the prediction of hydrogen bonding options that are proximal in energy [28][46][47]. Prediction of the organic solid state is challenged by the fact that many crystalline phases likely result from marginal differences in large opposing effects. While the

• be made about the most popular hydrogen bond motif followed by caveats regarding the use of crystal-structure derived atomic parameters to broadly characterize hydrogen bonding energies. 1: An intuitive prediction regarding the relationship between crude hydrogen bond donor/acceptor directionality

• obvious exceptions. See text. The icon legend is identical to Figure 8 and Figure 10. The Y-axis from Figure 8 energies (θ only) and the X-axis from Figure 10 energies are compared. The high and low energies of θ are mostly responsible for the two crystalline phases that lie outside the prediction that

Tether- directed synthesis of highly substituted oxasilacycles via an intramolecular allylation employing allylsilanes

• Peter J. Jervis and
• Liam R. Cox

Beilstein J. Org. Chem. 2007, 3, No. 6, doi:10.1186/1860-5397-3-6

• all four possible oxasilacycles in addition to appreciable quantities of a diene side-product. The results with anti-aldehydes are more interesting. In line with our prediction, substrates possessing this relative stereochemistry provide results which are comparable to those from aldehydes that lack a

Effect of transannular interaction on the redox- potentials in a series of bicyclic quinones

• Grigoriy Sereda,
• Jesse Van Heukelom,
• Miles Koppang,
• Sudha Ramreddy and
• Nicole Collins

Beilstein J. Org. Chem. 2006, 2, No. 26, doi:10.1186/1860-5397-2-26

• calculated parameters and to the nature and positions of substituents in the bicyclic system. Results and Discussion Accurate computational prediction of redox-potentials requires comparison of energies for both the starting quinone and its reduced forms. The open-shell nature of the reduced species and

• often the necessity to take into account solvation makes the prediction of the redox-potentials a challenging and time consuming computational problem. However, Koopmans' theorem [4] enabled us to relate redox-potentials of bicyclic quinones with their LUMO energies, which characterize solely the

• starting compound. Despite the neglected orbital relaxation that immediately follows the reduction, such correlations have proved to be an efficient tool for prediction of redox-potentials of anthracyclines [5], substituted anthracenes [6], and oligothiophenes [7]. For all chemical species, the