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

• : compliance constants; computational chemistry; drug design; molecular recognition; relaxed force constants; Introduction Antibiotic resistance is one of the major health problems in modern societies, causing millions of deaths per year [1][2][3]. Although Alexander Fleming recognized the importance of 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

• research grant is acknowledged. Special thanks go also to the Computational Chemistry Unit Cell (CCUC), the Vienna Scientific Cluster (VSC-2), the Starch and Cyclodextrin Research Unit of the CU and the Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, for providing

Computational study of productive and non-productive cycles in fluoroalkene metathesis

• Markéta Rybáčková,
• Jan Hošek,
• Ondřej Šimůnek,
• Viola Kolaříková and
• Jaroslav Kvíčala

Beilstein J. Org. Chem. 2015, 11, 2150–2157, doi:10.3762/bjoc.11.232

• mainly due to its variability and high compatibility with functional groups. It hence became the subject of multiple books [1][2][3] and reviews [4][5][6][7][8] discussing its synthetic applications, catalysts, mechanism, regio- and stereoselectivity. Computational chemistry proved to be extremely

Investigation of the role of stereoelectronic effects in the conformation of piperidones by NMR spectroscopy and X-ray diffraction

• Cesar Garcias-Morales,
• David Ortegón-Reyna and
• Armando Ariza-Castolo

Beilstein J. Org. Chem. 2015, 11, 1973–1984, doi:10.3762/bjoc.11.213

• -97 [69] and refined by the full-matrix least-squares method on F2 with SHELXL-97. Note that in this report we use our crystallography results of compounds 1, 3, 5, 6, and 7. Details of the calculations and computational methods The computational chemistry calculations were performed using the

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

• - and B-rings of fisetin. Acknowledgements This study was supported by the TRF-CHE Research Grant for New Scholars (MRG5580223), and Ratchadapiseksomphot Endowment Fund of Chulalongkorn University (RES560530176-FW). Chiang Mai University is also acknowledged. We thank the Computational Chemistry Unit

Atherton–Todd reaction: mechanism, scope and applications

• Stéphanie S. Le Corre,
• Mathieu Berchel,
• Hélène Couthon-Gourvès,
• Jean-Pierre Haelters and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2014, 10, 1166–1196, doi:10.3762/bjoc.10.117

• as a substrate, and cyclohexylamine as a nucleophilic amine. The formation of the salt 3 was observed when cyclohexylamine was added to dimethyl phosphite, thus pointing out the influence of the order of addition of the reactants. Roundhill et al. [17] used computational chemistry to further

Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines

• Andreas Gansäuer,
• Meriam Seddiqzai,
• Tobias Dahmen,
• Rebecca Sure and
• Stefan Grimme

Beilstein J. Org. Chem. 2013, 9, 1620–1629, doi:10.3762/bjoc.9.185

• indanes or dihydrobenzofurans are too slow to be useful synthetically. Keywords: aromatic substitution; computational chemistry; DFT-D3; free radical; polar effects; radical reaction; Introduction The development of efficient catalytic reactions is one of the central issues of chemistry [1][2]. Radical

Gold-catalyzed oxycyclization of allenic carbamates: expeditious synthesis of 1,3-oxazin-2-ones

• Benito Alcaide,
• Pedro Almendros,
• M. Teresa Quirós and
• Israel Fernández

Beilstein J. Org. Chem. 2013, 9, 818–826, doi:10.3762/bjoc.9.93

• gold-catalyzed synthetic routes to 1,3-oxazinan-2-ones (kinetically controlled products) and 1,3-oxazin-2-one derivatives (thermodynamically favored) from easily accessible allenic carbamates has been carried out. Keywords: allenes; computational chemistry; gold; gold catalysis; heterocycles; reaction

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

• ; Introduction Background Computational chemistry has become an indispensible tool for medicinal chemists, biologists and pharmacologists throughout all stages of the pharmaceutical research process. One application is in the selection or virtual screening of the, in many cases, numerous possible alternative

• slow, computationally costly and in many cases difficult to automate, and it also requires manual input from an expert in computational chemistry. In summary the property- or descriptor-based methods typically fulfill the requirements 3 and 4 above but fail 1 and 2, while the TS methods typically

On the mechanism of action of gated molecular baskets: The synchronicity of the revolving motion of gates and in/out trafficking of guests

• Keith Hermann,
• Stephen Rieth,
• Hashem A. Taha,
• Bao-Yu Wang,
• Christopher M. Hadad and
• Jovica D. Badjić

Beilstein J. Org. Chem. 2012, 8, 90–99, doi:10.3762/bjoc.8.9

• ΔG‡rac (i.e., opening and closing, see below in Figure 6) reveals a systematic disparity (ΔG° + ΔG‡rac + ΔG‡sterics ≠ ΔG‡out, see below in Figure 7). In order to address this conundrum, we have employed methods of experimental (dynamic NMR) and computational chemistry (steered molecular dynamics, SMD

Synthesis and oxidation of some azole-containing thioethers

• Andrei S. Potapov,
• Nina P. Chernova,
• Vladimir D. Ogorodnikov,
• Tatiana V. Petrenko and
• Andrei I. Khlebnikov

Beilstein J. Org. Chem. 2011, 7, 1526–1532, doi:10.3762/bjoc.7.179

• Elemental analyses were carried out on a Carlo Erba analyzer. Infrared (IR)-spectra of solid samples as KBr pellets were recorded on a Nicolet 5700 (4000–400 cm−1) spectrophotometer. NMR spectra were recorded on a Bruker AV300 operating at 300 MHz for 1H and 75 MHz for 13C. Computational chemistry details A

A gold-catalyzed alkyne-diol cycloisomerization for the synthesis of oxygenated 5,5-spiroketals

• Sami F. Tlais and
• Gregory B. Dudley

Beilstein J. Org. Chem. 2011, 7, 570–577, doi:10.3762/bjoc.7.66

• National Science Foundation (NSF-CHE 0749918). We thank Dr Tom Gedris (FSU) for assistance with NMR analysis and the FSU High Performance Computing group for assistance with the calculations. Helpful discussions with Dr. Abdulkader Baroudi (FSU) regarding computational chemistry and with Prof. Aaron

Catalysis: transition-state molecular recognition?

• Ian H. Williams

Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117

• most accessible route between reactants and products (Figure 1), it commands both the direction and the rate of chemical change. Questions of specificity and catalysis may be answered by knowledge of the structure and properties of the TS. Computational chemistry provides techniques for the generation

Physical organic chemistry

• John A. Murphy

Beilstein J. Org. Chem. 2010, 6, 1025–1025, doi:10.3762/bjoc.6.116

• kinetics of radical reactions. Applications to complex reactions in biology, polymer chemistry and electronic materials are ever more prevalent, and add to contributions in ‘small molecule’ chemistry. Novel experimental techniques combined with the revolution in computational chemistry give new impetus to

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

• experimental Epc are shown in Table 1. Overall, the test set had a mean signed error of −16 mV and a mean unsigned error of 99 mV. These results demonstrate that the training set correlation is transferable to the test set. Conclusion We have effectively used computational chemistry to predict the reduction