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

• ) 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

Enabling technologies and green processes in cyclodextrin chemistry

• Giancarlo Cravotto,
• Marina Caporaso,
• Laszlo Jicsinszky and
• Katia Martina

Beilstein J. Org. Chem. 2016, 12, 278–294, doi:10.3762/bjoc.12.30

• combinations has been done in two major databases [5][6]. The results were partially overlapped only in the full text searches and approximately 4000 records have been found. Further reduction of records, less than 2500, by searching in Title/Abstract/Keyword fields only resulted in more relevant publications

The Beilstein Journal of Organic Chemistry and the changing face of scientific publishing

• Martin G. Hicks and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2015, 11, 2242–2244, doi:10.3762/bjoc.11.242

• databases. In organic chemistry, laboratories are becoming digital in terms of process control, measurement and analytical techniques [2][3]. In terms of publishing, improvements would be beneficial in many areas of structure and data handling and linking. Slowly, the publishing infrastructure and workflows

• made available to experts working directly in a particular field. Further processing will allow it to be stored in structured databases for searching, and with further annotation, it can be linked or added to publications. The Protein Data Bank [15] and the Cambridge Structural Database [16] are two

• databases with inherent differences in precision and recall, as well as scientific social media [18], provide good substitutes for traditional browsing. The problems of plagiarism and self-plagiarism (also known as recycling) [19] are becoming more transparent thanks to open access and the CrossCheck system

Streptopyridines, volatile pyridine alkaloids produced by Streptomyces sp. FORM5

• Ulrike Groenhagen,
• Michael Maczka,
• Jeroen S. Dickschat and
• Stefan Schulz

Beilstein J. Org. Chem. 2014, 10, 1421–1432, doi:10.3762/bjoc.10.146

• the extract revealed that a small peak (7) eluted slightly earlier than compound 8. The mass spectrum of compound 7 matched that of 2-pentylpyridine, present in public databases [14]. From these data we concluded that the unknown compound 12 might be a 2-(pentadienyl)pyridine with conjugated side

Halogenated volatiles from the fungus Geniculosporium and the actinomycete Streptomyces chartreusis

• Tao Wang,
• Patrick Rabe,
• Christian A. Citron and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2013, 9, 2767–2777, doi:10.3762/bjoc.9.311

• . Their mass spectra pointed to the structures of a chlorodimethoxybenzene for X and a dichlorodimethoxybenzene for Y. The mass spectra of some constitutional isomers for X and Y were included in our databases and proved to be very similar, thus preventing a full structural assignment. For unambiguous

Synthesis of 5-(ethylsulfonyl)-2-methoxyaniline: An important pharmacological fragment of VEGFR2 and other inhibitors

• Miroslav Murár,
• Gabriela Addová and
• Andrej Boháč

Beilstein J. Org. Chem. 2013, 9, 173–179, doi:10.3762/bjoc.9.20

• mentioned in the patent literature [19]. No yield was given in this record. 5-(Ethylsulfonyl)-2-methoxy-1,3-dinitrobenzene (4a) is an unknown compound. No physicochemical properties or spectral data were found either in the Reaxys or in SciFinder databases. 5-(Ethylsulfonyl)-2-methoxyaniline (5), CAS [5339

• -62-8], is a compound with only limited commercial availability. For this compound no synthesis can be found in the Reaxys and SciFinder databases. There were 37 reactions in Reaxys and 191 reactions in SciFinder described. In all cases compound 5 was exclusively a starting material or reactant

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

• Jutta Erika Helga Köhler and
• Nicole Grczelschak-Mick

Beilstein J. Org. Chem. 2013, 9, 118–134, doi:10.3762/bjoc.9.15

• molecular conformers of up to 10 kcal mol−1 in the standard COSMO databases. These σ-profiles and σ-potentials were calculated with COSMOthermX for the empty β-CD models and are displayed in Figure 6 and Figure 7. Especially the σ-potentials (Figure 7) showed that the empty β-CD models were split into two

Beilstein Journal of Organic Chemistry: Open Access comes of age in Organic Chemistry

• Peter H. Seeberger

Beilstein J. Org. Chem. 2012, 8, 1284–1286, doi:10.3762/bjoc.8.145

• significant role in communicating the advantages of the Journal to colleagues, and in the selection of new Thematic Series, which have been particularly successful for the Journal. All articles are permanently stored in public archives, such as PubMed Central, and indexed by scientific databases. Impact

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

• been employed to generate thousands of the organic compounds that have been deposited in the NIH molecular repository for medicinal chemistry research. Deciphering the therapeutic potential of this many compounds is a continuing challenge. By combining chemogenomics databases, such as Protein Data Base

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

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

• that can be of use to glycobiologists, but also to chemists who work on the synthesis or analysis of carbohydrates. This article gives an overview of existing glyco-specific databases and tools, with a focus on their application to glycochemistry: Databases can provide information on candidate glycan

• structures for synthesis, or on glyco-enzymes that can be used to synthesize carbohydrates. Statistical analyses of glycan databases help to plan glycan synthesis experiments. 3D-Structural data of protein–carbohydrate complexes are used in targeted drug design, and tools to support glycan structure analysis

• aid with quality control. Specific problems of glycoinformatics compared to bioinformatics for genomics or proteomics, especially concerning integration and long-term maintenance of the existing glycan databases, are also discussed. Keywords: carbohydrates; databases; glycomics; software

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

• hydrogen bond motif to local, more directional forces. Should all molecules capable of hydrogen bonding build lattices of Ci symmetric aggregates with Z' = 1 at the expense of local interactions? No, local and dispersive forces can also synergize to construct the solid state. Crystal structure databases

• problem of calculating marginal differences in large energetic contributions to the organic solid state has been the subject of previous conjecture, this study is one example of the nature of the problem, unveiled and dissected. The results provide a caveat for mining crystal structure databases and