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Search for "software" in Full Text gives 484 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations
Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176
- similar groups, making it easier to define peaks manually. Open-source software is then used to determine peak areas of the manually defined peaks. We successfully applied this semi-automated method to a dataset (containing 391 glycoprofiles) of monoclonal antibody biosimilars from a bioreactor
- databases and software (among others) are discussed in a recent review [15]. A long standing problem associated with the analysis of large sets of electrophoretic data generated during bioprocessing is inevitably the drift of the peak migration time and area under the curve pertaining to glycan structures
- small peaks and peaks that can lose their “Gaussian-ness” when multiple peaks migrate close together. This is especially true for large sets of diverse CE electropherograms collected over days or months under varied conditions. Consequently, they are often processed with automated software using
How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates
Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171
- , namely the three gg, gt and tg conformations for each 1-6 torsion. The topology file for each structure was obtained using tleap [31], with parameters from the GLYCAM06-j1 [32] for the carbohydrate atoms and with TIP3P for water molecules [33]. All calculations were run with the AMBER18 software package
- cpptraj [31] and visually analysed with the Visual Molecular Dynamics (VMD) software package [34]. Root mean square deviation (RMSD) and torsion angles values were measured using VMD. A density-based clustering method was used to calculate the populations of occupied conformations for each torsion angle
Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides
Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167
- data produced per day. The high number of images generated by the automated microscope cannot be analysed manually, and therefore need to go through a completely automated analysis pipeline. For this purpose, dedicated software is used to first create specific masks that detect the objects of interest
Models of necessity
Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137
- Applied to Synthetic Analysis) [52], or implement an automatic ML approach that encodes the reactions based on a training set, as pioneered by Gelernter [53][54]. Latterly, hard- and software improvements have made advances possible (see, for example [55][56][57]), as has an unprecedented effort in the
- ], developing a ML-suitable model for intermolecular interactions is feasible. As noted above, old models such as Gasteiger–Marsili [38][39] charges or Hammett constants [59] have been used in recent applications. This development ignores the immense improvements in hard- and software of the last four decades
Rearrangement of o-(pivaloylaminomethyl)benzaldehydes: an experimental and computational study
Beilstein J. Org. Chem. 2020, 16, 1636–1648, doi:10.3762/bjoc.16.136
- ) spectrometer equipped with a Prodigy cryo-probehead. The pulse programs were taken from the Bruker software library (TopSpin 3.5) and full 1H and 13C assignments were achieved with widely accepted strategies [34][35]. 1H NMR assignments were accomplished using general knowledge of chemical shift dispersion
Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle
Beilstein J. Org. Chem. 2020, 16, 1564–1571, doi:10.3762/bjoc.16.128
- = 0.0450, Rsigma = 0.0402) which were used in all calculations. The final R1 was 0.0454 (I > 2σ(I)) and wR2 was 0.1180 (all data). CCDC Deposition Number 1968472. Molecular modelling Monte Carlo conformational searches with the MMFF force field were carried out with the Spartan ‘18 software [30]. For each
Heterogeneous photocatalysis in flow chemical reactors
Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125
In silico rationalisation of selectivity and reactivity in Pd-catalysed C–H activation reactions
Beilstein J. Org. Chem. 2020, 16, 1465–1475, doi:10.3762/bjoc.16.122
- computational data, a threshold to distinguish between two possible reaction mechanisms was established. Computational Methods The NWChem, an open source software package, was used for the DFT calculations. It is easily scalable and designed to solve large scientific computational problems efficiently employing
One-step route to tricyclic fused 1,2,3,4-tetrahydroisoquinoline systems via the Castagnoli–Cushman protocol
Beilstein J. Org. Chem. 2020, 16, 1456–1464, doi:10.3762/bjoc.16.121
- . The APEX 2 v.2014.11.0 software was used for all data processing [53]. The structure was solved and refined with SHELX [54] programs, ShelXT and ShelXL by using OLEX 2 software [55]. Hydrogen atoms were placed at idealized positions and refined. Crystallographic data (excluding structure factors) for
[3 + 2] Cycloaddition with photogenerated azomethine ylides in β-cyclodextrin
Beilstein J. Org. Chem. 2020, 16, 1296–1304, doi:10.3762/bjoc.16.110
- analysis using WinEQNMR software [51]. The titration was performed at 25 °C. NMR titrations with AN A solution of 2@β-CD (prepared by mixing 2 in the concentration of 2.71 mM with β-CD in the concentration of 8.20 mM), or 3@β-CD (prepared by mixing 3 in the concentration of 1.54 mM with β-CD in the
- concentration of 20.5 mM) in CD3CN/D2O (3:7 v/v, 1.0 mL) was titrated with acrylonitrile (AN). After each addition of AN, an 1H NMR spectrum was recorded. The changes of chemical shifts depending on the AN concentration were processed by nonlinear regression analysis using WinEQNMR software [51]. The titration
Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors
Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108
- biological activity methodology, computational details, and NMR/HRMS spectra of the final products. Acknowledgements Rodrigo Razo (RSRH) thanks to the Laboratorio Nacional de Supercómputo (LNS, Puebla) for the computer time, and Dr. Zeferino Gómez-Sandoval of the University of Colima for the software
Anthelmintic drug discovery: target identification, screening methods and the role of open science
Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105
- cost. Another open source resource with immediate applicability to target identification and validation is the Open Worm Movement Database [115]. This is an open platform for analysing and sharing worm behavioural data, such as that obtained from worm tracking software. For example, the researcher can
- how they have been applied to anthelmintic discovery. We concentrate on those where the software source code and/or hardware design is made clearly and openly available. Methods, applications, and location of source code/design are summarised in Table 3. Open tools for phenotypic screening of motility
- software (Automated WormScan) has recently been published [118]. The Lifespan Machine also uses a scanner to acquire images, and has the ability to monitor thousands of worms simultaneously and determine mortality time for individual worms on plates [120]. WormAssay is a combination of a video camera and
Development of fluorinated benzils and bisbenzils as room-temperature phosphorescent molecules
Beilstein J. Org. Chem. 2020, 16, 1154–1162, doi:10.3762/bjoc.16.102
- -deficient fluorinated aromatic ring. To confirm the electron-withdrawing effect of this fluorinated aromatic ring, the electronic charge at the adjacent C≡C bond was calculated by density functional theory (DFT) using the Gaussian 16 (Revision B.01) software package [35]. As typical examples, the molecular
Synthesis and properties of quinazoline-based versatile exciplex-forming compounds
Beilstein J. Org. Chem. 2020, 16, 1142–1153, doi:10.3762/bjoc.16.101
- with the Gaussian software [26]. Firstly, the equilibrium conformer search at the ground state was performed by using the MMFF (molecular mechanics force fields) method, and this geometry was used for further optimization. The vertical singlet and triplet energy values were calculated by using the
- energy values at the corresponding excited-state geometry. The time-dependent DFT (TD-DFT) calculations were carried out with the Gaussian 16 software package and molecular orbitals were visualized by using Gaussview. Photoelectron emission spectroscopy measurement was performed according to the
Synthesis of esters of diaminotruxillic bis-amino acids by Pd-mediated photocycloaddition of analogs of the Kaede protein chromophore
Beilstein J. Org. Chem. 2020, 16, 1111–1123, doi:10.3762/bjoc.16.98
- isotropic displacement parameter equal to 1.2–1.5 times the equivalent isotropic displacement parameter of its parent atom. For structure solving and refinement the SHELX-97 [70], and Bruker APEX3 software package [71] were used. The structures were refined to Fo2, and all reflections were used in the least
A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium
Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97
- (10''-NH); HRESITOFMS (m/z): [M − H]− calcd for C36H36N5O7, 650.2615; found, 650.2614. Computational procedure General information Conformational search was performed with MacroModel implemented in the Maestro 11.7 software package [46][47]. All DFT-based calculations were performed with the Gaussian
- 16 Rev B.01 program [48]. A part of these computations was conducted using the SuperComputer System, Institute for Chemical Research, Kyoto University. Molecular structures were visualized using the Maestro 11.7 software package. DP4+ analysis was performed with the Excel spreadsheet made by Sarotti
Aryl-substituted acridanes as hosts for TADF-based OLEDs
Beilstein J. Org. Chem. 2020, 16, 989–1000, doi:10.3762/bjoc.16.88
- ] and Gaussview 6 software. The ionization potential measurements of the solid samples were performed by the photoelectron emission method in air [36]. Cyclic voltammetry (CV) measurements of the liquid samples were carried out as described earlier [37]. Charge drift mobility measurements for the
Cation-induced ring-opening and oxidation reaction of photoreluctant spirooxazine–quinolizinium conjugates
Beilstein J. Org. Chem. 2020, 16, 904–916, doi:10.3762/bjoc.16.82
- : 125 MHz) at 25 °C, or with a Varian VNMR-S 600 (1H: 600 MHz, 13C: 150 MHz) at 25 °C. The spectra were processed with the software ACD/NMR Processor Academic Edition (version: 12.02) or MestReNova (version: 12.0.1) and referenced to the respective solvent (DMSO-d6: δH = 2.50, δC = 39.5; CDCl3: δH
- no more changes were observed in the absorption spectra. All spectrometric titrations were performed at least two times to ensure reproducibility. In general, the absorption spectra were determined in a range between 200 nm and 800 nm and subsequently smoothed with the Origin software function
Efficient synthesis of piperazinyl amides of 18β-glycyrrhetinic acid
Beilstein J. Org. Chem. 2020, 16, 798–808, doi:10.3762/bjoc.16.73
- using conventional or microwave methods had no effect on the conversion of intermediate 6 to compound 8. To explain the stable structure of the intermediate 6 (Figure 2a), energy minimization by MM2 was performed using the ChemBio3D Ultra 14.0 (CambridgeSoft Corporation, 2014) software force field [22
Towards triptycene functionalization and triptycene-linked porphyrin arrays
Beilstein J. Org. Chem. 2020, 16, 763–777, doi:10.3762/bjoc.16.70
- corrected for Lorentz and polarization effects by using the APEX software suite [53][54][55]. Using Olex2, the structures were solved with the XT structure solution program, using the intrinsic phasing solution method and refined against |F2| with XL using least-squares minimization [56][57]. Hydrogen atoms
Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0
Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40
- application [66]. Data collection [67] in combination with self-leaning software related to artificial intelligence (A.I.) drives their use in applications with more efficiency in large workflows. Such tools can recognize failures in industrial processes just by collection of data in a big database where data
Six-fold C–H borylation of hexa-peri-hexabenzocoronene
Beilstein J. Org. Chem. 2020, 16, 391–397, doi:10.3762/bjoc.16.37
- ) [24] and refined by full-matrix least-squares techniques against F2 (SHELXL-2018/3) [25] by using Olex2 software package [26]. The intensities were corrected for Lorentz and polarization effects. Non-hydrogen atoms were refined anisotropically, and hydrogen atoms were placed using AFIX instructions
p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies
Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33
- consideration, are shown in Table 2 and were calculated using Gaussian 09 software program package [77]. The BDE difference between the two compounds is about 10 kcal/mol, while that in their adiabatic excitation energies is 3.9 kcal/mol. Since Δ0 − D0 is higher for 12 than 11 someone would expect 12 to be more
Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus
Beilstein J. Org. Chem. 2020, 16, 297–304, doi:10.3762/bjoc.16.29
- (δC 33.1 for 2 vs 28.3 for 1), a decisive evidence was acquired from spin system simulations using the software ‘nmrpeak’ [19], which gave the best match to the experimentally obtained 1H NMR spectrum with the setting of 3JH8,H9 = 15.6 Hz and 3JH7,H8 = 9.5 Hz (Figure 3). Thus, the C8 geometry was
Combination of multicomponent KA2 and Pauson–Khand reactions: short synthesis of spirocyclic pyrrolocyclopentenones
Beilstein J. Org. Chem. 2020, 16, 200–211, doi:10.3762/bjoc.16.23
- inertia analysis was carried out by calculation of the lowest energy conformation of compounds 3–39 and block buster drugs. The conformation calculation was performed using the built-in AMMP molecular mechanics algorithm with default parameters of the VEGA ZZ molecular modelling software package v.3.0.1
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