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Search for "computational" in Full Text gives 514 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)
Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215
- synthesized through the serial addition of monosaccharides to form large polysaccharides. To build computational models of glycan synthesis, the biochemical reactions involved must be defined and described mathematically in a form that can be interpreted by computers [1][2][3]. Several groups have created
- monosaccharides and abbreviates the glycan symbols, thereby simplifying the representation without limiting flexibility. Given its readability and parsability, Linear Code has become a popular choice for representing reaction rules in computational models of glycan synthesis (Table 1). However, with the rise of
- reactions which add a galactose to an N-acetylglucosamine, but not necessarily the terminal one. The leftmost “ ( ”, therefore, can easily vary the glycan substrate substantially. Though Linear Code was developed with parsability in mind, some have found it useful to make a specific computational
Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding
Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206
- biological interaction, searching for structural data, and then searching for the molecular rationale. This is the connection between biology, chemical biology, and chemistry. The Galaxy project is a popular open web-based platform for accessible, reproducible, and transparent computational research [1
- . and others [14][16] provides a foundation for further investigation into the binding of glycopeptide antigens to antibodies using computational modeling. Molecular dynamics (MD) simulations and analysis thereof are a well-known ingredient of the in-silico process for mechanistic screening of
- of the analyses was carried out using Galaxy, the popular open web-based platform for bioinformatics and computational data analysis, which enables the creation of repeatable analysis pipelines (workflows). There are several well-known molecular dynamics analysis packages (MDAnalysis [37], Bio3D [38
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer
Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204
- glycan core to carry out further checks in the glycoprotein model (Figure 2). Availability and performance of the algorithm This new version of Privateer (MKIV) will be released as an update to CCP4 7.1. To demonstrate the capabilities of the computational bridge integrated in the newest version of
- demonstration was obtained from Atanasova et al. [18]. The computational analysis of the demonstration revealed a relatively small proportion of deposited glycoprotein models containing glycan chains that do not have a unique GlyTouCan accession ID assigned, raising questions about the provenance of their
- of gross modelling errors is currently a challenge due to the lack of publicly available tools. Our newly developed computational bridge between structural biology and glycomics databases makes the detection of gross modelling errors easier, as demonstrated by the following examples. Example 1 – 2H6O
NMR Spectroscopy of supramolecular chemistry on protein surfaces
Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203
- substituents binding to Cyt c was also studied by 15N-HSQC titrations [59]. Interestingly, large areas of the protein surface showed chemical shift perturbations, even though the binding curves clearly revealed a 1:1 stoichiometry. Crowley et al. concluded from the NMR data in combination with computational
- effect. While the computational results suggest that a specific basic residue in a given patch is bound by the tweezers, a dynamic complex involving “ligand hopping” in solution cannot be excluded. This challenge can be solved with the Lys and Arg-specific side chain NMR spectra described below. The
Dawn of a new era in industrial photochemistry: the scale-up of micro- and mesostructured photoreactors
Beilstein J. Org. Chem. 2020, 16, 2484–2504, doi:10.3762/bjoc.16.202
Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction
Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200
- conformers (II, VI, and VII), and with a rotatable C–C(F) bond that generates different conformers (I). The μ values for all herbicides were computed through theoretical calculations (see computational details section) and are presented in Table 2 along with their respective experimental log P data
- calculated molecular dipole moments as a descriptor of lipophilicity for small molecules, a more detailed analysis is required. Accordingly, a series of structurally simpler organofluorine compounds were retrieved (Figure 6), all from the same source [29], and a similar computational routine was carried out
- (see computational details section for a full description). Compounds 7, 9, and 10 have the dependence of the molecular dipole moment μ with the rotation around the C–C bond. The correlation plots between the experimental log P of compounds 1–11 and a) dipole moment and b) predicted log P are shown in
Computational tools for drawing, building and displaying carbohydrates: a visual guide
Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199
- carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools for the sketching, visualisation and modelling of glycans. The article also provides details on the standard representation of glycans, and
- areas of chemical and biochemical fragmentations followed by analysis using mass spectroscopy, nuclear magnetic resonance, crystallography and computational modelling. There have been some initiatives by independent research groups worldwide, that pushed the development of visual tools to improve some
- developments supported the construction and representation of glycan structures in symbolic form by computational tools like GlycanBuilder [10]. Since then, several advancements have been made to allow the user to both draw glycans manually or by importing and exporting the structure files in different text
Recent developments in enantioselective photocatalysis
Beilstein J. Org. Chem. 2020, 16, 2363–2441, doi:10.3762/bjoc.16.197
Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties
Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189
- Shimadzu 1800 UV–vis spectrophotometer in Britton–Robinson buffer solutions [63] with pH values ranging from 5.5 to 11 at room temperature (25 °C). The pKa values were obtained using the Origin software by recording the curve data. Computational methods The geometries of the dyes in their ground states
Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups
Beilstein J. Org. Chem. 2020, 16, 2141–2150, doi:10.3762/bjoc.16.182
- ). Interestingly, a two-carbon extension of I1 with concomitant vicinal difluorination (G7 [28]) or fluorinated cyclopropyl (E3) leads to a much smaller increase in logP compared to two-carbon extension as a cyclopropyl (E1). Computational results A number of open-access fragment-based calculation methods, as well
GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis
Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180
- quantitative glycoproteomic data analysis. GlypNirO takes Byonic and Proteome Discover output files, and user-defined sample information and processing parameters, performs a series of automated data integration and computational steps, and provides informative and intuitive output files with site or peptide
Muyocopronones A and B: azaphilones from the endophytic fungus Muyocopron laterale
Beilstein J. Org. Chem. 2020, 16, 2100–2107, doi:10.3762/bjoc.16.177
- –7.62 (m, 10H, phenyl groups of MTPAs). Computational methods Calculation of the ECD spectra were performed using CONFLEX 8, Gaussian 16, and SpecDis software as described previously [13][14]. Geometry optimizations were performed using DFT at the CAM-B3LYP/6-311+G(d,p) level of theory, while TDDFT
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
- optimization study. The key advantage of this computational approach is that all runs can be analyzed simultaneously with high accuracy in glycan identification and quantitation and there is no theoretical limit to the scale of this method. Keywords: capillary electrophoresis; clustering; data analysis
- . Here, we describe a computational solution for the identification and quantitation of glycans in a large glycomics CE dataset generated during process development of an anti-HER-2 antibody. The method is a semi-automated approach and improved accurate glycan assignments and quantitation compared to
- . To the best of our knowledge, we are the first to apply this computational approach to a large set of CE-LIF glycomic data. The result of this new method is that large cohorts (thousands) of bioreactor runs can be analyzed at once with high accuracy in quantitation and glycan identification. We
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
- also of how specific modifications affect molecular recognition. Computational Methods All starting structures were generated with the GLYCAM Carbohydrate Builder (http://www.glycam.org). For each sequence we selected the complete set of torsion angle values obtained by variation of the 1-6 dihedrals
- , respectively. Supporting Information Supporting Information File 516: Computational methods and supplementary figures and tables. Acknowledgements EF would like to thank Prof. Iain B.H. Wilson for insightful feedback on an earlier version of the manuscript. Funding The Irish Centre for High-End Computing
- (ICHEC) is gratefully acknowledged for generous allocation of computational resources. EF and CAF acknowledge the Irish Research Council (IRC) for funding through the Government of Ireland Postgraduate Scholarship Programme. EF and AMH acknowledge the John and Pat Hume Doctoral Scholarship Programme at
Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA
Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170
- with significant Stokes shifts (+60 nm) and quantum yields of 10–32% (Table 1). Theoretical calculations To get insight into the electronic and optical properties of the 2-amino-6-chloro-substituted NDIs, we carried out computational investigations by using the Gaussian 09 program suite [32]. In
Design, synthesis and application of carbazole macrocycles in anion sensors
Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157
- carboxylates were modelled computationally using COSMO-RS. Several observations were made from the computational structures. Intramolecular hydrogen bonds between the urea carbonyl and the carbazole NH protons were present in macrocycles MC001 and MC003, as indicated in Figure 4. The rings of these macrocycles
- started to decrease. The initial increase of the binding affinity suggested that just fitting into the ring was not a sufficient criterion for predicting binding affinity. This was because for the macrocycles MC003–MC005, the computational geometries suggested that the ring is too small to bind any of the
- computational geometries), allowing for more dynamic complexes to form. Such affinity was not entirely surprising as both, the open-chain receptor and the closed macrocycles, employed only aliphatic substituents in the 1 and 8 positions of the biscarbazolylurea moiety. Preparation and characterization of sensor
Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2
Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152
- substrate of mycobacterial galactofuranosyltransferase GlfT2 in the transition state, we evaluated these compounds by computational methods, as well as in an enzyme assay for the possible inhibition of the mycobacterial galactan biosynthesis. Our data show that despite favorable docking scores to the active
- mechanism studies using computational chemistry methods. The probable reaction mechanisms were studied by hybrid DFT QM/MM molecular dynamics simulations [11] where the possible transition state (TS) structures were localized. The observation of the possible TS structure opens the opportunities for the in
- synthesized. We performed docking studies of these compounds into the active site of GlfT2 by computational chemistry methods. Although the docking study showed good binding affinities of the prepared compounds towards the GlfT2 active site, their biological evaluation revealed a very poor effect on the
One-pot synthesis of oxazolidinones and five-membered cyclic carbonates from epoxides and chlorosulfonyl isocyanate: theoretical evidence for an asynchronous concerted pathway
Beilstein J. Org. Chem. 2020, 16, 1805–1819, doi:10.3762/bjoc.16.148
- isocyanate; computational modeling; cyclic carbonates; density functional theory; oxazolidinone; Introduction Oxazolidinones (1), five-membered heterocyclic rings containing an ester group adjacent to a nitrogen atom, are important compounds in synthetic and pharmaceutical chemistry because of their
- computational mechanistic study in the literature regarding the reaction of epoxides with CSI. On the other hand, the reactions of isocyanates with monofluoroalkenes and nitrones were modeled with the Møller–Plesset (MP2) perturbation theory and M06-2X functional, respectively [37][47]. According to these
- computational studies, such reactions of isocyanates may proceed through a concerted pathway. The remaining uncertainties in the mechanisms of the similar reactions inspired us to carry out quantum chemical calculations for the formation of oxazolidinone and five-membered cyclic carbonates. Results and
One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?
Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143
- particular, in situ kinetic studies by spectroscopic methods [31] correlated to computational chemistry approaches [32] might reveal specific interaction between reactants and catalysts as well as solvent effects at work in such a complex system that should provide an understanding of the underlying reason
Models of necessity
Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137
- these models be extended to cover all relevant properties and characteristics of chemical systems. This, in turn, imposes conditions such as completeness, compactness, computational efficiency and non-redundancy on the extensions to the almost universal Lewis and VSEPR bonding models. Thus, AI and ML
- approximation for computational quantum chemistry has long attained the status of a bonding model to such an extent that many chemists outside the theoretical community are unaware that it is an approximation. Molecular-orbital bonding models based on the LCAO approximation discuss chemical bonds in terms of
- computational studies. Furthermore, reactions often follow competing paths, where the dominance of one over another often depends on the specific reaction conditions and only minor variations can give rise to a different outcome. Biological systems have a network of pathways and it is often very difficult to
Rearrangement of o-(pivaloylaminomethyl)benzaldehydes: an experimental and computational study
Beilstein J. Org. Chem. 2020, 16, 1636–1648, doi:10.3762/bjoc.16.136
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
- studies of the 4-component macrocycle precursor were carried out. To reduce computational cost a model compound was considered, replacing the ferrocene by a hydrogen atom and replacing the hexyl chains of the template by methyl groups. Monte Carlo conformational searches were performed on the model
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
- of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, UK Benevolent AI, Minerva Building, Babraham Research Campus, Cambridge CB22 3AT, UK 10.3762/bjoc.16.122 Abstract A computational approach has been developed to automatically generate and analyse the structures of the
- transition metal coordination sphere; the energy of a new M–C bond formed and the thermodynamic stability of organometallic product. With new developments in computational chemistry, mechanistic studies using density functional theory (DFT) provide valuable insights into the reactivity of organometallic
- big challenge remaining which is to apply the computational analysis to a large number of mechanistically different transformations, both described and novel, in order to start generating accurate in silico reaction predictions. Here, we report an algorithm with high-performance computing (HPC
Highly selective Diels–Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole
Beilstein J. Org. Chem. 2020, 16, 1320–1334, doi:10.3762/bjoc.16.113
- provide compounds 12. To account for the strong endo preference of adducts 9, a computational study was performed to analyze the stationary points on the potential surfaces of the Diels–Alder reactions. Results and Discussion Synthesis Pyrroles 8a–j were prepared through a straightforward and efficient
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
- , angiogenesis, and metastasis in cancer [12][13][14][15], pointing at bisphosphonates as potential treatments for cancer and other inflammation-related diseases. In this respect, MMP inhibition by phosphonates or bisphosphonates has been previously studied through computational or X-ray diffraction analyses to
- biological targets of 3–6. Computational and theoretical analysis Ligands structure–activity relationship As a first approximation, we studied the structural and physicochemical features of the compounds to explain the antiinflammatory activity. The structure geometry used to obtain the molecular properties
- 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
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