Search results
Search for "calculations" in Full Text gives 854 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Understanding the competing pathways leading to hydropyrene and isoelisabethatriene
Beilstein J. Org. Chem. 2022, 18, 972–978, doi:10.3762/bjoc.18.97
- two byproducts, isoelisabethatrienes A and B. Fascinatingly, a single active site mutation (M75L) diverts the product distribution towards isoelisabethatrienes A and B. In the current work, we study the competing pathways leading to these products using quantum chemical calculations in the gas phase
- inherent chemistry in these reactions and also points to some understanding of the possible thermodynamic and kinetic control in the enzyme. Results Reaction mechanism To better understand the HP and IE reaction pathways, we performed quantum mechanics (QM) calculations using density functional theory (DFT
- ). We studied the inherent chemistry of the reaction leading to HP and IE using gas-phase calculations. This provided the free energy of distinct carbocation intermediates and transition states along the proposed reaction path leading to products in the gas phase. The gas phase is a natural choice as a
Electrochemical and spectroscopic properties of twisted dibenzo[g,p]chrysene derivatives
Beilstein J. Org. Chem. 2022, 18, 963–971, doi:10.3762/bjoc.18.96
- design of DBC-based materials. Here, the electrochemical and spectroscopic properties of DBC derivatives were investigated, and the effects of substituents and torsion of the naphthalene moiety were examined based on density functional theory (DFT) calculations. All the substituted DBC derivatives showed
- higher oxidation potentials than that for DBC-H, even for compounds that contained an electron-donating group such as DBC-Me and DBC-SMe. DFT calculations clearly indicate that these higher oxidation potentials are due to the ineffective conjugation of the MeO group, which is oriented perpendicular to
- states. Herein, we report on the electrochemical and spectroscopic properties of the DBC derivatives, where the effects of substituents and torsion were examined with the aid of DFT calculations. Consequently, the findings revealed that the substitution at the Z position induces a change in the
Electroreductive coupling of 2-acylbenzoates with α,β-unsaturated carbonyl compounds: density functional theory study on product selectivity
Beilstein J. Org. Chem. 2022, 18, 956–962, doi:10.3762/bjoc.18.95
- studied using DFT calculations. Keywords: 2-acylbenzoates; chlorotrimethylsilane; 3-(3-cyanoethyl)phthalides; 2-cyanonaphthalen-1-ols; electroductive coupling; Introduction The electroreductive coupling between carbon–heteroatom and carbon–carbon double bonds is one of the promising methods for carbon
- 2 and subsequent rearrangement to 3 are also discussed. In particular, the latter mechanism was studied using density functional theory (DFT) calculations and it was suggested that the ΔG for the cyclization step of an intermediate enolate anion determines the product selectivity. Results and
- -oxobutyl)phthalides 5 were produced as the sole products by the reaction of 1 with methyl vinyl ketone (2b). It was found by DFT calculations for the cyclization step of the intermediate enolate anions that the product selectivity was in good agreement with the free energy differences (∆G) in the
Introducing a new 7-ring fused diindenone-dithieno[3,2-b:2',3'-d]thiophene unit as a promising component for organic semiconductor materials
Beilstein J. Org. Chem. 2022, 18, 944–955, doi:10.3762/bjoc.18.94
- ] and Gaussview [74] programs. A frequency calculation showed that all frequencies are positive indicating that a minimum was found [75]. The calculations showed that the middle section consisting of seven fused ring systems is nearly planar (Figure 10). The thiophene groups carrying the ethylhexyl
Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa
Beilstein J. Org. Chem. 2022, 18, 916–925, doi:10.3762/bjoc.18.91
- -dependent density functional theory/electronic circular dichroism (TDDFT-ECD) calculations or X-ray diffraction analysis. A plausible biosynthetic pathway of these sesquiterpenoids and their internal correlation were proposed and discussed. In an in vitro bioassay, (+)-aristolone (3) exhibited promising
- from isoprene units rather than by the much more common routes to aromatics involving acetate or shikimate [37]. In addition, the absolute stereochemistry of (+)-1 was unambiguously elucidated by TDDFT-ECD calculations, and the complete structure of 2 was confirmed for the first time by X-ray
- Centre with CCDC number 2173439 (2). The data could be obtained free of charge via http://www.ccdc.cam.ac.uk/data_request/cif. Details of the crystallographic data were shown in Supporting Information File 1. Computational section. TDDFT-ECD calculations. Conformational searches were conducted using the
First series of N-alkylamino peptoid homooligomers: solution phase synthesis and conformational investigation
Beilstein J. Org. Chem. 2022, 18, 845–854, doi:10.3762/bjoc.18.85
- studied in detail. Computational studies For the theoretical calculations, acetyl N-(methylamino)dimethylamide model peptoids (Ac-N(NMe)n-NMe2) were used instead of the corresponding synthesized benzyl esters. The model structures were generated using the coordinates extracted from the single crystal X
Synthesis and HDAC inhibitory activity of pyrimidine-based hydroxamic acids
Beilstein J. Org. Chem. 2022, 18, 837–844, doi:10.3762/bjoc.18.84
- °C (Scheme 2). It is known that there are two possible tautomeric forms of each hydroxamic acid: the keto and enol tautomer. Furthemore, each tautomer can adopt an E or Z conformation (Figure 2) [32][33][34][35][36]. The results of NMR spectra and theoretical calculations showed that hydroxamic acids
Synthesis of bis-spirocyclic derivatives of 3-azabicyclo[3.1.0]hexane via cyclopropene cycloadditions to the stable azomethine ylide derived from Ruhemann's purple
Beilstein J. Org. Chem. 2022, 18, 769–780, doi:10.3762/bjoc.18.77
- experimentally observed stereoselectivity. Keywords: azomethine ylides; cycloaddition; cyclopropenes; DFT calculations; spiro heterocycles; Introduction Spiro compounds (molecules containing at least two rings with only one common atom) are an important class of both synthetic and naturally occurring
- ourselves exclusively to carrying out laboratory experiments. We turned to DFT calculations (M11 density functional theory) [42][43][44][45][46] to interpret the experimental results. At the beginning of the computational study, we evaluated the relative stability of prototropic tautomers which are formed
- diastereoselective approach for the synthesis of bis-spirocyclic derivatives of 3-azabicyclo[3.1.0]hexane through cycloaddition reactions of a stable azomethine ylide – protonated Ruhemann's purple to cyclopropenes. The cycloaddition reaction is compatible with a broad scope of cyclopropenes. DFT calculations
An isoxazole strategy for the synthesis of 4-oxo-1,4-dihydropyridine-3-carboxylates
Beilstein J. Org. Chem. 2022, 18, 738–745, doi:10.3762/bjoc.18.74
- intermediate 3, as shown for the reaction of isoxazole 1g (Scheme 2). Taking into account that compounds 2 can potentially exist in pyridone and pyridole tautomeric forms, we performed calculations at the DFT B3LYP-D3/6-311+G(d,p) level of theory with SMD solvent model to evaluate this tautomeric equilibrium
Structural basis for endoperoxide-forming oxygenases
Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71
- molecular dynamics analyses, as well as DFT calculations of the FtmOx1 reaction, suggested a modified mechanism [72][73][74]. In this mechanism, the tyrosyl radical at Tyr224 is generated by the Fe(IV)=O species, which abstracts a hydrogen atom at C21 to form an endoperoxide ring through the reaction with
Mechanochemical halogenation of unsymmetrically substituted azobenzenes
Beilstein J. Org. Chem. 2022, 18, 680–687, doi:10.3762/bjoc.18.69
- species, cyclopalladated intermediates, and products (Figure 1). The monitoring results confirmed the crucial role of TsOH and acetonitrile (MeCN) as additives in the catalytic bromination of the C–H bond in L1. The experimental results were supported by quantum-chemical calculations, which showed that
Syntheses of novel pyridine-based low-molecular-weight luminogens possessing aggregation-induced emission enhancement (AIEE) properties
Beilstein J. Org. Chem. 2022, 18, 580–587, doi:10.3762/bjoc.18.60
- -induced emission enhancement (AIEE) properties in aqueous media. Compounds 4a and 4e, bearing electron-withdrawing groups (Br and CF3, respectively) showed 7.0 and 15 times fluorescence enhancement. Time-dependent density functional theory (TD-DFT) calculations were performed to gain better insight into
- in AIEE. To compare the electronic natures of the compounds with and without AIEE, we performed TD-DFT calculations on each monomer of 3a, 4a, and 4e. The graphical representations of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) for the ground-state
- 464 to 468 nm. From calculations, a smaller solvent effect is seen in the Exmaxcalc values for compound 4a (484–488 nm) and 4e (404–407 nm), whereas the Exmaxobs were found at 476 nm in ethanol and 413 nm in water for 4a and at 378 nm in ethanol and 415 nm in water for compound 4e, respectively. This
Terpenoids from Glechoma hederacea var. longituba and their biological activities
Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58
- structure elucidation was performed for the five new compounds (1–5) using 1D and 2D NMR, HRESIMS, DP4+ and ECD calculations, and chemical methods. All the isolates (1–9) were assessed for their antineuroinflammatory activities on nitric oxide (NO) production in lipopolysaccharide (LPS)-activated BV-2 cells
- via an equation below [24] (: calculated 13C NMR chemical shift for nucleus x, σ0: shielding tensor for the carbon nuclei in tetramethylsilane, σx: shielding tensor for the carbon nucleus x) The calculated 13C NMR chemical shifit of 2 were averaged as described above and used for calculations of DP4
BINOL as a chiral element in mechanically interlocked molecules
Beilstein J. Org. Chem. 2022, 18, 508–523, doi:10.3762/bjoc.18.53
- for the non-interlocked mixture, see Figure 15). DFT calculations showed that the reaction takes place by cooperative action of the Li phosphate macrocycle and the amine thread, enabled by the mechanical bond. The Li phosphate acts as a Lewis acid to activate the malonic acid diethyl ester, which is
Substituent effect on TADF properties of 2-modified 4,6-bis(3,6-di-tert-butyl-9-carbazolyl)-5-methylpyrimidines
Beilstein J. Org. Chem. 2022, 18, 497–507, doi:10.3762/bjoc.18.52
- confirm the structures of the synthesized compounds (see Figures S1–S27 in Supporting Information File 1). DFT analysis To assess the structural and electronic properties of the chromophores tCbz-mPYR and 1–6, quantum chemical calculations were performed. DFT analysis revealed that all studied compounds
- 49 ms integration time. Solid-state samples were mounted in a closed cycle He cryostat (Cryo Industries 204 N) for PL measurements in oxygen-free conditions. Quantum chemical calculations were carried out by using density functional theory at the B3LYP/6-31G(d) level as implemented in a software
Comparative study of thermally activated delayed fluorescent properties of donor–acceptor and donor–acceptor–donor architectures based on phenoxazine and dibenzo[a,j]phenazine
Beilstein J. Org. Chem. 2022, 18, 459–468, doi:10.3762/bjoc.18.48
- efficiency (EQE) exceeds the theoretical maximum of those with prompt fluorescent emitters. Most importantly, comparative study of the D–A molecule and its D–A–D counterpart from the viewpoints of the experiments and theoretical calculations revealed the effect of the number of the electron donor on the
- on the physicochemical properties of the DBPHZ-cored D–A system, the properties of D–A compound 1 were compared with those of POZ-DBPHZ. Theoretical calculations further support the impact of the donor numbers in the DBPHZ-cored D–A system. Results and Discussion Synthesis of materials To synthesize
- ], indicating a dominant non-radiative decay of the excited state for the D–A type compound, which was supported by the theoretical calculations (vide infra). In the solid state, the D–A compound 1 showed an emission at around λem = 560 nm with a very low ΦPL (<0.1) (Figure S1 in Supporting Information File 1
Site-selective reactions mediated by molecular containers
Beilstein J. Org. Chem. 2022, 18, 309–324, doi:10.3762/bjoc.18.35
- (Figure 1c). This kind of unusual site-selectivity originated from the fixed orientation of the guest substrates confined to the cage host A before the reaction. Force-field calculations showed that the guest substrates 1 and 2 were parallel to each other with the double bond of 2 in close contact with
- reactions. Naphthalene is usually hard to undergo Diels–Alder reactions [44][45][46], even though the quantum-mechanical and thermochemical calculations suggest that the reaction is exothermic, which indicates the entropic cost is significant [47]. In 2010, the same group reported another interesting site
Iridium-catalyzed hydroacylation reactions of C1-substituted oxabenzonorbornadienes with salicylaldehyde: an experimental and computational study
Beilstein J. Org. Chem. 2022, 18, 251–261, doi:10.3762/bjoc.18.30
- density functional theory calculations. We set out to confirm the catalytic cycle in detail, the geometries of the intermediates, the energy profiles of the reactions, and most importantly, the origin of regioselectivity. Results and Discussion Experimental We began our investigation with C1-methyl
- electron-withdrawing groups inactivates the iridium catalyst, perhaps by chelation with the carbonyl and the bridging oxygen atom. Computational Computational details All density functional theory (DFT) calculations in this study were carried out with the Gaussian 16, C.01 suite of programs [68]. Geometry
- optimization and frequency calculations. Frequency analyses and single-point energies were calculated with the M06 functional [69] with the triple-ζ basis set def2TZVP [70] with the PCM (1,4-dioxane) solvent model [72]. The Gibbs free energies of formation of the reactants, products, and transition states were
1,2-Naphthoquinone-4-sulfonic acid salts in organic synthesis
Beilstein J. Org. Chem. 2022, 18, 53–69, doi:10.3762/bjoc.18.5
- equilibrium between A and B using semiempirical calculations (AM1 and PM3) and DFT (B3LYP/6-31G(d)) in the gas phase and water, where it was observed that in the gas phase B is the most stable, while in water A is formed, which is in agreement with the experimental results reported in the literature. There
The enzyme mechanism of patchoulol synthase
Beilstein J. Org. Chem. 2022, 18, 13–24, doi:10.3762/bjoc.18.2
- calculations; enzyme mechanisms; isotopes; terpenes; Introduction Patchouli oil, the essential oil of the shrub Pogostemon cablin, has a pleasant woody odour and is of high economic value for the perfumery and cosmetics industries. It is mainly composed of sesquiterpenes with patchoulol as the main compound
- contradictory. For this reason, we have reinvestigated the enzyme mechanism of PTS in isotopic labelling experiments through methods recently developed in our laboratory that make use of 13C and 2H-substituted terpene precursors, and by DFT calculations. The general strategy in these experiments is to use
- experiments and the DFT calculations were not only carried out in a way to gain support for one mechanism, but also to disprove some of the earlier reports in order to resolve the contradictions in the literature. Results and Discussion Absolute configurations of patchoulol and pogostol In order to
Peptide stapling by late-stage Suzuki–Miyaura cross-coupling
Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1
- in i + 4-position of the linear axin CBD sequence aAxWt were substituted by tryptophan and lysine, respectively, to have a higher analogy to the lysine modified SMC stapled peptides. Following the indications of DFT calculations, stapled peptide P5 was synthesised by modification of lysine in the i
- for support in the synthetic work. Funding The project was supported in part by a Bielefeld University Ph.D. fellowship to H.G. and by Deutsche Forschungsgemeinschaft (SE609/16-1). The DFT calculations were carried out using hardware and software resources of the Supercomputing and Networking Center
- in Wroclaw (grant no. 197). R.M. and A.M. gratefully acknowledge the support of NVIDIA Corporation with the donation of a Titan Xp GPU used for this research as well as TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) for additional calculations.
DABCO-promoted photocatalytic C–H functionalization of aldehydes
Beilstein J. Org. Chem. 2021, 17, 2959–2967, doi:10.3762/bjoc.17.205
- strategy for aldehyde C–H activation. The acyl radicals generated in this step were arylated with aryl bromides through a well stablished nickel cross-coupling methodology, leading to a variety of interesting aryl ketones in good yields. We also performed computational calculations to shine light in the
- HAT step energetics and determined an optimized geometry for the transition state, showing that the hydrogen atom transfer between aldehydes and DABCO is a mildly endergonic, yet sufficiently fast step. The same calculations were performed with quinuclidine, for comparison of both catalysts and the
- through this step were used in a well-stablished nickel-catalyzed cross-coupling reaction [19][27][28][29][30] with aryl bromides as a proof of concept, leading to the synthesis of aryl ketones. We also present computational calculations of the HAT reaction step with the DABCO radical cation as the
Effect of a twin-emitter design strategy on a previously reported thermally activated delayed fluorescence organic light-emitting diode
Beilstein J. Org. Chem. 2021, 17, 2894–2905, doi:10.3762/bjoc.17.197
- DICzTRZ were determined by a combination of NMR spectroscopy, mass spectrometry, and IR spectroscopy. Theoretical calculations Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations in the gas phase at the PBE0/6-31G(d,p) level reveal the potential of DICzTRZ as a TADF material. The
- , respectively, while the S1 level for DICzTRZ is more stabilized at 2.80 eV vs 2.94 eV for ICzTRZ). We can clearly observe that the phosphorescence spectrum presents a well-defined structure, typical for transitions coming from a local excited (LE) type state on the diindolocarbazole. TDA-DFT calculations in
- calculations showed a much larger density of triplet states, which suggests that RISC will be faster in this compound compared to its parent. The twin design strategy leads to an enhancement in the molar extinction coefficient of the low-lying CT states, accompanied by a red-shift in the emission. The 20 wt
Biological properties and conformational studies of amphiphilic Pd(II) and Ni(II) complexes bearing functionalized aroylaminocarbo-N-thioylpyrrolinate units
Beilstein J. Org. Chem. 2021, 17, 2812–2821, doi:10.3762/bjoc.17.192
- , C. tropicalis, and C. glabrata standard strains. A deep conformational survey was monitored using DFT calculations with the aim to explain the importance of the final conformation in the biological experimental results. Keywords: antituberculosis; bidentate ligands; DFT; nickel; palladium
- results of its corresponding nickel(II) [18] and palladium(II) [19][20] complexes with the analogous tests obtained in the case of having a benzylic substituent at the same position. Also, DFT calculations are run in order to study the conformational analysis of the synthetized complexes. Results and
- 62.50–125 μg/mL (Table 2) when compared to reference drugs. the L3-Ni complex has the highest activity against Candida glabrata. DFT calculations of complexes The survey of relationship between structure of the complex and activity (SAR) moved us to design DFT calculations. The difference of the
Recent advances in the asymmetric phosphoric acid-catalyzed synthesis of axially chiral compounds
Beilstein J. Org. Chem. 2021, 17, 2729–2764, doi:10.3762/bjoc.17.185
- functional calculations showed that the chiral phosphoric acid proton forms an H-bond with nitrogen atoms of 1 and the phosphate acts as a chiral counterion, resulting in a [3,3]-sigmatropic rearrangement with controlled stereoselectivity [14][41]. In 2017, Tan and co-workers developed an organocatalytic
- density functional theory calculations [46]. Recently, Shi, Lin and co-workers reported the atroposelective synthesis of axially chiral biaryls by Pd(II)-catalyzed free amine-directed atroposelective C–H olefination using chiral spirophosphoric acid CPA 5 as an efficient ligand and Ag2CO3 as the oxidant
- provide easy access to the privileged NOBIN (2-amino-2’-hydroxy-1,1’-binaphthyl) structures 41. The additional insights into the origins of enantiocontrol were described by DFT calculations. Owing to the presence of axially chiral indole-based biaryl scaffolds such as naphthylindoles and phenylindoles in
Other Beilstein-Institut Open Science Activities
