Asymmetric organocatalytic synthesis of chiral homoallylic amines

• Nikolay S. Kondratyev and
• Andrei V. Malkov

Beilstein J. Org. Chem. 2024, 20, 2349–2377, doi:10.3762/bjoc.20.201

• ]-rearrangement of ene-aldimines 149, catalysed by the BINOL-derived chiral phosphoric acid (CPA) (R)-151 (Scheme 31) [46]. DFT computational analysis suggested that the reaction proceeds via a complex cascade that involves the fragmentation of ene-aldimine 149 to form an imine methylene cation, which in turn

Synthesis and reactivity of the di(9-anthryl)methyl radical

• Tomohiko Nishiuchi,
• Kazuma Takahashi,
• Yuta Makihara and
• Takashi Kubo

Beilstein J. Org. Chem. 2024, 20, 2254–2260, doi:10.3762/bjoc.20.193

• two anthryl moieties (Figure 3b, Supporting Information File 1, Figure S1). DFT calculations for structural optimization revealed that the energy difference between two DAntM radical structures with different spin positions, spin localization at the central sp2 carbon and on the anthryl group, is

• Figure 6a and 6b, respectively. The DAntM radical exhibited a forbidden near-IR (NIR) band centered at 900 nm and relatively intense bands at 580 and 540 nm, whose spectral pattern is similar to the spectrum pattern of the TAntM radical [17]. The result of TD-DFT calculations could reproduce the obtained

• . Decomposition pathway of the DAntM radical under air conditions. Supporting Information Supporting Information File 81: Synthetic procedure and compound characterization data (1H, 13C NMR, MS, melting point, X-ray crystallography) of new compounds. DFT calculation results and optimized structural Cartesian

Metal-free double azide addition to strained alkynes of an octadehydrodibenzo[12]annulene derivative with electron-withdrawing substituents

• Naoki Takeda,
• Shuichi Akasaka,
• Susumu Kawauchi and
• Tsuyoshi Michinobu

Beilstein J. Org. Chem. 2024, 20, 2234–2241, doi:10.3762/bjoc.20.191

• substituents has a lower Ea than DBA with electron-donating substituents. DFT calculations The reaction mechanism was investigated by computational calculations. The reaction mechanism between 5 and benzyl azide was supported by the ωB97X-D/6-31G(d,p) calculations with the CH2Cl2 polarizable continuum model

• previously reported electron-donating hexyloxy substituents. The addition pattern was experimentally investigated by 2D NMR, which was also supported by DFT calculations. The bistriazole product displayed fluorescence in the visible range with a fluorescence quantum yield of 7.0%. Finally, the developed

• recorded on a JASCO FP-8500. All calculations were carried out using the Gaussian 16 program [21]. The DFT calculations were carried out using the long-range and dispersion-corrected ωB97X-D functional [22]. The 6-31G(d,p) basis set was used for H, C, O, and S atoms [23][24]. The solvent effect of CH2Cl2

Heterocycle-guided synthesis of m-hetarylanilines via three-component benzannulation

• Andrey R. Galeev,
• Maksim V. Dmitriev,
• Alexander S. Novikov and
• Andrey N. Maslivets

Beilstein J. Org. Chem. 2024, 20, 2208–2216, doi:10.3762/bjoc.20.188

• Russian Federation (FSNF-2023-0004). The DFT calculations were supported by the RUDN University Scientific Projects Grant System, project № 021342-2-000.

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

Beilstein J. Org. Chem. 2024, 20, 2171–2207, doi:10.3762/bjoc.20.187

Allostreptopyrroles A–E, β-alkylpyrrole derivatives from an actinomycete Allostreptomyces sp. RD068384

• Marwa Elsbaey,
• Naoya Oku,
• Mohamed S. A. Abdel-Mottaleb and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2024, 20, 1981–1987, doi:10.3762/bjoc.20.174

• : Allostreptomyces; β-alkylpyrrole; conformer; cytotoxic; DFT; 4-formylpyrrole-2-carboxylic acid; Introduction β-Alkylpyrroles are key structural motifs in biomolecules and functional organic materials [1]. For instance, β-alkylpyrroles are the main building blocks for the life-essential tetrapyrrole pigments

• to their populations [25]. The calculated specific rotations −11.4 and +16.1 were obtained for R-configured 2 and 3 from the DFT computations (see DFT methodology section), respectively, which were in good agreement with the experimentally obtained values, −6.1 for 2 and +15 for 3. Thus, R

• monitored by TLC. The solution was diluted with water and extracted with EtOAc three times. The organic layer was washed with brine and evaporated to dryness to afford bismethylated derivative of 1 (1a, 1.9 mg, 88% yield). DFT methodology Prior to the calculations of the molecular properties of compounds 2

Radical reactivity of antiaromatic Ni(II) norcorroles with azo radical initiators

• Siham Asyiqin Shafie,
• Ryo Nozawa,
• Hideaki Takano and
• Hiroshi Shinokubo

Beilstein J. Org. Chem. 2024, 20, 1967–1972, doi:10.3762/bjoc.20.172

• ) norcorrole. The radical reactivity of Ni(II) norcorroles was investigated by density functional theory (DFT) calculations. Keywords: 16π; antiaromatic; norcorrole; porphyrinoid; radical; Introduction Considerable attention has been directed toward antiaromatic norcorroles [1][2][3] due to the fascinating

• presented. We also discuss the selectivity of the radical addition to Ni(II) norcorroles using DFT calculations. Results and Discussion Reactivity with azo radical initiators We selected 2,2'-azobis(isobutyronitrile) (AIBN) as a radical source. Ni(II) dimesitylnorcorrole 1 was treated with AIBN in refluxing

• 2a obtained by TD DFT calculations at the M06/6-31G(d)+SDD//B3LYP-D3/6-31G(d)+SDD level of theory was consistent with the experimental results. Therein, the absorption band at 670 nm (f = 0.0026) was attributed to the transition from HOMO to LUMO+1. Next, the electrochemical properties of 2a in

Regioselective alkylation of a versatile indazole: Electrophile scope and mechanistic insights from density functional theory calculations

• Pengcheng Lu,
• Luis Juarez,
• Paul A. Wiget,
• Weihe Zhang,
• Krishnan Raman and
• Pravin L. Kotian

Beilstein J. Org. Chem. 2024, 20, 1940–1954, doi:10.3762/bjoc.20.170

• -carboxylate (6) and the use of density functional theory (DFT) to evaluate their mechanisms. Over thirty N1- and N2-alkylated products were isolated in over 90% yield regardless of the conditions. DFT calculations suggest a chelation mechanism produces the N1-substituted products when cesium is present and

• compounds 6, 18, and 21 via natural bond orbital (NBO) analyses which further support the suggested reaction pathways. Keywords: DFT; indazole; indazole substitution; mechanism; N1-substituted indazole; N2-substituted indazole; regioselectivity; Introduction Indazoles constitute an important class of

• isolated in >99% yield under conditions B albeit with low conversion. Both conditions provided >98:2 regioselectivity for their respective major products as determined by LC–MS. We again turned to DFT calculations to explore the mechanisms of these reactions and found very similar results to the parent

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

• diaryliodonium triflates such as 8 and 9 [13]. They studied a model reaction with 2-aminopyridine (1), p-tolualdehyde (10) and cyclohexyl isocyanide (11) both experimentally (by binding and kinetic studies) and theoretically (by density functional theory (DFT) calculations) (Scheme 5). Catalyst 8 was found to be

Hetero-polycyclic aromatic systems: A data-driven investigation of structure–property relationships

• Sabyasachi Chakraborty,
• Eduardo Mayo Yanes and
• Renana Gershoni-Poranne

Beilstein J. Org. Chem. 2024, 20, 1817–1830, doi:10.3762/bjoc.20.160

• ][33] level, including the D3 dispersion correction [29] by Grimme with Becke-Johnson damping [30]. We used the DFT-calculated dataset to generate fitting functions, such that all xTB-generated data was corrected to near DFT-level accuracy [9]. It is these corrected data that we use in this report to

Oxidative fluorination with Selectfluor: A convenient procedure for preparing hypervalent iodine(V) fluorides

• Samuel M. G. Dearman,
• Xiang Li,
• Yang Li,
• Kuldip Singh and
• Alison M. Stuart

Beilstein J. Org. Chem. 2024, 20, 1785–1793, doi:10.3762/bjoc.20.157

• (1–3 % spectroscopic yield) when BF3·OEt2 was added to the reaction mixture. X-ray crystallography and DFT calculations The solid-state structure of difluoroiodane 6 is shown in Figure 2 and displays the expected square pyramidal geometry around the iodine atom, with only minor distortion (τ5 = 0.191

• Supporting Information File 1). DFT calculations were carried out to gain further insight into the structures of iodine(V) fluorides 21 and 22 whose X-ray structures could not be obtained, and hypothetical iodine(V) amides 7a and 7b which could not be made. Comparisons were made with iodine(V) compounds 6

• . The only major difference between the bicyclic and monocyclic iodine(V) fluorides is the much smaller O–I–O bond angle (161.4(2) °) in difluoroiodane 6 compared to the F’–I–O bond angle (167.9(2) ° in 20) in the monocyclic iodanes 20–22. In fact, DFT calculations predicted that hypothetical

pKalculator: A pK_a predictor for C–H bonds

• Rasmus M. Borup,
• Nicolai Ree and
• Jan H. Jensen

Beilstein J. Org. Chem. 2024, 20, 1614–1622, doi:10.3762/bjoc.20.144

• identify the lowest-energy conformer. We then conduct re-optimization in ORCA (v. 5.0.4) [22][23], using the dispersion D4-corrected DFT functional CAM-B3LYP [24][25], the Karlsruhe [26][27] triple-ζ basis set, def2-TZVPPD, and the conductor-like polarizable continuum model (CPCM) [28] as the implicit

• solvation models. CAM-B3LYP is chosen as the optimal functional based on a benchmark study that evaluates the accuracy of different levels of theory, ranging from semiempirical methods (xTB) [21] over composite electronic structure methods (r2SCAN-3c) [29] to DFT methods (CAM-B3LYP) [24][25]. All these

• the XGBoost pKa predictor by Yang et al. [5]. Roszak et al. [3] used a mix of experimental data (414 compounds) [7], manually curated DFT data (212 compounds), and previously reported DFT data (194 C–H sites) [11]; they obtained a MAE of 2.18 pKa units for their test set. Yang et al. [5] used filtered

Divergent role of PIDA and PIFA in the AlX₃ (X = Cl, Br) halogenation of 2-naphthol: a mechanistic study

• Kevin A. Juárez-Ornelas,
• Manuel Solís-Hernández,
• Pedro Navarro-Santos,
• J. Oscar C. Jiménez-Halla and
• César R. Solorio-Alvarado

Beilstein J. Org. Chem. 2024, 20, 1580–1589, doi:10.3762/bjoc.20.141

• halogenation via PhIX2. Keywords: aromatic bromination; aromatic chlorination; density functional theory (DFT); hypervalent iodine; iodine(III); Introduction Hypervalent iodine(III) reagents have gained attention as strong oxidants with a low toxicity [1][2][3][4][5][6][7][8] and due to the ability to mimic

• , and transition-state structures were optimized by density functional theory (DFT) calculations employing the software Gaussian 16 [34]. Although the B3LYP functional could be suitable for these calculations, e.g., for tracing reaction pathways, nitrations, halogenations, or FC acylations in solution

Regio- and stereochemical stability induced by anomeric and gauche effects in difluorinated pyrrolidines

• Ana Flávia Candida Silva,
• Francisco A. Martins and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2024, 20, 1572–1579, doi:10.3762/bjoc.20.140

• each be subjected to quantum-chemical analysis. Results and Discussion In order to achieve the most accurate conformational depiction of the difluorinated pyrrolidines through density functional theory (DFT), a benchmark study was conducted. This study compares the crystallographic geometry of a

• pyrrolidinium salt [11] with the CCSD/DGTZVP geometry of the pyrrolidinium cation (with an exclusively axial C–F bond) and the energy of 3-fluoropyrrolidine conformations. Various combinations of DFT methods (B3LYP-D3BJ, ωB97XD, and PBEPBE) and basis sets (DGTZVP and 6-311++G**) were evaluated. The selection of

• (nN→σ*CF anomeric and σCH→σ*CF fluorine gauche effects) on the conformation of different stereoisomers is explored. MAE comparing the geometry parameters (bond length, bond angle, and dihedral angle) obtained from DFT calculations at the CCSD/DGTZVP level. The MAE for the crystal structure compared to

Predicting bond dissociation energies of cyclic hypervalent halogen reagents using DFT calculations and graph attention network model

• Yingbo Shao,
• Zhiyuan Ren,
• Zhihui Han,
• Li Chen,
• Yao Li and
• Xiao-Song Xue

Beilstein J. Org. Chem. 2024, 20, 1444–1452, doi:10.3762/bjoc.20.127

• both homolytic and heterolytic bond dissociation energies (BDEs) critical for assessing the chemical stability and functional group transfer capability of cyclic hypervalent halogen compounds using density functional theory (DFT) analysis. A moderate linear correlation was observed between the

• results of this study could aid in estimating the chemical stability and functional group transfer capabilities of hypervalent bromine(III) and chlorine(III) reagents, thereby facilitating their development. Keywords: BDE; cyclic hypervalent halogen reagents; DFT calculation; graph attention network

• DFT calculations for predicting key properties of organic molecules such as BDE, nucleophilicity, and electrophilicity [48][49][50][51][52][53][54][55][56][57][58][59][60]. Recently, applications of the Elastic Net model with Avalon fingerprints [55] and the deployment of artificial neural network

A comparison of structure, bonding and non-covalent interactions of aryl halide and diarylhalonium halogen-bond donors

• Nicole Javaly,
• Theresa M. McCormick and
• David R. Stuart

Beilstein J. Org. Chem. 2024, 20, 1428–1435, doi:10.3762/bjoc.20.125

• , monovalent, and hypervalent have been developed and studied. In this work we used density functional theory (DFT), natural bond orbital (NBO) theory, and quantum theory of atoms in molecules (QTAIM) to analyze aryl halogen-bond donors that are neutral, cationic, monovalent and hypervalent and in each series

• Cl, Br, I, and At. We have used density functional theory (DFT) to uncover periodic trends in the orbitals used by the central halogen atom in forming covalent and non-covalent interactions and how this impacts the interatomic distance and energy of halogen-bond interactions (Scheme 1c). Results and

• Discussion This study evolved from a parallel exploration of reactions involving unsymmetrical phenyl(mesityl)halonium salts, i.e., Ph(Mes)X+. DFT analysis revealed similar structural trends to our previous work [21] when we expanded the halogens to include astatine (At). Due to its radioactivity and short

Synthesis of cyclic β-1,6-oligosaccharides from glucosamine monomers by electrochemical polyglycosylation

• Md Azadur Rahman,
• Hirofumi Endo,
• Takashi Yamamoto,
• Shoma Okushiba,
• Norihiko Sasaki and
• Toshiki Nokami

Beilstein J. Org. Chem. 2024, 20, 1421–1427, doi:10.3762/bjoc.20.124

• disaccharide 16 was obtained as an exclusive product. The optimized structure of 15 calculated by DFT (B3LYP/6-31G(d)) suggested that the pyran ring preferred the boat conformation because the chair conformation of the pyran ring was controlled by the introduction of the 2,3-oxazolidinone protecting group (see

• DFT calculations in Supporting Information File 1). Therefore, it was proven that the 2,3-oxazolidinone protecting group was powerful enough to prevent intramolecular glycosylation of monomer 14. However, it did not prevent intramolecular glycosylation of the linear disaccharide and promote the

• monomers 6 with a 2-PhthN group. Electrochemical polyglycosylation of monomers 17 with a 2-azido group. Supporting Information Supporting Information File 18: Synthetic details, DFT calculations, and compound characterization data. Acknowledgements We thank Koganei Corporation (Tokyo, Japan) for donation

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

• Zining Li,
• Sana Jindani,
• Volga Kojasoy,
• Teresa Ortega,
• Erin M. Marshall,
• Khalil A. Abboud,
• Sandra Loesgen,
• Dean J. Tantillo and
• Jeffrey D. Rudolf

Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115

• rearrangement; DFT calculations; diterpene; electrophilic cyclization; eunicellane; Introduction The eunicellane diterpenoids are a family of nearly 400 natural products that present a conserved 6/10-bicyclic hydrocarbon framework [1][2][3]. Mostly known from soft corals [2], but with a growing number of

• anticipated that 1 would similarly undergo Cope rearrangement. However, when we heated 1 up to 200 °C for 5 h, we did not observe any Cope rearrangement products and we were able to recover >90% of 1. DFT calculations [mPW1PW91/6–31+G(d/p)/SMD(toluene)] on the Cope rearrangement of 2 revealed a free energy

• activation energy may allow for oxy-Cope rearrangement at 28 °C. DFT calculations (in toluene) of 5-hydroxyalbireticulene for both the pseudo-axial and pseudo-equatorial conformations of the C5 hydroxy moiety suggest that there is not a significant difference in the free energy barriers for the oxy-Cope

Sustainable tandem acylation/Diels–Alder reaction toward versatile tricyclic epoxyisoindole-7-carboxylic acids in renewable green solvents

• Ayhan Yıldırım

Beilstein J. Org. Chem. 2024, 20, 1308–1319, doi:10.3762/bjoc.20.114

• (Figure 3, path I) [132]. Similarly, Tomberg et al., note that in such reactions, amide is formed rapidly by opening the maleic anhydride ring first, followed by a slower cyclization [133]. On the other hand, according to the results of some DFT calculations, Naguib et al., state that [4 + 2

Diameter-selective extraction of single-walled carbon nanotubes by interlocking with Cu-tethered square nanobrackets

• Guoqing Cheng and
• Naoki Komatsu

Beilstein J. Org. Chem. 2024, 20, 1298–1307, doi:10.3762/bjoc.20.113

• complexation, a significant red-shift of the dipyrrin band to 465 nm was observed due to the metal coordination with the dipyrrin moieties in 4b. To compare the structures of 1a and 1b, they are calculated through geometry optimization with the density functional theory (DFT) method. The alkyl chains at the

• binding energy between SWNTs and the host molecules is calculated by the GFN2-xTB method, because the number of atoms is too large to use DFT methods. The binding energy Ebind is calculated by the following equation: The Ehost, ESWNTs and Ecomplex are the electronic energies of the host molecules, SWNTs

• -nanobrackets 1b. DFT-optimized structure of Cu-nanobrackets (a) 1a and (b) 1b. The yellow regions indicate their spherical cavities. (c) Experimental and calculated results of Raman spectra of 1b (λex = 488 nm). For calculation, Raman activity was transferred to Raman intensity (298.15 K, the full width at

Synthesis and physical properties of tunable aryl alkyl ionic liquids based on 1-aryl-4,5-dimethylimidazolium cations

• Stefan Fritsch and
• Thomas Strassner

Beilstein J. Org. Chem. 2024, 20, 1278–1285, doi:10.3762/bjoc.20.110

• start at 0 V. Structures of the imidazolium cations obtained by DFT calculations (B3LYP/6-311++G (d,p)). The electrostatic potentials are indicated by color (blue: positive; red: negative). Overview of the synthesis of compounds 1–63. Thermal decomposition point at 5% mass loss in °C for NTf2− TAAILs 37

Synthesis of indano[60]fullerene thioketone and its application in organic solar cells

• Yong-Chang Zhai,
• Shimon Oiwa,
• Shinobu Aoyagi,
• Shohei Ohno,
• Tsubasa Mikie,
• Jun-Zhuo Wang,
• Hirofumi Amada,
• Koki Yamanaka,
• Kazuhira Miwa,
• Naoyuki Imai,
• Takeshi Igarashi,
• Itaru Osaka and
• Yutaka Matsuo

Beilstein J. Org. Chem. 2024, 20, 1270–1277, doi:10.3762/bjoc.20.109

• differences between t-Bu-FIDO and t-Bu-FIDS, the density functional theory (DFT) method was employed using the B3LYP hybrid functional. The 6-31G* basis set was used for the geometry optimization and frequency calculation. The thiocarbonyl group in FIDS was found to have an out of plane bending vibration

Synthesis and optical properties of bis- and tris-alkynyl-2-trifluoromethylquinolines

• Stefan Jopp,
• Franziska Spruner von Mertz,
• Peter Ehlers,
• Alexander Villinger and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 1246–1255, doi:10.3762/bjoc.20.107

• different fine structures. However, TD-DFT calculations using the long-range correlated CAM-B3LYP/6-311G(d,p) level of theory reveal that the lowest energy band for all three derivatives 6a, 9a and 12a originate mainly from a HOMO→LUMO transition with some admixture of HOMO−1→LUMO+1 and HOMO−1→LUMO

Mechanistic investigations of polyaza[7]helicene in photoredox and energy transfer catalysis

• Johannes Rocker,
• Till J. B. Zähringer,
• Matthias Schmitz,
• Till Opatz and
• Christoph Kerzig

Beilstein J. Org. Chem. 2024, 20, 1236–1245, doi:10.3762/bjoc.20.106

• Aza-H•+ (red) were computed using TD-DFT (see Supporting Information File 1 for details). These computational results, which are included in Figure 1B, align well with the experimentally observed absorption bands in the visible region, supporting our assignment. The observed behavior of the Aza-H

Competing electrophilic substitution and oxidative polymerization of arylamines with selenium dioxide

• Vishnu Selladurai and
• Selvakumar Karuthapandi

Beilstein J. Org. Chem. 2024, 20, 1221–1235, doi:10.3762/bjoc.20.105

• with arylamines follows a complex reaction pathway, leading to a mixture of compounds. We established the possible reaction pathways using 77Se NMR spectroscopy and single-crystal X-ray crystallographic studies. Density functional theory (DFT) calculations were carried out to understand the relative

• interactions are rarely reported and currently gaining interest [59]. Computational studies To comprehend the role of electron-donating and -withdrawing groups in arylamine oxidation using SeO2 as oxidant, DFT calculations were carried out on the arylamines and SeO2 using Gaussian 16 [60]. The molecular