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

• Research Areas (A) (Grant Number JP20H05865, T. K.), and by research grant from The Murata Science Foundation (T. N.). Quantum chemical calculations were performed at the Research Center for Computational Science, Okazaki, Japan (Project: 23-IMS-C212 and 24-IMS-C214). This work was the result of using

Cell-free protein synthesis with technical additives – expanding the parameter space of in vitro gene expression

• Tabea Bartsch,
• Stephan Lütz and
• Katrin Rosenthal

Beilstein J. Org. Chem. 2024, 20, 2242–2253, doi:10.3762/bjoc.20.192

• from the 100% of pure water, additives decreased that value by the percentage of their contribution. Calculations and further details can be found in Supporting Information File 1. Cell-free protein synthesis The CFPS system was prepared and the reactions performed according to Rolf et al. [18] with

• Supporting Information File 75: Calculations of viscosity, macromolecules, inorganic ions, osmolarity and water content for CFPS in Table 1. Supporting Information File 76: Calculations of viscosity for CFPS with water-soluble solvents in Table 2. Supporting Information File 77: Fractional Yield of average

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

Selective hydrolysis of α-oxo ketene N,S-acetals in water: switchable aqueous synthesis of β-keto thioesters and β-keto amides

• Haifeng Yu,
• Wanting Zhang,
• Xuejing Cui,
• Zida Liu,
• Xifu Zhang and
• Xiaobo Zhao

Beilstein J. Org. Chem. 2024, 20, 2225–2233, doi:10.3762/bjoc.20.190

• yield is stated. Keto/enol ratio of 3 was determined by 1H NMR spectroscopy. Gram-scale hydrolysis reactions of 1a. Proposed mechanism for formation of β-keto thioesters 2 and β-keto amides 3. Optimization of the reaction conditions. EcoScale calculations and results for the synthesis of 2a and 3a [75

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

• /chemoinformatics calculations were also performed to correlate the observed reactivity with the charges on the carbonyl group of 1,3-diketones. Unfortunately, no reliable correlation was found between the charges and the reactivity of the 1,3-diketones with the present set of heterocyclic substituents or with the

• 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

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• bacterial sugars, the parametrisation of each building block is needed and requires the use of ab initio methodologies, including several steps of charges and electron density calculations, optimization and minimization, making the computational study of bacterial glycans difficult and time-consuming. 2

• involving unusual ligands, useful tools can be employed to provide the parameters needed for running MD simulations. Charge calculations and electron density computations for glycan units can be performed using tools like the online RED Server [70]. Although information on force fields is usually available

• , modifications can sometimes be required and can be achieved through ab initio calculations or programs like for example VFFDT [71]. Tools for the conformational analysis of glycans in the free state The structure and biological functions of glycans are closely intertwined; the roles they play are influenced not

Understanding X-ray-induced isomerisation in photoswitchable surfactant assemblies

• Beatrice E. Jones,
• Camille Blayo,
• Jake L. Greenfield,
• Matthew J. Fuchter,
• Nathan Cowieson and
• Rachel C. Evans

Beilstein J. Org. Chem. 2024, 20, 2005–2015, doi:10.3762/bjoc.20.176

• , SAXS using in-situ irradiation, models used for SAXS fitting, micelle dimensions from SAXS fits, calculations for the pH change on X-ray irradiation and UV–vis absorbance spectra for acid-induced isomerisation. Acknowledgements This work was carried out with the support of Diamond Light Source

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

• 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

• -3 as a bidentate ligand to the Na+ cation from NaH. The tight ion pair would direct alkylation under conditions A to N1. As this and other postulations exist, we explored the possible mechanisms of each reaction conditions computationally. All calculations were performed in implicit THF at the

• (NCI) in N1-s-cis, which accounts for the 2.1 kcal/mol difference in energy. Calculations showed that the sulfonate oxygens also chelate the cesium ion in both TSs. Thus, nitrogen NCIs with cesium, or lack thereof, seem to drive N1-product formation, which is both kinetically and thermodynamically

2-Heteroarylethylamines in medicinal chemistry: a review of 2-phenethylamine satellite chemical space

• Carlos Nieto,
• Alejandro Manchado,
• Ángel García-González,
• David Díez and
• Narciso M. Garrido

Beilstein J. Org. Chem. 2024, 20, 1880–1893, doi:10.3762/bjoc.20.163

• docking or QSAR calculations to describe the bioisostere, impact and rationalize the observed experimental binding or efficacy measurements. As it was stated in the introduction, only the rings described in this review, are the ones with reported activity, but there exists a plethora of other analogues

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

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

Synthesis and characterization of 1,2,3,4-naphthalene and anthracene diimides

• Adam D. Bass,
• Daniela Castellanos,
• Xavier A. Calicdan and
• Dennis D. Cao

Beilstein J. Org. Chem. 2024, 20, 1767–1772, doi:10.3762/bjoc.20.155

• been achieved as well. Other efforts have demonstrated that anthracene diimides (ADIs) can be tuned to achieve decent electron mobilities in electronic settings [13][14]. Although there have been calculations conducted that suggest 6-membered cyclic imides are more compelling than 5-membered cyclic

Syntheses and medicinal chemistry of spiro heterocyclic steroids

• Laura L. Romero-Hernández,
• Ana Isabel Ahuja-Casarín,
• Penélope Merino-Montiel,
• Sara Montiel-Smith,
• José Luis Vega-Báez and
• Jesús Sandoval-Ramírez

Beilstein J. Org. Chem. 2024, 20, 1713–1745, doi:10.3762/bjoc.20.152

• yields (82–85%) (Scheme 28). The authors proposed a free radical mechanism facilitated by hydrogen peroxide, generating a primary radical at the terminal nitrogen atom -CO-HN• which then adds to the carbon atom of the imino group. The reaction mechanism was substantiated by theoretical calculations

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

• methods are evaluated as single-point calculations or optimization and frequency calculations. For comprehensive details, refer to Supporting Information File 1, section “Benchmark study - computational methods”. Hereafter, we check the geometries for imaginary frequencies and use the total thermal energy

• Finkelmann et al. [30][31] and Ree et al. [14], we utilize the automated approach to compute CM5 atomic charges from semiempirical tight-binding (GFN1-xTB [37]) calculations. We modify the workflow to enhance the accuracy of the computed CM5 atomic charges. Instead of generating a single random conformer, we

• squared error. QM calculations were carried out at the CAM-B3LYP/def2-TZVPPD CPCM(DMSO)//GFN2-xTB ALPB(DMSO) level of theory. ML-predicted pKa values vs QM-computed pKa values of the held-out test set (155 compounds; 789 pKa values). r: Pearson correlation coefficient; ρ: Spearman’s rank correlation

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

• reported by our group, was elucidated via quantum chemical calculations using density functional theory. The chlorination mechanism using PIFA and AlCl3 demonstrated a better experimental and theoretical yield compared to using PIDA. Additionally, the lowest-energy chlorinating species was characterized by

• , 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

• , the 6-31G(d) basis set was used for the other atoms (i.e., H, C, O, F, Al, etc.). Geometry optimizations were carried out without any symmetry constraints, and the stationary points were characterized by analytical frequency calculations, i.e., energy minima (reactants, intermediates, and products

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

• the impact of gauche and anomeric effects on the conformer stabilities of different stereo- and regioisomers. Initially, we conducted a benchmark assessment comparing the optimal density functional theory method with coupled cluster with single and double excitations (CCSD) calculations and

• . In this study, initially, the conformational equilibrium of 3-fluoropyrrolidine and the corresponding cation were analyzed to establish a benchmark for selecting an appropriate theory level for subsequent calculations. Then, the different isomers of the 1,2- or 1,3-difluorinated pyrrolidines were

• (Table 1). Consequently, the B3LYP-D3BJ/6-311++G** level was selected for further calculations involving the difluorinated pyrrolidines shown in Figure 4. From the pool of 24 potential conformational, configurational, and constitutional isomers of the difluorinated pyrrolidines (i.e., 1–24), two pairs

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

• 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

• iodine [61][62][63][64][65][66][67][68][69][70][71][72][73][74][75][76] and the computational database of organic species by Paton and co-workers [77], geometry optimizations and single point energy calculations for homolytic BDEs are both performed using M06-2X/def2-TZVPP [78][79][80] in the gas phase

• at 298.15 K by Gaussian 16 [81]. Frequency calculations confirmed that optimized structures are minima (no imaginary frequency). The accuracy of computational BDEs of halides using M06-2X/def2-TZVPP is also evaluated and compared to experimental BDEs, demonstrating the reliability of the method (see

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

• the theoretical framework describing the structure, bonding, and reactivity of diarylhalonium compounds [27]. Although some relativistic effects of astatine may not be sufficiently incorporated in calculations [28], others have shown in theoretical and limited experimental studies that astatine does

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

• 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

• -eunicellane skeletons, respectively. Although the structures of these diterpenes only differed in their configuration at a single position, C1, they displayed distinct chemical and thermal reactivities. Here, we used a combination of quantum chemical calculations and chemical transformations to probe their

• 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

• chemically-induced cationic cyclization mechanisms, we performed quantum chemical calculations [mPW1PW91/6–31+G(d/p)/SMD(chloroform)] [13][14][15][16][17][18][19][20] to obtain the relative free energies of the cationic intermediates and transition states that interconvert them, as well as the relative free

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

• study indicates that the retro-IMDAF reaction does not occur under the reaction conditions developed. As seen in Figure 4b, the different sigma bond lengths formed in the exo transition state (calculations which were performed in Gaussian 16 Rev B.01 (Gaussian, Inc., Wallingford, CT, USA)) [135

• IMDAF reaction. IRC calculations of a) endo-, b) exo-transition structures and products for compound 2a (semi-empirical method, PM6) [136]. Synthesis of epoxyisoindole-7-carboxylic acids 2a–m and 2n–p. Possible side reactions of unsaturated fatty acids with maleic anhydride. Equilibrium of 2n–p with

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

• diameter range. The diameter selectivity is supported by the theoretical calculations with the GFN2-xTB method, indicating that the most preferred SWNT diameter for the square Cu-nanobrackets is 1.04 nm. Keywords: complexation; diameter; extraction; interlock; nanobracket; single-walled carbon nanotubes

• summarized in a graphene map (Figure 5c). This shows that Cu-nanobrackets 1b preferentially recognize larger diameters with wider range (0.94–1.10 nm) than 1a (0.90–0.92 nm) due to the larger cavity with more flexibility of 1b than 1a. Theoretical calculations To interpret the diameter selectivity, the

• diameters ranging from 0.94 to 1.10 nm among ≈20 kinds of SWNTs from 0.76 to 1.20 nm in their diameters. The most preferable SWNTs for 1b are found to be 1.04 nm in diameter by theoretical calculations, supporting the experimental results. Experimental Materials and instruments Reagents were purchased from