Sulfur-containing spiroketals from Breynia disticha and evaluations of their anti-inflammatory effect

• Ken-ichi Nakashima,
• Naohito Abe,
• Masayoshi Oyama,
• Hiroko Murata and
• Makoto Inoue

Beilstein J. Org. Chem. 2023, 19, 1604–1614, doi:10.3762/bjoc.19.117

• electrospray ionization HRESIMS analysis, and quantum chemical electronic CD calculations. Furthermore, the absolute configurations of sugar residues were determined by derivatization of the hydrolysates with ʟ-cysteine methyl ester and o-tolyl isothiocyanate followed by HPLC analysis. The anti-inflammatory

• ′, and 24 conformers for 3. The geometry of each conformer was optimized using DFT calculations at the B3LYP/6-31G(d) level of theory [20][21] with the conductor-like polarizable continuum model (CPCM) solvent model (MeOH) and Gibbs free energy was calculated subsequent frequency calculations. Time

• -dependent (TD)-DFT calculations at the B3LYP/6-31+G(d,p) level with CPCM solvent model (MeOH) [22] were performed for the optimized conformers. The resulting ECD spectra calculated for each conformer were averaged using Boltzmann populations evaluated at 300 K from Gibbs free energy calculated from the

Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions

• Waldemar Iwanek

Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109

• , finally, the structure with the lowest energy, with the functional PBE0-D4/mTZVPP/CPCM. The Hartree–Fock plus London dispersion (HFLD) method was used for the study of non-covalent interactions (NCI). The calculations lead to the conclusion that a reduction in electrostatic interactions and an increase in

• exchange and dispersion interactions in CHCl3 in relation to DMSO are the driving forces behind the placement of sec-amine molecules into the R[4]A cavity and the formation of “in” type complexes. Keywords: complexes; DFT calculations; hydrogen bond; resorcin[4]arene; supramolecular chemistry

• atoms, presenting a challenging and time-consuming task for geometry optimization calculations and screening via DFT methods. Recent advancements have introduced fast semi-empirical DFT methods such as xTB [15], which enable their use in preliminary screening for molecular dynamics or searching for

Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B

• Moe Nakano,
• Rintaro Gemma and
• Hajime Sato

Beilstein J. Org. Chem. 2023, 19, 1503–1510, doi:10.3762/bjoc.19.107

• possibility of through-space interactions with prenyl side chains using DFT calculations. Our calculations show that (i) the unstable secondary carbocation is stabilized by the cation–π interaction from prenyl side chains, thereby lowering the activation energy, (ii) the four-membered ring formation is

• , computational chemistry including DFT [5][6][7][8][9], QM/MM [10][11][12][13][14][15][16] and QM/MM MD [14][15][16][17] calculations have been used for the biosynthetic studies of terpene/terpenoids [18]. Terpene-forming reactions, which involve various types of carbocation species stabilized by

• investigated the biosynthetic pathways using DFT calculations to validate the above-mentioned aspects. Results and Discussion The detailed structures of the intermediates and transition states were elucidated by computational analysis. Interestingly, we have found an interaction between the secondary

N-Sulfenylsuccinimide/phthalimide: an alternative sulfenylating reagent in organic transformations

• Fatemeh Doraghi,
• Seyedeh Pegah Aledavoud,
• Mehdi Ghanbarlou,
• Bagher Larijani and
• Mohammad Mahdavi

Beilstein J. Org. Chem. 2023, 19, 1471–1502, doi:10.3762/bjoc.19.106

• first thiolation and intramolecular cyclization of propargyl azides the removal of N2 and a proton. Subsequently, monothiolated perroles were subjected to the second thiolation process to prepare 3,4-bisthiolated pyrroles. Cyclic voltammetry and DFT calculations revealed that the 3,4-bisthiolated

Cyclization of 1-aryl-4,4,4-trichlorobut-2-en-1-ones into 3-trichloromethylindan-1-ones in triflic acid

• Vladislav A. Sokolov,
• Andrei A. Golushko,
• Irina A. Boyarskaya and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2023, 19, 1460–1470, doi:10.3762/bjoc.19.105

• , the O-protonated forms ArC(=OH+)CH=CHCCl3, which are then cyclized into the target CCl3-indanones. These cations have been studied experimentally by means of NMR spectroscopy in TfOH and theoretically by DFT calculations. Under the same superacidic conditions in TfOH, CCl3-hydroxy ketones (1-aryl

• =CHC(=O)Me] with arenes in Brønsted superacid TfOH (triflic acid, CF3SO3H) furnishes 3-methyl-1-trichloromethylindenes (Scheme 1a) [11]. Based on NMR analysis in TfOH and theoretical DFT calculations, it has been found that the reaction proceeds through an intermediate formation of the O-protonated

• calculations, and to study their intramolecular cyclization in triflic acid into the synthetically and medicinally relevant (see recent reviews [12][13][14][15][16][17][18]) indan-1-ones. Results and Discussion The synthesis of 1-aryl-4,4,4-trichloro-3-hydroxybutan-1-ones (CCl3-hydroxy ketones) 1a–o was

Application of N-heterocyclic carbene–Cu(I) complexes as catalysts in organic synthesis: a review

• Nosheen Beig,
• Varsha Goyal and
• Raj K. Bansal

Beilstein J. Org. Chem. 2023, 19, 1408–1442, doi:10.3762/bjoc.19.102

• as σ-donor ligands only. However, subsequent experimental [18] and theoretical [19] studies revealed that a simultaneous back donation from the d-orbital of the metal to the π*-orbital of the NHC occurs in these species, which was also corroborated by energy decomposition analysis (EDA) calculations

• on C1 enhancing its nuceophilicity (Figure 9). The Mulliken charge, obtained from the NBO calculations, was found to be almost double at the C–H atom in the complexed alkyne (−0.294) as compared to the free alkyne (−0.129). Furthermore, as depicted in Figure 10, the HOMO–LUMO energy gap in the NHC–Cu

Organic thermally activated delayed fluorescence material with strained benzoguanidine donor

• Alexander C. Brannan,
• Elvie F. P. Beaumont,
• Nguyen Le Phuoc,
• George F. S. Whitehead,
• Mikko Linnolahti and
• Alexander S. Romanov

Beilstein J. Org. Chem. 2023, 19, 1289–1298, doi:10.3762/bjoc.19.95

• region of ca. 380–460 nm with ε up to 1900 M−1 cm−1 (Table 2). Both loCT and deCT bands are observed for the benchmark material 4CzIPN [16] while originating from HOMO to LUMO transition in line with the theoretical calculations (Tables S1, S3, and S4, Supporting Information File 1). All CT bands

• experience a very weak solvatochromic effect with increasing solvent polarity from cyclohexane to dichloromethane. This indicates only minor change of the dipole moment upon vertical excitation from S0 (6.4 D) to S1 (7.2 D) excited states according to the TD-DFT theoretical calculations (Table S2, Supporting

• π-conjugation. The twisted structure of the 4BGIPN ensures that the donor groups accommodate the highest occupied molecular orbital (HOMO) while the acceptor 4,6-dicyanobenzene moiety contains the lowest unoccupied molecular orbital (LUMO) and is supported by the TD-DFT calculations. A comparison of

Non-noble metal-catalyzed cross-dehydrogenation coupling (CDC) involving ether α-C(sp³)–H to construct C–C bonds

• Hui Yu and
• Feng Xu

Beilstein J. Org. Chem. 2023, 19, 1259–1288, doi:10.3762/bjoc.19.94

• the reaction mechanism supported by DFT calculations and concluded that FeF2 plays an important redox role in assisting the cleavage of oxidants and the oxidation of carbon radicals to cationic intermediates of oxygen. CDC reactions between C(sp3)–H/C(sp)–H bonds catalyzed by iron have been reported

Cyanothioacetamides as a synthetic platform for the synthesis of aminopyrazole derivatives

• Valeriy O. Filimonov,
• Alexandra I. Topchiy,
• Vladimir G. Ilkin,
• Tetyana V. Beryozkina and
• Vasiliy A. Bakulev

Beilstein J. Org. Chem. 2023, 19, 1191–1197, doi:10.3762/bjoc.19.87

• ) which were used in all calculations. The final R1 = 0.0403, wR2 = 0.0956 (I > 2σ(I)) and R1 = 0.0510, wR2 = 0.1042 (all data). Largest diff. peak/hole 0.281/−0.285 ēÅ−3. 6e: Crystal data for C15H15F3N4OS (M = 356.37 g/mol): triclinic, space group P-1 (no. 2), a = 6.1592(10) Å, b = 12.0568(18) Å, c

• = 12.1206(19) Å, α = 109.032 (14)°, β = 101.540 (13)°, γ = 100.648 (13), V = 802.7(2) Å3, Z = 2, μ(Mo Kα) = 0.244 mm−1, Dcalc = 1.474 g/cm3, 5870 reflections measured (6.154° ≤ 2Θ ≤ 58.47°), 3676 unique (Rint = 0.0326, Rsigma = 0.0537) were used in all calculations. The final R1 = 0.0513, wR2 = 0.1241 (I

• , Dcalc = 1.452 g/cm3, 7847 reflections measured (4.794° ≤ 2Θ ≤ 58.972°), 3663 unique (Rint = 0.0461, Rsigma = 0.0641) were used in all calculations. The final R1 = 0.0580, wR2 = 0.1295 (I > 2σ(I)) and R1 = 0.0993, wR2 = 0.1673(all data). Largest diff. peak/hole 0.244/−0.450 ēÅ−3. The experiments were

Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control

• Carlee A. Montgomery and
• Graham K. Murphy

Beilstein J. Org. Chem. 2023, 19, 1171–1190, doi:10.3762/bjoc.19.86

• energy adduct had fluoride residing in the weaker σ-hole (syn to the β-dicarbonyl) [16]. These calculations showed that a reductive elimination event was operative from both IntA/IntB, with a >25 kcal/mol energy difference between transitions states of the observed fluorination (TSA, path A) versus that

• calculations for enaminone synthesis from iodonium ylides and thioamides. Crystal structures of 76c (top) and 76e (bottom) [101], (CCDC# 2104180 & 2104181) [143][144]. Outline of possible reaction pathways between iodonium ylides and Lewis basic nucleophiles (top); and, reaction between 6 and HCl to give 7, as

Photoredox catalysis harvesting multiple photon or electrochemical energies

• Mattia Lepori,
• Simon Schmid and
• Joshua P. Barham

Beilstein J. Org. Chem. 2023, 19, 1055–1145, doi:10.3762/bjoc.19.81

Five new sesquiterpenoids from agarwood of Aquilaria sinensis

• Hong Zhou,
• Xu-Yang Li,
• Hong-Bin Fang,
• He-Zhong Jiang and
• Yong-Xian Cheng

Beilstein J. Org. Chem. 2023, 19, 998–1007, doi:10.3762/bjoc.19.75

• the correlation of H3-15/H2-6 (Figure 3), which results in ambiguity in the relative configuration assignment of 1. Thus, NMR chemical shift calculations and ECD calculations were used to confirm the relative and absolute configuration of 1. More specifically, NMR calculations were carried out at the

• PCM/mPW1PW91/6-311+G(d,p) [16] level for (7R*,10S*)-1 (1a) and (7S*,10S*)-1 (1b), which are possible diastereomers of 1. The results reveal that 1a has the highest probability score. Next, ECD calculations on (7R,10S)-1 and (7S,10R)-1 were conducted according to the results obtained from NMR

• calculations. The CD spectrum matched well with the calculated ECD spectrum of 1a (Figure 4), revealing the absolute configuration of 1 to be 7R,10S, and it was named aquisinenoid F. Compound 2 was isolated as pale yellow gum, and was assigned the molecular formula C15H24O2 as inferred from the HRESIMS m/z

Asymmetric tandem conjugate addition and reaction with carbocations on acylimidazole Michael acceptors

• Brigita Mudráková,
• Renata Marcia de Figueiredo,
• Jean-Marc Campagne and
• Radovan Šebesta

Beilstein J. Org. Chem. 2023, 19, 881–888, doi:10.3762/bjoc.19.65

• enolates in high enantiomeric purities. These enolates are reacted with highly electrophilic onium compounds to afford densely substituted acylimidazoles. DFT calculations helped to understand the reactivity of the zinc enolates derived from acylimidazoles and allowed their comparison with metal enolates

• , the configuration at the position C-3 is determined by the chiral ligand L1 and was determined previously as (R) [19]. To gain insight into the reactivity of enolates formed in this transformation, we evaluated properties of Zn enolates by DFT calculations (Figure 2). The corresponding (E) and (Z

• )-enolates were calculated for products 3b and 3d, which possess either an alkyl (ethyl) or an aryl (phenyl) substituent on the stereogenic center. To probe the nature of the imidazole moiety, enolates for products 3g and 3i were also calculated (with a shorter alkyl chain to simplify the calculations

Pyridine C(sp²)–H bond functionalization under transition-metal and rare earth metal catalysis

• Haritha Sindhe,
• Malladi Mounika Reddy,
• Karthikeyan Rajkumar,
• Akshay Kamble,
• Amardeep Singh,
• Anand Kumar and
• Satyasheel Sharma

Beilstein J. Org. Chem. 2023, 19, 820–863, doi:10.3762/bjoc.19.62

• significantly affect the C–H alkylation reaction and the reaction also proceeded well with hydrazones 13 obtained from aliphatic aldehydes or ketones. Based on mechanistic experiments and DFT calculations, the reaction presumably proceeds via a Cu–carbene migratory insertion (Scheme 4b). In the presence of CuI

Eschenmoser coupling reactions starting from primary thioamides. When do they work and when not?

• Lukáš Marek,
• Jiří Váňa,
• Jan Svoboda and
• Jiří Hanusek

Beilstein J. Org. Chem. 2023, 19, 808–819, doi:10.3762/bjoc.19.61

• ) level of theory. Quantum calculations (Figure 2) have shown that the reaction pathway that involves an intramolecular proton transfer between the α-carbon and imine nitrogen through TS1 is much more favorable for imidothioate derived from 4-bromoisoquinoline-1,3(2H,4H)-dione (3) and 3-bromooxindole (1

• nitrogen and carbonyl oxygen, generating both nucleophilic and electrophilic centers, i.e., a free amino group and protonated carbonyl group, which is much more prone to nucleophilic attack than a carbonyl group itself. Quantum calculations (see the left side of Figure 2) show that the relative stabilities

• each reaction medium. Unfortunately, the pKaN values of individual thioiminium salts 6a, 10a, 12a, and 15 are not available experimentally, and their exact determination using calculations is also not completely accurate, especially because of the uncertainty of the energy of a solvated proton. However

Non-peptide compounds from Kronopolites svenhedini (Verhoeff) and their antitumor and iNOS inhibitory activities

• Yuan-Nan Yuan,
• Jin-Qiang Li,
• Hong-Bin Fang,
• Shao-Jun Xing,
• Yong-Ming Yan and
• Yong-Xian Cheng

Beilstein J. Org. Chem. 2023, 19, 789–799, doi:10.3762/bjoc.19.59

• field (MMFF94) and DFT/TDDFT calculations, were performed for model compounds (3R,4R)-1, (3S,4S)-1, (2S,2″R)-4, (2S,2″S)-4, (2R,2″S)-4, and (2R,2″R)-4 using the Spartan'14 software package and the Gaussian 09 program package. The ECD calculations of the predominant conformers (80%) were conducted using

• DFT calculations at the B3LYP/6-311G(d,p) level of theory. The program SpecDis 1.62 was used to generate the CD spectra [31]. Biological evaluation Antitumor assay Panc02-h7-GP-GFP cells (derived from the transformation of mouse pancreatic cancer cell line Panc02-h7) were maintained at 37 °C in a 5

Synthesis, structure, and properties of switchable cross-conjugated 1,4-diaryl-1,3-butadiynes based on 1,8-bis(dimethylamino)naphthalene

• Semyon V. Tsybulin,
• Ekaterina A. Filatova,
• Alexander F. Pozharskii,
• Valery A. Ozeryanskii and
• Anna V. Gulevskaya

Beilstein J. Org. Chem. 2023, 19, 674–686, doi:10.3762/bjoc.19.49

• proposed for D–π–A systems. This parameter is a good indication for intramolecular charge transfer from the donor to the acceptor moiety in the ground state. In benzene, the qr value is equal to 0. In a fully quinoid ring, the qr was found to be equal to 0.10–0.12. Calculations based on the bond lengths in

Enolates ambushed – asymmetric tandem conjugate addition and subsequent enolate trapping with conventional and less traditional electrophiles

• Péter Kisszékelyi and
• Radovan Šebesta

Beilstein J. Org. Chem. 2023, 19, 593–634, doi:10.3762/bjoc.19.44

• thoroughly examined using DFT calculations. Other than the broad substrate scope, the synthetic utility of this method was demonstrated by a scale-up reaction (3.73 mmol scale, 87% yield, 88% ee), and by several different transformations of the tandem products. Similarly, Ghorai et al. studied a Cu-catalyzed

C3-Alkylation of furfural derivatives by continuous flow homogeneous catalysis

• Grédy Kiala Kinkutu,
• Catherine Louis,
• Myriam Roy,
• Juliette Blanchard and
• Julie Oble

Beilstein J. Org. Chem. 2023, 19, 582–592, doi:10.3762/bjoc.19.43

• reactor. Finally, after some optimizations, the temperature in the second reactor could be lowered to 180 °C leading to an NMR yield of C3-alkylated imine I2a of 79% (Scheme 3). Heat transfer calculations showed us that the reaction mixture rises to the set temperatures in two seconds, and more

A new oxidatively stable ligand for the chiral functionalization of amino acids in Ni(II)–Schiff base complexes

• Alena V. Dmitrieva,
• Oleg A. Levitskiy,
• Yuri K. Grishin and
• Tatiana V. Magdesieva

Beilstein J. Org. Chem. 2023, 19, 566–574, doi:10.3762/bjoc.19.41

• shown previously [31][37], this difference determines the stereochemical outcome of the reactions performed under thermodynamic control. To determine the conformational changes in the Ni(II) coordination environment induced by the additional tert-butyl group in the o-phenylene moiety, DFT calculations

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• dielectric constant and a lower polarity that influenced intramolecular stacking. To the best of our knowledge, this is the first reported phenanthridine–pyrene excimer in solution. Molecular dynamics calculations (see chapter Computational analysis) and hypochromism observed from UV–vis spectra pointed

• , and then did TD-DFT calculations at the same level of theory. Solvent effects were modeled using the SMD implicit water solvation. The obtained vertical transitions corresponding to absorption maxima at pH 7.0 are 260 and 372 nm (Phen-Py-1), and 270 and 397 nm (Phen-Py-2). At pH 5.0 vertical

• Scatchard equation [38] and Global Fit procedure [40]. Calculations mostly gave values of ratio n = 0.2 ± 0.05, but for easier comparison all Ka values were re-calculated for fixed n = 0.2. Values for Ka have satisfactory correlation coefficients (>0.98). In Scatchard equation values of association constant

Access to cyclopropanes with geminal trifluoromethyl and difluoromethylphosphonate groups

• Ita Hajdin,
• Romana Pajkert,
• Mira Keßler,
• Jianlin Han,
• Haibo Mei and
• Gerd-Volker Röschenthaler

Beilstein J. Org. Chem. 2023, 19, 541–549, doi:10.3762/bjoc.19.39

• good to very good yields. Keywords: alkenes; cyclopropanation; diazo compounds; difluoromethylphosphonate; DFT calculations; Introduction Cyclopropanes constitute a fascinating class of organic compounds due to their unique structure and bond properties [1]. However, their synthetic utility is

• confirm the lack of selectivity during the cyclopropanation process with terminal alkenes, the reaction mechanism between the diazo reagent 5 and styrene as a model substrate in the presence of CuI catalyst was investigated by density functional theory (DFT) calculations (Table 2). In the first step, CuI

• difluoromethylphosphonate-containing cyclopropanes in reactions with selected olefins, carried out under mild conditions with good to very good yields, in the presence of CuI, an inexpensive catalyst. As confirmed by quantum mechanical calculations and experimental results, the cyclopropane formation occurs always with a

Transition-metal-catalyzed domino reactions of strained bicyclic alkenes

• Austin Pounder,
• Eric Neufeld,
• Peter Myler and
• William Tam

Beilstein J. Org. Chem. 2023, 19, 487–540, doi:10.3762/bjoc.19.38

• little effect on the reaction (32b) with reactions involving unsymmetrically substituted bicyclic alkenes demonstrating complete regioselectivity for either 1,2,3- or 1,2,4-trisubstitued products (32a, 32f). DFT calculations were used to explain the syn-1,2-substitution experimentally observed rather

Computational studies of Brønsted acid-catalyzed transannular cycloadditions of cycloalkenone hydrazones

• Manuel Pedrón,
• Jana Sendra,
• Irene Ginés,
• Tomás Tejero,
• Jose L. Vicario and
• Pedro Merino

Beilstein J. Org. Chem. 2023, 19, 477–486, doi:10.3762/bjoc.19.37

• model [30] the distortion energy (ΔE≠d) corresponds to the difference between the single point corresponding to interacting 3 and 4, and the sum of single-point calculations for TS2-a and TS2b. The apparent activation energy (ΔE≠app) refers to the energy difference between TS2 and the interacting

• reagents 3 and 4 (single point calculations). The difference between ΔE≠app and ΔE≠ is the distortion energy of the tether (ΔE≠tether) (Equation 1). Since our system has two different tethers, we introduced an additional modification by calculating single points of the system with just one tether (Figure

• original geometry. From these calculations and applying the Houk’s model we can obtain the corresponding distortion energy for each different tether (ΔE≠t1 and ΔE≠t2; t1 and t2 correspond to tether A and B, respectively). Besides, we have added an additional term (ΔE≠ti) corresponding to the penalty (or

Combretastatins D series and analogues: from isolation, synthetic challenges and biological activities

• Jorge de Lima Neto and
• Paulo Henrique Menezes

Beilstein J. Org. Chem. 2023, 19, 399–427, doi:10.3762/bjoc.19.31

• combretastatin D on the use of computational calculations in order to find the intermediates with the lowest torsional energy for the cyclization step [43][44][45]. The authors came to the conclusion that both the formation of the double bond in compound 2 and the formation of the epoxide in compound 1 would