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

• 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

• reactive sites (aISS), for example, in the formation of supramolecular complexes [16]. The particularly fast GFN-xTB methods work well in geometry optimization, which is the most time-consuming step of the DFT calculation. There have also been developments in DFT methods concerning the energy distribution

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

• completed through bridging from the exomethylene group, and (iii) the annulation from the exomethylene group proceeds in a barrier-free manner. Keywords: biosynthesis; carbocation; cation–π interaction; DFT; terpene; Introduction Terpene/terpenoids are most abundant natural products in nature, more than

• , 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

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

• , we initiated this study on transformations of 1-aryl-4,4,4-trichlorobut-2-en-1-ones under superelectrophilic activation conditions (Scheme 1b). The main goals of this work were the investigation of the protonation of CCl3-enones (1-aryl-4,4,4-trichlorobut-2-en-1-ones) by NMR spectroscopy and DFT

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

• compounds, including diaryl- and dialkyl ketones and prochiral ketones, respectively (Scheme 36) [50]. Riant, Leyssens and co-workers investigated the mechanism of the hydrosilylation reaction of ketones using DFT, in situ FTIR, NMR, and kinetic methods [51][52]. The catalytic characteristics of sterically

• mentioned earlier, we recently reported the results of the theoretical investigation of different classes of NHCs and their NHC–Cu(I) complexes at the DFT level [21]. It was shown that in the NHC–Cu(I) complexes, the negative charge density is located mainly in the CuX region. The molecular electrostatic

• [Cu2(μBr)2(t-BuImCH2pyCH2L)]2 species 138 acting similar to the NHCs. A very low loading of these complexes was sufficient to catalyze the azide–alkyne cycloaddition. A theoretical investigation at the DFT level confirmed the participation of the dinuclear species [(CuBr)2(μ-t-BuImCH2pyCH2NEt2)] 139

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

• 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

• ). Computational results Computations were performed using density functional theory (DFT) for the ground state and time-dependent DFT (TD-DFT) with Tamm–Dancoff approximation [24][25] for the excited states calculations, using the global hybrid MN15 functional by Truhlar [26] in combination with the def2-TZVP

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

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

The effect of dark states on the intersystem crossing and thermally activated delayed fluorescence of naphthalimide-phenothiazine dyads

• Liyuan Cao,
• Xi Liu,
• Xue Zhang,
• Jianzhang Zhao,
• Fabiao Yu and
• Yan Wan

Beilstein J. Org. Chem. 2023, 19, 1028–1046, doi:10.3762/bjoc.19.79

• were studied by steady state UV–vis absorption spectroscopy, transient photoluminescence spectroscopy, nanosecond/femtosecond transient absorption spectroscopy, electrochemistry, as well as DFT/TDDFT computations. We observed experimental evidence for the spin–vibronic coupling effect in the TADF

• coupling, i.e., the 3LE mediate 3CS → 1CS rISC in TADF [27]. The photochemical properties of each compound in different solvents are summarized in Table 5. Computational investigations The optimized ground state geometry of the dyads at the DFT-B3LYP/6-31G (d) level of theory determined with Gaussian 09

• pulsed laser). The wavelength is tunable in the range of 410–2500 nm. Calculation study The geometries of the compounds in their ground state were optimized using density functional theory (DFT) with the B3LYP functional and the 6-31G(d) basis set [72]. The excited state geometries of S1 and T1 were

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

• ε) 200 (2.82) nm; HRESIMS (m/z): [M + Na]+ calcd for C15H26O2Na, 261.1825; found, 261.1825; 1H and 13C NMR data, see Table 3. Calculations of NMR spectra Using density functional theory (DFT) and B3LYP/6-31G(d,p) [28] levels in the Gaussian 09 software package [29], the obtained minimum energy

• conformation of the force field was optimized. DFT was used to calculate the gauge-independent atomic orbital [30] for 1H and 13C NMR chemical shifts using the PCM solvent model in Gaussian 09 software [29]. The NMR chemical shift was corrected by the isotope shift of TMS [31]. The calculated 13C NMR chemical

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

• determined by comparison of experimentally measured electronic circular dichroism (ECD) spectra with those of the DFT-calculated ones (Figure 1 and see Supporting Information File 1 for more details). CD spectra were calculated for the two most populated conformers for both diastereomers of product 4. The

• , 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

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

• DFT calculation, a plausible mechanism (Scheme 10b) has been proposed. Initially, a reversible ligand-to-ligand H-transfer process occurs for C–H activation between the intermediates 46 and 47. Next, isomerization of the η1-allyl complex 47 forms the η3-allylic nickel complex 48, which on reductive

• styrenes 64 using a Ni–Al bimetallic system and NHC ligand 65 through intermolecular hydroarylation with high levels of enantio- and regioselectivity in the alkylated products 66 (Scheme 13). Also, the authors performed DFT studies revealing the reaction mechanism and supported that the interaction of the

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

Bromination of endo-7-norbornene derivatives revisited: failure of a computational NMR method in elucidating the configuration of an organic structure

• Demet Demirci Gültekin,
• Arif Daştan,
• Yavuz Taşkesenligil,
• Cavit Kazaz,
• Yunus Zorlu and
• Metin Balci

Beilstein J. Org. Chem. 2023, 19, 764–770, doi:10.3762/bjoc.19.56

• Kutateladze claimed that based on an applied machine learning-augmented DFT method for computational NMR that the structure of the product, (1R,2R,3S,4S,7s)-2,3,7-tribromobicyclo[2.2.1]heptane was wrong. With the aid of their computational method, they revised a number of published structures, including ours

• have developed a machine learning-augmented DFT method for computational NMR, DU8ML, for fast and ‘accurate’ computational approaches [2]. They applied this computational method to a number of previously published organic compounds and claimed to have revised some structures and proposed new mechanisms

Construction of hexabenzocoronene-based chiral nanographenes

• Ranran Li,
• Di Wang,
• Shengtao Li and
• Peng An

Beilstein J. Org. Chem. 2023, 19, 736–751, doi:10.3762/bjoc.19.54

• , respectively by DFT calculation. The enantiopure isomers of the π-extended helicenes were evaluated as excellent circularly polarized luminescence (CPL) emitters with a glum of 7.44 × 10−3 for 37, which is around 10-fold higher than 35. Chiral “HBC-dimers” and “HBC trimers” The combination of two or more HBCs

• . Meanwhile, this NG 70 can also be synthesized from compound 68 through oxidative cyclodehydrognation and dimerization in one pot. The isomerization barrier was determined as over 35 kcal/mol at 170 °C, and 37 kcal/mol by DFT calculation, indicating a high degree of optical stability of pure enantiomers [51

• between two HBC layers suggested by DFT optimized structure. The furan containing NG 100 revealed a looser conformation than compound 96 with less overlap between two layers and a longer interlayer distance of 4.9 Å suggested by single crystal X-ray diffraction. The enantiomers of (P,P)-96 and (M,M)-96 or

Cassane diterpenoids with α-glucosidase inhibitory activity from the fruits of Pterolobium macropterum

• Sarot Cheenpracha,
• Ratchanaporn Chokchaisiri,
• Lucksagoon Ganranoo,
• Sareeya Bureekaew,
• Thunwadee Limtharakul and
• Surat Laphookhieo

Beilstein J. Org. Chem. 2023, 19, 658–665, doi:10.3762/bjoc.19.47

• , MeOH); lit. −44 (c 0.05, MeOH)) [18], confirming the same absolute configuration these compounds should be derived from the same biosynthetic pathway. In addition, the ECD spectra of (5S,8R,9S,10R,14S)-1 and its enantiomer were calculated at the B3LYP functional using a TD–DFT method [19]. As

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

• therefore be more accurate to consider as a precatalyst (Scheme 4, path b). The mononuclear complex would then initiate the alkylation reaction at 180 °C following elementary steps previously determined by DFT [21]. Conversely, a high starting temperature would favor the formation of ruthenium aggregates

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

• electrochemically induced oxidative modification of the amino acid side chain. Experimental and DFT studies showed that the additional tert-butyl group increases the dispersion interactions in the Ni coordination environment making the complexes more conformationally rigid and provides a higher level of

• heating of its MeOH/HCl solution at 60 °C under conditions similar to the ones previously reported for (RCysNi)L4 [42] (see Supporting Information File 1 for details). The corresponding amino acid was obtained, along with the L7 ligand which was recovered in ca. 70% yield and then reused. DFT study The

• 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

• , 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

• –vis spectra corresponding to isolated conjugates in the aqueous solution. For that purpose, we used the most abundant structure of each system in Figure 2 and performed the geometry optimization by the M06-2X DFT approach [53] together with the 6–31+G(d) basis set [54] in the Gaussian 16 program

• relative trends among similar systems, which is the focus here. This was followed by the TD-DFT computations at the same level of theory considering 32 lowest singlet electronic excitations. The choice of this setup was prompted by its recent success in modeling UV–vis spectra of organic and inorganic

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

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

• studied by using DFT. The Houk's distortion model has been employed to evaluate the influence of the tether in the cycloaddition reaction. That model has been extended to determine the contribution of each tether and, more importantly, the effect exerted between them. In addition to the distortion induced

• by the tethers, the entropy effects caused by them has also been studied. The analysis of the evolution of the electron localization function along the reaction revealed the highly concerted character of the reaction. Keywords: DFT; distortion model; hydrazones; transannular cycloadditions

CuAAC-inspired synthesis of 1,2,3-triazole-bridged porphyrin conjugates: an overview

• Dileep Kumar Singh

Beilstein J. Org. Chem. 2023, 19, 349–379, doi:10.3762/bjoc.19.29

• porphyrin subunits and was more efficient in DMSO as compared to chloroform. Also, a clear evidence of a folded conformer was found by electrostatic and CH–π interactions, which was also, confirmed by density functional theory (DFT) calculations. In another report, meso-triazole-bridged porphyrin-carborane

• groups by using a CuAAC click reaction between azide and acetylene-substituted porphyrins in good yields as shown in Scheme 21. The photophysical and electrochemical studies along with DFT calculations showed that these dyads possess suitable frontier orbital energy levels for the use as sensitizers in

Germacrene B – a central intermediate in sesquiterpene biosynthesis

• Houchao Xu and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 186–203, doi:10.3762/bjoc.19.18

• from L2 through similar reactions, or from L1 by 1,3-hydride shift to L1b and deprotonation (Scheme 16A). DFT calculations have shown that such 1,3-hydride shifts are only possible for trans-fused guaiane systems [120]. Without detailed knowledge about the structure, β-guaiene (56) was first obtained