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

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 and copper-corrole moieties upon photoexcitation. Moreover, the theoretical calculations suggested that the porphyrin moiety acted as a donor while the corrole unit acted as an acceptor in dimer 60. Recently S. Y. Yap and co-workers [38] used “click chemistry” to link a water-soluble porphyrin

• 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

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

• Robert N. Goldberg,
• Robert T. Giessmann,
• Peter J. Halling,
• Carsten Kettner and
• Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

• . Thermodynamic methods [12][13] can be used to calculate values of K′ if one knows the values of K for a chemical reference reaction and for the protonation and metal ion binding reactions of the ATP, ADP, and phosphate species. These calculations require activity coefficients (see section 3.6) which account for

• both long-range electrostatic interactions and the interactions of the ions with each other and with the solvent. The inverse calculation to obtain K from K′ can also be performed by using regression. The scientific principles behind these calculations and transformed thermodynamic quantities are

• reaction. Then, at equilibrium, the concentration of that reactant is known from its initial concentration with, perhaps, a small correction. All constraints on the reacting system and all auxiliary data used should be reported. The pH that should be reported and used in all calculations is the pH at

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• -mannosidase II (LManII) and JBMan). Finally, structural and physicochemical properties of inhibitor:enzyme complexes were investigated at the theoretical level using molecular docking, hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and fragmented molecular orbital pair interaction energy

• geometries of the resulting inhibitor:dGMII complexes (for 10, 20, 28–30 and DIM) were optimized at the hybrid QM/MM level (BP86/LACVP*:OPLS2005). Based on the previous pKa calculations [22] of DIM, 30 and 31 bound at the active site of dGMII (their pKa = 4.9–5.4 at pH 6 of Golgi), all imino-ᴅ-lyxitol

• (−578.74 kcal mol−1); and 10 (+4.13 kcal mol−1) < 20 (−43.01 kcal mol−1) < 29 (−49.25 kcal mol−1) < 30 (−50.99 kcal mol−1) < 28 (−56.07 kcal mol−1) < DIM (−64.16 kcal mol−1), respectively. The calculations predict that the functional group attached to C-5 of the inhibitor must bear one or two hydroxy

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

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

• main product [36]. Based on molecular mechanics calculations, four conformers 1a–d have been described for 1 (Scheme 3B) [37]. The calculations revealed all four conformers are of similar stability, with 1a being the most stable conformer. The fact that 1 shows a defined set of fifteen sharp signals in

• 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

• ), B) the four conformers of 1 established by molecular mechanics calculations (energies in black boxes are relative to 1a for which the energy was set to 0.00 kcal/mol), C) Cope rearrangement to 5 and formation from 6 by pyrolysis, D) dehydration of 7 to 5 and 8. The chemistry of germacrene B (1). A

Identification and determination of the absolute configuration of amorph-4-en-10β-ol, a cadinol-type sesquiterpene from the scent glands of the African reed frog Hyperolius cinnamomeoventris

• Angelique Ladwig,
• Markus Kroll and
• Stefan Schulz

Beilstein J. Org. Chem. 2023, 19, 167–175, doi:10.3762/bjoc.19.16

• discussions. Furthermore, we would like to thank Dr. Christian Schlawis for performing calculations with the MMFF94 method. We also thank Dr. Matthew Stell for language improvement of the manuscript. Funding We thank the Deutsche Forschungsgemeinschaft for grant Schu 984/10-2.

Insight into oral amphiphilic cyclodextrin nanoparticles for colorectal cancer: comprehensive mathematical model of drug release kinetic studies and antitumoral efficacy in 3D spheroid colon tumors

• Sedat Ünal,
• Gamze Varan,
• Juan M. Benito,
• Yeşim Aktaş and
• Erem Bilensoy

Beilstein J. Org. Chem. 2023, 19, 139–157, doi:10.3762/bjoc.19.14

• the dissolution medium drives the rate of release [35]. In our calculations, results compatible with first order kinetics were found for the poly-β-CD-C6 and it was considered to fit both models. The partially high “β” value for the Weibull model also confirmed the tendency towards first order

Organophosphorus chemistry: from model to application

• György Keglevich

Beilstein J. Org. Chem. 2023, 19, 89–90, doi:10.3762/bjoc.19.8

• chemistry and beyond. Quantum chemical calculations are a great support for organic chemists when exploring structures, reactivities, and mechanisms. In this thematic issue, the Diels–Alder cycloaddition of 2-phosphaindolizine, 1-aza-2-phosphaindolizine, 3-aza-2-phosphaindolizine, and 1,3-diaza-2

• studied by single-crystal X-ray diffraction by Khrizanforov et al., and the preferred conformations were substantiated by DFT calculations [6]. Finally, Hersh and Chan presented a method to improve the accuracy of 31P NMR chemical shift calculations by use of scaling methods [7]. György Keglevich Budapest

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• /RMSD = 6.9/8.5 ppm and 6.8/9.1 ppm, respectively, over an experimental chemical shift range of −181 to 356 ppm. Due to the unexplained failures observed, we recommend use of more than one method when looking at novel structures. Keywords: calculations; DFT; phosphorus NMR; scaling methods

• using such calculations is a powerful technique [9][10][11][12][13]. A set of recommendations for best practices has been proposed [1][2][3][14] and made available online [15] describing basis set choices, geometry optimization, incorporation of solvation, and use of scaling factors derived from linear

• experimental chemical shifts of relatively small molecules [17][18][19][20][21][22][23][24]. For instance, while calculations for 1H NMR are considered to be sufficiently reliable using DFT methods with the 6-311+G(2d,p) basis set [15], work on 31P NMR chemical shifts has favored [18][21][24] the use of larger