(Bio)isosteres of ortho- and meta-substituted benzenes

• H. Erik Diepers and
• Johannes C. L. Walker

Beilstein J. Org. Chem. 2024, 20, 859–890, doi:10.3762/bjoc.20.78

• efficiently (Scheme 18A) [70][71][72]. Experimental results and computational investigations by Stephenson and co-workers showed that the obtained ratio of 1,3-cunanes to 2,6-cuneanes is dependent on the cubane substituents [71]. Generally, at least one of the substituents needs to be electron donating to

Research progress on the pharmacological activity, biosynthetic pathways, and biosynthesis of crocins

• Zhongwei Hua,
• Nan Liu and
• Xiaohui Yan

Beilstein J. Org. Chem. 2024, 20, 741–752, doi:10.3762/bjoc.20.68

• CsCCD2 that exhibits broader substrate specificity and higher catalytic efficiency through computational modeling. Heterologous expression of the S323A mutant of CsCCD2 in yeast led to a 4-fold enhancement in the production of 1, with a crocetin (1) titer of 107 mg/L in a 5-liter fed-batch fermentation

Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization

• Senze Qiao,
• Zhongyu Cheng and
• Fuzhuo Li

Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66

• stability, etc. Emerging research methods on bioinformatics, computational modeling, deep learning, protein engineering, and high-throughput screening will accelerate the pace of enzyme discovery to provide a broader platform of tools for employing chemoenzymatic strategies [64][87][88][89]. More

Enhanced reactivity of Li⁺@C₆₀ toward thermal [2 + 2] cycloaddition by encapsulated Li⁺ Lewis acid

• Hiroshi Ueno,
• Yu Yamazaki,
• Hiroshi Okada,
• Fuminori Misaizu,
• Ken Kokubo and
• Hidehiro Sakurai

Beilstein J. Org. Chem. 2024, 20, 653–660, doi:10.3762/bjoc.20.58

• values of Li+@C60 are also listed as a reference. Supporting Information Supporting Information File 50: HPLC profiles, NMR, HRMS, UV–vis absorption spectra, and computational details. Acknowledgements We thank to Dr. N. Ikuma for a fruitful discussion. Generous support from the FRIS CoRE, Tohoku

Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

• Yasuhiro Oishi,
• Motoharu Kitatani and
• Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

• biosensing device. In oscillator-type biosensors, by arranging an appropriate surrounding environment, an improvement of the sensitivity is expected. Computational Method The density functional theory (DFT) calculation determined stable atomic configurations of conformation 1 and 2 of PASE on graphene. In

Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination

• Ruichen Lan,
• Brock Yager,
• Yoonsun Jee,
• Cynthia S. Day and
• Amanda C. Jones

Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43

• solvent and anion effects add complexity to mechanistic interpretation, and the reluctance of alkylgold complexes to undergo protodeauration under similar conditions give us pause [28]. While computational studies support protodeauration, the significantly lower reactivity of alkenes compared to alkynes

Spatial arrangements of cyclodextrin host–guest complexes in solution studied by ¹³C NMR and molecular modelling

• Konstantin Lebedinskiy,
• Ivan Barvík,
• Zdeněk Tošner,
• Ivana Císařová,
• Jindřich Jindřich and
• Radim Hrdina

Beilstein J. Org. Chem. 2024, 20, 331–335, doi:10.3762/bjoc.20.33

• supramolecular capsule with noradamantane-3-methyleneamine (2) as guest molecule (side and top view). Supporting Information Supporting Information File 38: General information, NMR spectra, NMR study, computational study, crystallographic data collection and refinement details. Funding This work has been

Unveiling the regioselectivity of rhodium(I)-catalyzed [2 + 2 + 2] cycloaddition reactions for open-cage C₇₀ production

• Cristina Castanyer,
• Anna Pla-Quintana,
• Anna Roglans,
• Albert Artigas and
• Miquel Solà

Beilstein J. Org. Chem. 2024, 20, 272–279, doi:10.3762/bjoc.20.28

• (fulleroid) derivatives. The aim is to shed light on the regioselectivity of the process through both experimental and computational approaches. In addition, the photooxidation of one of the C–C double bonds in the synthesized bis(fulleroids) affords open-cage C70 derivatives having a 12-membered ring

• group was substituted by a mesyl substituent and BIPHEP was used as a model phosphine ligand instead of Tol-BINAP to reduce the computational cost. The calculations, conducted at the B3LYP-D3/cc-pVTZ-PP(SMD=o-DCB)//B3LYP-D3/cc-pVDZ-PP level (see full computational details in Supporting Information File

Additive-controlled chemoselective inter-/intramolecular hydroamination via electrochemical PCET process

• Kazuhiro Okamoto,
• Naoki Shida and
• Mahito Atobe

Beilstein J. Org. Chem. 2024, 20, 264–271, doi:10.3762/bjoc.20.27

• oxidation current can be considered as a decrease in the diffusion coefficient of the hydrogen bond complex; thus, we attempted to reproduce the CV pattern by computational simulation (Figures S1 and S2 in Supporting Information File 1) [16]. The results indicated that an excessively small diffusion

Catalytic multi-step domino and one-pot reactions

• Svetlana B. Tsogoeva

Beilstein J. Org. Chem. 2024, 20, 254–256, doi:10.3762/bjoc.20.25

• . Zhang, Ma, and W. Zhang reflects the state of the art in the α-amino acid-based [3 + 2] cycloaddition reactions of N–H-type azomethine ylides in multicomponent, one-pot, and stepwise reactions for the synthesis of diverse bioactive heterocyclic compounds and natural products [9]. Computational studies

Photochromic derivatives of indigo: historical overview of development, challenges and applications

• Gökhan Kaplan,
• Zeynel Seferoğlu and
• Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

• the O atom (Figure 6b). Moreover, the data of the first systematic computational ab initio study of the molecular mechanism of the photostability of indigo [36] support these findings and additionally point out that the single proton transfer (SPT) is more favorable than the double proton transfer

• was prepared and the photoisomerization behavior of these compounds was studied. Surprisingly, all N,N'-diarylindigos were obtained as mixtures of E/Z isomers. The computational study showed the negligible energy differences between the Z- and E-isomers of 19a–h in the ground state, which explained

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• on the fullerene sphere. This was followed by a nucleophilic attack of the fullerene carbanion on one of the cyano groups, ultimately yielding 33. Computational calculations also suggested that the rearrangement was facilitated by the destabilization of the reactant due to steric interactions

• may not be apparent at a glance. Nevertheless, comprehensive computational analyses employing the matrix method suggest that the intense long-wavelength CD signal observed for 56 is due to the coupling of individual helicene-to-TCBD electric-transition dipole moments. The emergence of axial chirality

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

• Laura Abella,
• Gerard Novell-Leruth,
• Josep M. Ricart,
• Josep M. Poblet and
• Antonio Rodríguez-Fortea

Beilstein J. Org. Chem. 2024, 20, 92–100, doi:10.3762/bjoc.20.10

• the reaction either via singlet excitation or via radical cation formation (Scheme 1). Estimation of the activation barrier for the [2 + 2] cycloaddition when the nanotube acts as a sensitizer is 33.5 ± 6.8 kJ mol−1. This value agrees with computational predictions for the reaction via an excited

• , the interaction between the C60 surface and the walls of the armchair (10,10) CNT. The interaction or encapsulation energy of a fullerene inside the CNT, defined as Eencap = EFuller@CNT – EFuller – ECNT, amounts to −3.23 eV for C60 at our present computational settings (PBE/plane waves, see section

• Computational methods). This significant amount of energy, which could be overestimated, comes from the π–π interactions between the C60 surface and the CNT wall and is modelled in a first approximation using Grimme’s corrections to the dispersion energy [16]. This interaction energy is comparable to those in

NMRium: Teaching nuclear magnetic resonance spectra interpretation in an online platform

• Luc Patiny,
• Hamed Musallam,
• Alejandro Bolaños,
• Michaël Zasso,
• Julien Wist,
• Metin Karayilan,
• Eva Ziegler,
• Johannes C. Liermann and
• Nils E. Schlörer

Beilstein J. Org. Chem. 2024, 20, 25–31, doi:10.3762/bjoc.20.4

• Department, Universidad del Valle, Cali 76001, Colombia Australian National Phenome Center, and Center for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia Department of Chemistry, Case Western Reserve University (CWRU

Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway

• Seiji Kawai,
• Akito Yamada,
• Yohei Katsuyama and
• Yasuo Ohnishi

Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1

• vigorously used to search for novel compounds in recent years due to the rapid improvement of DNA sequence technologies and computational approaches to analyze BGCs [1][3]. Our research group previously identified the secondary metabolite-specific nitrous acid biosynthetic pathway, named ANS (aspartate

1-Butyl-3-methylimidazolium tetrafluoroborate as suitable solvent for BF₃: the case of alkyne hydration. Chemistry vs electrochemistry

• Marta David,
• Elisa Galli,
• Richard C. D. Brown,
• Marta Feroci,
• Fabrizio Vetica and
• Martina Bortolami

Beilstein J. Org. Chem. 2023, 19, 1966–1981, doi:10.3762/bjoc.19.147

• addition, with computational studies we demonstrated the greater stability of BF3 in BMIm-BF4 compared to BF3·Et2O [103]. Based on the ever increasing need to identify new eco-friendly catalysts and/or reaction media for the hydration of alkynes, and considering our previous works on ILs and

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• , computational approaches could be efficiently used to gain insight into protein–GAG interactions that take place at single-molecule levels [32]. More than a complementary tool, computational approaches provide a better understanding of the role of individual interaction partners (including GAGs, solvent, and

• ions) by bringing often new and experimentally inaccessible details [33][34]. However, for computational researchers, there are still many challenges to overcome that originate from the physicochemical properties of GAGs, viz. their highly polarized (anionic) nature, their periodicity, and the

• explanation and prediction of GAG specificity [35]. Computational methodologies like molecular docking and molecular dynamics (MD) have proven to be successful in modelling protein–GAG interactions, particularly examining the fundamental questions related to these interactions such as their specificity, the

Biphenylene-containing polycyclic conjugated compounds

• Cagatay Dengiz

Beilstein J. Org. Chem. 2023, 19, 1895–1911, doi:10.3762/bjoc.19.141

• compounds [12]. Research using computational methods to investigate how benzo and benzocyclobutadiene annulations impact the ring current density of biphenylene derivatives reveals that the antiaromatic (paratropic) current density in the 4-ring structure can range widely, shifting from highly antiaromatic

• phenomenon is a result of non-radiative deactivation was corroborated by detailed computational chemistry studies. In continuation of the aforementioned work by Wagner and co-workers [49], they have synthesized also "v" and "z"-shaped POAs, wherein biphenylene groups are angularly incorporated into the 1,4

Anion–π catalysis on carbon allotropes

• M. Ángeles Gutiérrez López,
• Mei-Ling Tan,
• Giacomo Renno,
• Augustina Jozeliūnaitė,
• J. Jonathan Nué-Martinez,
• Javier Lopez-Andarias,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2023, 19, 1881–1894, doi:10.3762/bjoc.19.140

• /23 = 4.6 of the respective monomer 22, which was already best among fullerene monomers. In computational simulations, the positive maximum of the MEP surface next to the amine base was the same for dimer 37 (+13.9 kJ mol−1) and monomer 22 (+13.8 kJ mol−1), supporting that the dramatic increase in

• below that of unsubstituted NDIs despite stronger π acidity. Supported by experimental and computational data, this poor performance of dyad 46 was explained by lone-pair π interactions of the fullerene with the donating oxygens. These lone-pair π interactions were even more impactful on the sulfone

• level. Compared to the sulfoxides in 46, the catalytic activity of dyad 47 decreased rather than increased despite stronger π acidity. Supported by computational predictions [80][81], record activities in anion–π catalysis with fullerene dimers called for higher oligomers. However, synthetic efforts

Thienothiophene-based organic light-emitting diode: synthesis, photophysical properties and application

• Recep Isci and
• Turan Ozturk

Beilstein J. Org. Chem. 2023, 19, 1849–1857, doi:10.3762/bjoc.19.137

• absorption and emission maxima of 411 and 520 nm, respectively, with a mega Stokes shift of 109 nm and fluorescence quantum yields both in the solid state (41%) and in solution (86%). The optical properties were supported by computational chemistry using density functional theory for optimized geometry and

• . The high thermal stability is profitable for the preparation of stable and durable OLED devices. Computational chemistry Ground-state geometry optimization of DMB-TT-TPA (8) was performed using density functional theory (DFT) calculations with the Gaussian 16 software at the B3LYP/6-31G (d,p) level

• model and synthesized in 85% yield. Its photophysical properties were investigated by UV–vis and fluorescence spectroscopy. The obtained experimental results were found to be in good agreement with computational investigations. An OLED fabrication, where DMB-TT-TPA (8) was employed as an emitter, showed

Recent advancements in iodide/phosphine-mediated photoredox radical reactions

• Tinglan Liu,
• Yu Zhou,
• Junhong Tang and
• Chengming Wang

Beilstein J. Org. Chem. 2023, 19, 1785–1803, doi:10.3762/bjoc.19.131

• novel metallaphotoredox catalysis by combining the NaI/PPh3 photoredox catalyst with a Cu(I) catalyst to accomplish diverse C–O/N cross-couplings of alkyl N-hydroxyphthalimide esters 3 with various phenols/secondary amines 30 (Scheme 13) [24]. It was anticipated the utilization of computational methods

• NHC catalyst acted as a stabilizer for the EDA complex and generates a radical species, which was confirmed by further computational studies. Monofluoromethylation The monofluoromethyl (CH2F) group, which is commonly found in a lot of agrochemicals, pharmaceuticals, and materials, serves as a powerful

Charge carrier transport in perylene-based and pyrene-based columnar liquid crystals

• Alessandro L. Alves,
• Simone V. Bernardino,
• Carlos H. Stadtlober,
• Edivandro Girotto,
• Giliandro Farias,
• Rodney M. do Nascimento,
• Sergio F. Curcio,
• Thiago Cazati,
• Marta E. R. Dotto,
• Juliana Eccher,
• Leonardo N. Furini,
• Hugo Gallardo,
• Harald Bock and
• Ivan H. Bechtold

Beilstein J. Org. Chem. 2023, 19, 1755–1765, doi:10.3762/bjoc.19.128

• transport [37][38]. Therefore, to better understand the charge mobility of compounds 1 and 2, we obtained their ground state geometry using DFT within the B3LYP/def2-TZVP(-f) level of theory (Figure 8a). To reduce computational efforts, isopropyl moieties were used instead of the large aliphatic

Trifluoromethylated hydrazones and acylhydrazones as potent nitrogen-containing fluorinated building blocks

• Zhang Dongxu

Beilstein J. Org. Chem. 2023, 19, 1741–1754, doi:10.3762/bjoc.19.127

• trifluoroacetaldehyde hydrazones. Jasiński et al. demonstrated that the CF3 group offered an appropriate electronic balance through experimental spectral analysis and computational DFT methods, and the hydrazones could be readily used to provide convenient access to azo tautomers under the acidic conditions [43]. The C

Unprecedented synthesis of a 14-membered hexaazamacrocycle

• Anastasia A. Fesenko and
• Anatoly D. Shutalev

Beilstein J. Org. Chem. 2023, 19, 1728–1740, doi:10.3762/bjoc.19.126

• File 12: Copies of IR, 1H and 13C NMR spectra of synthesized compounds and computational details. Funding This research was financially supported by the Russian Science Foundation (Grant No. 23-23-00324).

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• liquors and, in both cases, XRD confirmed the obtention of the (E)-isomer, in an anti-conformation. Computational calculations (gas and water phases) were performed in order to confirm some of the structural and vibrational aspects of the compounds. An important intramolecular H bond involving the

• calculate the electrostatic potential over an electronic density map as well. For hdz-NO2, results show the alternated slipped stack motif involves the assembly of portions with opposite electrostatic potentials. Computational calculations were performed in order to confirm some of the structural and

• maintained in DMSO-d6 solution. It is worth noting that the presence of the electron-withdrawing nitro substituent in hdz-NO2 makes the interaction stronger. An IR spectroscopy study, which was supported by computational calculations, as well as a complete NMR characterization of both compounds, align with