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

• stereoisomers to influence preferred conformations when designing functional molecules. Experimental Computational details The benchmark study was conducted for 3-fluoropyrrolidine and 3-fluoropyrrolidinium cation to determine the optimal theoretical level for further investigations involving 2,3-, 2,4-, and

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

• transfer capacity and chemical stability of different cyclic hypervalent halogen reagents. Results and Discussion We selected five different skeletons and twenty common transfer groups for combination (Figure 2) and calculated their BDEs. Referring to the previous computational studies of hypervalent

• 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

• . Comparison of E(r) for XB complexes 9–12, 42–44, and 53–56. Correlation of p-character and Vs,max on X of XB donor with ΔG of XB bond. Model for ΔG based on Equation 1. Supporting Information Supporting Information File 21: Computational data. Supporting Information File 22: Coordinates of optimized

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

• (S10 OD021758-01A1), and Jodie Johnson for GC–MS support. We thank Wenbo Ning for measuring the melting point of 9. Funding This work was funded in part by NIH grant R35 GM142574 (to J.D.R.), NSF grant CHE-1856416 (to D.J.T.), and NSF CHE-2020110 (to S.L.). Computational resources were provided by NSF

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

• (Figure 5b). Computational methods The geometry optimization and frequency analysis of Cu-nanobrackets 1a and 1b were performed at (U)ωB97X-D/6-31+G(d,p)-SDD(Cu) [30][31][32][33] level using the Gaussian 16 program [34], with calculating the pre-resonance Raman activities at 488 nm excitation wavelength

Synthesis of indano[60]fullerene thioketone and its application in organic solar cells

• Yong-Chang Zhai,
• Shimon Oiwa,
• Shinobu Aoyagi,
• Shohei Ohno,
• Tsubasa Mikie,
• Jun-Zhuo Wang,
• Hirofumi Amada,
• Koki Yamanaka,
• Kazuhira Miwa,
• Naoyuki Imai,
• Takeshi Igarashi,
• Itaru Osaka and
• Yutaka Matsuo

Beilstein J. Org. Chem. 2024, 20, 1270–1277, doi:10.3762/bjoc.20.109

• -withdrawing substituents. Computational studies with density functional theory revealed the unique vibrations of the thioketone group in FIDS. The molecular structure of FIDS was confirmed by single-crystal X-ray analysis. Bulk heterojunction organic solar cells using three evaporable fullerene derivatives

Mechanistic investigations of polyaza[7]helicene in photoredox and energy transfer catalysis

• Johannes Rocker,
• Till J. B. Zähringer,
• Matthias Schmitz,
• Till Opatz and
• Christoph Kerzig

Beilstein J. Org. Chem. 2024, 20, 1236–1245, doi:10.3762/bjoc.20.106

• Aza-H•+ (red) were computed using TD-DFT (see Supporting Information File 1 for details). These computational results, which are included in Figure 1B, align well with the experimentally observed absorption bands in the visible region, supporting our assignment. The observed behavior of the Aza-H

Competing electrophilic substitution and oxidative polymerization of arylamines with selenium dioxide

• Vishnu Selladurai and
• Selvakumar Karuthapandi

Beilstein J. Org. Chem. 2024, 20, 1221–1235, doi:10.3762/bjoc.20.105

• interactions are rarely reported and currently gaining interest [59]. Computational studies To comprehend the role of electron-donating and -withdrawing groups in arylamine oxidation using SeO2 as oxidant, DFT calculations were carried out on the arylamines and SeO2 using Gaussian 16 [60]. The molecular

Two-fold addition reaction of silylene to C₆₀: structural and electronic properties of a bis-adduct

• Masahiro Kako,
• Masato Kai,
• Masanori Yasui,
• Michio Yamada,
• Yutaka Maeda and
• Takeshi Akasaka

Beilstein J. Org. Chem. 2024, 20, 1179–1188, doi:10.3762/bjoc.20.100

• supplementary crystallographic data for this paper, and is obtainable free of charge from the Cambridge Crystallographic Data Centre. Computational method. All calculations were conducted using the Gaussian 16 program [60]. Optimized structures were obtained at the B3LYP [45][46][47] level of theory using basis

Kinetically stabilized 1,3-diarylisobenzofurans and the possibility of preparing large, persistent isoacenofurans with unusually small HOMO–LUMO gaps

• Qian Liu and
• Glen P. Miller

Beilstein J. Org. Chem. 2024, 20, 1099–1110, doi:10.3762/bjoc.20.97

• resistance to the most reactive 1,3-carbons of the furan ring. A combination of experimental and computational studies clarifies the impacts of these sterically congesting substituents on each molecule’s electronic structure. We further studied the reaction rates of 1,3-diarylisobenzofurans with the strong

• dienophiles dimethyl acetelyenedicarboxylate (DMAD) and acrylonitrile. We conclude that the synthesis of large, persistent, kinetically stabilized isoacenofurans with unusually small HOMO–LUMO gaps is an achievable goal. Results and Discussion Computational HOMO–LUMO gaps for isoacenofurans and comparable

• substituents, respectively, were also attempted but without success. In these cases, the sterically congesting ortho isopropyl and tert-butyl groups stymie the Friedel–Crafts acylation step leading to diketone (Scheme 1). Experimental and computational studies of 1,3-diarylisoacenofurans Purified

Novel route to enhance the thermo-optical performance of bicyclic diene photoswitches for solar thermal batteries

• Akanksha Ashok Sangolkar,
• Rama Krishna Kadiyam and
• Ravinder Pawar

Beilstein J. Org. Chem. 2024, 20, 1053–1068, doi:10.3762/bjoc.20.93

• results will certainly have a remarkable impact for applications in solar energy harvesting and storage. Computational Details The molecular structures of all studied dienes and photoproducts were fully relaxed without any geometrical or symmetrical constraints. The geometry optimization was performed

• ** level for the geometries optimized using the same level of theory. Further, the single point energy of the diene and photoproduct were also accounted at the DLPNO-CCSD(T)/Def2TZVP level of theory to predict the more accurate storage energy values at a low computational cost. This storage energy is

Structure–property relationships in dicyanopyrazinoquinoxalines and their hydrogen-bonding-capable dihydropyrazinoquinoxalinedione derivatives

• Tural N. Akhmedov,
• Ajeet Kumar,
• Daken J. Starkenburg,
• Kyle J. Chesney,
• Khalil A. Abboud,
• Novruz G. Akhmedov,
• Jiangeng Xue and
• Ronald K. Castellano

Beilstein J. Org. Chem. 2024, 20, 1037–1052, doi:10.3762/bjoc.20.92

• exhibits a noteworthy impact on the thermal stabilities (analyzed by TGA) of the compounds. The single-crystal X-ray diffraction of DPQD 2b exhibits a desirable herringbone solid-state arrangement for a potential OFET application. Complementary gas-phase computational analysis has provided insight into the

• illustrated in Figures S37–S41 (Supporting Information File 1). This serves as good evidence that the synthesized compounds exhibit no signs of aggregation in DMSO within the assessed concentration range (i.e., 2.5–45 μM). Electronic structure calculations Gas-phase computational investigations were conducted

• and DPQDs were established using gas-phase computational DFT analysis (B3LYP/6-31+G* level of theory), UV–visible spectroscopy, thermal analysis, and X-ray analysis in the solid state for 2b, 5b, and 6b. The primary takeaways from the work concern the attractive functional consequences of efficiently

(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