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

• the DFT calculation realized by the PWscf code of Quantum ESPRESSO [30][31][32], the DFT-D3 correlation [33] together with PBEsol functional [34] for the exchange-correlation functional described van der Waals interaction between graphene and pyrene fragment in PASE. Ultrasoft pseudopotentials [35

Enhanced host–guest interaction between [10]cycloparaphenylene ([10]CPP) and [5]CPP by cationic charges

• Eiichi Kayahara,
• Yoshiyuki Mizuhata and
• Shigeru Yamago

Beilstein J. Org. Chem. 2024, 20, 436–444, doi:10.3762/bjoc.20.38

• −/1,2-dichloroethane upon scanning in (a) positive and (b) negative directions. UV–vis–NIR spectra of [10]CPP⊃[5]CPP2+[B(C6F5)4−]2 (black), [10]CPP (blue), and [5]CPP2+[B(C6F5)4−]2 (red) in CH2Cl2. Top and side view of [10]CPP⊃[5]CPP2+ complexes a) 1, b) 2, and c) 3 obtained by DFT calculation at the

Tandem Hock and Friedel–Crafts reactions allowing an expedient synthesis of a cyclolignan-type scaffold

• Viktoria A. Ikonnikova,
• Cristina Cheibas,
• Oscar Gayraud,
• Alexandra E. Bosnidou,
• Nicolas Casaretto,
• Gilles Frison and
• Bastien Nay

Beilstein J. Org. Chem. 2024, 20, 162–169, doi:10.3762/bjoc.20.15

• number 2301977. Supporting Information File 41: Experimental procedures, compound characterizations, crystallographic data, DFT calculation, and spectra. Supporting Information File 42: Crystallographic information file of compound 6. Funding This work was supporting by the French Agence Nationale de la

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

• 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

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

• 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

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

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

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

Rhodium-catalyzed intramolecular reductive aldol-type cyclization: Application for the synthesis of a chiral necic acid lactone

• Motoyuki Isoda,
• Kazuyuki Sato,
• Kenta Kameda,
• Kana Wakabayashi,
• Ryota Sato,
• Hideki Minami,
• Yukiko Karuo,
• Atsushi Tarui,
• Kentaro Kawai and
• Masaaki Omote

Beilstein J. Org. Chem. 2022, 18, 1642–1648, doi:10.3762/bjoc.18.176

• the substrates through an η6 binding intermediate by DFT calculation [49]. Although another mechanism could not be denied in which a Z-enolate intermediate changes to an E-enolate under thermodynamic control, we propose the following mechanism on the basis of the above results (Scheme 3). The Rh–H

Dienophilic reactivity of 2-phosphaindolizines: a conceptual DFT investigation

• Nosheen Beig,
• Aarti Peswani and
• Raj Kumar Bansal

Beilstein J. Org. Chem. 2022, 18, 1217–1224, doi:10.3762/bjoc.18.127

• , electrophilicity and nucleophilicity indices as well as the Fukui functions computed from the conceptual DFT calculation at the B3LYP/6-31+G (d) level of theory could be used successfully to rationalize the experimentally observed dienophilic reactivites of four classes of 2-phosphaindolizenes. The energies of the

Electrochemical and spectroscopic properties of twisted dibenzo[g,p]chrysene derivatives

• Tomoya Imai,
• Ryuhei Akasaka,
• Naruhiro Yoshida,
• Toru Amaya and
• Tetsuo Iwasawa

Beilstein J. Org. Chem. 2022, 18, 963–971, doi:10.3762/bjoc.18.96

• , a strong photoluminescence was observed for DBC-H and DBC-Si. Keywords: DFT calculation; dibenzo[g,p]chrysenes; fluorescent compounds; oxidation; polycyclic aromatic hydrocarbon (PAH); twisted acenes; Introduction Polycyclic aromatic hydrocarbons (PAHs) have attracted interest as potential

• HOMO to LUMO and HOMO-1 to LUMO+1 (see Tables S1–S6 in Supporting Information File 1). The trend for the order of optical band gap is roughly consistent with that of the HOMO–LUMO gap obtained from DFT calculation [52]. In the photoluminescence spectra, the luminescence of DBC-Br was very weak. On the

Electroreductive coupling of 2-acylbenzoates with α,β-unsaturated carbonyl compounds: density functional theory study on product selectivity

• Naoki Kise and
• Toshihiko Sakurai

Beilstein J. Org. Chem. 2022, 18, 956–962, doi:10.3762/bjoc.18.95

• Information Supporting Information File 215: Characterization data for compounds, copies of 1H and 13C NMR spectra, X-ray crystallographic data (ORTEP) of 3b, CV data of compounds 1a–h, and DFT calculation data for cyclization of enolate anions. Supporting Information File 216: Cif for 3b. Acknowledgements

Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa

• Shou-Mao Shen,
• Qing Yang,
• Yi Zang,
• Jia Li,
• Xueting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 916–925, doi:10.3762/bjoc.18.91

• configuration determination of natural products with stereogenic centers near the chromophore groups [20], was applied, since there is an α,β-unsaturated ketone chromophore nearby C-5 and C-2 in compound (+)-1. Thus, the theoretical ECD spectrum of (+)-1 was calculated by the DFT calculation method at the b3lyp

Syntheses of novel pyridine-based low-molecular-weight luminogens possessing aggregation-induced emission enhancement (AIEE) properties

• Masayori Hagimori,
• Tatsusada Yoshida,
• Yasuhisa Nishimura,
• Yukiko Ogawa and
• Keitaro Tanaka

Beilstein J. Org. Chem. 2022, 18, 580–587, doi:10.3762/bjoc.18.60

• the electronic nature of the compounds with and without AIEE properties. Keywords: acceptor–donor–acceptor; AIEE; low molecular weight; one-pot reaction; ((pyridin-2-yl)amino)maleimide; TD-DFT calculation; Introduction Fluorescent compounds have attracted considerable attention as functional

Iridium-catalyzed hydroacylation reactions of C1-substituted oxabenzonorbornadienes with salicylaldehyde: an experimental and computational study

• Angel Ho,
• Austin Pounder,
• Krish Valluru,
• Leanne D. Chen and
• William Tam

Beilstein J. Org. Chem. 2022, 18, 251–261, doi:10.3762/bjoc.18.30

• this field. Potential energy profile of the PCM solvation model for the hydrometalation/reductive elimination pathway of the Ir/diene-catalyzed hydroacylation of MeOBD with salicylaldehyde (14) in 1,4-dioxane, as evaluated by DFT calculation (M06 [69]/def2SVP [70]/PCM [72]//M06 [69]/def2TZVP [70]/PCM

• PCM solvation model for the carbometalation/reductive elimination pathway of the Ir/diene-catalyzed hydroacylation of MeOBD with salicylaldehyde (14) in 1,4-dioxane, as evaluated by DFT calculation (M06 [69]/def2SVP [70]/PCM [72]//M06 [69]/def2TZVP [70]/PCM [72]). Calculated Gibbs free energies (in

• evaluated by DFT calculation (M06 [69]/def2SVP [70]/PCM [72]//M06 [69]/def2TZVP [70]/PCM [72]). Calculated Gibbs free energies (in kcal/mol; T = 338.15 K) are with respect to separated reactants Ir(COD)OH (Cat) + SaliK + MeOBD. Potential energy profile of the PCM solvation model for the Ir/diene-catalyzed

Synthesis of 5-arylacetylenyl-1,2,4-oxadiazoles and their transformations under superelectrophilic activation conditions

• Andrey I. Puzanov,
• Dmitry S. Ryabukhin,
• Anna S. Zalivatskaya,
• Dmitriy N. Zakusilo,
• Darya S. Mikson,
• Irina A. Boyarskaya and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2021, 17, 2417–2424, doi:10.3762/bjoc.17.158

• ], it was shown by means of NMR spectroscopy and DFT calculation that the protonation of these oxadiazoles in Brønsted superacids TfOH and FSO3H gave reactive N,C-diprotonated species. The protonation of oxadiazoles 1 takes place at the nitrogen N4 and the α-carbon of the side chain C=C bond. One would

Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura

• Zhiwei Zhang,
• Tao Zhou,
• Taehui Yang,
• Keisuke Fukaya,
• Enjuro Harunari,
• Shun Saito,
• Katsuhisa Yamada,
• Chiaki Imada,
• Daisuke Urabe and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141

• functional theory (DFT) calculation of the ECD spectrum for 4, for which the absolute configuration was established by the modified Mosher’s method in our previous work [15]. Since the acyltetronic acid exists as a mixture of keto–enol tautomers, the calculation was carried out using the four possible

Fritsch–Buttenberg–Wiechell rearrangement of magnesium alkylidene carbenoids leading to the formation of alkynes

• Tsutomu Kimura,
• Koto Sekiguchi,
• Akane Ando and
• Aki Imafuji

Beilstein J. Org. Chem. 2021, 17, 1352–1359, doi:10.3762/bjoc.17.94

• magnesium alkylidene carbenoids was studied by using 13C-labeled sulfoxides and by using DFT calculations. Keywords: alkyne; 1-chlorovinyl p-tolyl sulfoxide; DFT calculation; Fritsch–Buttenberg–Wiechell rearrangement; magnesium alkylidene carbenoid; Introduction Alkynes are important compounds in organic

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• formation of the crystal networks. This is complemented with the use of density functional theory (DFT) calculation of structures that have currently not been determined due to difficulties of obtained crystals of sufficient quality for X-ray determination. Additionally, DFT calculations were conducted for

Exploring the possibility of using fluorine-involved non-conjugated electron-withdrawing groups for thermally activated delayed fluorescence emitters by TD-DFT calculation

• Dongyang Chen and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2021, 17, 210–223, doi:10.3762/bjoc.17.21

• states between S1 and T1, thus likely leading to a very efficient reverse intersystem crossing in these compounds. Keywords: DFT calculation; pentafluorosulfanyl; spin-orbit coupling; TADF; trifluoromethoxy; trifluoromethylthio; Introduction Organic thermally activated delayed fluorescence (TADF

• states, followed by rISC [22]. This situation typically occurs when there are multiple donors about a single acceptor as exists in the molecules 5CzBN and 5CzTRZ. For 5CzBN, time-dependent density functional theory (TD-DFT) calculation revealed the existence of three intermediate triplet states [22]. The

UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation

• Tim Holtum,
• Vikas Kumar,
• Daniel Sebena,
• Jens Voskuhl and
• Sebastian Schlücker

Beilstein J. Org. Chem. 2020, 16, 2911–2919, doi:10.3762/bjoc.16.240

• ), and RGD (top). Supporting Information DFT calculated normal modes with the corresponding wavenumbers and Raman activities of GCI ethyl amide and detailed synthesis routes for GCP and GCI ethyl amide. Supporting Information File 410: DFT calculation results and detailed synthesis routes

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• for 4, 19 nm for 5, and 23 nm for 6 were observed. Similar behaviors were observed for the absorption spectra of compounds 8–12 (Table S1, Supporting Information File 1). The TD-DFT calculation results obtained for the values of absorption wavelengths for the dyes were in the order 3 > 4 > 5 > 6 > 7

Development of fluorinated benzils and bisbenzils as room-temperature phosphorescent molecules

• Shigeyuki Yamada,
• Takuya Higashida,
• Yizhou Wang,
• Masato Morita,
• Takuya Hosokai,
• Kaveendra Maduwantha,
• Kaveenga Rasika Koswattage and
• Tsutomu Konno

Beilstein J. Org. Chem. 2020, 16, 1154–1162, doi:10.3762/bjoc.16.102

• lobe is localized at the central benzene ring. Accordingly, it can be concluded that the absorption bands at the short-wavelength region (around 290–315 nm) stems from the π–π* transition. The TD-DFT calculation also reveals that n–π* transitions (e.g., HOMO–2→LUMO for 2a and HOMO–3→LUMO for 3a) have

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• comparison of experimental and simulated ECD spectra [26][27]. Quite interestingly, the DFT calculation suggested that 1a and 1b would possess the opposite axial chirality around the biaryl bond between C-6 and C-7'': Ra for 1a and Sa for 1b as dominant atropisomers (Figure 4). This conformational difference

Halogen-bonding-induced diverse aggregation of 4,5-diiodo-1,2,3-triazolium salts with different anions

• Xingyu Xu,
• Shiqing Huang,
• Zengyu Zhang,
• Lei Cao and
• Xiaoyu Yan

Beilstein J. Org. Chem. 2020, 16, 78–87, doi:10.3762/bjoc.16.10

• bonds. The DFT calculation also shows that σ hole of in diiodotriazolium D and 1,2,3-triazolium B are comparable, and much larger than the 1,2,3-triazole A and 1,2,3-triazolylidene complex C-CuI due to positive charge effect. Conclusion In summary, we synthesized 4,5-diiodo-1,3-dimesityl-1,2,3

• the former shows a boat conformation and the latter forms a rectangle conformation. Triazolium salts form a linear polymer with polyiodide. 2-BF4 forms co-crystals with 4,4'-bipyridine via halogen bonding. DFT calculation results show that the σ holes of 4,5-diiodo-1,2,3-triazolium is similar to the σ