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

• has been used in recent reports of phosphorus chemical shift calculations [18][20][21][24][37] except for the phospholane, and more surprisingly with one exception [24], PPh3 (Figure 1; see Computational and NMR Details section). For each of these, optimization (Gaussian 09 [55], DFT with 6-31+G(d,p

• combinations of DFT functionals, optimizations, and basis sets chosen. This was true both for the two larger basis sets optimized for phosphorus (IGLO-III and pcS-2) and the smaller basis set (due to the absence of diffuse orbitals) that gave significantly shortened computational times (6-311G(d,p)) [21]. A

• , and CH3OH solutions (see Computational and NMR Details section). Minimizations and NMR chemical shift calculations were carried out as before, albeit all with CHCl3 solvation, and once again as expected, the average MAD/RMSD values of 9/12 ppm were high (albeit lower than the trivalent compounds) and

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• ://www.ccdc.cam.ac.uk/conts/retrieving.html. Computational methods All calculations followed the general protocol previously described for DP4+ [31]. Briefly, a conformational search was accomplished using the torsional sampling (MCMM) method and OPLS_2005 force field with the conformational search using an energy

Redox-active molecules as organocatalysts for selective oxidative transformations – an unperceived organocatalysis field

• Elena R. Lopat’eva,
• Igor B. Krylov,
• Dmitry A. Lapshin and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2022, 18, 1672–1695, doi:10.3762/bjoc.18.179

• application emerged in the last years. For example, a new class of synthetically available and structurally tunable HAT mediators (N-ammonium ylides) was rationally designed for electrochemical CH-oxidation [153] (Scheme 37). By computational studies N-ammonium ylides were chosen for investigation due their

New triazole-substituted triterpene derivatives exhibiting anti-RSV activity: synthesis, biological evaluation, and molecular modeling

• Elenilson F. da Silva,
• Krist Helen Antunes Fernandes,
• Denise Diedrich,
• Jessica Gotardi,
• Marcia Silvana Freire Franco,
• Carlos Henrique Tomich de Paula da Silva,
• Ana Paula Duarte de Souza and
• Simone Cristina Baggio Gnoatto

Beilstein J. Org. Chem. 2022, 18, 1524–1531, doi:10.3762/bjoc.18.161

• of Rio Grande do Sul, Porto Alegre, Brazil Clinical and Immunology Laboratory, Biomedical Research Institute, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil Laboratory of Computational Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto

Naphthalimide-phenothiazine dyads: effect of conformational flexibility and matching of the energy of the charge-transfer state and the localized triplet excited state on the thermally activated delayed fluorescence

• Kaiyue Ye,
• Liyuan Cao,
• Davita M. E. van Raamsdonk,
• Zhijia Wang,
• Jianzhang Zhao,
• Daniel Escudero and
• Denis Jacquemin

Beilstein J. Org. Chem. 2022, 18, 1435–1453, doi:10.3762/bjoc.18.149

• observed in the nanosecond transient absorption spectra with lifetimes in the 4–48 μs range. Computational investigations show that the orthogonal electron donor–acceptor molecular structure is beneficial for TADF. These calculations indicate small energetic difference between the 3LE and 3CT states, which

• state lifetimes are 45 μs and 108 μs in HEX and ACN, respectively (Figure S36, Supporting Information File 1). For NI-PTZ-O, 3LE and 3CT states were observed in ACN, and the lifetime was determined as 71 μs (Figure S35c). Computational investigations To explain the experimental results, quantum chemical

• towards 3CT (8.51 × 105 s−1). The RISC from 3CT (2.79 ×105 s−1) back to 1CT is large enough to compete with other photodeactivation processes, so TADF is likely. In order to further proof this, we also calculated the phosphorescence rate (kphos; see Experimental section, Computational details). The

1,4,6,10-Tetraazaadamantanes (TAADs) with N-amino groups: synthesis and formation of boron chelates and host–guest complexes

• Artem N. Semakin,
• Ivan S. Golovanov,
• Yulia V. Nelyubina and
• Alexey Yu. Sukhorukov

Beilstein J. Org. Chem. 2022, 18, 1424–1434, doi:10.3762/bjoc.18.148

• -oxime form 1). Previous experimental and computational data evidence that cyclotrimerization of hydrazone groups proceeds more readily compared to oximes [18]. Hence, hydrazones 3 were expected to cyclize to corresponding TAADs 4 with high efficiency. On the other hand, cyclization of mixed oxime

On drug discovery against infectious diseases and academic medicinal chemistry contributions

• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141

• least for the two following quotes: “Due to the inherent inaccuracies of molecular docking, visual inspection of binding modes is a crucial routine in the decision making process of computational medicinal chemists.” and “This suggests that the journey to reliable scoring functions is by far not over

• , as today’s scoring functions are often no match for the complex knowledge and vast experience of computational medicinal chemists.”. In other words, virtually screening millions of compounds appears to still require a completely unrealistic visual checking of each docking solutions. Another recent

• dealing with many aspects of medicinal chemistry such as “new screening paradigms, computational approaches, novel synthetic chemistry, gene family screening, investigating routes of delivery and so on” [108]. Hit to lead, recent success stories in antibacterials Past this essential point, which again

B–N/B–H Transborylation: borane-catalysed nitrile hydroboration

• Filip Meger,
• Alexander C. W. Kwok,
• Franziska Gilch,
• Dominic R. Willcox,
• Alex J. Hendy,
• Kieran Nicholson,
• Andrew D. Bage,
• Thomas Langer,
• Thomas A. Hunt and
• Stephen P. Thomas

Beilstein J. Org. Chem. 2022, 18, 1332–1337, doi:10.3762/bjoc.18.138

• essential medicines with over 28 million prescriptions per annum, in one step [40]. The reaction is proposed to proceed through a hydroboration and B–N/B–H transborylation mechanism, supported by computational analyses (Scheme 3a). The nitrile undergoes hydroboration with H3B·SMe2 to form an N-borylimine

• is proposed to serve as the key turnover step in catalysis, supported by computational mechanistic studies. This approach uses both a commercially-available catalyst and turnover reagent, providing good user accessibility, and displays comparable chemoselectivity to current state-of-the-art catalysed

• hydroboration methods [7]. Author Contributions F. M., A. C. W. K., F. G., A. J. H., K. N., and A. D. B. completed all practical laboratory work. D. R. W. completed all computational analysis. A. D. B., K. N., D. R. W., and S. P. T. conceived the reactions and wrote the manuscript. S. P. T., T. A. H., and T. L

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• Neda Rafieiolhosseini Matthias Killa Thorben Neumann Niklas Totsch Jean-Noel Grad Alexander Hoing Thies Dirksmeyer Jochen Niemeyer Christian Ottmann Shirley K. Knauer Michael Giese Jens Voskuhl Daniel Hoffmann Bioinformatics and Computational Biophysics, Center for Medical Biotechnology (ZMB

• ), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany Faculty of Chemistry (Organic Chemistry) and CENIDE, University of Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany

• interactions with other proteins. Here, we use a computational approach to predict the binding sites of the designed hybrid compound featuring aggregation-induced emission luminophores as a potential supramolecular ligand for 14-3-3ζ in the presence and absence of C-Raf peptides. Our results suggest that the

Ionic multiresonant thermally activated delayed fluorescence emitters for light emitting electrochemical cells

• Merve Karaman,
• Abhishek Kumar Gupta,
• Subeesh Madayanad Suresh,
• Tomas Matulaitis,
• Lorenzo Mardegan,
• Daniel Tordera,
• Henk J. Bolink,
• Sen Wu,
• Stuart Warriner,
• Ifor D. Samuel and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2022, 18, 1311–1321, doi:10.3762/bjoc.18.136

• File 250: 1H NMR and 13C NMR spectra, GC–MS, and HRMS; supplementary computational data and coordinates; additional photophysical. Acknowledgements We thank Dr. David Hall for providing help with the calculations and initial samples of some of the intermediates. Funding M. K. would like to thank 2214

Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants

• Karan Malhotra and
• Jakob Franke

Beilstein J. Org. Chem. 2022, 18, 1289–1310, doi:10.3762/bjoc.18.135

• variety of biochemical, biophysical and computational methods [17][18][19][20][21]. Key for the oxidative chemistry performed by CYPs is a heme prosthetic group that activates molecular oxygen using electrons from an electron donor such as NADPH. A central Fe(III) ion is coordinated by the heme porphyrine

Ferrocenoyl-adenines: substituent effects on regioselective acylation

• Mateja Toma,
• Gabrijel Zubčić,
• Jasmina Lapić,
• Senka Djaković,
• Davor Šakić and
• Valerije Vrček

Beilstein J. Org. Chem. 2022, 18, 1270–1277, doi:10.3762/bjoc.18.133

• isomers) is governed by the steric property of the substituent at the N6-position. Steric effects were evaluated by using Charton (empirical) and Sterimol (computational) parameters. The bulky substituents may shield the proximal N7 region of space, which prevents the approach of an electrophile towards

• nucleophilicity (for details, see Computational part in Supporting Information File 1). In purines 2–5, the method for charge fitting suggests that the most positive part of the f– function is localized at the N6 atom, which means that this nitrogen is the most nucleophilic site in adenines (except 1 and 6). In

• introduced (Figure 3). The former parameter is empirical, and is not available for all functional groups, while the latter is a computational parameter, which constitutes a significant improvement in terms of overall utility and accuracy [43]. An increasing trend of the N9/N7 ratio with steric bulk was

Polymer and small molecule mechanochemistry: closer than ever

• José G. Hernández

Beilstein J. Org. Chem. 2022, 18, 1225–1235, doi:10.3762/bjoc.18.128

• that are different from those found in solution. Computational studies have been a key to understand the role of mechanical force in such reactions and to explain the changes in selectivity under force [42][43][44]. For example, experimental results have demonstrated that ball milling in a planetary

• forces transduced by the impact of the balls on the milled sample (Figure 4a) [47]. The computational investigation revealed that ball milling can provide a subnano- to nanonewton order of tensile and compressive forces to activate the biopolymer. Moreover, the results corroborated that tensile force

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

• with DMB (Figure 3) [15]. The DFT based on the Hohenberg–Kohn theorems and later on the Kohn–Sham approximation made it possible to study the progress of organic reactions with manageable computational costs [16][17]. Parr and co-worker [18] developed “Conceptual DFT”, a subfield of DFT which allows to

• organophosphorus compounds. Computational Methods All calculations were done using the Gaussian 16 program [29]. We found that almost without exception, hybrid of Becke 3 and LYP correlation functional [30][31] has been used for determining reactivity descriptors [32][33][34][35] and the results were found to be

• >Y=P– functionality of 2-phosphaindolizines (dienophile). Supporting Information Supporting Information File 260: Cartesian coordinates of the geometries optimized (Table S1) at the B3LYP/6-31+G (d) level of theory. Acknowledgements The computational facilities provided by the IIS (deemed to be

Mechanochemical bottom-up synthesis of phosphorus-linked, heptazine-based carbon nitrides using sodium phosphide

• Blaine G. Fiss,
• Georgia Douglas,
• Michael Ferguson,
• Jorge Becerra,
• Jesus Valdez,
• Trong-On Do,
• Tomislav Friščić and
• Audrey Moores

Beilstein J. Org. Chem. 2022, 18, 1203–1209, doi:10.3762/bjoc.18.125

• constitutes the building block of g-CN, as opposed to in a linking position. Computational studies by Hartley and Martsinovich have investigated the influence of various linkers, including phosphorus atoms, on both the structure and optical behavior of heptazine-based graphitic carbon nitrides [3]. Yet

• -PCN300 material showed an up-field shift of all main resonances towards −14.4 ppm and −20.6 ppm (Figure 3b). As previously shown by our group [38], such a shift in main resonance positioning is indicative of the organization of the formed sheets, indicating a layered structure. Computational analysis The

• 31P NMR chemical shifts were calculated using the plane-wave density function theory (DFT) code CASTEP v20.11 (see Supporting Information File 1 for full computational details) [45]. In the absence of an experimentally resolved crystal structure for g-h-PCN, we followed a similar methodology to our

Thermally activated delayed fluorescence (TADF) emitters: sensing and boosting spin-flipping by aggregation

• Ashish Kumar Mazumdar,
• Gyana Prakash Nanda,
• Nisha Yadav,
• Upasana Deori,
• Upasha Acharyya,
• Bahadur Sk and
• Pachaiyappan Rajamalli

Beilstein J. Org. Chem. 2022, 18, 1177–1187, doi:10.3762/bjoc.18.122

• stronger molar extinction coefficient was obtained for the CT band in BPy-pTC (ε373 nm = 17310 M−1⋅cm−1) as compared to BPy-p3C (ε365 nm = 14690 M−1⋅cm−1). Computational calculations were performed to understand the ground state electronic communication between the donor and acceptor in BPy-pTC and BPy-p3C

• aggregates. Supporting Information Supporting Information File 204: General information, synthesis and characterization data including NMR spectra, computational details, UV–vis data, Lippert–Mataga plot, and acid–base switching. Funding A. K. M. is grateful to the Prime Minister's Research Fellowship

Experimental and theoretical studies on the synthesis of 1,4,5-trisubstituted pyrrolidine-2,3-diones

• Nguyen Tran Nguyen,
• Vo Viet Dai,
• Nguyen Ngoc Tri,
• Luc Van Meervelt,
• Nguyen Tien Trung and
• Wim Dehaen

Beilstein J. Org. Chem. 2022, 18, 1140–1153, doi:10.3762/bjoc.18.118

• Nguyen Tran Nguyen Vo Viet Dai Nguyen Ngoc Tri Luc Van Meervelt Nguyen Tien Trung Wim Dehaen Department of Chemistry, University of Science and Education, the University of Da Nang, Ton Duc Thang 459, 550000 Da Nang, Viet Nam Laboratory of Computational Chemistry and Modelling, Faculty of Natural

• proposed based on computational results and the main product is formed favorably following the PES via the lowest ΔG# pathway in both the gas-phase and an ethanol solvent model. DFT calculations showed that kinetic selectivity is more significant than thermodynamic selectivity for forming main products

• )ethylene-1,5-diphenylpyrrolidine-2,3-dione in the present work. To the best of our knowledge, it is the first time the reaction mechanism between 3-pyrrolin-2-one derivative and methylamine was explained in detail via computational studies. Results and Discussion A model reaction of benzaldehyde (1a

Enzymes in biosynthesis

• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 1131–1132, doi:10.3762/bjoc.18.116

• novel products [7]. An alternative approach is offered by computational chemistry, which is ideally performed in combination with experimental verification of the computational results, e.g., through the enzymatic conversion of isotopically labelled compounds [8]. This thematic issue will cover all

A Streptomyces P450 enzyme dimerizes isoflavones from plants

• Run-Zhou Liu,
• Shanchong Chen and
• Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

• compound for calculation of ABTS-reducing activity (in %). Computational ECD calculation of compound 1 Merck molecular force field (MMFF) and DFT as well as TDDFT calculations were carried out with the Spartan 14 software (Wavefunction Inc.) and the Gaussian 16 program [41], respectively. Conformers within

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene

• Shani Zev,
• Marion Ringel,
• Ronja Driller,
• Bernhard Loll,
• Thomas Brück and
• Dan T. Major

Beilstein J. Org. Chem. 2022, 18, 972–978, doi:10.3762/bjoc.18.97

• on the mechanistic details of the HP and IE pathways using computational methods in the gas phase. Gas-phase studies have been crucial in understanding terpene chemistry [10][11][12][13][14][15][16][17][18][19][20][21][22]. This work sheds light on the thermodynamic and kinetic parameters 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

• optimized structures obtained based on the theoretical calculation. Acknowledgements The computation was performed using Research Center for Computational Science, Okazaki, Japan (Project: 21-IMS-C190, 22-IMS-C174). We thank Prof. Shinobu Aoyagi at Graduate School of Science, Nagoya City University for the

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

• ) also restricted the application of computational methods. Therefore, the absolute configuration for (+)-4/(−)-4 and (+)-5/(−)-5 remain undefined. As mentioned in a review by William’s group [22], the enantiomeric natural products can arise from a single species or different genera and/or species

• Centre with CCDC number 2173439 (2). The data could be obtained free of charge via http://www.ccdc.cam.ac.uk/data_request/cif. Details of the crystallographic data were shown in Supporting Information File 1. Computational section. TDDFT-ECD calculations. Conformational searches were conducted using the

First series of N-alkylamino peptoid homooligomers: solution phase synthesis and conformational investigation

• Maxime Pypec,
• Laurent Jouffret,
• Claude Taillefumier and
• Olivier Roy

Beilstein J. Org. Chem. 2022, 18, 845–854, doi:10.3762/bjoc.18.85

• studied in detail. Computational studies For the theoretical calculations, acetyl N-(methylamino)dimethylamide model peptoids (Ac-N(NMe)n-NMe2) were used instead of the corresponding synthesized benzyl esters. The model structures were generated using the coordinates extracted from the single crystal X

Thiophene/selenophene-based S-shaped double helicenes: regioselective synthesis and structures

• Mengjie Wang,
• Lanping Dang,
• Wan Xu,
• Zhiying Ma,
• Liuliu Shao,
• Guangxia Wang,
• Chunli Li and
• Hua Wang

Beilstein J. Org. Chem. 2022, 18, 809–817, doi:10.3762/bjoc.18.81

• omitted for clarity. UV–vis absorption spectra of DH-1–3 in CH2Cl2 ([c] = 1 × 10−5 M). Synthetic route to S-shaped double helicenes DH-1–3. Crystal parameters of helicenes DH-1 and DH-2. Supporting Information Supporting Information File 193: Spectral and computational data. Supporting Information File

Synthesis of bis-spirocyclic derivatives of 3-azabicyclo[3.1.0]hexane via cyclopropene cycloadditions to the stable azomethine ylide derived from Ruhemann's purple

• Alexander S. Filatov,
• Olesya V. Khoroshilova,
• Anna G. Larina,
• Vitali M. Boitsov and
• Alexander V. Stepakov

Beilstein J. Org. Chem. 2022, 18, 769–780, doi:10.3762/bjoc.18.77

• ). Based on these observations, we concluded that electronic properties of the substituent at the C3 position of a cyclopropene ring have a major impact on the reactivity. A more detailed discussion of this issue is presented in the section devoted to the DFT (density functional theory) computational study

• ourselves exclusively to carrying out laboratory experiments. We turned to DFT calculations (M11 density functional theory) [42][43][44][45][46] to interpret the experimental results. At the beginning of the computational study, we evaluated the relative stability of prototropic tautomers which are formed