1,2-Naphthoquinone-4-sulfonic acid salts in organic synthesis

• Ruan Carlos B. Ribeiro,
• Patricia G. Ferreira,
• Amanda de A. Borges,
• Luana da S. M. Forezi,
• Fernando de Carvalho da Silva and
• Vitor F. Ferreira

Beilstein J. Org. Chem. 2022, 18, 53–69, doi:10.3762/bjoc.18.5

• equilibrium between A and B using semiempirical calculations (AM1 and PM3) and DFT (B3LYP/6-31G(d)) in the gas phase and water, where it was observed that in the gas phase B is the most stable, while in water A is formed, which is in agreement with the experimental results reported in the literature. There

2,3-Dibutoxynaphthalene-based tetralactam macrocycles for recognizing precious metal chloride complexes

• Li-Li Wang,
• Yi-Kuan Tu,
• Huan Yao and
• Wei Jiang

Beilstein J. Org. Chem. 2019, 15, 1460–1467, doi:10.3762/bjoc.15.146

• −@1. Energy-minimized structure of a) AuCl4−@1 and b) AuCl4−@2 at the level of theory of PM3 by using Spartan ’14 (Wavefunction, Inc.). a) Fluorescence emission spectra of 1 (20 µM) upon addition of different amounts of TBA[AuCl4] (concentration range of 0.0−800 µM) and then recorded in

Water-soluble SNS cationic palladium(II) complexes and their Suzuki–Miyaura cross-coupling reactions in aqueous medium

• Alphonse Fiebor,
• Richard Tia,
• Banothile C. E. Makhubela and
• Henok H. Kinfe

Beilstein J. Org. Chem. 2018, 14, 1859–1870, doi:10.3762/bjoc.14.160

• complexes in the current study, the Pd(II) to Pd(IV) mechanism was proposed as shown in Scheme 2 [44]. In order to verify the viability of the Pd(II) to Pd(IV) mechanism proposed, an exploratory computational study using the semi-empirical PM3 method was performed on the oxidative addition stage of the

• mechanism to determine if the results obtained theoretically could support the experimental results. The oxidative addition stage was selected because it is also the rate-determining step for the catalytic cycle, and thus it can be used to compare the rate of conversions. The PM3 method has been

p-tert-Butylthiacalix[4]arenes functionalized by N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide fragments: synthesis and binding of anionic guests

• Alena A. Vavilova and
• Ivan I. Stoikov

Beilstein J. Org. Chem. 2017, 13, 1940–1949, doi:10.3762/bjoc.13.188

• −, H2PO4−, NO3−) was carried out at a semi-empirical level using the quantum-mechanical method, PM3 (HyperChem 7.0). The proposed model for the binding of anions by p-tert-butylthiacalix[4]arenes containing proton–donor (amide, hydroxy) groups was studied in order to identify steric and/or electronic

• hindrances to the complex formation. Review of literature data [62][63][64][65] indicate a good agreement between the results of calculations involving the complexes geometry determined by this method and experimental data. The PM3 method is used quite productively for molecular design and modeling of the

• the association constants of the complexes of the studied thiacalix[4]arenes with a series of anions) and the results of quantum mechanical calculations (energy change in the formation of guest–host complexes calculated by the PM3 method) (HyperChem 7.0) was the final stage of the work (Table 4). The

Regiochemistry of cyclocondensation reactions in the synthesis of polyazaheterocycles

• Patrick T. Campos,
• Leticia V. Rodrigues,
• Andrei L. Belladona,
• Caroline R. Bender,
• Juliana S. Bitencurt,
• Fernanda A. Rosa,
• Davi F. Back,
• Helio G. Bonacorso,
• Nilo Zanatta,
• Clarissa P. Frizzo and
• Marcos A. P. Martins

Beilstein J. Org. Chem. 2017, 13, 257–266, doi:10.3762/bjoc.13.29

• regiochemistry of the products [11]. Saiz et al. [14] synthesized 2-hydrazolyl-4-thiazolidinones with the aid of semi-empirical calculations (PM3 method). Through HOMO/LUMO energies, orbital coefficients, and charge distribution, a mechanism was proposed explaining the products observed. The authors claimed that

• between the HOMO/LUMO energies of electrophiles and nucleophiles (Table 2 and Table 3), and the reactions were controlled by frontier molecular orbitals rather than by charge density. Analogous calculations using the PM3 method for cyclocondensation reactions were performed by Saiz et al. [14] for the

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

• Vladimir A. Stepchenko,
• Anatoly I. Miroshnikov,
• Frank Seela and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2016, 12, 2588–2601, doi:10.3762/bjoc.12.254

• only 5-phenyl- and 5-tert-butyl-6-azauracils displayed very low substrate activity. The role of structural peculiarities and electronic properties in the substrate recognition by E. coli nucleoside phosphorylases is discussed. Keywords: enzymatic glycosylation; PM3 and ab initio calculations

• interaction contributes to the sp3 → sp2 transformation of the N-1 nitrogen atoms. With this aim in view, we constructed and geometry optimized [Bio+(CHARMM27) force field] and then re-optimized using semi-empirical PM3 method (HyperChem 8.1) the eight-member cyclic structures comprising two hydrogen bonds

• (conjugate gradient); basis set of parameters; HyperChem 8.1). Structures of 6-azapyrimidines 15–18 tested for E. coli UP and TP. Geometry optimized structures (PM3 method) of 5-tert-butyl-6-azauracil (15) and 5-phenyl-6-azauracil (16) (upper structures) vs those of 5-ethyluracil and (E)-5-(2-bromovinyl

Bis(vinylenedithio)tetrathiafulvalene analogues of BEDT-TTF

• Erdal Ertas,
• İlknur Demirtas and
• Turan Ozturk

Beilstein J. Org. Chem. 2015, 11, 403–415, doi:10.3762/bjoc.11.46

• detailed semi-empirical PM3 calculation indicated that the formation of the intermediate 10 is an endothermic process with ΔHrxn= 29.435 kcal/mol. The reaction of the intermediate 10 with itself could produce the 1,4-dithiin ring 11 and the side product thiophene 17 through the intermediates 21 and 22 by

Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

• Bodee Nutho,
• Wasinee Khuntawee,
• Chompoonut Rungnim,
• Piamsook Pongsawasdi,
• Peter Wolschann,
• Alfred Karpfen,
• Nawee Kungwan and
• Thanyada Rungrotmongkol

Beilstein J. Org. Chem. 2014, 10, 2789–2799, doi:10.3762/bjoc.10.296

• understand the two flavonoids/β-CD complexes, hesperetin and naringenin complexes, in aqueous solution. The PM3 method was applied to calculate the energy regarding the antioxidant property of the flavonoid chysin in the complex with β-CD [32]. Interestingly, the molecular docking study on the fisetin/β-CD

Staudinger ligation towards cyclodextrin dimers in aqueous/organic media. Synthesis, conformations and guest-encapsulation ability

• Malamatenia D. Manouilidou,
• Yannis G. Lazarou,
• Irene M. Mavridis and
• Konstantina Yannakopoulou

Beilstein J. Org. Chem. 2014, 10, 774–783, doi:10.3762/bjoc.10.73

• titration experiments: the binding constant with 1-adamantylamine was similar to that of natural β-CD. Theoretical calculations for isolated molecules (PM3 level of theory) and in the presence of solvent [water, PM3(COSMO)] as well as DFT calculations suggested that the compounds prefer to adopt

• ) satisfactory aqueous solubility and independent binding capacity of the cavities. Keywords: calculations; conformations; cyclodextrin; dimer; inclusion; PM3; Staudinger ligation; Introduction The Staudinger reaction [1] is a classical method for the preparation of amines from phosphines and azides [2][3

• over the cavity indicates that intermediate conformations, between extended and self-included may exist in water as well. Computational results Quantum mechanical calculations were carried out for monomer 4 and dimer 6 at the PM3 level of theory for isolated molecules, as well as in the presence of

Diastereoselective synthesis of nitroso acetals from (S,E)-γ-aminated nitroalkenes via multicomponent [4 + 2]/[3 + 2] cycloadditions promoted by LiCl or LiClO₄

• Leandro Lara de Carvalho,
• Robert Alan Burrow and
• Vera Lúcia Patrocinio Pereira

Beilstein J. Org. Chem. 2013, 9, 838–845, doi:10.3762/bjoc.9.96

• Domingos and co-workers in a PM3 study on domino reactions with nitroalkenes [34]. Additionally, it is possible that the high internal pressure of the solvent acts synergistically to promote the enhancement of the reaction rate of 5a–c and should not be neglected. In all cycloadditions, independent of the

High-spin intermediates of the photolysis of 2,4,6-triazido-3-chloro-5-fluoropyridine

• Sergei V. Chapyshev,
• Denis V. Korchagin,
• Patrik Neuhaus and
• Wolfram Sander

Beilstein J. Org. Chem. 2013, 9, 733–742, doi:10.3762/bjoc.9.83

• singlet excited states by using CIS/PM3 or CIS/6-311+G* calculations yield structures 11a-S1* and 11b-S1*, in which the azido groups in ortho-positions to the fluorine atom are locally excited (Scheme 3). These calculations confirm that the local excitation of such groups requires lower activation

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

• Jutta Erika Helga Köhler and
• Nicole Grczelschak-Mick

Beilstein J. Org. Chem. 2013, 9, 118–134, doi:10.3762/bjoc.9.15

• gaps of empty β-CD conformers, of benzene D6h (Table 1) and the eight complexes (Table 3) are of the same order of magnitude as the values calculated with PM3 in the literature [34] where they found for β-CD 12.44 eV, for benzene 10.15 eV and for the β-CD/benzene complex 10.15 eV. These authors found β

• eV in the complex, in agreement with other calculations (PM3) from the literature. All four hydrogen-bond models studied here (BCDO23lO6l, BCDO23rO6l, BCDO23lO6r and BCDO23rO6r) were energetically advantageous after geometry optimisations with BP86/TZVP-DISP3 in vacuo and in aquo, their relative

Theoretical study on β-cyclodextrin inclusion complexes with propiconazole and protonated propiconazole

• Adrian Fifere,
• Narcisa Marangoci,
• Stelian Maier,
• Adina Coroaba,
• Dan Maftei and
• Mariana Pinteala

Beilstein J. Org. Chem. 2012, 8, 2191–2201, doi:10.3762/bjoc.8.247

• -cyclodextrin/protonated propiconazole, established by the AM1 and PM3 semi-empirical methods. The affinity between different parts of the guest molecule and the cyclodextrin cavity was studied considering that propiconazole possesses three residues able to be included into the host cavity through primary or

• secondary hydroxyl rims. The results have revealed that the most stable complex is formed when the azole residue of the propiconazole enters the cavity of the cyclodextrin through the narrow hydroxyl’s rim. Keywords: β-cyclodextrin; inclusion complexes; PM3; propiconazole; Introduction The occurrence of

• methods, such as CNDO, AM1 and PM3 were widely used in the theoretical investigation of CDs. The PM3 method has proved to be a powerful tool in the conformational study of supramolecular systems, such as CD inclusion compounds and provides better performance compared to the AM1 method for molecular

Synthesis and anion recognition properties of shape-persistent binaphthyl-containing chiral macrocyclic amides

• Marco Caricato,
• Nerea Jordana Leza,
• Claudia Gargiulli,
• Giuseppe Gattuso,
• Daniele Dondi and
• Dario Pasini

Beilstein J. Org. Chem. 2012, 8, 967–976, doi:10.3762/bjoc.8.109

• . Preliminary conformational structures were optimized by using the semiempirical PM3 method [38]. The geometries were then subjected to further refinement by using DFT B3LYP/6-31G(d) methods. In order to locate conformers having the minimum energy, the structures obtained by preliminary optimization were then

• [guest], using the WinEQNMR for Windows software package [47], provided the Ka value. Molecular modeling. Geometry optimizations for the structures presented were carried out, first by using the semiempirical PM3 method, and then refined at the B3LYP/6-31G(d) level [48]. All calculations were performed

Synthesis and oxidation of some azole-containing thioethers

• Andrei S. Potapov,
• Nina P. Chernova,
• Vladimir D. Ogorodnikov,
• Tatiana V. Petrenko and
• Andrei I. Khlebnikov

Beilstein J. Org. Chem. 2011, 7, 1526–1532, doi:10.3762/bjoc.7.179

• conformational search by means of the semi-empirical PM3 method was performed for thioethers 3, 5 and sulfoxides 6, 8, taking into account rotations around all single bonds (C–C, C–S, C–N). Minimal energy conformations were used as starting points for further, more accurate geometry optimizations at the RI DFT

Long-range diastereoselectivity in Ugi reactions of 2-substituted dihydrobenzoxazepines

• Luca Banfi,
• Andrea Basso,
• Valentina Cerulli,
• Valeria Rocca and
• Renata Riva

Beilstein J. Org. Chem. 2011, 7, 976–979, doi:10.3762/bjoc.7.109

• conformation of imine 5a, as minimized using CSC Chem3D (MOPAC-PM3). a) TBAD [(t-BuO2C−N=)2], PPh3, THF, −15 °C → rt, 49% (3a), 62% (3b); b) LiAlH4, Et2O–THF, 0 °C, 90% (4a), 88% (4b); c) HCl, CH2Cl2–H2O, rt; d) R2NC, R3CO2H, MeOH, rt. Possible explanation of diastereoselectivity in Ugi reactions of imines 5

Alkene selenenylation: A comprehensive analysis of relative reactivities, stereochemistry and asymmetric induction, and their comparisons with sulfenylation

• Vadim A. Soloshonok and
• Donna J. Nelson

Beilstein J. Org. Chem. 2011, 7, 744–758, doi:10.3762/bjoc.7.85

• different methods are shown in the Supporting Information File 1. Four computational methods, including an ab initio method at HF level in five different basis sets (3-21G(*), 6-31G*, 6-31+G*, 6-311G*, and 6-311+G*), two semi-empirical methods (PM3 and MNDO), and a DFT method (B3LYP/6-31G*), were used to

Synthesis of some novel hydrazono acyclic nucleoside analogues

• Mohammad N. Soltani Rad,
• Ali Khalafi-Nezhad and
• Somayeh Behrouz

Beilstein J. Org. Chem. 2010, 6, No. 49, doi:10.3762/bjoc.6.49

• using phenylhydrazine. To interpret the dominant formation of (E)-hydrazone derivatives rather than (Z)-isomers, PM3 semiempirical quantum mechanic calculations were carried out which indicated that the (E)-isomers had the lower heats of formation. Keywords: acyclic nucleoside; chemotherapeutic agent

• compounds 2a–2o are expected to be produced as two geometrical isomers ((E)- or (Z)-isomer), 1H and 13C NMR analysis indicated that the (E)-isomer was obtained as major product; the minor (Z)-isomer was detected in trace amounts (<5%). To interpret the preference for the (E)-isomers, PM3 semiempirical

• the (E)-hydrazone derivatives rather than the (Z)-isomers, PM3 semiempirical quantum mechanical calculations were carried out which showed that the heats of formation of the (E)-isomers were lower. The biological studies of compounds 2a–2o are currently under investigation and will be reported in due

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32

Photosonochemical catalytic ring opening of α-epoxyketones

• Hamid R. Memarian and
• Ali Saffar-Teluri

Beilstein J. Org. Chem. 2007, 3, No. 2, doi:10.1186/1860-5397-3-2

• -f, the ratios of diastereomeric photoproducts have not been changed too much using ultrasound irradiation. In order to explain the results obtained, we have compared the results of the semi-empirical PM3 calculations on the complexes of 1a-f + 2 in the ground state with those of α-epoxyketones 1a-f

• . The semi-empirical PM3 calculations for interaction of 1a with NBTPT. Ultrasound-assisted photocatalytic ring opening of α-epoxyketones. Possible intermediates involved in the ring opening of α-epoxyketones. Possible formation of a complex involved in reaction in acetone. Interaction of oxygen lone

• the complexes of α-epoxyketones 1a-f with 2 in the ground state obtained from quantum mechanical PM3 calculations Supporting Information Supporting Information File 28: Supporting materials. comparison of the integral ratios of the hydrogen on C-2 for 3a-f and 4a-f. Acknowledgements We are thankful

An exceptional P-H phosphonite: Biphenyl- 2,2'-bisfenchylchlorophosphite and derived ligands (BIFOPs) in enantioselective copper- catalyzed 1,4-additions

• T. Kop-Weiershausen,
• J. Lex,
• J.-M. Neudörfl and
• B. Goldfuss

Beilstein J. Org. Chem. 2005, 1, No. 6, doi:10.1186/1860-5397-1-6

• between C1'-C2'-C3'-O2). The probability of ellipsoids is 40% (CCDC 270538). Computed geometry (PM3) of plus-(P)-BIFOP-Cl with unnatural plus-(P)-biaryl conformation. Distances are given in Å. (BAA = biaryl angle between C2-C1-C1'-C2'; FAA-lp = fenchyl-aryl dihedral angle between C1-C2-C3-O1; FAA