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

Synthesis and investigation on optical and electrochemical properties of 2,4-diaryl-9-chloro-5,6,7,8-tetrahydroacridines

• Najeh Tka,
• Mohamed Adnene Hadj Ayed,
• Mourad Ben Braiek,
• Mahjoub Jabli and
• Peter Langer

Beilstein J. Org. Chem. 2021, 17, 2450–2461, doi:10.3762/bjoc.17.162

• a PGSTAT30 Autolab potentiostat. Theoretical calculations The theoretical studies were realized in vacuum with the Gaussian 09 program [70]. The geometry of the equilibrium conformer at the ground state was first found at AM1 level. Then, further optimization through density functional theory (DFT

2,4-Bis(arylethynyl)-9-chloro-5,6,7,8-tetrahydroacridines: synthesis and photophysical properties

• Najeh Tka,
• Mohamed Adnene Hadj Ayed,
• Mourad Ben Braiek,
• Mahjoub Jabli,
• Noureddine Chaaben,
• Kamel Alimi,
• Stefan Jopp and
• Peter Langer

Beilstein J. Org. Chem. 2021, 17, 1629–1640, doi:10.3762/bjoc.17.115

• equilibrium conformer at ground state was first found at AM1 level. Then, further optimizations through density functional theory (DFT) approach [73] at the restricted Becke3–Lee–Yang–Parr hybrid functional (B3LYP) with standard basis set 6-31G were carried out. Experimental procedure and spectroscopic data

Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• this review will be on the AM1-type shown in Figure 1B, as this is the most studied and therapeutically promising modification of its class (a summary of other amide variations can be found elsewhere [74][75]). The strategy used to incorporate this modification into DNA or RNA has been to first

• necessary protecting groups are present on the nucleobase and sugar moieties [76][77]. Unlike the phosphodiester linkage of natural DNA, the AM1 modification is an example of a non-ionic backbone. The crystal structure of a 13-mer RNA duplex with a single central AM1 modification revealed that this

• 0.2–0.8 °C in the thermal stability of RNA/DNA hybrid duplexes for each AM1 modification [11][78]. NMR structural studies have shown that the AM1 modification is well tolerated in an RNA duplex, with little effect on the global structure [79]. Furthermore, siRNA duplexes with amide modifications at

Combination of multicomponent KA² and Pauson–Khand reactions: short synthesis of spirocyclic pyrrolocyclopentenones

• Riccardo Innocenti,
• Elena Lenci,
• Gloria Menchi and
• Andrea Trabocchi

Beilstein J. Org. Chem. 2020, 16, 200–211, doi:10.3762/bjoc.16.23

• performed using SPARTAN Version 5.11. Conformational searches of 36 were carried out using Monte Carlo method within MMFF94 force field, and the AM1 semiempirical method [72] was used to optimize the global minimum conformer. The geometry of the most abundant minimum energy conformer was successively

Synthesis and properties of sulfur-functionalized triarylmethylium, acridinium and triangulenium dyes

• Marco Santella,
• Eduardo Della Pia,
• Jakob Kryger Sørensen and
• Bo W. Laursen

Beilstein J. Org. Chem. 2019, 15, 2133–2141, doi:10.3762/bjoc.15.210

• method AM1). Normalized absorption and fluorescence spectra of 6 (S3-TOTA+), λex = 460 nm, and 8 (S2-TOTA+), λex = 470 nm, in CH2Cl2 solution. Synthesis of three novel SX-(DMP)3C+ PF6− ethylsulfanyl-substituted triarylmethylium salts. Synthetic route for the synthesis of S3-ADOTA+. Synthesis of S3-TOTA

Molecular recognition of N-acetyltryptophan enantiomers by β-cyclodextrin

• Spyros D. Chatziefthimiou,
• Mario Inclán,
• Petros Giastas,
• Athanasios Papakyriakou,
• Konstantina Yannakopoulou and
• Irene M. Mavridis

Beilstein J. Org. Chem. 2017, 13, 1572–1582, doi:10.3762/bjoc.13.157

• performed, while non-hydrogen atoms of β-CD are kept fixed in space. The XLEaP module of the AMBER 16 suite [45] was used and the GAFF parameters were applied to the β-CD molecules with AM1-BCC atomic charges using the Antechamber module [46], while the ff99SB parameters were employed for NAcTrp. Restraint

Deproto-metallation of N-arylated pyrroles and indoles using a mixed lithium–zinc base and regioselectivity-computed CH acidity relationship

• Mohamed Yacine Ameur Messaoud,
• Ghenia Bentabed-Ababsa,
• Madani Hedidi,
• Aïcha Derdour,
• Floris Chevallier,
• Yury S. Halauko,
• Oleg A. Ivashkevich,
• Vadim E. Matulis,
• Laurent Picot,
• Valérie Thiéry,
• Thierry Roisnel,
• Vincent Dorcet and
• Florence Mongin

Beilstein J. Org. Chem. 2015, 11, 1475–1485, doi:10.3762/bjoc.11.160

• , Figure 4, see Supporting Information File 2). Computational aspects There is a lack of data on the acidity of N-substituted pyrroles and indoles in the literature. NH acidity of unsubstituted pyrrole and indole in DMSO was measured by Bordwell [48] and computed by means of semi-empirical AM1 [49] and ab

Glycoluril–tetrathiafulvalene molecular clips: on the influence of electronic and spatial properties for binding neutral accepting guests

• Yoann Cotelle,
• Marie Hardouin-Lerouge,
• Stéphanie Legoupy,
• Olivier Alévêque,
• Eric Levillain and
• Piétrick Hudhomme

Beilstein J. Org. Chem. 2015, 11, 1023–1036, doi:10.3762/bjoc.11.115

• -empirical AM1 method in the case of 4 [19]. This distance was estimated to be equal to 9.7 Å indicating that this enlargement around 2 Å was the result mainly of the spatial contribution of the additional naphthoquinone spacer in molecular clip 4. Electrochemical properties The electrochemical behaviour of

The Flögel-three-component reaction with dicarboxylic acids – an approach to bis(β-alkoxy-β-ketoenamides) for the synthesis of complex pyridine and pyrimidine derivatives

• Mrinal K. Bera,
• Moisés Domínguez,
• Paul Hommes and
• Hans-Ulrich Reissig

Beilstein J. Org. Chem. 2014, 10, 394–404, doi:10.3762/bjoc.10.37

• of suitable crystals for an X-ray analysis, we calculated the energy for the two possible isomers of 34, suggesting that the E-isomer should be considerably more stable than the corresponding Z-isomer (Table 1). Using the semi-empirical AM1 method an energy difference of ΔEZ-E of 28.7 kJ/mol was

Studies on the interaction of isocyanides with imines: reaction scope and mechanistic variations

• Ouldouz Ghashghaei,
• Consiglia Annamaria Manna,
• Esther Vicente-García,
• Marc Revés and
• Rodolfo Lavilla

Beilstein J. Org. Chem. 2014, 10, 12–17, doi:10.3762/bjoc.10.3

• triple bonds should generate Z configurations [18][19], which are not observed in the solid-sate, thus suggesting isomerization processes affecting the C=N moieties, likely mediated by acid-catalyzed prototropy or other tautomerization steps. Computational calculations (MMFF, AM1 and BL3YP/6-31G

Self-assembly of 2,3-dihydroxycholestane steroids into supramolecular organogels as a soft template for the in-situ generation of silicate nanomaterials

• Valeria C. Edelsztein,
• Andrea S. Mac Cormack,
• Matías Ciarlantini and
• Pablo H. Di Chenna

Beilstein J. Org. Chem. 2013, 9, 1826–1836, doi:10.3762/bjoc.9.213

• -assembly to promote gelation. To get an insight of the necessary molecular spatial requirements for the 2,3-dihydroxy moiety to reach an optimal hydrogen bonding, we studied the possible mode of self-assembly of the four isomers by a molecular modeling simulation in vacuum (semiempirical AM1). A

• conformational study of a single molecule of LMOG 1 (semiempirical, AM1) showed a distance of 18.0 Å for the molecule with the elongated side chain (Figure 6) suggesting a repetitive unit involving a head-to-head self-assembly between two molecules, as explained above. Next, we minimized different modes of head

• in a similar manner as described in [25]. The computational experiments were performed with HyperChem 8.0.4, semiempirical optimization, AM1 method in vacuum. Algorithm: Fletcher–Reeves. Termination condition, RMS gradient: 0.05 kcal/(Å·mol). No bond or distance restrictions were imposed. The

Electron self-exchange activation parameters of diethyl sulfide and tetrahydrothiophene

• Martin Goez and
• Martin Vogtherr

Beilstein J. Org. Chem. 2013, 9, 1448–1454, doi:10.3762/bjoc.9.164

• . As we will show, the activation parameters provide evidence that the observed exchange indeed takes place between dimeric radical cations and D. Results and Discussion On the AM1 level, the heats of formation of D and are −92 kJ/mol and −14 kJ/mol for diethyl sulfide DES as opposed to −69 kJ/mol and

• was done with a Lambda Physik EMG 101 excimer laser (medium, XeCl; wavelength, 308 nm; pulse width, 15 ns) triggered by the computer of the spectrometer. The probe was thermostated to ±0.3 K. Quantum mechanical calculations were carried out with the Gaussian 09 package [53] using the AM1 Hamiltonian

Synthesis and spectroscopic properties of 4-amino-1,8-naphthalimide derivatives involving the carboxylic group: a new molecular probe for ZnO nanoparticles with unusual fluorescence features

• Laura Bekere,
• David Gachet,
• Vladimir Lokshin,
• Wladimir Marine and
• Vladimir Khodorkovsky

Beilstein J. Org. Chem. 2013, 9, 1311–1318, doi:10.3762/bjoc.9.147

• electron donating and accepting properties of this molecule. The geometry was optimized by using the semiempirical AM1 method and the electronic spectra were calculated by using the TD B3LYP/6-31G(d,p) method. The ionization potential (IP) and electron affinity (EA) were calculated at the B3LYP/6-31G(d,p

Thermotropic and lyotropic behaviour of new liquid-crystalline materials with different hydrophilic groups: synthesis and mesomorphic properties

• Alexej Bubnov,
• Miroslav Kašpar,
• Věra Hamplová,
• Ute Dawin and
• Frank Giesselmann

Beilstein J. Org. Chem. 2013, 9, 425–436, doi:10.3762/bjoc.9.45

• scattering. As an example, the temperature dependence of the smectic layer spacing d, for TL1 is shown in Figure 4. The MOPAC/AM1 model has been used to calculate the length of TL1 in the energy-optimized conformation, which gives 41 Å for the most extended conformer. In X-ray data taken at small scattering

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

• investigated by three different theoretical methods: classical quantum mechanics (QM) on AM1 and on the BP/TZVP-DISP3 level of approximation, and thirdly by classical molecular dynamics simulations (MD) at different temperatures (120 K and 273 to 300 K). The hydrogen bonds at the larger O2/O3 rim of empty β

• -CDs prefer the right-hand orientation, e.g., O3-H…O2-H in the same glucose unit and bifurcated towards …O4 and O3 of the next glucose unit on the right side. On AM1 level the complex energy was −2.75 kcal mol−1 when the benzene molecule was located parallel inside the β-CD cavity and −2.46 kcal mol−1

• when it was positioned vertically. The AM1 HOMO/LUMO gap of the empty β-CD with about 12 eV is lowered to about 10 eV in the complex, in agreement with data from the literature. AM1 IR spectra displayed a splitting of the O–H frequencies of cyclodextrin upon complex formation. At the BP/TZVP-DISP3

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

• 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

• theoretically investigates the interaction between PP, PPH+ and β-CD molecules by means of AM1 and PM3 semi-empirical quantum-mechanical calculations, to examine in detail the insertion pathways and to determine the intimate configurations of the β-CD/propiconazole (β-CD/PP and β-CD/PPH+) inclusion complexes

Synthesis and evaluation of new guanidine-thiourea organocatalyst for the nitro-Michael reaction: Theoretical studies on mechanism and enantioselectivity

• Tatyana E. Shubina,
• Matthias Freund,
• Sebastian Schenker,
• Timothy Clark and
• Svetlana B. Tsogoeva

Beilstein J. Org. Chem. 2012, 8, 1485–1498, doi:10.3762/bjoc.8.168

• and found that their system cannot be treated as conformationally rigid. Thus, a full conformational search of 7 was performed at the AM1 level by using the TORQUE algorithm within the VAMP program [58]. Based on the clustered semiempirical results, the four most stable structures were selected for

Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics

• Workalemahu M. Berhanu,
• Mohamed A. Ibrahim,
• Girinath G. Pillai,
• Alexander A. Oliferenko,
• Levan Khelashvili,
• Farukh Jabeen,
• Bushra Mirza,
• Farzana Latif Ansari,
• Ihsan ul-Haq,
• Said A. El-Feky and
• Alan R. Katritzky

Beilstein J. Org. Chem. 2012, 8, 1146–1160, doi:10.3762/bjoc.8.128

• program [52] and preoptimized using the molecular mechanics utility (MM2) [53] in Chem3D Ultra 12.0 software [54]. Final geometry optimization of the compounds was carried out by using the semiempirical quantum-mechanical AM1 parameterization [55]. Molecular descriptors The optimized geometries of the

Formation of smectic phases in binary liquid crystal mixtures with a huge length ratio

• Nadia Kapernaum,
• Friederike Knecht,
• C. Scott Hartley,
• Jeffrey C. Roberts,
• Robert P. Lemieux and
• Frank Giesselmann

Beilstein J. Org. Chem. 2012, 8, 1118–1125, doi:10.3762/bjoc.8.124

• Å calculated by using MOPAC/AM1 (Figure 2). For the short compound 2PhP, there is also a good agreement between the calculated value of 25.6 Å for the extended length of the molecule and the experimentally determined d-value of 25.1 Å from SAXS. Figure 5 shows the reduced layer spacings d/dA (where

• each molecular structure was minimized by molecular modelling with the semiempirical method MOPAC/AM1 for the most extended conformers. The phase diagram of the binary mixture system PhP16/2PhP. The layer spacing obtained by SAXS-measurements in the SmA phase at T = Tc is plotted against the mole

On the mechanism of action of gated molecular baskets: The synchronicity of the revolving motion of gates and in/out trafficking of guests

• Keith Hermann,
• Stephen Rieth,
• Hashem A. Taha,
• Bao-Yu Wang,
• Christopher M. Hadad and
• Jovica D. Badjić

Beilstein J. Org. Chem. 2012, 8, 90–99, doi:10.3762/bjoc.8.9

• Hoff analysis of the 1H NMR data revealed that the encapsulation is also driven by enthalpy (ΔH° = −3.56 ± 0.06 kcal/mol, Figure 2). Indeed, the computed electrostatic potential surface (AM1, Spartan) [20] of guest 2 is complementary to the one corresponding to the concave interior of 1 (Figure 1

• constants k*in and k*out. Chemical structure of gated molecular basket 1 and 1,1,1-trichloroethane (2). Electrostatic potential surfaces of basket 1 and guest 2 were computed with Spartan (AM1) [20]. (Left): 1H NMR spectra (400 MHZ, CD2Cl2) of 1 (0.67 mM) obtained upon incremental addition of 1,1,1

Imidazole as a parent π-conjugated backbone in charge-transfer chromophores

• Jiří Kulhánek and
• Filip Bureš

Beilstein J. Org. Chem. 2012, 8, 25–49, doi:10.3762/bjoc.8.4

• common synthetic approach to diimidazoles, with the rings connected at C2, is shown in Scheme 1. Typical diimidazole chromophores in D-π-A arrangement (Figure 9) were investigated by Wu and Ye et al. [16][17][18][50][51][52][53]. Compounds 27a (λmax = 384 nm; β(AM1) = 50.91 × 10−30 esu; TD = 377 °C) and

• 27c (λmax = 379 nm; β(AM1) = 29.5 × 10−30 esu; β(HRS) = 142 × 10−30 esu; TD = 360 °C) with free amino or hydroxy groups were further used as reactive species for the functionalization of various polymers (see below). Within the last ten years, diimidazole D-π-D systems were extensively studied, in

Lithium phosphonate umpolung catalysts: Do fluoro substituents increase the catalytic activity?

• Anca Gliga,
• Bernd Goldfuss and
• Jörg M. Neudörfl

Beilstein J. Org. Chem. 2011, 7, 1189–1197, doi:10.3762/bjoc.7.138

• ) [31][32]. The energy differences of the terpene-based conformers are between 5.1 and 5.8 kcal/mol [32][33] (B3LYP/6-31++G**:AM1). The conversion of diols 1–5, 7, and 8 to the desired phosphonates can be achieved by twofold addition to phosphorus trichloride and subsequent hydrolysis. Diol 6 could not

Catalysis: transition-state molecular recognition?

• Ian H. Williams

Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117

• results were consistent with the compression hypothesis for catalysis of methyl transfer. Origin of COMT catalytic power To assess whether compression actually operates in COMT-catalysed methyl transfer, hybrid QM/MM calculations have been performed at the AM1/MM level [17][18][19]. The secondary α-D3 KIE

• AM1/OPLS/TIP3P simulations [19] with ensemble averaging to include the effect of thermal fluctuations in the enzyme and solvent environments to obtain a value for the α-D3 KIE = 0.82 ± 0.05, which is in excellent accord with the experimental value [11] of VCH3 /VCD3 = 0.83 ± 0.05 for methylation of

• (PMF), computed from MD simulations at the AM1/CHARMM/TIP3P level with umbrella sampling along a reaction coordinate defined as the difference in bond lengths from Cα to the nucleophile and nucleofuge, predicted a 44 kJ mol−1 increase ΔG‡enz in free energy in going from the enzymic reactant complex