Synthesis, effect of substituents on the regiochemistry and equilibrium studies of tetrazolo[1,5-a]pyrimidine/2-azidopyrimidines

• Elisandra Scapin,
• Paulo R. S. Salbego,
• Caroline R. Bender,
• Alexandre R. Meyer,
• Anderson B. Pagliari,
• Tainára Orlando,
• Geórgia C. Zimmer,
• Clarissa P. Frizzo,
• Helio G. Bonacorso,
• Nilo Zanatta and
• Marcos A. P. Martins

Beilstein J. Org. Chem. 2017, 13, 2396–2407, doi:10.3762/bjoc.13.237

• , using ionic liquids and water as solvents, and short reaction times. In addition, 5-substituted isomers have proved to be excellent models in carrying out a thorough investigation of the azide–tetrazole equilibrium mechanism by density functional theory (DFT) and various experimental methods (e.g., NMR

• (R in the 4-position of the ring), which was attributed to an equilibrium of azide–tetrazole. In the solid state, all compounds were found as 2-azidopyrimidines. The regiochemistry of the reaction and the stability of the products are discussed on the basis of the data obtained by density functional

• theory (DFT) for energetic and molecular orbital (MO) calculations. Keywords: 5-aminotetrazol; azide–tetrazole equilibrium; 2-azidopyrimidine; β-enaminones; tetrazolo[1,5-a]pyrimidine; trifluoromethylatedtetrazolo[1,5-a]pyrimidines; Introduction Tetrazolo[1,5-a]pyrimidines have attracted attention in

Synthesis and photophysical properties of novel benzophospholo[3,2-b]indole derivatives

• Mio Matsumura,
• Mizuki Yamada,
• Atsuya Muranaka,
• Misae Kanai,
• Naoki Kakusawa,
• Daisuke Hashizume,
• Masanobu Uchiyama and
• Shuji Yasuike

Beilstein J. Org. Chem. 2017, 13, 2304–2309, doi:10.3762/bjoc.13.226

• corresponding vibronic band was seen in the absorption spectrum at 330–340 nm. Density functional theory (DFT) calculations [38] were carried out at the B3LYP/LanL2DZ level of theory. The HOMO and LUMO energies of the selected compounds are given in Table 3. For fluorescent compounds 3, 4, 7, and 9, the HOMO

Are boat transition states likely to occur in Cope rearrangements? A DFT study of the biogenesis of germacranes

• José Enrique Barquera-Lozada and
• Gabriel Cuevas

Beilstein J. Org. Chem. 2017, 13, 1969–1976, doi:10.3762/bjoc.13.192

• elemanschkuhriolide, but this transition state is questionable due to its high energy. The possible mechanisms of this transformation were studied in the density functional theory frame. The mechanistic differences between the transformation of (Z,E)-germacranes and (E,E)-germacranes were also studied. We found that

• stable elemanolide that is even more stable than its (Z,E)-germacrane. Keywords: biogenesis; density functional theory; reaction mechanism; sigmatropic rearrangement; terpenes; Introduction Germacranes are biogenetic precursors of elemanes [1][2][3][4], because germacranes can be easily transformed

• , stabilizing the transition state, or destabilizing the ground states energy of the reactants. An antibody-catalyzed oxy-Cope reaction has already been described [42] as well as a proposed reaction mechanism [43]. In the study presented in this paper, we performed density functional theory (DFT) calculations

Theoretical simulation of the infrared signature of mechanically stressed polymer solids

• Matthew S. Sammon,
• Milan Ončák and
• Martin K. Beyer

Beilstein J. Org. Chem. 2017, 13, 1710–1716, doi:10.3762/bjoc.13.165

• and widening of bond angles, which changes the infrared spectrum. Here, the infrared spectrum of solid polymer samples exposed to mechanical stress is simulated by density functional theory calculations. Mechanical stress is described with the external force explicitly included (EFEI) method. The

• infrared bands is not a shift of the peak position, but rather peak broadening and a characteristic change in the relative intensities of the strongest bands, which may serve for the identification and quantification of mechanical stress in polymer solids. Keywords: density functional theory; infrared

Correction: Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2017, 13, 1669–1669, doi:10.3762/bjoc.13.161

• Stephanie R. Hare Dean J. Tantillo Department of Chemistry, University of California–Davis, 1 Shields Avenue, Davis, CA 95616, USA 10.3762/bjoc.13.161 Keywords: carbocation; density functional theory; dynamics; mechanism; terpene; The originally published Figure 6 had several mis-drawn

Strategies toward protecting group-free glycosylation through selective activation of the anomeric center

• A. Michael Downey and
• Michal Hocek

Beilstein J. Org. Chem. 2017, 13, 1239–1279, doi:10.3762/bjoc.13.123

Sugar-based micro/mesoporous hypercross-linked polymers with in situ embedded silver nanoparticles for catalytic reduction

• Qing Yin,
• Qi Chen,
• Li-Can Lu and
• Bao-Hang Han

Beilstein J. Org. Chem. 2017, 13, 1212–1221, doi:10.3762/bjoc.13.120

• (BET) of SugPOP-1 was found to be as high as 1220 m2 g−1 and about 1000 m2 g−1 for SugPOP-2 and SugPOP-3. The PSD profiles for all polymers (based on the nonlinear density functional theory (NLDFT) method) are shown in Figure 2b. The dominant PSD peaks for polymer SugPOP-2 are located at around 0.53

Cycloheximide congeners produced by Streptomyces sp. SC0581 and photoinduced interconversion between (E)- and (Z)-2,3-dehydroanhydrocycloheximides

• Li Yang,
• Ping Wu,
• Jinghua Xue,
• Huitong Tan,
• Zheng Zhang and
• Xiaoyi Wei

Beilstein J. Org. Chem. 2017, 13, 1039–1049, doi:10.3762/bjoc.13.103

• . The column temperature was controlled at 40 °C and detection wavelength was set at 280 nm. Computational details Molecular Merck force field (MMFF) calculations were done using the Spartan'14 program (Wavefunction Inc., Irvine, CA, USA). Density functional theory (DFT) and time-dependent density

• functional theory (TDDFT) calculations were performed with the Gaussian 09 program package [24]. For computations of ECD spectra, the conformers generated by a MMFF conformational search in an energy window of 10 kcal/mol were subjected to geometry optimization using the dispersion-corrected DFT-D3 method

Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and ³J_HH coupling constant analyses

• Weslley G. D. P. Silva,
• Carolyne B. Braga and
• Roberto Rittner

Beilstein J. Org. Chem. 2017, 13, 925–937, doi:10.3762/bjoc.13.94

• calculations, such as the Møller–Plesset (MP2) method and density functional theory (DFT) calculations, together with experimental techniques have been combined to achieve more accurate results [20][21][22][23][24]. Some amino acid derivatives have been recently studied by our research group, including the

Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications

• Vinila N. Viswanathan,
• Arun D. Rao,
• Upendra K. Pandey,
• Arul Varman Kesavan and
• Praveen C. Ramamurthy

Beilstein J. Org. Chem. 2017, 13, 863–873, doi:10.3762/bjoc.13.87

• studied. The polymer, derived from dithienylated benzothiodiazole and fluorene, P1, exhibited a highest occupied molecular orbital (HOMO) energy level at −5.48 eV. Density functional theory (DFT) studies as well as experimental measurements suggested that upon substitution of the acceptor with fluorine

• stability with onset decomposition temperature of >410 °C. Computational modeling of the three polymers was performed to gain insight into the molecular energy levels along with band gaps using density functional theory (DFT) at the B3LYP/6-31G (d,p) level as implemented in Gaussian-09 software [37]. For

• bridge, a torsion angle of 179° is found between the benzothiadiazole and thienothiophene part. This clearly indicates an increased planarity of the polymer P3 compared to P1 due to the presence of the fused π-bridge. Moreover, time-dependent density functional theory (TDDFT) calculations were also

Continuous-flow processes for the catalytic partial hydrogenation reaction of alkynes

• Carmen Moreno-Marrodan,
• Francesca Liguori and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2017, 13, 734–754, doi:10.3762/bjoc.13.73

• selectivity trend was explained in terms of both adsorption mode on and relative accessibility to Pd active sites, depending on surface potentials and hindrance of modifiers, on the basis of density functional theory and molecular dynamics calculations. The rationale was summarized in the so-called

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• understand the binding mechanism, we have performed a density functional theory (DFT) simulation on the receptor molecules using the GAUSSIAN 09 software package [44]. A closed-shell Becke–Lee–Yang–Parr hybrid exchange–correlation three-parameter functional (B3LYP) [45] along with the 6-311++G(d,p) basis set

Self-optimisation and model-based design of experiments for developing a C–H activation flow process

• Alexander Echtermeyer,
• Yehia Amar,
• Jacek Zakrzewski and
• Alexei Lapkin

Beilstein J. Org. Chem. 2017, 13, 150–163, doi:10.3762/bjoc.13.18

• in self-optimisation and model-development frameworks is not well documented in the literature. Very recently we have shown that a priori knowledge in the form of density functional theory level (DFT) mechanistic calculations can be used to propose process models and to perform in silico design of

Characterization of the synthetic cannabinoid MDMB-CHMCZCA

• Carina Weber,
• Stefan Pusch,
• Dieter Schollmeyer,
• Sascha Münster-Müller,
• Michael Pütz and
• Till Opatz

Beilstein J. Org. Chem. 2016, 12, 2808–2815, doi:10.3762/bjoc.12.279

• functional theory, see Supporting Information File 1 for details), a comparison of the experimental and calculated ECD spectra did not allow for a safe assignment of the cannabimimetic’s absolute configuration (Figure 4). The main two positive ECD signals in the range above 230 nm are correctly predicted by

• CO and/or a cyclohexyl radical or methylenecyclohexane. As MDMB-CHMCZCA bears a stereogenic center at C-1', the elucidation of the absolute configuration of the sample was attempted by ECD spectroscopy. While the UV spectra can be adequately predicted by TD-DFT calculations (time-dependent density

Effects of solvent additive on “s-shaped” curves in solution-processed small molecule solar cells

• John A. Love,
• Shu-Hua Chou,
• Ye Huang,
• Guilllermo C. Bazan and
• Thuc-Quyen Nguyen

Beilstein J. Org. Chem. 2016, 12, 2543–2555, doi:10.3762/bjoc.12.249

• measured to be 32 mg/mL for p-SIDT(FBTThCA8)2 compared with over 50 mg/mL for p-SIDT(FBTTh2)2 in chloroform at room temperature. Frontier molecular energy levels were estimated by cyclic voltammograms (CV) in dichloromethane and calculated theoretically by density functional theory (DFT) (Supporting

High performance p-type molecular electron donors for OPV applications via alkylthiophene catenation chromophore extension

• Paul B. Geraghty,
• Calvin Lee,
• Jegadesan Subbiah,
• Wallace W. H. Wong,
• James L. Banal,
• Mohammed A. Jameel,
• Trevor A. Smith and
• David J. Jones

Beilstein J. Org. Chem. 2016, 12, 2298–2314, doi:10.3762/bjoc.12.223

• and overlap, density functional theory (DFT) calculations were performed. Geometry optimization and molecular orbital surfaces were determined and are shown in Figure 11. Geometries of the BXR series were obtained at the D2 dispersion corrected B3LYP/6-311G(d,p) level of theory. Subsequent time

Experimental and theoretical investigations into the stability of cyclic aminals

• Edgar Sawatzky,
• Antonios Drakopoulos,
• Martin Rölz,
• Christoph Sotriffer,
• Bernd Engels and
• Michael Decker

Beilstein J. Org. Chem. 2016, 12, 2280–2292, doi:10.3762/bjoc.12.221

• density functional theory (DFT) based studies were applied to support and explain the results obtained. Rapid decomposition is observed in acidic aqueous media for all cyclic aminals which occurs as a reversible reaction. Electronic effects do not seem relevant with regard to stability, but the magnitude

• test compounds were predicted using the empirical algorithm of MoKa [38] and validated with density functional theory (DFT) energy calculations of all protonation patterns for compounds 8a and 13b (cf. Supporting Information File 1). We used the B3LYP-D3 functional [39][40][41] in combination with the

The direct oxidative diene cyclization and related reactions in natural product synthesis

• Juliane Adrian,
• Leona J. Gross and
• Christian B. W. Stark

Beilstein J. Org. Chem. 2016, 12, 2104–2123, doi:10.3762/bjoc.12.200

• functional theory calculations both by Strassner and co-workers (Mn(VII) and Os(VIII)) [12][13] and by Kirchner and co-workers (Ru(VIII)) [14]. Reasonable fractions of the trans-THF isomer can be produced using ruthenium tetroxide in specifically optimized solvent compositions [15] (for other means to obtain

• stereochemistry of the vicinal hydroxy ether motif of the product (Scheme 2). The stereochemistry across the THF ring is set in the cyclization event. As a result of geometrical constraints it is usually predominantly or even exclusively cis (Scheme 2) – a fact that has recently been corroborated through density

Varioloid A, a new indolyl-6,10b-dihydro-5aH-[1]benzofuro[2,3-b]indole derivative from the marine alga-derived endophytic fungus Paecilomyces variotii EN-291

• Peng Zhang,
• Xiao-Ming Li,
• Xin-Xin Mao,
• Attila Mándi,
• Tibor Kurtán and
• Bin-Gui Wang

Beilstein J. Org. Chem. 2016, 12, 2012–2018, doi:10.3762/bjoc.12.188

• time-dependent density functional theory-electronic circular dichroism (TDDFT-ECD) calculations. A similar compound, whose planar structure was previously described but the relative and absolute configurations and 13C NMR data were not reported, was also identified and was tentatively named as

Stereo- and regioselectivity of the hetero-Diels–Alder reaction of nitroso derivatives with conjugated dienes

• Lucie Brulíková,
• Aidan Harrison,
• Marvin J. Miller and
• Jan Hlaváč

Beilstein J. Org. Chem. 2016, 12, 1949–1980, doi:10.3762/bjoc.12.184

• nitroso heterodienophiles 29 (Scheme 8) was determined at the B3LYP/6-31G** level [86]. All calculations were performed with density functional theory (DFT) using the B3LYP functional implemented in the Gaussian 98 software. Nitrosomethane (29a) was selected as a model heterodienophile for a preliminary

• formation of 109, on the other hand, the steric hindrance was greatly reduced, and consequently no complete regioselectivity was observed. These results were supported by ab initio [HF/6-31G(d)] and density functional theory [B3 LYP/6-31G(d)] calculations. The use of a copper(I) species, without a

Experimental and theoretical investigations on the high-electron donor character of pyrido-annelated N-heterocyclic carbenes

• Michael Nonnenmacher,
• Dominik M. Buck and
• Doris Kunz

Beilstein J. Org. Chem. 2016, 12, 1884–1896, doi:10.3762/bjoc.12.178

• of Heidelberg University. Calculations. All calculations were performed based on density functional theory at the BP86/def2-TZVP [81][82][83][84][85] or B3LYP/def2-TZVP [86][87][88] level implemented in Turbomole [89][90][91][92][93][94][95][96][97]. The RI-approximation [98][99][100][101][102][103

Synthesis and properties of fluorescent 4′-azulenyl-functionalized 2,2′:6′,2″-terpyridines

• Adrian E. Ion,
• Liliana Cristian,
• Mariana Voicescu,
• Masroor Bangesh,
• Augustin M. Madalan,
• Daniela Bala,
• Constantin Mihailciuc and
• Simona Nica

Beilstein J. Org. Chem. 2016, 12, 1812–1825, doi:10.3762/bjoc.12.171

• origin of the fluorescence emission will be also described by time-dependent density functional theory (TDDFT) calculations. The ability of the terpyridine compounds to bind poisoning metal cations was investigated by spectrophotometric titrations of methanolic 4′-azulenyl-substituted terpyridine

• oscillator strengths for the herein described compounds 4a and 4b were calculated with time-dependent density functional theory (TDDFT) utilizing the following functionals: B3LYP [34][35][36][37], Coulomb-attenuated B3LYP (CAMB3LYP) [38], hybrid TPSS (TPSSH) [39], and M06 with double Hartree–Fock exchange

Synthesis of the C8’-epimeric thymine pyranosyl amino acid core of amipurimycin

• Pramod R. Markad,
• Navanath Kumbhar and
• Dilip D. Dhavale

Beilstein J. Org. Chem. 2016, 12, 1765–1771, doi:10.3762/bjoc.12.165

• results on conformational preferences of 12 and 13 were corroborated using geometry-optimized density functional theory (DFT). The geometrically optimized preferred conformations of 12 and 13 are depicted in Figure 3, and geometrical parameters for torsion angles and intramolecular hydrogen bonding

Methylpalladium complexes with pyrimidine-functionalized N-heterocyclic carbene ligands

• Dirk Meyer and
• Thomas Strassner

Beilstein J. Org. Chem. 2016, 12, 1557–1565, doi:10.3762/bjoc.12.150

• -NHC ligand [33]. To study the differences between both systems we synthesized palladium [34] and platinum [35] “hybrid complexes” with ligands combining both structural elements the pyrimidine as well as the NHC fragment. We also used density functional theory (DFT) calculations to investigate the

• (Figure 1). This can be explained by the strong donor character of the carbene which makes the trans isomer less favorable. NMR analysis of the reaction products confirms that only one complex is formed. Additional proof comes from density functional theory (DFT) calculations which predict isomer B to be

Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides

• Franziska Hemmerling and
• Frank Hahn

Beilstein J. Org. Chem. 2016, 12, 1512–1550, doi:10.3762/bjoc.12.148

• to give the pyran ring. This terminal 6-endo-tet cyclisation is likewise facilitated by AurD, overriding the 5-exo-tet pathway that should be favoured in spontaneous reaction according to Baldwin’s rules. Density functional theory calculations suggested that this reaction pathway is favoured, if the