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

• that natural pyrimidine bases exist in the gas phase and in water solution in the canonical 2,4-diketo form (e.g. [42][43]). The tautomeric structures of 4- and 2-thioanalogues of thymine and uracil have been also investigated by diverse methods and the predominant population of the oxo/thioxo

Combined experimental and theoretical studies of regio- and stereoselectivity in reactions of β-isoxazolyl- and β-imidazolyl enamines with nitrile oxides

• Ilya V. Efimov,
• Marsel Z. Shafikov,
• Nikolai A. Beliaev,
• Natalia N. Volkova,
• Tetyana V. Beryozkina,
• Wim Dehaen,
• Zhijin Fan,
• Viktoria V. Grishko,
• Gert Lubec,
• Pavel A. Slepukhin and
• Vasiliy A. Bakulev

Beilstein J. Org. Chem. 2016, 12, 2390–2401, doi:10.3762/bjoc.12.233

• energies at 298.15 K in gas phase conditions. Structures of the localized transition states. Lengths of the forming bonds are given in Å. Summary of the calculated pathways of the cycloaddition reaction between enamine 1a and benzonitrile oxide 6a. The pathway leading to the observed product is highlighted

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

• of the reaction. Interestingly, plotting the data in water (Figure 5) as well as in the gas phase (cf. Supporting Information File 1) for all relevant fragments revealed an exothermic reaction (−6.7 kcal/mol in water) for the hydrolysis of 8a’ (II in Figure 5a) into the protonated fragments (III in

Elongated and substituted triazine-based tricarboxylic acid linkers for MOFs

• Arne Klinkebiel,
• Ole Beyer,
• Barbara Malawko and
• Ulrich Lüning

Beilstein J. Org. Chem. 2016, 12, 2267–2273, doi:10.3762/bjoc.12.219

• carboxylate plane relative to the central six-membered ring is in the same plane in the TATB based MOF PCN-6, the BTB analogue MOF-14 shows a tilt angle of ca. 35°. B3LYP//6-31G* calculations of the isolated linkers in the gas phase result in dihedral angles of 38.5° for BTB and 0.006° for TATB, respectively

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

• order to explore the possibility of axial chirality, torsional angle scans were performed on the lowest-energy M (conformer A) and P (conformer B) helicity gas-phase conformers or atropodiastereomers. Rotational energy barriers between the two isomers were estimated to be ca. 35–42 kJ/mol for TS1 (ωC12

• showed that there is no axial chirality in 1, and equilibrating conformers with M and P helicity are present in solution as obtained in the conformational analysis. The Boltzmann-weighted ECD spectra calculated for both the gas-phase and the solvent model conformers of (2R,3R)-1 at B3LYP/TZVP, BH&HLYP

• ), using dipole-velocity-computed rotational strengths. Boltzmann distributions were estimated from the ZPVE-corrected B3LYP/6-31G(d) energies in the gas-phase calculations and from the B97D/TZVP energies in the PCM model ones. Torsional energy scans and TS calculations were carried out at the B3LYP/6-31G

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

• central pyridine ring. The three pyridine rings are calculated to have higher coplanarity in comparison to the crystal structure, showing the easy rotation of pyridine rings about the interanullar axis in gas phase, in contrast to constraints imposed by the solid crystal. The electronic excitations and

A flow reactor setup for photochemistry of biphasic gas/liquid reactions

• Josef Schachtner,
• Patrick Bayer and
• Axel Jacobi von Wangelin

Beilstein J. Org. Chem. 2016, 12, 1798–1811, doi:10.3762/bjoc.12.170

• operation of various other reactions at light/liquid/gas interfaces in student, research, and industrial laboratories. Keywords: biphasic reactions; flow chemistry; gas phase; microreactor; oxygen; photochemistry; Introduction The recent developments of microreactor technologies have significantly

• phase, a gas phase, and an electromagnetic radiation field, where an effective interaction of three quasi mobile phases of different physical states is required for high selectivities and conversion rates. Such scenarios are highly relevant for photochemical reactions with reactive gases (e.g., air, O2

• possibly additives, the gas phase, containing the gaseous reagents, and the light (Figure 1). Only very few microreactor setups for such “quasi tri-phasic” processes have been reported [33][34]; most of them are film/falling film [22], microchannel [23][35] or simple tube reactors [35][36][37]. The reactor

Unusual traits of cis and trans-2,3-dibromo-1,1-dimethylindane on the way from 1,1-dimethylindene to 2-bromo-, 3-bromo-, and 2,3-dibromo-1,1-dimethylindene

• Rudolf Knorr,
• David S. Stephenson,
• Ernst Lattke,
• Petra Böhrer and
• Jakob Ruhdorfer

Beilstein J. Org. Chem. 2016, 12, 1178–1184, doi:10.3762/bjoc.12.113

• added Br2 to generate the thermolabile tribromide 5, whose HBr elimination gave 7; the required Br2 was visible in the weakly brownish gas phase and had been provided through the well-known reaction of HBr with the accompanying NBS. Consequently, three equivalents of NBS would be necessary for obtaining

• gas phase and was cooled in an ice bath (15 min). A 1H NMR spectrum of the solution revealed that the starting material 9 was completely consumed and that a mixture containing three gem-dimethyl compounds had been generated: 2,3-dibromo-1,1-dimethylindene (7, 76%), 1 (1%, trans/cis ca. 3:2), and an

Efficient syntheses of climate relevant isoprene nitrates and (1R,5S)-(−)-myrtenol nitrate

• Sean P. Bew,
• Glyn D. Hiatt-Gipson,
• Graham P. Mills and
• Claire E. Reeves

Beilstein J. Org. Chem. 2016, 12, 1081–1095, doi:10.3762/bjoc.12.103

• Pye et al. recently developed a system to study the formation and subsequent aerosol-phase partitioning of organic nitrates derived from both isoprene and monoterpenes. Their studies indicated the concentrations of organic aerosol and gas-phase organic nitrates increased when particulate organic

Scope and mechanism of the highly stereoselective metal-mediated domino aldol reactions of enolates with aldehydes

• M. Emin Cinar,
• Bernward Engelen,
• Martin Panthöfer,
• Hans-Jörg Deiseroth,
• Jens Schlirf and
• Michael Schmittel

Beilstein J. Org. Chem. 2016, 12, 813–824, doi:10.3762/bjoc.12.80

• calculations were carried out using the Gaussian 09 program [44]. Gas-phase optimization of geometries was performed by using the B3LYP [45][46][47] method with Pople’s split-valence 6-31G(d) basis set on C, H, O atoms and double-ζ quality basis set (LANL2DZ) [48][49][50] containing Hay and Wadt’s effective

Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics

• Maria C. Guimarães,
• Mariene H. Duarte,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76

• can cause misinterpretation of the QSAR model. The present computational work reports the conformational analysis of the volatile anesthetic isoflurane (2-chloro-2-(difluoromethoxy)-1,1,1-trifluoroethane) in the gas phase and also in polar and nonpolar implicit and explicit solvents to show that

• possible for isoflurane. However, geometry optimization at the MP2/6-311++g(d,p) and ωB97X-D/6-311++g(d,p) (a DTF method which includes dispersion effects) levels converged to five energy minima for the gas phase, implicit solvents (cyclohexane, DMSO and water, using the polarizable continuum model), and

• using one explicit water molecule as solvent to mimic a physiological medium (Figure 1). The results for the gas phase are in agreement with previous calculations [14] and microwave experiments [15], where five conformations were found, but only three could be experimentally detected, due to their lower

From steroids to aqueous supramolecular chemistry: an autobiographical career review

• Bruce C. Gibb

Beilstein J. Org. Chem. 2016, 12, 684–701, doi:10.3762/bjoc.12.69

• capsule formed by octa-acid is also capable of bringing about physical separations. One facile way to examine this is to consider the absorption of gases from the gas phase into a solution phase. We therefore examined the uptake of butane into an aqueous solution of octa-acid to form the corresponding 2:2

Creating molecular macrocycles for anion recognition

• Amar H. Flood

Beilstein J. Org. Chem. 2016, 12, 611–627, doi:10.3762/bjoc.12.60

• , to diatomic cyanide, and triatomic bifluoride. The halides fluoride, chloride and bromide largely follow experiment [29]. However, the cyanide study [30] produced some surprising results. We found in gas-phase calculations and solution-phase experiments that cyanide binds as well as chloride (Figure

• chloride and bifluoride had the same affinity in gas-phase calculations, they differed experimentally in solution (Figure 11b). Judging from the calculated geometry, we wagered that the bifluoride anion did not fit very well and that solvent was pulling it out of the binding pocket. We went through a few

• cycles of computer-aided receptor design to optimize the geometry of the complex. Out targets were to equalize chloride and bifluoride affinities in the gas phase, and to optimize geometries with the anions located in-plane with the macrocycle in order to avoid solvation effects. The hypothesis was that

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• particular potential function is able to reproduce a) the unbound and b) the bioactive structure of linezolid. Although the gas phase or solvent minimum structure of unbound linezolid is not known experimentally, we assume that it is very similar to the bioactive conformation [36][37]. Our strategy is based

• . Only the S-enantiomer is active. Superposition of all low energy minima of linezolid applying AMBER (left) and OPLS-AA (right) force field. Superposition of the found global linezolid gas phase minimum (AMBER on the left and OPLS-AA on the right) with the linezolid bioactive conformation (green). The

• OPLS-AA force field reproduces the conformation linezolid adopts in the solid state [38] or complexed by a transporter protein [39]. RMSD/Potential energy plots for linezolid in the gas phase. The OPLS-AA plot is characterized by an absence of conformers roughly between 25–34 kJ/mol. Model building

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• by Mosley et al. to study the experimental IR spectrum of the 2-norbornyl cation in the gas phase revealed a structural rearrangement to DMCP+, Jalife et al. set out to determine the isomerization mechanism using modern computational methods [64]. BOMD simulations using DFT were employed, with

Tandem processes promoted by a hydrogen shift in 6-arylfulvenes bearing acetalic units at ortho position: a combined experimental and computational study

• Mateo Alajarin,
• Marta Marin-Luna,
• Pilar Sanchez-Andrada and
• Angel Vidal

Beilstein J. Org. Chem. 2016, 12, 260–270, doi:10.3762/bjoc.12.28

• ring through transient intermediate 27a. As a final point, we have also explored the potential energy surface associated to these conversions by considering the effect of the solvent used in the experimental study, DMSO. The computed energy barriers in the gas phase and in DMSO are depicted in Table 3

• . In general, the values of the energy barriers do not vary noticeably in DMSO when compared with those in gas phase. Only ΔE8 and ΔE9 are appreciably lower in DMSO with respect to those in gas phase by 3.9 and 3.5 kcal·mol−1, respectively (Table 3). Consequently, according to these calculations, the

• rate determining step in the transformations 3a → 5a and 3a → 6a in DMSO should be the first one, i.e. the [1,9]-H shift, with an energy barrier slightly lower than that calculated in the gas phase. In summary, this computational study shows that the conversion of fulvene 3a into the benzindenes 5a and

Versatile deprotonated NHC: C,N-bridged dinuclear iridium and rhodium complexes

• Albert Poater

Beilstein J. Org. Chem. 2016, 12, 117–124, doi:10.3762/bjoc.12.13

• of Martin et al. [85] which consists of thermal corrections and entropy effects evaluated at 1354 atm [86][87][88][89], with the BP86-d3/TZVP method in the gas phase [90][91]. %VBur calculations: The buried volume calculations were performed with the SambVca package developed by Cavallo et al. [90

Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin

• Waratchada Sangpheak,
• Jintawee Kicuntod,
• Roswitha Schuster,
• Thanyada Rungrotmongkol,
• Peter Wolschann,
• Nawee Kungwan,
• Helmut Viernstein,
• Monika Mueller and
• Piamsook Pongsawasdi

Beilstein J. Org. Chem. 2015, 11, 2763–2773, doi:10.3762/bjoc.11.297

• binding free energies, or calculate the free energies of molecules in solution (∆Gbind) using the MM-PBSA/GBSA method. The free energy decomposition of each complex in terms of gas phase energy (∆EMM) including ∆Eele and ∆Evdw energies, solvation free energy (∆Gsol) and entropic term (T∆S) is shown in

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• The gas phase energy, ΔEMM, is a summation of bonded and non-bonded (electrostatic and van der Waals (vdW)) energies obtained from molecular mechanics calculation. The ΔGsolv is solvation free energy. In general, there are several methods for ΔGsolv prediction. Some methods calculate the ΔGsolv using

2-Hetaryl-1,3-tropolones based on five-membered nitrogen heterocycles: synthesis, structure and properties

• Yury A. Sayapin,
• Inna O. Tupaeva,
• Alexandra A. Kolodina,
• Eugeny A. Gusakov,
• Vitaly N. Komissarov,
• Igor V. Dorogan,
• Nadezhda I. Makarova,
• Anatoly V. Metelitsa,
• Valery V. Tkachev,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2015, 11, 2179–2188, doi:10.3762/bjoc.11.236

• estimation of relative stabilities of the tautomeric NH and OH forms of the representative derivatives of 1,3-tropolones 5 and 6 in the gas phase and in a polar solvent (DMSO, Table 2) revealed that the decrease in the electronegativity of the fragment X in the row 6a, 6d, 6g (X = O, S, C(CH3)2) shifts the

• energy correction (Etot + ZPE, а.u.) and relative energies (ΔE, kcal/mol) of the intermediates and corresponding transition states (Ts) occurring along the reaction path of the formation of 1,3-tropolones 5, and 6a,d,g calculated using the PBE0/6-311+G** method in the gas phase. Total energies with zero

• -point energy correction (Etot + ZPE, а.u.) and relative energies (ΔE, kcal/mol) of the NH and OH tautomeric forms of compounds 5 and 6 calculated using the PBE0/6-311+G** method in the gas phase and in DMSO solution. Optical properties of 2-(2-alkoxycarbonyl-6-hydroxyphenyl)benzoxazoles 11a–f in heptane

A comprehensive study of olefin metathesis catalyzed by Ru-based catalysts

• Albert Poater and
• Luigi Cavallo

Beilstein J. Org. Chem. 2015, 11, 1767–1780, doi:10.3762/bjoc.11.192

• and side, respectively. Next, by means of DFT calculations Goddard and co-workers indicated clearly that solvent effects were of paramount relevance to the relatively high stability of b [48], while in the gas phase structure a was much favored [13]. Moreover, Grubbs and co-workers reported the X-ray

• contributions of non-electrostatic terms have been estimated in single point calculations on the gas phase optimized structures, based on the polarizable continuous solvation model PCM using CH2Cl2 as a solvent [67]. The cavity is created via a series of overlapping spheres. For the sake of clarity we did not

Fe(II)/Et₃N-Relay-catalyzed domino reaction of isoxazoles with imidazolium salts in the synthesis of methyl 4-imidazolylpyrrole-2-carboxylates, its ylide and betaine derivatives

• Ekaterina E. Galenko,
• Olesya A. Tomashenko,
• Alexander F. Khlebnikov,
• Mikhail S. Novikov and
• Taras L. Panikorovskii

Beilstein J. Org. Chem. 2015, 11, 1732–1740, doi:10.3762/bjoc.11.189

• . entries 3 and 5) stabilize carbene tautomer 3 slightly. Changing N-alkyl for N-aryl substituents in the imidazolium ring has a relatively small effect on the tautomeric ratio (Table 3, entries 1 and 3). At the same time, the solvent has a dramatic effect on the equilibrium position. In the gas phase

• thermodynamic stability of tautomers 4–6 revealed (Table 3, entries 6–10) that solvent has a crucial impact on the equilibrium position. Betaines 6 are the most unstable species in the gas phase, whereas in solvents they become the most stable species and therefore dominate in solution. It is worth noting that

• and phenacylimidazolium bromides 9 under FeCl2·4H2O/Et3N catalysis. The preparation of ylides 2 and imidazolethiones 13. Relative free energies (carbene 3/ylide 2, ylide 4/betaine 6 and carbene 5/betaine 6) computed at the DFT B3LYP/6-31+G(d,p) level in the gas phase or with the PCM model for the

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

• recently [42][52]. The results of quantum chemical calculations on CH acidity of the different N-arylated pyrroles 1 and indoles 2, obtained both for THF solution (Figure 5) and gas phase (see Supporting Information File 1), are presented in the current paper. A potential acidity of the methoxy groups in

• allowed us to state that both 2a and 2b are likely to adopt a form in which the heteroatoms are far away from the benzo-fragment. The calculated values of gas-phase acidity of the investigated compounds (see Supporting Information File 1) lie within the range of 364.4–394.3 kcal mol−1 which is typical for

• weak CH acidic compounds while the pKa values in THF solution (Figure 5) covered a 28.8–45.0 span. These data allow the assignment of potential deprotonation sites in the investigated substrates. Also the correlation between gas-phase ΔGacid and the pKa(THF) values can be tracked. In all cases, the CH

Why base-catalyzed isomerization of N-propargyl amides yields mostly allenamides rather than ynamides

• Armando Navarro-Vázquez

Beilstein J. Org. Chem. 2015, 11, 1441–1446, doi:10.3762/bjoc.11.156

• ]. Interestingly, the kinetics of the reaction seem to be slow enough to allow the allenamide intermediate to be obtained by simply employing a short reaction time [20]. The computations for acridinone 11 gave isomerization energies and of −3.3 and −2.3 kcal/mol, in the gas phase, and −2.7 and −1.1 in DMSO

Antioxidant potential of curcumin-related compounds studied by chemiluminescence kinetics, chain-breaking efficiencies, scavenging activity (ORAC) and DFT calculations

• Adriana K. Slavova-Kazakova,
• Silvia E. Angelova,
• Timur L. Veprintsev,
• Petko Denev,
• Davide Fabbri,
• Maria Antonietta Dettori,
• Maria Kratchanova,
• Vladimir V. Naumov,
• Aleksei V. Trofimov,
• Rostislav F. Vasil’ev,
• Giovanna Delogu and
• Vessela D. Kancheva

Beilstein J. Org. Chem. 2015, 11, 1398–1411, doi:10.3762/bjoc.11.151

• UB3LYP/6-31+G(d,p) optimized structures of compounds and their radicals in the gas phase are given in Table 2. For all monomers only rotamers with intramolecular hydrogen bonds between the hydroxy and the methoxy groups (O atom) are considered. In case of monomer 4 the structures with hydrogen bonds

• Figure 6 are presented data for 1, 10, 11 and 13. In gas phase 6 has a BDE(r) value close to that of curcumin (1) (78.94 and 78.78 kcal·mol−1, respectively), which is in agreement with the experimental data. In water the BDE(r) values of 7 and of 6 are almost equal (76.40 and 76.71 kcal·mol−1). In gas

• phase 13 is characterized with BDE value in the range of that of the monomers, while in water higher value was evaluated. The BDE values calculated for 11 in gas phase and for 10 in water are much lower than the values determined for the compounds under study. This explains the experimentally obtained