First principle investigation of the linker length effects on the thermodynamics of divalent pseudorotaxanes

• Andreas J. Achazi,
• Doreen Mollenhauer and
• Beate Paulus

Beilstein J. Org. Chem. 2015, 11, 687–692, doi:10.3762/bjoc.11.78

• (CH2)3O– (n1) and –O(CH2)4O– (n2) have been investigated both experimentally in [16] and computationally. The results for the electronic association energy ΔE, the Gibbs energy of association ΔG in the gas phase and its enthalpic (ΔH) and entropic (−TΔS) contributions are given in Table 2. Comparing

• stacking of two benzene rings. The n1 and n2 guest do not perfectly fit with the host (Figure 2). In the n1-case the linker is folded away from the anthracene bridge, and for the n2-case one phenyl ring is twisted away due to steric constraints. The Gibbs energy of association ΔG in the gas phase of the

• compared to the calculated electronic association energies, Gibbs energies of association in the gas phase and to the measured experimental values. For the monovalently bound system Ph@C8 the computationally obtained value of ΔG (−12.6 kJ/mol) agrees well with the experimentally determined value (−15.0 kJ

Photocatalytic nucleophilic addition of alcohols to styrenes in Markovnikov and anti-Markovnikov orientation

• Martin Weiser,
• Sergej Hermann,
• Alexander Penner and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2015, 11, 568–575, doi:10.3762/bjoc.11.62

• methods. All chemicals were purchased from Aldrich, ABCR and TCI. GC–MS data were recorded on a Varian GC–MS System (gas-phase chromatograph 431-GC, mass spectrometer 210-MS). Absorption spectra were determined with a Perkin Elmer Lambda 750 UV–vis spectrometer. Fluorescence was measured with a Horiba

On the strong difference in reactivity of acyclic and cyclic diazodiketones with thioketones: experimental results and quantum-chemical interpretation

• Andrey S. Mereshchenko,
• Alexey V. Ivanov,
• Viktor I. Baranovskii,
• Grzegorz Mloston,
• Ludmila L. Rodina and
• Valerij A. Nikolaev

Beilstein J. Org. Chem. 2015, 11, 504–513, doi:10.3762/bjoc.11.57

• case of thioketone 2b, all calculations were performed for the gas phase. Reactions with thiobenzophenone (2a) By comparison with the literature data [16][17][18], one can assume that the multistep reactions of DDC 1a–d and thione 2a are initiated by 1,3-cycloaddition of the diazogroup with the C=S

• diazo compounds 1a–f with cycloaliphatic thioketone 2b were calculated (Table 2). All calculations refer to the gas phase, since all reactions of DDC 1 with the thioxocyclobutanedione 2b were carried out under solvent-free conditions [20]. The driving force behind the DDC 1a–d reactions with

• the polarizable continuum model (PCM) [22]. All calculations for the reactions of diazo compounds 1a,c,d with thiocyclobutanedione 2b were performed in the gas phase. To characterize the nature of the stationary points, the corresponding vibrational frequencies were calculated. The optimized structure

Synthesis of dinucleoside acylphosphonites by phosphonodiamidite chemistry and investigation of phosphorus epimerization

• William H. Hersh

Beilstein J. Org. Chem. 2015, 11, 184–191, doi:10.3762/bjoc.11.19

• cases the vibrational calculation exhibited one negative frequency that corresponded to the phosphorus inversion vibration. Not surprisingly, the phosphine transition state exhibited a trigonal planar geometry, and the gas-phase energy barrier of 32.5 kcal/mol was in excellent agreement with the values

• reported by Mislow for reactions carried out in non-polar toluene as a solvent. Similarly, the acylphosphine transition state exhibited a trigonal planar geometry, and the gas-phase energy barrier of 21.2 kcal/mol was also in excellent agreement with the typical values noted above. The phosphite, in

Cross-dehydrogenative coupling for the intermolecular C–O bond formation

• Igor B. Krylov,
• Vera A. Vil’ and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2015, 11, 92–146, doi:10.3762/bjoc.11.13

A one-pot multistep cyclization yielding thiadiazoloimidazole derivatives

• Debabrata Samanta,
• Anup Rana,
• Jan W. Bats and
• Michael Schmittel

Beilstein J. Org. Chem. 2014, 10, 2989–2996, doi:10.3762/bjoc.10.317

• computations on 1a at B3LYP/6-31+G* level in the gas phase as implemented in Gaussian 09 [14]. Several attempts to locate the intermediate 4 in the gas and solvent phase (dichloromethane) failed due to the absence of any minimum corresponding to 4 on the potential energy surface. A concerted TS search for the

• –π stacking. To take the solvent into consideration, the thermochemical analyses were performed in dichloromethane using the COSMO model with gas phase optimized geometries. Originally, DMAP should be hydrogen bonded to both amide protons in complex 8 increasing the nucleophilicity of both N-centers

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

• these two previous studies, the fisetin/β-CD inclusion complex was optimized in gas phase, the A- or B-rings of fisetin were not well inserted, but only partially occupied in the cavity, while the other ring entirely stayed outside of the β-CD moiety. Herein, the host–guest inclusion complexation

• ,p) optimization in gas phase and in water (Polarizable Continuum Model, PCM), also including BSSE correction was performed on this system. Materials and Methods System preparation The two possible conformations of fisetin (CAS 528-48-3), resulting from a single bond rotation between the chromone and

• (ΔG) can be calculated from enthalpy (ΔH) and entropy terms with constant temperature (TΔS). In solution, the ΔH term was divided into enthalpy energy in gas phase upon formation of complex (ΔEMM) and the free energy of solvation (ΔGsol), while the entropy term, T∆S, for conformational entropy change

Removal of volatile organic compounds using amphiphilic cyclodextrin-coated polypropylene

• Ludmilla Lumholdt,
• Sophie Fourmentin,
• Thorbjørn T. Nielsen and
• Kim L. Larsen

Beilstein J. Org. Chem. 2014, 10, 2743–2750, doi:10.3762/bjoc.10.290

• substitutions (DS) and location of these substitutions, as described elsewhere [21]. The structures, DS, average molecular weight, and label definitions are given in Table 3. Six VOCs (Table 2) were added to a 20 mL glass vial containing 10 mL of water and a piece of coated PP. Their presence in gas phase was

Preparation of neuroprotective condensed 1,4-benzoxazepines by regio- and diastereoselective domino Knoevenagel–[1,5]-hydride shift cyclization reaction

• László Tóth,
• Yan Fu,
• Hai Yan Zhang,
• Attila Mándi,
• Katalin E. Kövér,
• Tünde-Zita Illyés,
• Attila Kiss-Szikszai,
• Balázs Balogh,
• Tibor Kurtán,
• Sándor Antus and
• Péter Mátyus

Beilstein J. Org. Chem. 2014, 10, 2594–2602, doi:10.3762/bjoc.10.272

• Macromodel 9.9.223 software [25] using OPLS-2005 force field with implicit solvent model for chloroform applying a 42 kJ/mol energy window. Geometry reoptimizations (B3LYP/6-31G(d) level in gas phase and B3LYP/TZVP level with PCM solvent model for CHCl3) and TDDFT-ECD calculations were performed with

• strengths. Boltzmann distributions were estimated from the ZPVE-corrected B3LYP/6-31G(d) energies in the gas-phase calculations and from the B3LYP/TZVP energies in the PCM ones. The MOLEKEL [28] software package was used for visualization of the results. Bioassay on neuroprotective activity: SH-SY5Y cells

• compared with the computed ECD spectra of the gas-phase optimized conformers (>1%) of model compound (2S,15aS)-7d (1 conformer, B3LYP/TZVP) and (2S,15aS)-7b (2 conformers, BH&HLYP/TZVP). Bars represent the computed rotational strength values (R/8) of the lowest-energy conformer. c) Structure of the (2S

Molecular ordering at electrified interfaces: Template and potential effects

• Thanh Hai Phan and
• Klaus Wandelt

Beilstein J. Org. Chem. 2014, 10, 2243–2254, doi:10.3762/bjoc.10.233

• (UHV) based surface science in recent years. However, promising organic compounds may not remain intact volatile, and may thus not be deposited via the gas phase. In those cases, it may be a promising strategy to deposit these molecules from solution instead. Besides, this preparation route is probably

A new charge-tagged proline-based organocatalyst for mechanistic studies using electrospray mass spectrometry

• J. Alexander Willms,
• Rita Beel,
• Martin L. Schmidt,
• Christian Mundt and
• Marianne Engeser

Beilstein J. Org. Chem. 2014, 10, 2027–2037, doi:10.3762/bjoc.10.211

• charged proline catalyst has been tested in the direct asymmetric inverse aldol reaction between aldehydes and diethyl ketomalonate. Two intermediates in accordance with the List–Houk mechanism for enamine catalysis have been detected and characterized by gas-phase fragmentation. In addition, their

• for an extremely broad variety of substances [2], but has also been recognized as a valuable tool for studying reaction mechanisms by transferring species of a reacting solution directly into the gas phase of a mass spectrometer [3][4][5][6][7]. The technique allows glimpses into the reacting solution

• new proline catalyst with a non-interfering charge-label presented here as a tool to study the templating role of the hydroxy group in L-proline-catalyzed reactions in the gas-phase in the near future. Experimental Synthesis Reactions under inert gas atmosphere were performed under argon using

Efficient CO₂ capture by tertiary amine-functionalized ionic liquids through Li⁺-stabilized zwitterionic adduct formation

• Zhen-Zhen Yang and
• Liang-Nian He

Beilstein J. Org. Chem. 2014, 10, 1959–1966, doi:10.3762/bjoc.10.204

• chelated IL with LiNTf2. Calculation of the energy of the gas phase reaction between neutral ligands and Li+ gave a value for the enthalpy change in the range of −41.59 to −106.56 kcal mol−1 (Table 1, entries 1–11), indicating that the formation of chelated ILs is feasible. In addition, PEG

Proton transfers in the Strecker reaction revealed by DFT calculations

• Shinichi Yamabe,
• Guixiang Zeng,
• Wei Guan and
• Shigeyoshi Sakaki

Beilstein J. Org. Chem. 2014, 10, 1765–1774, doi:10.3762/bjoc.10.184

• complex 1. The reaction begins with the addition of NH3 to the carbonyl carbon of acetaldehyde to form a Mulliken charge-transfer complex 2. This complex was firstly proposed here. In 2, the C–O bond is elongated to1.345 Å, which has an alkoxide character and the complex is not stable in the gas phase

An experimental and theoretical NMR study of NH-benzimidazoles in solution and in the solid state: proton transfer and tautomerism

• Carla I. Nieto,
• Pilar Cabildo,
• M. Ángeles García,
• Rosa M. Claramunt,
• Ibon Alkorta and
• José Elguero

Beilstein J. Org. Chem. 2014, 10, 1620–1629, doi:10.3762/bjoc.10.168

• all nuclei have been reported for the three NH-benzimidazoles 1, 2 and 4 [16][17][18][19][20][21]; besides 13C and 15N NMR chemical shifts of 5 have been published [22][23]. Three kinds of calculations have been done: isolated molecules (gas phase), continuous model solvated molecules in DMSO, and

• have collected in Table 4 the different equations obtained from the data of Table 1, Table 2 and Table 3. i) The 1H chemical shifts are much more consistent with calculations for DMSO as solvent than with those of isolated molecules (gas phase). For 26 points, the R2 coefficient increases from 0.56 (eq

• for solution and for CPMAS, the gas phase and DMSO calculations are comparable in terms of R2 (eqs. 14–17), however, the values of the slopes (the closer to 1, the better) and intercepts (the closer to 0, the better), clearly favored the DMSO calculations. Surprisingly, the monomer appears preferable

Pd/C-catalyzed aerobic oxidative esterification of alcohols and aldehydes: a highly efficient microwave-assisted green protocol

• Marina Caporaso,
• Giancarlo Cravotto,
• Spyros Georgakopoulos,
• George Heropoulos,
• Katia Martina and
• Silvia Tagliapietra

Beilstein J. Org. Chem. 2014, 10, 1454–1461, doi:10.3762/bjoc.10.149

• resistant reactors (up to 200 bar) that are equipped with separate multiple gas inlets and can be considered autoclaves. Only a few publications have described this technique in heterogeneous gas-phase reactions that are important for industrial processes [51][52][53][54][55]. We have recently displayed the

Streptopyridines, volatile pyridine alkaloids produced by Streptomyces sp. FORM5

• Ulrike Groenhagen,
• Michael Maczka,
• Jeroen S. Dickschat and
• Stefan Schulz

Beilstein J. Org. Chem. 2014, 10, 1421–1432, doi:10.3762/bjoc.10.146

• components. In the gas phase, only the streptopyridines could be detected. Therefore, an orthogonal set of analysis is needed to assess the metabolic profile of bacteria, because volatile compounds are obviously overlooked by traditional analytical methods. The streptopyridines are strain specific volatiles

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

• Friedrich Malberg,
• Jan Gerit Brandenburg,
• Werner Reckien,
• Oldamur Hollóczki,
• Stefan Grimme and
• Barbara Kirchner

Beilstein J. Org. Chem. 2014, 10, 1299–1307, doi:10.3762/bjoc.10.131

• computational energy profile [22]. The formation of α-cyclodextrin-based [3]pseudorotaxanes in the gas phase was studied by means of density functional calculations [23]. Molecular mechanics calculations were used for a free energy calculation of an α-cyclodextrin rotaxane system and for the investigation of

• theory (MP2) calculations [29]. The contribution of the London dispersion interaction to the total interaction energy in the gas phase is of the same magnitude as the hydrogen bonding interaction (about −14 kcal/mol). The molecular functionality of rotaxanes is solely based on the interplay of different

• combination provides reliable results for both the gas phase and the solid state as shown in a number of publications by us [49][50][51] and other groups [45][52]. Structures under study The hereby considered pseuodorotaxanes (Figure 1) consist of an amide axle inside the cavity of a macrocycle, which

Atherton–Todd reaction: mechanism, scope and applications

• Stéphanie S. Le Corre,
• Mathieu Berchel,
• Hélène Couthon-Gourvès,
• Jean-Pierre Haelters and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2014, 10, 1166–1196, doi:10.3762/bjoc.10.117

• distinct mechanisms. First, some phosphorus compounds (e.g., DOPO, Scheme 34) act on the gas phase by the production of non-flammable compounds (e.g., water) or by the production of reactive species that act as hydroxyl radical scavengers. Alternatively, phosphorus-based flame retardants may act on the

• effects. Melamine polyphosphate (MPP, Scheme 34), illustrates this possibility: melamine decomposes endothermically and produces NH3 when burning (a gas-phase active agent), while polyphosphate, which is simultaneously produced, favors the charring process. The synergic effects of phosphorus and nitrogen

Homogeneous and heterogeneous photoredox-catalyzed hydroxymethylation of ketones and keto esters: catalyst screening, chemoselectivity and dilution effects

• Axel G. Griesbeck and
• Melissa Reckenthäler

Beilstein J. Org. Chem. 2014, 10, 1143–1150, doi:10.3762/bjoc.10.114

• the photolysis of TiO2 in the absence of additional acceptor compounds with formation of hydrogen and eventually formation of formaldehyde [46]. Both hydrogen and formaldehyde were also detected in our experiments by gas-phase analysis. Thus, higher amounts of hydroxymethyl radicals can be produced

Site-selective covalent functionalization at interior carbon atoms and on the rim of circumtrindene, a C₃₆H₁₂ open geodesic polyarene

• Hee Yeon Cho,
• Ronald B. M. Ansems and
• Lawrence T. Scott

Beilstein J. Org. Chem. 2014, 10, 956–968, doi:10.3762/bjoc.10.94

• the authors’, have been particularly successful in synthesizing geodesic polyarenes using flash vacuum pyrolysis (FVP) [6]. The FVP method involves slow sublimation of a starting material under vacuum, rapid passage of the gas-phase molecules through a hot zone, and subsequent capture of the products

Conformational analysis of 2,2-difluoroethylamine hydrochloride: double gauche effect

• Josué M. Silla,
• Claudimar J. Duarte,
• Rodrigo A. Cormanich,
• Roberto Rittner and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2014, 10, 877–882, doi:10.3762/bjoc.10.84

• a 2-substituted ethylamine fragment [1][2][3][4][5]. According to theoretical calculations, such conformational preference takes place in the gas phase and persists in water solution, where most biochemical processes occur. We have recently shown that, in water solution, the axial preference of 3

• and Discussion The conformational isomerism of 2,2-difluoroethylamine (1) was computationally investigated at the MP2/6-311++g(d,p) level, both in the gas phase and implicit water (using the Polarizable Continuum Model). The conformational preferences are consistent with those obtained elsewhere

• perturbation analysis of donor-acceptor interactions in the natural bond orbitals (NBOs) framework shows that the global minimum of 1 is more stabilized by hyperconjugation than the other conformers (both in the gas phase and implicit water), despite being significantly destabilized by Lewis-type interactions

Chromatographically separable rotamers of an unhindered amide

• Mario Geffe,
• Lars Andernach,
• Oliver Trapp and
• Till Opatz

Beilstein J. Org. Chem. 2014, 10, 701–706, doi:10.3762/bjoc.10.63

• - and Z-isomer of 4 is predicted to be 3.2 kJ/mol in hexane and 5.8 kJ/mol in vacuo, respectively. The transition states are located at 108.8 kJ/mol (TS1) and 105.5 kJ/mol (TS2) above the Z-isomer of 4 for hexane solvation as well as at 107.3 k/mol (TS1) and 102.1 kJ/mol (TS2) in the gas phase

• −284.0 cm−1 (TS1) and −362.2 cm−1 (TS2) in the gas phase). This imaginary frequency belongs to the rotational vibration of the formyl hydrogen and the formyl oxygen along the reaction pathway for the E/Z isomerization of 4. In both transition states geometries, the C–N bond (143 pm) is significantly

• , quant. Relative Gibbs free energy (kJ/mol) for E-4, Z-4, TS1, TS2, GSDMF, TS1DMF and TS2DMF in the gas phase and with COSMO solvation for hexane, ethanol and DMSO at 298 K (BP-D3/def2-SVP). Supporting Information Supporting Information File 168: Experimental procedures, HPLC chromatograms, copies of 1D

Continuous flow nitration in miniaturized devices

• Amol A. Kulkarni

Beilstein J. Org. Chem. 2014, 10, 405–424, doi:10.3762/bjoc.10.38

• nitration of thioureas is based on subsequent nitrosation and nitration steps. The same group also analyzed continuous processes to perform the strongly exothermic nitration of naphthalene (47) (Scheme 14) with N2O5, both in the gas phase and in the liquid phase [49][50]. The authors reported that the

Substrate dependent reaction channels of the Wolff–Kishner reduction reaction: A theoretical study

• Shinichi Yamabe,
• Guixiang Zeng,
• Wei Guan and
• Shigeyoshi Sakaki

Beilstein J. Org. Chem. 2014, 10, 259–270, doi:10.3762/bjoc.10.21

• at the reaction center was prepared by the use of Z matrices. For instance, in the gas phase SN2 reaction Cl− + H3C–Br → Cl–CH3 + Br−, Cl···C and C···Br intermediate distances were assumed. The geometry was optimized under the constraint of the fixed Cl–C and C–Br distances. After the partial

Less reactive dipoles of diazodicarbonyl compounds in reaction with cycloaliphatic thioketones – First evidence for the 1,3-oxathiole–thiocarbonyl ylide interconversion

• Valerij A. Nikolaev,
• Alexey V. Ivanov,
• Ludmila L. Rodina and
• Grzegorz Mlostoń

Beilstein J. Org. Chem. 2013, 9, 2751–2761, doi:10.3762/bjoc.9.309

• of quantum chemical programs. Geometry optimizations of intermediates, transition states, reactants, and products in the gas phase were performed at the PBE1PBE/6-31G(d) level by using Gaussian 09 [38]. Stationary points on the respective potential energy surfaces were characterized at the same level