Anion-driven encapsulation of cationic guests inside pyridine[4]arene dimers

• Anniina Kiesilä,
• Jani O. Moilanen,
• Anneli Kruve,
• Christoph A. Schalley,
• Perdita Barran and
• Elina Kalenius

Beilstein J. Org. Chem. 2019, 15, 2486–2492, doi:10.3762/bjoc.15.241

• and studied by multiple gas-phase techniques, ESI-QTOF-MS, IRMPD, and DT-IMMS experiments, as well as DFT calculations. The comparison of classical resorcinarenes with pyridinearenes by MS and NMR experiments reveals clear differences in their host–guest chemistry and implies that cation encapsulation

• complexes can template the formation of pyridinearene hexameric capsules in the gas phase [6]. Here, we report our novel findings on the ability of dimeric tetraisobutylpyridine[4]arene (compound 1 in Scheme 1) to encapsulate cationic guests. Despite of the obvious structural similarities between the

• "through-wall" electrostatic interactions. Results and Discussion We have previously shown that tetraisobutylpyridine[4]arene forms hydrogen-bonded dimers with eight intermolecular N–H···O(amide) hydrogen bonds in the solid state, in solution and in the gas phase [11]. Resorcinarene capsules of similar

Experimental and computational electrochemistry of quinazolinespirohexadienone molecular switches – differential electrochromic vs photochromic behavior

• Eric W. Webb,
• Jonathan P. Moerdyk,
• Kyndra B. Sluiter,
• Benjamin J. Pollock,
• Amy L. Speelman,
• Eugene J. Lynch,
• William F. Polik and
• Jason G. Gillmore

Beilstein J. Org. Chem. 2019, 15, 2473–2485, doi:10.3762/bjoc.15.240

• is an obvious inverse relationship between calculated bond orders and bond lengths. For D0, a longer bond length is observed for heteroN–C while a longer bond length is observed for benzoN–C in T0. These results, regardless of solvent or gas-phase considerations, are consistent with the discussion

• ) [22]. Gas-phase geometries were optimized at the B3LYP/6-31G(d) level of theory. Single point energies were computed at the same level of theory with implicit acetonitrile solvent implemented using the Conductor-like Polarizable Continuum Model with UAKS radii. These computations were performed using

• gas phase. Based on this starting point, geometries for S0, T0, and the one-electron reduced D0 states were then (re)optimized with an implemented acetonitrile conductor-like polarizable continuum model (CPCM) as the self-consistent reaction field (SCRF) [37]. It is from these implicit solvent

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• date, CotB2 represents the best studied bacterial diterpene synthase. Its reaction mechanism has been addressed by isoptope labeling, targeted mutagenesis and theoretical computations in the gas phase, as well as full enzyme molecular dynamic simulations. By X-ray crystallography different snapshots of

• rearrangement. Hong and Tantillo performed the first theoretical study of the reaction mechanism in CotB2 via gas phase density functional theory (DFT) calculations [33]. Simultaneously, Sato et al. also studied the CotB2 reaction mechanism in the gas phase using DFT, combined with experimental deuterium

• aromatic function [30][36][37][38] (Table 2 and Scheme 1), which significantly affect the product profile. Further support for the reaction mechanism was generated by gas-phase calculations [33][34] as well as in silico multiscale modeling [37], which suggest an active role of the enzyme during catalysis

Azologization and repurposing of a hetero-stilbene-based kinase inhibitor: towards the design of photoswitchable sirtuin inhibitors

• Christoph W. Grathwol,
• Nathalie Wössner,
• Sören Swyter,
• Adam C. Smith,
• Enrico Tapavicza,
• Robert K. Hofstetter,
• Anja Bodtke,
• Manfred Jung and
• Andreas Link

Beilstein J. Org. Chem. 2019, 15, 2170–2183, doi:10.3762/bjoc.15.214

• previously determined accuracy [56]. We notice a good agreement between ADC(2) gas phase calculations with CC2 gas phase calculations, which justifies the usage of the approximate ADC(2) method. Comparing the calculated absorption spectra for (E)-2b-B and (Z)-2b-A to the experimental spectra obtained from LC

Synthesis and anion binding properties of phthalimide-containing corona[6]arenes

• Meng-Di Gu,
• Yao Lu and
• Mei-Xiang Wang

Beilstein J. Org. Chem. 2019, 15, 1976–1983, doi:10.3762/bjoc.15.193

• adopt the conformation in which three phthalimide units are cis,trans-orientated. Acting as electron-deficient macrocyclic hosts, the synthesized O6-corona[3]arene[3]tetrazines self-regulated conformational structures to complex anions in the gas phase and in the solid state owing to the anion–π

• ability of 3a to bind various anion species in gas phase. To our delight, host molecule 3a co-crystalized with n-Bu4NX (X = Cl, Br) from diffusion of diethyl ether vapor into ethyl acetate solution at ambient temperature to give single crystals of the host–guest complexes (n-Bu4NX)3-3a (X = Cl, Br). X-ray

• conformational structures to complex anions in the gas phase and in the solid state owing to the anion–π noncovalent interactions between anions and the tetrazine rings. The easy accessibility, cylindroid cavity and diverse functionality would engender phthalimide-containing functionalized O6-corona[3]arene[3

Halide metathesis in overdrive: mechanochemical synthesis of a heterometallic group 1 allyl complex

• Ross F. Koby,
• Nicholas R. Rightmire,
• Nathan D. Schley,
• Timothy P. Hanusa and
• William W. Brennessel

Beilstein J. Org. Chem. 2019, 15, 1856–1863, doi:10.3762/bjoc.15.181

• Information File 1, Figure S3). Despite the gas-phase environment of the calculations, the distance between K+ and CH4 is 3.22 Å, a typical value for potassium–methyl interactions in the solid state, as is the ∆H° of almost 12 kJ mol−1, in the range of hydrogen bonds (Table 3, entries 1 and 2) [32]. The

Nanopatterns of arylene–alkynylene squares on graphite: self-sorting and intercalation

• Tristan J. Keller,
• Joshua Bahr,
• Kristin Gratzfeld,
• Nina Schönfelder,
• Marcin A. Majewski,
• Marcin Stępień,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2019, 15, 1848–1855, doi:10.3762/bjoc.15.180

• nanopores from the gas phase [15], the intercalation of organic molecules into nanopores is rather difficult to tailor from scratch, however, with prominent examples [16][17]. Likewise, larger polycyclic aromatic hydrocarbons (PAHs) and nanographenes form robust adsorbate films in a certain size range, and

Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding

• Stiliyana Pereva,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2019, 15, 1592–1600, doi:10.3762/bjoc.15.163

• ). Table 1 lists the enthalpies evaluated at the M062X/6-31G(d,p) level of theory for the stepwise water coordination to the host macrocycle in both the gas phase and aqueous solution. Negative ΔH1 and ΔH78 values imply favorable interactions in both media. Similar trends were observed for enthalpies

• against experimental data (dissociation energy, D0, in the gas phase) on water dimer. Frequency calculations for each M062X/6-31G(d,p) optimized construct were performed at the same level of theory. No imaginary frequency was found for the lowest energy configurations of any of the optimized structures

• . The frequencies were used to compute the respective thermal energy correction, Eth, including zero point energy, to the electronic energy yielding the gas phase enthalpy of the molecule/complex at T = 298.15 K (Equation 1). Solvation energies were evaluated by employing the solvation model based on

Transient and intermediate carbocations in ruthenium tetroxide oxidation of saturated rings

• Manuel Pedrón,
• Laura Legnani,
• Maria-Assunta Chiacchio,
• Pierluigi Caramella,
• Tomás Tejero and
• Pedro Merino

Beilstein J. Org. Chem. 2019, 15, 1552–1562, doi:10.3762/bjoc.15.158

• ]. Computations were done using the B3LYP functional [48][49] in conjunction with Grimme’s dispersion correction [50][51] (henceforth referred to as B3LYP-d3bj). The standard basis set Def2SVP was employed [52][53]. For the purpose of comparison optimizations at gas phase and considering solvent effects (both

• calculations are those indicated in Scheme 3. Results and Discussion We first studied the oxidations of cyclopentane (R1), tetrahydrofuran (R2) and tetrahydrothiophene (R3, Scheme 4). The geometries of all stationary points were optimized at the B3LYP-d3bj/Def2SVP level of theory in the gas phase and

An azobenzene container showing a definite folding – synthesis and structural investigation

• Abdulselam Adam,
• Saber Mehrparvar and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2019, 15, 1534–1544, doi:10.3762/bjoc.15.156

• unit as well as commercially available compounds. Investigation of the structure and the switching process To investigate the structures of the foldable container 10 in the gas phase, the geometric parameters of the trans,trans-, cis,trans- and cis,cis-isomers were fully optimized by means of the DFT

• performed by using the program package Gaussian 16 [62]. The geometries of the molecules were fully optimized in the gas phase by using the DFT potentials B3LYP [53][54][55] and B3LYP-D3 [56][57] as well as the 6-31G* [58][59] basis set. For all calculations, the default thresholds implemented in Gaussian

Selenophene-containing heterotriacenes by a C–Se coupling/cyclization reaction

• Pierre-Olivier Schwartz,
• Sebastian Förtsch,
• Astrid Vogt,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2019, 15, 1379–1393, doi:10.3762/bjoc.15.138

• (Figure 2b), because a completely flat geometry of the isolated molecule DST 3 (in the gas phase) was obtained from theoretical calculations (vide infra). Molecules of DST 3 order in a typical herringbone fashion, where the terminal hydrogen atoms form hydrogen bond-like C–H heteroatom interactions (2.819

Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study

• Valya K. Nikolova,
• Cristina V. Kirkova,
• Silvia E. Angelova and
• Todor M. Dudev

Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131

• between biological receptors and small ions. The complex formation behavior of water-soluble p-sulfonatocalix[4]arene and thiacalix[4]arene and group IA, IIA and f-block metal cations has been investigated computationally by means of density functional theory computations in the gas phase and in aqueous

• environment. The calculated Gibbs free energy values of the complex formation reaction of these ligands with the bare metal cations suggest a spontaneous and energy-favorable process for all metal cations in the gas phase and only for Na+, Mg2+, Lu3+ cations in water environment. For one of the studied

• descriptors of the group IA, IIA and f-block metal cations binding to the host calixarene systems have been evaluated and the factors that affect the interactions in the gas phase and in water medium have been unraveled. Available data on the experimental pKa values [31][33][34] imply that in acidic water

Extending mechanochemical porphyrin synthesis to bulkier aromatics: tetramesitylporphyrin

• Qiwen Su and
• Tamara D. Hamilton

Beilstein J. Org. Chem. 2019, 15, 1149–1153, doi:10.3762/bjoc.15.111

• under any traditional synthetic method. High-temperature (>170 °C) sealed-bomb reactions in the presence of metal salts will, after 2–3 days, yield 1–6% of meso-tetrakis[2,4,6-(trimethyl)phenyl]porphyrin (TMP) [20][21][23][24], and a gas-phase synthesis in the presence of TFA yielded 7% TMP [9]. Under

• -solvent-added routes to porphyrins, including high-temperature sealed-bomb methods [15][16][17], gas-phase synthesis [9], and microwave irradiation [10] do not employ a second oxidation step. Presumably for the latter two methods open to air, dioxygen serves as a rapid oxidizer under high-temperature

Precious metal-free molecular machines for solar thermal energy storage

• Meglena I. Kandinska,
• Snejana M. Kitova,
• Vladimira S. Videva,
• Stanimir S. Stoyanov,
• Stanislava B. Yordanova,
• Stanislav B. Baluschev,
• Silvia E. Angelova and
• Aleksey A. Vasilev

Beilstein J. Org. Chem. 2019, 15, 1096–1106, doi:10.3762/bjoc.15.106

• -crown-5 fragments) in the gas phase (Figure 5). The thermochemical data for these are calculated at 298.15 K and a pressure of 1 atm. In Table 3 we report the enthalpies (H) for the cis and trans isomers and the energy storage capacity (ΔH) calculated as the difference in enthalpy between the cis and

• trans isomers. B3LYP calculations in the gas phase predict the trans forms of the dyes 4a–d to be more stable. The cis forms are higher in energy by only 3.3 and 3.0 kJ mol−1 for 4a and 4b, respectively. The enthalpy differences calculated for dyes 4c and 4d are much higher (69.3 kJ mol−1 (4c) and 67.9

• displaced “above” the crown ether’s cavity. Figure 6 depicts the gas-phase geometries of the Ba2+ complexes of the cis and trans isomer of 4b. The calculated enthalpies for the complex-formation reaction dye + Ba2+ → [dye–Ba]2+ in the gas phase, where dye = 4a–d, with bare metal cations are listed in Table

Strong hyperconjugative interactions limit solvent and substituent influence on conformational equilibrium: the case of cis-2-halocyclohexylamines

• Camila B. Francisco,
• Cleverton S. Fernandes,
• Ulisses Z. de Melo,
• Roberto Rittner,
• Gisele F. Gauze and
• Ernani A. Basso

Beilstein J. Org. Chem. 2019, 15, 818–829, doi:10.3762/bjoc.15.79

• by the weighted averages of both conformers, considering the rotational populations in each. The negative values, both in gas phase and in solution, indicate that ea is the more stable conformation. A trend in energy values was observed at all the theory levels employed in this study, there being a

• small decrease of ΔEea from gas phase to solution. However, when we compare the ΔEea values for dichloromethane and methanol, the energy variation is too small (Table 3). Likewise, the nature of the halogen also showed a minimal variation in ΔEea values over the series, both in gas phase and in solution

• this theory level to describe the studied systems. The agreement of the energy values in gas phase with those in solution confers reliability to calculations such as natural bond orbitals (NBOs), which are made in the gas phase. With regard to rotamers, gX in ae conformer and a in ea are the least

Conformational signature of Ishikawa´s reagent using NMR information from diastereotopic fluorines

• Laize A. F. Andrade,
• Lucas A. Zeoly,
• Rodrigo A. Cormanich and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2019, 15, 506–512, doi:10.3762/bjoc.15.44

• . The calculations were carried out considering both the gas phase and implicit solvation, according to the polarizable continuum model [33]. The nine possible conformers were selected after a previous screening from 81 structures, which differed by the orientation of the N-ethyl groups. Subsequent

Study on the regioselectivity of the N-ethylation reaction of N-benzyl-4-oxo-1,4-dihydroquinoline-3-carboxamide

• Pedro N. Batalha,
• Luana da S. M. Forezi,
• Maria Clara R. Freitas,
• Nathalia M. de C. Tolentino,
• Ednilsom Orestes,
• José Walkimar de M. Carneiro,
• Fernanda da C. S. Boechat and
• Maria Cecília B. V. de Souza

Beilstein J. Org. Chem. 2019, 15, 388–400, doi:10.3762/bjoc.15.35

• hydrogen CON–H (equilibrium II), only presented negative values of ΔH and ΔG when considering gas phase and, even so, such values were not as significant as those from equilibrium I. Considering water and DMSO, the reaction becomes endergonic, suggesting that the carboxamide N–H site is not acidic enough

• crystallographic table was mounted using the OLEX2 software [36]. Computational details All the calculations were carried out with the Gaussian 09 software package [37] considering the absence (gas phase) and the presence of two implicit solvents (water and DMSO), using the polarized continuum solvation model

Silanediol versus chlorosilanol: hydrolyses and hydrogen-bonding catalyses with fenchole-based silanes

• Falco Fox,
• Jörg M. Neudörfl and
• Bernd Goldfuss

Beilstein J. Org. Chem. 2019, 15, 167–186, doi:10.3762/bjoc.15.17

• trajectories lead to three transition structures each, for the hydrolysis of BIFOXSiCl2 (7) and BIFOXSiCl(OH) (8, Figure 4). Geometry optimizations and frequency computations are performed in gas phase with B3LYP-D3BJ/6-31G(d) at 298 K. For single point energies, M06-2X-D3/6-311++G(d,p) in the solvent THF with

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• addressed issues regarding the various states of ThDP. For example, in some very early work, Jordan used semi-empirical methods to study the electronic structure and conformational space of the cofactor in the gas phase, acknowledging the difficulty of comparing these results to reactions in solution and on

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

• interaction with other electrons, they have different (orbital) energies but the charge is not changed. (Quasi)-atoms in a molecule have, for example, volumes and polarizabilities that differ from those of free atoms in the gas phase. Properties of such quasi-atoms are often calculated by using propagators

Mechanistic studies of an L-proline-catalyzed pyridazine formation involving a Diels–Alder reaction with inverse electron demand

• Anne Schnell,
• J. Alexander Willms,
• S. Nozinovic and
• Marianne Engeser

Beilstein J. Org. Chem. 2019, 15, 30–43, doi:10.3762/bjoc.15.3

• intermediates mimic single steps of the proposed catalytic cycle in the gas phase. Thus, the charge-tagged catalyst proved one more time its superior effectiveness for the detection and study of reactive intermediates at low concentrations. Keywords: charge-tag; electrospray ionization; enamine organocatalysis

• feature of high-resolution ESIMS is that each ionic species in the gas phase produces distinct signals which are unlikely to be overlaid with signals from other species [6]. As a consequence, reaction mixtures typically containing many different species can be analyzed without prior separation of the

• characterized as the oxazolidinone species [I3b]+ by infrared multiphoton dissociation (IRMPD) action spectroscopy in the gas phase [18][59]. The fragmentation already takes place at very low collision energies, so that some amount of fragmentation is expected to occur in the ESI source under normal ESI

A simple and effective preparation of quercetin pentamethyl ether from quercetin

• Jin Tatsuzaki,
• Tomohiko Ohwada,
• Yuko Otani,
• Reiko Inagi and
• Tsutomu Ishikawa

Beilstein J. Org. Chem. 2018, 14, 3112–3121, doi:10.3762/bjoc.14.291

• destabilized as compared with 2A, by 11.7 kcal/mol (in the gas phase) and 7.9 kcal/mol (in DMSO). This is probably due to rotation of the 2-phenyl group with respect to the chromenone plane (by 44°). Furthermore, loss of hydrogen bonding of the OH group at 5 position with the carbonyl group at 4 position due

• to rotation of the OH group at 5 position destabilizes the system dramatically, as in 2C, by 9.7 kcal/mol (in the gas phase) and 5.4 kcal/mol (in DMSO); however, the hydrogen bond is not crucial for the overall planar structure. The structures and energies of all possible isomeric mono-anions derived

• energy is shown in parentheses (gas phase) and in brackets (in DMSO, in kcal/mol). The dihedral angle around the biaryl structure (3–2–1'–2') is also shown. Structures of oxyanions derived from quercetin (2) by deprotonation of a single OH group. Top and side views are shown. The relative energy (in blue

1,8-Bis(dimethylamino)naphthyl-2-ketimines: Inside vs outside protonation

• A. S. Antonov,
• A. F. Pozharskii,
• P. M. Tolstoy,
• A. Filarowski and
• O. V. Khoroshilova

Beilstein J. Org. Chem. 2018, 14, 2940–2948, doi:10.3762/bjoc.14.273

• -arylketimines of 1,8-bis(dimethylamonio)naphthalene with a different number of methoxy groups in an aromatic substituent were investigated in solution by NMR (acetone, DMSO, MeCN), in solid state by X-ray analysis and in the gas phase by DFT calculations. Both mono- and diprotonated species were considered. It

• ], exists exclusively as a Z-isomer (Figure 2b). Moreover, gas phase quantum chemical calculations show that the E-form is preferable for 5a (ΔE = EZ − EE = 1.66 kcal/mol), 6a (ΔE = 1.19 kcal/mol), and 7a (ΔE = 1.90 kcal/mol), while the Z-form dominates for 4a (ΔE = −2.62 kcal/mol, Figure 3). The

• function are additionally stabilised by hydrogen bonds with solvent molecules and thus the amount of b’ forms correlates with the proton accepting ability of the medium [11]. The gas phase calculations show that without any additional interaction with the medium, the forms protonated at the imino group are

The influence of the cationic carbenes on the initiation kinetics of ruthenium-based metathesis catalysts; a DFT study

• Magdalena Jawiczuk,
• Angelika Janaszkiewicz and
• Bartosz Trzaskowski

Beilstein J. Org. Chem. 2018, 14, 2872–2880, doi:10.3762/bjoc.14.266

• . The solvation calculations were performed using the M06-D3/LACVP** level of theory and the gas-phase optimized structures. We also used the same polarizable continuum method to estimate the solvation energies in water (dielectric constant of 80.73 and the effective radius 1.40 Å) and these results are

Calixazulenes: azulene-based calixarene analogues – an overview and recent supramolecular complexation studies

• Paris E. Georghiou,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Hidetaka Nishimura,
• Jaehyun Lee,
• Atsushi Wakamiya and
• Lawrence T. Scott

Beilstein J. Org. Chem. 2018, 14, 2488–2494, doi:10.3762/bjoc.14.225

• (d) route was used (see Table 1 and Supporting Information File 1). For each of the individual components, i.e., the tetra-n-butylammonium salt, OPC4A and the respective corresponding 1:1 supramolecular complexes, unconstrained geometry optimizations were first conducted in the gas phase. Then