Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• ). The y- and Y-fragment ions of (glyco)peptides with Cys oxidation showed a characteristic neutral loss of 107.0041 Da (C2H5O2NS), as reported for singly oxidized carbamidomethylated Cys through an elimination reaction in the gas phase (Figures S13 and S16–S18, Supporting Information File 2) [27

UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation

• Tim Holtum,
• Vikas Kumar,
• Daniel Sebena,
• Jens Voskuhl and
• Sebastian Schlücker

Beilstein J. Org. Chem. 2020, 16, 2911–2919, doi:10.3762/bjoc.16.240

• –vis spectrometer (Perkin-Elmer Lambda 650) where liquid samples were kept in 2 mm fused silica cuvettes (Hellma). DFT calculations were performed with the Gaussian 16 program package [25]. The molecule was calculated in the gas phase in its protonated form with one positive net charge. The resulting

A heterobimetallic tetrahedron from a linear platinum(II)-bis(acetylide) metalloligand

• Matthias Hardy,
• Marianne Engeser and
• Arne Lützen

Beilstein J. Org. Chem. 2020, 16, 2701–2708, doi:10.3762/bjoc.16.220

• succeed to obtain single crystals of our metallosupramolecular assemblies that were suitable for single-crystal X-ray diffraction experiments. Therefore, we generated energy-minimized gas phase structures of 4, employing a force-field approach using the GFN2-xTB approach recently established to model

• equivalent positions of P atoms. Detailed excerpt of the 31P NMR spectrum of 4 (202 MHz, acetonitrile-d3, 298 K). 1H NMR and DOSY spectrum of heterobimetallic assembly 4 (500 MHz, acetonitilre-d3, 298 K). GFN2-xTB minimized gas phase models of the cationic units of all possible diastereomers of 4. Color code

Activation of pentafluoropropane isomers at a nanoscopic aluminum chlorofluoride: hydrodefluorination versus dehydrofluorination

• Maëva-Charlotte Kervarec,
• Thomas Braun,
• Mike Ahrens and
• Erhard Kemnitz

Beilstein J. Org. Chem. 2020, 16, 2623–2635, doi:10.3762/bjoc.16.213

• pentafluoropropanes (HFC-245 isomers) using chromia-based catalysts, or metal chloride/fluoride (AlF3, MgF2)-supported catalysts at elevated temperatures (350 °C) [11][14][15][17][18]. The group of Lu recently reported the gas-phase transformation of 1,1,1,3,3-pentafluoropropane (HFC-245eb) into 1,3,3,3

Dawn of a new era in industrial photochemistry: the scale-up of micro- and mesostructured photoreactors

• Emine Kayahan,
• Mathias Jacobs,
• Leen Braeken,
• Leen C.J. Thomassen,
• Simon Kuhn,
• Tom van Gerven and
• M. Enis Leblebici

Beilstein J. Org. Chem. 2020, 16, 2484–2504, doi:10.3762/bjoc.16.202

• using a spray system. The catalyst reactivity in the NETmix reactor was 70 times higher than for the monolithic photoreactor [62]. When the reactions involve a gas phase, a Taylor flow, also known as a slug flow, is commonly utilized in microstructured reactors. Su et al. studied the intrinsic kinetics

• ), and C is the concentration of the attenuating species (mol⋅m−3). Photoreactions are often heterogeneous, with solid particles in the reaction medium. In addition, some photoreactions contain a gas phase, which further complicates light field models. For heterogeneous photoreactions, the liquid

Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction

• Daniela Rodrigues Silva,
• Joyce K. Daré and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200

• geometry is quite similar among the three conformers. Only for Iga, where the gauche fluorine atom points to the opposite direction of the amine group, the triazole ring was farther away from the 1,2-disubstituted ethane moiety. Note that the gas-phase relative conformational energy ΔE increases, i.e

• the next section) and is naturally more stabilized by polar solvents. Therefore, further analysis will consider the gas phase, since in this way we are accounting for the intrinsic intramolecular interactions without the influence of solvent as an external factor. To better understand the relative

• known in the literature [23] and, accordingly, it differs from the energy minimum conformations computed in this work. However, a conformational search in the gas phase, as performed herein, is necessary to fully understand the intramolecular interactions and to establish the correlation between μ and

A proposed sustainability index for synthesis plans based on input provenance and output fate: application to academic and industrial synthesis plans for vanillin as a case study

• John Andraos

Beilstein J. Org. Chem. 2020, 16, 2346–2362, doi:10.3762/bjoc.16.196

• environmental and safety-hazard impacts of reactants and reagents become important since reaction solvent usage dramatically decreases. Reactions involving first generation feedstocks are typically gas-phase reactions run without any reaction solvent. However, as the synthesis chain extends to more complex

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• were calculated by Density Functional Theory at the B3LYP/6-31+G(d,p) level of theory in the gas phase [64][65]. This method was also applied to study the nonlinear optic (NLO) properties of the dyes in their ground states. The theoretical absorption spectra in different solvents were calculated using

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

• Benjamin Jeffries,
• Zhong Wang,
• Robert I. Troup,
• Anaïs Goupille,
• Jean-Yves Le Questel,
• Charlene Fallan,
• James S. Scott,
• Elisabetta Chiarparin,
• Jérôme Graton and
• Bruno Linclau

Beilstein J. Org. Chem. 2020, 16, 2141–2150, doi:10.3762/bjoc.16.182

• and geometry optimizations. Ho and co-worker showed that the use of the lowest-energy conformations as calculated in the respective solvents gave more accurate lipophilicities than the use of the lowest energy conformations in the gas phase [36]. Somewhat surprisingly, implicit solvent models proved

One-pot synthesis of oxazolidinones and five-membered cyclic carbonates from epoxides and chlorosulfonyl isocyanate: theoretical evidence for an asynchronous concerted pathway

• Esra Demir,
• Ozlem Sari,
• Yasin Çetinkaya,
• Ufuk Atmaca,
• Safiye Sağ Erdem and
• Murat Çelik

Beilstein J. Org. Chem. 2020, 16, 1805–1819, doi:10.3762/bjoc.16.148

• . The further investigation of the potential energy surfaces associated with two possible channels leading to oxazolidinones and five-membered cyclic carbonates disclosed that the cycloaddition reaction proceeds via an asynchronous concerted mechanism in gas phase and in DCM. Keywords: chlorosulfonyl

• N4 onto the less sterically encumbered C1 atom of the epoxide 7f forming intermediate 11. Optimized geometries of transition structures are depicted in Figure 1. Our calculated results for the reaction indicate 17.4 kcal/mol (gas phase) and 26.7 kcal/mol (in DCM) preference for the TS1 over the TS1

• energy profiles connecting each transition state to the two associated minima. The effect of the solvent environment on the reaction pathways has been taken into account by single-point energy calculations on the gas-phase stationary points using a polarizable continuum model (PCM) [64] at M06-2X/6-31+G

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

Activated carbon as catalyst support: precursors, preparation, modification and characterization

• Melanie Iwanow,
• Tobias Gärtner,
• Volker Sieber and
• Burkhard König

Beilstein J. Org. Chem. 2020, 16, 1188–1202, doi:10.3762/bjoc.16.104

• . Different methods can be used for the measurements. The volumetric method with determination of the gas removed from the gas phase and the gravimetric method, where the uptake of the gas by the adsorbent is determined by the increase in mass. In addition, static or dynamic techniques are available for the

• -containing surface groups on the activated carbon materials. They could observe that gas phase oxidation led to a higher amount of mainly hydroxy and carbonyl groups, whereas liquid phase treatment with nitric acid results in an increase of carboxylic acid groups [110]. Lillo-Ródenas et al. used TPD for the

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• structures 1a and 1b The conformational search on structure 1a began by applying 100,000 steps of the Monte-Carlo Multiple Minimum (MCMM) method with PRCG energy minimization using the OPLS3e force field (gas phase) to obtain 20 conformational isomers within 5.0 kcal/mol from the minimum energy conformer

Synthesis of 4-(2-fluorophenyl)-7-methoxycoumarin: experimental and computational evidence for intramolecular and intermolecular C–F···H–C bonds

• Vuyisa Mzozoyana,
• Fanie R. van Heerden and
• Craig Grimmer

Beilstein J. Org. Chem. 2020, 16, 190–199, doi:10.3762/bjoc.16.22

• H3···19F coupling (Figure 3). Evidence of a HOESY interaction between H5···19F and H3···19F indicates that neither the H3···19F nor the H5···19F interaction limits the C4–C1′ bond rotation. The geometry of coumarin 6 (single molecule, gas phase) was optimized using the B3LYP functional and the 6-311G

• angle Φ C2’–C1’–C4–C4a (°). Short contacts within the single-crystal X-ray structure of coumarin 6. Synthesis of 4-(2-fluorophenyl)-7-methoxycoumarin (6). Experimental and theoretical (gas phase) 1H and 13C chemical shift (δ) for atoms within six bonds from fluorine for coumarin 6 and RSMD values

The reaction of arylmethyl isocyanides and arylmethylamines with xanthate esters: a facile and unexpected synthesis of carbamothioates

• Narasimhamurthy Rajeev,
• Toreshettahally R. Swaroop,
• Ahmad I. Alrawashdeh,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Seegehalli M. Anil,
• Kuppalli R. Kiran,
• Chandra,
• Paris E. Georghiou,
• Kanchugarakoppal S. Rangappa and
• Maralinganadoddi P. Sadashiva

Beilstein J. Org. Chem. 2020, 16, 159–167, doi:10.3762/bjoc.16.18

• with Gaussian 09 [36]. The HF/6-31G(d) level of theory in the gas phase was only used to locate the transition state geometries. An intrinsic reaction coordinate (IRC) analysis was conducted for each transition state studied in this work to confirm that the transition states were associated with the

Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• active site cluster model. The results revealed the significant effect of the active site residues on the relative electronic energy of the intermediates and transition state structures with respect to gas phase data. A detailed understanding of the role of the enzyme environment on the CotB2 reaction

• ]. Theoretical quantum mechanical (QM) investigations on the chemistry of terpenes in the gas phase have provided a detailed understanding of the carbocation mechanisms underlying terpene synthase function [25][26][27]. Further, we have used multiscale modeling tools to study the effects of the enzyme

• cyclopropylcarbinyl cation, as shown by isotope labeling [41]. QM calculations support this unusual 1,3-alkyl shift that interconverts H and I [38][39]. Finally, the cyclopropyl ring opens by virtue of a nucleophilic water attack, and cyclooctat-9-en-7-ol is formed. Although gas phase calculations shed light on the

Two new aromatic polyketides from a sponge-derived Fusarium

• Mada Triandala Sibero,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Ocky K. Karna Radjasa,
• Agus Sabdono,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2941–2947, doi:10.3762/bjoc.15.289

• Supporting Information File 2. Computational search and NMR calculations of structures a and b The conformational search on structure a began by applying 100,000 steps of the Monte-Carlo Multiple Minimum (MCMM) method with PRCG energy minimization using the OPLS3e force field (gas phase) to obtain 42

Synthesis and optoelectronic properties of benzoquinone-based donor–acceptor compounds

• Daniel R. Sutherland,
• Nidhi Sharma,
• Georgina M. Rosair,
• Ifor D. W. Samuel,
• Ai-Lan Lee and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2019, 15, 2914–2921, doi:10.3762/bjoc.15.285

• carbazoles with respect to the bridging benzene of ca. 44° in both 3 and 4 (Figure 2). Theoretical properties Density functional theory (DFT) calculations were performed in the gas phase to assess the electronic structures of 2–5 (see Supporting Information File 1 for details). The S1 and T1 excited states

A chiral self-sorting photoresponsive coordination cage based on overcrowded alkenes

• Constantin Stuckhardt,
• Diederik Roke,
• Wojciech Danowski,
• Edwin Otten,
• Sander J. Wezenberg and
• Ben L. Feringa

Beilstein J. Org. Chem. 2019, 15, 2767–2773, doi:10.3762/bjoc.15.268

• insight in the self-sorting behavior of cages Pd2(stable Z-1)4 and Pd2(stable E-1)4. The structures of all possible cage diastereomers were optimized using B3LYP/6-31G(d) for C,H,N and LANL2DZ with ECP for Pd in the gas phase without counter ions. The optimized structure of Pd2(stable E-1)4 is in good

A combinatorial approach to improving the performance of azoarene photoswitches

• Joaquin Calbo,
• Aditya R. Thawani,
• Rosina S. L. Gibson,
• Andrew J. P. White and
• Matthew J. Fuchter

Beilstein J. Org. Chem. 2019, 15, 2753–2764, doi:10.3762/bjoc.15.266

• were optimized by using the Berny algorithm at the same level of theory [40]. Theoretical calculations were carried out in the gas phase. Theoretical kinetic studies were carried out at the PBE0-D3/6-31G** level of theory by considering all possible transition states and minimum-energy conformers for

• ground state geometries of both Z- and E-isomers were computed under the time-dependent density functional theory (TDDFT) approach [41][42]. The 20 lowest-lying singlet excited states were calculated in all conformers at the TD-PBE0/6-31G** level of theory in the gas phase. Solvent effects in

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