Deciphering the mechanism of γ-cyclodextrin’s hydrophobic cavity hydration: an integrated experimental and theoretical study

• Stiliyana Pereva,
• Stefan Dobrev,
• Tsveta Sarafska,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2024, 20, 2635–2643, doi:10.3762/bjoc.20.221

• process. An occupancy of up to 7 hydration water molecules has been found and a comparison between α-CD, β-CD, and γ-CD hydration mechanisms is provided. Results and Discussion Nonhydrated γ-CD As with the other two cyclodextrins (α- and β-), before proceeding to the complexes with water, we considered

Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• peptides or enhancement of the signal-to-noise ratio is necessary for successful analysis (Figure 1). The future challenge to complete the chemical proteomic analysis will include the absolute quantification of those identified NP–peptide conjugates to estimate protein occupancy (Figure 1). Although mass

Catalysing (organo-)catalysis: Trends in the application of machine learning to enantioselective organocatalysis

• Stefan P. Schmid,
• Leon Schlosser,
• Frank Glorius and
• Kjell Jorner

Beilstein J. Org. Chem. 2024, 20, 2280–2304, doi:10.3762/bjoc.20.196

• enantioselective formation of N,S-acetals catalysed by CPAs. To represent the catalysts, the authors developed the average steric occupancy (ASO) descriptors, a representation inspired by CoMFA [104][105][106], which recently also was applied in the selectivity prediction of aldehydes to nitroalkenes [68]. In ASO

• , all catalysts are aligned on a 3D-grid and the descriptor is calculated as the average occupancy of voxels on the 3D grid, where a voxel is occupied if it is within the van der Waals radius of an atom. The steric descriptors were combined with electronic descriptors called Average Electronic Indicator

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

Competing electrophilic substitution and oxidative polymerization of arylamines with selenium dioxide

• Vishnu Selladurai and
• Selvakumar Karuthapandi

Beilstein J. Org. Chem. 2024, 20, 1221–1235, doi:10.3762/bjoc.20.105

• arylamine reactivity. The NBO analysis was carried out using the same basis set, B3LYP/6-31G(d,p). The natural charge (q) of the nitrogen atom, occupancy of the nitrogen lone pair orbital, second-order perturbation energy (E) for intramolecular donor–acceptor interactions, and the donation of electron

• pair occupancy of methyl anthranilate, indicating poor electron density availability of the nitrogen atom for oxidation by SeO2. Therefore, the SeO2-mediated polymerization was slow for methyl anthranilate. The poor electron density of the nitrogen atom was due to the significant deviation of the

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• characterized. Each isolated homolog exhibited similar oligomerization and heme occupancy as Vs NnlA. Reduction of this heme was shown to be required for NnlA activity in each homolog, and each homolog degraded NNG to glyoxylate, NO2− and NH4+ in accordance with observations of Vs NnlA. It was also shown that

• experimental samples resulted from NNG degradation activity by the recombinantly expressed NnlA homologs. We conclude from these results that all five of the selected NnlA homologs exhibit NNG degradation activity. NnlA homologs exhibit similar heme and iron occupancy as Vs NnlA To better compare the NnlA

• nm/A280 nm ratio for each homolog was greater than 1.0, consistent with high occupancy of heme incorporation in the proteins. Iron analyses of each of the homologs were consistent with this conclusion; the heme iron concentrations per protein were consistent with stoichiometric or nearly

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• reaction coordinate which can affect the pulling away and pulling in processes and, therefore, the data described here. Furthermore, we analyzed in detail the most representative H-bonds (with the occupancy higher than 20%) established at different US windows that were the most distinguishable in the

• , 8, 10 in the forward and reverse processes for bFGF and ligand 1, respectively. The protein is in cartoon, the GAG and the protein residues establishing H-bonds with the GAG with the occupancy higher than 20% are in sticks. R101, K106, and K116 are labeled. Pearson correlation coefficients between

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• treated as a two-position model (O6A, O6B), being O6A the major position with 72% of occupancy. Figures were prepared with Mercury [56], Fourier maps, data and tables were prepared with Platon [57], and the Hirshfeld surfaces and fingerprint plots were calculated from the CIF files using Crystal Explorer

CO₂ complexation with cyclodextrins

• Cecilie Høgfeldt Jessen,
• Jesper Bendix,
• Theis Brock Nannestad,
• Heloisa Bordallo,
• Martin Jæger Pedersen,
• Christian Marcus Pedersen and
• Mikael Bols

Beilstein J. Org. Chem. 2023, 19, 1021–1027, doi:10.3762/bjoc.19.78

• two positions for each hydroxymethyl group with one of the positions leading to engagement in hydrogen bonding to water molecules bound at the narrow rim with a combined occupancy of 0.75. Additionally, five fully occupied water molecules are found in the structure one of which is best modeled as

• split over two positions yielding in total 5.75 mol of water per CO2. The hydration is similar to that of native α-CD [13] and that of the krypton inclusion complex which has 5.28 water/Kr [14]. The CO2 molecule refines with an optimal occupancy of 0.84 and linear geometry (178.2(6)o) with C–O bond

• lengths of 1.138(7) Å/1.146(5) Å. Refinement with full occupancy is also consistent with the diffraction data and yields realistic geometries. When the crystals were treated with water, CO2 was released as bubbles as the crystals were dissolving, which was also very clearly observed under a microscope. To

Synthesis, structure, and properties of switchable cross-conjugated 1,4-diaryl-1,3-butadiynes based on 1,8-bis(dimethylamino)naphthalene

• Semyon V. Tsybulin,
• Ekaterina A. Filatova,
• Alexander F. Pozharskii,
• Valery A. Ozeryanskii and
• Anna V. Gulevskaya

Beilstein J. Org. Chem. 2023, 19, 674–686, doi:10.3762/bjoc.19.49

• trifluoromethyl group of one independent molecule is disordered with an occupancy of fluorine atoms of 0.54/0.46, which makes the molecule asymmetric. The second independent molecule has an inversion center. Compared to the free bases 5 discussed above, the protonated form 11с demonstrates almost complete

Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements

• Alexios I. Vicatos,
• Zakiena Hoossen and
• Mino R. Caira

Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184

• , Oxford, U.K.). The data-collection was then performed and the collected intensity datasets were read into the program XPREP [52]. The structures were solved using isomorphous replacement, and the water oxygen atoms were refined anisotropically if they possessed full site-occupancy. No water hydrogen

Heteroleptic metallosupramolecular aggregates/complexation for supramolecular catalysis

• Prodip Howlader and
• Michael Schmittel

Beilstein J. Org. Chem. 2022, 18, 597–630, doi:10.3762/bjoc.18.62

• , introduced by Lehn, uses maximum site occupancy to afford heteroleptic aggregates [35]. While this principle is limited, the charge-separation approach by Stang is of much wider use [36]. Probably, most contributions in the literature, though, are based on using steric constraints in heteroleptic aggregation

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

Mesoionic tetrazolium-5-aminides: Synthesis, molecular and crystal structures, UV–vis spectra, and DFT calculations

• Vladislav A. Budevich,
• Sergei V. Voitekhovich,
• Alexander V. Zuraev,
• Vadim E. Matulis,
• Vitaly E. Matulis,
• Alexander S. Lyakhov,
• Ludmila S. Ivashkevich and
• Oleg A. Ivashkevich

Beilstein J. Org. Chem. 2021, 17, 385–395, doi:10.3762/bjoc.17.34

• for the molecule of 8a, a natural bond orbital (NBO) analysis was applied. In terms of the NBO theory, the "best Lewis structure" is the structure with the lowest non-Lewis occupancy. The NBO search for the molecule of 8a led to the best Lewis structure A (Scheme 3). The high non-Lewis occupancy shows

• slightly higher non-Lewis occupancy in comparison with structure A, and hence they are also good Lewis structures. Thus, the structures A, B, and D make a greater contribution to the overall structure of 8a in comparison with structures C and E having a C5–N5 single bond. As mentioned earlier, compounds 8a

Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• the modified CDs 7a–9a as sensitizing hosts and (Z)-6 as the guest (Figure 5 and Figure 6) [24]. The compounds 8a, 8b, and 8e could yield a higher enantiomeric excess (10.7% ee in 2 min at 25 °C, host occupancy 91%, 23.9% ee in 25 min at 40 °C, host occupancy 98%, and 8.1% ee in 30 min at 25 °C, host

• occupancy 95%) in MeOH/H2O solutions (0.25:0.75, 0.5:0.5, and 0:1, respectively). This may be due to fact that the CD-functionalized sensitizing group could increase the product yield through excited-state supramolecular interactions within the cavity. In addition, the spacer attached to the primary hydroxy

• various main factors, such as the percentage of the host occupancy, the temperature, and the solvent but not on the entropy of the system. In continuation of their previous work, Inoue, Yang, et al. reported an alternative approach so that the chiral slipped 5,8:9',10'-cyclodimers 14 and 15 were

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• , the peptide portion has hydrogen bonds between Arg5–Pro8 (26.69% and 26.58%), Arg5–Asp3 (12.45%), an Arg5–Pro2 interaction is observed with an occupancy of 7.13%, and an intramolecular hydrogen bond between the C3 alcohol and the carbonyl of the N-acetyl moiety of the GalNAc has an occupancy of 6.92

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• glycoprotein profile. Glycomics experiments are required to distinguish stereoisomers and the linkage information in order to obtain a full structural description about a glycan, whereas glycoproteomics are required to establish the glycan variability and occupancy at the glycosylation sites of the protein [43

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• statistical workflows. We used GlypNirO to analyse a published plasma glycoproteome dataset and identified changes in site-specific N- and O-glycosylation occupancy and structure associated with hepatocellular carcinoma as putative biomarkers of disease. Keywords: glycoproteomics; mass spectrometry; N

• ]. This heterogeneity can take the form of variable occupancy, also known as macroheterogeneity – the presence or absence of modification at a particular site in a protein, due to inefficient transfer of the initial glycan structure [5]. In addition, the non-template-driven synthesis of glycan structures

• means that there can be multiple different glycan structures attached at the same site in a pool of mature glycoproteins [6]. This structural heterogeneity is also known as microheterogeneity. This heterogeneity in glycan structure and occupancy can be influenced by many genetic and environmental

Isolation and structure determination of a tetrameric sulfonyl dilithio methandiide in solution based on crystal structure analysis and ⁶Li/¹³C NMR spectroscopic data

• Jürgen Vollhardt,
• Hans Jörg Lindner and
• Hans-Joachim Gais

Beilstein J. Org. Chem. 2020, 16, 2057–2063, doi:10.3762/bjoc.16.172

• symmetric tetramer, (2a)4·(THF)6, containing six THF molecules (Figure 2) [44]. The lithium atom Li4 is not exactly located on the C2 axis. It is resolved by two Li4 in general positions near the C2 axis each with an occupancy of 0.5. Therefore, Figure 2 shows two positions for Li4 and the attached THF

Towards triptycene functionalization and triptycene-linked porphyrin arrays

• Gemma M. Locke,
• Keith J. Flanagan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2020, 16, 763–777, doi:10.3762/bjoc.16.70

• three methyl groups on the TMS moiety was modelled over two position in a 55:45% occupancy. Two of the isopropyl group carbon atoms C24 and C26 were two positions in a 50:50% occupancy (see Supporting Information File 2 for full details). Crystal data for 16: C100H90N8NiZn (M =1527.87 g/mol): triclinic

• ) which were used in all calculations. The final R1 was 0.0695 (I > 2σ(I)) and wR2 was 0.1797 (all data). Both phenyl moieties at C15_1 and C15_2 were modelled over two positions in a 56:44% occupancy using the constrain EADP. The porphyrin ring from C17 to C3 in both residues one and two were modelled

• over two positions in a 50:50% occupancy using the restraint SADI and the constraint EADP. The hexyl groups at the C20_1 and C20_2 positions were modelled over two positions in a 50:50% occupancy using restraints (SADI, ISOR, DFIX) and the constraint EADP. The structure contained a highly disordered

Synthesis of C₇₀-fragment buckybowls bearing alkoxy substituents

• Yumi Yakiyama,
• Shota Hishikawa and
• Hidehiro Sakurai

Beilstein J. Org. Chem. 2020, 16, 681–690, doi:10.3762/bjoc.16.66

• enantiomers, however, they were disordered with 50% site occupancy (Figure 2a). The POAV (π-orbital axis vector) pyramidalization angle φ [27], which is often used for quantifying the curvature of curved π-conjugated materials (Figure 3a) showed 6.5° at C1 as the minimum value, and 7.6° at C3, which is

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

• change is generally due to a change in the oxidation state of a conjugated system. This change in the oxidation state is most often concomitant with conformational and orbital occupancy changes, rather than any σ-bond-forming or breaking processes. The viologens are perhaps the most ubiquitous example of

• likely be the first singlet excited state (S1), T0 and S1 possess equivalent orbital occupancy and differ only in their spin state. Our rationale for using T0 rather than S1 is that ignoring electron-exchange interaction introduces substantially less error than using different computational methods when

• -state calculation, as are the calculations of D0 (the radical anion) and S0. Clearly, as shown in Figure 7, the difference in reduction vs excitation is the occupancy in what was formerly the HOMO of SW. Because S0 is the common precursor to both T0 and D0, analysis of the S0 MOs was used to explain

Synthesis of a [6]rotaxane with singly threaded γ-cyclodextrins as a single stereoisomer

• Jason Yin Hei Man and
• Ho Yu Au-Yeung

Beilstein J. Org. Chem. 2019, 15, 1829–1837, doi:10.3762/bjoc.15.177

• between CB[6] and cyclodextrins via hydrogen bonds in rigid (pseudo)rotaxane systems has been previously reported [43][44][45][46][47][48]. The full occupancy of the axle by five macrocycles and the resulting close proximity of the macrocycles in 6R may hence resulted in similar interactions that

• structural assignment of 5R may not be straightforward unless more detailed structural characterization such as X-ray crystal data is available. Nevertheless, the observation that 5R was obtained as different stereoisomers further strengthens the proposal that it is the full occupancy of the axle by the

Selective detection of DABCO using a supramolecular interconversion as fluorescence reporter

• Indrajit Paul,
• Debabrata Samanta,
• Sudhakar Gaikwad and
• Michael Schmittel

Beilstein J. Org. Chem. 2019, 15, 1371–1378, doi:10.3762/bjoc.15.137

• Information File 1, Figure S21) to satisfy maximum site occupancy. Upon the addition of 2 equiv of rhodium porphyrin 3 [37], DABCO was selectively removed from complex 12 [38] affording the sandwich complex 7 = [(3)2(4)] leaving complex 11 untouched and liberating two equiv of 10 (incomplete self-sorting

Ugi reaction-derived prolyl peptide catalysts grafted on the renewable polymer polyfurfuryl alcohol for applications in heterogeneous enamine catalysis

• Alexander F. de la Torre,
• Gabriel S. Scatena,
• Oscar Valdés,
• Daniel G. Rivera and
• Márcio W. Paixão

Beilstein J. Org. Chem. 2019, 15, 1210–1216, doi:10.3762/bjoc.15.118

• reactor coupled to a HPLC system and the retention times of each substrate within the reactor were measured by UV detection at a wavelength of 210 nm. A retention time of 70 min for β-nitrostyrene at a flow rate of 0.1 mL/min into the reactor was observed. Then, this preferential occupancy of the packing