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

• , modifications can sometimes be required and can be achieved through ab initio calculations or programs like for example VFFDT [71]. Tools for the conformational analysis of glycans in the free state The structure and biological functions of glycans are closely intertwined; the roles they play are influenced not

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

CF₃-substituted carbocations: underexploited intermediates with great potential in modern synthetic chemistry

• Anthony J. Fernandes,
• Armen Panossian,
• Bastien Michelet,
• Agnès Martin-Mingot,
• Frédéric R. Leroux and
• Sébastien Thibaudeau

Beilstein J. Org. Chem. 2021, 17, 343–378, doi:10.3762/bjoc.17.32

• certain extent upon the electron demand in the system to which it is attached”. Thus, despite the strong intrinsic electron-withdrawing character, the trifluoromethyl group was shown to modestly act as a π-electron donor when substituting a carbenium ion. Ab initio calculations were performed to account

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• calculations use very space-extensive atomic orbitals (AOs, basis functions) that extend into the neighborhood of adjacent atoms (however that is defined). This problem manifests itself concretely as basis-set superposition error (BSSE) [21] in ab initio calculations but rears its ugly head in every AO-based

Influence of per-O-sulfation upon the conformational behaviour of common furanosides

• Alexey G. Gerbst,
• Vadim B. Krylov,
• Dmitry A. Argunov,
• Maksim I. Petruk,
• Arsenii S. Solovev,
• Andrey S. Dmitrenok and
• Nikolay E. Nifantiev

Beilstein J. Org. Chem. 2019, 15, 685–694, doi:10.3762/bjoc.15.63

• and β-galactose. Full exploration of the furanoside ring by means of ab initio calculations was performed and coupling constants were calculated for each of the low-energy conformers. The results demonstrated preferred trans-orientation of H4–H5 protons in the non-sulfated molecules which changed to

• of sulfates. Keywords: ab initio calculations; conformational analysis; furanosides; NMR; sulfation; Introduction Changes in the conformations of monosaccharides expectedly accompany their modification with different functional groups. Thus, spatial repulsion of silyl groups results in inversion or

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• oligonucleotides hybridized to RNA showed a similar structure than the natural DNA/RNA duplex. Furthermore, since the structural investigation on the nucleoside level by X-ray crystallography and ab initio calculations pointed to a furanose conformation in the southern region, a RNase H cleavage assay was

Correlation effects and many-body interactions in water clusters

• Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

• methods on an adequate level, e.g., random-phase approximation electron correlation methods. The relative magnitudes of the different interaction energy contributions obtained by accurate ab initio calculations can therefore provide useful insights that can be exploited to develop enhanced force field

Synthesis, effect of substituents on the regiochemistry and equilibrium studies of tetrazolo[1,5-a]pyrimidine/2-azidopyrimidines

• Elisandra Scapin,
• Paulo R. S. Salbego,
• Caroline R. Bender,
• Alexandre R. Meyer,
• Anderson B. Pagliari,
• Tainára Orlando,
• Geórgia C. Zimmer,
• Clarissa P. Frizzo,
• Helio G. Bonacorso,
• Nilo Zanatta and
• Marcos A. P. Martins

Beilstein J. Org. Chem. 2017, 13, 2396–2407, doi:10.3762/bjoc.13.237

• tendency while studying a series of substituents at the 5-position of tetrazolo[1,5-a]pyridines using ab initio calculations. Their findings indicated that electron-withdrawing groups stabilize the azide isomer while electron-donating groups stabilize the tetrazole ring. Additionally, it was observed that

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

• only 5-phenyl- and 5-tert-butyl-6-azauracils displayed very low substrate activity. The role of structural peculiarities and electronic properties in the substrate recognition by E. coli nucleoside phosphorylases is discussed. Keywords: enzymatic glycosylation; PM3 and ab initio calculations

Towards inhibitors of glycosyltransferases: A novel approach to the synthesis of 3-acetamido-3-deoxy-D-psicofuranose derivatives

• Maroš Bella,
• Miroslav Koóš and
• Chun-Hung Lin

Beilstein J. Org. Chem. 2015, 11, 1547–1552, doi:10.3762/bjoc.11.170

• carbohydrate substrates [9][16]. Investigations of the catalytic mechanism of inverting glycosyltransferases [18] and N-acetylglucosaminyltransferase I [19] by employing ab initio calculations resulted in the design of inhibitors based on carbohydrate mimetics that simulate the transition state of the

Single-molecule conductance of a chemically modified, π-extended tetrathiafulvalene and its charge-transfer complex with F₄TCNQ

• Raúl García,
• M. Ángeles Herranz,
• Edmund Leary,
• M. Teresa González,
• Gabino Rubio Bollinger,
• Marius Bürkle,
• Linda A. Zotti,
• Yoshihiro Asai,
• Fabian Pauly,
• Juan Carlos Cuevas,
• Nicolás Agraït and
• Nazario Martín

Beilstein J. Org. Chem. 2015, 11, 1068–1078, doi:10.3762/bjoc.11.120

• experimental resolution, based on the value we measure for the CT complex. Ab initio calculations To gain insight into the conduction mechanism of compound 5, we performed theoretical calculations based on a combination of density functional theory (DFT) and Green’s functions techniques within the framework of

Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy

• Manuel Gensler,
• Christian Eidamshaus,
• Maurice Taszarek,
• Hans-Ulrich Reissig and
• Jürgen P. Rabe

Beilstein J. Org. Chem. 2015, 11, 817–827, doi:10.3762/bjoc.11.91

• aqueous solutions of CuSO4 (Figure 1). As a result, rupture forces of both valencies were similar. Combining DFS with ab-initio calculations we suggested a stepwise bond-rupture including a hydrogen-bound intermediate. Thus in our system the bivalent effect did not increase the mechanical stability, but

• single-molecular level. For example, a Pd2+ pincer complex with two different pyridine ligands shows rupture lengths around 0.2 nm in DMSO [28]. Using ab-initio calculations we could show that a hydrogen-bound intermediate state stabilizes the interaction over a longer distance [27]. In this case, a

• in aqueous solution. The octahedral conformation of 1 with additional water ligands was suggested by ab-initio calculations [27]. For 2a a quasi-octahedral configuration was calculated with only three water ligands per Cu2+ due to steric reasons [27]. Schemes for 2b and 2c are suggested accordingly

Synthesis and characterization of a new photoinduced switchable β-cyclodextrin dimer

• Florian Hamon,
• Claire Blaszkiewicz,
• Marie Buchotte,
• Estelle Banaszak-Léonard,
• Hervé Bricout,
• Sébastien Tilloy,
• Eric Monflier,
• Christine Cézard,
• Laurent Bouteiller,
• Christophe Len and
• Florence Djedaini-Pilard

Beilstein J. Org. Chem. 2014, 10, 2874–2885, doi:10.3762/bjoc.10.304

• high solubility in water. The photoisomerization properties were studied by UV–vis and HPLC and supported by ab initio calculations. The cis/trans ratio of AZO-CDim 1 is 7:93 without irradiation and 37:63 after 120 min of irradiation at 365 nm; the reaction is reversible after irradiation at 254 nm

• times without causing side effects, as shown in Figure 3. Ab initio calculations were also performed but the cis/trans transition was not observed since molecular modeling methods are unable to break bonds. In order to collect data on this phenomenon, the two configurations of the system had to be taken

• into account separately. Thus, ab initio calculations were performed on the two configurations of the azobenzene linker, the so-called 4,4’-bis(N-methylcarboxamide)azobenzene linker, to determine the structures of minimal energy (Figure 4a and Figure 4b). Once optimized, the measured C4–C4’ distances

The chemoenzymatic synthesis of clofarabine and related 2′-deoxyfluoroarabinosyl nucleosides: the electronic and stereochemical factors determining substrate recognition by E. coli nucleoside phosphorylases

• Ilja V. Fateev,
• Konstantin V. Antonov,
• Irina D. Konstantinova,
• Tatyana I. Muravyova,
• Frank Seela,
• Roman S. Esipov,
• Anatoly I. Miroshnikov and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2014, 10, 1657–1669, doi:10.3762/bjoc.10.173

• ab initio calculations in terms of the electronic structure (natural purines vs analogues) and stereochemical features (2FAra-1P vs Ara-1P) of the studied compounds to determine the substrate recognition by E. coli nucleoside phosphorylases. The second approach starts with the cascade one-pot

• ), their analogues (5-aza-7-deazaguanine and 8-aza-7-deazahypoxanthine) and thymine. The results were compared with those of a similar reaction with α-D-arabinofuranose-1-phosphate (13a; Ara-1P). Differences of the reactivity of various substrates were analyzed by ab initio calculations in terms of the

• stereochemistry of both anomers as dilithium salts was analyzed by the ab initio calculations (3-21G; total charge equal to zero; Polak–Ribiere conjugate gradient) employing AMBER force field geometry optimization as a starting approximation. Two structures with the C-3-exo conformation of the pentofuranose ring

Theoretical studies on the intramolecular cyclization of 2,4,6-t-Bu₃C₆H₂P=C: and effects of conjugation between the P=C and aromatic moieties

• Masaaki Yoshifuji and
• Shigekazu Ito

Beilstein J. Org. Chem. 2014, 10, 1032–1036, doi:10.3762/bjoc.10.103

• Abstract The intramolecular C–H insertion of the Mes*-substituted phosphanylidenecarbene [Mes*P=C:] (Mes* = 2,4,6-t-Bu3C6H2) and physicochemical properties of the cyclized product, 6,8-di-tert-butyl-3,4-dihydro-4,4-dimethyl-1-phosphanaphthalene were studied based on ab initio calculations. Whereas the

Advancements in the mechanistic understanding of the copper-catalyzed azide–alkyne cycloaddition

• Regina Berg and
• Bernd F. Straub

Beilstein J. Org. Chem. 2013, 9, 2715–2750, doi:10.3762/bjoc.9.308

Stereoselectively fluorinated N-heterocycles: a brief survey

• Xiang-Guo Hu and
• Luke Hunter

Beilstein J. Org. Chem. 2013, 9, 2696–2708, doi:10.3762/bjoc.9.306

• investigated the reactivity of mono- and difluoroaziridines 2 and 3 (Figure 1) [15][16]. As well as the enhanced reactivity that 2 and 3 both show towards nucleophilic ring opening, there is an additional subtlety regarding the regioselectivity. While ab initio calculations predict that both 2 and 3 should

Establishing the concept of aza-[3 + 3] annulations using enones as a key expansion of this unified strategy in alkaloid synthesis

• Aleksey I. Gerasyuto,
• Zhi-Xiong Ma,
• Grant S. Buchanan and
• Richard P. Hsung

Beilstein J. Org. Chem. 2013, 9, 1170–1178, doi:10.3762/bjoc.9.131

• readily interconvertable 12 and 14. We found this controversy in the isolation and total synthesis papers an interesting one that deserves further investigations. Consequently, we performed ab initio calculations on 12 and 14 to gain insight into their relative thermodynamic stability. Models of the most

Synthesis and evaluation of new guanidine-thiourea organocatalyst for the nitro-Michael reaction: Theoretical studies on mechanism and enantioselectivity

• Tatyana E. Shubina,
• Matthias Freund,
• Sebastian Schenker,
• Timothy Clark and
• Svetlana B. Tsogoeva

Beilstein J. Org. Chem. 2012, 8, 1485–1498, doi:10.3762/bjoc.8.168

• . Extensive DFT calculations, including solvent effects and dispersion corrections, as well as ab initio calculations provide a plausible description of the reaction mechanism. Keywords: bifunctional organocatalyst; DFT calculations; guanidine-thiourea; Michael addition; organocatalysis; transition states

NMR studies of anion-induced conformational changes in diindolylureas and diindolylthioureas

• Damjan Makuc,
• Jennifer R. Hiscock,
• Mark E. Light,
• Philip A. Gale and
• Janez Plavec

Beilstein J. Org. Chem. 2011, 7, 1205–1214, doi:10.3762/bjoc.7.140

• along the C7–N7α bonds and the syn–syn conformer was preferred for anion–receptor complexes. The conformational changes upon anion binding are in good agreement with energetic preferences established by ab initio calculations. Keywords: anion recognition; conformation analysis; host–guest systems; NMR

• -anions, were studied by NMR spectroscopy and supported by energetic preferences established from ab initio calculations. Results and Discussion Synthesis Compounds 1–3 were synthesized following a previously reported methodology [36][37][38][39]. Compound 4 was prepared by reaction of 7-amino-N-phenyl-1H

• . Furthermore, binding of anions caused conformational changes along the C7–N7α bonds, and the syn–syn conformer was predominant in the anion–receptor complexes according to both NOE enhancements and ab initio calculations in solution. The freely optimized syn–syn conformer of the 1·AcO− complex retained a

Molecular rearrangements of superelectrophiles

• Douglas A. Klumpp

Beilstein J. Org. Chem. 2011, 7, 346–363, doi:10.3762/bjoc.7.45

• initio calculations were performed and revealed that the isomerization lowers the energy of the dication by about 26 kcal/mol. Moreover, isomerization increased the distance between the carbocation sites from 2.80 Å in 87 to 3.58 Å in 88. Olah and coworkers have described [30] an attempt to generate the

• (87) which was found to be stable at −105 °C. However, upon warming to −60 °C, the 3,7-dimethylbicyclo[3.3.1]nona-3,7-diyl dication (88) was formed. This isomerization is thought to occur through a series of hydride shifts, Wagner–Meerwein shifts, ring contractions, and methyl shifts (Scheme 18). Ab

Accuracy in determining interproton distances using Nuclear Overhauser Effect data from a flexible molecule

• Catharine R. Jones,
• Craig P. Butts and
• Jeremy N. Harvey

Beilstein J. Org. Chem. 2011, 7, 145–150, doi:10.3762/bjoc.7.20

• 0.03, 0.00, 0.20 and 0.14 kJ/mol, very close to the coupled-cluster values, suggesting that these quantities are reliable to ± 0.5 kJ/mol and perhaps better. Including the corrections for zero-point energy, thermal and entropic corrections, and solvation, these correlated ab initio calculations lead to

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32

• from Kebarle et al. who showed that binding of potassium ions to benzene and water in the gas phase is of similar energy [9][12]. Ammonium–π-interactions were experimentally investigated in detail as well as by ab initio calculations and are mainly based on electrostatic interactions. The binding

An enantiomerically pure siderophore type ligand for the diastereoselective 1 : 1 complexation of lanthanide(III) ions

• Markus Albrecht,
• Olga Osetska,
• Thomas Abel,
• Gebhard Haberhauer and
• Eva Ziegler

Beilstein J. Org. Chem. 2009, 5, No. 78, doi:10.3762/bjoc.5.78

• calculations In order to determine the configuration at the metal centres of the 1a·Ln (R = Et) complexes ab initio calculations were performed for the stereoisomers of complex 1b·La (R = Me) [37]. The difference between 1a and 1b is only the substitution of the ethyl groups in 1a by methyl groups in 1b. This

• ) ions, while smaller cations lead to an unspecific complex formation (probably oligomerization or polymerization). On the basis of ab initio calculations and CD spectroscopy we could show that the formed complex (1a)La exhibits exclusively Λ helicity. We were able to isolate the corresponding lanthanum

• following the absorption at 279 nm. Analysis of the titration data reveals high binding constants for lanthanum(III) (Ka = 8.3 × 105 M−1) as well as europium(III) (Ka = 7.8 × 105 M−1) for the reaction of deprotonated ligand 1a3− with the Ln3+ ion to form [(1a)Ln] in methanol at room temperature. Ab initio

The role of an aromatic group in remote chiral induction during conjugate addition of α-sulfonylallylic carbanions to ethyl crotonate

• Shlomo Levinger,
• Ranjeet Nair and
• Alfred Hassner

Beilstein J. Org. Chem. 2008, 4, No. 32, doi:10.3762/bjoc.4.32

• geometry of the aromatic ring during chelation with the lithiated species is as yet unknown, it evidently plays an important role in determining the approach of the carbanion to the conjugate acceptor and thus the stereoselectivity of the conjugate addition. Preliminary ab initio calculations [17] for the

• yields are obtained with aromatic rings possessing higher electron density (4-methoxyphenyl, 2-thienyl) while the employment of the 9-anthryl nucleus results in complete transmission of chirality to the newly formed stereogenic centers. Ab initio calculations assign an important role to Li+–aromatic π