Synthesis and conformational analysis of pyran inter-halide analogues of ᴅ-talose

• Olivier Lessard,
• Mathilde Grosset-Magagne,
• Paul A. Johnson and
• Denis Giguère

Beilstein J. Org. Chem. 2024, 20, 2442–2454, doi:10.3762/bjoc.20.208

• -halides motivated us to use density functional theory (DFT) calculations to understand the preference of talose analogues to adopt 4C1-like conformations. DFT computations were performed using Gaussian 16 revision B.01 [67] with the CAM-B3LYP [68][69][70] functional and the Def2TZVP basis set [71], which

Allostreptopyrroles A–E, β-alkylpyrrole derivatives from an actinomycete Allostreptomyces sp. RD068384

• Marwa Elsbaey,
• Naoya Oku,
• Mohamed S. A. Abdel-Mottaleb and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2024, 20, 1981–1987, doi:10.3762/bjoc.20.174

• to their populations [25]. The calculated specific rotations −11.4 and +16.1 were obtained for R-configured 2 and 3 from the DFT computations (see DFT methodology section), respectively, which were in good agreement with the experimentally obtained values, −6.1 for 2 and +15 for 3. Thus, R

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

• Laura Abella,
• Gerard Novell-Leruth,
• Josep M. Ricart,
• Josep M. Poblet and
• Antonio Rodríguez-Fortea

Beilstein J. Org. Chem. 2024, 20, 92–100, doi:10.3762/bjoc.20.10

Organic thermally activated delayed fluorescence material with strained benzoguanidine donor

• Alexander C. Brannan,
• Elvie F. P. Beaumont,
• Nguyen Le Phuoc,
• George F. S. Whitehead,
• Mikko Linnolahti and
• Alexander S. Romanov

Beilstein J. Org. Chem. 2023, 19, 1289–1298, doi:10.3762/bjoc.19.95

• ). (TD)-DFT computations were made possible by use of the Finnish Grid and Cloud Infrastructure resources (urn:nbn:fi:research-infras-2016072533). A.S.R. acknowledges the support from the EPSRC (grant code EP/K039547/1).

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• relative trends among similar systems, which is the focus here. This was followed by the TD-DFT computations at the same level of theory considering 32 lowest singlet electronic excitations. The choice of this setup was prompted by its recent success in modeling UV–vis spectra of organic and inorganic

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

• cooperative effect resulting from an additional η2-binding of the second copper(I) at the acetylene unit at which the second click reaction would take place. In case of distance mismatch, it is the formation of this copper–alkyne η2-complex that compensates for the build-up of strain as demonstrated by DFT

• computations [110]. Once the second click reaction has occurred, the rotaxane is liberated under release of strain in the catalyst if there was a distance mismatch. For cases with a close match of distances, product inhibition reduced the yield. Due to the high relevance of the CuAAC approach [111] for the

Efficient and regioselective synthesis of dihydroxy-substituted 2-aminocyclooctane-1-carboxylic acid and its bicyclic derivatives

• İlknur Polat,
• Selçuk Eşsiz,
• Uğur Bozkaya and
• Emine Salamci

Beilstein J. Org. Chem. 2022, 18, 77–85, doi:10.3762/bjoc.18.7

• -functional theory (DFT) computations were used to explain the reaction mechanism for the ring opening of the epoxide and the formation of five-membered lactones. The stereochemistry of the synthesized compounds was determined by 1D and 2D NMR spectroscopy. The configuration of methyl 6-hydroxy-9-oxo-8

• , which is a typical transesterification reaction. To explain the formation of lactone 10, we performed a series of DFT computations using the Gaussian 16 software [29]. For this purpose, we performed geometry optimizations using the B3LYP functional [30][31][32][33]. Vibrational frequencies were computed

• cyclic β-amino acid derivative, was achieved by oxirane ring opening in epoxide 7 with HCl(g)–MeOH, NaHSO4, or NH4Cl–DMF. The regioselectivity of oxirane ring-opening in 7 was attributed to the conformational effects. The mechanism for the formation of compound 10 was elucidated with DFT computations

Ring-closing metathesis of prochiral oxaenediynes to racemic 4-alkenyl-2-alkynyl-3,6-dihydro-2H-pyrans

• Viola Kolaříková,
• Markéta Rybáčková,
• Martin Svoboda and
• Jaroslav Kvíčala

Beilstein J. Org. Chem. 2020, 16, 2757–2768, doi:10.3762/bjoc.16.226

• -2,7-diyne reacted chemo- and stereoselectively in a Diels–Alder reaction with N-phenylmaleimide affording the tricyclic products as a mixture of two separable diastereoisomers, the configuration of which was estimated by DFT computations. The reported enediyne metathesis paves the way to the

• structures of which were estimated by DFT computations. The scope and limitations of the oxaenediyne ring-closing enyne metathesis disclosed here gave us essential information for continuing studies on the enantioselective variant of this reaction. Experimental General comments Temperature data were

Acid-catalyzed rearrangements in arenes: interconversions in the quaterphenyl series

• Sarah L. Skraba-Joiner,
• Carter J. Holt and
• Richard P. Johnson

Beilstein J. Org. Chem. 2019, 15, 2655–2663, doi:10.3762/bjoc.15.258

• . DFT computations with inclusion of implicit solvation support a complex network of phenyl and biphenyl shifts, with barriers to rearrangement in the range of 10–21 kcal/mol. Consistent with experiments, the lowest energy arenium ion located on this surface is due to protonation of m,p'-quaterphenyl

• assessed by high field NMR analysis. Under these reaction conditions, m,p'-quaterphenyl (13) is the equilibrium product. This isomer is unchanged by the reaction conditions and all other quaterphenyl isomers rearrange to m,p' as the dominant or sole product. DFT computations with inclusion of implicit

• facile acid-catalyzed interconversion, as well as the fact that m-terphenyl (2) is favored at equilibrium (observed ratio 1:2:3 is <1:69:31) and used theory to explain this product selectivity [25]. This preference is consistent with formation of the most stable arenium ion intermediate, as shown by DFT

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

• Information Supporting Information File 244: Additional data from DFT computations at the M062X/6-311++G(d,p)//M062X/6-31G(d,p) level of theory. Acknowledgements This work was supported by the Materials Networking Project H2020-TWINN-2015. S.P. acknowledges the financial support received from the program

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

• were established through 1H NMR (Figure 4) and UV–vis spectra (Figure 3b). DFT (B3LYP/6-31G(d)) calculations on rectangle 5 and sandwich complex 6 allow the modeling of the supramolecular architecture and provide some structural insights. The DFT computations demonstrate that the sandwich complex is

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

• ., H2O/THF reflux, 19 h (Scheme 3, Figure 2). DFT computations reveal two different hydrolysis mechanisms and explain the unusual low reactivity of BIFOXSiCl2 (7) and BIFOXSiCl(OH) (8, Table 3) with sterically demanding endo fenchone groups. For BIFOXSiCl(OH) (8) two isomers (8eq vs 8ax) are found

London dispersion as important factor for the stabilization of (Z)-azobenzenes in the presence of hydrogen bonding

• Andreas H. Heindl,
• Raffael C. Wende and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2018, 14, 1238–1243, doi:10.3762/bjoc.14.106

• -butyl methyl ether the hydrogen bonds dominate, the variation in stabilization of the different substituted azobenzenes in dimethyl sulfoxide can be rationalized by London dispersion interactions. These findings were supported by conformational analysis and DFT computations and reveal low-energy London

• density functional theory (DFT) computations, attractive LD forces were identified as the origin of this stability trend. Based on this study, LD interactions represent a valuable tool for the design of novel azobenzene photoswitches [24]. Herein we provide further evidence for the importance of LD as

• parentheses, see Figure S4 in Supporting Information File 1 for graphical representations of the compared conformers). Supporting Information Supporting Information File 338: NMR spectra of azobenzene 5, UV–vis data and detailed procedures, details for conformational analysis and DFT computations

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• -energy nπ* states are not present. This explanation is further substantiated using time-dependent density functional (TD-DFT) computations for pyrene–adenine conjugates 3 and 5. The molecular structures of compounds 3 and 5 were optimized at the B3LYP/6-311G(d,p) theory level. For the ground state

• geometry, ten excitations, five without spin flip and five to triplet excited states, respectively, were computed. The results for luminescence relevant transitions are summarized in Table 2. The TD-DFT computations predict, in particular, that the fluorescent state S1 of hydroxy compound 5 with the

Why base-catalyzed isomerization of N-propargyl amides yields mostly allenamides rather than ynamides

• Armando Navarro-Vázquez

Beilstein J. Org. Chem. 2015, 11, 1441–1446, doi:10.3762/bjoc.11.156

• support of ab initio and DFT computations, this work shows that observed results can be explained by assuming an exchange equilibrium between energetically close N-propargyl, allenyl and N-alkynyl forms and that the reaction outcome correlates to a particular equilibrium mixture. Due to the very small

• −4.3 kcal/mol (Table 1). As compared to CBS-QB3, all the DFT computations overestimated the exothermicity of this reaction by more than 1.5 kcal/mol save for the M06HF and ωB97 functionals with values of −5.0 and −5.3 kcal/mol, respectively. Particularly inadequate was the performance of M06L and

• is again reverted and the N-alkynyl compound 14c is more stable than the allenamide 14b by 1.2 kcal/mol. Note the more exothermic N-propargyl → N-allenyl gap for 14 caused by the higher electronic donation capability of the nitrogen atom. Hence, the DFT computations are in agreement with the observed

An unusually stable chlorophosphite: What makes BIFOP–Cl so robust against hydrolysis?

• Roberto Blanco Trillo,
• Jörg M. Neudörfl and
• Bernd Goldfuss

Beilstein J. Org. Chem. 2015, 11, 313–322, doi:10.3762/bjoc.11.36

• . Formation of the cyclofenchene derivative 7 is explained by rearrangement via a 2-fenchyl carbocation. The DFT computations of the hydrolysis revealed a higher degree of steric congestion in BIFOP–Cl (1) caused by the fenchane units, relative to the less-shielded and hence much more reactive O–BIFOP–Cl (3

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

• unit. The structure of the intricate heterocycle 2a was confirmed by single-crystal X-ray analysis and its mechanism of formation supported by DFT computations. Keywords: carbodiimide; cyclization; dithiourea; DFT; 1,2,4-thiadiazoles; Introduction Heterocyclic rings are key components in many

• is almost impossible, we had a look at the computed energetics of the intramolecular cyclization steps to check whether our suggestion would at least comply with a reaction cascade proceeding at room temperature. To obtain the energy for the first cyclization step (Scheme 2), we performed DFT

• 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

Rapid pseudo five-component synthesis of intensively blue luminescent 2,5-di(hetero)arylfurans via a Sonogashira–Glaser cyclization sequence

• Fabian Klukas,
• Alexander Grunwald,
• Franziska Menschel and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2014, 10, 672–679, doi:10.3762/bjoc.10.60

• interesting due to their bright blue luminescence with remarkably high quantum yields. The electronic structure of the title compounds is additionally studied with DFT computations. Keywords: C–C coupling; copper; DFT; fluorescence; furans; mircowave-assisted synthesis; multicomponent reactions; palladium

One-pot three-component synthesis and photophysical characteristics of novel triene merocyanines

• Christian Muschelknautz,
• Robin Visse,
• Jan Nordmann and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2014, 10, 599–612, doi:10.3762/bjoc.10.51

• -en-1-ylideneindolones are essentially nonemissive in films or in the solid state. TD-DFT computations rationalize the charge-transfer nature of the characteristic broad long-wavelength absorptions bands. Keywords: alkynes; cross coupling; enamines; fluorescence; heterocycles; multicomponent

• -2-enylidene indolones 8. Three-component synthesis of of 4-(1,3,3-trimethylindolin-2-ylidene)but-2-en-1-ylideneindolones 10. Selected computed electrostatic charges of zwitterion intermediates 16 (DFT computations with B3LYP functional and the 6-31G* basis set). Selected absorption and emission data

New hydrogen-bonding organocatalysts: Chiral cyclophosphazanes and phosphorus amides as catalysts for asymmetric Michael additions

• Helge Klare,
• Jörg M. Neudörfl and
• Bernd Goldfuss

Beilstein J. Org. Chem. 2014, 10, 224–236, doi:10.3762/bjoc.10.18

• . DFT computations reveal high hydrogen-bonding strengths of cyclodiphosphazane PV-amides compared to urea-based catalysts. Experimental results and computations on the enantiodetermining step with cis-cyclodiphosphazane 14a suggest a strong bidentate H-bond activation of the nitrostyrene substrate by

• the catalyst. Keywords: DFT computations; hydrogen bonding; Michael addition; organocatalysis; phosphazanes; Introduction Organocatalysis has gained great impact in promoting highly enantioselective [1][2][3][4] and eco-friendly [5] reactions. Within the field of organocatalysis hydrogen-bonding (HB

Tandem dinucleophilic cyclization of cyclohexane-1,3-diones with pyridinium salts

• Mostafa Kiamehr,
• Firouz Matloubi Moghaddam,
• Satenik Mkrtchyan,
• Volodymyr Semeniuchenko,
• Linda Supe,
• Alexander Villinger,
• Peter Langer and
• Viktor O. Iaroshenko

Beilstein J. Org. Chem. 2013, 9, 1119–1126, doi:10.3762/bjoc.9.124

• proceeds by regioselective attack of the central carbon atom of the 1,3-dicarbonyl unit to 4-position of the pyridinium salt and subsequent cyclization by base-assisted proton migration and nucleophilic addition of the oxygen atom to the 2-position, as was elucidated by DFT computations. Fairly extensive

• corroborated by X-ray [51] diffraction analysis (Supporting Information File 1, Figures S2, S3, S4) Reaction mechanism In order to shed light on the reaction mechanism we used DFT computations at the B3LYP/6-31G(d,p) [52][53][54] level, as implemented in the Gaussian 09 program [55], and acetonitrile was

Interplay of ortho- with spiro-cyclisation during iminyl radical closures onto arenes and heteroarenes

• Roy T. McBurney and
• John C. Walton

Beilstein J. Org. Chem. 2013, 9, 1083–1092, doi:10.3762/bjoc.9.120

• DFT computations, which gave insights into factors influencing the two cyclisation modes. Keywords: cyclisation; EPR spectroscopy; free radicals; heterocycles; oxime carbonates; Introduction Radical cyclisations onto aromatic acceptors take place readily, even though disruption of the 6π-electron

• arm is much more flexible. This paper reports our study of the chemistry of these compounds by means of product analyses, solution EPR spectroscopy and DFT computations. We encountered an intriguing interplay between spiro-cyclisation and ortho-cyclisation of the iminyl intermediates and factors

• . The ortho-product then accumulates because of thermodynamic control. Alternatively, spiro-radical 12a might rearrange via a tetracyclic aziridinyl intermediate (or transition state) at higher temperatures. DFT computations (see below) undermined this possibility however. EPR experiments with the

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

• -PCM), {MP2/6–31G(d)//B3PW91/6–31G(d)} and [DFT-D]. Supporting Information The Supporting Information File features data from DFT computations (computed absolute energies (Hartree) and zero-point vibrational energies (ZPVE, kcal·mol−1) at different levels of theory) as well as the respective GAUSSIAN

EPR and pulsed ENDOR study of intermediates from reactions of aromatic azides with group 13 metal trichlorides

• Giorgio Bencivenni,
• Riccardo Cesari,
• Daniele Nanni,
• Hassane El Mkami and
• John C. Walton

Beilstein J. Org. Chem. 2010, 6, 713–725, doi:10.3762/bjoc.6.84

• its electron-withdrawing substituent, did not react. In general the aromatic azides appeared to react most rapidly with AlCl3 but this reagent tended to generate much polymer. InCl3 was the least reactive group 13 halide. DFT computations of the radical cations provided corroborating evidence and

• explain the absence of the 19F high-frequency line in our spectrum. DFT computations of radical cation properties Quantum chemical calculations were carried out with the Gaussian 03 programme package [35][36]. Density functional theory with the UB3LYP functional was employed. The equilibrium geometries