Proton transfers in the Strecker reaction revealed by DFT calculations

• Shinichi Yamabe,
• Guixiang Zeng,
• Wei Guan and
• Shigeyoshi Sakaki

Beilstein J. Org. Chem. 2014, 10, 1765–1774, doi:10.3762/bjoc.10.184

• competitive TS8/18 has an energy barrier of 32.0 kcal/mol. Geometries along the unfavorable routes pathway II and pathway IB, are shown in Figures S4 and S5, Supporting Information File 1, respectively. The relative stability of these two transition states were checked with extended models TS10/11-ext and TS8

• kcal/mol and the large value corresponds to the high temperature conditions in Scheme 1(b). Geometries of transition states along the reaction from acetaldehyde (1) to the aminonitrile 8. Distances are in Å. TS1/2 means, for instance, a transition state for the step 1 → 2. Energy changes along

• elementary processes from acetaldehyde to aminonitrile. Bold numbers are defined in Scheme 5. Two transition states (A and B) of the nucleophilic addition of (S)-α-phenylethylamine to acetaldehyde. (H2O)10 is also included, and the molecular formula of the reaction system is C11H36N2O11. Energy changes along

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

• that the phosphate 12a is incapable to adopt a pentofuranose-ring conformation at the catalytic sites of E. coli UP and TP, which would be compatible with the coupling to pyrimidine bases. There are convincing arguments that the transition states of the phosphorolysis of pyrimidine [37] and purine [38

Dimerisation, rhodium complex formation and rearrangements of N-heterocyclic carbenes of indazoles

• Zong Guan,
• Jan C. Namyslo,
• Martin H. H. Drafz,
• Martin Nieger and
• Andreas Schmidt

Beilstein J. Org. Chem. 2014, 10, 832–840, doi:10.3762/bjoc.10.79

• to be true minima by the absence of imaginary frequencies or transition states by the occurrence of one negative frequency. Plots were obtained using Maestro 9.1.207, the graphical interface of Jaguar. Inversion barriers have been calculated fully relaxed, fixating one torsion angle around the

Domino reactions of 2H-azirines with acylketenes from furan-2,3-diones: Competition between the formation of ortho-fused and bridged heterocyclic systems

• Alexander F. Khlebnikov,
• Mikhail S. Novikov,
• Viktoriia V. Pakalnis,
• Roman O. Iakovenko and
• Dmitry S. Yufit

Beilstein J. Org. Chem. 2014, 10, 784–793, doi:10.3762/bjoc.10.74

• Supporting Information File 1). No intermediate structure was located on the way to the most stable conformation of trans-isomer 5a with the piperazine ring in a boat conformation. The free energies of the highest transition states on the pathways from 12a to cis-isomer 4a and trans-isomer 5a are practically

• , transition states, reactants, and products in benzene were performed using the PCM model. Intrinsic reaction coordinates were calculated to authenticate all transition states. Molecular structures of compounds 3а, 4b. Energy profiles for the reactions of azirines 2a,c and acylketene 6a, as well as acylketene

• experimental procedures including characterization data for all synthesized compounds, 1H and 13C NMR spectra for all new compounds. Computational details: energies of molecules, transition states and their Cartesian coordinates of atoms. Supporting Information File 191: Detailed experimental procedures and

Chromatographically separable rotamers of an unhindered amide

• Mario Geffe,
• Lars Andernach,
• Oliver Trapp and
• Till Opatz

Beilstein J. Org. Chem. 2014, 10, 701–706, doi:10.3762/bjoc.10.63

• ° and = 290°. The geometries of both minima were used as starting geometries for a geometry optimization followed by the calculation of the thermochemical data at 298 K. The coordinates of the maxima were used as starting points for the search for the transition states. After locating the transition

• - and Z-isomer of 4 is predicted to be 3.2 kJ/mol in hexane and 5.8 kJ/mol in vacuo, respectively. The transition states are located at 108.8 kJ/mol (TS1) and 105.5 kJ/mol (TS2) above the Z-isomer of 4 for hexane solvation as well as at 107.3 k/mol (TS1) and 102.1 kJ/mol (TS2) in the gas phase

• , respectively. The geometries of the E- and Z-ground states of 4 and both transition states (TS1 and TS2) are shown in Figure 6 together with the dihedral angle O–C–N–C1 () and the C–N bond length. Both transition states show a single imaginary frequency (−280.8 cm−1 (TS1) and −364.5 cm−1 (TS2) in hexane and at

Substrate dependent reaction channels of the Wolff–Kishner reduction reaction: A theoretical study

• Shinichi Yamabe,
• Guixiang Zeng,
• Wei Guan and
• Shigeyoshi Sakaki

Beilstein J. Org. Chem. 2014, 10, 259–270, doi:10.3762/bjoc.10.21

• product. For both ketone substrates, the diimines undergoing E2 reactions were found to be key intermediates. Keywords: acetone; acetophenone; DFT calculations; diimine intermediate; reduction reaction; transition states; Wolff–Kishner; Introduction The Wolff–Kishner (W-K) reduction is an organic

• process includes high-energy transition states, TS5 with +42.72 kcal/mol, TS7a with +53.81 kcal/mol and TS7b with +50.20 kcal/mol. The conversion of the acetone hydrazone to propane without the base catalyst is clearly improbable. A base-promoted reaction of acetone. The reaction model adopted here is

• effect was considered by the polarizable continuum model (PCM) [40][41][42]. Geometries of transition states (TSs) were determined by the input data consisting of two steps. For the first step, the initial geometry containing average and assumed distances between covalent and intermolecular interactions

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

• calculation of binding energies (Table 1) we considered different conformational binding patterns of the nitroolefin to the diamide moiety with either any one or both oxygen atoms participating in hydrogen bonding. This results in potentially twelve different transition states, some of which present the same

• stationary point on the potential energy surface resulting in 9 (see Supporting Information File 1 for all TS) competing transition states. Relative energies in Figure 9 suggest that TS-(pro-S)-14a is the most favored by 1.1 kcal/mol compared to the lowest competing TS in pro-R-configuration TS-(pro-R)-14a

• Hitachi together with the chiral column Chiralcel OJ-H in 25 cm length. The enantiomers of the product were determined by reference spectra. Crystal data, NMR spectra and coordinates of stationary points/transition states as well as experimental procedures for the preparation of catalysts 1–7f can be

Synthesis of the B-seco limonoid core scaffold

• Hanna Bruss,
• Hannah Schuster,
• Rémi Martinez,
• Markus Kaiser,
• Andrey P. Antonchick and
• Herbert Waldmann

Beilstein J. Org. Chem. 2014, 10, 194–208, doi:10.3762/bjoc.10.15

• ). This might be explained by the rigidity of the bicyclic system, such that transition states B and C can compete without preference for a conformation that clearly favours axial attack. Underscored by MM2 conformational calculations, it is furthermore plausible that the C11 oxygen can form an H-bond to

• transition states D and E seem to compete without any preference for a conformation that clearly favours axial attack (Figure 3b). Presumably because of the absence of electrostatic interactions in the pseudo-axial attack of the silyl ketene acetal (compare transition state B in Figure 3a: electrostatic

• precursor 30 and possible transition state involved in the Ireland–Claisen rearrangement. Conformations of rearrangement precursors 66 and 77 and possible transition states involved in the Ireland–Claisen rearrangements. R = MOM. Retrosynthetic analysis of the B-seco limonoid framework employing a [3,3

Recent applications of the divinylcyclopropane–cycloheptadiene rearrangement in organic synthesis

• Sebastian Krüger and
• Tanja Gaich

Beilstein J. Org. Chem. 2014, 10, 163–193, doi:10.3762/bjoc.10.14

• the Cope rearrangement, it has to be noted that the preference of transition states (chair/boat) is opposite. Whereas the Cope rearrangement of hexa-1,5-diene 12 usually proceeds through chair-like transition state 12' (see Scheme 2) and not through the energetically disfavoured boat-transition state

• 12'' [15], the DVCPR only proceeds via boat-like transition state 9nn' where both vinyl-moieties are in the endo-orientation reagarding the cyclopropane [16]. The other transition states (9xx'/9xn') would result in a cycloheptadiene with at least one E-configured double bond (13/14) after a

• characterization of cis-divinylcyclopropane by Brown. Transition states for the Cope rearrangement and the related DVCPR. Ts = transition state. Two possible mechanisms of trans-cis isomerizations of divinylcyclopropanes. Proposed biosynthesic pathway to ectocarpene (21), an inactive degradation product of a

Less reactive dipoles of diazodicarbonyl compounds in reaction with cycloaliphatic thioketones – First evidence for the 1,3-oxathiole–thiocarbonyl ylide interconversion

• Valerij A. Nikolaev,
• Alexey V. Ivanov,
• Ludmila L. Rodina and
• Grzegorz Mlostoń

Beilstein J. Org. Chem. 2013, 9, 2751–2761, doi:10.3762/bjoc.9.309

• , below −5 °C) the reaction was essentially ‘frozen’. According to the computational analysis, the transition states for the formation of 1,3,4-thiadiazoline 10a via the concerted cycloaddition of the corresponding reagents as well as for its decomposition to thiocarbonyl ylide 6a' and N2 display

• , Table S1). According to the computations, the transition states for the electrocyclizations of the initially formed thiocarbonyl ylide 6e' to 1,3-oxathiole 3e and to thiirane 8e' display activation barriers (ΔG#) of 8.6 and 15.2 kcal·mol−1, while the Gibbs free energy changes (ΔG) for the same processes

• are 15.2 and 26.6 kcal·mol−1, respectively (see Supporting Information File 1, Table S1). Based on these data domination of 1,5-electrocyclization of C=S-ylide 6e' at room temperature can be apparently explained by the rather high difference (6.6 kcal·mol−1) between transition states energy levels TS1

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

• ) complexes as calculated in a DFT study by Ahlquist and Fokin [125] (transition states with Cu–Cu distances of 2.54 Å for L = X = chloride and 2.64 Å for L = acetylide). They tested copper(I) acetate in the CuAAC model reaction of benzyl azide with phenylacetylene and reported an excellent performance of

Diastereoselectivity in the Staudinger reaction of pentafluorosulfanylaldimines and ketimines

• Alexander Penger,
• Cortney N. von Hahmann,
• Alexander S. Filatov and
• John T. Welch

Beilstein J. Org. Chem. 2013, 9, 2675–2680, doi:10.3762/bjoc.9.303

• highly charged transition states such as B. In both structures, consistent with the opposing dipole geometry of the Cornforth transition state, the N–C–C–S torsional angles remain near 170° (169° and 167° for 7a and 7c respectively). The 1,2-lk,ul ring closure product may be formed in the reaction of 5c

Garner’s aldehyde as a versatile intermediate in the synthesis of enantiopure natural products

• Mikko Passiniemi and
• Ari M.P. Koskinen

Beilstein J. Org. Chem. 2013, 9, 2641–2659, doi:10.3762/bjoc.9.300

• detected, instead the syn-adduct 30 was obtained as the sole stereoisomer. By lowering the temperature to −40 °C and keeping the amount of reagents the same, the selectivity was inverted! Only the anti-adduct 29 was isolated. This change in selectivity was explained with two different transition states. At

Bidirectional cross metathesis and ring-closing metathesis/ring opening of a C₂-symmetric building block: a strategy for the synthesis of decanolide natural products

• Bernd Schmidt and
• Oliver Kunz

Beilstein J. Org. Chem. 2013, 9, 2544–2555, doi:10.3762/bjoc.9.289

•  8) and to 67% for the 6,9-disubstituted compound 38 (Scheme 9). The presence of substituents and their relative configuration may have severe conformational effects on transition states, activation barriers and product stability [61][62]. An example for which a dramatically increased yield was

Synthetic scope and DFT analysis of the chiral binap–gold(I) complex-catalyzed 1,3-dipolar cycloaddition of azlactones with alkenes

• María Martín-Rodríguez,
• Luis M. Castelló,
• Carmen Nájera,
• José M. Sansano,
• Olatz Larrañaga,
• Abel de Cózar and
• Fernando P. Cossío

Beilstein J. Org. Chem. 2013, 9, 2422–2433, doi:10.3762/bjoc.9.280

• ball and stick and wireframe models, respectively. Blue surface represents the solvent-accessible surface with a probe radius of 1.9 Å. Main geometrical features and relative Gibbs free energies (in kcal mol−1) of the less energetic transition states associated with the 1,3-DC of 5aa and NPM catalyzed

• wireframe models, respectively. Blue surface represents the solvent-accessible surface with a probe radius of 1.9 Å. Main geometrical features and relative Gibbs free energies (in kcal mol−1) of the less energetic transition states associated with the 1,3-DC of 10 and tert-butyl acrylate catalyzed by (Sa

Sequential Diels–Alder/[3,3]-sigmatropic rearrangement reactions of β-nitrostyrene with 3-methyl-1,3-pentadiene

• Peter A. Wade,
• Alma Pipic,
• Matthias Zeller and
• Panagiota Tsetsakos

Beilstein J. Org. Chem. 2013, 9, 2137–2146, doi:10.3762/bjoc.9.251

• °C and 20 °C, respectively). Apparently, the developing cis-relationship between the phenyl and nitro groups in transition states leading to both 22b and 19 is unfavorable. On prolonged heating, product 22b is converted to the trans-isomer 23. It was postulated that the zwitterion 24 was an

• tetrasubstituted cycloalkenes 22a and 22b, respectively, whereas 2 and 3 give less stable trisubstituted alkenes 18 and 19 [22] which may explain the rate difference. Significant steric differences between the transition states leading to 22a and 22b versus 18 and19 appear to be absent. Nitronic esters 4–7 lack

Aerobic radical multifunctionalization of alkenes using tert-butyl nitrite and water

• Daisuke Hirose and
• Tsuyoshi Taniguchi

Beilstein J. Org. Chem. 2013, 9, 1713–1717, doi:10.3762/bjoc.9.196

• reactions of alkenes 5 and 7 could be rationalized by six-membered transition states 30 and 31 in the 1,5-hydrogen shift. If chair forms were postulated in both cases, more substituents should be arranged at equatorial positions to form more stable transition states. According to this presumption, the

Thermochemistry and photochemistry of spiroketals derived from indan-2-one: Stepwise processes versus coarctate fragmentations

• Götz Bucher,
• Gernot Heitmann and
• Rainer Herges

Beilstein J. Org. Chem. 2013, 9, 1668–1676, doi:10.3762/bjoc.9.191

• , involved in the reaction, one bond is made and one bond is broken. However, there are a number of reactions that include a linear system of atoms, or at least one atom, at which two bonds are made and two bonds broken simultaneously. Nevertheless, their transition states exhibit a cyclic overlap of basis

• orbitals. The orbital basis can be derived from the orbital basis of pericyclic transition states by constriction (coarctation, Figure 1). Hence, these reactions have been coined “coarctate” reactions [4][5]. Similar to pericyclic reactions [6], rules were derived to predict their stereochemistry, and

• overlap at each end is bound by terminating groups, e.g. a lone pair, or two atoms to form a three-ring, or four atoms to a five-ring, etc. Similar to pericyclic reactions, thermochemical coarctate reactions proceed via Hückel transition states, if the number of delocalized electrons in the transition

Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines

• Andreas Gansäuer,
• Meriam Seddiqzai,
• Tobias Dahmen,
• Rebecca Sure and
• Stefan Grimme

Beilstein J. Org. Chem. 2013, 9, 1620–1629, doi:10.3762/bjoc.9.185

• . In accordance with intuition, all transition states are ‘later’ than that of the 5-exo cyclization as indicated by the shorter distances between the radical center and the C-atom attacked for 1–3 (2.15–2.17 Å vs 2.30 in the 5-exo cyclization). Moreover, the trajectory of attack on the arene is very

• . Calculated kinetic and thermodynamic data (on the PW6B95-D3/QZVP//TPSS-D3/def2-TZVP level) and HOMO–SOMO gap ΔEH-S (on the TPSS-D3/TZVP level) of the reactions of 33 and 34 in benzene at 40 °C. Supporting Information Supporting Information File 352: Energies and coordinates of all radicals and transition

• states, tables with data on radicals with Me-substitution on N analogous to Tables 4, 5, and 6. Acknowledgements We thank the DFG (SFB 813, ‘Chemistry at Spin Centers’) and the Jürgen Manchot Stiftung (Fellowship to T. D.) for support.

A reductive coupling strategy towards ripostatin A

• Kristin D. Schleicher and
• Timothy F. Jamison

Beilstein J. Org. Chem. 2013, 9, 1533–1550, doi:10.3762/bjoc.9.175

• a β-ketoester. Retrosynthesis utilizing Rychnovsky’s cyanohydrin acetonide methodology. Nickel-catalyzed reductive coupling of alkynes and epoxides. Potential transition states and stereochemical outcomes for a concerted 1,5-hydrogen rearrangement. Rearrangements of vinylcyclopropanes to acylic 1,4

Thiourea-catalyzed Diels–Alder reaction of a naphthoquinone monoketal dienophile

• Carsten S. Kramer and
• Stefan Bräse

Beilstein J. Org. Chem. 2013, 9, 1414–1418, doi:10.3762/bjoc.9.158

• , 402.1 358.1, 357.1; HRMS–EI (m/z): [M]+ calcd for C28H40O8Si, 532.2491; found, 532.2493. Proposed favored and disfavored transition states during the thiourea catalyzed Diels–Alder reaction of dienophile 2 and diene 3. R = 3,5-bis(trifluoromethyl)phenyl. Retrosynthetic dissection of the ABC-ring system

True and masked three-coordinate T-shaped platinum(II) intermediates

• Manuel A. Ortuño,
• Salvador Conejero and
• Agustí Lledós

Beilstein J. Org. Chem. 2013, 9, 1352–1382, doi:10.3762/bjoc.9.153

• bending energy profile maintains the same basic features: the T-shaped configurations of the 14-electron species are energy minima, and their cis-like to trans-like interconversion occurs via transition states with Y-shaped configurations [2]. The X-ray structure of the recently reported three-coordinate

• cyclometalated T-shaped structure 27 is obtained, once again stabilized by an agostic interaction. The corresponding transition states for OA and RE processes are isoenergetic with respect to 25. Finally, the agostic coordination mode in 27 is displaced by a DMSO molecule forming the cyclometalated product 28

Host–guest complexes of mixed glycol-bipyridine cryptands: prediction of ion selectivity by quantum chemical calculations, part V

• Svetlana Begel,
• Ralph Puchta and
• Rudi van Eldik

Beilstein J. Org. Chem. 2013, 9, 1252–1268, doi:10.3762/bjoc.9.142

• .bpy]3+ are transition states for the movement of the metal ion inside the cavity of [2.2.bpy], as shown in Figure 5. This motion leads from one glycol molecular bar to the other, bringing the cation closer to the O donor atoms, hence supporting the coordination. The barrier for this movement lies at

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

• ). Frequency calculations were performed on all optimized geometries to ensure only positive eigenvalues for minima and one imaginary frequency for transition states. Free energies at 298.15 K and 1 bar pressure were calculated according to the recommendation of Gaussian, Inc. [57][58], and the frequency

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

• was in good accordance with the observed exclusive formation of phenanthridines derived from radicals 5a–f for these compounds. The possibility of the rearrangement of spiro- to ortho-species via aziridinyl intermediates (or transition states) (az) which contain benzyl stabilization was examined

• the ortho mode whereas the benzofuranyl- and benzothiophenyl-iminyls 11 prefer the spiro mode can be obtained by consideration of the structures of the transition states (TS, Figure 4). The top line shows the computed spin density (ρ) maps for the reactant iminyls. In agreement with the EPR spectra

• saddle points by frequency calculations. The experimental kinetic and spectroscopic data was all obtained in the nonpolar hydrocarbon solvents t-BuPh or cyclopropane. Solvent effects, particularly differences in solvation between the neutral reactants and neutral transition states, were therefore