Strecker degradation of amino acids promoted by a camphor-derived sulfonamide

• M. Fernanda N. N. Carvalho,
• M. João Ferreira,
• Ana S. O. Knittel,
• Maria da Conceição Oliveira,
• João Costa Pessoa,
• Rudolf Herrmann and
• Gabriele Wagner

Beilstein J. Org. Chem. 2016, 12, 732–744, doi:10.3762/bjoc.12.73

• developed by means of DFT calculations on potential transition states. Keywords: amino acids; camphorsulfonylimine; DFT calculations; NMR characterization; Strecker degradation; Introduction Among the many derivatives of natural camphor, oxoimine 1 (Figure 1) shows an especially versatile chemistry. The C

• (Figure 8) as the products [34][35]. We could indeed identify transition states for these reactions. Figure 8 (top) shows the reaction sequence and Figure 9 shows the TS and the change in salient atom distances along the path following the intrinsic reaction coordinate (IRC). A movie is available as

• is an obvious candidate as catalyst. Indeed, water inclusion in reaction paths with high-lying transition states is often observed in water as solvent, as in biochemical reactions, and was demonstrated for, e.g., the analytical detection of sulfenic acids with dimedone [36]. In these systems water

The aminoindanol core as a key scaffold in bifunctional organocatalysts

• Isaac G. Sonsona,
• Eugenia Marqués-López and
• Raquel P. Herrera

Beilstein J. Org. Chem. 2016, 12, 505–523, doi:10.3762/bjoc.12.50

• reaction pathway based on previously reported transition states (Figure 6). The catalyst ent-4 would activate and fix the electrophile through several hydrogen-bonding interactions with the NH groups of the thiourea. Simultaneously, the hydroxy group would be involved in the activation of the nucleophile

• external Brønsted acid. Proposed transition state TS7 for the Friedel–Crafts reaction of indole and α,β-unsaturated acyl phosphonates catalyzed by ent-4. Possible transition states TS8 and TS9 in the asymmetric addition of indoles 2 to the β,γ-unsaturated α-ketoesters 26 catalyzed by ent-4. Transition

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• trajectories initiated from minima and transition states have both been carried out on carbocations [25] and examples of each are described below. While many different quantum chemical methods can be used to carry out trajectory calculations, standard density functional theory (DFT) approaches are most

• structures in the vicinity of transition states, tend to have short lifetimes, on the order of the period of a single-bond stretching vibration. • These lifetimes can be increased via noncovalent interactions with electron-rich groups. Abietadiene – navigating past forks in the road Pathways to abietadiene

Diastereoselective synthesis of new O-alkylated and C-branched inositols and their corresponding fluoro analogues

• Charlotte Collet,
• Françoise Chrétien,
• Yves Chapleur and
• Sandrine Lamandé-Langle

Beilstein J. Org. Chem. 2016, 12, 353–361, doi:10.3762/bjoc.12.39

• substituted with the two carbon atoms arm where only compound myo-5 could be obtained. Indeed with the chain being longer, the formation of byproducts originating from cyclization and migration, favored by the proximity of the inositol ring and preferential transition states, was avoided. The synthetic routes

Tandem processes promoted by a hydrogen shift in 6-arylfulvenes bearing acetalic units at ortho position: a combined experimental and computational study

• Mateo Alajarin,
• Marta Marin-Luna,
• Pilar Sanchez-Andrada and
• Angel Vidal

Beilstein J. Org. Chem. 2016, 12, 260–270, doi:10.3762/bjoc.12.28

• into the isomeric spirotricycle 12a. The computed energy barriers for these processes are relatively small, 13.9 and 17.0 kcal·mol−1 respectively. Again the differences in the extent of the electronic conjugation in these electrocyclization transition states can give account of the relative stabilities

• characteristics of the respective transition states. The calculations have also shown that the tandem conversions of the starting fulvenes into benz[f]indenes are exergonics, the 9-substituted regioisomer being the thermodynamically-controlled major product, in accordance with the experimental results. Optimized

Synthesis and reactivity of aliphatic sulfur pentafluorides from substituted (pentafluorosulfanyl)benzenes

• Norbert Vida,
• Jiří Václavík and
• Petr Beier

Beilstein J. Org. Chem. 2016, 12, 110–116, doi:10.3762/bjoc.12.12

• Diels–Alder products (Table 1). Single-point energies of the transition states suggested that pathway a was preferred over b (difference of ca. 10–20 kJ/mol). This was further supported by comparison of Gibbs free energy values. Boltzmann distribution was used to calculate theoretical endo/exo

• selectivity of 16a (98:2) from the differences of Gibbs energy of the transition states. Geometries of the four transition states are depicted in Figure 1. The less abundant transition states (TS-endo-16b and TS-exo-16b) were asynchronous with the differences of bond lengths of 0.662 and 0.556 Å, respectively

• )acetic acid, which in aqueous solution exists in equilibrium with its enol form. Further experiments are underway to find out whether aerobic microbial degradation of SF5-substituted aromatic compounds follows the same pathway as our chemical oxidation method. Optimized geometries of transition states of

Solving the puzzling competition of the thermal C²–C⁶ vs Myers–Saito cyclization of enyne-carbodiimides

• Anup Rana,
• Mehmet Emin Cinar,
• Debabrata Samanta and
• Michael Schmittel

Beilstein J. Org. Chem. 2016, 12, 43–49, doi:10.3762/bjoc.12.6

• approach for the diradical species and the transition states (TSs) connecting them while the restricted method was used for closed shell species. The BLYP functional was chosen for computation because the benchmark studies done by Schreiner showed good applicability of BLYP for the enyne-allene system [3

Enantioselective additions of copper acetylides to cyclic iminium and oxocarbenium ions

• Jixin Liu,
• Srimoyee Dasgupta and
• Mary P. Watson

Beilstein J. Org. Chem. 2015, 11, 2696–2706, doi:10.3762/bjoc.11.290

• substrates, suggesting that more stable oxocarbenium ions result in more selective reactions, potentially because they lead to later enantiodetermining transition states. We have also discovered a CuSPh/Ph-Pybox catalyst that enables the formation of diaryl, tetrasubstituted stereocenters via an

2-Hetaryl-1,3-tropolones based on five-membered nitrogen heterocycles: synthesis, structure and properties

• Yury A. Sayapin,
• Inna O. Tupaeva,
• Alexandra A. Kolodina,
• Eugeny A. Gusakov,
• Vitaly N. Komissarov,
• Igor V. Dorogan,
• Nadezhda I. Makarova,
• Anatoly V. Metelitsa,
• Valery V. Tkachev,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2015, 11, 2179–2188, doi:10.3762/bjoc.11.236

• energy correction (Etot + ZPE, а.u.) and relative energies (ΔE, kcal/mol) of the intermediates and corresponding transition states (Ts) occurring along the reaction path of the formation of 1,3-tropolones 5, and 6a,d,g calculated using the PBE0/6-311+G** method in the gas phase. Total energies with zero

• solution at 293 K. Ф – Quantum yield of the fluorescence. Supporting Information Supporting Information File 519: Experimental section, crystallographic data for compounds 5g, 6e, 11b, 13; optimized geometries of the intermediates and transition states involved in the routes of the formation of 1,3

Computational study of productive and non-productive cycles in fluoroalkene metathesis

• Markéta Rybáčková,
• Jan Hošek,
• Ondřej Šimůnek,
• Viola Kolaříková and
• Jaroslav Kvíčala

Beilstein J. Org. Chem. 2015, 11, 2150–2157, doi:10.3762/bjoc.11.232

• partial bonding of alkene and the alkoxy group of the alkoxybenzylidene ligand to ruthenium was detected with the exception of a syn–cis arranged alkene, for which just a weak inflexion was observed in analogy to [42]. No large differences in the energies of transition states 3d preceeding the formation

• complex 2k. While both syn- and anti-coordinations of starting complex 2k and subsequent transition states 2l have nearly equal energies, the subsequent non-symmetrical productive metallacyclobutane 2PB is significantly more stable by ca. 60 kJ/mol than symmetrical non-productive metallacyclobutane 2NB

• . The difference in the energies was again more augmented for the subsequent transition states 2m and finally with the alkene coordinated to the alkylidene ruthenium, where the productive complex s2n, a complex of ethylene with difluororuthenium, is by ca. 80 kJ/mol more stable than the non-productive

Conformational equilibrium in supramolecular chemistry: Dibutyltriuret case

• Karina Mroczyńska,
• Małgorzata Kaczorowska,
• Erkki Kolehmainen,
• Ireneusz Grubecki,
• Marek Pietrzak and
• Borys Ośmiałowski

Beilstein J. Org. Chem. 2015, 11, 2105–2116, doi:10.3762/bjoc.11.227

• obtained (Eyring equation). Two forms in 1∙∙∙10 complexes are, most probably 1a∙∙∙10 (high temperature) and 1c∙∙∙10 (low temperature). Between these two rotational transition states exist and one form represented by a local energy minium (Figure 10). These are transition states related to a) conformational

• Gaussian with default settings. For all structures the frequency calculations were ran to be sure that the geometry is in an energy minimum. Except for transition states where one imaginary frequency was obtained all other structures gave only real frequencies. The AIM2000 [71] software was used to

• [62][63] model of solvation (chloroform). The M05 functional suggested for non-covalent interactions [64][65] was used to sustain the methodology from our previous publications [9][10][50][66]. The Synchronous Transit-Guided Quasi-Newton method [67][68] has been used for optimization of the transition

Synthesis of constrained analogues of tryptophan

• Elisabetta Rossi,
• Valentina Pirovano,
• Marco Negrato,
• Giorgio Abbiati and
• Monica Dell’Acqua

Beilstein J. Org. Chem. 2015, 11, 1997–2006, doi:10.3762/bjoc.11.216

• reaction of 1a with 2 and effective in the reaction of 1b with 2. In this latter case, the reaction outcome could be explained by the formation of two energetically comparable transition states (endo + exo TS) or by the occurrence of a stepwise mechanism. Finally, the results obtained with indole 1i

• 2 afforded the corresponding tetrahydrocarbazoles 5a and 5b in 1:1.3 diasteroisomeric ratio (Scheme 4). As reported for the reaction between 1b and 2 in chloroform, the reaction outcome could be explained by the formation of two energetically comparable transition states (endo + exo TS) or by the

Mechanism, kinetics and selectivity of selenocyclization of 5-alkenylhydantoins: an experimental and computational study

• Biljana M. Šmit,
• Radoslav Z. Pavlović,
• Dejan A. Milenković and
• Zoran S. Marković

Beilstein J. Org. Chem. 2015, 11, 1865–1875, doi:10.3762/bjoc.11.200

• the internal nucleophile, the amidic nitrogen, to the seleniranium cation yielding the intermediate imidazolinium cations. Their deprotonation is followed by the formation of the fused bicyclic reaction products. Important intermediates and key transition states are studied by using density functional

• -membered ((S,R)-INT3 and (S,S)-INT3) or six-membered ((S,R)-INT3’ and (S,S)-INT3’) intermediate bicyclic imidazolinium cations. Energy profiles for both 5-exo and 6-endo pathways are presented in Figure 3. The ring closure reactions are carried out via four transition states: two for the formation of the

• ’ the N-C(6) and Se-C(5) are almost completely formed. Optimized structures of seleniranium cations and transition states are given in Figure 4, while those for imidazolinium cations are given in Figure 5. From the charge analysis (data given in Supporting Information File 1, Table S2) it is possible to

A comprehensive study of olefin metathesis catalyzed by Ru-based catalysts

• Albert Poater and
• Luigi Cavallo

Beilstein J. Org. Chem. 2015, 11, 1767–1780, doi:10.3762/bjoc.11.192

• hand, complex 19 is an example of an asymmetric catalyst, suggesting that the NHC ligand is the source of asymmetry [52]. In this paper we contribute in the understanding of the side- and bottom-bound coordination intermediates and the stability of the corresponding transition states as well as the

• –2.60 Å away from the Ru atom. Transition state for metallacycle formation. The energy of the various transition states for metallacycle formation with respect to the uncoordinated C=C double bond are reported in the 5th column of Table 2, while in the 6th column it is reported the energy of the cis

• transition states with respect to the trans transition state. The numbers reported clearly indicate that at the transition state the bulkiness of the N-substituents plays a more remarkable role. Indeed, while cis C2H4 coordination is favored for all the systems we considered, the cis transition state is

Fe(II)/Et₃N-Relay-catalyzed domino reaction of isoxazoles with imidazolium salts in the synthesis of methyl 4-imidazolylpyrrole-2-carboxylates, its ylide and betaine derivatives

• Ekaterina E. Galenko,
• Olesya A. Tomashenko,
• Alexander F. Khlebnikov,
• Mikhail S. Novikov and
• Taras L. Panikorovskii

Beilstein J. Org. Chem. 2015, 11, 1732–1740, doi:10.3762/bjoc.11.189

• details: energies of molecules, transition states and their Cartesian coordinates of atoms. X-ray details. Acknowledgements We gratefully acknowledge the financial support of the Russian Foundation for Basic Research (Grant No. 14-03-00187) and Saint Petersburg State University (Grant No. 12.50.1565.2013

Surprisingly facile CO₂ insertion into cobalt alkoxide bonds: A theoretical investigation

• Willem K. Offermans,
• Claudia Bizzarri,
• Walter Leitner and
• Thomas E. Müller

Beilstein J. Org. Chem. 2015, 11, 1340–1351, doi:10.3762/bjoc.11.144

• the precursor and product states as the anchor points, the transition states were located for each L. All determined transition states were geometrically similar, depicting a cyclic arrangement around the cobalt(III) atom, an oxygen and carbon atom of CO2 and the oxygen atom of the original Co–O

• alkoxide bond (Figure 4). These configurations were identical to the arrangement of the reactive atoms in the transition states of the reaction between [Ni(OH)(pincer ligand)] complexes and CO2 [50]. Since the configurations of the reactive atoms are essentially identical in the reactant, precursor

• normal mode frequency analysis. The synchronous-transit method was applied to localize possible transition states [60]. These states were further optimized by following eigenvectors to gain the best predicted configuration of the transition state. Transition states were analysed by a normal mode

Cathodic hydrodimerization of nitroolefins

• Michael Weßling and
• Hans J. Schäfer

Beilstein J. Org. Chem. 2015, 11, 1163–1174, doi:10.3762/bjoc.11.131

• caused by the NH groups of the pyrroles. Their hydrogen bonds could influence the relative energies of the transition states leading to the diastereomers. One of the two meso-configurations can be assigned to isomer 22a because of the missing coupling between the benzylic methine protons. The 1H NMR data

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

• inverse rupture length rb and the x-intercept a measure of koff. Two linear regimes denote a change in two dominant transition states [45], a non-linear behavior may be due to a more complex PED [46]. A drawback of this method is the reduction of all measured rupture forces to one most-probable force

On the strong difference in reactivity of acyclic and cyclic diazodiketones with thioketones: experimental results and quantum-chemical interpretation

• Andrey S. Mereshchenko,
• Alexey V. Ivanov,
• Viktor I. Baranovskii,
• Grzegorz Mloston,
• Ludmila L. Rodina and
• Valerij A. Nikolaev

Beilstein J. Org. Chem. 2015, 11, 504–513, doi:10.3762/bjoc.11.57

• relative energy of the reagents, reaction intermediates, transition states, and reaction products on the potential energy surfaces were carried out. The results of the performed study are summarized and discussed in the present publication. Results and Discussion The subjects of the quantum-chemical

• transition states) on the potential energy surface of the reaction of the diazo compounds 1a–f with thiobenzophenone (2a) were located. The optimized structures of reagents, intermediates, and products were found to be characterized by the absence of the imaginary part of the frequency, and transition states

• through the single minimum energy transition state, TS1. This observation implies that the cycloaddition reaction proceeds via a concerted mechanism. In the case of an alternative, stepwise mechanism, one would expect the appearance of at least two transition states [29], which was not observed. In

Azirinium ylides from α-diazoketones and 2H-azirines on the route to 2H-1,4-oxazines: three-membered ring opening vs 1,5-cyclization

• Nikolai V. Rostovskii,
• Mikhail S. Novikov,
• Alexander F. Khlebnikov,
• Galina L. Starova and
• Margarita S. Avdontseva

Beilstein J. Org. Chem. 2015, 11, 302–312, doi:10.3762/bjoc.11.35

• ] adduct 6j, because the transition state TS9 leading to betaine 14′j, a precursor of [4.3.1] adduct 7j, has a higher energy than the transition state TS5 for the competitive pathway. In spite of the fact that the transition states TS3 and TS8 for alternative betaine 14j formation pathways are very close

Synthesis of dinucleoside acylphosphonites by phosphonodiamidite chemistry and investigation of phosphorus epimerization

• William H. Hersh

Beilstein J. Org. Chem. 2015, 11, 184–191, doi:10.3762/bjoc.11.19

• on the conformations about the P–O bonds, the energies are comparable (separated by less than 1 kcal/mol) and do not have a significant impact on the inversion barriers. Transition states were located using routines implemented in Gaussian (see Supporting Information File 1 for details), and in all

Microsolvation and sp²-stereoinversion of monomeric α-(2,6-di-tert-butylphenyl)vinyllithium as measured by NMR

• Rudolf Knorr,
• Monika Knittl and
• Eva C. Rossmann

Beilstein J. Org. Chem. 2014, 10, 2521–2530, doi:10.3762/bjoc.10.263

• migration across the β-unsubstituted H2C= region in 13 might be sterically much more comfortable than across the bulky β,β-di-tert-alkyl substituents in the transition states deriving from 1 or 2, this opportunity is apparently disdained in 13: The stereoinversion is not facilitated for 4, since the ΔGψ

Chiral phosphines in nucleophilic organocatalysis

• Yumei Xiao,
• Zhanhu Sun,
• Hongchao Guo and
• Ohyun Kwon

Beilstein J. Org. Chem. 2014, 10, 2089–2121, doi:10.3762/bjoc.10.218

• of yield, ee, or both. Based on previous literature, Zhao and co-workers speculated two possible transition states; in both cases, the dienolate adopts a conformation, featuring hydrogen bonding and O–P electrostatic attraction, that favors re-face attack of the imine (Scheme 44). 2.8 [4 + 2

Isoxazolium N-ylides and 1-oxa-5-azahexa-1,3,5-trienes on the way from isoxazoles to 2H-1,3-oxazines

• Alexander F. Khlebnikov,
• Mikhail S. Novikov,
• Yelizaveta G. Gorbunova,
• Ekaterina E. Galenko,
• Kirill I. Mikhailov,
• Viktoriia V. Pakalnis and
• Margarita S. Avdontceva

Beilstein J. Org. Chem. 2014, 10, 1896–1905, doi:10.3762/bjoc.10.197

• B3LYP/6-31G(d) level [34][35][36] by using the Gaussian 09 suite of quantum chemical programs [37] at the Resource center ‘Computer center of Saint Petersburg State University’. Geometry optimizations of intermediates, transition states, reactants and products in benzene were performed by means of a PCM

• model. Intrinsic reaction coordinates were calculated to authenticate all transition states. Energy profiles for the transformations of ylides C, (3Z)-1-oxa-5-azahexa-1,3,5-triene D and oxazines E derived from methoxycarbonylcarbene and isoxazole A. Relative free energies [kcal/mol, 298 K, CH2Cl2 (PCM

• compounds, 1H and 13C NMR spectra for all new compounds, and computational details (energies of molecules, transition states, and the Cartesian coordinates of atoms). Acknowledgements We gratefully acknowledge the financial support from the Russian Foundation for Basic Research (Grant No. 14-03-00187) and

Theoretical study of the adsorption of benzene on coinage metals

• Werner Reckien,
• Melanie Eggers and
• Thomas Bredow

Beilstein J. Org. Chem. 2014, 10, 1775–1784, doi:10.3762/bjoc.10.185

• adsorption sites for each surface. Other adsorption sites are higher in energy by 2 to 15 kJ/mol. This points to a relatively high mobility of benzene on the surfaces assuming that the corresponding activation barriers are of similar magnitude. We did not calculate the transition states because this was not