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

• activation barriers (ΔG#) of 30.2 and 26.0 kcal·mol−1, respectively. On the other hand, the Gibbs free energy changes (ΔG) for the same processes are −4.4 and +12.8 kcal·mol−1. If diazo compound 2a reacts with thioketone 2b via a concerted pathway A, the rate-determining step is the first one because of its

• , 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

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

• maleimides. Formation of the amide 8aa. Reaction Gibbs free energy associated with the 1,3-DC of 5aa and NPM catalyzed by (Sa)-Binap gold dimers computed at M06/Lanl2dz//ONIOM (b3lyp/Lanl2dz:UFF) level of theory. ΔG calculation for the recovery of the catalytic active species. 1,3-DC of azlactone 10 and tert

Synthesis of enantiomerically pure (2S,3S)-5,5,5-trifluoroisoleucine and (2R,3S)-5,5,5-trifluoro-allo-isoleucine

• Holger Erdbrink,
• Elisabeth K. Nyakatura,
• Susanne Huhmann,
• Ulla I. M. Gerling,
• Dieter Lentz,
• Beate Koksch and
• Constantin Czekelius

Beilstein J. Org. Chem. 2013, 9, 2009–2014, doi:10.3762/bjoc.9.236

• stereoisomers of Ile are less hydrophobic than Aha. F6Leu is similar to Aha in hydrophobicity, while exhibiting a much larger volume. In a free energy perturbation study, the hydration energy of F6Leu was shown to be 1.1 kcal/mol higher than that of leucine [29]. This, together with our previous and new

Cyclization of substitued 2-(2-fluorophenylazo)azines to azino[1,2-c]benzo[d][1,2,4]triazinium derivatives

• Aleksandra Jankowiak,
• Emilia Obijalska and
• Piotr Kaszynski

Beilstein J. Org. Chem. 2013, 9, 1873–1880, doi:10.3762/bjoc.9.219

• participation of metal ions. The computational studies were expanded by inclusion of 4g-Z– 4i-Z for a better understanding of the structure–reactivity relationship. The resulting free energy differences between the Z-isomers, relevant to the cyclization process, and the cyclic products, and free energy of

• activation for a series of diazenes are listed in Table 1 and Table 2. The results in Table 1 and Table 2 show that the free energy of activation, ΔG‡298, required for the cyclization of all considered azoazines is in a range of 18–25 kcal/mol, and the process is endergonic by about 5 kcal/mol. Thus, for all

• , CH2Cl2, rt, 25 h; ii) toluene, 50% NaOH, 50 °C, 25 min; iii) NCS, Me2S, CH2Cl2, –20 °C; iv) mCPBA, CH2Cl2, 0 °C; v) Oxone®, CH2Cl2/H2O rt, 25 h. Formation of cations 1 from diazenes 4. Calculated free energy activation and change (kcal/mol) for the cyclization of cis-azopyridine 4-Z to the nonaromatic

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

• -statistical corrections from energy to free energy at a given temperature and corrections for solvation free energy by the reliable (DFT-based) COSMO-RS continuum solvation model [29][30]. For recent applications of this procedure see [31][32][33]. The estimated accuracy is 1–2 kcal mol−1 for absolute free

• investigation [54][55]. In the transition state, the length of the forming C–C bond is assumed to be 2.341 Å and the attack of the radical at the olefin occurs at an angle of 105.8°. This value is close to the tetrahedral angle and the Bürgi–Dunitz angle [56]. In this study, the absolute free energy of

• activation as well as the free energy of the 5-exo cyclization of the hexenyl radical were calculated using the TPSS and PW6B95 functionals as described in computational details. From these values the absolute rate constants at 298 K (25 °C) in benzene were computed as summarized in Table 1 together with the

Electron self-exchange activation parameters of diethyl sulfide and tetrahydrothiophene

• Martin Goez and
• Martin Vogtherr

Beilstein J. Org. Chem. 2013, 9, 1448–1454, doi:10.3762/bjoc.9.164

• discussed above. Despite the obvious deviation of such an associative–dissociative process from a simple outer-sphere electron transfer, its experimental free energy of activation seems to be well reproduced by the Marcus theory in our case. That theory [1][2] predicts to be one quarter of the

• ) and THTP (filled circles and solid line; linear regression, 15.24 – 349/T, r2 = 0.88) in acetonitrile-d3; sensitizer TTP+. For all other experimental parameters and further explanation, see Figure 1 and text. Activation parameters (enthalpy entropy and free energy at room temperature (298K)) for

• arrives at utterly negligible effects on λi from all these bonds. As regards the sulfur–sulfur bond, from the shape of its associated optical absorption band its potential energy curve was concluded [24] to be quite broad and shallow, so it seems reasonable to identify its contribution to λi with the free

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

• 1.6 kcal/mol and 20.1 kcal/mol, respectively. The high value for the movement of Ga3+ inside the [2.2.bpy] results from the very effective complexation of earth metal ions by cryptands compared with single solvent molecules, e.g., H2O or NH3, and hence, a large amount of released free energy. The

Space filling of β-cyclodextrin and β-cyclodextrin derivatives by volatile hydrophobic guests

• Sophie Fourmentin,
• Anca Ciobanu,
• David Landy and
• Gerhard Wenz

Beilstein J. Org. Chem. 2013, 9, 1185–1191, doi:10.3762/bjoc.9.133

• space filling of host cavity plays a dominant role within such series of complexes, and that the applied force field was reasonable. All guests fitted completely into the cavity of host 4 without steric hindrance. The slope of the experimental Gibbs free energy versus the simulated interaction enthalpy

• (black) and 10 mM solution of β-CD 1 (red). Gibbs free energy of formation of the inclusion compound of benzene derivatives, and cyclohexane derivatives in host 4 as a function of the total number of carbon atoms of the guest n. Gibbs free energy of formation of the inclusion compounds of benzene and

• cyclohexane derivatives in host 4 as a function of the molecular volume VG = M/dNA. Gibbs free energy of formation of the inclusion compounds of benzene derivatives in host 4 as a function of the theoretical inclusion enthalpy, obtained by simulation by Macromodel (slope 0.69). Free binding enthalpy for

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

• action of hydrogencarbonate (TS 18 and intermediate 19). Structural rearrangement of 19 through TS 20 shows an intermediate 21. Finally 21 is protonated by coordinated H2CO3 (highest rate-determining TS 22a) to yield the final product 23 with a great release of free energy. It is worth mentioning that

• base and the reaction time was 4 days. The influence of K+ on the product free energy. Optimization of the reaction conditions. Supporting Information Supporting Information File 165: Details on synthetic procedures, list of pyridinium salts, characterization of new compounds, copies of NMR spectra, X

New core-pyrene π structure organophotocatalysts usable as highly efficient photoinitiators

• Sofia Telitel,
• Frédéric Dumur,
• Thomas Faury,
• Bernadette Graff,
• Mohamad-Ali Tehfe,
• Didier Gigmes,
• Jean-Pierre Fouassier and
• Jacques Lalevée

Beilstein J. Org. Chem. 2013, 9, 877–890, doi:10.3762/bjoc.9.101

• efficiency can be expected for this compound. The oxidation potentials of the Co_Pys (Table 1) range from 1.33 V (Py_1) to 0.6 V (Py_4, Py_12). The singlet-state energy is also affected by the core of the structure, i.e., 2.6 eV for Py_8 versus 3.44 eV for the reference Py_1. The free-energy change ΔG of the

• saturated calomel electrode-SCE). Ferrocene was used as a standard and the potentials were determined from half-peak potentials. The free energy change ΔGet for an electron-transfer reaction is calculated from the classical Rehm–Weller equation (Equation 1) [60] where Eox, Ered, ES and C are the oxidation

• wavelengths λmax,em), excited-state energy levels (ES), oxidation potentials (Eox) and free-energy changes ΔG (see text) [1]. Supporting Information Supporting Information File 2: Experimental procedures, characterization data, and additional spectra. Acknowledgements This work was partly supported by the

Kinetics and mechanism of the anilinolysis of aryl phenyl isothiocyanophosphates in acetonitrile

• Hasi Rani Barai and
• Hai Whang Lee

Beilstein J. Org. Chem. 2013, 9, 615–620, doi:10.3762/bjoc.9.68

• free-energy relationships with X in the nucleophiles were biphasic concave upwards with a break region between X = H and 4-Cl, giving unusual positive ρX and negative βX values with less basic anilines (X = 4-Cl and 3-Cl). A stepwise mechanism with rate-limiting bond breaking for more basic anilines

A computational study of base-catalyzed reactions of cyclic 1,2-diones: cyclobutane-1,2-dione

• Nargis Sultana and
• Walter M. F. Fabian

Beilstein J. Org. Chem. 2013, 9, 594–601, doi:10.3762/bjoc.9.64

• free energy of activation of the benzilic acid rearrangement (fission of the C1–C4 and concerted formation of the C2–C4 bond) via TS2 (ν = 246i cm–1) is ca. 15 kcal mol–1. The initial product P1a (1-carboxycyclopropanolate) is expected to easily convert to the final product 1

Electron and hydrogen self-exchange of free radicals of sterically hindered tertiary aliphatic amines investigated by photo-CIDNP

• Martin Goez,
• Isabell Frisch and
• Ingo Sartorius

Beilstein J. Org. Chem. 2013, 9, 437–446, doi:10.3762/bjoc.9.46

• polarizations. When escape predominates, all polarizations originate from the radical-ion pairs, when the in-cage deprotonation prevails, from the pairs of neutral radicals. Because the rate of in-cage deprotonation depends on the free energy of that reaction ∆Gdep, a threshold behaviour is observed: For

• . With Equation 2, the free energy of the relayed deprotonation can be estimated from the reduction potential Φred (DH•+) of the radical cation (see, Table 1, but taken relative to NHE instead of SCE), the pKa of the protonated amine (8.9 [43]), and the calculated heats of formation ∆Hf of D• (+208 kJ

• more excellently described by a single exponential, with the same implications for the mechanism as in the case of DABCO. The free energy for the deprotonation of the radical cation by the amine itself can again be calculated with Equation 2. The pKa value of is only known in aqueous diglyme, where it

Asymmetric Diels–Alder reaction with >C=P– functionality of the 2-phosphaindolizine-η¹-P-aluminium(O-menthoxy) dichloride complex: experimental and theoretical results

• Rajendra K. Jangid,
• Nidhi Sogani,
• Neelima Gupta,
• Raj K. Bansal,
• Moritz von Hopffgarten and
• Gernot Frenking

Beilstein J. Org. Chem. 2013, 9, 392–400, doi:10.3762/bjoc.9.40

• diastereoselectivity observed in the cycloisomerisations of triynes has been correlated with the Gibbs free energies of the diastereomers calculated at the DFT B3LYP/TZV+P level; a difference of ca. 2 kcal mol−1 of Gibbs free energy corresponded to 84% diastereoselectivity [55]. In the present case also, the observed

Presence or absence of a novel charge-transfer complex in the base-catalyzed hydrolysis of N-ethylbenzamide or ethyl benzoate

• Shinichi Yamabe,
• Wei Guan and
• Shigeyoshi Sakaki

Beilstein J. Org. Chem. 2013, 9, 185–196, doi:10.3762/bjoc.9.22

• [47]. The latter (amide) analogous one (N,N-dimethyltoluamide, Me–C6H4–C(C=O)–NMe2) was investigated and the experimental activation free energy was reported to be 27.1 kcal/mol [22]. The hydrolysis of the phenyl-group-containing substrate was studied computationally in a reaction between N

• energies was examined. The effect on free-energy changes of TS2(am), (+28.15 kcal/mol) and (+28.05 kcal/mol) was found to be small. Thus, in the amide hydrolysis of n = 16, the Na+ cation is separated well from the reaction center. Conclusion In this work, reaction paths of base-catalyzed hydrolyses of

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

• Jutta Erika Helga Köhler and
• Nicole Grczelschak-Mick

Beilstein J. Org. Chem. 2013, 9, 118–134, doi:10.3762/bjoc.9.15

• solvation-free-energy differences was used to distinguish amylose helices from cellulose sheets by analysing the different reactivity of oxygen atoms O2, O3 and O6 of the sugar units with and without methylation, in line with experimental data [13]. Cyclodextrin-complex formation with substituted benzenes

• the equation ΔG = −RT ln Ks they obtained the corresponding three free energy values ΔG of −11.5 kJ mol−1, −11.0 kJ mol−1 and −10.6 kJ mol−1, indicating rather weak interactions between the guest and host molecule, but still a thermodynamically exothermic reaction of complex formation. Here, our best

Influence of intramolecular hydrogen bonds on the binding potential of methylated β-cyclodextrin derivatives

• Gerhard Wenz

Beilstein J. Org. Chem. 2012, 8, 1890–1895, doi:10.3762/bjoc.8.218

• and the molar binding enthalpy ∆H° were obtained as fitting parameters, from which the binding free energy ∆G° and binding entropy ∆S° were derived. For those titrations with high binding constants, i.e., K > 5000 M−1, titrations were repeated with [host] = 10/K in the cell and [guest] = 13[host] in

A quantitative approach to nucleophilic organocatalysis

• Herbert Mayr,
• Sami Lakhdar,
• Biplab Maji and
• Armin R. Ofial

Beilstein J. Org. Chem. 2012, 8, 1458–1478, doi:10.3762/bjoc.8.166

• . Their rates can be calculated by the linear free-energy relationship log k(20 °C) = sN(E + N), where electrophiles are characterized by one parameter (E) and nucleophiles are characterized by the solvent-dependent nucleophilicity (N) and sensitivity (sN) parameters. Electrophilicity parameters in the

• their reactivities toward weak electrophiles, and to characterize weak nucleophiles, such as nonactivated alkenes, by their reactivities toward strong electrophiles. Recently we have explicitly outlined the reasons why we prefer Equation 1, a nonconventional version of a linear free-energy relationship

• , which defines nucleophilicities as the negative intercepts on the abscissa, over the conventional (mathematically equivalent) linear free-energy relationship depicted in the red frame at the top of Figure 1 [5]. The reactivity scales, developed on this basis, have not only be employed for designing

Cation affinity numbers of Lewis bases

• Christoph Lindner,
• Raman Tandon,
• Boris Maryasin,
• Evgeny Larionov and
• Hendrik Zipse

Beilstein J. Org. Chem. 2012, 8, 1406–1442, doi:10.3762/bjoc.8.163

• , methyl vinly ketone (MVK) and cyclohexenone as representative examples for synthetically useful Michael acceptors, the reaction with pyridine 63 and triphenylphosphane (89) is found to be significantly endergonic (Figure 12) [30]. In turn this implies that the free energy for dissociation of the

The preferred conformation of erythro- and threo-1,2-difluorocyclododecanes

• Yi Wang,
• Peer Kirsch,
• Tomas Lebl,
• Alexandra M. Z. Slawin and
• David O'Hagan

Beilstein J. Org. Chem. 2012, 8, 1271–1278, doi:10.3762/bjoc.8.143

• data to the Eyring equation [15] allowed determination of the activation parameters (see Table 1 and Supporting Information File 1). The overall free energy change (ΔG#) is similar in each case and both the erythro 5a and threo 5b stereoisomers have conformational energy barriers ~2–3 kcal·mol−1 higher

• ground state, thus this is most probably the major contributor to the enthalpy difference. The opposite sign in entropy (ΔS#) for each isomer makes a relatively small contribution to the overall free energy; however, the positive value for the erythro isomer is perhaps unexpected for progression towards

Formation of smectic phases in binary liquid crystal mixtures with a huge length ratio

• Nadia Kapernaum,
• Friederike Knecht,
• C. Scott Hartley,
• Jeffrey C. Roberts,
• Robert P. Lemieux and
• Frank Giesselmann

Beilstein J. Org. Chem. 2012, 8, 1118–1125, doi:10.3762/bjoc.8.124

• than the alkyl chains, which leads to a zig-zag shape of the molecules [3]. Due to this zig-zag shape, the molecules are “locked” in their layers and the free volume between them is no longer compensated. This costs a lot of free energy, which destabilizes the SmC phase in these bidisperse systems. For

On the mechanism of action of gated molecular baskets: The synchronicity of the revolving motion of gates and in/out trafficking of guests

• Keith Hermann,
• Stephen Rieth,
• Hashem A. Taha,
• Bao-Yu Wang,
• Christopher M. Hadad and
• Jovica D. Badjić

Beilstein J. Org. Chem. 2012, 8, 90–99, doi:10.3762/bjoc.8.9

• the basket: Specifically, the greater the affinity of the guest for occupying the basket, the less effective the gates are in “sweeping” the guest as the gates undergo their revolving motion. Keywords: dynamic NMR; host–guest chemistry; linear free-energy relationships; molecular encapsulation

• ]. This particular rate coefficient should more precisely describe the process of racemization. One could describe the free energy characterizing the guest departure (ΔG‡out) as a linear combination of ΔG‡rac′ + ΔG° + ΔG‡sterics representing (1) the opening of the gates (ΔG‡rac′), (2) the decomplexation

Thermodynamic and kinetic stabilization of divanadate in the monovanadate/divanadate equilibrium using a Zn-cyclene derivative: Towards a simple ATP synthase model

• Hanno Sell,
• Anika Gehl,
• Frank D. Sönnichsen and
• Rainer Herges

Beilstein J. Org. Chem. 2012, 8, 81–89, doi:10.3762/bjoc.8.8

• . The NMR tubes were then filled with 600 μL of the mixture. In all experiments a mixing time of 1 ms was applied. Simplified free energy scheme for driving an endergonic condensation (elimination/addition of water is omitted for simplicity). The non-driven reaction is depicted by a dashed line. a

On the control of secondary carbanion structure utilising ligand effects during directed metallation

• Andrew E. H. Wheatley,
• Jonathan Clayden,
• Ian H. Hillier,
• Alison Campbell Smith,
• Mark A. Vincent,
• Laurence J. Taylor and
• Joanna Haywood

Beilstein J. Org. Chem. 2012, 8, 50–60, doi:10.3762/bjoc.8.5

• optimisation of cis/trans-6-Lil·L (L = PMDTA, DGME) was carried out using the B3LYP density functional and a 6-311++G(2d,2p) basis and Gaussian 09 (see Supporting Information File 3). To give free energy differences relevant to the solid state, thermodynamic corrections (at the B3LYP/6-311G(2d,2p) level) and

Equilibrium constants and protonation site for N-methylbenzenesulfonamides

• José A. Moreira,
• Ana M. Rosa da Costa,
• Luis García-Río and
• Márcia Pessêgo

Beilstein J. Org. Chem. 2011, 7, 1732–1738, doi:10.3762/bjoc.7.203

• parameter than with σ, which indicates that the initial protonation site is the oxygen atom of the sulfonyl group. Keywords: linear free-energy relationships; N-methylbenzenesulfonamides; protonation equilibrium; Introduction Having a knowledge of the protonation equilibrium constants for N

• developed. The second approach to the problem considers that variations in the equilibrium or rate constants in aqueous acidic mixtures may be described by a free-energy linear correlation. This approach was developed by Bunnett and Olsen [25][26] according to the suggestion of Grunwald [27] and Kresge [28