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

Valence isomerization of cyclohepta-1,3,5-triene and its heteroelement analogues

• Helen Jansen,
• J. Chris Slootweg and
• Koop Lammertsma

Beilstein J. Org. Chem. 2011, 7, 1713–1721, doi:10.3762/bjoc.7.201

• NMR measurements showed that the slightly homoaromatic boat conformation is prone to undergo a degenerate ring flip via an antiaromatic C2v transition with a free energy barrier of 5.7 kcal·mol−1 in CBrF3 [18] and 6.3 kcal·mol−1 in CF2Cl2 [19][20][21]. Cycloheptatriene is in equilibrium with bicyclo

Dependency of the regio- and stereoselectivity of intramolecular, ring-closing glycosylations upon the ring size

• Patrick Claude,
• Christian Lehmann and
• Thomas Ziegler

Beilstein J. Org. Chem. 2011, 7, 1609–1619, doi:10.3762/bjoc.7.189

• size spacer n = 2 (constitutions 6d, 7d, 8d, and further the isomer β(1→2), were not observed). The various regio- and stereoisomers were modeled and subjected to molecular dynamics (MD) runs of at least 5000 ps, wherefrom the observed major diastereomer 8d emerged with a lowest free energy by more

• subjected to molecular dynamics (MD) runs of at least 5000 ps, wherefrom the observed major diastereomer 8c, α(1→2), in its lowest conformation was again obtained with a free energy that was 2.3 kcal/mol lower than that for the next highest diastereomer 7c, α(1→3). Most-stable product conformations for the

• diastereomer 7b, α(1→3), in its lowest conformation was obtained with a free energy that was 1.8 kcal/mol lower than that for the next highest diastereomer 8b, α(1→2). Most-stable product conformations for the cyclo-glycosidation reaction with ring size spacer n = 5 (constitutions 6a, 7a, 8a, and further the

Recent advances in direct C–H arylation: Methodology, selectivity and mechanism in oxazole series

• Cécile Verrier,
• Pierrik Lassalas,
• Laure Théveau,
• Guy Quéguiner,
• François Trécourt,
• Francis Marsais and
• Christophe Hoarau

Beilstein J. Org. Chem. 2011, 7, 1584–1601, doi:10.3762/bjoc.7.187

• demonstrating that the C5 (versus C2) position is slightly favoured under a carbonate-assisted internal CMD mechanism in the oxazole-4-carboxylate series, through DFT calculations of the Gibbs free energy of the CMD transition state calculated at the C2 and C5 positions (Scheme 22a), Hoarau developed novel

Chiral gold(I) vs chiral silver complexes as catalysts for the enantioselective synthesis of the second generation GSK-hepatitis C virus inhibitor

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

Beilstein J. Org. Chem. 2011, 7, 988–996, doi:10.3762/bjoc.7.111

• reaction proceeds to a concerted but highly asynchronous cycloaddition in which the endo-approach of the dipolarophile is favoured due to a stabilizing interaction of the carboxylic group and the metallic centre. The computed activation Gibbs free energy barrier associated with the formation of (2S,4S,5R

Alkene selenenylation: A comprehensive analysis of relative reactivities, stereochemistry and asymmetric induction, and their comparisons with sulfenylation

• Vadim A. Soloshonok and
• Donna J. Nelson

Beilstein J. Org. Chem. 2011, 7, 744–758, doi:10.3762/bjoc.7.85

• magnitude greater (Table 1, entries 20 versus 21, or 26 versus 27). 3. Alkyl branching α to C=C: The data obtained in this study pointed to a new steric effect in linear free energy relationships, which can be defined as alkyl group α-branching. Thus, within each line fit, there is a clear trend dependent

Gold-catalyzed heterocyclizations in alkynyl- and allenyl-β-lactams

• Benito Alcaide and
• Pedro Almendros

Beilstein J. Org. Chem. 2011, 7, 622–630, doi:10.3762/bjoc.7.73

• (DFT) calculations were performed to obtain insight on various aspects of this reactivity and indicated the selective activation of the allene and alkyne component. Free energy profile [kcal mol–1] for the transformation of γ-allenol I into the tetrahydrofuran type 9. Gold-catalyzed cyclization of 4

Kinetic evaluation of the solvolysis of isobutyl chloro- and chlorothioformate esters

• Malcolm J. D’Souza,
• Matthew J. McAneny,
• Dennis N. Kevill,
• Jin Burm Kyong and
• Song Hee Choi

Beilstein J. Org. Chem. 2011, 7, 543–552, doi:10.3762/bjoc.7.62

• activation values obtained from Arrhenius plots for 1 in these five solvents are reported. The specific rates of solvolysis were analyzed using the extended Grunwald–Winstein equation. Results obtained from correlation analysis using this linear free energy relationship (LFER) reinforce our previous

The arene–alkene photocycloaddition

• Ursula Streit and
• Christian G. Bochet

Beilstein J. Org. Chem. 2011, 7, 525–542, doi:10.3762/bjoc.7.61

• (simplified) Weller equation determines whether or not electron transfer will occur from an excited-state (Equation 1) [24][25]. For the reaction of an excited aromatic moiety with an alkene, this means that if the change in free energy, determined by the Weller equation, is negative. with ΔGET = free

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

• (vide supra) for each conformer by a range of populations (x) of 1a/b. The best fit to experiment is obtained at ~55% 1a/b, (and thus ~45% 2a/b), corresponding to a free energy difference of ca. 2.1–2.2 kJ/mol between conformers 1a/b and 2a/b. This compares extremely well with the highest level

• calculations, which suggest a corresponding free energy difference of ca. 1.5 kJ/mol. This remarkable match in populations and energies supports the proposition that fitting populations of conformers from the NOE-derived distances is an inherently accurate approach when the geometries of the contributing

Synthesis of Ru alkylidene complexes

• Renat Kadyrov and
• Anna Rosiak

Beilstein J. Org. Chem. 2011, 7, 104–110, doi:10.3762/bjoc.7.14

• these data gave activation enthalpy ΔH≠= 13.7 kcal/mol. From the rate constant at 303 K the value of free energy of activation (ΔG≠303K = 12.6 kcal/mol) was also calculated. This is substantially higher than several calculated (Ea = 4.4 kcal/mol) [11][12] and experimentally estimated (Ea = 5.7 kcal/mol

The intriguing modeling of cis–trans selectivity in ruthenium-catalyzed olefin metathesis

• Naeimeh Bahri-Laleh,
• Raffaele Credendino and
• Luigi Cavallo

Beilstein J. Org. Chem. 2011, 7, 40–45, doi:10.3762/bjoc.7.7

• metathesis with the Ru–propylidene moiety, or propene reactivity with the Ru–methylidene moiety, which would be the other Ru–alkylidene bonds present in the reaction mixture after complete activation of the starting precatalyst, are not considered. Results and Discussion The free energy profile in CH2Cl2 for

• into the most stable metallacycle. For this reason, the energy profile of Figure 1 suggests that the most likely event from Co2-cis and Co2-trans is not product release, but rather their transformation into MCy2-cis and MCy2-trans. The escape from Co2-cis and Co2-trans is controlled by the free energy

Stereoselectivity of supported alkene metathesis catalysts: a goal and a tool to characterize active sites

• Christophe Copéret

Beilstein J. Org. Chem. 2011, 7, 13–21, doi:10.3762/bjoc.7.3

• most acyclic alkenes) has a free energy close to 0 and is reversible, the (E/Z) ratio readily evolves towards a thermodynamic value [(E/Z) ≥ 3 for di-substituted alkenes] via metathesis, and all the valuable kinetic stereochemical information is easily lost, and consequently special care has to be

Kinetics and mechanism of vanadium catalysed asymmetric cyanohydrin synthesis in propylene carbonate

• Michael North and
• Marta Omedes-Pujol

Beilstein J. Org. Chem. 2010, 6, 1043–1055, doi:10.3762/bjoc.6.119

• energies of activation (ΔG‡) at 273 K are similar at 53.1 and 57.5 kJ mol−1 for reactions carried out in propylene carbonate and dichloromethane, respectively. (kB = Boltzmann’s constant, h = Planck’s constant, R = gas constant) Since differences in the Gibbs free energy of activation could not account for

Catalysis: transition-state molecular recognition?

• Ian H. Williams

Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117

• concept. It is shown that reactant binding is intrinsically inhibitory, and that attempts to design catalysts that focus simply upon attractive interactions in a binding site may fail. Free-energy changes along the reaction coordinate for SN2 methyl transfer catalysed by the enzyme catechol-O-methyl

• ) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically. Keywords: catalysis; computational simulation; enzymes; molecular recognition; transition state; Introduction “Molecular recognition of transition states” was the title of a paper presented by

• free energy surface) and a transition structure (corresponding to a saddle point on a potential energy surface). The commonly assumed identity between the two terms is often reasonable for small, “simple” systems in vacuum, for which it may be sufficient to model the TS by first finding a transition

Symmetry breaking and structure of a mixture of nematic liquid crystals and anisotropic nanoparticles

• Marjan Krasna,
• Matej Cvetko and
• Milan Ambrožič

Beilstein J. Org. Chem. 2010, 6, No. 74, doi:10.3762/bjoc.6.74

• magnetic field towards the perpendicular direction. Here we assume that originates from magnetic NPs, where μ0 is the magnetic permittivity constant and represents the magnetization of NPs due to the magnetic dipole moment . The resulting quadrupolar magnetic field free energy density change ΔfB is

• approximately given by where Δχ is the magnetic anisotropy of LC molecules [6] (which can be either positive or negative). Furthermore, introducing an elongated NP of length d into a LC, which via surface anchoring enforces elastic distortion in LC medium, typically gives rise to free energy penalties of the

RAFT polymers for protein recognition

• Alan F. Tominey,
• Julia Liese,
• Sun Wei,
• Klaus Kowski,
• Thomas Schrader and
• Arno Kraft

Beilstein J. Org. Chem. 2010, 6, No. 66, doi:10.3762/bjoc.6.66

• affinity. We therefore tentatively explain the gain in free energy by an increased classical hydrophobic effect due to the presence of additional nonpolar cyclohexyl residues throughout the polymer chain. For biological applications, it is desirable to keep the polymer size close to the size of the protein

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

Synthesis and binding studies of two new macrocyclic receptors for the stereoselective recognition of dipeptides

• Ana Maria Castilla,
• M. Morgan Conn and
• Pablo Ballester

Beilstein J. Org. Chem. 2010, 6, No. 5, doi:10.3762/bjoc.6.5

• showed neither enantio- nor diastereoselectivity in the recognition of the same substrates (Table 3). The difference in free energy measured for the complexes of 2 with the four diastereoisomers of Ala-Ala was in the order of 0.3 kcal/mol. We also investigated the complexation affinity of the cyclic

Mitomycins syntheses: a recent update

• Jean-Christophe Andrez

Beilstein J. Org. Chem. 2009, 5, No. 33, doi:10.3762/bjoc.5.33