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

• metallacycles are 7.7 kcal/mol above and 12.1 kcal/mol above the 14e species. To better understand the different stability of the metallacycle relative to the coordination intermediate of the 1st and 2nd generation catalysts we investigated the thermodynamics of the reaction shown in Figure 8. E1 is the energy

Is organic chemistry science – and does this question make any sense at all?

• Andreas Kirschning and
• Thomas A. C. Reydon

Beilstein J. Org. Chem. 2015, 11, 893–896, doi:10.3762/bjoc.11.100

• fundamental science. A well-known example is the reduction of thermodynamics to statistical mechanics [15][17], in which a bridge law would identify temperature with the mean kinetic energy of the constituent molecules of a gas. The science that is reduced is then explained by the science to which it is

Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands

• Katharina Koschek,
• Vedat Durmaz,
• Oxana Krylova,
• Marek Wieczorek,
• Shilpi Gupta,
• Martin Richter,
• Alexander Bujotzek,
• Christina Fischer,
• Rainer Haag,
• Christian Freund,
• Marcus Weber and
• Jörg Rademann

Beilstein J. Org. Chem. 2015, 11, 837–847, doi:10.3762/bjoc.11.93

• understanding of structure–activity relationships of polymeric ligands. For this purpose, the thermodynamics and the stoichiometry of protein binding events were determined experimentally for all multivalent ligands. Finally, atomistic molecular dynamics simulations were conducted in order to rationalize the

Impact of multivalent charge presentation on peptide–nanoparticle aggregation

• Daniel Schöne,
• Boris Schade,
• Christoph Böttcher and
• Beate Koksch

Beilstein J. Org. Chem. 2015, 11, 792–803, doi:10.3762/bjoc.11.89

• size of the peptide and finally the charge density plays an important role for its aggregation efficiency. Furthermore, we could show that the quaternary structure of the peptide has important consequences for the formed nanoparticle assemblies, as well as for the thermodynamics of aggregation. First

Discrete multiporphyrin pseudorotaxane assemblies from di- and tetravalent porphyrin building blocks

• Mirko Lohse,
• Larissa K. S. von Krbek,
• Sebastian Radunz,
• Suresh Moorthy,
• Christoph A. Schalley and
• Stefan Hecht

Beilstein J. Org. Chem. 2015, 11, 748–762, doi:10.3762/bjoc.11.85

• dealing with the daunting task to quantify the binding constants for the di- and tetravalent multiporphyrin complexes for example using isothermal calorimetry (ITC), in order to analyze the thermodynamics and kinetics of multivalent binding in these architectures in detail. In the future, we will continue

First principle investigation of the linker length effects on the thermodynamics of divalent pseudorotaxanes

• Andreas J. Achazi,
• Doreen Mollenhauer and
• Beate Paulus

Beilstein J. Org. Chem. 2015, 11, 687–692, doi:10.3762/bjoc.11.78

• the crown/ammonium binding motif. In this motif ammonium can bind on top of small crown ethers, e.g., crown-6, or can pass through larger crown ethers, e.g., crown-8. Jiang et al. [16] have investigated the assembly thermodynamics and kinetics of divalent crown-8/ammonium pseudorotaxanes with

Anionic sigmatropic-electrocyclic-Chugaev cascades: accessing 12-aryl-5-(methylthiocarbonylthio)tetracenes and a related anthra[2,3-b]thiophene

• Laurence Burroughs,
• John Ritchie,
• Mkhethwa Ngwenya,
• Dilfaraz Khan,
• William Lewis and
• Simon Woodward

Beilstein J. Org. Chem. 2015, 11, 273–279, doi:10.3762/bjoc.11.31

• NSCCS Computational Service. We thank Dr. Darren Walsh (University of Nottingham) for the help with the electrochemical studies. We thank European Thermodynamics for their involvement in the programme (JR) and use of the I19 Diamond Facility [31] is acknowledged.

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• requires a detailed knowledge of the energetics, thermodynamics and structural equilibrium – surprisingly few studies endeavoured to determine important parameters for such classical intercalator as ethidium bromide [49]. The most recent and very extensive theoretical study compared positively charged

Improving ITC studies of cyclodextrin inclusion compounds by global analysis of conventional and non-conventional experiments

• Eléonore Bertaut and
• David Landy

Beilstein J. Org. Chem. 2014, 10, 2630–2641, doi:10.3762/bjoc.10.275

• stability, enthalpy, or solubility. Keywords: cyclodextrins; global analysis; inclusion compounds; isothermal titration calorimetry; non-conventional experiments; Introduction The stability and thermodynamics of cyclodextrin inclusion compounds in solutions may be investigated with various analytical

Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

• Christine Beuck and
• Elmar Weinhold

Beilstein J. Org. Chem. 2014, 10, 2293–2306, doi:10.3762/bjoc.10.239

• helicases, which locally separate the two DNA strands, are important to enable vital cellular processes like DNA replication, DNA repair, chromatin remodeling and telomere maintenance [78][79][80][81]. Cross-linked DNA will not only provide a useful tool to study DNA binding and base flipping thermodynamics

Organic synthesis using photoredox catalysis

• Axel G. Griesbeck

Beilstein J. Org. Chem. 2014, 10, 1097–1098, doi:10.3762/bjoc.10.107

• synthesis, the principles of photoredox chemistry serve as guidelines, i.e., photoinduced electron transfer (PET) kinetics and thermodynamics as expressed in the Rehm–Weller and Marcus equations. For catalytic versions, the photoinduced redox processes require efficient and robust photocatalysts, and in

Tailoring of organic dyes with oxidoreductive compounds to obtain photocyclic radical generator systems exhibiting photocatalytic behavior

• Christian Ley,
• Julien Christmann,
• Ahmad Ibrahim,
• Luciano H. Di Stefano and
• Xavier Allonas

Beilstein J. Org. Chem. 2014, 10, 936–947, doi:10.3762/bjoc.10.92

• thermodynamics and the kinetics is necessary. Thermodynamics of the PCIS Obviously, every mixture of an acceptor, a donor and a dye, would not give rise to a photocatalytic behavior. The components should be selected with care in order to get a cyclic behavior instead of competitive parallel reactions [54] where

• electron acceptor. Photocatalytic behavior occurring in three component PIS. PS: photosensitizer; 1,3PS*: singlet and triplet PS excited states; A: electron acceptor; A•−: reduced form of acceptor; D: electron donor and D•+: oxidized donor. Thermodynamics of an oxidative three components PCIS, a) ground

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

• the rotamers which can readily be separated by HPLC as well as TLC. The experimental results of the different methods were compared to each other as well as to results obtained by DFT calculations. Keywords: amides; density functional calculations; dynamic HPLC; rotamers; thermodynamics

Continuous flow nitration in miniaturized devices

• Amol A. Kulkarni

Beilstein J. Org. Chem. 2014, 10, 405–424, doi:10.3762/bjoc.10.38

3-Pyridinols and 5-pyrimidinols: Tailor-made for use in synergistic radical-trapping co-antioxidant systems

• Luca Valgimigli,
• Daniele Bartolomei,
• Riccardo Amorati,
• Evan Haidasz,
• Jason J. Hanthorn,
• Susheel J. Nara,
• Johan Brinkhorst and
• Derek A. Pratt

Beilstein J. Org. Chem. 2013, 9, 2781–2792, doi:10.3762/bjoc.9.313

• same HBA ability as water [31], which is attributed a reliable  = 0.38 [29][30]. As such, we recommend a value of of 0.39 for acetonitrile. Computational thermodynamics. The rational design of synergistic co-antioxidant mixtures requires knowledge of not only the kinetics of the reactions of 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

• in intensity of the individual peaks. For tetrahydrothiophene THTP, the same polarization pattern (polarizations for Hα only, i.e., CIDNP originating from radical pairs ) and kinetic behavior of the polarizations was found, which is not surprising given the very similar thermodynamics (ionization

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

Establishing the concept of aza-[3 + 3] annulations using enones as a key expansion of this unified strategy in alkaloid synthesis

• Aleksey I. Gerasyuto,
• Zhi-Xiong Ma,
• Grant S. Buchanan and
• Richard P. Hsung

Beilstein J. Org. Chem. 2013, 9, 1170–1178, doi:10.3762/bjoc.9.131

• study was likely determined by the kinetics (kB versus kR) in the deprotonation step or the tautormerization process from the iminium salt 13, and not by thermodynamics as originally proposed. Resolving this interesting literature controversy added extra incentive for us to pursue propyleine

Spectroscopic characterization of photoaccumulated radical anions: a litmus test to evaluate the efficiency of photoinduced electron transfer (PET) processes

• Maurizio Fagnoni,
• Stefano Protti,
• Davide Ravelli and
• Angelo Albini

Beilstein J. Org. Chem. 2013, 9, 800–808, doi:10.3762/bjoc.9.91

• air equilibration of the 30 min photolyzed solution (green); (f) PME (4 × 10−4 M) in the presence of OXA (5.0 × 10−2 M) after 2 (red) and 30 (blue) min irradiation and after air equilibration of the 30 min photolyzed solution (green). Thermodynamics of the redox processes discussed (solid arrows

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

• . Structural drawing of β-CD [43], according to structural data (CSD-ID BUVSEQ03) from Zabel et al. [38], generated by VMD 1.8.4 showing the intramolecular hydrogen bonds between OH-3 and O-2. Thermodynamics of the inclusion of 4-tert-butyl-benzoate in β-cyclodextrin 1 and its methyl derivatives 2–6

• . Thermodynamics of the inclusion of adamantane-1-carboxylate in β-cyclodextrin 1 and its methyl derivatives 2–6. List of the methylated β-CD derivatives used in this contribution. Acknowledgements The author thanks Andreas Steffen for drawing the structure of β-CD (Figure 3), and Annegret Engelke for performing

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

• and H-transfer. The thermodynamics of both routes are comparable at all levels. Once ternary complex Init10 is formed, there are few C–C bond-forming pathways. Based on the extensive conformational search, we were able to find eleven competing transition states (Figure 3 and Figure 4), six of which

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

• thermodynamics of CH3CCl3 (2) entering and leaving the gated molecular basket 1. We found that the encapsulation is first-order in basket 1 and guest 2, while the decomplexation is zeroth-order in the guest. Importantly, the interchange mechanism in which a molecule of CH3CCl3 directly displaces the entrapped

• trap CH3CCl3 (2) as a guest, and we hereby elaborate on the equilibrium thermodynamics of the recognition event (Figure 2). The incremental addition of 2 to a CD2Cl2 solution of 1 (0.67 mM, 298.0 K) caused considerable 1H NMR chemical shifts of the resonances corresponding to the presence of the basket

(How) does 1,3,5-triethylbenzene scaffolding work? Analyzing the abilities of 1,3,5-triethylbenzene- and 1,3,5-trimethylbenzene-based scaffolds to preorganize the binding elements of supramolecular hosts and to improve binding of targets

• Xing Wang and
• Fraser Hof

Beilstein J. Org. Chem. 2012, 8, 1–10, doi:10.3762/bjoc.8.1

• rotational barriers Although kinetics has no bearing on binding thermodynamics, we sought also to understand computationally the dynamics of these different hosts. Molecular-dynamics simulations carried out at 300 K showed little or no dynamic exchange of conformations. Simulations carried out at the

Highly efficient cyclosarin degradation mediated by a β-cyclodextrin derivative containing an oxime-derived substituent

• Michael Zengerle,
• Florian Brandhuber,
• Christian Schneider,
• Franz Worek,
• Georg Reiter and
• Stefan Kubik

Beilstein J. Org. Chem. 2011, 7, 1543–1554, doi:10.3762/bjoc.7.182

• magnitude higher. More detailed information about the kinetics and thermodynamics of the reaction could be obtained by following the dependency of the rate of reaction on the GF concentration (Michaelis–Menten kinetics). These measurements are, however, demanding in light of the complexity of the currently

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

• kcal·mol−1, since the gas-phase rotational/translational entropy of coordination from classical statistical thermodynamics is generally considered to overestimate the coordination entropy in solution. The –TΔS contribution of 10 kcal·mol−1 is the experimental coordination entropy of C2H4 to a Pd-complex