Supramolecular polymer assembly in aqueous solution arising from cyclodextrin host–guest complexation

• Jie Wang,
• Zhiqiang Qiu,
• Yiming Wang,
• Li Li,
• Xuhong Guo,
• Duc-Truc Pham,
• Stephen F. Lincoln and
• Robert K. Prud’homme

Beilstein J. Org. Chem. 2016, 12, 50–72, doi:10.3762/bjoc.12.7

• the thermodynamics of the process [66]. As a result, the guest often exhibits a substantial change in its UV–vis, fluorescence and 1H NMR spectra upon complexation, and there is usually a significant enthalpy change. Consequently, UV–vis [67], fluorescence [68] and 1H NMR [69] spectroscopy and

Bright molecules for sensing, computing and imaging: a tale of two once-troubled cities

• A. Prasanna de Silva

Beilstein J. Org. Chem. 2015, 11, 2774–2784, doi:10.3762/bjoc.11.298

• needed to have a binding strength (βNa) of 10 M−1 in neutral water. An N-(2-methoxy)phenylaza-15-crown-5 ether [37] fitted the bill, besides having good selectivity characteristics. PET thermodynamics were matched by the use of a 4-aminonaphthalimide fluorophore [38][39][40], which, in the presence of

Learning from the unexpected in life and DNA self-assembly

• Jennifer M. Heemstra

Beilstein J. Org. Chem. 2015, 11, 2713–2720, doi:10.3762/bjoc.11.292

• validation of our hypothesis regarding the thermodynamics of split aptamer assembly. In the short term, this allowed us to overcome the challenge of background signal by reducing the ionic strength, and we were delighted to observe dose-dependent ligation of the split aptamer fragments with increasing

• concentrations of cocaine [11]. While the insight we gained into balancing the thermodynamics of split aptamer assembly seemed fairly straightforward, the lessons we learned from this unexpected experimental result played a critical role in our success with many of the experiments that soon followed. Having

• structurally biased library to generate aptamers having the necessary three-way junction architecture [15]. Using our insights regarding the thermodynamics of split aptamer assembly, we developed a method for rapidly and reliably converting these three-way junction aptamers into split aptamers (Figure 4b). We

Smart molecules for imaging, sensing and health (SMITH)

• Bradley D. Smith

Beilstein J. Org. Chem. 2015, 11, 2540–2548, doi:10.3762/bjoc.11.274

• ) Two views of the threaded complex highlighting the structural features controlling the threading kinetics and thermodynamics. Acknowledgements First and foremost, I am extremely grateful to all of the students who have worked in my lab over years, and the names of many are listed in the references

Biocatalysis for the application of CO₂ as a chemical feedstock

• Apostolos Alissandratos and
• Christopher J. Easton

Beilstein J. Org. Chem. 2015, 11, 2370–2387, doi:10.3762/bjoc.11.259

• the reductive TCA cycle (Scheme 2) isocitrate dehydrogenase catalyses the carboxylation of 2-oxoglutarate (6) to produce isocitrate (7). Exploitation in biotechnological applications has been challenging due to the unfavourable thermodynamics of the carboxylation. Recently, the use of purified

Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex

• Chompoonut Rungnim,
• Sarunya Phunpee,
• Manaschai Kunaseth,
• Supawadee Namuangruk,
• Kanin Rungsardthong,
• Thanyada Rungrotmongkol and
• Uracha Ruktanonchai

Beilstein J. Org. Chem. 2015, 11, 2306–2317, doi:10.3762/bjoc.11.251

• addition with complexation [2][3][6] have demonstrated that the thermodynamics underlying the interactions between host–guest molecules can be significantly changed in these instances. In these cases, the co-solvent can also occupy the CD cavity in conjunction with the guest (drug) molecules to form CD

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