Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• surface entropy and hinder crystal packing. For this reason, it is sometime necessary to manipulate the glycoform to facilitate the crystallization. In the case of the human IgE-FcεRIα [31], Man5-GlcNAc-GlcNAc-Asp-linked glycoforms produced better crystals than in the case where only the Man-GlcNAc-GlcNAc

From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

• function associated to this view is that the cell separates between an inside and an outside. In 1935, James Danielli proposed with Hugh Davson that this embodiment was achieved by formation of a bilayer made of amphiphilic lipid molecules [11]. This process is entropy-driven (life belongs to physics, it

• water by an entropy increase, if a selection process retains the macromolecules in a specific compartment. Surface metabolism at the origin of life is perhaps the simplest way to harness this ubiquitous property of thermodynamics. Samuel Granick, very early on, remarked the important role of transition

• recently proposed by the same author and his colleagues [24]. However, while these syntheses may operate under relatively mild conditions with compounds from volcanic emanations, they still need to be complemented by an entropy-driven process favouring polymerisation. Alternating dry and wet episodes might

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

• Addy Pross and
• Robert Pascal

Beilstein J. Org. Chem. 2017, 13, 665–674, doi:10.3762/bjoc.13.66

• develops these lines of thought and argues against the validity of a thermodynamic approach in which the maximisation of the rate of energy dissipation/entropy production is considered to direct the evolutionary process. More generally, our analysis reaffirms the predominant role of kinetics in the self

• living state? (2) If so, by what mechanistic means can a chemical system self-organise to yield the living state, consistent with the constraints of the Second Law. These considerations infer that an overall spontaneous decrease in entropy is statistically highly unlikely, and for macroscopic systems

• production of entropy in the environment. The identification of such a driving force would make it possible to determine the parameters influencing change, even though no historical information regarding its early expression is available. Furthermore, identification of that driving force could serve as a

Dimerization reactions of aryl selenophen-2-yl-substituted thiocarbonyl S-methanides as diradical processes: a computational study

• Michael L. McKee,
• Grzegorz Mlostoń,
• Katarzyna Urbaniak and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2017, 13, 410–416, doi:10.3762/bjoc.13.44

• with solvation effects (assuming ∆H(solv) = ∆G(solv)) to obtain enthalpies at 298 K in THF (Equation 1). The calculated entropy was used to determine the –T∆S term to form free energies at 298 K in THF (Equation 2). Structures of the reactive intermediates as a diradical 6 or a zwitterion 7 in the

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• of HP-β- and ME-β-CD is endothermic and entropy driven. As native and modified CDs are able to complex some amino acids which constitute peptides and proteins, these molecules can be useful for their separation by capillary zone electrophoresis. In this context, Rathore and Horváth reported that

Diels–Alder reactions in confined spaces: the influence of catalyst structure and the nature of active sites for the retro-Diels–Alder reaction

• Ángel Cantín,
• M. Victoria Gomez and
• Antonio de la Hoz

Beilstein J. Org. Chem. 2016, 12, 2181–2188, doi:10.3762/bjoc.12.208

• . The effect of confinement of the reactant within the pores of the catalyst can decrease the entropy of the activated complex [17][18][19][20][21][22][23][24][25][26][29][30] producing not only an increase of the reaction rate but also a modification of the selectivity. To study this effect, we have

Experimental and theoretical investigations on the high-electron donor character of pyrido-annelated N-heterocyclic carbenes

• Michael Nonnenmacher,
• Dominik M. Buck and
• Doris Kunz

Beilstein J. Org. Chem. 2016, 12, 1884–1896, doi:10.3762/bjoc.12.178

• preferred exchange of the cis-CO ligand (Scheme 2). This is in accordance with the experimental observation of the 13CO exchange. Although the formation of 3a NHC/COapic from 2a and CO is exothermic (ΔH298K,1bar = −11.4 kJ/mol), considering the entropy leads to an endergonic reaction (ΔG298K,1bar = 29.4 kJ

The hydrolysis of geminal ethers: a kinetic appraisal of orthoesters and ketals

• Sonia L. Repetto,
• James F. Costello,
• Craig P. Butts,
• Joseph K. W. Lam and
• Norman M. Ratcliffe

Beilstein J. Org. Chem. 2016, 12, 1467–1475, doi:10.3762/bjoc.12.143

• the anti rotamer 16c would lead to a more rapid elimination of methanol after protonation, consistent with an earlier transition state [29]. Compound 5, which does not have such an accessible flattened ring conformation cannot access this lower entropy trajectory and hence reacts more slowly

On the mechanism of imine elimination from Fischer tungsten carbene complexes

• Philipp Veit,
• Christoph Förster and
• Katja Heinze

Beilstein J. Org. Chem. 2016, 12, 1322–1333, doi:10.3762/bjoc.12.125

• a first order kinetics as anticipated in the absence of a base. An Eyring–Polanyi plot gives an activation enthalpy of ΔH‡ = 54.5 ± 10.4 kJ mol−1 and an activation entropy of ΔS‡ = –193 ± 30 J mol−1 K−1 (Supporting Information File 1, Figure S25). These values give a Gibbs free energy of activation

Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics

• Maria C. Guimarães,
• Mariene H. Duarte,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2016, 12, 760–768, doi:10.3762/bjoc.12.76

• MIA descriptors generated to build the model, a straightforward analysis would not be an easy task using the raw data. Thus, pre-filtration procedures were performed in order to reduce the number of variables. In this sense, the first approach was a measure of Shannon's entropy (SE), corresponding to

A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy

• Steven C. Zimmerman

Beilstein J. Org. Chem. 2016, 12, 125–138, doi:10.3762/bjoc.12.14

• entropy paid by the hydrogen bonding is sufficient to allow the enthalpy of the aromatic stacking to be observed. However, there are other explanations for the high stability observed in the 8·9 complex. The aromatic cleft may serve to desolvate the carboxylic acid, thereby improving its hydrogen bonding

• context of analyzing the vancomycin complex with D–Ala–D–Ala containing peptides, suggested the cost of freezing a free rotation to be between 0.4 to 0.9 kcal/mol – a value that is also close to what we had measured [25]. In Williams’ case, the value was derived from the entropy of fusion within a

Versatile deprotonated NHC: C,N-bridged dinuclear iridium and rhodium complexes

• Albert Poater

Beilstein J. Org. Chem. 2016, 12, 117–124, doi:10.3762/bjoc.12.13

• of Martin et al. [85] which consists of thermal corrections and entropy effects evaluated at 1354 atm [86][87][88][89], with the BP86-d3/TZVP method in the gas phase [90][91]. %VBur calculations: The buried volume calculations were performed with the SambVca package developed by Cavallo et al. [90

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

• Giuseppina Raffaini,
• Antonino Mazzaglia and
• Fabio Ganazzoli

Beilstein J. Org. Chem. 2015, 11, 2459–2473, doi:10.3762/bjoc.11.267

• configurational entropy. On the other hand, taken together the present results in water may provide some clues about the possible kinetics of aggregation: at first there is the fast formation of small clusters comprising few molecules, followed by the further aggregation of these cluster with may add individual

• the alkyl chains: their cooperative effect would then favour the micelle formation vs. the isolated molecules in spite of the entropy loss entailed by the clustering process. As a final remark, we point out that with atomistic MM and MD methods we can model the first nucleation steps which may take

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

• is successfully applied in other biological systems [29][34][35][48]. The non-polar contribution is calculated by the solvent-assessable surface area (SASA) as Where γ was set as 0.0072 kcal/(mol/A2) [49]. The TS term is a solute entropy contribution arising from changes in degrees of freedom

• higher than for electrostatic interactions (ΔEele). Through summation of the solvation free energy (ΔGsolv) and the entropy term (TΔS), the predicted binding free energies (ΔGbind) of the inclusion complexes I and II are similar with values of –8.86 ± 3.25 and –9.06 ± 2.87 kcal/mol, respectively. Thus

• inclusion complex, as seen by a reduction in ΔGsolv at high ethanol percentages. In contrast, the entropies of all systems were likely similar (−T∆S of ≈13 kcal/mol). After combining the interaction energy (1), solvation (2) and entropy (3) terms, the binding affinity of the α-MGS/β-CD complexation at 0–60

Synthesis, structure, and mechanical properties of silica nanocomposite polyrotaxane gels

• Kazuaki Kato,
• Daisuke Matsui,
• Koichi Mayumi and
• Kohzo Ito

Beilstein J. Org. Chem. 2015, 11, 2194–2201, doi:10.3762/bjoc.11.238

• polymer, their inhomogeneous distribution can generate entropic stress. Thus, the origin of elasticity is not the entropy of polymer chains but that of the CDs, and the abnormally small modulus of polyrotaxane gels can be explained by the characteristic elasticity. Similarly, the extremely low modulus of

• the nanocomposite polyrotaxane gels is attributable to the characteristic elasticity originated from the entropy of CDs. Since the infinite network was formed mainly by the covalent bonds between CDs and silica surface, the polymer chains are bound to neither CDs nor silica. If the polymer chains are

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

• between host (H) and guest (G) molecules. This is because, as Etter's rules [40] state, intramolecular hydrogen bonding is stronger than intermolecular one and more probable due to the entropy reasons. In order to construct a molecule capable to form intramolecular hydrogen bonds one should bear in mind

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

• and CO2 insertion occur simultaneously, whereby at a given time three molecules need to orientate themselves into a particular configuration to form the transition state (see Scheme 5). This is demanding with respect to the entropy effects. In both pathways, the CO2 addition to the epoxide was found

• and metal alkoxide. Formation of this associative complex is endergonic due to the entropy effects [45]. The transition state for the CO2 insertion into metal–oxygen bonds has been postulated to be a four-membered ring consisting of the metal, the carbon and two oxygen atoms (Scheme 9) [44]. For this

• each L, the precursor state (preS) was 10–20 kJ·mol−1 more stable than the reactant state (RS). Thus, the change in energy was small with respect to the reactant state. Consistent with an associative step, the entropy change was negative and the change in free energy was positive. Consistent with the

New palladium–oxazoline complexes: Synthesis and evaluation of the optical properties and the catalytic power during the oxidation of textile dyes

• Rym Hassani,
• Mahjoub Jabli,
• Yakdhane Kacem,
• Jérôme Marrot,
• Damien Prim and
• Béchir Ben Hassine

Beilstein J. Org. Chem. 2015, 11, 1175–1186, doi:10.3762/bjoc.11.132

• . Thermodynamic parameters To better understand the degradation process, the pseudo first-order kinetic equation was used to determine the kinetic parameters. The Arrhenius law was used to calculate the activation energy (Ea). The determination of the entropy and the enthalpy of activations (ΔS* and ΔH*) were

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

• matched in order to balance enthalpic gain with entropic loss of the system. In such a setting, a rigid multivalent ligand binding to a flexible receptor can be expected to reduce the entropy of the system upon binding, and thus will result in a partial or complete loss of the multivalent affinity

• and almost negligible entropic contributions , all polyhydroxy-based peptide–polymer conjugates showed significantly stronger generation of heat through binding (enthalpy) together with a pronounced loss in entropy. Binding in all cases was driven mainly by enthalpy, which clearly outweighed the

• observed entropy loss. In the seven peptide–polymer conjugates investigated, increased loading density of ligands led consistently to increased affinity of the multivalent ligand (Table 1). The most significant difference between dextran and the two other polymer carriers was the stoichiometry of the

Influence of length and flexibility of spacers on the binding affinity of divalent ligands

• Susanne Liese and
• Roland R. Netz

Beilstein J. Org. Chem. 2015, 11, 804–816, doi:10.3762/bjoc.11.90

• receptors [1]. Each multivalent ligand consists of several monovalent ligands that are connected via a scaffold. The binding affinity of such a multivalent ligand is determined by the interplay between gain in binding energy and loss of entropy associated with conformational degrees of freedom. The more

• flexible the scaffold is, the better it can adapt to the geometry of the receptor, but the more pronounced on the other hand is the entropy penalty. This simple, qualitative argument shows that the careful choice of the ligand scaffold is essential, in order to benefit from multivalent enhancement. It is

• monovalent ligand binds better than the divalent ligand. In this case the loss in entropy of the spacer is larger than the gain in binding energy due to the multiple binding of ligand units. Inserting the effective concentration from Equation 13 and Equation 23 into Equation 41 and Equation 47, the RBA can

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

• , and the enthalpy ΔH can be directly obtained from the measured data whereas the entropy ΔS is calculated. Due to very weak or absent interactions of R1A3 or R2A5 with Au/MUA nanoparticles it was not possible to determine thermodynamic parameters. Surprisingly, the obtained binding constants are not in

• energy. Nevertheless, all peptide–nanoparticle interactions are entropically favored processes as entropy increases with along with binding energy. Morphological studies of peptide-induced nanoparticle assemblies Cryo TEM was used to gain insight into the morphology of the peptide–nanoparticle aggregates

Probing multivalency in ligand–receptor-mediated adhesion of soft, biomimetic interfaces

• Stephan Schmidt,
• Hanqing Wang,
• Daniel Pussak,
• Simone Mosca and
• Laura Hartmann

Beilstein J. Org. Chem. 2015, 11, 720–729, doi:10.3762/bjoc.11.82

• generally low affinity between sugars and receptors and possibly also by the high flexibility of the polymeric mannose linkers [9]. High molecular flexibility causes a high degree of conformational entropy that negatively affects complex formation between ligands and receptors [23]. Also the design of the

Exploring monovalent and multivalent peptides for the inhibition of FBP21-tWW

• Lisa Maria Henning,
• Sumati Bhatia,
• Miriam Bertazzon,
• Michaela Marczynke,
• Oliver Seitz,
• Rudolf Volkmer,
• Rainer Haag and
• Christian Freund

Beilstein J. Org. Chem. 2015, 11, 701–706, doi:10.3762/bjoc.11.80

• peptides on the hPG particle are not engaged in the interaction with FBP21-tWW. The enthalpy of the interaction is twice as large for the hPG-peptide conjugate as for the monovalent ligand, while the entropy loss upon interaction (−19.5 cal/mol/deg for the interaction with the monovalent ligand and −45.9

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

• thermodynamically and kinetically favorable process for DDC with at least one electron-withdrawing acyl group. At higher temperatures, however, due to the entropy contribution, the dominating process becomes the 1,3-cyclization followed by desulfurization of the obtained thiiranes, which leads to the corresponding

Novel biphenyl-substituted 1,2,4-oxadiazole ferroelectric liquid crystals: synthesis and characterization

• Mahabaleshwara Subrao,
• Dakshina Murthy Potukuchi,
• Girish Sharada Ramachandra,
• Poornima Bhagavath,
• Sangeetha G. Bhat and
• Srinivasulu Maddasani

Beilstein J. Org. Chem. 2015, 11, 233–241, doi:10.3762/bjoc.11.26

• during the thermal studies at 5 °C/min are given in Supporting Information File 1. It is noticed that the mesomorphic thermal range is almost the same in both cases. The data of transition temperatures (TC), the enthalpy changes (∆H) across the transitions and entropy changes (∆S) of 13a (Ph.Ox.C*Cn) and

• changes (kJ/mol) and entropy changes (J/mol/K) of the 13a (Ph.Ox.C*Cn) series. Phase transition temperatures (°C), enthalpy changes (kJ/mol) and entropy changes (J/mol/K) of the 13b (C12Ox.C*Cn) series. Supporting Information The experimental procedure for the synthesis of 13ap–13as and 13bp–13bs with