Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

β-Cyclodextrin- and adamantyl-substituted poly(acrylate) self-assembling aqueous networks designed for controlled complexation and release of small molecules

• Liang Yan,
• Duc-Truc Pham,
• Philip Clements,
• Stephen F. Lincoln,
• Jie Wang,
• Xuhong Guo and
• Christopher J. Easton

Beilstein J. Org. Chem. 2017, 13, 1879–1892, doi:10.3762/bjoc.13.183

• ]. Generally, the retention and the release of the drug is controlled by the thermodynamics of drug complexation and in some systems the drug release is stimulated by either pH variation [28][30][34] or light irradiation [38][45]. The drug types include small molecular species, exemplified by diflunisal

Grip on complexity in chemical reaction networks

• Albert S. Y. Wong and
• Wilhelm T. S. Huck

Beilstein J. Org. Chem. 2017, 13, 1486–1497, doi:10.3762/bjoc.13.147

• reaction scheme and rate equations could be approximated based on the predictability in the thermodynamics of DNA binding. In presence of an excess of the source ssDNA (denoted by G for “Grass”), traveling waves of a predator–prey molecular network (similar to the spatio-temporal patterns in the BZ

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

• defying the second law of thermodynamics, as the system as a whole still evolves towards increasing entropy. With replicator complexification having been made feasible, it then only depends on evolutionary possibilities and benefits whether complexification also actually occurs. In order for the

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

• is not a fight against the second principle of thermodynamics), using the global distribution of water molecules as a driving force to order lipids into cell-like structures (of a considerable variety, even in bacteria [12]). Membranes also contain proteins as essential components. It took very long

• 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

Continuous-flow processes for the catalytic partial hydrogenation reaction of alkynes

• Carmen Moreno-Marrodan,
• Francesca Liguori and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2017, 13, 734–754, doi:10.3762/bjoc.13.73

• [34][35], thermodynamics [36][37], structure–activity relationships [38][39] have been extensively described elsewhere, therefore they are out of the scope of this review. Herein the focus is on the various catalytic reactor systems and technological solutions reported in the literature for this

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

• logical bridge connecting the general rules governing change in the universe with Darwin's theory of evolution. Indeed, analysis of the thermodynamics of the processes considered to underlie life’s emergence might assist in closing the conceptual gap that continues to separate the physical and life

• from equilibrium It has recently been claimed that thermodynamics could drive the self-organisation of life through an increase of energy dissipation rates [22][23], or, alternatively, in a continuing focus on the energy facet, that the evolutionary process takes place such that the total energy flux

• will be discussed, that thermodynamic approach is opposed by more recent theoretical considerations, as expressed by Ross et al. [37] and our own analyses, described subsequently. More detailed views on the role of thermodynamics in biology have been critical of the position that natural selection

Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

• Monica Ferro,
• Franca Castiglione,
• Nadia Pastori,
• Carlo Punta,
• Lucio Melone,
• Walter Panzeri,
• Barbara Rossi,
• Francesco Trotta and
• Andrea Mele

Beilstein J. Org. Chem. 2017, 13, 182–194, doi:10.3762/bjoc.13.21

• detail two models: the classical I–S model and the I–I*–S model. The classical I–S model This theoretical model, initially developed by Mehring [15], is based on the classical spin thermodynamics. The system is described as consisting of a lattice with a huge heat capacity and two subsystems, the

Effects of solvent additive on “s-shaped” curves in solution-processed small molecule solar cells

• John A. Love,
• Shu-Hua Chou,
• Ye Huang,
• Guilllermo C. Bazan and
• Thuc-Quyen Nguyen

Beilstein J. Org. Chem. 2016, 12, 2543–2555, doi:10.3762/bjoc.12.249

• extraction, it significantly reduces the magnitude of the effects, removing the dramatic s-shape of the curve. Thin film X-ray diffraction Changes in device performance upon addition of solvent additives are typically ascribed to improvements in the BHJ nanostructure by affecting the thermodynamics and

Organic chemistry meets polymers, nanoscience, therapeutics and diagnostics

• Vincent M. Rotello

Beilstein J. Org. Chem. 2016, 12, 1638–1646, doi:10.3762/bjoc.12.161

• –protein interactions using the tabula rasa-based particles mimicked the thermodynamics of protein–protein interactions quite well [49]. Once we were able to have proteins and nanoparticles work in harmony [50] we started working on designing systems with emergent behavior, i.e., where the particle–protein

Catalytic Chan–Lam coupling using a ‘tube-in-tube’ reactor to deliver molecular oxygen as an oxidant

• Carl J. Mallia,
• Paul M. Burton,
• Alexander M. R. Smith,
• Gary C. Walter and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2016, 12, 1598–1607, doi:10.3762/bjoc.12.156

• favourable thermodynamics with an increase in the electropositive nature of boron, which in turn increases the rate of the transmetallation step. Changing the group at the 4-position of the phenylboronic acid gave good yields for both electron-rich (19, 79% yield) and electron-poor (33, 76% yield

From steroids to aqueous supramolecular chemistry: an autobiographical career review

• Bruce C. Gibb

Beilstein J. Org. Chem. 2016, 12, 684–701, doi:10.3762/bjoc.12.69

• facet of these collaborations is the SAMPL exercise in which we and other supramolecular chemists a priori determine the thermodynamics of complexation for a series of processes, and keep the results under wraps whilst computational groups around the world attempt to predict the data [52]. This

• competition gives the computationalists a unique opportunity to try and hone their skills, which in return provides feedback to those interested in the a priori prediction of the thermodynamics of binding. For example, being able to predict ahead of time which ligands binds best to a protein binding-site has

• Emergency Management Administration (FEMA). Our first results that came out from this period demonstrated that the thermodynamics of guest binding to octa-acid were extremely perturbed by the presence of different salts [55]. As expected, the Hofmeister effect was indeed in operation: salting-out sodium

Creating molecular macrocycles for anion recognition

• Amar H. Flood

Beilstein J. Org. Chem. 2016, 12, 611–627, doi:10.3762/bjoc.12.60

• counter cations, their binding constants were not constant! In our case, when we changed concentrations, the binding constants for the 1:1 triazolophane–chloride complexes were not constant. We ended up taming our menagerie of ion pairing and complexation equilibria in a tour de force thermodynamics study

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

• 3H-H and 3H-T (where H-H = head-to-head and H-T = head-to-tail). By DFT calculations here we contribute in the understanding of the thermodynamics of the subsequent C,N-bridged dinuclear iridium and rhodium complexes [59], and the facility for the interconversion between these latter dimeric species

• the H-H coordination was not locate for 5, and further thermodynamics do not support the H-H coordination for 5, with an energy endergonicity of 6.7 kcal/mol with respect the previous corresponding complex 4. Oxidative addition of MeI to 5 affords complex 6, in an exergonic release of 16.5 kcal/mol

• NHC here have been studied in detail by DFT calculations. This is a contribution in the understanding of the thermodynamics of the subsequent C,N-bridged dinuclear iridium and rhodium complexes defined by Braunstein et al. [59] and the facility for the interconversion between these latter dimeric

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