Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics

• Laura Carro

Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267

• in fact there are focal points (i.e., hot spots or hot segments) that contribute to the majority of the binding energy [17][18]. Targeting these “druggable” sites can therefore be used for the rational design of new therapeutic compounds that can disrupt those critical interactions. However, their

Tetrathiafulvalene – a redox-switchable building block to control motion in mechanically interlocked molecules

• Hendrik V. Schröder and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2018, 14, 2163–2185, doi:10.3762/bjoc.14.190

• 303+ state and the 302(●+)/304+ states. The authors explain the discrepancy by the additional binding energy of the dihydroxynaphthalene stations in 294+ to the cyclobis(paraquat-4,4′-biphenylene) wheel. Therefore, the Coulomb repulsion and the subsequent expulsion of the TTF2+ units from the cavity

A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

• Claudia Lar,
• Adrian Woiczechowski-Pop,
• Attila Bende,
• Ioana Georgeta Grosu,
• Natalia Miklášová,
• Elena Bogdan,
• Niculina Daniela Hădade,
• Anamaria Terec and
• Ion Grosu

Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115

• the deformation potential of the cryptand is +11.85 kcal/mol giving an overall binding energy of −17.43 kcal/mol. The stacking distances between the aromatic ring of the 1,5-dihydroxynaphthalene molecule and the cryptand caps are 3.17 Å and 3.20 Å, respectively. Due to the discrepancies between the

• the anthracene depending on the constrained distance are: −6.00 kcal/mol (blue), −3.74 kcal/mol (green), −2.63 kcal/mol (red) and −0.76 kcal/mol (grey). This decrease of the binding energy tells us that even for the anthracene the fitting dynamics is not a straightforward process. Conclusion The 1,3,5

Novel unit B cryptophycin analogues as payloads for targeted therapy

• Eduard Figueras,
• Adina Borbély,
• Mohamed Ismail,
• Marcel Frese and
• Norbert Sewald

Beilstein J. Org. Chem. 2018, 14, 1281–1286, doi:10.3762/bjoc.14.109

• oriented towards the GDP binding site that might influence GTP hydrolysis. Compound 22 with the triethylene glycol-based substituent prevents correct binding, the binding energy was decreased and mainly nonspecific interactions outside the binding pocket were observed (Figure 3). This was not the case for

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

Synthesis and application of trifluoroethoxy-substituted phthalocyanines and subphthalocyanines

• Satoru Mori and
• Norio Shibata

Beilstein J. Org. Chem. 2017, 13, 2273–2296, doi:10.3762/bjoc.13.224

• is small [21][22]. As a result, compounds into which fluorine has been introduced may show beneficial changes in their properties. In addition, among the chemical bonds formed by carbon, fluorine bonds have the highest binding energy [23], such that fluorine-containing compounds often show resistance

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• possible interference, of the solvent molecules. The gas-phase stability of such a complex, depending on the nature of interactions occurring between molecules within a complex, may reflect the solution binding behavior, in particular when polar interactions greatly contribute to the overall binding energy

Encaging palladium(0) in layered double hydroxide: A sustainable catalyst for solvent-free and ligand-free Heck reaction in a ball mill

• Wei Shi,
• Jingbo Yu,
• Zhijiang Jiang,
• Qiaoling Shao and
• Weike Su

Beilstein J. Org. Chem. 2017, 13, 1661–1668, doi:10.3762/bjoc.13.160

• . The Pd loading of catalyst was 8.5 wt %, and the molar ratio of Mg and Al in LDH layers were 2.97, which is in accordance with the ratio of 3.00 employed in the synthesis step (see Table S1 in the Supporting Information File 1). Furthermore, the binding energy of Pd 3d5/2 and Pd 3d3/2 in LDH layers

Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications

• Vinila N. Viswanathan,
• Arun D. Rao,
• Upendra K. Pandey,
• Arul Varman Kesavan and
• Praveen C. Ramamurthy

Beilstein J. Org. Chem. 2017, 13, 863–873, doi:10.3762/bjoc.13.87

• binding energy [15]. While reducing the band gap by adjusting the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels, a downhill driving force for exciton dissociation should be maintained for optimum performance of the OPV. If not, the total exciton

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

• in support of that view. Results and Discussion From thermodynamic self-assembly to kinetic self-assembly Organised supramolecular structures are commonly formed when favourable interactions lead to the assembly of different components [18]. The release of chemical binding energy, i.e., the

• , as well as answering the ahistorical question, how was inanimate matter of whatever kind able to evolve into life. Self-assembly. (A) Macromolecular structures or patterns can form as the result of binding energy being released through the interaction of units which compensates for the decrease in

Sulfamide chemistry applied to the functionalization of self-assembled monolayers on gold surfaces

• Loïc Pantaine,
• Vincent Humblot,
• Vincent Coeffard and
• Anne Vallée

Beilstein J. Org. Chem. 2017, 13, 648–658, doi:10.3762/bjoc.13.64

• experiments were also performed to analyze the modified surfaces, and the data confirmed the formation of the sulfamide groups (mainly with the appearance of the SO2 spectroscopic signature at high binding energy around 168 eV). The conversion rate of the reaction has also been calculated with elemental

• must be very different from the one of thiol moiety. The all four samples highlight a strong S2p3/2,1/2 doublet at 162.0 ± 0.1 eV (S2p3/2) (blue) characteristic of the thiolate-gold bond [50] with an additional XPS peaks doublet at lower binding energy of 161.1 ± 0.1 eV (green) attributed to

• molecules in the SAM. It can be explained by the different preparation procedure. It is known that oxidised sulfur highlights a doublet at high binding energy 167–169 eV but since there was no XPS data to our knowledge in the literature on sulfamide, the analysis of the reference SAM 1 is crucial. The S2p

New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

• Pavel Nagorny and
• Zhankui Sun

Beilstein J. Org. Chem. 2016, 12, 2834–2848, doi:10.3762/bjoc.12.283

• of an electron-withdrawing group into the aryl ring (i.e., NO2, CN, CF3, etc.) could significantly enhance this binding and result in stronger hydrogen bonds between the arene and the anion. Thus, the gas-phase binding energy of the nitrobenzene and chloride anion complex containing two C–H hydrogen

• bonds was estimated to be −16.8 kcal/mol whereas the corresponding binding energy for the H2O/Cl− complex was determined to be −15.4 kcal/mol. Electron-deficient heterocyclic compounds such as 1,2,3-triazoles may also serve as strong C–H hydrogen bond donors. Substituted 1,2,3-triazoles possess a

Synthesis of spiro[isoindole-1,5’-isoxazolidin]-3(2H)-ones as potential inhibitors of the MDM2-p53 interaction

• Salvatore V. Giofrè,
• Santa Cirmi,
• Raffaella Mancuso,
• Francesco Nicolò,
• Giuseppe Lanza,
• Laura Legnani,
• Agata Campisi,
• Maria A. Chiacchio,
• Michele Navarra,
• Bartolo Gabriele and
• Roberto Romeo

Beilstein J. Org. Chem. 2016, 12, 2793–2807, doi:10.3762/bjoc.12.278

• -isoxazolidin isoindolinone scaffold in the receptor/ligand complex was difficult because of the open and lipophilic nature of the p53 binding site on MDM2. Therefore, prediction of the possible binding mode was based on two energy types, i.e., the lowest binding energy of the largest cluster and the

• biological evaluation, the compound (S,S)-6e has shown an intermolecular energy value comparable with that of the co-crystallized ligand (MI63 analogue). In addition to a lowest binding energy and intermolecular energy of docking success, we have also performed a visual inspection to confirm that all the

• . Synthesis of 6a–f by 1,3-dipolar cycloaddition. Reaction pathway. Synthesis of 6a–f by 1,3-dipolar cycloaddition. Relative free energies of TSs and percentages of the corresponding adducts at 408 K of the reaction of dipolarophiles (Z)-8 and (E)-8 with nitrone 4. Estimated lowest binding energy based on the

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• [123]. Here the binding energy of a target–ligand complex is solely estimated by a hydrogen bond term and a dehydration energy term. ChemScore [122] and SCORE [124] are two other scoring functions that are also empirical. Consensus-based scoring functions Current scoring functions are not perfect and

Robust C–C bonded porous networks with chemically designed functionalities for improved CO₂ capture from flue gas

• Damien Thirion,
• Joo S. Lee,
• Ercan Özdemir and
• Cafer T. Yavuz

Beilstein J. Org. Chem. 2016, 12, 2274–2279, doi:10.3762/bjoc.12.220

• hydroxylamine converted into amidoxime groups (COP-156-amidoxime). The COP-156-amine proved increased affinity towards CO2 with stronger binding energy, especially under moist conditions, reaching up to 7.8 wt % at 40 °C, a 2.1 wt % increase when compared to the original COP-156. Despite the promise

• pressure of CO2 in flue gas emission) and 273 K, the uptake is slightly higher than the starting COP-156. The chemisorptive behavior and stronger binding affinity is reflected in the higher Qst value of 49.9 kJ mol−1. The moderate binding energy is optimal for CO2 capture, as too strong binding requires

Synthesis and characterization of fluorinated azadipyrromethene complexes as acceptors for organic photovoltaics

• Forrest S. Etheridge,
• Roshan J. Fernando,
• Sandra Pejić,
• Matthias Zeller and
• Geneviève Sauvé

Beilstein J. Org. Chem. 2016, 12, 1925–1938, doi:10.3762/bjoc.12.182

• addition of fluorine decreases the energy of the highest occupied molecular orbitals (HOMO), thereby enhancing the open-circuit voltages (Voc) and PCEs [17][23][24][25][26]. A 2014 investigation by Luscombe and co-workers showed that a fluorine substitution lowered the charge transfer exciton (CTE) binding

• energy, in turn creating more free carriers and higher PCEs [19]. Additionally, enhancements to the short-circuit current density (Jsc), Voc, and fill-factor (FF) in OPVs have been attributed to the addition of fluorine substituents [17][18][20][21][27][28][29]. While fluorinated polymer donors are well

Ring-whizzing in polyene-PtL₂ complexes revisited

• Oluwakemi A. Oloba-Whenu,
• Thomas A. Albright and
• Chirine Soubra-Ghaoui

Beilstein J. Org. Chem. 2016, 12, 1410–1420, doi:10.3762/bjoc.12.135

• bond can be strengthened. The electron affinity for C6F6 is much larger than that for benzene [24]. Consequently interaction of the filled b2 fragment orbital with the LUMO of C6F6 is expected to be larger and the binding energy larger than that for benzene. The M and L that we shall use in this work

Molecular weight control in organochromium olefin polymerization catalysis by hemilabile ligand–metal interactions

• Stefan Mark,
• Hubert Wadepohl and
• Markus Enders

Beilstein J. Org. Chem. 2016, 12, 1372–1379, doi:10.3762/bjoc.12.131

• -ray diffraction data could be obtained from the active form of chromium polymerization catalysts [61][62][63]. However, DFT calculation is well suitable for studying such interactions. By such methods it is not only possible to estimate the binding energy but also to compare it with that of ethylene

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

• Jörg Grunenberg and
• Giuseppe Licari

Beilstein J. Org. Chem. 2016, 12, 415–428, doi:10.3762/bjoc.12.45

• analogues complexed inside the model ribosomal active site. Sampling the lowest energy wells in a 40 kJ/mol energy window the lowest enthalpy minimum was used to assess the relevant terms in Equation 1 below. Since the linezolid complex represents the zero point of our relative binding energy scale, a

• calculated relative binding energy of −15.6 kJ/mol seems to be lower bound for the prediction of an effective binder. The experimental ineffectiveness of compound 3 (MIC value >50 mg/L) is mirrored by our computed decrease of the enthalpic contribution by more than 12 kJ/mol. Two earlier in silico approaches

• the following we will discuss nevertheless not only the 15% good binders but all our candidates. Guest 8 shows a negative relative binding energy (−3.7 kJ/mol). Its lowest minimum conformation inside the receptor exactly fits the orientation of complexed linezolid. The small but negative relative

Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin

• Waratchada Sangpheak,
• Jintawee Kicuntod,
• Roswitha Schuster,
• Thanyada Rungrotmongkol,
• Peter Wolschann,
• Nawee Kungwan,
• Helmut Viernstein,
• Monika Mueller and
• Piamsook Pongsawasdi

Beilstein J. Org. Chem. 2015, 11, 2763–2773, doi:10.3762/bjoc.11.297

• three different cancer cell lines. The overall results suggested that solubilities and bioactivities of both flavanones were increased by complexation with methylated β-CDs. Keywords: binding energy; bioactivity; cyclodextrins; hesperetin; naringenin; Introduction Flavonoids are secondary metabolites

• calculation using the computational method (Table 1). From the result on the binding energy, the vdW energy was about six-fold greater than the electrostatic energy in both of the CDs complexes (Table 1 for hesperetin and Table S1, Supporting Information File 1 for naringenin). This implied that the complex

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

• influenced by the presence of β-CD and ethanol. MD simulations were performed to quantify the strength of inclusion complex formation in terms of binding energy, hydrogen bonding interactions, and displacement analysis. Materials and methods Experimental study Chemicals and reagents α-Mangostin (purity >90

• , the steric effect of the α-MGS functional groups influences only the inclusion geometry, but not the binding energy. Further details for MD simulations of the α-MGS/βCD inclusion complex in water solvation system appear in Supporting Information File 1. Solvation effect on the α-MGS/β-CD inclusion

• water and ethanol molecules always solvate around 2 Å from O3, compared to other oxygen atoms in α-MGS. Binding energy analysis Based on the MM-PBSA approach, the binding free energies of the α-MGS/β-CD complexes at various EtOH concentrations were predicted. The decomposition of free energy into

Ru complexes of Hoveyda–Grubbs type immobilized on lamellar zeolites: activity in olefin metathesis reactions

• Hynek Balcar,
• Naděžda Žilková,
• Martin Kubů,
• Michal Mazur,
• Zdeněk Bastl and
• Jiří Čejka

Beilstein J. Org. Chem. 2015, 11, 2087–2096, doi:10.3762/bjoc.11.225

• binding energy scale of the spectrometers was calibrated using the Au 4f7/2 (84.0 eV) and Cu 2p3/2 (932.6 eV) photoemission lines. The pressure of residual gases in the analysis chamber during spectra acquisition was 6 × 10−9 mbar. The powder samples were spread on an aluminum surface. The spectra were

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

• unfavorable entropic term of roughly 8–10 kcal/mol would reduce this internal binding energy to free energies of binding around 5–12 kcal/mol [13]. According to simple Boltzmann statistics, these energetics implies that the fraction of the naked 14e species in solution at 25 °C should be in the range of 10−11

• indeed coordinated to the Ru atom in place of the pyridine or phosphine to first dissociate. Pyridine and phosphine binding. The binding energy of the first (trans to the PR3 or NHC ligand) and of the second (trans to the ylidene group) pyridine ligands to the naked 14e species of 1–19 are reported in

• the 2nd and 3rd column of Table 1. These values indicate that the first pyridine is bonded quite strongly to the Ru atom. Indeed, it is competitive with PCy3 binding in the prototype 1st and 2nd generation systems based on 1 and 7 [74][75][76]. In precatalysts 1–7 the binding energy of the first

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

• determine the binding affinity, the enthalpic and entropic contributions to free binding energy, and the stoichiometry of binding for all peptide–polymer conjugates. Binding affinities of all multivalent ligands were in the µM range, strongly amplified compared to the monovalent ligand P1 with a KD > 1 mM

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

• energy ΔH. First of all a positive molar binding energy for VW05 was determined while this was found to be negative for R2A2, R2A3, and R2A4. This can be explained by the different quaternary structure of peptides R2A2, R2A3, and R2A4 compared to VW05. The latter forms coiled-coil trimers that are

• refolded into α-helical fibers in the presence of Au/MUA nanoparticles, whereas R2A2 and its analogues are already present as fibers before interacting with nanoparticles, which results in a negative molar binding energy. The molar binding energy of these peptides can be directly correlated with their

• binding constants, as, for example, R2A2 shows the highest binding affinity, produces the greatest release of energy and has the smallest binding energy. With increasing peptide length, the binding affinity decreases, as does the release of energy, which is indicated by the increase in molar binding