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

• 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

Synthesis of tripodal catecholates and their immobilization on zinc oxide nanoparticles

• Franziska Klitsche,
• Julian Ramcke,
• Julia Migenda,
• Andreas Hensel,
• Tobias Vossmeyer,
• Horst Weller,
• Silvia Gross and
• Wolfgang Maison

Beilstein J. Org. Chem. 2015, 11, 678–686, doi:10.3762/bjoc.11.77

• is a piezoelectronic semiconductor with a high exciton binding energy (60 meV) and a wide band-gap (3.37 eV) at room temperature [17][18]. ZnO is therefore employed in (bio-)sensors [19], ultraviolet (UV) light-emitting diodes [20], UV laser diodes [21] and in the field of catalysis [22][23]. ZnO

Organic chemistry on surfaces: Direct cyclopropanation by dihalocarbene addition to vinyl terminated self-assembled monolayers (SAMs)

• Malgorzata Adamkiewicz,
• David O’Hagan and
• Georg Hähner

Beilstein J. Org. Chem. 2014, 10, 2897–2902, doi:10.3762/bjoc.10.307

• generated from CHCl3. New signals at binding energies of 201 and 270 eV were detected. These were assigned to Cl 2p and Cl 2s [26]. Finally Figure 2c represents the surface after chemical modification with :CF2 generated from TMSCF3. A new signal at binding energy of 688.7 eV was detected and assigned to F

A small azide-modified thiazole-based reporter molecule for fluorescence and mass spectrometric detection

• Stefanie Wolfram,
• Hendryk Würfel,
• Stefanie H. Habenicht,
• Christine Lembke,
• Phillipp Richter,
• Eckhard Birckner,
• Rainer Beckert and
• Georg Pohnert

Beilstein J. Org. Chem. 2014, 10, 2470–2479, doi:10.3762/bjoc.10.258

• , bromine containing tags called isotope-differentiated binding energy shift tags (IDBEST™) were designed to introduce a mass-defect in peptides for better sequence coverage of proteins [25][42]. The reporter molecule BPT (1) contains bromine and tagged proteins can thus easily be identified with both

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

• extrahelical side and thus has an important contribution to the overall DNA-binding energy of M.TaqI. Experimental Solid-phase DNA synthesis was performed on an ABI DNA Synthesizer 392 in 1 µmol scale following the standard cycles recommended by Applied Biosystems with a coupling time of 30 s for the natural

Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water?

• Diogo Vila-Viçosa,
• Oscar Francesconi and
• Miguel Machuqueiro

Beilstein J. Org. Chem. 2014, 10, 1513–1523, doi:10.3762/bjoc.10.156

• , using MM/MD simulations, showed that the major contribution to the binding energy between both glucose and galactose to a proteic receptor, came from hydrogen bonds [38]. Moreover, Lerbret et al, suggested that hydrogen bonds are strongly related with the influence of sugar molecules in lysozyme

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

• Friedrich Malberg,
• Jan Gerit Brandenburg,
• Werner Reckien,
• Oldamur Hollóczki,
• Stefan Grimme and
• Barbara Kirchner

Beilstein J. Org. Chem. 2014, 10, 1299–1307, doi:10.3762/bjoc.10.131

• calculated crystal structure is in close agreement with the experimental X-ray data. Compared to a stiffer axle, a more flexible one results in a stronger binding by 1–3 kcal/mol. Alterations of the binding energy in the range of 5 kcal/mol could be achieved by substitution with different functional groups

• . Solvent effects As expected, the presence of the solvent decreases the binding energy by 11–14 kcal/mol, see Table 4. Even though the trends in the difference between single and double bond binding energy is constantly 1–4 kcal/mol. By comparison of the total energies of the complex, separated wheel, and

• systems in Table 5. Again the distances roughly follow the trend that with increasing binding energy the distances are shorter. The hydrogen bonding situation in the complexes with single bond is still less symmetrical, but the shorter N-H···O bond for the solvated is not shorter than in the DB complexes

Molecular recognition of isomeric protonated amino acid esters monitored by ESI-mass spectrometry

• Andrea Liesenfeld and
• Arne Lützen

Beilstein J. Org. Chem. 2014, 10, 825–831, doi:10.3762/bjoc.10.78

• to use this motif to achieve binding of the leucine isomers as their protonated ester derivatives. This provides the major part of the overall binding energy. However, to distinguish the three isomers the receptors need to provide further elements that either provide additional binding sites for the

A³-Coupling catalyzed by robust Au nanoparticles covalently bonded to HS-functionalized cellulose nanocrystalline films

• Jian-Lin Huang,
• Derek G. Gray and
• Chao-Jun Li

Beilstein J. Org. Chem. 2013, 9, 1388–1396, doi:10.3762/bjoc.9.155

• ) demonstrated that the binding energy of the Au species in the Au@HS-CNC (4.4 mol %) sample was 84.8 eV for the Au4f7/2 level corresponding to zero-valent Au, according to reference data reported by Li et al. [17], and no other peak was observed. This indicated that metal ions (Au3+) have been reduced to their

• the binding energy around 163.5 in the S2p level. Thermogravimetric analysis (Figure 3) showed that the deposition of AuNPs onto CNC apparently enhanced the thermal stability of the Au@HS-CNC (4.4 mol %) films, which might be due to a composite of the saline reagent (3-mercaptopropyltrimethoxysilane

Theoretical study on β-cyclodextrin inclusion complexes with propiconazole and protonated propiconazole

• Adrian Fifere,
• Narcisa Marangoci,
• Stelian Maier,
• Adina Coroaba,
• Dan Maftei and
• Mariana Pinteala

Beilstein J. Org. Chem. 2012, 8, 2191–2201, doi:10.3762/bjoc.8.247

• + inclusion compounds were selected by considering the binding energy as being the difference between the heat of formation of the complex and the heat of formation of the involved free molecules: where ECD/PP, EPP and ECD represent the heat of formation of the complex, of the free β-CD, and of the free guest

• PP deeply entered into the cavity during the calculation, demonstrating a high probability of complex formation. The binding energy is not very high, which could be explained by the absence of hydrogen bonds that strongly stabilize the molecular association. Analyzing the numerical values summarized

• fact suggests that a dipole–dipole coupling mechanism could be involved in the complex formation. The inclusion of the triazole ring is energetically favored, since the resulting binding energy is the lowest. The obtained theoretical results confirm the experimental data published on complexation of β

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

• additivity of free energies and the relationship ΔG‡rac′ + ΔG° + ΔG‡sterics ~ ΔG‡out still hold? When ΔG‡rac′ of 11.4 ± 0.1 kcal/mol (at 250.0 ± 0.1 K, Figure 7) is added to the intrinsic binding energy of CH3CCl3 (│ΔG°│ = 2.79 ± 0.09 kcal/mol at 250.0 ± 0.1 K, Figure 2), a value of 14.2 kcal/mol is obtained

(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

• total of the 5.4 kcal/mol favorable binding energy). However, we have turned up no report that was published since with such a dramatic difference in overall binding energy. While host 3Et has been shown to bind citrate in an entropy-driven manner, no comparison to 3H or 3Me was made, and the authors

Studies on Pd/NiFe₂O₄ catalyzed ligand-free Suzuki reaction in aqueous phase: synthesis of biaryls, terphenyls and polyaryls

• Sanjay R. Borhade and
• Suresh B. Waghmode

Beilstein J. Org. Chem. 2011, 7, 310–319, doi:10.3762/bjoc.7.41

• continuous flow of hydrogen gas [43]. The scanning electron microscope image shows that particle size of the catalyst is ~100 to 300 nm (Supporting Information File 1). The X-ray photoemission spectra confirms the formation of metallic Pd(0) particles, the binding energy values were 335.3 and 340.5 eV for Pd

Hoveyda–Grubbs type metathesis catalyst immobilized on mesoporous molecular sieves MCM-41 and SBA-15

• Hynek Balcar,
• Tushar Shinde,
• Naděžda Žilková and
• Zdeněk Bastl

Beilstein J. Org. Chem. 2011, 7, 22–28, doi:10.3762/bjoc.7.4

• remaining Ru species after washing was catalytically active; however, these species were rapidly deactivated. Figure 7 shows high-resolution spectra of the Ru 3d–C 1s photoelectrons of neat compound 3, catalyst 3/SBA-15 and the same catalyst after leaching in THF. The measured binding energy of the Ru 3d5/2

Catalysis: transition-state molecular recognition?

• Ian H. Williams

Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117

• ΔGRdist and the interaction energy ΔGRint is equal to the apparent binding energy ΔGRbind. The magnitude of the enzyme catalytic power ΔG‡aq − ΔG‡enz = 38 kJ mol−1 is equal to the difference in binding energies ΔGTbind − ΔGRbind of the enzyme with the TS and the solvent-separated ion-pair, neither of

• in enzyme catalysis has been that the TS need not be the same for both the catalysed and uncatalysed reactions [8]. Consequently, the previous analysis [17] should be modified by recognising that the apparent binding energy ΔGTbind is the sum of distortion energy ΔGTdist and interaction energy ΔGTint

• stabilisation. Free energy profiles for reactions of substrate S uncatalysed and catalysed by enzyme E, showing how the barrier height reduction is equal to the binding energy for transition state T offset by the binding energy for the reactant state R. Energetic analysis of the compression hypothesis for

En route to photoaffinity labeling of the bacterial lectin FimH

• Thisbe K. Lindhorst,
• Michaela Märten,
• Andreas Fuchs and
• Stefan D. Knight

Beilstein J. Org. Chem. 2010, 6, 810–822, doi:10.3762/bjoc.6.91

• of its free binding energy. Low (more negative) scores correlate with high affinities, whilst higher scores reflect diminished binding potency (Table 1). Docking was based on two different X-ray structures. In the first case, crystals with an open tyrosine gate were taken as the basis [7], whilst in

Chromo- and fluorophoric water-soluble polymers and silica particles by nucleophilic substitution reaction of poly(vinyl amine)

• Katja Hofmann,
• Ingolf Kahle,
• Frank Simon and
• Stefan Spange

Beilstein J. Org. Chem. 2010, 6, No. 79, doi:10.3762/bjoc.6.79

• + species (its binding energy is BE ≈ 401.4 eV while the binding energy of the non-protonated species is BE ≈ 399.5 eV). Table 1 summarizes the results of the BET analysis. In addition, Figure 3 shows the pore-size distribution histograms of bare silica, a typical PVAm/silica hybrid material and 1-Si. The

Symmetry breaking and structure of a mixture of nematic liquid crystals and anisotropic nanoparticles

• Marjan Krasna,
• Matej Cvetko and
• Milan Ambrožič

Beilstein J. Org. Chem. 2010, 6, No. 74, doi:10.3762/bjoc.6.74

• the chemical potential in the solid phase, kB is the Boltzmann constant, T is the temperature and Fb is the average binding energy of a NP with its surroundings. We further assume that the chemical potential in a diluted and solid NP state are comparable (depending on the chemical composition of both

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32

• a free electron pair of an electronegative atom (O, N, F). Crystal structures mainly show a linear arrangement of the three atoms but bifurcated hydrogen bonds can also be observed [9]. If exposed to a competing solvent, a single hydrogen bond cannot contribute much binding energy. Gas phase

• coulombic interactions are around 8 kJ/mol [15]. In aqueous medium ion pair formation is primarily driven by entropy, not directly by coulombic forces [16]. The binding energy is, in general, independent of the geometry, polarizability of the ions or the formation of a salt bridge. In addition, the

Templated versus non-templated synthesis of benzo-21-crown-7 and the influence of substituents on its complexing properties

• Wei Jiang and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2010, 6, No. 14, doi:10.3762/bjoc.6.14

• group and the binding energy increases, when phenyl is replaced by anthracenyl. Instead, the cavity of C7 is smaller and likely unable to adjust itself to the anthracenyl methyl-substituted axle. Some of the C-H•••O hydrogen bonds which can form with 6-H•PF6 do not form with 7-H•PF6 and thus weaken the