Titration Simulations for Understanding of the Binding Equilibrium

Author(s):  
Dae Hyup Sohn

<p>The reliability evaluation of the predicted binding constants in numerous models is also a challenge for supramolecular host-guest chemistry. Here, I briefly formulate binding isotherm with the derivation of the multivalent equilibrium model for the chemist who wants to determine the binding constants of their compounds. This article gives an in-depth understanding of the stoichiometry of binding equilibrium to take divalent binding equilibria bearing two structurally identical binding sites as an example. The stoichiometry of binding equilibrium is affected by (1) the cooperativity of complex, (2) the concentration of titration media, and (3) the equivalents of guests. The simulations were conducted with simple Python codes.</p>

2020 ◽  
Author(s):  
Dae Hyup Sohn

<p>The reliability evaluation of the predicted binding constants in numerous models is a challenge for supramolecular host-guest chemistry. Here, I briefly formulate binding isotherm with the derivation of the multivalent equilibrium model for the chemist who wants to determine the binding constants of their compounds. This article gives an in-depth understanding of the stoichiometry of binding equilibrium to take divalent binding equilibria bearing two structurally identical binding sites as an example. The stoichiometry of binding equilibrium is affected by (1) the cooperativity of complex, (2) the concentration of titration media, and (3) the equivalents of guests. The simulations were conducted with simple Python codes.</p>


2020 ◽  
Author(s):  
Dae Hyup Sohn

<p>The reliability evaluation of the predicted binding constants in numerous models is a challenge for supramolecular host-guest chemistry. Here, I briefly formulate binding isotherm with the derivation of the multivalent equilibrium model for the chemist who wants to determine the binding constants of their compounds. This article gives an in-depth understanding of the stoichiometry of binding equilibrium to take divalent binding equilibria bearing two structurally identical binding sites as an example. The stoichiometry of binding equilibrium is affected by (1) the cooperativity of complex, (2) the concentration of titration media, and (3) the equivalents of guests. The simulations were conducted with simple Python codes.</p>


2004 ◽  
Vol 69 (5) ◽  
pp. 1137-1148 ◽  
Author(s):  
Gennady V. Oshovsky ◽  
Willem Verboom ◽  
David N. Reinhoudt

Ureidocavitand 1 and thioureidocavitand 2 bind in CH3CN organic anions such as acetate, propionate, butyrate, etc. with K values of 2-8 × 105 l mol-1 and 2-9 × 106 l mol-1, respectively, as was determined with isothermal microcalorimetry (ITC). Bringing together four (thio)urea binding sites on a molecular platform gives rise to about 2000 times higher binding constants, compared with those of the corresponding single binding sites. Glucose- and galactose-containing thioureidocavitands 5 and 6 bind acetate in 1:1 CH3CN/water with a K-value of 2.15 × 103 l mol-1.


1985 ◽  
Vol 68 (3) ◽  
pp. 357-364 ◽  
Author(s):  
J. S. D. Scott ◽  
E. P. W. Bowman ◽  
W. G. E. Cooksley

1. Binding of cobalamin (Cbl) was compared in liver and kidney plasma membranes prepared from rat and human tissues. 2. Single, high-affinity, saturable (200 pmol/l), binding sites for TC II-Cbl were found in all tissues; by contrast no receptors were present for free cobalamin, for which only non-specific adsorption occurred. 3. Binding constants for TC II-CNCbl determined for liver and kidney plasma membranes were of a similar magnitude. Mean values for Ka (litre/nmol) were 16.7 (rat liver), 18.8 (rat kidney), 8.0 (human liver) and 7.5 (human kidney). 4. Results for binding TC II-OHCbl instead of TC II-CNCbl showed no difference in Ka and Bmax. values, although the non-specific adsorption was decreased to a third. 5. Competitive inhibition results showed that the receptors are specific for the TC II molecule and that binding is unaffected either by the cobalamin moiety or by the presence of free cobalamin. Degradation of the receptor protein molecules by trypsin (10 μg/ml) resulted in 90% inhibition of binding. 6. It is concluded that differences between liver and kidney in cobalamin uptake and accumulation cannot be attributed to differences in their TC II receptors.


2015 ◽  
Vol 51 (50) ◽  
pp. 10210-10213 ◽  
Author(s):  
Meng Zhang ◽  
Xianpeng Yin ◽  
Tian Tian ◽  
Yun Liang ◽  
Weina Li ◽  
...  

Synergetic combination of TPE and bile acid units could directly afford uniform fluorescent vesicles with amphiphilic binding sites.


2009 ◽  
Vol 23 (2) ◽  
pp. 103-111 ◽  
Author(s):  
Changyun Chen ◽  
Kai Chen ◽  
Qi Long ◽  
Meihua Ma ◽  
Fei Ding

A novel complex Sm(III) complex with ofloxacin was synthesized and characterized on the basis of elemental analyses, molar conductivities, IR spectra, thermal analysis (TG-DSC),1H-NMR spectra. Then, spectrometric titration, ethdium bromide displacement experiments by UV spectroscopy, ionic influence, viscosity measurements and Circular Dichroism (CD) spectroscopic measurements were conducted to characterize the interaction between the complex and CT-DNA. Results obtained indicate that the complex bound with CT-DNA via an intercalation mechanism. The binding constants and binding sites number of the Sm(III) complex with CT-DNA were 1.80×105l·mol−1and 1, respectively.


2008 ◽  
Vol 80 (9) ◽  
pp. 2025-2040 ◽  
Author(s):  
Frederick P. Schwarz ◽  
Timm Reinisch ◽  
Hans-Jürgen Hinz ◽  
Avadhesha Surolia

Isothermal titration calorimetry (ITC) is widely used to determine the thermodynamics of biological interactions including protein-protein, small molecule-protein, protein-DNA, small molecule-DNA, and antigen-antibody interactions. An ITC measurement consists of monitoring the transfer of heat between an analyte solution in a sample vessel and a reference solution in a reference vessel upon injection of a small aliquot of titrant solution into the sample vessel at a fixed ITC operating temperature. A binding isotherm is generated from the heat-transferred-per-injection data and values for the binding constants, the apparent binding enthalpies, and the apparent ratio of the amount of titrant to analyte for the binding reaction are then determined from fits of a binding model, whether it is a single site, identical multi-site, or an interacting multi-site binding model, to the binding isotherm. Prior to the fitting procedure, corrections should be made for contributions from extraneous heat of mixing determined separately from injections of the titrant into just the dialysate/buffer solution. Ultra-high binding constants, which cannot be directly determined from an ITC measurement, can be determined by a displacement ITC method where injections of the tight-binding titrant into a solution of a weaker-binding titrant-analyte complex displaces the weaker-binding titrant from the complex. The Michaelis and catalytic constants can be determined for an enzyme reaction from injections of a substrate or enzyme titrant into an enzyme or substrate analyte solution. Several binding reactions are suggested to check the operating performance of the ITC. The reporting of ITC results must be specific with regard to the composition of the titrant and the analyte solutions, the temperature, and the model used in the analysis.


1994 ◽  
Vol 353 ◽  
Author(s):  
M. Olin ◽  
J. Lehikoinen ◽  
A. Muurinen

AbstractA chemical equilibrium model has been developed for ion-exchange and to a limited extent for other reactions, such as precipitation or dissolution of calcite or gypsum, in compacted bentonite water systems. The model was successfully applied to some bentonite experiments, especially as far as monovalent ions were concerned. The fitted log-binding constants for the exchange of sodium for potassium, magnesium, and calcium were 0.27, 1.50, and 2.10, respectively. In addition, a coupled chemical and diffusion model has been developed to take account of diffusion in pore water, surface diffusion and ion-exchange. The model was applied to the same experiments as the chemical equilibrium model, and its validation was found pardy successful. The above values for binding constants were used also in the coupled model. The apparent (both for anions and cations) and surface diffusion (only for cations) constants yielding the best agreement between calculated and experimental data were 3.0×10-11 m2/s and 6.0×10-12m2/s, respectively. These values are questionable, however, as experimental results good enough for fitting are currently not available.


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