Theoretical Calculations of Heteroconjugation Equilibrium Constants in Systems Modeling Acid−Base Interactions in Side Chains of Biomolecules Using the Potential of Mean Force

2004 ◽  
Vol 108 (32) ◽  
pp. 12222-12230 ◽  
Author(s):  
Joanna Makowska ◽  
Mariusz Makowski ◽  
Artur Giełdoń ◽  
Adam Liwo ◽  
Lech Chmurzyński
Keyword(s):  
Theoretical Calculations ◽  
Equilibrium Constants ◽  
Potential Of Mean Force ◽  
Side Chains ◽  
Systems Modeling ◽  
Acid Base

Spectrophotometric study of the acid-base and optical properties of the 5-bromo and 5-chloro derivatives of 2-(2-pyridylazo)-5-(diethylamino)phenol (BrPADAP, ClPADAP) and their complexation equilibria with zinc(II) ions

1982 ◽  
Vol 47 (10) ◽  
pp. 2676-2691 ◽  
Author(s):  
Miroslav Macka ◽  
Vlastimil Kubáň
Keyword(s):  
Equilibrium Constants ◽  
Spectrophotometric Study ◽  
Graphical Analysis ◽  
Alkaline Media ◽  
Acid Base ◽  
Ethanol Medium ◽  
Triton X ◽  
Mixed Water ◽  
Derivatives Of

The optical and acid-base characteristics of BrPADAP and ClPADAP were studied in mixed water-ethanol and water-DMF media and in 10% ethanol medium in the presence of cationic, anionic and nonionic tensides. The composition, optical characteristics, molar absorption coefficients and equilibrium constants of the ML and ML2 complexes with zinc(II) ions were found by graphical analysis and numerical interpretation of the absorbance curves by the modified SQUAD-G program. Optimal conditions were found for the spectrophotometric determination of Zn(II) in the presence of 0.1% Triton X-100 or 1% Brij 35 in alkaline media with pH = 6.5-10. BrPADAP and ClPADAP are the most sensitive reagents (ε = 1.3-1.6 . 105 mmol-1 cm2 at 557 and 560 nm, respectively) for the determination of zinc with high colour contrast of the reaction (Δλ = 104 nm) and selectivity similar to that for the other N-heterocyclic azodyes (PAN, PAR, etc.).

Privileged hydration sites in aromatic side chains: effect on conformational equilibrium

2017 ◽  
Vol 19 (42) ◽  
pp. 28684-28695 ◽  
Author(s):  
Belén Hernández ◽  
Fernando Pflüger ◽  
Manuel Dauchez ◽  
Mahmoud Ghomi
Keyword(s):  
Conformational Equilibrium ◽  
Theoretical Calculations ◽  
Side Chains ◽  
Aromatic Side Chains

The most energetically favourable hydration sites of aromatic (Phe, Tyr, Trp and His) side chains revealed by DFT-based theoretical calculations.

scholarly journals Stabilization of phage T4 lysozyme by engineered disulfide bonds

1989 ◽  
Vol 86 (17) ◽  
pp. 6562-6566 ◽  
Author(s):  
M Matsumura ◽  
W J Becktel ◽  
M Levitt ◽  
B W Matthews
Keyword(s):  
Disulfide Bonds ◽  
Theoretical Calculations ◽  
Equilibrium Constants ◽  
T4 Lysozyme ◽  
Disulfide Bridges ◽  
Large Loop ◽  
Phage T4 ◽  
Flexible Part ◽  
Free Phage

Four different disulfide bridges (linking positions 9-164, 21-142, 90-122, and 127-154) were introduced into a cysteine-free phage T4 lysozyme at sites suggested by theoretical calculations and computer modeling. The new cysteines spontaneously formed disulfide bonds on exposure to air in vitro. In all cases the oxidized (crosslinked) lysozyme was more stable than the corresponding reduced (noncrosslinked) enzyme toward thermal denaturation. Relative to wild-type lysozyme, the melting temperatures of the 9-164 and 21-142 disulfide mutants were increased by 6.4 degrees C and 11.0 degrees C, whereas the other two mutants were either less stable or equally stable. Measurement of the equilibrium constants for the reduction of the engineered disulfide bonds by dithiothreitol indicates that the less thermostable mutants tend to have a less favorable crosslink in the native structure. The two disulfide bridges that are most effective in increasing the stability of T4 lysozyme have, in common, a large loop size and a location that includes a flexible part of the molecule. The results suggest that stabilization due to the effect of the crosslink on the entropy of the unfolded polypeptide is offset by the strain energy associated with formation of the disulfide bond in the folded protein. The design of disulfide bridges is discussed in terms of protein flexibility.

Thermodynamic of metal complexation of the macrocyclic antibiotic rifampicin

2001 ◽  
Vol 79 (1) ◽  
pp. 42-49
Author(s):  
I Shehatta ◽  
I Kenawy ◽  
A H Askalany ◽  
Ayman A Hassan
Keyword(s):  
Binding Sites ◽  
Equilibrium Constants ◽  
Ionic Species ◽  
Ligand Field ◽  
Water Medium ◽  
Acid Base ◽  
Distribution Diagram ◽  
Macrocyclic Antibiotic ◽  
Transition Series ◽  
Different Temperatures

The acid-base and complexation equilibria of rifampicin with H+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Hg2+, and Pb2+ were studied by means of potentiometry. The stoichiometric equilibrium constants were determined in 50% (v/v) methanol-water medium at different temperatures and constant ionic strength (0.05 M KCl). It was established that rifampicin has two proton-binding sites. The distribution diagram of the corresponding ionic species as a function of pH is given and indicated that rifampicin exists predominantly in the zwitterionic form at pH [Formula: see text] 5. The thermodynamic parameters of protonation and complexation were derived and discussed. The formation of the complexes is spontaneous, more favourable at lower temperatures, entropically unfavourable, and an enthalpy-driven process. The order of the changes in Gibbs energy and enthalpy accompanying the complexation was found to be Mn2+ < Co2+ < Ni2+ < Cu2+ > Pb2+ > Zn2+ > Cd2+ > Hg2+ in accordance with the well-known sequence of Irving and Williams. The transition series contraction energy (Er(Mn-Zn)), and the ligand field stabilization energy (δH) were calculated from the enthalpy changes.Key words: rifampicin, thermodynamics, potentiometry, and complexation.

Synthesis, and Acid–Base and DNA-Binding Properties of a Thiophen-Appended Ruthenium Complex

2011 ◽  
Vol 64 (2) ◽  
pp. 206 ◽  
Author(s):  
Hong Luo ◽  
Zhi-Ping Wang ◽  
An-Guo Zhang ◽  
Ke-Zhi Wang
Keyword(s):  
Dna Binding ◽  
Density Functional ◽  
Ruthenium Complex ◽  
Theoretical Calculations ◽  
Ionization Constants ◽  
Acid Base ◽  
Binding Properties ◽  
Emission Quenching ◽  
Melting Experiments ◽  
Dna Binding Properties

2-(5-Phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (Hptip) and its RuII complex [Ru(bpy)2(Hptip)](PF6)2 (where bpy = 2,2′-bipyridine) have been synthesized and characterized by elemental analysis, 1H NMR spectroscopy, and mass spectrometry. The acid–base properties of the complex were studied by UV-visible and luminescence spectrophotometric pH titrations, and ground- and excited-state acidity ionization constants were derived. The DNA-binding properties of [Ru(bpy)2(Hptip)](PF6)2 were also investigated by means of UV-vis and emission spectroscopy, salt effects, steady-state emission quenching by [Fe(CN)6]4–, DNA competitive binding with ethidium bromide, DNA melting experiments, and viscosity measurements. Density functional theoretical calculations were also carried out in order to understand the DNA binding properties.

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