![]() ![]() In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Riniker, Sereina Barandun, Luzi J Diederich, François Krämer, Oliver Steffen, Andreas van Gunsteren, Wilfred F This paper presents a systematic comparison of experimentally determined enthalpies of formation and enthalpies of sublimation or vaporization with the results ofįree enthalpies of replacing water molecules in protein binding pockets. The unknown property for the second group of compounds was predicted using the MEP model. Evidence of accuracy of experimental data for the first group of compounds was provided by the agreement with theoretical Δ f H 298 ° (g) value. For some of them, both the enthalpy of formation in the condensed phase and the enthalpy of sublimation or vaporization are available for other compounds, experimental data for only one of these properties exist. ![]() Different hydrazine derivatives have been also considered in this work. Thus, the difference between the values predicted by high-level theoretical calculations and the experimental value of Δ f H 298 ° (NH 2 NH 2 ,g) = 95.55 ± 0.19 kJ/mol recommended in the ATcT and other comprehensive reference sources is sufficiently large and requires further investigation. The calculated value is in excellent agreement with the reported results of the most accurate models based on coupled cluster theory (97.3 kJ/mol, the average of six calculations). The value of Δ f H 298 ° (NH 2 NH 2 ,g) = 97.0 ± 3.0 kJ/mol was determined from 75 isogyric reactions involving about 50 reference species for most of these species, the accurate Δ f H 298 ° (g) values are available in Active Thermochemical Tables (ATcT). To estimate the enthalpies of sublimation and vaporization with reasonable accuracy (5-20 kJ/mol), the method of molecular electrostatic potential (MEP) has been used. The composite G4 method has been used along with isodesmic reaction schemes to derive a set of self-consistent high-accuracy gas-phase enthalpies of formation. Based on a critical analysis of all thermodynamic information now available, a set of optimized parameters is identified and a table of thermodynamic data for GaN developed from 298.15 to 1400 K.Įnthalpies of Formation of Hydrazine and Its Derivatives.ĭorofeeva, Olga V Ryzhova, Oxana N Suchkova, Taisiya AĮnthalpies of formation, Δ f H 298 °, in both the gas and condensed phase, and enthalpies of sublimation or vaporization have been estimated for hydrazine, NH 2 NH 2, and its 36 various derivatives using quantum chemical calculations. Entropy of GaN is derived from heat-capacity measurements. are discussed in the light of other information on the Gibbs energy of formation available in the literature. It is shown that the experimental technique employed detects neither the equilibrium partial pressure of N 2 corresponding to the equilibrium between Ga and GaN at fixed temperatures nor the equilibrium temperature at constant pressure of N 2. Presented in this letter is a critical discussion of a recent paper on experimental investigation of the enthalpy, entropy and free energy of formation of gallium nitride (GaN) published in this journal. Discussion of enthalpy, entropy and free energy of formation of GaN
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