Search results for "THERMODYNAMICS"
showing 10 items of 2774 documents
Thermodynamics and kinetics of ion permeation in wild-type and mutated open active conformation of the human α7 nicotinic receptor
2020
Molecular studies of human pentameric ligand-gated ion channels (LGICs) expressed in neurons and at neuromuscular junctions are of utmost importance in the development of therapeutic strategies for neurological disorders. We focus here on the nicotinic acetylcholine receptor nAChR-α7, a homopentameric channel widely expressed in the human brain, with a proven role in a wide spectrum of disorders including schizophrenia and Alzheimer's disease. By exploiting an all-atom structural model of the full (transmembrane and extracellular) protein in the open, agonist-bound conformation we recently developed, we evaluate the free energy and the mean first passage time of single-ion permeation using …
Thermodynamics of binding between α- and β-cyclodextrins and some p-nitro-aniline derivatives: reconsidering the enthalpy–entropy compensation effect
2004
Abstract The thermodynamics of binding between native α- and β-cyclodextrin towards several p -nitro-aniline derivatives was examined, in order to gain further insights about the occurrence of different interaction modes for the two hosts. Valuable information was achieved regarding the ‘expanded hydrophobic sphere’ of α-cyclodextrin. Furthermore, very interesting and unexpected aspects of the behavior of β-cyclodextrin were enlightened, such as the crucial role played by hydrogen bond interactions. Experimental data were examined under the perspective of the ‘enthalpy–entropy compensation effect’, and some ideas about this topic are discussed.
Application of Grote-Hynes theory to the reaction catalyzed by thymidylate synthase.
2010
A theoretical study of dynamic effects on the rate-limiting step of the thymidylate synthase catalyzed reaction has been carried out by means of Grote-Hynes theory, successfully predicting the values of the recrossing effects for a chemical reaction that involves the transfer of a classical light particle. The transmission coefficients, obtained at 278, 293, 303, and 313 K, are almost invariant and in all cases far from unity, revealing a significant coupling of the environment motions and the reaction coordinate. Nevertheless, their energetic contribution to the activation free energy represents less than 0.50 kcal/mol for each of the four tested temperatures. Calculation of the transmissi…
Computational Modeling of Biological Systems: The LDH Story
2010
Lactate dehydrogenases, LDH, catalyzed reaction has been used in this chapter as a conductor wire to present the evolution and difficulties on computing methods to model chemical reactions in enzymes, since the early calculations based at semiempirical level carried out in gas phase to the recent sophisticated simulations based on hybrid Quantum Mechanical/Molecular Mechanics Dynamics (QM/MM MD) schemes. LDH catalyzes the reversible transformation of pyruvate into lactate. The chemical step consists in a hydride and a proton transfer from the cofactor (NADH) and a protonated histidine (His195), respectively. This fact has generated a lot of controversy about the timing of both transfers in …
Bringing a Molecular Plus One: Synergistic Binding Creates Guest-Mediated Three-Component Complexes
2020
Cethyl-2-methylresorcinarene (A), pyridine (B), and a set of 10 carboxylic acids (Cn) associate to form A·B·Cn ternary assemblies with 1:1:1 stoichiometry, representing a useful class of ternary systems where the guest mediates complex formation between the host and a third component. Although individually weak in solution, the combined strength of the multiple noncovalent interactions organizes the complexes even in a highly hydrogen-bond competing methanol solution, as explored by both experimental and computational methods. The interactions between A·B and Cn are dependent on the pKa values of carboxylic acids. The weak interactions between A and C further reinforce the interactions betw…
Phase Equilibria in the Binary and Ternary Systems Composed of Diethyl Ketone, 2-Pentanone, and 3-Pentanol at 101.3 kPa
2003
New vapor−liquid equilibrium data for the binary systems diethyl ketone + 2-pentanone, diethyl ketone + 3-pentanol and 2-pentanone + 3-pentanol and for the diethyl ketone + 2-pentanone + 3-pentanol ternary system are reported at 101.3 kPa. The data were found to be thermodynamically consistent according to the Van Ness−Byer−Gibbs method for the binary systems and according to the McDermott−Ellis method for the ternary one. The experimental results show that the diethyl ketone + 2-pentanone system is well represented by assuming ideal behavior. The other binary systems exhibit slight positive deviations from ideality, and no azeotrope is present. The VLE data have been correlated with the Wi…
Photochemical holes under pressure: Compressibility and volume fluctuations of a protein
1991
From the pressure induced frequency shift of photochemical holes burnt into mesomorphyrin substituted horseradish peroxidase, we determined the compressibility of the protein and the vacuum frequency of the chromophore. From the compressibility, an estimation of the volume fluctuations of the biomolecule is possible.
Thermodynamic studies of octyltrimethylammonium chloride in water
1992
Densities, heat capacities, enthalpies of dilution at 298 K and osmotic coefficients at 310 K of octyltrimethylammonium chloride were measured as functions of concentration. From the experimental data, the partial molar volumes, heat capacities, relative enthalpies, nonideal free energies and entropies at 298 K were derived as functions of concentration. A comparison between the above data and those of dodecyltrimethylammonium chloride reported in the literature shows that the increase of the alkyl chain length shifts the apparent molar volumevs. concentration curves towards greater values and the heat capacity, relative enthalpy and free energyvs. concentration curves towards smaller value…
Thermodynamic properties of some N-alkyl-N-methylpiperidinium chlorides and N-alkylpiperidine hydrochlorides in water
1993
Densities and heat capacities at 25[degrees]C were measured for N-octyl-, N-decyl- and N-dodecyl-N-methylpiperidinium chlorides and for N-octyl- and N-dodecylpiperidine hydrochlorides in water as functions of concentration. Enthalpies of dilution at 25[degrees]C and osmotic coefficients at 37[degrees]C of the N-methyl-N-alkylpiperidinium chlorides were also measured as functions of concentration. The partial molar volumes, heat capacities, relative enthalpies, nonideal Gibbs energies and entropies at 25[degrees]C were derived as functions of the surfactant concentration. By increasing the alkyl chain length of the surfactant, both the apparent molar volume vs. concentration curves are shift…
Continuum-uniform approach calculations of the solubility of hydrocarbons in water
1993
Abstract The ransfer free energies from gas phase to water for some hydrocarbons are calculated by means of a continuum-uniform model of the solvent. For the calculation of the cavitation energy a model based on the surface tension is proposed. The calculated values are compared with the experimental free energies obtained with and without a corrective factor that accounts for the difference in the solute—solvent sizes. Good agreement between the theoretical free energies and the corrected experimental data is obtained. Our calculations seem to show that the hydrophobic effect is directly related to the molecular surface area.