Search results for "Free Energy"
showing 10 items of 170 documents
Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: a QM/MM study
2019
AbstractCyclin-dependent kinase 2 (CDK2) is an important member of the CDK family exerting its most important function in the regulation of the cell cycle. It catalyzes the transfer of the gamma phosphate group from an ATP (adenosine triphosphate) molecule to a Serine/Threonine residue of a peptide substrate. Due to the importance of this enzyme, and protein kinases in general, a detailed understanding of the reaction mechanism is desired. Thus, in this work the phosphoryl transfer reaction catalyzed by CDK2 was revisited and studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our results show that the base-assisted mechanism is preferred over the substrat…
N-doped carbon networks: alternative materials tracing new routes for activating molecular hydrogen.
2014
The fragmentation of molecular hydrogen on N-doped carbon networks was investigated by using molecular (polyaromatic macrocycles) as well as truncated and periodic (carbon nanotubes) models. The computational study was focused on the ergonicity analysis of the reaction and on the properties of the transition states involved when constellations of three or four pyridinic nitrogen atom defects are present in the carbon network. Calculations show that whenever N-defects are embedded in species characterized by large conjugated π-systems, either in polyaromatic macrocycles or carbon nanotubes, the corresponding H2 bond cleavage is largely exergonic. The fragmentation Gibbs free energy is affect…
Calculation of partition coefficient and hydrophobic moment of the secondary structure of lysozyme
2001
A method that permits a semiquantitative estimate of the partitioning of any solute between any two media is presented. As an example, the partition coefficients and hydrophobic moment of the secondary structure of lysozyme are calculated. Program GSCAP is written as a version of Pascal's solvent-dependent conformational analysis (SCAP) program. The dipole moments calculated for the helices are trebled with respect to that for the sheet. For helices, the main contribution to the water-accessible surface area is the hydrophobic term, while the hydrophilic part dominates in the sheet. Molecular globularity and the three studied partition coefficients differentiate between helices and sheet.
Peptide Bond Formation Mechanism Catalyzed by Ribosome
2015
In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favorable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule. This transition state is similar to that described for the reaction in solution (J. Am. Chem. Soc. 2013, 135, 8708–871…
A Molecular Electron Density Theory Study of the Synthesis of Spirobipyrazolines through the Domino Reaction of Nitrilimines with Allenoates
2019
The reaction of diphenyl nitrilimine (NI) with methyl 1-methyl-allenoate yielding a spirobipyrazoline has been studied within molecular electron density theory (MEDT) at the MPWB1K/6-311G(d) computational level in dichloromethane. This reaction is a domino process that comprises two consecutive 32CA reactions with the formation of a pyrazoline intermediate. Analysis of the relative Gibbs free energies indicates that both 32CA reactions are highly regioselective, the first one being also completely chemoselective, in agreement with the experimental outcomes. The geometries of the TSs indicate that they are associated to asynchronous bond formation processes in which the shorter distance invo…
Phase diagrams calculated for sheared ternary polymer blends
1997
Abstract On the basis of the generalized Gibbs energy of mixing G γ (which is the sum of the Gibbs energy for zero shear and the energy the system stores in steady flow) phase diagrams were calculated as a function of shear rate γ for ternary model blends. This modelling uses simple equations for the description of the stagnant systems (Flory-Huggins) and for the contributions resulting from flow. Surface and alignment effects are neglected. A new procedure, which does not require the derivatives of G γ with respect to composition, was used to that end. Choosing typical values for the binary interaction parameters and molar masses, four classes of ternary systems were studied in greater det…
Suitability ofMMGBSAfor the selection of correct ligand binding modes from docking results
2018
The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics-generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescor…
Interaction of Nanometric Clay Platelets
2008
International audience; The free energy of interaction between two nanometric clay platelets immersed in an electrolyte solution has been calculated using Monte Carlo simulations as well as direct integration of the configurational integral. Each platelet has been modeled as a collection of charged spheres carrying a unit chargethe face of a platelet contains negative charges, and the edge, positive charges. The calculations predict that a configuration of “overlapping coins” is the global free energy minimum at intermediate salt concentrations (10−100 mM). A second weaker minimum, corresponding to the well-known “house of cards” configuration, also appears in this salt interval. At low sal…
Ab initio simulations of oxygen interaction with surfaces and interfaces in uranium mononitride
2012
Abstract The results of DFT supercell calculations of oxygen behavior upon the UN (0 0 1) and (1 1 0) surfaces as well as at the tilt grain boundary are presented. Oxygen adsorption, migration, incorporation into the surface N vacancies on (0 0 1) and (1 1 0) surfaces have been modeled using 2D slabs of different thicknesses and supercell sizes. The temperature dependences of the N vacancy formation energies and oxygen incorporation energies are calculated. We demonstrate that O atoms easily penetrate into UN surfaces and grain boundaries containing N vacancies, due to negative incorporation energies and a small energy barrier. The Gibbs free energies of N vacancy formation and O atom incor…
On the numerical solution of axisymmetric domain optimization problems by dual finite element method
1994
Shape optimization of an axisymmetric three-dimensional domain with an elliptic boundary value state problem is solved. Since the cost functional is given in terms of the cogradient of the solution, a dual finite element method based on the minimum of complementary energy principle is used. © 1994 John Wiley & Sons, Inc.