65 research outputs found
The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode
No full textThe thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H+ ) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H3 O+ ).
Using the computed solvation free energy of H+ as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pK a and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pK a , NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent. © 2011 American Institute of Physics
Electron transfer induced dissociation of chloro-cyano-benzene radical anion: Driving chemical reactions via charge restraints
No full textWe introduce a new quantum mechanics/molecular mechanics based method to drive electron transfer reactions. Our approach uses the dynamically restrained electrostatic potential derived charges of the quantum atoms(1) as a reaction coordinate, and allows an estimation of the free energy barrier of the electron transfer process. Moreover, it provides an accurate description of the electronic structure changes and of the nuclear reorganization associated with the reaction. We use the method to describe the electron-transfer induced dissociation of the m-chloro-cyano-benzene radical anion in aqueous solution. The reaction is triggered by solvent reorganization by a change in the coordination water shell around the cyano nitrogen atom. At the onset of the reaction, charge-spin segregation is observed. The negative charge is transferred to the leaving Cl, while the spin density localizes on the non-saturated carbon atom of the benzene ring. The calculated free energy barrier of dissociation is in good quantitative agreement with the experimental data
Shadow bands, gap and pseudogap in high-Tc superconductors
No full textWithin the framework of the Charge Density Wave Quantum Critical Point (CDW-QCP] scenario for high-Tc superconductors (HTCS) we introduce a model for tight-binding electrons coupled to quasi-critical fluctuations. In the normal state our model reproduces features the Fermi Surface (FS) observed in ARPES measurements on optimality doped Bi2212, such as the anisotropic suppression of spectral weight around the M points of the Brillouin zone. The spectral density is characterized by a transfer of spectral weight from the main quasiparticle peak to dispersing shadow peaks which originate branches of a shadow FS. In the superconducting state our model reproduces the d-wave symmetry of the gap parameter, which results from a balance between small-q attraction and large-q repulsion. The gap parameter is enhanced due to cooperative effects of charge and spin fluctuations
First principles study of alkali-tyrosine complexes: alkali solvation and redox properties.
No full textFermi surface and gap parameter in high-Tc superconductors: the Stripe Quantum Critical Point scenario
No full textWe study the single-particle spectral properties of electrons coupled to quasicritical charge and spin fluctuations close to a stripe-phase, which is governed by a Quantum Critical Point near optimum doping. We find that spectral weight is transferred from the quasiparticle peak to incoherent dispersive features. As a consequence, the distribution of low-laying spectral weight is modified with respect to the quasiparticle Fermi surface. The interplay of charge and spin fluctuations reproduces features of the observed Fermi surface, such as the asymmetric suppression of spectral weight near the M points of the Brillouin zone. Within the model, we also analyze the interplay between repulsive spin and attractive charge fluctuations in determining the symmetry and the peculiar momentum dependence of the superconducting gap parameter. When both spin and charge fluctuations are coupled to the electrons, we find dx2−y2-wave gap symmetry in a wide range of parameter. A crossover d- vs. s-wave symmetry of the gap may occur when the strength of charge fluctuations increases with respect to spin fluctuations
Ab initio molecular dynamics study of ascorbic acid in aqueous solution
No full textThe ascorbic radical anion A{*}(-) in aqueous solution was studied using ab initio molecular dynamics based on density functional theory. Calculations of the spin density indicate that, both in vacuum and in solution, the unpaired electron is largely shared between the two oxygens, which, in the fully reduced acid AH(2), constitute the acid hydroxyl groups, and the two carbon atoms connecting them. Of these two oxygens in RADAN, the one carrying in the reduced AN form the remaining proton is found to be the site with the largest unpaired electron density and also the site with (marginally) the higher affinity for hydrogen bonds. The hydrophilic character is almost completely lost upon oxidation of A{*}(-) to A. Reduction to AH(-) strengthens the hydrogen bonding of the deprotonated oxygen and weakens the hydrogen bonding of the protonated oxygen atom
Spray freeze-drying for inhalable L-leucine, mannitol-based microparticles: The impact of process variables, L-leucine, and crystallinity on Aerosolization properties
No full textIn this study, microparticles carrying salbutamol sulphate were produced by pneumatic spray freeze-drying. The optimal particle size was assessed through a model, associated with a design of experiments. Growing solid concentrations and N 2 f low rate led to decreasing geometric diameters, while an opposite effect was associated with the feed flow rate. The aerodynamic diameter, instead, increased at increasing solid concentrations. Moreover, the role of crystallinity in determining the microparticles’ flowability was evaluated upon the incorporation of L-leucine. The addition of the amino acid induced the formation of two morphologies with different degrees of crystallinity. The absence of recrystallization significantly improved the aerosolization properties of the microparticles up to a maximum fine particle fraction (48 %) and a minimum mass median aerodynamic diameter (2 μ m)at 10%(w/wdb)L-leucine. This result disclosed the influence of polymorphism on the microparticles’ cohesiveness, proving the dependency of the microparticles’ aerodynamics on L-leucine and mannitol crystallinity
Quantum Mechanical/Molecular Mechanical (QM/MM) Car-Parrinello Simulations in Excited States
No full textThe combination of time-dependent density functional theory (TDDFT) for the description of excited
states with a hybrid quantum mechanics/molecular mechanics (QM/MM) approach enables the study of photochemical
processes in complex environments. Here, we present a short overview of recent applications of TDDFT/
MM approaches to a variety of systems including studies of the optical properties of prototypical organic and
inorganic molecules in gas phase and solution, photoinduced electron transfer reactions in donor-bridge-acceptor
complexes, and in situ investigations of the molecular mechanisms of photoactive proteins. The application of
TDDFT/MM techniques to a wide range of systems enables an assessment of the current performance and limitations
of these methods for the characterization of photochemical processes in complex systems
Reaction mechanism of caspases: Insights from QM/MM Car-Parrinello simulations
No full textCaspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/mol. mechanics Car-Parrinello study of key steps of the enzymic reaction for a representative member of this family, caspase-3. The hydrolysis of the acyl-enzyme complex is described at the d. functional (BLYP) level of theory while the protein frame and solvent are treated using the GROMOS96 force field. These calcns. show that the attack of the hydrolytic water mol. implies an activation free energy of .apprx.DFA ~ 19+-4 kcal/mol in good agreement with exptl. data and leads to a previously unrecognized gem-diol intermediate that can readily (DFA ~ 5+-3 kcal/mol) evolve to the enzyme products. Our findings assist in elucidating the striking difference in catalytic activity between caspases and other structurally well-characterized cysteine proteases (papains and cathepsins) and may help design novel transition-state analog inhibitors. [on SciFinder (R)]LCB
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