Search results for "colloid"
showing 10 items of 1288 documents
Ligand-Stabilized Au13Cux (x = 2, 4, 8) Bimetallic Nanoclusters: Ligand Engineering to Control the Exposure of Metal Sites
2013
Three novel bimetallic Au-Cu nanoclusters stabilized by a mixed layer of thiolate and phosphine ligands bearing pyridyl groups are synthesized and fully characterized by X-ray single crystal analysis and density functional theory computations. The three clusters have an icosahedral Au13 core face-capped by two, four, and eight Cu atoms, respectively. All face-capping Cu atoms in the clusters are triply coordinated by thiolate or pyridyl groups. The surface ligands control the exposure of Au sites in the clusters. In the case of the Au13Cu8 cluster, the presence of 12 2-pyridylthiolate ligands still leaves open space for catalysis. All the 3 clusters are 8-electron superatoms displaying opti…
The Role of Adenine Excimers in the Photophysics of Oligonucleotides
2009
Energies and structures of different arrangements of the stacked adenine homodimer have been computed at the ab initio CASPT2 level of theory in isolation and in an aqueous environment. Adenine dimers are shown to form excimer singlet states with different degrees of stacking and interaction. A model for a 2-fold decay dynamics of adenine oligomers can be supported in which, after initial excitation in the middle UV range, unstacked or slightly stacked pairs of nucleobases will relax by an ultrafast internal conversion to the ground state, localizing the excitation in the monomer and through the corresponding conical intersection with the ground state. On the other hand, long-lifetime intra…
Motion, relaxation dynamics, and diffusion processes in two-dimensional colloidal crystals confined between walls
2012
The dynamical behavior of single-component two-dimensional colloidal crystals confined in a slit geometry is studied by Langevin dynamics simulation of a simple model. The colloids are modeled as pointlike particles, interacting with the repulsive part of the Lennard-Jones potential, and the fluid molecules in the colloidal suspension are not explicitly considered. Considering a crystalline strip of triangular lattice structure with n=30 rows, the (one-dimensional) walls confining the strip are chosen as two rigidly fixed crystalline rows at each side, commensurate with the lattice structure and, thus, stabilizing long-range order. The case when the spacing between the walls is incommensura…
Biomimetic oxygen reduction by cofacial porphyrins at a liquid-liquid interface.
2012
Oxygen reduction catalyzed by cofacial metalloporphyrins at the 1,2-dichlorobenzene−water interface was studied with two lipophilic electron donors of similar driving force, 1,1'-dimethylferrocene (DMFc) and tetrathiafulvalene (TTF). The reaction produces mainly water and some hydrogen peroxide, but the mediator has a significant effect on the selectivity, as DMFc and the porphyrins themselves catalyze the decomposition and the further reduction of hydrogen peroxide. Density functional theory calculations indicate that the biscobaltporphyr- in, 4,5-bis(5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl))-9,9-dimethylxanthene, Co2(DPX), actually catalyzes oxygen reduction to hydrogen p…
Role of Protein Flexibility in Enzymatic Catalysis: Quantum Mechanical−Molecular Mechanical Study of the Deacylation Reaction in Class A β-Lactamases
2002
We present a theoretical study of a mechanism for the hydrolysis of the acyl-enzyme complex formed by a class A beta-lactamase (TEM1) and an antibiotic (penicillanate), as a part of the process of antibiotic's inactivation by this type of enzymes. In the presented mechanism the carboxylate group of a particular residue (Glu166) activates a water molecule, accepting one of its protons, and afterward transfers this proton directly to the acylated serine residue (Ser70). In our study we employed a quantum mechanics (AM1)-molecular mechanics partition scheme (QM/MM) where all the atoms of the system were allowed to relax. For this purpose we used the GRACE procedure in which part of the system …
Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate const…
2014
Catalysis by dihydrofolate reductase from the moderately thermophilic bacterium Geobacillus stearothermophilus (BsDHFR) was investigated by isotope substitution of the enzyme. The enzyme kinetic isotope effect for hydride transfer was close to unity at physiological temperatures but increased with decreasing temperatures to a value of 1.65 at 5 °C. This behavior is opposite to that observed for DHFR from Escherichia coli (EcDHFR), where the enzyme kinetic isotope effect increased slightly with increasing temperature. These experimental results were reproduced in the framework of variational transition-state theory that includes a dynamical recrossing coefficient that varies with the mass of…
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…
Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.
2011
We here present a theoretical study of the alkaline hydrolysis of a phosphodiester (methyl p-nitrophenyl phosphate or MpNPP) in the active site of Escherichia coli alkaline phosphatase (AP), a monoesterase that also presents promiscuous activity as a diesterase. The analysis of our simulations, carried out by means of molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, shows that the reaction takes place through a D(N)A(N) or dissociative mechanism, the same mechanism employed by AP in the hydrolysis of monoesters. The promiscuous activity observed in this superfamily can be then explained on the basis of a conserved reaction mechanism. …
Dynamic Effects on Reaction Rates in a Michael Addition Catalyzed by Chalcone Isomerase. Beyond the Frozen Environment Approach
2008
We present a detailed microscopic study of the dynamics of the Michael addition reaction leading from 6'-deoxychalcone to the corresponding flavanone. The reaction dynamics are analyzed for both the uncatalyzed reaction in aqueous solution and the reaction catalyzed by Chalcone Isomerase. By means of rare event simulations of trajectories started at the transition state, we have computed the transmission coefficients, obtaining 0.76 +/- 0.04 and 0.87 +/- 0.03, in water and in the enzyme, respectively. According to these simulations, the Michael addition can be seen as a formation of a new intramolecular carbon-oxygen bond accompanied by a charge transfer essentially taking place from the nu…
Electrostatic control of the photoisomerization efficiency and optical properties in visual pigments: on the role of counterion quenching.
2009
Hybrid QM(CASPT2//CASSCF/6-31G*)/MM(Amber) computations have been used to map the photoisomerization path of the retinal chromophore in Rhodopsin and explore the reasons behind the photoactivity efficiency and spectral control in the visual pigments. It is shown that while the electrostatic environment plays a central role in properly tuning the optical properties of the chromophore, it is also critical in biasing the ultrafast photochemical event: it controls the slope of the photoisomerization channel as well as the accessibility of the S(1)/S(0) crossing space triggering the ultrafast decay. The roles of the E113 counterion, the E181 residue, and the other amino acids of the protein pock…