259 research outputs found
Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore
No full textThe structure and dynamics of the retinal chromophore of rhodopsin
are investigated systematically in different environments
(vacuum, methanol solution, and protein binding pocket) and
with different computational approaches (classical, quantum,
and hybrid quantum mechanics/molecular mechanics (QM/MM)
descriptions).Finite temperature effects are taken into account
by molecular dynamics simulations.The different components
that determine the structure and dynamics of the chromophore
in the protein are dissected, both in the dark state and in the
early photointermediates.In vacuum and in solution the chromophore
displays a very high flexibility, which is significantly reduced
by the protein environment.In the 11-cis chromophore,
the bond-length alternation, which is correlated with the dipole
moment, is found to be similar in solution and in the protein,
while it differs greatly with respect to minimum-energy vacuum
structures.In the model of the earliest protein photointermediate,
the highly twisted chromophore shows a very reduced bondlength
alternation
Three- and four-center trans effects in triply bonded ditungsten complexes: An ab initio molecular dynamics study of compounds with stoichiometry W2Cl4(NHEt)(2)(PMe3)(2)
No full textWe have performed ab initio molecular dynamics simulations based on density functional theory to characterize the structural, electronic, and dynamic properties of the three major isomeric forms of the title compound. In agreement with experimental results, calculations with two different parametrizations of the exchange-correlation functional (BLYP and BP) both indicate the cis-C-2 form as the most stable isomer. The relative energies of the different forms are, however, small (less than or similar to1-2 kcal/mol), and the three compounds show overall very similar ground-state properties. Larger differences exist in their finite temperature behavior, which is dominated by the facile dissociation of one or both phosphine ligands. The calculated activation energies for phosphine dissociation differ clearly for the trans and the cis isomers and vary in the order trans much less than cis-C-2 less than or similar to cis-C-i. Analysis of the electronic structure of the transition states shows that the difference in activation energy between cis and trans isomers can be rationalized in terms of a classic trans effect caused by a molecular orbital spanning the three atomic centers N-W-P. The subtle difference between the two cis isomers, on the other hand, is likely due to an analogous four-center trans effect N-W-W-P which is mediated via metal-metal orbitals and involves ligands on both tungsten atoms
Scanning Reactive Pathways with Orbital Biased Molecular Dynamics
No full textTo accelerate reactive events in molecular dynamics simulations we introduce a
general bias potential scheme which depends only on the electronic degrees of freedom of the
reactive system. This electronic reaction coordinate, which is expressed in terms of a penalty
function of the one-electron orbital energies, has been applied to study different reaction pathways
of s-cis-butadiene. Three different reactive channels have been identified: the cis/trans
isomerization, the s-cis/s-trans isomerization, and the symmetry allowed cyclization. For the
latter, despite the fact that the Woodward-Hoffmann rules are guided by the butadiene frontier
orbitals, biasing only these orbitals is not enough to drive the system toward cyclization, but a
low-lying valence shell orbital needs to be included
The role of pi-pi, stacking interactions in square planar palladium complexes. Combined quantum mechanics/molecular mechanics QM/MM studie
No full textDensity functional (DFT) studies and hybrid QM/MM-DFT calculations demonstrate the importance of pi-pi stacking interactions in determining the structural features of two exemplary d(8) palladium complexes, PdBr(p-NCC6H4)({S}-MeO-Biphep), 1, and PdBr(C6F5)-({S}-MeO-Biphep), 2. Despite the superficial similarity of the two compounds, the former shows marked distortions from square planar geometry, while the latter exhibits an almost ideal structure. Attractive pi-pi stacking interactions between two pairs of P-phenyl rings and the arene backbone of the MeO-Biphep are the main origin of the distortion in complex 1. The planar structure of complex 2 is preferred as a consequence of an additional stacking interaction between one P-phenyl ring and the pentafluorophenyl a-ligand. The artificial introduction of an analogous stacking interaction in complex 1 reestablishes an ideal square planar geometry, thus demonstrating that switching on/off specific pi-pi interactions distinctly alters the coordination geometry. These results reveal a previously unrecognized role for pi-pi stacking interactions in the stabilization of structural features in transition metal compounds. This suggests pi-pi stacking interactions as a potential new design principle in tailoring coordination compounds
Cis-trans isomerization in triply-bonded ditungsten complexes: A multitude of possible pathways
No full textWe have investigated different possible mechanisms for the cis-trans isomerization in triply bonded ditungsten complexes with stoichiometry W2Cl4(NHEt)(2)(PMe3)(2) using static density functional calculations as well as Car-Parrinello simulations. Our studies reveal an unexpected richness of possible reaction pathways that include both unimolecular and bimolecular mechanisms. Among the possible routes that have been identified are processes involving successive dissociation/reassociation of phosphine ligands, intramolecular chloride hopping, intertungsten phosphine exchange as well as numerous combinations of these basic reaction types. All pathways involve maximal activation barriers of less than 35 kcal/mol and include phosphine concentration dependent and independent routes. The energetically most favorable phosphine-dependent pathway is based on the dissociation/reassociation of phosphine ligands. This path is characterized by a maximal dissociation barrier of IS kcal/mol. The fastest alternative unimolecular route (with a maximal activation barrier of 24 kcal/mol) is based on a direct exchange of phosphine between the two metallic coordination centers. All the identified pathways, with the exception of a previously proposed internal flip mechanism that can be ruled out on energetic grounds, are competitive and may contribute in various combinations to the overall reaction rate. The identified isomerization mechanisms are fully consistent with the experimentally observed 3-state-kinetics and the dependence of the overall reaction rate on the excess concentration of phosphine which is demonstrated with a simplified kinetic model of the process
The protonation state of the Glu-71/Asp-80 residues in the KcsA Potassium Channel. A first principles QM/MM Molecular Dynamics Study
No full textAlthough a few x-ray structures of the KcsA K1 channel have been crystallized several issues concerning the
mechanisms of the ionic permeation and the protonation state of the selectivity filter ionizable side chains are still open. Using a
first-principles quantum mechanical/molecular mechanical simulation approach, wehave investigated the protonation state of Glu-
71 and Asp-80, two important residues located in the vicinity of the selectivity filter. Results from the dynamics show that a proton is
shared between the two residues, with a slight preference for Glu-71. The proton is found to exchange on the picosecond timescale,
an interesting phenomenon that cannot be observed in classical molecular dynamics. Simulations of different ionic loading states of
the filter show that the probability for the proton transfer is correlated with the filter occupancy. In addition, the Glu-71/Asp-80 pair is
able to modulate the potential energy profile experienced by a K1 ion as it translates along the pore axis. These theoretical
predictions, along with recent experimental results, suggest that changes of the filter structure could be associated with a shift in the
Glu-Asp protonation state, which in turn would influence the ion translocation
Study of the structural and dynamical properties of a biomimetic compound of diiron proteins via ab initio and hybrid (QM/MM) molecular dynamics simulations.
No full text13-ATOM CLUSTERS - EQUILIBRIUM GEOMETRIES, STRUCTURAL TRANSFORMATIONS, AND TRENDS IN NA, MG, AL, AND SI
No full textWe report the results of an extensive structural study of Na13, Mg13, Al13, and Si13 carried out with the Car-Parrinello method. Several and mostly unforeseen noncrystalline structures are discovered to characterize the low portion of the potential energy surface. Crystalline structures are shown either to correspond to high-energy local minima or to be highly unstable. The low-energy structural pattern appears to change significantly from one element to the other. Specific characteristics as well as trends are discussed
Enantioselective palladium-catalyzed hydrosilylation of styrene: Influence of electronic and steric effects on enantioselectivity and catalyst design via hybrid QM/MM molecular dynamics simulations
No full textThe factors determining the enantioselectivity of the palladium-catalyzed hydrosilylation of styrene have been rationalized by performing mixed QM/MM Car-Parrinello molecular dynamics simulations with styrene and 4-(dimethylamino)styrene as substrates. Our results demonstrate that the eta(3)-benzylic intermediate plays a crucial role in the stereoselectivity of the reaction. The relative thermodynamic stabilities (Delta E approximate to 1-2 kcal/mol) of the endo and exo eta(3) forms of the benzylic intermediates, precursors of the two enantiomeric products, are inverted as a function of the electron-releasing or -withdrawing nature of the para substituent of the substrate, and this trend holds also for the transition state of the reductive elimination step (the enantioselectivity-determining step). An electronic and structural characterization of the benzylic diasteroisomers shows that steric effects also play an important role in the inversion of the relative thermodynamic stability of the two allylic diasteroisomers. An analysis of the charge distribution of the free benzyl radical and a computational design of the catalyst suggest that the extent of the chiral induction may be moderately affected by the electronic properties of the substrate, but the sense is mainly dominated by steric effects of both the substrate and the ligands. Finally, we provide suggestions that may increase the observed enantiomeric excess (ee) of the reaction
Association of both inhibitory and stimulatory Gα subunits implies adenylyl cyclase 5 deactivation
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