1,721,119 research outputs found
Ground State Geometries of Polyacetylene Chains from Many-Particle Quantum Mechanics
Full text linkDue to the crucial role played by electron correlation, the accurate determination of ground state geometries of π-conjugated molecules is still a challenge for many quantum chemistry methods. Because of the high parallelism of the algorithms and their explicit treatment of electron correlation effects, Quantum Monte Carlo calculations can offer an accurate and reliable description of the electronic states and of the geometries of such systems, competing with traditional quantum chemistry approaches. Here, we report the structural properties of polyacetylene chains H-(C2H2)N-H up to N = 12 acetylene units, by means of Variational Monte Carlo (VMC) calculations based on the multi-determinant Jastrow Antisymmetrized Geminal Power (JAGP) wave function. This compact ansatz can provide for such systems an accurate description of the dynamical electronic correlation as recently detailed for the 1,3-butadiene molecule [J. Chem. Theory Comput. 2015 11 (2), 508-517]. The calculated Bond Length Alternation (BLA), namely the difference between the single and double carbon bonds, extrapolates, for N → ∞, to a value of 0.0910(7) Å, compatible with the experimental data. An accurate analysis was able to distinguish between the influence of the multi-determinantal AGP expansion and of the Jastrow factor on the geometrical properties of the fragments. Our size-extensive and self-interaction-free results provide new and accurate ab initio references for the structures of the ground state of polyenes. © 2015 American Chemical Society
Potassium permeation through the KcsA channel: a density functional study
No full textWe present a theoretical study on structural and electronic aspects of K+ permeation through the binding sites of the KcsA channel's selectivity filter. Density functional calculations are carried out on models taken from selected snapshots of a molecular dynamics simulation recently reported [FEBS Lett. 477 (2000) 37]. During the translocation process from one binding site to the other, the coordination number of the permeating K+ ion turns out to decrease and K+ ion polarizes significantly its ligands, backbone carbonyl groups and a water molecule. K+-induced polarization increases significantly at the transition state ITS) between the two binding sites. These findings suggest that polarization effects play a significant role in the microscopic mechanisms regulating potassium permeation. (C) 2002 Elsevier Science B.V All rights reserved
π-Conjugation in trans -1,3-Butadiene: Static and dynamical electronic correlations described through quantum monte carlo
No full textWe investigate the effects of the static and dynamical electronic correlations on the level of conjugation of the trans-1,3-butadiene molecule through Quantum Monte Carlo methods applied to an Antisymmetrized Geminal Power (AGP) wave function, with a Jastrow factor similar to the Gutzwiller ansatz. The degree of conjugation is measured through the convergence of the structural properties of 1,3-butadiene and in particular of the Bond Length Alternation (BLA), that is the difference between the lengths of the single and double carbon bonds. After verifying the different roles of the Fermionic AGP part of our wave function and of the Jastrow factor in recovering electronic correlation, we study the effects of a constrained Active Space AGP (AGPAS), similar to that used in the Complete Active Space (CAS) representation. Through this AGPAS, we are able to identify the effect of the limited active space on the degree of conjugation, showing that in the limit of infinite active space the structural properties converge exactly to those of the atomic AGP, giving a BLA for 1,3-butadiene around 0.1244(5) Å. © 2015 American Chemical Society
Reaction pathways by Quantum Monte Carlo: insight on the torsion barrier of 1,3-butadiene, and the conrotatory ring opening of cyclobutene
No full textQuantum Monte Carlo (QMC) methods are used to investigate the intramolecular
reaction pathways of 1,3-butadiene. The ground state geometries of the three con-
formers s-trans, s-cis and gauche, as well as the cyclobutene structure are fully opti-
mised at the Variational Monte Carlo (VMC) level, obtaining an excellent agreement
with the experimental results and other quantum chemistry high level calculations.
Transition state geometries are also estimated at the VMC level for the s-trans to
gauche torsion barrier of 1,3-butadiene and for the conrotatory ring opening of cy-
clobutene to the gauche-1,3-butadiene conformer. The energies of the conformers and
the reaction barriers are calculated at both variational and diffusional Monte Carlo
levels providing a precise picture of the potential energy surface of 1,3-butadiene and
supporting one of the two model profiles recently obtained by Raman spectroscopy
[Boopalachandran et al., J. Phys. Chem. A 115, 8920 (2011)]. Considering the
good scaling of QMC techniques with the system’s size, our results also demonstrate
how Variational Monte Carlo calculations can be applied in the future to properly
investigate the reaction pathways of large and correlated molecular systems
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
Pathway for Mn-cluster oxidation by tyrosine-Z in the S-2 state of photosystem II
No full textWater oxidation in photosynthetic organisms occurs through the five intermediate steps S-0-S-4 of the Kok cycle in the oxygen evolving complex of photosystem II (PSII). Along the catalytic cycle, four electrons are subsequently removed from the Mn4CaO5 core by the nearby tyrosine Tyr-Z, which is in turn oxidized by the chlorophyll special pair P680, the photo-induced primary donor in PSII. Recently, two Mn4CaO5 conformations, consistent with the S-2 state (namely, S-2(A) and S-2(B) models) were suggested to exist, perhaps playing a different role within the S-2-to-S-3 transition. Here we report multiscale ab initio density functional theory plus U simulations revealing that upon such oxidation the relative thermodynamic stability of the two previously proposed geometries is reversed, the S-2(B) state becoming the leading conformation. In this latter state a proton coupled electron transfer is spontaneously observed at similar to 100 fs at room temperature dynamics. Upon oxidation, the Mn cluster, which is tightly electronically coupled along dynamics to the Tyr-Z tyrosyl group, releases a proton from the nearby W1 water molecule to the close Asp-61 on the femtosecond timescale, thus undergoing a conformational transition increasing the available space for the subsequent coordination of an additional water molecule. The results can help to rationalize previous spectroscopic experiments and confirm, for the first time to our knowledge, that the water-splitting reaction has to proceed through the S-2(B) conformation, providing the basis for a structural model of the S-3 state
Early Steps of the Intramolecular Signaling Pathway in Rhodopsin Explored by Molecular Dynamics Simulations
No full textWe present molecular dynamics simulations of bovine rhodopsin in a membrane mimetic environment based on the recently refined X-ray structure of the pigment. The interactions between the protonated Schiff base and the protein moiety are explored both with the chromophore in the dark-adapted 11-cis and in the photoisomerized all-trans form. Comparison of simulations with Glu181 in different protonation states strongly suggests that this loop residue located close to the 11-cis bond bears a negative charge. Restrained molecular dynamics simulations also provide evidence that the protein tightly confines the absolute conformation of the retinal around the C12-C13 bond to a positive helicity. 11-cis to all-trans isomerization leads to an internally strained chromophore, which relaxes after a few nanoseconds by a switching of the ionone ring to an essentially planar all-trans conformation. This structural transition of the retinal induces in turn significant conformational changes of the protein backbone, especially in helix VI. Our results suggest a possible molecular mechanism for the early steps of intramolecular signal transduction in a prototypical G-protein-coupled receptor
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
Natural Orbitals and Sparsity of Quantum Mutual Information
No full textNatural orbitals, defined in electronic structure and quantum chemistry as the molecular orbitals diagonalizing the one-particle reduced density matrix of the ground state, have been conjectured for decades to be the perfect reference orbitals to describe electron correlation. In the present work we applied the Wave function-Adapted Hamiltonian Through Orbital Rotation (WAHTOR) method to study correlated empirical ansätze for quantum computing. In all representative molecules considered, we show that the converged orbitals are coinciding with natural orbitals. Interestingly, the resulting quantum mutual information matrix built on such orbitals is also maximally sparse, providing a clear picture that such orbital choice is indeed able to provide the optimal basis to describe electron correlation. The correlation is therefore encoded in a smaller number of qubit pairs contributing to the quantum mutual information matrix
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