119 research outputs found
Vibrational dynamics of zero-field-splitting hamiltonian in gadolinium-based MRI contrast agents from ab initio molecular dynamics
International audienceThe electronic relaxation of gadolinium complexes used as MRI contrast agents was studied theoretically by following the short time evolution of zero-field-splitting parameters. The statistical analysis of ab initio molecular dynamics trajectories provided a clear separation between static and transient contributions to the zero-field-splitting. For the latter, the correlation time was estimated at approximately 0.1 ps. The influence of the ligand was also probed by replacing one pendant arm of our reference macrocyclic complex by a bulkier phosphonate arm. In contrast to the transient contribution, the static zero-field-splitting was significantly influenced by this substitutio
Molecular hydrodynamics from memory kernels
The memory kernel for a tagged particle in a fluid, computed from molecular
dynamics simulations, decays algebraically as . We show how the
hydrodynamic Basset-Boussinesq force naturally emerges from this long-time tail
and generalize the concept of hydrodynamic added mass. This mass term is
negative in the present case of a molecular solute, at odds with incompressible
hydrodynamics predictions. We finally discuss the various contributions to the
friction, the associated time scales and the cross-over between the molecular
and hydrodynamic regimes upon increasing the solute radius.Comment: 5 pages, 4 figure
Challenges in first-principles NPT molecular dynamics of soft porous crystals: A case study on MIL-53(Ga)
Soft porous crystals present a challenge to molecular dynamics simulations
with flexible size and shape of the simulation cell (i.e., in the NPT
ensemble), since their framework responds very sensitively to small external
stimuli. Hence, all interactions have to be described very accurately in order
to obtain correct equilibrium structures. Here, we report a methodological
study on the nanoporous metal-organic framework MIL-53(Ga), which undergoes a
large-amplitude transition between a narrow- and a large-pore phase upon a
change in temperature. Since this system has not been investigated by density
functional theory (DFT)-based NPT simulations so far, we carefully check the
convergence of the stress tensor with respect to computational parameters.
Furthermore, we demonstrate the importance of dispersion interactions and test
two different ways of incorporating them into the DFT framework. As a result,
we propose two computational schemes which describe accurately the narrow- and
the large-pore phase of the material, respectively. These schemes can be used
in future work on the delicate interplay between adsorption in the nanopores
and structural flexibility of the host material
Quasi-classical simulations of resonance Raman spectra based on path integral linearization
Based on a linearization approximation coupled with path integral formalism,
we propose a method derived from the propagation of quasi-classical
trajectories to simulate resonance Raman spectra. This method is based on a
ground state sampling followed by an ensemble of trajectories on the mean
surface between the ground and excited states. The method was tested on three
models and compared to quantum mechanics solution based on a sum-over-states
approach: harmonic and anharmonic oscillators and the HOCl molecule
(hypochlorous acid). The method proposed is able to correctly characterize
resonance Raman scattering and enhancement, including the description of
overtones and combination bands. The absorption spectrum is obtained at the
same time and the vibrational fine structure can be reproduced for long excited
state relaxation times. The method can be applied also to dissociating excited
states (as is the case for HOCl)
Predicting the Charge Density Response in Metal Electrodes
The computational study of energy storage and conversion processes call for
simulation techniques that can reproduce the electronic response of metal
electrodes under electric fields. Despite recent advancements in
machine-learning methods applied to electronic-structure properties, predicting
the non-local behaviour of the charge density in electronic conductors remains
a major open challenge. We combine long-range and equivariant kernel methods to
predict the Kohn-Sham electron density of metal electrodes decomposed on an
atom-centered basis. By taking slabs of gold as an example, we show that
including long-range correlations into the learning model is essential to
accurately reproduce the charge density and potential in bare electrodes of
increasing size. A finite-field extension of the method is then introduced,
which allows us to predict the charge transfer and the electrostatic potential
drop induced by the application of an external electric field. Finally, we
demonstrate the capability of the method to extrapolate the non-local
electronic polarization generated by the interaction with an ionic species for
electrodes of arbitrary thickness. Our study represents an important step
forward in the accurate simulation of energy materials that include metallic
interfaces.Comment: 6 pages, 4 figure
On the mass of atoms in molecules: Beyond the Born-Oppenheimer approximation
Describing the dynamics of nuclei in molecules requires a potential energy
surface, which is traditionally provided by the Born-Oppenheimer or adiabatic
approximation. However, we also need to assign masses to the nuclei. There, the
Born-Oppenheimer picture does not account for the inertia of the electrons and
only bare nuclear masses are considered. Nowadays, experimental accuracy
challenges the theoretical predictions of rotational and vibrational spectra
and requires to include the participation of electrons in the internal motion
of the molecule. More than 80 years after the original work of Born and
Oppenheimer, this issue still is not solved in general. Here, we present a
theoretical and numerical framework to address this problem in a general and
rigorous way. Starting from the exact factorization of the electron-nuclear
wave function, we include electronic effects beyond the Born-Oppenheimer regime
in a perturbative way via position-dependent corrections to the bare nuclear
masses. This maintains an adiabatic-like point of view: the nuclear degrees of
freedom feel the presence of the electrons via a single potential energy
surface, whereas the inertia of electrons is accounted for and the total mass
of the system is recovered. This constitutes a general framework for describing
the mass acquired by slow degrees of freedom due to the inertia of light,
bounded particles. We illustrate it with a model of proton transfer, where the
light particle is the proton, and with corrections to the vibrational spectra
of molecules. Inclusion of the light particle inertia allows to gain orders of
magnitude in accuracy
Infrared spectroscopy in the gas and liquid phase from first principle molecular dynamics simulations - Application to small peptides
International audienceWe discuss the applicability of finite temperature Car-Parrinello molecular dynamics simulations for the calculation of infrared spectra of complex molecular systems, either in the gas phase or in the condensed phase, taking examples from the infrared spectroscopy of N-methylacetamide and small peptides. Band assignments for the simulation is still challenging and we introduce here a general method for obtaining effective normal modes of molecular systems from Molecular Dynamics simulations. The effective normal modes are defined as linear combination of internal coordinates such that the power spectra of these modes are as localized as possible in frequency. We further define band intensities for these modes from different levels of approximation of the infrared spectrum. Applications of this approach for assigning infrared bands from first-principle molecular dynamics simulations are presented for N-methylacetamide in gas phase and in solution, for the gas phase alanine dipeptide and the gas phase octa-alanine peptide
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