11 research outputs found
Well-Tempered Variational Approach to Enhanced Sampling
We
propose a simple yet effective iterative scheme that allows
us to employ the well-tempered distribution as a target distribution
for the collective variables in our recently introduced variational
approach to enhanced sampling and free energy calculations [Valsson and Parrinello Phys. Rev.
Lett. 2014, 113, 090601]. The performance of the scheme is evaluated for the
three-dimensional free energy surface of alanine tetrapeptide where
the convergence can be rather poor when employing the uniform target
distribution. Using the well-tempered target distribution on the other
hand results in a significant improvement in convergence. The results
observed in this paper indicate that the well-tempered distribution
is in most cases the preferred and recommended choice for the target
distribution in the variational approach
Gas-Phase Retinal Spectroscopy: Temperature Effects Are But a Mirage
We employ state-of-the-art first-principle approaches
to investigate whether temperature effects are responsible for the
unusually broad and flat spectrum of protonated Schiff base retinal
observed in photodissociation spectroscopy, as has recently been proposed.
We first carefully calibrate how to construct a realistic geometrical
model of retinal and show that the exchange–correlation M06-2X
functional yields an accurate description while the commonly used
complete active space self-consistent field method (CASSCF) is not
adequate. Using modern multiconfigurational perturbative methods (NEVPT2)
to compute the excitations, we then demonstrate that conformations
with different orientations of the β-ionone ring are characterized
by similar excitations. Moreover, other degrees of freedom identified
as active in room-temperature molecular dynamics simulations do not
yield the shift required to explain the anomalous spectral shape.
Our findings indicate that photodissociation experiments are not representative
of the optical spectrum of retinal in the gas phase and call for further
experimental characterization of the dissociation spectra
Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble
We
explore the performance of the well-tempered ensemble combined
with parallel tempering (PT-WTE) in obtaining a thermodynamical description
of a given molecular system. We carefully explain the theoretical
procedure employed to extract all the relevant thermodynamical quantities
from a PT-WTE simulation. As a specific molecular system, we consider
a Lennard–Jones cluster of 147 particles, which is a prototypical
case of a finite-size system exhibiting a quasi-first-order phase
transition, characterized by a range of temperatures where two distinct
phases are thermodynamically stable and coexist. Two separate PT-WTE
simulations, which investigate the thermodynamical behavior on different
levels of detail, give equally accurate descriptions of the critical
phase-coexistence region, indicating the good quality of the PT-WTE
results. The positive performance observed here clearly demonstrates
that the PT-WTE approach is an effective option when thermodynamical
properties are needed
Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling
In recent work, we
demonstrated that it is possible to obtain approximate
representations of high-dimensional free energy surfaces with variationally
enhanced sampling (Shaffer, P.;
Valsson, O.; Parrinello, M. Proc. Natl. Acad. Sci., 2016, 113, 17). The high-dimensional spaces considered in that work were the set
of backbone dihedral angles of a small peptide, Chignolin, and the
high-dimensional free energy surface was approximated as the sum of
many two-dimensional terms plus an additional term which represents
an initial estimate. In this paper, we build on that work and demonstrate
that we can calculate high-dimensional free energy surfaces of very
high accuracy by incorporating additional terms. The additional terms
apply to a set of collective variables which are more coarse than
the base set of collective variables. In this way, it is possible
to build hierarchical free
energy surfaces, which are composed of terms that act on different
length scales. We test the accuracy of these free energy landscapes
for the proteins Chignolin and Trp-cage by constructing simple coarse-grained
models and comparing results from the coarse-grained model to results
from atomistic simulations. The approach described in this paper is
ideally suited for problems in which the free energy surface has important
features on different length scales or in which there is some natural
hierarchy
The Crucial Role of Solvation Forces in the Steric Stabilization of Nanoplatelets
The steric stability
of inorganic colloidal particles in an apolar
solvent is usually described in terms of the balance between three
contributions: the van der Waals attraction, the free energy of mixing,
and the ligand compression. However, in the case of nanoparticles,
the discrete nature of the ligand shell and the solvent has to be
taken into account. Cadmium selenide nanoplatelets are a special case.
They combine a weak van der Waals attraction and a large facet to
particle size ratio. We use coarse grained molecular dynamics simulations
of nanoplatelets in octane to demonstrate that solvation forces are
strong enough to induce the formation of nanoplatelet stacks and by
that have a crucial impact on the steric stability. In particular,
we demonstrate that for sufficiently large nanoplatelets, solvation
forces are proportional to the interacting facet area, and their strength
is intrinsically tied to the softness of the ligand shell
The Crucial Role of Solvation Forces in the Steric Stabilization of Nanoplatelets
The steric stability
of inorganic colloidal particles in an apolar
solvent is usually described in terms of the balance between three
contributions: the van der Waals attraction, the free energy of mixing,
and the ligand compression. However, in the case of nanoparticles,
the discrete nature of the ligand shell and the solvent has to be
taken into account. Cadmium selenide nanoplatelets are a special case.
They combine a weak van der Waals attraction and a large facet to
particle size ratio. We use coarse grained molecular dynamics simulations
of nanoplatelets in octane to demonstrate that solvation forces are
strong enough to induce the formation of nanoplatelet stacks and by
that have a crucial impact on the steric stability. In particular,
we demonstrate that for sufficiently large nanoplatelets, solvation
forces are proportional to the interacting facet area, and their strength
is intrinsically tied to the softness of the ligand shell
The Crucial Role of Solvation Forces in the Steric Stabilization of Nanoplatelets
The steric stability
of inorganic colloidal particles in an apolar
solvent is usually described in terms of the balance between three
contributions: the van der Waals attraction, the free energy of mixing,
and the ligand compression. However, in the case of nanoparticles,
the discrete nature of the ligand shell and the solvent has to be
taken into account. Cadmium selenide nanoplatelets are a special case.
They combine a weak van der Waals attraction and a large facet to
particle size ratio. We use coarse grained molecular dynamics simulations
of nanoplatelets in octane to demonstrate that solvation forces are
strong enough to induce the formation of nanoplatelet stacks and by
that have a crucial impact on the steric stability. In particular,
we demonstrate that for sufficiently large nanoplatelets, solvation
forces are proportional to the interacting facet area, and their strength
is intrinsically tied to the softness of the ligand shell
The Crucial Role of Solvation Forces in the Steric Stabilization of Nanoplatelets
The steric stability
of inorganic colloidal particles in an apolar
solvent is usually described in terms of the balance between three
contributions: the van der Waals attraction, the free energy of mixing,
and the ligand compression. However, in the case of nanoparticles,
the discrete nature of the ligand shell and the solvent has to be
taken into account. Cadmium selenide nanoplatelets are a special case.
They combine a weak van der Waals attraction and a large facet to
particle size ratio. We use coarse grained molecular dynamics simulations
of nanoplatelets in octane to demonstrate that solvation forces are
strong enough to induce the formation of nanoplatelet stacks and by
that have a crucial impact on the steric stability. In particular,
we demonstrate that for sufficiently large nanoplatelets, solvation
forces are proportional to the interacting facet area, and their strength
is intrinsically tied to the softness of the ligand shell
The Crucial Role of Solvation Forces in the Steric Stabilization of Nanoplatelets
The steric stability
of inorganic colloidal particles in an apolar
solvent is usually described in terms of the balance between three
contributions: the van der Waals attraction, the free energy of mixing,
and the ligand compression. However, in the case of nanoparticles,
the discrete nature of the ligand shell and the solvent has to be
taken into account. Cadmium selenide nanoplatelets are a special case.
They combine a weak van der Waals attraction and a large facet to
particle size ratio. We use coarse grained molecular dynamics simulations
of nanoplatelets in octane to demonstrate that solvation forces are
strong enough to induce the formation of nanoplatelet stacks and by
that have a crucial impact on the steric stability. In particular,
we demonstrate that for sufficiently large nanoplatelets, solvation
forces are proportional to the interacting facet area, and their strength
is intrinsically tied to the softness of the ligand shell
Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls
Bovine rhodopsin is the most extensively
studied retinal protein
and is considered the prototype of this important class of photosensitive
biosystems involved in the process of vision. Many theoretical investigations
have attempted to elucidate the role of the protein matrix in modulating
the absorption of retinal chromophore in rhodopsin, but, while generally
agreeing in predicting the correct location of the absorption maximum,
they often reached contradicting conclusions on how the environment
tunes the spectrum. To address this controversial issue, we combine
here a thorough structural and dynamical characterization of rhodopsin
with a careful validation of its excited-state properties via the
use of a wide range of state-of-the-art quantum chemical approaches
including various flavors of time-dependent density functional theory
(TDDFT), different multireference perturbative schemes (CASPT2 and
NEVPT2), and quantum Monte Carlo (QMC) methods. Through extensive
quantum mechanical/molecular mechanical (QM/MM) molecular dynamics
simulations, we obtain a comprehensive structural description of the
chromophore–protein system and sample a wide range of thermally
accessible configurations. We show that, in order to obtain reliable
excitation properties, it is crucial to employ a sufficient number
of representative configurations of the system. In fact, the common
use of a single, ad hoc structure can easily lead to an incorrect
model and an agreement with experimental absorption spectra due to
cancelation of errors. Finally, we show that, to properly account
for polarization effects on the chromophore and to quench the large
blue-shift induced by the counterion on the excitation energies, it
is necessary to adopt an enhanced description of the protein environment
as given by a large quantum region including as many as 250 atoms