18,666 research outputs found
Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis
Given the piecewise approach to modeling intermolecular interactions for
force fields, they can be difficult to parameterize since they are fit to data
like total energies that only indirectly connect to their separable functional
forms. Furthermore, by neglecting certain types of molecular interactions such
as charge penetration and charge transfer, most classical force fields must
rely on, but do not always demonstrate, how cancellation of errors occurs among
the remaining molecular interactions accounted for such as exchange repulsion,
electrostatics, and polarization. In this work we present the first generation
of the (many-body) MB-UCB force field that explicitly accounts for the
decomposed molecular interactions commensurate with a variational energy
decomposition analysis, including charge transfer, with force field design
choices that reduce the computational expense of the MB-UCB potential while
remaining accurate. We optimize parameters using only single water molecule and
water cluster data up through pentamers, with no fitting to condensed phase
data, and we demonstrate that high accuracy is maintained when the force field
is subsequently validated against conformational energies of larger water
cluster data sets, radial distribution functions of the liquid phase, and the
temperature dependence of thermodynamic and transport water properties. We
conclude that MB-UCB is comparable in performance to MB-Pol, but is less
expensive and more transferable by eliminating the need to represent
short-ranged interactions through large parameter fits to high order
polynomials
van der Waals density functional calculations of binding in molecular crystals
A recent paper [J. Chem. Phys. 132, 134705 (2010)] illustrated the potential
of the van der Waals density functional (vdW-DF) method [Phys. Rev. Lett. 92,
246401 (2004)] for efficient first-principle accounts of structure and cohesion
in molecular crystals. Since then, modifications of the original vdW-DF version
(identified as vdW-DF1) has been proposed, and there is also a new version
called vdW-DF2 [ArXiv 1003.5255], within the vdW-DF framework. Here we
investigate the performance and nature of the modifications and the new version
for the binding of a set of simple molecular crystals: hexamine, dodecahedrane,
C60, and graphite. These extended systems provide benchmarks for computational
methods dealing with sparse matter. We show that a previously documented
enhancement of non-local correlations of vdW-DF1 over an asymptotic atom-based
account close to and a few A, beyond binding separation persists in vdW-DF2.
The calculation and analysis of the binding in molecular crystals requires
appropriate computational tools. In this paper, we also present details on our
real-space parallel implementation of the vdW-DF correlation and on the method
used to generate asymptotic atom-based pair potentials based on vdW-DF.Comment: 5 pages, 4 figure
Encounter complexes and dimensionality reduction in protein-protein association
An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein–protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures shows that the method captures both specific and non-specific encounter complexes. To explore the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the relative orientation of two solid bodies is projected onto a Euclidean space in which the shape of low energy regions is studied by principal component analysis. Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition
Chemical accuracy from quantum Monte Carlo for the Benzene Dimer
We report an accurate study of interactions between Benzene molecules using
variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC)
methods. We compare these results with density functional theory (DFT) using
different van der Waals (vdW) functionals. In our QMC calculations, we use
accurate correlated trial wave functions including three-body Jastrow factors,
and backflow transformations. We consider two benzene molecules in the parallel
displaced (PD) geometry, and find that by highly optimizing the wave function
and introducing more dynamical correlation into the wave function, we compute
the weak chemical binding energy between aromatic rings accurately. We find
optimal VMC and DMC binding energies of -2.3(4) and -2.7(3) kcal/mol,
respectively. The best estimate of the CCSD(T)/CBS limit is -2.65(2) kcal/mol
[E. Miliordos et al, J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate
that QMC methods give chemical accuracy for weakly bound van der Waals
molecular interactions, comparable to results from the best quantum chemistry
methods.Comment: Accepted for publication in the Journal of Chemical Physics, Vol.
143, Issue 11, 201
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