325 research outputs found
Toward transferable interatomic van der Waals interactions without electrons: The role of multipole electrostatics and many-body dispersion
We estimate polarizabilities of atoms in molecules without electron density,
using a Voronoi tesselation approach instead of conventional density
partitioning schemes. The resulting atomic dispersion coefficients are
calculated, as well as many-body dispersion effects on intermolecular potential
energies. We also estimate contributions from multipole electrostatics and
compare them to dispersion. We assess the performance of the resulting
intermolecular interaction model from dispersion and electrostatics for more
than 1,300 neutral and charged, small organic molecular dimers. Applications to
water clusters, the benzene crystal, the anti-cancer drug
ellipticine---intercalated between two Watson-Crick DNA base pairs, as well as
six macro-molecular host-guest complexes highlight the potential of this method
and help to identify points of future improvement. The mean absolute error made
by the combination of static electrostatics with many-body dispersion reduces
at larger distances, while it plateaus for two-body dispersion, in conflict
with the common assumption that the simple correction will yield proper
dissociative tails. Overall, the method achieves an accuracy well within
conventional molecular force fields while exhibiting a simple parametrization
protocol.Comment: 13 pages, 8 figure
The induction contribution to the lattice energy of organic crystals
A recently developed method for generating distributed, localized atomic polarizabilities
from the ab initio molecular charge density is used to assess the importance of the induction
energy in crystal structures of small organic molecules. Two models are first contrasted
based on large cluster representing the crystalline environment: one using the polarizability
model in which induced multipoles are evaluated in response to the electrostatic field due
to atomic multipoles; the other is a complementary procedure in which the same cluster is
represented by atomic point-charges and the molecular charge density is calculated ab initio
in this environment. The comparable results of these two methods show that the
contribution to the lattice energy from the induction term can differ significantly between
polymorphic forms, for a selection of organic crystal structures including carbamazepine
and oxalyl dihydrazide, and 3-azabicyclo[3,3,1]nonane-2,4-dione. The observed charge
density polarization of naphthalene in the crystalline state is also reproduced.
This demonstrates that explicit inclusion of the induction energy, rather than its absorption
into an empirically fitted repulsion-dispersion potential, will improve the relative ordering
of the lattice energies for computed structures, and that it needs to be included in crystal
structure prediction. Hence, the distributed atomic polarizability model was coded into the
lattice-energy minimization program DMACRYS (which was developed as a Fortran90
recoding of DMAREL) to allow the induction energy to be calculated
Transferable atomic multipole machine learning models for small organic molecules
Accurate representation of the molecular electrostatic potential, which is
often expanded in distributed multipole moments, is crucial for an efficient
evaluation of intermolecular interactions. Here we introduce a machine learning
model for multipole coefficients of atom types H, C, O, N, S, F, and Cl in any
molecular conformation. The model is trained on quantum chemical results for
atoms in varying chemical environments drawn from thousands of organic
molecules. Multipoles in systems with neutral, cationic, and anionic molecular
charge states are treated with individual models. The models' predictive
accuracy and applicability are illustrated by evaluating intermolecular
interaction energies of nearly 1,000 dimers and the cohesive energy of the
benzene crystal.Comment: 11 pages, 6 figure
Electronic Excitations in Complex Molecular Environments: Many-Body Green's Functions Theory in VOTCA-XTP
Many-body Green's functions theory within the GW approximation and the
Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP
software, aiming at the calculation of electronically excited states in complex
molecular environments. Based on Gaussian-type atomic orbitals and making use
of resolution of identify techniques, the code is designed specifically for
non-periodic systems. Application to the small molecule reference set
successfully validates the methodology and its implementation for a variety of
excitation types covering an energy range from 2-8 eV in single molecules.
Further, embedding each GW-BSE calculation into an atomistically resolved
surrounding, typically obtained from Molecular Dynamics, accounts for effects
originating from local fields and polarization. Using aqueous DNA as a
prototypical system, different levels of electrostatic coupling between the
regions in this GW-BSE/MM setup are demonstrated. Particular attention is paid
to charge-transfer (CT) excitations in adenine base pairs. It is found that
their energy is extremely sensitive to the specific environment and to
polarization effects. The calculated redshift of the CT excitation energy
compared to a nucelobase dimer treated in vacuum is of the order of 1 eV, which
matches expectations from experimental data. Predicted lowest CT energies are
below that of a single nucleobase excitation, indicating the possibility of an
initial (fast) decay of such an UV excited state into a bi-nucleobase CT
exciton. The results show that VOTCA-XTP's GW-BSE/MM is a powerful tool to
study a wide range of types of electronic excitations in complex molecular
environments
Non-empirical Force-Field Development for Weakly-Bound Organic Molecules
This thesis pioneers the development of non-empirical anisotropic atom-atom force-fields for organic molecules, and their use as state-of-the-art intermolecular potentials for modelling the solid-state. The long-range electrostatic, polarization and dispersion terms have been derived directly from the molecular charge density, while the short-range terms are obtained through fitting to the symmetry-adapted perturbation theory (SAPT(DFT)) intermolecular interaction energies of a large number of different dimer configurations. This study aims to establish how far this approach, previously used for small molecules, could be applied to specialty molecules, and whether these potentials improve on the current empirical force-fields FIT and WILLIAMS01. The scaling of the underlying electronic structure calculations with system size means many adaptions have been made. This project aims to generate force-fields suitable for use in Crystal Structure Prediction (CSP) and for modelling possible polymorphs, particularly high-pressure polymorphs. By accurately modelling the repulsive wall of the potential energy surface, the high pressure/temperature conditions typically sampled by explosive materials could be studied reliably, as shown in a CSP study of pyridine using a non-empirical potential. This thesis also investigates the transferability of these potentials from the gas to condensed-phase, as well as the transferability and importance of the intermolecular interactions of flexible functional groups, in particular NO2 groups. The charge distribution was found to be strongly influenced by variations in the observed NO2 torsion angle and the conformation of the rest of the molecule. This conformation dependence coupled with the novelty of the methods and size of the molecules has made developing non-empirical models for flexible nitro-energetic materials very challenging. The thesis culminates in the development of a bespoke non-empirical force-field for rigid trinitrobenzene and its use in a CSP study
Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field
Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed point charge models. The recent SAMPL4 challenge evaluated the AMOEBA polarizable force field in this regard, but showed substantially worse results than those using the fixed point charge GAFF model. Starting with a set of automatically generated AMOEBA parameters for the SAMPL4 dataset, we evaluate the cumulative effects of a series of incremental improvements in parameterization protocol, including both solute and solvent model changes. Ultimately the optimized AMOEBA parameters give a set of results that are not statistically significantly different from those of GAFF in terms of signed and unsigned error metrics. This allows us to propose a number of guidelines for new molecule parameter derivation with AMOEBA, which we expect to have benefits for a range of biomolecular simulation applications such as protein ligand binding studie
Combining Polarizable Embedding with the Frenkel exciton model:Applications to absorption spectra with overlapping solute-solvent bands
Modeling of spectral properties of extended chemical systems, such as the case of a solute in a solvent, is often performed based on so-called hybrid models in which only part of the complete system is given a quantum chemical description. The remaining part of the system is represented by an embedding potential treating the environment either by a discrete or continuum model. In order to successfully make use of minimally sized quantum chemical regions, theembedding potential should represent the environment as authentic as possible. Here, the importance of exactly such an accurate description of the embedding potential is investigated by comparing the performance of the Polarizable Embedding scheme against larger sized full quantum mechanical calculations. Our main conclusion is that as long as the solute and solvent do not overlap in their absorption spectra, the Polarizable Embedding approach shows results consistent with full quantum chemical calculations. For partly overlapping absorption spectra the Polarizable Embedding approach can furthermore successfully be expanded within a Frenkel exciton approach based on only economical monomeric quantum chemical calculations. Thus, by extending the Polarizable Embedding scheme to the exciton picture it is possible to cover computations of the whole absorption spectrum andstill reduce the computational cost compared to costly cluster calculations.<br
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