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Compressed intramolecular dispersion interactions.
The feasibility of the compression of localized virtual orbitals is explored in the context of intramolecular long-range dispersion interactions. Singular value decomposition (SVD) of coupled cluster doubles amplitudes associated with the dispersion interactions is analyzed for a number of long-chain systems, including saturated and unsaturated hydrocarbons and a silane chain. Further decomposition of the most important amplitudes obtained from these SVDs allows for the analysis of the dispersion-specific virtual orbitals that are naturally localized. Consistent with previous work on intermolecular dispersion interactions in dimers, it is found that three important geminals arise and account for the majority of dispersion interactions at the long range, even in the many body intramolecular case. Furthermore, it is shown that as few as three localized virtual orbitals per occupied orbital can be enough to capture all pairwise long-range dispersion interactions within a molecule
Extension of the B3LYP - Dispersion-Correcting Potential Approach to the Accurate Treatment of both Inter- and Intramolecular Interactions
We recently showed that dispersion-correcting potentials (DCPs),
atom-centered Gaussian-type functions developed for use with B3LYP (J. Phys.
Chem. Lett. 2012, 3, 1738-1744) greatly improved the ability of the underlying
functional to predict non-covalent interactions. However, the application of
B3LYP-DCP for the {\beta}-scission of the cumyloxyl radical led a calculated
barrier height that was over-estimated by ca. 8 kcal/mol. We show in the
present work that the source of this error arises from the previously developed
carbon atom DCPs, which erroneously alters the electron density in the C-C
covalent-bonding region. In this work, we present a new C-DCP with a form that
was expected to influence the electron density farther from the nucleus. Tests
of the new C-DCP, with previously published H-, N- and O-DCPs, with
B3LYP-DCP/6-31+G(2d,2p) on the S66, S22B, HSG-A, and HC12 databases of
non-covalently interacting dimers showed that it is one of the most accurate
methods available for treating intermolecular interactions, giving mean
absolute errors (MAEs) of 0.19, 0.27, 0.16, and 0.18 kcal/mol, respectively.
Additional testing on the S12L database of complexation systems gave an MAE of
2.6 kcal/mol, showing that the B3LYP-DCP/6-31+G(2d,2p) approach is one of the
best-performing and feasible methods for treating large systems dominated by
non-covalent interactions. Finally, we showed that C-C making/breaking
chemistry is well-predicted using the newly developed DCPs. In addition to
predicting a barrier height for the {\beta}-scission of the cumyloxyl radical
that is within 1.7 kcal/mol of the high-level value, application of
B3LYP-DCP/6-31+G(2d,2p) to 10 databases that include reaction barrier heights
and energies, isomerization energies and relative conformation energies gives
performance that is amongst the best of all available dispersion-corrected
density-functional theory approaches
Analysis of the conformational profiles of fenamates shows route towards novel, higher accuracy, force-fields for pharmaceuticals
In traditional molecular mechanics force fields, intramolecular non-bonded interactions are modelled as intermolecular interactions, and the form of the torsion potential is based on the conformational profiles of small organic molecules. We investigate how a separate model for the intramolecular forces in pharmaceuticals could be more realistic by analysing the low barrier to rotation of the phenyl ring in the fenamates (substituted N-phenyl-aminobenzoic acids), that results in a wide range of observed angles in the numerous fenamate crystal structures. Although the conformational energy changes by significantly less than 10 kJmol-1 for a complete rotation of the phenyl ring for fenamic acid, the barrier is only small because of small correlated changes in the other bond and torsion angles. The maxima for conformations where the two aromatic rings approach coplanarity arise from steric repulsion, but the maxima when the two rings are approximately perpendicular arise from a combination of an electronic effect and intramolecular dispersion. Representing the ab initio conformational energy profiles as a cosine series alone is ineffective; however, combining a cos2ξ term to represent the electronic barrier with an intramolecular atom-atom exp-6 term for all atom pairs separated by three or more bonds (1-4 interactions) provides a very effective representation. Thus we propose a new, physically motivated, generic analytical model of conformational energy, which could be combined with an intermolecular model to form more accurate force-fields for modelling the condensed phases of pharmaceutical-like organic molecules
Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles
We present a computational analysis of the terahertz spectra of the monoclinic and the orthorhombic polymorphs of 2,4,6-trinitrotoluene.
Very good agreement with experimental data is found when using density functional theory that includes
Tkatchenko–Scheffler pair-wise dispersion interactions. Furthermore, we show that for these polymorphs the theoretical results are
only weakly affected by many-body dispersion contributions. The absence of dispersion interactions, however, causes sizable shifts
in vibrational frequencies and directly affects the spatial character of the vibrational modes. Mode assignment allows for a distinction
between the contributions of the monoclinic and orthorhombic polymorphs and shows that modes in the range from 0 to
ca. 3.3 THz comprise both inter- and intramolecular vibrations, with the former dominating below ca. 1.5 THz. We also find that
intramolecular contributions primarily involve the nitro and methyl groups. Finally, we present a prediction for the terahertz spectrum
of 1,3,5-trinitrobenzene, showing that a modest chemical change leads to a markedly different terahertz spectrum
Computational design of metal-supported molecular switches: Transient ion formation during light- and electron-induced isomerisation of azobenzene
In molecular nanotechnology, a single molecule is envisioned to act as the
basic building block of electronic devices. Such devices may be of special
interest for organic photovoltaics, data storage, and smart materials. However,
more often than not the molecular function is quenched upon contact with a
conducting support. Trial-and-error-based decoupling strategies via molecular
functionalisation and change of substrate have in many instances proven to
yield unpredictable results. The adsorbate-substrate interactions that govern
the function can be understood with the help of first-principles simulation.
Employing dispersion-corrected Density-Functional Theory (DFT) and linear
expansion Delta-Self-Consistent-Field DFT, the electronic structure of a
prototypical surface-adsorbed functional molecule, namely azobenzene adsorbed
to (111) single crystal facets of copper, silver and gold, is investigated and
the main reasons for the loss or survival of the switching function upon
adsorption are identified. The light-induced switching ability of a
functionalised derivative of azobenzene on Au(111) and azobenzene on Ag(111)
and Au(111) is assessed based on the excited-state potential energy landscapes
of their transient molecular ions, which are believed to be the main
intermediates of the experimentally observed isomerisation reaction. We provide
a rationalisation of the experimentally observed function or lack thereof that
connects to the underlying chemistry of the metal-surface interaction and
provides insights into general design strategies for complex light-driven
reactions at metal surfaces.Comment: 14 pages, 5 figures, submitted to J. Phys. Condens. Matte
The Monomer Electron Density Force Field (MEDFF) : a physically inspired model for noncovalent interactions
We propose a methodology to derive pairwise-additive noncovalent force fields from monomer electron densities without any empirical input. Energy expressions are based on the symmetry-adapted perturbation theory (SAPT) decomposition of interaction energies. This ensures a physically motivated force field featuring an electrostatic, exchange repulsion, dispersion, and induction contribution, which contains two types of parameters. First, each contribution depends on several fixed atomic parameters, resulting from a partitioning of the monomer electron density. Second, each of the last three contributions (exchange-repulsion, dispersion, and induction) contains exactly one linear fitting parameter. These three so-called interaction parameters in the model are initially estimated separately using SAPT reference calculations for the S66x8 database of noncovalent dimers. In a second step, the three interaction parameters are further refined simultaneously to reproduce CCSD(T)/CBS interaction energies for the same database. The limited number of parameters that are fitted to dimer interaction energies (only three) avoids ill-conditioned fits that plague conventional parameter optimizations. For the exchange repulsion and dispersion component, good results are obtained for all dimers in the S66x8 database using one single value for the associated interaction parameters. The values of those parameters can be considered universal and can also be used for dimers not present in the original database used for fitting. For the induction component such an approach is only viable for the dispersion dominated dimers in the S66x8 database. For other dimers (such as hydrogen-bonded complexes), we show that our methodology remains applicable. However, the interaction parameter needs to be determined on a case-specific basis. As an external validation:, the force field predicts interaction energies in good agreement with CCSD(T)/CBS values for dispersion dominated dimers extracted from an HIV-II protease crystal structure with a bound ligand (indinavir). Furthermore, experimental second virial coefficients of small alkanes and alkenes are well reproduced
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