Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. ...To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn–Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.
Embedding beyond electrostatics-The role of wave function confinement Nåbo, Lina J; Olsen, Jógvan Magnus Haugaard; Holmgaard List, Nanna ...
Journal of chemical physics online/The Journal of chemical physics/Journal of chemical physics,
09/2016, Letnik:
145, Številka:
10
Journal Article
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We study excited states of cholesterol in solution and show that, in this specific case, solute wave-function confinement is the main effect of the solvent. This is rationalized on the basis of the ...polarizable density embedding scheme, which in addition to polarizable embedding includes non-electrostatic repulsion that effectively confines the solute wave function to its cavity. We illustrate how the inclusion of non-electrostatic repulsion results in a successful identification of the intense π → π(∗) transition, which was not possible using an embedding method that only includes electrostatics. This underlines the importance of non-electrostatic repulsion in quantum-mechanical embedding-based methods.
We establish the relationships between the metric of charge transfer excitation (Δr) for the bright ππ* state and the two-photon absorption probability as well as the first hyperpolarizability for ...two families of push–pull π-conjugated systems. As previously demonstrated by Guido et al. (J. Chem. Theory Comput. 2013, 9, 3118–3126), Δr is a measure for the average hole–electron distance upon excitation and can be used to discriminate between short- and long-range electronic excitations. We indicate two new benefits from using this metric for the analyses of nonlinear optical properties of push–pull systems. First, the two-photon absorption probability and the first hyperpolarizability are found to be interrelated through Δr; if β ∼ (Δr) k , then roughly, δTPA ∼ (Δr) k+1. Second, a simple power relation between Δr and the molecular hyperpolarizabilities of push–pull systems offers the possibility of estimating properties for longer molecular chains without performing calculations of high-order response functions explicitly. We further demonstrate how to link the hyperpolarizabilities with the chain length of the push–pull π-conjugated systems through the metric of charge transfer.
Based on the recently developed implementation of the full semi-classical field-matter interaction operator, we present a numerically accurate yet efficient scheme to perform rotational averaging of ...linear absorption spectra beyond the electric-dipole approximation. This allows for a gauge-origin independent determination of UV/vis and X-ray absorption spectra for randomly oriented systems such as multilayers, liquids, and gas phase samples. The approach is illustrated by the determination of spectral intensities of electric-dipole allowed π → π* transitions and electric-dipole forbidden n → π* transitions in the UV-vis region of the spectrum as well as electric-dipole forbidden 1s → 3d transitions in the X-ray region of the spectrum. The employed Lebedev quadrature scheme shows very fast convergence with respect to the number of symmetry-independent quadrature points - in all considered cases, the oscillator strengths for the randomly oriented systems are fully converged with use of only seven quadrature points.
The biophysical mechanism of the sense of smell, or olfaction, is still highly debated. The mainstream explanation argues for a shape-based recognition of odorant molecules by olfactory receptors, ...while recent investigations suggest the primary olfactory event to be triggered by a vibrationally-assisted electron transfer reaction. We consider this controversy by studying the influence of a receptor on the vibrational properties of an odorant in atomistic details as the coupling between electronic degrees of freedom of the receptor and the vibrations of the odorant is the key parameter of the vibrationally-assisted electron transfer. Through molecular dynamics simulations we elucidate the binding specificity of a receptor towards acetophenone odorant. The vibrational properties of acetophenone inside the receptor are then studied by the polarizable embedding density functional theory approach, allowing to quantify protein-odorant interactions. Finally, we judge whether the effects of the protein provide any indications towards the existing theories of olfaction.
Induced circular dichroism (ICD) of DNA-binding ligands is well known to be strongly influenced by the specific mode of binding, but the relative importance of the possible mechanisms has remained ...undetermined. With a combination of molecular dynamics simulations, CD response calculations, and experiments on an AT-sequence, we show that the ICD of minor-groove-bound 4′,6-diamidino-2-phenylindole (DAPI) originates from an intricate interplay between the chiral imprint of DNA, off-resonant excitonic coupling to nucleobases, charge-transfer, and resonant excitonic coupling between DAPIs. The significant contributions from charge-transfer and the chiral imprint to the ICD demonstrate the inadequacy of a standard Frenkel exciton theory of the DAPI–DNA interactions.
We present a formulation of molecular response theory for the description of a quantum mechanical molecular system in the presence of a weak, monochromatic, linearly polarized electromagnetic field ...without introducing truncated multipolar expansions. The presentation focuses on a description of linear absorption by adopting the energy-loss approach in combination with the complex polarization propagator formulation of response theory. Going beyond the electric-dipole approximation is essential whenever studying electric-dipole-forbidden transitions, and in general, non-dipolar effects become increasingly important when addressing spectroscopies involving higher-energy photons. These two aspects are examined by our study of the near K-edge X-ray absorption fine structure of the alkaline earth metals (Mg, Ca, Sr, Ba, and Ra) as well as the trans-polyenes. In following the series of alkaline earth metals, the sizes of non-dipolar effects are probed with respect to increasing photon energies and a detailed assessment of results is made in terms of studying the pertinent transition electron densities and in particular their spatial extension in comparison with the photon wavelength. Along the series of trans-polyenes, the sizes of non-dipolar effects are probed for X-ray spectroscopies on organic molecules with respect to the spatial extension of the chromophore.
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