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Plasmonic nanocavities enable the confinement of molecules and electromagnetic fields within nanometric volumes. As a consequence, the molecules experience a remarkably strong interaction with the electromagnetic field to such an extent that the quantum states of the system become hybrids between light and matter: polaritons. Here, we present a nonperturbative method to simulate the emerging properties of such polaritons: it combines a high-level quantum chemical description of the molecule with a quantized description of the localized surface plasmons in the nanocavity. We apply the method to molecules of realistic complexity in a typical plasmonic nanocavity, featuring also a subnanometric asperity (picocavity). Our results disclose the effects of the mutual polarization and correlation of plasmons and molecular excitations, disregarded so far. They also quantify to what extent the molecular charge density can be manipulated by nanocavities and stand as benchmarks to guide the development of methods for molecular polaritonics.

We develop an extension of the time-dependent equation-of-motion formulation of the polarizable continuum model (EOM-TDPCM) to introduce nonequilibrium cavity field effects in quantum mechanical calculations of solvated molecules subject to time-dependent electric fields. This method has been implemented in Octopus, a state-of-the-art code for real-space, real-time time-dependent density functional theory (RT-TDDFT) calculations. To show the potential of our methodology, we perform EOM-TDPCM/RT-TDDFT calculations of trans-azobenzene in water and in other model solvents with shorter relaxation times. Our results for the optical absorption spectrum of trans-azobenzene show (i) that cavity field effects have a clear impact in the overall spectral shape and (ii) that an accurate description of the solute shape (as the one provided within PCM) is key to correctly account for cavity field effects.

Protein aggregation is associated with various diseases, including Alzheimer and Parkinson as well as sickle cell disease (SCD). From a molecular point of view, protein aggregation depends on a complex balance of electrostatic and hydrophobic interactions mediated by water. An impressive manifestation of the importance of this balance concerns the human hemoglobin (HbA) mutant, HbS (sickle cell Hb), where a single substitution at the 6th position of HbA β-chains, from glutamic acid to valine, causes the polymerization of deoxygenated HbS (deoxy-HbS), responsible for SCD. HbS polymerization is believed to occur via a double nucleation mechanism initiated by the formation of HbS fibers (homogeneous nucleation), followed by fiber growth. Furthermore, it was proposed that homogeneous nucleation proceeds through a two-step mechanism, where metastable dense clusters play the role of nucleation precursors. Thus, hindering or delaying the formation of such precursors could represent a potential SCD therapeutic route. Here, we study, through molecular dynamics, the binding free energy and protein-protein contacts involved in the deoxy-HbS dimer aggregation and stabilization process. A binding free energy of ∼-14.0 ± 1 kcal/mol is estimated from a one-dimensional potential of mean force. Analysis of protein-protein interactions shows that both electrostatic and van der Waals interactions play an important role on the aggregation of HbS. With respect to the former, our results indicate that aggregation is largely favored by the formation of salt bridges (SB), mostly, Lys-Glu, Lys-Asp, and Heme-Lys SB, which outweigh electrostatic repulsions involving similar residues. Thus, our results suggest that a potential antisickling drug could be one with the ability to weaken or hinder the formation of a few SB between carboxylate and ammonium groups.

We combine classical and ring polymer molecular dynamics simulations with the molecular jump model to provide a molecular description of the nuclear quantum effects (NQEs) on water reorientation and hydrogen-bond dynamics in liquid H 2 O and D 2 O. We show that while the net NQE is negligible in D 2 O, it leads to a ∼13% acceleration in H 2 O dynamics compared to a classical description. Large angular jumps-exchanging hydrogen-bond partners-are the dominant reorientation pathway (just as in a classical description); the faster reorientation dynamics arise from the increased jump rate constant. NQEs do not change the jump amplitude distribution, and no significant tunneling is found. The faster jump dynamics are quantitatively related to decreased structuring of the OO radial distribution function when NQEs are included. This is explained, via a jump model analysis, by competition between the effects of water's librational and OH stretch mode zero-point energies on the hydrogen-bond strength.

The optical properties of molecules close to plasmonic nanostructures greatly differ from their isolated molecule counterparts. To theoretically investigate such systems from a quantum-chemistry perspective, one has to take into account that the plasmonic nanostructure (e.g., a metal nanoparticle-NP) is often too large to be treated atomistically. Therefore, a multiscale description, where the molecule is treated by an ab initio approach and the metal NP by a lower level description, is needed. Here we present an extension of one such multiscale model [Corni, S.; Tomasi, J. J. Chem. Phys.2001, 114, 3739], originally inspired by the polarizable continuum model, to a real-time description of the electronic dynamics of the molecule and of the NP. In particular, we adopt a time-dependent configuration interaction (TD CI) approach for the molecule, the metal NP is described as a continuous dielectric of complex shape characterized by a Drude-Lorentz dielectric function, and the molecule-NP electromagnetic coupling is treated by an equation-of-motion (EOM) extension of the quasi-static boundary element method (BEM). The model includes the effects of both the mutual molecule-NP time-dependent polarization and the modification of the probing electromagnetic field due to the plasmonic resonances of the NP. Finally, such an approach is applied to the investigation of the light absorption of a model chromophore, LiCN, in the presence of a metal-NP of complex shape.

When a solute charge density is evolving in time, e.g., due to an external perturbation, the solvent reaction field also becomes time-dependent, in a nontrivial way due to the delayed response of the solvent polarization rooted in its frequency-dependent dielectric constant. In polarizable continuum models, the time-dependent reaction field is represented by time-dependent apparent surface charges. Here, we derive general expressions for such charges. In particular, for all the main flavors of PCM, including IEF-PCM, we show how the frequency-dependent dielectric function terms can be singled-out in diagonal matrices, most convenient for Fourier transforming. For spherical cavities such formulation highlights the relation with multipolar solvation models and, when applied to the related context of metal nanoparticles, discloses a direct connection with multipolar plasmons. Using the Debye dielectric function, we derive a simple equation of motion for the apparent charges, free from system history. Such an equation has been coupled to real time time-dependent density functional theory (RT-TDDFT), to simulate the time evolution of the solute density rigorously accounting for the delayed solvent reaction field. The presented method seamlessly encompasses previous nonequilibrium approaches limited to an instantaneous solute potential change (e.g., a sudden electronic excitation), does not require additional assumptions besides the basic PCM's, and is not limited to iterative inversion procedures. Numerical examples are given, showing the importance of accounting for the delayed solvent-response effects.

The wettability properties of azobenzene self-assembled monolayers (SAMs), in the trans and cis forms, are investigated herein by classical Molecular Dynamics simulations of validated assembly structures described with a dedicated force field. The two different methodologies used for the calculation of the contact angle, one based on the Young's equation and the other on geometrical models, have provided a consistent description of the SAMs wettability in line with available experimental results. Furthermore, we provide an atomistic description of the first layers of water molecules at the solvent-SAM interface, which rationalizes the wettability difference between the cis- and trans-SAMs.

Azobenzene self-assembled monolayers (SAMs) are examples of optomechanical nanostructures capable of producing mechanical work through the well-known azobenzene photoisomerization process. Experimental studies have provided information on their structural properties, but an atomistic description of the SAMs in both the cis and trans forms is still lacking. In this work, a computational investigation of the SAM structures is conducted by classical molecular dynamics with a dedicated force. Experimental data on the SAM unit cell is used to set up SAM models of different molecular densities. The optimal structures are identified through the comparison with structural data from X-ray photoelectron and near-edge X-ray absorption fine structure spectroscopies. The resulting SAM atomistic models are validated by comparing simulated and experimental scanning tunneling microscopy images.