Strong Coupling between Localized Surface Plasmons and Molecules by Coupled Cluster Theory.

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.

Real-time dynamics of plasmonic resonances in nanoparticles described by a boundary element method with generic dielectric function.

Investigating nanoplasmonics in an explicit time-dependent perspective is a natural choice when light pulses are used and may also reveal aspects that are hidden in a frequency-based picture. In the past, we proposed a method time domain-boundary element method (TD-BEM) to simulate the time dependent polarization of nanoparticles based on a boundary element method that is particularly suitable to interface with a quantum atomistic description of nearby molecules. So far, however, metal dielectric functions in TD-BEM have been modeled through analytic expressions, such as those of Debye and Drude-Lorentz, which cannot account for multiple electronic resonances. Our approach allows us to include in the TD-BEM framework also the description of metals with complicate dielectric function profiles in the frequency domain. Particularly, among all metals, gold is a challenging case due to the presence of many transition frequencies. We applied our methods to different metals (gold, silver, and the less commonly investigated rhodium) and different shaped nanoparticles (spheres, ellipsoids, and cubes), the approach has been tested comparing TD-BEM and frequency domain BEM absorption spectra, and it has been used to investigate the time-dependent field acting locally close to nanoparticle vertices.

Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems.

Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light-matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).

Equation of motion for the solvent polarization apparent charges in the polarizable continuum model: Application to time-dependent CI.

The dynamics of the electrons for a molecule in solution is coupled to the dynamics of its polarizable environment, i.e., the solvent. To theoretically investigate such electronic dynamics, we have recently developed equations of motion (EOM) for the apparent solvent polarization charges that generate the reaction field in the Polarizable Continuum Model (PCM) for solvation and we have coupled them to a real-time time-dependent density functional theory (RT TDDFT) description of the solute [S. Corni et al., J. Phys. Chem. A 119, 5405 (2014)]. Here we present an extension of the EOM-PCM approach to a Time-Dependent Configuration Interaction (TD CI) description of the solute dynamics, which is free from the qualitative artifacts of RT TDDFT in the adiabatic approximation. As tests of the developed approach, we investigate the solvent Debye relaxation after an electronic excitation of the solute obtained either by a π pulse of light or by assuming the idealized sudden promotion to the excited state. Moreover, we present EOM for the Onsager solvation model and we compare the results with PCM. The developed approach provides qualitatively correct real-time evolutions and is promising as a general tool to investigate the electron dynamics elicited by external electromagnetic fields for molecules in solution.

Correction: Absolute stereochemistry and preferred conformations of urate degradation intermediates from computed and experimental circular dichroism spectra.

Correction for 'Absolute stereochemistry and preferred conformations of urate degradation intermediates from computed and experimental circular dichroism spectra' by Silvio Pipolo et al., Org. Biomol. Chem., 2011, 9, 5149-5155.

Equation of motion for the solvent polarization apparent charges in the polarizable continuum model: application to real-time TDDFT.

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.

Wettability of azobenzene self-assembled monolayers.

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.

The cavity electromagnetic field within the polarizable continuum model of solvation.

Cavity field effects can be defined as the consequences of the solvent polarization induced by the probing electromagnetic field upon spectroscopies of molecules in solution, and enter in the definitions of solute response properties. The polarizable continuum model of solvation (PCM) has been extended in the past years to address the cavity-field issue through the definition of an effective dipole moment that couples to the external electromagnetic field. We present here a rigorous derivation of such cavity-field treatment within the PCM starting from the general radiation-matter Hamiltonian within inhomogeneous dielectrics and recasting the interaction term to a dipolar form within the long wavelength approximation. To this aim we generalize the Göppert-Mayer and Power-Zienau-Woolley gauge transformations, usually applied in vacuo, to the case of a cavity vector potential. Our derivation also allows extending the cavity-field correction in the long-wavelength limit to the velocity gauge through the definition of an effective linear momentum operator. Furthermore, this work sets the basis for the general PCM treatment of the electromagnetic cavity field, capable to describe the radiation-matter interaction in dielectric media beyond the long-wavelength limit, providing also a tool to investigate spectroscopic properties of more complex systems such as molecules close to large nanoparticles.

Structural properties of azobenzene self-assembled monolayers by atomistic simulations.

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.

Absolute stereochemistry and preferred conformations of urate degradation intermediates from computed and experimental circular dichroism spectra.

The enzymatic oxidation of urate leads to the sequential formation of optically active intermediates with unknown stereochemistry: (-)-5-hydroxyisourate (HIU) and (-)-2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU). In accordance with the observation that a defect in HIU hydrolase causes hepatocarcinoma in mouse, a detoxification role has been proposed for the enzymes accelerating the conversion of HIU and OHCU into optically active (+)-allantoin. The enzymatic products of urate oxidation are normally not present in humans, but are formed in patients treated with urate oxidase. We used time-dependent density functional theory (TDDFT) to compute the electronic circular dichroism (ECD) spectra of the chiral compounds of urate degradation (HIU, OHCU, allantoin) and we compared the results with experimentally measured ECD spectra. The calculated ECD spectra for (S)-HIU and (S)-OHCU reproduced well the experimental spectra obtained through the enzymatic degradation of urate. Less conclusive results were obtained with allantoin, although the computed optical rotations in the transparent region supported the original assignment of the (+)-S configuration. These absolute configuration assignments can facilitate the study of the enzymes involved in urate metabolism and help us to understand the mechanism leading to the toxicity of urate oxidation products.

Salt-tolerance of alkyl-glyceryl ether carboxylates hydrotropes and surfactants. Dramatic effect of the methylation of the glyceryl spacer.

HYPOTHESIS: The insertion of polyether spacers between the anionic head and the alkyl chain of ionic surfactants significantly improves their salt-tolerance. The aim of this work is to study whether the petro-based polyethoxy spacer can be replaced by a glyceryl ether group for high salinity applications. EXPERIMENTS: A series of amphiphilic sodium salts of alkyl glyceryl ether carboxylates are synthesized with different alkyl chain lengths from 4 to 12 and various spacers between the glyceryl and the carboxylate groups. Their aggregation behavior is studied by tensiometry and their amphiphilicities are assessed by the PIT-slope method. The dramatic effect of the methylation of the glyceryl spacer on the salt-tolerance is highlighted, and rationalized by DFT calculations and molecular dynamics. FINDINGS: In contrast to the corresponding sodium soap, n-C6H13-CO2Na, and to the non-methylated counterpart, the sodium salt of 1-pentyl-3-methyl glyceryl ether methylene carboxylate ([5.0.1]-CH2CO2Na) exhibits an excellent salt-tolerance since it remains water-soluble with NaCl or CaCl2 concentrations greater than 20 wt% at 25 °C. Amphiphiles with short alkyl chains (

Nonequilibrium Solvent Polarization Effects in Real-Time Electronic Dynamics of Solute Molecules Subject to Time-Dependent Electric Fields: A New Feature of the Polarizable Continuum Model.

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.

On the Binding Free Energy and Molecular Origin of Sickle Cell Hemoglobin Aggregation.

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 ß-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.

Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation.

Heterogeneous crystal nucleation is ubiquitous in nature and at the heart of many industrial applications. At the molecular scale, however, major gaps in understanding this phenomenon persist. Here we investigate through molecular dynamics simulations how the formation of precritical crystalline clusters is connected to the kinetics of nucleation. Considering heterogeneous water freezing as a prototypical scenario of practical relevance, we find that precritical fluctuations connote which crystalline polymorph will form. The emergence of metastable phases can thus be promoted by templating crystal faces characteristic of specific polymorphs. As a consequence, heterogeneous classical nucleation theory cannot describe our simulation results, because the different substrates lead to the formation of different ice polytypes. We discuss how the issue of polymorphism needs to be incorporated into analysis and comparison of heterogeneous and homogeneous nucleation. Our results will help to interpret and analyze the growing number of experiments and simulations dealing with crystal polymorph selection.

Nuclear Quantum Effects in Water Reorientation and Hydrogen-Bond Dynamics.

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 H2O and D2O. We show that while the net NQE is negligible in D2O, it leads to a ∼13% acceleration in H2O 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.

Real-Time Description of the Electronic Dynamics for a Molecule Close to a Plasmonic Nanoparticle.

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.

Direct monitoring of opto-mechanical switching of self-assembled monolayer films containing the azobenzene group.

The potential for manipulation and control inherent in molecule-based motors holds great scientific and technological promise. Molecules containing the azobenzene group have been heavily studied in this context. While the effects of the cis-trans isomerization of the azo group in such molecules have been examined macroscopically by a number of techniques, modulations of the elastic modulus upon isomerization in self-assembled films were not yet measured directly. Here, we examine the mechanical response upon optical switching of bis[(1,1'-biphenyl)-4-yl]diazene organized in a self-assembled film on Au islands, using atomic force microscopy. Analysis of higher harmonics by means of a torsional harmonic cantilever allowed real-time extraction of mechanical data. Quantitative analysis of elastic modulus maps obtained simultaneously with topographic images show that the modulus of the cis-form is approximately twice that of the trans-isomer. Quantum mechanical and molecular dynamics studies show good agreement with this experimental result, and indicate that the stiffer response in the cis-form comprises contributions both from the individual molecular bonds and from intermolecular interactions in the film. These results demonstrate the power and insights gained from cutting-edge AFM technologies, and advanced computational methods.