FROG: Exploiting all-atom molecular dynamics trajectories to calculate linear and non-linear optical responses of molecular liquids within Dalton's QM/MM polarizable embedding scheme.

Quantum mechanical/molecular mechanics (QM/MM) methods are interesting to model the impact of a complex environment on the spectroscopic properties of a molecule. In this context, a FROm molecular dynamics to second harmonic Generation (FROG) code is a tool to exploit molecular dynamics trajectories to perform QM/MM calculations of molecular optical properties. FROG stands for "FROm molecular dynamics to second harmonic Generation" since it was developed for the calculations of hyperpolarizabilities. These are relevant to model non-linear optical intensities and compare them with those obtained from second harmonic scattering or second harmonic generation experiments. FROG's specificity is that it is designed to study simple molecular liquids, including solvents or mixtures, from the bulk to the surface. For the QM/MM calculations, FROG relies on the Dalton package: its electronic-structure models, response theory, and polarizable embedding schemes. FROG helps with the global workflow needed to deal with numerous QM/MM calculations: it permits the user to separate the system into QM and MM fragments, to write Dalton's inputs, to manage the submission of QM/MM calculations, to check whether Dalton's calculation finished successfully, and finally to perform averages on relevant QM observables. All molecules within the simulation box and several time steps are tackled within the same workflow. The platform is written in Python and installed as a package. Intermediate data such as local electric fields or individual molecular properties are accessible to the users in the form of Python object arrays. The resulting data are easily extracted, analyzed, and visualized using Python scripts that are provided in tutorials.

First hyperpolarizability of water in bulk liquid phase: long-range electrostatic effects included via the second hyperpolarizability.

The molecular first hyperpolarizability ß contributes to second-order optical non-linear signals collected from molecular liquids. For the Second Harmonic Generation (SHG) response, the first hyperpolarizability ß(2ω, ω, ω) often depends on the molecular electrostatic environment. This is especially true for water, due to its large second hyperpolarizability γ(2ω, ω, ω,0). In this study we compute the electronic γ(2ω, ω, ω,0) and ß(2ω, ω, ω) for water molecules in liquid water using QM/MM calculations. The average value of γ(2ω, ω, ω,0) is smaller than the one for the gaz phase, and its standard deviation among the molecules is relatively small. In addition, we demonstrate that the average bulk second hyperpolarizability 〈γ(2ω, ω, ω,0)〉 can be used to describe the electrostatic effects of the distant neighborhood on the first hyperpolarizability ß(2ω, ω, ω). In comparison with more complex schemes to take into account long-range effects, the approximation is simple, and does not require any modifications of the QM/MM implementation. The long-range correction can be added explicitly, using an average value of γ for water in the condensed phase. It can also be easily added implicitly in QM/MM calculations through an additional embedding electric field, without the explicit calculation of γ.

First hyperpolarizability of water at the air-vapor interface: a QM/MM study questions standard experimental approximations.

Surface Second-Harmonic Generation (S-SHG) experiments provide a unique approach to probe interfaces. One important issue for S-SHG is how to interpret the S-SHG intensities at the molecular level. Established frameworks commonly assume that each molecule emits light according to an average molecular hyperpolarizability tensor ß(-2ω,ω,ω). However, for water molecules, this first hyperpolarizability is known to be extremely sensitive to their environment. We have investigated the molecular first hyperpolarizability of water molecules within the liquid-vapor interface, using a quantum description with explicit, inhomogeneous electrostatic embedding. The resulting average molecular first hyperpolarizability tensor depends on the distance relative to the interface, and it practically respects the Kleinman symmetry everywhere in the liquid. Within this numerical approach, based on the dipolar approximation, the water layer contributing to the Surface Second Harmonic Generation (S-SHG) intensity is less than a nanometer. The results reported here question standard interpretations based on a single, averaged hyperpolarizability for all molecules at the interface. Not only the molecular first hyperpolarizability tensor significantly depends on the distance relative to the interface, but it is also correlated to the molecular orientation. Such hyperpolarizability fluctuations may impact the S-SHG intensity emitted by an aqueous interface.

Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c.

Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.

Molecular modeling of aqueous electrolytes at interfaces: Effects of long-range dispersion forces and of ionic charge rescaling.

Molecular dynamics simulations of aqueous electrolytes generally rely on empirical force fields, combining dispersion interactions-described by a truncated Lennard-Jones (LJ) potential-and electrostatic interactions-described by a Coulomb potential computed with a long-range solver. Recently, force fields using rescaled ionic charges [electronic continuum correction (ECC)], possibly complemented with rescaling of LJ parameters [ECC rescaled (ECCR)], have shown promising results in bulk, but their performance at interfaces has been less explored. Here, we started by exploring the impact of the LJ potential truncation on the surface tension of a sodium chloride aqueous solution. We show a discrepancy between the numerical predictions for truncated LJ interactions with a large cutoff and for untruncated LJ interactions computed with a long-range solver, which can bias comparison of force field predictions with experiments. Using a long-range solver for LJ interactions, we then show that an ionic charge rescaling factor chosen to correct long-range electrostatic interactions in bulk accurately describes image charge repulsion at the liquid-vapor interface, and the rescaling of LJ parameters in ECCR models-aimed at capturing local ion-ion and ion-water interactions in bulk- describes well the formation of an ionic double layer at the liquid-vapor interface. Overall, these results suggest that the molecular modeling of aqueous electrolytes at interfaces would benefit from using long-range solvers for dispersion forces and from using ECCR models, where the charge rescaling factor should be chosen to correct long-range electrostatic interactions.

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).

Liquid Water: When Hyperpolarizability Fluctuations Boost and Reshape the Second Harmonic Scattering Intensities.

Second harmonic scattering (SHS) is a method of choice to investigate the molecular structure of liquids. While a clear interpretation of SHS intensity exists for diluted solutions of dyes, the scattering due to solvents remains difficult to interpret quantitatively. Here, we report a quantum mechanics/molecular mechanics (QM/MM) approach to model the polarization-resolved SHS intensity of liquid water, quantifying different contributions to the signal. We point out that the molecular hyperpolarizability fluctuations and correlations cannot be neglected. The intermolecular orientational and hyperpolarizability correlations up to the third solvation layer strongly increase the scattering intensities and modulate the polarization-resolved oscillation that is predicted here by QM/MM without fitting parameters. Our approach can be generalized to other pure liquids to provide a quantitative interpretation of SHS intensities in terms of short-range molecular ordering.