Spectroscopic properties under vibrational strong coupling in disordered matter from path-integral Monte Carlo simulations.

Vibrational strong coupling (VSC), the strong coupling between a Fabry-Perrot cavity and molecular vibrations at mid-infrared frequencies, has received important attention in the last years due to its capacity of modifying both vibrational spectra and chemical reactivity. VSC is a collective effect, and in this work, we introduce Path Integral Monte Carlo (PIMC) simulations that not only take into account the quantum character of the molecular vibrations and of the optical resonance of the cavity but also reproduce this collective behavior by considering multiple replicas of the molecular system. Moreover, we show that it is possible to extract from the PIMC simulations the decomposition of the hybrid optical and molecular states in terms of the bare molecular modes.

Ultrafast fragmentation of highly-excited doubly-ionized deoxyribose: role of the liquid water environment.

molecular dynamics simulations are used to investigate the fragmentation dynamics following the double ionization of 2-deoxy-D-ribose (DR), a major component in the DNA chain. Different ionization scenarios are considered to provide a complete picture. First focusing on isolated DR, fragmentation patterns are determined for the ground electronic state, adding randomly distributed excitation energy to the nuclei.

Piezoelectric and microfluidic tuning of an infrared cavity for vibrational polariton studies.

We developed a microfluidic system for vibrational polariton studies, which consists of two microfluidic chips: one for solution mixing and another for tuning an infrared cavity made of a pair of gold mirrors and a PDMS (polydimethylsiloxane) spacer. We show that the cavity of the system can be accurately tuned with either piezoelectric actuators or microflow-induced pressure to result in resonant coupling between a cavity mode and a variational mode of the solution molecules. Acrylonitrile solutions were chosen to prove the concept of vabriational strong coupling (VSC) of a CN stretching mode with light inside the cavity.

Vibrational Circular Dichroism Spectroscopy with a Classical Polarizable Force Field: Alanine in the Gas and Condensed Phases.

Polarizable force fields are an essential component for the chemically accurate modeling of complex molecular systems with a significant degree of fluxionality, beyond harmonic or perturbative approximations. In this contribution we examine the performance of such an approach for the vibrational spectroscopy of the alanine amino acid, in the gas and condensed phases, from the Fourier transform of appropriate time correlation functions generated along molecular dynamics (MD) trajectories. While the infrared (IR) spectrum only requires the electric dipole moment, the vibrational circular dichroism (VCD) spectrum further requires knowledge of the magnetic dipole moment, for which we provide relevant expressions to be used with polarizable force fields.

Thermal dependence of the hydrated proton and optimal proton transfer in the protonated water hexamer.

Water is a key ingredient for life and plays a central role as solvent in many biochemical reactions. However, the intrinsically quantum nature of the hydrogen nucleus, revealing itself in a large variety of physical manifestations, including proton transfer, gives rise to unexpected phenomena whose description is still elusive. Here we study, by a combination of state-of-the-art quantum Monte Carlo methods and path-integral molecular dynamics, the structure and hydrogen-bond dynamics of the protonated water hexamer, the fundamental unit for the hydrated proton.

Quasi-classical simulations of resonance Raman spectra based on path integral linearization.

Based on a linearization approximation coupled with path integral formalism, we propose a method derived from the propagation of quasi-classical trajectories to simulate resonance Raman spectra. This method is based on ground state sampling followed by an ensemble of trajectories on the mean surface between the ground and excited states. The method was tested on three models and compared to a quantum mechanics solution based on a sum-over-states approach: harmonic and anharmonic oscillators and the HOCl molecule (hypochlorous acid).

Influence of the environment on the infrared spectrum of alanine: An effective mode analysis.

The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000-2000 cm, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine.

How Crystal Symmetry Dictates Non-Local Vibrational Circular Dichroism in the Solid State.

Solid-State Vibrational Circular Dichroism (VCD) can be used to determine the absolute structure of chiral crystals, but its interpretation remains a challenge in modern spectroscopy. In this work, we investigate the effect of a twofold screw axis on the solid-state VCD spectrum in a combined experimental and theoretical analysis of P2 crystals of (S)-(+)-1-indanol. Even though the space group is achiral, a single proper symmetry operation has an important impact on the VCD spectrum, which reflects the supramolecular chirality of the crystal.

Machine Learning Yield Prediction from NiCOlit, a Small-Size Literature Data Set of Nickel Catalyzed C-O Couplings.

Synthetic yield prediction using machine learning is intensively studied. Previous work has focused on two categories of data sets: high-throughput experimentation data, as an ideal case study, and data sets extracted from proprietary databases, which are known to have a strong reporting bias toward high yields. However, predicting yields using published reaction data remains elusive.

Why local and non-local terms are essential for second harmonic generation simulation?

Second Harmonic Generation (SHG) today represents one of the most powerful techniques to selectively probe all types of interfaces. However, the origin of the SHG signal at a molecular level is still debated since the local dipole contribution, which is strongly correlated to the molecular orientation can be counterbalanced by non-local quadrupole contributions. Here, we propose a method to simulate the SHG signal of a model water/air interface from the molecular response of each contribution.

Explaining and avoiding failure modes in goal-directed generation of small molecules.

Despite growing interest and success in automated in-silico molecular design, questions remain regarding the ability of goal-directed generation algorithms to perform unbiased exploration of novel chemical spaces. A specific phenomenon has recently been highlighted: goal-directed generation guided with machine learning models produce molecules with high scores according to the optimization model, but low scores according to control models, even when trained on the same data distribution and the same target. In this work, we show that this worrisome behavior is actually due to issues with the predictive models and not the goal-directed generation algorithms.

The trisulfur radical ion S controls platinum transport by hydrothermal fluids.

Platinum group elements (PGE) are considered to be very poorly soluble in aqueous fluids in most natural hydrothermal-magmatic contexts and industrial processes. Here, we combined in situ X-ray absorption spectroscopy and solubility experiments with atomistic and thermodynamic simulations to demonstrate that the trisulfur radical ion S forms very stable and soluble complexes with both Pt and Pt in sulfur-bearing aqueous solution at elevated temperatures (∼300 °C). These Pt-bearing species enable (re)mobilization, transfer, and focused precipitation of platinum up to 10,000 times more efficiently than any other common inorganic ligand, such as hydroxide, chloride, sulfate, or sulfide.

The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution.

We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water. We discuss the effect of the hydrogen bond network on the aggregation behaviour of the acid: while aggregates of the solute represent conditions encountered in a weakly interacting solvent, the presence of water drastically interferes with the clusters - more strongly than originally anticipated. For both scenarios we computed the VCD spectra by means of nuclear velocity perturbation theory (NVPT).

Computation of Solid-State Vibrational Circular Dichroism in the Periodic Gauge.

We introduce a new theoretical formalism to compute solid-state vibrational circular dichroism (VCD) spectra from molecular dynamics simulations. Having solved the origin-dependence problem of the periodic magnetic gauge, we present IR and VCD spectra of (1,2)--1,2-cyclohexanediol obtained from first-principles molecular dynamics calculations and nuclear velocity perturbation theory, along with the experimental results. Because the structure model imposes periodic boundary conditions, the common origin of the rotational strength has hitherto been ill-defined and was approximated by means of averaging multiple origins.

Assessing cluster models of solvation for the description of vibrational circular dichroism spectra: synergy between static and dynamic approaches.

Solvation effects are essential for defining the shape of vibrational circular dichroism (VCD) spectra. Several approaches have been proposed to include them into computational models for calculating VCD signals, in particular those resting on the "cluster-in-a-liquid" model. Here we examine the capabilities of this ansatz on the example of flexible (1S,2S)-trans-1-amino-2-indanol solvated in dimethyl sulfoxide (DMSO).

Direct observation of water-mediated single-proton transport between hBN surface defects.

Aqueous proton transport at interfaces is ubiquitous and crucial for a number of fields, ranging from cellular transport and signalling, to catalysis and membrane science. However, due to their light mass, small size and high chemical reactivity, uncovering the surface transport of single protons at room temperature and in an aqueous environment has so far remained out-of-reach of conventional atomic-scale surface science techniques, such as scanning tunnelling microscopy. Here, we use single-molecule localization microscopy to resolve optically the transport of individual excess protons at the interface of hexagonal boron nitride crystals and aqueous solutions at room temperature.

Adiabatic motion and statistical mechanics via mass-zero constrained dynamics.

In recent work [Coretti et al., J. Chem.

A first-principles computational comparison of defect-free and disordered, fluorinated anatase TiO (001) interfaces with water.

Chemical doping and other surface modifications have been used to engineer the bulk properties of materials, but their influence on the surface structure and consequently the surface chemistry are often unknown. Previous work has been successful in fluorinating anatase TiO with charge balance achieved the introduction of Ti vacancies rather than the reduction of Ti. Our work here investigates the interface between this fluorinated titanate with cationic vacancies and a monolayer of water density functional theory based molecular dynamics.

Spontaneous liquid water dissociation on hybridised boron nitride and graphene atomic layers from ab initio molecular dynamics simulations.

Two-dimensional materials such as graphene (G) and hexagonal boron nitride (BN) have demonstrated potential applications in membrane science and in particular for the harvesting of blue energy. Although pure G and BN atomic layers are known to remain inert towards neutral water, one may wonder about the aqueous reactivity of hybridized monolayers formed by joining BN and G sheets in a planar fashion. Here, we perform ab initio molecular dynamics calculations of liquid water in contact with all possible planar heterostructures.

The MgCO-CaCO-LiCO-NaCO-KCO melts: Thermodynamics and transport properties by atomistic simulations.

Atomistic simulations provide a meaningful way to determine the physicochemical properties of liquids in a consistent theoretical framework. This approach takes on a particular usefulness for the study of molten carbonates, in a context where thermodynamic and transport data are crucially needed over a large domain of temperatures and pressures (to ascertain the role of these melts in geochemical processes) but are very scarce in the literature, especially for the calcomagnesian compositions prevailing in the Earth's mantle. Following our work on LiCO-NaCO-KCO melts, we extend our force field to incorporate Ca and Mg components.

Versatile electrification of two-dimensional nanomaterials in water.

The recent emergence of nanofluidics has highlighted the exceptional properties of graphene and its boron-nitride counterpart as confining nanomaterials for water and ion transport. Surprisingly, ionic transport experiments have unveiled a consequent electrification of the water/carbon surfaces, with a contrasting response for its water/boron-nitride homologue. In this paper, we report free energy calculations based on ab initio molecular dynamics simulations of hydroxide OH ions in water near graphene and hexagonal boron nitride (h-BN) layers.

Atomistic simulations of molten carbonates: Thermodynamic and transport properties of the LiCO-NaCO-KCO system.

Although molten carbonates only represent, at most, a very minor phase in the Earth's mantle, they are thought to be implied in anomalous high-conductivity zones in its upper part (70-350 km). Besides, the high electrical conductivity of these molten salts is also exploitable in fuel cells. Here, we report quantitative calculations of their properties, over a large range of thermodynamic conditions and chemical compositions, which are a requisite to develop technological devices and to provide a better understanding of a number of geochemical processes.

Chiral Crystal Packing Induces Enhancement of Vibrational Circular Dichroism.

We demonstrate that molecular vibrations with originally low or zero intensity in a vibrational circular dichroism (VCD) spectrum attain chirality in molecular crystals by coordinated motion of the atoms. Ab initio molecular dynamics simulations of anharmonic solid-state VCD spectra of l-alanine crystals reveal how coherent vibrational modes exploit the space group's chirality, leading to non-local, enhanced VCD features, most significantly in the carbonyl region of the spectrum. The VCD-enhanced signal is ascribed to a helical arrangement of the oscillators in the crystal layers.

Proton Collision on Deoxyribose Originating from Doubly Ionized Water Molecule Dissociation.

In this work, we studied the fragmentation dynamics of 2-deoxy-d-ribose (DR) in solution that arises from the double ionization of a water molecule in its primary hydration shell. This process was modeled in the framework of ab initio molecular dynamics. The charge unbalanced in the solvent molecules produces a Coulomb explosion with the consequent release of protons with kinetic energy in the few electronvolts range, which collide with the surrounding molecules in solution inducing further chemical reactions.