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

Ab initio 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 DR2+, fragmentation patterns are determined for the ground electronic state, adding randomly distributed excitation energy to the nuclei. These patterns differ for the two isomers studied. To compare thermal and electronic excitation effects, Ehrenfest dynamics are also performed, allowing to remove the two electrons from selected molecular orbitals. Two intermediate-energy orbitals, localized on the carbon chain, were selected. The dissociation pattern corresponds to the most frequent pattern obtained when adding thermal excitation. On the contrary, targeting the four deepest orbitals, localized on the oxygen atoms, leads to selective ultrafast C-O and/or O-H bond dissociation. To probe the role of environment, a system consisting of a DR molecule embedded in liquid water is then studied. The two electrons are removed from either the DR or the water molecules directly linked to the sugar through hydrogen bonds. Although the dynamics onset is similar to that of isolated DR when removing the same deep orbitals localized on the sugar oxygen atoms, the subsequent fragmentation patterns differ. Sugar damage also occurs following the Coulomb explosion of neighboring H2O2+ molecules due to interaction with the emitted O or H atoms.

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. We also show that the Rabi splitting energy is linearly proportional to the square root of molecular concentration, thereby proving the relevance and reliability of the system for VSC studies.

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. The AMOEBA force field was employed here to model alanine in the neutral and zwitterionic isolated forms, solvated by water or nitrogen, and as a crystal. Within this framework, comparison of the electric and magnetic dipole moments to those obtained with nuclear velocity perturbation theory based on density-functional theory for the same MD trajectories are found to agree well with one another. The statistical convergence of the IR and VCD spectra is examined and found to be more demanding in the latter case. Comparisons with experimental frequencies are also provided for the condensed phases.

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. We report a remarkably low thermal expansion of the hydrogen bond from zero temperature up to 300 K, owing to the presence of short-Zundel configurations, characterised by proton delocalisation and favoured by the synergy of nuclear quantum effects and thermal activation. The hydrogen bond strength progressively weakens above 300 K, when localised Eigen-like configurations become relevant. Our analysis, supported by the instanton statistics of shuttling protons, reveals that the near-room-temperature range from 250 K to 300 K is optimal for proton transfer in the protonated water hexamer.

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). The method proposed is able to correctly characterize resonance Raman scattering and enhancement, including the description of overtones and combination bands. The absorption spectrum is obtained at the same time, and the vibrational fine structure can be reproduced for long excited state relaxation times. The method can also be applied to dissociating excited states (as is the case for HOCl).

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-1, 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. In condensed phases, the method provides invaluable insight into the molecular origins of the vibrational bands and further shows that peaks with similar positions can be traced to rather different molecular motions.

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 P21 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. Distinguishing between contributions originating from molecular chirality and from chiral crystal packing, we find that while IR absorption hardly depends on the symmetry of the space group, the situation is different for VCD, where completely new non-local patterns emerge. Understanding the two underlying mechanisms, namely gauge transport and direct coupling, will help to use VCD to distinguish polymorphic forms.

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. To fill the gap, we built a data set on nickel-catalyzed cross-couplings extracted from organic reaction publications, including scope and optimization information. We demonstrate the importance of including optimization data as a source of failed experiments and emphasize how publication constraints shape the exploration of the chemical space by the synthetic community. While machine learning models still fail to perform out-of-sample predictions, this work shows that adding chemical knowledge enables fair predictions in a low-data regime. Eventually, we hope that this unique public database will foster further improvements of machine learning methods for reaction yield prediction in a more realistic context.

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. This method includes both local and non-local terms, which are represented, respectively, by the dependency of the polarisability and hyperpolarisability upon the chemical environment of the molecule and by the bulk quadrupole response. The importance of both terms for the sound simulation of the SHG signals and their interpretation is assessed. We demonstrate that the sole dipole term is unable to simulate a SHG signal, even if the dependency of the hyperpolarisability on the local environment is considered. The inclusion of the bulk quadrupole contribution, which largely dominates the dipole contribution, is essential to predict the SHG response, although the accuracy of the prediction is increased when the dependency upon the local environment is considered.

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. We show that with appropriate predictive models, this issue can be resolved, and molecules generated have high scores according to both the optimization and the control models.

Deciphering second harmonic generation signals.

Second harmonic generation (SHG) has emerged as one of the most powerful techniques used to selectively monitor surface dynamics and reactions for all types of interfaces as well as for imaging non-centrosymmetric structures, although the molecular origin of the SHG signal is still poorly understood. Here, we present a breakthrough approach to predict and interpret the SHG signal at the atomic level, which is freed from the hyperpolarisability concept and self-consistently considers the non-locality and the coupling with the environment. The direct ab initio method developed here shows that a bulk quadrupole contribution significantly overwhelms the interface dipole term in the purely interfacial induced second-order polarisation for water/air interfaces. The obtained simulated SHG responses are in unprecedented agreement with the experimental signal. This work not only paves the road for the prediction of SHG response from more complex interfaces of all types, but also suggests new insights in the interpretation of the SHG signal at a molecular level. In particular, it highlights the modest influence of the molecular orientation and the high significance of the bulk quadrupole contribution, which does not depend on the interface, in the total experimental response.

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). The comparison with experimental data allows us to establish a VCD-structure relationship that includes the solvent network around the chiral solute. We suggest that fundamental modes with strong polarisation such as the carbonyl stretching vibration can borrow VCD from the chirally restructured solvent cage, which extends the common explanatory models of VCD generation in aqueous solution.

The trisulfur radical ion S3•- 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 S3•- forms very stable and soluble complexes with both PtII and PtIV 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. Our results imply a far more important contribution of sulfur-bearing hydrothermal fluids to PGE transfer and accumulation in the Earth's crust than believed previously. This discovery challenges traditional models of PGE economic concentration from silicate and sulfide melts and provides new possibilities for resource prospecting in hydrothermal shallow crust settings. The exceptionally high capacity of the S3•- ion to bind platinum may also offer new routes for PGE selective extraction from ore and hydrothermal synthesis of noble metal nanomaterials.

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 (1S,2S)-trans-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. The new formalism reconnects the periodic model with the finite physical system and restores gauge freedom. It nevertheless fully accounts for nonlocal spatial couplings from the gauge transport term. We show that even for small simulation cells the rich nature of solid-state VCD spectra found in experiments can be reproduced to a very satisfactory level.

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). We compare cluster sets obtained from static calculations with results from explicit molecular dynamics (MD) trajectories based on either force field (FF) or first-principles (FP) methods. While the FFMD approach provides a broader sampling of configurational space, FPMD and time-correlation functions of dipole moments account for anharmonicity and entropy effects in the VCD calculation. They provide a means to evaluate the immediate effect of the solvent on the spectrum. This survey singles out several challenges associated with the use of clusters to describe solvation effects in systems showing shallow potential energy surfaces and non-covalent interactions. Static structures of clusters involving a limited number of solvent molecules satisfactorily capture the main effects of solvation in the bulk limit on the VCD spectra, if these structures are correctly weighted. The importance of taking into consideration their fluxionality, i.e. different solvent conformations sharing a same hydrogen bond pattern, and the limitations of small clusters for describing the solvent dynamics are discussed.

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. Single excess proton trajectories are revealed by the successive protonation and activation of optically active defects at the surface of the crystal. Our observations demonstrate, at the single-molecule scale, that the solid/water interface provides a preferential pathway for lateral proton transport, with broad implications for molecular charge transport at liquid interfaces.

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

In recent work [Coretti et al., J. Chem. Phys., 2018, 149, 191102], a new algorithm to solve numerically the dynamics of the shell model for polarization was presented. The approach, broadly applicable to systems involving adiabatically separated dynamical variables, employs constrained molecular dynamics to strictly enforce the condition that the force on the fast degrees of freedom, modeled as having zero mass, is null at each time step. The algorithm is symplectic and fully time reversible, and results in stable and efficient propagation. In this paper we complete the discussion of the mechanics of mass-zero constrained dynamics by showing how to adapt it to problems where the fast degrees of freedom must satisfy additional conditions. This extension includes, in particular, the important case of first principles molecular dynamics. We then consider the statistical mechanics of the mass-zero constrained dynamical system demonstrating that the marginal probability sampled by the dynamics in the physical phase space recovers the form of the Born-Oppenheimer probability density. The effectiveness of the approach and the favorable scaling of the algorithm with system size are illustrated in test calculations of solid Na via orbital-free density functional 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. Remarkably, we could observe the spontaneous chemisorption and dissociation of the interfacial water molecule into its self-ions at one specific and non-standard one-dimensional border. Our simulations predict that this type of heterostructure is prone to ionize liquid water in the absence of any electrical gating.

A first-principles computational comparison of defect-free and disordered, fluorinated anatase TiO2 (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 TiO2 with charge balance achieved via 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 via density functional theory based molecular dynamics. We compute the projected density of states for only those atoms at the interface and for those states that fall within 1 eV of the Fermi level for various steps throughout the simulation, and we determine that the variation in this visualization of the density of states serves as a reasonable tool to anticipate where surfaces are most likely to be reactive. In particular, we conclude that water dissociation at the surface is the main mechanism that influences the anatase (001) surface whereas the change in the density of states at the surface of the fluorinated structure is influenced primarily through the adsorption of water molecules.

The MgCO3-CaCO3-Li2CO3-Na2CO3-K2CO3 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 Li2CO3-Na2CO3-K2CO3 melts, we extend our force field to incorporate Ca and Mg components. The empirical interaction potentials are benchmarked on the density data available in the experimental literature [for the crystals and the K2Ca(CO3)2 melt] and on the liquid structure issued from ab initio molecular dynamics simulations. Molecular dynamics simulations are then performed to study the thermodynamics, the microscopic structure, the diffusion coefficients, the electrical conductivity, and the viscosity of molten Ca,Mg-bearing carbonates up to 2073 K and 15 GPa. Additionally, the equation of state of a Na-Ca-K mixture representative of the lavas emitted at Ol Doinyo Lengai (Tanzania) is evaluated. The overall agreement between the MD results and the existing experimental data is very satisfactory and provides evidence for the ability of the force field to accurately model any MgCO3-CaCO3-Li2CO3-Na2CO3-K2CO3 melt over a large T-P range. Moreover, it is the first report of a force field allowing us to study the transport properties of molten magnesite (MgCO3) and molten dolomite [CaMg(CO3)2].