In both its gaseous and condensed forms, carbon dioxide has an ever-increasing impact on Earth's chemistry and human life and activities. However, many aspects of its high-pressure phase diagram remain unclear. In this work, we present a complete structural characterization of carbon dioxide fluids under geological conditions using extensive ab initio molecular dynamics simulations throughout a wide pressure and temperature range, corresponding to Earth's lower mantle. We identify and describe four different disordered regimes, including two polymeric forms and two molecular ones, all within the geothermal conditions of the lower mantle. At pressures below 40 GPa, we find that the molecular liquid becomes very reactive above 2000 K: the C-O double bond routinely breaks, resulting in small and transient chains composed of CO2 units and frequently leading to an exchange of oxygen atoms between molecules. At higher pressures, in addition to the polymeric fluid previously reported at 3000 K, we find a polymeric system with glass-like behavior at lower temperatures, suggesting a complex interplay between kinetics and stability.

Methane hydrate was recently shown, both experimentally and through simulations, to be stable up to the remarkably high pressure of 150 GPa. A new methane hydrate high-pressure (MH-IV) phase, reminiscent of ice at ambient pressure, was described for pressures above approximately 40 GPa. We disentangle here the main contributions to the relative stability of the lower pressure, denoted MH-III, and the high-pressure MH-IV structures. Through several simulation techniques, including metadynamics and path integral molecular dynamics for nuclear quantum effects, we analyze the phase transition mechanism, which implies hydrogen bond breaking and reforming, as well as methane reordering. The transition pathway is far from trivial, and the quantum delocalization of the hydrogen nuclei plays a significant role.

We propose an efficient method to explore the configuration space of nanoclusters by combining together ab initio molecular dynamics, metadynamics, and data clustering algorithms. On the one side, we employ collective variables sensitive to topological changes in the network of interatomic connections to map the configuration space; on the other side, we introduce an automatic approach to select, in such a space, representative structures to be optimized. In this way, we show that it is possible to sample thoroughly the set of relevant nanocluster geometries at a limited computational cost. We apply our method to explore MoS2 clusters that recently raised a sizable interest due to their remarkable electronic and catalytic properties. We demonstrate that the unsupervised algorithm is able to find a large number of low-energy structures at different cluster sizes, including both bulk-like geometries and very different topologies. We are thus able to recapitulate, in a single computational study on technologically relevant MoS2 clusters, the results of all previous works that employed distinct techniques like genetic algorithms or heuristic hypotheses. Furthermore, we found several new structures not previously reported. The ensemble of MoS2 cluster structures is deposited in a publicly accessible database.

In their high-pressure study of solid CO2, Yong et al. (1) claim: (i) that they recovered the polymeric phase V (CO2-V) at ambient pressure and 191 K, and (ii) that CO2-V may exist in different crystal structures. We demonstrate below that neither of these claims is supported by their data. First, in figure 5B of ref. 1, Yong et al. show as evidence for the recovery of CO2-V to ambient pressure a Raman spectrum of the sample labeled as “Ambient & 191 K.” This spectrum does contain CO2-V peaks at 360.8, 665.9, 880, and 978 cm−1. It also displays two more peaks at 113.8 and 166.8 cm−1, corresponding to the Fg− and Fg+ librons of CO2-I, respectively. This CO2-V/CO2-I coexistence originates from the kinetically limited back-transformation of CO2-V into CO2-I, which is the stable phase below …

In their high-pressure study of solid CO2, Yong et al. (1) claim: ( i ) that they recovered the polymeric phase V (CO2-V) at ambient pressure and 191 K, and ( ii ) that CO2-V may exist in different crystal structures. We demonstrate below that neither of these claims is supported by their data. First, in figure 5B of ref. 1, Yong et al. show as evidence for the recovery of CO2-V to ambient pressure a Raman spectrum of the sample labeled as “Ambient & 191 K.” This spectrum does contain CO2-V peaks at 360.8, 665.9, 880, and 978 cm−1. It also displays two more peaks at 113.8 and 166.8 cm−1, corresponding to the F g− and F g+ librons of CO2-I, respectively. This CO2-V/CO2-I coexistence originates from the kinetically limited back-transformation of CO2-V into CO2-I, which is the stable phase below … [↵][1]1To whom correspondence should be addressed. Email: Frederic.Datchi{at}impmc.upmc.fr. [1]: #xref-corresp-1-1

Single-particle imaging using X-ray free-electron lasers is an emerging technique that could provide high-resolution structures of macromolecules in the gas phase. One of the largest difficulties in realizing this goal is the unknown orientation of the individual sample molecules at the time of exposure. Preorientation of the molecules has been identified as a possible solution to this problem. Using molecular dynamics simulations, we identify a range of electric field strengths where proteins become oriented without losing their structure. For a number of experimentally relevant cases we show that structure determination is possible only when orientation information is included in the orientation-recovery process. We conclude that nondestructive field orientation of intact proteins is feasible and that it enables a range of new structural investigations with single particle imaging.

Dioxyde de carbone en conditions extrêmes : étude des phases liquide(s), crystallines, verre et leur transformations par méthodes topologiques ab initio Le dioxyde de carbone est un constituant important du manteau de la Terre et intervient dans de nombreux processus géologiques, notamment sismiques et volcaniques. Dans cette thèse, nous étudions les transformations du dioxyde de carbone dans les conditions extrêmes du manteau inférieur de la Terre. En effet, la compréhension du comportement du dioxyde de carbone et notamment de ses mécanismes de polymérisation dans ces conditions pourrait apporter un éclairage supplémentaire sur les propriétés du manteau inférieur. Nous utilisons ici des outils topologiques avancées et des méthodes de simulation aux premiers principes (ab initio) afin d’étudier ces mécanismes de polymérisation du dioxyde de carbone dans des conditions de températures et de pressions extrêmes du manteau. Ce faisant nous mettons en évidence quatre comportements fluides différents dans ces conditions géothermiques: le liquide moléculaire classique, avec des interactions faibles entre molécules de dioxyde de carbone ; un liquide moléculaire réactif dans lequel ces molécules réagissent fréquemment et forment d’éphèmes dimères permettant l’échange d’oxygène entre elles ; un liquide polymérique hautement réactif formant un réseau complexe de chaînes moléculaires en perpétuelles évolutions ; une forme liquide avec très peu de diffusion, semblable à un amorphe. Tous ces fluides peuvent apparaître dans les conditions expérimentales du manteau inférieur; leur propriétés peuvent donc impacter la réactivité et les propriétés de transport de ce dernier. Par exemple, le liquide moléculaire réactif semble indiquer une participation accrue du dioxyde de carbone dans les réactions du manteau.