arXiv subjects

Nore Stolte

Publications and source records attributed to Nore Stolte.

9 recordsLinked to original sources

arXiv2026

Aromatic Molecule Solvation in Liquid Water with Coupled Cluster Accuracy: The Balance of Pi-Interactions and Hydrophobicity

Aromatic organic solutes in water exhibit a delicate balance between hydrophobic solvation and directional O-H$\cdots \pi$ hydrogen bonds, yet widely used force fields and state-of-the-art density functional approaches struggle to provide a consistent picture of these pivotal interactions. We introduce a data-efficient upfitting strategy to train a machine learning interatomic potential (MLIP) based on the graph atomic cluster expansion for aqueous aromatic molecules with CCSD(T) accuracy for condensed phase simulations, using only finite molecular clusters. We apply our method to aqueous toluene (C$_6$H$_5$CH$_3$). The resulting CCSD(T)-quality MLIP reproduces coupled cluster energies and forces in bulk and reveals that commonly employed methods do not capture the crucial balance between hydrophilic and hydrophobic solvation, distorting the interactions of aromatic molecules with their environment. Representative biomolecular force fields substantially understructure the hydrophobic solvation shell and misorient interfacial water, while overestimating $\pi$-contacts, yielding an inconsistent solvation balance. Even hybrid DFT and MP2 overestimate barriers to breaking of water-$\pi$ hydrogen bonds. Our workflow provides a practical, general route to CCSD(T)-quality condensed-phase simulations of aqueous solutions, and thus constructed interaction potentials now open the door to consistent, highly accurate benchmark studies of $\pi$-contacts and hydrophobic effects in biomolecular contexts such as solvation of proteins and DNA in aqueous environments.

physics.chem-ph↗

arXiv2025

Formation of abiogenic hydrocarbons in supercritical fluids under Earth's upper mantle conditions

The formation of hydrocarbons in Earth's interior has traditionally been considered to have biogenic origins; however, growing evidence suggests that some hydrocarbons may instead originate abiotically in the deep carbon cycle. It is widely expected that the Fisher-Tropsch-type (FTT) process, which typically refers to the conversion of inorganic carbon to organic matter in geological settings,may also happen in Earth's interior, but the absence of industrial catalysts and aqueous conditions in deep environments suggest that the FTT process can be very different from that in the chemical industry. Here, we performed extensive \textit{ab initio} molecular dynamics (AIMD) simulations ($>$ 2.4 ns) to investigate the FTT synthesis in dry mixture and in aqueous solutions at 10-13 GPa and 1000-1400 K.We found that large hydrocarbon-related species containing C, O, and H($>$C$_2$) are abiotically synthesized via the polymerization of CO without any catalyst. Supercritical water, commonly found in the deep Earth, does not prevent organic molecule formation but restricts product size and carbon reduction.Our studies reveal a previously unrecognized abiogenic route for hydrocarbon synthesis in mantle geofluids. These carbon-containing fluids could potentially migrate from depth to shallower crustal reservoirs, thereby influencing Earth's surface carbon budget.

physics.comp-ph↗

arXiv2024

When Theory Meets Experiment: What Does it Take to Accurately Predict $^1$H NMR Dipolar Relaxation Rates in Neat Liquid Water from Theory?

In this contribution, we compute the $^1$H nuclear magnetic resonance (NMR) relaxation rate of liquid water at ambient conditions. We are using structural and dynamical information from Coupled Cluster Molecular Dynamics (CCMD) trajectories generated at CCSD(T) electronic structure accuracy while considering also nuclear quantum effects in addition to consulting information from X-ray and neutron scattering experiments. Our analysis is based on a recently presented computational framework for determining the frequency-dependent NMR dipole-dipole relaxation rate of spin $1/2$ nuclei from Molecular Dynamics (MD) simulations, which allows for an effective disentanglement of its structural and dynamical contributions, and is including a correction for finite-size effects inherent to MD simulations with periodic boundary conditions. A close to perfect agreement with experimental relaxation data is achieved if structural and dynamical informations from CCMD trajectories are considered including a re-balancing of the rotational and translational dynamics, according to the product of the self-diffusion coefficient and the reorientational correlation time of the H-H vector $D_0\times\tau_\mathrm{HH}$. The simulations show that this balance is significantly altered when nuclear quantum effects are taken into account. Our analysis suggests that the intermolecular and intramolecular contribution to the $^1$H NMR relaxation rate of liquid water are almost similar in magnitude, unlike to what was predicted earlier from classical MD simulations.

physics.chem-ph↗

arXiv2024

Nuclear Quantum Effects in Liquid Water Are Negligible for Structure but Significant for Dynamics

Isotopic substitution, which can be realized both in experiment and computer simulations, is a direct approach to assess the role of nuclear quantum effects on the structure and dynamics of matter. Yet, the impact of nuclear quantum effects on the structure of liquid water as probed in experiment by comparing normal to heavy water has remained controversial. To settle this issue, we employ a highly accurate machine-learned high-dimensional neural network potential to perform converged coupled cluster-quality path integral simulations of liquid H$_2$O versus D$_2$O at ambient conditions. We find substantial H/D quantum effects on the rotational and translational dynamics of water, in close agreement with the experimental benchmarks. However, in stark contrast to the role for dynamics, H/D quantum effects turn out to be unexpectedly small, on the order of 1/1000 \r{A}, on both intramolecular and H-bonding structure of water. The most probable structure of water remains nearly unaffected by nuclear quantum effects, but effects on fluctuations away from average are appreciable, rendering H$_2$O substantially more "liquid" than D$_2$O.

physics.chem-ph↗

arXiv2024

Random sampling versus active learning algorithms for machine learning potentials of quantum liquid water

Training accurate machine learning potentials requires electronic structure data comprehensively covering the configurational space of the system of interest. As the construction of this data is computationally demanding, many schemes for identifying the most important structures have been proposed. Here, we compare the performance of high-dimensional neural network potentials (HDNNPs) for quantum liquid water at ambient conditions trained to data sets constructed using random sampling as well as various flavors of active learning based on query by committee. Contrary to the common understanding of active learning, we find that for a given data set size, random sampling leads to smaller test errors for structures not included in the training process. In our analysis we show that this can be related to small energy offsets caused by a bias in structures added in active learning, which can be overcome by using instead energy correlations as an error measure that is invariant to such shifts. Still, all HDNNPs yield very similar and accurate structural properties of quantum liquid water, which demonstrates the robustness of the training procedure with respect to the training set construction algorithm even when trained to as few as 200 structures. However, we find that for active learning based on preliminary potentials, a reasonable initial data set is important to avoid an unnecessary extension of the covered configuration space to less relevant regions.

physics.chem-ph↗

arXiv2024

Synthesis and stability of biomolecules in C-H-O-N fluids under Earth's upper mantle conditions

How life started on Earth is an unsolved mystery. There are various hypotheses for the location ranging from outer space to the seafloor, subseafloor or potentially deeper. Here, we applied extensive ab initio molecular dynamics (AIMD) simulations to study chemical reactions between NH$_3$, H$_2$O, H$_2$, and CO at pressures (P) and temperatures (T) approximating the conditions of Earth's upper mantle (i.e. 10-13 GPa, 1000-1400 K). Contrary to the previous assumptions that larger organic molecules might readily disintegrate in aqueous solutions at extreme P-T conditions, we found that many organic compounds formed without any catalysts and persisted in C-H-O-N fluids under these extreme conditions, including glycine, ribose, urea, and uracil-like molecules. Particularly, our free energy calculations showed that the C-N bond is thermodynamically stable at 10 GPa and 1400 K. Moreover, while the pyranose (six-membered-ring) form of ribose is more stable than the furanose (five-membered-ring) form at ambient conditions, we observed the predominant formation of the five-membered-ring form of ribose at extreme conditions, which is consistent with the exclusive incorporation of $\beta$-D-ribofuranose in RNA. We have uncovered a previously unexplored pathway through which the crucial biomolecules could be abiotically synthesized from geofluids in the deep interior of Earth and other planets and these formed biomolecules could potentially contribute to the early stage of the emergency of life.

physics.bio-ph↗

arXiv2022

Nanoconfinement Facilitates Reactions of Carbon Dioxide in Supercritical Water

The reactions of CO$_2$ in water under extreme pressure-temperature conditions are of great importance to the carbon storage and transport below Earth's surface, which substantially affect the carbon budget in the atmosphere. We applied ab initio molecular dynamics simulations to study aqueous carbon solutions nanoconfined by graphene and stishovite (SiO$_2$) at 10 GPa and 1000$\sim$1400 K. We found that CO$_2$(aq) reacts more in nanoconfinement than in bulk. The stishovite-water interface makes the solutions more acidic, which shifts the chemical equilibria, and the interface chemistry also affects the reaction mechanisms. Our findings suggest that CO$_2$(aq) in deep Earth may be more active than previously thought, and confining CO$_2$ and water in nanopores may enhance the efficiency of mineral carbonation.

physics.chem-ph↗

arXiv2020

The Lightest 2D Nanomaterial: Freestanding Ultrathin Li Nanosheets by in-situ Electron Microscopy

Lithium (Li) is the simplest metal and the lightest solid element. Here we report the first demonstration of controlled growth of two-dimensional (2D) ultrathin Li nanosheets with large lateral dimensions up to several hundreds of nanometres and thickness limited to just a few nanometres by in-situ transmission electron microscopy (TEM). The nanoscale dynamics of nanosheets growth were unravelled by real-time TEM imaging, which, in combination with density function theory (DFT) calculations indicates that the growth of bcc structured Li into 2D nanosheets is a consequence of kinetic control as mediated by preferential oxidization of the (111) surfaces due to the trace amount of O2 (~10-6 Pa) within TEM chamber. The plasmonic optical properties of the as-grown Li nanosheets were probed by cathodoluminescence (CL) spectroscopy equipped within TEM, and a broadband visible emission was observed that contains contributions of both in-plane and out-of-plane plasmon resonance modes.

physics.chem-ph↗

arXiv2019

Large presence of carbonic acid in CO$_2$-rich aqueous fluids under Earth's mantle conditions

The chemistry of carbon in aqueous fluids at extreme pressure and temperature conditions is of great importance to Earth's deep carbon cycle, which substantially affects the carbon budget at Earth's surface and global climate change. At ambient conditions, the concentration of carbonic acid in water is negligible, so aqueous carbonic acid was simply ignored in previous geochemical models. However, by applying extensive ab initio molecular dynamics simulations at pressure and temperature conditions similar to those in Earth's upper mantle, we found that carbonic acid can be the most abundant carbon species in aqueous CO$_2$ solutions at ~10 GPa and 1000 K. The mole percent of carbonic acid in total dissolved carbon species increases with increasing pressure along an isotherm, while its mole percent decreases with increasing temperature along an isobar. In CO$_2$-rich solutions, we found significant proton transfer between carbonic acid molecules and bicarbonate ions, which may enhance the conductivity of the solutions. The effects of pH buffering by carbonic acid may play an important role in water-rock interactions in Earth's interior. Our findings suggest that carbonic acid is an important carbon carrier in the deep carbon cycle.

physics.chem-ph↗