382 citations · 1.1k across the 19 of their papers we have counts for
19 papers
How Alkali Metal Cations Affect the Structure and Reactivity of the Hydrated Dielectron
Tatiana Nemirovich, Pavel Jungwirth, Ondrej Marsalek
Hydrated electrons of opposite spins pair to form dielectrons at sufficiently high concentrations that can be achieved by dissolution of alkali metals in water. While experimental…
More converged, less accurate? Reassessing standard choices for ab initio water using machine learning potentials
Hubert Beck, Ondrej Marsalek
Accurately simulating the properties of liquid water remains a central challenge in molecular simulations. In this work, we use machine learning potentials to investigate how the c…
Multi-head committees enable direct uncertainty prediction for atomistic foundation models
Hubert Beck, Pavol Simko, Lars L. Schaaf +2
Machine learning potentials have become a standard tool for atomistic materials modelling. While models continue to become more generalisable, an open challenge relates to efficien…
Elucidating the Nature of -hydrogen Bonding in Liquid Water and Ammonia
Krystof Brezina, Hubert Beck, Ondrej Marsalek
Aromatic compounds form an unusual kind of hydrogen bond with water and ammonia molecules, known as the -hydrogen bond. In this work, we report ab initio path integral molecular…
Developing machine-learned potentials to simultaneously capture the dynamics of excess protons and hydroxide ions in classical and path integral simulations
Austin O. Atsango, Tobias Morawietz, Ondrej Marsalek +1
The transport of excess protons and hydroxide ions in water underlies numerous important chemical and biological processes. Accurately simulating the associated transport mechanism…
Reducing the cost of neural network potential generation for reactive molecular systems
Krystof Brezina, Hubert Beck, Ondrej Marsalek
Although machine-learning potentials have recently had substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, es…
Machine learning potentials for complex aqueous systems made simple
Christoph Schran, Fabian L. Thiemann, Patrick Rowe +3
Simulation techniques based on accurate and efficient representations of potential energy surfaces are urgently needed for the understanding of complex aqueous systems such as soli…
Benzene Radical Anion Microsolvated in Ammonia Clusters: Modelling the Transition from an Unbound Resonance to a Bound Species
Vojtech Kostal, Krystof Brezina, Ondrej Marsalek +1
The benzene radical anion, well-known in organic chemistry as the first intermediate in the Birch reduction of benzene in liquid ammonia, exhibits intriguing properties from the po…
Electronic Structure of the Solvated Benzene Radical Anion
Krystof Brezina, Vojtech Kostal, Pavel Jungwirth +1
The benzene radical anion is a molecular ion pertinent to several organic reactions, including the Birch reduction of benzene in liquid ammonia. The species exhibits a dynamic Jahn…
Significance of nuclear quantum effects in hydrogen bonded molecular chains
Aleš Cahlík, Jack Hellerstedt, Jesús I. Mendieta-Moreno +10
In hydrogen bonded systems, nuclear quantum effects such as zero-point motion and tunneling can significantly affect their material properties through underlying physical and chemi…
Committee neural network potentials control generalization errors and enable active learning
Christoph Schran, Krystof Brezina, Ondrej Marsalek
It is well known in the field of machine learning that committee models improve accuracy, provide generalization error estimates, and enable active learning strategies. In this wor…
Benzene radical anion in the context of the Birch reduction: when solvation is the key
Krystof Brezina, Pavel Jungwirth, Ondrej Marsalek
The benzene radical anion is an important intermediate in the Birch reduction of benzene by solvated electrons in liquid ammonia. Beyond organic chemistry, it is an intriguing subj…
i-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations
Venkat Kapil, Mariana Rossi, Ondrej Marsalek +23
Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomi…
The Interplay of Structure and Dynamics in the Raman Spectrum of Liquid Water over the Full Frequency and Temperature Range
Tobias Morawietz, Ondrej Marsalek, Shannon R. Pattenaude +3
While many vibrational Raman spectroscopy studies of liquid water have investigated the temperature dependence of the high-frequency O-H stretching region, few have analyzed the ch…
Decoding the spectroscopic features and timescales of aqueous proton defects
Joseph A. Napoli, Ondrej Marsalek, Thomas E. Markland
Acid solutions exhibit a variety of complex structural and dynamical features arising from the presence of multiple interacting reactive proton defects and counterions. However, di…
Unravelling the influence of quantum proton delocalization on electronic charge transfer through the hydrogen bond
Christoph Schran, Ondrej Marsalek, Thomas E. Markland
Upon hydrogen bond formation, electronic charge density is transferred between the donor and acceptor, impacting processes ranging from hydration to spectroscopy. Here we use ab in…
Quantum dynamics and spectroscopy of ab initio liquid water: the interplay of nuclear and electronic quantum effects
Ondrej Marsalek, Thomas E. Markland
Understanding the reactivity and spectroscopy of aqueous solutions at the atomistic level is crucial for the elucidation and design of chemical processes. However, the simulation o…
Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates
Joseph R. Cendagorta, Anna Powers, Timothy J. H. Hele +3
Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H and D diffusion through…
Ab initio molecular dynamics with nuclear quantum effects at classical cost: ring polymer contraction for density functional theory
Ondrej Marsalek, Thomas E. Markland
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of…