Protons display a high chemical activity and strongly affect the charge storage capability in confined interlayer spaces of two-dimensional (2D) materials. As such, an accurate representation of proton dynamics under confinement is important for understanding and predicting charge storage dynamics in these materials. While often ignored in atomistic-scale simulations, nuclear quantum effects (NQEs), e.g., tunneling, can be significant under confinement even at room temperature. Using the thermostatted ring polymer molecular dynamics implementation of path integral molecular dynamics (PIMD) in conjunction with the ReaxFF force field, density functional tight binding (DFTB), and NequIP neural network potential simulations, we investigate the role of NQEs on proton and water transport in bulk water and aqueous electrolytes under confinement in TiC MXenes. Although overall NQEs are relatively small, especially in bulk, we find that they can alter both quantitative values and qualitative trends on both proton transport and water self-diffusion under confinement relative to classical MD predictions. Therefore, our results suggest the need for NQEs to be considered to simulate aqueous systems under confinement for both qualitative and quantitative accuracy.
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Sci Rep
January 2025
Molecular Modeling and Simulation Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1, Anagawa, Inage-Ku, Chiba City, Chiba, 263-8555, Japan.
Sequence-dependent mechanical properties of DNA could play essential roles in nuclear processes by affecting histone-DNA interactions. Previously, we found that the DNA entry site of the first nucleosomes from the transcription start site (+ 1 nucleosome) in budding yeast enriches AA/TT steps, but not the exit site, and the biased presence of AA/TT in the entry site was associated with the transcription levels of yeast genes. Because AA/TT is a rigid dinucleotide step, we considered that AA/TT causes DNA unwrapping.
View Article and Find Full Text PDFStruct Dyn
January 2025
Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
Sub-ångström spatial resolution of electron density coupled with sub-femtosecond to few-femtosecond temporal resolution is required to directly observe the dynamics of the electronic structure of a molecule after photoinitiation or some other ultrafast perturbation, such as by soft X-rays. Meeting this challenge, pushing the field of quantum crystallography to attosecond timescales, would bring insights into how the electronic and nuclear degrees of freedom couple, enable the study of quantum coherences involved in molecular dynamics, and ultimately enable these dynamics to be controlled. Here, we propose to reach this realm by employing convergent-beam x-ray crystallography with high-power attosecond pulses from a hard-x-ray free-electron laser.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, USA.
Photosynthetic reaction center proteins (RCs) provide ideal model systems for studying quantum entanglement between multiple spins, a quantum mechanical phenomenon wherein the properties of the entangled particles become inherently correlated. Following light-generated sequential electron transfer, RCs generate spin-correlated radical pairs (SCRPs), also referred to as entangled spin qubit (radical) pairs (SQPs). Understanding and controlling coherence mechanisms in SCRP/SQPs is important for realizing practical uses of electron spin qubits in quantum sensing applications.
View Article and Find Full Text PDFChem Commun (Camb)
January 2025
Department of Chemistry, Quantum Chemistry, TU Darmstadt, Peter-Grünberg-Str. 4, 64287 Darmstadt, Germany.
The two key parameters extracted from Mössbauer spectroscopy, isomer shift and quadrupole splitting, have well-known temperature dependencies. While the behavior of the values following a temperature change has long been known, its microscopic origins are less clear. For quantum chemical calculations - formally representing the situation at 0 K - significant discrepancies with the experiment can arise, especially at elevated temperatures.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, D-70569 Stuttgart, Germany.
Effective potential methods, obtained by applying a quantum correction to a classical pair potential, are widely used for describing the thermophysical properties of fluids with mild nuclear quantum effects. In case of strong nuclear quantum effects, such as for liquid hydrogen and helium, the accuracy of these quantum corrections deteriorates significantly, but at present no simple alternatives are available. In this work, we solve this issue by developing a new, three-parameter corresponding-states principle that remains applicable in the regions of the phase diagram where quantum effects become significant.
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