Periodic Reporting for period 2 - GAS-WAT (Gases in Water)
Reporting period: 2023-02-01 to 2024-07-31
Water is the basis for life as we know it and is fundamental as a solvent in countless chemical and geochemical processes. It is often referred to as the "strangest" liquid due to its many unique physical properties. Among these are the density maximum at 4 C and the solid (ice) being less dense than the liquid. These properties make aquatic life possible also in the far north since lakes freeze from the top, while water at the bottom remains at 4 C. Its compressibility and heat capacity show a minimum at normal temperatures and then rapidly increase when the liquid is supercooled below the freezing point. Both depend on fluctuations in the liquid that for other liquids decrease upon cooling, but for water they instead increase. The origin of this anomalous behavior has been hotly debated, but from both experiment and simulations it is becoming increasingly clear that water, far from ambient conditions, can exist as a liquid in two different forms, a high-density (HDL) and low-density liquid (LDL). This still affects water under normal conditions through dynamical fluctuations as groups of molecules switch between local HDL and LDL structures. The ultimate goal of GAS-WAT is to determine how these structures are built, how they affect chemistry and how they affect the solvation of gases, most importantly oxygen, and how oxygen is transferred to fish gills.
Water can form so-called clathrates where water molecules form cages, typically around a solvated gas molecule, like methane or oxygen, but can such structures form locally in the liquid, even without the gas molecule? Would such more open structures be preferred for, e.g. oxygen in water? Irrespective of whether they pre-existed or formed around the oxygen, once the oxygen is in the cage, the question becomes how do fish get the oxygen out and into their gills? Has evolution found a way to change the structure of water in the vicinity of the gills to make it more attractive for the oxygen? To investigate this, we perform x-ray measurements at synchrotron radiation facilities to determine the arrangement of water molecules around Argon dissolved in water. Argon has a similar size and behavior as oxygen and we selectively look at the Argon in the water. We find a basic clathrate-like environment, but to answer the question if it existed without the Argon or formed because of the Argon we must turn to theoretical simulations and modeling.
For this we will put clathrate-like structures into simulation models of water and follow them as the simulation proceeds. Will they remain for any length of time or disappear? To be conclusive, the description of how the water molecules interact has to be very reliable and to this end we are finalizing a state-of-the-art computer model of water (FCM-GAP) that we will apply.
X-ray spectroscopic data indicate that the structures we find from advanced computer models of water need to be modified. These computer models give many other properties (density, diffusivity, compressibility, etc) in agreement with experiment, but will this still be the case for the modified structures we deduce from the x-ray spectra? To answer this we have developed a Monte Carlo code to calculate all the relevant properties, both for the original and modified structures to check the consistency.
Finally, the protons in the water molecule are light enough that we need to take quantum effects into account. This leads to water molecules existing in two different forms, ortho- and para-water, depending on how the proton nuclear spins are coupled and this affects how the molecules rotate. To include this we develop and implement methods to treat the protons on an equal basis with the electrons, i.e. as properly spin-coupled wave functions. The goal is to perform computer simulations where the protons are fully quantum mechanical and their spins properly described.
Water can form so-called clathrates where water molecules form cages, typically around a solvated gas molecule, like methane or oxygen, but can such structures form locally in the liquid, even without the gas molecule? Would such more open structures be preferred for, e.g. oxygen in water? Irrespective of whether they pre-existed or formed around the oxygen, once the oxygen is in the cage, the question becomes how do fish get the oxygen out and into their gills? Has evolution found a way to change the structure of water in the vicinity of the gills to make it more attractive for the oxygen? To investigate this, we perform x-ray measurements at synchrotron radiation facilities to determine the arrangement of water molecules around Argon dissolved in water. Argon has a similar size and behavior as oxygen and we selectively look at the Argon in the water. We find a basic clathrate-like environment, but to answer the question if it existed without the Argon or formed because of the Argon we must turn to theoretical simulations and modeling.
For this we will put clathrate-like structures into simulation models of water and follow them as the simulation proceeds. Will they remain for any length of time or disappear? To be conclusive, the description of how the water molecules interact has to be very reliable and to this end we are finalizing a state-of-the-art computer model of water (FCM-GAP) that we will apply.
X-ray spectroscopic data indicate that the structures we find from advanced computer models of water need to be modified. These computer models give many other properties (density, diffusivity, compressibility, etc) in agreement with experiment, but will this still be the case for the modified structures we deduce from the x-ray spectra? To answer this we have developed a Monte Carlo code to calculate all the relevant properties, both for the original and modified structures to check the consistency.
Finally, the protons in the water molecule are light enough that we need to take quantum effects into account. This leads to water molecules existing in two different forms, ortho- and para-water, depending on how the proton nuclear spins are coupled and this affects how the molecules rotate. To include this we develop and implement methods to treat the protons on an equal basis with the electrons, i.e. as properly spin-coupled wave functions. The goal is to perform computer simulations where the protons are fully quantum mechanical and their spins properly described.
We have performed three sets of measurements of Argon in water at four different temperatures (5, 15, 25 and 45 C) at the Stanford Synchrotron Radiation Lightsource in California. We have analyzed the data based on simulations of the scattering and advanced fitting techniques and find a clathrate-like cage around the Argon with 20 molecules.We have taken measurements at a lower pH to determine whether the stability of the cage is affected by a lower pH (as found in fish gills).
We have performed extensive simulations of x-ray absorption and emission spectra for water models to determine the connection between local structure and the measured spectra. We have performed calculations on larger models (in terms of number of molecules) and determined how structures from simulations should be modified to agree with the spectroscopies. The next step is to finalize a Monte Carlo code, which will allow determining if the derived distributions have an impact (positive or negative) on the thermodynamics of the model.
We have developed and implemented:
- the FCM-GAP model of water with focus on highly accurate machine-learned electrostatics and machine-learned two- and three-body quantum chemical short-range interactions. The three-body interactions have been a bottleneck in terms of efficiency and cpu time, but this has now been overcome and simulations to establish the properties of the model are underway.
- a non-orthogonal CI approach to rotational dynamics with the light nuclei as properly spin-coupled wave functions. We have tested on a Helium dimer confined inside a C60 molecule and applied to general HX, HXY and HXX molecules (X, Y stand for heavy atoms).
- real-time propagation both of electrons and protons (wave functions) in a time-dependent density functional theory formalism. This will allow us to follow the dynamics induced by absorption of an x-ray photon in the x-ray emission process and eliminate several current approximations.
We have performed extensive simulations of x-ray absorption and emission spectra for water models to determine the connection between local structure and the measured spectra. We have performed calculations on larger models (in terms of number of molecules) and determined how structures from simulations should be modified to agree with the spectroscopies. The next step is to finalize a Monte Carlo code, which will allow determining if the derived distributions have an impact (positive or negative) on the thermodynamics of the model.
We have developed and implemented:
- the FCM-GAP model of water with focus on highly accurate machine-learned electrostatics and machine-learned two- and three-body quantum chemical short-range interactions. The three-body interactions have been a bottleneck in terms of efficiency and cpu time, but this has now been overcome and simulations to establish the properties of the model are underway.
- a non-orthogonal CI approach to rotational dynamics with the light nuclei as properly spin-coupled wave functions. We have tested on a Helium dimer confined inside a C60 molecule and applied to general HX, HXY and HXX molecules (X, Y stand for heavy atoms).
- real-time propagation both of electrons and protons (wave functions) in a time-dependent density functional theory formalism. This will allow us to follow the dynamics induced by absorption of an x-ray photon in the x-ray emission process and eliminate several current approximations.
- Development of the FCM/GAP force-field and validating in large-scale PI-MD simulations
- Investigate the stability of clathrate-like clusters in simulations of ambient water
- Determine structural distributions consistent with x-ray spectroscopies and scattering and determine if they are also consistent with thermodynamics
- Develop and apply dynamics with protons as wave functions and intermolecular interactions by a force-field
- Develop and apply real-time time-dependent DFT including protons and apply to x-ray emission
- Determine experimentally the hydration sphere around a gas molecule/atom in water and factors affecting the stability
- Investigate oxygen diffusion in models of the mucuous contact layer between water and fish gills
- Investigate the stability of clathrate-like clusters in simulations of ambient water
- Determine structural distributions consistent with x-ray spectroscopies and scattering and determine if they are also consistent with thermodynamics
- Develop and apply dynamics with protons as wave functions and intermolecular interactions by a force-field
- Develop and apply real-time time-dependent DFT including protons and apply to x-ray emission
- Determine experimentally the hydration sphere around a gas molecule/atom in water and factors affecting the stability
- Investigate oxygen diffusion in models of the mucuous contact layer between water and fish gills