Can DFT-trained neural network potentials reproduce structure, solvation, and water-exchange properties in aqueous magnesium solutions?
Institute of Physics, University of Augsburg（奥格斯堡大学物理研究所）；Faculty of Physics, University of Vienna（维也纳大学物理学院）；Research Platform on Accelerating Photoreaction Discovery (ViRAPID), University of Vienna（维也纳大学光反应加速发现研究平台）
Sebastian Falkner, Pablo Montero de Hijes, Christoph Dellago, Nadine Schwierz
Magnesium ions play an essential role in many biological processes but remain challenging to model in biomolecular simulations. Despite considerable scientific effort, classical force fields fail to simultaneously reproduce key structural, thermodynamic and kinetic solution properties, likely due to their inability to explicitly account for quantum many-body effects. Here, we develop and systematically benchmark MACE neural network potentials (NNPs) for aqueous MgCl$_2$ solutions trained on revPBE-D3/zd and revPBE0-D3/zd density functional theory reference data and assess their ability to reproduce a broad range of experimental solution properties including the structure of the first hydration shell, diffusion coefficient, activity derivative, water-exchange rate and mechanism as well as solvation free energy. Both NNPs accurately reproduce the octahedral structure of the first hydration shell, ion pairing properties and diffusion coefficients. Combining the NNPs with transition path sampling and other enhanced sampling techniques allows us to capture the rare event of water exchange in the first hydration shell of Mg$^{2+}$ revealing a dissociative exchange mechanism. Transition interface sampling yields exchange rates within one order of magnitude of experiment, representing a substantial improvement over classical dissociative force fields. In contrast, the NNP-derived solvation free energy significantly underestimates the experimental value, revealing a limitation of the present local NNP architectures for describing ion solvation thermodynamics. Our results demonstrate that DFT-trained NNPs can accurately describe Mg$^{2+}$ hydration structure, diffusion, ion pairing, and exchange kinetics, while highlighting the need for explicit long-range electrostatic treatments to achieve quantitative agreement with experimental ion solvation free energies.
The performance of gold nanoparticles (NPs) in applications depends critically on the structure of the NP-solvent interface, at which the electrostatic surface polarization is one of the key characteristics that affects hydration, ionic adsorption, and electrochemical reactions. Here, we demonstrate significant effects of explicit metal polarizability on the solvation and electrostatic properties of bare gold NPs in aqueous electrolyte solutions of sodium salts of various anions (Cl$^-$, BF$_4$$^-$, PF$_6$$^-$, Nip$^-$(nitrophenolate), and 3- and 4-valent hexacyanoferrate (HCF)), using classic…
The current computational study investigates the changes in solvation dynamics of water when introducing hydrophobic side chains to the molecular probe N-methyl-6-oxyquinolinium betaine. High precision transient fluorescence and absorption measurements published in the companion paper revealed an influence of hydrophobic sidechain alterations on the observed solvation dynamics of a chromophore in water. As the influence of shape, size and structure of chromophores on the time-dependent Stokes shift was so far thought to play a role only in slowly rotating solvents compared to the solute or if …
Experiments on the formation of magnesium complexes in $^4$He nanodroplets were interpreted as the observation of the formation of weakly bound magnesium complexes. We present results for single Mg and Mg dimer solvation using the hypernetted chain / Euler-Lagrange method as well as path integral Monte Carlo simulations. We find that the phonon-mediated, indirect Mg-Mg interaction adds an oscillatory component to the direct Mg-Mg interaction. We undertake a step-by-step examination of the ingredients of the calculation of the phonon-induced interaction, comparing the results of semi-analytic H…
Pacific Northwest National Laboratory（太平洋西北国家实验室）；Lehigh University（理海大学）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）
The solvation free energy of organic molecules is a critical parameter in determining emergent properties such as solubility, liquid-phase equilibrium constants, and pKa and redox potentials in an organic redox flow battery. In this work, we present a machine learning (ML) model that can learn and predict the aqueous solvation free energy of an organic molecule using Gaussian process regression method based on a new molecular graph kernel. To investigate the performance of the ML model on electrostatic interaction, the nonpolar interaction contribution of solvent and the conformational entropy…
Structural, dynamical, bonding, and electronic properties of water molecules around a soluted methane molecule are studied from first principles. The results are compatible with experiments and qualitatively support the conclusions of recent classical Molecular Dynamics simulations concerning the controversial issue on the presence of "immobilized" water molecules around hydrophobic groups: the hydrophobic solute slightly reduces (by a less than 2 factor) the mobility of many surrounding water molecules rather than immobilizing just the few ones which are closest to methane, similarly to what …
We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained using the quasichemical organization of the potential distribution theorem, an approach that naturally provides the repulsive (solvophobic or cavity) and attractive (solvophilic) contributions to solvation. The solvophilic contribution is further parsed into a chemistry contribution arising from solute interaction with the solvent in the first sol…
Charge hydration asymmetry (CHA)--a characteristic dependence of hydration free energy on the sign of the solute charge--quantifies the asymmetric response of water to electric field at microscopic level. Accurate estimates of CHA are critical for understanding hydration effects ubiquitous in chemistry and biology. However, measuring hydration energies of charged species is fraught with significant difficulties, which lead to unacceptably large (up to 300%) variation in the available estimates of the CHA effect. We circumvent these difficulties by developing a framework which allows us to extr…
At room temperature, the quantum contribution to the kinetic energy of a water molecule exceeds the classical contribution by an order of magnitude. The quantum kinetic energy (QKE) of a water molecule is modulated by its local chemical environment and leads to uneven partitioning of isotopes between different phases in thermal equilibrium, which would not occur if the nuclei behaved classically. In this work, we use ab initio path integral simulations to show that QKEs of the water molecules and the equilibrium isotope fractionation ratios of the oxygen and hydrogen isotopes are sensitive pro…
Photoelectron spectroscopy experiments in ionic solutions reveal important electronic structure information, in which the interaction between hydrated ions and water solvent can be inferred. Based on many-body perturbation theory with GW approximation, we theoretically compute the quasiparticle electronic structure of chloride anion solution, which is modeled by path-integral $ab$ $initio$ molecular dynamics simulation by taking account the nuclear quantum effects (NQEs). The electronic levels of hydrated anion as well as water are determined and compared to the recent experimental photoelectr…
Nearly one third of all nitrogen oxides are removed from the atmosphere through the reactive uptake of N$_2$O$_5$ into aqueous aerosol. The primary step in reactive uptake is the rapid hydrolysis of N$_2$O$_5$, yet despite significant study, the mechanism and rate of this process are unknown. Here we use machine learning-based reactive many body potentials and methods of importance sampling molecular dynamics simulations to study the solvation and subsequent hydrolysis of N$_2$O$_5$. We find that hydrolysis to nitric acid proceeds through the coordinated fluctuation of intramolecular charge se…
Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting finite size effects can be substantial and may attenuate very slowly with increasing system size, as shown by previous work on dilute ions in bulk aqueous solution. Here we examine corrections for such effects, with an emphasis on solvation near interfaces. Our central assumption follows the perspective of Hünenberger and McCammon [J. Chem. Phys. 110, 1856 (19…
The solvation structure of protons in aqueous media is highly relevant to electric properties and to proton transport in liquids and membranes. At ambient temperature, polar liquids display structural fluctuations on femto- to picosecond time scales with a direct impact on proton solvation. We apply two-dimensional infrared (2D-IR) spectroscopy for following proton dynamics in acetonitrile/water mixtures with the Zundel cation H$_5$O$_2^+$ prepared in neat acetonitrile as a benchmark. The 2D-IR spectra of the proton transfer mode of H$_5$O$_2^+$ demonstrate stochastic large-amplitude motions i…
The Association of Zn$^{2+}$-SO$_4^{2-}$ and Mg$^{2+}$-SO$_4^{2-}$ in Aqueous MgSO$_4$/ZnSO$_4$ Hybrid Electrolytes: Insights from All-Atom Molecular Dynamics Simulations Molecular Dynamics Simulations
Path-integral ab initio molecular dynamics (PI-AIMD) calculations have been employed to probe the nature of chloride ion solvation in aqueous solution. Nuclear quantum effects (NQEs) are shown to weaken hydrogen bonding between the chloride anion and the solvation shell of water molecules. As a consequence, the disruptive effect of the anion on the solvent water structure is significantly reduced compared to what is found in the absence of NQEs. The chloride hydration structure obtained from PI-AIMD agrees well with information extracted from neutron scattering data. Inparticular, the observed…
Radiationless deactivation channels of 2-thiocytosine in aqueous environment are revisited by means of quantum-chemical simulations of excited-state absorption spectra, and investigations of potential energy surfaces of the chromophore clustered with two water molecules using the algebraic diagrammatic construction method to the second-order (ADC(2)), and multireference configuration interaction with single and double excitations (MR-CISD) methods. We argue that interactions of explicit water molecules with thiocarbonyl group might enable water-chromophore electron transfer (WCET) which leads …
The combinatorial explosion of empirical parameters in tens of thousands presents a tremendous challenge for extended Debye-Hückel models to calculate activity coefficients of aqueous mixtures of most important salts in chemistry. The explosion of parameters originates from the phenomenological extension of the Debye-Hückel theory that does not take steric and correlation effects of ions and water into account. In contrast, the Poisson-Fermi theory developed in recent years treats ions and water molecules as nonuniform hard spheres of any size with interstitial voids and includes ion-water and…
The transfer of a hydrated proton between water molecules in aqueous solution is accompanied by the large-scale structural reorganization of the environment as the proton relocates, giving rise to the Grotthus mechanism. The Zundel (H5O2+) and Eigen (H9O4+) cations are the main intermediate structures in this process. They exhibit radically different gas-phase infrared (IR) spectra, indicating fundamentally different environments of the solvated proton in its first solvation shell. The question arises: is there a least common denominator structure that explains the IR spectra of the Zundel and…
A major goal of many spectroscopic techniques is to provide comprehensive information on the local chemical environment. Electron transfer mediated decay (ETMD) is a sensitive probe of the environment since it is actively involved in this non-local radiationless decay process through electron and energy transfer steps. We report the first experimental observation of ETMD in the liquid phase. Using liquid-jet X-ray photoelectron spectroscopy we explore LiCl aqueous solution, and detect low-energy electrons unambiguously emerging from the ETMD processes of core-ionized Li+. We interpret the expe…
Recent advancements in thermogalvanic batteries offer a promising route to efficient harvesting of low-grade heat with temperatures below 100 °C. The thermogalvanic temperature coefficient α, usually referred to as effective thermopower, is the key parameter determining the power density and efficiency of thermogalvanic batteries. However, the current understanding of improving α of redox pairs remains at the phenomenological level without microscopic insights, and the development of electrolytes with high α largely relies on experimental trial and error. This work applies the free energy pert…
In this work, the solvation and electronic structure of the aqueous chloride ion solution was investigated using Density Functional Theory (DFT) based \textit{ab initio} molecular dynamics (AIMD). From an analysis of radial distribution functions, coordination numbers, and solvation structures, we found that exact exchange ($E_{\rm xx}$) and non-local van der Waals (vdW) interactions effectively \textit{weaken} the interactions between the Cl$^-$ ion and the first solvation shell. With a Cl-O coordination number in excellent agreement with experiment, we found that most configurations generate…
Using molecular dynamics simulations and methods of importance sampling, we study the thermodynamics and dynamics of sodium chloride in the aqueous premelting layer formed spontaneously at the interface between ice and its vapor. We uncover a hierarchy of timescales that characterize the relaxation dynamics of this system, spanning the picoseconds of ionic motion to the 10s-100s of nanoseconds associated with fluctuations of the liquid-crystal interface in their presence. We find that ions distort both local interfaces, incurring restoring forces that result in the ions preferentially residing…
Department of Engineering Physics and Computation, TUM School of Engineering and Design, Technical University of Munich（工程物理与计算系，TUM工程与设计学院，慕尼黑技术大学）；Atomistic Modeling Center (AMC), Munich Data Science Institute (MDSI), Technical University of Munich（原子建模中心（AMC），慕尼黑数据科学研究所（MDSI），慕尼黑技术大学）
Nuclear magnetic resonance relaxometry represents a powerful tool for extracting dynamic information. Yet, obtaining links to molecular motion is challenging for many ions that relax through the quadrupolar mechanism, which is mediated by electric field gradient fluctuations and lacks a detailed microscopic description. For sodium ions in aqueous electrolytes, we combine ab initio calculations to account for electron cloud effects with classical molecular dynamics to sample long-time fluctuations, and obtain relaxation rates in good agreement with experiments over broad concentration and tempe…
We study the solvation and electrostatic properties of bare gold (Au) nanoparticles (NPs) of $1$-$2$ nm in size in aqueous electrolyte solutions of sodium salts of various anions with large physicochemical diversity (Cl$^-$, BF$_4$$^-$, PF$_6$$^-$, Nip$^-$(nitrophenolate), 3- and 4-valent hexacyanoferrate (HCF)) using nonpolarizable, classical molecular dynamics computer simulations. We find a substantial facet selectivity in the adsorption structure and spatial distribution of the ions at the Au-NPs: while sodium and some of the anions (e.g., Cl$^-$, HCF$^{3-}$) adsorb more at the `edgy' (100…
Ion hydration structure and free energy establish criteria for understanding selective ion binding in potassium K+ ion channels, and may be significant to understanding blocking mechanisms as well. Recently, we investigated the hydration properties of Ba2+, the most potent blocker of K+ channels among the simple metal ions. Here, we use a similar method of combining ab initio molecular dynamics simulations, statistical mechanical theory, and electronic structure calculations to probe the fundamental hydration properties of Sr2+, which does not block bacterial K+ channels. The radial distributi…
The parasitic reactions associated with reduced oxygen species and the difficulty in achieving the high theoretical capacity have been major issues plaguing development of practical non-aqueous Li-O2 batteries. We hereby address the above issues by exploring the synergistic effect of 2,5-di-tert-butyl-1,4- benzoquinone and H2O on the oxygen chemistry in a non-aqueous Li-O2 battery. Water stabilizes the quinone monoanion and dianion, shifting the reduction potentials of the quinone and monoanion to more positive values (vs. Li+). When water and the quinone are used together in a (largely) non-a…
The extent of contact and solvent shared ion pairs of phosphate groups with Na$^+$, Ca$^{2+}$ and Mg$^{2+}$ ions in aqueous environment and their relevance for the stability of polyanionic DNA and RNA structures is highly debated. Employing the asymmetric phosphate stretching vibration of dimethyl phosphate (DMP), a model system of the sugar-phosphate backbone of DNA and RNA, we present linear infrared, femtosecond infrared pump-probe and absorptive 2D-IR spectra that report on contact ion pair formation via the presence of blue shifted spectral signatures. Compared to the linear infrared spec…
Protactinium ($Z$ = 91) is a very rare actinide with peculiar physico-chemical properties. Indeed, although one may naively think that it behaves similarly to either thorium or uranium by its position in the periodic table, it may in fact follow its own rules. Because of the quite small energy gap between its valence shells (in particular the 5$f$ and 6$d$ ones) and also the strong influence of relativistic effects on its properties, it is actually a challenging element for theoretical chemists. In this article, we combine experimental information, chemical arguments and standard first-princip…
Using a neural network potential (ANI-1ccx) generated from quantum data on a large data set of molecules and pairs of molecules, isothermal, constant volume simulations demonstrate that the model can be as accurate as ab initio molecular dynamics for simulations of pure liquid water and the aqueous solvation of a methane molecule. No theoretical or experimental data for the liquid phase is used to train the model, suggesting that the ANI-1ccx approach is an effective method to link high level ab initio methods to potentials for large scale simulations.
Theoretical Study of Reactivity Indices and Rough Potential Energy Curves for the Dissociation of 59 Fullerendiols in Gas-Phase and in Aqueous Solution with an Implicit Solvent Model
Metal oxide nanoparticles (NPs) are regarded as good candidates for many technological applications, where their functional environment is often an aqueous solution. The correct description of metal oxide electronic structure is still a challenge for local and semilocal density functionals, whereas hybrid functional methods provide an improved description, and local atomic function based codes such as CRYSTAL17 outperform plane wave codes when it comes to hybrid functional calculations. However, the computational cost of hybrids are still prohibitive for systems of real sizes, in a real enviro…
Transfer Learning Meets Embedded Correlated Wavefunction Theory for Chemically Accurate Molecular Simulations: Application to Calcium Carbonate Ion-Pairing
The interaction of phosphate groups with ions in an aqueous environment has a strong impact on the structure and folding processes of DNA and RNA. The dynamic variety of ionic arrangements, including both contact pairs and water separated ions, and the molecular coupling mechanisms are far from being understood. In a combined experimental and theoretical approach, we address the properties of contact ion pairs of the prototypical system dimethyl-phosphate with Na$^+$, Ca$^{2+}$, and Mg$^{2+}$ ions in water. Linear and femtosecond two-dimensional infrared (2D-IR) spectroscopy of the asymmetric …
Ion specificity and related Hofmeister effects, ubiquitous in aqueous systems, can have spectacular consequences in hydrated clays, where ion-specific nanoscale surface forces can determine large scale cohesive, swelling and shrinkage behaviors of soil and sediments. We have used a semi-atomistic computational approach and examined sodium, calcium and aluminum counterions confined with water between charged surfaces representative of clay materials, to show that ion-water structuring in nanoscale confinement is at the origin of surface forces between clay particles which are intrinsically ion-…
Excited states of polonium(IV): Electron correlation and spin-orbit coupling in the Po^{4+} free ion and in the bare and solvated [PoCl5]^- and [PoCl6]^{2-} complexes
