Ab Initio Molecular Dynamics Investigation Research Articles

Ab Initio Molecular Dynamics Investigation of Water and Butanone Adsorption on UiO-66 with Defects.

Volatile organic compounds (VOCs) are harmful chemicals that are found in minute quantities in the atmosphere and are emitted from a variety of industrial and biological processes. They can be harmful to breathe or serve as biomarkers for disease detection. Therefore, capture and detection of VOCs is important. Here, we have examined if the Zr-based UiO-66 metal-organic framework (MOF) can be used to capture butanone─a well-known VOC. Toward that end, we have performed Born-Oppenheimer ab initio molecular dynamics (AIMD) at 300 and 500 K to probe the energetics and molecular interactions between butanone [CH3C(O)CH2CH3] and open-cage Zr-UiO-66. Such interactions were systematically interrogated using three MOF structures: defective MOF with a missing 1,4-benzene-dicarboxylate linker and two H2O; pristine MOF with two H2O; and pristine dry MOF. These structures were loaded with one and four molecules of butanone to examine the effect of concentration as well. One-molecule loading interacted favorably with the defective structure at 300 K, only. In comparison, interactions with four-molecule loading were energetically favorable for all conditions. Persistent hydrogen bonds between the O atom of butanone, H2O, and μ3-OH hydroxyl attachments at Zr nodes substantially contributed to the intermolecular interactions. At higher loadings, butanone also showed a pronounced tendency to diffuse into the adjoining cages of Zr-UiO-66. The effect of such movement on interaction energies was rationalized using simple statistical mechanics-based models of interacting and noninteracting gases. Broadly, we learn that the presence of prior moisture within the interstitial cages of Zr-UiO-66 significantly impacts the adsorption behavior of butanone.

Ab Initio Molecular Dynamics Investigation on the Permeation of Sodium and Chloride Ions Through Nanopores in Graphene and Hexagonal Boron Nitride Membranes.

Nanoporous membranes promise energy-efficient water desalination. Hexagonal boron nitride (h-BN), like graphene, exhibits outstanding physical and chemical properties, making it a promising candidate for water treatment. We employed Car-Parrinello molecular dynamics simulations to establish an accurate modeling of Na+ and Cl- permeation through hydrogen passivated nanopores in graphene and h-BN membranes. We demonstrate that ion separation works well for the h-BN system by imposing a barrier of 0.13 eV and 0.24 eV for Na+ and Cl- permeation, respectively. In contrast, for permeation of the graphene nanopore, the Cl- ion faces a minimum of energy of 0.68 eV in the nanopore plane and is prone toward blockade of the nanopore, while the Na+ ion experiences a slight minimum of 0.03 eV. Overall, the desalination performance of h-BN nanopores surpasses that of their graphene counterparts.

An ab initio molecular dynamics investigation of the behaviour of amorphous substances in anodic aluminium oxide under electric field

In order to elucidate the diffusion behaviour of ions in alumina during the anodic alumina process, the effects of electric field strength, hydration content, and electrolyte on amorphous alumina and hydrated alumina were studied using ab initio molecular dynamics. The results show that the diffusion rate of ions in alumina increases with the increase in electric field strength, but there is an extreme value. The maximum diffusion rate of Al ions in alumina monohydrate is 21.8 μm2/ms/V, while in alumina trihydrate, it is 16.7 μm2/ms/V. The ionic diffusion rate of hydrated alumina is one to two orders of magnitude larger than that of anhydrous amorphous alumina due to the effect of the drag of H ions, which reduces the migration activation energy. Electrolytes also affect the diffusion rate of alumina through the action of H ions. The increase in H ions will not only enhance the diffusion rate of hydrated alumina but also render the hydrous compound more vulnerable to breakdown.

Interfacial structures and dissociation reactions of protic ionic liquids on Li metal surface: A combined first-principles and ab initio molecular dynamics investigation

Interfacial structures and dissociation reactions of protic ionic liquids (PILs) comprising five protic cations with two common sulfonylimide anions on the Li(001) surface were investigated using first-principles calculations and ab initio molecular dynamics simulations. Both the anions rapidly decompose, yielding LiF, Li2O and Li2S species as well as large fragments, e.g. NSO2CF3 and NSO2. Particularly, the proton attached to the N atom generally segregates from the cations and generates LiOH with the O atom from the anions and the surface Li atom. In addition, detailed comparisons of reaction mechanisms between PIL-based and AIL-based systems were also made.

Understanding of ammonium salts under-deposit corrosion: Electrochemical and AIMD investigations

In-situ electrochemical experiments and ab initio molecular dynamics (AIMD) simulations are combined to investigate the under-deposit corrosion and hygroscopicity of ammonium salts on SAE 1020 steel interdigital electrodes. The findings indicate that the hygroscopicity of ammonium salts influences the evolution of the interface and the accumulation of the product film. The corresponding simulations reveal that the hydrolysis of NH4+ leads to the generation of a proton transfer chain, resulting in an elevation of H+ concentration. This hydrolysis behavior is effectively catalyzed on the Fe(1 0 0) surface, promoting the occurrence of anodic adsorption and cathodic hydrogen evolution reaction, thereby inducing corrosion.

Ab initio molecular dynamics investigation of the Pt(111)-water interface structure in an alkaline environment with high surface OH-coverages.

In this study, we investigate the structure of the Pt(111)-water interface in an alkaline environment with large OH coverages of 1/3, 2/3 and 1 monolayer using a large well-equilibrated system. We observe that the OH coverage influences both the orientational distribution of the water molecules and their density, with more structure associated with higher coverage. At the same time, there is evidence of a highly dynamic hydrogen bond network on the lower coverage systems with substantial exchange of water between the surface and the solvent. In addition to OH and H2O species, which are preferentially located at the top sites, the 1/3 and 2/3 monolayer surfaces also contain O atoms, which are relatively stable and prefer the hollow sites. In contrast, the 1 monolayer surface shows none of these dynamics, and is unlikely to be active. The dynamic coexistence of O, OH and H2O on Pt(111) electrodes in alkaline conditions necessitates the investigation of several possible reaction paths for processess like ORR and water splitting. Finally, the exchange processes observed between the solvent and the interface underscore the need to explicitly include liquid water in simulations of systems similar to Pt(111).

Ab Initio Molecular Dynamics Investigation of the Solvation States of Hydrated Ions in Confined Water.

Ionic transport in nanoscale channels with a critical size comparable to that of ions and solutes exhibits exceptional performance in water desalination, ion separation, electrocatalysts, and supercapacitors. However, the solvation states (SSs), i.e., the hydration structures and probability distribution, of hydrated ions in nanochannels differ from those in the bulk and the perspective of continuum theory. In this work, we conduct ab initio enhanced-sampling atomistic simulations to investigate the ion-specific SSs of monovalent ions (including Li+, Na+, K+, F-, Cl-, and I-) in the graphene channel with a width of 1 nm. Our findings highlight that the SSs of those ions are primarily determined by ion-water hydration, where ion-wall interactions play a minor role. The distribution of ions in layered confined water is a result of ion-specific hydration, which arises from the synergy of entropy and enthalpy. The free energy barriers for transitions between SSs are on the order of 1kBT, allowing for modulation through applying external fields or modifying surface properties. As the ion-wall interaction strengthens, as observed in vermiculite and carbides and nitrides of transition metal channels, the probability of near-wall SSs increases. These results help to improve the performance of nanofluidic devices and provide crucial insights for developing accurate force fields of molecular simulations or advanced theoretical approaches for ion dynamics in confined channels.

Interaction of serotonin and histamine with water and ethanol: Evidence from theoretical investigations

This manuscript focuses on studying the interactions between two crucial neurotransmitters, serotonin and histamine, and common solvents such as water and ethanol. By examining the stable conformers of serotonin and histamine, we investigate their interactions with water and ethanol at various reactive sites, calculating the corresponding binding energies. To understand the qualitative solvent interaction, we employ RDG analysis and estimate the specific contributions to different types of interactions through energy decomposition analysis. We confirm the nature of solvent interaction using approaches based on natural bond orbitals and atoms in molecules. The optimization processes are carried out using PBE0-D3/def2-TZVP, while the energy decomposition analysis utilizes the DLPNO-CCSD(T) level. Additionally, we explore the solvation dynamics in detail through ab initio molecular dynamics (AIMD). Our findings indicate that the interaction energy between serotonin and water (pore2) surpasses that of histamine and water (pore1). Notably, hydrogen bonding plays a significant role in these interactions, as revealed by QTAIM analysis. Furthermore, our results indicate that ethanol exhibits approximately 16 times greater interaction with these molecules compared to water. AIMD investigations further demonstrate that the serotonin-ethanol system exhibits higher dynamic stability compared to the histamine system.

Atomic Ordering and Interfacial Interaction at Liquid-Mg/SiC{0 0 0 1} Interfaces: An Ab Initio Molecular Dynamics Study

We present the results of ab initio molecular dynamics investigations on the atomic ordering and chemical interactions at the interfaces between liquid Mg and SiC{0 0 0 1} interfaces. The simulations reveal distinct borders between the SiC substrates and liquid Mg. The liquid Mg atoms adjacent to the substrates are bonded to the outmost C/Si atoms and are positively charged. The terminating Mg layers contain a variety of atomic vacancies, being topologically rough. The liquid Mg atoms adjacent to the substrates display unusual prenucleation phenomenon with strong layering but weak in-plane ordering. The obtained information here is helpful to get insight into the formation and interfacial interactions in the SiC joined nano-sized magnesium matrix composites and the role of SiC particles as potential nucleation sites during solidification, and further helps understand interfacial interactions at the grain boundaries in ceramic/metal composites and welded parts, etc. in general.

Solvent Organization around Methane Dissolved in Archetypal Reline and Ethaline Deep Eutectic Solvents as Revealed by AIMD Investigation

Because of the rising concentration of harmful greenhouse gases like methane in the atmosphere, researchers are striving for developing novel techniques for capturing these gases. Recently, neoteric liquids such as deep eutectic solvents (DESs) have emerged as an efficient means of sequestration of methane. Herein, we have performed ab initio molecular dynamics (AIMD) simulations to elucidate the solvation structure around a methane molecule dissolved in reline and ethaline DESs. We aim to elicit the structural organization of different constituents of the DESs in the vicinity of methane, particularly highlighting the key interactions that stabilize such gases in DESs. We observe quite different solvation structures of methane in the two DESs. In ethaline, chloride ions play an active role in solvating methane. Instead, in reline, chloride ions do not interact much with the methane molecule in the first solvation shell. In reline, choline cations approach the methane molecule from their hydroxyl group side, whereas urea molecules approach methane from their carbonyl oxygen as well as amide group sides. In ethaline, ethylene glycol and Cl- dominate the nearest neighbor solvation structure around the methane molecule. In both the DESs, we do not observe any significant methane-DES charge transfer interactions, apart from what is present between choline cation and Cl- anion.

The chemical environment and structural ordering in liquid Mg-Y-Zn system: An ab-initio molecular dynamics investigation of melt for the formation mechanism of LPSO structure

In an effort to clarify the formation mechanism of LPSO structure in Mg-Y-Zn alloy, the chemical environment and structural ordering in liquid Mg-rich Mg-Y-Zn system are investigated with the aid of ab-initio molecular dynamics simulation. In liquid Mg-rich Mg-Y alloys, the strong Mg-Y interaction is determined, which promotes the formation of fivefold symmetric local structure. For Mg-Zn alloys, the weak Mg-Zn interaction results in the fivefold symmetry weakening in the liquid structure. Due to the coexistence of Y and Zn, the strong attractive interaction is introduced in liquid Mg-Y-Zn ternary alloy, and contributes to the clustering of Mg, Y, Zn launched from Zn. What is more, the distribution of local structures becomes closer to that in pure Mg compared with that in binary Mg-Y and Mg-Zn alloys. These results should relate to the origins of the Y/Zn segregation zone and close-packed stacking mode in LPSO structure, which provides a new insight into the formation mechanism of LPSO structure at atomic level.

Ab initio molecular dynamics investigation of [formula omitted]-(U,Zr) structural and thermal properties as a function of temperature and composition

Uranium in its metallic form is considered as a fuel for sodium fast reactors due to its higher thermal conductivity and high fissile material density relative to UO2 fuel. The metal is alloyed with zirconium to increase its stability at high temperatures and increase its solidus temperature. This work uses ab initio molecular dynamics to perform an evaluation of the mechanical and thermophysical properties of the γ-(U,Zr) system at temperatures between 1000 K and 1400 K. Among these properties are the equilibrium volume, bulk modulus, molar heat capacity, heat of formation, and the surface energy. The obtained results are compared to experimental data and previous computational work available in the literature. This is the first study of γ-(U,Zr) utilizing ab initio molecular dynamics, and reduces thermophysical property knowledge gaps that are currently present in the literature.

Ab-Initio Molecular Dynamics investigation of gas adsorption on α-quartz (001) for CO2 enhanced natural gas recovery

In this work, the interaction of methane and carbon dioxide on α-quartz with surface 001, with a siloxane termination (dense) surface was investigated by means of Ab-Initio Molecular Dynamics. Different temperatures were addressed, ranging from 298 to 423 K. For completeness, pure and mixed compositions were considered, to replicate the conditions present during Enhanced Gas Recovery processes by CO 2 injection. When considering pure compositions, both gases stick to the surface, except for the highest temperature (423 K), where most of CH 4 tend to desorb. When mixed compositions are addressed, carbon dioxide generally hinders the interaction of methane, except for high temperature, where both gases are equally distributed both close and far from the surface. To the goal of improving EGR processes on sandstone reservoirs, this work shows that a temperature of 323 K offers the best efficiency by increasing the interaction of carbon dioxide and pushing methane out of the surface. At the same time, this study would not recommend the use of very high temperatures (T > 373 K) and excessive concentration of CO 2 , as the majority of this gas would desorb, without improving methane extraction in a meaningful way. • With pure compositions, CH 4 possesses high mobility on α-quartz compared to CO 2 , though both gases are characterized by the same interaction. • At room temperature and mixed composition, both gases interact strongly with the surface, so the extraction of methane is usually inefficient. • A temperature of 323 K offers the best EGR efficiency, improving carbon dioxide interaction with the surface and pushing methane out. • Very high temperatures and excessive concentration of CO 2 could reduce gas recovery and sequestration.

Ab initio molecular dynamics investigation of Cs adsorption on Mo(0 0 1): Beyond a single monolayer coverage

Ab initio molecular dynamics simulations have been conducted to investigate the properties of cesiated surface Mo(0 0 1) at the typical operating temperature of the negative hydrogen ion sources (423 K). In the systems with sub-monolayer Cs coverages (θ), both the mobility and ionicity of the adatoms decrease with θ. The computed shape of the work function (ϕ) dependence on θ agrees with experiment, although our simulations underestimate the extent of the ϕ variation. In multilayer depositions, cesium forms two phases exhibiting distinctly different properties. The atoms laid directly on the substrate form an ordered layer with the atomic density and charges similar to those of the saturated monolayer (ML). A disordered phase with a much lower particle density is formed by the atoms stacked on the ordered layer and induces a positive shift in ϕ by 0.32 eV compared to ML. A similar behavior is observed for the Cs(0 0 1) and Cs(1 1 0) surfaces used as models for thick Cs depositions. The work function determined for multilayer Cs depositions at T = 423 K is nearly independent of the substrate face and of the presence/absence of Mo, indicating that ϕ of such systems is fully determined by the disordered surface phase.

Ab initio Molecular Dynamics Investigations of the Speciation and Reactivity of Deep Eutectic Electrolytes in Aluminum Batteries

Invited for this month's cover is the Section for Atomic Scale Materials Modelling led by Prof. Tejs Vegge at the Department of Energy Conversion and Storage, Technical University of Denmark. The central image of the cover picture illustrates one of the chemical reaction mechanisms observed in a deep eutectic electrolyte formed by AlCl3 and urea. This is a promising electrolyte for inexpensive and environmentally friendly next-generation batteries based on aluminum. We have developed the computational techniques needed to identify chemical species and track reaction mechanisms across an ab initio molecular dynamics trajectory. The reaction mechanisms and speciation observed help to gain more insight in the development of such batteries. The Full Paper itself is available at 10.1002/cssc.202100163.

Front Cover: Ab initio Molecular Dynamics Investigations of the Speciation and Reactivity of Deep Eutectic Electrolytes in Aluminum Batteries (ChemSusChem 9/2021)

Front Cover: Ab initio Molecular Dynamics Investigations of the Speciation and Reactivity of Deep Eutectic Electrolytes in Aluminum Batteries (ChemSusChem 9/2021)

Ab initio Molecular Dynamics Investigations of the Speciation and Reactivity of Deep Eutectic Electrolytes in Aluminum Batteries.

Deep eutectic solvents (DESs) have emerged as an alternative for conventional ionic liquids in aluminum batteries. Elucidating DESs composition is fundamental to understand aluminum electrodeposition in the battery anode. Despite numerous experimental efforts, the speciation of these DESs remains elusive. This work shows how ab initio molecular dynamics (AIMD) simulations can shed light on the molecular composition of DESs. For the particular example of AlCl3 :urea, one of the most popular DESs, we carried out a systematic AIMD study, showing how an excess of AlCl3 in the AlCl3 :urea mixture promotes the stability of ionic species vs neutral ones and also favors the reactivity in the system. These two facts explain the experimentally observed enhanced electrochemical activity in salt-rich DESs. We also observe the transfer of simple [AlClx (urea)y ] clusters between different species in the liquid, giving rise to free [AlCl4 ]- units. The small size of these [AlCl4 ]- units favors the transport of ionic species towards the anode, facilitating the electrodeposition of aluminum.

Ab initio molecular dynamics assessment of thermodynamic and transport properties in (K,Li)Cl and (K, Na)Cl molten salt mixtures

Molten salt mixtures are integral part of highly important technological applications such as nuclear reactors. However, due to inherent difficulties associated with experiment at high temperatures and the intrinsic complexity of liquid-phase multi-component systems, understanding their properties at a molecular level remains a challenge. Here, we report on an ab initio molecular dynamics investigation on structural, electronic, transport, and thermal properties of two common molten salt mixtures, (K, Li)Cl and (K,Na)Cl, at five different compositions and three temperatures. Most of the properties were found to depend on both composition and temperature. While properties, like atomic charges, show additive behaviors, other properties, such as electrical conductivity, show considerable deviations from additivity. We shall show that the mixing of the molten salt mixtures is mainly driven by entropy, and that the KCl and LiCl mix better than KCl and NaCl. Our computational results are in general consistent with available experimental data. Comparison with available theoretical data is also provided.

Solvent effect on the 195Pt NMR properties in pyridonate-bridged PtIII dinuclear complex derivatives investigated by ab initio molecular dynamics and localized orbital analysis.

An ab initio molecular dynamics investigation of the solvent effect (water) on the structural parameters, 195Pt NMR spin-spin coupling constants (SSCCs) and chemical shifts of a series of pyridonate-bridged PtIII dinuclear complexes is performed using Kohn-Sham (KS) Car-Parrinello molecular dynamics (CPMD) and relativistic hybrid KS NMR calculations. The indirect solvent effect (via structural changes) has a dramatic effect on the 1JPtPt SSCCs. The complexes exhibit a strong trans influence in solution, where the Pt-Pt bond lengthens with increasing axial ligand σ-donor strength. In the diaqua complex, where the solvent effect is more pronounced, the SSCCs averaged for CPMD configurations with explicit plus implicit solvation agree much better with the experimental data, while the calculations for static geometry and CPMD unsolvated configurations show large deviations with respect to experiment. The combination of CPMD with hybrid KS NMR calculations provides a much more realistic computational model that reproduces the large magnitudes of 1JPtPt and 195Pt chemical shifts. An analysis of 1JPtPt in terms of localized and canonical orbitals shows that the SSCCs are driven by changes in the s-character of the natural atomic orbitals of Pt atoms, which affect the 'Fermi contact' mechanism.

Tautomeric Equilibrium in Condensed Phases.

We present an ab initio molecular dynamics (MD) investigation of the tautomeric equilibrium for the aqueous solutions of glycine and acetone under realistic experimental conditions. Metadynamics is used to accelerate proton migration among tautomeric centers. Due to the formation of complex water-ion structures involved in the proton dynamics in the aqueous environment, standard enhanced sampling approaches may face severe limitations in providing a general description of the phenomenon. Recently, we have developed a set of collective variables (CVs) designed to study protons transfer reactions in complex condensed systems [Grifoni, E. Proc. Natl. Acad. Sci. U.S.A. 2019, 116, 4054 4057]. In this work, we applied this approach to study proton dissociation dynamics leading to tautomeric interconversion of biologically and chemically relevant prototypical systems, namely, glycine and acetone in water. Although relatively simple from a chemical point of view, the results show that even for these small systems, complex reaction pathways and nontrivial conversion dynamics are observed. The generality of our method allows obtaining these results without providing any prior information on the dissociation dynamics but only the atomic species that can exchange protons in the process. Our results agree with literature estimates and demonstrate the general applicability of this method in the study of tautomeric reactions.