Static Density Functional Theory Calculations Research Articles

Reactions of 2-chloropropionyl chloride on Cu(100): C-Cl bond cleavage and formation of methylketene and its dimer.

X-ray photoelectron spectroscopy, reflection-absorption infrared spectroscopy, and temperature-programmed reaction/desorption have been employed to investigate the reaction of CH3-CHCl-C(=O)Cl on Cu (100), with the aid of density functional theory (DFT) calculations. Experimentally, CH3-CH=C=O (methylketene) is found to be the product from the dechlorination of CH3-CHCl-C(=O)Cl on Cu(100) at 120K. The CH3-CH=C=O generated on the surface would dimerize to form 2,4-dimethylcyclobutane-1,3-dione below 180K. In agreement with the experimental findings, our DFT molecular dynamics simulations demonstrate that the dechlorination of CH3-CHCl-C(=O)Cl, resulting in CH3-CH=C=O and two Cl atoms, occurs readily, completing within 0.6ps at 300K. The simulations also indicate that the cleavage of the CH-Cl bond precedes that of the C(=O)-Cl bond. The static DFT calculations suggest that the dimerization of CH3-CH=C=O primarily occurs through the coupling of two C=C bonds, which has a lower barrier of 38.08 kJ mol-1 compared to the 69.05 kJ mol-1 barrier for C=C + C=O coupling.

Coordination structures and stabilities of Am(III) adsorption complexes at kaolinite(0 0 1)-water interface

Understanding the structures and stabilities of actinide species is crucial for comprehending the sorption mechanisms at mineral–water interfaces. However, the relevant molecular-level fundamental aspects of actinide coordination chemistry at the mineral–water interface remain unclear. We herein conduct a systematic theoretical study of coordination structures and adsorption energies of Am3+ and Am(OH)2+ sorption complexes at the kaolinite(001)-water interface by integrating static density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations. Computational results show that stable outer- and inner-sphere adsorption complexes are respectively formed through hydrogen bonding and coordinate bonding with surface aluminol groups. The most stable inner-sphere species are predicted to be tridentate surface complexes with an eight-folded coordination structure in the first coordination sphere of Am(III). This work deepens the understanding of Am(III) adsorption and complexation behaviors at the mineral–water interface, providing essential insights for actinide migration in natural environments and nuclear waste disposal. The synergy between static DFT calculations for initial screening and AIMD simulations for comprehensive dynamic analysis in this work enhances the efficiency and accuracy of theoretical predictions for actinide environmental chemistry and can be helpful for the broader research fields of geochemistry and environmental science.

Ion association behaviors in the initial stage of calcium carbonate formation: An ab initio study

In this work, we performed static density functional theory calculations and ab initio metadynamics simulations to systematically investigate the association mechanisms and dynamic structures of four kinds of ion pairs that could be formed before the nucleation of CaCO3. For Ca2+–HCO3− and Ca2+–CO32− pairs, the arrangement of ligands around Ca2+ evolves between the six-coordinated octahedral structure and the seven-coordinated pentagonal bipyramidal structure. The formation of ion pairs follows an associative ligand substitution mechanism. Compared with HCO3−, CO32− exhibits a stronger affinity to Ca2+, leading to the formation of a more stable precursor phase in the prenucleation stage, which promotes the subsequent CaCO3 nucleation. In alkaline environments, excessive OH− ions decrease the coordination preference of Ca2+. In this case, the formation of Ca(OH)+–CO32− and Ca(OH)2–CO32− pairs favors the dissociative ligand substitution mechanism. The inhibiting effects of OH− ion on the CaCO3 association can be interpreted from two aspects, i.e., (1) OH− neutralizes positive charges on Ca2+, decreases the electrostatic interactions between Ca2+ and CO32−, and thus hinders the formation of the CaCO3 monomer, and (2) OH− decreases the capacity of Ca2+ for accommodating O, making it easier to separate Ca2+ and CO32− ions. Our findings on the ion association behaviors in the initial stage of CaCO3 formation not only help scientists evaluate the impact of ocean acidification on biomineralization but also provide theoretical support for the discovery and development of more effective approaches to manage undesirable scaling issues.

Modeling separation of lanthanides via heterogeneous ligand binding.

Individual lanthanide elements have physical/electronic/magnetic properties that make each useful for specific applications. Several of the lanthanides cations (Ln3+) naturally occur together in the same ores. They are notoriously difficult to separate from each other due to their chemical similarity. Predicting the Ln3+ differential binding energies (ΔΔE) or free energies (ΔΔG) at different binding sites, which are key figures of merit for separation applications, will help design of materials with lanthanide selectivity. We apply ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) to calculate ΔΔG for Ln3+ coordinated to ligands in water and embedded in metal-organic frameworks (MOFs), and ΔΔE for Ln3+ bonded to functionalized silica surfaces, thus circumventing the need for the computational costly absolute binding (free) energies ΔG and ΔE. Perturbative AIMD simulations of water-inundated simulation cells are applied to examine the selectivity of ligands towards adjacent Ln3+ in the periodic table. Static DFT calculations with a full Ln3+ first coordination shell, while less rigorous, show that all ligands examined with net negative charges are more selective towards the heavier lanthanides than a charge-neutral coordination shell made up of water molecules. Amine groups are predicted to be poor ligands for lanthanide-binding. We also address cooperative ion binding, i.e., using different ligands in concert to enhance lanthanide selectivity.

Hydration Mechanisms of Tungsten Trioxide Revealed by Water Adsorption Isotherms and First-Principles Molecular Dynamics Simulations

WO3 is one of the most interesting materials for photocatalysis due to its optical absorption in UV–vis, good charge carrier transport, and stability against photocorrosion. A detailed knowledge of the hydration state of WO3 is indispensable to gain more precise mechanistic insights into its photocatalytic activity. To the best of our knowledge, the hydration process of WO3 has been scarcely studied so far and only from a theoretical point of view, mostly by means of static density functional theory calculations. Here, we use manometric gas sorption experiments combined with extensive ab initio molecular dynamics simulations to investigate the hydration mechanisms of WO3 at room temperature. We demonstrate that water adsorbs molecularly in a two-step mechanism: the first water sublayer interacts with the under-coordinated surface tungsten atoms through electrostatic interactions, and, in a second step, a full layer is formed through hydrogen bonds established with the pre-adsorbed water molecules and with the under-coordinated surface oxygen atoms. The computed value of −90 kJ·mol–1 for the isosteric enthalpy of adsorption of the first water molecules is in excellent agreement with the experimental value estimated using the Clausius–Clapeyron approach from the experimental adsorption isotherms. The isosteric enthalpy of adsorption steadily decreases in absolute value when the surface coverage is increased to tend toward the enthalpy of condensation of water after three adsorption layers.

Entropic influence on the generation of Fe(iv)O species at mononuclear Fe(ii) sites in metal–organic frameworks

We study the oxidation of mononuclear Fe(ii) centers in MOF-74 in the presence of nitric oxide, nitrogen dioxide, nitrous oxide, dinitrous dioxide, oxygen, ozone, and hydrogen peroxide using static density-functional theory calculations and ab initio molecular dynamics simulations.

Resolving the odd-even oscillation of water dissociation at rutile TiO2(110)-water interface by machine learning accelerated molecular dynamics.

Aqueous rutile TiO2(110) is the most widely studied water-oxide interface, and yet questions about water dissociation are still controversial. Theoretical studies have systematically investigated the influence of the slab thickness on water dissociation energy (Ediss) at 1 monolayer coverage using static density functional theory calculation and found that Ediss exhibits odd-even oscillation with respect to the TiO2 slab thickness. However, less studies have accounted for the full solvation of an aqueous phase using ab initio molecular dynamics due to high computational costs in which only three, four, and five trilayer models of rutile(110)-water interfaces have been simulated. Here, we report Machine Learning accelerated Molecular Dynamics (MLMD) simulations of defect-free rutile(110)-water interfaces, which allows for a systematic study of the slab thickness ranging from 3 to 17 trilayers with much lower costs while keeping ab initio accuracy. Our MLMD simulations show that the dissociation degree of surface water (α) oscillates with the slab thickness and converges to ∼2% as the TiO2 slab becomes thicker. Converting α into dissociation free energy (ΔAdiss) and comparing with dissociation total energy Ediss calculated with a single monolayer of water, we find that the full solvation of the interfaces suppresses surface water from dissociating. It is interesting to note that the machine learning potential trained from the dataset containing exclusively the five trilayer TiO2 model exhibits excellent transferability to other slab thicknesses and further captures the oscillating behavior of surface water dissociation. Detailed analyses indicate that the central plane in odd trilayer slabs modulates the interaction between double trilayers and, thus, the bonding strength between terminal Ti and water, which affects pKa of surface water and water dissociation degree.

Molecular dynamics study of structure and reactions at the hydroxylated Mg(0001)/bulk water interface.

A molecular level understanding of the aqueous Mg corrosion mechanism will be essential in developing improved alloys for battery electrodes, automobile parts, and biomedical implants. The structure and reactivity of the hydroxylated surface is expected to be key to the overall mechanism because (i) it is predicted to be the metastable surface state (rather than the bare surface) under a range of conditions and (ii) it provides a reasonable model for the outer corrosion film/water interface. We investigate the structure, interactions, and reactivity at the hydroxylated Mg(0001)/water interface using a combination of static Density Functional Theory calculations and second-generation Car-Parrinello ab initio molecular dynamics. We carry out detailed structural analyses into, among other properties, near-surface water orientations, favored adsorption sites, and near-surface hydrogen bonding behavior. Despite the short timescale (tens of ps) of our molecular dynamics run, we observe a cathodic water splitting event; the rapid timescale for this reaction is explained in terms of near-surface water structuring lowering the reaction barrier. Furthermore, we observe oxidation of an Mg surface atom to effectively generate a univalent Mg species (Mg+). Results are discussed in the context of understanding the Mg corrosion mechanism: For example, our results provide an explanation for the catalytic nature of the Mg corrosion film toward water splitting and a feasible mechanism for the generation of the univalent Mg species often proposed as a key intermediate.

Effect of temperature on CO oxidation over Pt(111) in two-dimensional confinement.

Confined catalysis between a two-dimensional (2D) cover and metal surfaces has provided a unique environment with enhanced activity compared to uncovered metal surfaces. Within this 2D confinement, weakened adsorption and lowered activation energies were observed using surface science experiments and density functional theory (DFT) calculations. Computationally, the role of electronic and mechanical factors responsible for the improved activity was deduced only from static DFT calculations. This demands a detailed investigation on the dynamics of reactions under 2D confinement, including temperature effects. In this work, we study CO oxidation on a 2D graphene covered Pt(111) surface at 90 and 593K using DFT-based ab initio molecular dynamics simulations starting from the transition state configuration. We show that CO oxidation in the presence of a graphene cover is substantially enhanced (2.3 times) at 90K. Our findings suggest that 2D confined spaces can be used to enhance the activity of chemical reactions, especially at low temperatures.

Solution-Phase Conformational/Vibrational Anharmonicity in Comonomer Incorporation Polyolefin Catalysis.

The prediction of comonomer incorporation statistics in polyolefin catalysis necessitates an accurate calculation of free energies corresponding to monomer binding and insertion, often requiring sub-kcal/mol resolution to resolve experimental free energies. Batch reactor experiments are used to probe incorporation statistics of ethene and larger α-olefins for three constrained geometry complexes which are employed as model systems. Herein, over 6 ns of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics is performed in combination with the zero-temperature string method to characterize the solution-phase insertion barrier and to analyze the contributions from conformational and vibrational anharmonicity arising both in vacuum and in solution. Conformational sampling in the solution-phase results in 0-2 kcal/mol corrections to the insertion barrier which are on the same scale necessary to resolve experimental free energies. Anharmonic contributions from conformational sampling in the solution phase are crucial energy contributions missing from static density functional theory calculations and implicit solvation models, and the accurate calculation of these contributions is a key step toward the quantitative prediction of comonomer incorporation statistics.

Structure and interactions at the Mg(0001)/water interface: An ab initio study.

A molecular level understanding of metal/bulk water interface structure is key for a wide range of processes, including aqueous corrosion, which is our focus, but their buried nature makes experimental investigation difficult and we must mainly rely on simulations. We investigate the Mg(0001)/water interface using second generation Car-Parrinello molecular dynamics (MD) to gain structural information, combined with static density functional theory calculations to probe the atomic interactions and electronic structure (e.g., calculating the potential of zero charge). By performing detailed structural analyses of both metal-surface atoms and the near-surface water, we find that, among other insights: (i) water adsorption causes significant surface roughening (the planar distribution for top-layer Mg has two peaks separated by ≈0.6Å), (ii) strongly adsorbed water covers only ≈14 of available surface sites, and (iii) adsorbed water avoids clustering on the surface. Static calculations are used to gain a deeper understanding of the structuring observed in MD. For example, we use an energy decomposition analysis combined with calculated atomic charges to show that adsorbate clustering is unfavorable due to Coulombic repulsion between adsorption site surface atoms. Results are discussed in the context of previous simulations carried out on other metal/water interfaces. The largest differences for the Mg(0001)/water system appear to be the high degree of surface distortion and the minimal difference between the metal work function and metal/water potential of zero charge (at least compared to other interfaces with similar metal-water interaction strengths). The structural information, in this paper, is important for understanding aqueous Mg corrosion, as the Mg(0001)/water interface is the starting point for key reactions. Furthermore, our focus on understanding the driving forces behind this structuring leads to important insights for general metal/water interfaces.

Insights into the thermal decomposition of plutonium(IV) oxalate – a DFT study of the intermediate structures

The thermal decomposition of plutonium oxalate to oxide is one of the most studied reactions in actinide chemistry but the intermediates have been the subject of debate for decades. Recent experimental data suggest that the decomposition of Pu(IV) oxalate in air undergoes dehydration first, then reduction to Pu(III) oxalate. The precise structural modifications that take place are unknown as experiments have not been able to fully characterize the intermediates at the microscopic level. To rectify this, we employed solid state density functional theory calculations at the PBE-D3 level with a Hubbard U correction to model the structures and energetics of potential dehydrated Pu(IV) and Pu(III) oxalate intermediate compounds. Based on the theoretical study presented here, the anhydrous analogues of the known hydrated Pu(IV) and Pu(III) oxalates are the preferred crystal structures formed through an overall exothermic reaction process. However, decomposition could proceed through the formation of a higher energy, more complicated 3D lattice structure with frustrated oxalate binding. It is expected that the intermediates presented here could be identified using spectroscopic techniques to enable further insight into the reaction mechanism.

Experiments and Direct Dynamics Simulations That Probe η2-Arene/Aryl Hydride Equilibria of Tungsten Benzene Complexes.

Key steps in the functionalization of an unactivated arene often involve its dihaptocoordination by a transition metal followed by insertion into the C-H bond. However, rarely are the η2-arene and aryl hydride species in measurable equilibrium. In this study, the benzene/phenyl hydride equilibrium is explored for the {WTp(NO)(PBu3)} (Bu = n-butyl; Tp = trispyrazoylborate) system as a function of temperature, solvent, ancillary ligand, and arene substituent. Both face-flip and ring-walk isomerizations are identified through spin-saturation exchange measurements, which both appear to operate through scission of a C-H bond. The effect of either an electron-donating or electron-withdrawing substituent is to increase the stability of both arene and aryl hydride isomers. Crystal structures, electrochemical measurements, and extensive NMR data further support these findings. Static density functional theory calculations of the benzene-to-phenyl hydride landscape suggest a single linear sequence for this transformation involving a sigma complex and oxidative cleavage transition state. Static DFT calculations also identified an η2-coordinated benzene complex in which the arene is held more loosely than in the ground state, primarily through dispersion forces. Although a single reaction pathway was identified by static calculations, quasiclassical direct dynamics simulations identified a network of several reaction pathways connecting the η2-benzene and phenyl hydride isomers, due to the relatively flat energy landscape.

Mechanisms of hydrogen atom interactions with MoS2 monolayer

The mechanisms of H atoms interactions with single-layer MoS2, a two-dimensional transition metal dichalcogenide, are studied by static and dynamic DFT (density functional theory) modeling. Adsorption energies for H atoms on MoS2, barriers for H atoms migration and recombination on hydrogenated MoS2 surface and effects of H atoms adsorptions on MoS2 electronic properties and sulfur vacancy production were obtained by the static DFT calculations. The dynamic DFT calculations give insight into the dynamics of reactive interactions of incident H atoms with hydrogenated MoS2 at H atoms energies in the range of 0.05–1 eV and elucidate the competitive mechanism of hydrogen adsorption and recombination that limits hydrogen surface coverage at the level of 30%. Various pathways of S-vacancies production and H atoms losses on MoS2 are calculated and the effects of MoS2 temperature on these processes are estimated and discussed.

Conformational diversity of the THF molecule in N2 matrix by means of FTIR matrix isolation experiment and Car-Parrinello molecular dynamics simulations.

Tetrahydrofuran (THF) is a widely used chemical compound, in particular as a solvent in organic and inorganic synthesis. The THF molecule has also an interesting property, namely, undergoes pseudorotation, similar to the case of the cyclopentane. Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. We study the influence of the molecular environment (N2) on the Cs-C2 equilibrium of tetrahydrofuran in the THF@N2 system utilizing nitrogen matrix isolation infrared spectroscopy. We observe a different ratio between envelope (Cs) and twisted (C2) conformations with respect to a change of the temperature. FTIR experimental studies are supported by the results of the static density functional theory calculations and Car-Parrinello molecular dynamics simulations. We focus on the dynamics of the pseudorotation process, in particular, the lifetime of the THF conformations and their mutual rearrangements. On the basis of the THF@N2 matrix model, with explicit nitrogen molecules, the anharmonic infrared spectra are generated from the Fourier transformation of the dipole moment autocorrelation function.

Excited state charge distribution and bond expansion of ferrous complexes observed with femtosecond valence-to-core x-ray emission spectroscopy.

Valence-to-core x-ray emission spectroscopy (VtC XES) combines the sample flexibility and element specificity of hard x-rays with the chemical environment sensitivity of valence spectroscopy. We extend this technique to study geometric and electronic structural changes induced by photoexcitation in the femtosecond time domain via laser-pump, x-ray probe experiments using an x-ray free electron laser. The results of time-resolved VtC XES on a series of ferrous complexes [Fe(CN)2n(2, 2'-bipyridine)3-n]-2n+2, n = 1, 2, 3, are presented. Comparisons of spectra obtained from ground state density functional theory calculations reveal signatures of excited state bond length and oxidation state changes. An oxidation state change associated with a metal-to-ligand charge transfer state with a lifetime of less than 100 fs is observed, as well as bond length changes associated with metal-centered excited states with lifetimes of 13 ps and 250 ps.

Environment-Sensitive Azepane-Substituted β-Diketones and Difluoroboron Complexes with Restricted C–C Bond Rotation

Luminescent β-diketones (bdks) and difluoroboron coordinated complexes (BF₂bdks) exhibit many environment-sensitive properties, such as solvatochromism, viscochromism, aggregation-induced emission (AIE), and thermal and mechanochromic luminescence (ML). In a previous study, an azepane-substituted bdk ligand (L1) and boron dye (D1) showed noteworthy luminescence properties but low quantum yields (Φ, L1: 0.26; D1: 0.02) due to free intramolecular bond rotation and twisted intramolecular charge transfer state formation with associated nonradiative decay. Thus, in order to improve the quantum yields, an azepane-substituted bdk ligand (L2) and boron complex (D2) with restricted C–C bond rotation were synthesized, and various luminescence properties were investigated. Restricting bond rotation blue-shifted absorptions and emissions, increased lifetimes, and greatly improved quantum yields (Φ, L2: 0.47; D2: 0.83). Excited state density functional theory calculations displayed twisted geometries for L1 and D1 but more planar geometries for L2 and D2. All compounds showed red-shifted emissions in more polar solvents. For viscochromism, L1 and D1 exhibited higher emission intensity in more viscous media. However, L2 and D2 did not show dramatic viscochromism, substantiating the relation between viscosity sensitivity and intramolecular bond twisting. Additionally, while both ligands showed quenched emission upon aggregation, the dyes exhibited AIE regardless of bond restriction. Thermal and ML studies showed a more dramatic emission shift for L2 than L1 between thermally annealed and melt-quenched states. In summary, the quantum yields of the azepane-substituted bdk ligand and boron dye were successfully improved by restricting the intramolecular C–C bond rotation, making various luminescence properties more promising for environment-sensitive applications.

Why the Reactive Oxygen Species of the Fenton Reaction Switches from Oxoiron(IV) Species to Hydroxyl Radical in Phosphate Buffer Solutions? A Computational Rationale.

It has been shown that the major reactive oxygen species (ROS) generated by the aqueous reaction of Fe(II) and H2O2 (i.e., the Fenton reaction) are high-valent oxoiron(IV) species, whereas the hydroxyl radical plays a role only in very acidic conditions. Nevertheless, when the Fenton reaction is conducted in phosphate buffer solutions, the resulting ROS turns into hydroxyl radical even in neutral pH conditions. The present density functional theory (DFT) study discloses the underlying principle for this phenomenon. Static and dynamic DFT calculations indicate that in phosphate buffer solutions, the iron ion is highly coordinated by phosphoric acid anions. Such a coordination environment substantially raises the pKa of coordinated water on Fe(III). As a consequence, the Fe(III)–OH intermediate, resulting from the reductive decomposition of H2O2 by ferrous ion is relatively unstable and will be readily protonated by phosphoric acid ligand or by free proton in solution. These proton-transfer reactions, which become energetically favorable when the number of phosphate coordination goes up to three, prevent the Fe(III)–OH from hydrogen abstraction by nascent •OH to form Fe(IV)=O species. On the basis of this finding, a ligand design strategy toward controlling the nature of ROS produced in the Fenton reaction is put forth. In addition, it is found that while phosphate buffers facilitate •OH radical generation in the Fenton reaction, phosphoric acid anions can act as •OH radical scavengers through hydrogen atom transfer reactions.

Charge transfer excitation energies from ground state density functional theory calculations.

Calculating charge transfer (CT) excitation energies with high accuracy and low computational cost is a challenging task. Kohn-Sham density functional theory (KS-DFT), due to its efficiency and accuracy, has achieved great success in describing ground state problems. To extend to excited state problems, our group recently demonstrated an approach with good numerical results to calculate low-lying and Rydberg excitation energies of an N-electron system from a ground state KS or generalized KS calculations of an (N - 1)-electron system via its orbital energies. In the present work, we explore further the same methodology to describe CT excitations. Numerical results from this work show that performance of conventional density functional approximations (DFAs) is not as good for CT excitations as for other excitations due to the delocalization error. Applying localized orbital scaling correction (LOSC) to conventional DFAs, a recently developed method in our group to effectively reduce the delocalization error, can improve the results. Overall, the performance of this methodology is better than time dependent DFT (TDDFT) with conventional DFAs. In addition, it shows that results from LOSC-DFAs in this method reach similar accuracy to other methods, such as ΔSCF, G0W0 with Bethe-Salpeter equations, particle-particle random phase approximation, and even high-level wavefunction methods like CC2. Our analysis shows that the correct 1/R trend for CT excitation can be captured from LOSC-DFA calculations, stressing that the application of DFAs with the minimal delocalization error is essential within this methodology. This work provides an efficient way to calculate CT excitation energies from ground state DFT.

CO2 Capture via Crystalline Hydrogen-Bonded Bicarbonate Dimers

Summary Limiting global temperature rises is increasingly dependent on the development of energy-efficient carbon-capture methods. Here, we report a simple CO2-separation cycle using an aqueous bis(iminoguanidine) (BIG) sorbent that reacts with CO2 and crystallizes into an insoluble bicarbonate salt. X-ray diffraction analysis of the bicarbonate crystals revealed “anti-electrostatic” hydrogen-bonded (HCO3−)2 dimers, stabilized by guanidinium cations and water. Mild heating of the crystals releases the CO2 and regenerates the BIG sorbent quantitatively, thereby closing the CO2-separation cycle. Experimental and computational investigations support a CO2-release mechanism consisting of surface-initiated low-barrier proton transfer from guanidinium groups to bicarbonate anions with the formation of carbonic acid dimers, followed by CO2 and H2O release in the rate-limiting step, with a measured activation energy of 102 ± 12 kJ/mol. The minimum energy required for sorbent regeneration is 151.5 kJ/mol CO2, which is 24% lower than the regeneration energy of monoethanolamine, a benchmark industrial sorbent.