Car-Parrinello Molecular Dynamics Simulations Research Articles

Hydrogen bridges of polycyclic aromatic systems with O-H···O bonds — a gas-phase vs. solid-state Car-Parrinello study

The current study belongs to a series of investigations of polycyclic aromatic compounds containing intramolecular hydrogen bonds. Close proximity of the coupled aromatic system and hydrogen bridges gives rise to resonance-assisted hydrogen bonding phenomena. Substituted naphthols are ideally suited for this kind of investigation. The parent compound, 1-hydroxy-8-methoxy-3-methylnaphthalene, and its derivative, 1-bromo-5-hydroxy-4-isopropoxy-7-methylnaphthalene, both with known crystal structure, are investigated. Car-Parrinello molecular dynamics (CPMD) is chosen as a theoretical background for this study. Gas phase and solid state simulations are carried out. The effect of Grimme’s dispersion corrections is also included. The report presents time evolution of structural parameters, spectroscopic signatures based on the CPMD simulations, and comparison with available experimental data. We show that the proton transfer phenomena do not occur within the simulations, which is consistent with evaluation based on the acidity of the donor and acceptor sites. The effects of the substitution in the aromatic system and change of the environment (gas vs. condensed phase) are of similar magnitude.

UO2(NH3)5]Br2·NH3: synthesis, crystal structure, and speciation in liquid ammonia solution by first-principles molecular dynamics simulations.

Pentaammine dioxido uranium(VI) dibromide ammonia (1/1), [UO2(NH3)5]Br2·NH3, was synthesized in the form of yellow crystals by the reaction of uranyl bromide, UO2Br2, with dry liquid ammonia. The compound crystallizes orthorhombic in space group Cmcm and is isotypic to [UO2(NH3)5]Cl2·NH3 with a = 13.2499(2), b = 10.5536(1), c = 8.9126(1) Å, V = 1246.29(3) Å(3) and Z = 4 at 123 K. The UO2(2+) cation is coordinated by five ammine ligands and the coordination polyhedron can be best described as pentagonal bipyramid. Car-Parrinello molecular dynamics simulations are reported for [UO2(NH3)5](2+) in the gas phase and in liquid NH3 solution (using the BLYP density functional). According to free-energy simulations, solvation by ammonia has only a small effect on the uranyl-NH3 bond strength.

Estimating successive pKa values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers

Estimation of the dissociation constant, or pKa, of weak acids continues to be a central goal in theoretical chemistry. Here we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free energy profile of the dissociation reaction can provide reasonable estimates of the successive pKa values of polyprotic acids. We use the distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic group as the collective variable to explore the free energy profile of the dissociation process. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. Two distinct minima corresponding to the dissociated and un-dissociated states of the acid are observed and the difference in their free energy values provides the estimate for pKa, the acid dissociation constant. We show that the method predicts the pKa value of benzoic acid in good agreement with experiment and then show using phthalic acid (benzene dicarboxylic acid) as a test system that both the first and second pKa values as well, as the subtle difference in their values for different isomers can be predicted in reasonable agreement with experimental data.

Tuning the reactivity of a dissociative force field: proton transfer properties of aqueous H3O(+) and their dependence on the three-body interaction.

The proton transfer properties of the dissociative water potential developed by Garofalini et al. were closely examined by carefully analyzing the pairwise screening functions of the three-body interaction. It was shown that a simultaneous adjustment of the exponential screening factor and the three-body cutoff distance enables a selective adjustment of the diffusive properties of an excess proton, while at the same time structural and other dynamical data remain unaffected to a large extend. To investigate proton transfer properties without the influence of nuclear quantum effects, deuterated systems have been investigated in addition to their hydrogen counterparts. It was shown that the suggested parameter set A leads to significantly improved diffusion coefficients and proton hopping rates. Comparison of proton transfer correlation functions to simulation data obtained from Car-Parrinello molecular dynamics simulations confirms the improved performance of the adjusted parametrization.

Dissociation constants of weak acids from ab initio molecular dynamics using metadynamics: influence of the inductive effect and hydrogen bonding on pKa values.

The theoretical estimation of the dissociation constant, or pKa, of weak acids continues to be a challenging field. Here, we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pKa value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pKa. We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pKa values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pKa values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pKa values.

Interplay of Orientational Order and Electronic Structure in Methylammonium Lead Iodide: Implications for Solar Cell Operation

We report on ab initio electronic structure and Car–Parrinello molecular dynamics simulations for several structural models of the prototype MAPbI3 perovskite for solar cells applications. We considered both configurations having a preferred orientation of the MA cations, giving rise to a net dipole alignment, and configurations with an isotropic distribution of the MA cations, respectively representative of polar (ferroelectric) and apolar (antiferroelectric) structures. Our calculations demonstrate the preferred stability of a set of polar structures over apolar ones, with an energy difference within 0.1 eV and a conversion barrier within 0.2 eV per unit cell (four MAPbI3), thus possibly accessible at room temperature. Ferroelectric-like orientations lead to a quasi I4cm structure for the inorganic component, characterized by lack of inversion symmetry, while the antiferroelectric-like orientations are associated to a quasi I4/mcm structure. Ab initio molecular dynamics simulations on the polar structur...

Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.

The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water molecules have also been found to be strongly dependent on their initial hydrogen-bonding state. Finally, the dependence of the librational and vibrational modes of water molecules on the local hydrogen-bonding network has been carefully examined, revealing a significant effect upon the libration and bond-stretching peak frequencies. The calculated low frequency peaks come in agreement with previously reported interpretations of the experimental low-frequency Raman spectrum of liquid water.

New insights into the oxygen dissociation and migration on Pt(1 1 1) surface from the Car–Parrinello molecular dynamics study

Car–Parrinello molecular dynamics simulations were performed to study the dissociation of oxygen molecule on the Pt(111) surface at 350K. The results show oxygen dissociation is a step-by-step process. The dissociated oxygen atoms can form fcc–fcc or fcc–hcp adsorption structure on the Pt(111) surface, which is consistent with the results of previous experiments. The Kohn–Sham energy evolutions indicate that the hcp–hcp adsorption structure possesses relatively high energy, and would transform into an fcc–hcp adsorption structure with low energy barrier. This study provides important information in understanding the oxygen dissociation dynamics at the atomic level.

Thermal decomposition of solid phase nitromethane under various heating rates and target temperatures based on ab initio molecular dynamics simulations.

The Car-Parrinello molecular dynamics simulation was applied to study the thermal decomposition of solid phase nitromethane under gradual heating and fast annealing conditions. In gradual heating simulations, we found that, rather than C-N bond cleavage, intermolecular proton transfer is more likely to be the first reaction in the decomposition process. At high temperature, the first reaction in fast annealing simulation is intermolecular proton transfer leading to CH3NOOH and CH2NO2, whereas the initial chemical event at low temperature tends to be a unimolecular C-N bond cleavage, producing CH3 and NO2 fragments. It is the first time to date that the direct rupture of a C-N bond has been reported as the first reaction in solid phase nitromethane. In addition, the fast annealing simulations on a supercell at different temperatures are conducted to validate the effect of simulation cell size on initial reaction mechanisms. The results are in qualitative agreement with the simulations on a unit cell. By analyzing the time evolution of some molecules, we also found that the time of first water molecule formation is clearly sensitive to heating rates and target temperatures when the first reaction is an intermolecular proton transfer.

Pt-free counter electrode for dye-sensitized solar cells with high efficiency.

Dye-sensitized solar cells (DSSCs) have attracted widespread attention in recent years as potential cost-effective alternatives to silicon-based and thin-film solar cells. Within typical DSSCs, the counter electrode (CE) is vital to collect electrons from the external circuit and catalyze the I3- reduction in the electrolyte. Careful design of the CEs can improve the catalytic activity and chemical stability associated with the liquid redox electrolyte used in most cells. In this Progress Report, advances made by our groups in the development of CEs for DSSCs are reviewed, highlighting important contributions that promise low-cost, efficient, and robust DSSC systems. Specifically, we focus on the design of novel Pt-free CE catalytic materials, including design ideas, fabrication approaches, characterization techniques, first-principle density functional theory (DFT) calculations, ab-initio Car-Parrinello molecular dynamics (CPMD) simulations, and stability evaluations, that serve as practical alternatives to conventional noble metal Pt electrodes. We stress the merits and demerits of well-designed Pt-free CEs, such as carbon materials, conductive polymers, transition metal compounds (TMCs) and their corresponding hybrids. Also, the prospects and challenges of alternative Pt catalysts for their applications in new-type DSSCs and other catalytic fields are discussed.

Quantum molecular dynamics simulations of the oxidation of aluminum-cyclopentadienyl clusters

We report Car-Parrinello molecular dynamics simulations of the oxidation of aluminum-cyclopentadienyl clusters currently being considered as novel fuels or energetic materials. These clusters contain a small aluminum core surrounded by a single organic ligand layer. The aromatic cyclopentadienyl ligands form a very strong bond with surface Al atoms, giving rise to a stable organometallic cluster which crystallizes into a low-symmetry solid-state material. Our calculations of an isolated cluster in oxygen show minimal reaction between the ligand and oxygen molecules at simulation temperatures of 300 and 1000 K. Rather, in all cases O2 diffuses through the ligand barrier, splits into atomic oxygen upon contact with the aluminum, and forms an amorphous aluminum oxide core. Loss of aluminum-ligand units, as expected from bond strength calculations, is not observed except following significant oxidation. We present simple metrics to quantitatively compare the steric barrier of the outer ligands that limits the oxidation process.

Peculiar Structure of Water in Slightly Superhydrated Vermiculite Clay Studied by Car–Parrinello Molecular Dynamics Simulations

An unusual water structure was found using Car–Parrinello Molecular Dynamics simulations of a slightly superhydrated Na–vermiculite clay, containing six water molecules per sodium cation, corresponding to that of recent experiments performed to detect dynamical crossovers in the adsorbed supercooled water. In our simulations we observe that water forms two closed packed hexagonal plane layers parallel to aluminosilicate sheets and linked to their surface oxygens by hydrogen bonds. The presence of these hydrogen bonds and the coordination to Na cations lying midway between the clay layers, lowers the number of water–water hydrogen bonds, thus making the closed-packed structure thermodynamically accessible. Remarkably, we have found that this structure is stable across a wide range of temperatures. At the best of our knowledge, this kind of water structure was never reported before, except for a similar hexatic phase (liquid-like, but with a local hexagonal compact symmetry) resulting from a two-dimensional model of water proposed by Vilanova and Franzese.

Oxidation of ligand-protected aluminum clusters: An ab initio molecular dynamics study

We report Car-Parrinello molecular dynamics simulations of the oxidation of ligand-protected aluminum clusters that form a prototypical cluster-assembled material. These clusters contain a small aluminum core surrounded by a monolayer of organic ligand. The aromatic cyclopentadienyl ligands form a strong bond with surface Al atoms, giving rise to an organometallic cluster that crystallizes into a low-symmetry solid and is briefly stable in air before oxidizing. Our calculations of isolated aluminum/cyclopentadienyl clusters reacting with oxygen show minimal reaction between the ligand and O2 molecules at simulation temperatures of 500 and 1000 K. In all cases, the reaction pathway involves O2 diffusing through the ligand barrier, splitting into atomic oxygen upon contact with the aluminum, and forming an oxide cluster with aluminum/ligand bonds still largely intact. Loss of individual aluminum-ligand units, as expected from unimolecular decomposition calculations, is not observed except following significant oxidation. These calculations highlight the role of the ligand in providing a steric barrier against oxidizers and in maintaining the large aluminum surface area of the solid-state cluster material.

Structural flexibility of 4,4′-methylene diphenyl diisocyanate (4,4′-MDI): evidence from first principles calculations

A reactant used globally in the production of polyurethane is the molecule 4,4′-methylene diphenyl diisocyanate (4,4′-MDI). The structural flexibility of 4,4′-MDI is one of the most important molecular properties influencing the polymerization process and this property was therefore modeled using density functional theory (DFT) calculations and Car-Parrinello molecular dynamics (MD) simulations. Global and local minima structures were found and confirmed by vibrational analysis. The energy barriers related to rotation of the aromatic rings were estimated by DFT calculations. The stability of global and local minima was verified by Car-Parrinello (MD) runs at finite temperature. The presence of weak C–H⋯π hydrogen bonds was confirmed by atoms in molecules analysis and found to be responsible for the low energy barriers.

Interplay between molecule–molecule and molecule–substrate interactions: first-principles study of fluoroform aggregates on a hexagonal ice (0001) surface

The adsorption of fluoroform molecules on a hexagonal ice (0001) surface was studied using static density functional theory (DFT) calculations and Car-Parrinello molecular dynamics (CP-MD) simulations. Extending our previous work on isolated molecules we focus in the present study on the interplay between molecule-molecule and molecule-substrate interactions. Coverages of up to a full monolayer were modeled by introducing two, three and four fluoroform molecules per unit cell of the ice (0001) substrate. Lowest-energy structures of fluoroform aggregates on the ice surface were determined in a systematic search by performing geometry optimizations from a large set of initial configurations chosen by chemical intuition and from snapshots taken from CP-MD simulations. In the vibrational analysis of the optimized geometries both conventional red- and unusual blue-shifting hydrogen bonds were found. The finite temperature stability of the lowest-energy configurations was probed by CP-MD simulations and conformational changes were analyzed in terms of transformations between the global and local minima structures.

Structure of a uranyl peroxo complex in aqueous solution from first-principles molecular dynamics simulations

Static ab initio and density-functional computations, as well as Car-Parrinello molecular dynamics simulations in aqueous solution are reported for [UO2(OH)(κ(2)-O2)(H2O)2](-) and [UO2(OH)2(κ(1)-O2H)(H2O)](-). Whereas the κ(1)-hydroperoxo isomer is found to be more stable than the κ(2)-peroxo form in the gas phase, the order of stability is reversed in explicit bulk solution. Based on free energies from thermodynamic integration (BLYP functional), the peroxo form is favoured by ca. 32 kJ mol(-1) in water. This stabilisation is discussed in terms of the hydration shells about the individual ligands and dipole moments of the complexes in water, and highlights the importance of explicit solute-solvent interactions and bulk solvation for the speciation of uranyl(vi) compounds.

Structure of the hexagonal NaYF4 phase from first-principles molecular dynamics

The hexagonal phase of NaYF4 is one of the most popular hosts for the synthesis of upconverting phosphors. The local structure of the lattice is known to have an impact on the optical properties of the doped NaYF4, however despite extensive research being conducted in this field, the structure of the crystalline β-NaYF4 phase is little understood. In this paper, the bulk β-NaYF4 is investigated by means of Car–Parrinello Molecular Dynamics simulations. Three different space groups proposed in the literature are compared. The results show that models based on P and P2m space groups converge to the same structure with nine-fold coordination sites only, while the model based on the P63/m space group is distinct and contains sodium atoms in six-fold coordination sites. Besides coordination numbers, analysis of the distances and average structure, the paper also presents a study of the dynamics of the lattice. Depending on the model, anisotropic thermal vibrations are observed and quantified, as well as oscillations of the sodium atoms between adjacent sites. A different scale of oscillation is observed, depending on the element (sodium or yttrium) and coordination site. In some cases, a reduced symmetry of the coordination shell is observed.

Nature of Zr-Monosubstituted Monomeric and Dimeric Polyoxometalates in Water Solution at Different pH Conditions: Static Density Functional Theory Calculations and Dynamic Simulations

Static density functional theory (DFT) calculations with a continuous solvent model as well as classical and Car-Parrinello molecular dynamics (MD) simulations with explicit solvent molecules were performed to study the nature of Zr-monosubstituted monomeric and dimeric polyoxometalates (POMs) in water at different pHs. We have analyzed Zr-aqua, -hydroxo, and -aqua-hydroxo species derived from Linqvist- and Keggin-type anions. Both DFT and Car-Parrinello MD methods suggest that the Zr center tends to have coordination number greater than 6 and can bind up to 3 water molecules. Car-Parrinello MD simulations also show that the Zr atom fluctuates within the oxide POM framework, providing a flexible coordination environment. There is a small thermodynamic preference for the Zr-aqua species over the protonated Zr-hydroxo species; however the prevalence of one or the other species might depend on the pH. Classical MD simulations show that H3O(+) interacts mainly with hydroxo ligand, while OH(-) anions prefer the protons of the H2O ligands. In general, an increase of the acidity favors the formation of Zr-aqua species, explaining why dimer dissociation is promoted at low pH. At basic conditions Zr-hydroxo species are generated, providing the reactive groups to form Zr···Zr linkages.

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Coordination and Hydrolysis of Plutonium Ions in Aqueous Solution Using Car–Parrinello Molecular Dynamics Free Energy Simulations

Car-Parrinello molecular dynamics (CPMD) simulations have been used to examine the hydration structures, coordination energetics, and the first hydrolysis constants of Pu(3+), Pu(4+), PuO2(+), and PuO2(2+) ions in aqueous solution at 300 K. The coordination numbers and structural properties of the first shell of these ions are in good agreement with available experimental estimates. The hexavalent PuO2(2+) species is coordinated to five aquo ligands while the pentavalent PuO2(+) complex is coordinated to four aquo ligands. The Pu(3+) and Pu(4+) ions are both coordinated to eight water molecules. The first hydrolysis constants obtained for Pu(3+) and PuO2(2+) are 6.65 and 5.70, respectively, all within 0.3 pH unit of the experimental values (6.90 and 5.50, respectively). The hydrolysis constant of Pu(4+), 0.17, disagrees with the value of -0.60 in the most recent update of the Nuclear Energy Agency Thermochemical Database (NEA-TDB) but supports recent experimental findings. The hydrolysis constant of PuO2(+), 9.51, supports the experimental results of Bennett et al. [Radiochim. Acta 1992, 56, 15]. A correlation between the pKa of the first hydrolysis reaction and the effective charge of the plutonium center was found.