Principles Molecular Dynamics Study Research Articles

CO2 Absorption in the Protic Ionic Liquid Ethylammonium Nitrate

We present a first principles molecular dynamics study of carbon dioxide solvation by protic ionic liquids using ethylammonium nitrate as an example solvent. Microheterogeneity of the alkyl chains and the extended hydrogen bond network could be observed. Thus, the entire structure of the investigated protic ionic liquid mixed with CO2 closely resembles the one of the pure liquid. Our data indicates that CO2 most likely creates an energy loss due to entering the liquid via the too-small voids. But this is fully compensated by specific attractive interactions of CO2 with the cation and anions of ethylammonium nitrate. This result might serve as an explanation for the question of why the volume of the ionic liquid is not increasing through CO2 uptake. The CO2 cluster formation, which shows a structure similar to supercritical CO2, is guided by the dominance of the nonpolar groups in the CO2 solvation shell.

Biased interface between solid ion conductor LiBH4 and lithium metal: A first principles molecular dynamics study

We use first-principles molecular dynamics to study the electrochemical solid-solid interface between lithium metal and lithium electrolyte LiBH4. An external bias is applied by using an effective screening medium. We observe large polarization in the LiBH4, because the lithium cations in LiBH4 are shifted more on one side of the double-well potential of Li+. This results in a large potential drop in the interface region and a large double-layer capacity corresponding to ca. 70 μF/cm2. H-coordination to the Li atoms plays an important role in the charge-transfer reaction and ion transfer.

First and Second One-Electron Reduction of Lumiflavin in Water-AFirst Principles Molecular Dynamics Study.

Flavins are ubiquitously found in nature as cofactors in proteins that regulate electron and proton transfer reactions. The electron and proton affinities of flavins are modulated by their molecular environment. Using density functional theory based molecular dynamics simulations, we have studied the first and second reduction reactions of the prototypical flavin named lumiflavin in aqueous solution. We find that the reduction potential, calculated using free energy perturbation simulations, has the typical parabolic shape as predicted by Marcus' theory of electron transfer. The water solvent structure undergoes significant changes within the first coordination shell upon lumiflavin reduction. These structural changes account largely for the reorganization free energy term in the measured redox potential. However, in the second reduction reaction, from semiquinone to fully reduced lumiflavin, also the inner-sphere reorganization contributes significantly via the increased "butterfly" bending of the flavin. This butterfly bending causes a deviation from the linear response approximation that underlies Marcus' theory of electron transfer.

First principles molecular dynamics study of proton dynamics and transport in phosphoric acid/imidazole (2:1) system

Phosphoric acid based polymer electrolyte membranes (e.g. poly(benzimidazole)/phosphoric acid) are the only quasi-anhydrous separator electrolytes for medium temperature fuel cells currently in use. Pure phosphoric acid has the highest known intrinsic proton conductivity of any substance, which is very sensitive towards doping with Brønsted–Lowry bases or even acids. Proton conductivity shows the most dramatic decrease upon addition of basic species, e.g. polymers containing N-heterocyclic groups, and high phosphoric acid contents, are required to ensure high conductivities in these materials. We perform first principles molecular dynamics simulations in order to investigate these processes at the fundamental molecular level. Proton dynamics and transport are studied in a system of phosphoric acid and imidazole having 2:1 molar ratio. This model system represents a first step towards the more detailed understanding of the proton conduction mechanisms in realistic phosphoric acid based polymer electrolyte materials. Our results indicate that imidazole molecules have a much stronger proton affinity (basicity) than phosphoric acid, forming very stable imidazolium–dihydrogenphosphate complexes. We evaluate a number of properties which are important for the proton conduction and compare them to the previously obtained data on pure phosphoric acid. The reduced proton density in the proton conducting H3PO4 phase is shown to have strong effects on the energetics of proton transfer, local proton dynamics, electrostatic proton–proton interactions as well as on the structure of the hydrogen bond network. These effects are suggested to be the reason for the impaired proton conducting properties of this, and similar, phosphoric acid based systems containing N-heterocycles.

Understanding surface acidity of gibbsite with first principles molecular dynamics simulations

In this paper, we report a first principles molecular dynamics (FPMD) study of the acid–base chemistry of gibbsite. With FPMD based vertical energy gap technique, the acidity constants of the sites on the basal surface (i.e. (001)) and the edge surface (100) are derived and the results overall indicate that l(OH2)2 groups on the edge surface are the major acidic sites. The free-energy calculation indicates that both the 6-fold (i.e. Al(OH2)2) and 5-fold (i.e. Al(OH2)) coordination states of edge Al atoms are probable with the former being much more stable. The 6-fold forms have very similar 1st and 2nd acidity constants in 9.0–10.0, which agrees with the experimental PZC (point of zero charge) range. The 5-fold forms have a very low pKa of about 2.0, which indicates that its common form is Al(OH) within normal pH range. The doubly coordinated site (i.e. Al2(OH)) on the edge surface has a very high pKa of about 13.0, indicating that the proton dissociation rarely happens. For the basal surface, the hydroxyl groups almost do not have contribution to the acid–base chemistry of gibbsite. On this surface, some OHs keep orientation parallel to the surface and therefore they can only perform as proton acceptors. However, their protonated states have very low pKas of around 1.3. The other OHs have an extremely high pKa (about 22.0), indicating no dissociation in common pH. Overall, this study provides atomic-scale understanding on the acid–base chemistry of gibbsite and the derived interfacial structures and acidity constants form a basis for future research on the interfacial processes of Al–hydroxides.

Organic Synthesis in the Interstellar Medium by Low-Energy Carbon Irradiation

We present a first principles molecular dynamics (FPMD) study of the interaction of low-energy neutral carbon projectiles with amorphous solid water clusters at 30 K. Reactions involving the carbon atom at an initial energy of 11 and 1.7 eV with 30-molecule clusters have been investigated. Simulations indicate that the formation of hydroxymethylene, an intermediate in formaldehyde production, dominates at the higher energy. The reaction proceeds by fragmenting a water molecule, binding the carbon to the OH radical, and saturating the C valence with a hydrogen atom that can arise from the originally dissociated water molecule, or through a chain of proton transfer events. We identified several possible pathways for the formation of HCOH. When the initial collision occurs at the periphery of the cluster, we observe the formation of CO and the evaporation of water molecules. At the lower energy water fragmentation is not favorable, thus leading to the formation of weakly bound carbon-water complexes.

The structure of liquid GeSe revisited: A first principles molecular dynamics study

Early first-principles molecular dynamics results on liquid GeSe were characterized by shortcomings in the description of Ge-Ge (and to a lesser extent Se-Se) short range correlations. In that case the exchange-correlation functional adopted was the one devised by Perdew and Wang (PW91). In the search of improvements in the atomic-scale modelling of this liquid, we have produced new sets of data by employing two different schemes for the exchange-correlation part within the density functional theory approach. The two functionals selected are those proposed by Becke, Lee, Yang, and Parr (BLYP) and by Perdew, Burke, and Ernzerhof (PBE). The PBE results turned out to be quite similar to the PW91 ones. The BLYP results feature instead a better account of the Ge-Ge first shell of neighbors, correctly exhibiting two clear maxima separated by a deep minimum. Due to the increase in the number of the tetrahedral structural units, the atomic mobility of Ge and Se atoms in the network is reduced with respect to the PW91 case. This brings the diffusion coefficients of the two species down to values close to those of liquid Ge2Se3 and liquid GeSe2.

Frequency dependence of the reorientational motion of OD bonds of deuterated methanol in liquid phase: A first principles molecular dynamics study

We present an ab initio molecular dynamics study of the frequency dependence of rotational motion of OD bonds of deuterated methanol in liquid phase. A time series analysis of the simulated trajectories is performed to calculate the fluctuating frequencies of the OD bonds and the frequency-resolved rotational dynamics are investigated through calculations of the first and second-rank rotational correlation functions of the OD bond vectors. The short-time dynamics is found to depend on the chosen frequency which, in turn, is related to different hydrogen bonded environments of methanol molecules. The long time dynamics is found to be independent of the frequency of OD bonds. The effects of dispersion interactions on the calculated results are also discussed. The current first principles results are compared with the available experiments on frequency dependence of rotational dynamics of similar alcoholic systems.

Hydration, acidity and metal complexing of polysulfide species: A first principles molecular dynamics study

We report a first principles molecular dynamics study on hydration and acidity of polysulfide species. Hydration structures of (poly)sulfides species are pictured by analyzing the trajectories. With the vertical energy gap technique, our calculations reproduce the acidity constants of H2S and predict chain length independent acidity for polysulfanes: pKa1s are about 7.0 and pKa2s are around 9.0. This indicates H2Sn, HSn− and Sn2− can all be dominant under common pH. Furthermore, our simulations show that stable Au+–HSn− complexes can form in solutions, which implies that polysulfides can perform as metal complexing agents in hydrothermal processes.

A first principles molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in liquid methanol

We present a first principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in liquid methanol at room temperature. The dynamics of spectral diffusion of OD modes of deuterated methanol reveals two times scales: a short time scale of about 120fs and a longer time scale of about 3.2ps. A damped oscillation is also found at around 120–180fs. Calculations of power spectrum of relative velocities and hydrogen bond correlation functions reveal that the short time dynamics originates from intermolecular motion of hydrogen bonded methanol pairs while the long time relaxation corresponds to the breaking dynamics of hydrogen bonds. The quantitative details of the time constants are found to depend on the frequency of tagged OD bonds.

First principles molecular dynamics study of filled ice hydrogen hydrate

We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C(2) by using first principles molecular dynamics simulation. It was found that the experimentally reported "cubic" structure is unstable at low temperature and/or high pressure: The "cubic" structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the "cubic" symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in "cubic" symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules' rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and/or low temperatures.

Communication: Hydration structure and polarization of heavy alkali ions: A first principles molecular dynamics study of Rb+ and Cs+

Hydration structure and polarization of Rb(+) and Cs(+) in liquid water at ambient conditions were studied by first principles molecular dynamics. Our systematic analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H(2)O molecules in the first solvation shell of the ions slightly increases with increasing the atomic number. We also found that the polarization of heavy alkali ions, particularly Cs(+), tends to stabilize a peculiar asymmetric hydration structure with relevant consequences in the extraction of the harmful (137)Cs resulting from nuclear wastes.

First principles molecular dynamics study of nitrogen vacancy complexes in boronitrene

We present the results of first principles molecular dynamics simulations of nitrogen vacancy complexes in monolayer hexagonal boron nitride. The threshold for local structure reconstruction is found to be sensitive to the presence of a substitutional carbon impurity. We show that activated nitrogen dynamics triggers the annihilation of defects in the layer through formation of Stone–Wales-type structures. The lowest energy state of nitrogen vacancy complexes is negatively charged and spin polarized. Using the divacancy complex, we show that their formation induces spontaneous magnetic moments, which is tunable by electron or hole injection. The Fermi level s-resonant defect state is identified as a unique signature of the ground state of the divacancy complex. Due to their ability to enhance structural cohesion, only the divacancy and the nitrogen vacancy carbon-antisite complexes are able to suppress the Fermi level resonant defect state to open a gap between the conduction and valence bands.

A first principles molecular dynamics study of the solvation structure and migration kinetics of an excess proton and a hydroxide ion in binary water-ammonia mixtures

We have investigated the solvation structure and migration kinetics of an excess proton and a hydroxide ion in water-ammonia mixed liquids of varying composition by means of ab initio molecular dynamics simulations. The excess proton is always found to be attached to an ammonia molecule to form the ammonium ion. Migration of the excess proton is found to occur very occasionally from one ammonia to the other but no proton transfer to a water molecule is observed during the entire simulations. Also, when the ammonium ion is solvated in water only, its hydrogen bond dynamics and rotation are found to occur at a faster rate than those in water-ammonia mixtures. For water-ammonia mixtures containing a proton less, the defect is found to stay like the hydroxide ion. For these systems, occasional proton transfer is found to occur only through the hydrogen bonded chains of water molecules in these water-ammonia mixtures. No proton transfer is found to take place from an ammonia molecule. The presence of ammonia molecules makes the realization of proper presolvated state of the hydroxide ion to accept a proton a more difficult process and, as a result, the rate of proton transfer and migration kinetics of the hydroxide ion in water-ammonia mixtures are found to be slower than that in liquid water and these rates are found to slow down further with increase of ammonia concentration.

Hydrogen bond dynamics and vibrational spectral diffusion in aqueous solution of acetone: A first principles molecular dynamics study#

We present an ab initio molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution of acetone at room temperature. It is found that the frequencies of OD bonds in the acetone hydration shell have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the acetone–water hydrogen bond distance. The vibrational spectral diffusion of the hydration shell water molecules reveals three time scales: A short-time relaxation (~80fs) corresponding to the dynamics of intact acetone–water hydrogen bonds, a slower relaxation (~1.3ps) corresponding to the lifetime of acetone–water hydrogen bonds and another longer time constant (~12ps) corresponding to the escape dynamics of water from the solute hydration shell. The present first principles results are compared with those of available experiments and classical simulations. Vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution containing an acetone molecule are studied through ab initio molecular dynamics simulations and time series analysis. The present theoretical results are also compared with those of available experiments and classical simulations.

A first principles molecular dynamics study of excess electron and lithium atom solvation in water–ammonia mixed clusters: Structural, spectral, and dynamical behaviors of [(H $_2$2O) $_5$5NH $_3]^-$3]− and Li(H $_2$2O) $_5$5NH $_3$3 at finite temperature

First principles molecular dynamics simulations are carried out to investigate the solvation of an excess electron and a lithium atom in mixed water-ammonia cluster (H(2)O)(5)NH(3) at a finite temperature of 150 K. Both [(H(2)O)(5)NH(3)](-) and Li(H(2)O)(5)NH(3) clusters are seen to display substantial hydrogen bond dynamics due to thermal motion leading to many different isomeric structures. Also, the structures of these two clusters are found to be very different from each other and also very different from the corresponding neutral cluster without any excess electron or the metal atom. Spontaneous ionization of Li atom occurs in the case of Li(H(2)O)(5)NH(3). The spatial distribution of the singly occupied molecular orbital shows where and how the excess (or free) electron is primarily localized in these clusters. The populations of single acceptor (A), double acceptor (AA), and free (NIL) type water and ammonia molecules are found to be significantly high. The dangling hydrogens of these type of water or ammonia molecules are found to primarily capture the free electron. It is also found that the free electron binding motifs evolve with time due to thermal fluctuations and the vertical detachment energy of [(H(2)O)(5)NH(3)](-) and vertical ionization energy of Li(H(2)O)(5)NH(3) also change with time along the simulation trajectories. Assignments of the observed peaks in the vibrational power spectra are done and we found a one to one correlation between the time-averaged populations of water and ammonia molecules at different H-bonding sites with the various peaks of power spectra. The frequency-time correlation functions of OH stretch vibrational frequencies of these clusters are also calculated and their decay profiles are analyzed in terms of the dynamics of hydrogen bonded and dangling OH modes. It is found that the hydrogen bond lifetimes in these clusters are almost five to six times longer than that of pure liquid water at room temperature.

A first principles molecular dynamics study of lithium atom solvation in binary liquid mixture of water and ammonia: Structural, electronic, and dynamical properties

The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li(+) ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li(+) ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li(+) ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen bonds.

Interfacial water: A first principles molecular dynamics study of a nanoscale water film on salt

Density functional theory (DFT) molecular dynamics simulations of a thin (approximately 15 A) water film on NaCl(001) have been performed, with the aim of understanding the structural and dynamic properties of this important interfacial water system. The interaction of the water film with the surface orders the water molecules in the immediate vicinity of the interface. This is reflected by oscillations in the planar-averaged water density distribution along the surface normal that extend to about 8 A from the surface. The interaction with the substrate leaves many of the water molecules in the immediate vicinity with broken hydrogen bonds and as a consequence considerably reduced dipole moments. Indeed a clear correlation between the number of hydrogen bonds which a water molecule is involved in and its dipole moment for both water on NaCl and bulk water is observed. How the DFT results obtained here compare to those obtained with various empirical potentials is briefly discussed.

L‐Lactate dehydrogenation in flavocytochrome b2

First principles molecular dynamics studies on active-site models of flavocytochrome b2 (L-lactate : cytochrome c oxidoreductase, Fcb2), in complex with the substrate, were carried out for the first time to contribute towards establishing the mechanism of the enzyme-catalyzed L-lactate oxidation reaction, a still-debated issue. In the calculated enzyme-substrate model complex, the L-lactate alpha-OH hydrogen is hydrogen bonded to the active-site base H373 Nepsilon, whereas the Halpha is directed towards flavin N5, suggesting that the reaction is initiated by alpha-OH proton abstraction. Starting from this structure, simulation of L-lactate oxidation led to formation of the reduced enzyme-pyruvate complex by transfer of a hydride from lactate to flavin mononucleotide, without intermediates, but with alpha-OH proton abstraction preceding Halpha transfer and a calculated free energy barrier (12.1 kcal mol(-1)) consistent with that determined experimentally (13.5 kcal mol(-1)). Simulation results also revealed features that are of relevance to the understanding of catalysis in Fcb2 homologs and in a number of flavoenzymes. Namely, they highlighted the role of: (a) the flavin mononucleotide-ribityl chain 2'OH group in maintaining the conserved K349 in a geometry favoring flavin reduction; (b) an active site water molecule belonging to a S371-Wat-D282-H373 hydrogen-bonded chain, conserved in the structures of Fcb2 family members, which modulates the reactivity of the key catalytic histidine; and (c) the flavin C4a-C10a locus in facilitating proton transfer from the substrate to the active-site base, favoring the initial step of the lactate dehydrogenation reaction.

Insights from first principles molecular dynamics studies toward infrared multiple-photon and single-photon action spectroscopy: Case study of the proton-bound dimethyl ether dimer

We have used finite temperature ab initio molecular dynamics simulations in conjunction with computation of critical quantum nuclear effects to probe the differences between single-photon argon tagged action spectral results and infrared multiple-photon dissociation experiments for a proton bound molecular ion system. We find that the principal difference between the results in these experimental techniques is essentially that of cluster temperature. The multiple-photon dissociation experiments conducted using room temperature ions reflect a larger degree of conformational freedom compared to the colder single-photon argon tagged action spectral results. Our ab initio molecular dynamics simulation techniques accurately capture the effects of conformational sampling, adequately reproduce both spectra, and can be utilized to assign the dynamically averaged finite temperature spectra.