Charge-transfer-to-solvent-driven dissolution dynamics of I- (H2O)2-5 upon excitation: excited-state ab initio molecular dynamics simulations

In contrast to the extensive theoretical investigation of the solvation phenomena, the dissolution phenomena have hardly been investigated theoretically. Upon the excitation of hydrated halides, which are important substances in atmospheric chemistry, an excess electron transfers from the anionic precursor (halide anion) to the solvent and is stabilized by the water cluster. This results in the dissociation of hydrated halides into halide radicals and electron-water clusters. Here we demonstrate the charge-transfer-to-solvent (CTTS)-driven femtosecond-scale dissolution dynamics for I-(H2O)n=2-5 clusters using excited state (ES) ab initio molecular dynamics (AIMD) simulations employing the complete-active-space self-consistent-field (CASSCF) method. This study shows that after the iodine radical is released from I-(H2O)n=2-5, a simple population decay is observed for small clusters (2 相似文献   

Photodissociation of diiodomethane in acetonitrile solution and fragment recombination into iso-diiodomethane studied with ab initio molecular dynamics simulations

Series of hydrates of the most stable glycine-H+/2H2+ in the gas phase are presented at the B3LYP level. The results show that only the amino hydrogens and hydroxyl hydrogens can be monohydrated for the glycine-H+, and the amino hydrogens are preferred. The H6(O4) of glycine-2H2+ is the best site for a water molecule to attach, i.e., the corresponding hydrate is the most stable one among its isomers. Calculations reveal that the binding energies of hydrated hydrogens decrease relative to their counterparts in the isolated glycine-H+/2H2+ complexes and they are positive values and without proton transfer except those of monohydrated glycine-2H2+ complexes with the combination modes of H3O+...(glycine-H+). The complex H3O+...(glycine-H+) is formed by the combination of a H2O molecule and one hydroxyl-site proton of glycine-2H2+, and with the proton transfer to H2O. Here the interaction between the proton of H3O+ and the glycine-H+ mainly depends on an electronic one instead of an initial covalent one of the isolated glycine-2H2+. The generation of the bond between the H3O+ and the glycine-H+ makes the energy of the complex higher than the energy sum of its two separated species (or two reactants of the complex), just like the case of M+...(glycine-H+) bond (M = Li,Na). The observation can explain satisfactorily why the combinations of both a proton and an alkali ion or two alkali ions to a glycine molecule can make the corresponding complex hold reservation energy bond(s), while the combination of two protons and a glycine in our previous work cannot [H. Ai et al., J. Chem. Phys. 117, 7593 (2002)]. For the glycine-2H2+, monohydration at the any site of its amino hydrogens can make the binding strength of any other neighboring proton (hydrogens) stronger relative to its counterpart in the isolated glycine-2H2+. Further hydration, especially at the site of either of hydroxyl hydrogens, would disfavor the reservation energy of the system.     

The nature of NOx species on BaO(100): an ab initio molecular dynamics study

The dynamics of NO(x) species adsorbed on BaO(100) have been investigated with ab initio molecular dynamics simulations at a temperature of 300 degrees C. Nitrites are found to continuously interconvert between different adsorption configurations. For both nitrites and nitrates, diffusion events between anion sites are observed. These findings support the use of spillover mechanisms often postulated in mechanistic models of catalysts based on the NO(x)() storage and reduction concept. The large number of possible adsorption configurations are reflected in broad calculated vibrational signatures. These results explain the corresponding property observed in experimental infrared measurements of NO(x)() species on BaO. The dynamic response of the BaO(100) surface is found to strongly depend on the nature of the surface-adsorbate interaction. The largest distortions are predicted for nitrite adsorption.     

Density functional theory for efficient ab initio molecular dynamics simulations in solution

We present a density functional for first-principles molecular dynamics simulations that includes the electrostatic effects of a continuous dielectric medium. It allows for numerical simulations of molecules in solution in a model polar solvent. We propose a smooth dielectric model function to model solvation into water and demonstrate its good numerical properties for total energy calculations and constant energy molecular dynamics.     

Oxygen adsorption on Mo(112) surface studied by ab initio genetic algorithm and experiment

Density functional theory in combination with genetic algorithm is applied to determine the atomic models of p(1x2) and p(1x3) surface structures observed upon oxygen adsorption on a Mo(112) surface. The authors' simulations reveal an unusual flexibility of Mo(112) resulting in oxygen-induced reconstructions and lead to more stable structures than any suggested so far. Comparison of the stabilities of the predicted models shows that different p(1x2) and p(1x3) structures may coexist over a wide range of oxygen pressures. A pure p(1x2) structure can be obtained only in a narrow region of oxygen pressures. In contrast, a pure p(1x3) structure cannot exist as a stable phase. The results of simulations are fully supported by a multitude of experimental data obtained from low energy electron diffraction, x-ray photoelectron spectroscopy, and scanning tunneling microscopy.     

Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations

We apply DFT+U-based ab initio molecular dynamics simulations to study the hydration structures of U(III) and U(IV) ions, pertinent to redox reactions associated with uranium salts in aqueous media. U(III) is predicted to be coordinated to 8 water molecules, while U(IV) has a hydration number between 7 and 8. At least one of the innershell water molecules of the hydrated U(IV) complex becomes spontaneously deprotonated. As a result, the U(IV)-O pair correlation function exhibits a satellite peak at 2.15 A? associated with the shorter U(IV)-(OH(-)) bond. This feature is not accounted for in analysis of extended x-ray absorption fine structure and x-ray adsorption near edge structure measurements, which yield higher estimates of U(IV) hydration numbers. This suggests that it may be useful to include the effect of possible hydrolysis in future interpretation of experiments, especially when the experimental pH is close to the reported hydrolysis equilibrium constant value.     

Structure of docosahexaenoic acid-containing phospholipid bilayers as studied by (2)H NMR and molecular dynamics simulations.

Polyunsaturated phospholipids are known to be important with regard to the biological functions of essential fatty acids, for example, involving neural tissues such as the brain and retina. Here we have employed two complementary structural methods for the study of polyunsaturated bilayer lipids, viz. deuterium ((2)H) NMR spectroscopy and molecular dynamics (MD) computer simulations. Our research constitutes one of the first applications of all-atom MD simulations to polyunsaturated lipids containing docosahexaenoic acid (DHA; 22:6 cis-Delta(4,7,10,13,16,19)). Structural features of the highly unsaturated, mixed-chain phospholipid, 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC), have been studied in the liquid-crystalline (L(alpha)) state and compared to the less unsaturated homolog, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). The (2)H NMR spectra of polyunsaturated bilayers are dramatically different from those of less unsaturated phospholipid bilayers. We show how use of MD simulations can aid in interpreting the complex (2)H NMR spectra of polyunsaturated bilayers, in conjunction with electron density profiles determined from small-angle X-ray diffraction studies. This work clearly demonstrates preferred helical and angle-iron conformations of the polyunsaturated chains in liquid-crystalline bilayers, which favor chain extension while maintaining bilayer flexibility. The presence of relatively long, extended fatty acyl chains may be important for solvating the hydrophobic surfaces of integral membrane proteins, such as rhodopsin. In addition, the polyallylic DHA chains have a tendency to adopt back-bended (hairpin-like) structures, which increase the interfacial area per lipid. Finally, the material properties have been analyzed in terms of the response of the bilayer to mechanical stress. Simulated bilayers of phospholipids containing docosahexaenoic acid were less sensitive to the applied surface tension than were saturated phospholipids, possibly implying a decrease in membrane elasticity (area elastic modulus, bending rigidity). The above features distinguish DHA-containing lipids from saturated or monounsaturated lipids and may be important for their biological modes of action.     

Insights into mechanistic photodissociation of acetyl chloride by ab initio calculations and molecular dynamics simulations

The potential energy surfaces of dissociation and elimination reactions for CH(3)COCl in the ground (S0) and first excited singlet (S1) states have been mapped with the different ab inito calculations. Mechanistic photodissociation of CH(3)COCl has been characterized through the intrinsic reaction coordinate and ab initio molecular dynamics calculations. The alpha-C-C bond cleavage along the S1 pathway leads to the fragments of COCl((2)A' ') and CH(3) ((2)A') in an excited electronic state and a high barrier exists on the pathway. This channel is inaccessible in energy upon photoexcitation of the CH(3)COCl molecules at 236 nm. The S1 alpha-C-Cl bond cleavage yields the Cl((2)P) and CH(3)CO(X(2)A') fragments in the ground state and there is very small or no barrier on the pathway. The S1 alpha-C-Cl bond cleavage proceeds in a time scale of picosecond in the gas phase, followed by CH(3)CO decomposition to CH(3) and CO. The barrier to the C-Cl bond cleavage on the S1 surface is significantly increased by effects of the argon matrix. The S1 alpha-C-Cl bond cleavage in the argon matrix becomes inaccessible in energy upon photoexcitation of CH(3)COCl at 266 nm. In this case, the excited CH(3)COCl(S1) molecules cannot undergo the C-Cl bond cleavage in a short period. The internal conversion from S1 to S0 becomes the dominant process for the CH(3)COCl(S1) molecules in the condensed phase. As a result, the direct HCl elimination in the ground state becomes the exclusive channel upon 266 nm photodissociation of CH(3)COCl in the argon matrix at 11 K.     

Insights into photodissociation dynamics of propionyl chloride from ab initio calculations and molecular dynamics simulations

The potential energy surfaces of isomerization, dissociation, and elimination reactions for CH3CH2COCl in the S0 and S1 states have been mapped with the different ab initio calculations. Mechanistic photodissociation of CH3CH2COCl at 266 nm has been characterized through the computed potential energy surfaces, the optimized surface crossing structure, intrinsic reaction coordinate, and ab initio molecular dynamics calculations. Photoexcitation at 266 nm leads to the CH3CH2COCl molecules in the S1 state. From this state, the C-Cl bond cleavage proceeds in a time scale of picosecond in the gas phase. The barrier to the C-Cl bond cleavage on the S1 surface is significantly increased by effects of the matrix and the internal conversion to the ground state prevails in the condensed phase. The HCl eliminations as a result of internal conversion to the ground state become the dominant channel upon photodissociation of CH3CH2COCl in the argon matrix at 10 K.     

Combined ab initio and classical molecular dynamics simulations of alkyl-lithium aggregates in ethereal solutions

Molecular dynamics simulations of organolithium aggregates in solution are reported for the first time. We use a combined quantum/classical force field (the so-called QM/MM approach) and study ethyl-lithium aggregates in dimethyl ether (DME) solvent. The solutes are described at the Density Functional Theory level while solvent molecules are described using molecular mechanics. NVT Molecular Dynamics simulations at 200 K are carried out in the Born–Oppenheimer approximation. After equilibration, the production phase was run for 80 ps (monomer), 40 ps (dimer) and 26 ps (tetramer). The analysis of the results focuses on Li coordination as a function of aggregate size and we show that the total Li coordination number is always 4. No decoordination has been observed along the simulations. Fluctuations of the structures are predicted to be large in some cases and possible implications on reactivity are discussed.     

Proton transport in triflic acid pentahydrate studied via ab initio path integral molecular dynamics

Trifluoromethanesulfonic acid hydrates provide a well-defined system to study proton dissociation and transport in perfluorosulfonic acid membranes, typically used as the electrolyte in hydrogen fuel cells, in the limit of minimal water. The triflic acid pentahydrate crystal (CF(3)SO(3)H·5H(2)O) is sufficiently aqueous that it contains an extended three-dimensional water network. Despite it being extended, however, long-range proton transport along the network is structurally unfavorable and would require considerable rearrangement. Nevertheless, the triflic acid pentahydrate crystal system can provide a clear picture of the preferred locations of local protonic defects in the water network, which provides insights about related structures in the disordered, low-hydration environment of perfluorosulfonic acid membranes. Ab initio molecular dynamics simulations reveal that the proton defect is most likely to transfer to the closest water that has the expected presolvation and only contains water in its first solvation shell. Unlike the tetrahydrate of triflic acid (CF(3)SO(3)H·4H(2)O), there is no evidence of the proton preferentially transferring to a water molecule bridging two of the sulfonate groups. However, this could be an artifact of the crystal structure since the only such water molecule is separated from the proton by long O-O distances. Hydrogen bonding criteria, using the two-dimensional potential of mean force, are extracted. Radial distribution functions, free energy profiles, radii of gyration, and the root-mean-square displacement computed from ab initio path integral molecular dynamics simulations reveal that quantum effects do significantly extend the size of the protonic defect and increase the frequency of proton transfer events by nearly 15%. The calculated IR spectra confirm that the dominant protonic defect mostly exists as an Eigen cation but contains some Zundel ion characteristics. Chain lengths and ring sizes determined from the hydrogen bond network, counted using graph theory techniques, are only moderately sensitive to quantum effects. Deliberately introducing a structural defect into the native crystal yields a protonic defect with one hydrogen bond to a sulfonate group that was found to be metastable for at least 10 ps.     

The nature of [PdCl(2)(C(2)H(4))(H(2)O)] as an active species in the Wacker process: new insights from ab initio molecular dynamics simulations

First-principles molecular dynamics coupled with metadynamics have been used to gain a deeper insight into the reaction mechanism of the Wacker process by determining the nature of the active species. An explicit and dynamic representation of the aqueous solvent, which was essential for modeling this reaction, was efficiently included into the simulations. Prompted by our earlier results, which showed that the configuration of the catalytically active species [PdCl(2)(H(2)O)(C(2)H(4))] was crucial in the subsequent steps of the Wacker process, herein we focused on the preceding equilibria that led to the formation of both the cis and trans isomers. Starting from the initial catalyst, [PdCl(4)](2-), the free-energy barriers for the forward and backward reactions were calculated. These results confirmed the relevance of the trans intermediate in the reaction mechanism, whilst conversely, they showed that the cis configuration played no role in it. This sole participation of the trans intermediate has some very important implications; besides the mechanistic interpretation of the initial steps in the Wacker reaction mechanism, the analysis of these equilibria provides additional information about the chemical nature of these ligand-substitution processes.     

Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl

Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25 kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl- +H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH...H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.     

The origin of the site preference of H adsorption on Pd(100)

Spin-polarized density functional theory(DFT)calculations are carried out to determine the site preference of H adsorption on Pd(100)surface and subsurface.We carefully scrutinize the energy difference between different patterns at=0.50 ML and confirm the LEED observation that surface adsorption can form c(2×2)ordering structure.On the contrary,we disclose that p(2×1)structure become more favorable than c(2×2)for subsurface adsorption.These site preferences are rationalized via an analysis of the layer and orbital resolved density of states.Furthermore,we propose that the interstitial charge as a key factor determining the preferred H adsorbed site.     

Characterization of dynamics and reactivities of solvated ions by ab initio simulations

Based on a systematic investigation of trajectories of ab initio quantum mechanical/molecular mechanical simulations of numerous cations in water a standardized procedure for the evaluation of mean ligand residence times is proposed. For the characterization of reactivity and structure-breaking/structure-forming properties of the ions a measure is derived from the mean residence times calculated with different time limits. It is shown that ab initio simulations can provide much insight into ultrafast dynamics that are presently not easily accessible by experiment.     

Using force-matching to reveal essential differences between density functionals in ab initio molecular dynamics simulations

The exchange-correlation (XC) functional and value of the electronic fictitious mass μ can be two major sources of systematic errors in ab initio Car-Parrinello Molecular Dynamics (CPMD) simulations, and have a significant impact on the structural and dynamic properties of condensed-phase systems. In this work, an attempt is made to identify the origin of differences in liquid water properties generated from CPMD simulations run with the BLYP and HCTH∕120 XC functionals and two different values of μ (representative of "small" and "large" limits) by analyzing the effective pairwise atom-atom interactions. The force-matching (FM) algorithm is used to map CPMD interactions into non-polarizable, empirical potentials defined by bonded interactions, pairwise short-ranged interactions in numerical form, and Coulombic interactions via atomic partial charges. The effective interaction models are derived for the BLYP XC functional with μ=340 a.u. and μ=1100 a.u. (BLYP-340 and BLYP-1100 simulations) and the HCTH∕120 XC functional with μ=340 a.u. (HCTH-340 simulation). The BLYP-340 simulation results in overstructured water with slow dynamics. In contrast, the BLYP-1100 and HCTH-340 simulations both produce radial distribution functions (indicative of structure) that are in reasonably good agreement with experiment. It is shown that the main difference between the BLYP-340 and HCTH-340 effective potentials arises in the short-ranged nonbonded interactions (in hydrogen bonding regions), while the difference between the BLYP-340 and BLYP-1100 interactions is mainly in the long-ranged electrostatic components. Collectively, these results demonstrate how the FM method can be used to further characterize various simulation ensembles (e.g., density-functional theory via CPMD). An analytical representation of each effective interaction water model, which is easy to implement, is presented.     

Sulfur dioxide in water: structure and dynamics studied by an ab initio quantum mechanical charge field molecular dynamics simulation

An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 ?, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.     

Collisional dynamics of Ag19 on Pd(100): a molecular dynamics study

By means of molecular dynamics simulations based on realistic n-body potentials we investigate structural and dynamical features inherent to the energetic collision of a silver cluster (Ag₁₉) on the Pd(100) substrate. Both the system and the impact energy (E_i = 95 eV) adopted have been chosen to parallel an experimental study of size selected Ag cluster deposition on Pd(100). Our results indicate that the experimental cross section obtained via thermal energy atom scattering at the same collision energy is well reproduced by the simulations.The modeling allows to rationalize the collision outcome in terms of defect production and cluster atoms implantation. The adsorbed structures have an heterogenous nature and are mostly two-dimensional.