Ab initio model potential and molecular dynamics simulation of Ag6 clusters

We present an approach to generate a model potential with parameters fitted to ab initio energetic surfaces. The potential includes two-, three- and four-body terms. Each of them consists of an exponential exchange and dispersion terms. The analytical form of the latter was taken from perturbation theory up to fourth order. We illustrate the present approach by constructing an ab initio model potential for the Ag₆ cluster. A molecular dynamics simulation using this potential reveals interesting features in the isomerization of the C _2v structure. A two step isomerization transition is observed: First, at temperatures around 350 K, the cluster structures fluctuate between two-dimensional isomers. At higher temperatures (450 K), fast transitions occur between two- and three-dimensional cluster configurations.     

Density functional theory study of the isomerization conversion of the cluster ConMoS (n = 1–5)

To investigate the isomerization transition of cluster Co_nMoS (n = 1–5), we employ density functional theory and transition state theory methods in this study. The cluster is optimized at the B3LYP/def2tzvp quantum chemical level. The results reveal eight isomerization reactions for the clusters Co_nMoS (n = 3, 5). Analyzing the activation energies shows a greater propensity for the isomerization transformation in the forward reaction compared to the reverse reaction. At room temperature, six isomerization transformation processes exhibit rapid conversion to the product configurations. Investigation of the equilibrium constants and application of the Arrhenius formula demonstrate that the cluster isomerization reactions are primarily driven by the forward reactions, with four reactions displaying efficient reactant to product conversion rates. Furthermore, there exists a consistent relationship between the structural complexity of the cluster and the change in entropy value. This study provides theoretical insights into reaction rates and optimization of reaction pathways, facilitating mutual validation and development between experimental and theoretical approaches.     

Some aspects of dynamic chaos in small Lennard-Jones clusters

For the purpose of studying stochastic phenomena in the clusters due to an instability of their trajectories in phase space, an evolution of ensembles of the clusters with the representative points initially located in small regions of phase space is investigated using the molecular dynamics method. A path of a cloud of the representative points through the subspace of phase space available for the clusters, and cloud growth in size and in volume are considered. Specific results are presented for Ar₄. A “cold” cluster (subjected to neither an isomerization nor an evaporation) is examined in details. A brief comparison with a “hot” cluster (both the phenomena are available) is given.     

Stabilization of cluster dimers by centrifugal effects

The influence of finite angular momentum on the stabilization of an (Ar₁₃)₂ cluster dimer in Ar₁₃+Ar₁₃ collisions is investigated with simulations and simple models. Local optimizations on the effective rovibrational potentialenergy surface show that the centrifugal effects favor the mechanical stability of strongly prolate shapes. Molecular dynamics simulations are performed to study the collisions between two Ar₁₃ subclusters. At low collisional energy and large impact parameter, trapping of the product cluster in its dimer-like configuration is found. For larger values of the angular momentum, the “molecular” cluster is found to remain in this dimer-like structure during the time of the simulation. Intermediate values of the angular momentum allow isomerization into more compact structures, but still dimer-like. Again, the final product appears as dynamically stable. All of these dimer-like products have the thermodynamical properties of a rotating rigid-like body. At high energy, unimolecular evaporation rates from collisional heating are calculated and comparisons with the predictions of the Rice, Ramsperger, Kassel (RRK) and Weisskopf models are discussed. Qualitative agreement with the simulations, in particular concerning the evolution of the rates versus angular momentum is found. The rates decrease when angular momentum is increased, especially when the total energy is low. Thus, the enhancement of the stability of the product cluster by centrifugal effects has also a statistical character.     

Quantum chemical study of the charged gold atom influence on the mechanism of allylbenzene double bond migration

The DFT calculations of allylbenzene double bond migration were performed in the presence of gold ions Au^? and Au⁺ and the cluster Au₄, which are models of active sites of the gold-containing catalysts. The mechanism of isomerization is determined by the charge of the metal. For the allylbenzene + Au⁺ system, the most appropriate mechanism is the multistage metal-allylic process passing through either the formation of a gold-hydride complex, or no hydride complex is formed in the presence of Au^?. The calculated rate constant of the rate-determining step of the catalytic reaction increases in the order Au₀ < Au^? < Au⁺. The Au^??+ particles are active sites in allylbenzene isomerization. Additional routes of accumulation of the trans-isomer result in the selective formation of trans-??-methylstyrene observed in the catalytic conversion of allylbenzene in the presence of gold nanoparticles. The metal-allylic mechanism is the most preferential in the presence of Au₄ cluster. The high energy of the bond of allylbenzene with the cluster is possibly due to the high reactivity of the latter.     

Capturing Lacunary Iron–Oxo Keggin Clusters and Insight Into the Keggin-Fe13 Cluster Rotational Isomerization

The formation mechanism of ferrihydrite is the key to understand its treatment of pollutants in waste water and purification of surface water and groundwater. Although emerging evidence suggests that formation of the ferrihydrite occurs through the aggregation of prenucleation clusters, rather than classical atom-by-atom growth, its formation mechanism remains unclear. Herein, an iron–oxo anionic cluster of [Fe₂₂(μ₄-O)₈(μ₃-OH)₂₀(μ₂-OH)₁₈(CH₃COO)₁₆(H₂O)₂]⁴⁻ viewed as a dimer of bivacant β-Keggin-Fe₁₃ clusters was for the first time obtained by using lanthanide ions as stabilizers. Upon dissolution in a mixed solution of isopropanol and water, the lacunary β-Keggin-Fe₁₃ cluster can transform into an α-Keggin-Fe₁₃ cluster, distinctly demonstrating that the Keggin-Fe₁₃ cluster rotational isomerization can be realized through the vacant Keggin-Fe₁₃ cluster.     

Ultrafast fragmentation and ionisation dynamics of ammonia clusters

The formation of protonated and unprotonated ammonia cluster ions is studied by femtosecond two colour two photon pump-probe techniques applied to (NH₃) _n and (ND₃) _n clusters withn up to 8. The fourth harmonic (～ 200 nm, 6.2 eV, 160 fs) of a Ti: Sapphire laser pulse is used to excite the clusters in a state corresponding to theà state of NH₃ while the third harmonic (267 nm, 4.65 eV) is used for the subsequent ionisation step. Employing a combination of the optical Bloch equations for the excitation process and rate equations for the cluster dynamics we calibrate the zero time delay and carefully analyse the time dependence of the pump-probe signal. Several distinct intermediate steps in the time evolution can be distinguished, having characteristic time constants ranging from 40 fs to over 100 ps. They are discussed in a consistent scheme for the excitation, ionisation and protonation dynamics, accounting also for characteristic differences observed between deuterated and undeuterated species. A particularly remarkable time dependence of the homogeneous (NH₃) ₂ ⁺ cluster ion signal is interpreted as a fingerprint of internally protonated neutral precursors of the type NH₃NH₂NH₄.     

Structures and isomerization of neutral and zwitterion serine–water clusters: Computational study

Calculations are presented for the structure and the isomerization reaction of various conformers of the bare serine, neutral serine–(H₂O)_n and serine zwitterion–(H₂O)_n (n = 1, 2) clusters. The effects of binding water molecules on the relative stability and the isomerization processes are examined. Hydrogen bonding between serine and the water molecule(s) may significantly affect the relative stability of conformers of the neutral serine–(H₂O)_n (n = 1, 2) clusters. The sidechain (OH group) in serine is found to have a profound effect on the structure and isomerization of serine–(H₂O)_n (n = 1, 2) clusters. Conformers with the hydrogen bonding between water and the hydroxyl group of serine are predicted. A detailed analysis is presented of the isomerization (proton transfer) pathways between the neutral serine–(H₂O)₂ and serine zwitterion–(H₂O)₂ clusters by carrying out the intrinsic reaction coordinate analysis. At least two water molecules need to bind to produce the stable serine zwitterion–water cluster in the gas phase. The isomerization for the serine–(H₂O)₂ cluster proceeds by the concerted double and triple proton transfer mechanism occurring via the binding water molecules, or via the hydroxyl group. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

The mechanism of allyl isomerization of unsaturated compounds catalyzed by organomagnesium clusters

The paper presents a density functional theory investigation of the mechanism of allyl isomerization of olefins on magnesium clusters for the example of the Mg₄-allylbenzene system. The rearrangement of the cluster compound corresponding to the insertion of the tetranuclear cluster at a C-H allylbenzene bond into a structure derivative from 2-methylstyrene is an activationless reaction. The limiting step is the liberation of the cluster nucleus capable of interacting with another allylbenzene molecule. Cluster decomposition competes with this process; this conclusion is in agreement with experimental short lifetimes of cluster magnesium hydride catalysts.     

Photoisomerization of linear merocyanines in salt solutions

The trans-cis isomerization in the excited state of linear merocyanine L-Mero4 and phenyl substituted linear merocyanine P-L-Mero4 in salt solution and in ionic liquid was investigated using frequency upconversion measurements. Strontium chloride and cesium iodide were added to solvent dimethyl sulfoxide (DMSO) and dimethylformamide (DMF) to vary the ionic strength. The time-resolved fluorescence curves of merocyanines displayed multiple exponential decay behavior. The second temporal component with time constant τ₂ ≈ 2.8 (11) ps of L-Mero4 (P-L-Mero4) in DMSO was assigned to the duration to reach the isomerization equilibrium between the trans and the twisted conformers. The τ₂ increased at higher salt concentrations and was explained by the attachment of salt ions on the polar excited merocyanines decelerating the isomerization rate. The rotational correlation time constants obtained from the anisotropy decay of fluorescence were 360 and 240 ps in neat DMSO for L-Mero4 and P-L-Mero4, respectively, and they increased to 790 and 450 ps in the most concentrated SrCl₂. Using Perrin relation, we estimated the increase in the rotating volume at [SrCl₂] = 536 mM, revealing ≈15 SrCl₂ molecules surrounding L-Mero4 and 7 SrCl₂ on P-L-Mero4. The experimental data indicated that the ion–molecule interaction was stronger with SrCl₂ and on L-Mero4 than on P-L-Mero4.     

Thermal cis–trans isomerization and decomposition of polyacetylene

Thermal cis-trans isomerization and decomposition of polyacetylene film prepared with a Ti(OC₄H₉)₄–Al(C₂H₅)₃ (Al/Ti = 4) system were investigated under inert gas or in vacuum by means of thermal analysis and infrared spectroscopy. Thermograms of differential thermal analysis of cis-polyacetylene revealed the existence of two exothermic peaks at 145 and 325°C and one endothermic peak at 420°C which were assigned to cis-trans isomerization, hydrogen migration accompanied with crosslinking reaction, and thermal decomposition, respectively. The isomerization was followed by infrared spectroscopy over the temperature range 75–115°C. The reaction did not obey simple kinetics. The apparent activation energy for the cis-trans isomerization was 17.0 kcal/mole for the polymer containing 88% cis configuration and increased with increasing trans content up to 38.8 kcal/mole for 80% trans content.     

A dynamic study of isomerization on MoOx catalyst

The dynamics of n-heptane isomerization on the reduced MoO₃ catalyst have been studied in a fixed bed flow reactor. In the reaction temperature ranging from 523 to 673 K, the apparent energy for n-heptane isomerization obtained from the Arrhenius plot was 49.3 kJ/mol. At 573 K, the reaction orders of 0.33 in n-heptane and 0.35 in H₂ have been obtained.     

Path-integral molecular dynamics simulations of hydrated hydrogen chloride cluster HCl(H2O)4 on a semiempirical potential energy surface

Path-integral molecular dynamics simulations for the HCl(H₂O)₄ cluster have been performed on the ground-state potential energy surface directly obtained on-the-fly from semiempirical PM3-MAIS molecular orbital calculations. It is found that the HCl(H₂O)₄ cluster has structural rearrangement above the temperature of 300 K showing a liquid-like behavior. Quantum mechanical fluctuation of hydrogen nuclei plays a significant role in structural arrangement processes in this cluster.     

A comparative study of neighbouring group effects on the isomerization of imines in platinum-imine complexes by 1H, 13C, 31P and 195Pt NMR spectroscopy

¹⁹⁵Pt-, ³¹P-, ¹³C- and ¹H-chemical shifts are reported for the first time for complexes of the type trans-[PtCl₂ (η²-C₂H₄) (imine)], I, trans-[PtCl₂ (η²-C₂H₄) (amine)] II, and trans-[PtCl₂(PR′₃) (imine)] III (the imine ligand being derived from cyclopropyl-2-thienylketone and primary amines; PR′₃ = PBuⁿ₃ and PPh₃; amine; the amine ligand obtained by the reduction of the appropriate imine). The use of multinuclear spectroscopy provides strong evidence for E-Z isomerization of imine ligands coordinated to platinum (II) of the type trans-[PtCl₂ (η²-C₂H₄)(imine)]. Tertiary phosphine ligands trans to imine ligand (III) are not strongly labilizing groups, in contrast to η²-C₂H₄, which shows a strong labilizing effect. The effect of neighbouring groups on E-Z isomerization indicates that increase of the bulky substituents close to the imino group tends to increase the rate of isomerization, and increasing the degree of substitution on the imine carbon atoms slows the rate of isomerization. Furthermore, addition of a trace of amine will catalyze the E-Z isomerization. Also, isomerization takes place in the liquid state to give one isomer during the coordination with platinum.     

Isomerization of hydrocarbon ions. VI—parameters determining the isomerization of aliphatic hydrocarbon ions

The radical or non-radical character of aliphatic hydrocarbon ions determines the extent to which these ions equilibrate to a mixture of interconverting structures prior to decomposition. It is suggested that the radical (odd electron) ions have both lower thresholds for decomposition and higher barriers for isomerization that non-radical (even electron) ions, thus explaining their reduced tendency for isomerization. Moreover, the molecular size seems to be a major influencing factor for the isomerization of unsaturated hydrocarbon molecular ions. With decreasing molecular size isomerization prior to decomposition becomes more pronounced. Collisional activation spectra of fragment ions (formed by loss of H₂O from the corresponding alcohols) and of [C₅H₁₀]⁺ and [C₄H₈]⁺ molecular ions are reported in support of these conclusions.     

Rotating clusters: centrifugal distortion,isomerization, fragmentation

The effect of the overall rotation, as characterized by the total angular momentum, on the structure of an Ar₁₃ cluster is studied by using a new technique for separation of the rotational motion from vibrations. No a priori limitation on the degree of nonrigidity of the cluster is imposed. The different structures for different total angular momenta of the cluster are arrived at by a thermal quenching procedure which preserves the overall rotation. It is shown that the centrifugal distortion is anisotropic and it may lead to isomerization transitions and even fragmentation of the cluster.     

Size dependent melting mechanisms of iron nanoclusters

Molecular dynamics simulations were used to study the change in the mechanism of iron cluster melting with increasing cluster size. Melting of smaller clusters (e.g., Fe₅₅ and Fe₁₀₀) occurs over a large temperature interval where the phase of the cluster repeatedly oscillates between liquid and solid. In contrast, larger clusters (e.g., Fe₃₀₀) have sharper melting points with surface melting preceding bulk melting. The importance of the simulation time, the force field and the definition of cluster melting is also discussed.     

Molecular dynamics calculation of half-lives for thermal decay of Lennard-Jones clusters

Molecular dynamics has been used with a Lennard-Jones (6–12) potential in order to study the decay behavior of neutral Argon clusters containing between 12 and 14 atoms. The clusters were heated to temperatures well above their melting points and then tracked in time via molecular dynamics until evaporation of one or more atoms was observed. In each simulation, the mode of evaporation, energy released during evaporation, and cluster lifetime were recorded. Results from roughly 2000 simulation histories were combined in order to compute statistically significant values of cluster half-lives and decay energies. It was found that cluster half-life decreases with increasing energy and that for a given value of excess energy (defined asE=(E _tot ?E _gnd)/n), the 13 atom cluster is more stable against decay than clusters containing either 12 or 14 atoms. The dominant decay mechanism for all clusters was determined to be single atom emission.