Chemical Dynamics Simulations of Thermal Desorption of Protonated Dialanine from a Perfluorinated Self-Assembled Monolayer Surface.

Classical chemical dynamics simulation results are presented for the thermal desorption kinetics and energetics of protonated dialanine ions (ala2-H+) physisorbed on/in a perfluorinated self-assembled monolayer (F-SAM) surface. Previously developed analytic potentials were used for the F-SAM and the ala2-H+/F-SAM intermolecular interaction, and the AMBER valence force field was used for ala2-H+. The activation energy, Ea = 13.2 kcal/mol, determined from the simulations is consistent with previous simulations of the ala2-H+/F-SAM binding energy. The A-factor, 7.8 × 1011 s-1, is about an order of magnitude lower than those representative of small molecule desorption from metal and semiconductor surfaces. This finding is consistent with the decreased entropies of ala2-H+ and the F-SAM upon desorption. Using the Arrhenius parameters for ala2-H+ desorption from the F-SAM, the lifetime of ala2-H+ adsorbed on the F-SAM at 300 K is 5 × 10-3 s. Larger peptide ions are expected to have longer adsorption lifetimes.

Energy and temperature dependent dissociation of the Na(+)(benzene)1,2 clusters: importance of anharmonicity.

Chemical dynamics simulations were performed to study the unimolecular dissociation of randomly excited Na(+)(Bz) and Na(+)(Bz)2 clusters; Bz = benzene. The simulations were performed at constant energy, and temperatures in the range of 1200-2200 K relevant to combustion, using an analytic potential energy surface (PES) derived in part from MP2/6-311+G* calculations. The clusters decompose with exponential probabilities, consistent with RRKM unimolecular rate theory. Analyses show that intramolecular vibrational energy redistribution is sufficiently rapid within the clusters that their unimolecular dynamics is intrinsically RRKM. Arrhenius parameters, determined from the simulations of the clusters, are unusual in that Ea is ∼10 kcal/mol lower the Na(+)(Bz) → Na(+) + Bz dissociation energy and the A-factor is approximately two orders-of-magnitude too small. Analyses indicate that temperature dependent anharmonicity is important for the Na(+)(Bz) cluster's unimolecular rate constants k(T). This is consistent with the temperature dependent anharmonicity found for the Na(+)(Bz) cluster from a Monte Carlo calculation based on the analytic PES used for the simulations. Apparently temperature dependent anharmonicity is quite important for unimolecular dissociation of the Na(+)(Bz)1,2 clusters.

Direct dynamics simulation of dissociation of the [CH3--I--OH]- ion-molecule complex.

Direct dynamics simulations were used to study dissociation of the [CH3--I--OH](-) complex ion, which was observed in a previous study of the OH(-) + CH3I gas phase reaction ( J. Phys. Chem. A 2013 , 117 , 7162 ). Restricted B97-1 simulations were performed to study dissociation at 65, 75, and 100 kcal/mol and the [CH3--I--OH](-) ion dissociated exponentially, in accord with RRKM theory. For these energies the major dissociation products are CH3I + OH(-), CH2I(-) + H2O, and CH3OH + I(-). Unrestricted B97-1 and restricted and unrestricted CAM-B3LYP simulations were also performed at 100 kcal/mol to compare with the restricted B97-1 results. The {CH3I + OH(-)}:{CH2I(-) + H2O}:{CH3OH + I(-)} product ratio is 0.72:0.15:0.13, 0.81:0.05:0.14, 0.71:0.19:0.10, and 0.83:0.13:0.04 for the restricted B97-1, unrestricted B97-1, restricted CAM-B3LYP, and unrestricted CAM-B3LYP simulations, respectively. Other product channels found are CH2 + I(-) + H2O, CH2 + I(-)(H2O), CH4 + IO(-), CH3(-) + IOH, and CH3 + IOH(-). The CH3(-) + IOH singlet products are only given by the restricted B97-1 simulation and the lower energy CH3 + IOH(-) doublet products are only formed by the unrestricted B97-1 simulation. Also studied were the direct and indirect atomic-level mechanisms for forming CH3I + OH(-), CH2I(-) + H2O, and CH3OH + I(-). The majority of CH3I + OH(-) were formed through a direct mechanism. For both CH2I(-) + H2O and CH3OH + I(-), the direct mechanism is overall more important than the indirect mechanisms, with the roundabout like mechanism the most important indirect mechanism at high excitation energies. Mechanism comparisons between the B97-1 and CAM-B3LYP simulations showed that formation of the CH3OH---I(-) complex is favored for the B97-1 simulations, whereas formation of the HO(-)---HCH2I complex is favored for the CAM-B3LYP simulations. The unrestricted simulations give a higher percentage of indirect mechanisms than the restricted simulations. The possible role of the self-interaction error in the simulations is also discussed. The work presented here gives a detailed picture of the [CH3--I--OH](-) dissociation dynamics and is very important for unraveling the role of [CH3--I--OH](-) in the dynamics of the OH(-)(H2O)(n=1,2) + CH3I reactions.

Dynamics of energy transfer and soft-landing in collisions of protonated dialanine with perfluorinated self-assembled monolayer surfaces.

Chemical dynamics simulations are reported which provide atomistic details of collisions of protonated dialanine, ala2-H(+), with a perfluorinated octanethiolate self-assembled monolayer (F-SAM) surface. The simulations are performed at collision energies Ei of 5.0, 13.5, 22.5, 30.00, and 70 eV, and incident angles 0° (normal) and 45° (grazing). Excellent agreement with experiment (J. Am. Chem. Soc., 2000, 122, 9703-9714) is found for both the average fraction and distribution of the collision energy transferred to the ala2-H(+) internal degrees of freedom. The dominant pathway for this energy transfer is to ala2-H(+) vibration, but for Ei = 5.0 eV ∼20% of the energy transfer is to ala2-H(+) rotation. Energy transfer to ala2-H(+) rotation decreases with increase in Ei and becomes negligible at high Ei. Three types of collisions are observed in the simulations: i.e. those for which ala2-H(+) (1) directly scatters off the F-SAM surface; (2) sticks/physisorbs on/in the surface, but desorbs within the 10 ps numerical integration of the simulations; and (3) remains trapped (i.e. soft-landed) on/in the surface when the simulations are terminated. Penetration of the F-SAM by ala2-H(+) is important for the latter two types of events. The trapped trajectories are expected to have relatively long residence times on the surface, since a previous molecular dynamics simulation (J. Phys. Chem. B, 2014, 118, 5577-5588) shows that thermally accommodated ala2-H(+) ions have an binding energy with the F-SAM surface of at least ∼15 kcal mol(-1).

A unified model for simulating liquid and gas phase, intermolecular energy transfer: N2 + C6F6 collisions.

Molecular dynamics simulations were used to study relaxation of a vibrationally excited C6F6* molecule in a N2 bath. Ab initio calculations were performed to develop N2-N2 and N2-C6F6 intermolecular potentials for the simulations. Energy transfer from "hot" C6F6 is studied versus the bath density (pressure) and number of bath molecules. For the large bath limit, there is no heating of the bath. As C6F6* is relaxed, the average energy of C6F6* is determined versus time, i.e., ⟨E(t)⟩, and for each bath density ⟨E(t)⟩ is energy dependent and cannot be fit by a single exponential. In the long-time limit C6F6 is fully equilibrated with the bath. For a large bath and low pressures, the simulations are in the fixed temperature, independent collision regime and the simulation results may be compared with gas phase experiments of collisional energy transfer. The derivative d[⟨E(t)⟩]/dt divided by the collision frequency ω of the N2 bath gives the average energy transferred from C6F6* per collision ⟨ΔE(c)⟩, which is in excellent agreement with experiment. For the ~100-300 ps simulations reported here, energy transfer from C6F6* is to N2 rotation and translation in accord with the equipartition model, with no energy transfer to N2 vibration. The energy transfer dynamics from C6F6* is not statistically sensitive to fine details of the N2-C6F6 intermolecular potential. Tests, with simulation ensembles of different sizes, show that a relatively modest ensemble of only 24 trajectories gives statistically meaningful results.

Intermolecular potential for binding of protonated peptide ions with perfluorinated hydrocarbon surfaces.

An analytic potential energy function was developed to model both short-range and long-range interactions between protonated peptide ions and perfluorinated hydrocarbon chains. The potential function is defined as a sum of two-body potentials of the Buckingham form. The parameters of the two-body potentials were obtained by fits to intermolecular potential energy curves (IPECs) calculated for CF4, which represents the F and C atoms of a perfluoroalkane chain, interacting with small molecules chosen as representatives of the main functional groups and atoms present in protonated peptide ions: specifically, CH4, NH3, NH4(+), and HCOOH. The IPECs were calculated at the MP2/aug-cc-pVTZ level of theory, with basis set superposition error (BSSE) corrections. Good fits were obtained for an energy range extending up to about 400 kcal/mol. It is shown that the pair potentials derived from the NH3/CF4 and HCOOH/CF4 fits reproduce acceptably well the intermolecular interactions in HCONH2/CF4, which indicates that the parameters obtained for the amine and carbonyl atoms may be transferable to the corresponding atoms of the amide group. The derived potential energy function may be used in chemical dynamics simulations of collisions of peptide-H(+) ions with perfluorinated hydrocarbon surfaces.

Temperature dependence of the OH(-) + CH3I reaction kinetics. experimental and simulation studies and atomic-level dynamics.

Direct dynamics simulations and selected ion flow tube (SIFT) experiments were performed to study the kinetics and dynamics of the OH(-) + CH3I reaction versus temperature. This work complements previous direct dynamics simulation and molecular beam ion imaging experiments of this reaction versus reaction collision energy (Xie et al. J. Phys. Chem. A 2013, 117, 7162). The simulations and experiments are in quite good agreement. Both identify the SN2, OH(-) + CH3I → CH3OH + I(-), and proton transfer, OH(-) + CH3I → CH2I(-) + H2O, reactions as having nearly equal importance. In the experiments, the SN2 pathway constitutes 0.64 ± 0.05, 0.56 ± 0.05, 0.51 ± 0.05, and 0.46 ± 0.05 of the total reaction at 210, 300, 400, and 500 K, respectively. For the simulations this fraction is 0.56 ± 0.06, 0.55 ± 0.04, and 0.50 ± 0.05 at 300, 400, and 500 K, respectively. The experimental total reaction rate constant is (2.3 ± 0.6) × 10(-9), (1.7 ± 0.4) × 10(-9), (1.9 ± 0.5) × 10(-9), and (1.8 ± 0.5) × 10(-9) cm(3) s(-1) at 210, 300, 400, and 500 K, respectively, which is approximately 25% smaller than the collision capture value. The simulation values for this rate constant are (1.7 ± 0.2) × 10(-9), (1.8 ± 0.1) × 10(-9), and (1.6 ± 0.1) × 10(-9) cm(3)s(-1) at 300, 400, and 500 K. From the simulations, direct rebound and stripping mechanisms as well as multiple indirect mechanisms are identified as the atomic-level reaction mechanisms for both the SN2 and proton-transfer pathways. For the SN2 reaction the direct and indirect mechanisms have nearly equal probabilities; the direct mechanisms are slightly more probable, and direct rebound is more important than direct stripping. For the proton-transfer pathway the indirect mechanisms are more important than the direct mechanisms, and stripping is significantly more important than rebound for the latter. Calculations were performed with the OH(-) quantum number J equal to 0, 3, and 6 to investigate the effect of OH(-) rotational excitation on the OH(-) + CH3I reaction dynamics. The overall reaction probability and the probabilities for the SN2 and proton-transfer pathways have little dependence on J. Possible effects on the atomistic mechanisms were investigated for the SN2 pathway and the probability of the direct rebound mechanism increased with J. However, the other atomistic mechanisms were not appreciably affected by J.

Determination of viscoelastic properties by analysis of probe-particle motion in molecular simulations.

We present a technique for the determination of viscoelastic properties of a medium by tracking the motion of an embedded probe particle by using molecular dynamics simulations. The approach involves the analysis of the simulated particle motion by continuum theory; it is shown to work in both passive and active modes. We demonstrate that, for passive rheology, an analysis based on the generalized Stokes-Einstein relationship is not adequate to obtain the values of the viscoelastic moduli over the frequency range studied. For both passive and active modes, it is necessary to account for the medium and particle inertia when analyzing the particle motion. For a polymer melt system consisting of short chains, the values calculated from the proposed approach are in good quantitative agreement with previous literature results that were obtained using completely different simulation approaches. The proposed particle rheology simulation technique is general and could provide insight into the characterization of the mechanical properties in biological systems, such as cellular environments and polymeric systems, such as thin films and nanocomposites that exhibit spatial variation in properties over the nanoscale.

Effect of nanoconfinement on kinetics of cross-linking reactions: a molecular simulation study.

We have used molecular dynamics simulations to study the effect of nanoconfinement on the kinetics of cross-linking reactions. Specifically, a bead-spring model is used to carry out reactive molecular dynamics simulations of the autocatalytic epoxy curing reactions. In this simple model, if two colliding molecules arrive in spatial proximity, they react to form a new bond with a specified probability. The kinetics of the reaction in the bulk was compared with that in a cylindrical pore. Our simulations show that confinement leads to an increase in both the translational mobility of the beads as well as the average displacement undergone by the beads from their initial position to the position of reaction. The net result of these opposing factors is that the rate of curing reaction in the confinement is quantitatively similar to that in the bulk. We also observed heterogeneity of reaction rates in the confined system. As compared to the reaction rate in the bulk, the reaction rate in the first layer near the pore wall is lower, whereas the reaction rate in the central core domain of the nanopore hardly shows any difference from the bulk value except in the high conversion stage. The results suggest that the reaction rate in the confined system relative to the bulk will vary with the relative volume fractions of the first layer near the wall and the central core domain.

Molecular dynamics simulation study of friction force and torque on a rough spherical particle.

Recent developments in techniques of micro- and nanofluidics have led to an increased interest in nanoscale hydrodynamics in confined geometries. In our previous study [S. C. Kohale and R. Khare, J. Chem. Phys. 129, 164706 (2008)], we analyzed the friction force experienced by a smooth spherical particle that is translating in a fluid confined between parallel plates. The magnitude of three effects--velocity slip at particle surface, the presence of confining surfaces, and the cooperative hydrodynamic interactions between periodic images of the moving particle--that determine the friction force was quantified in that work using molecular dynamics simulations. In this work, we have studied the motion of a rough spherical particle in a confined geometry. Specifically, the friction force experienced by a translating particle and the torque experienced by a rotating particle are studied using molecular dynamics simulations. Our results demonstrate that the surface roughness of the particle significantly reduces the slip at the particle surface, thus leading to higher values of the friction force and hence a better agreement with the continuum predictions. The particle size dependence of the friction force and the torque values is shown to be consistent with the expectations from the continuum theory. As was observed for the smooth sphere, the cooperative hydrodynamic interactions between the images of the sphere have a significant effect on the value of the friction force experienced by the translating sphere. On the other hand, the torque experienced by a spherical particle that is rotating at the channel center is insensitive to this effect.

Cross stream chain migration in nanofluidic channels: Effects of chain length, channel height, and chain concentration.

We use molecular dynamics simulations to study the shear flow of a polymer solution in a nanochannel by using an explicit, atomistic model of the solvent. The length scales representing the chain size, channel size, and the molecular scale structure in these nanochannels are comparable. The diffusion and hydrodynamic interactions in the system are governed by the intermolecular interactions in the explicit solvent model that is used in the simulations. We study the cross stream migration of flexible polymer chains in a solution that is subjected to a planar Couette flow in a nanochannel. We present a detailed study of the effects of chain length, channel size, and solution concentration on the cross stream chain migration process. Our results show that when a dilute solution containing a longer and a shorter chain is subjected to shear flow, the longer chains that are stretched by the flow migrate away from the channel walls, while the shorter chains that do not stretch also do not exhibit this migration behavior. The thickness of the chain depletion layer at the channel surface resulting from cross stream migration is found to increase with an increase in the channel height. On the other hand, this degree of migration away from the channel walls is found to decrease with an increase in the solution concentration. In solutions with concentrations comparable to or greater than the overlap concentration, the depletion layer thickness in shear flow is found to be comparable or slightly smaller than that observed in the absence of flow.

Molecular simulation of cooperative hydrodynamic effects in motion of a periodic array of spheres between parallel walls.

We use molecular dynamics simulations to investigate the cooperative hydrodynamic interactions involved in the collective translation of a periodic array of spheres in a fluid which is confined between two atomistic surfaces. In particular, we study a spherical particle that is moving with a constant velocity parallel to the two confining surfaces. This central sphere along with its periodic images forms the translating two dimensional periodic grid. The cooperative hydrodynamic effects between neighboring spheres in the grid are determined by monitoring the friction force experienced by the spheres that are moving through an atomistic solvent. The dependence of the hydrodynamic cooperativity on the grid spacing is quantified by running simulations in systems with different sizes of the periodic box. Our results show a clear evidence of hydrodynamic cooperation between the spherical particles for grid spacing of 90sigma and larger, where sigma is the solvent molecular diameter. These cooperative interactions lead to a reduced value of the friction force experienced by these spheres as opposed to the case for a single sphere moving in an infinite quiescent fluid. The simulated friction force values are compared with the recent continuum mechanics predictions [Bhattacharya, J. Chem. Phys. 128, 074709 (2008)] for the same problem of the motion of a periodic grid of particles through a confined fluid. The simulated values of friction force were found to follow the same qualitative trend as the continuum results but the continuum predictions were consistently larger than the simulation results by approximately 22%. We attribute this difference to the fluid slip at the surface of the spherical particle, as measured in the simulations.