Classical trajectory study of collisions of Ar with alkanethiolate self-assembled monolayers: Potential-energy surface effects on dynamics

Computational Studies of Uranium Hexafluoride Interacting with Functionalized Organics. I. Screening Intermolecular Potentials between UF6 and Small Organic Functional Groups

We report the intermolecular binding energies (IBEs) between UF₆ and over 50 different functionalized small organic molecules as predicted by electronic structure calculations. Optimized geometries of UF₆-molecule dimers were found at the MP2/aug-cc-pwCVDZ (non-U), cc-pVDZ-PP (U) level. IBEs were calculated using MP2 and dispersion-corrected DFT theory. We characterize the various functional groups based on the inclusion of specific heteroatoms. Those functional groups containing "nitrogen only" heteroatoms result in larger IBEs than groups containing both nitrogen and oxygen or oxygen alone. Halogen-containing and regular hydrocarbon molecules show the lowest IBEs with UF₆. Nonorganic phosphoryl species are also shown to display large IBEs with UF₆. These interactions are characterized in part by how much the impinging functionalized molecule distorts the UF₆ from its optimal octahedral geometry. Of all the investigated groups, the amine group displayed the largest IBE values (IBE ∼ >12-14 kcal/mol for methyl amine), while hydrocarbons and perfluorocarbons both showed the weakest interactions (IBE ∼ 0.5-1.5 and 0.1-0.8 kcal/mol for methane and perfluoromethane, respectively). The study examines how the strength of the IBE is contingent on a combination of conformational deformation, stabilizing nonbonding interactions, and sterics.

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.

Quantum state-resolved CO2 collisions at the gas-liquid interface: surface temperature-dependent scattering dynamics

Energy transfer dynamics at the gas-liquid interface are investigated as a function of surface temperature both by experimental studies of CO2 + perfluorinated polyether (PFPE) and by molecular dynamics simulations of CO2 + fluorinated self-assembled monolayers (F-SAMs). Using a normal incident molecular beam, the experimental studies probe scattered CO2 internal-state and translational distributions with high resolution infrared spectroscopy. At low incident energies [Einc = 1.6(1) kcal/mol], CO2 J-state populations and transverse Doppler velocity distributions are characteristic of the surface temperature (Trot approximately Ttrans approximately TS) over the range from 232 to 323 K. In contrast, the rotational and translational distributions at high incident energies [Einc = 10.6(8) kcal/mol] show evidence for both trapping-desorption (TD) and impulsive scattering (IS) events. Specifically, the populations are surprisingly well-characterized by a sum of Boltzmann distributions where the two components include one (TD) that equilibrates with the surface (TTD approximately TS) and a second (IS) that is much hotter than the surface temperature (TIS > TS). Support for the superthermal, yet Boltzmann, nature of the IS channel is provided by molecular dynamics (MD) simulations of CO2 + F-SAMs [Einc = 10.6 kcal/mol], which reveal two-temperature distributions, sticking probabilities, and angular distributions in near quantitative agreement with the experimental PFPE results. Finally, experiments as a function of surface temperature reveal an increase in both sticking probability and rotational/translational temperature of the IS component. Such a trend is consistent with increased surface roughness at higher surface temperature, which increases the overall probability of trapping, yet preferentially leads to impulsive scattering of more highly internally excited CO2 from the surface.

Quantum-State-Resolved CO2 Scattering Dynamics at the Gas−Liquid Interface: Dependence on Incident Angle

Energy transfer dynamics at the gas-liquid interface have been probed with a supersonic molecular beam of CO2 and a clean perfluorinated-liquid surface in vacuum. High-resolution infrared spectroscopy measures both the rovibrational state populations and the translational distributions for the scattered CO2 flux. The present study investigates collision dynamics as a function of incident angle (thetainc = 0 degrees, 30 degrees, 45 degrees, and 60 degrees), where column-integrated quantum state populations are detected along the specular-scattering direction (i.e., thetascat approximately thetainc). Internal state rovibrational and Doppler translational distributions in the scattered CO2 yield clear evidence for nonstatistical behavior, providing quantum-state-resolved support for microscopic branching of the gas-liquid collision dynamics into multiple channels. Specifically, the data are remarkably well described by a two-temperature model, which can be associated with both a trapping desorption (TD) component emerging at the surface temperature (Trot approximately TS) and an impulsive scattering (IS) component appearing at hyperthermal energies (Trot > TS). The branching ratio between the TD and IS channels is found to depend strongly on thetainc, with the IS component growing dramatically with increasingly steeper angle of incidence.

Collision-induced annealing of octanethiol self-assembled monolayers by high-kinetic-energy xenon atoms

Collisions with high-energy xenon atoms (1.3 eV) induce structural changes in octanethiol self-assembled monolayers on Au(111). These changes are characterized at the molecular scale using an in situ scanning tunneling microscope. Gas-surface collisions induce three types of structural transformations: domain boundary annealing, vacancy island diffusion, and phase changes. Collision-induced changes that occur tend to increase order and create more stable structures on the surface. We propose a mechanism where monolayer transformations are driven by large amounts of vibrational energy localized in the alkanethiol molecules. Because we monitor incremental changes over small regions of the surface, we can obtain structural information about octanethiol monolayers that cannot be observed directly in scanning tunneling microscopy images.

Diffusion on a Self-Assembled Monolayer: Molecular Modeling of a Bound + Mobile Lubricant

The diffusion of tricresyl phosphate molecules on an octadecyltrichlorosilane self-assembled monolayer (SAM) was characterized using molecular dynamics simulations. The simulations predict that when placed on the top of a close-packed SAM, the molecules remain mobile on the surface with an isotropic diffusion activation energy of approximately 9 kJ/mol. In contrast, an anisotropic barrier that results from chain tilt within the SAM is predicted for diffusion into a defect created by reducing the alkane chain length within a cylinderical region of the surface. Once in the defect, the molecules become trapped by embedding part of the molecule into the side of the SAM.

Quantum-state resolved reaction dynamics at the gas-liquid interface: Direct absorption detection of HF(v,J) product from F(P2)+Squalane

Exothermic reactive scattering of F atoms at the gas-liquid interface of a liquid hydrocarbon (squalane) surface has been studied under single collision conditions by shot noise limited high-resolution infrared absorption on the nascent HF(v,J) product. The nascent HF(v,J) vibrational distributions are inverted, indicating insufficient time for complete vibrational energy transfer into the surface liquid. The HF(v=2,J) rotational distributions are well fit with a two temperature Boltzmann analysis, with a near room temperature component (T(TD) approximately equal to 290 K) and a second much hotter scattering component (T(HDS) approximately equal to 1040 K). These data provide quantum state level support for microscopic branching in the atom abstraction dynamics corresponding to escape of nascent HF from the liquid surface on time scales both slow and fast with respect to rotational relaxation.

Structural changes of an octanethiol monolayer via hyperthermal rare-gas collisions

In situ scanning tunneling microscopy is used to measure the effect of hyperthermal rare-gas bombardment on octanethiol self-assembled monolayers. Close-packed monolayers remain largely unchanged, even after repeated collisions with 0.4 eV argon and 1.3 eV xenon atoms. In contrast, gas-surface collisions do induce structural changes in the octanethiol film near defects, domain boundaries, and disordered regions, with relatively larger changes observed for xenon-atom bombardment.

Ab initio and direct quasiclassical-trajectory study of the Cl+CH4→HCl+CH3 reaction

We present an electronic structure and dynamics study of the Cl + CH(4)--> HCl + CH(3) reaction. We have characterized the stationary points of the ground-state potential-energy surface using various electronic structure methods and basis sets. Our best calculations, CCSD(T) extrapolated to the complete basis-set limit based on geometries and harmonic frequencies obtained at the CCSD(T)/aug-cc-pvtz level, are in agreement with the experimental reaction energy and indirect measurements of the barrier height. Using ab initio information, we have reparametrized a semiempirical Hamiltonian so that the predictions of the improved Hamiltonian agree with the higher-level calculations in various regions of the potential-energy surface. This improved semiempirical Hamiltonian is then used to propagate quasiclassical trajectories and characterize the reaction dynamics. The good agreement of the calculated HCl rotational and angular distributions with the experiment indicates that reparametrizing semiempirical Hamiltonians is a promising approach to derive accurate potential-energy surfaces for polyatomic reactions. However, excessive energy leakage from the initial vibrational energy of the CH(4) molecule to the reaction coordinate in the trajectory calculations calls into question the suitability of the standard quasiclassical-trajectory method to describe energy partitioning in polyatomic reactions.

Dynamics of HCl Collisions with Hydroxyl- and Methyl-Terminated Self-Assembled Monolayers

Molecular beam scattering techniques are used to explore the energy exchange and thermal accommodation efficiencies of HCl in collisions with long-chain OH- and CH(3)-terminated self-assembled monolayers (SAMs) on gold. Upon colliding with the nonpolar methyl-terminated SAM, HCl (E(i) = 85 kJ/mol) is found to transfer the majority, 83%, of its translational energy to the surface. The extensive energy loss for HCl helps to bring the molecules into thermal equilibrium with the monolayer. Specifically, 72% of the HCl approaches thermal equilibrium prior to desorption. For the molecules that do not thermally accommodate, but scatter after an impulsive collision with the surface, the final translational energy is observed to be directly proportional to the surface temperature as the thermal surface energy and gas translational energy exchange during the collision. For the OH-terminated SAM, the impulsively scattered HCl escapes from the surface with slightly more average energy. The rigid nature of the OH-terminated SAM is due to the extended intra-monolayer hydrogen-bonding network that restricts some of the low-energy modes of the surface. However, despite the rigid nature of this system, the extent of thermal accommodation for HCl on these two surfaces is remarkably similar. It appears that the potential energy well between the impinging HCl and the polar surface groups is sufficient enough to trap HCl molecules that would otherwise scatter impulsively from this rigid SAM.

Theoretical Study of the Effect of Surface Density on the Dynamics of Ar + Alkanethiolate Self-Assembled Monolayer Collisions

We present a classical-trajectory study of energy transfer in collisions of Ar atoms with alkanethiolate self-assembled monolayers (SAMs) of different densities. The density of the SAMs is varied by changing the distance between the alkanethiolate chains in the organic monolayers. Our calculations indicate that SAMs with smaller packing densities absorb more energy from the impinging Ar atoms, in agreement with recent molecular-beam scattering experiments. We find that energy transfer is enhanced by a decrease in the SAM density because (1) less dense SAMs increase the probability of multiple encounters between Ar and the SAM, (2) the vibrational frequencies of large-amplitude motions of the SAM chains decrease for less dense SAMs, which makes energy transfer more efficient in single-encounter collisions, and (3) increases in the distance between chains promote surface penetration of the Ar atom. Analysis of angular distributions reveals that the polar-angle distributions do not have a cosine shape in trapping-desorption processes involving penetration of the Ar atom into the alkanethiolate self-assembled monolayers. Instead, there is a preference for Ar atoms that penetrate the surface to desorb along the chain-tilt direction.