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ABSTRACT: We have studied structural and dynamic properties of water confined between hydrophobic alkanethiol self-assembled monolayers (SAMs) using molecular-dynamics simulations. After quantifying the hydrophobic nature of the SAM surfaces via contact-angle calculations involving water droplets, we analyze the effect that the hydrophobic surfaces have on structural properties of the confined water such as density, tetrahedral ordering, orientational structure at the SAM-water interface, and on dynamical properties via calculation of diffusion coefficients. Both the SPC/E and TIP5P water models have been utilized in the calculations. All of the analyses of the structure and dynamics of water are performed as a function of separation from the surface with a focus on determining the range of the effect of hydrophobic surfaces on the water film. We show that the effects of the surface are not noticeable at water-film depths of approximately 1 nm for the structural properties examined. However, calculated diffusion coefficients in the plane of the surface indicate the SAMs induce enhancement of water motion clearly beyond 1 nm. While the enhanced lateral diffusion coefficients persist into deeper regions of the water film than any other measure of the hydrophobic effect examined in this work, the range of influence of the surface on the dynamics of water falls dramatically short of the range for hydrophobic interactions measured in some experiments.
The Journal of Physical Chemistry B 04/2011; 115(16):4662-70. · 3.70 Impact Factor
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ABSTRACT: We present a classical-trajectory study of collisions of HCl with hydroxylated alkanethiol self-assembled monolayers. The potential-energy surface used in the trajectory propagation is a combination of the standard OPLS force field to describe the surface and an analytical potential for the gas/surface interaction developed in this work. The gas/surface potential has been derived based on high-quality electronic-structure calculations of model HCl−alcohol systems in the gas phase and includes a flexible Buckingham term and a Coulombic term. The results of the trajectories calculations are in good agreement with recent molecular-beam experiments on the same system, thereby lending support to the accuracy of the calculations. The collision dynamics differ vastly from prior scattering studies involving rare gases and CO, primarily because the gas/surface attraction governed by hydrogen bonding dramatically increases the ability of the gas molecules to trap on the surface for extended times. The properties of the desorbing HCl molecules are largely insensitive to the initial collision energy and are only mildly affected by the incident angle. An analysis of the reaction mechanism reveals the distinct dynamics of trajectories that either recoil from the surface directly or undergo multiple collisions with the surface and result in thermalization.
01/2011;
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ABSTRACT: The dynamics of the reactions of F atoms with octanethiol self-assembled monolayers (SAMs) has been studied using theoretical methods. F+SAM classical trajectories have been propagated directly using a quantum-mechanics (QM)/molecular-mechanics scheme in which the QM portion is described using a specific-reaction-parameters (SRP) semiempirical Hamiltonian. This SRP Hamiltonian has been derived using ab initio information of model gas-phase F+alkane reactions and its accuracy has been calibrated via comparison of the result of direct-dynamics calculations with available experiments on the F+CH(4)-->HF+CH(3) and F+C(2)H(6)-->HF+C(2)H(5) reactions. The F+SAM calculations are used to analyze HF product-energy distributions at collision energies ranging from 0.80 to 11.53 kcal mol(-1) and 0 degrees, 30 degrees, and 60 degrees incident angles with respect to the surface normal. The calculations show that while the HF product is vibrationally excited, it desorbs translationally and rotationally cold at all collision energies and incident angles explored. The calculated results shed light into recent experiments of F-atom reactions with liquid alkane surfaces by providing mechanistic understanding of the factors that govern the amount of energy deposited into the various degrees of freedom of the HF product. Specifically, examination of the dynamics of postreaction HF collisions with the surface shows the role that secondary collisions play in quenching rotational and translational excitation of HF before desorption from the surface.
The Journal of chemical physics 04/2010; 132(13):134307. · 3.09 Impact Factor
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ABSTRACT: The hydroxyl radical (HO*) is a highly reactive oxygen-centered radical whose bimolecular rate constants for reaction with organic compounds (hydrogen atom abstraction) approach the diffusion-controlled limit in aqueous solution. The results reported herein show that hydroxyl radical is considerably less reactive in dipolar, aprotic solvents such as acetonitrile. This diminished reactivity is explained on the basis of a polarized transition state for hydrogen abstraction, in which the oxygen of the hydroxyl radical becomes highly negative and can serve as a hydrogen bond acceptor. Because acetonitrile cannot participate as a hydrogen bond donor, the transition state cannot be stabilized by hydrogen bonding, and the reaction rate is lower; the opposite is true when water is the solvent. This hypothesis explains hydroxyl radical reactivity both in solution and in the gas phase and may be the basis for a "containment strategy" used by Nature when hydroxyl radical is produced endogenously.
Journal of the American Chemical Society 02/2010; 132(9):2907-13. · 9.91 Impact Factor
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ABSTRACT: The reactions between ground-state oxygen atoms (O((3)P)) and the ammonia (NH(3)) and hydrazine (N(2)H(4)) molecules have been studied using electronic-structure and dynamics calculations. Ab initio calculations have been used to characterize the primary reaction channels accessible at hyperthermal energies. These reaction channels are i) hydrogen abstraction, O + NH(3)(N(2)H(4)) --> OH + NH(2)(N(2)H(3)), ii) H-elimination O + NH(3)(N(2)H(4)) --> H + ONH(2)(ON(2)H(3)), and iii) N-N breakage (in the reaction involving hydrazine), O + N(2)H(4) --> ONH(2) + NH(2). Hydrogen abstraction is the lowest-barrier process, followed by N-N breakage and H-elimination. Comparison of our highest-accuracy calculations (CCSD(T)/CBS//MP2/aug-cc-pVDZ) with a variety of lower-cost electronic-structure methods shows that the BHandHLYP method, in combination with the 6-31G* basis set, captures remarkably well the essential features of the potential-energy surface of all of the reaction channels investigated in this work. Using directly the BHandHLYP/6-31G* combination, we have propagated quasiclassical trajectories to characterize the dynamics of the O + NH(3) and O + N(2)H(4) reactions at hyperthermal energies. The trajectory calculations reveal that hydrogen abstraction is the dominant reaction channel, with cross sections between a factor of 2 and an order of magnitude larger than those for the H-elimination and N-N breakage channels. The dynamics calculations also indicate that most of the energy is partitioned into products relative translation but significant vibrational excitation of products is possible as well. Analysis of angular distributions and opacity functions suggests that whereas the hydrogen-abstraction reactions proceed through a mechanism with a substantial component of stripping dynamics, H-elimination and N-N breakage are dominated by rebound dynamics.
The Journal of Physical Chemistry A 11/2009; 113(50):13863-70. · 2.95 Impact Factor
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ABSTRACT: We present a classical-trajectory study of CO collisions with regular (CH3-terminated) and omega-fluorinated (CF3-terminated) alkanethiol self-assembled monolayers (SAMs) with a focus on analyzing the stereodynamics properties of the collision. The CO molecule is scattered with incident angles of either 30 degrees or 60 degrees with respect to the surface normal and with 60 kJ x mol(-1) collision energy, and we analyze final translational and rotational energy, mechanism of the collisions, and orientation and alignment of the rotational angular momentum. Analysis of the alignment of the final rotational angular momentum in collisions involving initially rotationally cold CO indicates a slight preference for "cartwheel" and "corkscrew" rotational motions. In contrast, collisions of initially excited CO slightly favor "helicopter" motion of the recoiling molecule. Moreover, studies of final orientation reveal that, while cartwheel "topspin" motion is favored for collisions in which initially cold CO becomes rotationally excited, no preferred handedness is observed when CO leaves the surfaces with "helicopter" motion. Analysis of trajectories involving initially rotationally excited CO in which the initial rotational angular momentum is aligned and/or oriented shows a non-negligible effect of the initial rotational motion on the dynamics of energy transfer. For instance, CO approaching the SAMs with helicopter motion retains a larger fraction of its initial rotation than molecules colliding with cartwheel-type motions. Conservation of the alignment and orientation of the initial rotational angular momentum vector is also enhanced with helicopter motion relative to cartwheel or random motions. The calculated trends in the stereodynamic properties for the two SAMs indicate that the CH3-SAM is effectively more corrugated than the CF3-SAM.
The Journal of Physical Chemistry A 03/2009; 113(16):4155-67. · 2.95 Impact Factor
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ABSTRACT: We present an experimental and theoretical study of the dynamics of collisions of the CO molecule with organic surfaces. Experimentally, we scatter CO at 60 kJ mol(-1) and 30 degrees incident angle from regular (CH(3)-terminated) and omega-fluorinated (CF(3)-terminated) alkanethiol self-assembled monolayers (SAMs) and measure the time-of-flight distributions at the specular angle after collision. At a theoretical level, we carry out classical-trajectory simulations of the same scattering process using CO/SAM potential-energy surfaces derived from ab initio calculations. Agreement between measured and calculated final translational energy distributions justifies use of the calculations to examine dynamical behavior of the gas/surface system not available directly from the experiment. Calculated state-to-state energy-transfer properties indicate that the collisions are notably vibrationally adiabatic. Similarly, translational energy transfer from and to CO rotation is relatively weak. These trends are examined as a function of collision energy and incident angle to provide a deeper understanding of the factors governing state-to-state energy transfer in gas/organic-surface collisions.
The Journal of chemical physics 03/2009; 130(8):084702. · 3.09 Impact Factor
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ABSTRACT: We present a theoretical study of the dynamics of the first few members of the F + alkane --> HF + alkyl family of reactions (alkane = CH(4), C(2)H(6), C(3)H(8), and i-C(4)H(10)). Quasiclassical trajectories have been propagated employing a reparameterized semiempirical Hamiltonian that was derived in this work based on ab initio information of the global potential-energy surfaces of all reactions studied. The accuracy of the Hamiltonian is probed via comparison of the calculated dynamics properties with experimental results in the F + CH(4) --> HF + CH(3), F + CD(4) --> DF + CD(3), and F + C(2)H(6) --> HF + C(2)H(5) reactions. Additional calculations on the F + C(3)H(8) --> HF + C(3)H(7) and F + i-C(4)H(10) --> HF + C(4)H(9) reactions have been analyzed with emphasis on the difference in the dynamics of reactions occurring at primary, secondary, and tertiary sites. We learn that at low collision energies, the amount of energy going into HF vibration increases very slightly along the primary --> secondary --> tertiary sequence. In addition, reactions involving larger alkane molecules tend to channel more energy toward alkyl products at the expense of the rest of the degrees of freedom. Angular distributions are also dependent on the abstraction site, with tertiary abstractions resulting in slightly more backward scattering than reactions at primary sites.
The Journal of Physical Chemistry A 03/2009; 113(16):4294-304. · 2.95 Impact Factor
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ABSTRACT: We present a classical-trajectory study of the dynamics of energy exchange in collisions between hyperthermal Ar (6-12 eV collision energy) and a fluorinated self-assembled monolayer (SAM). Product translational-energy, polar-angle, and azimuthal-angle distributions as a function of collision energy and incidence angle are presented to provide a detailed description of the gas/surface energy exchange dynamics. Our results indicate that while the properties of the scattered Ar atom at normal and 30 degrees incidence are notably similar and essentially independent of collision energy in the 6-12 eV range, the dynamics of energy exchange when Ar impinges at 60 degrees are remarkably different and depend on collision energy. This behavior is understood via analysis of the microscopic mechanism of the collisions. Three main collision mechanisms-direct collisions without surface penetration, direct collisions involving surface penetration, and surface-penetrating non-direct collisions-are found to govern the dynamics, and the ratio of these mechanisms determines the properties of the scattered Ar atom. Our study also reveals that the Ar atoms that penetrate the organic monolayer do not desorb following a direct-ejection mechanism proposed in recent studies of Xe collisions with a hydrogenated SAM. The vast amount of energy transferred to the surface found in the calculations lends support to recent experiments showing degradation of fluorinated surfaces in collisions with hyperthermal Ar.
Physical Chemistry Chemical Physics 11/2008; 10(37):5776-86. · 3.57 Impact Factor
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ABSTRACT: Molecular beam scattering experiments are used to explore collisions of 60 kJ/mol Ne, CD4, ND3, and D2O with long-chain CH3-, NH2-, and OH-terminated self-assembled monolayers (SAMs) created via the chemisorption of alkanethiols on gold. Time-of-flight measurements for the scattered gases reveal the extent of energy exchange and the propensity for a gas to thermally accommodate with the surface during a collision. Of the four gases studied, Ne transfers the least amount of translational energy into the monolayers and D2O the most. Neon atoms recoil from the OH-SAM with an average of 14.4 kJ/mol of energy, while D2O retains only 6.4 kJ/mol of its 60 kJ/mol incident energy when scattering from the same surface. Overall, the trend in final translational energies follows the order Ne > CD4 > ND3 > D2O for scattering from all three SAMs. The observed trend in the energy exchange is correlated with the gas−surface attractive forces, as determined by ab initio calculations. The thermal accommodation efficiencies of the four gases follow the opposite trend. Thermalization for the Ne atoms is nearly negligible for all three monolayers, whereas D2O and ND3 approach near complete accommodation on all of the monolayers studied. The overall energy exchange and thermal accommodation efficiencies also depend markedly on the terminal group of the SAM. For Ne scattering, the trend for the overall energy transfer follows: CH3- > NH2- ≈ OH-SAMs. In contrast, the overall D2O energy transfer is greater when colliding with the OH-SAM than the nonpolar CH3-SAM. Together, the results show that the extent of energy transfer depends on a balance between the rigidity of the surface, as affected by intrasurface hydrogen bonding, and the strength of the gas−surface attractive forces, as determined by intermolecular interactions.
10/2008;
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ABSTRACT: We present an electronic-structure and dynamics study of the Cl + C2H6 --> HCl + C2H5 reaction. The stationary points of the ground-state potential energy surface have been characterized using various electronic-structure methods and basis sets. Our best calculations, CCSD(T) extrapolated to the complete basis limit, using geometries and harmonic frequencies obtained at the MP2/aug-cc-pVTZ level, are in agreement with the experimental reaction energy. Ab initio information has been used to reparameterize a semiempirical Hamiltonian so that the predictions of the improved Hamiltonian agree with the higher-level calculations in key regions of the potential energy surface. The improved semiempirical Hamiltonian is then used to propagate quasiclassical trajectories. Computed kinetic energy release and scattering angle distributions at a collision energy of approximately 5.5 kcal mol(-1) are in reasonable agreement with experiments, but no evidence was found for the low translational energy HCl products scattered in the backward hemisphere reported in recent experiments.
The Journal of Physical Chemistry A 10/2008; 112(39):9387-95. · 2.95 Impact Factor
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ABSTRACT: Experiments and simulations on the scattering of hyperthermal Ar from a C(0001) surface have been conducted. Measurements of the energy and angular distributions of the scattered Ar flux were made over a range of incident angles, incident energies (2.8-14.1 eV), and surface temperatures (150-700 K). In all cases, the scattering is concentrated in a narrow superspecular peak, with significant energy exchange with the surface. The simulations closely reproduce the experimental observations. Unlike recent experiments on hyperthermal Xe scattering from graphite [Watanabe et al., Eur. Phys. J. D 38, 103 (2006)], the angular dependence of the energy loss is not approximated by the hard cubes model. The simulations are used to investigate why parallel momentum conservation describes Xe scattering, but not Ar scattering, from the surface of graphite. These studies extend our knowledge of gas-surface collisional energy transfer in the hyperthermal regime, and also demonstrate the importance of performing realistic numerical simulations for modeling such encounters.
The Journal of chemical physics 07/2008; 128(22):224708. · 3.09 Impact Factor
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ABSTRACT: We present a theoretical study of the reactions of hydrogen atoms with methane and ethane molecules and isotopomers. High-accuracy electronic-structure calculations have been carried out to characterize representative regions of the potential-energy surface (PES) of various reaction pathways, including H abstraction and H exchange. These ab initio calculations have been subsequently employed to derive an improved set of parameters for the modified symmetrically-orthogonalized intermediate neglect of differential overlap (MSINDO) semiempirical Hamiltonian, which are specific to the H+alkane family of reactions. The specific-reaction-parameter (SRP) Hamiltonian has then been used to perform a quasiclassical-trajectory study of both the H+CH4 and H+C2H6 reactions. The calculated values of dynamics properties of the H+CH4-->H2+CH3 reaction and isotopologues, including alkyl product speed distributions, diatomic product internal-state distributions, and cross sections, are generally in good agreement with experiment and with the results provided by the ZBB3 PES [Z. Xie et al., J. Chem. Phys. 125, 133120 (2006)]. The results of trajectories propagated with the SRP Hamiltonian for the H+C2H6-->H2+C2H5 reaction also agree with experiment. The level of agreement between the results calculated with the SRP Hamiltonian and experiment in both the H+methane and H+ethane reactions indicates that semiempirical Hamiltonians can be improved for not only a specific reaction but also a family of reactions.
The Journal of Chemical Physics 05/2008; 128(19):194302. · 3.33 Impact Factor
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ABSTRACT: The effect of mass on gas/organic-surface energy transfer is explored via investigation of the scattering dynamics of rare gases (Ne, Ar, and Kr) from regular (CH3-terminated) and omega-fluorinated (CF3-terminated) alkanethiol self-assembled monolayers (SAMs) at 60 kJmol collision energy. Molecular-beam scattering experiments carried out in ultrahigh vacuum and molecular-dynamics simulations based on high-accuracy potentials are used to obtain the rare-gases' translational-energy distributions after collision with the SAMs. Simulations indicate that mass is the most important factor in determining the changes in the energy exchange dynamics for Ne, Ar, and Kr collisions on CH3- and CF3-terminated SAMs at 60 kJmol collision energy. Other factors, such as changes in the gas-surface potential and intrasurface interactions, play only a minor role in determining the differential dynamics behavior for the systems studied.
The Journal of Chemical Physics 02/2008; 128(1):014713. · 3.33 Impact Factor
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Diego Troya
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ABSTRACT: We present an extensive study of the barriers of hydrogen abstraction from primary, secondary, and tertiary sites of acyclic alkanes by ground-state oxygen atoms. Our studies include the characterization of the lowest-energy transition states of the O(3P) reactions with methane, ethane, propane, isobutane, and isopentane using high-level ab initio methods. The order of the calculated barriers heights is primary > secondary > tertiary, in agreement with the trends gleaned from kinetic measurements. Analysis of the transition-state geometry reveals a shift toward more reagents-like structures in the primary --> secondary --> tertiary sequence, which concurs with the expectation from Hammond's postulate. Using the ab initio data, we calculate thermal rate constants via transition-state theory. Our highest-level calculations indicate that the room-temperature relative reactivities of primary, secondary, and tertiary alkane sites in hydrogen-abstraction reactions by ground-state oxygen atoms are 1, 29, and 422, respectively. These results are used to interpret recent experiments on the reactions of O(3P) with liquid alkanes.
The Journal of Physical Chemistry A 11/2007; 111(42):10745-53. · 2.95 Impact Factor
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ABSTRACT: We present a classical-trajectory study of the dynamics of high-energy (5-12 eV) collisions between Ar atoms and the C2H6 and C2F6 molecules. We have constructed the potential-energy surfaces for these systems considering separately the Ar-molecule interactions (intermolecular potential) and the interactions within the molecule (intramolecular potential). The intermolecular surfaces consist of pairwise empirical potentials derived from high-accuracy ab initio calculations. The intramolecular potentials for C2H6 and C2F6 are described using specific-reaction-parameters semiempirical Hamiltonians and are calculated "on the fly", i.e., while the trajectories are evolving. Trajectory analysis shows that C2F6 absorbs more energy than C2H6 and is more susceptible to collision-induced dissociation (CID). C-C bond-breakage processes are more important than C-H or C-F bond breakage at the energies explored in this work. Analysis of the reaction mechanism for CID processes indicates that, although C-C breakage is mostly produced by side-on collisions, head-on collisions are more efficient in producing C-F or C-H dissociation. Our results suggest that high-energy collisions between closed-shell species of the natural low-Earth-orbit environment and spacecraft can contribute to the observed degradation of polymers that coat spacecraft surfaces.
The Journal of Physical Chemistry A 06/2007; 111(18):3618-32. · 2.95 Impact Factor
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ABSTRACT: We present a theoretical study of the intermolecular potentials for the Ar, Kr, and Xe-CH4, -CF4 systems. The potential-energy surfaces of these systems have been calculated utilizing second-order Möller-Plesset perturbation theory and coupled-cluster theory in combination with correlation-consistent basis sets (aug-cc-pvnz; n = d, t, q). The calculations show that the stabilizing interactions between the rare gases and the molecules are slightly larger for CF4 than for CH4. Moreover, the rare-gas-CX4 (X = H, F) potentials are more attractive for Xe than for Kr and Ar. Our highest quality ab initio data (focal-point-CCSD(T) extrapolated to the complete basis set limit) have been used to develop pairwise analytical potentials for rare-gas-hydrocarbon (-fluorocarbon) systems. These potentials can be applied in classical-trajectory studies of rare gases interacting with hydrocarbon surfaces.
The Journal of Physical Chemistry A 10/2006; 110(37):10834-43. · 2.95 Impact Factor
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ABSTRACT: We have studied the reactions of hyperthermal atomic oxygen with perfluorinated hydrocarbons using quantum-mechanical and
molecular dynamics methods. Electronic structure calculations reveal that the reaction barriers for all of the primary reaction
channels in the O(3P) + CF4 and C2F6 systems are larger than those in the analogous reactions with methane and ethane.
07/2006: pages 365-375;
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ABSTRACT: This paper presents experimental and theoretical studies of the product energy partitioning associated with the H + CD4 (nu = 0) --> HD + CD3 reaction for the collision energy range 0.5-3.0 eV. The theoretical results are based on quasiclassical trajectories from (1) first principles direct dynamics calculations (B3LYP/6-31G), (2) an empirical surface developed by Espinosa-García [J. Chem. Phys. 2002, 116, 10664] (EG), and (3) two semiempirical surfaces (MSINDO and reparametrized MSINDO). We find that most of the energy appears in product translation at energies just above the reactive threshold; however, HD vibration and rotation become quite important at energies above 1 eV, each accounting for over 20% of the available energy above 1.5 eV, according to the B3LYP calculations. The barrier on the B3LYP surface, though being later than that on EG, predicts significantly higher HD vibrational excitation than EG. This deviation is contradictory to what would be expected on the basis of the Polanyi rules and derives from modest differences in the potential energy surfaces. The CD3 internal energy is generally quite low, and we present detailed rotational state distributions which show that the CD3 rotational distribution is largely independent of collision energy in the 0.75-1.95 eV range. The most populated rotational levels are N = 5 and 6 on B3LYP, with most of that excitation being associated with motion about the C2 axes, rather than C3 axis, of the CD3 product, in good agreement with the experimental results. Through our extensive studies in this and previous work concerning the scattering dynamics, we conclude that B3LYP/6-31G provides the best available description of the overall dynamics for the title reaction at relatively high collision energies.
The Journal of Physical Chemistry A 04/2006; 110(9):3017-27. · 2.95 Impact Factor
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ABSTRACT: 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.
The Journal of Physical Chemistry A 03/2006; 110(4):1319-26. · 2.95 Impact Factor
