Gas-surface scattering dynamics of CO2, NO2, and O3 in collisions with model organic surfaces

High-energy (70 kJ/mol) molecular beams of CO(2), NO(2), and O(3) were scattered from long-chain methyl (CH(3)-), hydroxyl (OH-), and perfluoro (CF(3)(CF(2))(8)-, or F-) ω-functionalized alkanethiol self-assembled monolayers (SAMs) on gold to study the dynamics of energy exchange and thermal accommodation of atmospherically important triatomic molecules on model organic surfaces. Overall, the extent of energy transfer in gas collisions with all of the surfaces studied was substantial. Specifically, the triatomics scatter from each surface only after dissipating greater than 80% of their incident energy. Furthermore, although the OH-SAM is a more rigid surface, the extent of energy transfer and accommodation of these molecules to the CH(3)- and OH-SAMs were approximately the same. The similar scattering dynamics are likely due to significant gas-surface attractive forces between the triatomics and the OH terminal groups, which compensate for the rigidity of this monolayer. In contrast to the OH- and CH(3)-SAMs, the dominant pathway in collisions of the gases with the F-SAM was impulsive scattering. The portion of molecules that accommodated (<40%) to the F-SAM was about half of the amount that accommodated (～70%) to the CH(3)- and OH-SAMs. Although differences in the surface properties had a significant effect on the dynamics, variances in the chemical and physical properties of the three gases, CO(2), NO(2), and O(3), were found to have little effect on the extent of energy transfer and accommodation for collisions with any one surface.     

Packing density and structure effects on energy-transfer dynamics in argon collisions with organic monolayers

A combined experimental and molecular-dynamics simulation study has been used to investigate energy-transfer dynamics of argon atoms when they collide with n-alkanethiols adsorbed to gold and silver substrates. These surfaces provide the opportunity to explore how surface structure and packing density of alkane chains affect energy transfer in gas-surface collisions while maintaining the chemical nature of the surface. The chains pack standing up with 12 degrees and 30 degrees tilt angles relative to the surface normal and number densities of 18.9 and 21.5 A(2)molecule on the silver and gold substrates, respectively. For 7-kJmol argon scattering, the two surfaces behave equivalently, fully thermalizing all impinging argon atoms. In contrast, these self-assembled monolayers (SAMs) are not equally efficient at absorbing the excess translational energy from high-energy, 35 and 80 kJmol, argon collisions. When high-energy argon atoms are scattered from a SAM on silver, the fraction of atoms that reach thermal equilibrium with the surface and the average energy transferred to the surface are lower than for analogous SAMs on gold. In the case of argon atoms with 80 kJmol of translational energy scattering from long-chain SAMs, 60% and 45% of the atoms detected have reached thermal equilibrium with the monolayers on gold and silver surfaces, respectively. The differences in the scattering characteristics are attributed to excitation efficiencies of different types of surface modes. The high packing density of alkyl chains on silver restricts certain low-energy degrees of freedom from absorbing energy as efficiently as the lower-density monolayers. In addition, molecular-dynamics simulations reveal that the extent to which argon penetrates into the monolayer is related to packing density. For argon atoms with 80-kJmol incident energy, we find 16% and 7% of the atoms penetrate below the terminal methyl groups of C(10) SAMs on gold and silver, respectively.     

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.     

Surface structure and interface dynamics of alkanethiol self-assembled monolayers on Au(111)

Scanning tunneling microscopy (STM) and high-resolution electron energy loss spectroscopy (HREELS) were used to examine the structural transitions and interface dynamics of octanethiol (OT) self-assembled monolayers (SAMs) caused by long-term storage or annealing at an elevated temperature. We found that the structural transitions of OT SAMs from the c(4 x 2) superlattice to the (6 x square root 3) superlattice resulting from long-term storage were caused by both the dynamic movement of the adsorbed sulfur atoms on several adsorption sites of the Au(111) surface and the change of molecular orientation in the ordered layer. Moreover, it was found that the chemical structure of the sulfur headgroups does not change from monomer to dimer by the temporal change of SAMs at room temperature. Contrary to the results of the long-term-stored SAMs, it was found that the annealing process did not modify either the interfacial or chemical structures of the sulfur headgroups or the two-dimensional c(4 x 2) domain structure. Our results will be very useful for a better understanding of the interface dynamics and stability of sulfur atoms in alkanethiol SAMs on Au(111) surfaces.     

Hyperthermal organic thin film growth on surfaces terminated with self-assembled monolayers. I. The dynamics of trapping

We have examined the initial stages of growth of a crystalline small molecule organic thin film, diindenoperylene (DIP), on SiO(2) surfaces terminated with a series of self-assembled monolayers (SAMs). In this study we make use of supersonic molecular beam techniques to vary the incident kinetic energy of the DIP molecules, and we use in situ, real time synchrotron x-ray scattering to monitor the buildup of each molecular layer in the growing thin film. We find that the effects of the SAMs are most apparent concerning growth in the sub-monolayer regime, before the substrate is entirely covered by the DIP thin film. In this coverage regime on bare SiO(2), and SiO(2) terminated with either hexamethyldisilazane or perflurooctyltrichlorosilane the adsorption dynamics are consistent with trapping-mediated adsorption as observed in more simple systems, where the probability of adsorption decreases significantly with increasing kinetic energy. Once these surfaces are covered with DIP, however, the adsorption probability increases, particularly at the highest incident kinetic energy, and the probability of adsorption exhibits only a weak dependence on the incident kinetic energy. In contrast, on surfaces terminated by octyl- (OTS) and octadecyltrichlorosilane (ODTS) the trapping probability is high and exhibits little dependence on the incident kinetic energy, essentially the same as what is observed on these same surfaces covered by DIP. We postulate, which is backed by the results of molecular dynamics simulations, that direct molecular insertion into the OTS and ODTS layers is a primary explanation for efficient trapping on these surfaces.     

Hydroxyl radical at the air-water interface

Interaction of the hydroxyl radical with the liquid water surface was studied using classical molecular dynamics computer simulations. From a series of scattering trajectories, the thermal and mass accommodation coefficients of OH on liquid water at 300 K were determined to be 0.95 and 0.83, respectively. The calculated free energy profile for transfer of OH across the air-water interface at 300 K exhibits a minimum in the interfacial region, with the free energy of adsorbtion (DeltaGa) being about 1 kcal/mol more negative than the hydration free energy (DeltaGs). The propensity of the hydroxyl radical for the air-water interface manifests itself in partitioning of OH radicals between the bulk water and the surface. The enhancement of the surface concentration of OH relative to its concentration in the aqueous phase suggests that important OH chemistry may be occurring in the interfacial layer of water droplets, aqueous aerosol particles, and thin water films adsorbed on solid surfaces. This has profound consequences for modeling heterogeneous atmospheric chemical processes.     

Rotationally inelastic scattering from surfaces CO(g) + LiF(OO1)

The rotationally inelastic scattering of a supersonic, rotanonally cold (T_rot^I = 4–30 k) CO molecular beam from a clean LiF(001) surface has been investigated by VUV laser-induced fluorescence. Rotational accommodation was incomplete for surface temperatures 350 <T_s < 900 K. The degree of accommodation decreased with T_s and was independent of collision energy.     

Experimental and theoretical studies of the effect of mass on the dynamics of gas/organic-surface energy transfer

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.     

Probing Chemical Dynamics at Surfaces

An account is given of recent progress concerning chemical reaction dynamics at surfaces. The goal is to elucidate the reaction dynamics at the molecular level, both as time and distance is concerned. The methods of study include molecular beam scattering, scanning tunnelling microscopy, and (femtosecond) laser spectroscopy. Systems studied include elementary interactions of NO, CO, and O₂ at single crystal metal surfaces.     

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

We have investigated collisions between Ar and alkanethiolate self-assembled monolayers (SAMs) using classical trajectory calculations with several potential-energy surfaces. The legitimacy of the potential-energy surfaces is established through comparison with molecular-beam data and ab initio calculations. Potential-energy surfaces used in previous work overestimate the binding of Ar to the SAM, leading to larger energy transfer than found in the experiments. New calculations, based on empirical force fields that better reproduce ab initio calculations, exhibit improved agreement with the experiments. In particular, polar-angle-dependent average energies calculated with explicit-atom potential-energy surfaces are in excellent agreement with the experiments. Polar- and azimuthal-angle-dependent product translational energies are examined to gain deeper insight into the dynamics of Ar+SAM collisions.     

New sights into the electrochemical interface provided by in situ X-ray absorption fine structure and surface X-ray scattering

Various important processes, such as electron transfer reactions, adsorption/desorption, solvation/desolvation, and formation/cleavage of chemical bonds, take place at electrolyte/electrode interfaces during electrocatalytic reactions. Those processes have been understood on the basis of changes in the surface composition, atomic arrangement, and molecular and electronic structures of the interfaces by using various in situ analysis techniques. To date, in situ analysis and observation of those interfacial processes at an ideal single-crystal surface are indispensable not only for fundamental understanding of the reaction mechanism but also for rational design of the highly efficient and durable electrocatalytic materials. Here, historical and recent progress of in situ studies on electrocatalytic reactions is briefly reviewed with a focus on two major techniques, X-ray absorption fine structure and surface X-ray scattering.     

Scattering, accommodation, and trapping of HCl in collisions with a hydroxylated self-assembled monolayer

Time-of-flight molecular beam scattering techniques are used to explore the energy exchange, thermal accommodation, and residence time of HCl in collisions with an OH-terminated self-assembled monolayer. The monolayer, consisting of 16-mercapto-1-hexadecanol (HS(CH(2))(16)OH) self-assembled on gold, provides a well-characterized surface containing hydroxyl groups located at the gas-solid interface. Upon colliding with the hydroxylated surface, the gas-phase HCl is found to follow one of three pathways: direct impulsive scattering, thermal accommodation followed by prompt desorption, and temporary trapping through HO--- HCl hydrogen bond formation. For an incident energy of 85 kJ/mol, the HCl transfers the majority, >80%, of its translational energy to the surface. The extensive energy exchange facilitates thermalization, leading to very large accommodation probabilities on the surface. Under the experimental conditions used in this work, over 75% of the HCl approaches thermal equilibrium with the surface before desorption and, for a 6 kJ/mol HCl beam, nearly 100% of the molecules that recoil from the surface can be described by a thermal distribution at the temperature of the surface. For the molecules that reach thermal equilibrium with the surface prior to desorption, a significant fraction appear to form hydrogen bonds with surface hydroxyl groups. The adsorption energy, determined by measuring the HCl residence time as a function of surface temperature, is 24 +/- 2 kJ/mol.     

Molecular dynamics simulations of low-ordered alzheimer β-amyloid oligomers from dimer to hexamer on self-assembled monolayers

Accumulation of small soluble oligomers of amyloid-β (Aβ) in the human brain is thought to play an important pathological role in Alzheimer's disease. The interaction of these Aβ oligomers with cell membrane and other artificial surfaces is important for the understanding of Aβ aggregation and toxicity mechanisms. Here, we present a series of exploratory molecular dynamics (MD) simulations to study the early adsorption and conformational change of Aβ oligomers from dimer to hexamer on three different self-assembled monolayers (SAMs) terminated with CH(3), OH, and COOH groups. Within the time scale of MD simulations, the conformation, orientation, and adsorption of Aβ oligomers on the SAMs is determined by complex interplay among the size of Aβ oligomers, the surface chemistry of the SAMs, and the structure and dynamics of interfacial waters. Energetic analysis of Aβ adsorption on the SAMs reveals that Aβ adsorption on the SAMs is a net outcome of different competitions between dominant hydrophobic Aβ-CH(3)-SAM interactions and weak CH(3)-SAM-water interactions, between dominant electrostatic Aβ-COOH-SAM interactions and strong COOH-SAM-water interactions, and between comparable hydrophobic and electrostatic Aβ-OH-SAM interactions and strong OH-SAM-water interactions. Atomic force microscopy images also confirm that all of three SAMs can induce the adsorption and polymerization of Aβ oligomers. Structural analysis of Aβ oligomers on the SAMs shows a dramatic increase in structural stability and β-sheet content from dimer to trimer, suggesting that Aβ trimer could act as seeds for Aβ polymerization on the SAMs. This work provides atomic-level understanding of Aβ peptides at interface.     

Neutralization of methyl cation via chemical reactions in low-energy ion-surface collisions with fluorocarbon and hydrocarbon self-assembled monolayer films

Low-energy ion-surface collisions of methyl cation at hydrocarbon and fluorocarbon self-assembled monolayer (SAM) surfaces produce extensive neutralization of CH3+. These experimental observations are reported together with the results obtained for ion-surface collisions with the molecular ions of benzene, styrene, 3-fluorobenzonitrile, 1,3,5-triazine, and ammonia on the same surfaces. For comparison, low-energy gas-phase collisions of CD3+ and 3-fluorobenzonitrile molecular ions with neutral n-butane reagent gas were conducted in a triple quadrupole (QQQ) instrument. Relevant MP2 6-31G*//MP2 6-31G* ab initio and thermochemical calculations provide further insight in the neutralization mechanisms of methyl cation. The data suggest that neutralization of methyl cation with hydrocarbon and fluorocarbon SAMs occurs by concerted chemical reactions, i.e., that neutralization of the projectile occurs not only by a direct electron transfer from the surface but also by formation of a neutral molecule. The calculations indicate that the following products can be formed by exothermic processes and without appreciable activation energy: CH4 (formal hydride ion addition) and C2H6 (formal methyl anion addition) from a hydrocarbon surface and CH3F (formal fluoride addition) from a fluorocarbon surface. The results also demonstrate that, in some cases, simple thermochemical calculations cannot be used to predict the energy profiles because relatively large activation energies can be associated with exothermic reactions, as was found for the formation of CH3CF3 (formal addition of trifluoromethyl anion).     

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.     

Mechanisms and Beyond: Elucidation of Fluxional Dynamics by Exchange NMR Spectroscopy

Detailed mechanistic information is crucial to our understanding of reaction pathways and selectivity. Dynamic exchange NMR techniques, in particular 2D exchange spectroscopy (EXSY) and its modifications, provide indispensable intricate information on the mechanisms of organic and inorganic reactions and other phenomena, for example, the dynamics of interfacial processes. In this Review, key results from exchange NMR studies of small molecules over the last few decades are systemised and discussed. After a brief introduction to the theory, the key types of dynamic processes are identified and fundamental examples given of intra- and intermolecular reactions, which, in turn, could involve, or not, bond-making and bond-breaking events. Following that logic, internal molecular rotation, intramolecular stereomutation and molecular recognition will first be considered because they do not typically involve bond breaking. Then, rearrangements, substitution-type reactions, cyclisations, additions and other processes affecting chemical bonds will be discussed. Finally, interfacial molecular dynamics and unexpected combinations of different types of fluxional processes will also be highlighted. How exchange NMR spectroscopy helps to identify conformational changes, coordination and molecular recognition processes as well as quantify reaction energy barriers and extract detailed mechanistic information by using reaction rate theory in conjunction with computational techniques will be shown.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Vibrational Stark shift spectroscopy of catalysts under the influence of electric fields at electrode–solution interfaces

External control of chemical processes is a subject of widespread interest in chemical research, including control of electrocatalytic processes with significant promise in energy research. The electrochemical double-layer is the nanoscale region next to the electrode/electrolyte interface where chemical reactions typically occur. Understanding the effects of electric fields within the electrochemical double layer requires a combination of synthesis, electrochemistry, spectroscopy, and theory. In particular, vibrational sum frequency generation (VSFG) spectroscopy is a powerful technique to probe the response of molecular catalysts at the electrode interface under bias. Fundamental understanding can be obtained via synthetic tuning of the adsorbed molecular catalysts on the electrode surface and by combining experimental VSFG data with theoretical modelling of the Stark shift response. The resulting insights at the molecular level are particularly valuable for the development of new methodologies to control and characterize catalysts confined to electrode surfaces. This Perspective article is focused on how systematic modifications of molecules anchored to surfaces report information concerning the geometric, energetic, and electronic parameters of catalysts under bias attached to electrode surfaces.

Heterogeneous electrocatalysis: characterization of interfacial electric field within the electrochemical double layer.     

Differentiation of isomeric oxygenated adsorbates using low-energy ion/surface collisions

Reactive scattering of polyatomic ions in the hyperthermal collision energy range (<100 eV) is used to distinguish isomeric oxygenated adsorbates and to quantify their relative amounts when co-adsorbed at a surface. The self-assembled monolayers (SAMs) of interest are constructed from HO-terminated, CH₃O-terminated, and CH₃CH₂O-terminated dialkyl disulfides. Projectile ions used for ion/surface scattering experiments include CF₃⁺, SiCl₃⁺, and the molecular ion of pyridine, C₅H₅N√⁺. Each of these ions exhibits a unique scattered ion profile upon collision with the SAM monolayer surfaces, and so provides different information about the surfaces. Hydrogen atom abstraction by the C₅H₅N√⁺ ion is more prominent at the CH₃CH₂O- and CH₃O-terminated surfaces than the HO-terminated surface, while collisions of SiCl₃⁺ yield reactively scattered products which reflect the chemical composition of these surfaces. For instance, SiCl₂OH⁺ and SiCl₂OCH₃⁺ are scattered from the HO-terminated and CH₃O-terminated surfaces, respectively. Ion/surface collisions involving the CF₃⁺ ion produce chemically sputtered ions from the oxygenated adsorbates, which are valuable for quantitation of those groups. Preferential sputtering of the CH₃O-terminated versus the HO-terminated SAM surface is ascribed to favored thermochemistry and the more accessible CH₃O-terminated adsorbate. Fundamental ion/surface scattering processes, such as inelastic collisions leading to surface-induced dissociation (SID), ion/surface reaction, and chemical sputtering are examined over a range of collision energies for each of the ion/surface types mentioned, and their value in surface analysis is demonstrated.