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Oxygen atoms on transition metal surfaces are highly mobile under the demanding pressures and temperatures typically employed for heterogeneously catalyzed oxidation reactions. This mobility allows for rapid surface diffusion of oxygen atoms, as well as absorption into the subsurface and reemergence to the surface, resulting in variable reactivity. Subsurface oxygen atoms play a unique role in the chemistry of oxidized metal catalysts, yet little is known about how subsurface oxygen is formed or returns to the surface. Furthermore, if oxygen diffusion between the surface and subsurface is mediated by defects, there will be localized changes in the surface chemistry due to the elevated oxygen concentration near the emergence sites. We observed that oxygen atoms emerge preferentially along the boundary between surface phases and that subsurface oxygen is depleted before the surface oxide decomposes.

The physics-based molecular force field (PMFF) was developed by integrating a set of potential energy functions in which each term in an intermolecular potential energy function is derived based on experimental values, such as the dipole moments, lattice energy, proton transfer energy, and X-ray crystal structures. The term "physics-based" is used to emphasize the idea that the experimental observables that are considered to be the most relevant to each term are used for the parameterization rather than parameterizing all observables together against the target value. PMFF uses MM3 intramolecular potential energy terms to describe intramolecular interactions and includes an implicit solvation model specifically developed for the PMFF. We evaluated the PMFF in three ways. We concluded that the PMFF provides reliable information based on the structure in a biological system and interprets the biological phenomena accurately by providing more accurate evidence of the biological phenomena.

We explored the interaction of a molecular beam of dimethyl methylphosphonate with a multilayer graphene surface to better understand the fate of chemical warfare agents in the environment. The experiments were done at surface temperatures between 120 and 900 K and translational energies between 200 and 1500 meV. At the lowest temperatures, the dimethyl methylphosphonate is adsorbed, with the molecules next to the carbon surface held slightly more strongly than the bulk molecular film that grows with continued dosing. We measured the desorption energy for submonolayer coverage using modulated beam techniques and found a value of 290 meV (28 kJ/mol). At higher surface temperatures, where the residence times are very short, we measured the scattering of the dimethyl methylphosphonate as a function of angle and translational kinetic energy. For a surface temperature of 250 K, with translational kinetic energies between 200 and 1500 meV, much of the incident flux has nearly been accommodated by the surface temperature and has no memory of the incident momentum. The internal energy also seems to be at least partially accommodated. As the surface temperature increases, the scattering transitions to direct-inelastic reflection, where much of the incident translational energy is retained, and the intensity of the scattering peaks superspecularly toward glancing final angles. These results demonstrate the efficacy of using kinetic energy controlled molecular beams to probe the interactions of complex organic molecules with well-defined surfaces, extending our fundamental understanding of how the dynamics for such systems crossover from trapping-desorption to direct inelastic scattering. Moreover, these results indicate that simulations that model the dispersal of chemical warfare agents using common interfaces in the environment need to account for multiple bounce trajectories and survival of the impinging molecules.

We present the first study detailing the capture and aggregation of hyperthermal CO2 molecules by amorphous solid water (ASW) under ultra-high vacuum conditions at 125 K, near the amorphous/crystalline transition. Using time-resolved in situ reflection-absorption infrared spectroscopy (RAIRS), CO2 molecules with translational energies above 3.0 eV are observed to directly embed underneath the vacuum-solid interface to become absorbed within the ice films despite an inability to adsorb at 125 K; this behavior is not observed for crystalline films. Upon embedding, the mobility of CO2 within 125 K amorphous ice and the strength of its intermolecular interactions result in its segregation into clusters within the ice films. Tracing the kinetics of CO2 embedding events under different energetic conditions allows for elucidation of the underlying dynamics, and we draw comparison with other projectiles we have studied to promote generalized conclusions in regard to empirical prediction of a projectile's embedding probability. Through application of a classical model of the entrance barrier for projectiles colliding with amorphous ice, we provide direct evidence for a unified connection between embedding probability and projectile momentum; an account of all embedding data measured by our group traces a unified barrier model. This work highlights the interplay between translational energy and momentum accommodation during collisions with ice in high speed gas flows.

We have conducted a comprehensive study of ground-state O((3)P) atomic oxygen reactions with 1-hexadecanethiolate (CH3(CH2)15SH) and 1-undecanethiolate (CH3(CH2)10SH) self-assembled monolayers adsorbed onto Au/mica substrates, using X-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, ellipsometry, and contact angle measurements. In general, the reactions are not limited to the terminal methyl groups. Apparently, the incident O((3)P) (translational energy per atom of 0.11 kJ mol(-1)) can penetrate below the surface of the monolayer. The ability of the atoms to penetrate, and thus the reaction rate of the backbone -CH2-, is dependent upon both the temperature and the chain length, with the longer chain having a large difference between the rate at room temperature and 150 K. In particular, the long-chain SAM exhibits clearly reduced reactivity with respect to the incident beam of atomic oxygen when the film is cooled to 150 K as compared to room temperature. This is a notable finding and demonstrates the crucial importance that structural order and dynamical fluctuations, both of which depend on chain length and substrate temperature, have in determining the surface passivation and protection characteristics of SAM overlayers with respect to attack by energetic reagents.

He diffraction has been used to investigate changes in the surface morphology of reconstructed Au(111) when small quantities of O atoms are adsorbed. It is proposed that the electronegative oxygen removes charge from the surface, which causes the surface to revert to the (111) structure. The extent of this deconstruction is dependent on the initial O coverage and the surface temperature. These results further delineate and emphasize the delicate interplay of adsorbate coverage and surface structure for the oxygen-gold system, a topic of current high interest due to the remarkable and technologically relevant catalytic properties of gold interfaces and clusters spanning atomic through nanoscale dimensions.

A study of the interaction of hyperthermal Xe with a well-ordered standing-up phase of 1-decanethiol adsorbed on Au(111) is presented. Experimentally, double-differential measurements were made of the postcollision Xe kinetic energy as a function of incident and final angles. These experiments are compared to classical trajectory calculations. The results show the two expected channels: direct-inelastic scattering from the surface and accommodated Xe due to trapping-desorption. There is also evidence of a further interaction mechanism. This involves the penetration of the atom deep into the channels between the aligned chains of the monolayer. When the collision energy has been dissipated, the implanted Xe is expelled as the chains return to their equilibrium positions. The expelled Xe leaves the surface with an energy much higher than expected for trapping-desorption, and with an angular-intensity distribution peaked close to the direction of the 1-decanethiol chain orientation. For this reason, we call this new scattering mechanism directed ejection.

The solution structure of murine epidermal growth factor (mEGF) at pH 3.1 and a temperature of 28 degrees C has been determined from NMR data, using distance geometry calculations and restrained energy minimization. The structure determination is based on 730 conformational constraints derived from NMR data, including 644 NOE-derived upper bound distance constraints, constraints on the ranges of 32 dihedral angles based on measurements of vicinal coupling constants, and 54 upper and lower bound constraints associated with nine hydrogen bonds and the three disulfide bonds. The distance geometry interpretation of the NMR data is based on previously published sequence-specific 1H resonance assignments [Montelione et al. (1988) Biochemistry 27, 2235-2243], supplemented here with individual assignments for some side-chain amide, methylene, and isopropyl methyl protons. The molecular architecture of mEGF is the same as that described previously [Montelione et al. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 5226-5230], but the structure is overall more precisely determined by a more extensive set of NMR constraints. Analysis of proton NMR line widths, amide proton exchange rates, and side-chain 3J(H alpha-H beta) coupling constants provides evidence for internal motion in several regions of the mEGF molecule. Because mEGF is one member of a large family of homologous growth factors and protein domains for which X-ray crystal structures are not yet available, the atomic coordinates resulting from the present structure refinement (which we have deposited in the Brookhaven Protein Data Bank) are important data for understanding the structures of EGF-like proteins and for further detailed comparisons of these structures with mEGF.

The human alpha 2(V) collagen chain when cleaved with cyanogen bromide yields ten peptides which can be recovered in approximately equimolar quantities. Characterization of the purified peptides with regard to molecular weight and amino acid composition establishes the uniqueness of the peptides and reveals that the alpha 2(V) chain recovered following limited pepsin digestion contain 956 amino acid residues. Possible homologies between the alpha 2(V) peptides and peptides derived from other collagen chains were noted. In addition, a high-performance liquid chromatography system is described for the separation of three of the alpha 2(V) chain peptides which were not resolved by using conventional separation techniques.