Vibrational dynamics and band structure of methyl-terminated Ge(111)

A combined synthesis, experiment, and theory approach, using elastic and inelastic helium atom scattering along with ab initio density functional perturbation theory, has been used to investigate the vibrational dynamics and band structure of a recently synthesized organic-functionalized semiconductor interface. Specifically, the thermal properties and lattice dynamics of the underlying Ge(111) semiconductor crystal in the presence of a commensurate (1 × 1) methyl adlayer were defined for atomically flat methylated Ge(111) surfaces. The mean-square atomic displacements were evaluated by analysis of the thermal attenuation of the elastic He diffraction intensities using the Debye-Waller model, revealing an interface with hybrid characteristics. The methyl adlayer vibrational modes are coupled with the Ge(111) substrate, resulting in significantly softer in-plane motion relative to rigid motion in the surface normal. Inelastic helium time-of-flight measurements revealed the excitations of the Rayleigh wave across the surface Brillouin zone, and such measurements were in agreement with the dispersion curves that were produced using density functional perturbation theory. The dispersion relations for H-Ge(111) indicated that a deviation in energy and lineshape for the Rayleigh wave was present along the nearest-neighbor direction. The effects of mass loading, as determined by calculations for CD_3-Ge(111), as well as by force constants, were less significant than the hybridization between the Rayleigh wave and methyl adlayer librations. The presence of mutually similar hybridization effects for CH_3-Ge(111) and CH_3-Si(111) surfaces extends the understanding of the relationship between the vibrational dynamics and the band structure of various semiconductor surfaces that have been functionalized with organic overlayers

Experimental and theoretical study of rotationally inelastic diffraction of H_2(D_2) from methyl-terminated Si(111)

Fundamental details concerning the interaction between H_2 and CH_3–Si(111) have been elucidated by the combination of diffractive scattering experiments and electronic structure and scattering calculations. Rotationally inelastic diffraction (RID) of H_2 and D_2 from this model hydrocarbon-decorated semiconductor interface has been confirmed for the first time via both time-of-flight and diffraction measurements, with modest j = 0 → 2 RID intensities for H_2 compared to the strong RID features observed for D_2 over a large range of kinematic scattering conditions along two high-symmetry azimuthal directions. The Debye-Waller model was applied to the thermal attenuation of diffraction peaks, allowing for precise determination of the RID probabilities by accounting for incoherent motion of the CH_3–Si(111) surface atoms. The probabilities of rotationally inelastic diffraction of H_2 and D_2 have been quantitatively evaluated as a function of beam energy and scattering angle, and have been compared with complementary electronic structure and scattering calculations to provide insight into the interaction potential between H_2 (D_2) and hence the surface charge density distribution. Specifically, a six-dimensional potential energy surface (PES), describing the electronic structure of the H_2(D_2)/CH_3−Si(111) system, has been computed based on interpolation of density functional theory energies. Quantum and classical dynamics simulations have allowed for an assessment of the accuracy of the PES, and subsequently for identification of the features of the PES that serve as classical turning points. A close scrutiny of the PES reveals the highly anisotropic character of the interaction potential at these turning points. This combination of experiment and theory provides new and important details about the interaction of H_2 with a hybrid organic-semiconductor interface, which can be used to further investigate energy flow in technologically relevant systems

Experimental and theoretical study of rotationally inelastic diffraction of H_2(D_2) from methyl-terminated Si(111)

Fundamental details concerning the interaction between H_2 and CH_3–Si(111) have been elucidated by the combination of diffractive scattering experiments and electronic structure and scattering calculations. Rotationally inelastic diffraction (RID) of H_2 and D_2 from this model hydrocarbon-decorated semiconductor interface has been confirmed for the first time via both time-of-flight and diffraction measurements, with modest j = 0 → 2 RID intensities for H_2 compared to the strong RID features observed for D_2 over a large range of kinematic scattering conditions along two high-symmetry azimuthal directions. The Debye-Waller model was applied to the thermal attenuation of diffraction peaks, allowing for precise determination of the RID probabilities by accounting for incoherent motion of the CH_3–Si(111) surface atoms. The probabilities of rotationally inelastic diffraction of H_2 and D_2 have been quantitatively evaluated as a function of beam energy and scattering angle, and have been compared with complementary electronic structure and scattering calculations to provide insight into the interaction potential between H_2 (D_2) and hence the surface charge density distribution. Specifically, a six-dimensional potential energy surface (PES), describing the electronic structure of the H_2(D_2)/CH_3−Si(111) system, has been computed based on interpolation of density functional theory energies. Quantum and classical dynamics simulations have allowed for an assessment of the accuracy of the PES, and subsequently for identification of the features of the PES that serve as classical turning points. A close scrutiny of the PES reveals the highly anisotropic character of the interaction potential at these turning points. This combination of experiment and theory provides new and important details about the interaction of H_2 with a hybrid organic-semiconductor interface, which can be used to further investigate energy flow in technologically relevant systems

Dimensionality-reduction techniques for complex mass spectrometric datasets: Application to laboratory atmospheric organic oxidation experiments

Oxidation of organic compounds in the atmosphere produces an immensely complex mixture of product species, posing a challenge for both their measurement in laboratory studies and their inclusion in air quality and climate models. Mass spectrometry techniques can measure thousands of these species, giving insight into these chemical processes, but the datasets themselves are highly complex. Data reduction techniques that group compounds in a chemically and kinetically meaningful way provide a route to simplify the chemistry of these systems but have not been systematically investigated. Here we evaluate three approaches to reducing the dimensionality of oxidation systems measured in an environmental chamber: positive matrix factorization (PMF), hierarchical clustering analysis (HCA), and a parameterization to describe kinetics in terms of multigenerational chemistry (gamma kinetics parameterization, GKP). The evaluation is implemented by means of two datasets: synthetic data consisting of a three-generation oxidation system with known rate constants, generation numbers, and chemical pathways; and the measured products of OH-initiated oxidation of a substituted aromatic compound in a chamber experiment. We find that PMF accounts for changes in the average composition of all products during specific periods of time but does not sort compounds into generations or by another reproducible chemical process. HCA, on the other hand, can identify major groups of ions and patterns of behavior and maintains bulk chemical properties like carbon oxidation state that can be useful for modeling. The continuum of kinetic behavior observed in a typical chamber experiment can be parameterized by fitting species' time traces to the GKP, which approximates the chemistry as a linear, first-order kinetic system. The fitted parameters for each species are the number of reaction steps with OH needed to produce the species (the generation) and an effective kinetic rate constant that describes the formation and loss rates of the species. The thousands of species detected in a typical laboratory chamber experiment can be organized into a much smaller number (10-30) of groups, each of which has a characteristic chemical composition and kinetic behavior. This quantitative relationship between chemical and kinetic characteristics, and the significant reduction in the complexity of the system, provides an approach to understanding broad patterns of behavior in oxidation systems and could be exploited for mechanism development and atmospheric chemistry modeling.National Science Foundation (U.S.) (Grant AGS-1638672)Erwin-Schrödinger-Stipendium (Grant J-3900

Influence of the NO/NO2 Ratio on Oxidation Product Distributions under High-NO Conditions

Organic oxidation reactions in the atmosphere can be challenging to parse due to the large number of branching points within each molecule’s reaction mechanism. This complexity can complicate the attribution of observed effects to a particular chemical pathway. In this study, we simplify the chemistry of atmospherically relevant systems, and particularly the role of NO[subscript x], by generating individual alkoxy radicals via alkyl nitrite photolysis (to limit the number of accessible reaction pathways) and measuring their product distributions under different NO/NO₂ ratios. Known concentrations of NO in the classically “high-NO” range are maintained in the chamber, thereby constraining first-generation RO₂ (peroxy radicals) to react nearly exclusively with NO. Products are measured in both the gas phase (with a proton-transfer reaction mass spectrometer) and the particle phase (with an aerosol mass spectrometer). We observe substantial differences in measured products under varying NO/NO₂ ratios (from ∼0.1 to >1); along with modeling simulations using the Master Chemical Mechanism (MCM), these results suggest indirect effects of NO[subscript x] chemistry beyond the commonly cited RO₂ + NO reaction. Specifically, lower-NO/NO₂ ratios foster higher concentrations of secondary OH, higher concentrations of peroxyacyl nitrates (PAN, an atmospheric reservoir species), and a more highly oxidized product distribution that results in more secondary organic aerosol (SOA). The impact of NO[subscript x] concentration beyond simple RO₂ branching must be considered when planning laboratory oxidation experiments and applying their results to atmospheric conditions.NSF (Grant CHE-1709993

Atomic Surface Structure of CH_3-Ge(111) Characterized by Helium Atom Diffraction and Density Functional Theory

The atomic-scale surface structure of methyl-terminated germanium (111) has been characterized by using a combination of helium atom scattering and density functional theory. High-resolution helium diffraction patterns taken along both the ⟨1̅21̅⟩ and the ⟨011̅⟩ azimuthal directions reveal a hexagonal packing arrangement with a 4.00 ± 0.02 Å lattice constant, indicating a commensurate (1 × 1) methyl termination of the primitive Ge(111) surface. Taking advantage of Bragg and anti-Bragg diffraction conditions, a step height of 3.28 ± 0.02 Å at the surface has been extracted using variable de Broglie wavelength specular scattering; this measurement agrees well with bulk values from CH_3-Ge(111) electronic structure calculations reported herein. Density functional theory showed that methyl termination of the Ge(111) surface induces a mild inward relaxation of 1.66% and 0.60% from bulk values for the first and second Ge–Ge bilayer spacings, respectively. The DFT-calculated rotational activation barrier of a single methyl group about the Ge–C axis on a fixed methyl-terminated Ge(111) surface was found to be approximately 55 meV, as compared to 32 meV for a methyl group on the H-Ge(111) surface, sufficient to hinder the free rotation of the methyl groups on the Ge(111) surface at room temperature. However, accurate MD simulations demonstrate that cooperative motion of neighboring methyl groups allows a fraction of the methyl groups to fully rotate on the picosecond time scale. These experimental data in conjunction with theory provide a quantitative evaluation of the atomic-scale surface structure for this largely unexplored, yet technologically interesting, hybrid organic–semiconductor interface

Mechanistic study of the formation of ring-retaining and ring-opening products from the oxidation of aromatic compounds under urban atmospheric conditions

Aromatic hydrocarbons make up a large fraction of anthropogenic volatile organic compounds and contribute significantly to the production of tropospheric ozone and secondary organic aerosol (SOA). Four toluene and four 1,2,4-trimethylbenzene (1,2,4-TMB) photooxidation experiments were performed in an environmental chamber under relevant polluted conditions (NOx ~ 10 ppb). An extensive suite of instrumentation including two proton-transferreaction mass spectrometers (PTR-MS) and two chemical ionisation mass spectrometers (NHC 4 CIMS and I- CIMS) allowed for quantification of reactive carbon in multiple generations of hydroxyl radical (OH)-initiated oxidation. Oxidation of both species produces ring-retaining products such as cresols, benzaldehydes, and bicyclic intermediate compounds, as well as ring-scission products such as epoxides and dicarbonyls. We show that the oxidation of bicyclic intermediate products leads to the formation of compounds with high oxygen content (an O V C ratio of up to 1.1). These compounds, previously identified as highly oxygenated molecules (HOMs), are produced by more than one pathway with differing numbers of reaction steps with OH, including both auto-oxidation and phenolic pathways. We report the elemental composition of these compounds formed under relevant urban high-NO conditions. We show that ringretaining products for these two precursors are more diverse and abundant than predicted by current mechanisms. We present the speciated elemental composition of SOA for both precursors and confirm that highly oxygenated products make up a significant fraction of SOA. Ring-scission products are also detected in both the gas and particle phases, and their yields and speciation generally agree with the kinetic model prediction.NSF award (AGS-1638672)Core Center grant (grant no. P30-ES002109) from the National Institute of Environmental Health Sciences, National Institutes of HealthNational Science Foundation (grant no. AGS-1638672)National Institute of Environmental Health Sciences (grant no. P30-ES002109)Austrian Science Fund (grant no. J-3900