Internal molecular conformation of organic glasses: A NEXAFS study.

The origin of the exceptional stability of molecular glasses grown by physical vapor deposition (PVD) is not well understood. Differences in glass density have been correlated with thermodynamic stability for thin films of N,N'-Bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD) grown by PVD at specific substrate temperatures below the glass transition temperature. However, the relationship between the internal conformation of glass molecules and the thermodynamic properties of molecular glasses is not well studied. We use carbon 1s near edge x-ray absorption fine structure (NEXAFS) spectroscopy to examine different TPD sample preparations in which differences in the thermodynamic stability of the glass are known. Density functional theory simulations of the NEXAFS spectra of TPD allow us to attribute spectroscopic differences to changes in the internal conformation of the TPD molecule and relate this conformation to the stability of the TPD glass. This provides a direct experimental measurement of the internal conformation of molecules forming an organic glass.

Temperature Dependence in the NEXAFS Spectra of n-Alkanes.

The near edge X-ray absorption fine structure (NEXAFS) spectra of orthorhombic single crystals of n-octacosane ( n-C28H58), recorded at room temperature (298 K) and at cryogenic temperatures (93 K), show distinct differences. The characteristic carbon 1s → σ*C-H band in the NEXAFS spectrum of n-C28H58 is broader and has a lower-energy onset in its room temperature spectrum than in its NEXAFS spectrum recorded at cryogenic temperatures. Density functional theory simulations show that nuclear motion and molecular disorder contribute to the observed spectral broadness and are the origin of the low-energy onset of the C-H band in the room temperature spectrum.

Systematic Investigation of π-π Interactions in Near-Edge X-ray Fine Structure (NEXAFS) Spectroscopy of Paracyclophanes.

NEXAFS spectroscopy has potential for study of packing and order in organic materials but only if intermolecular effects are understood. This work studies how π-π interactions between adjacent unsaturated groups affect their NEXAFS spectra, with a broader goal of building a general understanding of the role of intermolecular effects in NEXAFS spectroscopy. These effects are examined using paracyclophane (PCP) molecules, in which the benzene-benzene separation distance is controlled by varying the length of the alkyl groups separating the benzene rings. NEXAFS spectroscopy and density functional theory (DFT) simulations are used to examine spectroscopic changes related to the strength of these π-π interactions. A characteristic red shift is observed as adjacent benzene rings get closer together. This shift is attributed to Coulombic and orbital interactions between the adjacent benzene rings, mediated through overlapping π/π* orbitals.

Indirect molecular epitaxy: deposition of n-alkane thin films on Au coated NaCl(001) and HOPG(0001) surfaces.

The epitaxial growth of organic molecules can lead to the formation of complex orientated morphologies. In previous work, we studied the kinetic and thermodynamic factors that drive the epitaxial growth of n-alkane thin films on HOPG(0001) and NaCl(001) by physical vapor deposition. A wide variety of morphologies are observed as a function of deposition conditions (substrate temperature, n-alkane chain length, etc.). In the current study we examine how a modified substrate (Au deposited on a HOPG(0001) or NaCl(001) substrate) affects the epitaxial growth of n-C36H74 (50 nm thick) relative to the uncoated substrates. This "indirect epitaxy", in which the patterned attractive forces of the substrate are transferred through a thin metal film, can tailor the conditions for epitaxial growth. The observation of fourfold symmetry for n-alkane growth on Au/NaCl(001) and sixfold symmetry for n-alkane growth on Au/HOPG(0001) demonstrates indirect epitaxy over a wide range of substrate temperatures during deposition.

Sulfur 1s near edge x-ray absorption fine structure spectroscopy of thiophenic and aromatic thioether compounds.

Thiophenic compounds are major constituents of fossil fuels and pose problems for fuel refinement. The quantification and speciation of these compounds is of great interest in different areas such as biology, fossil fuels studies, geology, and archaeology. Sulfur 1s Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy has emerged as a qualitative and quantitative method for sulfur speciation. A firm understanding of the sulfur 1s NEXAFS spectra of organosulfur species is required for these analytical studies. To support this development, the sulfur 1s NEXAFS spectra of simple thiols and thioethers were previously examined, and are now extended to studies of thiophenic and aromatic thioether compounds, in the gas and condensed phases. High-resolution spectra have been further analyzed with the aid of Improved Virtual Orbital (IVO) and Δ(self-consistent field) ab initio calculations. Experimental sulfur 1s NEXAFS spectra show fine features predicted by calculation, and the combination of experiment and calculation has been used to improve the assignment of spectroscopic features important for the speciation and quantification of sulfur compounds. Systematic differences between gas and condensed phases are also explored; these differences suggest a significant role for conformational effects in the NEXAFS spectra of condensed species.

Effect of substrate temperature on the epitaxial growth of oriented n-alkane thin films on graphite.

A complex orientational morphology is observed when n-alkane thin films are vapor deposited on highly oriented pyrolytic graphite surfaces. Substrate temperature can be used to tune the orientation and morphology of n-alkane thin films. The molecular orientation changes from lateral to normal to the surface when the substrate temperature is raised sufficiently. Under specific substrate temperature conditions, the n-alkane molecules are aligned in the plane of the sample surface, in directions reflecting the 6-fold symmetry of the graphite substrate. A series of different morphologies, from uniform thin films to oriented bars, are observed as a function of chain length and substrate temperature. The systematic evolution of these oriented morphologies is mapped as a function of deposition conditions, and the kinetic and thermodynamic factors that govern the formation of different in-plane and normal domains are considered.

X-ray Spectroptychography.

X-ray spectroptychography is an emerging method for the chemical microanalysis of advanced nanomaterials such as catalysts and batteries. This method builds upon established synchrotron X-ray microscopy and spectromicroscopy techniques with added spatial resolution from ptychography, an algorithmic imaging technique. This minireview will introduce the technique of X-ray spectroptychography, where ptychography is performed with variable photon energy, and discuss recent results and prospects for this method.

Sulfur 1s near-edge x-ray absorption fine structure (NEXAFS) of thiol and thioether compounds.

The speciation and quantification of sulfur species based on sulfur K-edge x-ray absorption spectroscopy is of wide interest, particularly for biological and petroleum science. These tasks require a firm understanding of the sulfur 1s near-edge x-ray absorption fine structure (NEXAFS) spectra of relevant species. To this end, we have examined the gas phase sulfur 1s NEXAFS spectra of a group of simple thiol and thioether compounds. These high-resolution gas phase spectra are free of solid-state broadening, charging, and saturation effects common in the NEXAFS spectra of solids. These experimental data have been further analyzed with the aid of improved virtual orbital Hartree-Fock ab initio calculations. The experimental sulfur 1s NEXAFS spectra show fine features predicted by calculation, and the combination of experiment and calculation has been used to improve assignment of spectroscopic features relevant for the speciation and quantification of the sulfur compounds.

Electron-vibron coupling in halogenated acenaphthenequinone upon O K-edge soft x-ray absorption.

We present high resolution oxygen K near-edge x-ray absorption spectra of the acenaphthenequinone (ANQ) derivative 3,8-dibromo-5,6-dichloro-ANQ (Br(2)Cl(2)-ANQ). The spectral features exhibit an almost identical vibronic fine structure compared to that shown by ANQ. The unequal distances of the vibronic levels as derived from the least-squares fit analysis of the vibronic progressions allows us to determine the anharmonicity of the excited state potentials involved. We conclude that a single vibrational progression couples to the resonant excitation of O 1s core electrons preferentially. Comparison of the two ANQ derivatives gives a clear indication that the vibronic mode corresponds to a C=O stretching mode, rather than coupling to a C-H mode as suggested previously. These conclusions are supported by density functional theory calculations.

Strong double excitation and open-shell features in the near-edge x-ray absorption fine structure spectroscopy of ferrocene and ferrocenium compounds.

We have recorded the iron 2p and carbon 1s near-edge x-ray absorption fine structure (NEXAFS) spectra of decamethyl ferrocene (Fe 3d(6)) and ferrocenium hexafluorophosphate (Fe 3d(5)), two low spin compounds with closed- and open-shell electron configurations, respectively. These species have a similar covalent bonding environment but a different electron configuration, allowing us to examine the role of ligand-metal interactions and electron correlation responsible for their NEXAFS spectra. We have interpreted these spectra with the aid of ab initio configuration interaction (CI) calculations. The CI calculations indicate that double excitation is essential to interpret the Fe 2p NEXAFS spectra of not only the open-shell ferrocenium ion but also the closed-shell ferrocene species, even though the ground states of both species are well described within the Hartree-Fock single-configuration approximation.

Phase separation of palmitic acid and perfluorooctadecanoic acid in mixed Langmuir-Blodgett monolayer films.

Deposition of mixtures of palmitic acid (C15H31COOH) and perfluorooctadecanoic acid (C17F35COOH) onto solid substrates gives rise to irregularly shaped, phase-separated domains under a variety of deposition conditions. The morphology and chemical composition of these phase-separated domains have been investigated using a combination of surface pressure-area isotherms, atomic force microscopy, X-ray photoemission electron microscopy, and confocal fluorescence microscopy imaging. While domain morphology and composition in 2D phase-separated mixed monolayer systems can typically be rationalized in terms of an interplay between line tension and dipole-dipole repulsion effects, it was found that for this system additional kinetic factors, including domain growth rates and the rate of dissolution of the fatty acid component into the aqueous subphase, also play a major role in controlling film properties. The potential importance of these effects for the controlled patterning of solid substrates is discussed.

Effect of chain length and substrate temperature on the growth and morphology of n-alkane thin films.

Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and microscopy has been used to study the orientational morphology of thin films of the linear alkanes n-C36H74 and n-C60H122, prepared by vacuum deposition onto NaCl (001) surfaces at ambient and elevated substrate temperatures. The orientational morphology, specifically, the nature of domains with lateral and normal orientation, is explored as a function of the chain length and the substrate temperature. It is found that the longer n-C60H122 molecules are laterally oriented on the substrate surface within the investigated substrate temperatures but that the morphology of these thin films varies with substrate temperature. The shorter n-C36H74 molecules are partially laterally oriented at low substrate temperature and are completely normally oriented at high substrate temperature. The relative magnitude of "side-by-side" and "end-to-end" intermolecular interactions leads to the formation of highly ordered alkane structures with a high aspect ratio. The formation of complex, nanoscale orientational morphologies are rationalized by considering kinetic and thermodynamic effects, in particular, the relative enthalpic and entropic contributions to the free energy associated with the different molecular orientations.

Matrix effects in the carbon 1s near edge x-ray absorption fine structure spectra of condensed alkanes.

The carbon 1s near edge x-ray absorption fine structure (NEXAFS) spectra of simple gaseous alkane molecules differ from the spectra of the same alkane molecules in the condensed phase. The origin of these large, systematic differences is poorly understood. The NEXAFS spectra of gaseous alkanes are interpreted as a progression of core-->Rydberg transitions with distinctive vibronic structure. The interpretation of the NEXAFS spectra of condensed phase alkanes is varied. Specifically, the degree of Rydberg character in the pre-edge core excited states of condensed alkanes is controversial. We determined the character of core excited states in condensed alkanes with a combination of experiment and computational study. From this, we have determined the nature of matrix effects for these species. The high-resolution carbon 1s NEXAFS spectrum of gaseous neopentane is dramatically different from its condensed phase spectrum, a striking illustration of the dramatic spectroscopic changes that occur upon condensation. High quality ab initio calculations of a cluster designed to model the solid phase environment provide definitive evidence for the reduction of Rydberg character and support the assignment of sigma*C-H) valence character in the pre-edge features in the NEXAFS spectra of condensed alkanes.

Nitrogen 1s near-edge X-ray absorption fine structure spectroscopy of amino acids: Resolving zwitterionic effects.

Considerable variation is observed in the near-edge X-ray absorption fine structure (NEXAFS) spectra of amino acids. To unambiguously characterize the chemical origin of this variation, we have acquired the nitrogen 1s NEXAFS spectra of several amino acids and other model compounds and complemented these experimental measurements with ab initio calculations of isolated molecules and molecular clusters. The systematic differences observed between the zwitterionic and un-ionized forms of amino acids arise directly from the structural difference (-NH2 vs -NH3+), which leads to a change in the degree of Rydberg-valence mixing. Further change arises from quenching of this Rydberg character in the spectra of condensed amino acids. Ab initio calculations are used to explore the degree of Rydberg-valence mixing in the solid state.

Rydberg-valence mixing in the carbon 1s near-edge X-ray absorption fine structure spectra of gaseous alkanes.

We have acquired high-resolution carbon 1s near-edge X-ray absorption fine structure (NEXAFS) spectra of methane, ethane, propane, isobutane, and neopentane. These experimental measurements are complemented by high-quality ab initio calculations, performed with the improved virtual orbital approximation. The degree and character of Rydberg-valence mixing in the preedge of the NEXAFS spectra of these species is explored. Significant Rydberg-valence mixing only occurs when there are excited states of valence sigma(C-H) character that have the appropriate symmetry to interact with excited states of Rydberg character. Our results show that this mixing is only present when there are C-H bonds to the core excited carbon atom.

Linear dichroism in the X-ray absorption spectra of linear n-alkanes.

The nature of the linear dichroism in the near-edge X-ray absorption fine structure (NEXAFS) spectra of linear n-alkanes is a matter of long-standing controversy. Linear dichroism in the carbon 1s --> sigma*(C-C) transition has been interpreted within a building block model and a molecular orbital model, leading to two different descriptions for the angular dependence of this feature. When used for measurement of molecular orientation, the application of these two different models will lead to different results. We have explored the linear dichroism in the carbon 1s NEXAFS spectra of single crystals of the linear n-alkane hexacontane (n-C60H122). An analysis of the angular dependence in this spectrum shows that the transition dipole moment associated with the carbon 1s --> sigma*(C-C) transition is oriented along the macromolecular chain axis, contradicting the predictions of the building block model. However, other transitions are observed in the sigma*(C-H) and the sigma*(C-C) bands that are orthogonal to the dominant transitions for each band. We also observe that radiation damage can be manifest in the form of molecular reorientation in highly ordered organic thin films.