Core level study of alanine and threonine

Core level X-ray photoemission spectra (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectra of alanine and threonine in the gas phase have been measured at the carbon, nitrogen, and oxygen K edges and interpreted in the light of theoretical calculations. For the computations, a set of approximations is made which allows sufficiently accurate calculations of several conformers to be performed in reasonable computing time. The accuracy has been checked by comparing results obtained for proline to our previous, higher level calculations. The photoemission spectra at the carbon and oxygen edges are assigned and compared. The nitrogen 1s photoemission peaks show anomalous broadening which we relate to the populations and types of conformers. The carbon K-edge NEXAFS spectra of alanine and threonine are compared with our previous data on glycine and resonances assigned accordingly. The nitrogen K-edge NEXAFS spectra of alanine and threonine do not show measurable effects due to the population of conformers, in contrast to the photoemission results. At the oxygen K edge, the spectra of these amino acids are similar with two prominent peaks assigned to transitions of O 1s electrons from the oxo and hydroxyl groups to vacant pi* and sigma* orbitals and additional intensity for threonine due to the second OH group. Conformer effects are observable in photoemission but appear to be more difficult to resolve in photoabsorption. We explain this by energetic shifts of opposite sign for the core hole states and unoccupied orbitals, which causes partial cancelation in NEXAFS but not in photoemission.     

Self-assembled carbon nanotubes on gold: polarization-modulated infrared reflection-absorption spectroscopy, high-resolution X-ray photoemission spectroscopy, and near-edge X-ray absorption fine structure spectroscopy study

Recently we reported noncovalent functionalization of nanotubes in an aqueous medium with ionic liquid-based surfactants, 1-dodecyl-3-methylimidazolium bromide (1) and 1-(12-mercaptododecyl)-3-methylimidazolium bromide (2), resulting in positively charged single-wall carbon nanotube (SWNT)-1,2 composites. Thiolation of SWNTs with 2 provides their self-assembly on gold as well as templating gold nanoparticles on SWNT sidewalls via a covalent -S-Au bond. In this investigation, we studied the electronic structure, intermolecular interactions, and packing within noncovalently thiolated SWNTs and also nanotube alignment in the bulk of SWNT-2 dried droplets and self-assembled submonolayers (SAMs) on gold by high-resolution X-ray photoemission spectroscopy (HRXPS), C K-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS). HRXPS data confirmed the noncovalent nature of interactions within the nanocomposite of thiolated nanotubes. In PM-IRRAS spectra of SWNT SAMs on gold, the IR-active vibrational SWNT modes have been observed and identified. According to PM-IRRAS data, the hydrocarbon chains of 2 are oriented with less tilt angle to the bare gold normal in a SAM deposited from an SWNT-2 dispersion than those of 1 deposited from an SWNT-1 dispersion on the mercaptoethanesulfonic acid-primed gold. For both the dried SWNT-2 bulk and the SWNT-2 SAM on gold, the C K-edge NEXAFS spectra revealed the presence of CH-pi interactions between hydrocarbon chains of 2 and the pi electronic nanotube structure due to the highly resolved vibronic fine structure of carbon 1s --> R*/sigma*C-H series of states in the alkyl chain of 2. For the SWNT-2 bulk, the observed splitting and upshift of the SWNT pi* orbitals in the NEXAFS spectrum indicated the presence of pi-pi interactions. In the NEXAFS spectrum of the SWNT-2 SAM on gold, the upshifted values of the photon energy for R*/sigma*C-H transitions indicated close contact of 2 with nanotubes and with a gold surface. The angle-dependent NEXAFS for the SWNT-2 bulk showed that most of the molecules of 2 are aligned along the nanotubes, which are self-organized with orientation parallel to the substrate plane, whereas the NEXAFS for the SWNT-2 SAM revealed a more normal orientation of functionality 2 on gold compared with that in the SWNT-2 bulk.     

Probing weak molecular orbital interactions in non-conjugated diene molecules by means of near-edge X-ray absorption spectroscopy

Carbon and oxygen near-edge X-ray absorption fine structure (NEXAFS) spectra of 1,4-cyclohexadiene, p-benzoquinone, norbornadiene, norbornadienone, and cis-cis-[4,4,2]propella-3,8-diene-11,12-dione were calculated by means of Hartree-Fock and hybrid density functional theory using the static-exchange (STEX) approximation. The NEXAFS spectra are used as a probe to identify weak molecular interactions between the two non-conjugated ethylenic pi* orbitals present in these molecules. We show that the X-ray absorption spectrum of 1,4-cyclohexadiene exhibits some particular spectral structures in the discrete energy region that evidence diene through-bond orbital interaction, whereas absorption peaks are identified in the norbornadiene and norbornadienone spectra that indicate effective through-space orbital interactions. The molecular structure of the cis-cis-[4,4,2]propella-3,8-diene-11,12-dione isomer is such that the indirect through-bond or through-space diene orbital interactions are too weak to be assigned by its C1s NEXAFS spectrum.     

Electronic states of o-nitrobenzaldehyde: a combined experimental and theoretical study

The experimental UV/vis absorption spectrum of ortho-nitrobenzaldehyde (o-NBA) has been assigned by means of MS-CASPT2/CASSCF, TD-DFT, and RI-CC2 theoretical computations. Additional information on the nature of the absorbing bands was obtained by comparing the o-NBA spectrum with that of related compounds, as, e.g., nitrobenzene and benzaldehyde. For wavelengths larger than approximately 280 nm, the absorption spectrum of o-NBA is dominated by a series of weak n pi* absorptions from the NO2 and CHO groups. These weak transitions are followed in energy by a more intense band, peaking at 250 nm and arising from charge transfer pi pi* excitations involving mainly benzene and nitro orbitals. Finally, the most intense band centered at 220 nm has its origin in the overlap of two different absorptions: the first one localized in the NO2 substituent and the second one arising from a charge transfer excitation involving the NO2 and the CHO fragments, respectively.     

pH dependence of the electronic structure of glycine

The carbon, nitrogen, and oxygen K-edge spectra were measured for aqueous solutions of glycine by total electron yield near-edge X-ray absorption fine structure (TEY NEXAFS) spectroscopy. The bulk solution pH was systematically varied while maintaining a constant amino acid concentration. Spectra were assigned through comparisons with both previous studies and ab initio computed spectra of isolated glycine molecules and hydrated glycine clusters. Nitrogen K-edge solution spectra recorded at low and moderate pH are nearly identical to those of solid glycine, whereas basic solution spectra strongly resemble those of the gas phase. The carbon 1s --> pi*(C=O) transition exhibits a 0.2 eV red shift at high pH due to the deprotonation of the amine terminus. This deprotonation also effects a 1.4 eV red shift in the nitrogen K-edge at high pH. Two sharp preedge features at 401.3 and 402.5 eV are also observed at high pH. These resonances, previously observed in the vapor-phase ISEELS spectrum of glycine, have been reassigned as transitions to sigma* bound states. The observation of these peaks indicates that the amine moiety is in an acceptor-only hydrogen bond configuration at high pH. At low pH, the oxygen 1s --> pi*(C=O) transition exhibits a 0.25-eV red shift due to the protonation of the carboxylic acid terminus. These spectral differences indicate that the variations in electronic structure observed in the NEXAFS spectra are determined by the internal charge state and hydration environment of the molecule in solution.     

Theoretical study of the electronic spectroscopy of CO adsorbed on Pt(111)

The excited states of CO adsorbed on the Pt(111) surface are studied using a time-dependent density functional theory formalism. To reduce the computational cost, electronic excitations are computed within a reduced single excitation space. Using cluster models of the surface, excitation energies are computed for CO in the on-top, threefold, and bridge binding sites. On adsorption, there is a lowering of the 5sigma orbital energy. This leads to a large blueshift in the 5sigma- -> pi(CO*) excitation energy for all adsorption sites. The 1pi and 4sigma orbital energies are lowered to a lesser extent, and smaller shifts in the corresponding excitation energies are predicted. For the larger clusters, pi* excitations at lower energies are observed. These transitions correspond to excitations to virtual orbitals of pi* character which lie below the pi* orbitals of gas phase CO. These orbitals are associated predominantly with the metal atoms of the cluster. The excitation energies are also found to be sensitive to changes in the adsorption geometry. The electronic spectrum of CO on Pt(111) is simulated and the assignment of the bands observed in experimental electron energy loss spectroscopy discussed.     

High-resolution inner-shell excitation spectroscopy of H2-phthalocyanine

We report on a combined experimental and theoretical carbon and nitrogen K-edge near-edge x-ray absorption fine structure investigation on condensed metal-free phthalocyanine (H2Pc). Based on the results from improved virtual orbital calculations, all resonances in the experimental high-resolution data can be assigned to various electronic transitions. The comparison between experiments and calculations further shows that a significant influence of the core hole, which affects both the transition energies and the cross sections, is present and must be considered in theoretical approaches. Moreover, additional fine structure is clearly resolved for the first N 1s-->pi* transition, which can be interpreted as vibronic coupling to the electronic core excitation.     

Kβ X-ray emission spectroscopy offers unique chemical bonding insights: revisiting the electronic structure of ferrocene

Kβ X-ray emission spectroscopy (XES) is emerging as a powerful tool for the study of chemical bonding. Analyses of the Kβ XES of ferrocene (Fc) and ferrocenium (Fc(+)) are presented as further demonstrations of the capabilities of the technique. Assignments of the valence to core (V2C) region of these spectra as electric dipole-allowed cyclopentadienyl (Cp) → Fe 1s transitions demonstrate that XES affords electronic structural insight into the energetics of ligand-based molecular orbitals (MOs). Combined with K-edge X-ray absorption spectroscopy (XAS), we show that XES can provide analogous information to photoemission spectroscopy (PES). Density functional theory (DFT) analyses reveal that the V2C transitions in Fc/Fc(+) derive their intensity from Fe 4p admixture (on the order of 5-10%) into the Cp-based MOs from which they originate. These 4p admixtures confer bonding character to the Cp-based a(2u) and e(1u) MOs to at least the extent of backbonding contributions to frontier MOs from higher-lying Cp π* MOs.     

Directly probing the hybrid bonding of styrene on Cu111

The interfacial electronic structure of chemisorbed styrene on Cu(111) was successfully investigated with two-photon photoemission spectroscopy. We observed unoccupied states 3.5 eV above the Fermi level and occupied states 2.0 eV below the Fermi level. Polarization results reveal that the occupied and unoccupied states arise from bonding and antibonding orbitals formed by hybridization of copper (surface state and d-band orbitals) and styrene (pi1* and pi2* orbitals).     

Photophysics of aromatic molecules with low-lying pi sigma* states: excitation-energy dependence of fluorescence in jet-cooled aromatic nitriles

Excitation-energy dependence of fluorescence intensity and fluorescence lifetime has been measured for 4-dimethylaminobenzonitrile (DMABN), 4-aminobenzonitrile (ABN), 4-diisopropylaminobenzonitrile (DIABN), and 1-naphthonitrile (NN) in a supersonic free jet. In all cases, the fluorescence yield decreases rather dramatically, whereas the fluorescence lifetime decreases only moderately for S1 (pi pi*, L(b)) excess vibrational energy exceeding about 1000 cm(-1). This is confirmed by comparison of the normalized fluorescence excitation spectrum with the absorption spectrum of the compound in the vapor phase. The result indicates that the strong decrease in the relative fluorescence yield at higher energies is due mostly to a decrease in the radiative decay rate of the emitting state. Comparison of the experimental results with the TDDFT potential energy curves for excited states strongly suggests that the decrease in the radiative decay rate of the aminobenzonitriles at higher energies is due to the crossing of the pi pi* singlet state by the lower-lying pi sigma*(C[triple bond]N) singlet state of very small radiative decay rate. The threshold energy for the fluorescence "break-off" is in good agreement with the computed energy barrier for the pi pi*/pi sigma* crossing. For NN, on the other hand, the observed decrease is in fluorescence yield at higher excitation energies can best be attributed to the crossing of the pi pi* singlet state by the pi sigma* triplet state.     

The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase

Near edge x-ray absorption fine structure spectra have been measured and interpreted by means of density functional theory for five different azabenzenes (pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine) in the gas phase. The experimental and theoretical spectra at the N 1s and C 1s edges show a strong resonance assigned to the transition of the 1s electron in the respective N or C atoms to the lowest unoccupied molecular orbital with pi(*) symmetry. As opposed to the N 1s edge, at the C 1s edge this resonance is split due to the different environments of the core hole atom in the molecule. The shift in atomic core-level energy due to a specific chemical environment is explained with the higher electronegativity of the N atom compared to the C atom. The remaining resonances below the ionization potential (IP) are assigned to sigma or pi [corrected] orbitals with mixed valence/Rydberg [corrected] character. Upon N addition, a reduction of intensity is observed in the Rydberg region at both edges as compared to the intensity in the continuum. Above the IP one or more resonances are seen and ascribed here to transitions to sigma(*) orbitals. Calculating the experimental and theoretical Delta(pi) term values at both edges, we observe that they are almost the same within +/-1 eV as expected for isoelectronic bonded pairs. The term values of the pi(*) and sigma(*) resonances are discussed in terms of the total Z number of the atoms participating in the bond.     

Absorption spectrum and solvatochromism of the [Ru(4,4'-COOH-2,2'-bpy)2(NCS)2] molecular dye by time dependent density functional theory

We present a combined Density Functional/Time Dependent Density Functional study of the molecular structure, electronic states, and optical absorption spectrum of [Ru(4,4'-COOH-2,2'-bpy)(2)(NCS)(2)], a widely used charge-transfer sensitizer in nanocrystalline TiO(2) solar cells. Calculations have been performed both for the complex in vacuo and in ethanol and water solvents, using a continuum model to account for solute-solvent interactions. Inclusion of the solvent leads to important changes of the energies and composition of the molecular orbitals of the complex; as a consequence, whereas the computed spectrum for the Ru-complex in vacuo deviates from the experimental one in both energy and shape, the spectra calculated in the presence of the solvent are in good agreement with the experiment. The first two absorption bands are found to originate from mixed ruthenium-NCS to bipyridine-pi* transitions rather than to pure metal-to-ligand-charge-transfer (MLCT) transitions, whereas the third band arises from intraligand pi --> pi* transitions. The experimentally observed blue-shift of the spectrum in water with respect to ethanol is well reproduced by our calculations and appears to be related to a decreased dipole moment in the excited state.     

Photoemission and near-edge X-ray absorption fine structure studies of the bacterial surface protein layer of Bacillus sphaericus NCTC 9602

The electronic structure of the regular, two-dimensional bacterial surface protein layer of Bacillus sphaericus NCTC 9602 has been examined by photoemission (PE) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Both the O 1s and the N 1s core-level PE spectra show a single structure, whereas the C 1s core-level spectrum appears manifold, suggesting similar chemical states for each oxygen atom and also for each nitrogen atom, while carbon atoms exhibit a range of chemical environments in the different functional groups of the amino acids. This result is supported by the element-specific NEXAFS spectra of the unoccupied valence electronic states, which exhibit a series of characteristic NEXAFS peaks that can be assigned to particular molecular orbitals of the amino acids by applying a phenomenological building-block model. The relative contributions of the C-O, C-N, and C-C bond originating signals into the C 1s PE spectrum are in good agreement with the number ratios of the corresponding bonds calculated from the known primary structure of the bacterial surface protein. First interpretation of the PE spectrum of the occupied valence states is achieved on the basis of electronic density-of-states calculations performed for small peptides. It was found that mainly the pi clouds of the aromatic rings contribute to both the lowest unoccupied and the highest occupied molecular orbitals.     

Excited states of porphyrin macrocycles

S1 --> S(n) spectra of porphyrin, diprotonated porphyrin, and tetraoxaporphyrin dication have been measured in the energy range 2-3 eV above S1 at room temperature in solution by means of transient absorption spectroscopy exciting with femtosecond pulses. Highly excited pi pi* states not active in the conventional S0 --> S(n) spectrum have been observed. The experimental data are discussed on the basis of the time dependent density functional theory taking advantage of large scale calculations of configuration interaction between singly excited configurations (DF/SCI). The DF/SCI calculation on porphyrin has allowed to assign g states active in the S1 --> S(n) spectrum. Applying the same calculation method to tetraoxaporphyrin dication the S0 --> S(n) spectrum is reproduced relatively to the Q and B (Soret) bands as well as to the weaker E(u) bands at higher energy. According to our calculation the S1 --> S(n) transient spectrum is related to states of g symmetry mainly arising from excitations between doubly degenerate pi and pi* orbitals such as 2e(g) --> 4e(g). In the case of diprotonated porphyrin it is shown that the complex of the macrocycle with two trifluoroacetate anions plays a significant role for absorption. Charge transfer excitations from the anions to the macrocycle contribute to absorption above the Soret band, justifying the intensity enhancement of the S0 --> S(n) spectrum with respect to the other two macrocyclic systems.     

Spectroscopic analysis of small organic molecules: a comprehensive near-edge x-ray-absorption fine-structure study of C6-ring-containing molecules

We report high-resolution C 1s near-edge x-ray-absorption fine-structure (NEXAFS) spectra of the C6-ring-containing molecules benzene (C6H6), 1,3- and 1,4-cyclohexadiene (C6H8), cyclohexene (C6H10), cyclohexane (C6H12), styrene (C8H8), and ethylbenzene (C8H10) which allow us to examine the gradual development of delocalization of the corresponding pi electron systems. Due to the high experimental resolution, vibrational progressions can be partly resolved in the spectra. The experimental spectra are compared with theoretical NEXAFS spectra obtained from density-functional theory calculations where electronic final-state relaxation is accounted for. The comparison yields very good agreement between theoretical spectra and experimental results. In all cases, the spectra can be described by excitations to pi*- and sigma*-type final-state orbitals with valence character, while final-state orbitals of Rydberg character make only minor contributions. The lowest C 1s-->1pi* excitation energy is found to agree in the (experimental and theoretical) spectra of all molecules except for 1,3-cyclohexadiene (C6H8) where an energy smaller by about 0.6 eV is obtained. The theoretical analysis can explain this result by different binding properties of this molecule compared to the others.     

X-ray absorption near edge structure study of BN nanotubes and nanothorns

Two boron nitride (BN) nanostructures, the bamboo-like nanotubes and nanothorns where the nanosize h-BN layers are randomly stacked looking like thorns, were synthesized selectively via thermal chemical vapor deposition of B/B(2)O(3) under the NH(3) flow at 1200 degrees C. Electron energy-loss spectroscopy reveals the N-rich h-BN layers with a ratio of B/N = 0.75-0.85. Angle-resolved X-ray absorption near edge structure of these two N-rich nanostructures has been compared with that of h-BN microcrystals. The pi transition in the N K-edge shifts to the lower energy by 0.8-1.0 eV from that of h-BN microcrystals, and the second-order signals of N 1s electrons become significant. We suggest that the N enrichment would decrease the band gap of nanostructures from that of h-BN microcrystals. The Raman spectrum shows the peak broadening due to the defects of N-rich h-BN layers.     

Shape resonances and partial photoemission cross sections of solid SF6 and CCl4

Photoelectron energy distribution curves from solid films of SF₆ and CCl₄ have been measured in the photon energy range 10 ? hr ? 40 eV using synchrotron radiation. The binding energies, peak widths and relative partial cross sections have been determined. In the photoelectron spectra a 1:1 correspondence to the gas phase is observed for the occupied molecular orbitals, and a straightforward assignment of the occupied valence bands emerges. Furthermore, the cross sections of the individual orbitals show for both samples great similarities to the gas phase. For SF₆ detailed structures are visible in the cross sections which are only partly interpreted as shape resonances. A new assignment for the 6t_1u shape resonance is proposed and the resonance energies are related to X-ray absorption and electron scattering data. Furthermore a comparison of the total photoemission cross section to the optical reflection spectrum of solid SF₆ is presented. For CCl₄ less structures are ob served in the partial cross sections. They are all interpreted as shape resonances. An energetic scheme of the virtual orbitals is proposed for CCl₄.     

Quantum Monte Carlo for the x-ray absorption spectrum of pyrrole at the nitrogen K-edge

Fixed-node diffusion Monte Carlo (FNDMC) is used to simulate the x-ray absorption spectrum of a gas-phase pyrrole molecule at the nitrogen K-edge. Trial wave functions for core-excited states are constructed from ground-state Kohn-Sham determinants substituted with singly occupied natural orbitals from configuration interaction with single excitations calculations of the five lowest valence-excited triplet states. The FNDMC ionization potential (IP) is found to lie within 0.3 eV of the experimental value of 406.1 ± 0.1 eV. The transition energies to anti-bonding virtual orbitals match the experimental spectrum after alignment of IP values and agree with the existing assignments.     

Resonant processes and Coulomb interactions in (C59N)2

We have determined the on-site molecular Coulomb interaction energy U of a (C59N)2 bulk film and find values ranging from 1.10+/-0.10 eV for the highest occupied molecular orbital to 1.35+/-0.10 eV for the deeper lying orbitals, comparable to values found in C60. The on-site Coulomb interaction between a carbon core hole and valence electrons, Uc, is, however, substantially lower than in C60 at 1.35+/-0.07 eV. Resonant photoemission (RESPES) results show a weakened participator decay channel, especially around the N 1s threshold, where resonance of the highest occupied molecular orbital shoulder is absent. Near-edge x-ray absorption fine structure and constant initial state measurements, taken in parallel with the RESPES data, indicate, however, that matrix element effects cannot be ruled out.