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.     

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.     

Towards a detailed understanding of the NEXAFS spectra of bulk polyethylene copolymers and related alkanes

High energy resolution C 1s near-edge X-ray absorption fine structure (NEXAFS) spectra of ethylene-1-alkene copolymers with systematic variations in comonomer content and thus systematic changes in branch length, branching ratio, and degree of crystallinity are presented. Spectral changes of the σ^*_C–H/Rydberg and σ^*_C–C features in these ideal model systems provide unambiguous experimental evidence for intermolecular interactions with profound effects on the spectral intensity, but only very small energy shifts. Ab initio calculations reproduce the experimental results in detail. The intermolecular interaction observed suggests that interpretation of NEXAFS spectra based on calculations of isolated molecules can be insufficient even in relatively weakly interacting macromolecules.     

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.     

A theoretical study of the XP and NEXAFS spectra of alanine: gas phase molecule, crystal, and adsorbate at the ZnO(10 ̅10) surface

The adsorption of alanine on the mixed-terminated ZnO(10 ?10) surface is studied by means of quantum-chemical ab initio calculations. Using a finite cluster model and the adsorption geometry as obtained both by periodic CPMD and embedded cluster calculations, the C1s, N1s and O1s X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra are calculated for single alanine molecules on ZnO(10 ?10). These spectra are compared with the spectra calculated for alanine in the gas phase and in its crystalline form and with experimental XPS and NEXAFS data for the isolated alanine molecule and for alanine adsorbed on ZnO(10 ?10) at multilayer and monolayer coverage. The excellent agreement between the experimental and calculated XP and NEXAFS spectra confirms the calculated adsorption geometry: A single alanine molecule is bound to ZnO(10 ?10) in a dissociated bidentate form with the two O atoms of the acid group bound to two Zn atoms of the surface and the proton transferred to one O atom of the surface. Other possible structures, such as adsorption of alanine in one of its neutral or zwitterionic forms in which the proton of the -COOH group remains at this group or is transferred to the amino group, can be excluded since they would give rise to quite different XP spectra. In the multilayer coverage regime, on the other hand, alanine is in its crystalline form as is also shown by the analysis of the XP spectra.     

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.     

Using intrinsic X-ray absorption spectral differences to identify and map peptides and proteins

The intrinsic variation in the near-edge X-ray absorption fine structure (NEXAFS) spectra of peptides and proteins provide an opportunity to identify and map them in various biological environments, without additional labeling. In principle, with sufficiently accurate spectra, peptides (<50 amino acids) or proteins with unusual sequences (e.g., cysteine- or methionine-rich) should be differentiable from other proteins, since the NEXAFS spectrum of each amino acid is distinct. To evaluate the potential for this approach, we have developed X-SpecSim, a tool for quantitatively predicting the C, N, and O 1s NEXAFS spectra of peptides and proteins from their sequences. Here we present the methodology for predicting such spectra, along with tests of its precision using comparisons to the spectra of various proteins and peptides. The C 1s, N 1s, and O 1s spectra of two novel antimicrobial peptides, Indolicidin (ILPWKWPWWPWRR-NH2) and Sub6 (RWWKIWVIRWWR-NH2), as well as human serum albumin and fibrinogen are reported and interpreted. The ability to identify, differentiate, and quantitatively map an antimicrobial peptide against a background of protein is demonstrated by a scanning transmission X-ray microscopy study of a mixture of albumin and sub6.     

Geometric and electronic structures of NO dimer layers on Rh(111) studied with near edge x-ray absorption fine structure spectroscopy: experiment and theory

Adsorption of NO on the Rh(111) surface has been studied in the monolayer, bilayer, and multilayer regimes with near edge x-ray absorption fine structure (NEXAFS) spectroscopy. NO dimer layers are formed on a chemisorbed monomer layer. The polarization dependence in the NEXAFS spectra of the dimer components has contradicted the previous assignments. To determine the structure of the NO dimer layers from the polarization analysis of the NEXAFS spectra, ab initio configuration interaction calculations have been carried out for some low-lying core excited states of the weakly bound NO dimer with cis-ONNO planar geometry. It is revealed that the NO dimers in the multilayer are standing with the N-N bond perpendicular to the surface, while in the second layer they are rather lying on the first monomer layer.     

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.     

Core excitations of naphthalene: vibrational structure versus chemical shifts

High-resolution x-ray photoelectron emission (XPS) and near-edge x-ray absorption fine structure (NEXAFS) spectra of naphthalene are analyzed in terms of the initial state chemical shifts and the vibrational fine structure of the excitations. Carbon atoms located at peripheral sites experience only a small chemical shift and exhibit rather similar charge-vibrational coupling, while the atoms in the bridging positions differ substantially. In the XPS spectra, C-H stretching modes provide important contributions to the overall shape of the spectrum. In contrast, the NEXAFS spectrum contains only vibrational progressions from particular C-C stretching modes. The accuracy of ab initio calculations of absolute electronic transition energies is discussed in the context of minute chemical shifts, the vibrational fine structure, and the state multiplicity.     

X-ray spectroscopy of heterocyclic biochemicals: xanthine, hypoxanthine, and caffeine

The electronic structures of the purine derivatives xanthine, hypoxanthine and caffeine have been investigated in the gas phase using C, N, and O 1s X-ray photoemission (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The results have been interpreted by means of ab initio calculations using the third-order algebraic-diagrammatic construction (ADC(3)) method for the one-particle Green's function and the second-order ADC method (ADC(2)) for the polarization propagator. The carbon, nitrogen and oxygen K-edge NEXAFS spectra of xanthine and caffeine are very similar, since the molecules differ only by substitution of three hydrogen atoms by methyl groups. For hypoxanthine, the electronic structure and spectra differ considerably from xanthine as the purine ring is more highly conjugated, and there is one less oxo group. Effects due to oxo-hydroxy tautomerism were not observed. However, the two oxo tautomeric forms of hypoxanthine oxo-N(9)-H and oxo-N(7)-H are populated in the gas phase, and the C 1s spectra can be simulated only by taking account of these two tautomers, with appropriate Boltzmann population ratios which we have also calculated. For xanthine and caffeine, single tautomeric forms were observed.     

Activity difference between alpha-COOH and beta-COOH in N-phosphorylaspartic acids

N-phosphorylamino acids are chemically active species that have many biomimic activities. alpha-COOH in amino acids and peptides behaviors rather differently than beta-COOH in many biochemical processes and takes a more important role in the origin of life. Activity differences between alpha-COOH and beta-COOH in the peptide formation of phosphoryl amino acids are studied by 1D, 2D NMR techniques and by ab initio and density functional theory (DFT) calculations in this paper. Phosphoryl dipeptide is formed directly from phosphoryl aspartic acids without any coupling reagents. Only the alpha-dipeptide ester is observed by 1D (1)H, (13)C, and (31)P NMR and 2D NMR. In the ab initio and DFT calculations, the pentacoordinate phosphorane intermediates containing five-membered rings are predicted to be more favored than those with six-membered rings. Both the experimental results and the theoretical calculations suggest that only the alpha-COOH group is activated by N-phosphorylation in N-phosphorylaspartic acid under mild conditions.     

Ne3-NH3 van der Waals tetramer: rotational spectra and ab initio study of the microsolvation of NH3 with rare gas atoms

Microwave rotational spectra of eleven isotopomers of the Ne(3)-NH(3) van der Waals tetramer were measured using a pulsed jet, Balle-Flygare type Fourier transform microwave spectrometer. The transitions measured fall between 4 and 17 GHz and correspond to the ground internal rotor state of the weakly bound complex. The (20)Ne(3)- and (22)Ne(3)-containing species are symmetric top molecules while the mixed (20)Ne(2)(22)Ne- and (20)Ne(22)Ne(2)-isotopomers are asymmetric tops. For each of the deuterium-containing isotopomers, a tunneling splitting was observed due to the inversion of NH(3) within the tetramer. The (14)N nuclear quadrupole hyperfine structures were resolved and included in the spectroscopic fits of the various isotopomers. The rotational constants obtained from the fits were used to estimate the van der Waals bond lengths of the tetramer while the (14)N nuclear quadrupole coupling contants and the observed inversion tunneling splittings provided information about the internal dynamics of the NH(3) moiety. The experimental results were complemented by the construction of three ab initio potential energy surfaces [CCSD(T)] for the Ne(3)-NH(3) complex, each corresponding to a different internal geometry of NH(3) ( 90 degree angle HNH = 106.67 degrees, 90 degree angle HNH = 113.34 degrees, and 90 degree angle HNH = 120.00 degrees ). The topologies of the surfaces are related to the structures and dynamics of the tetramer. Extensive comparisons are made between the results obtained for the Ne(3)-NH(3) tetramer in this work and previous experimental and ab initio studies of related Rg(n)-NH(3) van der Waals clusters.     

Discrimination between peptide 3(10)- and alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra

Detailed spectral simulations based on ab initio density functional theory computations of the amide I and II infrared (IR) and vibrational circular dichroism (VCD) spectra for Ac-(Ala)(4)-NH(2), Ac-(Aib-Ala)(2)-NH(2), and Ac-(Aib)(4)-NH(2) constrained to 3(10)- and alpha-helical conformations are presented. Parameters from these ab initio calculations are transferred onto corresponding larger oligopeptides to simulate the spectra for dodecamers. The differences between conformations and for different Aib substitution patterns within a conformation are reflected in observable spectral patterns where data are available. Simulated IR spectra show small frequency shifts in the amide I maxima between 3(10)- and alpha-helices, but the same magnitude shifts occur within one conformation upon Aib substitution. Thus, from a computational basis, the frequency of the amide I maximum does not discriminate between the 3(10)- or alpha-helical conformations. Calculated VCD band shapes for 3(10)-helices showed more significant changes in amplitude, with change in the fraction of Aib, than those for alpha-helices. Generally, with increasing Aib content, the overall amide I VCD intensity becomes weaker and the amide I couplet becomes more conservative, while the amide II VCD is less affected. Although the detailed band shape is shown to be sensitive to alpha-Me substitution, the basic pattern of amide I and II relative VCD intensities still differs between alpha- and 3(10)-helices and, as a consequence, successfully discriminates between them. These predictions are all borne out in experimental spectra of Aib, mixed Aib-Ala, and Ala-based helical peptides, where available.     

pH-dependent x-ray absorption spectra of aqueous boron oxides

Near edge x-ray absorption fine structure (NEXAFS) spectra at the boron K-edge were measured for aqueous boric acid, borate, and polyborate ions, using liquid microjet technology, and compared with simulated spectra calculated from first principles density functional theory in the excited electron and core hole (XCH) approximation. Thermal motion in both hydrated and isolated molecules was incorporated into the calculations by sampling trajectories from quantum mechanics∕molecular mechanics simulations at the experimental temperature. The boron oxide molecules exhibit little spectral change upon hydration, relative to mineral samples. Simulations reveal that water is arranged nearly isotropically around boric acid and sodium borate, but the calculations also indicate that the boron K-edge NEXAFS spectra are insensitive to hydrogen bonding, molecular environment, or salt interactions.     

Local hydration environments of amino acids and dipeptides studied by X-ray spectroscopy of liquid microjets

The nitrogen K-edge spectra of aqueous proline and diglycine solutions have been measured by total electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at neutral and high pH. All observed spectral features have been assigned by comparison to the recently reported spectrum of aqueous glycine and calculated spectra of isolated amino acids and hydrated amino acid clusters. The sharp preedge resonances at 401.3 and 402.6 eV observed in the spectrum of anionic glycine indicate that the nitrogen terminus is in an "acceptor-only" configuration, wherein neither amine proton is involved in hydrogen bonding to the solvent, at high pH. The analogous 1s --> sigma(NH) preedge transitions are absent in the NEXAFS spectrum of anionic proline, implying that the acceptor-only conformation observed in anionic glycine arises from steric shielding induced by free rotation of the amine terminus about the glycine CN bond. Anionic diglycine solutions exhibit a broadened 1s --> pi(CN) resonance at 401.2 eV and a broad shoulder resonance at 403 eV, also suggesting the presence of an acceptor-only species. Although this assignment is not as unambiguous as for glycine, it implies that the nitrogen terminus of most proteins is capable of existing in an acceptor-only conformation at high pH. The NEXAFS spectrum of zwitterionic lysine solution was also measured, exhibiting features similar to those of both anionic and zwitterionic glycine, and leading us to conclude that the alpha amine group is present in an acceptor-only configuration, while the end of the butylammonium side chain is fully solvated.     

Photodissociation dynamics of hydroxybenzoic acids

Aromatic amino acids have large UV absorption cross-sections and low fluorescence quantum yields. Ultrafast internal conversion, which transforms electronic excitation energy to vibrational energy, was assumed to account for the photostability of amino acids. Recent theoretical and experimental investigations suggested that low fluorescence quantum yields of phenol (chromophore of tyrosine) are due to the dissociation from a repulsive excited state. Radicals generated from dissociation may undergo undesired reactions. It contradicts the observed photostability of amino acids. In this work, we explored the photodissociation dynamics of the tyrosine chromophores, 2-, 3- and 4-hydroxybenzoic acid in a molecular beam at 193 nm using multimass ion imaging techniques. We demonstrated that dissociation from the excited state is effectively quenched for the conformers of hydroxybenzoic acids with intramolecular hydrogen bonding. Ab initio calculations show that the excited state and the ground state potential energy surfaces change significantly for the conformers with intramolecular hydrogen bonding. It shows the importance of intramolecular hydrogen bond in the excited state dynamics and provides an alternative molecular mechanism for the photostability of aromatic amino acids upon irradiation of ultraviolet photons.     

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.     

Ab initio DFT studies of oxygen K edge NEXAFS spectra for the V2O3(0001) surface

Theoretical near edge X-ray absorption fine structure (NEXAFS) spectra describing oxygen 1s core excitation have been evaluated for the differently coordinated oxygen species appearing near the V₂O₃(0001) surface with half metal layer V^′OV termination. Adsorption of oxygen above vanadium centers of the V^′OV terminated surface (O_tV^′O termination) results in very strongly bound vanadyl oxygen, which has also been considered for core excitation in this study. The angle-resolved spectra are based on electronic structure calculations using ab initio density functional theory (DFT) together with model clusters. Experimental NEXAFS spectra for V₂O₃(0001) show a rather strong dependence of peak positions and relative intensities on the photon polarization direction. This dependence is well described by the present theoretical spectra and allows us to assign spectral details in the experiment to specific O 1s core excitations where final state orbitals are determined by the local binding environments of the differently coordinated oxygen centers. As a result, a combination of the present theoretical spectra with experimental NEXAFS data enables an identification of differently coordinated surface oxygen species at the V₂O₃(0001) surface.     

2-amino-1-propanol versus 1-amino-2-propanol: valence band and C 1s core-level photoelectron spectra

Valence band and C 1s core-level photoelectron spectra of S-(+)-2-amino-1-propanol (alaninol) and S-(+)-1-amino-2-propanol (isopropanolamine) have been studied by means of synchrotron radiation photoelectron spectroscopy in gas phase. The alaninol, the reduced derivative of the alanine, is a good test system of amino acid-like structures. The isopropanolamine, presenting the inversion of the two functional groups of the alaninol at the chiral carbon, offers the opportunity to study the effect of -OH and -NH(2) structural position on the photoelectron spectra. The influence of the conformational contribution on the electronic structure and the photoelectron spectra has been interpreted using density functional and ab initio theoretical calculations. Agreement has been achieved by taking into account the presence, in gas phase, of two conformers with different population ratios in both chiral systems. The C 1s core-level spectra of alaninol and isopropanolamine are reported and the peak positions of the three carbon atoms of the molecules are assigned.