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.     

Surface sensitive study to determine the reactivity of soot with the focus on the European emission standards IV and VI

Diesel soot (Euro IV and Euro VI) was investigated with spectroscopic methods such as near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray photoemission spectroscopy (XPS). C and O K-edge NEXAFS show that structural disorder on the surface is accompanied by a higher amount of oxygen functional groups. O K-edge NEXAFS and O1s XPS results are discussed with the aim to elucidate the nature of the oxygen surface species. The analysis of the data presented here allows the postulation of a hypothetical structure for soot samples emitted by diesel engines.     

Oxygen-containing functional groups on single-wall carbon nanotubes: NEXAFS and vibrational spectroscopic studies.

Single-walled nanotubes (SWNTs) produced by plasma laser vaporization (PLV) and containing oxidized surface functional groups have been studied for the first time with NEXAFS. Comparisons are made to SWNTs made by catalytic synthesis over Fe particles in high-pressure CO, called HiPco material. The results indicate that the acid purification and cutting of single-walled nanotubes with either HNO3/H2SO4 or H2O2/H2SO4 mixtures produces the oxidized groups (O/C = 5.5-6.7%), which exhibit both pi*(CO) and sigma*(CO) C K-edge NEXAFS resonances. This indicates that both carbonyl (C=O) and ether C-O-C functionalities are present. Upon heating in a vacuum to 500-600 K, the pi*(CO) resonances are observed to decrease in intensity; on heating to 1073 K, the sigma*(CO) resonances disappear as the C-O-C functional groups are decomposed. Raman spectral measurements indicate that the basic tubular structure of the SWNTs is not perturbed by heating to 1073 K, based on the invariance of the ring breathing modes upon heating. The NEXAFS studies agree well with infrared studies which show that carboxylic acid groups are thermally destroyed first, followed by the more difficult destruction of ether and quinone groups. Single-walled nanotubes produced by the HiPco process, and not treated with oxidizing acids, exhibit an O/C ratio of 1.9% and do not exhibit either pi*(CO) or sigma*(CO) resonances at the detection limit of NEXAFS. It is shown that heating (to 1073 K) of the PLV-SWNTs containing the functional groups produces C K-edge NEXAFS spectra very similar to those seen for the HiPco material. The NEXAFS spectra are calibrated against spectra measured for a number of fused-ring aromatic hydrocarbon molecules containing various types of oxidized functional groups present on the oxidized SWNTs.     

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.     

NEXAFS光谱分析聚合物修饰的单壁碳纳米管

利用C1s、O1s、N1s近边X射线吸收精细结构(Near Edge X-Ray Absorption Fine Structure,NEXAFS)光谱对聚合物修饰的碳纳米管进行了分析,研究了氧化及偶联聚合物对碳纳米管结构的影响。氧化碳纳米管及十八胺修饰的、聚合物/十八胺双修饰的碳纳米管的NEXAFS光谱均出现了碳/氧K边π*(C=O)和σ*(C-O)共振峰;而十八胺修饰的、聚合物/十八胺双修饰的碳纳米管则出现了氮K边π*(N-C=O)和σ*(N1s)共振峰。分析表明,NEXAFS光谱可有效表征聚合物修饰的碳纳米管。     

Asymmetric Acceptor–Donor–Acceptor Polymers with Fast Charge Carrier Transfer for Solar Hydrogen Production

Construction of local donor–acceptor architecture is one of the valid means for facilitating the intramolecular charge transfer in organic semiconductors. To further accelerate the interface charge transfer, a ternary acceptor–donor–acceptor (A₁-D-A₂) molecular junction is established via gradient nitrogen substituting into the polymer skeleton. Accordingly, the exciton splitting and interface charge transfer could be promptly liberated because of the strong attracting ability of the two different electron acceptors. Both DFT calculations and photoluminescence spectra elucidate the swift charge transfer at the donor-acceptor interface. Consequently, the optimum polymer, N₃-CP, undergoes a remarkable photocatalytic property in terms of hydrogen production with AQY_{405 nm}=26.6 % by the rational design of asymmetric molecular junctions on organic semiconductors.     

Theoretical characterization and design of small molecule donor material containing naphthodithiophene central unit for efficient organic solar cells

To seek for high‐performance small molecule donor materials used in heterojunction solar cell, six acceptor–donor–acceptor small molecules based on naphtho[2,3‐b:6,7‐b′]dithiophene ( NDT ) units with different acceptor units were designed and characterized using density functional theory and time‐dependent density functional theory. Their geometries, electronic structures, photophysical, and charge transport properties have been scrutinized comparing with the reported donor material NDT(TDPP)₂ ( TDPP = thiophene‐capped diketopyrrolopyrrole). The open circuit voltage (V_oc), energetic driving force(ΔE_L‐L), and exciton binding energy (E_b) were also provided to give an elementary understanding on their cell performance. The results reveal that the frontier molecular orbitals of 3–7 match well with the acceptor material PC₆₁BM , and compounds 3–5 were found to exhibit the comparable performances to 1 and show promising potential in organic solar cells. In particular, comparing with 1 , system 7 with naphthobisthiadiazole acceptor unit displays broader absorption spectrum, higher V_oc, lower E_b, and similar carrier mobility. An in‐depth insight into the nature of the involved excited states based on transition density matrix and charge density difference indicates that all S₁ states are mainly intramolecular charge transfer states with the charge transfer from central NDT unit to bilateral acceptor units, and also imply that the exciton of 7 can be dissociated easily due to its large extent of the charge transfer. In a word, 7 maybe superior to 1 and may act as a promising donor candidate for organic solar cell. © 2013 Wiley Periodicals, Inc.     

Direct observation of defect levels in InN by soft X-ray absorption spectroscopy

We have used synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to study the electronic structure of nitrogen-related defects in InN(0001). Several defect levels within the band gap or the conduction band of InN were clearly resolved in NEXAFS spectra around the nitrogen K-edge. We attribute the level observed at 0.3 eV below the conduction band minimum (CBM) to interstitial nitrogen, the level at 1.7 eV above the CBM to antisite nitrogen, and a sharp resonance at 3.2 eV above the CBM to molecular nitrogen, in full agreement with theoretical simulations.     

S K-edge XAS and DFT calculations on SAM dependent pyruvate formate-lyase activating enzyme: nature of interaction between the Fe4S4 cluster and SAM and its role in reactivity

S K-edge X-ray absorption spectroscopy on the resting oxidized and the S-adenosyl-l-methionine (SAM) bound forms of pyruvate formate-lyase activating enzyme are reported. The data show an increase in pre-edge intensity, which is due to additional contributions from sulfide and thiolate of the Fe(4)S(4) cluster into the C-S σ* orbital. This experimentally demonstrates that there is a backbonding interaction between the Fe(4)S(4) cluster and C-S σ* orbitals of SAM in this inner sphere complex. DFT calculations that reproduce the data indicate that this backbonding is enhanced in the reduced form and that this configurational interaction between the donor and acceptor orbitals facilitates the electron transfer from the cluster to the SAM, which otherwise has a large outer sphere electron transfer barrier. The energy of the reductive cleavage of the C-S bond is sensitive to the dielectric of the protein in the immediate vicinity of the site as a high dielectric stabilizes the more charge separated reactant increasing the reaction barrier. This may provide a mechanism for generation of the 5'-deoxyadenosyl radical upon substrate binding.     

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.     

Adsorption of nitrogen oxides on graphene and graphene oxides: insights from density functional calculations

The interactions of nitrogen oxides NO(x) (x = 1,2,3) and N(2)O(4) with graphene and graphene oxides (GOs) were studied by the density functional theory. Optimized geometries, binding energies, and electronic structures of the gas molecule-adsorbed graphene and GO were determined on the basis of first-principles calculations. The adsorption of nitrogen oxides on GO is generally stronger than that on graphene due to the presence of the active defect sites, such as the hydroxyl and carbonyl functional groups and the carbon atom near these groups. These active defect sites increase the binding energies and enhance charge transfers from nitrogen oxides to GO, eventually leading to the chemisorption of gas molecules and the doping character transition from acceptor to donor for NO(2) and NO. The interaction of nitrogen oxides with GO with various functional groups can result in the formation of hydrogen bonds OH???O (N) between -OH and nitrogen oxides and new weak covalent bonds C???N and C???O, as well as the H abstraction to form nitrous acid- and nitric acidlike moieties. The spin-polarized density of states reveals a strong hybridization of frontier orbitals of NO(2) and NO(3) with the electronic states around the Fermi level of GO, and gives rise to the strong acceptor doping by these molecules and remarkable charge transfers from molecules to GO, compared to NO and N(2)O(4) adsorptions on GO. The calculated results show good agreement with experimental observations.     

Decoration of nitrogen vacancies by oxygen atoms in boron nitride nanotubes

Decoration of nitrogen vacancies by oxygen atoms has been studied by near-edge X-ray absorption fine structure (NEXAFS) around B K-edge in several boron nitride (BN) structures, including bamboo-like and multi-walled BN nanotubes. Breaking of B-N bonds and formation of nitrogen vacancies under low-energy ion bombardment reduces oxidation resistance of BN structures and promotes an efficient oxygen-healing mechanism, in full agreement with some recent theoretical predictions. The formation of mixed O-B-N and B-O bonds is clearly identified by well-resolved peaks in NEXAFS spectra of excited boron atoms.     

Investigating the electronic structure and bonding in uranyl compounds by combining NEXAFS spectroscopy and quantum chemistry

The nature of the reactivity of the "yl" oxygens has been a subject of constant interest for a long time in uranyl chemistry. Thus, the electron-donor ability of the equatorial ligands plays an important role in the nature of the uranyl U=O bond. In this paper, a combination of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and both ground-state and time-dependent density functional theory (DFT) calculations have been used to examine the effect of equatorial plane ligation on the U=O bonding in two uranyl complexes: [UO(2)(py)(3)I(2)] and [UO(2)(CN)(5)][NEt(4)](3). By coupling experimental data and theory, spectral features observed in the oxygen K-edge NEXAFS spectra have been assigned. Despite the inert character of the U=O bond, we observe that the electron-donating or withdrawing character of the equatorial ligands has a measurable effect on features in the NEXAFS spectra of these species and thereby on the unoccupied molecular orbitals of {UO(2)}(2+).     

Observations on the Crystal Structures of Electron Donor-Acceptor Complexes

The theoretical interpretation of electron donor-acceptor complex formation in terms of charge transfer interactions has stimulated many structure determinations for these complexes. These fall into three classes, depending on the type of orbitals involved in charge transfer. In σ-σ complexes, intermolecular bonds become shorter and intramolecular bonds become longer as charge transfer increases. Relative orientations correspond to overlap of donor and acceptor molecules in directions of “preferred polarizability”. Intermolecular bond lengths in σ-π complexes show similar trends, and the axial orientation in the benzene-halogen complexes is probably the result of the best compromise between orbital overlap and energy factors. π-π Complexes contain stacks of alternate plane-to-plane donor and acceptor molecules, arranged in three characteristic ways. There is little correlation between interplanar spacing in these stacks and charge transfer properties. The relative orientations of donor and acceptor molecules within the stacks are determined by a combination of charge transfer interactions (maximized when aromatic rings of donor and acceptor molecules are displaced by half a ring diameter) and dipole-induced dipole interactions (maximized, for example, when a polar bond of one molecule overlaps a polarizable region of another). Crystal packing requirements and dispersion forces modify these effects, and no satisfactory theoretical treatment of this complex combination of interactions is yet available.     

Mechanistic insights on how hydroquinone disarms OH and OOH radicals

Phenol derivatives are distinguished as successful free radical scavengers. We present a detailed analysis of hydroxyl hydrogen abstraction from hydroquinone by hydroxyl and hydroperoxyl radical with emphasis on changes that take place in the vicinity of the transition state. Quantum theory of atoms in molecules is employed to elucidate the sequence of positive and negative charge transfer by studying selected properties of the three key atoms (the transferring hydrogen, the donor atom, and the acceptor atom) along intrinsic reaction path. The presented results imply that in both reactions, which are examples of proton coupled electron transfer, proton, and electron get simultaneously transferred to the radical oxygen atom. The fact that the hydrogen's charge and volume do not monotonously change in the vicinity of the transition state in the product valley results from the adjacency of the proton and the electron to the donor and the acceptor oxygen atoms. Obtaining a detailed understanding of mechanisms by which free radicals are disarmed is of paramount importance given the effects of those highly reactive species on biological systems. A comprehensive analysis of hydroxyl hydrogen abstraction from hydroquinone by hydroxyl and hydroperoxyl radicals, based on changes of selected electronic properties of the three most relevant atoms (hydrogen donor, hydrogen acceptor, and the hydrogen itself), along the reaction coordinate, can be obtained by first‐principles calculations.     

Hydrogen bonding in methanol clusters probed by inner-shell photoabsorption spectroscopy in the carbon and oxygen K-edge regions

Hydrogen bonding in methanol clusters has been investigated by using inner-shell photoabsorption spectroscopy and density functional theory (DFT) calculations in the carbon and oxygen K-edge regions. The partial-ion-yield (PIY) curves of H(CH(3)OH)(n)(+) were measured as the soft x-ray absorption spectra of methanol clusters. The first resonance peak in the PIY curves, which is assigned to the sigma*(O-H) resonance transition, exhibits a 1.20 eV blueshift relative to the total-ion-yield (TIY) curves of molecular methanol in the oxygen K-edge region, while it exhibits a shift of only 0.25 eV in the carbon K-edge region. Decreased intensities of the transitions to higher Rydberg orbitals were observed in the PIY curves of the clusters. The drastic change in the sigma*(O-H) resonance transition is interpreted by the change in the character of the sigma*(O-H) molecular orbital at the H-donating OH site due to the hydrogen-bonding interaction.     

Charge transfer complexes between 4,4′-disubstituted diphenyldiacetylenes: experimental and theoretical study

Novel charge transfer (CT) complexes containing donor and acceptor derivatives of diphenyldiacetylene have been synthesised and characterised. The structure of CT complexes was modelled at the B3LYP/6-31G(d)//B3LYP/6-31G(d) level of theory. It was found that the complex formation is mainly due to dipole–dipole interaction between side groups of diacetylene molecules and there was no significant charge transfer between donor and acceptor in the ground state. On the other hand, optical excitation of CT complexes leads to strong charge transfer from donor to acceptor molecule as followed from the modelling using time-dependent density functional theory (DFT) method. Diacetylene molecules adopt strongly bent configuration in CT complexes which is prohibitive for solid-state topochemical polymerisation of diacetylenes     

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.     

Fluorescence Quenching over Short Range in a Donor‐DNA‐Acceptor System

A new donor‐DNA‐acceptor system has been synthesized containing Nile red‐modified 2′‐deoxyuridine as charge donor and 6‐N,N‐dimethylaminopyrene‐modified 2′‐deoxyuridine as acceptor to investigate the charge transfer in DNA duplexes using fluorescence spectroscopy and time‐resolved femtosecond pump‐probe techniques. Fluorescence quenching experiments revealed that the quenching efficiency of Nile red depends on two components: 1) the presence of a charge acceptor and 2) the number of intervening CG and AT base pairs between donor and acceptor. Surprisingly, the quenching efficiency of two base pairs (73 % for CG and the same for AT) is higher than that for one base pair (68 % for CG and 37 % for AT), while at a separation of three base pairs less than 10 % quenching is observed. A comparison with the results of time‐resolved measurements revealed a correlation between quenching efficiency and the first ultrafast time constant suggesting that quenching proceeds via a charge transfer from the donor to the acceptor. All transients are satisfactorily described with two decays: a rapid charge transfer with 600 fs (～10¹² s^?1) that depends strongly and in a non‐linear fashion on the distance between donor and acceptor, and a slower time constant of a few picoseconds (～10¹¹ s^?1) with weak distance dependence. A third time constant on a nanosecond time scale represents the fluorescence lifetime of the donor molecule. According to these results and time‐dependent density functional theory (TDDFT) calculations a combination of single‐step superexchange and multistep hopping mechanisms can be proposed for this short‐range charge transfer. Furthermore, significantly less quenching efficiency and slower charge transfer rates at very short distances indicate that the direct interaction between donor and acceptor leads to a local structural distortion of DNA duplexes which may provide some uncertainty in identifying the charge transfer rates in short‐range systems.     

Second hyperpolarizabilities of singlet polycyclic diphenalenyl radicals: effects of the nature of the central heterocyclic ring and substitution to diphenalenyl rings

Adopting density functional theory and a hybrid exchange-correlation functional, the relationship between the second hyperpolarizability (gamma) and the diradical character has been investigated for diphenalenyl-based compounds containing different heterocyclic five-membered central rings (C(4)H(4)X, where X = NH, PH, O, S, CH(2), SiH(2), BH, GaH, C=O, C=S, and C=Se) or substituted by donor (NH(2))/acceptor(NO(2)) groups. It turns out that these structural modifications can tune the diradical character from 0.0 to 0.968 and lead to variations of gamma over more than 1 order of magnitude, demonstrating the controllability of gamma in this family of compounds. In particular, when the central ring is strongly aromatic, the diradical character is larger than 0.7, which is associated with pretty large gamma values except for almost the pure diradical case (y approximately 1). On the other hand, when the aromaticity decreases--or the antiaromaticity increases--the diradical character and the second hyperpolarizability get smaller. These relationships are correlated to structural (bond length alternation) and charge distribution (charge transfer between the phenalenyl rings and the central ring) properties, which account for the relative importance of the resonance diradical, zwitterionic, and quinoid forms. Therefore, the diradical character and the second hyperpolarizability can be controlled by the aromaticity of the ring while the paradigm of the enhancement of gamma for intermediate diradical character is globally verified. Then, upon introducing donor groups, the zwitterionic character increases, leading to closed-shell species and small second hyperpolarizabilities. In the case of substitution by acceptor groups, the charge transfer is reduced but the diradical character and the second hyperpolarizability hardly changes.