Electron propagator theory study of N-/O-methylglycine conformers

The low-lying conformers of N-/O-methylglycine are studied by ab initio calculations at the B3LYP, MP3, and MP4(SDQ) levels of theory with the aug-cc-pVDZ basis set. The conformers having the intramolecular hydrogen bonds N-H...O=C or O-H...N are more stable than the others. Vertical ionization energies for the valence molecular orbitals of each conformer predicted with the electron propagator theory in the partial third-order quasiparticle approximation are in good agreement with the experimental data available in the literatures. The relative energies of the conformers and comparison between the simulated and the experimental photoelectron spectra demonstrate that there are at least three and two conformers of N- and O-methylglycine, respectively, in the gas-phase experiments. The intramolecular hydrogen bonding O-H...N effects on the molecular electronic structures are discussed for the glycine methyl derivatives, on the basis of the ab initio electronic structure calculations, natural orbital bond, and atoms-in-molecules analyses. The intramolecular hydrogen bonding O-H...N interactions hardly affect the electronic structures of the O-NH2-CH2-C(=O)-O-CH3 and alpha-methylated NH2-CH2-C(CH3)OOH conformers, while the similar intramolecular interactions lead to the significantly lower-energy levels of the highest occupied molecular orbitals for the N-(CH3-NH-CH2-COOH) and beta-methylated (NH2-CH2-CH2-COOH) conformers.     

Electronic structures of acyl nitrites and nitrates

The gas phase electronic structures of CM(3)C(O)ONO and CM(3)C(O)ONO(2) (M=H, Cl, F) are studied by photoelectron spectroscopy (PES) combined with the outer valence Green's function (OVGF) calculations at 6-311+G(d, p) basis sets. The highest occupied molecular orbital (HOMO) for each compound is the carbonyl oxygen lone pair (n(O)), the ionizations of these orbitals are associated with the vibrational frequency about 1750 and 1820 cm(-1) reflected on the first band, respectively, for acyl nitrites and nitrate. Comparing with the calculated energies, it can be concluded that the syn conformers with Cs overall symmetry, a planar CC(O)ONO skeleton in nitrites, and a planar CC(O)ON skeleton in nitrates, respectively, are the most stable in the gas phase.     

Chiral signatures in angle-resolved valence photoelectron spectroscopy of pure glycidol enantiomers

Photoionization of the chiral molecule glycidol has been investigated in the valence region. Photoelectron circular dichroism (PECD) curves have been obtained at various photon energies by using circularly polarized VUV synchrotron radiation and a velocity map imaging technique to record angle-resolved photoelectron spectra (PES). The measured chiral asymmetries vary dramatically with the photon energy as well as with the ionized orbital, improving the effective orbital resolution of the PECD spectrum with respect to the PES. Typical asymmetry factors of 5% are observed, but the peak values measured range up to 15%. The experimental results are interpreted by continuum multiple scattering (CMS-Xalpha) calculations for several thermally accessible glycidol conformers. We find that a nearly quantitative agreement between theory and experiments can be achieved for the ionization of several molecular orbitals. Owing to the sensitivity of PECD to molecular conformation this allows us to identify the dominant conformer. The influence of intramolecular hydrogen bond orbital polarization is found to play a small yet significant role in determining the chiral asymmetry in the electron angular distributions.     

Electron Momentum Spectroscopy of Outer Valence Orbitals of 2-Fluoroethanol

The binding energy spectra and electron momentum distributions for the outer valence molecular orbitals of gaseous 2-fluoroethanol have been measured by the non-coplanar asymmetric (e, 2e) spectrometer at impact energy of 2.5 keV plus binding energy. The quantitative calculations of the ionization energies and the relevant molecular orbitals have been carried out by using the outer-valence Green’s function method and the density functional theory with B3LYP hybrid functional. The observed ionization bands in binding energy spectra, as well as the previous photoelectron spectrum which was not assigned, have been assigned for the first time through the comparison between experiment and theory. In general, the theoretical electron momentum distributions calculated by B3LYP method with aug-cc-pVTZbasis set are in line with the experimental ones when taking into account the Boltzmannweighted thermo-statistical abundances of five conformers of 2-fluoroethanol.     

Comparison of a calculated and measured XANES spectrum of α-Fe2O3

Comparison and prediction of the experimental XANES spectrum is a good measurement of the quality of the electronic structure calculations employed, and their ability to predict electronic transitions in solids. Here we present a comparison between BLYP + U and hybrid-BLYP calculations regarding the geometric, magnetic and electronic structures of α-Fe(2)O(3) (hematite). Several values of U and different percentages of Fock-exchange have been screened to see how their contributions affect different properties of hematite, paying particular attention to the electronic structure. To estimate the quality of the various methods the calculated density-of-states were compared to the experimentally collected XANES spectrum of the iron K-edge, providing information about the orbitals describing the conduction band. We find that in agreement with previous studies DFT + U and hybrid-functional simulations can correctly predict the character of the valence band, but only Fock-exchange higher than 30% or U-values equal or larger than 6 eV properly reproduce the order between the t(g) and e orbitals in the conduction band, and can, therefore, be used to study and predict XANES spectra and electronic transitions in hematite.     

NMR, UV, FT-IR, FT-Raman spectra and molecular structure (monomeric and dimeric structures) investigation of nicotinic acid N-oxide: A combined experimental and theoretical study

In this work, the experimental and theoretical UV, NMR, and vibrational features of nicotinic acid N-oxide (abbreviated as NANO, C(6)H(5)NO(3)) were studied. The ultraviolet (UV) absorption spectrum of studied compound that dissolved in water was examined in the range of 200-800nm. FT-IR and FT-Raman spectra in solid state were observed in the region 4000-400cm(-1) and 3500-50cm(-1), respectively. The (1)H and (13)C NMR spectra in DMSO were recorded. The geometrical parameters, energies and the spectroscopic properties of NANO were obtained for all four conformers from density functional theory (DFT) B3LYP/6-311++G(d,p) basis set calculations. There are four conformers, C(n), n=1-4 for this molecule. The computational results identified the most stable conformer of title molecule as the C1 form. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. (13)C and (1)H nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies, were performed by CIS approach. Finally the calculation results were applied to simulate infrared, Raman, and UV spectra of the title compound which show good agreement with observed spectra.     

Spectroscopic and theoretical studies of optically active porphyrin dimers: a system uninterpretable by exciton coupling theory.

The electronic excited states of a meso-meso beta-beta doubly linked bis-porphyrin are comprehensively investigated by measuring its circular dichroism (CD) and magnetic circular dichroism (MCD) spectra. The observed spectroscopic properties are rationalized by DFT calculations. The frontier molecular orbitals (MOs) are constructed by the linear combinations of the constituent monomers' four MOs. Comparison of a theoretical CD spectrum based on time-dependent DFT (TDDFT) with the experimental spectra resulted in the assignment of the helical conformation of the dimer. This assignment is contrary to the previous assignment based on the point-dipole approximation (exciton coupling theory).     

The outer valance orbital electron densities of cyclopentane by binary (e,2e) spectroscopy

The binding energy spectra and electron distributions in momentum space of the valence orbitals of cyclopentane (C(5)H(10)) are studied by Electron Momentum Spectroscopy (EMS) in a noncoplanar symmetric geometry. The impact energy was 1200 eV plus binding energy and energy resolution of the EMS spectrometer was 1.2 eV. The experimental momentum profiles of the outer valence orbitals are compared with the theoretical momentum distributions calculated using Hartree-Fock and density functional theory (DFT) methods. The shapes of the experimental momentum distributions are generally quite well described by both the Hartree-Fock and DFT calculations when the large and diffuse basis sets are used.     

Photoelectron spectra of some antibiotic building blocks: 2-azetidinone and thiazolidine-carboxylic Acid

X-ray photoelectron spectra of the core and valence levels of the fundamental building blocks of β-lactam antibiotics have been investigated and compared with theoretical calculations. The spectra of the compounds 2-azetidinone and the 2- and 4-isomers of thiazolidine-carboxylic acid are interpreted in the light of theoretical calculations. The spectra of the two isomers of thiazolidine-carboxylic acid are rather similar, as expected, but show clear effects due to isomerization. Both isomers are analogues of proline, which is well-known to populate several low energy conformers in the gas phase. We have investigated the low energy conformers of thiazolidine-4-carboxylic acid theoretically in more detail and find some spectroscopic evidence that multiple conformers may be present. The measured valence levels are assigned for all three compounds, and the character of the frontier orbitals is identified and analyzed.     

Ultrafast hybridization screening in Fe3+ aqueous solution

We report here on the electron binding energies and ultrafast electronic relaxation of the Fe(3+)(aq) complex in FeCl(3) aqueous solution as measured by soft X-ray photoelectron (PE) spectroscopy from a vacuum liquid microjet. Covalent mixing between the 3d valence orbitals of the iron cation and the molecular orbitals of water in the ground-state solution is directly revealed by spectroscopy of the highest partially occupied molecular orbitals. Valence PE spectra, obtained for photon energies near the iron 2p absorption edge, exhibit large resonant enhancements. These resonant PE features identify 3d-O2p transient hybridization between iron and water-derived orbitals and are an indication of charge transfer within the electronically excited Fe(3+)(aq)* complex. Charge transfer from water to iron is also revealed by the 2p core-level PE spectrum, and the asymmetric peak shape additionally identifies the characteristic multiplet interactions in the 2p core-hole state. The electronic structure of water molecules in the first hydration shell is selectively probed by Auger decay from water molecules, at excitation energies well below the O1s absorption edge of neat water. These experiments lay the groundwork for establishing resonant PE spectroscopy for the study of electronic-structure dynamics in the large family of transition metal (aqueous) solutions.     

CFCl3分子2e和4a1轨道的电子动量谱研究

由于工业的迅速发展,使得空气质量急剧下降,因此对影响大气的分子进行深入研究变得非常必要．本实验室已经对影响环境的甲烷[1]、丙烷[2]、CO2[3]等分子进行了电子动量谱研究,为环保提供了有用的数据．CFCl3作为工业广泛应用的气雾剂和制冷剂原料,它的大量使用导致了大气中臭氧的减少[4]．前人已用光电子谱学的方法[5-8]研究了CFCl3,我们又用电子动量谱的手段对CFCl3分子进行了进一步的研究,即从波函数的层次上详细了解CFCl3的电子结构．     

Valence band structure of cellulose and lignin studied by XPS and DFT

In this report, X-ray induced photoelectron spectroscopy (XPS) measurements of the valence band structure of cellulose and lignin are combined with a theoretical reconstruction of the spectra based on density functional theory (DFT) calculations. These calculations involve an analysis of the valence band structures and their respective orbitals in which basic units of cellulose and lignin are considered. In addition, photoionization cross sections are incorporated for reconstruction of the XPS spectra. This combination of theoretical calculations and experimental measurements revealed that an emission present up to 10 eV in the valence band structure is dominated by oxygen rather than by carbon, as reported in literature. Furthermore, a quantitative elemental analysis shows significant carbon contributions at binding energies above 13 eV. The valence band analysis supported by DFT provides a powerful basis for a detailed interpretation of spectroscopic data and enables a profound insight into application relevant processes in future.     

Probing the molecular and electronic structure of capsaicin: a spectroscopic and quantum mechanical study

The conformational preferences of capsaicin were investigated by using the hybrid meta density functional theory (DFT) method MPWB1K. Its flexible, pendant side chain allows for a multitude of conformations only slightly different in energy. The distinctive vibrational features of the most stable conformers were characterized. To elucidate the most favorable reaction sites of capsaicin for radical scavenging, various homolytic bond-dissociation energies were also calculated. Of the possible radical intermediates, the allyl and benzyl radicals are energetically preferred. The filled and empty electronic structures of capsaicin were investigated by exploiting the photoelectron and electron-transmission spectra also of reference molecules and suitable quantum-mechanical calculations. On this basis, a reliable pattern of the vertical ionization energies and electron-attachment energies of capsaicin was proposed. The frontier pi molecular orbitals are concentrated over the vanillyl moiety, with a modest influence of the amidic-aliphatic chain. The (negative) first vertical electron affinity is predicted to be similar to that of benzene. The absorption spectrum of capsaicin and its change by conversion into a phenolic deprotonated anion (modest bathochromic displacement) or a phenoxyl neutral radical (from colorless to red) were interpreted with time-dependent DFT calculations. ESR measurements following chemical or electrochemical reduction of capsaicin did not lead to detection of the corresponding radical anion. The spectra show fragmentation of the original molecule and formation of a variety of radical species which are believed to have a semiquinonic structure.     

Electronic structure of copper phthalocyanine: an experimental and theoretical study of occupied and unoccupied levels

An experimental and theoretical study of the electronic structure of copper phthalocyanine (CuPc) molecule is presented. We performed x-ray photoemission spectroscopy (XPS) and photoabsorption [x-ray absorption near-edge structure (XANES)] gas phase experiments and we compared the results with self-consistent field, density functional theory (DFT), and static-exchange theoretical calculations. In addition, ultraviolet photoelectron spectra (UPS) allowed disentangling several outer molecular orbitals. A detailed study of the two highest occupied orbitals (having a(1u) and b(1g) symmetries) is presented: the high energy resolution available for UPS measurements allowed resolving an extra feature assigned to vibrational stretching in the pyrrole rings. This observation, together with the computed DFT electron density distributions of the outer valence orbitals, suggests that the a(1u) orbital (the highest occupied molecular orbital) is mainly localized on the carbon atoms of pyrrole rings and it is doubly occupied, while the b(1g) orbital, singly occupied, is mainly localized on the Cu atom. Ab initio calculations of XPS and XANES spectra at carbon K edge of CuPc are also presented. The comparison between experiment and theory revealed that, in spite of being formally not equivalent, carbon atoms of the benzene rings experience a similar electronic environment. Carbon K-edge absorption spectra were interpreted in terms of different contributions coming from chemically shifted C 1s orbitals of the nonequivalent carbon atoms on the inner ring of the molecule formed by the sequence of CN bonds and on the benzene rings, respectively, and also in terms of different electronic distributions of the excited lowest unoccupied molecular orbital (LUMO) and LUMO+1. In particular, the degenerate LUMO appears to be mostly localized on the inner pyrrole ring.     

Quadricyclanes. Part I: Photoelectron spectra and electronic structure

The photoelectron spectra of quadricyclane ( 3 ) and 3-methylidene quadricyclane ( 4 ) have been measured. The results served as a basis for the elucidation of the electronic structure of these compounds, which agreed with theoretical calculations. It is found that the symmetry of the HOMO of 3 is different when compared to that of its valence isomer norbornadiene ( 1 ). The results also indicate that the structure of the highest occupied orbitals cannot be derived by only considering the Walsh-orbitals of the two three-membered rings. In addition one of the Walsh-components of the four-memebered ring has to be taken into account.     

Benchmark Dyson orbital study of the ionization spectrum and electron momentum distributions of ethanol in conformational equilibrium

An extensive study, throughout the valence region, of the electronic structure, ionization spectrum, and electron momentum distributions of ethanol is presented, on the ground of a model that focuses on a mixture of the gauche and anti conformers in their energy minimum form, using weight coefficients obtained from thermostatistical calculations that account for the influence of hindered rotations. The analysis is based on accurate calculations of valence one-electron and shakeup ionization energies and of the related Dyson orbitals, using one-particle Green's Function (1p-GF) theory in conjunction with the so-called third-order Algebraic Diagrammatic Construction scheme [ADC(3)]. The confrontation against available UPS (HeI) measurements indicates the presence in the spectral bands of significant conformational fingerprints at outer-valence ionization energies ranging from approximately 14 to approximately 18 eV. The shakeup onset is located at approximately 24 eV, and a shoulder at approximately 14.5 eV in the He I spectrum can be specifically ascribed to the minor anti (C(s)) conformer fraction. Thermally and spherically averaged Dyson orbital momentum distributions are computed for seven resolvable bands in model (e, 2e) ionization spectra at an electron impact energy of 1.2 keV. A comparison is made with results obtained from standard (B3LYP) Kohn-Sham orbitals and EMS measurements employing a high-resolution spectrometer of the third generation. The analysis is qualitatively in line with experiment and reveals a tremendously strong influence of the molecular conformation on the outermost electron momentum distributions. Quantitatively significant discrepancies with experiment can nonetheless be tentatively ascribed to strong dynamical disorder in the gas phase molecular structure.     

Ab initio assessment of the electronic structure of 5α-reduced progestins

Progesterone (P) yields to 5α-reduced progestins, namely 5α-pregnanedione (DHP), tetrahydroprogesterone (THP), and allopregnanolone (ALLO-P). The geometries and electronic structure of these steroids were assessed by ab initio calculations using the 6-31G* basis set. The parameters measured were bond distances, valence angles, and dihedral angles. Likewise, the following were calculated: total energy; frontier orbitals, i.e., highest occupied molecular orbital (HOMO); lowest unoccupied molecular orbital (LUMO); dipole moment; atomic charges; and electrostatic potentials. The frontier orbitals of P were located at the π-double bond. However, the HOMO of the 5α-progestins was extended into the molecule, while the LUMO was confined at the C20 carbonyl group. The atomic charges, electronic density surfaces and electrostatic potentials showed patterns according to the stereochemical arrangement of the C3 and C20 carbonyl and hydroxyl functional groups. Interestingly, P and THP showed the larger dipole moment and high electronic density at the A-ring because the double bond and the 3α-hydroxy group, respectively. The present results might explain to some extent the metabolism of the studied progestins. Similarly, some physicochemical properties, such as dipole moments and electrostatic potentials, seem related with important biological actions such as uterine contractility and control of gonadotropin secretion. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 329–338, 1998     

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.     

Determining relative f and d orbital contributions to M-Cl covalency in MCl6(2-) (M = Ti, Zr, Hf, U) and UOCl5(-) using Cl K-edge X-ray absorption spectroscopy and time-dependent density functional theory

Chlorine K-edge X-ray absorption spectroscopy (XAS) and ground-state and time-dependent hybrid density functional theory (DFT) were used to probe the electronic structures of O(h)-MCl(6)(2-) (M = Ti, Zr, Hf, U) and C(4v)-UOCl(5)(-), and to determine the relative contributions of valence 3d, 4d, 5d, 6d, and 5f orbitals in M-Cl bonding. Spectral interpretations were guided by time-dependent DFT calculated transition energies and oscillator strengths, which agree well with the experimental XAS spectra. The data provide new spectroscopic evidence for the involvement of both 5f and 6d orbitals in actinide-ligand bonding in UCl(6)(2-). For the MCl(6)(2-), where transitions into d orbitals of t(2g) symmetry are spectroscopically resolved for all four complexes, the experimentally determined Cl 3p character per M-Cl bond increases from 8.3(4)% (TiCl(6)(2-)) to 10.3(5)% (ZrCl(6)(2-)), 12(1)% (HfCl(6)(2-)), and 18(1)% (UCl(6)(2-)). Chlorine K-edge XAS spectra of UOCl(5)(-) provide additional insights into the transition assignments by lowering the symmetry to C(4v), where five pre-edge transitions into both 5f and 6d orbitals are observed. For UCl(6)(2-), the XAS data suggest that orbital mixing associated with the U 5f orbitals is considerably lower than that of the U 6d orbitals. For both UCl(6)(2-) and UOCl(5)(-), the ground-state DFT calculations predict a larger 5f contribution to bonding than is determined experimentally. These findings are discussed in the context of conventional theories of covalent bonding for d- and f-block metal complexes.