Core Electron Binding Energies Research Articles

Relativistic study of tautomerism and core electron binding energies of thio- and selenocytosine

We applied the spin-free relativistic infinite-order two-component method to calculate the core-electron binding energies of different tautomeric structures of thio- and selenocytosine. The importance of relativistic effects in the ionization of 1s electrons was studied for selenocytosine. The present method provides a reasonably simple and reliable computational tool for calculating the core electron binding energies of molecules containing heavy atoms. The method can also be used for characterization of different tautomeric structures of nucleic acid basis.

Local Electronic Structure and Density of Edge and Facet Atoms at Rh Nanoclusters Self-Assembled on a Graphene Template

The chemical and physical properties of nanoclusters largely depend on their sizes and shapes. This is partly due to finite size effects influencing the local electronic structure of the nanocluster atoms which are located on the nanofacets and on their edges. Here we present a thorough study on graphene-supported Rh nanocluster assemblies and their geometry-dependent electronic structure obtained by combining high-energy resolution core level photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory. We demonstrate the possibility to finely control the morphology and the degree of structural order of Rh clusters grown in register with the template surface of graphene/Ir(111). By comparing measured and calculated core electron binding energies, we identify edge, facet, and bulk atoms of the nanoclusters. We describe how small interatomic distance changes occur while varying the nanocluster size, substantially modifying the properties of surface atoms. The properties of under-coordinated Rh atoms are discussed in view of their importance in heterogeneous catalysis and magnetism.

Core-to-Rydberg band shift and broadening of hydrogen bonded ammonia clusters studied with nitrogen K-edge excitation spectroscopy

Nitrogen 1s (N 1s) core-to-Rydberg excitation spectra of hydrogen-bonded clusters of ammonia (AM) have been studied in the small cluster regime of beam conditions with time-of-flight (TOF) fragment-mass spectroscopy. By monitoring partial-ion-yield spectra of cluster-origin products, "cluster" specific excitation spectra could be recorded. Comparison of the "cluster" band with "monomer" band revealed that the first resonance bands of clusters corresponding to N 1s → 3sa(1)/3pe of AM monomer are considerably broadened. The changes of the experimental core-to-Rydberg transitions ΔFWHM (N 1s → 3sa(1)/3pe) = ~0.20/~0.50 eV compare well with the x ray absorption spectra of the clusters generated by using density functional theory (DFT) calculation. The broadening of the core-to-Rydberg bands in small clusters is interpreted as being primarily due to the splitting of non-equivalent core-hole N 1s states caused by both electrostatic core-hole and hydrogen-bonding (H(3)N···H-NH(2)) interactions upon dimerization. Under Cs dimer configuration, core-electron binding energy of H-N (H-donor) is significantly decreased by the intermolecular core-hole interaction and causes notable redshifts of core-excitation energies, whereas that of lone-pair nitrogen (H-acceptor) is slightly increased and results in appreciable blueshifts in the core-excitation bands. The result of the hydrogen-bonding interaction strongly appears in the n-σ* orbital correlation, destabilizing H-N donor Rydberg states in the direction opposite to the core-hole interaction, when excited N atom with H-N donor configuration strongly possesses the Rydberg component of anti-bonding σ* (N-H) character. Contributions of other cyclic H-bonded clusters (AM)(n) with n ≥ 3 to the spectral changes of the N 1s → 3sa(1)/3pe bands are also examined.

Tautomerism in 5-aminotetrazole investigated by core-level photoelectron spectroscopy and ΔSCF calculations

The C 1s and N 1s photoelectron spectra of gas-phase 5-aminotetrazole (5ATZ) were recorded using synchrotron radiation, with the aim of evaluating 1H/2H tautomer population ratios. The core–electron binding energies (CEBEs) were estimated from computational results, using the delta self-consistent-field (ΔSCF) approach. Simulated spectra were generated using these CEBEs and the results from Gaussian-n (Gn, n=1, 2 and 3) and Complete Basis Set (CBS-4M and CBS-Q) methods. Results reveal the almost exclusive predominance of the 2H-tautomer, with a 1H/2H ratio of ca. 0.12/0.88, taken from a gross analysis of the XPS C 1s spectrum, recorded at 365K.

Density functional theory study of the vertical ionization energies of the valence and core electrons of cyclopentadiene, pyrrole, furan, and thiophene

The procedure abbreviated as ΔPBE0(SAOP)/et-pVQZ, based on density functional theory, was developed recently for the calculation of vertical ionization energies of the valence electrons of organic and other small molecules and succeeded in giving results with an average absolute deviation of 0.21 eV from experiment for a collection of 115 reliable test cases of nonperhalo molecules. The objective of this work is to add a number of test cases to the benchmark database. We chose the set of molecules cyclo-C4H4X, with X = CH2, NH, O, and S, previously studied by many workers both experimentally and theoretically. The results show that the ΔPBE0(SAOP)/et-pVQZ procedure is not only as good as ab initio methods such as SAC-CI, OVGF, and ADC(3) in performance, but also handles inner valence ionized cations more efficiently. Although the core-electron binding energies of the titled molecules have not been as well investigated theoretically, we apply the methods we developed in recent years to calculate the binding energies of C1s, N1s, O1s, S1s, and S2p, which compare well with available experimental data.

Tautomerism in 5-methyltetrazole investigated by core-level photoelectron spectroscopy and ΔSCF calculations

The relative populations of the 1H- and 2H-tautomer of gas-phase 5-methyltetrazole (5MTZ) have been assessed through core-level photoelectron spectroscopy, and compared with the results obtained from Gaussian-n (Gn, n=1, 2 and 3) and Complete Basis Set methods (CBS-4M and CBS-Q). The C 1s and N 1s core–electron binding energies (CEBEs) for each ionization site of both tautomers have been computed using the Δself-consistent-field (ΔSCF) approach. The C 1s and N 1s XPS spectra, obtained at 313K, yield a 1H/2H tautomer ratio of ca. 0.16/0.84 and 0.21/0.79, respectively.

Substituent effects in chain and ring π-systems studied by core-electron binding energies calculated by density functional theory

The substituent effects of X- in 1-X-hexatrienes, which are chain π-systems with conjugated double bonds, was compared with those in Ph X, which are ring π-systems, using core electron binding energy shifts (ΔCEBE) of the carbon atoms in the molecules. The ΔCEBE of C 1 C 4 in 1-X-hexatrienes are generally close to ΔCEBE of C 1 C 4 in Ph X. The ΔCEBE of carbon atoms in the 1-X-hexatrienes are not only highly correlated to the Hammett σ substituent constants, but their numerical values are also close to each other. The core electron binding energies (CEBE) of the six carbons in 1-X-hexatriynes, which are the chain π-systems with conjugated triple bonds, were calculated by density functional theory (DFT) and the substituent effect was investigated. Average ΔCEBE of the five carbon atoms between C 2 and C 6 in 1-X-hexatriyne were calculated. The magnitude and sign of the average ΔCEBE provides quantitative strength and direction, electron withdrawing or donating, of a substituent X.

Calibration and applications of the ΔMP2 method for calculating core electron binding energies

We calibrated a method for the evaluation of core electron binding energies, based on the energy differences between the cation and neutral molecule evaluated at the level of Møller-Plesset perturbation theory. The central feature of the method is the use of a mixed basis set: a large all-electron basis set is used for the atom whose core electron is removed, while the model core potential basis set is employed for all remaining atoms. Calibration was carried out for 55 molecules and 114 binding energies of 1s core electrons for the atoms C, N, O, and F. The average absolute deviation for all the core electron binding energies is 0.163 eV. The method was applied to the calculation of the core electron binding energies of five nucleic acid bases (uracil, adenine, cytosine, guanine, and thymine) and several of their low-energy tautomers.

K-shell core-electron binding energies for phosphorus- and sulfur-containing molecules calculated by density functional theory

In this paper, 1s ionization energies for P- and S-containing molecules were calculated using energy-difference method by DFT. Using observed core-electron binding energies (CEBEs) as reference, we found that the Becke00x(xc) exchange-correlation functional ( E xc) is the best choice for CEBEs(P1s), with an average absolute deviation (AAD) of 0.20 eV, and that the best choice for CEBEs(S1s) is E xc = BmTau1, with an average absolute deviation (AAD) of 0.22 eV. However, the best single functional for calculation of both P and S is E xc = VS98, resulting in the weighted AAD of 0.43 eV. Our results are also showing that the quality of AAD changes slightly with the apparent orbital hybridization of the atom.

Accurate calculation of C1s core electron binding energies of some carbon hydrates and substituted benzenes

Approaches, using density functional theory (DFT), to calculate accurate adiabatic and vertical carbon 1s core electron binding energies (CEBE) of some alkanes, alkenes, alkynes and methyl- and fluorine-substituted benzenes are investigated. The approaches tested can be schematized as follows; Δ E KS ( PW 86 × - PW 91 c / TZP + C rel ) / / DFT ( PW 86 × - PW 91 c / TZP ) where Δ E KS is the difference between the Kohn–Sham total energy of the core–hole cation M +, E KS(M +), and the Kohn–Sham total energy of the neutral ground state molecule M, E KS(M). The geometry of M is optimized with DFT(PW86x-PW91c/TZP). For the adiabatic C1s CEBE calculation, the geometry of M + is optimized whereas, for the vertical C1s CEBE calculation, the geometry of M + is identical to the neutral ground state molecule M. C rel represents relativistic corrections. We tested two cases; C rel = 0 eV, and C rel = 0.05 eV. The relativistic correction turned out to be not necessary, because inclusion of the relativistic correction always increased deviation. The current results suggest a systematic error in the calculations that is fortuitously offset by the neglect of relativistic effects. The best approach resulted in average absolute deviations (maximum absolute deviations) from adiabatic experimental values of 0.045 eV (0.130 eV) for calculations of the corresponding C1s CEBE of the alkanes, alkenes, and substituted benzenes for 120 cases. The absolute uncertainty in the experimental measurements is estimated to be 0.03 eV. The average absolute deviation of 0.045 eV is close to the magnitude of the experimental uncertainty. Agreement between theory and experiment is better for adiabatic C1s CEBE than for vertical C1s CEBE.

Excitation and ionization energies of substituted anilines calculated with density functional theory

Valence electron singlet excitation energies (VEExE), valence electron ionization energies (VEIE), core electron binding energies (CEBE), and non-resonant X-ray emission energies of substituted anilines and related molecules were calculated using density functional theory (DFT). The energy calculations were done with TZP basis set of Slater Type Orbitals. PW86x-PW91c, turned out to be the best XC functional among eight functionals tested for time dependent DFT (TDDFT) calculation of the singlet excitation energies of the substituted anilines. Using the XC functional, average absolute deviation (AAD) from experiment was 0.223 eV for eighteen cases with maximum absolute deviation of 0.932 eV. The valence electron ionization energies of the substituted benzenes were calculated by ΔSCF method with PW86x-PW91c. AAD from experiment was 0.21 eV. The CEBEs were calculated with the previously established method, named as scheme 2003. ΔCEBE(SMS),, sum of mono substituted (SMS) CEBE shift , and mutual interference effect (MIE) were defined and their values were calculated. Magnitude of MIE provides the degree of mutual interference between two substituents in a phenyl ring. Average absolute value of MIE was ca. 0.1 eV for the three isomers of phenetidine. Using the calculated valence electron ionization energies and the core electron binding energies of one of the phenetidines, some X-ray emission energies were calculated.

Experimental and theoretical studies of 2‐amino‐3‐methylimidazo[4,5‐f]quinoline derivatives: Cooked‐food mutagens

AbstractThe UV absorption spectra of two potent mutagens, 2‐amino‐3‐methylimidazo[4,5‐f]quinoline (IQ) and NO2‐IQ, dissolved in ethanol, were observed at room temperature. General appearance of the two spectra is somewhat different. The absorption spectra show five bands in the region above 200 nm. The peak positions of the five bands are similar in the two spectra. The observed bands in the two molecules were assigned using transition energies calculated with time‐dependent density functional theory with triple‐zeta polarized basis set with the statistical average of orbital potentials exchange‐and‐correlation functional. The emission spectra of the two molecules dissolved in ethanol were obtained at 77 K. Only fluorescence emission was observed in IQ. No phosphorescence emission of the molecule was observed. Both fluorescence and phosphorescence emissions were observed in NO2‐IQ. These observations were interpreted with the aid of the calculated transition energy spectra. Some lowest vertical ionization energies of the two molecules were also calculated. The first ionization energy of NO2‐IQ is greater than that of IQ by 1.2 eV. Core electron binding energies (CEBEs) of the two molecules were calculated as well. Using CEBE shifts of atoms in the molecules, it was possible to observe the changes of chemical environment when substituent changes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

An X-ray photoelectron and absorption spectroscopic investigation of the electronic structure of cubanite, CuFe2S3

X-ray photoelectron and absorption spectra have been obtained for natural specimens of cubanite and compared with the corresponding spectra for chalcopyrite. Synchrotron X-ray photoelectron spectra of surfaces prepared by fracture under ultra-high vacuum revealed some clear differences for the two minerals, most notably those reflecting their different structures. In particular, the concentration of the low binding energy S species formed at cubanite fracture surfaces was approximately double that produced at chalcopyrite surfaces. However, the core electron binding energies for the two S environments in cubanite were not significantly different, and were similar to the corresponding values for the single environment in chalcopyrite. High binding energy features in the S 2p and Cu 2p spectra were not related to surface species produced either by the fracture or by oxidation, and most probably arose from energy loss due to inter-band excitation. Differences relating to the Fe electronic environments were detectable, but were smaller than expected from some of the observed physical properties and Mossbauer spectroscopic parameters for the two minerals. X-ray absorption and photoelectron spectra together with the calculated densities of states for cubanite confirmed an oxidation state of CuI in the mineral. It was concluded that the best formal oxidation state representation for cubanite is CuI(Fe2)VS 3 −II .

Substituent effect in n-hexanes and n-hexatrienes based on core-electron binding energies calculated with density-functional theory

It was shown that core-electron binding energy (CEBE) is a very convenient quantity to monitor substituent effect at each carbon atom in a substituted n-hexane (1-X–hexane), a chain σ-system, and a substituted n-hexatriene (1-X–hexatriene), a chain π-system. The core-electron binding energy was calculated using the density-functional theory with a scheme: Δ E KS ( PW86 – PW91 ) / TZP + C rel / / HF / 6 - 31 G ∗ The calculated CEBE( i) of ith orbital is equal to the sum of the ionization energy (− ε i ) due to the Koopmans’ theorem and relaxation energy ( R). The variation of the ionization energy (− ε i ) parallels closely to that of CEBE( i). The relaxation energy curve does not follow the CEBE curve. The behavior of CEBE in a molecule M depends almost exclusively upon the electronic structure of its neutral parent molecule M, and not upon its core-ionized cation M +. The substituent effect in the σ-system is considered as inductive effect. The substituent effect in the π-system consists of inductive and resonant/π-electron effects. Assuming that the inductive effect of the π-system, 1-X–hexatriene, can be approximated by that of the σ-systems, 1-X–hexane, resonant effect of the π-system was estimated.

Correlation and multiplet hole theory of core-electron energy splittings in transition-metal ions

A theory of multiplet hole splittings of core-electron binding energies in transition-metal ions is developed including correlation effects. Correlation effects are found to be important for understanding the magnitude and intensity ratios of the observed splittings. New multiplet structure is predicted for the 3s multiplets, a structure which does not exist in any rigorous one-electron theory and which has now been observed by Kowalczyk et al.

Oxygen chemisorption on the PbS(001) surface: Quantum-chemical modeling

The structure and stability of local centers involving a different number of oxygen atoms on the surface of crystalline lead sulfide (001) were calculated in the framework of the cluster approach by the hybrid density functional theory B3LYP method. The trends of the formation of such centers and changes in the core electron binding energies for the sulfur and lead atoms constituting these centers were considered.

Self-consistent-field calculations of core excited states

The accuracy of core excitation energies and core electron binding energies computed within a Delta self-consistent-field framework is assessed. The variational collapse of the core excited state is prevented by maintaining a singly occupied core orbital using an overlap criterion called the maximum overlap method. When applied to a wide range of small organic molecules, the resulting core excitation energies are not systematically underestimated as observed in time-dependent density functional theory and agree well with experiment. The accuracy of this approach for core excited states is illustrated by the calculation of the pre-edge features in x-ray absorption spectra of plastocyanin, which shows that accurate results can be achieved with Delta self-consistent-field calculations when used in conjunction with uncontracted basis functions.

X-ray photoelectron spectra of organoelement compounds and polarizability effect

The literature data on substituent influence on the core–electron binding energies E for K, B, Al, Si, Ge, Sn, P, Mo, Mn, Co, and Pt central atoms obtained mainly from X-ray photoelectron spectra have been analyzed for 22 series of the organoelement compounds. It was established for the first time that the E values depend not only on the inductive and resonance effects but also on the polarizability of substituents. The polarizability effect is caused by an electrostatic attraction between the positive charge on the central atom and the dipole moments induced by this charge in the substituents. The polarizability contribution ranges from 2 to 56%.

XPS study of nitrogen dioxide adsorption on metal oxide particle surfaces under different environmental conditions

The adsorption of nitrogen dioxide on gamma aluminium oxide (gamma-Al(2)O(3)) and alpha iron oxide (alpha-Fe(2)O(3)) particle surfaces under various conditions of relative humidity, presence of molecular oxygen and UV light has been investigated. X-Ray photoelectron spectroscopy (XPS) is used to monitor the different surface species that form under these environmental conditions. Adsorption of NO(2) on aluminum oxide particle surfaces results primarily in the formation of surface nitrate, NO(3)(-) with an oxidation state of +5, as indicated by a peak with binding energy of 407.3 eV in the N1s region. An additional minority species, sensitive to the presence of relative humidity and molecular oxygen, is also observed in the N1s region with lower binding energy of 405.9 eV. This peak is assigned to a surface species in the +4 oxidation state. When irradiated with UV light, other species form on the surface. These surface-bound photochemical products all have lower binding energy, between 400 and 402 eV, indicating reduced nitrogen species in the range of N oxidations states spanning +1 to -1. Co-adsorbed water decreases the amount of these reduced surface-bound products while the presence of molecular oxygen completely suppresses the formation of all reduced nitrogen species on aluminum oxide particle surfaces. For NO(2) on iron oxide particle surfaces, photoreduction is enhanced relative to gamma-Al(2)O(3) and surface bound photoreduced species are observed under all environmental conditions. Complementing the experimental data, N1s core electron binding energies (CEBEs) were calculated using DFT for a number of nitrogen-containing species in the gas phase and adsorbed on an Al(8)O(12) cluster. A range of CEBEs is calculated for various nitrogen species in different adsorption modes and oxidation states. These calculated values are discussed in light of the peaks observed in the XPS N1s region and the possible species that form following NO(2) adsorption and photoreaction on metal oxide particle surfaces under different conditions of relative humidity, presence of molecular oxygen and UV light.

Relativistic effects in K-shell ionizations: SAC-CI general-R study based on the DK2 Hamiltonian

Relativistic effects in K-shell ionizations were studied using the symmetry adapted cluster-configuration interaction (SAC-CI) general-R method based on the spin-free part of the second-order Douglass–Kroll–Hess (DK2) Hamiltonian. The core–electron binding energies (CEBEs) of F, Si, P, S, and Cl atoms of several molecules were calculated. The relativistic effect in the CEBEs of the second-row atoms was 4–9eV. The relativistic effect was mostly overestimated by the Koopmans’ theorem and was reduced to the extent of 0.15–0.4eV by including the orbital relaxation and electron correlations. The present method provides a simple and reliable computational tool for calculating the CEBEs of molecules containing heavy elements.