On the origins of core-electron chemical shifts of small biomolecules in aqueous solution: insights from photoemission and ab initio calculations of glycine(aq)

The local electronic structure of glycine in neutral, basic, and acidic aqueous solution is studied experimentally by X-ray photoelectron spectroscopy and theoretically by molecular dynamics simulations accompanied by first-principle electronic structure and spectrum calculations. Measured and computed nitrogen and carbon 1s binding energies are assigned to different local atomic environments, which are shown to be sensitive to the protonation/deprotonation of the amino and carboxyl functional groups at different pH values. We report the first accurate computation of core-level chemical shifts of an aqueous solute in various protonation states and explicitly show how the distributions of photoelectron binding energies (core-level peak widths) are related to the details of the hydrogen bond configurations, i.e. the geometries of the water solvation shell and the associated electronic screening. The comparison between the experiments and calculations further enables the separation of protonation-induced (covalent) and solvent-induced (electrostatic) screening contributions to the chemical shifts in the aqueous phase. The present core-level line shape analysis facilitates an accurate interpretation of photoelectron spectra from larger biomolecular solutes than glycine.     

Calculation of core-level electron spectra of ionic liquids

On the example of 40 ion pairs (5 cations times 8 anions), this study demonstrates how the core-level binding energy values can be calculated and used to plot theoretical spectra at low computational cost using density functional theory methods. Three approaches for obtaining the binding energy values are based on delta Kohn–Sham (ΔKS) calculations, 1s KS orbital energies, and atomic charges. The ΔKS results show reasonable agreement with the available experimental X-ray photoelectron data. The 1s KS orbital energies correlate well with the ΔKS results. Atomic charge correlation with ΔKS is improved by accounting for the charges of neighboring atoms. Assignment of binding energies to atoms and the applicability of the mentioned methods to model systems of ionic liquids are discussed.     

Interaction of atomic hydrogen with the beta-SiC(100) 3 x 2 surface and subsurface

We investigate clean and atomic hydrogen exposed beta-SiC(100) 3 x 2 surfaces by synchrotron radiation-based Si 2p core-level photoemission spectroscopy. The clean 3 x 2 surface reconstruction exhibits three surface and subsurface components. Upon hydrogen exposures, those surface and subsurface components are shifted to lower binding energies by large values, indicating significant charge transfer to the surface and subsurface regions, in excellent agreement with the recently discovered H-induced beta-SiC(100) 3 x 2 surface metallization. In addition, the interaction of hydrogen results in a large reactive component at Si 2p supporting an asymmetric charge transfer in the third plane below the surface, in agreement with previous experimental investigations. However, the results are inconsistent with recent ab initio theoretical "frozen" calculations predicting H atom to be in a bridge-bond position.     

An iterative method for obtaining accurate atomic inner shell binding energies

A new method based on an iterative procedure for obtaining accurate atomic inner shell binding energies is described. The method makes use of the doubly modi-fied Moseley plot as the starting point. As an illustration accurate binding energies for the M ₁ shell in the atomic number range 57 ≤ Z ≤ 71 have been obtained. This has also resulted in the removal of the anomaly in the M ₁ binding energy of Z = 68. Our calculations point to a need for a fresh look at the theoretical calculations of inner shell binding energies for Z = 57 to 71 in which some unsuspected effects appear to occur when the 4f shell is opened, half filled and closed.     

Relativistic theory of an inhomogeneous electron liquid in relation to atomic binding energies

Experimentally determined ionization potentials in the literature are used to plot the binding energies for neutral atoms as a function of atomic number Z for Z?=?2–30, 32, 36, 42. From this pretty smooth plot we have subtracted non-relativistic Hartree–Fock binding energies, using both available numerical values and the almost analytical result, based on the non-relativistic Thomas–Fermi statistical theory valid for large Z. The difference is still relatively smooth. For Mo, with Z?=?42, the difference is about 70 atomic units. This difference is then analyzed using first relativistic theory of an inhomogeneous electron liquid and then the Local Density Approximation (LDA), and for Mo their results yield approximately 88 and 67 atomic units respectively. We infer that a highly accurate relativistic many-electron theory will therefore be needed before reliable electron correlation energies can be extracted from the experimental binding energies for atoms heavier than Argon. This fact has prompted us to use available LDA calculations to confront three theoretical predictions of the Z dependence of non-relativistic electron correlation energies at large Z.     

Energetics of surface atomic processes and effects on growth of ultrathin films and nanoislands

Real surfaces of a crystal, especially those of nanometer in size, have many steps and all types of lattice imperfections. Moreover, there are atoms of different atomic environments: adatoms sit at a flat terrace, kink-site atoms sit in kink sites, and step-edge atoms of various coordination numbers sit in different step-edge sites. Using field-ion and atom-probe field-ion microscopy, it is possible to measure site specific binding energies of these surface atoms, and determine the mechanisms and activation energies of the various elementary surface atomic processes, i.e. surface diffusion. For kink-site atoms, our measurements with several metals find the binding energy to be equal to the cohesive energy of these metals. Atoms at other sites have slightly smaller binding energies. However, they are not proportional to the coordination numbers of the atoms, as assumed in many calculations. Such information will not only shed light on the binding mechanisms of solids, but is also needed for understanding the mechanisms of growth phenomena, such as crystal growth and epitaxial growth of thin films and nanoislands.     

Site-sensitive X-ray photoelectron spectroscopy of Fe3O4 by photoelectron diffraction

Fe 2p core-level photoelectron spectra of magnetite were measured using soft X-ray and hard X-ray, and its emission angle dependence was investigated. The photoelectron diffraction pattern from different atomic sites differs because the atomic arrangement surrounding each site is different. By selecting the forward-focusing-peak (FFP) directions characteristic to each atomic site and measuring the kinetic energy dependence of the FFP intensities at the Fe 2p core-level range, we succeed in detecting the variation of the peak intensity of Fe 2p core-level spectra at different emission directions. This result, consistent with recent results, suggests that the lower-binding-energy peak of the Fe 2p core-level spectrum may be assigned as the B site component.     

First-principles calculation of local atomic polarizabilities

Common methods of determining atomic polarizabilities suffer from the inclusion of nonlocal effects such as charge polarization. A new method is described for determining fully ab initio atomic polarizabilities based on calculating the response of atomic multipoles to the local electrostatic potential. The localized atomic polarizabilities are then used to calculate induction energies that are compared to ab initio induction energies to test their usefulness in practical applications. These polarizabilities are shown to be an improvement over the corresponding molecular polarizabilities, in terms of both absolute accuracy and the convergence of the multipolar induction series. The transferability of localized polarizabilities for the alkane series is also discussed.     

X-ray photoelectron spectroscopic study of the mechanism of palladium matrix modification in the electrothermal atomic absorption spectrometric determination of lead and bismuth

The mechanism of palladium matrix modification is studied for the determination of lead and bismuth by graphite-furnace atomic absorption spectrometry. The binding energies of the charring products for lead and bismuth in the presence or absence of palladium obtained at the initial stage of atomization were measured. The binding energies indicated the formation of PbPd and BiPd bonds, thus explaining the increase in appearance temperatures of lead and bismuth in the presence of palladium.     

ESCA applied to polymers. XXVI. Investigation of a series of aliphatic,aromatic, and fluorine-containing polycarbonates

The absolute and relative binding energies for the C_1s, O_1s, and F_1s core levels have been determined using x-ray photoelectron spectroscopy (ESCA) for a series of aliphatic, aromatic, and fluorine-containing polycarbonates. Comparisons of these experimentally determined, core-level binding energies with theoretical calculations using the ground-state potential model in the CNDO/2 SCF MO formalism as well as model compounds have been made on the C_1s and O_1s core levels. The degree of polymerization for low-molecular-weight fluorine-containing polycarbonates, as determined from ESCA measurements, is compared to measurements by vapor-phase osmometry and ¹⁹F-NMR.     

Bi-Sr-Ca-Cu-O超导体与氧化物衬底材料的反应性估计

测定了一系列氧化物的电子结合能，显示了铋系超导体与二元氧化物衬底材料的化学反应性可以用固态酸碱反应理论来描述，其反应性大小除了可以用衬底氧化物的酸碱参数估计以外，还可以用衬底氧化物氧离子的内层电子结合能估计．     

Hydrogen-induced Sulfur Vacancies on the MoS2 Basal Plane Studied by Ambient Pressure XPS and DFT Calculations

Sulfur vacancy on an MoS₂ basal plane plays a crucial role in device performance and catalytic activity; thus, an understanding of the electronic states of sulfur vacancies is still an important issue. We investigate the electronic states on an MoS₂ basal plane by ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) and density functional theory calculations while heating the system in hydrogen. The AP-XPS results show a decrease in the intensity ratio of S 2p to Mo 3d, indicating that sulfur vacancies are formed. Furthermore, low-energy components are observed in Mo 3d and S 2p spectra. To understand the changes in the electronic states induced by sulfur vacancy formation at the atomic scale, we calculate the core-level binding energies for the model vacancy surfaces. The calculated shifts for Mo 3d and S 2p with the formation of sulfur vacancy are consistent with the experimentally observed binding energy shifts. Mulliken charge analysis indicates that this is caused by an increase in the electronic density associated with the Mo and S atoms around the sulfur vacancy as compared to the pristine surface. The present investigation provides a guideline for sulfur vacancy engineering.     

Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges

A method is presented for the rapid calculation of atomic charges in σ-bonded and nonconjugated π-systems. Atoms are characterized by their orbital electronegativities. In the calculation only the connectivities of the atoms are considered. Thus only the topology of a molecule is of importance. Through an iterative procedure partial equalization of orbital electronegativity is obtained. Excellent correlations of the atomic charges with core electron binding energies and with acidity constants are observed. This establishes their value in predicting experimental data.     

Related upper and lower bounds to atomic binding energies

The method proposed by Singh for the calculations of lower bounds to atomic binding energies has been generalized to encompass upper bounds as well. The result is a pair of related matrix eigenvalue problems, constructed from similar sets of basic matrix elements, with the solution of one yielding the tower bound, and of the other, the upper bound. The upper bounds are identical to those calculated by the Rayleigh–Ritz method, which can be useful when the inversion of the normalization matrix is ill-conditioned. The lower bounds are comparable with the best available in the literature. © 1993 John Wiley & Sons, Inc.     

X-ray photoelectron spectra of ruthenium(II) phthalocyanines

Summary The Ru 3d_5/2 and 3p_3/2 x-ray photoelectron spectra of mono-and non-chlorinated ruthenium phthalocyanines were measured and the collected data on the core-level binding energies of ruthenium have been used to assess the oxidation state of the metal and the composition of the macrocyclic ligands.     

An exactly soluble base problem for atomic systems

An exactly soluble base problem for atomic systems is presented which approximates the atomic Hamiltonian as a sum of identical one‐electron operators. The eigenfunctions of the one‐electron operator consist of a radial function multiplied by a spherical harmonic. Energies for many‐electron atoms are found by summing the one‐electron energy eigenvalues according to the Pauli principle. These energies are rigorous lower bounds to the exact energies. This revised version was published online in July 2006 with corrections to the Cover Date.     

A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets

We report here a new and fast approach [Transferable Partial Atomic Charge Model (TPACM4)-upto four bonds] for deriving the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. We have created a look-up table of 5302 atom types to cover the chemical space of C, H, O, N, S, P, F, Cl, and Br atoms in small molecules together with their quantum mechanical RESP fit charges. The atom types defined span diverse plausible chemical environments of each atom in a molecule. The partial charge on any atom in a given molecule is then assigned by a reference to the look-up table. We tested the sensitivity of the TPACM4 partial charges in estimates of hydrogen bond dimers energies, solvation free energies and protein-ligand binding free energies. An average error ±1.11 kcal/mol and a correlation coefficient of 0.90 is obtained in the calculated protein-ligand binding free energies vis-à-vis an RMS error of ±1.02 kcal/mol and a correlation coefficient of 0.92 obtained with RESP fit charges in comparison to experiment. Similar accuracies are realized in predictions of hydrogen bond energies and solvation free energies of small molecules. For a molecule containing 50-55 atoms, the method takes on the order of milliseconds on a single processor machine to assign partial atomic charges. The TPACM4 programme has been web-enabled and made freely accessible at http://www.scfbio-iitd.res.in/software/drugdesign/charge.jsp.     

Theoretical and experimental study of the reactivity of PbTe in interaction with oxygen: Effect of germanium impurity atoms

High-resolution X-ray photoelectron spectroscopy (BESSY II, Berlin) has shown that germanium atoms doped into lead telluride are the centers of the oxidation reaction with dioxygen. The structure, stability, and core-level binding energies in the reaction centers have been calculated in the framework of the cluster approach with the use of the hybrid density functional (B3LYP); i.e., theoretical X-ray photoelectron spectra have been obtained. Different variants of the attachment of one to three O₂ molecules to the Ge atom located at the surface of a crystal or in the subsurface layer have been considered. It has been shown that chemisorption leads to structures with close energies, which give rise to a set of components in the spectra with unresolvable binding energies. The calculation and experimental results are in good agreement.     

Evidence from x-ray photoelectron spectroscopy on the charge distribution in various chromium compounds

Measurements of various core-level binding energies in the compounds K₃CrF₆, K₃Cr(CN)₆ and Cr(acac)₃ are reported. The binding energies of the L_III level of Cr in these compounds, and in Cr(CO)₆ and K₂CrO₄, are analyzed to yield charge differences between the chromium atom in Cr(acac)₃ and in the other compounds.     

Electron ionization cross sections for atomic subshells.

Ionization of atoms is the first step in many analytical procedures. The cross section for ionizing a particular atomic shell is essential for calculating the magnitude of analytical signals. Calculations using atomic wave functions for various shells of all elements relevant for X-ray microanalysis over a range of electron energies up to 400 keV were performed. The calculations for high energies above threshold can be considerably simplified by using the mathematical form of the Bethe ridge that dominates the scattering in this region. Corrections for exchange at low energies above threshold are incorporated in these calculations. A selection of results showing the effects of different approximations on ionization cross sections for K, L, and M shells is presented.