Outer Valence Region Research Articles

DFT Conformational, Wavefunction Based Reactivity Analysis, Docking and MD Simulations of a Carboxamide Derivative with Potential Anticancer Activity

The aim of this article is to use electronic structure approaches to investigate the chemical characteristics of N-[2-(diethylamino)ethyl]-5-[(Z)- (5-fluoro-2-oxo-1H-indol-3-ylidene) methyl] − 2,4-dimethyl-1H-pyrrole-3-carboxamide (Sunitinib) (DFDC), a carboxamide derivative with antitumor activity. For the dihedral angle of C13-C9-C16-N6 (160.0°) of DFDC, conformational analysis predicted the lowest energy conformer. Except for heptane, UV absorptions in various solvents and air give nearly identical. The hydrogen atom for which electron density exceeds upper limit of the color scale in localized orbital locator (LOL) analysis, whereas the blue color circles around the selected atoms in DFDC are for oxygen, and there are few carbon atoms with the electron depleted regions between inner and outer valence regions in DFDC. The biological impacts of the reactivity descriptors were addressed. Studies of wavefunction dependent properties such as LOL, electron localization function (ELF), and others provide a wealth of knowledge on electronic properties that is sufficient for predicting the bioactivity. Docking is done with several PDBs due to the anticancer activity of DFDC and bovine serum albumin corresponding to 3V03 yields the highest binding energy and MD simulations of DFDC with 3V03 are investigated in detail.

Electronic structure and nature of the metal-ligand chemical bond of Be, Mg, and Zn β-diketonates by quantum chemistry methods

The electronic structure of Be (II), Mg (II), and Zn (II) acetylacetonates and hexafluoroacetylacetonates was calculated in the DFT approximation. The energies of MOs and ionization energies calculated by the OVGF method were compared with the published data of photoelectron spectroscopy (HeI). The outer valence region of the spectra is equally effectively reproduced by DFT and OVGF methods. The calculations allowed determining the ionization energies of the π2 orbitals of the chelate cycles. It was determined that an increase in the binding energy of the electrons of the valence and core levels upon substitution of CH3>CF3 by 1,7–2,1 eV was correlated with a change of the negative charge of the carbon atom of the substituted groups on positive one. The polarity of M − O bonds increases in the series of Be, Mg, Zn. It was found that in addition to outer valence orbitals, a covalent bonding was also significantly affected by the deep valence σ-orbital 4a1 with a high degree of overlap with metal s-orbitals.

The Renner–Teller effect observed in the and electronic states of H2S+

In 1995, Balzer et al. recorded a well-resolved photoelectron spectrum of the outer valence region of H2S between 12.7 and 14.5 eV. The vibronic energies were identified with the aid of calculated ionisation potentials. Following on from this, vacuum ultraviolet pulsed-field ionisation spectroscopy was used by Hochlaf et al. in 2004 to record partially resolved rotational spectra of H2S+. Finally, in 2010, Han, Kang and Kim recorded rotationally resolved electronic spectra of the transitions of H2S+ above the barrier to linearity, by use of mass-analysed threshold ionisation photo-fragment excitation spectroscopy. By making use of new high-resolution jet-cooled electronic spectra recorded in Basel, and the rotational analyses carried out in 1972 and 1983, the different methods have been linked to provide a detailed picture of the relationship between the four different types of spectroscopy.

Spin–orbit effects, electronic decay and breakdown phenomena in the photoelectron spectra of iodomethane

In this work we discuss the theoretical photo-double ionization spectrum of iodomethane which was obtained by the newly developed relativistic two-particle propagator and compare it to experimental data. For a correct interpretation of the spectral features in the outer valence region, spin–orbit effects play a major role and induce new features to the spectra. Additionally, wide-energy range single and double ionization spectra of iodomethane were calculated revealing possible electronic decay reactions after high-energy primary ionization. In the low energy region of the single ionization spectrum pronounced breakdown was observed resulting in a highly correlated manifold which was characterized in detail via population analysis.

Size selective spectroscopy of Se microclusters

The electronic structure and photofragmentation in outer and inner valence regions of Se(n) (n ≤ 8) clusters produced by direct vacuum evaporation have been studied with size-selective photoelectron-photoion coincidence technique by using vacuum-ultraviolet synchrotron radiation. The experimental ionization potentials of these clusters were extracted from the partial ion yield measurements. The calculations for the possible geometrical structures of the Se(n) microclusters have been executed. The ionization energies of the clusters have been calculated and compared with the experimental results. In addition, theoretical fragment ion appearance energies were estimated. The dissociation energies of Se(n) clusters were derived from the recurrent relation between the gas phase enthalpies of the formation of corresponding cationic clusters and experimental ionization energies.

Soft X-ray photoemission spectroscopy of selected neurotransmitters in the gas phase

The valence molecular orbitals and core levels of tyramine, tryptamine and tryptophol in the gas phase have been studied using X-ray photoelectron spectroscopy (XPS) and theoretical methods. The energies of the outer valence region spectrum are found to be in agreement with previously reported He I spectra, while new data on the inner valence molecular orbitals are reported. The structures in the carbon, nitrogen and oxygen core level spectra of these molecules have been identified and assigned. These compounds are characterised by conformers with hydrogen bonding in which the π systems of the phenol and indole groups act as hydrogen acceptors, but a spectroscopic signature of this hydrogen bond was not observed. This is in contrast with our previous spectra of amino acids, where conformers with specific hydrogen bonding showed strong effects in core level spectra. We attribute the difference to the weaker strength of the π-hydrogen bonding.

Dyson orbitals of N2O: Electron momentum spectroscopy and symmetry adapted cluster-configuration interaction calculations

Electron momentum spectroscopy and symmetry adapted cluster-configuration interaction (SAC-CI) theory were combined to study electron correlation effects in nitrous oxide molecule (N(2)O). The SAC-CI General-R method accurately reproduced the experimental ionization spectrum. This bench-marked method was also introduced for calculating the momentum distributions of N(2)O Dyson orbitals. Several calculated momentum distributions with different theoretical methods were compared with the high resolution experimental results. In the outer-valence region, Hartree-Fock (HF), density functional theory (DFT), and SAC-CI theory can well describe the experimental momentum distributions. SAC-CI presented a best performance among them. In the inner-valence region, HF and DFT cannot work well due to the severe breaking of the molecular orbital picture, while SAC-CI still produced an excellent description of experimental momentum profiles because it can accurately take into account electron correlations. Moreover, the thermally averaged calculation showed that the geometrical changes induced by the vibration at room temperature have no noticeable effects on momentum distribution of valence orbitals of N(2)O.

High-resolution electron momentum spectroscopy of valence satellites of carbon disulfide

The binding energy spectrum of carbon disulphide (CS(2)) in the energy range of 9-23 eV has been measured by a high-resolution (e,2e) spectrometer employing asymmetric noncoplanar kinematics at an impact energy of 2500 eV plus the binding energy. Taking the advantage of the high energy resolution of 0.54 eV, four main peaks and five satellites in the outer-valence region are resolved. The assignments and pole strengths for these satellite states are achieved by comparing the experimental electron momentum profiles with the corresponding theoretical ones calculated using Hartree-Fock and density functional theory methods. The results are also compared in detail with the recent SAC-CI general-R calculations. General agreement is satisfactory, while the present experiment suggests cooperative contributions from (2)Π(u), (2)Σ(g)(+) states to satellite 2 and (2)Σ(g)(+), (2)Π(g) states to satellite 3. Besides, relatively low pole strength for X (2)Π(g) state is obtained which contradicts all the theoretical calculations [2ph-TDA, ADC(3), SAC-CI general-R, ADC(4)] so far.

A photoelectron and double photoionization study of the valence electronic structure of 1,4-bromofluorobenzene

Conventional photoelectron and time-of-flight photoelectron-photoelectron coincidence (TOF-PEPECO) spectra have been measured for the outer valence region of the 1,4-bromofluorobenzene molecule. The photoelectron spectra were recorded using HeI alpha radiation from a resonance source, and the TOF-PEPECO spectra were recorded using HeII alpha radiation from a pulsed resonance source. The former provide energies of the cationic states and the latter of the dicationic states. The spectra are adequately interpreted with the aid of accurate Green's function calculations, showing very significant correlation effects. The lowest double ionization energy is found at 23.45 eV associated with the (4b(1))(-2)X (1)A(1) dicationic state.

Dynamical (e,2e) studies using tetrahydrofuran as a DNA analogue

We present triply differential cross sections for the electron impact ionization of the outer valence regions of formic acid and tetrahydrofuran by 250eV incident electrons, measured in the coplanar asymmetric geometry in a conventional (e,2e) spectrometer.

Investigation of the molecular conformations of ethanol using electron momentum spectroscopy

The valence electronic structure and momentum-space electron density distributions of ethanol have been investigated with our newly constructed high-resolution electron momentum spectrometer. The measurements are compared to thermally averaged simulations based on Kohn–Sham (B3LYP) orbital densities as well as one-particle Green's function calculations of ionization spectra and Dyson orbital densities, assuming Boltzmann's statistical distribution of the molecular structure over the two energy minima defining the anti and gauche conformers. One-electron ionization energies and momentum distributions in the outer-valence region were found to be highly dependent upon the molecular conformation. Calculated momentum distributions indeed very sensitively reflect the distortions and topological changes that molecular orbitals undergo due to the internal rotation of the hydroxyl group, and thereby exhibit variations which can be traced experimentally. The B3LYP model Kohn–Sham orbital densities are overall in good agreement with the experimental distributions, and closely resemble benchmark ADC(3) Dyson orbital densities. Both approaches fail to quantitatively reproduce the experimental momentum distributions characterizing the highest occupied molecular orbital. Since electron momentum spectroscopy measurements at various electron impact energies indicate that the plane wave impulse approximation is valid, this discrepancy between theory and experiment is tentatively ascribed to thermal disorder, i.e. large-amplitude and thermally induced dynamical distortions of the molecular structure in the gas phase.

Valence photoionization and photofragmentation of aromatic amino acids

The valence photoelectron spectra of the aromatic amino acids phenylalanine, tyrosine, tryptophan and 3-methylindole in the gas phase have been investigated by soft X-ray radiation. The photoemission spectra of the outer valence regions are similar to previously reported He I spectra, although relative peak intensities are different due to the different photon energy. The spectral range has been extended to the inner valence region and new information has been obtained. The photofragmentation mass spectra of the aromatic amino acids were measured after ionization by noble gas resonance radiation at energies from 8.4 to 21.2 eV. The main peak in the mass spectra of phenylalanine corresponds to loss of the aromatic functional group, while for tyrosine and tryptophan it is due to the loss of the carboxylic and amino groups. Lower photon energies lead to ‘softer’ ionization, with reduced fragmentation and increased parent ion signal.

The Chemical Bond between Au(I) and the Noble Gases. Comparative Study of NgAuF and NgAu+ (Ng = Ar, Kr, Xe) by Density Functional and Coupled Cluster Methods

The nature of the chemical bond between gold and the noble gases in the simplest prototype of Au(I) complexes (NgAuF and NgAu+, where Ng = Ar, Kr, Xe), has been theoretically investigated by state of art all-electron fully relativistic DC-CCSD(T) and DFT calculations with extended basis sets. The main properties of the molecules, including dipole moments and polarizabilities, have been computed and a detailed study of the electron density changes upon formation of the Ng-Au bond has been made. The Ar-Au dissociation energy is found to be nearly the same in both Argon compounds. It almost doubles along the NgAuF series and nearly triples in the corresponding NgAu+ series. The formation of the Ng-Au(I) bonds is accompanied by a large and very complex charge redistribution pattern which not only affects the outer valence region but reaches deep into the core-electron region. The charge transfer from the noble gas to Au taking place in the NgAu+ systems is largely reduced in the fluorides but the Ng-Au chemical bond in the latter systems is found to be tighter near the equilibrium distance. The density difference analysis shows, for all three noble gases, a qualitatively identical nature of the Ng-Au bond, characterized by the pronounced charge accumulation in the middle of the Ng-Au internuclear region which is typical of a covalent bond. This bonding density accumulation is more pronounced in the fluorides, where the Au-F bond is found to become more ionic, while the overall density deformation is more evident and less localized in the NgAu+ systems. Accurate density difference maps and charge-transfer curves help explain very subtle features of the chemistry of Au(I), including its peculiar preference for tight linear bicordination.

A study of the valence shell electronic structure and photoionization dynamics of selenophene

The photoelectron spectrum of selenophene has been recorded using synchrotron radiation in the photon energy range 20–80 eV and the inner valence region has been studied in detail for the first time. Green's function methods have been employed to evaluate the energies and spectral intensities of all valence shell ionization transitions and the results have facilitated an interpretation of the experimental spectra. Strong configuration interaction results in a redistribution of the intensity associated with the low lying π1(1b1) orbital amongst several satellite states located in the outer valence region. The continuum multiple scattering approach has been used to calculate photoelectron asymmetry parameters for selenophene, thiophene and hydrogen sulphide, and these theoretical predictions have been compared with the corresponding experimental data to assess the influence of Cooper minima and shape resonances. The comparison indicates that the Se 4p and the S 3p Cooper minima have little effect on the valence shell photoionization dynamics of selenophene and thiophene, respectively. This outcome is discussed in connection with the closely related hydrogen selenide and hydrogen sulphide molecules where strong resonant phenomena are observed.

Fragment anion spectroscopy of water in the inner and outer valence regions

Photoion-pair formation in H2O and D2O has been studied using synchrotron radiation within the energy range 15–50 eV. Appearance potentials for the formation of O−, OH− and H− have been determined and coincide with their thermochemical thresholds. Above threshold it is shown that superexcited states play an important role in the polar photodissociation process. Substantial isotope effects have been observed.

Understanding glycine conformation through molecular orbitals

The four most stable C(s) conformers of glycine have been investigated using a variety of quantum-mechanical methods based on Hartree-Fock theory, density-functional theory (B3LYP and statistical average of orbital potential), and electron propagation (OVGF) treatments. Information obtained from these models were analyzed in coordinate and momentum spaces using dual space analysis to provide insight based on orbitals into the bonding mechanisms of glycine conformers, which are generated by rotation of C-O(H) (II), C-C (III), and C-N (IV) bonds from the global minimum structure (I). Wave functions generated from the B3LYP/TZVP model revealed that each rotation produced a unique set of fingerprint orbitals that correspond to a specific group of outer valence orbitals, generally of a' symmetry. Orbitals 14a', 13a', 12a', and 11a' are identified as the fingerprint orbitals for the C-O(H) (II) rotation, whereas fingerprint orbitals for the C-C (III) bond rotation are located as 16a' [highest occupied molecular orbital (HOMO)], 15a' [next highest molecular occupied molecular orbital (NHOMO)], 14a', and 12a' orbitals. Fingerprint orbitals for IV generated by the combined rotations around the C-C, C-O(H), and C-N bonds are found as 16a', 15a', 14a', 13a', and 11a', as well as in orbitals 2a" and 1a". Orbital 14a' is identified as the fingerprint orbital for all three conformational processes, as it is the only orbital in the outer valence region which is significantly affected by the conformational processes regardless rotation of which bond. Binding energies, molecular geometries, and other molecular properties such as dipole moments calculated based on the specified treatments agree well with available experimental measurements and with previous theoretical calculation.

Experimental and calculated momentum densities for the complete valence orbitals of the antimicrobial agent diacetyl

The first electronic structural study of the complete valence shell binding energy spectra of the antimicrobial agent diacetyl, encompassing both the outer and inner valence regions, is reported. The binding energy spectra as well as the individual orbital momentum profiles have been measured by using a high resolution (e, 2e) electron momentum spectrometer (EMS) at an impact energy of 1200eV plus the binding energy and using symmetric noncoplanar kinematics. The experimental orbital electron momentum profiles are compared with self-consistent field (SCF) theoretical profiles calculated using the Hartree–Fock approximation and Density Functional theory predictions in the target Kohn-Sham approximation which includes some treatment of correlation via the exchange and correlation potentials with a range of basis sets. The pole strengths of the main ionization peaks from the inner valence orbitals are estimated.

A fluorescence polarisation study of the CS2+ and the transitions

Abstract The fluorescence yields and polarisations of the CS 2 + A 2 Π u → X 2 Π g and the B 2 Σ u + → X 2 Π g transitions have been measured between their thresholds and 30 eV using synchrotron radiation. In the outer valence region the fluorescence yields display prominent structure due to autoionising Rydberg states. New features, associated with multi-electron transitions, have been observed between 16 and 30 eV, and most have been assigned through reference to the inner valence shell photoelectron spectrum. Some of the new features exhibit vibrational progressions involving excitation of the ν 1 ′ mode. The influence of shape resonances on the photoionisation partial cross-sections has been considered. The polarisation measurements for the A 2 Π u → X 2 Π g and the B 2 Σ u + → X 2 Π g transitions have been compared with predictions derived from theoretical photoionisation partial cross-sections. The predictions for the B 2 Σ u + → X 2 Π g fluorescence polarisation display a rapid increase in the threshold region, in agreement with the experimental results. Resonant excitation and decay processes produce significant variations in the fluorescence polarisation, and these changes can be used to deduce the symmetry of the excited state. This information has allowed the assignments of some of the Rydberg series converging onto the B 2 Σ u + or the C 2 Σ g + ionisation thresholds to be clarified.

An experimental and theoretical study of the valence shell photoelectron spectraof purine and pyrimidine molecules

The valence shell photoelectron spectrum of purine has been studied experimentallyand theoretically. Synchrotron radiation has been used to record spectra at photonenergies of 45 and 85 eV. Photoelectron angular distributions have been determinedand these provide an experimental means of distinguishing between σ-and π-typeorbitals. Vertical ionization energies and photoelectron spectral intensities havebeen evaluated using the many-body Green function method. The calculatedspectra agree well with the experimental results in the outer valence region andhave proved to be indispensable for interpreting the structure at higher bindingenergies where the single particle model of ionization breaks down. Thephotoelectron spectrum of pyrimidine has also been studied and is compared tothat of purine.

Theoretical investigation on the valence ionization spectra of Cl2O, ClOOCl, and F2O by correlation-based configuration interaction methods

We report on theoretical valence ionization spectra of molecules relevant in the stratosphere photochemistry obtained by all-electron SAC–CI (symmetry-adapted-cluster–configuration-interaction) calculations. Vertical ionization energies and pole strengths of the one- and two-electron processes of Cl2O and F2O were calculated beyond the energy region so far explored in the few other available theoretical and experimental studies to interpret the electronic structure of these molecules. Early and recently proposed incomplete assignments of the available He I photoelectron spectra are discussed and completed at least up to 20–21 eV binding energy on firmer grounds relying on valuable and accurate results based on different basis sets and an adequate treatment of electron correlations. Our theoretical data predict satellite states of Cl2O starting already in the outer-valence region because of strong correlation effects; the (2b1−1), (8a1−1), and (6b2−1) states interact with the two-electron processes and they split into more-than-two peaks. On the other hand, Koopmans’ picture is valid for the main peaks of F2O and no prominent satellites with strong intensity were found in the outer-valence region. The (4b2−1), (6a1−1), and (1a2−1) were attributed to the second band of F2O, for which different assignments or orderings of the states have previously been proposed in some experimental and theoretical works. Differences of the valence-ionization spectra of Cl2O and F2O for the appearance of the satellites in the intermediate energy region have been discussed with the aid of the calculated ionization potentials and excitation energies. For ClOOCl, we have presented the first theoretical low-energy ionization spectrum and discussed the character of the calculated states referring to the available ionization spectra of ClO radical.