Study of Nb2O(y) (y = 2-5) anion and neutral clusters using anion photoelectron spectroscopy and density functional theory calculations

A study combining anion photoelectron spectroscopy and density functional theory calculations on the transition metal suboxide series, Nb(2)O(y)(-) (y = 2-5), is described. Photoelectron spectra of the clusters are obtained, and Franck-Condon simulations using calculated anion and neutral structures and frequencies are used to evaluate the calculations and assign transitions observed in the spectra. The spectra, several of which exhibit partially resolved vibrational structure, show an increase in electron affinity with increasing cluster oxidation state. Hole-burning experiments suggest that the photoelectron spectra of both Nb(2)O(2)(-) and Nb(2)O(3)(-) have contributions from more than one structural isomer. Reasonable agreement between experiment and computational results is found among all oxides.     

Adsorption of C2H radical on cobalt clusters: anion photoelectron spectroscopy and density functional calculations

We investigated the adsorption of C(2)H radical on small cobalt clusters by mass spectrometry and by measuring the photoelectron spectra of Co(n)C(2)H(-) (n = 1-5) cluster anions. The most stable structures of Co(n)C(2)H(-) (n = 1-5) and their neutrals were determined by comparing the experimental results with theoretical calculations. Our studies show that C(2)H radical still maintains its integrity as a structural unit in Co(n)C(2)H(-) clusters, rather than being divided by Co(n) clusters. The most stable isomers of Co(1-2)C(2)H(-) clusters are linear with the C(2)H interacting with only one Co atom, while those of Co(3-5)C(2)H(-) cluster anions are quasi-planar structures with the carbon-carbon bonds bending slightly toward the Co(3-5) clusters. The carbon-carbon bond of C(2)H is lengthened more in Co(3-5)C(2)H(-) clusters than in Co(1-2)C(2)H(-).     

Phenyl-coinage metal (Ag, Au) complexes: an anion photoelectron spectroscopy and density functional study

The important intermediate phenyl-coinage metal complexes (Ag(m)C6H5(-), Au(m)C6H5(-)), which are produced from the reactions between coinage metal clusters formed by laser ablation and the benzene molecules seeded in argon carrier gas, are studied by PES (photoelectron spectroscopy) and DFT (density functional theory). The EAs (adiabatic electron affinities) of these complexes are obtained from PES at both 308 and 193 nm photon energies and show odd-even alternation. Calculations with DFT are carried out on the structural and electronic properties of Ag(m)C6H5(-) and Au(m)C6H5(-); the adiabatic detachment energy and the calculated DOS (density of states) for the ground state of a given anion are in good agreement with the experimental PES results. The observed spectra are also compared with those of the pure coinage metal clusters, which reveal that there are some similarities between them and the phenyl acts like an additional metal atom in the clusters. Furthermore, the bonding between phenyl and metal is analyzed, suggesting that phenyl group binds perpendicularly on metal clusters through C-M sigma bond.     

Lithium cluster anions: photoelectron spectroscopy and ab initio calculations

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.     

Hydrogen bonds in the nucleobase-gold complexes: photoelectron spectroscopy and density functional calculations

The nucleobase-gold complexes were studied with anion photoelectron spectroscopy and density functional calculations. The vertical detachment energies of uracil-Au(-), thymine-Au(-), cytosine-Au(-), adenine-Au(-), and guanine-Au(-) were estimated to be 3.37 ± 0.08 eV, 3.40 ± 0.08 eV, 3.23 ± 0.08 eV, 3.28 ± 0.08 eV, and 3.43 ± 0.08 eV, respectively, based on their photoelectron spectra. The combination of photoelectron spectroscopy experiments and density functional calculations reveals the presence of two or more isomers for these nucleobase-gold complexes. The major isomers detected in the experiments probably are formed by Au anion with the canonical tautomers of the nucleobases. The gold anion essentially interacts with the nucleobases through N-H···Au hydrogen bonds.     

Methylation of zebularine investigated using density functional theory calculations

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1‐(β‐D ‐ribofuranosyl)‐2‐pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1‐(β‐D ‐ribofuranosyl)‐5‐methyl‐2‐pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital‐based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Studies of iridium nanoparticles using density functional theory calculations

The energetics and the electronic and magnetic properties of iridium nanoparticles in the range of 2-64 atoms were investigated using density functional theory calculations. A variety of different geometric configurations were studied, including planar, three-dimensional, nanowire, and single-walled nanotube. The binding energy per atom increases with size and dimensionality from 2.53 eV/atom for the iridium dimer to 6.09 eV/atom for the 64-atom cluster. The most stable geometry is planar until four atoms are reached and three-dimensional thereafter. The simple cubic structure is the most stable geometric building block until a strikingly large 48-atom cluster, when the most stable geometry transitions to face-centered cubic, as found in the bulk metal. The strong preference for cubic structure among small clusters demonstrates their rigidity. This result indicates that iridium nanoparticles intrinsically do not favor the coalescence process. Nanowires formed from linear atomic chains of up to 4-atom rings were studied, and the wires formed from 4-atom rings were extremely stable. Single-walled nanotubes were also studied. These nanotubes were formed by stacking 5- and 6-atom rings to form a tube. The ring stacking with each atom directly above the previous atom is more stable than if the alternate rings are rotated.     

Structures of Mo2Oy- and Mo2Oy (y=2, 3, and 4) studied by anion photoelectron spectroscopy and density functional theory calculations

The competitive structural isomers of the Mo(2)O(y) (-)Mo(2)O(y) (y=2, 3, and 4) clusters are investigated using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. The PE spectrum and calculations for MoO(3) (-)MoO(3) are also presented to show the level of agreement to be expected between the spectra and calculations. For MoO(3) (-) and MoO(3), the calculations predict symmetric C(3v) structures, an adiabatic electron affinity of 3.34 eV, which is above the observed value 3.17(2) eV. However, there is good agreement between observed and calculated vibrational frequencies and band profiles. The PE spectra of Mo(2)O(2) (-) and Mo(2)O(3) (-) are broad and congested, with partially resolved vibrational structure on the lowest energy bands observed in the spectra. The electron affinities (EA(a)s) of the corresponding clusters are 2.24(2) and 2.33(7) eV, respectively. Based on the calculations, the most stable structure of Mo(2)O(2) (-) is Y shaped, with the two Mo atoms directly bonded. Assignment of the Mo(2)O(3) (-) spectrum is less definitive, but a O-Mo-O-Mo-O structure is more consistent with overall electronic structure observed in the spectrum. The PE spectrum of Mo(2)O(4) (-) shows cleanly resolved vibrational structure and electronic bands, and the EA of the corresponding Mo(2)O(4) is determined to be 2.13(4) eV. The structure most consistent with the observed spectrum has two oxygen bridge bonds between the Mo atoms.     

Electronic structure of ReO3Me by variable photon energy photoelectron spectroscopy,absorption spectroscopy and density functional calculations

Valence photoelectron (PE) spectra have been measured for ReO(3)Me using a synchrotron source for photon energies ranging between 20 and 110 eV. Derived branching ratios (BR) and relative partial photoionization cross sections (RPPICS) are interpreted in the context of a bonding model calculated using density functional theory (DFT). Agreement between calculated and observed ionization energies (IE) is excellent. The 5d character of the orbitals correlates with the 5p --> 5d resonances of the associated RPPICS; these resonances commence around 47 eV. Bands with 5d character also show a RPPICS maximum at 35 eV. The RPPICS associated with the totally symmetric 4a(1) orbital, which has s-like character, shows an additional shape resonance with an onset of 43 eV. The PE spectrum of the inner valence and core region measured with photon energies of 108 and 210 eV shows ionization associated with C 2s, O 2s, and Re 4f and 5p electrons. Absorption spectra measured in the region of the O1s edge showed structure assignable to excitation to the low lying empty "d" orbitals of this d(0) molecule. The separation of the absorption bands corresponded with the calculated orbital splitting and their intensity with the calculated O 2p character. Broad bands associated with Re 4d absorption were assigned to (2)D(5/2) and (2)D(3/2) hole states. Structure was observed associated with the C1s edge but instrumental factors prevented firm assignment. At the Re 5p edge, structure was observed on the (2)P(3/2) absorption band resulting from excitation to the empty "d" levels. The intensity ratios differed from that of the O 1s edge structure but were in good agreement with the calculated 5d character of these orbitals. An absorption was observed at 45 eV, which, in the light of the resonance in the 4a(1) RPPICS, is assigned to a 4a(1) --> ne, na(2) transition. The electronic structure established for ReO(3)Me differs substantially from that of TiCl(3)Me and accounts for the difference in chemical behavior found for the two complexes.     

Valence electronic structure of benzo-2,1,3-chalcogenadiazoles studied by photoelectron spectroscopy and density functional theory

The He I photoelectron spectra of benzo-2,1,3-thia-, selena-, and telluradiazole were measured, and the observed ionization bands were assigned by comparison with the results of DFT calculations. Whereas the B3LYP exchange-correlation functional provided orbital energies that permitted a preliminary assignment by application of Koopman's theorem, a more-accurate interpretation was established by calculation of the vertical ionization energies with the PW91 functional and analysis of the correlation of energy levels along the homologous series. This strategy clarified earlier disagreements in the assignment of the spectrum of benzo-2,1,3-thiadiazole.     

Communication: Avoiding unbound anions in density functional calculations

Converged approximate density functional calculations usually do not bind anions due to large self-interaction error. But Hartree-Fock (HF) calculations have no such problem, producing negative HOMO energies. Thus, electron affinities can be calculated from density functional total energy differences using approximations such as PBE and B3LYP, evaluated on HF densities (for both anion and neutral). This recently proposed scheme is shown to work very well for molecules, better than the common practice of restricting the basis set except for cases such as CN, where the HF density is too inaccurate due to spin contamination.     

Studies on the encapsulation of various anions in different fullerenes using density functional theory calculations and Born-Oppenheimer molecular dynamics simulation

The density functional theory (DFT)-based Becke's three parameter hybrid exchange functional and Lee-Yang-Parr correlation functional (B3LYP) calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations have been performed to understand the stability of different anions inside fullerenes of various sizes. As expected, the stability of anion inside the fullerene depends on its size as well as on the size of the fullerene. Results show that the encapsulation of anions in larger fullerenes (smaller fullerene) is energetically favorable (not favorable). The minimum size of the fullerene required to encapsulate F(-) is equal to C(32). It is found from the results that C(60) can accommodate F(-), Cl(-), Br(-), OH(-), and CN(-). The electron density topology analysis using atoms in molecule (AIM) approach vividly delineates the interaction between fullerene and anion. Although F(-)@C(30) is energetically not favorable, the BOMD results reveal that the anion fluctuates around the center of the cage. The anion does not exhibit any tendency to escape from the cage.     

Electronic structure of guanidine and its derivatives from X-ray photoelectron spectroscopy and density functional theory studies

Electronic structure of guanidine, diphenylguanidine, their protonated forms, and guanidinium chloride have been studied by X-ray photoelectron spectroscopy and quantum-chemical modeling. From the derived geometry parameters and electronic structure, the effect of protonation on localization of the electron density has been revealed. The lines in the valence region of the X-ray photoelectron spectra have been assigned.     

Electronic structures of WAlO(y) and WAlO(y) (-) (y = 2-4) determined by anion photoelectron spectroscopy and density functional theory calculations

The anion photoelectron spectra of WAlO(y) (-) (y = 2-4) are presented and assigned based on results of density functional theory calculations. The WAlO(2) (-) and WAlO(3) (-) spectra are both broad, with partially resolved vibrational structure. In contrast, the WAlO(4) (-) spectrum features well-resolved vibrational structure with contributions from three modes. There is reasonable agreement between experiment and theory for all oxides, and calculations are in particular validated by the near perfect agreement between the WAlO(4) (-) photoelectron spectrum and a Franck-Condon simulation based on computationally determined spectroscopic parameters. The structures determined from this study suggest strong preferential W-O bond formation, and ionic bonding between Al(+) and WO(y) (-2) for all anions. Neutral species are similarly ionic, with WAlO(2) and WAlO(3) having electronic structure that suggests Al(+) ionically bound to WO(y) (-) and WAlO(4) being described as Al(+2) ionically bound to WO(4) (-2). The doubly-occupied 3sp hybrid orbital localized on the Al center is energetically situated between the bonding O-local molecular orbitals and the anti- or non-bonding W-local molecular orbitals. The structures determined in this study are very similar to structures recently determined for the analogous MoAlO(y) (-)∕MoAlO(y) cluster series, with subtle differences found in the electronic structures [S. E. Waller, J. E. Mann, E. Hossain, M. Troyer, and C. C. Jarrold, J. Chem. Phys. 137, 024302 (2012)].     

Assignment of photoelectron spectra by the help of density functional calculations

First adiabatic and vertical ionization energies were calculated by the density functional method using Becke's correlated functional for water, ammonia, the silyl radical, five-membered heterocycles, and naphtalene. The structure of the ionic ground state and that of the neutral was optimized separately. The calculated ionization energies and harmonic frequencies are in acceptable agreement with the observed values. The calculated geometrical changes are in agreement with the information deduced from the photoelectron spectra. © 1997 John Wiley & Sons, Inc.     

Intrinsic electrophilic properties of nucleosides: photoelectron spectroscopy of their parent anions

The nucleoside parent anions 2(')-deoxythymidine(-), 2(')-deoxycytidine(-), 2(')-deoxyadenosine(-), uridine(-), cytidine(-), adenosine(-), and guanosine(-) were generated in a novel source, employing a combination of infrared desorption, electron photoemission, and a gas jet expansion. Once mass selected, the anion photoelectron spectrum of each of these was recorded. In the three cases in which comparisons were possible, the vertical detachment energies and likely adiabatic electron affinities extracted from these spectra agreed well with the values calculated both by Richardson et al. [J. Am. Chem. Soc. 126, 4404 (2004)] and by Li et al. [Radiat. Res. 165, 721 (2006)]. Through the combination of our experimental results and their theoretical calculations, several implications emerge. (1) With the possible exception of dG(-), the parent anions of nucleosides exist, and they are stable. (2) These nucleoside anions are valence anions, and in most cases the negative charge is closely associated with the nucleobase moiety. (3) The nucleoside parent anions we have generated and studied are the negative ions of canonical, neutral nucleosides, similar to those found in DNA.     

Anion photoelectron spectroscopy and density functional investigation of vanadium carbide clusters

The influence of source conditions on vanadium-carbon cluster formation in a methane-vanadium plasma is explored and analyzed by photoelectron spectroscopy, revealing that the metal-carbon ratio has substantial influence over the cluster products. Experiments that employ large methane content produce carbon-rich mono- and divanadium carbides. The carbon-rich clusters show a preference for the formation of cyclic neutral and linear ionic structures. When the methane concentration is decreased, VmCn clusters are formed with m = 1-4 and n = 2-8. The photoelectron spectra of clusters formed under these conditions are indicative of a three-dimensional network. We have measured a significantly lower vertical electron affinity for the VC2, V2C3, and V4C6 clusters compared with proximate species. Interestingly, the VC2 species is a proposed building block of the M8C12 Met-Car cluster, and the 2,3 and 4,6 clusters correspond to the 1/4 and 1/2 Met-Car cages, respectively. This correlation is taken as evidence of their importance in the formation of the larger Met-Car species. These results are supported by density functional theory (DFT) calculations carried out at the PBE/GGA level.     

Interaction of Co(m)O(-) (m = 1-3) with water: anion photoelectron spectroscopy and density functional calculations

We investigated the reactions between cobalt-oxides and water molecules using photoelectron spectroscopy and density functional calculations. It has been confirmed by both experimental observation and theoretical calculations that dihydroxide anions, Co(m)(OH)(2)(-) (m = 1-3), were formed when Co(m)O(-) clusters interact with the first water molecule. Addition of more water molecules produced solvated dihydroxide anions, Co(m)(OH)(2)(H(2)O)(n)(-) (m = 1-3). Hydrated dihydroxide anions, Co(m)(OH)(2)(H(2)O)(n)(-), are more stable than their corresponding hydrated metal-oxide anions, Co(m)O(H(2)O)(n+1)(-).     

Microscopic solvation of NaBO2 in water: anion photoelectron spectroscopy and ab initio calculations

We investigated the microscopic solvation of NaBO(2) in water by conducting photoelectron spectroscopy and ab initio studies on NaBO(2)(-)(H(2)O)(n) (n = 0-4) clusters. The vertical detachment energy (VDE) of NaBO(2)(-) is estimated to be 1.00 ± 0.08 eV. The photoelectron spectra of NaBO(2)(-)(H(2)O)(1) and NaBO(2)(-)(H(2)O)(2) are similar to that of bare NaBO(2)(-), except that their VDEs shift to higher electron binding energies (EBE). For the spectra of NaBO(2)(-)(H(2)O)(3) and NaBO(2)(-)(H(2)O)(4), a low EBE feature appears dramatically in addition to the features observed in the spectra of NaBO(2)(-)(H(2)O)(0-2). Our study shows that the water molecules mainly interact with the BO(2)(-) unit in NaBO(2)(-)(H(2)O)(1) and NaBO(2)(-)(H(2)O)(2) clusters to form Na-BO(2)(-)(H(2)O)(n) type structures, while in NaBO(2)(-)(H(2)O)(3) and NaBO(2)(-)(H(2)O)(4) clusters, the water molecules can interact strongly with the Na atom, therefore, the Na-BO(2)(-)(H(2)O)(n) and Na(H(2)O)(n)···BO(2)(-) types of structures coexist. That can be seen as an initial step of the transition from a contact ion pair (CIP) structure to a solvent-separated ion pair (SSIP) structure for the dissolution of NaBO(2).