The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase

Near edge x-ray absorption fine structure spectra have been measured and interpreted by means of density functional theory for five different azabenzenes (pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine) in the gas phase. The experimental and theoretical spectra at the N 1s and C 1s edges show a strong resonance assigned to the transition of the 1s electron in the respective N or C atoms to the lowest unoccupied molecular orbital with pi(*) symmetry. As opposed to the N 1s edge, at the C 1s edge this resonance is split due to the different environments of the core hole atom in the molecule. The shift in atomic core-level energy due to a specific chemical environment is explained with the higher electronegativity of the N atom compared to the C atom. The remaining resonances below the ionization potential (IP) are assigned to sigma or pi [corrected] orbitals with mixed valence/Rydberg [corrected] character. Upon N addition, a reduction of intensity is observed in the Rydberg region at both edges as compared to the intensity in the continuum. Above the IP one or more resonances are seen and ascribed here to transitions to sigma(*) orbitals. Calculating the experimental and theoretical Delta(pi) term values at both edges, we observe that they are almost the same within +/-1 eV as expected for isoelectronic bonded pairs. The term values of the pi(*) and sigma(*) resonances are discussed in terms of the total Z number of the atoms participating in the bond.     

Photophysics of aromatic molecules with low-lying pi sigma* states: fluorinated benzenes

Unlike fluorinated benzenes with four or less fluorine atoms, pentafluorobenzene (PFB) and hexafluorobenzene (HFB) exhibit very small fluorescence yields and short fluorescence lifetimes. These emission anomalies suggest that the nature of the first excited singlet (S(1)) state may be different for the two classes of fluorobenzenes. Consistent with this conjecture, the time-dependent density-functional theory calculations yield S(1) state of pi pi(*) character for fluorinated benzenes with four or less F atoms, and S(1) state of pi sigma(*) character for PFB and HFB. The pi sigma(*) character of the S(1) state of PFB and HFB has been confirmed by laser-induced fluorescence, which reveal the presence of a new electronic transition to the red of the (1)pi pi(*) (L(b))<--S(0) transition, which can be identified with the predicted low-energy (1)pi sigma(*)<--S(0) absorption. The low fluorescence yields and the short fluorescence lifetimes of PFB and HFB are consistent with the small radiative decay rate of the (1)pi sigma(*) state and efficient S(1) (pi sigma(*))-->S(0) internal conversion between two electronic states of very different geometries.     

Low energy electron-induced reactions in gas phase 1,2,3,5-tetra-O-acetyl-beta-D-ribofuranose: a model system for the behavior of sugar in DNA

Dissociative electron attachment to 1,2,3,5-tetra-O-acetyl-beta-D-ribofuranose (TAR) is studied in a crossed electron-molecular beam experiment with mass spectrometric detection of the observed fragment ions. Since in TAR acetyl groups are coupled at the relevant positions to the five membered ribose ring, it may serve as an appropriate model compound to study the response of the sugar unit in DNA towards low energy electrons. Intense resonances close to 0 eV are observed similar to the pure gas phase sugars (2-deoxyribose, ribose, and fructose). Further strong resonances appear in the range of 1.6-1.8 eV (not present in the pure sugars). Based on calculations on transient anions adopting the stabilization method, this feature is assigned to a series of closely spaced shape resonances of pi* character with the extra electron localized on the acetyl groups outside the ribose ring system. Further but weaker resonant contributions are observed in the range of 7-11 eV, representing core excited resonances and/or sigma* shape resonances. The decomposition processes involve single bond ruptures but also more complex reactions associated with substantial rearrangement. The authors hence propose that the sugar unit in DNA plays an active role in the molecular mechanism towards single strand breaks induced by low energy electrons.     

Radiation damage of biosystems mediated by secondary electrons: resonant precursors for uracil molecules

Calculations are presented for the energy locations and spatial structures of low-energy resonant states describing transient negative ions (TNIs) of the uracil molecule in the gas phase. The resonant states are modeled using scattering calculations of low energy electrons interacting with isolated molecules in their equilibrium geometry. The interaction forces used in this model are described in detail. Examination of the spatial densities of the excess resonant electrons for the various TNIs found by the calculations allows one to associate the metastable anions with specific features of the experimentally observed fragmentation patterns.     

Low-energy electron collisions with gas-phase uracil

We have studied gas-phase collisions between slow electrons and uracil molecules with a view to understanding the resonance structure of the scattering cross section. Our symmetry-resolved results for elastic scattering, computed in the fixed-nuclei, static-exchange and static-exchange-plus-polarization approximations, provide locations for the expected pi* shape resonances and indicate the possible presence of a low-energy sigma* resonance as well. Electron-impact excitation calculations were carried out for low-lying triplet and singlet excitation channels and yield a very large singlet cross section. We discuss the connection between the resonances found in our elastic cross section and features observed in dissociative attachment.     

Spectroscopy of excited states of carbon anions above the photodetachment threshold

Electronic transitions of C3- and C5- to states lying above the electron affinity of the neutral (EA) have been recorded in the gas phase by laser photodetachment spectroscopy. The excited states are identified by comparison with absorption spectra for the mass-selected ions deposited in neon matrices and with ab initio calculations. The C 2 sigma u (+)-X 2 pi g transition and two higher energy band systems are observed for C3-, corresponding to excitation energies more than 1.5 eV above the EA. In the case of C5- the strongest features, at about 0.6 eV above the EA, are attributed to close lying 2 delta g-X 2 pi u and 2 sigma g(-)-X 2 pi u transitions. The dominant configurations in these states identify them as long-lived Feshbach resonances. Lifetimes for these resonances in C3- are estimated to be between 200 fs and 3 ps from the band widths.     

Photochemistry of pyrrole: time-dependent quantum wave-packet description of the dynamics at the 1pi sigma*-S0 conical intersections

The photoinduced hydrogen-elimination reaction in pyrrole via the conical intersections of the two (1)pi sigma(*) excited states with the electronic ground states [(1)B(1)(pi sigma(*))-S(0) and (1)A(2)(pi sigma(*))-S(0)] have been investigated by time-dependent quantum wave-packet calculations. Model potential-energy surfaces of reduced dimensionality have been constructed on the basis of accurate multireference ab initio electronic-structure calculations. For the (1)B(1)-S(0) conical intersection, the model includes the NH stretching coordinate as the tuning mode and the hydrogen out-of-plane bending coordinate as the coupling mode. For the (1)A(2)-S(0) conical intersection, the NH stretching coordinate and the screwing coordinate of the ring hydrogens are taken into account. The latter is the dominant coupling mode of this conical intersection. The electronic population-transfer processes at the conical intersections, the branching ratio between the dissociation channels, and their dependence on the initial preparation of the system have been investigated for pyrrole and deuterated pyrrole. It is shown that the excitation of the NH stretching mode strongly enhances the reaction rate, while the excitation of the coupling mode influences the branching ratio of different dissociation channels. The results suggest that laser control of the photodissociation of pyrrole via mode-specific vibrational excitation should be possible. The calculations provide insight into the microscopic details of ultrafast internal-conversion processes in pyrrole via hydrogen-detachment processes, which are aborted at the (1)pi sigma(*)-S(0) conical intersections. These mechanisms are of relevance for the photostability of the building blocks of life (e.g., the DNA bases).     

Origin of threefold symmetric torsional potential of methyl group in 4-methylstyrene

To understand the effect of the para position vinyl group substitution in toluene on methyl torsion, we investigated 4-methylstyrene, a benchmark molecule with an extended pi conjugation. The assignment for a 33 cm(-1) band in the excitation spectrum to the 3a(2) torsional transition, in addition to the assignments suggested previously for the other bands in the excitation spectrum, leads to the model potentials for the ground as well as excited states with V(3) (")=19.6 cm(-1), V(6) (")=-16.4 cm(-1) and V(3) (')=25.6 cm(-1), V(6) (')=-30.1 cm(-1), respectively. These potentials reveal that both in ground and excited states, the methyl group conformations are staggered with a 60 degrees phase shift between them. MP2 ab initio calculations support the ground state conformations determined from experiments, whereas Hartree-Fock calculations fail to do so. The origin of the modified ground state potential has been investigated by partitioning the barrier energy using the natural bond orbital (NBO) theoretical framework. The NBO analysis shows that the local delocalization (bond-antibond hyperconjugation) interactions of the methyl group with the parent molecule is sixfold symmetric. The threefold symmetric potential, on the other hand, stems from the interaction of the vinyl group and the adjacent ring pi bond. The threefold symmetric structural energy arising predominantly from the pi electron contribution is the barrier forming term that overwhelms the antibarrier contribution of the delocalization energy. The observed 60 degrees phase shift of the excited state potential is attributed to the pi(*)-sigma(*) hyperconjugation between out of plane hydrogens of the methyl group and the benzene ring.     

Electron-attachment resonances of glycine zwitterions from quantum scattering calculations: modeling macrosolvation effects

A computational study of the quantum dynamics for low-energy electrons scattered by the isolated zwitterionic species of the glycine molecule is carried out using a model interaction potential described in the main text. The macroscopic effects of water solvation on the target molecule in the electron scattering problem are described through a continuum polarizable model (CPCM) which modifies the target molecular structure. In such a way, realistic molecular orbitals depicting the glycine zwitterion in solution are used to model the electron-molecule interaction. The results of the calculations indicate the presence of five different transient negative ions (TNIs) formed at energies from the threshold and up to about 6 eV. Although no nuclear motion was explicitly considered in the ensuing decay processes, the analysis of the nodal structures and density distributions for the resonant excess electron wavefunctions over the molecular space suggests possible anionic fragmentations that produce (Gly-H)-, H-, -CO2-, and -NH3. The likely consequences of such releases into the medium are briefly discussed.     

Bound states and scattering resonances of OH(A)-He

The OH-He complex has been observed using laser excitation of the A 2sigma+-X 2pi transition. The bands of the complex were close to the monomer rotational lines that terminate on the n = 0, 1, and 2 levels of OH(A). The unresolved band associated with He.OH (A,n=0) was redshifted from the OH parent line by 1.6 cm(-1), providing a direct measurement of D0'-D0". The complex features associated with n = 1 and 2 were identified as scattering resonances. They have been assigned by comparison with resonance structures derived from close-coupling calculations. The ab initio potential energy surface of H.-S. Lee, A.B. McCoy, R.R. Toczylowski, and S.M. Cybulski, [J. Chem. Phys. 113, 5736 (2000)] was used in these calculations. The level of agreement between the observed and predicted resonances indicated that the ab initio surface is reasonably accurate.     

Experimental and theoretical study of the photodissociation reaction of thiophenol at 243 nm: intramolecular orbital alignment of the phenylthiyl radical

The photoinduced hydrogen (or deuterium) detachment reaction of thiophenol (C(6)H(5)SH) or thiophenol-d(1) (C(6)H(5)SD) pumped at 243 nm has been investigated using the H (D) ion velocity map imaging technique. Photodissociation products, corresponding to the two distinct and anisotropic rings observed in the H (or D) ion images, are identified as the two lowest electronic states of phenylthiyl radical (C(6)H(5)S). Ab initio calculations show that the singly occupied molecular orbital of the phenylthiyl radical is localized on the sulfur atom and it is oriented either perpendicular or parallel to the molecular plane for the ground (B(1)) and the first excited state (B(2)) species, respectively. The experimental energy separation between these two states is 2600+/-200 cm(-1) in excellent agreement with the authors' theoretical prediction of 2674 cm(-1) at the CASPT2 level. The experimental anisotropy parameter (beta) of -1.0+/-0.05 at the large translational energy of D from the C(6)H(5)SD dissociation indicates that the transition dipole moment associated with this optical transition at 243 nm is perpendicular to the dissociating S-D bond, which in turn suggests an ultrafast D+C(6)H(5)S(B(1)) dissociation channel on a repulsive potential energy surface. The reduced anisotropy parameter of -0.76+/-0.04 observed at the smaller translational energy of D suggests that the D+C(6)H(5)S(B(2)) channel may proceed on adiabatic reaction paths resulting from the coupling of the initially excited state to other low-lying electronic states encountered along the reaction coordinate. Detailed high level ab initio calculations adopting multireference wave functions reveal that the C(6)H(5)S(B(1)) channel may be directly accessed via a (1)(n(pi),sigma(*)) photoexcitation at 243 nm while the key feature of the photodissociation dynamics of the C(6)H(5)S(B(2)) channel is the involvement of the (3)(n(pi),pi(*))-->(3)(n(sigma),sigma(*)) profile as well as the spin-orbit induced avoided crossing between the ground and the (3)(n(pi),sigma(*)) state. The S-D bond dissociation energy of thiophenol-d(1) is accurately estimated to be D(0)=79.6+/-0.3 kcalmol. The S-H bond dissociation energy is also estimated to give D(0)=76.8+/-0.3 kcalmol, which is smaller than previously reported ones by at least 2 kcalmol. The C-H bond of the benzene moiety is found to give rise to the H fragment. Ring opening reactions induced by the pi-pi(*)n(pi)-pi(*) transitions followed by internal conversion may be responsible for the isotropic broad translational energy distribution of fragments.     

H atom transfer along an ammonia chain: tunneling and mode selectivity in 7-hydroxyquinoline.(NH3)3

Excitation of the 7-hydroxyquinoline(NH(3))(3) [7HQ(NH(3))(3)] cluster to the S(1) (1)pi pi(*) state results in an O-H-->NH(3) hydrogen atom transfer (HAT) reaction. In order to investigate the entrance channel, the vibronic S(1)<-->S(0) spectra of the 7HQ.(NH(3))(3) and the d(2)-7DQ.(ND(3))(3) clusters have been studied by resonant two-photon ionization, UV-UV depletion and fluorescence techniques, and by ab initio calculations for the ground and excited states. For both isotopomers, the low-frequency part of the S(1)<--S(0) spectra is dominated by ammonia-wire deformation and stretching vibrations. Excitation of overtones or combinations of these modes above a threshold of 200-250 cm(-1) for 7HQ.(NH(3))(3) accelerates the HAT reaction by an order of magnitude or more. The d(2)-7DQ.(ND(3))(3) cluster exhibits a more gradual threshold from 300 to 650 cm(-1). For both isotopomers, intermolecular vibrational states above the threshold exhibit faster HAT rates than the intramolecular vibrations. The reactivity, isotope effects, and mode selectivity are interpreted in terms of H atom tunneling through a barrier along the O-H-->NH(3) coordinate. The barrier results from a conical intersection of the optically excited (1)pi pi(*) state with an optically dark (1)pi sigma(*) state. Excitation of the ammonia-wire stretching modes decreases both the quinoline-O-H...NH(3) distance and the energetic separation between the (1)pi pi(*) and (1)pi sigma(*) states, thereby increasing the H atom tunneling rate. The intramolecular vibrations change the H bond distance and modulate the (1)pi pi(*)<-->(1)pi sigma(*) interaction to a much smaller extent.     

Interaction of low-energy electrons with the purine bases, nucleosides, and nucleotides of DNA

The authors report results from computational studies of the interaction of low-energy electrons with the purine bases of DNA, adenine and guanine, as well as with the associated nucleosides, deoxyadenosine and deoxyguanosine, and the nucleotide deoxyadenosine monophosphate. Their calculations focus on the characterization of the pi* shape resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. Results are obtained for adenine and guanine both with and without inclusion of polarization effects, and the resonance energy shifts observed due to polarization are used to predict pi* resonance energies in associated nucleosides and nucleotides, for which static-exchange calculations were carried out. They observe slight shifts between the resonance energies in the isolated bases and those in the nucleosides.     

Parameters for excess electron transfer in DNA. Estimation using unoccupied Kohn-Sham orbitals and TD DFT

We show that the energetics and electronic couplings for excess electron transfer (EET) can be accurately estimated by using unoccupied Kohn-Sham orbitals (UKSO) calculated for neutral pi stacks. To assess the performance of different DFT functionals, we use MS-PT2 results for seven pi stacks of nucleobases as reference data. The DFT calculations are carried out by using the local spin density approximation SVWN, two generalized gradient approximation functionals BP86 and BLYP, and two hybrid functionals B3LYP and BH&HLYP. Best estimations within the UKSO approach are obtained by the B3LYP and SVWN methods. TD DFT calculations provide less accurate values of the EET parameters as compared with the UKSO data. Also, the excess charge distribution in the radical anions is well described by the LUMOs of neutral systems. In contrast, spin-unrestricted DFT calculations of radical anions considerably overestimate delocalization of the excess electron. The excellent results obtained for the ground and excited states of the radical anions (excitation energy, transition dipole moment, electronic coupling, and excess electron distribution) by using UKSO of neutral dimers suggest an efficient strategy to calculate the EET parameters for DNA pi stacks.     

Are there pi* shape resonances in electron scattering from phosphate groups?

The temporary anion states of trimethyl phosphate and several compounds bearing the P=O group were explored using electron transmission spectroscopy and ab initio calculations to determine if these states have the characteristics of the pi* resonances usually associated with multiple bonds. No evidence was found for this in (CH3O)3PO and, by extension, we do not expect them to appear in the phosphate group of DNA. Cl3PO, however, does display such characteristics to some extent, and we show that they arise from the spatial properties of the sigma* (P-Cl) orbitals rather than from multiple PO bonding. A novel computational means to explore effects due to the relative size of a molecular orbital and that of the angular momentum barrier responsible for confining the additional electron is presented.     

Selective bond breaking in beta-D-ribose by gas-phase electron attachment around 8 eV

Electron attachment experiments are carried out on the beta-d-ribose molecule in the gas phase for the energy region around 8 eV, and clear fragmentation products are observed for different mass values. A computational analysis of the relevant dynamics is also carried out for the beta-d-ribose in both the furanosic and pyranosic form as gaseous targets around that energy range. The quantum scattering attributes obtained from the calculations reveal in both systems the presence of transient negative ions (TNIs). An analysis of the spatial features of the excess resonant electron, together with the computation and characterization of the target molecular normal modes, suggests possible break-up pathways of the initial, metastable molecular species.     

Electron transport across the alkanethiol self-assembled monolayer/Au(111) interface: role of the chemical anchor

Alkanethiol self-assembled monolayers (SAMs) on Au(111) are model systems for molecular electronics. We probe the role of the chemisorption bond on electron dynamics at the SAM/Au interface using time-resolved two-photon photoemission. Formation of the Au-S bond is evidenced by a localized sigma resonance, which broadens and shifts upward in energy when the lying-down chemisorbed molecules stand up. The localized chemisorption bond does not affect the electronic coupling between delocalized image resonances and the metal substrate. Instead, lifetimes of image resonances are decreased due to scattering with S atoms within the thiol or thiolate monolayer.     

The role of pi sigma* state in intramolecular electron-transfer dynamics of 4-dimethylaminobenzonitrile and related molecules

Evidence is presented which indicates that the photoinduced intramolecular charge transfer (ICT) in 4-dimethylaminobenzonitrile proceeds by a new mechanism in which pi sigma(C triple bond N) (*) state is the intermediate of a consecutive process that takes the initially excited pi pi(*) state to the fully charge-separated ICT state. The absence of the ICT-state formation in 4-aminobenzonitrile is attributed to the smaller electron-donor strength of the amino group relative to the dimethylamino group, which hinders the pi sigma(*)-->ICT charge-shift reaction.     

Electron spectroscopy, molecular structures, and binding energies of Al- and Cu-imidazole

Al- and Cu-imidazole are produced in laser-vaporization supersonic molecular beams and studied with pulsed field ionization-zero electron kinetic energy (ZEKE) spectroscopy and second-order M?ller-Plesset (MP2) theory. The sigma and pi structures of these complexes are predicted by MP2 calculations, but only the sigma structures are identified by the experimental measurements. For these sigma structures, adiabatic ionization energies and several vibrational frequencies are measured from the ZEKE spectra, the ground electronic states of the neutral and ionized complexes are determined by comparing the observed and calculated spectra, and the metal-ligand bond dissociation energies of the neutral states are derived by using a thermochemical relation. The measured vibrational modes include the metal-ligand stretch and bend and ligand ring distortions. The metal-ligand stretch frequencies of these transient complexes are compared with those of coordinately saturated, stable metal compounds, and the ligand-based distortion frequencies are compared with those of the free ligand. Al-imidazole has a larger bond dissociation energy than Cu-imidazole, although the opposite order was previously found for the corresponding ions. The weaker bonding of the Cu complex is attributed to the antibonding interaction and the electron repulsion between the Cu 4s and N lone-pair electrons.     

The weak hydrogen bond in the fluorobenzene-ammonia van der Waals complex: Insights into the effects of electron withdrawing substituents on pi versus in-plane bonding

The fluorobenzene-ammonia van der Waals complex has been studied using a combination of two-color resonance enhanced multiphoton ionization (REMPI) spectroscopy, counterpoise corrected RICC2 ab initio molecular orbital calculations, and multidimensional Franck-Condon analysis. The experimental REMPI spectrum is characterized by a dominant, blueshifted band origin, and weak activity in intermolecular vibrational modes. RICC2 geometry optimizations and numerical vibrational frequency calculations of the neutral ground and first excited states have been performed on a number of different structural isomers of the complex using basis sets ranging from augmented double-zeta to quadruple-zeta level. Ground state basis set superposition error corrected zero-point binding energies show the in-plane sigma complex, forming a pseudo-six-membered ring connecting the fluorine atom and ortho-hydrogen, to be consistently the most stable of all six conformations considered, at all levels of theory. Comparison of computed zero-point excitation energies for the most stable pi and sigma conformers with fluorobenzene show that the sigma complex is the only conformer predicted to exhibit a spectral blueshift upon electronic excitation. The computed neutral ground and first excited state geometries and frequencies were used to perform multidimensional Franck-Condon simulations of the S(1)-S(0) vibronic spectrum for each of the most stable conformers. These simulations yielded null spectra for transitions involving the most stable of the pi complexes, pi(bridge); a spectrum rich in strong intermolecular vibrational structure for the second of the pi complexes, in complete contrast to the experimental spectrum; and for the sigma complex, a spectrum exhibiting weak intermolecular activity in line with that observed experimentally. This last simulation allowed an almost complete vibrational assignment of the intermolecular structure in the REMPI spectrum. The agreement between computational results and experiment overwhelmingly favors assignment of the spectrum to the in-plane sigma complex.