Base and phosphate electron detachment energies of deoxyribonucleotide anions

Photoelectron spectra of deoxyribonucleotide anions are interpreted with ab initio, electron propagator calculations. Ground-state structures display hydrogen bonds which are not present in less stable minima that resemble Watson-Crick fragment geometries. For the adenosine and thymidine anions, there are two vertical electron detachment energies (VEDEs) within 0.1 eV of each other that correspond to phosphate- and base-centered Dyson orbitals (DOs). The first VEDE of the cytidine anion belongs to a phosphate-centered DO. The anomalously low VEDE of the guanosine anion is assigned to a base-centered, pi DO. Higher VEDEs of all four anions also are assigned.     

Deprotonated cytosine anions: a theoretical prediction of photoelectron spectra

Predictions on the photoelectron spectra of deprotonated cytosine anions (cytosinate, Cye(-)) have been made with ab initio electron propagator methods. Two imino-oxo forms are most stable, but four other isomers have energies within 10 kcal/mol. The first vertical electron detachment energies (VEDEs) for the three most stable Cye(-) isomers are approximately 3.4 eV. Imino-oxy VEDEs are about 0.3 eV smaller. For each anion, the lowest VEDE corresponds to a pi Dyson orbital. The order of higher final states is changed when relaxation and correlation effects are considered. Considerable mixing between lone-pair and bonding lobes occurs in the sigma Dyson orbitals.     

OH(3) (-) and O(2)H(5) (-) double Rydberg anions: predictions and comparisons with NH(4) (-) and N(2)H(7) (-)

A low barrier in the reaction pathway between the double Rydberg isomer of OH(3) (-) and a hydride-water complex indicates that the former species is more difficult to isolate and characterize through anion photoelectron spectroscopy than the well known double Rydberg anion (DRA), tetrahedral NH(4) (-). Electron propagator calculations of vertical electron detachment energies (VEDEs) and isosurface plots of the electron localization function disclose that the transition state's electronic structure more closely resembles that of the DRA than that of the hydride-water complex. Possible stabilization of the OH(3) (-) DRA through hydrogen bonding or ion-dipole interactions is examined through calculations on O(2)H(5) (-) species. Three O(2)H(5) (-) minima with H(-)(H(2)O)(2), hydrogen-bridged, and DRA-molecule structures resemble previously discovered N(2)H(7) (-) species and have well separated VEDEs that may be observable in anion photoelectron spectra.     

Photoelectron spectroscopy of hydrated adenine anions

We report the observation of hydrated adenine anions, A(-)(H(2)O)(n), n=1-7, and their study by anion photoelectron spectroscopy. Values for photoelectron threshold energies, E(T), and vertical detachment energies are tabulated for A(-)(H(2)O)(n) along with those for hydrated uracil anions, U(-)(H(2)O)(n), which are presented for comparison. Analysis of these and previously measured photoelectron spectra of hydrated nucleobase anions leads to the conclusion that threshold energies significantly overstate electron affinity values in these cases, and that extrapolation of hydrated nucleobase anion threshold values to n=0 leads to incorrect electron affinity values for the nucleobases themselves. Sequential shifts between spectra, however, lead to the conclusion that A(-)(H(2)O)(3) is likely to be the smallest adiabatically stable, hydrated adenine anion.     

Theoretical study of neutral, anionic, and cationic uracil-Ag and uracil-Au systems: nonconventional hydrogen bonds

The interaction of Ag and Au with uracil has been studied using the B3LYP density-functional approach. Neutral, cationic, and anionic systems were analyzed in order to study the influence of the atomic charge on bond formation. This interaction becomes stronger as the charge increases. In the case of neutral systems, a weak association is present. In the case of cations, the interaction is mainly electrostatic. The extra electron of the anions is localized on the metal atom. Consequently, nonconventional hydrogen bonds are formed. The ionization energy of uracil-Ag and uracil-Au is lower than the corresponding values for the metal atoms and uracil molecule, while the electron affinity is higher for uracil-Ag and uracil-Au than the analogous values for the isolated Ag, Au, and uracil. This might have significance for further experiments and possibly for applications, where the movement of the electrons is important. In the case of uracil-Ag and uracil-Au (anions), it may be possible to induce the detachment of one electron from the anion and also to remove a single hydrogen atom. It is possible that tight competition exists between the H dissociation and electron aloofness.     

Interaction of the uracil dipole-bound electron with closed-shell systems (Ar and N2)

A very diffuse, but spatially confined, electron trapped in a dipole–bound state of a polar molecule provides an excellent target for testing the interaction of a localized electron positioned outside the molecular frame of its host molecule with other atomic or molecular systems. In this work we use ab initio calculations to investigate systems where a dipole–bound electron attached to a uracil molecule is interacting with an N₂ molecule and an Ar atom. Neither of the two systems forms a stable anion and in the aducts they form with the dipole–bound electron the electron becomes suspended between the uracil molecule and Ar or N₂. Calculations are performed to determine the vertical electron detachment energies of these anions and to determine the molecular rearrangements occurring when the excess electron is removed from them.Contribution to the Jacopo Tomasi Honorary Issue     

Products of the addition of water molecules to Al3O3- clusters: structure, bonding, and electron binding energies in Al3O4H2-, Al3O5H4-, Al3O4H2, and Al3O5H4

Two stable products of reactions of water molecules with the Al3O3- cluster, Al3O4H2- and Al3O5H4-, are studied with electronic structure calculations. There are several minima with similar energies for both anions and the corresponding molecules. Dissociative absorption of a water molecule to produce an anionic cluster with hydroxide ions is thermodynamically favored over the formation of Al3O3-(H2O)n complexes. Vertical electron detachment energies of Al3O4H2- and Al3O5H4- calculated with ab initio electron propagator methods provide a quantitative interpretation of recent anion photoelectron spectra. Contrasts and similarities in these spectra may be explained in terms of the Dyson orbitals associated with each transition energy.     

Non-conventional hydrogen bonds: pterins-metal anions

In this paper, we present an analysis of the interaction of metal ions (Cu, Ag and Au) with three different pterins (pterin, isoxanthopterin and sepiapterin) to provide insights concerning the formation of conventional and non-conventional H bonds. Density functional theory calculations were performed in order to reveal the optimized structures of pterin molecules, dimers and tetramers compounds, both with and without metal anions (M). The interaction with small metal clusters (M(3)) is also considered. The formation of different systems is characterized in terms of the structural parameters and hydrogen binding energies (HBE). The HBE values for pterin-M systems presented in this study lie between 22 and 60 kcal mol(-1) and can therefore be classified as strong conventional and strong non-conventional hydrogen bonds. The HBE with small metal clusters (pterin-M(3)) are smaller than the HBE with metal atoms. Vertical electron detachment energies (VEDEs) are also reported in order to analyze the influence of the hydrogen bond on electronic properties. A direct correlation between VEDEs and HBE was found for pterin-M and pterin-M(3) complexes; i.e. as the VEDEs increase, the HBE also augment. The only exception is with Ag(3). The main conclusion derived from this study is that the strong non-conventional hydrogen bonds formed between pterins, dimers and tetramers do not affect the formation of conventional hydrogen bonds between pterins but they do influence the VEDEs.     

Microsolvation pattern of the hydrated radical anion of uracil: U-(H2O)n (n = 3-5)

The microsolvation patterns of the uracil radical anion in water clusters U-(H2O)n with n ranging from 3 to 5 were investigated by the density functional theory approach. The electron detachment energies (VDE) of the stable anionic complexes with different numbers of hydration water are predicted. The linear dependence of the VDE value of the most stable anionic complexes with respect to the hydration number suggests the importance of the clustered waters in the microsolvation of the radical anion of the nucleobases. The formation of the water clusters is found to be necessary in the most stable conformers of the tri-, tetra-, and pentahydrated radical anion of uracil. The microsolvation pattern with three or more well-separated hydration water molecules in the first hydration layer is less stable than the arrangement with the waters in tight clusters. The charge transfer between the anionic uracil and the hydration water is high. Good agreement between the experimental and the theoretical vertical detachment energy yield in this study further demonstrates the practicability of the B3LYP/DZP++ approach in the study of radical anions of the DNA subunits.     

Pseudopotential and electron propagator methods for the calculation of the photoelectron spectra of anionic silicon clusters: predictions on Si10-

Photoelectron spectra of anionic clusters of silicon require reliable theoretical calculations for their assignment and interpretation. Electron propagator calculations in the outer valence Green's-function approximation with two well-characterized, all-electron basis sets on vertical electron detachment energies (VEDEs) of anions are compared to similar calculations that employ Stuttgart pseudopotentials. Tests on Si(n) (-) clusters with n=3-7 exhibit an encouraging agreement between the all-electron and pseudopotentials results and between electron propagator predictions and experiments and values obtained from coupled-cluster calculations. To illustrate the capabilities of the new approach based on a Si pseudopotential and electron propagator methods, VEDE calculations on Si(10) (-) are presented.     

MX3(-) superhalogens (M = Be, Mg, Ca; X = Cl, Br): a photoelectron spectroscopic and ab initio theoretical study

Gas-phase alkaline earth halide anions, MgX3(-) and CaX3(-) (X = Cl, Br), were produced using electrospray and investigated using photoelectron spectroscopy at 157 nm. Extremely high electron binding energies were observed for all species and their first vertical detachment energies were measured as 6.60 +/- 0.04 eV for MgCl3(-), 6.00 +/- 0.04 eV for MgBr3(-), 6.62 +/- 0.04 eV for CaCl3(-), and 6.10 +/- 0.04 eV for CaBr3(-). The high electron binding energies indicate these are very stable anions and they belong to a class of anions, called superhalogens. Theoretical calculations at several levels of theory were carried out on these species, as well as the analogous BeX3(-). Vertical detachment energy spectra were predicted to compare with the experimental observations, and good agreement was obtained for all species. The first adiabatic detachment energies were found to be substantially lower (by about 1 eV) than the corresponding vertical detachment energies for all the MX3(-) species, indicating extremely large geometry changes between MX3(-) and MX3. We found that all the MX3(-) anions possess D3h ((1)A1') structures and are extremely stable against dissociation into MX2 and X-. The corresponding neutral species MX3, however, were found to be only weakly bound with respect to dissociation toward MX2 + X. The global minimum structures of all the MX3 neutrals were found to be C2v ((2)B2), which can be described as (X2(-))(MX+) charge-transfer complexes, whereas the MX2...X (C2v, (2)B1) van der Waals complexes were shown to be low-lying isomers.     

Structure and conformation properties of 1-alkyl-3-methylimidazolium halide ionic liquids: a density-functional theory study

The structures and conformational properties of 1-alkyl-3-methylimidazolium halide ionic liquids have been studied with a Becke's 3 Parameter functional method. The interaction mechanisms between the cation and the anion in 1-ethyl-3-methylimidazolium (Emim+) halide and 1-butyl-3-methylimidazolium (Bmim+) halide ionic liquids were investigated using 6-31G*, 6-31++G**, and 6-311++G** basis sets. Forty structures of different ion pairs were optimized and geometrical parameters of them have been discussed in details. Halide ions (Cl- or Br-) have been gradually placed in different regions around imidazolium cation and the interaction energies between the anion and the cation have been calculated. Theoretical results indicate that there are four activity regions in the vicinity of the imidazolium cations, in these regions the imidazolium cations and the halide anions formed stable ion pairs. Imidazolium cations can form hydrogen bond interactions with one, two or three but no more than three nearest halide anions. The halide ions are situated in hydrogen bond positions rather than at random.     

Photoelectron spectrum of valence anions of uracil and first-principles calculations of excess electron binding energies

The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree-Fock and second-order Moller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within +/-1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of approximately -0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics of biomolecular anions are highly dependent on their tautomeric form. If indeed the third most stable anion is observed in the experiment, then it remains an open question why and how this species is formed under the given conditions.     

Photoelectron spectroscopy of anions at 118.2 nm: observation of high electron binding energies in superhalogens MCl4- (M=Sc, Y, La)

High energy photon is needed for photoelectron spectroscopy (PES) of anions with high electron binding energies, such as superhalogens and O-rich metal oxide clusters. The highest energy photon used for anion PES in the laboratory has been 157 nm (7.866 eV) from F2 eximer lasers. Here, we report an anion PES experiment using coherent vacuum ultraviolet radiation at 118.2 nm (10.488 eV) by tripling the third harmonic output (355 nm) of a Nd:YAG laser in a XeAr cell. Our study focuses on a set of superhalogen species, MCl(4) (-) (M=Sc, Y, La), which were expected to possess very high electron binding energies. While the 157 nm photon can only access the ground state detachment features for these species, more transitions to the excited states at binding energies higher than 8 eV are observed at 118.2 nm. The adiabatic detachment energies are shown to be, 6.84, 7.02, and 7.03 eV for ScCl(4) (-), YCl(4) (-), and LaCl(4) (-) eV, respectively, whereas their corresponding vertical detachment energies are measured to be 7.14, 7.31, and 7.38 eV.     

Theoretical study of guanine-Cu and uracil-Cu (neutral, anionic, and cationic). Is it possible to carry out a photoelectron spectroscopy experiment?

The structure and bonding of guanine-Cu and uracil-Cu (neutral, anionic, and cationic) are discussed on the basis of the calculated structures and energies. The interaction of the metal atom with guanine and uracil has been analyzed using the B3LYP density-functional approach. The removal of one electron from the neutral complexes produces the stabilization of one of the isomers, while the addition of one electron leads to a system where the metal atom is weakly bounded to guanine or uracil, according to the metal-bases bond distance that is long (2.29-2.90). For guanine-Cu and uracil-Cu, the vertical ionization energy of the anion is close to the dissociation energy of one hydrogen atom from guanine-Cu or uracil-Cu. In these cases, it could be possible to produce the detachment of one electron from the anion and also the removal of one hydrogen atom. This is important since the photoelectron spectroscopy of atomic or mixed-atomic cluster anions has proven to be a very effective tool in the study of small systems. For the analysis of copper atoms with DNA bases such as guanine and uracil, it is expected that the photoelectron spectra of the anion-bases complexes strongly resemble the spectrum of Cu(-1), just shifted to higher electron binding energies due to the product stabilization. Hopefully, this information will be useful for the experimental groups.     

Spectroscopic, structural, and theoretical studies of halide complexes with a urea-based tripodal receptor

A urea-based tripodal receptor L substituted with p-cyanophenyl groups has been studied for halide anions using (1)H NMR spectroscopy, density functional theory (DFT) calculations, and X-ray crystallography. The (1)H NMR titration studies suggest that the receptor forms a 1:1 complex with an anion, showing a binding trend in the order of fluoride > chloride > bromide > iodide. The interaction of a fluoride anion with the receptor was further confirmed by 2D NOESY and (19)F NMR spectroscopy in DMSO-d(6). DFT calculations indicate that the internal halide anion is held by six NH···X interactions with L, showing the highest binding energy for the fluoride complex. Structural characterization of the chloride, bromide, and silicon hexafluoride complexes of [LH(+)] reveals that the anion is externally located via hydrogen bonding interactions. For the bromide or chloride complex, two anions are bridged with two receptors to form a centrosymmetric dimer, while for the silicon hexafluoride complex, the anion is located within a cage formed by six ligands and two water molecules.     

Addition of water, methanol, and ammonia to Al3O3- clusters: reaction products, transition states, and electron detachment energies

Products of reactions between the book and kite isomers of Al3O3- and three important molecules are studied with electronic structure calculations. Dissociative adsorption of H2O or CH3OH is highly exothermic and proton-transfer barriers between anion-molecule complexes and the products of these reactions are low. For NH3, the reaction energies are less exothermic and the corresponding barriers are higher. Depending on experimental conditions, Al3O3- (NH3) coordination complexes or products of dissociative adsorption may be prepared. Vertical electron detachment energies of stable anions are predicted with ab initio electron propagator calculations and are in close agreement with experiments on Al3O3- and its products with H2O and CH3OH. Changes in the localization properties of two Al-centered Dyson orbitals account for the differences between the photoelectron spectra of Al3O3- and those of the product anions.     

Are structures with Al-H bonds represented in the photoelectron spectrum of Al3O4H2-?

Photoelectron spectra of Al3O4H2- clusters formed by reactions of Al3O3- with water molecules have been interpreted recently in terms of dissociative absorption products with hydroxide and oxide anions that are coordinated to aluminum cations. Alternative isomers with Al-H bonds have lower energies, but barriers to hydrogen migrations that break O-H bonds and create Al-H bonds are high. Ab initio electron propagator calculations of the vertical electron detachment energies of the anions indicate that the species with hydrides cannot be assigned to the chief features in the photoelectron spectrum. Therefore, the previously studied dissociative absorption products are the structures that are most likely to be probed in the photoelectron spectra.     

Unexpectedly strong anion–π interactions on the graphene flakes

Interactions of anions with simple aromatic compounds have received growing attention due to their relevancy in various fields. Yet, the anion–π interactions are generally very weak, for example, there is no favorable anion–π interaction for the halide anion F^? on the simplest benzene surface unless the H‐atoms are substituted by the highly negatively charged F. In this article, we report a type of particularly strong anion–π interactions by investigating the adsorptions of three halide anions, that is, F^?, Cl^?, and Br^?, on the hydrogenated‐graphene flake using the density functional theory. The anion–π interactions on the graphene flake are shown to be unexpectedly strong compared to those on simple aromatic compounds, for example, the F^?‐adsorption energy is as large as 17.5 kcal/mol on a graphene flake (C₈₄H₂₄) and 23.5 kcal/mol in the periodic boundary condition model calculations on a graphene flake C₁₁₃ (the supercell containing a F^? ion and 113 carbon atoms). The unexpectedly large adsorption energies of the halide anions on the graphene flake are ascribed to the effective donor–acceptor interactions between the halide anions and the graphene flake. These findings on the presence of very strong anion–π interactions between halide ions and the graphene flake, which are disclosed for the first time, are hoped to strengthen scientific understanding of the chemical and physical characteristics of the graphene in an electrolyte solution. These favorable interactions of anions with electron‐deficient graphene flakes may be applicable to the design of a new family of neutral anion receptors and detectors. © 2012 Wiley Periodicals, Inc.     

LDHs主体层板与卤素阴离子超分子作用的理论研究

构建了LDHs主客体作用模型, 采用混合密度泛函B3LYP方法, 在6-31G(d)水平上进行结构优化和频率分析, 然后分别用6-31G(d)和6-311++G(d, p)基组计算主客体相互作用能, 从几何参数、电荷布居、前线轨道、能量以及热力学参数等角度探讨LDHs主体层板与卤素阴离子(F?, Cl?)间的超分子作用. 计算结果表明, LDHs主体层板复合卤素阴离子是一个自发过程. LDHs主客体间存在着较强的超分子作用, 主要包括静电和氢键作用, 相互作用能分别为?592.45和?444.01 kJ·mol?1. LDHs主体层板与卤素阴离子的前线轨道发生作用, 电子容易从卤素阴离子的HOMO向层板的LUMO转移, 形成的组装产物Mg6Al(OH)14+?F?比Mg6Al(OH)14+?Cl?稳定.