Resonant Fragmentation of the Water Cation by Electron Impact: a Wave-Packet Study

We have investigated the dissociation of a resonant state that can be formed in low energy electron scattering from H₂O⁺. We have chosen the second triplet resonance above the state of H₂O⁺ whose autoionization mainly produces H₂O⁺ ( ). We have considered both dissociation of the resonant state itself, dissociative recombination (DR), or the dissociation of the H₂O⁺ cation after autodetachment, dissociative excitation (DE). The time-evolution of a wave packet on the potential energy surfaces of the resonance and cationic states shows, for the initial conditions studied, that the probability for DR is about 38 % while the probability for DE is negligible.     

Theoretical Study on the Kinetics of Electron Transfer for Bond—breaking Reaction

ＩｎｔｒｏｄｕｃｔｉｏｎＦｒｅｅｒａｄｉｃａｌｆｏｒｍａｔｉｏｎｆｒｏｍｈａｌｏｇｅｎａｔｅｄｈｙｄｒｏｃａｒｂｏｎｓｈａｓｒｅｃｅｉｖｅｄｃｏｎｓｉｄｅｒａｂｌｅａｔｔｅｎｔｉｏｎｂｅｃａｕｓｅｏｆｉｔｓｓｃｉｅｎｔｉｆ ｉｃａｎｄｅｎｖｉｒｏｎｍｅｎｔａｌｒｅｌｅｖａｎｃｅ .1 6 Ｔｈｉｓｒｅａｃｔｉｏｎｓｅｅｍｓｔｏｐｌａｙａｎｉｍｐｏｒｔａｎｔｒｏｌｅｉｎｖａｒｉｏｕｓｐｒｏｃｅｓｓｅｓ .Ｂｏｎｄ ｂｒｅａｋ ｉｎｇｒｅａｃｔｉｏｎｉｓａｐｏｗｅｒｆｕｌｓｙｎｔｈｅｔｉｃｔｏｏｌｔｏｐｒｏｖ…     

The possibility of the decomposition of 2'-deoxyribose moiety of thymidine induced by the low energy electron attachment

To evaluate the possibility of the decomposition of 2-deoxyribose moiety of thymidine induced by low energy electrons (LEE) attachment, the transition states and the energy barriers of the bond breaking processes of the ribose of the nucleoside have been studied theoretically by applying the density functional theory with the double zeta basis sets (DZP++). The energy barriers for the breakage of the C-C bonds (C(1')-C(2'), C(2')-C(3'), C(3')-C(4'), and C(4')-C(5')) of the ribose group of the radical anion of thymidine are found to be high (ca. 42-57 kcal/mol). The total energies of the C-C bond-broken products are significantly higher than that of the radical anion dT(*-). The decomposition of dT(*-) through the C-C bond rupture is unlikely to take place. The rupture of the C(1')-O(4') bond of dT(*-) needs an activation energy as low as 10.4 kcal/mol. However, the reversed reaction (C(1')-O(4') bond formation) needs the activation energy low as 0.3 kcal/mol. Therefore, the intermediate product LM1(C1')-(O4') is unlikely to be stable and the C(1')-O(4') bond-broken is not favored. The activation energy of the C(4')-O(4') bond rupture process amounts to 20.5 kcal/mol. The total energy of the C(4')-O(4') bond broken product is about 6.5 kcal/mol lower than that of the reactant dT(*-). The subsequent N1-glycosidic bond breaking process is found to have a very low energy barrier. Therefore, the LEE-induced base release through the C(4')-O(4') bond rupture might be a possible pathway.     

One‐, two‐, and three‐electron bonding: An “in vitro” theoretical study using noninteger nuclear charges evidences the crucial role of electronegativity in the strength of symmetrical bonds

Fictitious hydrogen atoms H*_A of variable nuclear charge 0.5 ≤ Z_A ≤ 2 (and thus of variable electronegativity) are used to study the intrinsic dependency of chemical bonding on electronegativity. Dissociation energy and equilibrium distance are reported for symmetrical 1‐, 2‐ and 3‐electron H*_AH*_A systems and 2‐electron dissymmetrical H*_A‐H ones. Dealing with symmetrical systems, the strongest two‐electron bonds are found for Z_A ≈ 1.2. Oneelectron and three‐electron strongest bonds occur respectively with low (ca. 0.7) and high (ca. 1.7) Z_A values and can become stronger than the corresponding 2‐electron system. Comparison with data on real systems leads to conclude that electronegativity is a prevailing atomic property in the control of the dissociation energy of symmetrical 1‐, 2‐ and 3‐electron bonds. A simplified mathematical model at Hartree‐Fock or Heitler‐London level with a minimal basis set reproduces these trends semi‐quantitatively and provides the overall shape of the dissociation curves. Finally some points are qualitatively discussed from MO analysis, which emphasize the dependence of the bonding/antibonding properties on the nucleus charge Z_A and their occupancy number. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low‐Energy Electron Attachment

To elucidate the role of guanosine in DNA strand breaks caused by low‐energy electrons (LEEs), theoretical investigations of the LEE attachment‐induced C? O σ‐bonds and N‐glycosidic bond breaking of 2′‐deoxyguanosine‐3′,5′‐diphosphate (3′,5′‐dGMP) were performed using the B3LYP/DZP++ approach. The results reveal possible reaction pathways in the gas phase and in aqueous solutions. In the gas phase LEEs could attach to the phosphate group adjacent to the guanosine to form a radical anion. However, the small vertical detachment energy (VDE) of the radical anion of guanosine 3′,5′‐diphosphate in the gas phase excludes either C? O bond cleavage or N‐glycosidic bond breaking. In the presence of the polarizable surroundings, the solvent effects dramatically increase the electron affinities of the 3′,5′‐dGDP and the VDE of 3′,5′‐dGDP^?. Furthermore, the solvent–solute interactions greatly reduce the activation barriers of the C? O bond cleavage to 1.06–3.56 kcal mol^?1. These low‐energy barriers ensure that either C_5′? O_5′ or C_3′? O_3′ bond rupture takes place at the guanosine site in DNA single strands. On the other hand, the comparatively high energy barrier of the N‐glycosidic bond rupture implies that this reaction pathway is inferior to C? O bond cleavage. Qualitative agreement was found between the theoretical sequence of the bond breaking reaction pathways in the PCM model and the ratio for the corresponding bond breaks observed in the experiment of LEE‐induced damage in oligonucleotide tetramer CGTA. This concord suggests that the influence of the surroundings in the thin solid film on the LEE‐induced DNA damage resembles that of the solvent.     

Origin of the Electron Transport Properties of Aromatic and Antiaromatic Single Molecule Circuits

Antiaromatic molecules have been predicted to exhibit increased electron transport properties when placed between two nanoelectrodes compared to their aromatic analogues. While some studies have demonstrated this relationship, others have found no substantial increase. We use atomistic simulations to establish a general relationship between the electronic spectra of aromatic, antiaromatic, and quinoidal molecules and illustrate its implications for electron transport. We compare the electronic properties of a series of aromatic-antiaromatic counterparts and show that antiaromaticity effectively p-dopes the aromatic electronic spectra. As a consequence, the conducting properties of aromatic-antiaromatic analogues are closely related. For similar attachment points to the electrodes, an interference feature is expected in the HOMO-LUMO gap of one whenever it is absent in the other one. We demonstrate how the relative conductance of aromatic-antiaromatic pairs can be tuned and even reversed through the choice of chemical linker groups. Our work provides a general picture relating connectivity, (anti)aromaticity, and quantum interference and establishes new design rules for single molecule circuits.     

On the Possibility of Uphill Intramolecular Electron Transfer in Multicopper Oxidases: Electrochemical and Quantum Chemical Study of Bilirubin Oxidase

The catalytic cycle of multicopper oxidases (MCOs) involves intramolecular electron transfer (IET) from the Cu‐T1 copper ion, which is the primary site of the one‐electron oxidations of the substrate, to the trinuclear copper cluster (TNC), which is the site of the four‐electron reduction of dioxygen to water. In this study we report a detailed characterization of the kinetic and electrochemical properties of bilirubin oxidase (BOx) – a member of the MCO family. The experimental results strongly indicate that under certain conditions, e.g. in alkaline solutions, the IET can be the rate‐limiting step in the BOx catalytic cycle. The data also suggest that one of the catalytically relevant intermediates (most likely characterized by an intermediate oxidation state of the TNC) formed during the catalytic cycle of BOx has a redox potential close to 0.4 V, indicating an uphill IET process from the T1 copper site (0.7 V) to the Cu‐T23. These suggestions are supported by calculations of the IET rate, based on the experimentally observed Gibbs free energy change and theoretical estimates of reorganization energy obtained by combined quantum and molecular mechanical (QM/MM) calculations.     

Origin of Extraordinary Stability of Square‐Planar Carbon Atoms in Surface Carbides of Cobalt and Nickel

Surface carbides of cobalt and nickel are exceptionally stable, having stabilities competitive with those of graphitic C on these surfaces. The unusual structure of these carbides has attracted much attention: C assumes a tetracoordinate square‐planar arrangement, in‐plane with the metal surface, and its binding favors a spontaneous p4g clock surface reconstruction. A chemical bonding model for these systems is presented and explains the unusual structure, special stability, and the reconstruction. C promotes local two‐dimensional aromaticity on the surface and the aromatic arrangement is so powerful that the required number of electrons is taken from the void M₄ squares, thus leading to Peierls instability. Moreover, this model predicts a series of new transition‐metal and main‐group‐element surface alloys: carbides, borides, and nitrides, which feature high stability, square‐planar coordination, aromaticity, and a predictable degree of surface reconstruction.     

Computational studies on electron and proton transfer in phenol‐imidazole‐base triads

The electron and proton transfer in phenol‐imidazole‐base systems (base = NH₂^? or OH^?) were investigated by density‐functional theory calculations. In particular, the role of bridge imidazole on the electron and proton transfer was discussed in comparison with the phenol‐base systems (base = imidazole, H₂O, NH₃, OH^?, and NH₂^?). In the gas phase phenol‐imidazole‐base system, the hydrogen bonding between the phenol and the imidazole is classified as short strong hydrogen bonding, whereas that between the imidazole and the base is a conventional hydrogen bonding. The n value in spⁿ hybridization of the oxygen and carbon atoms of the phenolic CO sigma bond was found to be closely related to the CO bond length. From the potential energy surfaces without and with zero point energy correction, it can be concluded that the separated electron and proton transfer mechanism is suitable for the gas‐phase phenol‐imidazole‐base triads, in which the low‐barrier hydrogen bond is found and the delocalized phenolic proton can move freely in the single‐well potential. For the gas‐phase oxidized systems and all of the triads in water solvent, the homogeneous proton‐coupled electron transfer mechanism prevails. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

A New Conformation With an Extraordinarily Long, 3.04 Å Two‐Electron,Six‐Center Bond Observed for the π‐[TCNE]22− Dimer in [NMe4]2[TCNE]2 (TCNE=Tetracyanoethylene)

[NMe₄]₂[TCNE]₂ (TCNE=tetracyanoethenide) formed from the reaction of TCNE and (NMe₄)CN in MeCN has ν_CN IR absorptions at 2195, 2191, 2172, and 2156 cm^?1 and a ν_CC absorption at 1383 cm^?1 that are characteristic of reduced TCNE. The TCNEs have an average central C?C distance of 1.423 Å that is also characteristic of reduced TCNE. The reduced TCNE forms a previously unknown non‐eclipsed, centrosymmetric π‐[TCNE]₂^2? dimer with nominal C₂ symmetry, 12 sub van der Waals interatomic contacts <3.3 Å, a central intradimer separation of 3.039(3) Å, and comparable intradimer C???N distances of 3.050(3) and 2.984(3) Å. The two pairs of central C???C atoms form a ?C?C???C?C of 112.6° that is substantially greater than the 0° observed for the eclipsed D_2h π‐[TCNE]₂^2? dimer possessing a two‐electron, four‐center (2e^?/4c) bond with two C???C components from a molecular orbital (MO) analysis. A MO study combining CAS(2,2)/MRMP2/cc‐pVTZ and atoms‐in‐molecules (AIM) calculations indicates that the non‐eclipsed, C₂ π‐[TCNE]₂^2? dimer exhibits a new type of a long, intradimer bond involving one strong C???C and two weak C???N components, that is, a 2e^?/6c bond. The C₂ π‐[TCNE]₂^2? conformer has a singlet, diamagnetic ground state with a thermally populated triplet excited state with J/k_B=1000 K (700 cm^?1; 86.8 meV; 2.00 kcal mol^?1; H=?2 JS_a?S_b); at the CAS(2,2)/MBMP2 level the triplet is computed to be 9.0 kcal mol^?1 higher in energy than the closed‐shell singlet ground state. The results from CAS(2,2)/NEVPT2/cc‐pVTZ calculations indicate that the C₂ and D_2h conformers have two different local metastable minima with the C₂ conformer being 1.3 kcal mol^?1 less stable. The different natures of the C₂ and D_2h conformers are also noted from the results of valence bond (VB) qualitative diagram that shows a 10e^?/6c bond with one C???C and two C???N bonding components for the C₂ conformer as compared to the 6e^?/4c bond for the D_2h conformer with two C???C bonding components.     

Theoretical Study of Electron Density Delocalization in the Excited States of Transition Metal Complexes

This paper presents a theoretical study of electron density delocalization effects over an electron-accepting ligand in metal-to-ligand charge-transfer (MLCT) complexes in the excited states, where the ligand is 4,4'-X₂-2,2'-bpy (X = H, NH₂, CH₃, Ph, Cl, CO₂Et, NO₂, bpy = 2,2'-bipyridine) or terpy (2,2':6',2'-terpyridine). Optimal geometry calculations are performed for neutral ligand molecules and their radical anions modeling the state of the ligands during MLCT excitations. Spin density distribution over atoms in the radical anions is used as a measure of the degree of delocalization. The role of spin density distribution in excitation-induced changes of geometrical parameters of the ligands is considered.     

Strength of the [Z–I···Hal]− and [Z–Hal···I]− Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy

Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, E_int, using relationships between E_int and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between E_int and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z–I···Hal]⁻ and [Z–Hal···I]⁻ types bearing halogen bonds and involving iodine as interacting atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06–4.76 kcal/mol.     

Reply to “Comment on the Comparative Use of the Electron Density and Its Laplacian”

In our reply to the preceding comment by Richard Bader we show that the statements of the author are not justified and that he contradicts his own previous work.     

An alternative way of characterising the bonding in compounds featuring main-group elements and with the potential for multiple bonding: on the dissociation of binary main-group hydrides

Herein the bonding in compounds featuring main-group elements and with the potential for multiple bonding is studied theoretically by examination of their fragmentation into two fragments that still exhibit the same structure as they had in the molecule prior to dissociation. The fragments were calculated both in their electronic ground state and in an excited electronic state, in which the number of unpaired electrons is equal to the maximal number of bonds in the compounds before dissociation. The energies of the fragmentation processes (DeltaE(frag)) can be more directly linked to the bond strengths than the dissociation energies (DeltaE(diss)), because of the absence of any secondary effects like relaxation of the electronic state or of the geometry of the fragments. These relaxation energies of the fragments (DeltaE(frag)) are also studied herein. The energies derived in this work allow for an accurate comparison of the bonding properties in main-group-element hydrides. The trends of the fragmentation and relaxation energies are discussed in detail. It will be shown that the relaxation energies allow for a classification of the bonds ("classical" sigma and pi bonds or donor-acceptor interactions), while the fragmentation energies are good quantitative measures for the total bond strength. Similar calculations are on the way to explore the bonding in systems in which the hydrogen atoms are replaced by organic groups or halogen atoms.     

Gold Behaves as Hydrogen in the Intermolecular Self‐Interaction of Metal Aurides MAu4 (M=Ti,Zr, and Hf)

We performed density functional calculations to examine the intermolecular self‐interaction of metal tetraauride MAu₄ (M=Ti, Zr, and Hf) clusters. We found that the metal auride clusters have strong dimeric interactions (2.8–3.1 eV) and are similar to the metal hydride analogues with respect to structure and bonding nature. Similarly to (MH₄)₂, the (μ‐Au)₃ C_s structures with three three‐center two‐electron (3c–2e) bonds were found to be the most stable. Natural orbital analysis showed that greater than 96 % of the Au 6s orbital contributes to the 3c–2e bonds, and this predominant s orbital is responsible for the similarity between metal aurides and metal hydrides (>99 % H 1s). The favorable orbital interaction between occupied Au 6s and unoccupied metal d orbitals leads to a stronger dimeric interaction for MAu₄‐MAu₄ than the interaction for MH₄‐MH₄. There is a strong relationship between the dimeric interaction energy and the chemical hardness of its monomer for (MAu₄)₂ and (MH₄)₂.     

Triplet‐State Aromaticity of 4nπ‐Electron Monocycles: Analysis of Bifurcation in the π Contribution to the Electron Localization Function

The π contribution to the electron localization function (ELF) is used to compare 4nπ‐ and (4n+2)π‐electron annulenes, with particular focus on the aromaticity of 4nπ‐electron annulenes in their lowest triplet state. The analysis is performed on the electron density obtained at the level of OLYP density functional theory, as well as at the CCSD and CASSCF ab initio levels. Two criteria for aromaticity of all‐carbon annulenes are set up: the span in the bifurcation values ΔBV(ELF_π) should be small, ideally zero, and the bifurcation value for ring closure of the π basin RCBV(ELF_π) should be high (≥ 0.7). On the basis of these criteria, nearly all 4nπ‐electron annulenes are aromatic in their lowest triplet states, similar to (4n+2)π‐electron annulenes in their singlet ground states. For singlet biradical cyclobutadiene and cyclooctatetraene constrained to D_4h and D_8h symmetry, respectively, the RCBV(ELF_π) at the CASSCF level is lower (0.531 and 0.745) than for benzene (0.853), even though they have equal proportions of α‐ and β‐electrons.