Ab initio study of long-range electron transfer between biphenyl anion radical and naphthalene

After the separation of the donor, the acceptor, and the σ-type bridge from the π-σ-π system, the geometries of biphenyl, biphenyl anion radical, naphthalene, and naphthalene anion radical are optimized, and then the reorganization energy for the intermolecular electron transfer (ET) at the levels of HF/4-31G and HF/DZP is calculated. The ET matrix elements of the self-exchange reactions of theπ-σ-π systems have been calculated by means of both the direct calculation based on the variational principle, and the transition energy between the molecular orbitals at the linear coordinateR = 0.5. For the cross reactions, the ET matrix element and the geometry of the transition state are determined by searching the minimum energy splitting Δ_min along the reaction coordinate. In the evaluation of the solvent reorganization energy of the ET in solution, the Marcus’ two- sphere model has been invoked. A few of ET rate constants for the intramolecular ET reactions for the π-σ-π systems, which contain the biphenylyl as the donor and both biphenylyl and naphthyl as the acceptor, have been obtained. Project supported by the National Natural Science Foundation of China (Grant Nos. 29706104 and 29573112), the State Key Laboratory of Theoretical and Computational Chemistry of Jilin University.     

Computational Insights into the Charge Relaying Properties of β‐Turn Peptides in Protein Charge Transfers

Density functional theory calculations suggest that β‐turn peptide segments can act as a novel dual‐relay elements to facilitate long‐range charge hopping transport in proteins, with the N terminus relaying electron hopping transfer and the C terminus relaying hole hopping migration. The electron‐ or hole‐binding ability of such a β‐turn is subject to the conformations of oligopeptides and lengths of its linking strands. On the one hand, strand extension at the C‐terminal end of a β‐turn considerably enhances the electron‐binding of the β‐turn N terminus, due to its unique electropositivity in the macro‐dipole, but does not enhance hole‐forming of the β‐turn C terminus because of competition from other sites within the β‐strand. On the other hand, strand extension at the N terminal end of the β‐turn greatly enhances hole‐binding of the β‐turn C terminus, due to its distinct electronegativity in the macro‐dipole, but does not considerably enhance electron‐binding ability of the N terminus because of the shared responsibility of other sites in the β‐strand. Thus, in the β‐hairpin structures, electron‐ or hole‐binding abilities of both termini of the β‐turn motif degenerate compared with those of the two hook structures, due to the decreased macro‐dipole polarity caused by the extending the two terminal strands. In general, the high polarity of a macro‐dipole always plays a principal role in determining charge‐relay properties through modifying the components and energies of the highest occupied and lowest unoccupied molecular orbitals of the β‐turn motif, whereas local dipoles with low polarity only play a cooperative assisting role. Further exploration is needed to identify other factors that influence relay properties in these protein motifs.     

Charge transport and electronic properties of N-heteroquinones: quadruple weak hydrogen bonds and strong π–π stacking interactions

The charge transport and photophysical properties of N-heteroquinones, which can function as n-type organic semiconductors in organic field-effect transistors (OFETs) with high electron mobility, were systematically investigated using hopping model, band theory, and time-dependent density functional theory (TDDFT). The calculated absorption spectra and electron mobility are in good agreement with experimental results. To the studied compounds, subtle structural modifications can greatly reduce the reorganization energy. There are two main kinds of intermolecular interaction forces of the studied compounds in the crystal, which result from intermolecular π–π and hydrogen bonds interactions, respectively. The results of hopping model show that the electron transport properties are mainly determined by pathways containing intermolecular π–π interactions, and hole transport properties are mainly determined by pathways containing intermolecular hydrogen bonds from the standpoint of transfer integral. Moreover, electronic transfer integral value increases with the enhancement of intermolecular overlap corresponding to the overlap extent of π–π packing. Hole transfer integral value decreases with decreasing the number of hydrogen bonds. This means that charge transport properties can be efficiently tuned by controlling the relative positions of the molecules and the number of hydrogen bonds. The analysis of band structure also supports the conclusion of hopping model.     

A new algorithm for the fixed-node quantum Monte Carlo method

A novel algorithm is proposed for the fixed-node quantum Monte Carlo (FNQMC) method.In contrast to previous procedures,its "guiding function" is not optimized prior to diffusion quantum Monte Carlo (DMC) computation but synchronistically in the diffusion process The new algorithm can not only save CPU time,but also make both of the optimization and diffusion carried out according to the same sampling fashion,reaching the goal to improve each other This new optimizing procedure converges super-linearly,and thus can accelerate the particle diffusion During the diffusion process,the node of the "guiding function" changes incessantly,which is conducible to reducing the "fixed-node error" The new algorithm has been used to calculate the total energies of states X3B1 and a1A1 of CH2 as well as π-X2B1 and λ-2A1 of NH2 The singlet-triplet energy splitting (λEsT) in CH2 and π energy splitting in NH2 obtained with this present method are (45 542±1.840) and (141.644±1.589) kJ/mol,respectively The calculated     

Anomalous temperature-isotope dependence in proton-coupled electron transfer

Motivated by the experiments of Hodgkiss et al. [J. Phys. Chem. (submitted)] on electron transfer (ET) through a H-bonding interface, we present a new theoretical model for proton-coupled electron transfer (PCET) in the condensed phase, that does not involve real proton transfer. These experiments, which directly probe the joint T-isotope effects in coupled charge transfer reactions, show anomalous T dependence in k(H)k(D), where k(H) and k(D) are the ET rates through the H-bonding interface with H-bonded protons and deuterons, respectively. We address the anomalous T dependence of the k(H)k(D) in our model by attributing the modulation of the electron tunneling dynamics to bath-induced fluctuations in the proton coordinate, so that the mechanism for coupled charge transfer might be better termed vibrationally assisted ET rather than PCET. We argue that such a mechanism may be relevant to understanding traditional PCET processes, i.e., those in which protons undergo a transfer from donor to acceptor during the course of ET, provided there is an appropriate time scale separating both coupled charge transfers. Likewise, it may also be useful in understanding long-range ET in proteins, where tunneling pathways between redox cofactors often pass through H-bonded amino acid residues, or other systems with sufficiently decoupled proton and electron donating functionalities.     

Dynamic relaying properties of a β-turn peptide in long-range electron transfer

The relay stations play a significant role in long-range charge hopping transfer in proteins. Although studies have clarified that many more protein structural motifs can function as relays in charge hopping transfers by acting as intermediate charge carriers, the relaying properties are still poorly understood. In this work, taking a β-turn oligopeptide as an example, we report a dynamic character of a relay with tunable relaying properties using the density functional theory calculations. Our main finding is that a β-turn peptide can serve as an effective electron relay in facilitating long-range electron migration and its relay properties is vibration-tunable. The vibration-induced structural transient distortions remarkably affect the lowest occupied molecular orbital (LUMO) energy, vertical electron affinity and electron-binding mode of the β-turn oligopeptide and the singly occupied molecular orbital (SOMO) energy of the corresponding electron adduct and thus the relaying properties. Different vibration modes lead to different structural distortions and thus have different effects on the relaying properties and ability of the β-turn peptide. For the relaying properties, there approximately is a linear negative correlation of electron affinity with the LUMO energy of the β-turn or the SOMO energy of its electron adduct. Besides, such relaying properties also vary in the vibration evolution process, and the electron-binding modes may be tunable. As an important addition to the known static charge relaying properties occurring in various protein structural motifs, this work reports the dynamic electron-relaying characteristics of a β-turn oligopeptide with variable relaying properties governed by molecular vibrations which can be applied to different proteins in mediating long-range charge transfers. Clearly, this work reveals molecular vibration effects on the electron relaying properties of protein structural motifs and provides new insights into the dynamics of long-range charge transfers in proteins. © 2018 Wiley Periodicals, Inc.     

Direct-space analysis of the Si–Si bonding pattern in the π-bonded chain reconstructed Si(111)(2 × 1) surface

Atomic and bond properties of silicon atoms in the buckled π-bonded chain reconstructed Si(111)(2 × 1) system were investigated by applying the quantum theory of atoms in molecules to a number of wavefunctions from periodic ab initio calculations using a slab model for the surface and geometries from experiment. Reconstruction involves much larger surface-cell charge distortions than in the unrelaxed surface and drastic changes in the atomic polarizations of the surface layer atoms. The effect of buckling is to largely differentiate the properties (charge, energy, volume, atomic polarizations) of the two unique atoms of each surface layer. The direction of electronic charge transfer in the topmost chain (from the “up” to the “down” atom) was found to be opposite to what was claimed previously. The π conjugation is not strictly localized along the topmost layer chains (where it is also largely incomplete), but rather it extends over a 2D array of bonds between the topmost and the lower surface layers. Received: 19 July 2000 / Accepted: 2 October 2000 / Published online: 23 January 2001     

Redox induced reactions of transition metal π- and σ,π-complexes

In this review, redox-induced reactions of π- and σ,π-complexes leading to the selective formation (or cleavage) of C–H, C–C, and C–O bonds have been summarized. To illustrate the synthetic potential of such methodology, the following representative reactions studied in our group are discussed: (1) oxidatively induced hydrogen elimination from “open” cyclic diene and dienyl complexes resulting in formation of “closed” dienyl and arene complexes, respectively; (2) reductive activation of C–H bonds in diene, vinylidene, and carbyne complexes forming new multiple C–C bonds; (3) oxidative dehydrodimerization of vinylidene complexes into binuclear μ-divinylidene species; and (4) oxidatively induced addition of oxygen nucleophiles to μ-divinylidene complexes affording cyclic μ-dicarbene derivatives. Oleg V. Gusev, deceased on October 31.     

Cation-modulated electron-transfer channel: H-atom transfer vs proton-coupled electron transfer with a variable electron-transfer channel in acylamide units

The mechanism of proton transfer (PT)/electron transfer (ET) in acylamide units was explored theoretically using density functional theory in a representative model (a cyclic coupling mode between formamide and the N-dehydrogenated formamidic radical, FF). In FF, PT/ET normally occurs via a seven-center cyclic proton-coupled electron transfer (PCET) mechanism with a N-->N PT and an O-->O ET. However, when different hydrated metal ions are bound to the two oxygen sites of FF, the PT/ET mechanism may significantly change. In addition to their inhibition of PT/ET rate, the hydrated metal ions can effectively regulate the FF PT/ET cooperative mechanism to produce a single pathway hydrogen atom transfer (HAT) or a flexible proton coupled electron transfer (PCET) mechanism by changing the ET channel. The regulation essentially originates from the change in the O...O bond strength in the transition state, subject to the binding ability of the hydrated metal ions. In general, the high valent metal ions and those with large binding energies can promote HAT, and the low valent metal ions and those with small binding energies favor PCET. Hydration may reduce the Lewis acidity of cations, and thus favor PCET. Good correlations among the binding energies, barrier heights, spin density distributions, O...O contacts, and hydrated metal ion properties have been found, which can be used to interpret the transition in the PT/ET mechanism. These findings regarding the modulation of the PT/ET pathway via hydrated metal ions may provide useful information for a greater understanding of PT/ET cooperative mechanisms, and a possible method for switching conductance in nanoelectronic devices.     

Charge hopping in DNA.

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G(+) with water. In addition, it has been assumed that the presence of units with several adjacent stacked G bases on the same strand leads to the additional vibronic relaxation process (G(+)G...G) --> (GG...G)(+). The latter may also compete with the hole transfer from (G(+)G...G) to a single G site, depending on the relative positions of energy levels for G(+) and (G(+)G...G). A hopping model is proposed to take the competition of these three rate steps into account. It is shown that the model includes two important limits. One corresponds to the situation where the charge relaxation inside a multiple guanine unit is faster than hopping. In this case hopping is terminated by several adjacent G bases located on the same strand, as has been observed for the GGG triple. In the opposite, slow relaxation limit the GG...G unit allows a hole to migrate further in accord with experiments on strand cleavage exploiting GG pairs. We demonstrate that for base pair sequences with only the GGG triple, the fast relaxation limit of our model yields practically the same sequence- and distance dependencies as measurements, without invoking adjustable parameters. For sequences with a certain number of repeating adenine:thymine pairs between neighboring G bases, our analysis predicts that the hole transfer efficiency varies in inverse proportion to the sequence length for short sequences, with change to slow exponential decay for longer sequences. Calculations performed within the slow relaxation limit enable us to specify parameters that provide a reasonable fit of our numerical results to the hole migration efficiency deduced from experiments with sequences containing GG pairs. The relation of the results obtained to other theoretical and experimental studies of charge transfer in DNA is discussed. We propose experiments to gain a deeper insight into complicated kinetics of charge-transfer hopping in DNA.     

Theoretical study of electron, proton, and proton-coupled electron transfer in iron bi-imidazoline complexes.

A comparative theoretical investigation of single electron transfer (ET), single proton transfer (PT), and proton-coupled electron transfer (PCET) reactions in iron bi-imidazoline complexes is presented. These calculations are motivated by experimental studies showing that the rates of ET and PCET are similar and are both slower than the rate of PT for these systems (Roth, J. P.; Lovel, S.; Mayer, J. M. J. Am. Chem. Soc. 2000, 122, 5486). The theoretical calculations are based on a multistate continuum theory, in which the solute is described by a multistate valence bond model, the transferring hydrogen nucleus is treated quantum mechanically, and the solvent is represented as a dielectric continuum. For electronically nonadiabatic electron transfer, the rate expressions for ET and PCET depend on the inner-sphere (solute) and outer-sphere (solvent) reorganization energies and on the electronic coupling, which is averaged over the reactant and product proton vibrational wave functions for PCET. The small overlap of the proton vibrational wave functions localized on opposite sides of the proton transfer interface decreases the coupling for PCET relative to ET. The theory accurately reproduces the experimentally measured rates and deuterium kinetic isotope effects for ET and PCET. The calculations indicate that the similarity of the rates for ET and PCET is due mainly to the compensation of the smaller outer-sphere solvent reorganization energy for PCET by the larger coupling for ET. The moderate kinetic isotope effect for PCET arises from the relatively short proton transfer distance. The PT reaction is found to be dominated by solute reorganization (with very small solvent reorganization energy) and to be electronically adiabatic, leading to a fundamentally different mechanism that accounts for the faster rate.     

Influence of the out-of-plane distortions of nuclear configurations of molecules with then-AO of the heteroatom directed along theC 2 symmetry axis on spin-orbit coupling between thenπ*- and ππ*-states

This paper studies changes in the matrix elements (U_mp) of spin-orbit coupling between the nπ^*- and ππ^*-states, which are induced by the (“chair,” “bath”) distortions of the nuclear configurations of molecules. The analysis is performed for acridine molecules in which the n-p_z atomic orbital (AO) of the heteroatom is directed along the C₂ symmetry axis. Earlier, for molecules with a planar nuclear configuration of C_2v symmetry and with the heteroatom lying on the C₂ axis, we established the dependence of U_mp on the symmetry of ππ^*-states [Γ(ππ^*)=A₁ or B₂]. The values of U_mp differ by more than one order of magnitude; this is in line with the difference between the interconversion rate constants (K_isc; two or three orders). In this work we have found that this contrast in U_mp (and, accordingly, in K_isc) is retained when the nuclear configuration of the acridine molecule is distorted to the “chair” (AC-A) configuration, although the individuality of both molecular orbital types (nσ-MO and π-MO) and states nπ^* and ππ^* is annihilated to a certain extent. For the “bath” (AC-B) conformation the difference in U_mp considerably diminishes. Reasons for the changes in the matrix elements of spin-orbit coupling and rate constants of the S-T conversion are analyzed. The available energy level diagram is critically analyzed, and a slightly different diagam as well as a scheme of nonradiating deactivation of acridine are suggested. L. Ya. Karpov Physicochemical Scientific Research Institute. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 292–297, March–April, 1995. Translated by L. Smolina     

Intramolecular electron-hole transfer in binuclear transition metal compounds-theoretical methods and model studies

A theoretical framework for intramolecular electron or hole migration is developed starting from the convenient canonical molecular orbitals of an ordinary Hartree-Fock (HF) calculation. The necessary unitary transformations from the canonical MO basis via localized orbitals to a transfer Fockian are presented. A simple procedure for the consideration of relaxation and correlation effects during the time evolution is developed. Computational results for the hole migration between different metal 3d electron-hole pairs in bis(-pentadienyl)dinickel (1) are discussed. The contribution of the direct transfer channel as well as the participation of ligand and channels in the various propagation processes are analyzed.     

Cocrystal Assembled by 1,2-Diiodotetrafluorobenzene and Acridine via C-I…N Halogen Bond and Tr-hole…F Bonds

The concepts on o-hole and ~-hole bonds are suggested. A cocrystal with repeated 8-F-atom unit as basic struc- tural motif is assembled based on bifurcated C-I…N…I-C halogen/σ-hole bond and antiparallel double π-hole… F bonds by 1,2-diiodotetrafluorobenzene and acridine and characterized well by XRD, powder XRD and solid 19F NMR, etc. Also the calculated interaction energies are -26.8 and -31.5 kJ/mol for bifurcated C-I…N sp……2 halogen bonds, and -14.3 kJ/mol for a pair of n-hole…F bonds. In this system C-I…N halogen bond has stronger competitive ability to C-I…π halogen bond due to stronger basicity of N than π-system in acridine. The combination of the halogen/σ-hole and π-hole bonds or together with other weak interactions could play a key role in assembling function materials, molecular recognition and design of drugs and so on.     

Proton-coupled electron transfer in a model for tyrosine oxidation in photosystem II

Theoretical calculations of a model for tyrosine oxidation in photosystem II are presented. In this model system, an electron is transferred to ruthenium from tyrosine, which is concurrently deprotonated. This investigation is motivated by experimental measurements of the dependence of the rates on pH and temperature (Sj?din et al. J. Am. Chem. Soc. 2000, 122, 3932). The mechanism is proton-coupled electron transfer (PCET) at pH < 10 when the tyrosine is initially protonated and is single electron transfer (ET) for pH > 10 when the tyrosine is initially deprotonated. The PCET rate increases monotonically with pH, whereas the single ET rate is independent of pH and is 2 orders of magnitude faster than the PCET rate. The calculations reproduce these experimentally observed trends. The pH dependence for the PCET reaction arises from the decrease in the reaction free energies with pH. The calculations indicate that the larger rate for single ET arises from a combination of factors, including the smaller solvent reorganization energy for ET and the averaging of the coupling for PCET over the reactant and product hydrogen vibrational wave functions (i.e., a vibrational overlap factor in the PCET rate expression). The temperature dependence of the rates, the solvent reorganization energies, and the deuterium kinetic isotope effects determined from the calculations are also consistent with the experimental results.     

Electron Transfer around a Molecular Corner

The distance dependence of electron transfer (ET) is commonly investigated in linear rigid rod‐like compounds, but studies of molecular wires with integrated corners imposing 90° angles are very rare. By using spirobifluorene as a key bridging element and by substituting it at different positions, two isomeric series of donor‐bridge‐acceptor compounds with either nearly linear or angled geometries were obtained. Photoinduced ET in both series is dominated by rapid through‐bond hole hopping across oligofluorene bridges over distances of up to 70 Å. Despite considerable conformational flexibility, direct through‐space and through‐solvent ET is negligible even in the angled series. The independence of the ET rate constant on the total number of fluorene units in the angled series is attributed to a rate‐limiting tunneling step through the spirobifluorene corner. This finding is relevant for multidimensional ET systems and grids in which individual molecular wires are interlinked at 90° angles.     

Proton-coupled electron transfer versus hydrogen atom transfer: generation of charge-localized diabatic states

The distinction between proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms is important for the characterization of many chemical and biological processes. PCET and HAT mechanisms can be differentiated in terms of electronically nonadiabatic and adiabatic proton transfer, respectively. In this paper, quantitative diagnostics to evaluate the degree of electron-proton nonadiabaticity are presented. Moreover, the connection between the degree of electron-proton nonadiabaticity and the physical characteristics distinguishing PCET from HAT, namely, the extent of electronic charge redistribution, is clarified. In addition, a rigorous diabatization scheme for transforming the adiabatic electronic states into charge-localized diabatic states for PCET reactions is presented. These diabatic states are constructed to ensure that the first-order nonadiabatic couplings with respect to the one-dimensional transferring hydrogen coordinate vanish exactly. Application of these approaches to the phenoxyl-phenol and benzyl-toluene systems characterizes the former as PCET and the latter as HAT. The diabatic states generated for the phenoxyl-phenol system possess physically meaningful, localized electronic charge distributions that are relatively invariant along the hydrogen coordinate. These diabatic electronic states can be combined with the associated proton vibrational states to generate the reactant and product electron-proton vibronic states that form the basis of nonadiabatic PCET theories. Furthermore, these vibronic states and the corresponding vibronic couplings may be used to calculate rate constants and kinetic isotope effects of PCET reactions.     

Characterization of a sealed Americium–Beryllium (AmBe) source by inductively coupled plasma mass spectrometry

Two Americium–Beryllium neutron sources were dismantled, sampled (sub-sampled) and analyzed via inductively coupled plasma mass spectrometry (ICP-MS). Characteristics such as “age” since purification, actinide content, trace metal content and inter and intra source composition were determined. The “age” since purification of the two sources was determined to be 25.0 and 25.4 years, respectively. The systematic uncertainties in the “age” determination were ±4% 2σ. The amount and isotopic composition of U and Pu varied substantially between the sub-samples of Source 2 (n = 8). This may be due to the physical means of sub-sampling or the way the source was manufactured. Source 1 was much more consistent in terms of content and isotopic composition (n = 3 sub-samples). The Be–Am ratio varied greatly between the two sources. Source 1 had an Am–Be ratio of 6.3 ± 52% (1σ). Source 2 had an Am–Be ratio of 9.81 ± 3.5% (1σ). In addition, the trace element content between the samples varied greatly. Significant differences were determined between Sources 1 and 2 for Sc, Sr, Y, Zr, Mo, Ba and W.     

Base sequence effects on transport in DNA

Given the success of the polaron model based on solvation in accounting for the width of a hole polaron on an all-adenine (A) sequence on DNA, we extend the calculations to other sequences. We find excellent agreement with the free energy differences measured by Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037-12038) between a guanine (G) cation and a pair of bases, GG, or a triple of bases, GGG, in all cases surrounded by As, by treating AGGA and AGGGA as solvated polarons. There is additional support for hole polaron formation in DNA from experiments in which oxidative damage due to injected holes is investigated in sequences involving Gs and As. Theory and comparison with transport measurements on repeated sequences involving multiple thymines (Ts) or combinations such as ATs or GCs, where C is cytosine, led to the suggestion that the basic sequences in these cases must be polarons whose wave functions have substantial amplitudes on both chains in a duplex. The size of an electron polaron in DNA is predicted to be similar to that of a hole polaron, approximately 4 or 5 bases. Although experiments have shown that polaron hopping is the dominant mode of charge transport in DNA with repeated sequences such as AGGA, further investigations, particularly of temperature dependence of site energies and transfer integrals, are needed to determine to what extent hole transport takes place by polaron hopping for arbitrary DNA sequences.