Parameters For Excess Electron Transfer in DNA. Estimation Using Unoccupied Kohn−Sham Orbitals and TD DFT

The recently developed Quasiparticle Energy (QE) scheme, based on a DFT calculation with one more (or less) electron, offers a good description of excitation energies, even with charge transfer characters. In this work, QE is further extended to calculate electron transfer (ET) couplings involving two excited states. We tested it with a donor-acceptor complex, consisting of a furan and a 1,1-dicyanoethylene (DCNE), in which two low lying charge transfer and local excitation states are involved. With generalized Mülliken-Hush and fragment charge-difference schemes, couplings from the QE approach generally agree well with those obtained from TDDFT, except that QE couplings exhibit better exponential distance dependence. Couplings from half-energy gaps with an external field are also calculated and reported. Our results show that the QE scheme is robust in calculating ET couplings with greatly reduced computational time.

In the past few decades, charge transfer in DNA has attracted considerable attention from researchers in a wide variety of fields, including bioscience, physical chemistry, and nanotechnology. Charge transfer in DNA has been investigated using various techniques. Among them, time-resolved spectroscopic methods have yielded valuable information on charge transfer dynamics in DNA, providing an important basis for numerical practical applications such as development of new therapy applications and nanomaterials. In DNA, holes and excess electrons act as positive and negative charge carriers, respectively. Although hole transfer dynamics have been investigated in detail, the dynamics of excess electron transfer have only become clearer relatively recently. In the present paper, we summarize studies on the dynamics of hole and excess electron transfer conducted by several groups including our own.

The electronic structure of a charged polysilane molecule is studied. The transient absorption spectroscopy was carried out for radical cations and anions of aryl-substituted polysilane molecules with Si-based defects by means of the nanosecond pulse radiolysis technique. Radical cations and anions of polysilanes displayed near-UV and IR absorption maxima at ca. 3.2−3.4 and 0.5−1 eV, respectively. They are ascribed to interband and subband transitions of polaron states and/or charge resonance states (CR) between σ-conjugated segments. The transition energy of the bands was strongly affected by the defects, showing a remarkable blue shift in IR absorption. The energy of the IR absorption band was interpreted as the degree of electron−phonon coupling. The energy rapidly increased from ca. 0.5 eV with an increase in the defect density and saturated at ca. 0.85 eV for radical cations and 0.95 eV for radical anions. It indicated that excess electrons and holes relatively localized at the defect structures, whereas the charges were delocalized in a conjugated segment in linear polysilanes.

Engineering couplings for exciton transport using synthetic DNA scaffolds

In this work we focus on the binding of excess electrons to water clusters, a problem for which dispersion interactions, which originate from long-range correlation effects, are especially important. Two different model potential approaches, one using quantum Drude oscillators and the other using polarization potentials, are investigated for describing the long-range correlation effects between the weakly bound excess electron and the more tightly bound electrons of the monomers. We show that these two approaches are related in that the polarization potential models can be derived from the quantum Drude model approach by use of an adiabatic separation between the excess electron and the Drude oscillators. The model potential approaches are applied to clusters containing up to 45 water monomers. Where possible, comparison is made with the results of ab initio electronic structure calculations. Overall, the polarization potential approach is found to give electron binding energies in good agreement with those from the Drude model and ab initio calculations, with the greatest discrepancies being found for "cavity-bound" anion states.

Electronic coupling is a key parameter that controls the efficiency of excitation energy transfer (EET) and exciton delocalization. A new approach to estimate electronic coupling is introduced. Within a two-state model, the EET coupling V of two chromophores is expressed via the vertical excitation energies (Ei and Ej), transition dipole moments (Mi and Mj) of the system and transition moments (μA and μB) of the individual chromophores: V = (Ei – Ej){[(MiMj)(μA2 – μB2) – (μAμB)(Mi2 – Mj2)]/[(Mi2 – Mj2)2 + 4(MiMj)2]}. These quantities are directly available from quantum mechanical calculations. As the estimated coupling accounts for both short-range and long-range interactions, this approach allows for the treatment of systems with short intermolecular distances, in particular, π-stacked chromophores. For a system of two identical chromophores, the coupling is given by V = (Ei – Ej)[(EiFj – EjFi)/(EiFj + EjFi)][1/(2 cos θ)] where Fi and Fj are the corresponding oscillator strengths and cos θ is determined by the relative position of the chromophores in the dimer. Thus, the coupling can be derived from purely experimental data. The developed approach is used to calculate the EET coupling and exciton delocalization in two π-stacks of pyrimidine nucleobases 5′-TT-3′ and 5′-CT-3′ showing quite different EET properties.

To better understand the cause of the diversity in reported values of the electron affinities (EAs) for DNA bases, we performed a series of DFT (B3LYP functional) calculations at different basis set sizes. Through investigation of (1) trends in the values of EAs, (2) the excess electron spin distribution of the anion radical dependence on basis set size, (3) effect of the excess electron on ZPEs, we are able to identify the features of a basis set that allows for dipole-bound and continuum states to compete with molecular states for the electron. Smaller basis sets that confine the excess electron to the molecule allow for reasonable estimates of relative valence electron affinities excluding dipole-bound states and suggest the order of adiabatic valence electron affinities to be U ≈ T > C ≈ I (hypoxanthine) > A > G with G nearly 1 eV less electron affinic than U. Combining the best estimates from theory and experiment we place the adiabatic valence electron affinities of the pyrimidines as zero to +0.2 eV, whereas the purines A and G are predicted to be clearly negative with electron affinities of ca. −0.35 and −0.75 eV, respectively. The virtual states (i.e., negative electron affinities) for A and G in the gas-phase become relevant to biology when their energies are lowered to bound states in solvated systems. Indeed, our calculations performed including the effect of solvation (PCM model) show that all EAs for the DNA bases are positive and have the same relative order as found with the compact basis sets in the gas-phase calculations.

Focusing on the interesting new concept of all-metal electride, centrosymmetric molecules e^− + M^(2+) (Ni@Pb_12)^(2−) M^(2+) + e^− (M = Be, Mg, and Ca) with two anionic excess electrons located at the opposite ends of the molecule are obtained theoretically. These novel molecular all-metal electrides can act as infrared (IR) nonlinear optical (NLO) switches. Whereas the external electric field (F) hardly changes the molecular structure of the all-metal electrides, it seriously deforms their excess electron orbitals and average static first hyperpolarizabilities (β0 e (F)). For e^− + Ca^(2+) (Ni@Pb_12)^(2−) Ca^(2+) + e^−, a small external electric field F = 8 × 10−4 au (0.04 V/Å) drives a long-range excess electron transfer from one end of the molecule through the middle all-metal anion cage (Ni@Pb_12)^(2−) to the other end. This long-range electron transfer is shown by a prominent change of excess electron orbital from double lobes to single lobe, which forms an excess electron lone pair and electronic structure Ca^(2+) (Ni@Pb_12)^(2−) Ca^(2+) + 2e^−. Therefore, the small external electric field induces a dramatic β_0 e (F) contrast from 0 (off form) to 2.2 × 106 au (on form) in allmetal electride molecule Ca(Ni@Pb_12)Ca. Obviously, such switching is high sensitive. Interestingly, in the switching process, such long-range excess electron transfer does not alter the valence and chemical bond nature. Then, this switching mechanism is a distinct nonbonding evolution named electronic structure isomerization, which means that such switching has the advantages of being fast and reversible. Besides, these all-metal electride molecules also have a rare IR transparent characteristic (1.5−10 μm) in NLO electride molecules, and hence are commendable molecular IR NLO switches. Therefore, this work opens a new research field of electric field manipulated IR NLO switches of molecular all-metal electrides

Spiropyrans and spirooxazines (SP) are known to undergo photochromism to form merocyanines (MC). In this study, upon pulsed electron radiolysis of SP in organic solvents, we observed the transient absorption spectra of SP radical ions in the visible wavelength region. Based on first-order kinetics in the microsecond time domain, the absorption spectra changed to different ones, which were plausibly due to the radical ions of the corresponding MC. The reaction rates from SP radical ions to MC ones were determined. Using heats of formation for the radical ions of SP and MC evaluated with DFT calculations, the differences in heats of formation between the radical ions of SP and MC were determined to be exothermic. The reaction rate correlated with the difference in heat of formation, which depended on the parity of the radical ions. Time-dependent DFT calculations provided the SOMO surfaces of the radical ions of SP and MC. Comparing the SOMO with the LUMO, HOMO, and HOMO-1 surfaces of the neutral SP, we found that the attached electron locates on the LUMO upon one-electron reduction in SP, whereas the HOMO-1 of SP is involved in one-electron oxidation of SP rather than the HOMO.

The anion photoelectron (PE) spectra of EuH(-) and the PE spectrum of overlapping EuOH(-) and EuO(-) anions are presented and analyzed with supporting results from density functional theory calculations on the various anions and neutrals. Results point to ionically bound, high-spin species. EuH and EuOH anions and neutrals exhibit analogous electronic structures: Transitions from (8)Σ(-) anion ground states arising from the 4f(7)σ(6s)(2) superconfiguration to the close-lying neutral (9)Σ(-) and (7)Σ(-) states arising from the 4f(7)σ(6s) superconfiguration are observed spaced by an energy interval similar to the free Eu(+) [4f(7)6s] (9)S - (7)S splitting. The electron affinities (EAs) of EuH and EuOH are determined to be 0.771 ± 0.009 eV and 0.700 ± 0.011 eV, respectively. Analysis of spectroscopic features attributed to EuO(-) photodetachment is complicated by the likely presence of two energetically competitive electronic states of EuO(-) populating the ion beam. However, based on the calculated relative energies of the close-lying anion states arising from the 4f(7)σ(6s) and 4f(6)σ(6s)(2) configurations and the relative energies of the one-electron accessible 4f(7) and 4f(6)σ(6s) neutral states based on ligand-field theory [M. Dulick, E. Murad, and R. F. Barrow, J. Chem. Phys. 85, 385 (1986)], the remaining features are consistent with the 4f(6)σ(6s)(2) (7)Σ(-) and 4f(7)σ(6s) (7)Σ(-) anion states lying very close in energy (the former was calculated to be 0.15 eV lower in energy than the latter), though the true anion ground state and neutral EA could not be established unambiguously. Calculations on the various EuO anion and neutral states suggest 4f-orbital overlap with 2p orbitals in species with 4f(6) occupancy.

Two-dimensional photon-echo experiments indicate that excitation energy transfer between chromophores near the reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides occurs coherently with decoherence times of hundreds of femtoseconds, comparable to the energy transfer time scale in these systems. The original explanation of this observation suggested that correlated fluctuations in chromophore excitation energies, driven by large scale protein motions could result in long lived coherent energy transfer dynamics. However, no significant site energy correlation has been found in recent molecular dynamics simulations of several model light harvesting systems. Instead, there is evidence of correlated fluctuations in site energy-electronic coupling and electronic coupling-electronic coupling. The roles of these different types of correlations in excitation energy transfer dynamics are not yet thoroughly understood, though the effects of site energy correlations have been well studied. In this paper, we introduce several general models that can realistically describe the effects of various types of correlated fluctuations in chromophore properties and systematically study the behavior of these models using general methods for treating dissipative quantum dynamics in complex multi-chromophore systems. The effects of correlation between site energy and inter-site electronic couplings are explored in a two state model of excitation energy transfer between the accessory bacteriochlorophyll and bacteriopheophytin in a reaction center system and we find that these types of correlated fluctuations can enhance or suppress coherence and transfer rate simultaneously. In contrast, models for correlated fluctuations in chromophore excitation energies show enhanced coherent dynamics but necessarily show decrease in excitation energy transfer rate accompanying such coherence enhancement. Finally, for a three state model of the Fenna-Matthews-Olsen light harvesting complex, we explore the influence of including correlations in inter-chromophore couplings between different chromophore dimers that share a common chromophore. We find that the relative sign of the different correlations can have profound influence on decoherence time and energy transfer rate and can provide sensitive control of relaxation in these complex quantum dynamical open systems.

A density functional study of the effects of microhydration on the guanine-cytosine (GC) base pair and its anion radical is presented. Geometries of the GC base pair in the presence of 6 and 11 water molecules were fully optimized in the neutral (GC-nH2O) and anion radical [(GC-nH2O)*-] (n = 6 and 11) states using the B3LYP method and the 6-31+G** basis set. Further, vibrational frequency analysis at the same level of theory (B3LYP/6-31+G**) was also performed to ensure the existence of local minima in these hydrated structures. It was found that water molecules surrounding the GC base pair have significant effects on the geometry of the GC base pair and promote nonplanarity in the GC base pair. The calculated structures were found to be in good agreement with those observed experimentally and obtained in molecular dynamics (MD) simulation studies. The water molecules in neutral GC-nH2O complexes lie near the ring plane of the GC base pair where they undergo hydrogen bonding with both GC and each other. However, in the GC anion radical complexes (GC-nH2O, n = 6, 11), the water molecules are displaced substantially from the GC ring plane. For GC-11H2O*-, a water molecule is hydrogen-bonded with the C6 atom of the cytosine base. We found that the hydration shell initially destabilizes the GC base pair toward electron capture as a transient anion. Energetically unstable diffuse states in the hydration shell are suggested to provide an intermediate state for the excess electron before molecular reorganization of the water molecules and the base pair results in a stable anion formation. The singly occupied molecular orbital (SOMO) in the anion radical complexes clearly shows that an excess electron localizes into a pi orbital of cytosine. The zero-point-energy (ZPE-) corrected adiabatic electron affinities (AEAs) of the GC-6H2O and GC-11H2O complexes, at the B3LYP/6-31+G** level of theory, were found to be 0.74 and 0.95 eV, respectively. However, the incorporation of bulk water as a solvent using the polarized continuum model (PCM) increases the EAs of these complexes to 1.77 eV.

The absorption and fluorescence properties of the non-natural amino acid p-cyanophenylalanine (PheCN) were examined using high-level ab initio methods and were compared to those of natural amino acids phenylalanine and tyrosine. Single-reference and multireference methods were surveyed for their accuracy in predicting the excited state energies and transition dipole moments of the chromophores and the corresponding amino acids. The excitation energies were found to be very similar between the chromophores and the various conformers of the amino acids for all three amino acids studied here, but the transition dipole moments and consequently the radiative lifetimes were very sensitive to conformation. In agreement with experimental data, PheCN is predicted to have increased fluorescence intensity compared to phenylalanine and the amino acid group is partly responsible for this effect.KeywordsExcited statesFluorescenceAmino acidsCyanophenylalanineTyrosinePhenylalanineRadiative lifetime

We present a general framework for analyzing how molecular structure and dynamics control the effective tunneling coupling in electron transfer reactions. Using combined molecular dynamics and electronic structure calculations, we explore four principal issues that could not be quantitatively addressed at the Pathways level: sensitivity to the choice of the electronic Hamiltonian, interference among pathways, sensitivity to the electron transfer bridge conformation and modulation by the dynamical motion of the bridge. To be able to categorize the electronic orbital interactions, to identify the most relevant ones and to investigate their sensitivity to the bridge structure and dynamics, we introduce the dynamic overlap-coupling (S – H) maps. Using this framework, we identify dominant pathways mediated by these interactions and analyze the effects of the interference among them on the effective coupling. This approach provides a clear view of how the bridge structure and dynamics controls the effective coupling, allowing for a more quantitative understanding of biological ET reactions, guiding detailed calculations and de novo design of ET proteins.

Optically induced charge transfer between adsorbed molecules and a metal electrode was predicted by Hush to lead to new electronic absorption features but has not been experimentally observed. However, Gerischer characterized photocurrents arising from such absorption between adsorbed metal atoms and semiconductor conduction bands. Interfacial charge-transfer absorption (IFCTA) provides information concerning the barriers to charge transfer between molecules and the metal/semiconductor and the magnitude of the electronic coupling and could thus provide a powerful tool for understanding interfacial charge-transfer kinetics. Here we provide a framework for modeling and predicting IFCTA spectra. The key feature of optical charge transfer to or from a band of electronic levels (taken to have a constant density of states and electronic coupling element) is that the absorption probability reaches half intensity at lambda + DeltaG(theta), where lambda and DeltaG(theta) are the reorganization energy and free-energy gap for the optical charge transfer, attains >90% intensity at lambda + DeltaG(theta) + 0.9 square root[4lambdak(B)T], and remains essentially constant until the top (bottom) level of the band is attained. However, when the electronic coupling and transition moment are assumed to be independent of photon energy (Mulliken-Hush model), a peaked, highly asymmetric absorption profile is predicted. We conclude that, in general, the electronic coupling between molecular adsorbates and the metal levels is so small that absorption is not detectable, whereas for semiconductors there may be intense features involving coupling to surface states.