Estimation of Electronic Coupling for Singlet Excitation Energy Transfer

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 <i>V</i> of two chromophores is expressed via the vertical excitation energies (<i>E</i>_<i>i</i> and <i>E</i>_<i>j</i>), transition dipole moments (M_<i>i</i> and M_<i>j</i>) of the system and transition moments (μ_A and μ_B) of the individual chromophores: <i>V</i> = (<i>E</i>_<i>i</i> – <i>E</i><i>_j</i>)­{[(M_<i>i</i>M_<i>j</i>)­(μ_A² – μ_B²) – (μ_Aμ_B)­(M_<i>i</i>² – M_<i>j</i>²)]/[(M_<i>i</i>² – M_<i>j</i>²)² + 4­(M_<i>i</i>M_<i>j</i>)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 <i>V</i> = (<i>E</i>_<i>i</i> – <i>E</i><i>_j</i>)­[(<i>E</i><i>_i</i><i>F</i>_<i>j</i> – <i>E</i>_<i>j</i><i>F</i><i>_i</i>)/(<i>E</i><i>_i</i><i>F</i><i>_j</i> + <i>E</i><i>_j</i><i>F</i><i>_i</i>)]­[1/(2 cos θ)] where <i>F</i>_<i>i</i> and <i>F</i>_<i>j</i> 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

Estimation of Electronic Coupling for Photoinduced Charge Separation and Charge Recombination Using the Fragment Charge Difference Method

Photoinduced electron transfer reactions play an important role in chemistry, biochemistry, and material sciences. Electronic coupling of donor and acceptor is a key parameter that controls the rate of charge separation and charge recombination processes. The fragment charge difference (FCD) method is extended to calculate the electronic couplings and diabatic energies for the photoinduced reactions. It is shown that FCD provides consistent values of the ET parameters for any 3-state model system. We compare the matrix elements obtained within the 2- and 3-state treatment for different situations and suggest how to check adiabatic states included in the diabatization procedure. Two examples demonstrate the use of the FCD method in combination with MS-CASPT2 calculations to derive the ET parameters

Distance Dependence of Triplet Energy Transfer in Water and Organic Solvents: A QM/MD Study

The possibility to optimize optoelectronic devices, such as organic light-emitting diodes or solar cells, by exploiting the special characteristics of triplet electronic states and their migration ability is attracting increased attention. In this study, we analyze how an intervening solvent modifies the distance dependence of triplet electronic energy transfer (TEET) processes by combining molecular dynamics simulations with quantum chemical calculations of the transfer matrix elements using the Fragment Excitation Difference (FED) method. We determine the β parameter characterizing the exponential distance decay of TEET rates in a stacked perylene dimer in water, chloroform, and benzene solutions. Our results indicate that the solvent dependence of β (β_vacuum = 5.14 Å^–1 > β_water = 3.77 Å^–1 > β_chloroform = 3.61 Å^–1 > β_benzene = 3.44 Å^–1) can be rationalized adopting the McConnell model of superexchange, where smaller triplet energy differences between the donor and the solvent lead to smaller β constants. We also estimate the decay of hole transfer (HT) and excess electron transfer (EET) processes in the system using the Fragment Charge Difference (FCD) method and find that β_TEET can be reasonably well approximated by the sum of β_EET and β_HT constants

Single Amino Acid Mutation Controls Hole Transfer Dynamics in DNA-Methyltransferase <i>Hha</i>I Complexes

Different mutagenic effects are generated by DNA oxidation that implies the formation of radical cation states (so-called holes) on purine nucleobases. The interaction of DNA with proteins may protect DNA from oxidative damage owing to hole transfer (HT) from the stack to aromatic amino acids. However, how protein binding affects HT dynamics in DNA is still poorly understood. Here, we report a computational study of HT in DNA complexes with methyltransferase <i>Hha</i>I with the aim of elucidating the molecular factors that explain why long-range DNA HT is inhibited when the glutamine residue inserted in the double helix is mutated into a tryptophan. We combine molecular dynamics, quantum chemistry, and kinetic Monte Carlo simulations and find that protein binding stabilizes the energies of the guanine radical cation states and significantly impacts the corresponding electronic couplings, thus determining the observed behavior, whereas the formation of a tryptophan radical leads to less efficient HT

In-silico Assessment of Protein-Protein Electron Transfer. A Case Study: Cytochrome c Peroxidase – Cytochrome c

<div><p>The fast development of software and hardware is notably helping in closing the gap between macroscopic and microscopic data. Using a novel theoretical strategy combining molecular dynamics simulations, conformational clustering, <i>ab-initio</i> quantum mechanics and electronic coupling calculations, we show how computational methodologies are mature enough to provide accurate atomistic details into the mechanism of electron transfer (ET) processes in complex protein systems, known to be a significant challenge. We performed a quantitative study of the ET between Cytochrome c Peroxidase and its redox partner Cytochrome c. Our results confirm the ET mechanism as hole transfer (HT) through residues Ala194, Ala193, Gly192 and Trp191 of CcP. Furthermore, our findings indicate the fine evolution of the enzyme to approach an elevated turnover rate of 5.47×10⁶ s⁻¹ for the ET between Cytc and CcP through establishment of a localized bridge state in Trp191.</p> </div

Average distances <i>d</i> in Å, Electronic coupling <i>rmsV</i> in eV, Δ<i>G</i>° in eV, λ in eV and in s⁻¹ calculated for HT between donor and acceptor (DA), donor and bridge (DB), and bridge and acceptor (BA), respectively.

<p>The electronic coupling is calculated applying QM setups <i>direct</i>, <i>full</i>, <i>path1</i> and <i>path2</i>. <i>k_ET</i> is calculated by Marcus theory applying the respective highest electronic coupling of the system. Fluctuations are depicted through the coherence factor given in parentheses.</p

Electron transfer region of the CcP/Cytc complex.

<p>The ET pathway proposed by Pelletier and Kraut is shown in red, the ET pathway suggested by Siddarth is shown in blue.</p

Influence of Base Stacking Geometry on the Nature of Excited States in G‑Quadruplexes: A Time-Dependent DFT Study

G-quadruplexes are four-stranded structures of nucleic acids that are formed from the association of guanine nucleobases into cyclical arrangements known as tetrads. G-quadruplexes are involved in a host of biological processes and are of interest in nanomaterial applications. However, not much is known about their electronic properties. In this paper, we analyze electronic excited states of G-quadruplexes using a combination of time-dependent DFT calculations and molecular dynamics simulations. We systematically consider experimentally observed arrangements of stacked guanine tetrads. The effects of structural features on exciton delocalization and photoinduced charge separation are explored using a quantitative analysis of the transition electron density. It is shown that collective coherent excitations shared between two guanine nucleobases dominate in the absorption spectrum of stacked G-tetrads. These excitations may also include a significant contribution of charge transfer states. Large variation in exciton localization is also observed between different structures with a general propensity toward localization between two bases. We reveal large differences in how charge separation occurs within different nucleobase arrangements, with some geometries favoring separation within a single tetrad and others favoring separation between tetrads. We also investigate the effects of the coordinating K⁺ ion located in the central cavity of G-quadruplexes on the relative excited state properties of such systems. Our results demonstrate how the nature of excited states in G-quadruplexes depends on the nucleobase stacking geometry resulting from the mutual arrangement of guanine tetrads

Conformationally Gated Charge Transfer in DNA Three-Way Junctions

Molecular structures that direct charge transport in two or three dimensions possess some of the essential functionality of electrical switches and gates. We use theory, modeling, and simulation to explore the conformational dynamics of DNA three-way junctions (TWJs) that may control the flow of charge through these structures. Molecular dynamics simulations and quantum calculations indicate that DNA TWJs undergo dynamic interconversion among “well stacked” conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes. The studies further indicate that this conformational gating would control charge flow through these TWJs, distinguishing them from conventional (larger size scale) gated devices. Simulations also find that structures with polyethylene glycol linking groups (“extenders”) lock conformations that favor CT for 25 ns or more. The simulations explain the kinetics observed experimentally in TWJs and rationalize their transport properties compared with double-stranded DNA