Benchmarking Quantum Mechanical Methods for the Description of Charge-Transfer States in π-Stacked Nucleobases.

Charge-transfer (CT) states are of special interest in photochemical research because they can facilitate chemical reactions through the rearrangement of electrons and subsequently chemical bonds in a molecular system. Of particular importance to this research is the transfer of electrons between π-stacked nucleobases in DNA because they play an important role in its photophysics and photochemistry. Computational methods are paramount for the study of CT states because of the current inability of experimental methods to easily detect such states. However, many ab-initio wavefunction-based and density functional theory (DFT) methods fail to accurately describe these CT states. Here, we benchmark how 40 different quantum mechanical methods describe the excited states of a guanine-thymine π-stacked nucleobase dimer system, both in 5'-TG-3' and 5'-GT-3' conformations. We find that the distance between the nucleobases plays a major role in the energy of the CT state and in the difference of the dipole moments between the CT and ground state. There is a larger range of values (and errors) for the energies of CT states compared to those of states localized on one nucleobase. Wavefunction-based methods have similar errors for the CT and localized valence states, while DFT methods are very sensitive to the amount of Hartree-Fock exchange. Long-range-corrected functionals with a careful balance of the Hartree-Fock exchange included can predict very accurate CT states and a balanced description with the localized states.

Plasmon damping depends on the chemical nature of the nanoparticle interface.

The chemical nature of surface adsorbates affects the localized surface plasmon resonance of metal nanoparticles. However, classical electromagnetic simulations are blind to this effect, whereas experiments are typically plagued by ensemble averaging that also includes size and shape variations. In this work, we are able to isolate the contribution of surface adsorbates to the plasmon resonance by carefully selecting adsorbate isomers, using single-particle spectroscopy to obtain homogeneous linewidths, and comparing experimental results to high-level quantum mechanical calculations based on embedded correlated wavefunction theory. Our approach allows us to indisputably show that nanoparticle plasmons are influenced by the chemical nature of the adsorbates 1,7-dicarbadodecaborane(12)-1-thiol (M1) and 1,7-dicarbadodecaborane(12)-9-thiol (M9). These surface adsorbates induce inside the metal electric dipoles that act as additional scattering centers for plasmon dephasing. In contrast, charge transfer from the plasmon to adsorbates-the most widely suggested mechanism to date-does not play a role here.

Mechanistic Insights into Photocatalyzed Hydrogen Desorption from Palladium Surfaces Assisted by Localized Surface Plasmon Resonances.

Nanoparticles synthesized from plasmonic metals can absorb low-energy light, producing an oscillation/excitation of their valence electron density that can be utilized in chemical conversions. For example, heterogeneous photocatalysis can be achieved within heterometallic antenna-reactor complexes (HMARCs), by coupling a reactive center at which a chemical reaction occurs to a plasmonic nanoparticle that acts as a light-absorbing antenna. For example, HMARCs composed of aluminum antennae and palladium (Pd) reactive centers have been demonstrated recently to catalyze selective hydrogenation of acetylene to ethylene. Here, we explore within a theoretical framework the rate-limiting step of hydrogen photodesorption from a Pd surface-crucial to achieving partial rather than full hydrogenation of acetylene-to understand the mechanism behind the photodesorption process within the HMARC assembly. To properly describe electronic excited states of the metal-molecule system, we employ embedded complete active space self-consistent field and n-electron valence state perturbation theory to second order within density functional embedding theory. The results of these calculations reveal that the photodesorption mechanism does not create a frequently invoked transient negative ion species but instead enhances population of available excited-state, low-barrier pathways that exhibit negligible charge-transfer character.

Substituent Effects on the Absorption and Fluorescence Properties of Anthracene.

Substitution can be used to efficiently tune the photophysical properties of chromophores. In this study, we examine the effect of substituents on the absorption and fluorescence properties of anthracene. The effects of mono-, di-, and tetrasubstitution of electron-donating and -withdrawing functional groups were explored. In addition, the influence of a donor-acceptor substituent pair and the position of substitution were investigated. Eleven functional groups were varied on positions 1, 2, and 9 of anthracene, and on position 6 of 2-methoxyanthracene and 2-carboxyanthracene. Moreover, the donor-acceptor pair NH2/CO2H was added on different positions of anthracene for additional studies of doubly substituted anthracenes. Finally, we looked into quadruple substitutions on positions 1,4,5,8 and 2,3,6,7. Vertical excitation energies and oscillator strengths were computed using density functional theory with the hybrid CAM-B3LYP functional and 6-311G(d) basis set. Correlations between the excitation energies or oscillator strengths of the low-lying bright La state and the Hammett sigma parameter, σp+, of the substituents were examined. The energy is red-shifted for all cases of substitution. Oscillator strengths increase when substituents are placed along the direction of the transition dipole moment of the bright La excited state. Substitution of long chain conjugated groups significantly increases the oscillator strength in comparison to the cases for other substituents. In addition, the results of quadruply substituted geometries reveal symmetric substitution at the 1,4,5,8 positions significantly increases the oscillator strength and can lower the band gap compared to that of the unsubstituted anthracene molecule by up to 0.5 eV.

Photophysical properties of pyrrolocytosine, a cytosine fluorescent base analogue.

The photophysical behavior of pyrrolocytosine (PC), a fluorescent base analogue of cytosine, has been investigated using theoretical approaches. The similarities between the PC and cytosine structures allow PC to maintain the pseudo-Watson-Crick base-pairing arrangement with guanine. Cytosine, similar to the other natural nucleobases, is practically non-fluorescent, because of ultrafast radiationless decay occurring through conical intersections. PC displays a much higher fluorescence quantum yield than cytosine, making it an effective fluorescent marker to study the structure, function, and dynamics of DNA/RNA complexes. Similar to 2-aminopurine, a constitutional isomer of adenine that base-pairs with thymine, PC's fluorescence is quenched when it is incorporated into a dinucleotide or a trinucleotide. In this work we examine the photophysical properties of isolated PC, microhydrated PC, as well as, complexes where PC is either base-stacked or hydrogen-bonded with guanine. Our results indicate that hydration affects the radiationless decay pathways in PC by destabilizing conical intersections. The calculations of dimers and trimers show that the radiative decay is affected by π stacking, while the presence of charge transfer states between PC and guanine may contribute to radiationless decay.

Excimers and Exciplexes in Photoinitiated Processes of Oligonucleotides.

A lot has been learned about the physical and chemical transformations that originate from the absorption of light by DNA, and computational chemistry has played a critical role in revealing the mechanisms of how these transformations occur. Nucleic acids consist of chromophores interacting via π stacking and hydrogen bonding. The fate of these systems after they absorb light is determined by the interplay and competition between pathways involving one chromophore or interacting chromophores. This Perspective highlights the role of π stacking in photophysical and photochemical processes in oligonucleotides and reveals the importance of excimers and exciplexes. Special types of excimers/exciplexes, characterized as bonded excimers/exciplexes, are also found to be important.

Photophysical deactivation pathways in adenine oligonucleotides.

In this work we study deactivation processes in adenine oligomers after absorption of UV radiation using Quantum Mechanics combined with Molecular Mechanics (QM/MM). Correlated electronic structure methods appropriate for describing the excited states are used to describe a π-stacked dimer of adenine bases incorporated into (dA)20(dT)20. The results of these calculations reveal three different types of excited state minima which play a role in deactivation processes. Within this set of minima there are minima where the excited state is localized on one adenine (monomer-like) as well as minima where the excited state is delocalized on two adenines, forming different types of excimers and bonded excimers of varying but inter-related character. The proximity of their energies reveals that the minima can decay into one another along a flat potential energy surface dependent on the interbase separation. Additionally, analysis of the emissive energies and other physical properties, including theoretical anisotropy calculations, and comparison with fluorescence experiments, provides evidence that excimers play an important role in long-lived signals in adenine oligonucleotides while the subpicosecond decay is attributed to monomer-like minima. The necessity for a close approach of the nucleobases reveals that the deactivation mechanism is tied to macro-molecular motion.

Role of excitonic coupling and charge-transfer states in the absorption and CD spectra of adenine-based oligonucleotides investigated through QM/MM simulations.

In this work, we study the photophysical properties of an adenine-based oligonucleotide using an ensemble of about 200 configurations obtained from molecular dynamics simulations. Specifically, a QM/MM approach is used to obtain the excited-state energies and properties of (dA)20(dT)20 with a dimer of π-stacked adenine bases included in the quantum region. The absorption and circular dichroism spectra are computed and analyzed using the algebraic diagrammatic construction through second order level of theory method (ADC(2)) combined with classical mechanics. We find that the experimentally observed red-shifted shoulder in the absorption spectrum is due to excitonic interactions, while charge-transfer states are present within the absorption band at the higher-energy end of the spectrum. More importantly, low-energy states with charge-transfer mixing exist, which could lead to excimers and bonded excimers. These observations suggest that mixing between charge-transfer and excitonic states plays an important role in the photophysics of oligonucleotides. They also highlight the importance of taking into account the conformational flexibility of the oligonucleotide when investigating photophysical properties.

Bonded excimer formation in π-stacked 9-methyladenine dimers.

The interaction of DNA with UV radiation is an area of intense interest not only because of its biological implications but also because of the complicated excited state dynamics. To channel the excess energy associated with the absorption of UV radiation, the nucleobases undergo ultrafast nonradiative decay facilitated by conical intersections. In this work we extend the role of conical intersections in π-stacked dimers of nucleobases. We present a novel conical intersection between the excited state and the ground state for a π-stacked 9-methyladenine homodimer system, where a bond is partially formed between the two bases, and the wave function shows charge-transfer character between the monomers. These characteristics lead us to assign this state to a bonded excimer, a model that has been proposed in the past to explain the observed electron transfer in systems where this process is not thermodynamically favored. Gas-phase excited state calculations are carried out using perturbation theory corrected configuration interaction singles methods and complete active space self-consistent field, and physical observables are calculated and analyzed to understand the behavior of the system. A polarizable continuum solvent model is used to test the changes of the energies of the excited states along the pathway subject to solvation and reveals small changes in aqueous solution. Molecular dynamics simulations have also been performed on a poly(dA)20·(dT)20 B-DNA strand to find how the backbone affects the proximity of the bases which can facilitate access to the conical intersection.