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.

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.

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.

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.

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.

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.

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.

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.

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.