Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

Fullerene dimerization inside a peapod is analyzed at DFT level by characterizing the stationary points and deriving the energy profile of the initial and reversible process named phase 1. We find that the barriers for the radical cation mechanism are significantly lower than those found for the neutral pathway. The peapod is mainly providing one-dimensional confinement for the reaction to take place in a more efficient way. Car-Parrinello metadynamics simulations provide hints on structures for the initial steps of the irreversible phase 2 where bond formation and breaking lead to important structural reorganizations within the coalescence process.

Ionization and electron excitation of C60 in a carbon nanotube: A variable temperature/voltage transmission electron microscopic study

The destruction of specimen molecules by an electron beam (e-beam) is either beneficial, as in mass spectrometry capitalizing on ion formation, or deleterious, as in electron microscopy. In the latter application, the e-beam not only produces the specimen image, but also causes information loss upon prolonged irradiation. However, the atomistic mechanism of such loss has been unclear. Performing single-molecule kinetic analysis of C₆₀ dimerization in a carbon nanotube (CNT) under variable-temperature/voltage conditions, we identified three reactive species—that is, radical cation, singlet, and triplet excited states—reacting competitively as the voltage and the properties of the CNT were changed. The key enabler was in situ continuous recording of the whole reaction process, suggesting an upcoming new era of “cinematic chemistry.”

There is increasing attention to chemical applications of transmission electron microscopy, which is often plagued by radiation damage. The damage in organic matter predominantly occurs via radiolysis. Although radiolysis is highly important, previous studies on radiolysis have largely been descriptive and qualitative, lacking in such fundamental information as the product structure, the influence of the energy of the electrons, and the reaction kinetics. We need a chemically well-defined system to obtain such data and have chosen as a model a variable-temperature and variable-voltage (VT/VV) study of the [2 + 2] dimerization of a van der Waals dimer [60]fullerene (C₆₀) to C₁₂₀ in a carbon nanotube (CNT), as studied for several hundred individual reaction events at atomic resolution. We report here the identification of five reaction pathways that serve as mechanistic models of radiolysis damage. Two of them occur via a radical cation of the specimen generated by specimen ionization, and three involve singlet or triplet excited states of the specimen, as initiated by electron excitation of the CNT, followed by energy transfer to the specimen. The [2 + 2] product was identified by measuring the distance between the two C₆₀ moieties, and the mechanisms were distinguished by the pre-exponential factor and the Arrhenius activation energy—the standard protocol of chemical kinetic studies. The results illustrate the importance of VT/VV kinetic analysis in the studies of radiation damage and show that chemical ionization and electron excitation are inseparable, but different, mechanisms of radiation damage, which has so far been classified loosely under the single term “ionization.”

Direct Microscopic Analysis of Individual C60 Dimerization Events: Kinetics and Mechanisms

Modern transition state theory states that the statistical behavior of a chemical reaction is the sum of individual chemical events that occur randomly. Statistical analysis of each event for individual molecules in a three-dimensional space however is practically impossible. We report here that kinetics and mechanisms of chemical reactions can be investigated by using a one-dimensional system where reaction events can be observed in situ and counted one by one using variable-temperature (VT) atomic-resolution transmission electron microscopy (TEM). We thereby provide direct proof that the ensemble behavior of random events conforms to the Rice-Ramsperger-Kassel-Marcus theory, as illustrated for [2 + 2] cycloaddition of C₆₀ molecules in carbon nanotubes (CNTs). This method gives kinetic and structural information for different types of reactions occurring simultaneously in the microscopic view field, suggesting that the VT-TEM opens a new dimension of chemical kinetics research on molecules and their assemblies in their excited and ionized states. The study carried out at 393-493 K showed that pristine CNT primarily acts as a singlet sensitizer of the cycloaddition reaction that takes place with an activation energy of 33.5 ± 6.8 kJ/mol. On the other hand, CNT suffers electron damage of the conjugated system at 103-203 K and promotes a reactive radical cation path that takes place with an activation energy of only 1.9 ± 0.7 kJ/mol. The pre-exponential factor of the Arrhenius plot gave us further mechanistic insights.

Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer

The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules.

Slow Relaxation of Surface Plasmon Excitations in Au55: The Key to Efficient Plasmonic Heating in Au/TiO2

Gold nanoparticles distinguish themselves from other nanoparticles due to their unique surface plasmon resonance properties that can be exploited for a multiplicity of applications. The promise of plasmonic heating in systems of Au nanoparticles on transition metal oxide supports, for example, Au/TiO2, rests with the ability of the surface plasmon in Au nanoparticles to effectively transfer energy into the transition metal oxide. Here, we report a critical observation regarding Au nanoparticle (Au55) surface plasmon excitations, that is, the relaxation of the surface plasmon excitation is very slow, on the order of several picoseconds. Starting from five plasmon states in Au55 nanoparticles using nonadiabatic molecular dynamics simulations, we find that the relaxation time constant resulting from these simulations is ∼6.8 ps, mainly resulting from a long-lived intermediate state found at around -0.8 eV. This long-lived intermediate state aligns with the conduction band edge of TiO2, thereby facilitating energy transfer injection from the Au55 nanoparticle into the TiO2. The current results rule out the previously reported molecular-like relaxation dynamics for Au55.