Spiridoula Matsika

Nonadiabatic Events and Conical Intersections

Nonadiabatic events, in which the Born-Oppenheimer approximation breaks down, are ubiquitous in chemistry and biology. It is now widely accepted that they are facilitated by conical intersections (CIs), actual degeneracies between electronic states. We review the basic theory of CIs and how they can be studied using modern quantum chemistry and nuclear dynamics. We highlight their importance by presenting their role in radiationless decay pathways present in the building blocks of DNA and proteins. The presence of CIs may contribute to the photostability of these important biomolecules.

Three-state conical intersections in cytosine and pyrimidinone bases

Three-state conical intersections have been located and characterized for cytosine and its analog 5-methyl-2-pyrimidinone using multireference configuration-interaction ab initio methods. The potential energy surfaces for each base contain three different three-state intersections: two different S(0)-S(1)-S(2) intersections (gs/pi pi(*)/n(N)pi(*) and gs/pi pi(*)/n(O)pi(*)) and an S(1)-S(2)-S(3) intersection (pi pi(*)/n(N)pi(*)/n(O)pi(*)). Two-state seam paths from these intersections are shown to be connected to previously reported two-state conical intersections. Nonadiabatic coupling terms have been calculated, and the effects of the proximal third state on these quantities are detailed. In particular, it is shown that when one of these loops incorporates more than one seam point, there is a profound and predictable effect on the phase of the nonadiabatic coupling terms, and as such provides a diagnostic for the presence and location of additional seams. In addition, it is shown that each of the three three-state conical intersections located on cytosine and 5-methyl-2-pyrimidinone is qualitatively similar between the two bases in terms of energies and character, implying that, like with the stationary points and two-state conical intersections previously reported for these two bases, there is an underlying pattern of energy surfaces for 2-pyrimidinone bases, in general, and this pattern also includes three-state conical intersections.

Two-Dimensional Ultrafast Fourier Transform Spectroscopy in the Deep Ultraviolet

We demonstrate two-dimensional ultrafast fourier transform spectroscopy in the deep ultraviolet (approximately 260 nm) using an acousto-optic modulator based pulse shaper. The use of a pulse shaper in the ultraviolet allows for rapid scanning, high phase (time) stability (approximately 0.017 rad) and phase cycling. We present measurements on the DNA nucleobase Adenine.

Absorption, circular dichroism, and photoluminescence in perylene diimide bichromophores: polarization-dependent H- and J-aggregate behavior.

Using a single-mode Holstein Hamiltonian with through-space excitonic couplings evaluated quantum mechanically, the absorption, circular dichroism, and photoluminescence spectral line shapes of a chiral perylene diimide dimer complex were accurately reproduced. In general, a dimer consisting of two chromophores related through a C(2) rotation is neither a J- nor an H-aggregate because oscillator strength is divided between the top and bottom of the exciton band. The division gives rise to the two Davydov components per vibronic band in the absorption spectrum. Nevertheless, it is shown that the vibronic structure of the absorption component polarized in the same direction as the lower (upper) Davydov component is identical to what one would obtain from an ideal J- (H-) aggregate. Emission generally contains both polarization components, but the component polarized in the same direction as the lower (upper) Davydov component behaves similarly to the emission from an ideal J- (H-) aggregate. The basic photophysical behavior also applies to molecular crystals containing two molecules per unit cell in which the interactions between inequivalent molecules dominate over interactions between equivalent molecules.

Accidental conical intersections of three states of the same symmetry. I. Location and relevance

An efficient algorithm for locating conical intersections of three states of the same symmetry is presented. The algorithm, which derives its efficiency from the use of analytic gradient techniques, is used to locate a three state intersection for the excited 3p Rydberg states of the ethyl radical. The existence of a seam of three state conical intersections in a 3p Rydberg manifold is expected to be a general occurrence.

Solvatochromic Shifts of Uracil and Cytosine Using a Combined Multireference Configuration Interaction/Molecular Dynamics Approach and the Fragment Molecular Orbital Method†

A recently developed combined quantum mechanics/molecular mechanics (QM/MM) approach has been applied to the calculation of solvatochromic shifts of the excited states of the pyrimidine nucleobases uracil and cytosine in aqueous solution. In this procedure the quantum mechanical solute is described using a multireference configuration interaction method while molecular dynamics simulations are used to obtain the structure of the solvent around the solute. The fragment molecular orbital multiconfiguration self-consistent field (FMO-MCSCF) method of Fedorov and Kitaura is also used and compared with the QM/MM results. The two methods give similar results. The solvatochromic shifts in uracil are found to be +0.41 (+0.44) eV for the S(1) excited state and -0.05 (-0.19) eV for the S(2) state at the QM/MM (FMO-MCSCF) level. Solvatochromic shifts in cytosine are calculated to be +0.25 (+0.19), +0.56 (+0.62), and +0.83 (+0.83) eV for the S(1), S(2), and S(3) states, respectively, at the QM/MM (FMO-MCSCF) level.

Closed-loop learning control of isomerization using shaped ultrafast laser pulses in the deep ultraviolet

We demonstrate the use of shaped ultrafast laser pulses in the deep ultraviolet to control the ring opening isomerization of 1,3-cyclohexadiene to form 1,3,5-hexatriene. The experiments are performed with a gas phase sample and the isomerization yield is probed with dissociative ionization driven by a time-delayed, intense infrared laser pulse. Differences in the electronic structure of the ions for the two isomers, as shown by ab initio calculations, result in very different fragmentation products following strong-field ionization. We find that a shaped pulse yields a approximately 37% increase in the isomerization over an unshaped laser pulse.

Excited-State Energies and Electronic Couplings of DNA Base Dimers

The singlet excited electronic states of two pi-stacked thymine molecules and their splittings due to electronic coupling have been investigated with a variety of computational methods. Focus has been given on the effect of intermolecular distance on these energies and couplings. Single-reference methods, CIS, CIS(2), EOM-CCSD, TDDFT, and the multireference method CASSCF, have been used, and their performance has been compared. It is found that the excited-state energies are very sensitive to the applied method but the couplings are not as sensitive. Inclusion of diffuse functions in the basis set also affects the excitation energies significantly but not the couplings. TDDFT is inadequate in describing the states and their coupling, while CIS(2) gives results very similar to EOM-CCSD. Excited states of cytosine and adenine pi-stacked dimers were also obtained and compared with those of thymine dimers to gain a more general picture of excited states in pi-stacked DNA base dimers. The coupling is very sensitive to the relative position and orientation of the bases, indicating great variation in the degree of delocalization of the excited states between stacked bases in natural DNA as it fluctuates.

What We Can Learn from the Norms of One-Particle Density Matrices, and What We Can't: Some Results for Interstate Properties in Model Singlet Fission Systems

The utility of the norms of one-particle density matrices, ∥γ∥, for understanding the trends in electronic properties is discussed. Using several model systems that are relevant in the context of singlet fission (butadiene, octatetraene, and ethylene dimer), the dependence of interstate properties (such as transition dipole moments and nonadiabatic couplings, NACs) on molecular geometries is investigated. ∥γ∥ contains the principal information about the changes in electronic states involved, such as varying degree of one-electron character of the transition; thus, it captures leading trends in one-electron interstate properties (i.e., when ∥γ∥ is small, the respective interstate matrix elements are also small). However, finer variations in properties that arise due to the dependence of the matrix elements of the respective operators may not be reproduced. Analysis of NACs in ethylene dimer reveals that intermolecular components of NACs follow the trends in ∥γ∥ well, as they are determined primarily by the characters of the two wave functions; however, intramolecular components depend on the relative orientation of the two moieties via the dependence in the derivative of the electron-nuclear Coulomb operator. Therefore, intramolecular NACs may exhibit large variations even when the changes in ∥γ∥ are small. We observe large NACs at perfectly stacked geometry; however, larger values (by a factor of 1.6) are observed at slip-stacked (along the long axis) geometries. Larger values of NACs at slip-stacked configurations are due to the breaking of symmetry of the local environment of the heavy atoms and not due to the wave function composition. We found that the variations in ∥γ∥ for ethylene dimer are due to a varying admixture of the charge-resonance configurations in the S1 state, whereas the (1)ME state retains its pure multiexciton character.

Two-Dimensional Fourier Transform Spectroscopy of Adenine and Uracil Using Shaped Ultrafast Laser Pulses in the Deep UV

We compare two-dimensional (2D) ultrafast Fourier transform spectroscopy measurements in the deep UV (262 nm) for adenine and uracil in solution. Both molecules show excited-state absorption on short time scales and ground-state bleaching extending for over 1 ps. While the 2D spectrum for uracil shows changes in the center of gravity during the first few hundred femtoseconds, the center of gravity of the 2D spectrum for adenine does not show similar changes. We discuss our results in light of ab initio electronic structure calculations.