8 research outputs found
Challenges in simulating light-induced processes in DNA
© 2016 by the authors; licensee MDPI, Basel, Switzerland. In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments
Intersystem Crossing Pathways in the Noncanonical Nucleobase 2‑Thiouracil: A Time-Dependent Picture
The deactivation mechanism after
ultraviolet irradiation of 2-thiouracil
has been investigated using nonadiabatic dynamics simulations at the
MS-CASPT2 level of theory. It is found that after excitation the S<sub>2</sub> quickly relaxes to S<sub>1</sub>, and from there intersystem
crossing takes place to both T<sub>2</sub> and T<sub>1</sub> with
a time constant of 400 fs and a triplet yield above 80%, in very good
agreement with recent femtosecond experiments in solution. Both indirect
S<sub>1</sub> → T<sub>2</sub> → T<sub>1</sub> and direct
S<sub>1</sub> → T<sub>1</sub> pathways contribute to intersystem
crossing, with the former being predominant. The results contribute
to the understanding of how some noncanonical nucleobases respond
to harmful ultraviolet light, which could be relevant for prospective
photochemotherapeutic applications
A Static Picture of the Relaxation and Intersystem Crossing Mechanisms of Photoexcited 2‑Thiouracil
Accurate
excited-state quantum chemical calculations on 2-thiouracil, employing
large active spaces and up to quadruple-ζ quality basis sets
in multistate complete active space perturbation theory calculations,
are reported. The results suggest that the main relaxation path for
2-thiouracil after photoexcitation should be S<sub>2</sub> →
S<sub>1</sub> → T<sub>2</sub> → T<sub>1</sub>, and that
this relaxation occurs on a subpicosecond time scale. There are two
deactivation pathways from the initially excited bright S<sub>2</sub> state to S<sub>1</sub>, one of which is nearly barrierless and should
promote ultrafast internal conversion. After relaxation to the S<sub>1</sub> minimum, small singlet–triplet energy gaps and spin–orbit
couplings of about 130 cm<sup>–1</sup> are expected to facilitate
intersystem crossing to T<sub>2</sub>, from where very fast internal
conversion to T<sub>1</sub> occurs. An important finding is that 2-thiouracil
shows strong pyramidalization at the carbon atom of the thiocarbonyl
group in several excited states
Cyclobutane Thymine Photodimerization Mechanism Revealed by Nonadiabatic Molecular Dynamics
The formation of
cyclobutane thymine dimers is one of the most
important DNA carcinogenic photolesions induced by ultraviolet irradiation.
The long debated question whether thymine dimerization after direct
light excitation involves singlet or triplet states is investigated
here for the first time using nonadiabatic molecular dynamics simulations.
We find that the precursor of this [2 + 2] cycloaddition reaction
is the singlet doubly π<sup>2</sup>π*<sup>2</sup> excited
state, which is spectroscopically rather dark. Excitation to the bright <sup>1</sup>ππ* or dark <sup>1</sup>nπ* excited states
does not lead to thymine dimer formation. In all cases, intersystem
crossing to the triplet states is not observed during the simulated
time, indicating that ultrafast dimerization occurs in the singlet
manifold. The dynamics simulations also show that dimerization takes
place only when conformational control happens in the doubly excited
state
Femtosecond Intersystem Crossing in the DNA Nucleobase Cytosine
Ab initio molecular dynamics including nonadiabatic and
spin–orbit
couplings on equal footing is used to unravel the deactivation of
cytosine after UV light absorption. Intersystem crossing (ISC) is
found to compete directly with internal conversion in tens of femtoseconds,
thus making cytosine the organic compound with the fastest triplet
population calculated so far. It is found that close degeneracy between
singlet and triplet states can more than compensate for very small
spin–orbit couplings, leading to efficient ISC. The femtosecond
nature of the ISC process highlights its importance in photochemistry
and challenges the conventional view that large singlet–triplet
couplings are required for an efficient population flow into triplet
states. These findings are important to understand DNA photostability
and the photochemistry and dynamics of organic molecules in general
Solvatochromic Effects on the Absorption Spectrum of 2‑Thiocytosine
The
solvatochromic effects of six different solvents on the UV
absorption spectrum of 2-thiocytosine have been studied by a combination
of experimental and theoretical techniques. The steady-state absorption
spectra show significant shifts of the absorption bands, where in
more polar solvents the first absorption maximum shifts to higher
transition energies and the second maximum to lower energies. The
observed solvatochromic shifts have been rationalized using three
popular solvatochromic scales and with high-level multireference quantum
chemistry calculations including implicit and explicit solvent effects.
It has been found that the dipole moments of the excited states account
for some general shifts in the excitation energies, whereas the explicit
solvent interactions explain the differences in the spectra recorded
in the different solvents
Efficient and Flexible Computation of Many-Electron Wave Function Overlaps
A new algorithm for the computation
of the overlap between many-electron
wave functions is described. This algorithm allows for the extensive
use of recurring intermediates and thus provides high computational
efficiency. Because of the general formalism employed, overlaps can
be computed for varying wave function types, molecular orbitals, basis
sets, and molecular geometries. This paves the way for efficiently
computing nonadiabatic interaction terms for dynamics simulations.
In addition, other application areas can be envisaged, such as the
comparison of wave functions constructed at different levels of theory.
Aside from explaining the algorithm and evaluating the performance,
a detailed analysis of the numerical stability of wave function overlaps
is carried out, and strategies for overcoming potential severe pitfalls
due to displaced atoms and truncated wave functions are presented
OpenMolcas: From source code to insight
In this article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already
includes a large number of new developments realized during the transition from
the commercial MOLCAS product to the open-source platform. The paper initially
describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features
of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density
matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations
include an array of additional options and functionalities. The paper proceeds and
describes developments related to explorations of potential energy surfaces. Here
we present methods for the optimization of conical intersections, the simulation of
adiabatic and nonadiabatic molecular dynamics and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the article describes
features unique to simulations of spectroscopic and magnetic phenomena such as
the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism and properties. Finally, the paper
describes a number of built-in and add-on features to support the OpenMolcas platform with post calculation analysis and visualization, a multiscale simulation option
using frozen-density embedding theory and new electronic and muonic basis sets