1 3
Top Curr Chem (Z) (2018) 376:24
introduce energy splitting in the main signal trace along Ω 1 , i.e. that associated with the fundamental S 0 → S 3–4 transitions (with S 3 and S 4 being the lowest
ππ* bright state of the two adenines, namely
1
L a ), which results in an effective
additional broadening of the GSB signals. Analogous broadening along Ω 1 is
observed in the 2DUV–Vis spectrum (Fig. 13b) for the dominant ESA signals
arising from excitations to the adenine doubly excited state (referred to as HL
2
),
lying at Ω 3 around 28,000–30,000 cm
−1
.
The solvated ApA dinucleoside is a highly flexible system, featuring conformations ranging from T-shaped to quasi-planar π-stacked, to completely unstacked
adenines along the MD trajectory. Cluster analysis has been used to group molecular conformations and select those that are most representative, a few of which are
depicted in Fig. 13c. Generally, short inter-chromophore distance in the 3.5–4.5
Å range (measured as C5–C5 distance) is associated with rotated π-stacked structures that yield substantial broadening in 2D maps along Ω 1 (i.e.
1
L a trace splitting),
while also featuring CT signals in the low-energy Vis probing window (at Ω 3 around
16,000 cm
−1
). At inter-chromophore distances of around 5 Å, the ApA structures
can be found in T-shaped conformations, usually with the amino group of one adenine pointing towards the 5-ring of the opposite adenine moiety. Generally, these
T-stacked conformations can be differentiated from the others because the presence
of ESA signals from CT states is not accompanied by broadening along Ω 1 in this
case. As expected, unstacked conformations behave as non-interacting dimeric systems, featuring dark CT states (thus not contributing to the 2DUV–Vis maps) and
ESA signals with negligible Ω 1 broadening.
Overall, these results demonstrate how 2DUV spectroscopy is theoretically
able to characterize the conformational space of a dinucleoside monophosphate by
exploiting the two-dimensional spectral resolution, representing a powerful alternative or complement to standard pump–probe experiments for elucidating the role
of structural arrangements on nucleic acid photophysics and photochemistry. However, the spectral line shapes reported in the examples above are not realistic, as
they account for only partial contributions to the spectral line broadening. Various effects (coupling to nuclear degrees of freedom, coupling to environment, finite
excited-state lifetimes) are the source of dephasing-induced broadening. In real
2D, electronic spectra broadening could obscure the spectral fingerprints predicted
by ab initio simulations. Therefore, inclusion of dynamic effects is indispensable
to move towards accurate 2DES simulation, and this is the focus of the next two
sections.
4.3 Excited‑State Coherent Vibrational Dynamics Resolved by 2DES
Real quantum systems are not closed. Upon interaction with the incident electric
field, the electron density of the molecular system rearranges instantaneously in
a new discrete quantum state. The changed electron density exerts a force on the
nuclei, which are set in motion, and vibrational dynamics is initiated. As the nuclei
are much heavier than electrons, their vibrations have vibrational periods from 10 fs
(fast hydrogen stretch vibrations) to a few hundred femtoseconds (for wagging,
93
Reprinted from the journal
Top Curr Chem (Z) (2018) 376:24
introduce energy splitting in the main signal trace along Ω 1 , i.e. that associated with the fundamental S 0 → S 3–4 transitions (with S 3 and S 4 being the lowest
ππ* bright state of the two adenines, namely
1
L a ), which results in an effective
additional broadening of the GSB signals. Analogous broadening along Ω 1 is
observed in the 2DUV–Vis spectrum (Fig. 13b) for the dominant ESA signals
arising from excitations to the adenine doubly excited state (referred to as HL
2
),
lying at Ω 3 around 28,000–30,000 cm
−1
.
The solvated ApA dinucleoside is a highly flexible system, featuring conformations ranging from T-shaped to quasi-planar π-stacked, to completely unstacked
adenines along the MD trajectory. Cluster analysis has been used to group molecular conformations and select those that are most representative, a few of which are
depicted in Fig. 13c. Generally, short inter-chromophore distance in the 3.5–4.5
Å range (measured as C5–C5 distance) is associated with rotated π-stacked structures that yield substantial broadening in 2D maps along Ω 1 (i.e.
1
L a trace splitting),
while also featuring CT signals in the low-energy Vis probing window (at Ω 3 around
16,000 cm
−1
). At inter-chromophore distances of around 5 Å, the ApA structures
can be found in T-shaped conformations, usually with the amino group of one adenine pointing towards the 5-ring of the opposite adenine moiety. Generally, these
T-stacked conformations can be differentiated from the others because the presence
of ESA signals from CT states is not accompanied by broadening along Ω 1 in this
case. As expected, unstacked conformations behave as non-interacting dimeric systems, featuring dark CT states (thus not contributing to the 2DUV–Vis maps) and
ESA signals with negligible Ω 1 broadening.
Overall, these results demonstrate how 2DUV spectroscopy is theoretically
able to characterize the conformational space of a dinucleoside monophosphate by
exploiting the two-dimensional spectral resolution, representing a powerful alternative or complement to standard pump–probe experiments for elucidating the role
of structural arrangements on nucleic acid photophysics and photochemistry. However, the spectral line shapes reported in the examples above are not realistic, as
they account for only partial contributions to the spectral line broadening. Various effects (coupling to nuclear degrees of freedom, coupling to environment, finite
excited-state lifetimes) are the source of dephasing-induced broadening. In real
2D, electronic spectra broadening could obscure the spectral fingerprints predicted
by ab initio simulations. Therefore, inclusion of dynamic effects is indispensable
to move towards accurate 2DES simulation, and this is the focus of the next two
sections.
4.3 Excited‑State Coherent Vibrational Dynamics Resolved by 2DES
Real quantum systems are not closed. Upon interaction with the incident electric
field, the electron density of the molecular system rearranges instantaneously in
a new discrete quantum state. The changed electron density exerts a force on the
nuclei, which are set in motion, and vibrational dynamics is initiated. As the nuclei
are much heavier than electrons, their vibrations have vibrational periods from 10 fs
(fast hydrogen stretch vibrations) to a few hundred femtoseconds (for wagging,
93
Reprinted from the journal