Computational mechanistic photochemistry: The central role of conical intersections

Abstract

In this thesis, I review my own contributions in the field of computational photochemistry. This manuscript is written as an introduction to this field of research. It is not intended to be a textbook, as more emphasis has been made on illustrations rather than on methodologies and technical guidelines. In this way, I hope that it will be accessible to a large audience, from undergraduate students to more experienced scientists who would be interested in learning about this fascinating and relatively young field of research.

Full text

Computational mechanistic photochemistry: The central
role of conical intersections
Martial Boggio-Pasqua
To cite this version:
Martial Boggio-Pasqua. Computational mechanistic photochemistry: The central role of conical
intersections. Theoretical and/or physical chemistry. Universit´e Toulouse III, 2015. <tel-
01184241>
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Manuscrit
en vue de la soutenance de
l’Habilitation à Diriger les Recherches
par
Martial BOGGIO-PASQUA
Computational mechanistic photochemistry:
The central role of conical intersections
Soutenue le 22 Juillet 2015
JURY
Pr. Maurizio PERSICO Professeur, Université de Pise Rapporteur
Pr. Nicolas FERRÉ Professeur, Université d’Aix-Marseille Rapporteur
Dr. Daniel BORGIS Directeur de recherche, ENS Paris Rapporteur
Pr. Isabelle DEMACHY Professeur, Université Paris Sud Examinateur
Dr. Thomas GUSTAVSSON Directeur de recherche, CEA-Saclay Examinateur
Pr. Fabienne ALARY Professeur, Université Toulouse III Présidente
Ecole doctorale : Sciences de la Matière
Unité de Recherche : Laboratoire de Chimie et Physique Quantiques (UMR 5626)

Foreword
1. Introduction p. 7
1.1. Computational mechanistic photochemistry
1.2. Role of conical intersections
2. Conical intersections and associated crossing seams p. 10
2.1. Introduction to the theoretical concept of conical intersections
2.2. Topological features
2.3. The important coordinates in photochemistry
3. Mechanistic photochemistry: theoretical aspects p. 15
3.1. Determination of potential energy surfaces and reaction pathways
3.1.1. Electronic structure methods
3.1.2. Photochemical reaction path
3.2. Excited-state molecular dynamics
4. Applications: from organic photochemistry to photobiochemistry and inorganic
photochemistry p. 24
4.1. Organic photochemistry
4.1.1. Photostability of polycyclic aromatic hydrocarbons
4.1.2. Photochromic systems
4.1.3. Intramolecular charge transfer
4.2. Photobiochemistry
4.2.1. Photostability and photodamage in DNA
4.2.2. Photoisomerizations in proteins
4.3. Inorganic photochemistry
4.3.1. Photophysical properties of ruthenium complexes
4.3.2. Photochromic ruthenium complexes
5. Perspectives p. 57
5.1. Electronic energy transfer
5.2. Photoswitchable systems
5.2.1. Organic photoswitches
5.2.2. Reversibly switchable fluorescent proteins
5.2.3. Inorganic photochromes
5.2.4. Hybrid photochromes
5.3. SOC nonadiabatic dynamics in transition metal complexes

6. Conclusion p. 63
7. References p. 64
8. Curriculum Vitæ p. 75

Foreword
This manuscript is written as an introduction to the field of computational photochemistry. It is not
intended to be a textbook, as more emphasis has been made on illustrations rather than on
methodologies and technical guidelines. In this way, I hope that it will be accessible to a large
audience, from undergraduate students to more experienced scientists who would be interested in
learning about this fascinating and relatively young field of research.
This manuscript would have never appeared without many of the people I had the chance to study
or work with along these last twenty years or so. First, I would like to thank Prof. Jean-Claude Rayez
who taught me quantum chemistry and transmitted his passion to me. I am indebted to Prof. Mike
Robb and Dr. Mike Bearpark for all the knowledge they have imparted to me on computational
photochemistry and for their support during my scientific career as a post-doctoral researcher. A large
part of this manuscript is devoted to the work we have done together. My collaborator, Dr. Gerrit
Groenhof, also played a critical role in some of the most successful stories I am presenting in this
report. I would also like to thank Prof. Fabienne Alary and Dr. Jean-Louis Heully for giving me the
opportunity to work in their team, for sharing their passion of theoretical chemistry with me and for
their support during the writing of this manuscript.
Finally, I would like to dedicate this manuscript to my wife, Marjorie. Her support is a great
source of motivation for me, and our two children, Lina (4 years old) and Timéo (2 years old) are a
source of joy.

7
1. Introduction
In the past three decades or so, computational photochemistry has gained considerable credit as a
tool to investigate photochemical reaction mechanisms in organic, inorganic and even biological
chromophores.1 This reputation has been gained thanks to the concomitant growing of computational
power and theoretical developments in the field of quantum chemistry. These advances allow peering
beyond the traditional interpretations of photochemistry focused on vertical excitations at the Franck–
Condon geometry. The exploration of other regions of the complex multidimensional potential energy
surfaces is becoming routine, and the synergy between accurate and global static calculations and
either quantum or semiclassical nonadiabatic molecular dynamics simulations has allowed major
breakthroughs in the understanding of photochemical and photophysical processes. Nowadays,
computational investigations of photochemical processes such as photoisomerization, photoinduced
electron transfer, photosensitization and photodissociation have become a standard practice.
While standard state-of-the-art ab initio quantum chemical methods are already capable of
providing a complete description of what happens at the molecular level during bond-breaking and
bond-forming processes in thermal reactions, the task is much more challenging when contemplating
photochemical reactions. The main reasons are as follows: i) the description of electronic excited
states can become very difficult because of their usual multiconfigurational character, ii) the reaction
path cannot be described by a single potential energy surface, but rather two branches at least are
required: one located on an excited state (reactant side) and the other located on the ground-state
potential energy surface (product side), and iii) the Born-Oppenheimer approximation breaks down in
the ‘funnel’ region where the excited-state reactant or intermediate is delivered to the ground state.
The main difficulty associated with computations of photochemical processes lies in the correct
description and practical computation of this ‘funnel’ region. Computational tools have been
developed and strategies discovered to explore electronically excited-state reaction paths involving so-
called conical intersections, which act as funnels for efficient radiationless electronic transitions. The
goal of such computational approaches in the study of photochemical mechanisms is the complete
description of what happens at the molecular level from photonic energy absorption to product
formation.
In this manuscript, I will review my own contributions in this fascinating field of research. I will
start by giving a short introduction on what is called computational mechanistic photochemistry and
the central role played by conical intersections. Then I will review the basic concepts and
computational strategy, which permit such investigations. Next I will give some illustrations based on
the most interesting systems I had the chance to study. These include the study of organic and
inorganic photochromic systems, the photoisomerization of a protein, the photostability of polycyclic
aromatic hydrocarbons, photoinduced intramolecular charge transfer in donor-acceptor systems, and
photoinduced proton-coupled electron transfer in biological systems. Finally, I will present some
perspectives of future work.
1.1. Computational mechanistic photochemistry
The terminology computational mechanistic photochemistry is used in the present manuscript to
designate theoretical studies aimed at understanding excited-state mechanisms involved in
photochemical processes. The term photochemistry (or photochemical processes) is used here in the

8
broadest sense, i.e. it also includes photophysical processes such as nonradiative decay back to the
original ground state (photostability) and radiative emission (photoluminescence). To understand the
fate of a molecular system after photoexcitation, it is not only necessary to understand the excited-
state properties of the molecule but also to determine how the system will evolve chemically in terms
of bond making and bond breaking in these excited states. Thus, it is crucial to understand the reaction
pathway describing the passage from the ground-state reactants to the final photoproducts evolving
along the potential energy surfaces (PESs) of the photochemically relevant electronic states. This
reaction path is called photochemical reaction path or photochemical pathway. As explained in more
details later (see section 3.1.2), the photochemical pathway is determined by following the detailed
relaxation and reaction paths of the molecule along the relevant potential energy surfaces from the
Franck-Condon (FC) point (i.e., vertically excited geometry) to the ground state. Static calculations
are performed to investigate the topology of the PESs. It requires finding all the relevant critical
structures (minima, saddle points, barriers, surface crossings) involved along the reaction path and
understanding how all these critical points are interconnected on the PESs. This interconnection is
often determined by minimum energy path (MEP) calculations. Once the potential energy landscape
for all the relevant electronic states is understood, very detailed mechanistic information can be
derived on the photochemistry of the system. To give an illustration, we show in Figure 1 the
mechanistic picture first derived more than twenty years ago on benzene photochemistry.2 With this
information in hand, one can interpret the experimental data regarding the competition between
fluorescence and benzene to benzvalene photoisomerization depending on the photoexcitation
wavelength.
The information obtained from this static approach is mainly structural, i.e. the calculated path
describes the motion of a vibrationally cold molecule moving with infinitesimal momenta. While this
path does not represent any real trajectory, it allows for a qualitative understanding of different
Figure 1. Schematic S0 and S1 potential energy landscapes along the benzene →
benzvalene
photochemical pathway. Red arrows show photon absorption followed by fluorescence. Blue arrows
show photon absorption of higher energy followed by photoproduct formation.

9
experimental data such as excited-state lifetimes, nature of the photoproducts formed, quantum yields
and transient absorption and emission spectra. Beyond the static approach, detailed information about
the time-evolution of a molecule after photoexcitation can be obtained from ab initio excited-state
molecular dynamics (MD). Dynamics studies become all the more important when the system does
not follow MEPs. In such cases, regions of the PES far from the computed photochemical pathway
may become important and mechanistic pictures deduced solely from the topological investigation of
the PESs may be erroneous. Moreover, dynamics simulations can bring semi-quantitative information
on important experimental data such as excited-state lifetimes and quantum yields provided that a
sufficient sampling of the system can be achieved (more details in section 3.2). Thus, static
calculations of PESs and characterization of the photochemical pathway are often complemented by
dynamics simulations to gain a more complete understanding of the molecular photochemistry.
1.2. Role of conical intersections
Back in the late 60s, the consensual view of a photochemical reaction was that the decay of an
excited species was taking place at an excited-state energy minimum coinciding with an avoided
crossing region between the excited- and ground-state PESs (Scheme 1a).3 However, a conceptual
shift was about to take place when Zimmerman,4 Teller5 and Michl6 introduced independently the
concept of photochemical funnels. These authors were the first to suggest that some photoproducts
may be produced from the nonradiative decay of the excited-state species through a degeneracy (i.e., a
real crossing point) between the excited- and ground-state PESs, rather than an avoided crossing
(Scheme 1b). These degenerate points were first coined conical crossings7 and are more commonly
known as conical intersections.8
While conical intersections were thought to be an exception rather than the rule, more than two
decades of computational photochemical studies have established that they are ubiquitous in
polyatomic systems, and their involvement in excited-state processes represents a general mechanistic
feature,9,10,11,12 in analogy with transition states for thermal reactions.13 Thus, the likeliness that an
excited-state species enters a region where the excited state crosses the ground state is high. Such
crossings provide very efficient funnels for radiationless deactivation (i.e., internal conversion). In
other words, the transition probability at the crossing is very high (close to unity) and the associated
kinetics is ultrafast (within a single molecular vibration, that is, on a femtosecond timescale). Not
surprisingly, then, the search of photochemical funnels has become the grail of all the computational
investigations in mechanistic photochemistry. Therefore, conical intersections deserve to be
understood and the following section is dedicated to these intriguing critical points.
Scheme 1. Schematic potential energy profiles from reactants (R) to products (P) and deactivation
pathways through (a) an avoided crossing, and (b) a conical intersection.

10
2. Conical intersections and associated crossing seams
2.1. Introduction to the theoretical concept of conical intersections
Condition of existence. The concept of conical intersection first appeared in the thirties of the 20th
century.7 But it is only about thirty to forty years later that the detailed study of this phenomenon
began with the work of Herzberg,8 Longuet-Higgins,8 Zimmerman,4 Teller,5 Michl,6 Mead,14 Truhlar,15
Robb,9–12 Yarkony16 and Baer17 to cite just a few. This is when the idea that conical intersections act as
funnels through which the excited state transfers nonradiatively to a lower state emerged. At first,
conical intersections were regarded as a mathematical curiosity rather than a useful concept for
explaining nonadiabatic events, and they were considered as extremely rare objects. Modern
theoretical advances, however, have enabled the location of conical intersections routinely leading to
the realization that they are much more common than previously thought. In fact, it is well established
that they are ubiquitous in polyatomic systems18 and in this new paradigm they play a central role in
many photochemical transformations.19 This has been confirmed experimentally thanks to the progress
in ultrafast (femtosecond) techniques, which have enabled the determination of subpicosecond
lifetimes for nonadiabatic events. These very fast processes cannot be explained with the traditional
theories for avoided crossings and point to the involvement of conical intersections.
Given the importance of these conical intersections in photochemistry,13,20 an obvious question
involves the requirements for their existence. To address this question, we consider an electronic
Hamiltonian, 𝑯!", through which two electronic states, 𝜙! and 𝜙!, are interacting.21
𝑯!" =
𝐻!! (𝑅)𝐻!"(𝑅)
𝐻!" (𝑅)𝐻!!(𝑅)
where 𝐻!" =𝜙!𝐻!" 𝜙!, 𝜙! are called diabatic wave functions and
R
represents the nuclear
coordinates. The eigenvalues of 𝑯!" !are obtained by diagonalization of the two-by-two matrix, giving
the following adiabatic energies:
𝐸!,!=𝐻±Δ𝐻!+𝐻!"
!
where 𝐻=𝐻!! +𝐻!! 2 and Δ𝐻=𝐻!! −𝐻!! 2. For the adiabatic energies to be degenerate,
two independent conditions must be satisfied:
𝐻!! 𝑅=𝐻!! 𝑅
𝐻!" 𝑅=0
Thus, at least two internal degrees of freedom are necessary to fulfill these two conditions. These
conditions for degeneracy are well-known since 1929 when von Neumann and Wigner formulated
what is known as the non-crossing rule.22 For a diatomic molecule that has only one internal degree of
freedom, it is not possible for two electronic states of the same symmetry to become degenerate. When
two states have different (spatial or spin) symmetry, then the second condition (𝐻!" =0) is satisfied
and the two states may cross (they will cross if 𝐻!! =𝐻!!). This non-crossing rule is only valid for

11
diatomic molecules, as larger polyatomic molecules have many nuclear degrees of freedom, which
may permit to satisfy the two necessary conditions for degeneracy. Thus, the correct view is that two
electronic states of a polyatomic molecule can in principle intersect even if they belong to the same
spatial and spin symmetry.
Branching space and intersection seam. If we denote the two independent coordinates fulfilling
the degeneracy requirements by x1 and x2, and take the origin at the point where the two above
conditions are satisfied, in the hypothesis of the first order (i.e., linear) approximation,23 it can be
demonstrated24 that these two directions are given as the gradient difference vector
𝐱𝟏=
𝜕𝐸!−𝐸!
𝜕𝑅
and the gradient of the interstate coupling vector
𝐱𝟐=𝜓!
𝜕𝐻!"
𝜕𝑅 𝜓!
where 𝜓! are the adiabatic wave functions The first vector x1 is often denoted g. The second vector is
parallel to the nonadiabatic coupling vector (also called derivative coupling vector) often denoted h.
𝐡𝟏𝟐 =𝜓!
𝜕𝜓!
𝜕𝑅 =
𝜓!
𝜕𝐻!"
𝜕𝑅 𝜓!
𝐸!−𝐸!
The vector h12 is the coupling term that gives the magnitude of the coupling between the adiabatic
(Born-Oppenheimer) states 𝜓! and 𝜓! as a function of the nuclear motion along
R
. Note that this
coupling becomes singular (infinite) at the conical intersection where 𝐸!=𝐸!.
The two first-order degeneracy-lifting coordinates x1!and! x2 form the so-called branching space
(also known as g*h space).23 If one moves away from the conical intersection in the plane spanned by
these two directions, the degeneracy is lifted at first order. As a consequence, the two crossing PESs
intersect as a double cone (Figure 2a). Another consequence of the non-crossing rule concerns the
dimensionality of the conical intersection. Because of the 2-dimensional branching space, conical
intersections are not isolated points in space, but rather they are made of an infinite number of
connected conical intersection points forming what is called the intersection seam or crossing seam.
For a molecule with
Nint
internal degrees of freedom, it is possible to find
Nint
!–!2 coordinates
orthogonal to the branching space, which maintain the degeneracy at first order. This (
Nint
!–!2)*
dimensional space is a hyperline of degeneracy and is also called intersection space (Figure 2b).
Consequently, conical intersections have a high dimensionality, which makes them all the more
accessible during the course of the photochemical reaction. The search for the most relevant
photochemical funnels aims therefore at finding minimum energy points along the crossing seams.
These critical points are called minimum energy conical intersections (MECI) and can be efficiently
optimized24,25 using standard quantum chemistry codes.

12
Figure 2. (a) Typical double cone topology for a conical intersection, and (b) relation between the
branching space (x1,!x2) and the intersection space (spanning the remainder of the (
Nint
!–!2)*
dimensional space of internal geometric variables).
Analogy with transition states. To understand the relationship between PES crossings and
photochemical reactivity, it is useful to draw a parallel between the role of a transition state in thermal
reactivity and that of a conical intersection in photochemical reactivity.10 In a thermal reaction, the
transition state (TS) forms a bottleneck through which the reaction must pass, on its way from
reactants (R) to products (P) (Figure 3a). The motion through the TS is described by a single vector,
called transition vector xtv (i.e., the normal mode associated with the unique imaginary vibrational
frequency). A transition state separates the reactant and product energy wells along the reaction path.
An accessible conical intersection (Figure 3b) also forms a bottleneck but separates the excited-state
branch of the reaction path from the ground-state branch. The crucial difference between conical
intersections and transition states is that, while the transition state must connect the reactant energy
well to a single product well via a single reaction path, an intersection is a ‘spike’ on the ground-state
PES (see Figure 3b), and thus it may connect the excited-state reactant (R*) to two or more products
(e.g., P1, P2, P3) on the ground state via a branching of the excited-state reaction path (in the plane x1
and!x2) into different ground-state relaxation pathways. The nature of the products generated
following decay at a surface crossing will depend on the ground-state valleys (relaxation paths) that
can be accessed from that particular structure.
Figure 3. Comparison of the role of (a) a transition state (TS) in thermal reactivity and (b) of a conical
intersection (CI) in photochemical reactivity.

13
2.2. Topological features
Different topological situations are possible for real crossings between PESs. One can have
intersections between states of same spin multiplicity (e.g., between two singlets) giving rise to an
(
Nint
!–!2)-dimensional conical intersection hyperline (Figure 4a). Or intersections can be found
between states of different spin multiplicity (e.g., singlet/triplet crossing) giving rise to an (
Nint
!–!1)-
dimensional intersection space, as the interstate coupling vector vanishes by symmetry (Figure 4b).
(
Nint
!–!1)-dimensional crossing seams can also be encountered between states of same spin multiplicity
in two distinct cases: 1) when the vector x2!vanishes for other reasons than symmetry (this situation is
encountered in photoinduced electron and energy transfer processes), or 2) when vectors x1 and x2
become parallel reducing the dimensionality of the branching space to one coordinate. Note that in
these last two cases, the real crossing is not anymore a conical intersection strictly speaking, as there is
only one degeneracy-lifting coordinate remaining. Thus, the crossing does not display anymore a
double-cone topology and it is not possible anymore to get a change of sign of the wave function by
making a loop around the locus of the crossing, which is a particular feature of conical intersections.16a
Note also that in the case of singlet/triplet crossings, the interstate coupling is restored upon including
the spin-orbit coupling (SOC).
Figure 4. Possible topologies for real crossings between two states: (a) typical (
Nint
!–!2)-dimensional
conical intersection between states of same spin multiplicity (e.g., two singlets or two triplets), and (b)
(
Nint
!–!1)-dimensional intersection between states of different spin multiplicity (e.g., singlet and triplet)
or between states of same spin multiplicity with a branching space reduced to one dimension (x1).
The topology of the PESs in the vicinity of a conical intersection can also be characterized by the
relative orientation of the two potential surfaces, as discussed by Ruedenberg et al.23 According to
Ruedenberg’s terminology, two limiting cases can be distinguished depending on the relative
orientation of the slopes of the PESs. In the first case called peaked conical intersection (Figure 5a,
top), the excited-state gradient points in opposite direction to the ground-state gradient, whereas in the
second case called sloped (or tipped) conical intersection (Figure 5b, top), the two gradients are
pointing toward the same direction. A direct consequence is that, in the peaked topology, there are at
least two ground-state relaxation pathways, one leading to at least one photoproduct, the other one
returning to the reactant (Figure 5a bottom). In the sloped topology, there may exist only one ground-
state relaxation pathway pointing directly back to the original reactant (Figure 5b bottom). As a result,

14
peaked conical intersections are ideal candidate for photochemistry providing efficient funnels for
products formation, while sloped conical intersections are more interesting for photophysics providing
efficient funnels for ultrafast reactant recovery.
Figure 5. Possible topologies for conical intersections characterized according to Ruedenberg’s
terminology: (a) peaked conical intersection, and (b) sloped conical intersection.
2.3. The important coordinates in photochemistry
For a discussion of mechanistic photochemistry, one needs a minimum of three geometric
variables to describe the nonadiabatic event: the reaction path, and the two vectors which span the
branching space.26 When the reaction path is contained in the branching space, one has a ‘sand in the
funnel’ model (Figure 6a). However, as we shall show, there are many chemical problems where the
reaction path lies almost parallel to the seam of the conical intersection. In this type of problem,
dynamics is essential.
The ‘sand in the funnel’ model is characterized by a passage through the tip of the upper cone
associated with the conical intersection. It can be described as sand flowing through a funnel or an
hourglass. This situation is encountered when the reaction path is included in the branching space (i.e.,
the reaction path can be described as a linear combination of x1 and x2, Figure 6a). In this case, a
minimum energy path will drive directly the system to the apex of the double cone corresponding to
the MECI. Thus, the system will most likely decay in the region of the MECI. A different case is
encountered when the reaction path is orthogonal to the branching space (i.e., the reaction path is
included in the intersection space, Figure 6b). In such a case, a conical intersection seam can be found
along the reaction path, as this coordinate preserves the degeneracy. Two possible scenarios can be
found depending on how the seam is laid out. The seam may intersect the minimum energy path in
which case the system will most likely decay along the crossing seam in a region necessarily higher
than the MECI. This case will be illustrated in DHA/VHF photochromism (see section 4.1.2).

15
Alternatively, the seam remains located higher in energy than the minimum energy path, even at the
MECI, and access to the seam requires some energy flow into the degeneracy-lifting coordinates x1
and/or x2. Depending on the amount of vibrational kinetic energy available in these modes, the system
may decay at different regions of the seam. In Figure 6b, an illustration of an unreactive trajectory
(blue arrow) and a reactive trajectory (white arrow) is shown depending on the vibrational kinetic
energy available in the {x1, x2} space. Thus, when the ‘sand in the funnel’ model is not appropriate
because the reaction path does not lie in the branching space, a study of the reaction path and
knowledge of the MECI is not enough to understand the photoreactivity. Only dynamics can provide
reliable mechanistic information, as it will allow the exploration of the chemically relevant parts of the
seam. In conclusion, the central idea in photochemistry should be the relationship between the reaction
coordinate, the intersection seam and the path actually followed by the system.
Figure 6. Representation of a conical intersection along the reaction path (Rx) (a) when Rx is included
in the branching space (‘sand in the funnel’ model), and (b) when Rx is orthogonal to the branching
space (conical intersection seam). In case (a), the MEP leads directly to the MECI. The inset shows the
trajectory followed by a (classical) ball rolling through the intersection. In case (b), access to the
conical intersection seam depends on vibrational motion within the branching space.
3. Mechanistic photochemistry: theoretical aspects
3.1. Determination of potential energy surfaces and reaction pathways
3.1.1. Electronic structure methods. To describe the electronic excited states, one needs a
quantum mechanical method that provides a balanced description of all the states involved in the
dynamics of the system. It needs to describe these states consistently along the entire photochemical
pathway, meaning that the important electronic rearrangements taking place in all the states considered
must be accounted for along the reaction path. In addition, a method with analytical energy gradients
available is also required to explore any photochemical process, whether statically through geometry
optimizations and MEP calculations, or dynamically through MD simulations. Because of the

16
important nonadiabatic effects often involved in the excited-state dynamics, particularly around
conical intersections,27 it is also desirable to use a multiconfigurational method that allows a proper
description of the electronic state mixing in the corresponding regions of the PESs. For all these
reasons, the complete active space self-consistent field (CASSCF) method has often been used to
compute the PESs of excited states, or to investigate nonadiabatic dynamics on-the-fly.28,29,30,31 Within
the CASSCF framework, one chooses a set of active orbitals over which the active electrons can be
distributed to generate all the electronic configurations, as in a configuration interaction (CI)
calculation. Both CI coefficients and orbitals are optimized for a given (set of) state(s). The most
critical feature of this kind of calculations is the choice of the active orbitals, known as the active
space. A judicious choice of active space has to be selected in order to describe all the electronic
rearrangements that will occur during the photochemical process under investigation.32,33 It allows a
reliable description of the static (or non-dynamical) electron correlation. However, to obtain accurate
PESs, post-CASSCF treatments are usually necessary to recover the dynamic electron correlation
missing at the CASSCF level.34 This is the case in the popular complete active space second-order
perturbation theory (CASPT2),35 which has become one of the most popular post-CASSCF methods
employed in photochemistry today.36 ,37 To obtain useful mechanistic information in photochemical
studies, the CASSCF approximation is often sufficient. However, if quantitative agreement with
experiment is sought or if CASSCF does not provide a balanced description of the excited states
because of the lack of dynamic electron correlation, then CASPT2 is necessary.
However, a computational bottleneck arises as the number of electronic configurations generated
by the CI expansion in CASSCF quickly increases with the number of active orbitals along with the
computational cost. Thus, it may be desirable to use a smaller set of electronic configurations in order
to perform the CASSCF calculations. Furthermore, the computational demand in CASPT2
calculations will also depend on the size of the reference active space. One possible strategy is to use
the restricted active space self-consistent field (RASSCF) approach. This method can be used either to
reduce the number of electronic configurations that are considered in order to treat large polyatomic
systems,38 or to enlarge the active space to include dynamic electron correlation.39 Another possible
approach is to reduce the size of the active space in the CASSCF approach.40 This is rather useful
when one contemplates direct molecular dynamics simulations (see section 3.2) for which evaluation
of CASSCF energy and gradient are required at every integration step along the trajectory. Therefore,
simulations can rapidly become prohibitively expensive if the size of the active space gets too large.
Note that there exist other computational approaches to describe excited-state electronic
structures, such as time-dependent density functional theory (TD-DFT) and equation-of-motion
coupled cluster (EOM-CCSD), which have been used in excited-state molecular dynamics
simulations.41,42 Both approaches however suffer from deficiencies of the underlying mono-
configurational description of the ground state in regions of bond breaking and bond formation.
Moreover, TD-DFT is known to encounter severe problems in describing valence states of molecules
exhibiting extended π systems, doubly excited states, charge-transfer excited states,43 and conical
intersections between ground and excited states.44,45 Still, recent progress has been made to correct
these problems in order to make TD-DFT a promising method for general photochemical studies.46
Other approaches based on semiempirical configuration interaction methods have been developed
specifically for excited-state calculations.47,48 These low-cost methods can be considered an alternative
to the ab initio methods described above for studies of photochemical processes in large size

17
molecules or when a large number of trajectories is necessary to simulate the dynamics of the system.
One particular semiempirical method, which has proved very useful in the context of the present
manuscript, is the Molecular Mechanics Valence Bond (MMVB) hybrid method.49 MMVB uses a
parameterised Heisenberg Hamiltonian50 to simulate CASSCF active orbitals in a valence bond space
and the molecular mechanics MM2 force field51 to describe an inert molecular
σ
framework. In short,
the molecular system is divided into two parts: one to be treated by Valence Bond (VB) theory and the
other to be treated by Molecular Mechanics (MM). VB wave functions can be written as
eigenfunctions of what is known as the Heisenberg spin Hamiltonian. The parameters of this
Hamiltonian have a simple physical interpretation in terms of Coulomb and exchange integrals and
they are molecule- and state-independent. In the MMVB method they have been parameterised from
CASSCF calculations on small model systems. The result is a parameterised VB Hamiltonian from ab
initio data, which can reproduce CASSCF geometries and energies for covalent excited states,52,53 and
be used to study the nonadiabatic dynamics of the system.54 The main advantage of the MMVB
method is that it provides a description of excited states in large conjugated systems taking into
account static correlation. Nevertheless, an important drawback is that it can be used for a limited
number of problems at present since the VB part has only been parameterised for sp2 and sp3 carbon
atoms and for covalent electronic states.55 Besides MMVB, conventional quantum mechanical /
molecular mechanics (QM/MM) methodology has been applied to study the photochemistry of
chromophores embedded in a solvent bath or in a protein environment.56,57
3.1.2. Photochemical reaction path. Important mechanistic information on the
photochemical behavior of the system can be derived by computing and analyzing the photochemical
reaction path, i.e. the reaction coordinates and energies connecting the Franck-Condon point to the
excited-state intermediate M* (if existing) to the ground-state products possibly via conical
intersections. As illustrated in Scheme 2, the strategy used in computational photochemistry is based
on the mapping of the photochemical reaction path computed by following the MEP from the starting
(e.g., Franck-Condon structure FC) to the final points (e.g., ground-state product P) through a conical
intersection. This strategy provides information on the structure and accessibility of the photochemical
reaction path from a chosen starting point (e.g., the FC point). This technique has the advantage of
limiting the investigation only to the region of the PES that is relevant for the description of the
photochemical reaction. In other words, by following the MEP, we immediately focus on the driving
forces responsible for the photoinduced nuclear motion. Critical structures directly accessible by the
system such as intermediates, transition states and funnels will be located as travelling points along
the MEP. Other stationary points and crossing regions may be very far from the MEP, both in terms of
energy and geometry. They may or may not be important for the description of the process depending
on the dynamical behavior of the system. For example, the decay point (i.e., the photochemical funnel)
intercepted by the MEP may differ from the MECI such as in the case of DHA/VHF photochromism
(see section 4.1.2). Thus, the information given by the MEP may be different (or complementary)
from that provided by locating stationary points and minimum energy crossing points, yielding a more
general and extended description of the potential energy landscape. Another example is the case of the
conical intersection and the associated crossing seam lying close to the reaction coordinate but not
intercepted by the MEP (see Figure 6b). In this instance, the crossing seam is obviously highly
important to account for the nonradiative decay but only dynamics can account for this process.

18
From a practical point of view, standard methods for geometry optimizations are used to locate the
various stationary points on the PESs. The MEP is determined by computing the intrinsic reaction
coordinate (IRC).58 Finding MECI requires special methods as two potential energy surfaces become
degenerate and the gradient and Hessian cannot be unambiguously computed. Several algorithms are
available (e.g., gradient projection method,24,25 Lagrange multiplier method,59 penalty function
method60) to optimize MECIs and are implemented in various quantum chemistry codes (e.g.,
Gaussian61 and Molpro62 mostly used to perform the calculations reported in this manuscript employ
the gradient projection method).
Scheme 2. Illustration of reaction path modeling.
Determining the various MEPs arising from a conical intersection where the branching of the
photochemical reaction path occurs upon decay from a higher to a lower electronic state is not so
standard. The interstate nature of such paths requires special methodologies to locate the energy
valleys describing the relaxation process (e.g., the ground-state relaxation occurring after the decay at
an MECI). Methods for computing relaxation paths starting from a crossing point are still not widely
distributed. As explained earlier, an accessible conical intersection forms a structural bottleneck that
separates the excited-state branch of a photochemical reaction path from one or more ground-state
branches connecting the excited-state reactant to one or more ground-state products. The number and
nature of the products generated following decay at a surface crossing will depend on the population
of such branches, each one corresponding to a different relaxation path. To locate and characterize all
the accessible branches developing on the lower cone of a conical intersection, the calculation of the
initial relaxation directions (IRD)63 departing from such a conical intersection can be performed.
The MEP connecting the reactant (R) to the product (P) of a thermal reaction is uniquely defined
by the associated transition structure (TS). The direction of the transition vector xtv (i.e., the normal
mode corresponding to the imaginary frequency at the TS) is used to start an IRC calculation. One

19
takes a small step along this vector (shown in Figure 7a) towards P or R and then follows the IRC
connecting this point to the product or reactant well. The small initial step vector defines the IRD
towards the product or reactant. This procedure cannot be used to find the IRD for a photochemical
reaction since, as discussed above, a conical intersection is a "singularity" and there is no such unique
direction for this first step. However, note that if one computes the energy of the system along a
circular cross section centered at the TS as illustrated in Figure 7a, then provided the radius of the
circle is small enough, the energy minima M1 and M2 located on the circular cross section provide an
alternative but equivalent definition of the IRD. Thus, this strategy can be transposed to the conical
intersection for which several IRDs may develop. In this case, one can systematically search for
minima on a hypersphere of a given radius and centered on the conical intersection. Figure 7b
illustrates this approach in the case of a model elliptic conical intersection (i.e., in the first-order
approximation). In this case, two steep sides exist on the ground-state surface in the immediate
vicinity of the apex of the cone. It is thus obvious there are two preferential directions of downhill
motion along these steep sides of the ground-state cone surface. As one moves away from the apex
along these steep directions, real reaction valleys eventually develop (leading to the final photoproduct
minima). A simple procedure for defining these directions involves the computation of the energy
profile along a circular cross-section centered on the vertex of the cone. It can be seen that the profile
contains two different energy minima. These minima (M1 and M2 in Figures 7b and 7c) uniquely
define the two IRDs from the vertex of the cone. The two steepest descent lines starting at M1 and M2
define two MEPs that describe the relaxation processes in the same way the transition vector xtv
defines the MEP connecting reactants to products from a TS. Thus, while there is no analogue for the
transition vector in conical intersections, the simple case of an elliptic cone shows that the IRDs are
still uniquely defined in terms of M1 and M2. At this stage, one should notice that while the IRD from
a TS connects the reactant to the product, there are two distinct IRDs from an elliptic conical
intersection leading to two different photoproduct valleys (where one of these photoproducts may
actually correspond to the original reactant).
Figure 7. (a) Model PES showing a transition state (TS) and the corresponding energy profile along a
circular cross section centered on the TS. (b) Model ground- (Egs) and excited-state (Eex) PESs for an
elliptic conical intersection and the corresponding energy profile along a circular cross section
centered on the crossing point. (c) Egs energy profile along the circle defined in Figure 7b. The points
M1 and M2 correspond to the two energy minima located along the circular cross section. The points
TS12 and TS21 correspond to the two transition structures connecting M1 and M2. (Adapted from
reference [63b])

20
In fact, for the elliptic cone model discussed above, there can be at most two minima (M1 and M2)
defining two distinct IRDs (excluding the case where the cone becomes circular in which case there
are an infinite number of equivalent directions of relaxation).23 These minima are located within the
branching space {x1, x2}. However, this model of the potential energy sheets at a conical intersection
point is not general enough to give a correct description of all relaxation paths for a real system.
Firstly, as illustrated in Figure 3b, there may be more than two possible IRDs originating from the
same conical intersection. Secondly, some IRDs may lie “out” of the branching space since the real
{x1, x2} space is, in general, curved. However, the ideas introduced above can be easily extended to
search for IRDs in the full n-dimensional space surrounding a conical intersection point by replacing
the circular cross section with a hyperspherical cross section centered at the vertex of the cone. Thus
the search for energy minima in a one-dimensional circular cross section (i.e., the circle in Figure 7b)
is merely extended to an n–1 dimensional spherical cross section of the ground-state PES (i.e., a
hypersphere), and the IRD will then be defined by the energy minima located on the hypersphere.
We must emphasize that the procedure outlined above is designed to locate the points where the
relaxation paths begin (i.e., they define the IRDs). Once these points have been found for some small
value of the hypersphere radius, then one must compute the associated MEP which defines the
relaxation paths leading to a ground-state energy minimum. The standard IRC method58 can be used
for that purpose. As a consequence, the approach outlined above provides a systematic way to find the
MEP connecting the vertex of the cone to the various ground-state photoproduct wells.
The whole procedure described above allows a reliable description of the photochemical reaction
path. However, computations of MEP can become prohibitively expensive depending on the actual
cost of the electronic structure method used to determine the PES. Alternative but more approximate
methodologies exist such as relaxed potential energy surface scans along a given coordinate, and
linearly-interpolated transit path (also called linear least motion path) calculations. Relaxed scans can
lead to wrong pathways if the coordinate chosen for the scan is too approximate. Pathways based on
intermediate geometries obtained from linearly-interpolated structures in internal coordinates are
simple but very approximate. This method is useful for locating transition states and for providing an
upper bound on the energy profile associated with a reaction path.
3.2. Excited-state molecular dynamics
The techniques outlined above provide information on the structure and accessibility of the
photochemical reaction paths. As mentioned, this information is structural (i.e., non-dynamical) and
provides insight into the mechanism of photoproduct formation from vibrationally “cold” excited-state
reactants such as those encountered in many experiments where slow excited-state motion or/and
thermal equilibration is possible (in cool jets, in cold matrices and in solution). In many cases, such
structural or static information is not sufficient. Since reacting molecules have usually a finite amount
of kinetic energy, a trajectory will not follow the MEP and may, in principle, deviate quite
dramatically from it (e.g., in the case of "hot" systems where there is substantial vibrational energy). In
this case, regions of the potential energy surface far from the computed photochemical reaction path
may become important and a dynamical treatment of the reaction is unavoidable. In other words, in
these cases, the photochemical reaction path may not provide a realistic nuclear motion followed by
the system. We already discussed (see section 2.3) that to understand photochemical reactivity it may

21
be necessary to go beyond the idea of following a reaction path through a minimum energy conical
intersection, and to look not only at how the reaction coordinate relates to the intersection seam, but
also at the actual dynamical path of the system. In short, we need to know where the system meets the
intersection seam in order to determine where it crosses to the ground state, and this depends not only
on the topology of the potential energy surfaces but also on the dynamics of the system, i.e. the
momenta of the particles. In addition, knowing the dynamics of a molecular system will provide
detailed information about its time-evolution after photoexcitation giving access to timescales of the
reaction and important experimental observables such as excited-state lifetimes, products quantum
yield and branching ratios. Thus, understanding the underlying ultrafast dynamics of a molecule
undergoing a photochemical process will help interpreting experimental data, be a powerful tool to
predict the photochemical behavior of systems for which no experimental data are available, and even
help designing new devices with a particular function.
If the PESs are known, the time-dependent Schrödinger equation can in principle be solved
directly using what are termed wavepacket dynamics.64 Here, a time-independent basis set expansion
is used to represent the wavepacket and the Hamiltonian. The evolution is then carried by the
expansion coefficients. While providing a complete description of the system dynamics, this approach
represents however a formidable computational task and in practice, these methods are restricted to the
study of typically 3 to 6 degrees of freedom. Even the highly efficient multi-configuration time-
dependent Hartree (MCTDH) method,65 which uses a time-dependent basis set expansion, can handle
no more than 30 degrees of freedom. Recent developments66 based on the variational
multiconfiguration Gaussian (vMCG) wavepacket method30 look very promising to treat larger
molecules, but the description of such a method is out of the scope of this manuscript, as it has not
been used here. Instead, we resorted to semiclassical simulations.
In the classical limit of the Schrödinger equation and in the case of an evolution on a single sheet
of PES (adiabatic or Born-Oppenheimer approximation), the evolution of the wavepacket density can
be simulated by a ‘swarm’ of classical trajectories driven by Newton’s equations of motion
𝑀𝑹=−𝛁𝑉
where
V
is the potential and 𝑹 is the second-derivative of the position with respect to time, that is the
acceleration. This approach is called molecular dynamics (MD). In ab initio MD, the potential
V
is
obtained by solving the electronic Schrödinger equation. Then, the dynamics is designated as
semiclassical because nuclei motion is treated classically, while the electrons are described quantum
mechanically. In addition, we have to resort to direct or on-the-fly MD.28–31,67 In contrast to standard
dynamics simulations that require a predefined (analytical) PES over which the nuclei move, the PES
(i.e.,
V
) is provided here by explicit evaluation of the electronic wavefunction at every integration step
along the trajectory. This makes the method very general and powerful, particularly for the study of
polyatomic systems where the determination of an analytical multidimensional potential function is an
impossible task. Because of the size of the systems reported in this manuscript, we have only carried
out on-the-fly semiclassical dynamics simulations and we present in the following the two different
approaches that we used to include nonadiabatic effects.
To add nonadiabatic effects to semiclassical methods, it is necessary to allow the trajectories to
sample the different surfaces in a way that simulates the population transfer between electronic states.
The simplest way to add a nonadiabatic correction is to use what is known as trajectory surface

22
hopping (TSH). First introduced on an intuitive basis by Bjerre and Nikitin,68 and Tully and Preston,69
a number of variations have been developed and reviews on the TSH methodology can be found in
reference [70]. These methods all use standard semiclassical trajectories which use the hopping
procedure to sample the different states, and so add nonadiabatic effects. The motivation comes from
the early work of Landau71 and Zener.72 The Landau-Zener model is for a classical particle moving on
two coupled one-dimensional potential energy curves. If the diabatic states cross so that the energy
gap is linear with time, and the velocity of the particle is constant through the nonadiabatic region,
then the probability of transition from adiabatic state 2 to adiabatic state 1 is given by
𝑃
!→!=exp!(−
1
4𝜋𝜉)
where !𝜉 is the so-called Massey parameter73
𝜉=
Δ𝐸
ℏ𝜕𝑅
𝜕𝑡 𝜓!
𝜕𝜓!
𝜕𝑅
=
Δ𝐸
ℏ𝑹∙𝒉𝟏𝟐
where Δ
E
is the energy gap between the two adiabatic states and 𝑹∙𝒉𝟏𝟐 is the product of the velocity
of the particle by the nonadiabatic coupling vector. This product can be rewritten as 𝜓!𝜕𝜓!𝜕𝑡 and
is often referred to as the time-dependent nonadiabatic coupling (also called kinetic coupling or
dynamic coupling) responsible for the nonadiabatic transitions. Indeed, according to the Landau-Zener
formula given above, for a vanishingly small energy gap, or a very large nonadiabatic coupling, such
as encountered when the system approaches a conical intersection, the probability of changing
adiabatic states approaches unity. We used two different surface hopping procedures to perform our
on-the-fly TSH simulations. They are briefly presented below.
Tully’s fewest switches surface hopping. The most popular implementation of the TSH method is
based on Tully’s fewest switches algorithm (FSA),69,74 which gives a good compromise between
accuracy and computational efficiency. In the FSA the quantum amplitudes are propagated coherently
along the trajectory and the transition (i.e., hopping) probabilities are proportional to the variation of
the quantum state populations with the constraint that the number of transitions (i.e., hops) is required
to be as small as possible. In the adiabatic representation, the probability of hopping from the adiabatic
surface 2 to the adiabatic surface 1 is given by
𝑃
!→!=max!(0,𝑞!")
with
𝑞!" =
2𝑅𝑒 𝑐!
∗(𝜏)𝑐!(𝜏)𝑹∙𝒉𝟏𝟐 d𝜏
!!!!
!
𝑐!(𝑡)𝑐!
∗(𝑡)
The complex-valued coefficients c are the quantum amplitudes of the expansion of the total electronic
wavefunction in the basis of the adiabatic states and are obtained from the solution of the time-
dependent Schrödinger equation.
To determine whether a switch from state 2 to state 1 will occur at each time step, a uniform
random number 𝜁 between 0 and 1 is generated and, in a two-state case, the hopping is performed if

23
𝜁<𝑃
!→!
In the case a surface hop is achieved, the velocity components are adjusted in the direction of the
nonadiabatic coupling vector
h
12 in order to conserve the total energy of the system. If there is not
enough velocity (kinetic energy) in the direction of the nonadiabatic coupling vector to maintain
energy conservation during a hop, the hop is classically forbidden and is rejected.
Although the FSA is conceptually very simple, its implementation requires the computation of
nonadiabatic coupling vectors and the integration of quantum amplitudes at every point of the
trajectory. Moreover, the exact transition probability is given by a complex expression that involves,
in addition to nonadiabatic couplings, also the relative phases of the real and imaginary components of
the quantum amplitudes. For these reasons the use of the FSA may be impractical for the study of
large systems or for QM/MM applications, where the explicit computation of nonadiabatic coupling
vectors may no longer be feasible. In such cases it is desirable to use more approximate switching
methods that involve a numerical evaluation of the nonadiabatic couplings in terms of wavefunction
overlap at successive time steps, as proposed in the following approach.
Diabatic surface hopping. To decide when to undergo a transition to a different potential energy
surface, one would in principle need to compute ψ!∂ψ!∂t at every time step (Δ
t
) of the
simulation. In practice, however, it is possible to approximate !ψ!∂ψ!∂t! as
!ψ!(𝑡)ψ!(𝑡+Δ𝑡)Δ𝑡, i.e. the overlap between the excited-state wavefunction at the current time
step and the ground-state wavefunction at the previous time step. In the case of simulations performed
at the CASSCF level with state-averaged (SA) orbitals to model the wavefunctions, one can compute
the overlap as the inner product of the corresponding SA-CASSCF eigenvectors
C
1 and
C
2:
ψ!(𝑡)ψ!(𝑡+Δ𝑡)=𝑪!
!∙𝑪!
!!!!
Calculating the energy gap Δ
E
and 𝑪!
!∙𝑪!
!!!!!at every time step is straightforward, and we can use the
Landau–Zener formula to calculate the probability of a transition between the two electronic states. In
principle, the transition probability can be used to spawn a new trajectory on the other surface.
However, since this procedure would lead to multiple trajectories that have to be computed
simultaneously, spawning is too demanding in practice. In our diabatic surface hopping approach,56 we
only restrict hopping to situations where the transition probability approaches unity. This happens at
the conical intersection seam, where Δ
E
≈ 0 and 𝑪!
!∙𝑪!
!!!!! ≈ 1.
Because surface hopping is only allowed at the conical intersection seam, classical trajectories
follow the same diabatic state at the crossing. Therefore, energy and momentum are obviously
conserved. In principle, this strict diabatic hopping criterion could lead to an underestimation of the
population transfer probability, because a surface hop in regions with strong nonadiabatic couplings
far from the intersection is prohibited. In practice, however, the high dimensionality of the seam
ensures that all trajectories encounter such regions of high transfer probability. A major advantage of
restricting hopping to the seam is that we obtain information on the location of the seam in our
trajectories. The latter is important for example to understand how the interactions between a
chromophore and its environment alter the topology of the surfaces and the seam and thereby control
the outcome of the photochemical process. The Landau–Zener model is clearly an approximation, but
can help to keep a proper physical insight, which is crucial for understanding complex systems.

24
4. Applications: from organic photochemistry to photobiochemistry and inorganic
photochemistry
After presenting some of the concepts and tools required to investigate photochemical processes
from a theoretical point of view, we will now illustrate the power of computational photochemistry to
rationalize and sometimes predict the excited-state behavior of various molecular systems, ranging
from simple organic chromophores to biomolecules and transition metal complexes.
4.1. Organic photochemistry
4.1.1. Photostability of polycyclic aromatic hydrocarbons. The main aim of this series of
studies is to present a consistent mechanistic picture for the photophysics of small cationic polycyclic
aromatic hydrocarbons (PAHs). PAHs and their cations are of great interest in the field of
astrophysics. PAH cations are extremely photostable following electronic photoexcitation and have
been extensively studied as the leading candidates for the diffuse interstellar bands (DIBs).75 Very
little is known about their photophysics and reactivity, partly because of their inherent
nonfluorescence and difficulties in isolating charged species. Gas-phase photofragmentation studies of
a variety of PAH monocations have shown the high photostability of these species (dissociation onsets
of 4-4.5 eV) and suggest fast relaxation times.76 Their tendency to return efficiently on an ultrafast
timescale to the ground-state reactant structure after electronic photoexcitation, without forming new
photoproducts directly, was later confirmed and shown to be remarkable.77 In the following, we
present the main theoretical results obtained on naphthalene (N•+),78 pyrene (Py•+)79 and perylene
(Pe•+)80 radical cations, which allow a rationalization of their distinct photophysical behaviors.
Naphthalene cation. Relaxation dynamics study of cold (10–100 K) N•+ isolated in boric acid glass
using transient grating spectroscopy revealed rapid and efficient relaxation of N•+ down to its ground
state after photoexcitation at 680 nm to its D2 state. A two-step relaxation kinetics was unveiled with a
fast component (<200 fs) and a slow component (ca. 20 ps). The two steps were interpreted as an
initial rapid D2 to D0 internal conversion, followed by slow vibrational relaxation of the hot D0 state.
The authors of this study further postulated that the observed fast step is due to the D1→D0 relaxation,
concluding that the D2→D1 relaxation occurs on a timescale too short to be measured by their
apparatus (<1 fs). Our computational study aimed at understanding this photophysical behavior from a
simple static approach.78
The results of our CASSCF and CASPT2 calculations are summarized in Figures 8, 9 and 10.
Figures 8 and 9 show the CASSCF potential energy profiles of the three electronic states involved in
the photophysics of the naphthalene cation. These states are the ground, D0(Au), and the first two
excited states, D1(B1u) and D2(B2g) (where the label Dn refers to the order obtained for vertical
transitions). The potential surface is displayed on two separate diagrams for clarity, because the
reaction coordinate is not the same in both cases. All the optimized minima and crossings have D2h
point group symmetry and the structures are drawn up on these figures. The energy gradient vectors of
the states at the Franck-Condon points and crossings are opposite to the forces acting on the molecule.
These are shown to the right in Figures 8 and 9 to illustrate the driving force for the photophysics and
the nature of the reaction coordinate, which is along the symmetry-preserving gradient difference
vector (x1) in each case.

25
Figure 8. Optimized critical points of the naphthalene radical cation using CASSCF/6-31G* on the D0
and D1 states. Energies in kcal/mol. Vectors to the right display the energy gradients at the intersection
and FC geometry.
Figure 9. Optimized critical points of the naphthalene radical cation using CASSCF/6-31G* on the D1
and D2 states. Energies in kcal/mol. Vectors to the right display the energy gradients at the intersection
and FC geometry.
Upon excitation to the D2 state, the system will relax to the nearby D2 minimum. The initial forces
acting on the system correspond to the opposite of the gradient difference vector and points directly
towards a D1/D2 MECI. This crossing is located over 20 kcal/mol above the D2 minimum however.
Upon nonradiative decay at the crossing region, the system further relaxes on the D1 PES. The forces
then drive the system directly towards the D1 minimum. Along the same direction is located an easily
accessible D0/D1 MECI less than 2 kcal/mol above this minimum. This funnel allows for a fast internal
conversion back to the ground state. The photophysical mechanistic picture that emerges from these
calculations is thus rather simple. It is illustrated in Figure 10. The efficient and ultrafast ground-state

26
recovery upon photoexcitation of N•+ results from easily accessible funnels between the populated
electronic states. These funnels correspond to sloped conical intersections and the forces acting on the
nuclei drive the system efficiently toward these funnels. Note however that, at the CASSCF level, the
D1/D2 MECI is too high in energy to account for the ultrafast decay observed experimentally. Only at
the CASPT2 level is the picture in better agreement with the experimental measurements. Indeed, at
this level of calculation, the D1/D2 MECI is lowered in energy relative to the D2 minimum energy.
This is a direct consequence of larger correlation energy in the D0 and D2 states compared to the D1
state.
Figure 10. Schematic representation of the electronic relaxation mechanism of the naphthalene radical
cation. Dashed curve: original CASSCF/6-31G* result for D1 state. Solid curve: predicted relative
increase in D1 energies indicated by CASPT2 calculations, suggesting a lower energy D1/D2 MECI,
allowing for nonradiative relaxation.
It is remarkable to note that the photophysics of N•+ is very different from that of its neutral
counterpart. Neutral naphthalene (N) is known to exhibit mainly fluorescence in the near ultra-violet
(UV) after photoexcitation to the S1 excited state.81 Like in benzene, it can probably undergo
photoisomerization reactions to produce valence isomers such as naphthvalene and/or benzofulvene.
This is in contrast with the ultrashort excited-state lifetime observed in N•+. Figure 11 compares the
potential energy profiles of neutral and cationic naphthalene in the ground and first excited states. The
S0→S1 vertical transition energy in N is much larger than the corresponding D0→D1 vertical transition
energy in N•+. This is expected based on the nature of the excited states. The S1 state of N results from
transitions between occupied π orbitals to unoccupied (virtual) π* orbitals (π→π* transitions), while
the D1 state of N•+ results from a transition between occupied π orbitals (π→π transition). Therefore, it
is not surprising that the energy gap is much lower in the cationic species. Upon geometry
optimization of the excited state, the structure remains highly-symmetric (i.e., D2h symmetry) both in

27
N and N•+. However, the energy gap with the ground state remains very large in N, while it is
considerably reduced in N•+. As a consequence, crossing with the ground state can only occur in N
upon pyramidalization of a benzene ring, which is an activated process with a barrier of about 30
kcal/mol. Thus, unless the system has enough vibrational kinetic energy to overcome this barrier, the
system will remain trapped in the S1 minimum until radiative decay (fluorescence) occurs. If the
excitation energy is high enough to provide the system with sufficient energy to overcome the barrier,
then the S0/S1 conical intersection can be reached and nonradiative decay to the ground state becomes
efficient. The system can either return back to its original naphthalene structure, or, because of the
peaked topology of the MECI, lead to new photoproducts corresponding to valence isomers. This
behavior is very similar to the one observed in benzene (see Figure 1).
Figure 11. Comparison of the CASSCF potential energy profiles in the ground and first excited states
of (a) neutral naphthalene and (b) naphthalene radical cation. The neutral PAH exhibits fluorescence
or photoproducts formation depending on excitation energy, while the cationic PAH is highly
photostable.
Pyrene cation. Regarding Py•+ no time-resolved photodynamics study has been reported so far.
Because this cation is often considered to be a strong candidate for one of the DIB carriers,82 we have
investigated the topological features of the relevant PESs for this system.79 The results are summarized
in Figure 12. The presence of two easily accessible sloped D1/D2 and D0/D1 conical intersections
suggests that Py•+ is highly photostable, with ultrafast nonradiative decay back to the initial ground-
state geometry predicted via a mechanism similar to the one found in N•+. However, the two funnels
involved are even more accessible in Py•+ compared to N•+, suggesting a shorter excited-state lifetime
in this case. Thus, like for N•+, our model also predicts Py•+ to be nonfluorescent.

28
Figure 12. Schematic representation of the potential energy landscape and nonradiative electronic
relaxation mechanism of the pyrene radical cation.
Perylene cation. By contrast with other PAH radical cations, Pe•+ seems to present a different
photophysical behavior. While most small PAH cations display ultrafast ground-state recovery (<200
fs) in boric acid glass,77 much longer times from 19 ps77 up to 35 ps83 were needed in the case of Pe•+.
Even longer ground-state recovery times of up to 100 ps were obtained in a Freon glass at 77 K.84 An
exceptionally large D0–D1 energy gap inhibiting the internal conversion was put forward as a possible
explanation for this behavior.77 Photoinduced fluorescence of Pe•+ has been observed in neon and
argon matrices at ~10 K.85 This was the first report of the fluorescence spectrum of a PAH cation in
any phase. However, a gas-phase experiment failed to reproduce these matrix results, for reasons that
remain unclear.86 Because of the distinct photophysical behavior of Pe•+ and apparently controversial
experimental observations on the luminescence property of this radical cation, we were interested in
investigating the ground and lowest excited-state PESs of this cation in order to rationalize the
experimental results.80 Figure 13 synthesizes the results. Photoexcitation to the D2 state in the vicinity
of a peaked D1/D2 MECI leads to ultrafast nonradiative decay to the D1 state. Vibrational relaxation
can then lead to populate two distinct excited-state minima on the D1 PES. The most important result
concerns the absence of accessible in-plane surface crossings between the D0 and D1 states; crossings
which we have previously found for N•+ and Py•+, as discussed above. This accounts for the longer
excited-state lifetime in Pe•+ and the most likely decay mechanism from the first excited state is a
radiative deexcitation, in agreement with reference [85]. Note that we cannot completely rule out a
competition with a nonradiative decay route via out-of-plane distortions, which may explain the
absence of emission observed in reference [86], although fragmentation may also be connected with
this.

29
Figure 13. Schematic representation of the potential energy landscape and radiative electronic
relaxation mechanism of the perylene radical cation.
4.1.2. Photochromic systems. Photochromism represents an increasing area of research in
photochemistry because of its actual and potential applications. It is defined as a reversible
phototransformation of a molecule between two forms having different spectral properties. This
process, however, may not only induce spectral changes, but also change of refractive index, dielectric
constant, dipole moment, oxidation/reduction potential or geometry of a molecule. The reverse
(backward) transformation may proceed photochemically using light irradiation of different
wavelength, thermally, or in redox processes. Photochromic molecular systems have entered the new
generation of innovative functional materials with high added value. Applications are already
widespread in nanosciences, biology, and photonic or optoelectronic devices as light-activated
switches.87,88,89 Whether in molecular information storage, holography, or as photomechanical
actuators, photochromic compounds convert photonic energy into chemical energy (e.g., selective
bond-breaking and bond-making reactions) within an ultrafast (picosecond or sub-picosecond)
timescale. The change in electronic and molecular structures following electronic excitation results in
a change of physical properties, which forms the basis of the applications listed above.
While the ultimate interest for these compounds is device applications, we are compelled to
understand the mechanism of action of these and other photoactive molecules. Thus, knowledge and
understanding of the precise reaction mechanisms underlying their photochromic activity at the
molecular level are of particular interest because they are necessary for a rational design of new
molecular systems with improved photochromic properties, potentially leading to innovative devices.
Various classes of photochromic compounds are currently under study as photochromic materials.
The vast majority of them rely on organic compounds. One of the largest groups of photochromic
switches is based on ring-opening/ring-closure reactions in photoinduced electrocyclic reactions. The
systems presented below belong to this main class of molecular switches.
Dihydroazulene / vinylheptafulvene photochromism. The photochemical ring-opening reaction of
dihydroazulene (DHA) to give vinylheptafulvene (VHF) (Scheme 3) is rapid and efficient, but VHF is
photostable and does not react photochemically from the S1 state to give DHA; the backward reaction
only takes place thermally or via two-photon excitation.90 We will show in the following that most of

30
these experimental observations can be explained by a conical intersection between the S1 and S0
states.91
Scheme 3. The dihydroazulene (DHA) / vinylheptafulvene (VHF) photochromic system.
The S0 and S1 potential energy profiles along the reaction coordinate are shown in Figure 14 along
with the main relaxation pathways. Upon photoexcitation to the S1 state of DHA, the system relaxes to
a local S1 DHA diradicaloid minimum (M* on Fig. 14) following a complete inversion of single and
double bonds within the π-system. Then, upon stretching the σ-bond that breaks to produce VHF, the
system reaches a transition state TS* (11 kcal/mol above M* but 24 kcal/mol below the S1 Franck-
Condon energy) characterized by a transition vector dominated by adiabatic σ-bond breaking. Beyond
the transition structure, the system proceeds downhill and barrierless to a conical intersection, S0/S1
MECI, which corresponds to the lowest energy point on the S1 PES (over 50 kcal/mol below M*).
This crossing presents a VHF-like structure, i.e. the 5-membered ring is opened, and at this funnel,
efficient radiationless decay to S0 will take place producing the VHF isomer (MVHF). This picture is
consistent with the observation of fluorescence following photoexcitation of DHA, as there is a local
DHA S1 minimum. The DHA→VHF isomerization quantum yield increases, at the expense of the
emission efficiency, when the temperature is increased. This is consistent with the activated process to
reach the funnel for photoisomerization.
Figure 14. S0 and S1 potential energy profiles along the reaction paths of a relevant DHA/VHF model
system. DHA→VHF photochemical path indicated by blue arrows. VHF→VHF photophysical path
indicated by red arrows. Red and blue crosses indicate the S0 and S1 energies at various critical points.

31
In fact, the MEP calculated from TS* in the VHF direction does not actually reach S0/S1 MECI
itself, the lowest-energy point optimized on the intersection. Instead, the MEP terminates at a higher
energy point on the crossing seam, denoted S0/S1 X, which is over 30 kcal/mol above the MECI. This
is made possible because the ring-opening reaction coordinate involves mainly a C-C σ-bond
breaking, while the degeneracy-lifting coordinates at the S0/S1 MECI are dominated by rearrangements
of the fulvene ring alone in the DHA/VHF model system (or of the seven-membered ring in the real
system shown in Scheme 3). Thus, a crossing hyperline persists along the DHA→VHF reaction path
(Figure 15). In addition to its higher energy, S0/S1 X is characterized by a shorter C-C bond distance
for the broken σ-bond of 2.45 Å compared to the 3.45 Å C-C bond distance at S0/S1 MECI. This
confirms that the MEP is intercepted by the crossing seam well before reaching the MECI. Analysis of
the decay routes at S0/S1 X shows that the system may return to MDHA or form MVHF but, for inertial
reasons, product formation will be highly favored over reactant regeneration.
Figure 15. S0 and S1 potential energy landscape along the reaction path corresponding to the
DHA→VHF photoisomerization. The IRC computed at TS* is indicated by the white line and shows
how it is intercepted by the conical intersection seam at the structure S0/S1 X, lying much higher in
energy than the minimum energy conical intersection, S0/S1 MECI. The relevant coordinates for
mechanistic photochemistry are shown on the left for a DHA/VHF model system: the reaction
coordinate Rx is orthogonal to the branching space.

32
Upon photoexcitation to the S1 state of VHF, the system relaxes directly towards the S0/S1 MECI.
The relaxation coordinate corresponds to the gradient difference vector characterizing the S0/S1 MECI.
Consequently, the MEP on S1 is naturally driven to the MECI like in the ‘sand in the funnel’ model
(Figure 16). The topological feature on S0 around this conical intersection only allows the system to
reform VHF. After nonradiative decay to S0 at the MECI, the system relaxes towards a transition state
(TS2). TS2 has a very similar geometry to the S0/S1 MECI and is the lowest point along the x1 reaction
path leading from MVHF through the MECI onto S0. Continuing on the same path through TS2 leads to
a steep rise in energy (Figures 14 and 16), and molecules approaching the S0/S1 MECI from the VHF
side will therefore be reflected on this barrier back toward MVHF. These particular topological features
around the conical intersection account for the high photostability of VHF. Moreover, the presence of
the S0/S1 MECI as the lowest critical point on the S1 PES in the VHF region also explains the lack of
fluorescence upon excitation of VHF.
Figure 16. Topology of S0 and S1 PES in the vicinity of the S0/S1 MECI. Grid obtained by CASSCF
single-point energy calculations at scanned structures along x1 and x2. The relaxation coordinate
following VHF excitation to S1 corresponds to x1. Thus, the MEP leads directly to S0/S1 MECI, as
indicated by the orange arrow. After decay to S0, a steep rise in energy is encountered along x1 and the
system reverts back toward VHF.
Both the highly efficient DHA→VHF photoisomerization and high VHF photostability were
confirmed by on-the-fly CASSCF91 and MMVB54 molecular dynamics. All the trajectories performed
from TS* ended up producing VHF, while none of the trajectories started from VHF produced DHA.
In addition, these dynamics simulations also illustrated the access of the higher energy part of the
crossing seam in the region of S0/S1 X during the DHA→VHF photoisomerization.
Dithienylethenes photochromism. Dithienylethenes (DTEs) belong to the diarylethene family and
are remarkable photochromic systems where the chemical transformation involves a ring-opening
reaction via single bond breaking (Scheme 4). These systems exhibit remarkable switching sensitivity
and rapid response: both ring-opening (cycloreversion) and ring-closure (cyclization) reactions occur
with high quantum yields and in the picosecond time domain.88a

33
Scheme 4. Dithienylethene (DTE) photochromic system.
Because the distribution of π-bonds is different in both isomers, they have distinct absorption
spectra. We will show that the photophysics and the efficiency of the system are completely controlled
by the relationship between the reaction path and the degeneracy-lifting coordinates at an S0/S1 MECI.
Figure 17 shows a cartoon of the dithienylethene S0 and S1 PESs that can be derived from the static
and dynamics computations reported in reference [92]. There is a ground-state thermal reaction path
involving a transition state TS connecting the closed-ring isomer (DTEc) to the open-ring isomer
(DTEo). In addition, there is an adiabatic reaction path on the excited state involving a closed-ring
minimum (DTEc*), a transition state TS*, and an open-ring minimum (DTEo*). Finally, a conical
intersection seam, S0/S1 CI, runs along the reaction path as a result of the orthogonal character of the
reaction coordinate with the branching space. Thus, decay to S0 is controlled by motion orthogonal to
the reaction path and dynamics simulations are necessary to explain why the conical intersection is
accessible. Furthermore, the transition state (TS*) is a narrow bottleneck. Just because the system has
enough energy to get over the transition state does not mean that it will find it. In fact, passing through
the transition state will be a rare event: not only the energy needs to be sufficient, but also it needs to
be distributed in exactly the right mode (i.e., the transition vector). A trajectory started at the Franck-
Condon structure on the DTEo side of the reaction will remain in the DTEo* minimum for a “long”
time and will not necessarily find the transition state. By contrast, the conical intersection is a many-
dimensional hypersurface, and consequently more accessible. It is not a dynamical bottleneck in the
same way as a transition state. Once the crossing seam is reached, decay to S0 is immediate.
Figure 17. S0 and S1 potential energy landscape along the reaction path corresponding to the
DTEc→DTEo photoisomerization. The reaction coordinate Rx is orthogonal to the branching space
and the conical intersection appears as a seam running along Rx. The S0/S1 MECI structure is shown
on the right.

34
The MECI on the conical intersection hyperline is shown in Figure 17. While it appears quite
close to the transition state on the excited state, it is actually on the DTEo side of the barrier. In the
dynamics computations,92 a typical trajectory (as shown in Figure 18) started from the Franck-Condon
region on the DTEo side of the reaction path lives in the DTEo* minimum for almost two picoseconds,
until a vibration that has enough energy inside the branching space (i.e., orthogonal to the reaction
coordinate) drives it towards the CI seam and decay takes place to the ground state. The central point
is that knowledge of the excited-state reaction path does not yield an understanding of the
photochromism of this system. Simply finding the conical intersection points does not yield a
complete picture, because they do not lie on the reaction path (note that the situation was different in
DHA/VHF, as the intersection seam was intercepted by the reaction path). Indeed, a large segment of
the intersection seam in this region is energetically accessible. However, to demonstrate and
understand this, dynamics simulations need to be performed. Moreover, the MD simulations confirm
that the crossing seam is reached before finding the “bottleneck” formed by the transition structure
TS* on S1. These simulations confirm the highly effective and ultrafast cyclization reaction.
Figure 18. Description of the four phases in a typical MMVB trajectory on a prototype hydrocarbon
model system started on the DTEo side: 1) ultrafast relaxation to DTEo*, 2) motion on S1 in the DTEo*
minimum well, 3) energy flowing in one of the degeneracy-lifting coordinates and system decaying at
the S0/S1 CI, and 4) ring-closure on S0.
Experimentally, one observes fluorescence that is red-shifted, confirming that the position of the
minimum is different on the excited state, as shown in Figure 17. The cyclization quantum yield
(DTEo* to DTEc) is high, which arises from the fact that a trajectory from DTEo* can sample the
whole intersection seam, at right angles to the reaction path. On the other hand, for a trajectory starting
from DTEc*, the probability of decay to S0 is low, because the main locus of the conical intersection
seam appears to be on the DTEo* side of the transition state. Thus, to reach DTEo from DTEc*, the
system has to pass through the transition state TS* on the adiabatic excited-state reaction path. Hence,
there is a competition between passing through the transition state to reach the reactive conical
intersection on the DTEo* side of TS*, decay at a nearby crossing on the DTEc* side of the transition
state (not shown in Figure 17), which does not lead to any reaction, and fluorescence from DTEc*.
This accounts for the relatively low cycloreversion quantum yield and its temperature-dependent
character.

35
Dihydropyrenes photochromism. Dihydropyrenes (DHPs) also belong to the diarylethene family.
However, in contrast with DTEs, DHPs have the particularity to be negative photochromes, which
makes them highly interesting because the thermally stable isomer is the more colored one, while
positive photochromes such as DTEs have the more stable form colorless. The colored form bleaches
upon exposure to visible light corresponding to the formation of the cyclophanediene (CPD) isomer
and returns to the colored DHP isomer upon exposure to UV light or in some cases thermally (Scheme
5).93 However, the low DHP to CPD isomerization quantum yields and a fast rate of thermal back
reaction in these compounds were representing an obstacle for their use as efficient photochromic
systems.
Scheme 5. The dimethyldihydropyrene (DHP) / cyclophanediene (CPD) photochromic system.
The reasons behind this lack of efficiency was rationalized based on an extensive
CASSCF/CASPT2 ab initio study of the reference compound shown in Scheme 5.94 The very low
ring-opening quantum yield observed upon irradiation of DHP was explained by the quenching of the
photoisomerization channel by internal conversion of the initially excited zwitterionic (Z) state to the
lowest locally-excited (LE) state minimum (blue arrow, Figure 19), where the system can fluoresce or
decay back to the ground state via another internal conversion. To undergo the DHP to CPD ring-
opening reaction, the system needs to reach a biradical intermediate (correlating with the S4 state at the
Franck-Condon geometry denoted B state) via the population of a CPD precursor (CPD*) on S2
followed by internal conversion at a conical intersection between the zwitterionic and biradicaloid
states. Upon population of the biradical intermediate, the system can then decay to the ground state at
a nearby conical intersection (photochemical funnel) leading to product formation. An elongated
Figure 19. CASPT2 potential energy profiles of the relevant electronic states involved in the DHP /
CPD photochromism. GS: ground state, LE: locally excited, Z: zwitterionic, B: biradicaloid, IC:
internal conversion. A doubly-excited S3 state quasi-degenerate with the B state at the FC geometry is
not shown for simplicity.

36
transannular bond and a loss of planarity of the DHP core relative to the ground-state structure
characterize the CPD precursor and represent the triggering process. On the other hand, irradiation of
CPD leads to the formation of a biradical excited-state minimum along the ring-closure reaction path.
Internal conversion back to the ground state can then occur at the same photochemical funnel, leading
to the DHP photoproduct (purple arrows, Figure 19). Thus, our results point unambiguously towards a
stepwise mechanism involving the formation of a biradical intermediate on a singlet excited state. The
fact that this intermediate does not correspond to the lowest excited-state minimum is mainly
responsible for the inefficiency of this system. The internal conversion mechanism responsible for the
photochromic properties of these compounds is also controlled by the accessibility of a crossing seam,
similar to the one found in dithienylethenes.92 Based on our proposed mechanism, one could increase
the efficiency of these systems by using substituents in order to energetically lower the biradical
intermediate relative to the other excited-state minima and/or by suppressing the internal conversion of
the initially excited Z state to the lowest LE state.
Attempts to synthesize more efficient DHP derivatives were successful using benzo[e]-fused-
DHPs,93 isobutenyl- and naphthoyl-DHPs,95 and pyridinium-appended-DHPs.96 We investigated
theoretically the excited-state photoswitching mechanism in these improved DHP derivatives denoted
DHP-1 to DHP-4, respectively (Chart 1).96,97 Because of the size of these derivatives, we did not use
the highly accurate CASSCF/CASPT2 approach employed to study the reference compound. We used
DFT and TD-DFT calculations instead. While the biradicaloid state cannot be described with TD-DFT
because of the doubly-excited nature of this electronic state, TD-DFT is expected to describe the
S2→S1 deactivation pathway, as both states results from single excitations. This was first verified for
the reference compound. After validation of the description of the S2→S1 photophysical path at the
TD-DFT level, we investigated the pathway leading to CPD* for the improved DHP derivatives 1 to 4
shown in Chart 1. In DHP-1, the efficient ring-opening reaction is made possible by the inversion of
states occurring between S1 and S2. Thus, CPD* formation takes place directly on the lowest S1 PES
and no internal conversion with another excited state is involved (Figure 20a). In DHP-2 and DHP-3,
the S1 and S2 states are in the same order as in the reference DHP, but CPD* corresponds to the lowest
minimum on the S1 PES and the topology and accessibility of the S2/S1 conical intersection render
CPD* formation efficient (Figure 20b). In DHP-4, the pyridinium electron withdrawing groups create
excited states of charge transfer (CT) character and CPD* formation takes place directly on the lowest
S1 PES (Figure 20c).
Chart 1. DHP derivatives investigated theoretically: benzo[e]-fused-DHP (DHP-1), isobutenyl-DHP
(DHP-2), naphthoyl-DHP (DHP-3), pyridinium-appended-DHP (DHP-4) and benzo[e]-fused-
naphthoyl-DHP (DHP-5).

37
Figure 20. Computed photochemical pathways leading to CPD precursor (CPD*) formation in (a)
DHP-1, (b) DHP-3, (c) DHP-4, and (d) DHP-5. Calculations performed at TD-DFT level using a
linearly-interpolated transit path (LITP).
The previous results show that two distinct effects come into play in the improved efficiency of
these DHP derivatives. In DHP-1 and DHP-4, the inversion of electronic states between S1 and S2 is
the main factor (with the subtlety that CT character is present in both states of DHP-4), allowing the
efficient formation of CPD* directly on S1. In DHP-2 and DHP-3, no inversion between S1 and S2 is
observed but the stabilization of CPD* on the S1 PES in association with a more substantial elongation
of the transannular bond is the key factor. A reasonable strategy to propose a rationally-designed
improved system is to try combining both effects using a benzo[e]-fused version of DHP-3. The main
result for the as yet unsynthesized benzo[e]-fused-naphthoyl-DHP (DHP-5, Chart 1) is presented in
Figure 20d. It shows that we can combine the two effects separately responsible for improved ring-
opening isomerization efficiency in DHP-1,4 and DHP-2,3, i.e. i) having the zwitterionic state
producing CPD* as the lowest excited state and ii) having CPD* as the lowest-lying S1 minimum
along with a substantial elongation of the transannular bond. We may thus anticipate an unprecedented
efficiency for DHP-5. This is a nice illustration of the power of computational photochemistry to
deliver guidelines for designing new chromophores with improved potentials.
4.1.3. Intramolecular charge transfer.
We now move to photoinduced charge transfer processes, which are of utmost importance in
photochemistry. The example we will use is the intramolecular charge transfer (ICT) potentially
occurring in aminobenzonitrile compounds (Scheme 6).98 4-Aminobenzonitrile (ABN) and 4-
dimethylaminobenzonitrile (DMABN) will be used as prototype examples. In such compounds there

38
are two low-lying excited states: a locally excited (LE) state where the excitation is localized on the
phenyl ring (anti-Kekule structure), and the intramolecular charge transfer (ICT) state, where there is a
transfer of charge from the amino group to the benzene ring. The ICT state is thus similar
(electronically) to a benzene radical anion. This zwitterionic state is characterized by a large dipole
moment. In spectroscopy, with suitable substitution R and in the appropriate solvent, one can see
emission from each state.98 The mechanism accounting for the observation of this dual fluorescence is
highly controversial and has been the subject of many experimental and theoretical studies. The
central issues relate to i) the molecular and electronic structures of the emitting ICT species, ii) the
nature of the adiabatic reaction pathway which connects the LE species to the ICT emitting state, and
iii) the nature of the nonadiabatic reaction path via a conical intersection which connects the FC
structure on S2 to the LE and ICT species which emit from S1.99 Regarding the first issue, the lowest
energy equilibrium geometry of the ICT state is usually assumed to be twisted; hence the acronym
TICT (Scheme 6), but other ICT structures have been proposed such as a planar ICT (PICT) structure
which have long been debated in the literature. Since one can observe dual fluorescence, there must be
two S1 minima, associated with the LE and ICT electronic structures. An adiabatic reaction path must
therefore connect these two electronic structures on S1. Thus, there is an adiabatic reaction coordinate
associated with the electron transfer process. This is related to the second issue. However, the
absorption from the ground state to the LE state in the Franck–Condon region is “forbidden”. Rather
the absorption takes place to S2, which is the ICT state at the Franck–Condon geometry. Thus, there is
also a nonadiabatic ICT process associated with the radiationless decay from S2(ICT) to S1(LE). This
is the third aspect that we need to investigate.
Scheme 6. Schematic representation of the ICT process and the generation of LE, PICT or TICT
states.
The problematics just discussed above can be summarized in the potential energy profile shown in
Figure 21a. From this figure it is clear that the (adiabatic) state labels S1 and S2 and the (diabatic)
structure labels ICT or LE are independent. The adiabatic reaction path (solid arrow), involving a
transition state (i.e., avoided crossing) appears to be associated with the real crossing. The TICT
coordinate (amino group torsion) is assumed to be the reaction path. The transition state on this
reaction path is associated with a state change from LE to ICT. This state change can also be
associated with the nonadiabatic process via the real crossing. However, the real crossing and the
nature of the branching space and its relationship to the adiabatic reaction path can be understood only
by moving to higher dimensions and by consideration of the relationship between the branching space

39
coordinates and the torsion coordinate. In other words, we need to consider the PES model including
the reaction path and the branching space coordinates. This is shown in Figure 21b for the particular
case of ABN.
Figure 21. Adiabatic and nonadiabatic reaction profiles for the TICT process. (a) Schematic potential
energy profiles represented along the reaction coordinate (mainly amino group torsion). (b) Schematic
potential energy landscape represented in the space that includes the reaction coordinate and one of the
two branching space coordinates, along with the S1/S2 MECI (distances in Å) and the associated
branching space coordinates. The dotted arrows show the nonadiabatic pathways. The solid arrow
shows the adiabatic pathway. In (b), the S1-TICT minimum is represented higher in energy than the
S1-LE minimum, as this potential energy landscape is based on calculations in the gas phase of ABN.
In Figure 21b, we show the geometry of the S1/S2 LE/ICT MECI, together with the degeneracy-
lifting coordinates x1 and x2 in ABN. The crossing occurs between the LE and ICT quinoid structures.
The most important point about the geometry is that the amino group is not twisted. The directions x1
and x2 are mainly skeletal deformations of the phenyl ring and do not involve the amino group torsion.
This is completely consistent with the fact that the LE and ICT quinoid structures differ essentially
only in the phenyl ring (Figure 22). A local minimum for the ICT quinoid structure is found on S2 with
a planar conformation (S2-PICT, Figures 21b and 22) and the system can access the S1/S2 conical
intersection seam from this minimum. Thus, we have established that the nonadiabatic decay does not
necessarily involve the amino group torsion, since the directions x1 and x2 exclude this coordinate.
Figure 22. CASSCF geometries, electronic structures (in red) and dipole moments (
µ
) of the ground
state (GS), LE, PICT, TICT, and RICT minima in ABN. All bond lengths are in Å.

40
Thus, the ICT mechanism in ABN and DMABN can be summarized as follows. After excitation
to the S2 state, the system relaxes quickly to a shallow S2-PICT minimum. No significant barrier
occurs between S2-PICT and the S1/S2 MECI. Because of the extended conical intersection seam,
ultrafast nonradiative S2→S1 decay can take place at various torsion angles of the amino group leading
to either S1-LE or S1-TICT geometries (green dotted arrows in Figure 21b). Experimentally, the
ultrafast decay through the S1/S2 CI leads to both LE and TICT simultaneously.100 The branching at
the CI favors the formation of the LE state because the lowest energy point on the crossing seam is not
twisted. Equilibration can then occur on S1 so the dual fluorescence is controlled by the S1-LE and S1-
TICT adiabatic reaction path. In ABN, because the equilibrium is displaced towards the LE minimum,
the S1-TICT minimum is not populated, and fluorescence occurs only from the S1-LE state (no ICT
reaction). For DMABN, population of LE and TICT can occur since the two species have similar
stabilities. This explains why dual fluorescence can be observed in DMABN but not in ABN. Our
mechanistic picture derived from static calculations has recently been confirmed by semi-classical and
quantum dynamics simulations.101,102
4.2. Photobiochemistry
4.2.1. Photostability and photodamage in DNA. Deoxyribonucleic acid (DNA) carries the
genetic information of all cellular forms of life. DNA is usually found as a double helix, in which the
nucleoside bases of the single strands are stacked upon each other, forming strong hydrogen bonds
with the bases in the complementary strand (Watson-Crick configuration).103 Due to the absorbance of
the bases in the harmful UV region of the spectrum (wavelength < 400 nm), DNA is vulnerable to
photochemical damage. To protect the genetic information, highly elaborate mechanisms have evolved
to repair damaged DNA. More important, however, is the robustness of DNA with respect to UV
damage. Indeed, when arranged in the Watson-Crick configuration, the isolated base pairs have an
extremely short excited-state lifetime,104 suggesting a very high photostability. Excited-state decay
Figure 23. Illustration of the excited-state dynamics of a Watson-Crick cytosine-guanine base pair
after light absorption. The snapshots show the light-induced transfer of the central proton from a
guanine to a cytosine. After this transfer, a radiationless transition to the ground state takes place (18
fs). The proton then rapidly returns to the guanine, restoring the Watson-Crick base pair (200 fs).

41
measurements of bases and model base pairs suggest a subpicosecond repopulation of the ground
state.104,105 Experimental evidences indicate that the excited state of an isolated cytosine-guanine (C-G)
base pair has a lifetime in the order of a few tens of femtoseconds.106 Quantum chemistry calculations
on the isolated C-G suggested that this ultrafast deactivation may be triggered by a barrierless single
proton transfer in the excited state.107 We investigated the photostability of C-G both in the gas phase
and embedded in DNA.108 This study provided detailed structural and dynamical insights into the
ultrafast radiationless deactivation mechanism.
Figure 23 shows the sequence of events that follows excitation of a C-G base pair in DNA.
According to our QM/MM simulations, photon absorption induces the transfer of a proton from the
guanine to the cytosine. This proton transfer enhances ultrafast decay of the excited state. After the
radiationless transition to the ground state, the original Watson-Crick configuration is quickly
restored. The entire photochemical reaction is completed within about 200 fs. The absorbed energy is
converted into heat and therefore does not lead to structural damage. These findings have been
corroborated by experimental observations.109 The existence of such ultrafast deactivation channel
confirmed the static picture provided by ab initio calculations performed in the gas phase.107 We
investigated in detail the potential energy landscape of the electronic states involved in this
mechanism and the results are summarized in Figure 24. Radiationless decay occurs along an extended
crossing seam that lies parallel to the proton transfer coordinate in the vicinity the excited-state
minimum. The gradient difference vector x1!and the derivative coupling vector x2!are collinear and
thus span a one-dimensional branching space. The seam is displaced from the proton path along a
skeletal deformation of the bases. Decay can thus occur anywhere along the proton transfer coordinate,
accounting for the remarkably short lifetime of the excited base pair.109 Note that during the dynamics
the system can encounter the seam more than once and recrossings between the excited and ground
Figure 24. S0 and S1 potential energy landscape of the cytosine-guanine (C-G) base pair along the
proton transfer reaction coordinate (Rx) and skeletal deformations of the bonds corresponding to the
collinear branching space coordinates x1 and x2. Motion along the proton transfer coordinate
connects the Franck-Condon (FC) geometry to the minimum of the S1 charge transfer (CT) state.
Nonradiative decay occurs along the intersection seam between the surfaces.

42
states can occur repeatedly due to the unusual (n-1) dimensional seam with a sloped topology. Another
important point is that in the gas phase decay occurs after a complete proton transfer, whereas in
DNA, decay can also occur much earlier. The origin of this effect lies in a temporal electrostatic
stabilization of the dipole in the excited charge transfer state by the solvated DNA environment.
One important question that we still need to answer is the origin of the driving force for such
excited-state proton transfer mechanism. A useful insight can be obtained from the various valence
bond structures (Scheme 7) involved along the reaction coordinate. According to our calculations,
photoexcitation to the CT state induces an electron transfer from guanine to cytosine giving rise to a
zwitterionic structure (a→d, Scheme 7) in which guanine is positively charged and cytosine is
negatively charged. This charge separation is the main driving force for the proton transfer from
guanine to cytosine giving rise to a photoinduced proton-coupled electron transfer process. Upon the
central proton transfer, the CT state is stabilized by restoring a non-zwitterionic electronic structure
(d→d’, Scheme 7). Along this relaxation coordinate, the ground-state structure is destabilized by
acquiring a zwitterionic character (a’, Scheme 7) in which guanine is negatively charged and cytosine
is positively charged this time. Thus, this opposite charge transfer provides the driving force for the
central proton to return to guanine (a’→a, Scheme 7) after S1→S0 nonradiative decay. Note that there
are low-lying locally excited (LE) states in the Franck-Condon region (b and c, Scheme 7) but these
states are destabilized upon the central proton transfer coordinate giving rise to low-lying conical
intersections between the LE states and the CT state.
To conclude, understanding the dynamics of the ultrafast deactivation processes in the C-G base
pair represents a major challenge. Here we demonstrated that, by using a combined static and
dynamical study of the system in the gas phase and in its biological environment, it is possible not
only to reproduce the experimental excited-state lifetime, but also to provide detailed mechanistic
Scheme 7. Valence bond representations of the C-G base pair in the relevant electronic states.

43
insights into the deactivation process.
Intrastrand thymine photodimerization (Figure 25a) is recognized as the most common process
leading to DNA damage under UV irradiation.110 The formation of thymine dimers has potentially
important physiological consequences. This mutagenic photoproduct can disrupt the function of DNA
and thereby trigger complex biological responses, including apoptosis, immune suppression, and
carcinogenesis.111
Figure 25. (a) Stacked thymines in DNA. (b) CASSCF potential energy landscape for the
photochemical [2+2] cycloaddition of two stacked thymines along with the structure of the S0/S1
MECI. Gradient difference (x1) and derivative coupling (x2) vectors forming the branching space are
shown. Interatomic distances are given in Å.
A recent study based on femtosecond time-resolved infrared spectroscopy showed that thymine
dimers are fully formed around 1 ps after UV excitation.112 The authors concluded that this ultrafast
photolesion rate points to an excited-state reaction that is nearly barrierless for bases that are properly
oriented at the instant of light absorption. It was suggested that the low quantum yield of this
photoreaction results from infrequent conformational states in the unexcited system. However, this
study did not provide a mechanistic picture of the photoactivated thymine dimerization process. Our
theoretical investigation was aimed at finding the photochemical pathway leading to the formation of
the thymine dimer in the gas phase and characterizing the funnel required for this ultrafast process.113
The mechanistic picture is summarized in Figure 25b. Unlike the ground-state reaction pathway,
which involves a highly activated stepwise process, the excited-state photochemical [2+2]
cycloaddition takes place through a concerted mechanism. The process is barrierless and leads to a
low-lying minimum energy conical intersection, S0/S1 MECI, where ultrafast nonradiative decay to the
ground state is extremely efficient. Such a nonadiabatic pathway is reminiscent of the one found in the
ethylene-ethylene photochemical cycloaddition.63a,114 The peaked topology of the CI suggests that
upon decay to the ground state at S0/S1 MECI the system can either evolve to the dimeric
photoproduct or reverse back to the original reactant. It has been suggested that photodimer formation
occurs with a quantum yield close to unity when the molecule is excited in a favorable conformation,
while in the more common unfavorable conformations the excited state will be unreactive.112 The very
low overall quantum yield of the thymine photodimerization can be mainly explained by the fact that
the photoreactive state is not easily accessible at the Franck-Condon geometry (it corresponds to state
S6 with a weaker oscillator strength than lower LE states at CASPT2 level)115 and its population

44
requires excitation of the stacked thymines at favorable but rare conformations where the two bases
are close to each other as in the funnel region.
4.2.2. Photoisomerizations in proteins. In this subsection, we give a brief overview of our
work on the photoisomerization in the photoactive yellow protein (PYP). Our choice for this system is
motivated by the fact that the photochemistry of this protein and of its chromophore has been
extensively studied by both experiments and computations, so that there is a wealth of data to compare
the outcome of our calculations to. PYP is known to be the primary photoreceptor for the
photoavoidance of the salt-tolerant bacterium Halorhodospira halophila. It contains a deprotonated 4-
hydroxy-cinnamic acid (or p-coumaric acid, pCA, Scheme 8) chromophore that is covalently linked to
the γ-sulfur atom of a cysteine amino acid (Cys69) via a thioester bond. Upon absorbing a blue-light
photon, PYP undergoes a complete photocycle involving several intermediates on timescales ranging
from a few hundred femtoseconds to seconds.116 Our focus is on the primary photochemical event,
which involves a trans-to-cis photoisomerization of the chromophore.
To understand how the protein mediates the photoisomerization of the chromophore, we have
performed atomistic simulations of the chromophore and related analogues in various molecular
environments.117,118 The results of these computations not only provided a detailed mechanistic picture
of the isomerization process, but also revealed the influence of the interactions with the environment.
With such detailed information new experiments can be designed, which will ultimately enhance our
understanding of the photochemistry of PYP.
Isolated chromophore. To investigate the intrinsic excited-state dynamics of the deprotonated
chromophore, we performed MD simulations of two isolated chromophore analogues (thiomethyl
para-coumaric acid, thio-pCA–, and para-coumaric-ketone, pCK–, Scheme 8). Because the
chromophore is deprotonated in the protein, we focused our attention on the anionic species. Note that
these anionic chromophores in isolation are autoionizing (i.e., unstable with respect to electron
detachment) upon electronic excitation. As our aim is to understand the effect of different molecular
environments on the photoisomerization processes, we need to study these hypothetical chromophore
models in vacuum as a reference.
Scheme 8. Schematic drawings of the p-coumaric acid (pCA) chromophore and the two analogues
used in our study.
After vertical excitation to S1, both chromophores rapidly relax from the Franck–Condon region
by twisting around the formal single bond adjacent to the chromophore ring (Scheme 8). After
reaching a single-bond-twisted minimum, no decay to the ground state occurred within 5 ps, which
was the total time of our MD simulations. The observation of a fast vibrational relaxation into the
single-bond-twisted S1 minimum for both thio-pCA– and pCK– is consistent with the topology of the
excited-state PES for these chromophores. Indeed, the topology of the S1 PES reveals that in both

45
chromophores there are two minima on S1, associated with bond twisting: the single-bond-twisted
minimum, in which the bond adjacent to the phenol ring is rotated by 90° (Figure 26a), and the
double-bond-twisted minimum, in which the ethylenic bond is twisted by 90° (Figure 26b). In the
isolated chromophores, there is no barrier for reaching the single-bond-twisted S1 minimum from the
Franck–Condon region, whereas there is a significant barrier to double-bond rotation (9.4 kJ/mol for
pCK– and 14.0 kJ/mol for thio-pCA– at the CASSCF level). Thus, in agreement with the MD
simulations, the main initial relaxation channel after excitation should involve rotation of the single
bond to 90°. Furthermore, we found that the S0/S1 CI seam lies rather far away from the single-bond-
twisted minimum. The seam can be accessed only upon rotation of the double bond. Based on these
findings we suggest that radiationless decay is not very efficient in vacuum. This observation is in line
with the relatively long excited-state lifetime of 52 ps for the isolated pCK– chromophore, measured
by means of time-resolved photoelectron spectroscopy.119 In the following, we have probed the effect
of different environments on the photochemistry of the chromophore.
Figure 26. Schematic overview of the S0 and S1 potential energy landscape along the (a) single-bond
and (b) double-bond torsion coordinates in the gas phase and in a micro-solvated environment.

46
Structures of the single-bond-twisted and double-bond-twisted S1 minima are shown along with the
corresponding S1 charge distributions. S0-S1 energy gaps at these minima and activation energies to
reach the S0/S1 MECI are also indicated.
Chromophore in water. To examine the effect of an aqueous environment, we have investigated
the excited-state dynamics of the deprotonated pCK– chromophore analogue in water using QM/MM
excited-state MD.118a The pCK– chromophore was chosen because experimental data are available
both in the gas phase119 and in water.120 Static calculations were also performed in order to investigate
the change in the PES landscape brought by the aqueous environment. Thus, we have computed the
PESs for the micro-solvated chromophore, including explicit water molecules at key positions (based
on the MD simulations) in the CASSCF calculations.
The results of the simulations demonstrate that radiationless decay is very efficient in water. The
predominant excited-state decay channel involves twisting of the single bond (88%) rather than
twisting of the double bond (12%), as illustrated in Figure 27. In contrast to the gas phase simulations,
decay takes place very near these minima. Inspection of the trajectories revealed that decay is
mediated by specific hydrogen-bond interactions with water molecules. These hydrogen bonds are
different for the single- and double-bond-twisted S1 minima. This reflects the difference in charge
distribution of the electronic structures at these minima. In the single-bond-twisted S1 minimum, the
negative charge resides on the alkene moiety of the chromophore (Figure 26a). Thus, it corresponds to
a twisted-intramolecular charge transfer (TICT) state. Three strong hydrogen bonds to the carbonyl
oxygen stabilize this charge distribution to such an extent that the crossing seam becomes accessible
from the single-bond-twisted S1 minimum (Figure 26a): the S0/S1 MECI presents a single-bond-
twisted structure lying only 8.1 kJ/mol above this minimum. In the double-bond-twisted S1 minimum,
the negative charge is localized on the phenolate ring (Figure 26b). Transient stabilization of this
charge distribution by two or more strong hydrogen bonds to the phenolate oxygen brings the seam
much closer to this S1 minimum (Figure 26b): the activation energy to reach the S0/S1 MECI with a
double-bond-twisted structure from this S1 minimum decreases from 29.3 kJ/mol in the gas phase to
13.5 kJ/mol in water. Thus, in water the ultrafast excited-state decay is clearly mediated by hydrogen
bonds. Note that among the 12% of trajectories that show twisting of the double bond, the
chromophore continued isomerizing towards the cis configuration after decay to S0 in just over half
the trajectories. In the other simulations, the trans configuration was restored.
Figure 27. In water, pCK– undergoes both single- (88%) and double-bond (12%) photoisomerizations.
Excited-state decay from the corresponding twisted minima is very efficient due to the stabilization of
the S1 charge distribution of the chromophore by specific hydrogen bond interactions.

47
To summarize, the predominant excited-state relaxation process of pCK– in water involves a
rotation of the single bond, adjacent to the phenolate ring, rather than rotation of the ethylenic double
bond. In the gas phase, only the double-bond torsion can lead to radiationless decay, whereas in water,
both channels lead to decay. This decay becomes ultrafast in water because of the proximity of the
S0/S1 intersection seam with the photochemical pathway. Because single-bond photoisomerization is
strongly favored over double-bond photoisomerization for pCK– in water, the probability of finding
the chromophore in the cis configuration is very low. This result is in good agreement with the
observed ultrashort excited-state lifetime of pCK– in water (~1 ps) and a negligible trans-to-cis
photoisomerization quantum yield.120
Effect of the protein environment. By displacing the S0/S1 crossing seam very close to the S1
minima, hydrogen-bond interactions between the chromophore and water molecules enhance excited-
state decay in water.118a Yet, the major decay channel involves torsion around the single bond, rather
than torsion around the double bond of the chromophore. To find out the effect of the protein
environment on the excited-state dynamics of the chromophore, QM/MM MD simulations of the wild-
type PYP, as well as on the Arg52Gln mutant, were carried out.117
Figure 28 shows the primary events after photoexcitation in the simulation of the wild-type
PYP.117a In the majority of the trajectories the chromophore rapidly decays to the ground state via a
90° torsion around the double bond. During this photoisomerization process, the hydrogen bonds
between the phenolate oxygen atom of the thio-pCA– chromophore and the side chains of the highly
conserved tyrosine (Tyr42) and glutamic acid (Glu46) residues remain intact. Just as in water, these
hydrogen bonds are essential to promote excited-state decay from the double-bond-twisted S1
minimum (Figure 26b). Upon returning to the ground state, the chromophore either relaxes back to the
original trans conformation (70% of the trajectories) or it continues isomerizing to a cis conformation
(remaining 30%). In the latter case, the relaxation also involves a flip of the thioester linkage, which
causes the carbonyl group to rotate by 180°. During this rotation, the hydrogen bond between the
carbonyl oxygen and the Cys69 backbone amino group is broken (Figure 28). The loss of this hydrogen
bond has been observed in time-resolved infrared spectroscopy121 as well as in time-resolved Laue
crystallography studies.122
Figure 28. Snapshots from QM/MM MD simulations of wild-type PYP, showing the thio-pCA–
chromophore in the active site pocket. The first snapshot is at the excitation. The second shows the
configuration at the S1→S0 radiationless transition. The third snapshot shows the photoproduct, in
which the carbonyl oxygen of the thioester linkage has flipped and is no longer hydrogen bonded to
the backbone of Cys69.
Although the number of trajectories is too small (only 14 QM/MM MD simulations could be run
back in 2004) to rule out that single-bond isomerization could also occur in the wild-type protein, no

48
single-bond isomerization was observed.117a Because in water single-bond isomerization is the main
decay channel, the latter observation implies that the protein not only provides the hydrogen bonds
required for ultrafast decay, but also controls which of the chromophore bonds isomerizes upon
photoexcitation. It was speculated at the time that a positive guanidinium moiety of an arginine amino
acid (Arg52) located just above the chromophore ring, acts as the ‘catalytic’ residue that enforces
double-bond isomerization. This hypothesis was tested by removing the charge from the Arg52 side
chain in a snapshot taken at the S1→S0 hop, and recalculating the energy gap. The gap increased by 40
kJ/mol.117a This result suggested that a preferential electrostatic stabilization of the double-bond
twisted S1 minimum by the positive Arg52 favors double-bond isomerization over single-bond
isomerization in the wild-type protein. Recent theoretical works on an isolated pCK– chromophore in
the presence of an external electric field confirms that the photoisomerization can indeed be controlled
by electrostatic interactions.123
To elucidate the role of Arg52 in the activation process in more detail, we investigated the excited-
state dynamics of the Arg52Gln mutant of PYP (R52Q), in which the positively charged Arg52 has
been replaced by a neutral glutamine (Gln52) residue.117b Such PYP mutant can still enter the
photocycle, albeit with lower rate and quantum yield.124 Without the positive Arg52, the predominant
photochemical reaction path in the simulations involved isomerization of the single bond in the
chromophore, rather than isomerization of the double bond (Figure 29).117b Although the latter was
also observed in one of the trajectory, it is a minor decay channel. Again, the number of trajectories (a
few tens) is too low to make quantitative predictions. Nevertheless, the R52Q mutant simulations
confirm that within our model the role of Arg52 is to steer the initial events after photon absorption to
ensure rotation of the double bond rather than that of the single bond in the chromophore.
Figure 29. Snapshots from QM/MM MD simulations of Arg52Gln mutant of PYP (R52Q), showing
the thio-pCA– chromophore in the active site pocket. The first snapshot is at the excitation. The second
shows the configuration at the S1→S0 radiationless transition. The third snapshot shows the
photoproduct. In this mutant, isomerization takes place around the single-bond. Like in the wild-type
protein, the carbonyl oxygen of the thioester linkage flips, causing the break of the hydrogen bond to
the backbone of Cys69 (20% of the trajectories).
Remarkably, the hydrogen-bonding interactions play also an essential role in the decay process of
the mutant. During rotation of the single bond, the hydrogen bond between the carbonyl oxygen and
the Cys69 backbone amino group is broken. In contrast to the wild-type, the rupture of this bond occurs
before the decay. Therefore this may seem at conflict with the observation that in water three
hydrogen bonds at the carbonyl group are required to make the S0/S1 crossing seam accessible from
the single-bond-twisted minimum. However, as shown in Figure 30, new hydrogen bonds are rapidly
formed between the carbonyl oxygen atom and the backbone amino groups of Tyr98 and Asp97. A
water molecule enters the chromophore pocket to donate a third hydrogen bond. This is possible

49
because the chromophore pocket has become more exposed to the solvent due to the replacement of
the rather bulky arginine side chain by the much smaller glutamine side chain. With these three
hydrogen bonds stabilizing the negative charge on the alkene moiety, the chromophore rapidly decays
to S0. Thus, the decay mechanisms in the Arg52Gln mutant and in water are essentially the same in
our simulations.
Figure 30. Snapshots from an excited-state trajectory of the Arg52Gln mutant of PYP (R52Q),
demonstrating that three hydrogen bonds to the carbonyl moiety are essential for S1→S0 radiationless
decay near the single-bond-twisted minimum. The first snapshot (a) is at the excitation to S1. The
second snapshot (b) shows the twisted configuration without hydrogen bonds to the carbonyl. The gap
between S1 and S0 is far too high for decay at this configuration. However, as the third snapshot (c)
shows, two backbone amino groups and a bulk water that has moved into the chromophore pocket
during the excited-state dynamics donate the three hydrogen bonds that are required for efficient decay
from the S1 minimum.
Although single-bond isomerization does not result in the formation of the cis chromophore, a
180° flip of the thioester group and a rupture of the hydrogen bond to Cys69 were observed in 20% of
the trajectories (Figure 29). Together with the experimental observation that the mutant can still enter
the photocycle, this suggests that the key step to enter the photocycle may be the carbonyl flip rather
than the double-bond isomerization. This suggestion is further supported by the observation that when
the protein is reconstituted with chromophore analogues that cannot isomerize,125 PYP can still enter
the photocycle.126 In these chromophores the isomerization is prevented by either a covalent bridge
that blocks both single- and double-bond rotations, or by oxidation of the double bond to a triple bond.
However, since trans-to-cis isomerization of the double bond was also observed in R52Q, we cannot
rule out the possibility that only the latter process is responsible for photoactivation and that the
single-bond isomerization pathway is a dead-end in the process, responsible for the lower activation
yield in the mutant. Support for the involvement of the double-bond photoisomerization comes from
time-resolved absorption spectroscopy measurements that show the appearance of the cis
photoproduct on a sub-picosecond timescale in this mutant.127 In these experiments, the lower
quantum yield and slower deactivation dynamics as compared to the wild-type PYP were attributed to
a lower structural integrity of the chromophore pocket. Based on our simulations, however, we would
attribute the difference in efficiency to the involvement of the single-bond isomerization channel.
To summarize, the simulations have provided detailed structural and dynamical information at a
resolution well beyond that achievable by other means. From the simulations, we have identified key
amino acids and the mechanism by which they control the primary events in the photocycle of PYP.
These are i) the trans-to-cis photoisomerization around the double bond and ii) the break of a

50
hydrogen bond between the chromophore and the protein backbone. These events trigger a proton
transfer from the protein to the chromophore, which ultimately leads to the signaling state of PYP.128
4.3. Inorganic photochemistry
One of my main research line is devoted to the study of polypyridine ruthenium complexes. Such
complexes are extensively studied in coordination chemistry, material science and biochemistry due to
their remarkable photophysical and photochemical properties.129,130 In particular, ligands can be
chosen to tune these properties in order to design for example new photoluminescent or photovoltaic
systems with the aim to improve lighting devices131 or solar cells.132
In order to rationalize theoretically the photophysical and photochemical properties of such metal
complexes, it is important to understand the nature of the electronic states involved in the various
photoinduced processes. Our first studies were aimed at describing and characterizing the various
electronic excited states of archetypal ruthenium polypyridine complexes.133 As shown by the
simplified Jablonski diagram in Scheme 9, upon initial photoexcitation to singlet metal-to-ligand
charge transfer (1MLCT) states, the system relaxes to lower triplet states of either metal-to-ligand
charge transfer character (3MLCT states) or metal centered character (3MC state, also known as
ligand-field state or d-d state). This is made possible by the efficient intersystem crossing (ISC)
encountered in these 2nd row metal complexes for which spin-orbit coupling (SOC) is significant.134
The photophysical properties and photochemical reactivity are largely governed by the position of the
lowest 3MLCT state relative to that of the 3MC state and the associated equilibration pathway between
these states on the lowest triplet PES. While 1MLCT states are very short lived (fs timescale) because
of efficient ISC and mainly permit ultrafast electron transfer processes (e.g., such as the injection of an
electron in the conduction band of a semi-conductor in dye-sensitized solar cells132), 3MLCT states
have substantially longer lifetimes (ps up to µs timescale). For most polypyridine Ru(II) complexes,
the lowest 3MLCT state undergoes relatively slow radiationless transitions and thus exhibits fairly
long lifetime and intense luminescence.129 This state is also responsible for photoinduced electron
transfer reactions and photoreactivity with biomolecules (e.g., DNA and polypeptides).130a In contrast,
3MC states are short lived due to efficient radiationless transitions back to the ground state.129,134 The
dissociative character encountered in these 3MC states133 also allows for photoinduced ligand
dissociation, trans-to-cis photoisomerization and photosubstitution.135 In the following, we will
Scheme 9. Simplified Jablonski diagram indicating the main electronic states involved in various
photophysical and photochemical processes of the studied polypyridine ruthenium complexes. MLCT:
metal-to-ligand charge transfer, MC: metal centered, ISC: intersystem crossing.

51
present our main contribution as regard to designing efficient photoluminescent polypyridine
ruthenium complexes and understanding the linkage photoisomerization mechanisms in ruthenium
photochromic compounds.
Figure 31. Potential energy landscape of the triplet PES: comparison between (a) [Ru(bpy)3]2+ and (b)
[Ru(bpy)2(HN= CH–CH=NH)]2+. Red lines correspond to MEPs between 3MLCT and 3MC states
belonging to the C2 point group. CI: conical intersection, TS: transition state, SP: saddle point. Solid
arrows indicate the emission process from the 3MLCT state.
4.3.1. Photophysical properties of ruthenium complexes. As explained above, the lowest
3MLCT state is responsible for the observation of luminescence in polypyridine ruthenium complexes
provided that its lifetime is sufficiently long to undergo a radiative transition. One of the main reasons
for luminescence quenching is the depopulation of the 3MLCT in favor of a non-luminescent low-
lying 3MC state,129,134 as illustrated in Figure 31a. Thus, the excited-state lifetime of the 3MLCT state
is largely governed by the 3MLCT↔3MC equilibration pathway on the lowest triplet PES. To design a
long-lived photoluminescent candidate, one has to find a ruthenium complex with a 3MLCT state
sufficiently lower in energy than the 3MC state to improve the emission quantum yield. Two strategies
can be contemplated to increase the stability of the 3MLCT state relative to the 3MC state. One can
either use strong π-accepting ligands that will stabilize the 3MLCT state, or use strong σ-donating
ligands that will destabilize the 3MC state. These are the two strategies that we followed.
First, we used strong π-accepting acyclic α-diimine ligands such as 1,4-diaza-1,3-butadiene
(HN=CH–CH=NH). We substituted the 2,2’-bipyridine (bpy) ligands of the reference [Ru(bpy)3]2+
complex and investigated the effects of successive substitutions by this diazabutadiene ligand (Figure
32). We have investigated the absorption properties of these systems and the triplet potential energy
Figure 32. Series of [Ru(bpy)n(HN=CH
–
CH=NH)3-n]2+ (n=0–3) studied complexes.

52
landscape along the 3MLCT↔3MC equilibration path.136 This study showed a high stabilization of the
MLCT state due to the presence of the strong π-accepting diazabutadiene ligands, making these
complexes luminescent in the IR region (Figure 31b). In addition, the 3MC state became unstable on
the triplet PES, as the corresponding stationary point corresponds to a first-order saddle-point (Figure
31b). Thus, the 3MLCT→3MC deactivation pathway is efficiently suppressed in these complexes.137
Following the second strategy, strong σ-donating ligands were used in order to destabilize the
lowest 3MC state. To achieve this goal, we resorted to original organophosphorus ligands. Most
examples of Ru(II) complexes combining polypyridine and phosphorus ligands make use of phosphine
ligands.138 Here, we investigated polypyridine ruthenium complexes incorporating aminophosphine
and phosphoryl ligands, which displayed unprecedented luminescent properties for polypyridine
Ru(II) organophosphorus complexes.139,140 More precisely, we studied the following complexes:
[Ru(bpy)(tpy)(R2P–N=CH–N(i-Pr)2)]2+ (tpy = 2,2’:6’,2”-terpyridine, R = i-Pr, Ph) denoted [Ru-
P(N)]2+ and [Ru(bpy)(tpy)(PPh2O)]+, denoted [RuPO]+. The use of an aminophosphine ligand on the
one hand and of a phosphoryl ligand on the other hand proved largely successful to destabilize the
3MC state. Indeed, room-temperature luminescence in the visible range was observed for the complex
[Ru-P(N)]2+ (R = i-Pr), which was the first account of such photoluminescent behavior in the
[Ru(bpy)(tpy)(L)]2+ family of complexes.139 The [RuPO]+ complex synthesized subsequently proved
to be the complex with the longer emission lifetime at room temperature (57 ns),140 whereas it was
only 1.2 ns in [Ru-P(N)]2+.
In order to rationalize these results, we performed calculations of the Gibbs energy profiles
corresponding to the lowest triplet excited state along the 3MLCT↔3MC equilibration pathway for
[Ru-P(N)]2+ (R = Ph), [RuPO]+ and compared these to the one of the reference
[Ru(bpy)(tpy)(PPh2H)]2+ complex, denoted [Ru-PH]2+. Figure 33 collects these results and clearly
shows that the 3MC state has been destabilized relative to the 3MLCT state by substitution of an –H by
the –N=CH–N(i-Pr)2 group, and even more so by substitution with the anionic group –O–. In the case
of the [RuPO]+ complex, the minimum of the 3MC state becomes even higher in energy than the
minimum of the 3MLCT state. In addition, the 3MLCT→3MC activation energy increases substantially
in the following order [Ru-PH]2+ < [Ru-P(N)]2+ < [RuPO]+. This means that from a kinetic point of
view, we expect a longer 3MLCT excited-state lifetime in [RuPO]+ compared to that of [Ru-P(N)]2+,
Figure 33. Schematic Gibbs energy profiles computed using DFT in acetonitrile at 298 K for the three
complexes [Ru-PH]2+, [Ru-P(N)]2+ and [RuPO]+. 3MLCT states are set at the same energy for clarity.

53
being itself longer than that of [Ru-PH]2+. At low temperature (77 K), the three complexes are
photoluminescent because the system can remain trapped in the 3MLCT well for a long enough time to
undergo radiative decay. At room temperature, the system disposes of more vibrational kinetic energy
to overcome the 3MLCT→3MC barrier. The [Ru-PH]2+ complex becomes non-luminescent, as only a
small energy barrier has to be crossed to undergo 3MLCT→3MC deactivation. In [Ru-P(N)]2+ and
[RuPO]+, this barrier is increased significantly and provides a rationale for explaining the increased
3MLCT excited-state lifetime along with the room-temperature emission. Thus, these calculations
accounted for the substitution effects on the evolution of the photoluminescent behaviors at room
temperature in this series of complexes. Both favorable thermodynamic and kinetic factors are
responsible for the remarkable room-temperature luminescence properties of the phosphoryl complex.
4.3.2. Photochromic ruthenium complexes. Although transition metal complexes represent a
relatively small fraction within the realm of photochromic compounds, they offer a large flexibility to
tune the photochemical and photophysical properties with the use of different ligands. These systems
are often based on linkage isomerizations between the metal center, M, and various ambidentate
ligands. There are three main groups of inorganic compounds that are commonly used in
photochromic materials: nitrosyl (M-NO),141 sulfoxide (M-SO)142 and sulfur dioxide (M-SO2)143
complexes. First, we will focus on the photoisomerization mechanism in photochromic polypyridine
ruthenium sulfoxide complexes, which have attracted considerable interest over the past fifteen years
or so. An intriguing complex, [Ru(bpy)2(OSO)]+ (OSO = 2-methylsulfinylbenzoate, Scheme 10), for
which nonadiabatic photoisomerization via a conical intersection was deduced from the absence of
spectroscopic and kinetic signatures of an O-bonded 3MLCT state, has recently been synthesized.144
The photoisomerization was suspected to occur nonadiabatically from an S-bonded 3MLCT state or
from an
η
2-sulfoxide excited-state species. Further support of a nonadiabatic mechanism comes from
the fast timescale of the isomerization (124 ps) and time-resolved transient absorption spectroscopy.145
Our theoretical study of this compound focused on characterizing both the adiabatic and
nonadiabatic pathways for the S→O linkage photoisomerization on the lowest triplet PES.146 The
results are synthesized in Figure 34. The adiabatic route requires a multistep process involving both
3MLCT and 3MC states. The nonadiabatic mechanism was characterized by locating minimum energy
crossing points (MECPs) between the lowest triplet state and the singlet ground state. We know that,
at these critical points, efficient intersystem crossing due to significant spin-orbit interactions will take
place.134 The most important conclusions we can infer from Figure 34 are the following: i) the 3MC
states play a crucial role in the adiabatic mechanism: the isomerization route on the triplet PES going
from the S-bonded isomer to the O-bonded isomer can only proceed through the population of 3MC
states for which decoordination of S and O from the metal center are favorable energetically. The
critical step involving the rotation of the sulfoxide group to get from an S-bonded structure to an O-
bonded structure occurs via a transition state (SO-MC-TS, Figure 34) of 3MC character and with an
η
2
Scheme 10. Illustration of the [Ru(bpy)2(OSO)]+ photochromic system.

54
coordination; ii) the 3MC states also play a critical role in the nonadiabatic mechanism: the funnels
(conical intersections) for efficient triplet to singlet nonradiative decay (ISC) were all located in the
region of the 3MC states on the lowest triplet PES; iii) the nonadiabatic pathways are kinetically more
favorable than the adiabatic path: the activation energies required to access the funnels from the
respective nearby 3MC minima are lower than the barrier associated with the transition states on the
adiabatic triplet PES (in particular for the formation of the O-bonded 3MLCT state, O-MLCT1 in
Figure 34). All these results are in agreement with the experimental observations that no O-bonded
3MLCT state is formed and that the mechanism is taking place nonadiabatically through a conical
intersection. However, the calculations also demonstrate that the photoisomerization will involve an
excursion on the triplet PES in the region of 3MC states, which was not inferred from the reported
experimental observations.142,144,145
We then studied the [Ru(bpy)2(DMSO)2]2+ (DMSO = dimethyl sulfoxide) complex147 in order to
investigate the photoisomerization mechanisms of the DMSO ligands in the cis and trans isomers
(Scheme 11). When the DMSO ligands are in the cis position in the ground state, the stable species
corresponds to two S-bonded DMSO ligands (cis-SS). Upon photoexcitation, the cis-SS isomer is
converted into a species with two O-bonded DMSO ligands (cis-OO).147,148 The cis-OO isomer is
metastable and thermally reverts back to the cis-SS isomer. The thermal OO→SS linkage
Figure 34. Schematic representation of the lowest triplet excited-state Gibbs energy profile of
[Ru(bpy)2(OSO)]+ in methanol at 298 K for the S→
O linkage photoisomerization path. The adiabatic
pathway is shown as a black line. The region where nonadiabatic transitions can occur is represented
by a purple shaded area, and funnels for such transitions are shown as double cone pictograms.
Scheme 11. Schematic representation of the cis- and trans-[Ru(bpy)2(DMSO)2]2+ complexes.

55
isomerization occurs through a two-step process with the formation of an intermediate species with
one S-bonded DMSO and one O-bonded DMSO (cis-SO). For the trans complex, it is the trans-SO
isomer that is observed experimentally as a stable species, and its photoexcitation leads to the
formation of the trans-OO isomer.148 Our theoretical investigation aimed at elucidating the double
linkage photoisomerization mechanism in the cis complex (cis-SS→cis-OO) and the single linkage
photoisomerization mechanism in the trans complex (trans-SO→trans-OO).149
For the cis complex, reaction pathways that allow the adiabatic SS → OO isomerization on the
lowest triplet excited PES were identified. Along these paths, the S→O linkage isomerization of the
two S-bonded DMSO ligands occurs sequentially following one-photon excitation of the cis-SS
isomer and is thermodynamically allowed throughout. As for the linkage photoisomerization of the
bidentate OSO ligand in [Ru(bpy)2(OSO)]+, following the population of the lowest 3MLCT state that
already elongates the Ru−S bond, the intervention of highly distorted 3MC states is required to allow
the large structural rearrangements occurring during the linkage isomerization of DMSO ligands.146
The two possible adiabatic routes are i) SS-3MLCT→SO-3MC→OO-3MC→OO-3MLCT, or ii) SS-
3MLCT→SO-3MLCT→OO-3MC→OO-3MLCT (Figure 35a). In addition, some nonradiative
deactivations toward the ground state are favorable from 3MC states, especially after the linkage
isomerization of the first DMSO ligand, due to the presence of singlet/triplet conical intersections. In
this nonadiabatic scenario, the SO-bonded ground state is populated and a second photoexcitation is
required to isomerize the second S-bonded DMSO ligand, which results in a proposed two-photon
mechanism (Figure 35b).
For the trans complex, the mechanism is far simpler. As summarized in Figure 36, upon
photoexcitation, the system relaxes to the OO-3MC species leading to the ground-state photoproduct
OO-GS following nonradiative decay (ISC at a funnel near OO-3MC). This process is barrierless (no
Figure 35. (a) Gibbs energy profile of cis-[Ru(bpy)2(DMSO)2]2+ in DMSO at 298 K for the adiabatic
cis-SS → cis-OO photoisomerization paths. The Gibbs energies are arbitrarily given relative to the SS-
3MLCT state. The black line represents the lowest energy reaction path and the cyan line, an
alternative path. The inset schematically shows a possible bifurcation occurring after the first
transition state encountered along the back path. (b) Schematic depiction of the major events involved
in the stepwise cis-SS → cis-OO double photoisomerization mechanism. The various steps are labeled
sequentially for the one-photon mechanism (1−7) and the two-photon mechanism (1′−11′). Solid
arrows are used for absorption and emission, dashed arrows for intersystem crossings and curly arrows
for adiabatic processes.

56
minimum corresponding to the SO-3MLCT species) and population of the OO-3MLCT is highly
unlikely due to its high energy relative to the funnel near OO-3MC. This peculiarity implies that the
trans complex has probably the same behavior at room temperature and at low temperature, namely
the absence of emission from the SO-3MLCT state and a photochromic behavior.
Our interest in using organophosphorus ligand to tune the photophysical properties of
polypyridine ruthenium complexes (see subsection 4.3.1) also incited us to use this type of ligands to
design original photoswitchable and possibly photochromic complexes. While the aminophosphine
and phosphoryl ambidentate ligands reported above were successful in improving the luminescence
efficiency of polypyridine ruthenium complexes, they did not confer any photoisomerizable properties
to these systems. However, the phosphinidene oxide ligand (R-P=O) proved to be a completely
different story. We performed a DFT-based computational study in the gas phase and in acetonitrile
on the yet to be synthesized [Ru(tpy)(bpy)(POPh)]2+ (Ru–P, Figure 37a) and [Ru(tpy)(bpy)(OPPh)]2+
(Ru-O, Figure 37a) complexes and predicted that they would constitute a prototype for a new family
of inorganic photochromic systems.150
The computed P→O linkage photoisomerization pathways are schematized in Figure 37b. The P-
bonded isomer (Ru–P) and the O-bonded isomer (Ru–O) are characterized by distinct UV-visible
Figure 36. Schematic depiction of the SO→OO photoisomerization mechanism of trans-
[Ru(bpy)2(DMSO)2]2+. The various steps, which result in the population of the OO-GS state, are
labeled sequentially (1−4) and their nature is specified using the same code as in Figure 35.
Figure 37. (a) UV-visible absorption spectra of Ru–P and Ru–O linkage isomers of
[Ru(tpy)(bpy)(POPh)]2+ computed by TD-DFT. (b) Schematic representation of the adiabatic (green
line) and nonadiabatic (red line) mechanisms of the Ru–P → Ru–O photoisomerization process.
Triplet/singlet funnels are represented by double cone pictograms.

57
absorption spectra (Figure 37a): Ru–P is expected to be colorless, while Ru–O should be colored. The
main result is that the thermal isomerization is both kinetically and thermodynamically unfavorable,
whereas photoisomerization can readily take place either by adiabatic or nonadiabatic routes (Figure
37b). The adiabatic mechanism is based on a triplet potential energy profile that connects various
excited states of the two isomers. Although this mechanism can lead to the photoproduct formation,
the location of triplet/singlet funnels in the vicinity of the lowest energy minima along the excited-
state profile will favor the nonadiabatic pathways. We have shown that upon nonradiative decay (ISC)
at these funnels, the photoisomerization can complete on the ground state PES. Another consequence
of the presence of these funnels will be the absence of luminescence in this system. The reverse RuO
to RuP isomerization was found to be achievable only thermally. The backward isomerization barrier
is relatively large allowing the photoproduct to be long-lived (several hours), as found for example in
ruthenium sulfoxide complexes.151 Thus, the predicted bistability of the complex, the different
absorption properties (different colors) of the two isomers and their photoswitching properties make
this complex a promising candidate for photochromic devices.
5. Perspectives
5.1. Electronic energy transfer
Electronic energy transfer (EET) between chromophores is an important process in biology and
chemistry. In photosynthesis special antennae complexes harvest light, but the absorbed energy must
be transferred into another part of the system to be used. A famous example of EET is fluorescence
resonance energy transfer (FRET), where light is absorbed in one part of the system and emitted in
another part. FRET has become one of the most important tools for studying structure and dynamics of
biological systems.152 However, our understanding of how energy transfer occurs at the molecular
level is still rather limited and mostly based upon empirical theories, such as Förster theory153 and
Dexter theory154 that are of limited use to design new systems.
Our plan is to provide a general theoretical framework to rationalize EET processes at the
molecular level. We will use ab initio quantum chemistry approaches in combination with on-the-fly
nonadiabatic MD simulations to provide evidence for an EET mechanism that is based on chemical
reaction pathways on nonadiabatically coupled PESs. Our investigation will focus on a bridged
bichromophoric system155 shown in Figure 38. This dyad consists of a cyclic α-diketone incorporating
a para-substituted benzene ring. Upon photoexcitation to the (π,π*) state on benzene, EET takes place
to the (n,π*) state on the α-diketone moiety. By varying the length of the linkers connecting the two
chromophore units, Speiser and coworkers were able to control the distance and relative orientation
Figure 38. Illustration of EET in the P44 bichromophore.

58
between the chromophores. In the smallest dyad, with four aliphatic carbon atoms in both linkers
(denoted P44), excitation of benzene at 268 nm induces fluorescence of α-diketone at 480 nm with a
100% efficiency.155 We will thus try to understand the EET mechanism in P44 and account for the very
efficient energy transfer process that occurs in this bichromophoric system. We will also attempt to
rationalize the decrease of EET efficiency upon increasing the length of the aliphatic bridges by
studying the P55 and P66 systems.
5.2. Photoswitchable systems
5.2.1. Organic photoswitches. Another aspect that I would like to investigate in organic
photochromic systems is the improvement of photoisomerization efficiency with the use of
multiphoton excitation. For example, while DHA to VHF photoconversion is highly efficient in the
first electronic excited state, the backward isomerization can only take place thermally or via two-
photon excitation.90 The mechanistic picture obtained from our theoretical study back in 2002
provided an explanation for the forbidden VHF to DHA photoisomerization in the S1 state (see section
4.1.2).91 However, no investigation of the higher excited states has been performed to rationalize the
results from the two-pulse experiments.90c Similarly, dithienylethene photochromism has been
extensively studied both experimentally and theoretically. Our theoretical contribution provided a
detailed mechanistic picture for the cyclization and cycloreversion reactions in the first electronic
state.92 However, no theoretical data are available to interpret the recently observed increase of the
cycloreversion quantum yield following sequential two-photon excitation.156 One objective could be to
extend our theoretical studies to the excited states involved in these multiphoton excitation
experiments and rationalize the experimental data. Following this line of thought, we could also
consider whether the use of nonlinear optical processes (two-photon excitations) can improve the DHP
to CPD photoizomerization efficiency.
5.2.2. Reversibly switchable fluorescent proteins. Reversibly switchable fluorescent proteins
(RSFPs) are proteins homologous to the Green Fluorescent Protein (GFP) developed over the last
decade, that can be switched back and forth between a fluorescent state (ON state) and a non-
fluorescent state (OFF state) by irradiation at appropriate wavelengths (see Figure 39 for examples).
Figure 39. Schematic representation of the reversible thermal and photoinduced transitions of the
RSFP variants to be investigated: a) Dronpa, b) Padron and c) Dreiklang. The wavelengths driving the
different photoinduced processes are written at the end of the excitation flashes, and the associated
quantum yields on the side of the arrows. The emission wavelengths of the ON forms are indicated at
the lower right edge of the explosion pictograms symbolizing fluorescence. The half-lives of the
metastable forms are given at the right of the dashed arrows representing thermal recovery reactions.

59
The number of ON-OFF cycles that can actually be achieved varies from one RSFP to the other. It is
determined by the competition between reversible ON-OFF switching and irreversible photoreactions
equivalent to those responsible for the photobleaching of conventional fluorescent proteins.157 In
addition to the photoinduced transitions, RSFPs exhibit a thermal recovery reaction, which
spontaneously restores the most stable form (ON or OFF depending on the protein).
Thanks to their reversible photoconversion properties, RSFPs show great promise for numerous
new imaging techniques, in particular in the field of super-resolution imaging. As an example, in
PALM (photoactivation and localization microscopy) super-resolution imaging, a sparse subset of
RSFPs are switched ON, localized with subdiffraction spatial precision by fitting of the diffraction-
limited spots corresponding to single molecules, and then switched OFF.158 This process is repeated
many times, and the position information from all sequentially photoactivated subsets is assembled
into a super-resolution image.
One of the main drawbacks of available RSFPs is their low photoswitching quantum yields.
Higher photoswitching efficiencies would increase the number of achievable ON-OFF cycles, by
favoring reversible photoswitching over irreversible photoreactions. The ability to perform a high
number of ON-OFF cycles is important for applications (e.g., in PALM, it would increase the duration
of the super-resolution movies that can be acquired). Higher photoswitching efficiencies would
moreover decrease the irradiation time and/or power needed to drive the ON-OFF transitions.
It would be highly desirable to establish detailed models of the photophysics and photochemistry
of RSFPs, aimed in particular at understanding why some photoswitching quantum yields are so low.
It could then be used to rationally design new mutants with increased efficiency. For this purpose, we
would like to investigate both reactive processes leading to the photoswitched state and competitive
nonreactive excited-state relaxation processes leading back to the initial ground state in three RSFPs
named Dronpa, Padron and Dreiklang (Figure 39). As far as the photoswitching process is concerned,
X-ray crystallography studies revealed two types of mechanisms: the photoswitching of Dronpa159 and
Padron160 consists in cis/trans isomerization of the chromophore double bond and
protonation/deprotonation of its phenol group, while Dreiklang161 exhibits a completely different
photoswitching mechanism based on the reversible addition of a water molecule on the C-N double
bond of the imidazolinone ring (Figure 40).
Figure 40. Chromophore states in the ON and OFF forms of Dronpa, Padron and Dreiklang. The
molecular changes associated with the photoswitching reactions at chromophore level are indicated on
the side of the corresponding arrows. c and t stand for cis and trans, respectively.

60
Computational photochemistry is a formidable help to understand and interpret the extremely
complex time-resolved experimental data on such biological photoactive systems. To systematically
exploit the potential of such photoswitchable proteins and to enable rational improvements to their
properties require a detailed understanding of the molecular switching mechanism, which is still
largely unknown. In the past, we were able to unravel the photoswitching mechanism in asFP595
based on extensive CASSCF calculations and QM/MM excited-state MD simulations.162 Using a
similar strategy, our goal here will be to get insight into the nature of the intermediate states leading to
the final products identified by X-ray crystallography and to identify the amino acids that are
transiently involved in the photoswitching mechanism of these three RSFPs. We might then be in a
position to propose new variants of Dronpa, Padron and Dreiklang with increased photoswitching
quantum yields by mutagenesis at rationally selected amino acid positions. It is important to note that,
considering the complexity of the processes involved, this kind of studies can only be successful if a
close partnership between experiment and theory is established.
5.2.3. Inorganic photochromes. As mentioned in section 4.3.2, there exist inorganic
photochromic compounds which typically involve optical switching of an ambidentate ligand such as
NO+, SO2 or RR’S=O. Two families of complexes will be the center of my interest in the next future.
First, ruthenium nitrosyl complexes have found utility in a variety of applications, such as optical
switches and data storage,163 or medicine.164 Depending on the ancillary ligands, environment, and
irradiation wavelength, these complexes can undergo either intramolecular N→O linkage
photoisomerization141,165 or NO photorelease166 (Figure 41). A recent theoretical study has investigated
the initial part of the NO photorelease mechanism,167 but so far the mechanistic picture associated with
the intramolecular N→O linkage photoisomerization remains unclear. Our main objective will be to
investigate the photoreactivity of ruthenium nitrosyl complexes in realistic conditions in order to
understand the factors that govern the competition between intramolecular N→O linkage
photoisomerization and NO photorelease.
Figure 41. Illustration of the competing photoisomerization and photorelease mechanisms taking
place in the triplet states of a ruthenium nitrosyl complex. IC: internal conversion, ISC: intersystem
crossing, SOC: spin-orbit coupling.

61
Another family of inorganic photochromic complexes which we are interested in is the sulfoxide
(RR’S=O) family. Our recent theoretical studies of ruthenium sulfoxide complexes146,149 have revealed
the involvement of 3MC states in the nonadiabatic S→O linkage photoisomerization mechanism,
which was not inferred from the experimental observations.142 One of the reasons was that osmium
sulfoxide complexes can also undergo S→O linkage photoisomerization despite the fact that these MC
states are inaccessible for third-row transition metals.168 Thus, I will investigate theoretically the S→O
linkage photoisomerization in osmium sulfoxide complexes for which I expect to find a different
mechanism compared to their ruthenium counterparts.
5.2.4. Hybrid photochromes. In the context of elaborating multifunctional materials, two
main strategies can be followed. The first one consists in combining several photochromic units onto a
single molecule to allow for multiswitchable systems.89a,169 This approach has been successfully
applied for the first time between dihydroazulene and diarylethene chromophores.170 The second
promising approach is to covalently link organic photochromic derivatives with metal complexes.171
An example is the bridging of bisterpyridine ruthenium complexes with DHP/CPD photochromes.172
One strategy we are considering is the possibility to merge these two distinct approaches by linking
DHP/CPD photochromes to photochromic ruthenium nitrosyl or sulfoxide complexes (Scheme 12 for
an illustration using ruthenium nitrosyl complexes). To our knowledge, it would be the first attempt to
attach an organic negative photochrome to an inorganic positive photochrome. We anticipate that from
the Ru-NO/DHP stable ground-state isomer, we may be able to control the reversible transformation to
the metastable states Ru-ON/DHP and Ru-NO/CPD. These two states should have distinct optical
signatures and we will investigate whether the Ru-ON/CPD isomer formation can be controlled,
providing an original cyclic multistep switch. In the case of ruthenium nitrosyl complexes, it will also
be interesting to verify if the NO photorelease properties is modulated by the presence of the organic
photochrome.
5.3. SOC nonadiabatic dynamics in transition metal complexes
So far, all our theoretical studies of ruthenium complexes have been limited to the exploration of
the excited-state PESs to rationalize their photochemical and photophysical properties. The static
Scheme 12. Example of a hybrid multiswitchable system based on ruthenium nitrosyl complexes
linked with DHP/CPD photochromes.

62
information gained from these calculations has been enlightening (see section 4.3). Two main
hypotheses were made to derive the mechanistic features from the excited-state potential energy
landscapes: i) we assumed that the photochemical and photophysical properties of the studied
complexes could be rationalized based only on the population of the lowest triplet excited state, and ii)
nonradiative deactivations by ISC were assumed to take place at singlet/triplet crossings only. While it
is reasonable to think that the lowest excited state will eventually be populated, the relaxations
pathways from the initially excited singlet states and their possible deactivation to higher triplet states
by ISC have been ignored. In other words, the initial part of the photochemical path is completely
overlooked and assumed to lead to the lowest excited state on an ultrafast timescale. Moreover, while
we know that efficient ISC will take place at singlet/triplet crossings, SOC will also allow ISC to take
place away from the crossing regions. It would therefore be desirable to go beyond the “simple” static
approach and investigate the photochemistry of these systems from the initially excited singlet states
to the final photoproducts using a dynamical strategy which allows the computation of the
nonadiabatic transition probabilities between singlet and triplet states like in the case of internal
conversion (see section 3.2).
The TSH method74 was originally formulated to consider only nonadiabatic couplings between
electronic states of the same spin multiplicity and has been therefore extensively used to describe
nonadiabatic excited-state dynamics involving internal conversion. By introducing SOC in the surface
hopping procedure, dynamical studies can be extended to describe ISC. Several approaches of
increasing complexity have been proposed to achieve this purpose. On the simplest level, hopping
between states of different spin multiplicity is performed “manually”. This can be done by exploring
first the deactivation mechanism within, for example, the singlet manifold with conventional TSH and
then identifying singlet/triplet crossings, where ISC is assumed to occur, along these trajectories.
These regions then serve as starting points for independent simulations (a procedure known as
spawning) in the triplet manifold. This oversimplified approach was first used by Warshel and
Karplus173 in the 70s but is still considered a viable option to treat complex systems (see reference
[167] for example). On the next level of sophistication, conventional TSH is applied between states of
different spin multiplicity by computing hopping probabilities only at crossing points based on
Landau-Zener theory.71,72 In this approach, internal conversions and intersystem crossings are treated
inconsistently. A more reliable way to treat ISC is to properly include SOC in the equation of motion
which governs the evolution of the electronic populations and hence the hopping probabilities. Thus,
ISC can occur in principle at every time step of the simulation and not just at singlet/triplet crossings.
Two alternative approaches can be considered. In the case of weak SOC, spin-diabatic states can be
used174 but the more reliable approach consists in using spin-adiabatic (or spin-coupled) states which
are eigenstates of the total electronic Hamiltonian including SOC.174,175,176
I would like to apply this type of methods to study the photodynamics of ruthenium nitrosyl
complexes in order to describe the competition between intramolecular N→O linkage
photoisomerization and NO photorelease. While the static approach can provide useful information
about the most likely photochemical pathways for these two processes, simulating the competition
between them requires a dynamical approach in order to understand the factors favoring one process
over the other. This project will involve designing model systems small enough to apply nonadiabatic
on-the-fly SOC dynamics. The reason is that the evaluation of the energy and forces on-the-fly is very
time-consuming even for relatively small ruthenium complexes.

63
6. Conclusion
In this manuscript, I have tried to convince the reader that computational photochemistry is a
powerful tool to investigate the underlying mechanisms of photochemical reactions that determine the
fate of a molecular system from energy absorption to photoproduct formation. I hope that, through the
different studies I have participated in, I have provided evidence that conical intersections and their
associated crossing seams were playing a central role in these mechanisms. Research performed in
computational photochemistry in recent years has made it evident that these extended crossing seams
are key mechanistic features of excited-state mechanisms.1,9,12,13,177 In this manuscript, I have given
examples in the fields of organic photochemistry (photoswitching mechanisms of organic
photochromic systems, photostability of PAHs, photoinduced intramolecular charge transfer in donor-
acceptor systems), photobiochemistry (photoisomerization of a protein, photostability and
photodamage in DNA) and inorganic photochemistry (photoswitching mechanisms of photochromic
ruthenium complexes). These studies rely on exploring the relevant PESs involved in the investigated
photochemical processes, including the characterization of the all-important conical intersections
accessible along the photochemical path(s). This (or these) photochemical path(s) is (are) determined
by a series of minimum energy path calculations allowing the connection of the excited reactant
(Franck-Condon point on the corresponding excited-state PES) to the ground-state photoproduct(s).
Based on this static information, one can already obtain a detailed insight into the mechanistic picture
of the photochemistry and/or photophysics of the system. These studies can sometimes be
complemented by a dynamical approach. The underlying molecular mechanisms of light-driven
processes are typically governed by sub-picosecond atomic motions. Mechanisms on such ultrafast
timescales are very challenging to probe by experiment, in particular in complex systems like proteins.
Thus, molecular dynamics simulations have become an invaluable tool to understand such processes
in atomic detail. In addition, I have shown that, depending on the orientation of the photochemical
reaction path with the branching space coordinates, the extended crossing seam may require
vibrational motion within the branching space to be accessed. Only a dynamical investigation can then
determine if the seam is really accessible and on which timescale. Also, these seams may play the role
of reactive or quenching funnels depending on the local topology of the PESs at the crossing region.
Dynamics can then help to determine quantum yields and branching ratios provided that one properly
samples the initial conditions and performs enough simulations to analyze the results on a statistical
basis.
Any mechanistic study undertaken using quantum chemistry methods requires considerable
physical and chemical insight. Thus, for a thermal reaction, there is no method that will generate
automatically all the possible mechanistic pathways that might be relevant. Rather, one still needs to
apply skills of chemical intuition and make sensible hypotheses that can then be explored
computationally. In excited-state chemistry, these problems are even more difficult, and I hope the
examples given in this manuscript are a step in providing this required insight. In addition to the
conceptual and physical problems associated with mechanistic studies in photochemistry, the actual
computations are technically difficult to carry out. Whether the calculations are aimed at obtaining
static or dynamical information on the photochemical process, I believe that only a well-trained
scientist in computational photochemistry can be in a position to perform these calculations and
interpret their results with a critical viewpoint.

64
To finish, it is clear that we are now living a new era where experimental and theoretical
chemistry can talk to each other on an equal footing. I have been privileged to work on fascinating
systems, which I would never have studied without the efforts of experimental groups to synthesize
these systems and without their willingness to understand how their systems physically operate. The
work I have carried out with my coworkers was often the outcome of a constructive interplay between
the experimental and theoretical viewpoints, and has been rewarding in many different ways as a
result.
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8. Curriculum Vitæ
Personal Information!
Date of birth: 3 October 1973 Status: Married, two children
Nationality: French Personal address: 10 rue Germaine Tillion
31400 Toulouse, France
Professional Experience!
Permanent Researcher 2007–
Employed as Chargé de Recherche 1st class (CR1) in CNRS working at Laboratoire de Chimie et
Physique Quantiques – IRSAMC at Université Paul Sabatier (Toulouse, France) since 1st October
2007. Theme: Computational photochemistry of organic, inorganic and biological systems.
Associate Researcher 2000-2007
Employed as a post-doctoral research associate at King’s College London (4 years), then at Imperial
College London (3 years) in the group of Prof. Mike Robb. Theme: Computational photochemistry of
organic and biological systems.
Temporary Lecturer 1999-2000
Employed as Attaché Temporaire à l’Enseignement et à la Recherche at Université Bordeaux 1.
Doctoral Fellowship and Instructor. 1996-1999
Employed as a doctoral researcher and instructor for teaching chemistry at Université Bordeaux 1.

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Academic Education!
PhD 1996-1999
Doctoral thesis in Physical Chemistry at Laboratoire de Physico-Chimie Moléculaire at Université de
Bordeaux 1. Title of the thesis: Theoretical study of the reaction C+CH. Date of viva: 23rd November
1999. Grade Highly Honorable.
MSc 1994-1996
Master of Science in Physical Chemistry obtained at Université de Bordeaux 1. Grade Very Good.
BSc 1991-1994
Bachelor of Science in Physical Chemistry obtained at Université de Bordeaux 1. Grade Good.
Specific Skills!
• Expert in computational photochemistry.
• In-depth knowledge of ab initio methods, in particular for electronic excited state calculations.
• Expert in the studies of reaction paths and topologies of potential energy surfaces of molecular
systems (e.g., photochemical paths involving conical intersections).
• Experienced in semiclassical nonadiabatic molecular dynamics.
• Qualified user of quantum chemistry packages, in particular Gaussian and Molpro.
• Experienced in hybrid methods (MMVB, ONIOM and QM/MM)
• Experienced in teaching physical chemistry and supervising students.
• Fluent in English (more than 7 years spent in London)
Scientific Production!
Peer-reviewed articles!
1. Rationalization and design of enhanced photoinduced cycloreversion in photochromic
dimethyldihydropyrenes by theoretical calculations
M. Boggio-Pasqua, M. Garavelli, J. Phys. Chem. A., DOI: 10.1021/jp5118773.
2. A multi-addressable switch based on the dimethyldihydropyrene photochrome with
remarkable proton-triggered photo-opening efficiency
D. Roldan, S. Cobo, F. Lafolet, N. Vilà, C. Bochot, C. Bucher, E. Saint-Aman, M. Boggio-Pasqua,
M. Garavelli, G. Royal, Chem. Eur. J. 21, 2015, 455–467.
3. Probing the photophysical capability of mono and bis(cyclometallated) Fe(II) polypyridine
complexes using inexpensive ground state DFT
I. M. Dixon, S. Khan, F. Alary, M. Boggio-Pasqua, J.-L. Heully, Dalton Trans. 43, 2014, 15898–
15905.
4. Unravelling the S→O linkage photoisomerization mechanisms in cis- and trans-
[Ru(bpy)2(DMSO)2]2+ using density functional theory
A. J. Göttle, F. Alary, I. M. Dixon, J.-L. Heully, M. Boggio-Pasqua, Inorg. Chem. 53, 2014, 6752–
6760.
5. Steering the excited state dynamics of a photoactive yellow protein chromophore analogue
with external electric fields
F. Knoch, D. Morozov, M. Boggio-Pasqua, G. Groenhof, Comput. Theor. Chem. 1040–1041, 2014,
120–125.
6. On the use of reduced active space in CASSCF calculations

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M. Boggio-Pasqua, G. Groenhof, Comput. Theor. Chem. 1040–1041, 2014, 6–13.
7. Phosphoryl group as a strong σ-donor anionic phosphine-type ligand: A combined
experimental and theoretical study on long-lived room temperature luminescence of the
[Ru(tpy)(bpy)(Ph2PO)]+ complex
E. Lebon, R. Sylvain, R. E. Piau, C. Lanthony, J. Pilmé, P. Sutra, M. Boggio-Pasqua, J.-L. Heully, F.
Alary, A. Juris, A. Igau, Inorg. Chem. 53, 2014, 1946–1948.
8. Enantiomerization pathway and atropochiral stability of the BINAP ligand: a density
functional theory study
J. Sanz Garcia, C. Lepetit, Y. Canac, R. Chauvin, M. Boggio-Pasqua, Chem. Asian J. 9, 2014, 462–
465.
9. A roaming wavepacket in the dynamics of electronically excited 2-hydroxypyridine
L. Poisson, D. Nandi, B. Soep, M. Hochlaf, M. Boggio-Pasqua, J.-M. Mestdagh, Phys. Chem. Chem.
Phys. 16, 2014, 581–587.
10. Theoretical investigation of phosphinidene oxide polypyridine ruthenium(II) complexes:
toward the design of a new class of photochromic compounds
O. P. J. Vieuxmaire, R. E. Piau, F. Alary, J.-L. Heully, P. Sutra, A. Igau, M. Boggio-Pasqua, J. Phys.
Chem. A 117, 2013, 12821–12830.
11. The (N4C2)2– donor set as promising motif for bis(tridentate) Fe(II) photoactive compounds
I. Dixon, F. Alary, M. Boggio-Pasqua, J.-L. Heully, Inorg. Chem. 52, 2013, 13369–13374.
12. Giant Ising-type magnetic anisotropy in trigonal bipyramidal Ni(II) complexes: experiment
and theory
R. Ruamps, R. Maurice, L. Batchelor, M. Boggio-Pasqua, R. Guillot, A. L. Barra, J. Liu, E.-E.
Bendeif, S. Pillet, S. Hill, T. Mallah, N. Guihéry, J. Am. Chem. Soc. 135, 2013, 3017–3026.
13. Photophysical and electrochemical properties of polypyridine imine ruthenium(II) complexes:
a comparative experimental and theoretical study
R. E. Piau, T. Guillon, E. Lebon, N. Perrot, F. Alary, M. Boggio-Pasqua, J.-L. Heully, A. Juris, P.
Sutra, A. Igau, New J. Chem. 36, 2012, 2484–2492.
14. Photochemical reactions in biological systems: probing the effect of the environment by
means of hybrid quantum chemistry/molecular mechanics simulations
M. Boggio-Pasqua, C. F. Burmeister, M. A. Robb, G. Groenhof, Phys. Chem. Chem. Phys. 14, 2012,
7912–7928.
15. Can a functionalized phosphine ligand promote room temperature luminescence of the
[Ru(bpy)(tpy)]2+ core?
E. Lebon, S. Bastin, P. Sutra, L. Vendier, R. E. Piau, I. M. Dixon, M. Boggio-Pasqua, F. Alary, J.-L.
Heully, A. Igau, A. Juris, Chem. Commun. 48, 2012, 741–743.
16. Adiabatic versus nonadiabatic photoisomerization in photochromic ruthenium sulfoxide
complexes: a mechanistic picture from density functional theory calculations
A. J. Göttle, I. M. Dixon, F. Alary, J.-L. Heully, M. Boggio-Pasqua, J. Am. Chem. Soc. 133, 2011,
9172–9174.
17. Controlling the photoreactivity of the photoactive yellow protein chromophore by substituting
at the p-coumaric acid group
M. Boggio-Pasqua, G. Groenhof, J. Phys. Chem. B 115, 2011, 7021–7028.
18. Towards the limit of atropochiral stability: H-MIOP, an N-heterocyclic carbene precursor and
cationic analogue of the H-MOP ligand
I. Abdellah, M. Boggio-Pasqua, Y. Canac, C. Lepetit, C. Duhayon, R. Chauvin, Chem. Eur. J. 17,
2011, 5110–5115.
19. Theoretical investigation on the photophysical properties of model ruthenium complexes with
diazabutadiene ligands [Ru(bpy)3–x(dab)x]2+ (x=1–3)

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T. Guillon, M. Boggio-Pasqua, F. Alary, J.-L. Heully, E. Lebon, P. Sutra, A. Igau, Inorg. Chem. 49,
2010, 8862–8872.
20. Computer simulations of photobiological processes: the effect of the protein environment
G. Groenhof, M. Boggio-Pasqua, L. V. Schäfer, M. A. Robb, Adv. Quantum Chem. 59, 2010, 181–
212.
21. Fluorescence of the perylene radical cation and an inaccessible D0/D1 conical intersection: An
MMVB, RASSCF and TD-DFT computational study
A. M. Tokmachev, M. Boggio-Pasqua, D. Mendive-Tapia, M. J. Bearpark, M. A. Robb, J. Chem.
Phys. 132, 2010, 044306.
22. Spin-orbit effects on the photophysical properties of Ru(bpy)32+
J.-L. Heully, F. Alary, M. Boggio-Pasqua, J. Chem. Phys. 131, 2009, 184308.
23. Hydrogen bonding controls excited-state decay of the photoactive yellow protein
chromophore
M. Boggio-Pasqua, M. A. Robb, G. Groenhof, J. Am. Chem. Soc. 131, 2009, 13580–13581.
24. A counterintuitive absence of an excited-state intramolecular charge transfer reaction with
2,4,6-tricyanoanilines. Experimental and computational results
K. A. Zachariasse, S. I. Druzhinin, V. A. Galievsky, S. Kovalenko, T. A. Senyushkina, P. Mayer, M.
Noltemeyer, M. Boggio-Pasqua, M. A. Robb, J. Phys. Chem. A 113, 2009, 2693–2710.
25. Ligand selection in RuII complexes for direct one-electron photooxidation of guanine: a
combined computational and experimental study
M. Boggio-Pasqua, P. Vicendo, M. Oubal, F. Alary, J.-L. Heully, Chem. Eur. J. 15, 2009, 2759–
2762.
26. Photostability via sloped conical intersections: a computational study of the pyrene radical
cation
A. M. Tokmachev, M. Boggio-Pasqua, M. J. Bearpark, M. A. Robb, J. Phys. Chem. A 112, 2008,
10881–10886.
27. Theoretical characterization of the lowest triplet excited states of the tris-(1,4,5,8-
tetraazaphenanthrene) ruthenium dication complex
F. Alary, M. Boggio-Pasqua, J.-L. Heully, C. Marsden, P. Vicendo, Inorg. Chem. 47, 2008, 5259–
5266.
28. Chromophore protonation state controls photoswitching of the fluoroprotein asFP595
L. V. Schäfer, G. Groenhof, M. Boggio-Pasqua, M. A. Robb, H. Grubmüller, PLoS Comput. Biol. 4,
2008, e1000034.
29. Arginine52 controls the photoisomerization process in photoactive yellow protein
G. Groenhof, L. V. Schäfer, M. Boggio-Pasqua, H. Grubmüller, M. A. Robb, J. Am. Chem. Soc. 130,
2008, 3250–3251.
30. Ultrafast deactivation channel for thymine dimerization
M. Boggio-Pasqua, G. Groenhof, L. V. Schäfer, H. Grubmüller, M. A. Robb, J. Am. Chem. Soc. 129,
2007, 10996–10997.
31. Molecular mechanics-valence bond method for planar conjugated hydrocarbon cations
K. F. Hall, A. M. Tokmachev, M. J. Bearpark, M. Boggio-Pasqua, M. A. Robb, J. Chem. Phys. 127,
2007, 134111.
32. CASSCF calculations for photoinduced processes in large molecules: choosing when to use
the RASSCF, ONIOM and MMVB approximations
M. J. Bearpark, F. Ogliaro, T. Vreven, M. Boggio-Pasqua, M. J. Frisch, S. M. Larkin, M. Morrison,
M. A. Robb, J. Photochem. Photobiol. A 190, 2007, 207–227.
33. Ultrafast deactivation of an excited cytosine-guanine base pair in DNA

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G. Groenhof, L. V. Schäfer, M. Boggio-Pasqua, M. Goette, H. Grubmüller, M. A. Robb, J. Am.
Chem. Soc. 129, 2007, 6812–6819.
34. Towards a mechanistic understanding of the photochromism of dimethyldihydropyrenes
M. Boggio-Pasqua, M. J. Bearpark, M. A. Robb, J. Org. Chem. 72, 2007, 4497–4503.
35. Photoswitching of the fluorescent protein asFP595: mechanism, proton pathways, and
absorption spectra
L. V. Schäfer, G. Groenhof, A. R. Klingen, G. M. Ullmann, M. Boggio-Pasqua, M. A. Robb, H.
Grubmüller, Angew. Chem. Int. Ed. 46, 2007, 530–536.
36. Photostability via sloped conical intersections: a computational study of the excited states of
the naphthalene radical cation
K. F. Hall, M. Boggio-Pasqua, M. J. Bearpark, M. A. Robb, J. Phys. Chem. A 110, 2006, 13591–
13599.
37. Photochemical reactivity of 2-vinylbiphenyl and 2-vinyl-1,3-terphenyl: the balance between
nonadiabatic and adiabatic photocyclization
M. Boggio-Pasqua, M. J. Bearpark, F. Ogliaro, M. A. Robb, J. Am. Chem. Soc. 128, 2006, 10533–
10540.
38. Excited states of conjugated hydrocarbons using the Molecular Mechanics – Valence Bond
(MMVB) method: conical intersections and dynamics
M. J. Bearpark, M. Boggio-Pasqua, M. A. Robb, F. Ogliaro, Theor. Chem. Acc. 116, 2006, 670–682.
39. Photostability via a sloped conical intersection: a CASSCF and RASSCF study of pyracylene
M. Boggio-Pasqua, M. J. Bearpark, M. A. Robb, J. Phys. Chem. A 109, 2005, 8849–8856.
40. Intramolecular charge transfer in 4-aminobenzonitriles does not necessarily need the twist
I. Gómez, M. Reguero, M. Boggio-Pasqua, M. A. Robb, J. Am. Chem. Soc. 127, 2005, 7119–7129.
41. A computational strategy for geometry optimization of ionic and covalent excited states,
applied to butadiene and hexatriene
M. Boggio-Pasqua, M. J. Bearpark, M. Klene, M. A. Robb, J. Chem. Phys. 120, 2004, 7849–7860.
42. Can diarylethene photochromism be explained by a reaction path alone? A CASSCF study
with model MMVB dynamics
M. Boggio-Pasqua, M. Ravaglia, M. J. Bearpark, M. Garavelli, M. A. Robb, J. Phys. Chem. A 107,
2003, 11139–11152.
43. Excited states of conjugated hydrocarbon radicals using the molecular mechanics – valence
bond (MMVB) method
M. J. Bearpark, M. Boggio-Pasqua, Theor. Chem. Acc. 110, 2003, 105–114.
44. Dihydroazulene/Vinylheptafulvene photochromism: A model for one-way photochemistry via
a conical intersection
M. Boggio-Pasqua, M. J. Bearpark, P. A. Hunt, M. A. Robb, J. Am. Chem. Soc. 124, 2002, 1456–
1470.
45. Visible emission from the vibrationally hot C2H radical following vacuum-ultraviolet
photolysis of acetylene: Experiment and theory
S. Boyé, A. Campos, S. Douin, C. Fellows, D. Gauyacq, N. Shafizadeh, P. Halvick, M. Boggio-
Pasqua, J. Chem. Phys. 116, 2002, 8843–8855.
46. Trajectory surface hopping study of the C + CH reaction
P. Halvick, M. Boggio-Pasqua, L. Bonnet, A. I. Voronin, J.-C. Rayez, Phys. Chem. Chem. Phys. 4,
2002, 2560–2567.
47. Coupled ab initio potential energy surfaces for the two lowest 2A’ electronic states of the C2H
molecule
M. Boggio-Pasqua, A. I. Voronin, P. Halvick, J.-C. Rayez, A. J. C. Varandas, Mol. Phys. 98, 2000,
1925–1938.

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48. Global analytical representations of the three lowest potential energy surfaces of C2H, and rate
constant calculations for the C(3P) + CH(2P) reaction
M. Boggio-Pasqua, A. I. Voronin, P. Halvick, J.-C. Rayez, Phys. Chem. Chem. Phys. 2, 2000, 1693–
1700.
49. Analytical representations of high level ab initio potential energy curves of the C2 molecule
M. Boggio-Pasqua, A. I. Voronin, P. Halvick, J.-C. Rayez, J. Mol. Struct. (Theochem) 531, 2000,
159–167.
50. Ab initio study of the potential energy surfaces for the reaction C + CH → C2 + H
M. Boggio-Pasqua, P. Halvick, M.-T. Rayez, J.-C. Rayez, J.-M. Robbe, J. Phys. Chem. A 102, 1998,
2009–2015.
51. Ab initio study of the structure, cooperativity and vibrational properties of the H2O:(HCl)2
hydrogen bonded complex
M. Kreissler, L. Lavialle, M. Boggio-Pasqua, Y. Hannachi, J. Mol. Struct. (Theochem) 542, 1998,
55–66.
Invited conferences
1. Computational studies of photoactivable and photoswitchable systems, International
Collaborative Laboratory for Supraphotoactive Systems meeting, 10 March 2015, Toulouse,
France.
2. Theoretical mechanistic studies of photoinduced linkage isomerizations in ruthenium
complexes, Breaking and Making Bonds with Light (TSRC workshop), 30 June – 4 July 2014,
Telluride (Colorado), USA.
3. On the role of extended intersection seams in ultrafast photochemistry, Chemical Reactivity
2014: From accurate theories to simple models, 21–23 January 2014, Bordeaux, France.
4. CASSCF and CASPT2 study of 2-hydroxypyridine, EPSRC UK National Service for
Computational Chemistry Software (NSCCS) workshop, 28–29 September 2013, London, UK.
5. Photophysique de monocations d’hydrocarbures aromatiques polycycliques isolés:
contribution théorique, Spectroscopie et modélisation moléculaire d’assemblages complexes
(symposium), 28 September 2012, Toulouse, France.
6. Theoretical mechanistic studies of photochromic systems: the central role of conical
intersections, Breaking and making bonds with light (TSRC workshop), 2–6 July 2012,
Telluride (Colorado), USA.
7. On the role of extended intersection seams in ultrafast photochemistry, International Meeting
on Atomic and Molecular Physics and Chemistry (IMAMPC 2011), 5–8 July 2011, Rennes,
France.
8. The role of extended conical intersection seams in photochromic systems, VIIIth International
Conference of Computational Methods in Sciences and Engineering (ICCMSE 2010), 3–8
October 2010, Kos, Greece.
9. How do conical intersections control photostability and photochemical reactivity?, Radiation
Damage in Biomolecular Systems (RADAM’04) workshop, 24–27 June 2004, Lyon, France.
Conference proceedings
1. The role of extended conical intersection seams in photochromic systems
M. Boggio-Pasqua, M. J. Bearpark, M. A. Robb, AIP Conf. Proc. 1642, 2015, 453–456.
2. Computer simulations of photochemistry in complex environments: Photo-isomerization and
excitation energy transfer
G. Groenhof, D. Morozov, C. F. Burmeister, L. Vukovic, M. Boggio-Pasqua, Abstracts of Papers of
the American Chemical Society 247, 2014, PHYS 29.

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3. Light-induced processes in biological systems: From first principles to biotechnology
G. Groenhof, L. V. Schaefer, M. Boggio-Pasqua, H. Grubmüller, M. A. Robb, Abstracts of Papers of
the American Chemical Society 236, 2008, COMP 334.
4. CASSCF calculations for excited states of large molecules: Choosing when to use the
RASSCF, ONIOM and MMVB approximations
M. J. Bearpark, F. Ogliaro, T. Vreven, M. Boggio-Pasqua, M. J. Frisch, S. M. Larkin, M. A. Robb,
AIP Conf. Proc. 963, 2007, 583–585.
5. MMVB for conjugated hydrocarbon cations: Method development and application to
photochemistry in interstellar clouds
K. F. Hall, M. J. Bearpark, A. M. Tokmachev, M. Boggio-Pasqua, M. A. Robb, Abstracts of Papers
of the American Chemical Society 234, 2007, PHYS 729.
6. Excited state CASSCF/forcefield dynamics computations on systems of biological interest
G. Groenhof, L. V. Schaefer, H. Grubmüller, M. Boggio-Pasqua, M. A. Robb, Abstracts of Papers of
the American Chemical Society 234, 2007, PHYS 282.
Other articles
1. Methods for controlling photochemical reactivity: applications to photochemical switches and
photostability
M. Boggio-Pasqua, M. J. Bearpark, M. A. Robb, The Spectrum 21, 2008, 28–31.
Communications in congress, symposium
Oral communications
1. Mechanistic pictures of linkage photoisomerizations in photochromic ruthenium complexes
from DFT calculations, Modeling Photoactive Molecules. (MPM 2015 conference), 21–24
April 2015, Nantes, France.
2. A mechanistic picture of the photoisomerization in photochromic ruthenium sulfoxide
complexes, Excited states and non-adiabatic processes in complex systems. Theoretical
approaches. (WATOC 2011 Satellite meeting), 25–27 July 2011, Sant Feliu de Guíxols
(Girona), Spain.
3. The role of hydrogen bonds in the ultrafast non-radiative decay of the photoactive yellow
protein chromophore, XXIIIrd IUPAC symposium on photochemistry, 11–16 July 2010,
Ferrara, Italy.
4. Ultrafast deactivation of an excited guanine-cytosine base pair in DNA, Radiation Damage in
Biomolecular Systems (RADAM’07) workshop, 19–22 June 2007, Dublin, Ireland.
5. Role of the extended intersection seam in photoswitchable molecules, From molecular
switches to molecular motors BIOMACH workshop, 20–23 September 2005, Ascona,
Switzerland.
Posters
1. Rationalization and design of enhanced photoinduced cycloreversion in photochromic
dihydropyrenes by theoretical calculations, Modeling Photoactive Molecules. (MPM 2015
conference), 21–24 April 2015, Nantes, France.
2. Photoisomerization of photoactive yellow protein chromophores in water, Modelling of
biologically-inspired photoactive systems workshop, 30 mars – 1 April 2011, Marseilles,
France.
3. Photostability of polycyclic aromatic hydrocarbons in the interstellar medium, PAHs and the
Universe symposium, 31 May – 4 June 2010, Toulouse, France.
4. Ligand selection in Ru(II) complexes for direct one-electron photooxidation of guanine, XXIV
International Conference on Photochemistry (ICP 2009), 19–24 July 2009, Toledo, Spain.

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5. Use of acyclic alpha-diimine ligands to tune the photophysical properties of Ru(II)
polypyridyl complexes, XXIV International Conference on Photochemistry (ICP 2009), 19–24
July 2009, Toledo, Spain.
6. DFT and TD-DFT studies of the lowest excited states of polypyridyl ruthenium complexes,
XXIInd IUPAC symposium on photochemistry, 28 July – 1er August 2008, Gothenburg,
Sweden.
7. Etude de la photophysique des radicaux pyrène•+ et pérylène•+ par la méthode hybride MMVB,
XIème Rencontre des Chimistes Théoriciens Francophones (RCTF 2008), 30 June – 4 July
2008, Dinard, France.
8. Intramolecular charge transfer in 4-aminobenzonitriles: internal conversion without twist, 7th
Congress of the World Association of Theoretically Oriented Chemists (WATOC 2005), 16–21
January 2005, Cape Town, South Africa.
9. Can diarylethene photochromism be explained by a reaction path alone? A CASSCF study
with model MMVB dynamics, Faraday Discussion 127, 5–7 April 2004, Oxford, UK.
Seminars, workshops
1. Rôle des liaisons hydrogène sur la désactivation non-radiative ultra-rapide du chromophore de
la protéine jaune photo-active, invited seminar, Ecole Normale Supérieure de Paris, 18
November 2011, Paris, France.
2. Rôle des liaisons hydrogène sur la désactivation non-radiative ultra-rapide du chromophore de
la protéine jaune photo-active, invited seminar, Laboratoire de Chimie Physique, 15 April
2011, Orsay, France.
3. Le rôle des liaisons hydrogène dans la désactivation non-radiative du chromophore de la
protéine jaune photo-active, local symposium, Journées Expérience – Théorie, 4 December
2009, Toulouse, France.
4. Photochimie ultra-rapide: modélisation moléculaire mécanistique, invited seminar,
Laboratoire des IMRCP, 31 March 2009, Toulouse, France.
5. Photochimie ultra-rapide: modélisation moléculaire mécanistique, invited seminar, IRSAMC,
8 December 2008, Toulouse, France.
6. Theoretical study of the photophysics of isolated PAH radical cations, Toulouse Interstellar
Nanograin workshop, 13–14 November 2008, Toulouse, France.
7. Le rôle des intersections coniques dans le contrôle de la photoréactivité et de la photostabilité,
invited seminar, Laboratoire Francis Perrin (CEA Saclay), 29 May 2008, Gif sur Yvette,
France.
8. Désactivation non-radiative ultra-rapide d’une paire de bases cytosine-guanine excitée dans
l’ADN, local symposium, Journées de Dynamique du Sud-Ouest, 20–21 May 2008,
Montpellier, France.
9. On the role of the extended intersection seam in ultrafast photochemistry, invited seminar,
Max Planck Institute for Biophysical Chemistry, 21 May 2007, Göttingen, Germany.
10. Désactivation non-radiative ultra-rapide d’une paire de bases cytosine-guanine excitée dans
l’ADN, invited seminar, Laboratoire de Chimie et Physique Quantiques, 22 March 2007,
Toulouse, France.
11. The role of the extended intersection seam in photochemistry, invited seminar, Laboratoire de
Chimie et Physique Quantiques, 11 January 2006, Toulouse, France.
12. The RASSCF method with correlation adapted orbitals: applications to excited-state
photochemistry, COST (European Cooperation in Science and Technology) meeting, June
2005, Valencia, Spain.

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13. The extended nature of the conical intersection seam: implications for mechanistic
photochemistry, invited seminar, 21 February 2005, Imperial College London, London, UK.
14. Intramolecular charge transfer in 4-aminobenzonitrile, Radiation Damage in Biomolecular
Systems (RADAM) working group meeting, 30 October 2004, Brussels, Belgium.
Book chapters
1. Excited state dynamics in biomolecules
G. Groenhof, L. V. Schäfer, M. Boggio-Pasqua, M. A. Robb, In Handbook of Molecular Biophysics,
Ed. H. Bohr, Wiley-VCH, Weinheim, 2009, pp. 93–134.
2. Conical intersections and photochemical mechanisms: characterizing the conical intersection
hyperline using gradients, second derivatives, and dynamics
M. A. Robb, M. J. Bearpark, M. Boggio-Pasqua, P. A. Hunt, M. Paterson, M. Olivucci, L. Blancafort,
G. Groenhof, In Quantum Dynamics at Conical Intersections, Eds. S. Althorpe and G. Worth, CCP6,
Warrington, 2004, pp.1–3.
Others
1. Suivez le guide !, written contribution in the magazine 2011, une année avec le CNRS en
Midi-Pyrénées.
2. Qu’est-ce-que la photobiologie ?, written contribution in the magazine 2009, une année avec
le CNRS en Midi-Pyrénées.
3. Extended MC-SCF Calculations on Conjugated Polycyclic Hydrocarbons, M. J. Bearpark, M.
Boggio-Pasqua, Scientific highlight in EPSRC UK National Service for Computational
Chemistry Software (NSCCS) editorial, issue 11, 23 July 2007, pp. 2–4.
4. Exhibitor for Gaussian Inc., 7th Congress of the World Association of Theoretically Oriented
Chemists (WATOC 2005), 16–21 January 2005, Cape Town, South Africa.
5. Contribution in Faraday Discussion 127: Non-adiabatic effects in chemical dynamics, 5–7
April 2004, Oxford, UK.
Teaching and Overseeing!
Teaching!
• 4-hour lecture given to M2 Erasmus Mundus TCCM students (2014). Computational Mechanistic
Photochemistry.
• 10-hour lecture given to PhD students of Ecole Doctorale des Sciences de la Matière in Toulouse
(2014). Computational photochemistry.
• 2-hour lecture given to ENSIACET students in Toulouse (2014). Towards understanding
photochromic materials at the molecular level: how can theoretical chemistry be helpful?
• Master lecture for Pôle Sud-Ouest du Réseau Français de Chimie Théorique (2008, 2010 and
2012). 6-hour lecture and practical work. QM/MM calculations of excited states.
• Numerical labs and tutorials in physical chemistry for 1st year students at Imperial College London
(2004-2007).
• Exercise corrections and practical labs in physical chemistry for 1st and 2nd year students at
Université de Bordeaux 1 (1996-2000).
Overseeing
• Tatiana Lemishko (TCCM Erasmus Mundus Master)
3-month assignment, February-April 2015.
Theoretical study of the fragmentation of guanine upon electron attachment.

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• Juan Sanz Garcia (PhD)
3-year PhD thesis, October 2013–October 2016. Co-direction (50%) with J.-L. Heully.
Theoretical study of ruthenium nitrosyl complexes.
• Serra Arslancan (TCCM Erasmus Mundus Master)
4-month assignment, March-June 2014.
Theoretical study of the photochemistry of dimers of thiosubstituted pyridine bases.
• Mohamed Elshakre (mobility of an Egyptian researcher from Cairo)
1-month placement, December 2013.
Theoretical study of the photoisomerization of heterocyclic aromatic azides.
• Kathy Chen (TCCM Erasmus Mundus Master)
4-month assignment, January-April 2013.
Theoretical study of the deactivation pathways in 4-thiouracil and 2,4-dithiouracil.
• Juan Sanz Garcia (BSc research project)
4-month assignment, September 2012-January 2013.
Theoretical calculations of enantiomerization barriers in atropochiral biaryls.
• Olivier Vieuxmaire (post-doctoral researcher, ANR funding)
2-year assignment, October 2011-October 2013.
Theoretical study of the P
→
O linkage photoisomerization in a phosphinidene oxide ruthenium
complex.
• Adrien Göttle (PhD)
3-year PhD thesis, October 2010–October 2013. Co-direction (50%) with F. Alary.
Theoretical study of the photophysical and photochemical properties of ruthenium complexes.
• Cloé Lanthony (Master)
5-month assignment, January-June 2010.
Theoretical study of ruthenium complexes functionalized with organophosphorus ligands for solar
energy conversion in photovoltaic systems.
• Thomas Guillon (temporary lecturer)
10-month assignment, October 2008-July 2009.
Theoretical study of ruthenium complexes with diazabutadiene ligands.
• Mohamed Oubal (Master)
5-month assignment, January-June 2008.
Photoreactivity of ruthenium complexes with a DNA basis.
• Moira Prete (Master)
6-month Erasmus assignment at King’s College London, September 2001-March 2002. Co-
supervision with M. Robb.
A theoretical study of the Bergman reaction: A CASSCF approach for modeling the enediyne
anticancer drugs.
• Anna Zagolin (Master 2ème année)
6-month Erasmus assignment at King’s College London, October 2000-April 2001. Co-supervision
with M. Robb.
Theoretical study of an iron complex.
Scientific and Administrative Duties!
• In charge of the organization of the lab (LCPQ) and institute (IRSAMC) seminars.
• Member of the Scientific Board of CALMIP since 2010. Reviewer in the evaluation process of the
projects for getting HPC computing resources on Hyperion (2010–2014) and Eos (2014–).

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• Member of the Scientific Board of the “Labex” NEXT (2015–).
• Regular reviewer in journals of ACS, RSC, Springer, AIP and Elsevier. Occasional reviewer for
Wiley, Taylor & Francis and Biophysical Society.
• Reviewer of ANR, ERC and FNRS projects.
• Member of the tribunal of the international PhD defense of Lara Martinez (Madrid, 4 November
2014).
• Member of the organization committee of RCET (Toulouse, 2015).
• Member of the organization committee of PEM2 symposium (Toulouse, 2015).
• Partner in ANR programs PhosphoRuIr (2010–2014) and Gasparim (2010–2013).

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To my beloved wife, Marjorie