The photochemistry of benzophenone, a paradigmatic organic molecule for photosensitization, was investigated by means of surface-hopping ab initio molecular dynamics. Different mechanisms were found to be relevant within the first 600 fs after excitation; the long-debated direct (S₁ → T₁) and indirect (S₁ → T₂ → T₁) mechanisms for population of the low-lying triplet state are both possible, with the latter being prevalent. Moreover, we established the existence of a kinetic equilibrium between the two triplet states, never observed before. This fact implies that a significant fraction of the overall population resides in T₂, eventually allowing one to revisit the usual spectroscopic assignment proposed by transient absorption spectroscopy. This finding is of particular interest for photocatalysis as well as for DNA damages studies because both T₁ and T₂ channels are, in principle, available for benzophenone-mediated photoinduced energy transfer toward DNA.

Molecular switches based on E/Z photoisomerization have been used in different contexts in order to control a variety of processes in different systems, from peptide conformation control to molecular data storage devices, from catalysis to smart materials. The syntheses, properties and applications of several types of E/Z photochemical switches are presented with special attention paid to azobenzenes, overcrowded alkenes and switches based on the protonated Schiff base chromophore of rhodopsins.

The emergence in late 2019 of the coronavirus SARS-CoV-2 has resulted in the breakthrough of the COVID-19 pandemic that is presently affecting a growing number of countries. The development of the pandemic has also prompted an unprecedented effort of the scientific community to understand the molecular bases of the virus infection and to propose rational drug design strategies able to alleviate the serious COVID-19 morbidity. In this context, a strong synergy between the structural biophysics and molecular modeling and simulation communities has emerged, resolving at the atomistic level the crucial protein apparatus of the virus and revealing the dynamic aspects of key viral processes. In this Review, we focus on how in silico studies have contributed to the understanding of the SARS-CoV-2 infection mechanism and the proposal of novel and original agents to inhibit the viral key functioning. This Review deals with the SARS-CoV-2 spike protein, including the mode of action that this structural protein uses to entry human cells, as well as with nonstructural viral proteins, focusing the attention on the most studied proteases and also proposing alternative mechanisms involving some of its domains, such as the SARS unique domain. We demonstrate that molecular modeling and simulation represent an effective approach to gather information on key biological processes and thus guide rational molecular design strategies.

Channelrhodopsin (ChR) is a key protein of the optogenetic toolkit. C1C2, a functional chimeric protein of Chlamydomonas reinhardtii ChR1 and ChR2, is the only ChR whose crystal structure has been solved, and thus uniquely suitable for structure-based analysis. We report C1C2 photoreaction dynamics with ultrafast transient absorption and multi-pulse spectroscopy combined with target analysis and structure-based hybrid quantum mechanics/molecular mechanics calculations. Two relaxation pathways exist on the excited (S₁) state through two conical intersections CI₁ and CI₂, that are reached via clockwise and counter-clockwise rotations: (i) the C13=C14 isomerization path with 450 fs via CI₁ and (ii) a relaxation path to the initial ground state with 2.0 ps and 11 ps via CI₂, depending on the hydrogen-bonding network, hence indicating active-site structural heterogeneity. The presence of the additional conical intersection CI₂ rationalizes the relatively low quantum yield of photoisomerization (30 ± 3%), reported here. Furthermore, we show the photoreaction dynamics from picoseconds to seconds, characterizing the complete photocycle of C1C2.

We present the study of optical and photophysical properties of chlorin e6, a known photosensitizer producing singlet oxygen. The linear and non-linear optical properties have been studied taking into account the dynamical and vibrational effects both by using Wigner distribution or coupling with molecular dynamics. A force field correctly describing the out-of-plane vibrations has been properly parameterized. The photophysical study revealed a possible efficient population of the triplet manifold, from the S₁ minimum region. Hence, fluorescence and singlet oxygen production are shown to coexist. Two-photon absorption high cross-section and far infrared absorption also suggest the possible use of chlorin e6 as an efficient sensitizer in two-photon absorption based phototherapy.