How to Find Molecules with Long-lasting Charge Migration?

Under certain conditions, the ionization of a molecule may create a superposition of electronic states, leading to ultrafast electron dynamics. If controlled, this motion could be used in attochemistry applications, but it has been shown that the decoherence induced by the nuclear motion typically happens in just a few femtoseconds. We recently developed an efficient algorithm for finding molecules exhibiting long-lasting electronic coherence and charge migration across the molecular structure after valence ionization. Here, we first explain why the but-3-ynal molecule is a promising candidate to study this type of ultrafast electron dynamics. Then, we use the 3-oxopropanenitrile molecule, which does not induce long-lasting charge migration in any of three different ionization scenarios, as an example demonstrating that several different properties must be fulfilled simultaneously to make the attochemistry applications possible.

Search for long-lasting electronic coherence using on-the-fly ab initio semiclassical dynamics.

Using a combination of high-level ab initio electronic structure methods with efficient on-the-fly semiclassical evaluation of nuclear dynamics, we performed a massive scan of small polyatomic molecules searching for a long-lasting oscillatory dynamics of the electron density triggered by the outer-valence ionization. We observed that in most of the studied molecules, either the sudden removal of an electron from the system does not lead to the appearance of the electronic coherence or the created coherences become damped by the nuclear rearrangement on a time scale of a few femtoseconds. However, we report several so far unexplored molecules with the electronic coherences lasting up to 10 fs, which can be good candidates for experimental studies. In addition, we present the full-dimensional simulations of the electronic coherences coupled to nuclear motion in several molecules which were studied previously only in the fixed nuclei approximation.

Tuning the Thermal Stability and Photoisomerization of Azoheteroarenes through Macrocycle Strain*.

Azobenzene and its derivatives are one of the most widespread molecular scaffolds used in a range of modern applications, as well as in fundamental research. After photoexcitation, azo-based photoswitches revert back to the most stable isomer on a timescale ( t 1 / 2 ) that determines the range of potential applications. Attempts to bring t 1 / 2 to extreme values prompted the development of azobenzene and azoheteroarene derivatives that either rebalance the E- and Z-isomer stabilities, or exploit unconventional thermal isomerization mechanisms. In the former case, one successful strategy has been the creation of macrocycle strain, which tends to impact the E/Z stability asymmetrically, and thus significantly modify t 1 / 2 . On the bright side, bridged derivatives have shown an improved optical switching owing to the higher quantum yields and absence of degradation. However, in most (if not all) cases, bridged derivatives display a reversed thermal stability (more stable Z-isomer), and smaller t 1 / 2 than the acyclic counterparts, which restricts their potential interest to applications requiring a fast forward and backwards switch. In this paper, the impact of alkyl bridges on the thermal stability of phenyl-azoheteroarenes is investigated by using computational methods, and it is revealed that it is indeed possible to combine such improved photoswitching characteristics while preserving the regular thermal stability (more stable E-isomer), and increased t 1 / 2 values under the appropriate connectivity and bridge length.

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power.

The ATLAS of Biochemistry is a repository of both known and novel predicted biochemical reactions between biological compounds listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG). ATLAS was originally compiled based on KEGG 2015, though the number of KEGG reactions has increased by almost 20 percent since then. Here, we present an updated version of ATLAS created from KEGG 2018 using an increased set of generalized reaction rules. Furthermore, we improved the accuracy of the enzymes that are predicted for catalyzing novel reactions. ATLAS now contains ∼150 000 reactions, out of which 96% are novel. In this report, we present detailed statistics on the updated ATLAS and highlight the improvements with regard to the previous version. Most importantly, 107 reactions predicted in the original ATLAS are now known to KEGG, which validates the predictive power of our approach. The updated ATLAS is available at https://lcsb-databases.epfl.ch/atlas.