Constructing grids for molecular quantum dynamics using an autoencoder

A challenge for molecular quantum dynamics (QD) calculations is the curse of dimensionality with respect to the nuclear degrees of freedom. A common approach that works especially well for fast reactive processes is to reduce the dimensionality of the system to a few most relevant coordinates. Identifying these can become a very difficult task, since they often are highly unintuitive. We present a machine learning approach that utilizes an autoencoder that is trained to find a low-dimensional representation of a set of molecular configurations. These configurations are generated by trajectory calculations performed on the reactive molecular systems of interest. The resulting low-dimensional representation can be used to generate a potential energy surface grid in the desired subspace. Using the G-matrix formalism to calculate the kinetic energy operator, QD calculations can be carried out on this grid. In addition to step-by-step instructions for the grid construction, we present the application to a test system.Comment: 24 pages, 6 figures, articl

Cavity sideband cooling of trapped molecules

The efficiency of cavity sideband cooling of trapped molecules is theoretically investigated for the case where the IR transition between two rovibrational states is used as a cycling transition. The molecules are assumed to be trapped either by a radio-frequency or optical trapping potential, depending on whether they are charged or neutral, and confined inside a high-finesse optical resonator which enhances radiative emission into the cavity mode. Using realistic experimental parameters and COS as a representative molecular example, we show that in this setup cooling to the trap ground state is feasible

Visualizing Conical Intersection Passages via Vibronic Coherence Maps Generated by Stimulated Ultrafast X--Ray Raman Signals

The rates and outcomes of virtually all photophysical and photochemical processes are determined by Conical Intersections. These are regions of degeneracy between electronic states on the nuclear landscape of molecules where electrons and nuclei evolve on comparable timescales and become strongly coupled, enabling radiationless relaxation channels upon optical excitation. Due to their ultrafast nature and vast complexity, monitoring Conical Intersections experimentally is an open challenge. We present a simulation study on the ultrafast photorelaxation of uracil, which demonstrates a new window into Conical Intersections obtained by recording the transient wavepacket coherence during this passage with an x-ray free electron laser pulse. We report two major findings. First, we find that the vibronic coherence at the conical intersection lives for several hundred femtoseconds and can be measured during this entire time. Second, the time-dependent energy splitting landscape of the participating vibrational and electronic states is directly extracted from Wigner spectrograms of the signal. These offer a novel physical picture of the quantum Conical Intersection pathways through visualizing their transient vibronic coherence distributions. The path of a nuclear wavepacket around the Conical Intersection is directly mapped by the proposed experiment.Comment: 7 pages, 5 Figures, to be published in PNA

Photochemical formation of intricarene

Sunlight is the ultimate driver of biosynthesis but photochemical steps late in biosynthetic pathways are very rare. They appear to play a role in the formation of certain furanocembranoids isolated from Caribbean corals. One of these compounds, intricarene, has been suspected to arise from an intramolecular 1,3-dipolar cycloaddition involving an oxidopyrylium. Here we show, by a combination of experiments and theory, that the oxidopyrylium forms under photochemical conditions and that its cycloaddition occurs via a triplet state. The formation of a complex by-product can be rationalized by another photochemical step that involves a conical intersection. Our work raises the question whether intricarene is biosynthesized in the natural habitat of the corals or is an artefact formed during workup. It also demonstrates that the determination of exact irradiation spectra, in combination with quantum chemical calculations, enables the rationalization of complex reaction pathways that involve multiple excited states

Hole-transfer induced energy transfer in perylene diimide dyads with a donor–spacer–acceptor motif

We investigate the photoinduced dynamics of perylene diimide dyads based on a donor–spacer–acceptor motif with polyyne spacers of varying length by pump–probe spectroscopy, time resolved fluorescence, chemical variation and quantum chemistry. While the dyads with pyridine based polyyne spacers undergo energy transfer with near-unity quantum efficiency, in the dyads with phenyl based polyyne spacers the energy transfer efficiency drops below 50%. This suggests the presence of a competing electron transfer process from the spacer to the energy donor as the excitation sink. Transient absorption spectra, however, reveal that the spacer actually mediates the energy transfer dynamics. The ground state bleach features of the polyyne spacers appear due to the electron transfer decay with the same time constant present in the rise of the ground state bleach and stimulated emission of the perylene energy acceptor. Although the electron transfer process initially quenches the fluorescence of the donor it does not inhibit energy transfer to the perylene energy acceptor. The transient signatures reveal that electron and energy transfer processes are sequential and indicate that the donor–spacer electron transfer state itself is responsible for the energy transfer. Through the introduction of a Dexter blocker unit into the spacer we can clearly exclude any through bond Dexter-type energy transfer. Ab initio calculations on the donor–spacer and the donor–spacer–acceptor systems reveal the existence of a bright charge transfer state that is close in energy to the locally excited state of the acceptor. Multipole–multipole interactions between the bright charge transfer state and the acceptor state enable the energy transfer. We term this mechanism coupled hole-transfer FRET. These dyads represent a first example that shows how electron transfer can be connected to energy transfer for use in novel photovoltaic and optoelectronic devices

Stereoselective Csp3−Csp2 Cross‐Couplings of Chiral Secondary Alkylzinc Reagents with Alkenyl and Aryl Halides

We report palladium‐catalyzed cross‐coupling reactions of chiral secondary non‐stabilized dialkylzinc reagents, prepared from readily available chiral secondary alkyl iodides, with alkenyl and aryl halides. This method provides α‐chiral alkenes and arenes with very high retention of configuration (dr up to 98:2) and satisfactory overall yields (up to 76 % for 3 reaction steps). The configurational stability of these chiral non‐stabilized dialkylzinc reagents was determined and exceeded several hours at 25 °C. DFT calculations were performed to rationalize the stereoretention during the catalytic cycle. Furthermore, the cross‐coupling reaction was applied in an efficient total synthesis of the sesquiterpenes (S)‐ and (R)‐curcumene with control of the absolute stereochemistry

Photoprotecting uracil by coupling with lossy nanocavities

We analyze how the photorelaxation dynamics of a molecule can be controlled by modifying its electromagnetic environment using a nanocavity mode. In particular, we consider the photorelaxation of the RNA nucleobase uracil, which is the natural mechanism to prevent photodamage. In our theoretical work, we identify the operative conditions in which strong coupling with the cavity mode can open an efficient photoprotective channel, resulting in a relaxation dynamics twice as fast as the natural one. We rely on a state-of-the-art chemically detailed molecular model and a non-Hermitian Hamiltonian propagation approach to perform full-quantum simulations of the system dissipative dynamics. By focusing on the photon decay, our analysis unveils the active role played by cavity-induced dissipative processes in modifying chemical reaction rates, in the context of molecular polaritonics. Remarkably, we find that the photorelaxation efficiency is maximized when an optimal trade-off between light-matter coupling strength and photon decay rate is satisfied. This result is in contrast with the common intuition that increasing the quality factor of nanocavities and plasmonic devices improves their performance. Finally, we use a detailed model of a metal nanoparticle to show that the speedup of the uracil relaxation could be observed via coupling with a nanosphere pseudomode, without requiring the implementation of complex nanophotonic structuresThis work has been funded by the European Research Council through Grants ERC-2016-StG- 714870 (S. Felicetti, J. Feist, and J. Fregoni) and ERC-2015- CoG-681285 (J. Fregoni, PI Stefano Corni) and by the Spanish Ministry for Science, Innovation, and Universities - Agencia Estatal de Investigación through Grants RTI2018- 099737-B-I00, PCI2018-093145 (through the QuantERA program of the European Commission), and MDM-2014- 0377 (through the Marıá de Maeztu program for Units of Excellence in R&D). T. Schnappinger and R. de Vivie-Riedle gratefully acknowledge the DFG Normalverfahren. S. Reiter gratefully acknowledges financial support by the International Max Planck Research School of Advanced Photon Science (IMPRS-APS

Substituent effects on the relaxation dynamics of furan, furfural and β-furfural: a combined theoretical and experimental approach

For the series furan, furfural and β-furfural we investigated the effect of substituents and their positioning on the photoinduced relaxation dynamics in a combined theoretical and experimental approach. Using time resolved photoelectron spectroscopy with a high intensity probe pulse, we can, for the first time, follow the whole deactivation process of furan through a two photon probe signal. Using the extended 2-electron 2-orbital model [Nenov et al., J. Chem. Phys., 2011, 135, 034304] we explain the formation of one central conical intersection and predict the influence of the aldehyde group of the derivatives on its geometry. This, as well as the relaxation mechanisms from photoexcitation to the final outcome was investigated using a variety of theoretical methods. Complete active space self consistent field was used for on-the-fly calculations while complete active space perturbation theory and coupled cluster theory were used to accurately describe critical configurations. Experiment and theory show the relaxation dynamics of furfural and β-furfural to be slowed down, and together they disclose an additional deactivation pathway, which is attributed to the nO lonepair state introduced with the aldehyde group