MLatom Software Ecosystem for Surface Hopping Dynamics in Python with Quantum Mechanical and Machine Learning Methods.

We present an open-source MLatom@XACS software ecosystem for on-the-fly surface hopping nonadiabatic dynamics based on the Landau-Zener-Belyaev-Lebedev algorithm. The dynamics can be performed via Python API with a wide range of quantum mechanical (QM) and machine learning (ML) methods, including ab initio QM (CASSCF and ADC(2)), semiempirical QM methods (e.g., AM1, PM3, OMx, and ODMx), and many types of ML potentials (e.g., KREG, ANI, and MACE). Combinations of QM and ML methods can also be used. While the user can build their own combinations, we provide AIQM1, which is based on Δ-learning and can be used out-of-the-box. We showcase how AIQM1 reproduces the isomerization quantum yield of trans-azobenzene at a low cost. We provide example scripts that, in dozens of lines, enable the user to obtain the final population plots by simply providing the initial geometry of a molecule. Thus, those scripts perform geometry optimization, normal mode calculations, initial condition sampling, parallel trajectories propagation, population analysis, and final result plotting. Given the capabilities of MLatom to be used for training different ML models, this ecosystem can be seamlessly integrated into the protocols building ML models for nonadiabatic dynamics. In the future, a deeper and more efficient integration of MLatom with Newton-X will enable a vast range of functionalities for surface hopping dynamics, such as fewest-switches surface hopping, to facilitate similar workflows via the Python API.

New insights into the photocyclization reaction of a popular diarylethene switch: a nonadiabatic molecular dynamics study.

Diarylethene (DAE) molecular switches have continued to attract the attention of researchers for over 20 years. Their remarkable photophysical properties endow them with countless applications in photonics and molecular technologies. However, despite extensive experimental and theoretical research, the mechanism of DAE photoswitching is not yet fully rationalized. In this work, we investigate the ring closure dynamics of a popular DAE switch, 1,2-bis(3-methyl-5-phenyl-2 thienyl)perfluorocyclopentene (PT), using nonadiabatic molecular dynamics (NAMD) simulations. Employing the fewest switches surface hopping protocol, along with the semi-empirical multireference ODM2/MRCI-SD method, we investigate possible reaction pathways for this photoprocess, as well as their timescales and resulting photoproducts. Furthermore, using a dynamic configuration-space sampling procedure, we elucidate the role of triplet states in the photocyclization of PT, supporting available experimental data for the closely related DMPT molecule, which indicate an ultrafast intersystem crossing (ISC) transition competing with the singlet-driven photoswitching reaction. Our findings not only corroborate experimental studies on DAE switches, but also provide new mechanistic insights into the potential use in the rational design of DAE switches tailored for specific technological applications.

Photo-oxidation of methanol in complexes with pyrido[2,3-b]pyrazine: a nonadiabatic molecular dynamics study.

Excited-state Proton-Coupled Electron Transfer (PCET) constitutes a key step in the photo-oxidation of small, electron-rich systems possessing acidic hydrogen atoms, such as water or alcohols, which can play a vital role in green hydrogen production. In this contribution, we employ ab initio quantum-chemical methods and on-the-fly nonadiabatic molecular dynamics simulations to study the mechanism and the photodynamics of PCET in 1 : 1 pyrido[2,3-b]pyrazine complexes with methanol. We find the process to be ultrafast and efficient when the intramolecular hydrogen bond is formed with one of the ß-positioned nitrogen atoms. The complex exhibiting a hydrogen bond with an isolated nitrogen site, on the contrary, shows much lower reactivity. We explain this effect with the stabilization of the reactive ππ* charge-transfer electronic state in the former case.

Interrelations between Linkage Isomers of an Efficient Square-planar Nickel(II) Nitrite Photoswitch in the Solid State.

An efficient nitrite nickel(II) photoswitch, with the 1-phenyl-2-hydroxyimino-3-[(2'-dimethylamino)ethyl]imino-1-propanone moiety used as the ancillary ligand, is reported. In the ground-state ('dark') crystal structure, the studied compound exists predominantly as the nitro-(η1 -N(O)2 ) isomer, however, traces of the exo- and endo-nitrito-(η1 -ONO) forms are detected both at 100 K (4-5 % each) and under ambient conditions (~9 % each). When excited with the 405-530 nm LED light, the nitro-to-nitrito isomerization takes place. The total conversion exceeds 90 %. The exo-nitrito linkage isomer constitutes the dominant photo-generated form, whereas the relative population of both nitrito species depends on temperature. The reaction is fully reversible and reproducible. The photo-products are stable up to 200 K. The system constitutes a good model case for the reaction mechanism studies. Thus, experimental and theoretical investigations on the photo-isomerism were conducted and are presented in detail. Eventually, the nitro→exo-nitrito→endo-nitrito reaction pathway is proposed.

The radiative surface hopping (RSH) algorithm: Capturing fluorescence events in molecular systems within a semi-classical non-adiabatic molecular dynamics framework.

In this article, we present the radiative surface hopping algorithm, which enables modeling fluorescence within a semi-classical non-adiabatic molecular dynamics framework. The algorithm has been tested for the photodeactivation dynamics of trans-4-dimethylamino-4'-cyanostilbene (DCS). By treating on equal footing the radiative and non-radiative processes, our method allows us to attain a complete molecular movie of the excited-state deactivation. Our dynamics rely on a semi-empirical quantum mechanical/molecular mechanical Hamiltonian and have been run for hundreds of picoseconds, both in the gas phase and in isopropyl ether. The proposed approach successfully captures the first fluorescence processes occurring in DCS, and it succeeds in reproducing the experimental fluorescence lifetime and quantum yield, especially in the polar solvent. The analysis of the geometrical features of the emissive species during the dynamics discards the hypothesis of a twisted intramolecular charge transfer state to be responsible for the dual emission observed experimentally in some polar solvents. In a nutshell, our method opens the way for theoretical studies on early fluorescence events occurring up to hundreds of picoseconds in molecular systems.

Modern Theoretical Approaches to Modeling the Excited-State Intramolecular Proton Transfer: An Overview.

The excited-state intramolecular proton transfer (ESIPT) phenomenon is nowadays widely acknowledged to play a crucial role in many photobiological and photochemical processes. It is an extremely fast transformation, often taking place at sub-100 fs timescales. While its experimental characterization can be highly challenging, a rich manifold of theoretical approaches at different levels is nowadays available to support and guide experimental investigations. In this perspective, we summarize the state-of-the-art quantum-chemical methods, as well as molecular- and quantum-dynamics tools successfully applied in ESIPT process studies, focusing on a critical comparison of their specific properties.

Ultrafast nonradiative deactivation of photoexcited 8-oxo-hypoxanthine: a nonadiabatic molecular dynamics study.

In the scientific endeavor to understand the chemical origins of life, the photochemistry of the smallest life building blocks, nucleobases, has been a constant object of focus and intense research. Here, we report the results of the first theoretical study on the photo-properties of an 8-oxo-hypoxanthine molecule, the chromophore of 8-oxo-inosine, which is relevant to the recently proposed, prebiotically plausible synthetic routes to the formation of purine- and pyrimidine-nucleotides. With ab initio and semi-empirical OM2/MRCI quantum-chemistry calculations, we predict a strong photostability of the 8-oxo-hypoxanthine system and see the origin of this effect in ultrafast nonradiative relaxation through puckering of the 6-membered heterocyclic ring.

Ehrenfest and classical path dynamics with decoherence and detailed balance.

We present a semiclassical approach for nonadiabatic molecular dynamics based on the Ehrenfest method with corrections for decoherence and detailed balance. Decoherence is described via a coherence penalty functional that drives dynamics away from regions in Hilbert space characterized by large values of coherences. Detailed balance is incorporated by modification of the off-diagonal matrix elements with a quantum correction factor used in semiclassical approximations to quantum time-correlation functions. Both decoherence and detailed balance corrections introduce nonlinear terms to the Schrödinger equation. At the same time, the simplicity of fully deterministic dynamics and a single trajectory for each initial condition is preserved. In contrast, surface hopping is stochastic and requires averaging over multiple realization of the stochastic process for each initial condition. The Ehrenfest-decoherence-detailed-balance (Ehrenfest-DDB) method is adapted to the classical path approximation and ab initio time-dependent density functional theory and applied to an experimentally studied nanoscale system consisting of a fluorophore molecule and an scanning tunneling microscopy tip and undergoing current-induced charge injection, cooling, and recombination. Ehrenfest-DDB produces time scales that are similar to those obtained with decoherence induced surface hopping, which is a popular nonadiabatic molecular dynamics technique applied to condensed matter. At long times, Ehrenfest-DDB dynamics slows down considerably because the detailed balance correction makes off-diagonal elements go to zero on approach to Boltzmann equilibrium. The Ehrenfest-DDB technique provides efficient means to study quantum dynamics in large systems.

Real-Time Atomistic Dynamics of Energy Flow in an STM Setup: Revealing the Mechanism of Current-Induced Molecular Emission.

Detailed understanding of the current-induced fluorescence mechanism constitutes an exciting challenge as it can open the way to efficient coupling between an electric field and light at the nanoscale. At the same time, a number of published experimental studies give an unclear, contradictory picture of this phenomenon working principle. Here, for a system consisting of a silver tip and a porphyrin molecule, we perform for the first time fully atomistic, real-time nonadiabatic dynamics simulations to study the process of energy transfer and relaxation in an STM setup. We calculate time scales of all crucial processes and explain their atomic details. On this basis, we confirm and characterize the dual mechanism of the observed emission based on competing elastic and inelastic electron transfer between the metal tip and the molecule.

Strong Influence of Ti Adhesion Layer on Electron-Phonon Relaxation in Thin Gold Films: Ab Initio Nonadiabatic Molecular Dynamics.

Electron-phonon relaxation in thin metal films is an important consideration for many ultrasmall devices and ultrafast applications. Recent time-resolved experiments demonstrate a significant, more than a factor of five, increase in the electron-phonon coupling and acceleration in the electron-phonon relaxation rate when a narrow Ti adhesion layer is introduced between an Au film and a nonmetal substrate. Using nonadiabatic molecular dynamics combined with real-time time-dependent density functional theory, we identify the reasons that give rise to this strong effect. First, the Ti layer greatly enhances the density of states (DOS) in the energy region starting at 1 eV below the Fermi level and extending several electronvolts above it. Second, Ti atoms are four times lighter than Au atoms and therefore generate larger nonadiabatic (NA) electron-phonon coupling. Because the transition rates depend on coupling and DOS, both the factors accelerate the dynamics. Showing good agreement with the experiments, the time-domain atomistic simulations provide a detailed mechanistic understanding of the electron-phonon relaxation dynamics in thin gold films and related nanomaterials.

Ferroelectric Alignment of Organic Cations Inhibits Nonradiative Electron-Hole Recombination in Hybrid Perovskites: Ab Initio Nonadiabatic Molecular Dynamics.

Hybrid organic-inorganic perovskites show impressive potential for photovoltaic applications and currently give rise to one of the most vibrant research areas in the field. Until recently, the electrostatic interactions between their organic and inorganic components were considered mostly for stabilization of the fragile perovskite structure. We study the effect of local interactions of polar C-N bonds in the organic layer on the nonradiative electron-hole recombination in the recently reported room-temperature ferroelectric hybrid perovskite, (benzylammonium)2PbCl4. Using nonadiabatic molecular dynamics and real-time time-dependent density functional theory, we show that ferroelectric alignment of the polar groups weakens the electron-phonon nonadiabatic coupling and inhibits the nonradiative charge recombination. The effect is attributed to suppression of contributions of higher frequency phonons to the electron-phonon coupling. The coupling is dominated in the ferroelectric phase by slower collective motions. We also demonstrate the importance of van der Waals interactions for the charge-phonon relaxation in the hybrid perovskite systems. Combined with the long-range charge separation achievable in the ferroelectric phase, the weakened electron-phonon coupling indicates that ferroelectric order in hybrid perovskites can lead to increased excited-state lifetimes and improved solar energy conversion performance.

Tailoring the Schiff base photoswitching - a non-adiabatic molecular dynamics study of substituent effect on excited state proton transfer.

Small molecular systems exhibiting Excited State Intramolecular Proton Transfer (ESIPT) attract considerable attention due to their possible role as ultrafast, efficient, and photostable molecular photoswitches. Here, by means of static potential energy profile scan and on-the-fly non-adiabatic dynamics simulations we study the photodeactivation process of a minimal-chromophore aromatic Schiff base, salicylidene methylamine (SMA), and its two derivatives 6-cyano-salicylidene methylamine (6-CN-SMA) and 3-hydroxy-salicylidene methylamine (3-OH-SMA). We show that the dominant character of the lowest excited singlet state - ππ* vs. nπ* - plays a crucial role in the system's photophysics and controls the ESIPT efficiency. We also show that the relative alignment of the ππ* and nπ* states may be controlled through chemical substitutions made to the aromatic ring of the Schiff-base molecule. We believe that our findings will improve the rational-design strategies employed for the ESIPT systems, especially in the context of their possible photoswitching.

Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations.

In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H)-ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale of this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other.

Electric field control of proton-transfer molecular switching: molecular dynamics study on salicylidene aniline.

In this letter, we propose a novel, ultrafast, efficient molecular switch whose switching mechanism involves the electric field-driven intramolecular proton transfer. By means of ab initio quantum chemical calculations and on-the-fly dynamics simulations, we examine the switching performance of an isolated salicylidene aniline molecule and analyze the perspectives of its possible use as an electric field-controlled molecular electronics unit.

Photoswitching of salicylidene methylamine: a theoretical photodynamics study.

Photoswitching of simple photochromic molecules attracts substantial attention because of its possible role in future photon-driven molecular electronics. Here we model the full photoswitching cycle of a minimal photochromic Schiff base-salicylidene methylamine (SMA). We perform semiempirical nonadiabatic on-the-fly photodynamics simulations at the OM2/MRCI level and thoroughly analyze the structural time evolution and switching efficiency of the system. We also identify and examine in detail the crucial steps in the SMA photochemistry ruled by excited-state intramolecular proton transfer. The results place the investigated model aromatic Schiff base among the promising candidates for novel photoswitching molecular materials. Our study also shows the potential of the semiempirical multireference photodynamics simulations as a tool for early stage molecular photodevice design.

Excited-state intramolecular proton transfer: photoswitching in salicylidene methylamine derivatives.

The effect of chemical substitutions on the photophysical properties of the salicylidene methylamine molecule (SMA) (J. Jankowska, M. F. Rode, J. Sadlej, A. L. Sobolewski, ChemPhysChem, 2012, 13, 4287-4294) is studied with the aid of ab initio electronic structure methods. It is shown that combining π-electron-donating and π-electron-withdrawing substituents results in an electron-density push-and-pull effect on the energetic landscape of the ground and the lowest excited ππ* and nπ* singlet states of the system. The presented search for the most appropriate SMA derivatives with respect to their photoswitching functionality offers an efficient prescreening tool for finding chemical structures before real synthetic realization.

Photophysics of Schiff bases: theoretical study of salicylidene methylamine.

The proton-transfer reaction in a model aromatic Schiff base, salicylidene methylamine (SMA), in the ground and in the lowest electronically-excited singlet states, is theoretically analyzed with the aid of second-order approximate coupled-cluster model CC2, time-dependent density functional theory (TD-DFT) using the Becke, three-parameter Lee-Yang-Parr (B3LYP) functional, and complete active space perturbation theory CASPT2 electronic structure methods. Computed vertical-absorption spectra for the stable ground-state isomers of SMA fully confirm the photochromism of SMA. The potential-energy profiles of the ground and the lowest excited singlet state are calculated and four photophysically relevant isomeric forms of SMA; α, ß, γ, and δ are discussed. The calculations indicate two S(1)/S(0) conical intersections which provide non-adiabatic gates for a radiationless decay to the ground state. The photophysical scheme which emerges from the theoretical study is related to recent experimental results obtained for SMA and its derivatives in the low-temperature argon matrices (J. Grzegorzek, A. Filarowski, Z. Mielke, Phys. Chem. Chem. Phys. 2011, 13, 16596-16605). Our results suggest that aromatic Schiff bases are potential candidates for optically driven molecular switches.

Iron(II) and zinc(II) complexes with designed pybox ligand for asymmetric aqueous Mukaiyama-aldol reactions.

An iron(II) complex with a hindered hydroxyethyl-pybox (he-pybox) ligand shows improved catalytic activity and enantioselectivity for asymmetric Mukaiyama-aldol reactions in aqueous media. This water-stable chiral Lewis acid promotes condensation of aromatic silyl enol ethers with a range of aldehydes with good yields, excellent syn-diastereoselectivity and up to 92% ee. The combination of the same ligand with ZnII salt is also demonstrated as a remarkably efficient and water-compatible chiral Lewis acid.

Zn(pybox)-complex-catalyzed asymmetric aqueous Mukaiyama-aldol reactions.

Catalytic asymmetric aldol reactions in aqueous media have been developed using chiral zinc complex. The aldol products have been obtained in high yields, high diastereocontrol, and good level of enantioselectivity. Various aromatic and alpha,beta-unsaturated aldehydes and silyl enol ethers derived from ketones can be employed in this reaction to provide the aldol adducts in good to high yield. The elaborated catalytic system has been found as selective for aliphatic aldehydes as well.

Direct asymmetric aldol-Tishchenko reaction of aliphatic ketones catalyzed by syn-aminoalcohol-Yb(III) complexes.

The asymmetric direct aldol condensation of aldehydes with ethyl- and propylketones is catalyzed by syn-alpha-aminoalcohol-Yb(OTf)3 complexes, yielding the anti-1,3-diol monoesters with high diastereocontrol and good enantioselectivity. Three adjacent stereogenic centers are created in a simultaneous aldol condensation and Evans-Tishchenko reduction in an acyclic system.