arXiv subjects

Petr Slavíček

Publications and source records attributed to Petr Slavíček.

13 recordsLinked to original sources

arXiv2026

Real-Time Emergence of Charge-Transfer-to-Solvent States from Core Excitation

Charge-transfer-to-solvent (CTTS) excitations provide a chemically central route to generating hydrated electrons and initiating redox chemistry in solution, yet the earliest stage of CTTS---the formation of the excited state itself---is usually treated as instantaneous. Here we present a time-domain perspective of how CTTS character builds up during core-level photoexcitation of an aqueous metal ion. Using time-dependent configuration interaction, we simulate the coherent evolution of a dense manifold of core-excited states and track the ultrafast flow of electronic charge from the initially localized site into solvent-supported final states. We find that the dynamics evolves from a few-state, oscillatory behavior to effectively irreversible delocalization, as the charge disperses among many coupled configurations, providing a microscopic mechanism for the early-time emergence of CTTS character. Our results offer a transparent real-time interpretation of what core-level spectroscopies and core-hole-clock-type measurements can probe in solutions, outlining experimental signatures for probing the build-up of CTTS states on the core-hole-lifetime timescale. Looking ahead, attosecond and sub-femtosecond X-ray pump--probe approaches at X-ray free-electron lasers provide a realistic route to directly time-resolve the core-excited CTTS wave packets in solution.

physics.chem-ph↗

arXiv2026

Proton transfer and hydronium formation in ionized water

Aqueous radiation chemistry emerges through ultrafast proton transfer and ion-radical formation with unexplored energy-redistribution dynamics steering the subsequent reactions. We performed a time-resolved disruptive-probing experiment on pure water dimer, (H$_2$O)$_2$, to disentangle the elementary post-ionization reactions. Through kinetic-energy-resolved ion imaging, we unraveled the dynamics in the (H$_2$O)$_2^+$ ground state: at low-energy ($\sim$0.05~eV) ultrafast proton transfer ($\sim$19~fs) is followed by H$_3$O$^+$+OH fragmentation ($\sim$360~fs). At higher energies, proton transfer becomes hindered ($\sim$60~fs) while the subsequent fragmentation becomes faster ($\sim$210~fs), eventually ($>0.15$~eV) merging into coupled dynamics ($\sim$100~fs). Additionally, we observed H$_2$O)$_2^+$ stabilization proceeding through a Zundel-like structure. These timescales and product energies reveal how ion-radical formation in ionized hydrogen-bonded networks shapes reactivity in aqueous dynamics.

physics.chem-ph↗

arXiv2026

On the interpretation of molecular photoexcitation with long and ultrashort laser pulses

Photoexcitation is an inherent part of any photochemical or spectroscopic experiment, yet its impact on the excited-state dynamics is often overlooked. However, it is the excited molecular state, built upon photoexcitation and shaped by the characteristics of the light source, that determines the fate of the excited molecule and its subsequent photochemical reactions. In this work, we investigate how excited molecular states are built by different laser pulses, leveraging two representations of the molecular wave function: the Born-Huang expansion and the exact factorization. We explore the generation of two limiting cases: a stationary molecular state generated with a long laser pulse and an electronic wave packet created by an ultrashort (attosecond) laser pulse. The standard concepts of population transfer between electronic states, the resonance condition, or sudden vertical excitation, inherent to the Born-Huang representation and used by chemists to approximate the impact of photoexcitation on molecular systems, are brought to a new light by the exact factorization.

physics.chem-ph↗

arXiv2026

Perspective on a challenge: predicting the photochemistry of cyclobutanone

This Perspective is part of a Special Topic that explored the maturity of nonadiabatic molecular dynamics for predicting photochemical processes. In 2023, a prediction challenge was issued to the community of computational photochemists to simulate the photochemistry of cyclobutanone, photoexcited at 200 nm, and the resulting time-resolved MeV-UED signal. The challenge attracted 15 theoretical predictions from more than 70 researchers, employing a wide range of strategies for electronic structure and nonadiabatic molecular dynamics to predict the time-resolved MeV-UED signal before the experiment had been conducted at SLAC (Stanford, USA). The MeV-UED instrument at Shanghai Jiao Tong University was also used to provide a second independent time-resolved MeV-UED signal for the photochemistry of cyclobutanone. This Perspective discusses the various approaches and strategies used by the participants to predict the photochemistry of cyclobutanone. This work also summarizes the strengths and weaknesses of various methods used for photoexcitation, electronic structure, nonadiabatic dynamics, and calculation of observables, as agreed by the participants during a CECAM workshop dedicated to the results of the challenge and organized in Lausanne in April 2025. This Perspective also collects all the predicted time-resolved MeV-UED signals into a single figure, together with the experimental signal. This challenge (i) demonstrated the qualitative predictive power of nonadiabatic molecular dynamics and (ii) underscore the impact of electronic-structure theory on the outcome of the excited-state dynamics and the need for its careful benchmarking. This effort allowed the community to share practical strategies to perform nonadiabatic dynamics (discussed in the present Perspective) and constitutes a 'calibration' exercise for computational photochemistry.

physics.chem-ph↗

arXiv2026

Limitations of MRSF-TDDFT for Applications in Photochemistry

Mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) has recently emerged as an attractive electronic-structure method for studying photochemical processes, given that it bridges the computational efficiency of single-reference approaches with the versatility of multireference methods. In the following, we critically assess the general applicability of MRSF-TDDFT to photochemistry and identify two important limitations. First, the doubly-excited configurations included in MRSF-TDDFT come at the cost of missing some singly-excited configurations. Second, MRSF-TDDFT provides unreliable excited-state energies when its triplet reference - a cornerstone of the method - abruptly changes its nature, e.g., when the T$_1$ and T$_2$ triplet states become nearly degenerate and exchange electronic character. This change of character of the triplet reference can induce discontinuities or sharp distortions in electronic potential energy curves of the response states in unsuspected regions of the nuclear configuration space. We propose strategies and diagnostics to detect these limitations in the exploration of potential energy surfaces and nonadiabatic molecular dynamics using MRSF-TDDFT.

physics.chem-ph↗

arXiv2025

Best practices for nonadiabatic molecular dynamics simulations

Nonadiabatic molecular dynamics simulations aim to describe the coupled electron-nuclear dynamics of molecules in excited electronic states. These simulations have been applied to understand a plethora of photochemical and photophysical processes, and, as a result, the number of nonadiabatic dynamics simulations has been growing significantly over the past decade. Yet, the field remains in its infancy, and a potential user may find it difficult to approach this type of simulation, given their complexity and the number of elements that should be considered for a (hopefully) successful nonadiabatic dynamics simulation. Nonadiabatic molecular dynamics relies on several key steps: finding a level of electronic-structure theory to describe the molecule in its Franck-Condon region and beyond, describing the photoexcitation process, selecting a method to perform the nonadiabatic dynamics, and analyzing the final results before calculating observables for a more direct comparison with experiment. This Best Practices guide aims to provide a general guide for the user of nonadiabatic molecular dynamics by (i) discussing the fundamentals of nonadiabatic molecular dynamics and the various trajectory-based methods developed for molecular systems, (ii) introducing the different electronic-structure methods and concepts - adiabatic/diabatic representation, conical intersections - that can be used with nonadiabatic molecular dynamics (or for benchmarking), (iii) providing details on the various steps required to perform a nonadiabatic dynamics simulation and their practical use, as well as guided examples and a discussion on the calculation of observables, (iv) proposing a FAQ with the typical questions a user may have when performing nonadiabatic dynamics, and (v) sketching a checklist for the key practical steps when performing a (trajectory-based) nonadiabatic molecular dynamics.

physics.chem-ph↗

arXiv2025

Diffusive vs. non-diffusive paths to interstellar hydrogen peroxide. A machine learning-based molecular dynamics study

Context. Radical chemical reactions on cosmic dust grains play a crucial role in forming various chemical species. Among different radicals, the hydroxyl (OH) is one of the most important ones, with a rather specific chemistry. Aims. The goal of this work is to simulate the recombination dynamics of hydroxyl radicals and the subsequent formation of hydrogen peroxide (H$_{2}$O$_{2}$). Mthods. We employed neural network potentials trained on ONIOM(QM/QM) data, combining multi-reference (CASPT2) and density functional theory (DFT) calculations. This approach allows us to model the recombination of hydroxyl radicals on ice surfaces with high computational efficiency and accuracy. Results. Our simulations reveal that the initial position of the radicals plays a decisive role in determining recombination probability. We found that the formation of hydrogen-bond between radicals, competes with the formation of hydrogen peroxide, reducing the recombination efficiency, contrary to expectancy. This competition reduces the recombination probability for radicals that are initially formed approximately 3 Å apart. Recombination probabilities also depend on the kinetic energy of the added radicals, with values around 0.33 for thermal radicals and a wide range of values between 0.33 and 1.00 for suprathermal OH radicals. Conclusions. Based on our calculations we provide recommendations for introducing OH radical recombination into kinetic astrochemical models, differentiating between thermal and suprathermal radicals. The recombination behavior varies significantly between these two cases: while thermal radicals are sometimes trapped in hydrogen-bonded minima, the case of suprathermal radicals varies with the added energy. Our most important conclusion is that OH radical recombination probability cannot be assumed 1.0 for a wide variety of cases.

astro-ph.GA↗

arXiv2024

Including photoexcitation explicitly in trajectory-based nonadiabatic dynamics at no cost

Over the last decades, theoretical photochemistry has produced multiple techniques to simulate the nonadiabatic dynamics of molecules. Surprisingly, much less effort has been devoted to adequately describing the first step of a photochemical or photophysical process: photoexcitation. Here, we propose a formalism to include the effect of a laser pulse in trajectory-based nonadiabatic dynamics at the level of the initial conditions, with no additional cost. The promoted density approach (PDA) decouples the excitation from the nonadiabatic dynamics by defining a new set of initial conditions, which include an excitation time. PDA with surface hopping leads to nonadiabatic dynamics simulations in excellent agreement with quantum dynamics using an explicit laser pulse and highlights the strong impact of a laser pulse on the resulting photodynamics and the limits of the (sudden) vertical excitation. Combining PDA with trajectory-based nonadiabatic methods is possible for any arbitrary-sized molecules using a code provided in this work.

physics.chem-ph↗

arXiv2024

How Does Mg$^{2+}_{(aq)}$ Interact with ATP$_{(aq)}$? Biomolecular Structure through the Lens of Liquid-Jet Photoelectron Spectroscopy

Site-specific information on how adenosine triphosphate in the aqueous phase (ATP$_{(aq)}$) interacts with magnesium (Mg$^{2+}_{(aq)}$) is a prerequisite to understanding its complex biochemistry. To gather such information, we apply liquid-jet photoelectron spectroscopy (LJ-PES) assisted by electronic-structure calculations to study ATP$_{(aq)}$ solutions with and without dissolved Mg$^{2+}$. Valence photoemission data reveal spectral changes in the phosphate and adenine features of ATP$_{(aq)}$ due to interactions with the divalent cation. Chemical shifts in Mg 2p, Mg 2s, P 2p, and P 2s core-level spectra as a function of the Mg$^{2+}$/ATP concentration ratio are correlated to the formation of [MgATP]$^{-2}_{(aq)}$ and Mg$_2$ATP$_{(aq)}$ complexes, demonstrating the element-sensitivity of the technique to Mg$^{2+}$-phosphate interactions. In addition, we report and compare P 2s data from ATP$_{(aq)}$ and adenosine mono- and di-phosphate (AMP$_{(aq)}$ and ADP$_{(aq)}$, respectively) solutions, probing the electronic structure of the phosphate chain and the local environment of individual phosphate units in ATP$_{(aq)}$. Finally, we have recorded intermolecular Coulombic decay (ICD) spectra initiated by ionization of Mg 1s electrons to probe ligand exchange in the Mg$^{2+}$-ATP$_{(aq)}$ coordination environment, demonstrating the unique capabilities of ICD for revealing structural information. Our results provide an overview of the electronic structure of ATP$_{(aq)}$ and Mg$^{2+}$-ATP$_{(aq)}$ moieties relevant to phosphorylation and dephosphorylation reactions that are central to bioenergetics in living organisms.

physics.chem-ph↗

arXiv2024

Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water

Solvent interactions, particularly hydration, are vital in chemical and biochemical systems. Model systems unveil microscopic details of such interactions. We uncover a specific hydrogen-bonding motif of the biomolecular building block indole (C$_8$H$_7$N), tryptophan's chromophore, in water: a strong localized $\text{N-H}\cdots\text{OH}_2$ hydrogen bond, alongside unstructured solvent interactions. This insight is revealed from a combined experimental and theoretical analysis of indole's electronic structure in aqueous solution. We have recorded the complete X-ray photoemission and Auger spectrum of aqueous-phase indole, quantitatively explaining all peaks through \emph{ab initio} modeling. The efficient and accurate technique for modeling valence and core photoemission spectra involves the maximum-overlap method and the non-equilibrium polarizable-continuum model. A two-hole electron-population analysis quantitatively describes the Auger spectra. Core-electron binding energies for nitrogen and carbon highlight the specific interaction with a hydrogen-bonded water molecule at the N-H group and otherwise nonspecific solvent interactions.

physics.chem-ph↗

arXiv2024

Predicting the photodynamics of cyclobutanone triggered by a laser pulse at 200 nm and its MeV-UED signals -- a trajectory surface hopping and XMS-CASPT2 perspective

This work is part of a prediction challenge that invited theoretical/computational chemists to predict the photochemistry of cyclobutanone in the gas phase, excited at 200 nm by a laser pulse, and the expected signal that will be recorded during a time-resolved megaelectronvolt ultrafast electron diffraction (MeV-UED). We present here our theoretical predictions based on a combination of trajectory surface hopping with XMS-CASPT2 (for the nonadiabatic molecular dynamics) and Born-Oppenheimer molecular dynamics (BOMD) with MP2 (for the athermal ground-state dynamics following internal conversion), coined (NA+BO)MD. The initial conditions were sampled from BOMD coupled to a quantum thermostat. Our simulations indicate that the main photoproducts after 2 ps of dynamics are CO + cyclopropane (50%), CO + propene (10%), and ethene and ketene (34%). The photoexcited cyclobutanone in its second excited electronic state S$_2$ can follow two pathways for its nonradiative decay: (i) a ring-opening in S$_2$ and a subsequent rapid decay to the ground electronic state, where the photoproducts are formed, or (ii) a transfer through a closed-ring conical intersection to S$_1$, where cyclobutanone ring opens and then funnels to the ground state. Lifetimes for the photoproduct and electronic populations were determined. We calculated a stationary MeV-UED signal [difference pair distribution function - $Δ$PDF$(r)$] for each (interpolated) pathway as well as a time-resolved signal [$Δ$PDF$(r,t)$ and $ΔI/I(s,t)$] for the full swarm of (NA+BO)MD trajectories. Furthermore, our analysis provides time-independent basis functions that can be used to fit the time-dependent experimental UED signals and potentially recover the population of photoproducts. We also offer a detailed analysis of the limitations of our model and their potential impact on the predicted experimental signals.

physics.chem-ph↗

arXiv2019

Direct detection of polar structure formation in helium nanodroplets by beam deflection measurements

Long-range intermolecular forces are able to steer polar molecules submerged in superfluid helium nanodroplets into highly polar metastable configurations. We demonstrate that the presence of such special structures can be identified, in a direct and determinative way, by electrostatic deflection of the doped nanodroplet beam. The measurement also establishes the structures' electric dipole moments. In consequence, the introduced approach is complementary to spectroscopic studies of low-temperature molecular assembly reactions. It is enabled by the fact that within the cold superfluid matrix the molecular dipoles become nearly completely oriented by the applied electric field. As a result, the massive (tens of thousands of helium atoms) nanodroplets undergo significant deflections. The method is illustrated here by an application to dimers and trimers of dimethyl sulfoxide (DMSO) molecules. We interpret the experimental results with ab initio theory, mapping the potential energy surface of DMSO complexes and simulating their low temperature aggregation dynamics.

physics.atm-clus↗

arXiv2015

Electric dipole moments of nanosolvated acid molecules in water clusters

The electric dipole moments of $(H_{2}O)_{n}DCl$ ($n=3-9$) clusters have been measured by the beam deflection method. Reflecting the (dynamical) charge distribution within the system, the dipole moment contributes information about the microscopic structure of nanoscale solvation. The addition of a DCl molecule to a water cluster results in a strongly enhanced susceptibility. There is evidence for a noticeable rise in the dipole moment occurring at $n\approx5-6$. This size is consistent with predictions for the onset of ionic dissociation. Additionally, a molecular dynamics model suggests that even with a nominally bound impurity an enhanced dipole moment can arise due to the thermal and zero point motion of the proton and the water molecules. The experimental measurements and the calculations draw attention to the importance of fluctuations in defining the polarity of water-based nanoclusters, and generally to the essential role played by motional effects in determining the response of fluxional nanoscale systems under realistic conditions.

physics.atm-clus↗