How Does Mg2+(aq) Interact with ATP(aq)? Biomolecular Structure through the Lens of Liquid-Jet Photoemission Spectroscopy.

Liquid-jet photoemission spectroscopy (LJ-PES) allows for a direct probing of electronic structure in aqueous solutions. We show the applicability of the approach to biomolecules in a complex environment, exploring site-specific information on the interaction of adenosine triphosphate in the aqueous phase (ATP(aq)) with magnesium (Mg2+(aq)), highlighting the synergy brought about by the simultaneous analysis of different regions in the photoelectron spectrum. In particular, we demonstrate intermolecular Coulombic decay (ICD) spectroscopy as a new and powerful addition to the arsenal of techniques for biomolecular structure investigation. We apply LJ-PES assisted by electronic-structure calculations to study ATP(aq) solutions with and without dissolved Mg2+. Valence photoelectron 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 Mg2+/ATP concentration ratio are correlated to the formation of [Mg(ATP) 2]6-(aq), [MgATP]2-(aq), and [Mg2ATP](aq) complexes, demonstrating the element sensitivity of the technique to Mg2+-phosphate interactions. The most direct probe of the intermolecular interactions between ATP(aq) and Mg2+(aq) is delivered by the emerging ICD electrons following ionization of Mg 1s electrons. ICD spectra are shown to sensitively probe ligand exchange in the Mg2+-ATP(aq) coordination environment. In addition, we report and compare P 2s data from ATP(aq) and adenosine mono- and diphosphate (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). Our results provide a comprehensive view of the electronic structure of ATP(aq) and Mg2+-ATP(aq) complexes relevant to phosphorylation and dephosphorylation reactions that are central to bioenergetics in living organisms.

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 with MP2 (for the athermal ground-state dynamics following internal conversion), coined (NA+BO)MD. The initial conditions were sampled from Born-Oppenheimer molecular dynamics 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 S2 can follow two pathways for its nonradiative decay: (i) a ring-opening in S2 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 S1, 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-ΔPDF(r)] for each (interpolated) pathway as well as a time-resolved signal [ΔPDF(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 [both ΔPDF(r,t) and ΔI/I(s,t)] 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.

Fast and accurate excited states predictions: machine learning and diabatization.

The efficiency of machine learning algorithms for electronically excited states is far behind ground-state applications. One of the underlying problems is the insufficient smoothness of the fitted potential energy surfaces and other properties in the vicinity of state crossings and conical intersections, which is a prerequisite for an efficient regression. Smooth surfaces can be obtained by switching to the diabatic basis. However, diabatization itself is still an outstanding problem. We overcome these limitations by solving both problems at once. We use a machine learning approach combining clustering and regression techniques to correct for the deficiencies of property-based diabatization which, in return, provides us with smooth surfaces that can be easily fitted. Our approach extends the applicability of property-based diabatization to multidimensional systems. We utilize the proposed diabatization scheme to achieve higher prediction accuracy for adiabatic states and we show its performance by reconstructing global potential energy surfaces of excited states of nitrosyl fluoride and formaldehyde. While the proposed methodology is independent of the specific property-based diabatization and regression algorithm, we show its performance for kernel ridge regression and a very simple diabatization based on transition multipoles. Compared to most other algorithms based on machine learning, our approach needs only a small amount of training data.

Unveiling the Borohydride Ion through Force-Field Development.

The borohydride ion, BH4-, is an essential reducing agent in many technological processes, yet its full understanding has been elusive, because of at least two significant challenges. One challenge arises from its marginal stability in aqueous solutions outside of basic pH conditions, which considerably limits the experimental thermodynamic data. The other challenge comes from its unique and atypical hydration shell, stemming from the negative excess charge on its hydrogen atoms, which complicates the accurate modeling in classical atomistic simulations. In this study, we combine experimental and computer simulation techniques to devise a classical force field for NaBH4 and deepen our understanding of its characteristics. We report the first measurement of the ion's activity coefficient and extrapolate it to neutral pH conditions. Given the difficulties in directly measuring its solvation free energies, owing to its instability, we resort to quantum chemistry calculations. This combined strategy allows us to derive a set of nonpolarizable force-field parameters for the borohydride ion for classical molecular dynamics simulations. The derived force field simultaneously captures the solvation free energy, the hydration structure, as well as the activity coefficient of NaBH4 salt across a broad concentration range. The obtained insights into the hydration shell of the BH4- ion are crucial for accurately modeling and understanding its interactions with other molecules, ions, materials, and interfaces.

Photocatalytic Generation of Trifluoromethyl Nitrene for Alkene Aziridination.

N-Trifluoromethylated organics may be applied in drug design, agrochemical synthesis, and materials science, among other areas. Yet, despite recent advances in the synthesis of aliphatic, cyclic and heterocyclic N-trifluoromethyl compounds, no strategy based on trifluoromethyl nitrene has hitherto been explored. Here we describe the formation of triplet trifluoromethyl nitrene from azidotrifluoromethane, a stable and safe-to-use precursor, by visible light photocatalysis. The addition of CF3 N to alkenes via biradical intermediates afforded previously unknown aziridines substituted with trifluoromethyl group on the nitrogen atom. The obtained aziridines were converted into either N-trifluoromethylimidazolines, via formal [3+2] cycloaddition with nitriles, mediated by a Lewis acid, or into N-trifluoromethylaldimines, via ring opening and aryl group migration mediated by a strong Brønsted acid. Our findings open new opportunities for the development of novel classes of N-CF3 compounds with possible applications in the life sciences.

Spin-Vibronic Coupling Controls the Intersystem Crossing of Iodine-Substituted BODIPY Triplet Chromophores.

4,4-Difluoro-4-borata-3a-azonia-4a-aza-s-indacene (BODIPY) dyes are extensively used in various applications of their triplet states, ranging from photoredox catalysis, through triplet sensitization to photodynamic therapy. However, the rational design of BODIPY triplet chromophores by ab initio modelling is limited by their strong interactions of spin, electronic and vibrational dynamics. In particular, spin-vibronic coupling is often overlooked when estimating intersystem crossing (ISC) rates. In this study, a combined experimental and theoretical approach using spin-vibronic coupling to correctly describe ISC in BODIPY dyes was developed. For this purpose, seven π-extended BODIPY derivatives with iodine atoms in different positions were examined. It was found that the heavy-atom effect of iodine atoms is site specific, causing high triplet yields in only some positions. This site-specific ISC was explained by El-Sayed rules, so both the contribution and character of the molecular orbitals involved in the excitation must be considered when predicting the ISC rates. Overall, the rational design of BODIPY triplet chromophores requires using (i) the high-quality electronic structure theory, including both static and dynamical correlations; and (ii) the two-component wave function Hamiltonian, and rationalizing; and (iii) ISC based on the character of the molecular orbitals of heavy atoms involved in the excitation, expanding El-Sayed rules beyond their traditional applications.

Visible-Light-Activated Carbon Monoxide Release from Porphyrin-Flavonol Hybrids.

We report on porphyrin-flavonol hybrids consisting of a porphyrin antenna and four covalently bound 3-hydroxyflavone (flavonol) groups, which act as highly efficient photoactivatable carbon monoxide (CO)-releasing molecules (photoCORMs). These bichromophoric systems enable activation of the UV-absorbing flavonol chromophore by visible light up to 650 nm and offer precise spatial and temporal control of CO administration. The physicochemical properties of the porphyrin antenna system can also be tuned by inserting a metal cation. Our computational study revealed that the process occurs via endergonic triplet-triplet energy transfer from porphyrin to flavonol and may become feasible thanks to flavonol energy stabilization upon intramolecular proton transfer. This mechanism was also indirectly supported by steady-state and transient absorption spectroscopy techniques. Additionally, the porphyrin-flavonol hybrids were found to be biologically benign. With four flavonol CO donors attached to a single porphyrin chromophore, high CO release yields, excellent uncaging cross sections, low toxicity, and CO therapeutic properties, these photoCORMs offer exceptional potential for their further development and future biological and medical applications.

Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water.

Solvent interactions, particularly hydration, are vital in chemical and biochemical systems. Model systems reveal microscopic details of such interactions. We uncover a specific hydrogen-bonding motif of the biomolecular building block indole (C8H7N), tryptophan's chromophore, in water: a strong localized N-H···OH2 hydrogen bond, alongside unstructured solvent interactions. This insight is revealed from a combined experimental and theoretical analysis of the electronic structure of indole in aqueous solution. We recorded the complete X-ray photoemission and Auger spectrum of aqueous-phase indole, quantitatively explaining all peaks through ab initio modeling. The efficient and accurate technique for modeling valence and core photoemission spectra involves the maximum-overlap method and the nonequilibrium 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.

What Controls the Quality of Photodynamical Simulations? Electronic Structure Versus Nonadiabatic Algorithm.

The field of nonadiabatic dynamics has matured over the last decade with a range of algorithms and electronic structure methods available at the moment. While the community currently focuses more on developing and benchmarking new nonadiabatic dynamics algorithms, the underlying electronic structure controls the outcome of nonadiabatic simulations. Yet, the electronic-structure sensitivity analysis is typically neglected. In this work, we present a sensitivity analysis of the nonadiabatic dynamics of cyclopropanone to electronic structure methods and nonadiabatic dynamics algorithms. In particular, we compare wave function-based CASSCF, FOMO-CASCI, MS- and XMS-CASPT2, density-functional REKS, and semiempirical MRCI-OM3 electronic structure methods with the Landau-Zener surface hopping, fewest switches surface hopping, and ab initio multiple spawning with informed stochastic selection algorithms. The results clearly demonstrate that the electronic structure choice significantly influences the accuracy of nonadiabatic dynamics for cyclopropanone even when the potential energy surfaces exhibit qualitative and quantitative similarities. Thus, selecting the electronic structure solely on the basis of the mapping of potential energy surfaces can be misleading. Conversely, we observe no discernible differences in the performance of the nonadiabatic dynamics algorithms across the various methods. Based on the above results, we discuss the present-day practice in computational photodynamics.

On the Wavelength-Dependent Photochemistry of the Atmospheric Molecule CF3COCl.

The wavelength control of photochemistry usually results from ultrafast dynamics following the excitation of different electronic states. Here, we investigate the CF3COCl molecule, exhibiting wavelength-dependent photochemistry both via (i) depositing increasing internal energy into a single state and (ii) populating different electronic states. We reveal the mechanism behind the photon-energy dependence by combining nonadiabatic ab initio molecular dynamics techniques with the velocity map imaging experiment. We describe a consecutive mechanism of photodissociation where an immediate release of Cl taking place in an excited electronic state is followed by a slower ground-state dissociation of the CO fragment. The CO release is subject to an activation barrier and is controlled by excess internal energy via the excitation wavelength. Therefore, a selective release of CO along with Cl can be achieved. The mechanism is fully supported by both the measured kinetic energy distributions and anisotropies of the angular distributions. Interestingly, the kinetic energy of the released Cl atom is sensitively modified by accounting for spin-orbit coupling. Given the atmospheric importance of CF3COCl, we discuss the consequences of our findings for atmospheric photochemistry.

Direct tracking of ultrafast proton transfer in water dimers.

Upon ionization, water forms a highly acidic radical cation H2O+· that undergoes ultrafast proton transfer (PT)-a pivotal step in water radiation chemistry, initiating the production of reactive H3O+, OH[Formula: see text] radicals, and a (hydrated) electron. Until recently, the time scales, mechanisms, and state-dependent reactivity of ultrafast PT could not be directly traced. Here, we investigate PT in water dimers using time-resolved ion coincidence spectroscopy applying a free-electron laser. An extreme ultraviolet (XUV) pump photon initiates PT, and only dimers that have undergone PT at the instance of the ionizing XUV probe photon result in distinct H3O+ + OH+ pairs. By tracking the delay-dependent yield and kinetic energy release of these ion pairs, we measure a PT time of (55 ± 20) femtoseconds and image the geometrical rearrangement of the dimer cations during and after PT. Our direct measurement shows good agreement with nonadiabatic dynamics simulations for the initial PT and allows us to benchmark nonadiabatic theory.

Spin-Vibronic Control of Intersystem Crossing in Iodine-Substituted Heptamethine Cyanines.

Spin-orbit coupling between electronic states of different multiplicity can be strongly coupled to molecular vibrations, and this interaction is becoming recognized as an important mechanism for controlling the course of photochemical reactions. Here, we show that the involvement of spin-vibronic coupling is essential for understanding the photophysics and photochemistry of heptamethine cyanines (Cy7), bearing iodine as a heavy atom in the C3' position of the chain and/or a 3H-indolium core, as potential triplet sensitizers and singlet oxygen producers in methanol and aqueous solutions. The sensitization efficiency was found to be an order of magnitude higher for the chain-substituted than the 3H-indolium core-substituted derivatives. Our ab initio calculations demonstrate that while all optimal structures of Cy7 are characterized by negligible spin-orbit coupling (tenths of cm-1) with no dependence on the position of the substituent, molecular vibrations lead to its significant increase (tens of cm-1 for the chain-substituted cyanines), which allowed us to interpret the observed position dependence.

Excitation and fragmentation of the dielectric gas C4F7N: Electrons vs photons.

C4F7N is a promising candidate for the replacement of sulfur hexafluoride as an insulating medium, and it is important to understand the chemical changes initiated in the molecule by collision with free electrons, specifically the formation of neutral fragments. The first step of neutral fragmentation is electronic excitation, yet neither the absorption spectrum in the vacuum ultraviolet (VUV) region nor the electron energy loss spectrum have previously been reported. Here, we experimentally probed the excited states by VUV photoabsorption spectroscopy and electron energy loss spectroscopy (EELS). We found that the distribution of states populated upon electron impact with low-energy electrons is significantly different from that following photoabsorption. This difference was confirmed and interpreted with ab initio modeling of both VUV and EELS spectra. We propose here a new computational protocol for the simulation of EELS spectra combining the Born approximation with approximate forms of correlated wave functions, which allows us to calculate the (usually very expensive) scattering cross sections at a cost similar to the calculation of oscillator strengths. Finally, we perform semi-classical non-adiabatic dynamics simulations to investigate the possible neutral fragments of the molecule formed through electron-induced neutral dissociation. We show that the product distribution is highly non-statistical.

Redox Potentials with COSMO-RS: Systematic Benchmarking with Different Databases.

Recent techniques of computational electrochemistry can yield redox potentials with accuracy as good as 0.1 V. Yet, many such methods are not universal, easy to use, or computationally efficient. Herein, we provide a systematic benchmarking of a relatively cheap and straightforward computational approach for fairly accurate computations of redox potentials. It is based on a combination of the conductor-like screening model for real solvents (COSMO-RS) and the density functional theory (DFT). The benchmarking is done with databases covering diverse redox systems, including transition-metal aquacomplexes and various organic and inorganic compounds. In addition, we also present our own test set aiming at maximum chemical diversity and maximum range of redox potential values. We assess the performance of the fairly efficient computational protocol combining the COSMO-RS with the BP86 DFT functional. This is done by calibrating it against different high-level state-of-the-art techniques, in particular, polarizable continuum model (PCM) connected to composite G3(MP2,CC)(+) method, domain-based pair natural orbital implementation of coupled cluster theory, or complete basis set CBS-QB3 method. We also elaborate on the absolute reduction potential value of standard hydrogen electrode to be used with COSMO-RS, and we propose the value of approx. 4.4 V. The COSMO-RS/BP86-D3(BJ) combination outperforms other methods on a wide range of redox systems. However, we show that its accuracy is based on a balanced error cancelation and, therefore, it cannot be further systematically improved. As a result, the proposed procedure represents a pragmatic choice for large-scale screening, yet it could be combined with more advanced methods for detailed studies.

Ultrafast Charge and Proton Transfer in Doubly Ionized Ammonia Dimers.

We investigate the ultrafast energy and charge transfer processes between ammonia molecules following ionization reactions initiated by electron impact. Exploring ionization-induced processes in molecular clusters provides us with a detailed insight into the dynamics using experiments in the energy domain. We ionize the ammonia dimer with 200 eV electrons and apply the fragment ions coincident momentum spectroscopy and nonadiabatic molecular dynamics simulations. We identify two mechanisms leading to the doubly charged ammonia dimer. In the first one, a single molecule is ionized. This initiates an ultrafast proton transfer process, leading to the formation of the NH2+ + NH4+ pair. Alternatively, a dimer with a delocalized charge is formed dominantly via the intermolecular Coulombic decay, forming the NH3+·NH3+ dication. This dication further dissociates into two NH3+ cations. The ab initio calculations have reproduced the measured kinetic energy release of the ion pairs and revealed the dynamical processes following the double ionization.

Observation of intermolecular Coulombic decay and shake-up satellites in liquid ammonia.

We report the first nitrogen 1s Auger-Meitner electron spectrum from a liquid ammonia microjet at a temperature of ∼223 K (-50 °C) and compare it with the simultaneously measured spectrum for gas-phase ammonia. The spectra from both phases are interpreted with the assistance of high-level electronic structure and ab initio molecular dynamics calculations. In addition to the regular Auger-Meitner-electron features, we observe electron emission at kinetic energies of 374-388 eV, above the leading Auger-Meitner peak (3a1 2). Based on the electronic structure calculations, we assign this peak to a shake-up satellite in the gas phase, i.e., Auger-Meitner emission from an intermediate state with additional valence excitation present. The high-energy contribution is significantly enhanced in the liquid phase. We consider various mechanisms contributing to this feature. First, in analogy with other hydrogen-bonded liquids (noticeably water), the high-energy signal may be a signature for an ultrafast proton transfer taking place before the electronic decay (proton transfer mediated charge separation). The ab initio dynamical calculations show, however, that such a process is much slower than electronic decay and is, thus, very unlikely. Next, we consider a non-local version of the Auger-Meitner decay, the Intermolecular Coulombic Decay. The electronic structure calculations support an important contribution of this purely electronic mechanism. Finally, we discuss a non-local enhancement of the shake-up processes.

Different timescales during ultrafast stilbene isomerization in the gas and liquid phases revealed using time-resolved photoelectron spectroscopy.

Directly contrasting ultrafast excited-state dynamics in the gas and liquid phases is crucial to understanding the influence of complex environments. Previous studies have often relied on different spectroscopic observables, rendering direct comparisons challenging. Here, we apply extreme-ultraviolet time-resolved photoelectron spectroscopy to both gaseous and liquid cis-stilbene, revealing the coupled electronic and nuclear dynamics that underlie its isomerization. Our measurements track the excited-state wave packets from excitation along the complete reaction path to the final products. We observe coherent excited-state vibrational dynamics in both phases of matter that persist to the final products, enabling the characterization of the branching space of the S1-S0 conical intersection. We observe a systematic lengthening of the relaxation timescales in the liquid phase and a red shift of the measured excited-state frequencies that is most pronounced for the complex reaction coordinate. These results characterize in detail the influence of the liquid environment on both electronic and structural dynamics during a complete photochemical transformation.

Porphyrin as a versatile visible-light-activatable organic/metal hybrid photoremovable protecting group.

Photoremovable protecting groups (PPGs) represent one of the main contemporary implementations of photochemistry in diverse fields of research and practical applications. For the past half century, organic and metal-complex PPGs were considered mutually exclusive classes, each of which provided unique sets of physical and chemical properties thanks to their distinctive structures. Here, we introduce the meso-methylporphyrin group as a prototype hybrid-class PPG that unites traditionally exclusive elements of organic and metal-complex PPGs within a single structure. We show that the porphyrin scaffold allows extensive modularity by functional separation of the metal-binding chromophore and up to four sites of leaving group release. The insertion of metal ions can be used to tune their spectroscopic, photochemical, and biological properties. We provide a detailed description of the photoreaction mechanism studied by steady-state and transient absorption spectroscopies and quantum-chemical calculations. Our approach applied herein could facilitate access to a hitherto untapped chemical space of potential PPG scaffolds.

Electron-induced fragmentation of water droplets: Simulation study.

The transport of free electrons in a water environment is still poorly understood. We show that additional insight can be brought about by investigating fragmentation patterns of finite-size particles upon electron impact ionization. We have developed a composite protocol aiming to simulate fragmentation of water clusters by electrons with kinetic energies in the range of up to 100 eV. The ionization events for atomistically described molecular clusters are identified by a kinetic Monte Carlo procedure. We subsequently model the fragmentation with classical molecular dynamics simulations, calibrated by non-adiabatic quantum mechanics/molecular mechanics simulations of the ionization process. We consider one-electron ionizations, energy transfer via electronic excitation events, elastic scattering, and also the autoionization events through intermolecular Coulombic decay. The simulations reveal that larger water clusters are often ionized repeatedly, which is the cause of substantial fragmentation. After losing most of its energy, low-energy electrons further contribute to fragmentation by electronic excitations. The simultaneous measurement of cluster size distribution before and after the ionization represents a sensitive measure of the energy transferred into the system by an incident electron.

Probing aqueous ions with non-local Auger relaxation.

Non-local analogues of Auger decay are increasingly recognized as important relaxation processes in the condensed phase. Here, we explore non-local autoionization, specifically Intermolecular Coulombic Decay (ICD), of a series of aqueous-phase isoelectronic cations following 1s core-level ionization. In particular, we focus on Na+, Mg2+, and Al3+ ions. We unambiguously identify the ICD contribution to the K-edge Auger spectrum. The different strength of the ion-water interactions is manifested by varying intensities of the respective signals: the ICD signal intensity is greatest for the Al3+ case, weaker for Mg2+, and absent for weakly-solvent-bound Na+. With the assistance of ab initio calculations and molecular dynamics simulations, we provide a microscopic understanding of the non-local decay processes. We assign the ICD signals to decay processes ending in two-hole states, delocalized between the central ion and neighbouring water. Importantly, these processes are shown to be highly selective with respect to the promoted water solvent ionization channels. Furthermore, using a core-hole-clock analysis, the associated ICD timescales are estimated to be around 76 fs for Mg2+ and 34 fs for Al3+. Building on these results, we argue that Auger and ICD spectroscopy represents a unique tool for the exploration of intra- and inter-molecular structure in the liquid phase, simultaneously providing both structural and electronic information.