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One of the major challenges in cancer therapy lies in the limited targeting specificity exhibited by existing anti-cancer drugs. Tumor-homing peptides (THPs) have emerged as a promising solution to this issue, due to their capability to specifically bind to and accumulate in tumor tissues while minimally impacting healthy tissues. THPs are short oligopeptides that offer a superior biological safety profile, with minimal antigenicity, and faster incorporation rates into target cells/tissues. However, identifying THPs experimentally, using methods such as phage display or in vivo screening, is a complex, time-consuming task, hence the need for computational methods. In this study, we proposed StackTHPred, a novel machine learning-based framework that predicts THPs using optimal features and a stacking architecture. With an effective feature selection algorithm and three tree-based machine learning algorithms, StackTHPred has demonstrated advanced performance, surpassing existing THP prediction methods. It achieved an accuracy of 0.915 and a 0.831 Matthews Correlation Coefficient (MCC) score on the main dataset, and an accuracy of 0.883 and a 0.767 MCC score on the small dataset. StackTHPred also offers favorable interpretability, enabling researchers to better understand the intrinsic characteristics of THPs. Overall, StackTHPred is beneficial for both the exploration and identification of THPs and facilitates the development of innovative cancer therapies.

The emergence of drug resistance among pathogens has become a major challenge to human health on a global scale. Among them, antibiotic resistance is already a critical issue, and finding new therapeutic agents to address this problem is therefore urgent. One of the most promising alternatives to antibiotics are antibacterial peptides (ABPs), i.e., short peptides with antibacterial activity. In this study, we propose a novel ABP recognition method, called ABPCaps. It integrates a convolutional neural network (CNN), a long short-term memory (LSTM), and a new type of neural network named the capsule network. The capsule network can extract critical features automatically from both positive and negative samples, leading to superior performance of ABPCaps over all baseline models built on hand-crafted peptide descriptors. Evaluated on independent test sets, ABPCaps achieves an accuracy of 93.33% and an F1-score of 91.34%, and consistently outperforms the baseline models in other extensive experiments as well. Our study demonstrates that the proposed ABPCaps, built on the capsule network method, is a valuable addition to the current state-of-the-art in the field of ABP recognition and has significant potential for further development.

When employing molecular dynamics (MD) simulations for computer-aided drug design, the quality of the used force fields is highly important. Here we present reparametrisations of the force fields for the core molecules from 9 different $$\beta$$ β -lactam classes, for which we utilized the force field Toolkit and Gaussian calculations. We focus on the parametrisation of the dihedral angles, with the goal of reproducing the optimised quantum geometry in MD simulations. Parameters taken from CGenFF turn out to be a good initial guess for the multiplicity of each dihedral angle, but the key to a successful parametrisation is found to lie in the phase shifts. Based on the optimised quantum geometry, we come up with a strategy for predicting the phase shifts prior to the dihedral potential fitting. This allows us to successfully parameterise 8 out of the 11 molecules studied here, while the remaining 3 molecules can also be parameterised with small adjustments. Our work highlights the importance of predicting the dihedral phase shifts in the ligand parametrisation protocol, and provides a simple yet valuable strategy for improving the process of parameterising force fields of drug-like molecules.

MicroRNAs (miRNAs) are noncoding RNAs with 18–26 nucleotides; they pair with target mRNAs to regulate gene expression and produce significant changes in various physiological and pathological processes. In recent years, the interaction between miRNAs and their target genes has become one of the mainstream directions for drug development. As a large-scale biological database that mainly provides miRNA–target interactions (MTIs) verified by biological experiments, miRTarBase has undergone five revisions and enhancements. The database has accumulated >2 200 449 verified MTIs from 13 389 manually curated articles and CLIP-seq data. An optimized scoring system is adopted to enhance this update’s critical recognition of MTI-related articles and corresponding disease information. In addition, single-nucleotide polymorphisms and disease-related variants related to the binding efficiency of miRNA and target were characterized in miRNAs and gene 3′ untranslated regions. miRNA expression profiles across extracellular vesicles, blood and different tissues, including exosomal miRNAs and tissue-specific miRNAs, were integrated to explore miRNA functions and biomarkers. For the user interface, we have classified attributes, including RNA expression, specific interaction, protein expression and biological function, for various validation experiments related to the role of miRNA. We also used seed sequence information to evaluate the binding sites of miRNA. In summary, these enhancements render miRTarBase as one of the most research-amicable MTI databases that contain comprehensive and experimentally verified annotations. The newly updated version of miRTarBase is now available at https://miRTarBase.cuhk.edu.cn/.

Release of toxic cyanobacterial secondary metabolites threatens biosecurity, foodwebs and public health. Microcystis aeruginosa (Ma), the dominant species in global freshwater cyanobacterial blooms, produces exudates (MaE) that cause adverse outcomes including nerve damage. Previously, we identified300 chemicals in MaE. It is critical to investigate neurotoxicity mechanisms of active substances among this suite of Ma compounds. Here, we screened 103 neurotoxicity assays from the ToxCast database to reveal targets of action of MaE using machine learning. We then built a potential Adverse Outcome Pathway (AOP) to identify neurotoxicity mechanisms of MaE as well as key targets. Finally, we selected potential neurotoxins matched with those targets using molecular docking. We found 38 targets that were inhibited and eight targets that were activated, collectively mainly related to neurotransmission (i.e. cholinergic, dopaminergic and serotonergic neurotransmitter systems). The potential AOP of MaE neurotoxicity could be caused by blocking calcium voltage-gated channel (CACNA1A), because of antagonizing neurotransmitter receptors, or because of inhibiting solute carrier transporters. We identified nine neurotoxic MaE compounds with high affinity to those targets, including LysoPC(16:0), 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine, egonol glucoside, polyoxyethylene (600) monoricinoleate, and phytosphingosine. Our study enhances understanding of neurotoxicity mechanisms and identifies neurotoxins in cyanobacterial bloom exudates, which may help identify priority compounds for cyanobacteria management.

When employing molecular dynamics (MD) simulations for computer-aided drug design, the quality of the used force fields is highly important. Here we present reparametrisations of the force fields for the core molecules from 9 different [Formula: see text]-lactam classes, for which we utilized the force field Toolkit and Gaussian calculations. We focus on the parametrisation of the dihedral angles, with the goal of reproducing the optimised quantum geometry in MD simulations. Parameters taken from CGenFF turn out to be a good initial guess for the multiplicity of each dihedral angle, but the key to a successful parametrisation is found to lie in the phase shifts. Based on the optimised quantum geometry, we come up with a strategy for predicting the phase shifts prior to the dihedral potential fitting. This allows us to successfully parameterise 8 out of the 11 molecules studied here, while the remaining 3 molecules can also be parameterised with small adjustments. Our work highlights the importance of predicting the dihedral phase shifts in the ligand parametrisation protocol, and provides a simple yet valuable strategy for improving the process of parameterising force fields of drug-like molecules.

Radiation of the plant pyridoxal 5’-phosphate (PLP)-dependent aromatic L-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic L-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.SignificancePlants biosynthesize their own proteinogenic aromatic L-amino acids, namely L-phenylalanine, L-tyrosine and L-tryptophan, not only for building proteins but also for the production of a plethora of aromatic-amino-acid-derived natural products. Pyridoxal 5’-phosphate (PLP)-dependent aromatic L-amino acid decarboxylase (AAAD) family enzymes play important roles in channeling various aromatic L-amino acids into diverse downstream specialized metabolic pathways. Through comparative structural analysis of four functionally divergent plant AAAD proteins together with biochemical characterization and molecular dynamics simulations, we reveal the structural and mechanistic basis for the rich divergent and convergent evolutionary development within the plant AAAD family. Knowledge learned from this study aids our ability to engineer high-value aromatic-L-amino-acid-derived natural product biosynthesis in heterologous chassis organisms.

In this work we performed force field parameter optimisation for various β-lactams using the Force Field Toolkit (FFTK) and Gaussian calculations. Two problems that users are likely to encounter when optimising other drug molecules are identified. First, inappropriate CGenFF parameters without penalty prediction could cause a difficulty in optimisation. Second, multiple dihedral parameter sets may produce the same molecular mechanics (MM) potentials of similar quality, raising the question on how to choose the right parameter set as the best solution. A systematic protocol incorporating molecular dynamics simulations and a principle for selecting the dihedral phase shifts are introduced. Using the protocol, we then successfully optimised both neutral and anionic forms of penam and of cephem. Our results highlight the importance of selecting proper phase shifts during the dihedral optimisation, and the protocol proposed in this work is beneficial to other users.

Steroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-Δ4 structure, such as testosterone or progesterone, are catalyzed by steroid 5α-reductases (SRD5As) to generate their corresponding 3-oxo-5α steroids, which are essential for multiple physiological and pathological processes. SRD5A2 is already a target of clinically relevant drugs. However, the detailed mechanism of SRD5A-mediated reduction remains elusive. Here we report the crystal structure of PbSRD5A from Proteobacteria bacterium, a homolog of both SRD5A1 and SRD5A2, in complex with the cofactor NADPH at 2.0 Å resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic substrate binding cavity, whereas TM5-7 coordinate cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with biochemical characterization, define the substrate binding pocket of SRD5As, explain the properties of disease-related mutants and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-Δ4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible., Steroid 5α-reductase 2 (SRD5A2), a testosterone metabolism enzyme, is implicated in human disease. Structural and biochemical analyses of PbSRD5A, a bacterial homolog, reveal SRD5A2 substrate binding pocket and provide framework for the design of new drugs targeting this enzyme.

Methicillin‐resistant Staphylococcus aureus (MRSA) tolerates β‐lactam antibiotics by carrying out cell wall synthesis with the transpeptidase Penicillin‐binding protein 2a (PBP2a), which cannot be inhibited by β‐lactams. It has been proposed that PBP2a's active site is protected by two loops to reduce the probability of it binding with β‐lactams. Previous crystallographic studies suggested that this protected active site opens for reaction once a native substrate binds at an allosteric domain of PBP2a. This opening was proposed for the new β‐lactam ceftaroline's mechanism in successfully treating MRSA infections, i. e. by it binding to the allosteric site, thereby opening the active site to inhibition. In this work, we investigate the binding of ceftaroline at this proposed allosteric site using molecular dynamics simulations. Unstable binding was observed using the major force fields CHARMM36 and Amber ff14SB, and free energy calculations were unable to confirm a strong allosteric effect. Our study suggests that the allosteric effect induced by ceftaroline is weak at best.

Selective bond breaking in a molecule with the use of photons opens the way to control chemical reactions. We demonstrate here that dissociation of a molecule can be efficiently achieved by first photoexciting a neighboring atom or molecule. On the example of the giant $\mathrm{He}\ensuremath{-}{\mathrm{H}}_{2}$ dimer, we show that simultaneous ionization and excitation of the helium atom induces ${\mathrm{H}}_{2}$ dissociation with a high probability. The excited ${\mathrm{He}}^{+}$ ion transfers its excess energy via interatomic Coulombic decay (ICD) or electron transfer mediated decay (ETMD) to ${\mathrm{H}}_{2}$ which is then singly or doubly ionized, respectively. In both cases, the molecular ion dissociates effectively within a few tens of femtoseconds. Molecular-bond breaking induced by ICD and ETMD are expected to be general phenomena, which provide alternatives to standard photochemistry.

With the rapid expansion of our computing power, molecular dynamics (MD) simulations ranging from hundreds of nanoseconds to microseconds or even milliseconds have become increasingly common. The majority of these long trajectories are obtained from plain (vanilla) MD simulations, where no enhanced sampling or free energy calculation method is employed. To promote the "recycling" of these trajectories, we developed the Virtual Substitution Scan (VSS) toolkit as a plugin of the open-source visualization and analysis software VMD. Based on the single-step free energy perturbation (sFEP) method, VSS enables the user to post-process a vanilla MD trajectory for a fast free energy scan of substituting aryl hydrogens by small functional groups. Dihedrals of the functional groups are sampled explicitly in VSS, which improves the performance of the calculation and is found particularly important for certain groups. As a proof-of-concept demonstration, we employ VSS to compute the solvation free energy change upon substituting the hydrogen of a benzene molecule by 12 small functional groups frequently considered in lead optimization. Additionally, VSS is used to compute the relative binding free energy of four selected ligands of the T4 lysozyme. Overall, the computational cost of VSS is only a fraction of the corresponding multi-step FEP (mFEP) calculation, while its results agree reasonably well with those of mFEP, indicating that VSS offers a promising tool for rapid free energy scan of small functional group substitutions. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 324-336, 2016.

Flavonoids are important polyphenolic natural products, ubiquitous in land plants, that play diverse functions in plants' survival in their ecological niches, including UV protection, pigmentation for attracting pollinators, symbiotic nitrogen fixation, and defense against herbivores. Chalcone synthase (CHS) catalyzes the first committed step in plant flavonoid biosynthesis and is highly conserved in all land plants. In several previously reported crystal structures of CHSs from flowering plants, the catalytic cysteine is oxidized to sulfinic acid, indicating enhanced nucleophilicity in this residue associated with its increased susceptibility to oxidation. In this study, we report a set of new crystal structures of CHSs representing all five major lineages of land plants (bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms), spanning 500 million years of evolution. We reveal that the structures of CHS from a lycophyte and a moss species preserve the catalytic cysteine in a reduced state, in contrast to the cysteine sulfinic acid seen in all euphyllophyte CHS structures. In vivo complementation, in vitro biochemical and mutagenesis analyses, and molecular dynamics simulations identified a set of residues that differ between basal-plant and euphyllophyte CHSs and modulate catalytic cysteine reactivity. We propose that the CHS active-site environment has evolved in euphyllophytes to further enhance the nucleophilicity of the catalytic cysteine since the divergence of euphyllophytes from other vascular plant lineages 400 million years ago. These changes in CHS could have contributed to the diversification of flavonoid biosynthesis in euphyllophytes, which in turn contributed to their dominance in terrestrial ecosystems.

Quantum molecular dynamics simulations with MCTDH or ML-MCTDH perform best if the potential energy surface (PES) has a sum-of-products (SOP) or multi-layer operator (MLOp) structure. Here we investigate four different POTFIT-based methods for representing a general PES as such a structure, among them the novel random-sampling multi-layer Potfit (RS-MLPF). We study how the format and accuracy of the PES representation influences the runtime of a benchmark (ML-)MCTDH calculation, namely the computation of the ground state of the ${\text{H}_3\text{O}_2}^-$ ion. Our results show that compared to the SOP format, the MLOp format leads to a much more favorable scaling of the (ML-)MCTDH runtime with the PES accuracy. At reasonably high PES accuracy, ML-MCTDH calculations thus become up to 20 times faster, and taken to the extreme, the RS-MLPF method yields extremely accurate PES representations (global root-mean-square error of $\sim 0.1\,\text{cm}^{-1}$) which still lead to only moderate computational demands for ML-MCTDH., (C) 2017. This manuscript version is made available under the CC-BY-NC-ND 4.0 license. http://creativecommons.org/licenses/by-nc-nd/4.0/

In recent years the laser-induced interatomic Coulombic decay (ICD) process in paired quantum dots has been predicted (Bande, 2013). In this work we target the enhancement of ICD by scanning over a range of strong-field laser intensities. The GaAs quantum dots are modeled by a one-dimensional double-well potential in which simulations are done with the space-resolved multi-configuration time-dependent Hartree method including antisymmetrization to account for the fermions. As a novelty a complementary state-resolved ansatz is developed to consolidate the interpretation of transient state populations, widths obtained for the ICD and the competing direct ionization channel, and Fano peak profiles in the photoelectron spectra. The major results are that multi-photon processes are unimportant even for the strongest fields. Further, below- π to π pulses display the highest ICD efficiency while the direct ionization becomes less dominant.

Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT) is an essential acyltransferase that mediates flux through plant phenylpropanoid metabolism by catalyzing a reaction between p-coumaroyl CoA and shikimate, yet it also exhibits broad substrate permissiveness in vitro. How do enzymes like HCT avoid functional derailment by cellular metabolites that qualify as non-native substrates? Here, we combine X-ray crystallography and molecular dynamics to reveal distinct dynamic modes of HCT under native versus non-native catalysis. We find that essential electrostatic and hydrogen-bonding interactions between the ligand and active site residues, enabled by active site plasticity, are elicited more effectively by shikimate than by other non-native substrates. This work provides a structural basis for how dynamic conformational states of HCT favor native over non-native catalysis by reducing the number of futile encounters between the enzyme and shikimate.

Since their theoretical prediction in 1997, interatomic (intermolecular) Coulombic decay (ICD) and related processes have been in the focus of intensive theoretical and experimental research. The spectacular progress in this direction has been stimulated both by the fundamental importance of the discovered electronic decay phenomena and by the exciting possibility of their practical application, for example in spectroscopy of interfaces. Interatomic decay phenomena take place in inner-shell-ionized clusters due to electronic correlation between two or more cluster constituents. These processes lead to the decay of inner-shell vacancies by electron emission and often also to disintegration of the resulting multiply ionized cluster. Here we review the recent progress in the study of interatomic decay phenomena in singly and multiply ionized clusters.

With the rapid expansion of our computing power, molecular dynamics (MD) simulations ranging from hundreds of nanoseconds to microseconds or even milliseconds have become increasingly common. The majority of these long trajectories are obtained from plain (vanilla) MD simulations, where no enhanced sampling or free energy calculation method is employed. To promote the "recycling" of these trajectories, we developed the Virtual Substitution Scan (VSS) toolkit as a plugin of the open-source visualization and analysis software VMD. Based on the single-step free energy perturbation (sFEP) method, VSS enables the user to post-process a vanilla MD trajectory for a fast free energy scan of substituting aryl hydrogens by small functional groups. Dihedrals of the functional groups are sampled explicitly in VSS, which improves the performance of the calculation and is found particularly important for certain groups. As a proof-of-concept demonstration, we employ VSS to compute the solvation free energy change upon substituting the hydrogen of a benzene molecule by 12 small functional groups frequently considered in lead optimization. Additionally, VSS is used to compute the relative binding free energy of four selected ligands of the T4 lysozyme. Overall, the computational cost of VSS is only a fraction of the corresponding multi-step FEP (mFEP) calculation, while its results agree reasonably well with those of mFEP, indicating that VSS offers a promising tool for rapid free energy scan of small functional group substitutions. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 324-336, 2016.

A scheme utilizing excitation of core electrons followed by the resonant-Auger - interatomic Coulombic decay (RA-ICD) cascade was recently proposed as a means of controlling the generation site and energies of slow ICD electrons. This control mechanism was verified in a series of experiments in rare gas dimers. In this article, we present fully ab initio computed ICD electron and kinetic energy release spectra produced following 2p(3/2) → 4s, 2p(1/2) → 4s, and 2p(3/2) → 3d core excitations of Ar in Ar2. We demonstrate that the manifold of ICD states populated in the resonant Auger process comprises two groups. One consists of lower energy ionization satellites characterized by fast interatomic decay, while the other consists of slow decaying higher energy ionization satellites. We show that accurate description of nuclear dynamics in the latter ICD states is crucial for obtaining theoretical electron and kinetic energy release spectra in good agreement with the experiment.

Single-step free energy perturbation (sFEP) has often been proposed as an efficient tool for a quick free energy scan due to its straightforward protocol and the ability to recycle an existing molecular dynamics trajectory for free energy calculations. Although sFEP is expected to fail when the sampling of a system is inefficient, it is often expected to hold for an alchemical transformation between ligands with a moderate difference in their sizes, e.g., transforming a benzene into an ethylbenzene. Yet, exceptions were observed in calculations for anisole and methylaniline, which have similar physical sizes as ethylbenzene. In this study, we show that such exceptions arise from the sampling inefficiency on an unexpected rigid degree of freedom, namely, the bond angle θ. The distributions of θ differ dramatically between two end states of a sFEP calculation, i.e., the conformation of the ligand changes significantly during the alchemical transformation process. Our investigation also reveals the interrelation between the ligand conformation and the intramolecular nonbonded interactions. This knowledge suggests a best combination of the ghost ligand potential and the dual topology setting, which improves the accuracy in a single reference sFEP calculation by bringing down its error from around 5kBT to kBT.

We investigate the exact wavefunction as a single product of electronic and nuclear wavefunction for a model conical intersection system. Exact factorized spiky potentials and nodeless nuclear wavefunctions are found. The exact factorized potential preserves the symmetry breaking effect when the coupling mode is present. Additionally the nodeless wavefunctions are found to be closely related to the adiabatic nuclear eigenfunctions. This phenomenon holds even for the regime where the non-adiabatic coupling is relevant, and sheds light on the relation between the exact wavefunction factorization and the adiabatic approximation.

In this paper we study the impact of interatomic Coulombic decay (ICD) on molecular photodissociation. The investigation reveals the hitherto unrecognized ability of ICD to quench processes involving nuclear rearrangements. Numerical computations of the nuclear dynamics, initiated by photoexciting the B(1)Σ(+) Rydberg state of CO in CO·Mg complexes, are carried out. The efficiencies of ICD and photoinduced predissociation are compared for the four lowest vibrational levels of the corresponding electronic state. We also show the impact of CO vibrations on the ICD electron spectrum. Finally, we discuss the growing efficiency of ICD to quench the dissociation as the number of neighboring Mg atoms is increased.

A time-dependent approach for the kinetic energy release (KER) spectrum is developed for a fragmentation of a diatomic molecule after an electronic decay process, e.g. Auger process. It allows one to simulate the time-resolved spectra and provides more insight into the molecular dynamics than the time-independent approach. Detailed analysis of the time-resolved emitted electron and KER spectra sheds light on the interrelation between wave packet dynamics and spectra., This article has been modified and the newest version can be found in (J. Chem. Phys. 136, 114111 (2012)) at (http://link.aip.org/link/?JCP/136/114111). Copyright (2012) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics

The dynamics of the resonant Auger (RA) process of the core-excited C$^\ast$O(1s$^{-1}\pi^\ast,v_r=0$) molecule in an intense X-ray laser field is studied theoretically. The theoretical approach includes the analogue of the conical intersections of the complex potential energy surfaces of the ground and `dressed' resonant states due to intense X-ray pulses, taking into account the decay of the resonance and the direct photoionization of the ground state, both populating the same final ionic states coherently, as well as the direct photoionization of the resonance state itself. The light-induced non-adiabatic effect of the analogue of the conical intersections of the resulting complex potential energy surfaces gives rise to strong coupling between the electronic, vibrational and rotational degrees of freedom of the diatomic CO molecule. The interplay of the direct photoionization of the ground state and of the decay of the resonance increases dramatically with the field intensity. The coherent population of a final ionic state via both the direct photoionization and the resonant Auger decay channels induces strong interference effects with distinct patterns in the RA electron spectra. The individual impact of these physical processes on the total electron yield and on the CO$^+(A^2\Pi)$ electron spectrum are demonstrated., Comment: 13 figs, 1 tabel

Using momentum-resolved electron-ion multicoincidence spectroscopy, we have investigated interatomic Coulombic decay (ICD) in the heteronuclear NeAr dimer following Ne $1s$ Auger decay. The measured intensity ratio for the three ICD transitions Ne${}^{2+}$($2{s}^{\ensuremath{-}1}2{p}^{\ensuremath{-}1} {}^{1}P$)Ar to Ne${}^{2+}$($2{p}^{\ensuremath{-}2} {}^{1}S$)--Ar${}^{+}$($3{p}^{\ensuremath{-}1}$), Ne${}^{2+}$($2{s}^{\ensuremath{-}1}2{p}^{\ensuremath{-}1} {}^{1}P$)Ar to Ne${}^{2+}$($2{p}^{\ensuremath{-}2} {}^{1}D$)-Ar${}^{+}$($3{p}^{\ensuremath{-}1}$), and Ne${}^{2+}$($2{s}^{\ensuremath{-}1}2{p}^{\ensuremath{-}1} {}^{3}P$)Ar to Ne${}^{2+}$($2{p}^{\ensuremath{-}2} {}^{3}P$)-Ar${}^{+}$($3{p}^{\ensuremath{-}1}$) reasonably agree with predictions. The kinetic energy release distribution for the fragmentation to Ne${}^{2+}$($2{p}^{\ensuremath{-}2} {}^{1}D$)-Ar${}^{+}$($3{p}^{\ensuremath{-}1}$) after the ICD transition from singlet Ne${}^{2+}$($2{s}^{\ensuremath{-}1}2{p}^{\ensuremath{-}1} {}^{1}P$)Ar state, which is a mirror image of the kinetic energy distribution of the emitted ICD electrons, suggests that the corresponding ICD rate is roughly two times lower than predicted by ab initio calculations.

In an electronic decay process followed by fragmentation the kinetic energy release and electron spectra can be measured. Classically they are the mirror image of each other, a fact which is often used in practice. Quantum expressions are derived for both spectra and analyzed. It is demonstrated that these spectra carry complementary quantum information and are related to the nuclear dynamics in different participating electronic states. Illustrative examples show that the classical picture of a mirror image can break down and shed light on the underlying physics.

The resonant Auger process is studied in intense x-ray laser fields. It is shown that the dressing of the initial and decaying states by the field leads to coupled complex potential surfaces which, even for diatomic molecules, possess intersections at which the nonadiabatic couplings are singular. HCl is studied as an explicit showcase example. The exact results differ qualitatively from those without rotations. A wealth of nonadiabatic phenomena is expected in decay processes in intense x-ray fields.

The time-dependent theory of an atomic cascade decay process is discussed. We show that it is useful to measure the spectra of the emitted particles (electrons or photons) as a function of time and introduce time-dependent spectra and time-dependent coincidence spectra. The analysis reveals that there are several timescales involved in the atomic cascades and in the respective spectra. The work prepares the ground for the discussion of molecules, clusters, and solids, where the nuclear dynamics strongly participate in the cascade decay process making it much more complex.

We analyze in detail the accessible relaxation pathways via electron emission of the Ne2+Ar states populated via the K-LL Auger decay of Ne+(1s−1)Ar. In particular, we concentrate on the “direct” interatomic Coulombic decay (ICD) of the Ne2+(2s−12p−1)Ar weakly bound doubly ionized states into the manifold of the Ne2+(2p−2)–Ar+(3p−1) repulsive triply ionized ones. To carry out the present study the potential energy curves of the NeAr ground state, the core ionized state Ne+(1s−1)Ar, the relevant dicationic and tricationic states, and the corresponding ICD transition rates have been computed using accurate ab initio methods and basis sets. The total and partial ICD electron spectra are computed within the framework of the time-dependent theory of wave packet propagation. Thereby, the impact of nuclear dynamics accompanying the electronic decay on the computed ICD-electron spectra is investigated in detail.

Here we demonstrate the smallest possible implementation of an antenna-receiver complex which consists of a single (helium) atom acting as the antenna and a second (neon) atom acting as a receiver.

The resonant-Auger - interatomic Coulombic decay (ICD) cascade was recently suggested as an efficient means of controlling the course of the ICD process. Recent theoretical and experimental works show that control over the energies of the emitted ICD electrons can be achieved either by varying the photon energy to produce different initial core excitations or by changing the neighboring species. This work presents a theoretical investigation on the role of the rare-gas neighbor and clarifies how the latter influences the ICD process. For this purpose, we compare fully ab initio computed ICD-electron and kinetic energy release spectra following the 2p(3/2) → 4s, 2p(1/2) → 4s and 2p(3/2) → 3d of Ar in ArKr and Ar2. We demonstrate that the presence of the chemically "softer" partner atom results in an increase in the energies of the emitted ICD electrons, and also in the appearance of additional ICD-active states. The latter leads to a threefold increase in the ICD yield for the case of the 2p(3/2, 1/2) → 4s parent core excitations.

Using momentum-resolved electron-ion multicoincidence, we have investigated interatomic Coulombic decay (ICD). We observed ICD processes in NeAr dimers following Ar LMM and Ne KLL Auger decay. From Auger final state of Ar2+(3s?2), we observed ICD where three electrons participate in.