Low-energy Collisions Research Articles

Isobaric Stable Isotope N‐Phosphorylation Labeling (iSIPL) for Ultrasensitive Proteome Quantification

AbstractStable isotope chemical labeling methods have been widely used for high‐throughput mass spectrometry (MS)‐based quantitative proteomics in biological and clinical applications. However, the existing methods are far from meeting the requirements for high sensitivity detection. In the present study, a novel isobaric stable isotope N‐phosphorylation labeling (iSIPL) strategy was developed for quantitative proteome analysis. The tryptic peptides were selectively labeled with iSIPL tag to generate the novel reporter ions containing phosphoramidate P−N bond with high intensities under lower collision energies. iSIPL strategy are suitable for peptide sequencing and quantitative analysis with high sensitivity and accuracy even for samples of limited quantity. Furthermore, iSIPL coupled with affinity purification and mass spectrometry was applied to measure the dynamics of cyclin dependent kinase 9 (CDK9) interactomes during transactivation of the HIV‐1 provirus. The interaction of CDK9 with PARP13 was found to significantly decrease during Tat‐induced activation of HIV‐1 gene transcription, suggesting the effectiveness of iSIPL strategy in dynamic analysis of protein‐protein interaction in vivo. More than that, the proposed iSIPL strategy would facilitate large‐scale accurate quantitative proteomics by increasing multiplexing capability.

Isobaric Stable Isotope N-Phosphorylation Labeling (iSIPL) for Ultrasensitive Proteome Quantification.

Stable isotope chemical labeling methods have been widely used for high-throughput mass spectrometry (MS)-based quantitative proteomics in biological and clinical applications. However, the existing methods are far from meeting the requirements for high sensitivity detection. In the present study, a novel isobaric stable isotope N-phosphorylation labeling (iSIPL) strategy was developed for quantitative proteome analysis. The tryptic peptides were selectively labeled with iSIPL tag to generate the novel reporter ions containing phosphoramidate P-N bond with high intensities under lower collision energies. iSIPL strategy are suitable for peptide sequencing and quantitative analysis with high sensitivity and accuracy even for samples of limited quantity. Furthermore, iSIPL coupled with affinity purification and mass spectrometry was applied to measure the dynamics of cyclin dependent kinase 9 (CDK9) interactomes during transactivation of the HIV-1 provirus. The interaction of CDK9 with PARP13 was found to significantly decrease during Tat-induced activation of HIV-1 gene transcription, suggesting the effectiveness of iSIPL strategy in dynamic analysis of protein-protein interaction in vivo. More than that, the proposed iSIPL strategy would facilitate large-scale accurate quantitative proteomics by increasing multiplexing capability.

Globally Accurate Gaussian Process Potential Energy Surface and Quantum Dynamics Studies on the Li(2S) + Na2 → LiNa + Na Reaction at Low Collision Energies.

The LiNa2 reactive system has recently received great attention in the experimental study of ultracold chemical reactions, but the corresponding theoretical calculations have not been carried out. Here, we report the first globally accurate ground-state LiNa2 potential energy surface (PES) using a Gaussian process model based on only 1776 actively selected high-level ab initio training points. The constructed PES had high precision and strong generalization capability. On the new PES, the quantum dynamics calculations on the Li(2S) + Na2(v = 0, j = 0) → LiNa + Na reaction were carried out in the 0.001-0.01 eV collision energy range using an improved time-dependent wave packet method. The calculated results indicate that this reaction is dominated by a complex-forming mechanism at low collision energies. The presented dynamics data provide guidance for experimental research, and the newly constructed PES could be further used for ultracold reaction dynamics calculations on this reactive system.

Dynamics of Dissociative Chemisorption of NH3 on Fe(111) on a Twelve-Dimensional Potential Energy Surface

We constructed a new, accurate twelve-dimensional potential energy surface (PES) for ammonia dissociative chemisorption (DC) on a rigid Fe(111) surface using the fundamental invariant-neural network fitting to a large number of density functional theory data points. The DC dynamics simulations were carried out by the quasi-classical trajectory (QCT) approach. At very low collision energies, the molecules experienced a large number of rebounds due to the deep pre-transition-state adsorption well and finally decomposed around the global transition state. At high collision energies, the bridge site with a loose transition state was the most favorable site for dissociation. The mode-specific dynamics revealed that excitations in symmetric stretch and umbrella modes were most efficient in promoting the dissociation and were more efficacious than the same amount of translational energy. The computed large dissociation probability for NH3/Fe(111) supported the fact that iron is an effective catalyst for ammonia dissociation, which is of practical importance in producing clean hydrogen.

Quantum state-resolved molecular dipolar collisions over four decades of energy.

Collisions between cold polar molecules represent a fascinating research frontier but have proven hard to probe experimentally. We report measurements of inelastic cross sections for collisions between nitric oxide (NO) and deuterated ammonia (ND3) molecules at energies between 0.1 and 580 centimeter-1, with full quantum state resolution. At energies below the ~100-centimeter-1 well depth of the interaction potential, we observed backward glories originating from peculiar U-turn trajectories. At energies below 0.2 centimeter-1, we observed a breakdown of the Langevin capture model, which we interpreted in terms of a suppressed mutual polarization during the collision, effectively switching off the molecular dipole moments. Scattering calculations based on an ab initio NO-ND3 potential energy surface revealed the crucial role of near-degenerate rotational levels with opposite parity in low-energy dipolar collisions.

Low-Energy Collisions of Zeeman-Decelerated NH Radicals with He Atoms.

We report an experimental study of state-to-state inelastic scattering of NH (X 3Σ-, N = 0, j = 1) radicals with He atoms. Using a crossed molecular beam apparatus that combines a Zeeman decelerator and velocity map imaging, we study both integral and differential cross sections in the N = 0, j = 1 → N = 2, j = 3 inelastic channel. We developed various new REMPI schemes to state-selectively detect NH radicals, and tested their performance in terms of sensitivity and ion recoil velocity. We found a 1 + 2' + 1' REMPI scheme using the A 3Π ← X 3Σ- resonant transition, which yields acceptable recoil velocities and is more than an order of magnitude more sensitive than conventional one-color REMPI schemes to detect NH. We used this REMPI scheme to probe state-to-state integral and differential cross sections around the channel opening at 97.7 cm-1, as well as at higher energies where structure in the scattering images could be resolved. The experimental results are in excellent agreement with the predictions from quantum scattering calculations which are based on an ab initio NH-He potential energy surface.

Rigorous Negative Ion Binding Energies in Low-Energy Electron Elastic Collisions with Heavy Multi-Electron Atoms and Fullerene Molecules: Validation of Electron Affinities

Dramatically sharp resonances manifesting stable negative ion formation characterize Regge pole-calculated low-energy electron elastic total cross sections (TCSs) of heavy multi-electron systems. The novelty of the Regge pole analysis is in the extraction of rigorous and unambiguous negative ion binding energies (BEs), corresponding to the measured electron affinities (EAs) of the investigated multi-electron systems. The measured EAs have engendered the crucial question: is the EA of multi-electron atoms and fullerene molecules identified with the BE of the attached electron in the ground, metastable or excited state of the formed negative ion during a collision? Inconsistencies in the meaning of the measured EAs are elucidated and new EA values for Bk, Cf, Fm, and Lr are presented.

Molecular dynamics simulations of cascade events in AlN

The radiation tolerance and the ability to retain its piezoelectric response make aluminum nitride (AlN) a good candidate for emerging sensing technologies in nuclear reactor environments. Furthermore, it has been shown that doping the ceramic with additional metals can further improve the piezoelectric response. Fundamental understanding of the response of AlN to radiation is important for ultimately improving the material's properties. In this paper, we use molecular dynamics and a recently developed interatomic potential fitted to defect energies to investigate low energy collision cascades in AlN. We additionally investigate the electronic stopping effect in the damage production for 20 keV Al ions. Our results show that for all energies the number of Al surviving defects is larger than that of N defects. Additionally, we find that even though the ballistic energy loss is the dominating mechanism, it is important to take into account the electronic stopping in order not to overestimate the number of defects.

Theoretical study of low-energy electron collision with normal-pentane using R-matrix method

Low-energy electron collisions with normal-pentane (n-C5H12) that initiate the plasma to assist combustion are critical in understanding the underlying physics and chemistries. In the present work, we studied this collisional process using the R-matrix method at the static-exchange plus polarization and close-coupling model levels. The scattering calculation was performed by running the UKRmol+ code using the Quantemol Electron Collision interface to obtain elastic differential, momentum transfer, integral, and electronic excitation cross sections up to 20 eV and ionization cross sections up to 1000 eV. Our computed cross-section data are in better agreement with the available experimental results both regarding the magnitude and shape. We also demonstrated the importance of using a diffuse basis set in describing the scattering due to the Rydberg nature of the lowest unoccupied molecular orbitals of n-C5H12.

Probing neutron-star matter in the lab: Similarities and differences between binary mergers and heavy-ion collisions

Binary neutron-star mergers and heavy-ion collisions are related through the properties of the hot and dense nuclear matter formed during these extreme events. In particular, low-energy heavy-ion collisions offer exciting prospects to recreate such {extreme} conditions in the laboratory. However, it remains unexplored to what degree those collisions can actually reproduce hot and dense matter formed in binary neutron star mergers. As a way to understand similarities and differences between these systems, we {discuss their geometry and }perform a direct numerical comparison of the thermodynamic conditions probed in both collisions. To enable a direct comparison, we employ a finite-temperature equation of state able to describe the entire high-energy phase diagram of Quantum Chromodynamics. Putting side by side the evolution of both systems, we find that laboratory heavy-ion collisions at the energy range of $E_{\mathrm{lab}}=0.4 - 0.6\ A$ MeV probe (thermodynamic) states of matter that are very similar to those created in binary neutron-star mergers. These results can inform future low-energy heavy-ion collisions probing this regime.

Bremsstrahlung photons from a hadronizing quark-gluon plasma

Assuming that quark and antiquark numbers are separately conserved during hadronization, we calculate Bremsstrahlung photon from a hadronizing quark-gluon plasma. The quark and antiquark numbers are obtained from the hadron numbers in the statistical model and the transition amplitudes for the hadronization from the constraint that all quarks and antiquarks must be consumed in the hadronization. Then Bremsstrahlung photon from the hadronization is obtained in the soft photon approximation, and we find that its contribution to the direct photon increases in low-energy heavy-ion collisions and in peripheral collisions where the lifetime of a quark-gluon plasma (QGP) is relatively short.

The topology of the reaction stereo-dynamics in chemi-ionizations

Details on the stereo-dynamic topology of chemi-ionizations highlight the role of the centrifugal barrier of colliding reactants: it acts as a selector of the orbital quantum number effective for reaction in a state-to-state treatment. Here, an accurate internally consistent formulation of the Optical interaction potentials, obtained by the combined analysis of scattering and spectroscopic experimental findings, casts light on structure, energy and angular momentum couplings of the precursor (pre-reactive) state controlling the stereo-dynamics of prototypical chemi-ionization reactions. The closest approach (turning point) of reagents, is found to control the relative weight of two different reaction mechanisms: (i) A direct mechanism stimulated by exchange chemical forces mainly acting at short separation distances and high collision energy; (ii) An indirect mechanism, caused by the combination of weak chemical and physical forces dominant at larger distances, mainly probed at low collision energy, that can be triggered by a virtual photon exchange between reagents.

Collision centrality and energy dependence of strange hadron production in Au + Au collisions at sNN=7.7 –54.4 GeV

We apply an equal-velocity quark combination model to systematically study the transverse momentum (${p}_{T}$) spectra of identified hadrons ${K}_{S}^{0}, \ensuremath{\phi}, \mathrm{\ensuremath{\Lambda}}, {\mathrm{\ensuremath{\Xi}}}^{\ensuremath{-}}, {\mathrm{\ensuremath{\Omega}}}^{\ensuremath{-}}, \overline{\mathrm{\ensuremath{\Lambda}}}, {\overline{\mathrm{\ensuremath{\Xi}}}}^{+}, {\overline{\mathrm{\ensuremath{\Omega}}}}^{+}, p, \overline{p}, {\ensuremath{\pi}}^{+}$, and ${\ensuremath{\pi}}^{\ensuremath{-}}$ at midrapidity in $\mathrm{Au}+\mathrm{Au}$ collisions at $\sqrt{{s}_{NN}}=7.7$, 11.5, 19.6, 27, 39, 54.4 GeV. The relative deviation between model calculations and experimental data of these 12 hadrons is generally about 10% in central collisions even at low collision energies and is weakly increased in peripheral collisions. We systematically explain the dependence of two baryon-to-meson ratios $\overline{\mathrm{\ensuremath{\Lambda}}}/{K}_{S}^{0}$ and $\mathrm{\ensuremath{\Omega}}/\ensuremath{\phi}$ on ${p}_{T}$, collision centrality, and collision energy by the property of quark ${p}_{T}$ spectra at hadronization. We derive the analytic relations between ${R}_{CP}$ of hadrons and those of quarks, and we use them to naturally explain the species and ${p}_{T}$ dependence of ${R}_{CP}$ of those strange hadrons.

Reaction of an Ion and a Free Radical near 0 K: He++NO→He+N++O.

The reactions between ions and free radicals are among the fastest chemical reactions. They are predicted to proceed with large rates, even near 0 K, but so far, this prediction has not been verified experimentally. We report on measurements of the rate coefficient of the reaction between the ion He+ and the free radical NO at collision energies in the range between 0 and ∼ kB·10 K. To avoid heating of the ions by stray electric fields, the reaction is observed within the large orbit of a Rydberg electron of principal quantum number n ≥ 30, which shields the ion from external electric fields without affecting the reaction. Low collision energies are reached by merging a supersonic beam of He Rydberg atoms with a supersonic beam of NO molecules and adjusting their relative velocity using a chip-based Rydberg-Stark decelerator and deflector. We observe a strong enhancement of the reaction rate at collision energies below ∼kB·2 K. This enhancement is interpreted on the basis of adiabatic-channel capture-rate calculations as arising from the near-degenerate rotational levels of opposite parity resulting from the Λ-doubling in the X 2Π1/2 ground state of NO. With these new results, we examine the reliability of broadly used approximate analytic expressions for the thermal rate constants of ion-molecule reactions at low temperatures.

Luminescence Measurements of the Hyperthermal Reactions of N/N+ + NH3.

Chemiluminescence from a system of collisions, N+/N/Kr+/Kr/Xe+/Xe + NH3, at collision energies between 10 and 170 eV (center of mass, COM), was measured in the spectral range 300-1000 nm. The energy dependence of the emission excitation cross sections was quantified, and molecular signatures were fit to known spectroscopic constants to determine vibrational-state populations. For both N and N+ collision species, the strongest features were assigned to emissions from NH (A-X) and the atomic hydrogen Balmer series. For each of the spectra resulting from collisions with primary cations, the NH (A-X) emissions had the largest cross sections reaching values of (1.0-1.5) × 10-18 cm2 by 100 eV. Additional features originating from atomic nitrogen and NH (c-a) emissions were also observed. The NH (c-a) emissions accounted for about 8%, 13%, and 15% for total excited populations in collisions with Xe+, N+, and Kr+, respectively. These transitions were consistent with short-range interactions resulting in collision-induced dissociation of the NH3 molecule with apparent energy thresholds between 20 and 30 eV and emission cross sections decreasing with ion mass. Evidence of charge exchange in the N+ + NH3 collisions was observed in the resulting spectra as broad transitions between 420 and 480 nm and were assigned to NH+ emitting from the (B) state. Differences between the spectra were observed as changes in the emission signal with the neutral collisions producing only 30% or 65% of the NH (A-X) emission cross sections compared to the cation results for xenon and krypton, respectively. For N and N+, NH (A) was created in equal amounts at lower collision energies, but the emission for the neutral system increases above that of the cation at collision energies greater than 80 eV COM. In both cases, the threshold energy for appearance was below 10 eV, suggesting an additional pathway for NH (A) formation, namely, hydrogen abstraction or charge exchange and abstraction for the N and N+, respectively. In all cases, the neutral NH (c-a) emission intensity was similar between neutral and cation pairs. The H-α emission line (n = 3-2) decreased to about 10%, 33%, and 50% of the corresponding cation spectra for xenon, krypton, and nitrogen, respectively.

Development of a Machine Learning Algorithm for Drug Screening Analysis on High-Resolution UPLC-MSE/QTOF Mass Spectrometry.

Ultra-performance liquid chromatography (UPLC)-MSE/quadrupole time-of-flight (QTOF) high-resolution mass spectrometry employs untargeted, data-independent acquisition in a dual mode that simultaneously collects precursor ions and product ions at low and ramped collision energies, respectively. However, algorithmic analysis of large-scale multivariate data of comprehensive drug screening as well as the positivity criteria of drug identification have not been systematically investigated. It is also unclear whether ion ratio (IR), the intensity ratio of a defined product ion divided by the precursor ion, is a stable parameter that can be incorporated into the MSE/QTOF data analysis algorithm. IR of 91 drugs were experimentally determined and variation of IR was investigated across 5 concentrations measured on 3 different days. A data-driven machine learning approach was employed to develop multivariate linear regression (MLR) models incorporating mass error, retention time, number of detected fragment ions and IR, accuracy of isotope abundance, and peak response using drug-supplemented urine samples. Performance of the models was evaluated in an independent data set of unknown clinical urine samples in comparison with the results of manual analysis. IR of most compounds acquired by MSE/QTOF were low and concentration-dependent (i.e., IR increased at higher concentrations). We developed an MLR model with composite score outputs incorporating 7 parameters to predict positive drug identification. The model achieved a mean accuracy of 89.38% in the validation set and 87.92% agreement in the test set. The MLR model incorporating all contributing parameters can serve as a decision-support tool to facilitate objective drug identification using UPLC-MSE/QTOF.

H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage.

Radiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This work reports the first experimental study of the ion-molecule reactions of the H2O˙+ and OH+ ions, produced by photoionization with synchrotron radiation, with a furan (c-C4H4O) molecule, a template for deoxyribose sugar in DNA. The present experiments, performed as a function of the collision energy of the ions and the tunable photoionization energy, provide key parameters for the theoretical modelling of the effect of radiation dose, like the absolute cross sections for producing protonated furan (furanH+) and a radical cation (furan˙+), the most abundant products, which can amount up to 200 Å2 at very low collision energies (<1.0 eV). The experimental results show that furanH+ is more fragile, indicating how the protonation of the sugar component of the DNA may favor its dissociation with possible major radiosensitizing effects. Moreover, the ring opening of furanH+ isomers and the potential energy surface of the most important fragmentation channels have been explored by molecular dynamics simulations and quantum chemistry calculations. The results show that, in the most stable isomer of furanH+, the ring opening occurs via a low energy pathway with carbon-oxygen bond cleavage, followed by the loss of neutral carbon monoxide and the formation of the allyl cation CH2CHCH2+, which instead is not observed in the fragmentation of furan˙+. At higher energies the ring opening through the carbon-carbon bond is accompanied by the loss of formaldehyde, producing HCCCH2+, the most intense fragment ion detected in the experiments. This work highlights the importance of the secondary processes, like the ion-molecule reactions at low energies in the radiation damage due to their very large cross sections, and it aims to provide benchmark data for the development of suitable models to approach this low collision energy range.

Feshbach resonances in the F + CHD3 → HF + CD3 reaction.

The signature of dynamics resonances was observed in the benchmark polyatomic F + CH4/CHD3 reactions more than a decade ago; however, the dynamical origin of the resonances is still not clear due to the lack of reliable quantum dynamics studies on accurate potential energy surfaces. Here, we report a six-dimensional state-to-state quantum dynamics study on the F + CHD3 → HF + CD3 reaction on a highly accurate potential energy surface. Pronounced oscillatory structures are observed in the total and product rovibrational-state-resolved reaction probabilities. Detailed analysis reveals that these oscillating features originate from the Feshbach resonance states trapped in the peculiar well on the HF(v' = 3)-CD3 vibrationally adiabatic potential caused by HF chemical bond softening. Most of the resonance structures on the reaction probabilities are washed out in the well converged integral cross sections (ICS), leaving only one distinct peak at low collision energy. The calculated HF vibrational state-resolved ICS for CD3(v = 0) agrees quantitatively with the experimental results, especially the branching ratio, but the theoretical CD3 umbrella vibration state distribution is found to be much hotter than the experiment.

Photoassociation spectra of cesium 31D&lt;sub&gt;5/2&lt;/sub&gt;+6S&lt;sub&gt;1/2&lt;/sub&gt;(&lt;i&gt;F&lt;/i&gt; = 4) ultralong-range Rydberg molecules

In this paper, we conduct the experiment and simulation on 31D&lt;sub&gt;5/2&lt;/sub&gt;+6S&lt;sub&gt;1/2&lt;/sub&gt;(&lt;i&gt;F&lt;/i&gt; = 4) Cs&lt;sub&gt;2&lt;/sub&gt; ultralong-range Rydberg molecules (ULRMs). These molecules are prepared by employing a two-photon photoassociation scheme. Two distinct ultralong-range Rydberg molecular signals are observed at the detuning –162.8 MHz and –66.6 MHz of 31D&lt;sub&gt;5/2&lt;/sub&gt; atomic resonant line, which are bound by the pure triplet potential and mixed singlet-triplet potential, respectively. We use the model of scattering interaction between the Rydberg electron and ground-state atom to perform the simulation. The molecular potential-energy curves are obtained by solving the Hamiltonian on a grid of intermolecular distances &lt;i&gt;R&lt;/i&gt;. The calculations of the binding energy of pure triplet and mixed singlet-triplet &lt;i&gt;v&lt;/i&gt; = 0 vibrational states are compared with the experimental measurements. The calculated and measured values of the binding energy are in good agreement. The s-wave pure triplet and singlet zero-energy scattering length are obtained to be &lt;inline-formula&gt;&lt;tex-math id="M3"&gt;\begin{document}${a}_{{\rm{s}}}^{{\rm{T}}}({0})=-{19.16}{a}_{0}$\end{document}&lt;/tex-math&gt;&lt;alternatives&gt;&lt;graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="14-20230520_M3.jpg"/&gt;&lt;graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="14-20230520_M3.png"/&gt;&lt;/alternatives&gt;&lt;/inline-formula&gt; and &lt;inline-formula&gt;&lt;tex-math id="M4"&gt;\begin{document}$ {a}_{{\rm{s}}}^{{\rm{S}}}(0)=-{1.92}{a}_{0} $\end{document}&lt;/tex-math&gt;&lt;alternatives&gt;&lt;graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="14-20230520_M4.jpg"/&gt;&lt;graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="14-20230520_M4.png"/&gt;&lt;/alternatives&gt;&lt;/inline-formula&gt;, respectively. This kind of molecule with large size, abundant vibrational states and large permanent electric dipole moment is an excellent candidate for studying low-energy collision dynamics. The study of these molecules will further deepen and enrich the understanding of the special binding mechanism and exotic properties of the ULRMs.

Triatomic Photoassociation in an Ultracold Atom–Molecule Collision

Ultracold collisions of neutral atoms and molecules have been of great interest since experimental advances enabled the cooling and trapping of such species. This study develops a simplified theoretical treatment of a low-energy collision between an alkali atom and a diatomic molecule accompanied by absorption of a photon from an external electromagnetic field. The long-range interaction between the two species is treated, including the atomic spin-orbit interaction. The long-range potential energy curves for the triatomic complex are calculated in realistic detail, while effects of the short-range behavior are mimicked by applying different boundary conditions at the van der Waals length. For neutral colliding species, the leading interaction term is the dipole-dipole interaction. In the case of nonpolar dimers like Cs2, the second leading term is the quadrupole-quadrupole interaction. However, there is also a strong dipole-quadrupole interaction for dimers with a large permanent dipole moment such as NaCs, making the dipole-quadrupole interaction the second leading term for an atom colliding with a polar dimer. Our applications of the simplified treatment show a higher density of trimer states for a polar dimer compared to the case of a nonpolar dimer like Cs2. This is a consequence of the strong quadrupole-dipole coupling between the atom and the dimer dipole moment.