Molecular Ions Research Articles

Cold trapped molecular ions and hybrid platforms for ions and neutral particles

Cold trapped molecular ions and hybrid platforms for ions and neutral particles

Formation of antihydrogen molecular ions by associative ionization

Formation of antihydrogen molecular ions by associative ionization

Qualitative analysis of licorice and strychnine decoction before and after combination using UPLC-QE-Orbitrap-MS.

Glycyrrhiza glabra L. (GG) and Strychnos nux-vomica L. (NV) are traditional Chinese medicines (TCMs). Changes in the chemical composition may occur before and after the GG-NV compatibility. Ultra-performance liquid chromatography Q-exactive Orbitrap mass spectrometry (UPLC-QE-Orbitrap-MS) was applied here to study the difference in the components of the GG and NV decoctions before and after they were combined. The changes in the chemical composition of GG and NV before and after the combination were determined. The precise molecular weight, retention time, and fragment ion peak of the different components of the decoctions before and after compatibility were obtained through UPLC-QE-Orbitrap-MS. Differential analysis methods, such as principal component analysis, were used for comparison. In the positive ion mode, 200 new components were added, whereas six components were lost. In the negative ion mode, 144 new compounds were identified, whereas three components were missing. The compatibility difference between GG and NV was studied through UPLC-QE-Orbitrap-MS. The chemical composition of GG and NV changed before and after compatibility, and a class of compounds different from GG and NV was identified in the co-decoction. This study provides an experimental basis for subsequent research into detoxification mechanisms of the GG-NV combination and offers a new analytical method for investigating the compatibility of various other TCM pairs.

PyQCAMS: Python Quasi-Classical Atom–Molecule Scattering

We present Python Quasi-classical atom–molecule scattering (PyQCAMS v0.1.0), a new Python package for atom–diatom scattering within the quasi-classical trajectory approach. The input consists of the mass, collision energy, impact parameter, and pair-wise/three-body interactions. As the output, the code provides the vibrational quenching, dissociation, and reactive cross sections along with the rovibrational energy distribution of the reaction products. We benchmark the program for a reaction involving a molecular ion in a high-density ultracold gas, RbBa+ + Rb. Furthermore, we treat H2 + Ca → CaH + H reactions as a prototypical example to illustrate the properties and performance of the software. Finally, we study the parallelization performance of the code by looking into the speedup of the program as a function of the number of CPUs used.

MolDStruct: Modeling the dynamics and structure of matter exposed to ultrafast x-ray lasers with hybrid collisional-radiative/molecular dynamics.

We describe a method to compute photon-matter interaction and atomic dynamics with x-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically determined based on changes to their electronic occupations and the formation of a free electron cloud created from the irradiation of photons in the x-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, reducing the number of non-bonded interactions. In combination with parallelization through domain decomposition, the hybrid code handles large-scale molecular dynamics and ionization. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters, and crystals) that, when exposed to an x-ray laser pulse, turn into a plasma in the first few femtoseconds of the interaction. We present four examples demonstrating the applicability of the method. We investigate the non-thermal heating and scattering of bulk water and damage-induced dynamics of a protein crystal using an x-ray pump-probe scheme. In both cases, we compare to the experimental data. For single particle imaging, we simulate the ultrafast dynamics of a methane cluster exposed to a femtosecond x-ray laser. In the context of coherent diffractive imaging, we study the fragmentation as given by an x-ray pump-probe setup to understand the evolution of radiation damage in the time range of hundreds of femtoseconds.

Coherence mapping to identify the intermediates of multi-channel dissociative ionization

Identifying the short-lived intermediates and reaction mechanisms of multi-channel radical cation fragmentation processes remains a current and important challenge to understanding and predicting mass spectra. We find that coherent oscillations in the femtosecond time-dependent yields of several product ions following ultrafast strong-field ionization represent spectroscopic signatures that elucidate their mechanism of formation and identify the intermediate(s) they originate from. Experiments on endo-dicyclopentadiene show that vibrational frequencies from various intermediates are mapped onto their resulting products. Aided by ab initio methods, we identify the vibrational modes of both the cleaved and intact molecular ion intermediates. These results confirm stepwise and concerted fragmentation pathways of the dicyclopentadiene ion. This study highlights the power of tracking the femtosecond dynamics of all product ions simultaneously and sheds further light onto one of the fundamental reaction mechanisms in mass spectrometry, the retro-Diels Alder reaction.

Constructing Self-Healing Polydimethylsiloxane through Molecular Structure Design and Metal Ion Bonding

Self-healing polydimethylsiloxane (PDMS) has garnered significant attention due to its potential applications across various fields. In this study, a functionalized modification of PDMS containing di-aminos was initially conducted using 2,6-pyridinedicarbonyl chloride to synthesize pyridine-PDMS (Py-PDMS). Subsequently, rare earth metal europium ions (Eu3+) were incorporated into Py-PDMS. Due to the coordination interaction between Eu3+ and organic ligands, a coordination cross-linking network was created within the Py-PDMS matrix, resulting in the fabrication of Eu3+-Py-PDMS elastomer. At a molar ratio of Eu3+ to ligands of 1:1, the tensile strength of Eu3+-Py-PDMS reached 1.4 MPa, with a fracture elongation of 824%. Due to the dynamic reversibility of coordination bonds, Eu3+-Py-PDMS with a metal-to-ligand molar ratio of 1:2 exhibited varying self-healing efficiencies at different temperatures. Notably, after 4 h of repair at 60 °C, its self-healing efficiency reached nearly 100%. Furthermore, the gas barrier properties of Eu3+-Py-PDMS with a molar ratio of 1:1 was improved compared with that of Eu3+-Py-PDMS with a molar ratio of 1:1. This study provides an effective strategy for the design and fabrication of PDMS with high mechanical strength, high gas barrier properties, and exceptional self-healing efficiency.

Characterization of arsenic species by liquid sampling-atmospheric pressure glow discharge ionization mass spectrometry.

A liquid sampling-atmospheric pressure glow discharge (LS-APGD) ionization source operating at a nominal power of 30 W and solution flow rate of 30 µL min-1 and supported in a He sheath gas flow rate of 500 mL min-1 was interfaced to an Orbitrap mass spectrometer and assessed for use in rapid identification of inorganic and organic arsenic species, including As(III), As(V), monomethylarsonic acid, dimethylarsinic acid, and arsenobetaine in a 2% (v/v) nitric acid medium. Mass spectral acquisition in low-resolution mode, using only the ion trap analyzer, provided detection of protonated molecular ions for AsBet (m/z 179), DMA (m/z 139), MMA (m/z 141), and As(V) (m/z 143). As(III) is oxidized to As(V), likely due to in-source processes. Typical fragmentation of these compounds resulted in the loss of either water or methyl groups, as appropriate, i.e., introducing DMA also generated ions corresponding to MMA and As(V) as dissociation products. Structure assignments were also confirmed by high-resolution Orbitrap measurements. Spectral fingerprint assignments were based on the introduction of solutions containing 5 µg mL-1 of each arsenic compound.

Characteristic structures of liquid crystal monomers in EI-MS analysis and the potential application in suspect screening

Liquid crystal monomers (LCMs) are of emerging concern due to their ubiquitous presence in indoor and outdoor environments and their potential negative impacts on human health and ecosystems. Suspect screening approaches have been developed to monitor thousands of LCMs that could enter the environment, but an updated suspect list of LCMs is difficult to maintain given the rapid development of material innovations. To facilitate suspect screening for LCMs, in-silico mass fragmentation model and quantitative structure-activity relationship (QSPR) models were applied to predict electron ionization (EI) mass spectra of LCMs. The in-silico model showed limited predictive power for EI mass spectra, while the QSPR models trained with 437 published mass spectra of LCMs achieved an acceptable absolute error of 12 percentage points in predicting the relative intensity of the molecular ion, but failed to predict the mass-to-charge ratio of the base peak. A total of 41 characteristic structures were identified from an updated suspect list of 1606 LCMs. Multi-phenyl groups form the rigid cores of 85% of LCMs and produce 154 characteristic peaks in EI mass spectra. Monitoring the characteristic structures and fragments of LCMs may help identify new LCMs with the same rigid cores as those in the suspect list.

MINDS: The JWST MIRI Mid-INfrared Disk Survey

The study of protoplanetary disks has become increasingly important with the Kepler satellite finding that exoplanets are ubiquitous around stars in our galaxy and the discovery of enormous diversity in planetary system architectures and planet properties. High-resolution near-IR and ALMA images show strong evidence for ongoing planet formation in young disks. The JWST MIRI mid-INfrared Disk Survey (MINDS) aims to (1) investigate the chemical inventory in the terrestrial planet-forming zone across stellar spectral type, (2) follow the gas evolution into the disk dispersal stage, and (3) study the structure of protoplanetary and debris disks in the thermal mid-IR. The MINDS survey will thus build a bridge between the chemical inventory of disks and the properties of exoplanets. The survey comprises 52 targets (Herbig Ae stars, T Tauri stars, very low-mass stars and young debris disks). We primarily obtain MIRI/MRS spectra with high signal-to-noise ratio (∼100–500) covering the complete wavelength range from 4.9 to 27.9 μm. For a handful of selected targets we also obtain NIRSpec IFU high resolution spectroscopy (2.87–5.27 μm). We will search for signposts of planet formation in thermal emission of micron-sized dust—information complementary to near-IR scattered light emission from small dust grains and emission from large dust in the submillimeter wavelength domain. We will also study the spatial structure of disks in three key systems that have shown signposts for planet formation, TW Hya and HD 169142 using the MIRI coronagraph at 15.5 μm and 10.65 μm respectively and PDS 70 using NIRCam imaging in the 1.87 μm narrow and the 4.8 μm medium band filter. We provide here an overview of the MINDS survey and showcase the power of the new JWST mid-IR molecular spectroscopy with the TW Hya disk spectrum where we report the detection of the molecular ion CH3+ and the robust confirmation of HCO+ earlier detected with Spitzer.

Unveiling the Therapeutic Potential of Organotellurium(IV) Schiff Base Complexes through Structural Elucidation, Antimalarial, Antioxidant and Antimicrobial Studies

Infectious diseases have long been a formidable adversary to human health and well-being, presenting a persistent global challenge with far-reaching implication for individuals, communities and societies at large. Thus, with the aim of a combating agent against malarial and oxidant causing ailments, the newly synthesized Organotellurium(IV) complexes with a hydroxynaphthaldehyde Schiff base ligand are proposed in the present research. The structures of the complexes were established through various physical and spectral analysis. The weak electrolytic (8.77 to 35.08 ohm−1 cm2 mol−1) and crystalline nature of the compounds were demonstrated by molar conductivity and TGA, respectively. The ligand and complexes (7a-7f) shows molecular ion peaks at m/z 458.3563, 726.1039, 713.6978, 727.6179, 799.4780, 771.3178 and 799.3978 amu which were well consistent with their formula, revealing formation of compounds. The shifting of ligand's azomethine peak (7.74 ppm) and disappearance of naphthyl hydroxyl proton (12.28 ppm) in 1H NMR spectra confirmed the chelation of ligand with metal ion in proposed manner. In the FT-IR spectra, the complexation of ligand with metal ion was confirmed by disappearance of hydroxyl group (3355 cm−1) band and shifting of C=N (1245 cm−1) and C-O (1632 cm−1) band whereas appearance of Te-O (of 285-293 cm−1) and Te-N (458-467 cm−1) bands, revealed the bonding of metal with metal and octahedral nature of the complexes. Optimized structures, HOMO-LUMO energies and associated chemical reactivity descriptors of the compounds were computed by DFT calculations. The in vitro studies demonstrate that the complexes 7c (1.06 ± 0.11 μM) and 7f (1.22 ± 0.05 μM) exhibited moderate inhibition of the Plasmodium falciparum 3D7 strain, complexes 7a (100.96 ± 0.32 μg/mL) and 7d (96.32 ± 0.40 μg/mL) demonstrated the highest free radical quenching ability. Complex 7c displayed the highest antibacterial actions, whereas 7f exhibited the highest antifungal actions against the tested pathogens. Molecular docking and ADMET studies demonstrated enhanced binding affinity of the complexes compared to the Schiff base and their drug-like qualities.

Optical cycling in charged complexes with Ra–N bonds

The extension of laser cooling and trapping techniques to polyatomic molecular ions would have advanced scientific applications such as search of physics outside of the Standard Model, ultracold chemistry etc. We apply the Fock space relativistic coupled cluster method to study low-lying electronic states of molecular ions with Ra–N bonds, namely RaNCH+, RaNH3+ and RaNCCH3+. Prospects of laser cooling of these species are estimated, and the peculiarities of unpaired-electron distributions are analyzed from the point of view of the molecular electronic structure. RaNH3+ and RaNCCH3+ are the first symmetric top molecular ions expected to be suitable for direct laser cooling.

Investigation of pyruvic acid photolysis at the air-liquid interface as a source of aqueous secondary organic aerosols

Pyruvic acid (PA) is a ubiquitous 2-oxocarboxylic acid in the atmosphere. Its photochemical process at the air-liquid (a-l) interface has been suggested as an important source of aqueous secondary organic aerosols. We investigated the photochemical reaction pathways of PA at the a-l interface using synchrotron-based vacuum ultraviolet single-photon ionization mass spectrometry (VUV SPI-MS) coupled with the System for Analysis at the Liquid Vacuum Interface (SALVI) microreactor. Results from mass spectral analysis and the determination of appearance energies (AEs) indicate that photolysis of PA can generate radicals, then they recombine with carboxylic acids and simple molecular oligomers. Furthermore, the preliminary products could form larger oligomers via radical reaction or esterification in the presence of hydroxyl and carboxyl functional groups. Mass spectral comparison shows that most photochemical reactions would complete within 4 h. The expanded photochemistry-driven reaction flowchart of PA is proposed based on the newly discovered products. Our results reveal that the interfacial PA photochemical reactions have different mechanisms from the bulk liquid due to the interfacial properties, such as molecular density, composition, and ion concentration. Our findings show that in situ mass spectral analysis with bright photon ionization is useful to elucidate the contribution of a-l interfacial reactions leading to aqSOA formation.

Valorization of waste engine oil to mono- and di-rhamnolipid in a sustainable approach to circular bioeconomy.

This study aims to valorize waste engine oil (WEO) for synthesizing economically viable biosurfactants (rhamnolipids) to strengthen the circular bioeconomy concept. It specifically focuses on investigating the influence of key bioprocess parameters, viz. agitation and aeration rates, on enhancing rhamnolipid yield in a fed-batch fermentation mode. The methodology involves conducting experiments in a stirred tank bioreactor (3 L) using Pseudomonas aeruginosa gi |KP 163922| as the test organism. Central composite design and response surface methodology (CCD-RSM) are employed to design the experiments and analyze the effects of agitation and aeration rates on various parameters, including dry cell biomass (DCBM), surface tension, tensoactivity, and rhamnolipid yield. It is also essential to determine the mechanistic pathway of biosurfactant production followed by the strain using complex hydrophobic substrates such as WEO. The study reveals that optimal agitation and aeration rates of 200rpm and 1 Lpm result in the highest biosurfactant yield of 29.76g/L with minimal surface tension (28 mN/m). Biosurfactant characterization using FTIR, 1H NMR, and UPLC-MS/MS confirm the presence of dominant molecular ion peaks m/z 543.9 and 675.1. This suggests that the biosurfactant is a mixture of mono- and di-rhamnolipids (RhaC10C10, RhaRhaC10C12:1, RhaRhaC12:1C10). The findings present a sustainable approach for biosurfactant production in a fed-batch bioreactor. This research opens the possibility of exploring the use of pilot or large-scale bioreactors for biosurfactant production in future investigations.

Prospects for the determination of fundamental constants with beyond-state-of-the-art uncertainty using molecular hydrogen ion spectroscopy

Prospects for the determination of fundamental constants with beyond-state-of-the-art uncertainty using molecular hydrogen ion spectroscopy

Impact of Cavity on Molecular Ionization Spectra.

Ionization phenomena have been widely studied for decades. With the advent of cavity technology, the question arises how quantum light affects molecular ionization. As the ionization spectrum is recorded from the neutral ground state, it is usually possible to choose cavities which exert negligible effect on the neutral ground state, but have significant impact on the ion and the ionization spectrum. Particularly interesting are cases where the ion exhibits conical intersections between close-lying electronic states, which gives rise to substantial nonadiabatic effects. Assuming single-molecule strong coupling, we demonstrate that vibrational modes irrelevant in the absence of a cavity play a decisive role when the molecule is in the cavity. Here, dynamical symmetry breaking is responsible for the ion-cavity coupling and high symmetry enables control of the coupling via molecular orientation relative to the cavity field polarization. Significant impact on the spectrum by the cavity is found and shown to even substantially increase for less symmetric molecules.

Two-dimensional nonlinear spectroscopy in the extreme ultraviolet to study dynamics of atomic and molecular gases

We present a two-dimensional (2D) nonlinear four-wave mixing scheme in the extreme ultraviolet (XUV) to investigate ultrafast electronic wave-packets dynamics of multi-electron states in the above-threshold ionization region, using atomic argon and molecular nitrogen as examples. Coherent light sources in the range between 24 and 45 eV is generated by phase-matched cascaded four-wave mixing processes with a collinear configuration of laser fields 800 nm and 1400 nm. Motion of the electrons involving the excited states 3s3p6np (1P10) of argon gas, theF2Σg+ state and the predissociation state C2Σu+ of molecular nitrogen ion N2+ are unravelled through the ‘on-axis’ and ‘off-axis’ features of the two-dimensional spectra. Interpretation of the experimental data is supported by a theoretical dipole control model. Hence, results of this study may be promising for studies of dynamics of electrons in more complex systems.

Isolation of Human Milk Difucosyl Nona- and Decasaccharides by Ultrahigh-Temperature Preparative PGC-HPLC and Identification of Novel Difucosylated Heptaose and Octaose Backbones by Negative-Ion ESI-MSn.

Despite their many important physiological functions, past work on the diverse sequences of human milk oligosaccharides (HMOs) has been focused mainly on the highly abundant HMOs with a relatively low degree of polymerization (DP) due to the lack of efficient methods for separation/purification and high-sensitivity sequencing of large-sized HMOs with DP ≥ 10. Here we established an ultrahigh-temperature preparative HPLC based on a porous graphitized carbon column at up to 145 °C to overcome the anomeric α/β splitting problem and developed further the negative-ion ESI-CID-MS/MS into multistage MSn using a combined product-ion scanning of singly charged molecular ion and doubly charged fragment ion of the branching Gal and adjacent GlcNAc residues. The separation and sequencing method allows efficient separation of a neutral fraction with DP ≥ 10 into 70 components, among which 17 isomeric difucosylated nona- and decasaccharides were further purified and sequenced. As a result, novel branched difucosyl heptaose and octaose backbones were unambiguously identified in addition to the conventional linear and branched octaose backbones. The novel structures of difucosylated DF-novo-heptaose, DF-novo-LNO I, and DF-novo-LNnO I were corroborated by NMR. The various fucose-containing Lewis epitopes identified on different backbones were confirmed by oligosaccharide microarray analysis.

Synthesis of Calix[4]arene-Based Porous Organic Cages and Their Gas Adsorption.

Two crystalline large-sized porous organic cages (POCs) based on conical calix[4]arene (C4A) were designed and synthesized. The four-jaw C4A unit tends to follow the face-directed self-assembly law with the planar triangular building blocks such as tris(4-aminophenyl)amine (TAPA) or 1,3,5-tris(4-aminophenyl)benzene (TAPB) to generate a predictable cage with a stoichiometry of [6+8]. The formation of the large cages is confirmed through their relative molecular mass measured using MALDI-TOF/TOF spectra. The protonated molecular ion peaks of C4A-TAPA and C4A-TAPB were observed at m/z 5109.0 (calculated for C336H240O24N32: m/z 5109.7) and m/z 5594.2 (calculated for C384H264O24N24: m/z 5598.4). C4A-POCs exhibit I-type N2 adsorption-desorption isotherms with the BET surface areas of 1444.9 m2×g-1 and 1014.6 m2×g-1. The CO2 uptakes at 273 K are 62.1 cm3×g-1 and 52.4 cm3×g-1 at a pressure of 100 KPa. The saturated iodine vapor static uptakes at 348 K are 3.9 g∙g-1 and 3.5 g∙g-1. The adsorption capacity of C4A-TAPA for SO2 reaches to 124.4 cm3×g-1 at 298 K and 1.3 bar. Additionally, the adsorption capacities of C4A-TAPA for C2H2, C2H4, and C2H6 were evaluated.

Control of quantum paths in harmonic generation through orthogonal fields specific frequency ratios

By solving a two-dimensional, time-dependent Schrödinger equation, we investigate high-order harmonic generation for the H2+ molecular ion in orthogonally polarized two-color laser pulses. We find that harmonic generation depends on the frequency ratio n=ωyωx . When the wavelength is 800 nm and n = 1.2, the harmonic plateau becomes smoother, and the quantum orbital interference decreases. We change the fundamental wavelength and find that the harmonic spectrum exhibits a supercontinuum structure, and the quantum orbital is controllable. When the wavelength is 1600 nm and 2000 nm, and n = 1.2, we gain a deeper understanding of the physical process of harmonics. We have provided the time-frequency distribution and the probability density of an electron wave packet picture. Next, we analyzed the impact of the carrier-envelope phase on harmonics, and we combined Lissajous figures to continue our analysis. The research results find that when the carrier-envelope phase is 0, 0.5π, π, and 1.5π, the harmonic intensity becomes higher, and all exhibit a supercontinuum structure. We chose certain orders of harmonics, and isolated attosecond pulses can be synthesized.