Ion molecule reactions in the HBr+ + CH4 system: a combined experimental and theoretical study.

Reactions in the system HBr+ + CH4 have been investigated inside a guided ion-beam apparatus under single-collision conditions. The HBr+ is vibrational and rotational state selected in the electronic X2Π1/2 state created by (2+1)-REMPI. Due to the exitation scheme employed different rotational states of the HBr+ are accessible. Four reaction channels have been observed. The cross section, σ, for the exothermic proton transfer channel (PT) decreases with increasing collision energy, steeper than predicted by the Langevin model. The cross section also decreases with increasing rotational energy in the HBr+, with the effect of the rotational energy being stronger than that of translational energy. The cross section for the endothermic charge transfer (CT) increased with increasing collision energy. The energy dependence is well reproduced by a simple line of center (loc) model. Although the bromine transfer (BT) is exothermic the observed cross section increased with increasing collision energy due to an activation barrier on the potential energy surface (PES). Analysis by a modified loc model suggest the relevance of an angle dependence of σ. The cross section for the endothermic hydrogen atom abstraction (HA) exhibits a maximum at 2 eV Ecm. The measured cross sections are rationalized by means of reaction dynamics simulations which show good agreement with the experimental cross sections. The dynamics simulations are carried out with a machine learning potential that is developed and benchmarked with ab initio molecular dynamics simulation. The absolute cross sections predicted by reaction dynamics simulations are well within the same order of magnitude while reproducing the trends over three different collision energies for all four reaction channels. Furthermore, the simulations demonstrate various reaction mechanisms for these reaction channels, including a very interesting HBr+ orientation selectivity for the BT reaction channel.

Atomistic Insight into the Lipid Nanodomains of Synaptic Vesicles.

Membrane curvature, once regarded as a passive consequence of membrane composition and cellular architecture, has been shown to actively modulate various properties of the cellular membrane. These changes could also lead to segregation of the constituents of the membrane, generating nanodomains with precise biological properties. Proteins often linked with neurodegeneration (e.g., tau, alpha-synuclein) exhibit an unintuitive affinity for synaptic vesicles in neurons, which are reported to lack distinct, ordered nanodomains based on their composition. In this study, all-atom molecular dynamics simulations are used to study a full-scale synaptic vesicle of realistic Gaussian curvature and its effect on the membrane dynamics and lipid nanodomain organization. Compelling indicators of nanodomain formation, from the perspective of composition, surface areas per lipid, order parameter, and domain lifetime, are identified in the vesicle membrane, which are absent in a flat bilayer of the same lipid composition. Therefore, our study supports the idea that curvature may induce phase separation in an otherwise fluid, disordered membrane.

Hypergolic ionic liquids: to be or not to be?

Hypergolic ionic liquids (HIL) - ionic liquids which ignite spontaneously upon contact with an oxidizer - emerged as green space propellants. Exploiting the previously marked hypergolic [EMIM][CBH] - WFNA (1-ethyl-3-methylimidazolium cyanoborohydride - white fuming nitric acid) system as a benchmark, through the utilization of a novel chirped-pulse droplet-merging technique in an ultrasonic levitation environment and electronic structure calculations, this work deeply questions the hypergolicity of the [EMIM][CBH]-WFNA system. Molecular oxygen is critically required for the [EMIM][CBH]-WFNA system to ignite spontaneously. State-of-the-art electronic structure calculations identified the resonantly stabilized N-boryl-N-oxo-formamide [(H3B-N(O)-CHO)-; BOFA] radical anion as the key intermediate in driving the oxidation chemistry upon reaction with molecular oxygen of the ionic liquid. These findings challenge conventional wisdom of 'well-established' test protocols as indicators of the hypergolicity of ionic liquids thus necessitating truly oxygen-free experimental conditions to define the ignition delay upon mixing of the ionic liquid and the oxidizer and hence designating an ionic liquid as truly hypergolic at the molecular level.

Unraveling the initial steps of the ignition chemistry of the hypergolic ionic liquid 1-ethyl-3-methylimidazolium cyanoborohydride ([EMIM][CBH]) with nitric acid (HNO3) exploiting chirped pulse triggered droplet merging.

The composition of the products and the mechanistic routes for the reaction of the hypergolic ionic liquid (HIL) 1-ethyl-3-methylimidazolium cyanoborohydride ([EMIM][CBH]) and nitric acid (HNO3) at various concentrations from 10% to 70% were explored using a contactless single droplet merging within an ultrasonic levitation setup in an inert atmosphere of argon to reveal the initial steps that cause hypergolicity. The reactions were initiated through controlled droplet-merging manipulation triggered by a frequency chirp pulse amplitude modulation. Utilizing the high-speed optical and infrared cameras surrounding the levitation process chamber, intriguing visual images were unveiled: (i) extensive gas release and (ii) temperature rises of up to 435 K in the merged droplets. The gas development was validated qualitatively and quantitatively with Fourier Transform Infrared Spectroscopy (FTIR) indicating the major gas-phase products to be hydrogen cyanide (HCN) and nitrous oxide (N2O). The merged droplet was also probed by pulsed Raman spectroscopy which deciphered features for key functional groups of the reaction products and intermediates (-BH, -BH2, -BH3, -NCO); reaction kinetics revealed that the reaction was initiated by the interaction of the [CBH]- anion of the HIL with the oxidizer (HNO3) through proton transfer. Computations indicate the formation of a van-der-Waals complex between the [CBH]- anion and HNO3 initially, followed by proton transfer from the acid to the anion and subsequent extensive isomerization; these rearrangements were found to be essential for the formation of HCN and N2O. The exoergicity observed during the merging process provides a molar enthalpy change up to 10 kJ mol-1 to the system, which could be sufficient for a significant fraction of the reactants of about 11% to overcome the reaction barriers in the individual steps of the computationally determined minimum energy pathways.

Ion-molecule reactions in the HBr+ + HCl (DCl) system: a combined experimental and theoretical study.

Reactions in the system HBr+ + HCl (DCl) were investigated inside a guided ion-beam apparatus under single-collision conditions. In the HBr+ + HCl system, the proton transfer (PTHCl) and charge transfer (CT) are observable. In the HBr+ + DCl system, proton transfer (PTDCl) and deuterium abstraction (DA) are accessible. The cross sections for all reaction channels were measured as a function of the collision energy Ecm and of the rotational energy Erot of the ion. The rotationally state-selective formation of the ionic species was realized by resonance-enhanced multiphoton ionization (REMPI). As expected, the PT-channels are exothermic, and the cross section decreases with increasing collision energy for both PTHCl and PTDCl. The cross section for DA also decreases with an increasing Ec.m.. In the case of a considerably endothermic CT-channel, the reaction efficiency increases with increasing collision energy but has an overall much smaller cross sections compared to PT and DA reactions. Both PT-reactions are hindered by ion rotation, whereas DA is independent of Erot. The CT-channel shows a rotational enhancement near the thermochemical threshold. The experiment is complemented by theory, using ab initio molecular dynamics (AIMD, also known as direct dynamics) simulations and taking the rotational enhancement of HBr+ into account. The simulations show good agreement with the experimental results. The cross section of PTHCl decreases with an increase of the rotational energy. Furthermore, the absolute cross sections are in the same order of magnitude. The CT channel shows no reactions in the simulation.

Unsupervised Reaction Pathways Search for the Oxidation of Hypergolic Ionic Liquids: 1-Ethyl-3-methylimidazolium Cyanoborohydride (EMIM+/CBH-) as a Case Study.

Hypergolic ionic liquids have come under increased study for having several desirable properties as a fuel source. One particular ionic liquid, 1-ethyl-3-methylimidazolium/cyanoborohydride (EMIM+/CBH-), and oxidant, nitric acid (HNO3), has been reported to be hypergolic experimentally, but its mechanism is not well-understood at a mechanistic level. In this computational study, the reaction is first probed with ab initio molecular dynamics simulations to confirm that anion-oxidant interactions likely are the first step in the mechanism. Second, the potential energy surface of the anion-oxidant system is studied with an in-depth search over possible isomerizations, and a network of possible intermediates are found. The critical point search is unsupervised and thus has the potential of identifying structures that deviate from chemical intuition. Molecular graphs are employed for analyzing 3000+ intermediates found, and nudged elastic band calculations are employed to identify transition states between them. Finally, the reactivity of the system is discussed through examination of minimal energy paths connecting the reactant to various common products from hypergolic ionic liquid oxidation. Eight products are reported for this system: NO, N2O, NO2, HNO, HONO, HNO2, HCN, and H2O. All reaction paths leading to these exothermic products have overall reaction barriers of 6-7 kcal/mol.

Directed gas phase preparation of ethynylallene (H2CCCHCCH; X1A') via the crossed molecular beam reaction of the methylidyne radical (CH; X2Π) with vinylacetylene (H2CCHCCH; X1A').

The gas-phase bimolecular reaction of the methylidyne (CH; X2Π) radical with vinylacetylene (H2CCHCCH; X1A') was conducted at a collision energy of 20.3 kJ mol-1 under single collision conditions exploiting the crossed molecular beam experimental results merged with ab initio electronic structure calculations and ab initio molecular dynamics (AIMD) simulations. The laboratory data reveal that the bimolecular reaction proceeds barrierlessly via indirect scattering dynamics through long-lived C5H5 reaction intermediate(s) ultimately dissociating to C5H4 isomers along with atomic hydrogen with the latter predominantly originating from the vinylacetylene reactant as confirmed by the isotopic substitution experiments in the D1-methylidyne-vinylacetylene reaction. Combined with ab initio calculations of the potential energy surface (PES) and statistical Rice-Ramsperger-Kassel-Marcus (RRKM) calculations, the experimental determined reaction energy of -146 ± 26 kJ mol-1 along with the distribution minimum of T(θ) at 90° and isotopic substitution experiments suggest ethynylallene (p1; ΔrG = -230 ± 4 kJ mol-1) as the dominant product. The ethynylallene (p1) may be formed with extensive rovibrational excitation, which would result in a lower maximum translational energy. Further, AIMD simulations reveal that the reaction dynamics leads to p1 (ethynylallene, 75%) plus atomic hydrogen with the dominant initial complex being i1 formed by methylidyne radical addition to the double CC bond in vinylacetylene. Overall, combining the crossed molecular beam experimental results with ab initio electronic structure calculations and ab initio molecular dynamics (AIMD) simulations, ethynylallene (p1) is expected to represent the dominant product in the reaction of the methylidyne (CH; X2Π) radical with vinylacetylene (H2CCHCCH; X1A').

The Potential Energy Profile of the HBr+ + HCl Bimolecular Collision.

Recently, the HBr+ + HCl bimolecular reaction has been exploited by guided ion beam studies to probe the effect of rotational excitations and collision energies on the dynamics of the ion-molecule reactions. The current manuscript employs high-level ab initio calculations and reports the potential energy of pathways leading to various products, including HBr + HCl+, H2Cl+ + Br, H2Br+ + Cl, and H2 + BrCl+. The study shows that the intermediates involved in this reaction are connected by low-lying transition states, thus frequent isomerizations and diverse products are expected. Further, this manuscript screens the performance of 192 different combinations of computationally efficient methods and basis sets in order to identify the optimal quantum chemical method for further dynamics simulations.

Assessing the Intestinal Permeability of Small Molecule Drugs via Diffusion Motion on a Multidimensional Free Energy Surface.

A protocol that accurately assesses the intestinal permeability of small molecule compounds plays an essential role in decreasing the cost and time in inventing a new drug. This manuscript presents a novel computational method to study the passive permeation of small molecule drugs based on the inhomogeneous solubility-diffusion model. The multidimensional free energy surface of the drug transiting through a lipid bilayer is computed with transition-tempered metadynamics that accurately captures the mechanisms of passive permeation. The permeability is computed by following the diffusion motion of the drug molecules along the minimal free energy path found on the multidimensional free energy surface. This computational method is assessed by studying the permeability of five small molecule drugs (ketoprofen, naproxen, metoprolol, propranolol, and salicylic acid). The results demonstrate a remarkable agreement between the computed permeabilities and those measured with the intestinal assay. The in silico method reported in this manuscript also reproduces the permeability measured from the intestinal assay (in vivo) better than the cell-based assays (e.g., PAMPA and Caco-2) do. In addition, the multidimensional free energy surface reveals the interplay between the structure of the small molecule and its permeability, shedding light on strategies of drug optimization.

A chemical dynamics study of the reaction of the methylidyne radical (CH, X2Π) with dimethylacetylene (CH3CCCH3, X1A1g).

The gas-phase reaction of the methylidyne (CH; X2Π) radical with dimethylacetylene (CH3CCCH3; X1A1g) was studied at a collision energy of 20.6 kJ mol-1 under single collision conditions with experimental results merged with ab initio calculations of the potential energy surface (PES) and ab initio molecule dynamics (AIMD) simulations. The crossed molecular beam experiment reveals that the reaction proceeds barrierless via indirect scattering dynamics through long-lived C5H7 reaction intermediate(s) ultimately dissociating to C5H6 isomers along with atomic hydrogen with atomic hydrogen predominantly released from the methyl groups as verified by replacing the methylidyne with the D1-methylidyne reactant. AIMD simulations reveal that the reaction dynamics are statistical leading predominantly to p28 (1-methyl-3-methylenecyclopropene, 13%) and p8 (1-penten-3-yne, 81%) plus atomic hydrogen with a significant amount of available energy being channeled into the internal excitation of the polyatomic reaction products. The dynamics are controlled by addition to the carbon-carbon triple bond with the reaction intermediates eventually eliminating a hydrogen atom from the methyl groups of the dimethylacetylene reactant forming 1-methyl-3-methylenecyclopropene (p28). The dominating pathways reveal an unexpected insertion of methylidyne into one of the six carbon-hydrogen single bonds of the methyl groups of dimethylacetylene leading to the acyclic intermediate, which then decomposes to 1-penten-3-yne (p8). Therefore, the methyl groups of dimethylacetylene effectively 'screen' the carbon-carbon triple bond from being attacked by addition thus directing the dynamics to an insertion process as seen exclusively in the reaction of methylidyne with ethane (C2H6) forming propylene (CH3C2H3). Therefore, driven by the screening of the triple bond, one propynyl moiety (CH3CC) acts in four out of five trajectories as a spectator thus driving an unexpected, but dominating chemistry in analogy to the methylidyne - ethane system.

Theoretical Study of the Dynamics of the HBr+ + CO2 → HOCO+ + Br Reaction.

The dynamics of the HBr+ + CO2 → HOCO+ + Br reaction was recently investigated with guided ion beam experiments under various excitations (collision energy of the reactants, rotational and spin-orbital states of HBr+, etc.), and their impacts were probed through the change of the cross section of the reaction. The potential energy profile of this reaction has also been accurately characterized by high-level ab initio methods such as CCSD(T)/CBS, and the UMP2/cc-pVDZ/lanl08d has been identified as an ideal method to study its dynamics. This manuscript reports the first ab initio molecular dynamics simulations of this reaction at two different collision energies, 8.1 kcal/mol and 19.6 kcal/mol. The cross sections measured from the simulations agree very well with the experiments measured with HBr+ in the 2∏1/2 state. The simulations reveal three distinct mechanisms at both collision energies: direct rebound (DR), direct stripping (DS), and indirect (Ind) mechanisms. DS and Ind make up 97% of the total reaction. The dynamics of this reaction is also compared with nucleophilic substitution (SN2) reactions of X- + CH3Y → CH3X + Y- type. In summary, this research has revealed interesting dynamics of the HBr+ + CO2 → HOCO+ + Br reaction at different collision energies and has laid a solid foundation for using this reaction to probe the impact of rotational excitation of ion-molecule reactions in general.