Metastable Dimers Research Articles

Composition of the Water Dimer and the Heterodimers of Water with N2 and O2 in Earth's Atmosphere.

The mole fractions χ and number concentrations n of the water dimer and the heterodimers H2O-N2 and H2O-O2 in Earth's atmosphere are reported up to 20 km. The water dimer data is obtained from published values of the equilibrium constant based on the water equation of state. The mixed equilibrium constants for the heterodimers are obtained from the respective second virial coefficients using an approach introduced by Stogryn and Hirschfelder that extracts the components pertaining to pairwise interactions producing bound and metastable dimers. From these calculations, χ and n for the water dimer and the (H2O)(N2) and (H2O)(O2) heterodimers at standard sea level are 1.79(6) × 10-5, 4.77(12) × 10-5 and 9.90(5) × 10-6 and 4.55(15) × 1014, 1.23(3) × 1016 and 2.56(1) × 1015, respectively. Analytical expressions are provided for these quantities for altitudes between 0-20 km and temperatures from 200-300 K. Sea level values of χ and n are given for two specific locations.

Thermodynamics of the van der Waals Dimers of O2, N2 and the Heterodimer (N2)(O2) and Their Presence in Earth's Atmosphere.

The dimerization thermodynamics of N2 and O2, the principal components of Earth's atmosphere, have been determined from the respective second virial coefficients of the bound and metastable dimers calculated using the method of Stogryn and Hirschfelder that utilizes the Lennard-Jones (LJ) potential to account for intermolecular interactions. In addition, the thermodynamic properties of the heterodimer (N2)(O2) have been obtained using the same approach, employing combining rules to construct the LJ potential. Thus, Keq, ΔH, and ΔS for the three dimers are reported between 80-120 K. Over this temperature range, the ranking of Keq is (N2)(O2) > (O2)(O2) > (N2)(N2). The same trend is found for the exoethalpicity of dimer formation. For example, at 100 K, the Keq values are, respectively, 0.0406(14), 0.0215(5), and 0.0181(10), and the corresponding ΔH values are -2401(5), -2344(7), and -2279(1) J/mol. The mole fraction composition of the dimers in the atmosphere was calculated for altitudes up to 20 km. These calculations show that in the troposphere and the lower stratosphere (up to 20 km), the three dimers rank fifth to seventh in abundance, between CO2 and Ne. In this region, the average mole fractions of (N2)(N2), (O2)(O2), and (N2)(O2) are calculated to be 3.4(2) × 10-4, 2.80(9) × 10-5, and 1.95(7) × 10-4, respectively.

Metastable Charged Dimers in Organometallic Species: A Look into Hydrogen Bonding between Metallocene Derivatives.

Multiply charged complexes bound by noncovalent interactions have been previously described in the literature, although they were mostly focused on organic and main group inorganic systems. In this work, we show that similar complexes can also be found for organometallic systems containing transition metals and deepen in the reasons behind the existence of these species. We have studied the structures, binding energies, and dissociation profiles in the gas phase of a series of charged hydrogen-bonded dimers of metallocene (Ru, Co, Rh, and Mn) derivatives isoelectronic with the ferrocene dimer. Our results indicate that the carboxylic acid-containing dimers are more strongly bonded and present larger barriers to dissociation than the amide ones and that the cationic complexes tend to be more stable than the anionic ones. Additionally, we describe for the first time the symmetric proton transfer that can occur while in the metastable phase. Finally, we use a density-based energy decomposition analysis to shine light on the nature of the interaction between the dimers.

A simple quantum model for solving two-electron diatomics approximately

Analytical expressions are obtained for the total energy of two-electron heteronuclear diatomics using a minimal basis set consisting of a 1S-Gaussian orbital centered on each atom and a Heitler-London trial wavefunction. The equations are applied to the recently discovered helium hydride cation (2019, Nature 568, 357–9) to understand its stability. Special attention was given to the fulfillment of the virial theorem and the different limiting cases (homonuclear diatomics, short and long internuclear distances). The correctness of equations and numerical results was confirmed via a brute-force Metropolis Monte Carlo integration. Expressions for the moments of the electron density (including the dipole moments) were obtained. The effect of the spin state on the dipole moment is discussed and the model agrees qualitatively with results from more advanced ab initio calculations. I also applied the model to study the metastable helium dimer dication () and the predicted bond length (0.7359 Å) is in good agreement with the experimental value (0.75 ± 0.02 Å). The advantages and limitations of this simple quantum model are discussed.

Expanding the Scope of Metastable Species in Hydrogen Bonding-Directed Supramolecular Polymerization.

We reveal unique hydrogen (H‐) bonding patterns and exploit them to control the kinetics, pathways and length of supramolecular polymers (SPs). New bisamide‐containing monomers were designed to elucidate the role of competing intra‐ vs. intermolecular H‐bonding interactions on the kinetics of supramolecular polymerization (SP). Remarkably, two polymerization‐inactive metastable states were discovered. Contrary to previous examples, the commonly assumed intramolecularly H‐bonded monomer does not evolve into intermolecularly H‐bonded SPs via ring opening, but rather forms a metastable dimer. In this dimer, all H‐bonding sites are saturated, either intra‐ or intermolecularly, hampering elongation. The dimers exhibit an advantageous preorganization, which upon opening of the intramolecular portion of the H‐bonding motif facilitates SP in a consecutive process. The retardation of spontaneous self‐assembly as a result of two metastable states enables length control in SP by seed‐mediated growth.

CO oxidation by Pt2/Fe3O4: Metastable dimer and support configurations facilitate lattice oxygen extraction.

Heterogeneous catalysts based on subnanometer metal clusters often exhibit strongly size-dependent properties, and the addition or removal of a single atom can make all the difference. Identifying the most active species and deciphering the reaction mechanism is extremely difficult, however, because it is often not clear how the catalyst evolves in operando. Here, we use a combination of atomically resolved scanning probe microscopies, spectroscopic techniques, and density functional theory (DFT)-based calculations to study CO oxidation by a model Pt/Fe3O4(001) "single-atom" catalyst. We demonstrate that (PtCO)2 dimers, formed dynamically through the agglomeration of mobile Pt-carbonyl species, catalyze a reaction involving the oxide support to form CO2. Pt2 dimers produce one CO2 molecule before falling apart into two adatoms, releasing the second CO. Olattice extraction only becomes facile when both the Pt-dimer and the Fe3O4 support can access metastable configurations, suggesting that substantial, concerted rearrangements of both cluster and support must be considered for reactions occurring at elevated temperature.

The atmospheric continuum in the “terahertz gap” region (15–700 cm−1): Review of experiments at SOLEIL synchrotron and modeling

The results of our recent water vapor related continuum studies in the range of the “terahertz gap” at the AILES beam line of the SOLEIL synchrotron using a Fourier transform spectrometer are reviewed and summarized. The continuum of pure water vapor and its mixture with N2, O2 and dry air were investigated in the 15–700 cm−1 range in conditions close to the atmospheric ones. Analysis of the frequency and temperature dependence of the self-continuum revealed a significant contribution of a stable water dimer to the observed absorption, which is not taken into account by the MT_CKD semi-empirical model of the continuum widely used for atmospheric applications. We propose a physically based approach to continuum modeling, which explicitly accounts for the contribution of dimers and far wings of monomer resonance lines. We applied the suggested approach for the water vapor self-continuum modeling in the H2O rotational band and supported it by comparing with the SOLEIL data. The frequency dependence of the relative contributions of far wings, stable and metastable dimers to the self-continuum is evaluated. Prospects for further developments of the atmospheric continuum modeling are considered.

Monovalent ion-mediated charge-charge interactions drive aggregation of surface-functionalized gold nanoparticles.

Monolayer-protected metal nanoparticles (NPs) are not only promising materials with a wide range of potential industrial and biological applications, but they are also a powerful tool to investigate the behaviour of matter at nanoscopic scales, including the stability of dispersions and colloidal systems. This stability is dependent on a delicate balance between attractive and repulsive interactions that occur in the solution, and it is described in quantitative terms by the classic Derjaguin-Landau-Vewey-Overbeek (DLVO) theory, that posits that aggregation between NPs is driven by van der Waals interactions and opposed by electrostatic interactions. To investigate the limits of this theory at the nanoscale, where the continuum assumptions required by the DLVO theory break down, here we investigate NP dimerization by computing the Potential of Mean Force (PMF) of this process using fully atomistic MD simulations. Serendipitously, we find that electrostatic interactions can lead to the formation of metastable NP dimers at physiological ion concentrations. These dimers are stabilized by complexes formed by negatively charged ligands belonging to distinct NPs that are bridged by positively charged monovalent ions present in solution. We validate our findings by collecting tomographic EM images of NPs in solution and by quantifying their radial distribution function, that shows a marked peak at interparticle distance comparable with that of MD simulations. Taken together, our results suggest that not only van der Waals interactions, but also electrostatic interactions mediated by monovalent ions at physiological concentrations, contribute to attraction between nano-sized charged objects at very short length scales.

Fluorescence Quenching in J-Aggregates through the Formation of Unusual Metastable Dimers.

Molecular aggregation alters the optical properties of a system as fluorescence may be activated or quenched. This is usually described within the well-established framework of H- and J-aggregates. While H-aggregates show nonfluorescent blueshifted absorption bands with respect to the isolated monomer, J-aggregates are fluorescent displaying a redshifted peak. In this publication, we employ a combined approach of experiment and theory to study the complex aggregation features and photophysical properties of diaminodicyanoquinone derivatives, which show unusual and puzzling nonfluorescent redshifted absorption bands upon aggregation. Our theoretical analysis demonstrates that stable aggregates do not account for the experimental observations. Instead, we propose an unprecedented mechanism involving metastable dimeric species formed from stable dimers to generate nonfluorescent J-aggregates. These results represent a novel kind of aggregation-induced optical effect and may have broad implications for the photophysics of dye aggregates.

Stability of Human Serum Amyloid A Fibrils.

In systemic amyloidosis, serum amyloid A (SAA) fibril deposits cause widespread damages to tissues and organs that eventually may lead to death. A therapeutically intervention therefore has either to dissolve these fibrils or inhibit their formation. However, only recently has the human SAA fibril structure been resolved at a resolution that is sufficient for development of drug candidates. Here, we use molecular dynamic simulations to probe the factors that modulate the stability of this fibril model. Our simulations suggest that fibril formation starts with the stacking of two misfolded monomers into metastable dimers, with the stacking depending on the N-terminal amyloidogenic regions of different chains forming anchors. The resulting dimers pack in a second step into a 2-fold two-layer tetramer that is stable enough to nucleate fibril formation. The stability of the initial dimers is enhanced under acidic conditions by a strong salt bridge and side-chain hydrogen bond network in the C-terminal cavity (residues 23-51) but is not affected by the presence of the disordered C-terminal tail.

Optical and spectroscopic study of a supersonic flowing helium plasma: energy transport in the afterglow

Flowing plasma jets are increasingly investigated and used for surface treatments, including biological matter, and as soft ionization sources for mass spectrometry. They have the characteristic capability to transport energy from the plasma excitation region to the flowing afterglow, and therefore to a distant application surface, in a controlled manner. The ability to transport and deposit energy into a specimen is related to the actual energy transport mechanism. In case of a flowing helium plasma, the energy in the flowing afterglow may be carried by metastable helium atoms and long-lived helium dimer ions. In this work a systematic investigation of the optical and spectroscopic characteristics of a supersonic flowing helium plasma in vacuum and its afterglow as function of the helium gas density is presented. The experimental data are compared with numerical modeling of the plasma excitation and helium dimer ion formation supported by a Computational Fluid Dynamic simulation of the helium jet. The results indicate that the plasma afterglow is effectively due to helium dimer ions recombination via a three-body reaction.

Shifting formic acid dimers into perspective: vibrational scrutiny in helium nanodroplets.

A metastable dimer of formic acid has been prepared inside superfluid helium nanodroplets and examined using IR spectroscopy and quantum chemical calculations. This dimer has one strong O-HO[double bond, length as m-dash]C hydrogen bond and one weak C[double bond, length as m-dash]OH-C bond, which is the same bonding motif that exists between adjacent molecules in catemer chains found in the crystalline phase. The strongly bound OH stretching vibration of the metastable dimer shows clear evidence of significant coupling to other vibrational modes, but it is far less extensive than that seen for the doubly hydrogen bonded global energy minimum dimer structure, which dominates in the gas phase but is not observed in helium droplets. The width and shape of the resonance pattern can be qualitatively reproduced by B3LYP-D3(BJ)/aVTZ VPT2 calculations, if additional intensity scaling is applied. However, it is the MP2/aVTZ level of theory that consistently provides the closest agreement between calculated (VPT2) and experimental frequencies for the OH stretching vibration in the formic acid monomer and metastable dimer.

Probing Elusive Cations: Infrared Spectroscopy of Protonated Acetic Acid.

Protonated carboxylic acids, (RCOOH)H+, are the initial intermediates in acid-catalyzed (Fischer) esterification reactions. However, the identity of the isomeric form has been debated. Surprisingly, no optical spectra have been reported for any isomer of the protonated carboxylic acid monomer, despite it being a fundamental organic cation. Here, we address these issues by using a new approach to prepare cold He-tagged cations of protonated acetic acid (AA), which entails electron ionization of helium nanodroplets containing metastable dimers of AA. The protonated species is subsequently probed using infrared photodissociation spectroscopy, and following a comparison with calculations, we identify the two isomers whose roles in Fischer esterification are debated. These are the carbonyl-protonated E, Z isomer and the metastable hydroxyl-protonated isomer. Our technique provides a novel approach that can be applied to other elusive ionic species.

Dimers of acetic acid in helium nanodroplets.

The structural arrangement of small carboxylic acid molecules in the liquid phase remains a controversial topic. Some studies indicate a dominance of the cyclic dimer that prevails in the gas phase, whilst other studies favor short fragments of the infinite catemer chains that are found in the crystalline phase. Furthermore, difficulties in preparing and probing size-selected catemer segments have resulted in a lack of benchmark data upon which theoretical models of the condensed phases can be built. To address these issues, we have combined infrared spectroscopy and quantum chemical calculations to explore regions of the intermolecular potential energy surface associated with the formation of metastable dimer isomers. The OH stretching region of the spectrum shows that aggregation of acetic acid molecules inside liquid helium nanodroplets yields two distinct metastable dimers, whilst negligible signal is observed from the cyclic dimer that typically overwhelms this spectral region. We deduce that the most abundant isomer in superfluid helium has one strong O-HO[double bond, length as m-dash]C and one weak C-HO[double bond, length as m-dash]C hydrogen bond. Since this bonding motif is common to the dimeric repeating unit of the catemer, it is of fundamental importance for understanding intermolecular interactions in the condensed phases of small carboxylic acids.

Plasma kinetics in a nanosecond pulsed filamentary discharge sustained in Ar–H2O and H2O

The plasma kinetics of Ar–H2O and H2O at atmospheric pressure are of interest for applications in biotechnology where rare-gas plasma jets treat liquid surfaces and in water treatment where discharges are generated in bubbles or directly in liquid water. Due to evaporation resulting from heat transfer to the liquid, for many conditions the mole fraction of water in the plasma can be large—approaching nearly pure water. In this paper, results are discussed from a combined experimental and computational investigation of the chemical kinetics in a high electron density plasma filament sustained in Ar–H2O at atmospheric pressure. The chemical kinetics were simulated using a 0D global model, validated by measurements of the absolute OH and H densities by laser induced fluorescence (LIF) and two-photon absorption LIF. The primary sources of H and OH during the discharge pulse are dissociative excitation transfer from metastable Ar atoms and Ar dimer excimers at low water concentration and electron impact dissociation of H2O at high water concentration. In spite of their similar sources, the density of OH was measured to be two orders of magnitude smaller than that of H at power densities on the order of 105 Jm−3. This disparity is due to electron impact dissociation of OH during the discharge pulse and rapid reactions of OH in the presence of high H and O densities in the afterglow. It is often assumed that OH is the dominant non-selective reactive species in water-containing plasmas. These results reinforce the importance of atomic species such as H and O in water containing high energy density plasmas. A numerical parametric study revealed that the lowest energy cost for H2O2 production is achieved at low energy densities in pure water. The high concentration of atomic radicals, which rapidly recombine, results in an overall lower energy efficiency of reactive species production. In particular, the selectivity of H2O2 production decreases with increasing power density which instead favors H2 and O2 production.

A Natively Monomeric Deubiquitinase UCH-L1 Forms Highly Dynamic but Defined Metastable Oligomeric Folding Intermediates.

Oligomerization of misfolded protein species is implicated in many human disorders. Here we showed by size-exclusion chromatography-coupled multiangle light scattering (SEC-MALS) and small-angle X-ray scattering (SEC-SAXS) that urea-induced folding intermediate of human ubiquitin C-terminal hydrolase, UCH-L1, can form well-defined dimers and tetramers under denaturing conditions despite being highly disordered. Introduction of a Parkinson disease-associated mutation, I93M, resulted in increased aggregation propensity and formation of irreversible precipitants in the presence of a moderate amount of urea. Since UCH-L1 exhibits highly populated partially unfolded forms under native conditions that resemble urea-induced folding intermediates, it is likely that these metastable dimers and tetramers can form under physiological conditions. Our findings highlighted the unique strength of integrated SEC-MALS/SAXS in quantitative analyses of the structure and dynamics of oligomeric folding intermediates that enabled us to extract information that is inaccessible to conventional biophysical techniques.

Dinitrogen as a Sensor for Metastable Carboxylic Acid Dimers and a Weak Hydrogen Bond Benchmarking Tool.

Molecular nitrogen as a weak hydrogen bond acceptor is added to formic and acetic acid and their monodeuterated isotopologues. FTIR spectroscopy of supersonic expansions in the O-H stretching region reveals the formation of the weakly bound N2-carboxylic acid complexes. Their respective spectral downshifts from the monomer fundamental vibration are used to benchmark electronic structure calculations and vibrational perturbation theory. The small size of the investigated systems allows for a wide range of electronic structure levels to be explored. The O-H stretching vibration of an open dimer of acetic acid can be discriminated from the cyclic dimer vibrations by its higher susceptibility to coexpanded nitrogen.

Benzimidazolines Convert Sulfur Dioxide to Bisulfate at Room Temperature and Atmospheric Pressure Utilizing Aerial Oxygen

By employing a simple strategy of reacting SO2 gas with easily attainable hydride donors such as 2-substituted-1,3-dimethyl-2,3-dihydro-1H-benzo[d]imidazole, benzimidazoline and SO2 were converted into benzimidazolium bisulfate at room temperature and atmospheric pressure. Bisulfate originated from SO2 and hydride from benzimidazoline and aerial oxygen. Metastable dimers of bisulfate anions were observed in the solid state and in solution where the anions are not stabilized by encapsulation in cages but through hydrogen bonding from benzimidazolium cations. All three benzimidazolines and resulted benzimidazolium bisulfates have been characterized using 1H and 13C NMR spectroscopy, high-resolution electrospray ionization mass spectrometry, and single crystal X-ray diffraction techniques.

Effect of stable and metastable dimers on collision-induced rototranslational spectra: Carbon dioxide – rare gas mixtures

The role of stable and metastable dimers as well as of free collisions in the collision-induced rototranslational absorption by the compressed CO2–Ar and CO2–Xe gas mixtures is elucidated using the classical three-dimensional trajectories method. The contribution from the stable dimers is obtained via Fourier transform of the dipole correlation function. The spectral bandshape due to the unbound trajectories (metastable dimers and free collisions) is calculated as an averaged Fourier spectrum of the collision-induced dipole moment. The mean lifetimes of metastable dimers have been estimated as 3.8 ps for CO2–Ar and 5.9 ps for CO2–Xe pairs. Trajectory computations are complemented by calculations of zero spectral moments using pair distribution functions. The stable and metastable dimer contribution to the zero spectral moment is shown to be comparable with that from free collisions.

Dichlorosilylene Transfer to a P‐Fluorophosphaalkene: The Route to a C‐Dichlorofluorosilyl‐Functionalized Dialkyldiphosphene

Reactions of the (trichlorosilyl)germane Me3GeSiCl3 and of the unsymmetric disilane Me3SiSiCl3 with the P‐fluorophosphaalkene (Me3Si)2C=PF (1) proceed with transfer of SiCl2 (2) leading to the new C‐dichlorofluorosilyl‐functionalized dialkyldiphosphene (Cl2FSi)(Me3Si)2CP=PC(SiCl2F)(SiMe3)2 (6), which was characterized by X‐ray crystallography. The P‐phosphanylphosphaalkene (Me3Si)2C=PP[C(SiCl2F)(SiMe3)2]SiCl2F (8a) was detected in the reaction mixtures by 31P NMR spectroscopy, accompanied by its isomer 8b, presumably (Cl2FSi)(Me3Si)C=PP[C(SiCl2F)(SiMe3)2]SiMe3. The unsymmetric dimers 8a and 8b rearrange by a 1,3‐(P→C) silyl group shift, providing the inversion‐symmetric diphosphene 6. Compound 6 was transformed with selenium into a selenadiphosphirane (9). Quantum chemical calculations were performed on intermediates on the route from 1 and 2 to the metastable unsymmetric dimers 8a and 8b. The addition of SiCl2 to the P=C bond of 1, followed by ring opening of the silaphosphirane 4, provides the phosphinidene (Me3Si)2(Cl2FSi)CP (5), which rearranges further to isomeric P‐silylphosphaalkenes (Me3Si)2C=PSiCl2F (7a) and (Cl2FSi)(Me3Si)C=PSiMe3 (7b). Rapid phosphinidene–phosphaalkene P–P coupling reactions of 5 with 7a and with 7b followed by 1,2‐(P→P) silyl group shift of ylide‐type dimers 11a and 11b explain the formation of the observed species 8a and 8b. The absence of species related to 8b in previous experiments on the reactions of the P‐chlorophosphaalkene (Me3Si)2C=PCl (1′) with Si2Cl6, with Me3GeSiCl3, and with Me3SiSiCl3, allows us to suggest that in the P‐chlorophosphaalkene case nucleophile‐supported SiCl2 insertion into the P–Cl bond or the substitutive Cl–/SiCl3– exchange are the preferred routes to the metastable P‐(trichlorosilyl)phosphaalkene (Me3Si)2C=PSiCl3.