Gas-phase Data Research Articles

Theoretical study of the efficiencies of graphyne supported Mo single-atom catalyst (SAC) and Mo-Ni dual-atom catalyst (DAC) on hydrogen evolution reaction

In this work, by adding one molybdenum atom or two molybdenum and nickel atoms on the surface graphyne support, single atom catalyst (SAC) and dual atoms catalyst (DAC) were designed. The different spin multiplicities for both catalysts were analyzed by the relative energies, adsorption energies and frontier orbitals. The results showed in both case of SACs and DACs, the catalyst with spin multiplicity = 3 is desired. Then, the efficiency of these two catalysts as high-performance and cost-effective catalysts in the HER process was investigated theoretically. All calculations were performed using M06-2X/def2SV level of theory. In the HER mechanism, it has been found that the DAC has higher favorability than the SAC. Both steps (Volmer reaction and Tafel or Heyrovsky reaction) are more exothermic using DAC, and the difference between SAC and DAC is higher in the second step. The effect of solvent on these steps has been studied using water and methanol as two common solvents. The reactions are less exothermic in the solvent; but they are still highly exothermic and thermodynamically favorable. Moreover, despite the gas phase data, in both solvents, the use of DAC gives less favorable data versus the SAC. The data also showed the little preference of water versus the methanol as solvent.

Quantum computations on a new neural network potential for the proton-bound noble-gas Ar[formula omitted]H[formula omitted] complex: Isotopic effects

High-quality data-driven potentials were developed aiming to predict rovibrational traits and analyze the influence of the isotopic substitution on the molecular spectroscopic properties of Ar2H+. Neural networks machine-learning approaches trained on CCSD(T)/CBS datasets were implemented. Our full-dimensional quantum MCTDH results were discussed in comparison with experimental data in gas phase and solid matrix environments, as well as against theoretical estimates available. The new data indicate that both fundamental and progression bands are dominantly driven by the strength and shape of the underlying interactions. Our simulations could enable the spectroscopic characterization of these species, assisting investigations for their astrophysical observation.

Measuring the Electric Fields of Ions Captured in Crown Ethers.

Controlling reactivity with electric fields is a persistent challenge in chemistry. One approach is to tether ions at well-defined locations near a reactive center. To quantify fields arising from ions, we report crown ethers that capture metal cations as field sources and a covalently bound vibrational Stark shift probe as a field sensor. We use experiments and computations in both the gas and liquid phases to quantify the vibrational frequencies of the probe and estimate the electric fields from the captured ions. Cations, in general, blue shift the probe frequency, with effective fields estimated to vary in the range of ∼0.2-3 V/nm in the liquid phase. Comparison of the gas and liquid phase data provides insight into the effects of mutual polarization of the molecule and solvent and screening of the ion's field. These findings reveal the roles of charge, local screening, and geometry in the design of tailored electric fields.

Electron interaction with DNA constituents in aqueous phase.

Electron driven chemistry of biomolecules in aqueous phase presents the realistic picture to study molecular processes. In this study we have investigated the interactions of electrons with the DNA constituents in their aqueous phase in order to obtain the quantities useful for DNA damage assessment. We have computed the inelastic mean free path (IMFP), mass stopping power (MSP) and absorbed dose (D) for the DNA constituents (Adenine, Cytosine, Guanine, Thymine and Uracil) in the aqueous medium from ionisation threshold to 5000 eV. We have modified complex optical potential formalism to include band gap of the systems to calculate inelastic cross sections which are used to estimate these entities. This is the maiden attempt to report these important quantities for the aqueous DNA constituents. We have compared our results with available data in gas and other phase and have observed explicable accord for IMFP and MSP. Since these are the first results of absorbed dose (D) for these compounds, we have explored present results vis-a-vis dose absorption in water.

On using an aerosol thermodynamic model to calculate aerosol acidity of coarse particles

Thermodynamic modeling is still the most widely used method to characterize aerosol acidity, a critical physicochemical property of atmospheric aerosols. However, it remains unclear whether gas-aerosol partitioning should be incorporated when thermodynamic models are employed to estimate the acidity of coarse particles. In this work, field measurements were conducted at a coastal city in northern China across three seasons, and covered wide ranges of temperature, relative humidity and NH3 concentrations. We examined the performance of different modes of ISORROPIA-II (a widely used aerosol thermodynamic model) in estimating aerosol acidity of coarse and fine particles. The M0 mode, which incorporates gas-phase data and runs the model in the forward mode, provided reasonable estimation of aerosol acidity for coarse and fine particles. Compared to M0, the M1 mode, which runs the model in the forward mode but does not include gas-phase data, may capture the general trend of aerosol acidity but underestimates pH for both coarse and fine particles; M2, which runs the model in the reverse mode, results in large errors in estimated aerosol pH for both coarse and fine particles and should not be used for aerosol acidity calculations. However, M1 significantly underestimates liquid water contents for both fine and coarse particles, while M2 provides reliable estimation of liquid water contents. In summary, our work highlights the importance of incorporating gas-aerosol partitioning when estimating coarse particle acidity, and thus may help improve our understanding of acidity of coarse particles.

Reaction nanoscopy of ion emission from sub-wavelength propanediol droplets

Abstract Droplets provide unique opportunities for the investigation of laser-induced surface chemistry. Chemical reactions on the surface of charged droplets are ubiquitous in nature and can provide critical insight into more efficient processes for industrial chemical production. Here, we demonstrate the application of the reaction nanoscopy technique to strong-field ionized nanodroplets of propanediol (PDO). The technique’s sensitivity to the near-field around the droplet allows for the in-situ characterization of the average droplet size and charge. The use of ultrashort laser pulses enables control of the amount of surface charge by the laser intensity. Moreover, we demonstrate the surface chemical sensitivity of reaction nanoscopy by comparing droplets of the isomers 1,2-PDO and 1,3-PDO in their ion emission and fragmentation channels. Referencing the ion yields to gas-phase data, we find an enhanced production of methyl cations from droplets of the 1,2-PDO isomer. Density functional theory simulations support that this enhancement is due to the alignment of 1,2-PDO molecules on the surface. The results pave the way towards spatio-temporal observations of charge dynamics and surface reactions on droplets.

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation.

Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.

A DFT Study on the Excited Electronic States of Cyanopolyynes: Benchmarks and Applications.

Highly unsaturated chain molecules are interesting due to their potential application as nanowires and occurrence in interstellar space. Here, we focus on predicting the electronic spectra of polyynic nitriles HC2m+1N (m = 0–13) and dinitriles NC2n+2N (n = 0–14). The results of time-dependent density functional theory (TD-DFT) calculations are compared with the available gas-phase and noble gas matrix experimental data. We assessed the performance of fifteen functionals and five basis sets for reproducing (i) vibrationless electronic excitation energies and (ii) vibrational frequencies in the singlet excited states. We found that the basis sets of at least triple-ζ quality were necessary to describe the long molecules with alternate single and triple bonds. Vibrational frequency scaling factors are similar for the ground and excited states. The benchmarked spectroscopic parameters were shown to be acceptably reproduced with adequately chosen functionals, in particular ωB97X, CAM-B3LYP, B3LYP, B971, and B972. Select functionals were applied to study the electronic excitation of molecules up to HC27N and C30N2. It is demonstrated that optical excitation leads to a shift from the polyyne- to a cumulene-like electronic structure.

Experimental Investigations and Numerical Assessment of Liquid Velocity Profiles and Turbulence for Single- and Two-phase Flow in a Constricted Vertical Pipe

In this work, the capabilities of state-of-the-art turbulence models are compared for a three-dimensional flow (3D) field within a constricted vertical pipe. The considered flow domain is a vertical pipe section with a baffle-shaped flow constriction which leads to the development of a jet flow through and a recirculation flow region behind the constriction. Different Reynolds-Averaged Navier-Stokes (RANS) and Large Eddy Simulation (LES) models were tested for single- and two-phase flow simulations. In the two-phase simulations, bubble-induced turbulence (BIT) was also considered by adding source terms in the k and ε/ω equations. The results are validated against experimental data. We employed hot-film anemometry (HFA) for liquid velocity measurement and combined it with ultrafast X-ray computed tomography (UFXCT), which provides gas phase data. Based on the local phase-indicator function obtained from the tomographic image data, we can correct HFA signals, which become corrupted by bubble contacts. We found that for single-phase flow all RANS models predict axial velocity well while radial velocity prediction is inadequate. LES models, however, achieve a better prediction of the latter. For two-phase flow, the axial component of the liquid velocity is well captured by all RANS models and the radial component of the liquid velocity is predicted better than for single-phase flow. In general, the computationally less costly RNG k-ε model performs similar to the SSG RSM model and can therefore be recommended for simulation of complex flow scenarios.

Structural insights into some sterically demanding heterocyclic β-diketones: Optimized molecular structure, optimized energy, stability and Mulliken charge distribution based on DFT analysis

Density functional theory is a quantum chemical theory based computational tool for theoretical analysis of molecular structures and electronic properties of organic compounds and new materials. The present synergistic investigation between experimental spectroscopic data and theoretical data is focused to gain structural insights and to study the optimized molecular structures, optimized energies, stabilities and Mulliken charge distribution based on DFT analysis of some sterically demanding heterocyclic β-diketones. The B3LYP functionals with 6-31G* basis set was used for calculations in gas phase as well as in polar and nonpolar solvents. The experimental spectroscopic data (1H and 13C NMR) of sterically demanding heterocyclic β-diketones were compared with the corresponding theoretical data (in gas phase and polar solvent). There was a synergy between experimental spectroscopic data and theoretical data of these organic compounds. The atomic charges at all the atoms were calculated to ascertain the electrophilic and nucleophilic centres in these compounds. Global reactivity descriptors have also been calculated from the energies of frontier molecular orbitals (HOMO-LUMO energy values). The presence of various groups such as -CH3, -CH2CH3, - C6H5 and p-ClC6H4- in these compounds provided an opportunity to examine the steric and electronic effects of these groups on the stability, optimized energy, Mulliken charge distribution and spectroscopic properties of these sterically demanding heterocyclic β-diketones.

Wavefunction-based quantum-chemical ab initio calculations for core electron binding energies of small open shell molecules

Core electron binding energies (CEBEs), i.e. ionization energies of 1s core orbitals, are calculated by means of wavefunction-based quantum-chemical ab initio methods for a series of small open-shell molecules containing first-row atoms. The calculations are performed in three steps: (a) Koopmans’ theorem, where the orbitals of the electronic ground state are used unchanged also for the ions, (b) Hartree–Fock or self consistent field (SCF) approximation in which the orbitals are allowed to relax after 1s ionization (ΔSCF), (c) dynamic correlation effects on top of SCF. For open-shell molecules 1s ionization leads to ions in several spin states, mostly to a pair of a triplet and a singlet state. In several cases one or both of these ionic states are only poorly described by a single-reference SCF wavefunction, therefore a multi-reference complete active space self consistent field (CAS-SCF) wavefunction is used instead. The correlation effects are evaluated by means of our multi-reference coupled electron pair approximation program. The accuracy of the calculated CEBEs is in the order of 0.1–0.4 eV. This is in agreement with experimental results for NO and O2. But there exist only very few gas phase data for CEBEs of open-shell molecules.

Thermodynamics of equilibrium alkali plasma. Simple and accurate analytical model for non-trivial case

Analytical equation of state for pure alkali metals (lithium, sodium, potassium, rubidium and cesium) in equilibrium gas phase is proposed. This equation has a simple form, generalizes the equation of state for a perfect gas and is universal for all alkali elements. It correctly reproduces the experimental data for the equilibrium gas phase over a wide range of pressures (up to ∼105 Pa) and temperatures (up to ∼3⋅103 K). On the basis of this equation of state, expressions for thermal and caloric coefficients as well as for other physical characteristics are obtained. The results of this study confirm feasibility of the principle of corresponding states in relation to the group of alkali elements.

Operando Fourier-transform infrared-mass spectrometry reactor cell setup for heterogeneous catalysis with glovebox transfer process to surface-chemical characterization.

We describe a new type of operando Fourier transform infrared (FTIR)-mass spectrometry setup for surface-chemical and reactivity characterization of heterogeneous catalysts. On the basis of a sophisticated all-quartz FTIR reactor cell, capable of operating between room temperature and 1000 °C in reactive gas atmospheres, the setup offers a unique opportunity to simultaneously collect and accordingly correlate FTIR surface-chemical adsorption data of the active catalyst state and FTIR gas phase data with complementary reactivity data obtained via mass spectrometry in situ. The full set of catalytic operation modes (recirculating static and flow reactor conditions) is accessible and can be complemented with a variety of temperature-programmed reaction modes or thermal desorption. Due to the unique transfer process involving a home-built portable glovebox to avoid air exposure, a variety of complementary quasi in situ characterization methods for the pre- and post-reaction catalyst states become accessible. We exemplify the capabilities for additional x-ray photoelectron spectroscopy characterization of surface-chemical states, highlighting the unique strength of combining adsorption, electronic structure, and reactivity data to gain detailed insight into the reactive state of a Cu/ZrO2 heterogeneous catalyst during methanol steam reforming operation.

Comparison of Reaction Field Schemes for Coupling Continuum Solvation Models with Wave Function Methods for Excitation Energies.

We address in this work the question to which extend reaction field schemes for correlated wave function methods give accurate excitation energies and, at the same time, physically consistent potential energy surfaces. The performance of the perturbation on energy (PTE), perturbation on energy and density (PTED), and post-SCF reaction field schemes is compared for the algebraic diagrammatic construction through second-order, ADC(2), as electronic structure and the conductor-like screening model COSMO as solvation model. The conditions on reaction field schemes to give physically consistent potential energies surfaces are discussed at the example of 4-(N,N-dimethylamino)benzonitrile, which is used as a test case to assess the artifacts introduced by state-specific contributions to the effective Hamiltonian. To evaluate the accuracy for excitation energies, we use two benchmark sets with data in gas phase and solution for ππ* and nπ* electronic transitions. The experimental solvatochromic shifts are compared to the corresponding calculated values at the COSMO-ADC(2) level with the PTE scheme within the frozen solvent approximation, PTED with the linear response (LR) and corrected linear response (cLR) and post-SCF with LR schemes and with the approximate coupled-cluster singles and doubles method CC2 combined with COSMO in the post-SCF (LR) scheme. The PTE scheme gives at the COSMO-ADC(2) level less accurate solvent shifts than the PTED(LR), PTED(cLR), and post-SCF(LR) schemes. The most accurate prediction of solvatochromism is obtained with the post-SCF(LR) scheme. In most cases, PTED(cLR) performs similar to post-SCF, although its nonlinear perturbative correction causes problems for potential energy surfaces.

Understanding the role of active site residues in CotB2 catalysis using a cluster model.

Terpene cyclases are responsible for the initial cyclization cascade in the multistep synthesis of a large number of terpenes. CotB2 is a diterpene cyclase from Streptomyces melanosporofaciens, which catalyzes the formation of cycloocta-9-en-7-ol, a precursor to the next-generation anti-inflammatory drug cyclooctatin. In this work, we present evidence for the significant role of the active site's residues in CotB2 on the reaction energetics using quantum mechanical calculations in an active site cluster model. The results revealed the significant effect of the active site residues on the relative electronic energy of the intermediates and transition state structures with respect to gas phase data. A detailed understanding of the role of the enzyme environment on the CotB2 reaction cascade can provide important information towards a biosynthetic strategy for cyclooctatin and the biomanufacturing of related terpene structures.

Large Amplitude Motions in Fruit Flavors: The Case of Alkyl Butyrates.

To accurately characterize the large amplitude motions and soft degrees of freedom of isolated molecules, sampling their conformational landscape by molecular mechanics and quantum chemical calculations may provide a valuable insight into the structure and dynamics. However, the resulting models need to be validated by a reliable experimental counterpart. For ethyl pentanoates, which belong to the family of fruit esters, benchmark calculations at different levels of theory showed that the C-C bond in proximity to the ester carbonyl group exhibits a large amplitude motion that is extremely sensitive to the choice of quantum chemical method and basis set. In such cases, insights from high-resolution molecular jet techniques are ideal to accurately identify and characterize soft degrees of freedom. Here, we report on the most abundant conformer of ethyl 2-ethyl butyrate using Fourier-transform microwave spectroscopy. We show that - unlike other structurally related pentanoates for which gas-phase and crystallographic data is available - ethyl 2-ethyl butyrate possesses a Cs symmetry plane under molecular jet conditions.

Testing the Robustness of Solution Force Fields for MD Simulations on Gaseous Protein Ions.

It is believed that electrosprayed proteins and protein complexes can retain solution-like conformations in the gas phase. However, the lack of high-resolution structure determination methods for gaseous protein ions implies that their properties remain poorly understood. Many practitioners tackle this difficulty by complementing mass spectrometry-based experiments with molecular dynamics (MD) simulations. It is a potential problem that the standard MD force fields used for this purpose (such as OPLS-AA/L and CHARMM) were optimized for solution conditions. The question whether these force fields produce meaningful gas-phase data has received surprisingly little attention. Standard force fields are overpolarized to account for an aqueous environment, i.e., atomic charges and intramolecular dipole moments are ∼20% larger than predicted by gas-phase ab initio methods. Here, we examined the implications of this overpolarization by conducting a series of MD simulations on electrosprayed proteins. Force fields were modified via a charge scaling factor (CSF), while ensuring that the net protein charge remained unchanged. CSF = 0.8 should roughly eliminate water-associated overpolarization. Gas-phase CHARMM simulations on myoglobin with CSF = 0.8 and with unmodified parameters (CSF = 1) yielded similar results, preserving a compact structure that was consistent with ion mobility experiments. Major structural changes caused by weakened charge-dipole and dipole-dipole contacts occurred only when lowering CSF to physically unreasonable values (0.5 and 0.1). Similar results were obtained in mobile-proton OPLS-AA/L simulations on the collision-induced dissociation of transthyretin. Our data support the view that gas-phase MD simulations with standard (solution) force fields are suitable for modeling gaseous protein ions in a semiquantitative manner. Although this is welcome news for the mass spectrometry community, it is hoped that dedicated gas-phase MD force fields will become available in the near future.

Combining Planar Laser-Induced Fluorescence with Stagnation Point Flows for Small Single-Crystal Model Catalysts: CO Oxidation on a Pd(100)

A stagnation flow reactor has been designed and characterized for both experimental and modeling studies of single-crystal model catalysts in heterogeneous catalysis. Using CO oxidation over a Pd(100) single crystal as a showcase, we have employed planar laser-induced fluorescence (PLIF) to visualize the CO2 distribution over the catalyst under reaction conditions and subsequently used the 2D spatially resolved gas phase data to characterize the stagnation flow reactor. From a comparison of the experimental data and the stagnation flow model, it was found that characteristic stagnation flow can be achieved with the reactor. Furthermore, the combined stagnation flow/PLIF/modeling approach makes it possible to estimate the turnover frequency (TOF) of the catalytic surface from the measured CO2 concentration profiles above the surface and to predict the CO2, CO and O2 concentrations at the surface under reaction conditions.

Gaseous [formula omitted] measurements for propane (R290) + trifluoroiodomethane (R13I1) system

An experimental study of the pressure–volume–temperature-composition (PVTx) properties in the gas phase for the R290 + R13I1 system was performed with an isochoric method. The measurements of R290 + R13I1 mixtures were conducted in the range of temperatures from 283.37 K to 353.29 K, pressures from 242.2 kPa to 1065.0 kPa, densities from 0.1091 mol dm−3 to 0.4133 mol dm−3, and compositions from 0.4502 to 0.8524 mol fraction of propane. The uncertainties in the present work were estimated to be within ±10 mK for temperature, ± 2.4 kPa for pressure, ± 0.1 mol% for mole composition and ±0.16% for density, respectively. On the basis of the experimental PVTx property data, a truncated virial equation of state was developed for the R290 + R13I1 system. This equation reproduces the experimental data in gas phase with relative deviation within ±0.23% in pressure and within ±0.25% in density.

Experimental Approach to the Study of Anharmonicity in the Infrared Spectrum of Pyrene from 14 to 723 K.

Quantifying the effect of anharmonicity on the infrared spectrum of large molecules such as polycyclic aromatic hydrocarbons (PAHs) at high temperatures is the focus of a number of theoretical and experimental studies, many of them motivated by astrophysical applications. We recorded the IR spectrum of pyrene C16H10 microcrystals embedded inKBr pellets over a wide range of temperatures (14-723 K) and studied the evolution of band positions, widths, and integrated intensities with temperature. We identified jumps for some of the spectral characteristics of some bands in the 423-473 K range. These were attributed to a change of phase from crystal to molten in condensed pyrene, which appears to affect more strongly bands involving large CH motions. Empirical anharmonicity factors that quantify the linear evolution of band positions and widths with temperature for values larger than ∼150-250 K, depending on the band, were retrieved from both phases and averaged to provide recommended values for these anharmonicity factors. The derived values were found to be consistent with available gas phase data. We conclude about the relevance of the methodology to produce data that can be compared with calculated anharmonic IR spectra and provide input for models that simulate the IR emission of astro-PAHs.