Single-photon ionization of SiC in the gas phase: experimental and ab initio characterization of SiC. Phys Chem Chem Phys 2023;25:23568-23578. [PMID: 37656136 DOI: 10.1039/d3cp02775a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

We report the first experimental observation of single-photon ionization transitions of the SiC radical between 8.0 and 11.0 eV performed on the DESIRS beamline at the SOLEIL synchrotron facility. The SiC radical, very difficult to synthesize in the gas phase, was produced through chemical reactions between CHx (x = 0-3) and SiHy (y = 0-3) in a continuous microwave discharge flow tube, the CHx and SiHy species being formed by successive hydrogen-atom abstractions induced by fluorine atoms on methane and silane, respectively. Mass-selected ion yield and photoelectron spectra were recorded as a function of photon energy using a double imaging photoelectron/photoion coincidence spectrometer. The photoelectron spectrum enables the first direct experimental determinations of the X+ 4Σ- ← X 3Π and 1+ 2Π ← X 3Π adiabatic ionization energies of SiC (8.978(10) eV and 10.216(24) eV, respectively). Calculated spectra based on Franck-Condon factors are compared with the experimental spectra. These spectra were obtained by solving the rovibrational Hamiltonian, using the potential energy curves calculated at the multireference single and double configuration interaction level with Davidson correction (MRCI + Q) and the aug-cc-pV5Z basis set. MRCI + Q calculations including the core and core-valence electron correlation were performed using the aug-cc-pCV6Z basis set to predict the spectroscopic properties of the six lowest electronic states of SiC+. Complete basis set extrapolations and relativistic energy corrections were also included in the determination of the energy differences characterizing the photoionization process. Using our experimental and theoretical results, we derived semi-experimental values for the five lowest ionization energies of SiC.

Dynamics of the isotope exchange reaction of D with H3 +, H2D+, and D2H. J Chem Phys 2021;154:084307. [PMID: 33639774 DOI: 10.1063/5.0038434]

We have measured the merged-beams rate coefficient for the titular isotope exchange reactions as a function of the relative collision energy in the range of ∼3 meV-10 eV. The results appear to scale with the number of available sites for deuteration. We have performed extensive theoretical calculations to characterize the zero-point energy corrected reaction path. Vibrationally adiabatic minimum energy paths were obtained using a combination of unrestricted quadratic configuration interaction of single and double excitations and internally contracted multireference configuration interaction calculations. The resulting barrier height, ranging from 68 meV to 89 meV, together with the various asymptotes that may be reached in the collision, was used in a classical over-the-barrier model. All competing endoergic reaction channels were taken into account using a flux reduction factor. This model reproduces all three experimental sets quite satisfactorily. In order to generate thermal rate coefficients down to 10 K, the internal excitation energy distribution of each H₃ ⁺ isotopologue is evaluated level by level using available line lists and accurate spectroscopic parameters. Tunneling is accounted for by a direct inclusion of the exact quantum tunneling probability in the evaluation of the cross section. We derive a thermal rate coefficient of <1×10^-12 cm³ s^-1 for temperatures below 44 K, 86 K, and 139 K for the reaction of D with H₃ ⁺, H₂D⁺, and D₂H⁺, respectively, with tunneling effects included. The derived thermal rate coefficients exceed the ring polymer molecular dynamics prediction of Bulut et al. [J. Phys. Chem. A 123, 8766 (2019)] at all temperatures.

Reactivity of Hydrated Hydroxide Anion Clusters with H and Rb: An ab Initio Study

We present a theoretical investigation of the hydrated hydroxide anion clusters, OH(H₂O)_n^-, and of the collisional complexes, H-OH(H₂O)_n^- and Rb-OH(H₂O)_n^- (with n = 1-4). The MP2 and CCSD(T) methods are used to calculate interaction energies, optimized geometries, and vertical detachment energies. Parts of the potential energy surfaces are explored with a focus on the autodetachment region. We point out the importance of diffuse functions to correctly describe the latter. We use our results to discuss the different water loss and electronic detachment channels, which are the main reaction routes at room temperature and below. In particular, we have considered a direct and an indirect process for the electronic detachment, depending on whether water loss follows or precedes the detachment of the excess electron. We use our results to discuss the implications for astrochemistry and hybrid trap experiments in the context of cold chemistry.

Experimental and theoretical investigations of H2O-Ar

We have used continuous-wave cavity ring-down spectroscopy to record the spectrum of H₂O-Ar in the 2OH excitation range of H₂O. 24 sub-bands have been observed. Their rotational structure (T_rot = 12 K) is analyzed and the lines are fitted separately for ortho and para species together with microwave and far infrared data from the literature, with a unitless standard deviation σ=0.98 and 1.31, respectively. Their vibrational analysis is supported by a theoretical input based on an intramolecular potential energy surface obtained through ab initio calculations and computation of the rotational energy of sub-states of the complex with the water monomer in excited vibrational states up to the first hexad. For the ground and (010) vibrational states, the theoretical results agree well with experimental energies and rotational constants in the literature. For the excited vibrational states of the first hexad, they guided the assignment of the observed sub-bands. The upper state vibrational predissociation lifetime is estimated to be 3 ns from observed spectral linewidths.

Ab initio study of the neutral and anionic alkali and alkaline earth hydroxides: Electronic structure and prospects for sympathetic cooling of OH. J Chem Phys 2017;146:194309. [PMID: 28527437 PMCID: PMC5438307 DOI: 10.1063/1.4983627]

We have performed a systematic ab initio study on alkali and alkaline earth hydroxide neutral (MOH) and anionic (MOH-) species where M = Li, Na, K, Rb, Cs or Be, Mg, Ca, Sr, Ba. The CCSD(T) method with extended basis sets and Dirac-Fock relativistic effective core potentials for the heavier atoms has been used to study their equilibrium geometries, interaction energies, electron affinities, electric dipole moment, and potential energy surfaces. All neutral and anionic species exhibit a linear shape with the exception of BeOH, BeOH-, and MgOH-, for which the equilibrium structure is found to be bent. Our analysis shows that the alkaline earth hydroxide anions are valence-bound whereas the alkali hydroxide anions are dipole bound. In the context of sympathetic cooling of OH- by collision with ultracold alkali and alkaline earth atoms, we investigate the 2D MOH- potential energy surfaces and the associative detachment reaction M + OH→- MOH + e-, which is the only energetically allowed reactive channel in the cold regime. We discuss the implication for the sympathetic cooling of OH- and conclude that Li and K are the best candidates for an ultracold buffer gas.

Histidine-Aromatic Interactions in Proteins and Protein-Ligand Complexes: Quantum Chemical Study of X-ray and Model Structures

His-aromatic complexes, with the His located above the aromatic plane, are stabilized by π-π, δ(+)-π and/or cation-π interactions according to whether the His is neutral or protonated and the partners are in stacked or T-shape conformations. Here we attempt to probe the relative strength of these interactions as a function of the geometry and protonation state, in gas phase, in water and protein-like environments (acetone, THF and CCl4), by means of quantum chemistry calculations performed up to second order of the Møller-Plesset pertubation theory. Two sets of conformations are considered for that purpose. The first set contains 89 interactions between His and Phe, Tyr, Trp, or Ade, observed in X-ray structures of proteins and protein-ligand complexes. The second set contains model structures obtained by moving an imidazolium/imidazole moiety above a benzene ring or an adenine moiety. We found that the protonated complexes are much more stable than the neutral ones in gas phase. This higher stability is due to the electrostatic contributions, the electron correlation contributions being equally important in the two forms. Thus, π-π and δ(+)-π interactions present essentially favorable electron correlation energy terms, whereas cation-π interactions feature in addition favorable electrostatic energies. The protonated complexes remain more stable than the neutral ones in protein-like environments, but the difference is drastically reduced. Furthermore, the T-shape conformation is undoubtedly more favorable than the stacked one in gas phase. This advantage decreases in the solvents, and the stacked conformation becomes even slightly more favorable in water. The frequent occurrence of His-aromatic interactions in catalytic sites, at protein-DNA or protein-ligand interfaces and in 3D domain swapping proteins emphasize their importance in biological processes.

Potential energy surface and bound states of the NH3-Ar and ND3-Ar complexes

A new, four-dimensional potential energy surface for the interaction of NH3 and ND3 with Ar is computed using the coupled-cluster method with single, double, and perturbative triple excitations and large basis sets. The umbrella motion of the ammonia molecule is explicitly taken into account. The bound states of both NH3-Ar and ND3-Ar are calculated on this potential for total angular momentum values from J = 0 to 10, with the inclusion of Coriolis interactions. The energies and splittings of the rovibrational levels are in excellent agreement with the extensive high-resolution spectroscopic data accumulated over the years in the infrared and microwave regions for both complexes, which demonstrates the quality of the potential energy surface.

Determination of the ground electronic state in transition metal halides: ZrF

The spectroscopy of the ZrF radical, produced by a laser ablation-molecular beam experimental setup, has been investigated for the first time using a two-color two-photon (1 + 1') REMPI scheme and time-of-flight (TOF) mass spectrometry detection. The region of intense bands 400-470 nm has been studied, based upon the first spectroscopic observations of the isovalent ZrCl radical by Carroll and Daly. The overall spectrum observed is complex. However, simultaneous and individual ion detection of the five naturally occurring isotopologues of ZrF has provided a crucial means of identifying band origins and characterization via the isotopic shift, δ(iso), of the numerous vibronic transitions recorded. Hence, five (0-0) transitions, of which only two were free of overlap with other transitions, have been identified. The most intense (0-0) transition at 23113 cm(-1) presented an unambiguously characteristic RQP rotational structure. From rotational contour simulations of the observed spectra, the nature of the ground electronic state is found to be unambiguously of (2)Δ symmetry, leading to the assignment of this band as (0-0) (2)Δ ← X(2)Δ at 23113 cm(-1). A set of transitions (1-0) (2)Δ ← X(2)Δ at 22105 cm(-1) and (2-0) (2)Φ ← X(2)Δ at 22944 cm(-1) involving the X(2)Δ state has also been identified and analyzed. Furthermore, a second series of transitions with lesser intensity has also been related to the long-lived metastable (4)Σ(-) state: (3-0) (4)Π(-1/2) ← (4)Σ(-) at 21801 cm(-1), (2-0) (4)Π(-1/2) ← (4)Σ(-) at 21285 cm(-1) and (2-0) (4)Σ(-) ← (4)Σ(-) at 23568 cm(-1). These spectroscopic assignments are supported by MRCI ab initio calculations, performed using the MOLPRO quantum chemistry package, and show that the low-lying excited states of the ZrF radical are the (4)Σ(-) and (4)Φ states lying at 2383 and 4179 cm(-1) respectively above the ground X(2)Δ state. The difference in the nature of ground state and ordering of the first electronic states with TiF (X(4)Φ)(2-4) and ZrCl,(5) respectively, is examined in terms of the ligand field theory (LFT)(7) applied to diatomic molecules. These results give a precise description of the electronic structure of the low lying electronic states of the ZrF transition metal radical.

Comparison of the experimental, semi-experimental and ab initio equilibrium structures of acetylene: influence of relativisitic effects and of the diagonal Born-Oppenheimer corrections

The equilibrium structure of acetylene (also named ethyne) has been reinvestigated to resolve the small discrepancies noted between different determinations. The size of the system as well as the large amount of available experimental data provides the quite unique opportunity to check the magnitude and relevance of various contributions to equilibrium structure as well as to verify the accuracy of experimental results. With respect to pure theoretical investigation, quantum-chemical calculations at the coupled-cluster level have been employed together with extrapolation to the basis set limit, consideration of higher excitations in the cluster operator, inclusion of core correlation effects as well as relativistic and diagonal Born-Oppenheimer corrections. In particular, it is found that the extrapolation to the complete basis set limit, the inclusion of higher excitations in the electronic-correlation treatment and the relativistic corrections are of the same order of magnitude. It also appears that a basis set as large as a core-valence quintuple-zeta set is required for accurately accounting for the inner-shell correlation contribution. From a pure experimental point of view, the equilibrium structure has been determined using very accurate rotational constants recently obtained by a "global analysis" (that is to say that all non-negligible interactions are explicitly included in the Hamiltonian matrix) of rovibrational spectra. Finally, a semi-experimental equilibrium structure (where the equilibrium rotational constants are obtained from the experimental ground state rotational constants and computed rovibrational corrections) has been obtained from the available experimental ground-state rotational constants for ten isotopic species corrected for computed vibrational corrections. Such a determination led to the revision of the ground-state rotational constants of two isotopologues, thus showing that structural determination is a good method to identify errors in experimental rotational constants. The three structures are found in a very good agreement, and our recommended values are r(CC) = 120.2958(7) pm and r(CH) = 106.164(1) pm.

Reactions of laser-ablated zirconium atoms within a supersonic expansion: insertion versus radical mechanism

In a laser ablation type microreactor followed by supersonic expansion, zirconium atoms have been reacted with methyl fluoride, CH(3)F (MeF), and mixtures of MeF and dimethylether, CH(3)-O-CH(3) (DME) seeded in He. With both mixtures, only a number of simple fluorinated products are formed, and they have been identified by one-photon ionization. All products can be linked to radical reactions either with F atoms, CH(3), or ZrF(1, 2, 3) radicals. No insertion products of the Grignard reagent type, F -Zr-CH(3) could be identified with or in the absence of DME. On the other hand, evidence has been found for the presence of organometallic compounds of the type ZrC(2)H(n=2, 4, 6), which could result from radical attack. Thus, even in conditions where intense solvation is at work, induced by clustering with polar DME molecules, which can act as stabilizing agents, a direct insertion mechanism into the C-F bond involving barrier suppression is not at work in our conditions. The reactivity due to radicals is very effective in this type of reactor, and the products that are efficiently formed can be quickly stabilized in the expansion. The radical attack supersedes, in the case of zirconium solvated by DME, the metastable mechanism with Zr(4d)(3)(5s)(1), that is certainly energetically impossible in the absence of strong reaction barrier suppression by a solvent. High level ab initio calculations performed at the CASPT2 level of theory are used for characterizing the electronic and geometric structure of the inserted products. They also reveal striking features of the reaction mechanism that support the absence of observation of inserted products within solvated clusters of zirconium.

A comparison of two methods for selecting vibrational configuration interaction spaces on a heptatomic system: ethylene oxide

Two recently developed methods for solving the molecular vibrational Schrodinger equation, namely, the parallel vibrational multiple window configuration interaction and the vibrational mean field configuration interaction, are presented and compared on the same potential energy surface of ethylene oxide, c-C(2)H(4)O. It is demonstrated on this heptatomic system with strong resonances that both approaches converge towards the same fundamental frequencies. This confirms their ability to tackle the vibrational problem of large molecules for which full configuration interaction calculations are not tractable.

Ab initio study of the ionization of the DNA bases: ionization potentials and excited states of the cations

The ionization of the four DNA bases is investigated by means of ab initio calculations. Accurate values of the gas-phase vertical and adiabatic ionization potentials (IP) are obtained at the MP2/6-31G(2d(0.8,alpha(d)),p) level of theory. The need of introducing extra polarization to the standard 6-31G(d,p) basis set is demonstrated by test calculations and an optimal value of alpha(d) = 0.1 is obtained. Ionization to electronically excited radical cations is also considered. The low-lying excited states of the cations are characterized for the first time. The topology of the corresponding potential energy surfaces is qualitatively described in terms of the stationary points (minima and saddle points) located on these surfaces. A conical intersection is characterized for the first time on the ground-state potential energy surface of all cations. It arises from the crossing of the adiabatic surfaces of the ground and first excited state at planar geometries. A nonplanar minimum is observed for the cytosine cation only. The geometry and electronic changes occurring along these surfaces are analyzed, leading to a comparison between the different nucleobase cations. The study of larger ionized systems related to DNA is rendered possible thanks to the optimized medium size basis set proposed in this work, as exemplified by the calculation of the IP of a stacked dimer of guanines.

Anharmonic force field ofcis- andtrans-formic acid from high-levelab initiocalculations, and analysis of resonance polyads

The quadratic, cubic, and semidiagonal quartic force fields of cis- and trans-formic acid have been calculated using three different levels of theory. They all give satisfactory results, including the one at the lowest level of theory which is the MP2 method employing a basis set of triple-zeta quality. The results are used to theoretically analyze resonance polyads, including the one involving the 4(1), 5(1), 6(1), 8(1), 7(1)9(1), and 9(2) vibrational states. A semiexperimental equilibrium structure is derived from experimental ground state rotational constants and rovibrational interaction parameters calculated from the ab initio force field. The ab initio structure calculated at the CCSD(T) level of theory using a basis set of quintuple-zeta quality is in excellent agreement with the semiexperimental structure.

Equilibrium Structure of Sulfuric Acid

The equilibrium structure of the more stable conformer of H2SO4, of C2 symmetry, has been calculated ab initio using the CCSD(T) method and taking into account the core correlation correction. The accuracy of this structure has been checked by comparing it to that of similar molecules and by estimating the effects of basis set enlargement and of diffuse functions. Furthermore, the quadratic, cubic, and quartic force fields have been calculated at the MP2 level of theory using a basis set of triple-zeta quality. The spectroscopic constants derived from the force field are in satisfactory agreement with the experimental ones. The resulting band origins are compared to literature infrared values, including those for overtone and combination bands. Normal modes of vibration are pictured. Using this force field, semiexperimental equilibrium rotational constants are determined which allows us to check the accuracy of the ab initio structure and to refine it using a mixed regression method.

Vinylidene-acetylene cation isomerization investigated by large scale ab initio calculations

The planar isomerization routes of the vinylidene/acetylene cation in the lowest electronic states are accurately examined for the first time, by using large scale MRCI and CCSDT calculations in a complementary way. They are compared with the similar calculations performed for the neutral ground state isomerization. An accurate value of the adiabatic ionization potential of vinylidene (11.26 eV) is predicted. The vinylidene cation lowest state, 1 2A1, follows an almost flat pathway with a shallow secondary minimum on the 1 2A' potential energy surface, before suddenly dropping to the stable acetylene cation ground state, X 2Piu. It is therefore confirmed to be completely unstable with respect to isomerization. The first excited state of the vinylidene cation, 1 2B1, which also correlates with the 2Piu ground state of acetylene cation along a 2A' isomerization route, has been studied at the same level of calculation. This 1 2B1 state is lying only 0.15 eV above the 1 2A1 state, and exhibits a potential energy barrier of 0.55 eV which explains the earlier assignment of this symmetry to the ground state of vinylidene cation. In addition to large scale calculations, a comprehensive description of the important steps of isomerization drawn from a very simple model involving monoconfigurational states is presented. In particular, the behavior of one unique orbital, namely, the 5a1 outer molecular orbital, is shown to completely govern the molecular geometry and energy evolution along the isomerization route of the ground state cation C2H2+.

The VMFCI method: a flexible tool for solving the molecular vibration problem

The present article introduces a general variational scheme to find approximate solutions of the spectral problem for the molecular vibration Hamiltonian. It is called the "vibrational mean field configuration interaction" (VMFCI) method, and consists in performing vibrational configuration interactions (VCI) for selected modes in the mean field of the others. The same partition of modes can be iterated until self-consistency, generalizing the vibrational self-consistent field (VSCF) method. As in contracted-mode methods, a hierarchy of partitions can be built to ultimately contract all the modes together. So, the VMFCI method extends the traditional variational approaches and can be included in existing vibrational codes based on the latter approaches. The flexibility and efficiency of this new method are demonstrated on several molecules of atmospheric interest.

Contribution of cation-pi interactions to the stability of protein-DNA complexes

Cation-pi interactions between an aromatic ring and a positive charge located above it have proven to be important in protein structures and biomolecule associations. Here, the role of these interactions at the interface of protein-DNA complexes is investigated, by means of ab initio quantum mechanics energy calculations and X-ray structure analyses. Ab initio energy calculations indicate that Na ions and DNA bases can form stable cation-pi complexes, whose binding strength strongly depends on the type of base, on the position of the Na ion, and whether the base is isolated or included in a double-stranded B-DNA. A survey of protein-DNA complex structures using appropriate geometrical criteria revealed cation-pi interactions in 71% of the complexes. More than half of the cation-pi pairs involve arginine residues, about one-third asparagine or glutamine residues that only carry a partial charge, and one-seventh lysine residues. The most frequently observed pair, which is also the most stable as monitored by ab initio energy calculations, is arginine- guanine. Arginine-adenine interactions are also favorable in general, although to a lesser extent, whereas those with thymine and cytosine are not. Our calculations show that the major contribution to cation-pi interactions with DNA bases is of electrostatic nature. These interactions often occur concomitantly with hydrogen bonds with adjacent bases; their strength is estimated to be from three to four times lower than that of hydrogen bonds. Finally, the role of cation-pi interactions in the stability and specificity of protein-DNA complexes is discussed.