Structure of Pyridazine in the S1 State: Experiment and Theory

The molecular structure of pyridazine in the first electronically excited state (S₁) is deduced from the combined use of resonance‐enhanced two‐photon ionization and mass‐analyzed threshold ionization spectroscopic methods. The equation‐of‐motion coupled‐cluster single and double (EOM–CCSD) calculation gives the distorted planar geometry for the most stable structure of the S₁ pyridazine. The symmetry constraint of C_2v is relaxed to that of C_s, and consequently many in‐plane vibrational modes are found to be optically active in both S₁–S₀ and D₀–S₁ excitation spectra, being appropriately assigned from the comparison of their frequencies with ab initio values. This indicates that the S₁–S₀ excitation is partially localized, and provides an alternative explanation for the long‐standing spectroscopic puzzle in S₁ pyridazine.     

(Noble Gas)n-NC+ Molecular Ions in Noble Gas Matrices: Matrix Infrared Spectra and Electronic Structure Calculations

An investigation of pulsed-laser-ablated Zn, Cd and Hg metal atom reactions with HCN under excess argon during co-deposition with laser-ablated Hg atoms from a dental amalgam target also provided Hg emissions capable of photoionization of the CN photo-dissociation product. A new band at 1933.4 cm⁻¹ in the region of the CN and CN⁺ gas-phase fundamental absorptions that appeared upon annealing the matrix to 20 K after sample deposition, and disappeared upon UV photolysis is assigned to (Ar)_nCN⁺, our key finding. It is not possible to determine the n coefficient exactly, but structure calculations suggest that one, two, three or four argon atoms can solvate the CN⁺ cation in an argon matrix with C−N absorptions calculated (B3LYP) to be between 2317.2 and 2319.8 cm⁻¹. Similar bands were observed in solid krypton at 1920.5, in solid xenon at 1935.4 and in solid neon at 1947.8 cm⁻¹. H¹³CN reagent gave an 1892.3 absorption with shift instead, and a 12/13 isotopic frequency ratio–nearly the same as found for ¹³CN⁺ itself in the gas phase and in the argon matrix. The CN⁺ molecular ion serves as a useful infrared probe to examine Ng clusters. The following ion reactions are believed to occur here: the first step upon sample deposition is assisted by a focused pulsed YAG laser, and the second step occurs on sample annealing: (Ar)₂⁺+CN→Ar+CN⁺→(Ar)_nCN⁺.     

Theoretical Investigation of the OH.‐Initiated Oxidation of Benzaldehyde in the Troposphere

A mechanistic and kinetic study of the OH^.‐initiated oxidation of benzaldehyde is carried out using quantum chemical methods and classical transition state theory. We calculate the rate constant for this reaction within the temperature range of 200–350 K at atmospheric pressure. All possible hydrogen abstraction and OH^. addition channels are considered and branching ratios are obtained. Tunneling corrections are taken into account for abstraction channels, assuming unsymmetrical Eckart barriers. The aldehydic abstraction is by far the most important reaction channel within the entire range of temperatures studied, especially at room temperature and lower—the temperatures relevant to atmospheric chemistry. The relative importance of all the other possible channels increases slightly with temperature. Branching ratios show that addition at the ring and abstraction of an ortho hydrogen contribute about 1 % each at about 300 K, while the branching ratio for the main reaction decreases from 99 % at 200 K to 93 % at 350 K. The results are compared with available experimental measurements.     

Spin-orbit ab initio investigation of the photolysis of bromoiodomethane.

The photodissociation of bromoiodomethane has been investigated by spin-orbit ab initio calculations. The experimentally observed A- and B-bands and the corresponding photoproducts were assigned by multistate second-order multiconfigurational perturbation theory in conjunction with spin-orbit interaction through complete active space state interaction potential energy curves, vertical excitation energies, and oscillator strengths of low-lying excited states. The present conclusions with respect to the dissociation process in the B-band are different compared with those of previous studies. The reaction between the iso-CH(2)Br-I and iso-CH(2)I-Br species has also been studied. Finally, a set of stable excited states was identified for both isomers. These species might be of importance in the recombination process that follows the photodissociation in a solvent.     

Criteria for the elucidation of the pseudopericyclic character of the cyclization of (Z)-1,2,4,6-heptatetraene and its heterosubstituted analogues: magnetic properties and natural bond orbital analysis

The electrocyclization of heterosubstituted derivatives of (Z)-1,2,4,6-heptatetraene, (2Z)-2,4,5-hexatrien-1-imine and (2Z)-2,4,5-hexatrienal exhibit some features which suggest a pseudopericyclic mechanism. In order to examine this, a comprehensive study including the determination of magnetic properties to estimate aromaticity and an NBO analysis throughout the reaction path was conducted. The cyclization of 5oxo-2,4-pentadienal, a process of unequivocal pseudopericyclic nature, was studied for comparison. The results suggest that, although the lone electron pair on the heteroatom in the heptatetraene derivatives seemingly plays a crucial role in the reaction mechanism, it does not suffice to deprive the reaction from the essential features of a pericyclic disrotatory electrocyclization.     

How Frustrated Lewis Acid/Base Systems Pass through Transition‐State Regions: H2 Cleavage by [tBu3P/B(C6F5)3]

We investigate the transition‐state (TS) region of the potential energy surface (PES) of the reaction tBu₃P+H₂+B(C₆F₅)₃→tBu₃P‐H⁽⁺⁾+^(?)H?B(C₆F₅)₃ and the dynamics of the TS passage at room temperature. Owing to the conformational inertia of the phosphane???borane pocket involving heavy tBu₃P and B(C₆F₅)₃ species and features of the PES E(P???H, B???H | B???P) as a function of P???H, B???H, and B???P distances, a typical reactive scenario for this reaction is a trajectory that is trapped in the TS region for a period of time (about 350 fs on average across all calculated trajectories) in a quasi‐bound state (scattering resonance). The relationship between the timescale of the TS passage and the effective conformational inertia of the phosphane???borane pocket leads to a prediction that isotopically heavier Lewis base/Lewis acid pairs and normal counterparts could give measurably different reaction rates. Herein, the predicted quasi‐bound state could be verified in molecular collision experiments involving femtosecond spectroscopy.     

Semiconducting Clathrates Meet Gas Hydrates: Xe24[Sn136]

Semiconducting Group 14 clathrates are inorganic host–guest materials with a close structural relationship to gas hydrates. Here we utilize this inherent structural relationship to derive a new class of porous semiconductor materials: noble gas filled Group 14 clathrates (Ng_x[M₁₃₆], Ng=Ar, Kr, Xe and M=Si, Ge, Sn). We have carried out high‐level quantum chemical studies using periodic Local‐MP2 (LMP2) and dispersion‐corrected density functional methods (DFT‐B3LYP‐D3) to properly describe the dispersive host–guest interactions. The adsorption of noble gas atoms within clathrate‐II framework turned out to be energetically clearly favorable for several host–guest systems. For the energetically most favorable noble gas filled clathrate, Xe₂₄[Sn₁₃₆], the adsorption energy is ?52 kJ mol^?1 per guest atom at the LMP2/TZVPP level of theory, corresponding to ?9.2 kJ mol^?1 per framework Sn atom. Considering that a hypothetical guest‐free Sn clathrate‐II host framework is only 2.6 kJ mol^?1 per Sn atom less stable than diamond‐like α‐Sn, the stabilization resulting from the noble gas adsorption is very significant.     

A theoretical investigation of the gas-phase oxidation reaction of the saturated tert-butyl radical.

The radical-radical reaction mechanisms and dynamics of ground-state atomic oxygen [O(3P)] with the saturated tert-butyl radical (t-C4H9) are investigated using the density functional method and the complete basis set model. Two distinctive reaction pathways are predicted to be in competition: addition and abstraction. The barrierless addition of O(3P) to t-C4H9 leads to the formation of an energy-rich intermediate (OC4H9) on the lowest doublet potential energy surface, which undergoes subsequent direct elimination or isomerization-elimination leading to various products: C3H6O + CH3, iso-C4H8O + H, C3H7O + CH2, and iso-C4H8 + OH. The respective microscopic reaction processes examined with the aid of statistical calculations, predict that the major addition pathway is the formation of acetone (C3H6O) + CH3 through a low-barrier, single-step cleavage. For the direct, barrierless H-atom abstraction mechanism producing iso-C4H8 (isobutene) + OH, which was recently reported in gas-phase crossed-beam investigations, the reaction is described in terms of both an abstraction process (major) and a short-lived addition dynamic complex (minor).     

Structure and Stability of (NG)nCN3Be3+ Clusters and Comparison with (NG)BeY0/+

The noble gas binding ability of CN₃Be₃⁺ clusters was assessed both by ab intio and density functional studies. The global minimum structure of the CN₃Be₃⁺ cluster binds with four noble‐gas (NG) atoms, in which the Be atoms are acting as active centers. The electron transfer from the noble gas to the Be atom plays a key role in binding. The dissociation energy of the Be? NG bond gradually increases from He to Rn, maintaining the periodic trend. The HOMO–LUMO gap, an indicator for stability, gives additional insight into these NG‐bound clusters. The temperature at which the NG‐binding process is thermodynamically feasible was identified. In addition, we investigated the stability of two new neutral NG compounds, (NG)BeSe and (NG)BeTe, and found them to be suitable candidates to be detected experimentally such as (NG)BeO and (NG)BeS. The dissociation energies of the Be? NG bond in monocationic analogues of (NG)BeY (Y=O, S, Se, Te) were found to be larger than in the corresponding neutral counter‐parts. Finally, the higher the positive charge on the Be atoms, the higher the dissociation energy for the Be? NG bond becomes.     

Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes

Activation and reaction energies for four model systems capturing the essential physicochemical features of the hydrolysis of the peptide bond have been calculated at various level of theory, including the presumably accurate CCSD(T) calculations. The models studied covered a part of the spectrum encountered in biological systems: the hydrolysis in the absence of metal ions (represented by formamide and Ala–Ala) and the hydrolysis in the presence of one and two zinc(II) ions, mimicking the active sites of mono‐ and dizinc metallopeptidases, respectively (by using thermolysin and glutamate carboxypeptidase II as the model catalytic systems and formamide as the model substrate). The results obtained using CCSD(T)/def2‐TZVP and CCSD(T)/aug‐cc‐pVTZ calculations were used as the benchmark values to which the set of cheaper methods, such as (RI‐)DFT, (RI‐)MP2, and SCS‐MP2, were referenced. It was shown that deviations of 3–5 kcal mol^?1 (translating to 2–3 orders in reaction constants) with respect to the reference CCSD(T) barriers are frequently encountered for many correlated methods and most of studied DFT functionals. It has been concluded that from the set of wave‐function methods, both MP2 and SCS‐MP2 methods can be recommended for smaller models (measured by the mean absolute deviation of the activation barriers over the four systems studied), whereas among the popular DFT functionals, B3LYP and especially M06‐2X are likely to be reasonable choices for calculating the activation barriers of zinc metallopeptidases. Finally, with the model of glutamate carboxypeptidase II, issues related to the convergence of the calculated barriers with the size of the model system used as the representative of the enzyme active site were addressed. The intricacies related to system truncation are demonstrated, and suggest that the correlated wave‐function methods may suffer from problems, such as intramolecular BSSE, which make their usage for the larger system questionable. Altogether, the presented data should contribute to efforts to understand enzymatic catalysis more deeply and to gain control of the accuracy and deficiencies of the available theoretical methods and computational approaches.     

Electron Localization Dynamics in the Triplet Excited State of [Ru(bpy)3]2+ in Aqueous Solution

Hybrid DFT/classical molecular dynamics of the long‐lived triplet excited state of [Ru(bpy)₃]²⁺ (bpy=2,2′‐bipyridine) in aqueous solution is used to investigate the solvent‐mediated electron localization and dynamics in the triplet metal‐to‐ligand charge‐transfer (MLCT) state. Our studies reveal a solvent‐induced breaking of the coordination symmetry with consequent localization of the photoexcited electron on one or two bipyridine units for the entire length of our simulation, which amounts to several picoseconds. Frequent electronic “hops” between the ligands constituting the pair are observed with a characteristic time of approximately half a picosecond.     

Quantum chemical study of the reaction mechanism of ozone and methane with fluorine and chlorine atoms

Ab initio calculations of the potential energy surface for the F + O₃ and Cl + O₃ reactions have been performed using the G3 and G3MP2 methods, which optimize the geometry configuration of reactants, products, intermediates, and transition states. The results show that fluorine atoms react with ozone as violently as chlorine atoms. At the same time, we have studied the reaction mechanisms of F atoms and Cl atoms with methane. It is found that fluorine atoms prefer to react with methane and chlorine atoms with ozone when there is competition between ozone and methane. Therefore, we can reasonably explain why chlorine atoms play the main role of reactants depleting ozone, while the more active fluorine atoms deplete less ozone. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/qua.10119     

The gas-phase reaction between O3 and HO radical: a theoretical study.

We report a theoretical study on the reaction of ozone with hydroxyl radical, which is important in the chemistry of the atmosphere and in particular participates in stratospheric ozone destruction. The reaction is a complex process that involves, in the first stage, a pre-reactive hydrogen-bonded complex (C1), which is formed previous to two transition states (TS1 and TS2) involving the addition of the hydroxyl radical to ozone, and leads to the formation of HO4 polyoxide radical before the release of the products HO2 and O2. The reaction is computed to be exothermic by 42.72 kcal mol(-1), which compares quite well with the experimental estimate, and the energy barriers of TS1 and TS2 with respect to C1 are computed to be 1.80 and 2.26 kcal mol(-1) at 0 K. A kinetic study based on the variational transition state theory (VTST) predicts a rate constant, at 298 K, of 7.37 x 10(-14) cm3 molecule(-1) s(-1), compared to the experimentally recommended value of 7.25 x 10(-14) cm3 molecule(-1) s(-1).     

Ab initio static and molecular dynamics study of 4-styrylpyridine.

We report an in‐depth theoretical study of 4‐styrylpyridine in its singlet S₀ ground state. The geometries and the relative stabilities of the trans and cis isomers were investigated within density functional theory (DFT) as well as within Hartree–Fock (HF), second‐order Møller–Plesset (MP2), and coupled cluster (CC) theories. The DFT calculations were performed using the B3LYP and PBE functionals, with basis sets of different qualities, and gave results that are very consistent with each other. The molecular structure is thus predicted to be planar at the energy minimum, which is associated with the trans conformation, and to become markedly twisted at the minimum of higher energy, which is associated with the cis conformation. The results of the calculations performed with the post‐HF methods approach those obtained with the DFT methods, provided that the level of treatment of the electronic correlation is high enough and that sufficiently flexible basis sets are used. Calculations carried out within DFT also allowed the determination of the geometry and the energy of the molecule at the biradicaloid transition state associated with the thermal cis?trans isomerization and at the transition states associated with the enantiomerization of the cis isomer and with the rotations of the pyridinyl and phenyl groups in the trans and cis isomers. Car–Parrinello molecular dynamics simulations were also performed at 50, 150, and 300 K using the PBE functional. The studies allowed us to evidence the highly flexible nature of the molecule in both conformations. In particular, the trans isomer was found to exist mainly in a nonplanar form at finite temperatures, while the rotation of the pyridinyl ring in the cis isomer was incidentally observed to take place within ≈1 ps during the simulation carried out at 150 K on this isomer.