Calculated properties of the active site complex of oxidized rubredoxins

The active site of rubredoxins, the simplest class of iron-sulfur, electron-transfer proteins consists of a single Fe atom surrounded by a distorted tetrahedral array of four cysteine sulfur atoms. With the aid of a newly formulated computer program, we have calculated the electric field gradient at the Fe⁵⁷ nucleus, the resultant quadrupole splitting (ΔE _Q) and the isotropic and anisotropic parts of the hyperfine interaction between the Fe nuclear spin and the net electron spin in the sextet ground state for ten conformational variations of the active site complex. For each conformer we used an electron distribution obtained from an Iterated Extended Huckel Theory (IEHT) molecular orbital calculation. Comparison of calculated and experimental results of (ΔE _Q) obtained from Mossbauer resonance spectra indicated that a number of conformers have field gradient values in excellent agreement with experiment. Good agreement with experiment was also found for the calculated hyperfine coupling constant. In this interaction, the isotropic contribution is dominant while the anisotropic contribution is more symmetry dependent. Since a single average experimental value is observed, hyperfine interaction in this system is not a very sensitive probe of active site conformation.     

Cross sections and rate coefficients for electronic excitation of the triplet states of the hydrogen molecule in different vibrational levels

Cross sections for the excitation of the triplet state of H₂ from different vibrational levels of the ground electronic state have been calculated by using the Gryzinski approximation. The results for the ground vibrational level are in satisfactory agreement with the corresponding values obtained by the quantum mechanical close coupling method. The calculated cross sections have been used to generate rate coefficients for the excitation of the triplet states by using a self-consistent electron energy distribution function, obtained by numerical integration of the Boltzmann equation. The results show a strong increase of the different rate coefficients with increasing the vibrational quantum number.     

Large configuration interaction calculations of nuclear spin-spin coupling constants: III. Vibrational effects in ammonia

Large configuration interaction calculations of the proton—proton coupling constant for several geometrical configurations of the ammonia molecules are reported. The analytical expressions for the energy surface and the coupling constant as functions of two cartesian displacement coordinates are fitted to the calculated values. The potential is used for the calculation of the vibrational wavefunctions for ¹⁵NH₃ and ¹⁵ND₃ species and the vibrational averaging of the coupling constant is carried out using these functions. Though the value of the coupling constants shows a very strong geometry dependence, the vibrational corrections are found to be small. A possible correlation of the proton—proton coupling constant with an angular parameter in the NH₂ group in RNH₂ compounds is indicated.     

Non-condon scheme of radiationless transitions for the morse oscillator model

The non-adiabatic coupling matrix elements responsible for radiationless deactivation of an electronically excited molecule are calculated without invoking the Condon approximation. Assuming the Morse potential surfaces for vibrational motion along the local and totally symmetric normal coordinates, the vibronic part of the radiationless rate constant is calculated. It is shown that the rate constant in the non-Condon scheme exceeds that obtained in the Condon approximation by about two orders of magnitude. The calculated dependence of the radiationless rate constant on the energy gap is in good agreement with the experimentally observed energy gap law for intersystem crossing T₁ → S₀ rate constants in aromatic hydrocarbons.     

Structure and electron paramagnetic resonance parameters of the manganese site of concanavalin A studied by density functional methods

The EPR parameters of the manganese site in the saccharide-binding protein concanavalin A have been studied by density functional methods, with an emphasis on metal (⁵⁵Mn) and ligand (¹H and ¹⁷O) hyperfine couplings, in comparison with high-field EPR and ENDOR data. Results for gradient-corrected and hybrid functionals with different exact-exchange admixture have been compared with experiment for the ⁵⁵Mn and the ¹H ligand hyperfine coupling and have been predicted for ¹⁷O hyperfine coupling based on comparison with experiment for the related [Mn(H₂O)₆]²⁺. Appreciable exact-exchange admixture in the hybrid functional is needed to obtain an adequate spin-density distribution and thus near-quantitative agreement with experimental EPR parameters. The common use of experimental proton hyperfine coupling tensors together with the point-dipole approximation for determination of bond lengths is evaluated by explicit calculations.     

On the excess-energy dependence of radiationless decay rate constants

The results of calculations of the dependence of the radiationless rate constant on the excess of excitation energy within the two-electronic states model under the weak coupling and statistical limits are presented. It is assumed that the exact molecular states for a given electronic configuration are global in character containing equal contributions from all degenerated vibrational levels at a given excitation energy due to intramolecular vibrational relaxation (IVR). The results of calculations indicate an important role of the low-frequency vibrational modes, the potential energy surfaces of which cross between the two electronic states involved into the radiationless process. The sharp increase of the rate constant is predicted for the excitation energy below the diabatic crossing point, followed by saturation at higher energies. The calculated rate constants for the T₁→S₀ intersystem crossing in pyrazine and benzene are in good agreement with experimental observations. Some comments concerning the “channel-three” phenomenon in benzene are presented.     

Optical band shape for the A1gEu transition in D4h symmetry: Eu×(β1g+β2g)

The optical band shape for the A_1gE_u transition in D_4h symmetry has been calculated quantum mechanically. It is shown that the band shape for moderately strong coupling with two vibrational modes has a doubly peaked structure even if the two coupling constants are different and the two vibrations have different frequencies. The calculation is compared with experiment and qualitative agreement is found.     

Ab initio configuration interaction study of the structure and magnetic properties of radicals and radical ions derived from group 13–15 trihydrides

The structures, characteristic vibrations and magnetic properties of two isoelectronic series of radicals and radical ions derived from group 13–15 trihydrides have been investigated by post-Hartree-Fock theoretical techniques. Møller-Plesset perturbation theory based on an unrestricted Hartree-Fock determinant has been employed to determine the structures and vibrational frequencies in the 9-electron series, BH⁻₃, CH₃, and NH⁺₃. These species are found to be planar. Spin density distributions and ionization energetics have been estimated using a variational configuration interaction procedure. A positive electron affinity for BH₃ has not been demonstrated. The effect of out-of-plane vibrations on the hyperfine coupling constants is determined at a similar level of theory. In the 17-electron series AlH⁻₃, SiH₃, and PH⁺₃, pyramidal structures are found by using and extended split-valence basis at the SCF level. The computed harmonic force field suggests that a tentative assignment of a matrix isolated infrared spectrum to SiH₃ is incorrect. This conclusion is reinforced by calculation of the vibrational intensity patterns. Hyperfine interaction tensors computed at the optimized geometries from the UHF wavefunction with a more complete polarized double-zeta basis set are in accord with experiment. Vibrational effects are estimated by averaging the UHF spin density over an energy surface determined by second-order perturbation theory. Corrections due to vibrations are smaller than in the carbon series and single-point configuration interaction calculations confirm the reliability of the UHF spin densities.     

An ab initio potential energy surface and spectroscopic constants for the XΣg state of NO2

A three-dimensional potential energy function has been calculated for the X¹Σ⁺_g state of NO⁺₂ from ab initio MRD-CI data. With this PE function, converged vibrational calculations have also been performed for ten vibrational states, with the aid of a computer program developed in the present work for this purpose. The calculated harmonic frequencies, vibrational term values and rotational constants are in good agreement with experimental data.     

Vibrational frequency shifts of free to complexed PF3: Tetrakis(trifluorophosphine)-nickel

The vibrational frequencies of Ni(PF₃)₄ are studied. Frequency shifts from free to complexed PF₃ are calculated on the basis of kinematic coupling. The results are compared with experimental data from literature. Many of the general trends in the observed frequency shifts are found to be in qualitative agreement with the theory, but several quantitative discrepancies remain.     

LIF measurement of the vibrational dependence of the N2(B 3Π g ) hyperfine splitting parameters

From very high resolution (8 MHz FWHM) LIF measurements, the hyperfine coupling constants of N₂(A ³Σ _u ⁺ ) and N₂(B ³Π _g ) have been obtained for three pairs of vibrational quantum numbersv′,v″. TheA-state constants are in very good agreement with accurate literature data. The vibrational dependence of some of theB-state constants is found to be much more pronounced. This is qualitatively explained in terms of the electronic structure of the two states.     

Experimental determination of level shift and broadening by predissociation of the B3Π0· state of ICl

From the semiclassical analysis of the coupling between discrete molecular levels and continuum levels simple relations for the level shift and the level broadening are known. Laser spectroscopy on the transition is B³Π₀·?X¹Σ⁺ is applied to demonstrate the overall validity of these relations in the rotational ladder of the vibrational state υ′ = 3 of B³Π₀·. Deviations for low rotational quantum numbers might be attributed to the still unresolved hyperfine structure and the possible hyperfine predissociation and for very large rotational quantum numbers to the distortion through a coupling with a second continuum.     

An INDO investigation of the electronic structure and hyperfine coupling constants of the radicals HBO−, HCO and HCN−

The equilibrium geometry and hyperfine coupling constants in the isoelectronic radicals HBO^–, HCO and HCN^– have been calculated using the INDO method. The calculated coupling constants are in reasonable agreement with experiment for these -radicals, provided the geometry is optimised in the calculations.     

Fully converged sudden rotation total integral cross sections for 4He + H2 (ν = 0, j = 0) → 4He + H2 (ν′ = 1, j′)

Total integral cross sections for ⁴He + H₂ (ν = 0, j = 0) → ⁴He + H₂ (ν′ = 1, j′ = 0, 2) have been calculated in the total energy range 1.2 to 5.5 eV, according to a quantal sudden approximation for the H₂ rotational degrees of freedom and a close coupling expansion of the vibrational degree of freedom. Convergence of the above cross sections is investigated by employing four vibration basis sets in the close coupling calculations, i.e., ν = 0,1, ν = 0,1, 2, ν = 0, 1, 2, 3 and ν = 0, 1, 2, 3, 4. Between 4.2 and 5.5 eV calculations were done with three vibration basis sets; ν = 0.–4, ν = 0–5, and ν = 0–6. It is found that at least four vibrational basis functions are needed to converge (to within 5–10%) these cross sections in the above energy range. Comparison of breathing sphere calculations and summed sudden rotation results shows good agreement for the (weakly anisotropic) Mies-Krauss potential. However, as expected the former results underestimate the vibrational 0 → 1 total integral cross sections.     

Dissociative excitation of water by metastable argon

The reaction Ar(²P_2,0) + H₂O → Ar + H + OH(A²Σ⁺)was studied in crossed molecular beams by observing the luminescence from OH(A²Σ⁺). No significant dependence of the spectrum on collision energy was found over the 22–52 meV region. Spectral simulation was used to obtain the OH(A) vibrational distribution and rotational temperature, assuming a Boltzmann rotational distribution. Since predissociation is known to strongly affect the rovibrational distribution, the individual rotational state lifetimes were included in the simulation program and were used to obtain the average vibrational state lifetimes. Excellent agreement with experiment was obtained for vibrational population ratios N₀/N₁/N₂ of 1.00/ 0.40/0.013 and a rotational temperature of 4000 K. Correction for the different average vibrational lifetimes gave formation rate ratios P₀/P₁/P₂ of 1.00/0.49/0.25. The differences between these results and those from flowing afterglow studies on the same system are discussed. Three reaction mechanisms are considered, and the vibrational prior distributions are calculated from a simple density-of-states model. Only fair agreement with experiment is obtained. The best agreement for the mechanisms giving OH(A) in two 2-body dissociation steps is obtained by assuming 1.0 eV of internal energy remains in the second step. The OH(A) vibrational population distribution of the present work is similar to that found in the photolysis of H₂O at 122 nm, where there is 1.10 eV of excess internal energy.     

SCF MO INDO calculation of anisotropie hyperfine coupling tensors for σ-type radicals

The anisotropic hyperfine coupling tensors for some -type radicals (HCO, FCO, NO₂, CO ₂ ^– , CN, phenyl, vinyl) were calculated. The calculation was performed with an all-valence-electron approximate open-shell MO method using the INDO approximation and with the dipolar integrals evaluated over Slater-type AO's. The diagonalyzed tensors were in reasonable agreement with the available data of experiment.     

Theoretical investigation of the isomers photolysis reaction for chlorine nitrate

For the reactant ClONO₂ the equilibrium geometry and energy have been calculated by using various density functional (DFT) theory methods. The harmonic vibrational frequencies were computed using the B3LYP method for the ground state of the reactant; the results were in good agreement with those of the experiment. It was shown that the DFT methods were superior to other ab initio methods in optimizing geometry and predicting vibrational frequencies. In the process of forming the products from the dissociation reactions of ClONO₂, the results indicated it undergoes the TS₂, but not the TS₁ transition state. According to the relative energies of various species, the potential energy surface reflected intuitively the mechanisms of these dissociation reactions. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 44–50, 2003     

The isomers of ionized ethane

The previously reported ²A_g, ²A_1g, and ²B_g states of ionized ethane are characterized at several levels of theory. The diborane-like ²A_g state, which gives rise to the observed ESR spectrum, is predicted by SCF and CCD calculations not to exist in a separate minimum from the ²A_1g state formed by ionization of the C(SINGLE BOND)C bond. However, as reported by Lunell and Huang, second-order Moller-Plesset theory places the ²A_g lowest, provided polarization functions are included on carbon. QCISD theory predicts that both A states correspond to potential energy minima, but places the long-bond ²A_1g state lower, at least with moderately large basis sets. F orbitals on carbon stabilize the diborane structure more than the long-bond one. When a potential energy surface is generated for a series of fixed C(SINGLE BOND)C bond lengths by optimizing all variables except for the C(SINGLE BOND)C bond length with MP2 theory and calculating the energy with QCISD(T), the ²A_g state is predicted to be the lowest energy state with the ²A_1g state 1.83 kJ/mol above it. The two A states are predicted to be separated by a barrier 2.79 kJ/mol above the lower state. This barrier is above the zero-point energy in the C(SINGLE BOND)C stretch for the lower state but below the ZPE for this stretch in the upper state, which is therefore predicted not to exist as a stable species. A single quantum of vibrational excitation in the low frequency C(SINGLE BOND)C stretch is predicted to yield an ion with a poorly defined C(SINGLE BOND)C bond length. The highest levels of theory employed give poor agreement with the experimental hyperfine coupling constants. The discrepancy could either be due to neglect of vibrational effects, to poor inherent accuracy of the calculation, as one author has concluded, or to compression of the ion by the matrix as suggested by another. The ²B_g state is found to be higher in energy than the A states at all theoretical levels and is predicted to have a large (160.2–177.4 G) hyperfine coupling from four hydrogens. The transition state for simultaneous exchange of two hydrogen atoms between the carbons by a diborane structure is predicted to lie above the lowest energy fragmentation threshold, in agreement with experiment. © 1996 by John Wiley & Sons, Inc.     

Non-empirical calculations on the conformation and hyperfine structure of the silyl radical influence of vibrational effects

An ab-initio spin-restricted SCF and perturbative configuration interaction study of the silyl radical is presented. The vibrational dependence of isotropic coupling constants is investigated using double-zeta and double-zeta plus polarization basis sets. The calculations predict a nearly tetrahedral geometry for the radical with an inversion barrier of 5.85 kcal/mol. The vibrational treatment leads to coupling constants (α_Si = ?190.20 G;α_H = +5.03 G) in excellent agreement with experiment.     

Excited states of gaseous ions. V. The predissociation of the h2o+ ion

The B?² state of H₂O⁺ is predissociated twice. First, by the ã⁴B₁ state, giving OH⁺ + H fragments via spinorbit coupling interaction. Secondly, by a²A state, giving H ⁺ OH fragments via spin-orbit coupling and Coriolis interactions. A vibrational analysis of the photoelectron band of the B? state of H₂O⁺ and D₂O⁺ is carried out. This provides the vibrational frequencies of the H₂O⁺, D₂O⁺ and HDO⁺ ions, as well as a vibrational assignment of the peaks. The H₂O⁺ ion in its B?²B₂ state is found to have a OH bond length of 1.12 A and a valence angie of 78°.In order to describe the unimolecular fragmentation process, a distinction is introduced between the totally symmetric, optically active vibrational modes, and the antisymmetric ones which are coupled to the continuum. The former are supplied with photon or electron impact energy, but only the latter are chemically efficient. The dynamics of the dissociation process depends therefore on the couplings among normal modes. This is studied in the framework of two models. In Model 1, it is assumed that, as a result of the anharmonicity of the potential energy surface, only even overtones of the antisymmetric vibration are excited by Fermi resonance. In Model II, excitation of the odd overtones is provided by vibronic coupling. Model II is in better agreement with experiment than Model I. Calculated and experimental results have been compared on the following points: isotopic shift on the appearance potential of OH⁺ and OD⁺ ions, shapes of the photoionization curves, fragmentation pattern with 21 eV photons, presence of a unimolecular metastable transition, production of O⁺ ions. All the vibrational levels situated above the dissociation asymptote are totally predissociated. Autoionization is shown in this case to contribute only to the formation of molecular H₂O⁺ ions, and not to that of the OH⁺ fragments. For 21 eV electrons, the contribution due to direct ionization is calculated to represent about 25% of the total cross section, the rest being due to autoionization.