On the nature of the first excited states of the uranyl ion

Results of calculations on the uranylion using the LCAO MO Hartree—Fock—Slater method including relativistic effects are reported. The highest occupied molecular orbital is calculated to be σ_u, consisting predominantly of U 5f character. The σ_u orbital is the HOMO partly because of “pushing-from-below” by the U 6p orbital, but also as a result of the change in potential of the U 5f electrons with the uranium core elections brought about by relativistic contraction of the core electrons. This effect also determines the character of the first virtual levels (δ_u and Φ_u, respectively) in equatorial ligand fields.     

Watson-crick base pairs with thiocarbonyl groups: How sulfur changes the hydrogen bonds in DNA

We have theoretically analyzed mimics of Watson-Crick AT and GC base pairs in which N-H···O hydrogen bonds are replaced by N-H···S, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P level. The general effect of the above substitutions is an elongation and a slight weakening of the hydrogen bonds that hold together the base pairs. However, the precise effects depend on how many, and in particular, on which hydrogen bonds AT and GC are substituted.. Another purpose of this work is to clarify the relative importance of electrostatic attraction versus orbital interaction in the hydrogen bonds involved in the mimics, using a quantitative bond energy decomposition scheme. At variance with widespread believe, the orbital interaction component in these hydrogen bonds is found to contribute more than 40% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining attraction.      

A vibrational circular dichroism implementation within a Slater-type-orbital based density functional framework and its application to hexa- and hepta-helicenes

We describe the implementation of the rotational strengths for vibrational circular dichroism (VCD) in the Slater-type orbital based Amsterdam Density Functional (ADF) package. We show that our implementation, which makes use of analytical derivative techniques and London atomic orbitals, yields origin independent rotational strengths. The basis set dependence in the particular case of Slater-type basis functions is also discussed. It turns out that the triple zeta STO basis sets with one set of polarization functions (TZP) are adequate for VCD calculations. The origin- dependence of the atomic axial tensors is checked by a distributed origin gauge implementation. The distributed and common origin gauge implementations yield virtually identical atomic axial tensors with the Slater-type basis sets employed here, proving that our implementation yields origin independent rotational strengths. We verify the implementation for a set of benchmark molecules, for which the dependence of the VCD spectra on the particular choice of the exchange–correlation functional is studied. The pure functionals BP86 and OLYP show a particularly good performance. Then, we apply this approach to study the VCD spectra of hexa- and hepta- helicenes. In particular we focus on relationships between the sign of the rotational strengths of the two helicenes. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

A kinetic study of chlorine radical reactions with ketones by laser photolysis technique

Rate coefficients for reactions between Cl radicals and four ketones were determined at 294 ± 1 K with a relative rate method using a laser photolysis technique. The experiments were conducted in synthetic air in a flow system at atmospheric pressure. A mixture of Cl₂/ClONO₂ was photolyzed and the formation of NO₃ through the reaction Cl + ClONO₂ → Cl₂ + NO₃ was measured with and without ketones in the reaction mixture. The NO₃ radical concentration was measured by optical absorption using a diode laser as the light source. The rate coefficients for the Cl-ketone reactions could then be evaluated. The following rate coefficients were obtained (in units of cm³ molecule⁻¹ s⁻¹): cyclohexanone (7.00 ± 1.15) × 10⁻¹¹; cyclopentanone (4.76 ± 0.33) × 10⁻¹¹; acetone (1.69 ± 0.32) × 10⁻¹²; and 2,3-butanedione (7.62 ± 1.66) × 10⁻¹³. The accuracy of the method employed was tested by using the well-studied reaction between Cl and methane and a rate coefficient of (9.37 ± 1.04) × 10⁻¹⁴ cm³ molecule⁻¹ s⁻¹ was obtained, which is in good agreement with previous work. The errors are at the 95% confidence level. The results in this work indicate that a carbonyl group in a ketone lowers the reactivity towards α-hydrogen abstraction by Cl radicals, compared to the corresponding Cl-alkane reactions. © 1997 John Wiley & Sons, Inc. Int J Chem Kinet 29: 195–201, 1997.     

On the optimal mixing of the exchange energy and the electron-electron interaction part of the exchange-correlation energy

The optimal mixing coefficient C of the exchange energy E_x and the electron-electron interaction part of the exchange-correlation energy W¹_xc in the formula for the total exchange-correlation energy E_xc was expressed through the ratio of the kinetic T_c and potential W_c contributions to the correlation energy E_c. This expression can be derived from a Heavyside step function model of the dependence of W^λ_xc on the coupling parameter of the electron interaction λ. Values of T_c and W_c obtained from ab initio wave functions were used to estimate C for a number of atoms and molecules. A strong dependence of T_c, W_c, and C on the bond distance was demonstrated for the case of the H₂ molecule. T_c and C approach zero in the bond-dissociation limit; so for an electron-pair bond, the admixing of exact exchange to obtain an accurate E_xc is strongly dependent on the bond length and has to disappear for weak interaction/large bond distances. The potential of the exchange-correlation hole constructed for H₂ from an ab initio second-order density matrix was compared with its generalized gradient approximation (GGA). © 1996 John Wiley & Sons, Inc.     

Pulse radiolysis study of reactions of alkyl and alkylperoxy radicals originating from methyl tert-butyl ether in the gas phase

UV spectra and kinetics for the reactions of alkyl and alkylperoxy radicals from methyl tert-butyl ether (MTBE) were studied in 1 atm of SF₆ by the pulse radiolysis-UV absorption technique. UV spectra for the radical mixtures were quantified from 215 to 340 nm. At 240 nm. σ_R = (2.6 ± 0.4) × 10⁻¹⁸ cm² molecule⁻¹ and σ_RO2 = (4.1 ± 0.6) × 10⁻¹⁸ cm² molecule⁻¹ (base e). The rate constant for the self-reaction of the alkyl radicals is (2.5 ± 1.1) × 10⁻¹¹ cm³ molecule⁻¹ s⁻¹. The rate constants for reaction of the alkyl radicals with molecular oxygen and the alkylperoxy radicals with NO and NO₂ are (9.1 ± 1.5) × 10⁻¹³, (4.3 ± 1.6) × 10⁻¹² and (1.2 ± 0.3) × 10⁻¹¹ cm³ molecule⁻¹ s⁻¹, respectively. The rate constants given above refer to reaction at the tert-butyl side of the molecule.     

Coenzyme B induced coordination of coenzyme M via its thiol group to Ni(I) of F430 in active methyl-coenzyme M reductase

Methyl-coenzyme M reductase (MCR) catalyzes the reaction of methyl-coenzyme M (CH3-S-CoM) with coenzyme B (HS-CoB) to methane and CoM-S-S-CoB. At the active site, it contains the nickel porphinoid F430, which has to be in the Ni(I) oxidation state for the enzyme to be active. How the substrates interact with the active site Ni(I) has remained elusive. We report here that coenzyme M (HS-CoM), which is a reversible competitive inhibitor to methyl-coenzyme M, interacts with its thiol group with the Ni(I) and that for interaction the simultaneous presence of coenzyme B is required. The evidence is based on X-band continuous wave EPR and Q-band hyperfine sublevel correlation spectroscopy of MCR in the red2 state induced with 33S-labeled coenzyme M and unlabeled coenzyme B.     

Structural, optical, and photophysical properties of nickel(II) alkylthioporphyrins: insights from experimental and DFT/TDDFT studies

The ground- and excited-state properties of a Ni(II) porphyrin bearing peripheral alkylthio group, NiOMTP (OMTP = 2,3,7,8,12,13,17,18-octakis methylthio porphyrinate) have been investigated by steady-state and time-resolved absorption spectrometry and DFT/TDDFT theoretical methods. Several conformations corresponding to different deformations of the porphyrin core and to different orientations of the alkylthio groups have been theoretically explored. The nearly degenerate, purely ruffled D(2d) and hybrid (ruffled with a modest degree of saddling) D(2) conformations, both characterized by an up-down (ud) orientation of the vicinal methylthio groups are by far the preferred conformations in the "gas phase". In contrast to NiOEP, it is the orientation of the peripheral substituents rather than the type and degree of distortions of the porphyrin core that determines the stability of the NiOMTP conformers. The ground-state electronic absorption spectra of NiOMTP exhibit significant changes compared to its parent NiP and beta-alkylated analogues, such as NiOEP, resulting in a considerable red shift of the B and the Q bands, intensification and broadening of the Q band, and additional weak absorptions in the region between the Q and B bands. These spectral changes can be understood in terms of the electronic effects of the methylthio groups with nonplanar distortions of the porphyrin ring playing a very minor role. Transient absorption measurements with sub-picosecond resolution performed in toluene and TDDFT calculations reveal that following photoexcitation, NiOMTP deactivates by the pathway 1(pi,pi) --> 3(d(z2),d(x2-y2))--> ground state. The (d,d) state exhibits complex spectral evolution over ca. 8 ps, interpreted in terms of vibrational relaxation and cooling. The cold ligand-field excited state decays with a lifetime of 320 ps. At variance with the highly distorted nickel porphyrins but similar to the planar analogues, the (d,d) spectrum of NiOMTP has transient absorption bands immediately to the red of the bleaching of the ground-state Q and B bands.     

Improving numerical integration through basis set expansion

Calculations are presented to assess a theorem presented by S.F. Boys [(1969) Proc. R. Soc. A. 309:195], regarding the accuracy of numerical integration in quantum chemical calculations. The theorem states that the error due to numerical integration can be made proportional to the error due to basis set truncation, and thus goes to zero in the limit of a complete basis. We test this theorem on the hydrogen atom, showing that with a solution-spanning basis, the numerically exact orbital energy can indeed be calculated with a small number of integration points. Moreover, tests for H and H₂⁺ demonstrate that even when only a near-complete basis is employed, Boys Theorem can significantly reduce integration error. However, for other systems, like the oxygen atom and the CO₂ molecule, the theorem yields no advantage for some occupied orbitals. It is concluded that the theorem would be most useful for calculations that demand large basis sets.