Assignment of a perturbation in the FT-ICLAS spectrum of 12C2H2 around 12 709.5 cm−1

The vibrational state perturbing the J = 17 and 18 rotational states of the zero-order v ₁ + 3v ₃ state of ¹²C₂H₂ is assigned to the state with vibrational energy predicted at G _ν = 12 685.1 cm^?1 using the cluster model (El Idrissi, M. I., Liévin, J., Campargue, A. and Herman, M., 1999, J. chem. Phys., 110, 2074). The assignment is discussed also in terms of the very special pressure shift behaviour demonstrated previously for absorption lines reaching these levels (Herregodts, F., Hepp, M., Hurtmans, D., Vander Auwera, J. and Herman, M., 1999, J. chem. Phys., 111, 7961). The experimental information arising from a set-up newly running at ULB, called FT-ICLAS brings decisive information in the assignment process. This set-up is described briefly.     

Ernest Roy Davidson: A career of distinction

A simple method is described for the production of Fortrat diagrams during computation of rotational band contours. Assignments of rotational details in the 0-0 bands of the electronic transitions of phenol at 2750 å and aniline at 2938 å are made with the aid of Fortrat diagrams. Rotational features which may be common in type A and B bands in the electronic spectra of large asymmetric rotor molecules are discussed.     

The absorption spectrum of 12C2D2 in the 10000–12500 cm−1 spectral region

The absorption spectrum of dideuteroacetylene has been recorded by intracavity laser absorption spectroscopy (ICLAS) in the 10 200–12 500cm^?1 spectral region. Among 25 absorption bands of ¹²C₂D₂ rotationally analysed in this spectral region, 17 are newly observed. They include one II_u-Σ⁺ _g and thirteen Σ⁺ _u-Σ⁺ _g bands starting from the vibrational ground state and eleven hot bands from the V ₄ = 1 and V ₅ = 1 lower states. The rotational structure of two excited levels is affected by a strongly J-dependent interaction with a perturber which induces intensity transfer to extra lines. The coupling is identified as a I-resonance interaction with δ_u dark states and the vibrational assignment of the perturbers is discussed. Two Σ-Σ bands of the ¹²C¹³ CD₂ species, present in natural abundance in the sample, could also be identified and rotationally analysed. Most of the corresponding excited vibrational levels of ¹²C₂D₂ were unambiguously assigned using the polyad model [Herman, M., el idrissi, M. I., Pisarchik, A., Campargue, A., Gaillot, A.-C., Biennier, L., di lonardo, G. and Fusina, L., 1998, J. chem. Phys., 108, 1377] which allows vibrational energies and B _V rotational constants to be predicted. In particular the previously highlighted 1/244 anharmonic resonance is confirmed by energy and intensity features in several {(V ₁, V ₂, V ₃, V ₄ = 0, V ₅ = 0),(V ₁ ?1, V ₂ + 1, V ₃ V ₄ = 2, V ₅ = 0)} dyads. Significant deviations between predicted and experimental energy levels are observed for a few levels and discussed.     

Vibrational-rotational Einstein coefficients for HF/DF and HCl/DCl

The RKR potential functions have been combined with the best experimentally based dipole functions to calculate the Einstein coefficients for HF/DF and HCl/DCl. Calculations were done for the Δν = 1,2,3 transitions for a wide range of ν′ (?15 for HF/DF and ?8 for HCl/ DCl) and J′ (?25). Experimental tests involving comparison of P- and R-branch line intensities for high-J′ transitions of the HF (ν₁ → ν₀, ν₂ → ν₁ and ν₃ → ν₂ bands) and the Δν = 2 and Δν = 1 transitions for HF/DF and HCl are done to examine the reliability of the Einstein coefficients for the rotational and vibrational levels, respectively. Good agreement is obtained for HF/DF even for the high-J′ R-branch intensities which vary markedly with J′. But the data suggest improvement is needed in the dipole functions for HCl (and DCl).     

Singlet–triplet transitions in three-atomic molecules studied by time-dependent MCSCF and density functional theory

Singlet–triplet transition moments and phosphorescence lifetimes have been calculated for the three-atomic molecules HCN, O₃, H₂O, H₂S, GeF₂, GeCl₂ and GeBr₂ by time-dependent density functional theory (DFT) utilizing quadratic response functions in order to qualify DFT which recently has become available for studies of this kind [TUNELL, I., Rinkevivius, Z., VAHTRAS, O., SALEK, P., HELGAKER, T., and ÅGREN, H., 2003, J. chem. phys., 119, 11024]. Comparison with ab initio and experimental data indicates that DFT exhibit results of similar quality as explicitly correlated methods which indicates that it indeed is a viable approach for singlet–triplet transitions. O₃ provides an intriguing example in that a systematic investigation of the singlet–triplet transition moment of its Wulf band indicates a clear advantage of the DFT technique despite the multiconfigurational character of the electronic structure of this molecule. The electronic spin–spin coupling and the hyperfine nuclear coupling constants have also been calculated in order to further characterize the triplet state in the spectra of the investigated systems.     

Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules

The force constants and equilibrium geometry of water were calculated ab initio from Hartree-Fock self-consistent field wavefunctions using the force method, and a 53/31, a 73/3 + 1 and a 95/41 + 2 gaussian lobe basis set. The force method proved to be very economic and numerically accurate.

The calculated values agree well with the experimental ones. Especially good is the agreement for the interaction constant F_rα . Calculated force constants for the 95/41 + 2 basis are: F_r = 9·158 mdyn/å, F_α = 0·8513 mdyn/å, F_rα = +0·3007, F_rr = -0·1724; the experimental values from isotope frequencies are: F_r = 8·456, F_α = 0·762, F_rα = +0·246, F_rr = -0·100 mdyn/å. The agreement in the geometry is also good for the 95/41 + 2 basis r _e = 0·9518 å, α = 107·49°, and the experimental r _e = 0·9572 å, α = 104·52°.

Force constants were found to be quite insensitive to variation in the basis functions, all three sets giving almost the same result. On the other hand, the dipole moment derivative is very sensitive.     

The equilibrium geometry of the SC3H radical: an ab initio study

The SC₃H radical is known by experiment to have a linear equilibrium structure, but even rather high-level ab initio computations give a bent equilibrium geometry. A theoretical study of the SCCCH radical has been carried out in order to analyse the influence of several factors in the computed equilibrium structure. Quadratic configuration interaction QCISD(T) and restricted coupled cluster RCCSD(T) computations have been performed in combination with large basis sets. Spin-orbit effects have been taken into account through the Breit-Pauli Hamiltonian using multi-configuration SCF and configuration interaction wavefunctions. Our final results indicate that the equilibrium structure must be linear, in agreement with the experimental studies [McCarthy, M. C., Vrtilek, J. M., Gottlieb, C. A., Wang, W., and Thaddeus, P., 1994, Astrophys. J., 431, L127; Hirahara, Y., Ohshima, Y, and Endo, Y, 1994, J. chem. Phys., 101, 7342]. Both spin-orbit and electron correlation effects appear to be of comparable importance, but an adequate computation of the correlation energy has been much more difficult and has ultimately required basis set extrapolations.     

Reflections on Ernest Roy Davidson: the UW years 1962–1984

In the following research acetylation as an unexplored factor in the anomeric effect in carbohydrate chemistry has been examined. Crystallographic data for methyl glycosides and their acetates have been compared and discussed. Some of the methyl glycosides form hydrogen bonding with the participation of acetal oxygen atoms. This seems to have the most significant influence on the structural diagnostic parameters for anomeric effect.

Abbreviations: Me-α-Glc: methyl α-D-glucopyranoside; Me-β-Glc: methyl β-D-glucopyranoside; Me-α-Gal: methyl α-D-galactopyranoside; Me-β-Gal: methyl β-D-galactopyranoside; Me-α-Man: methyl α-D-mannopyranoside; Me-β-Man: methyl β-D-mannopyranoside; Ac-Me-α-Glc: methyl 2,3,4,6-tetra-O-acetyl-α-D-glucopyranoside; Ac-Me-β-Glc: methyl 2,3,4,6-tetra-O-acetyl-β-D-glucopyranoside; Ac-Me-α-Gal: methyl 2,3,4,6-tetra-O-acetyl-α-D-galactopyranoside; Ac-Me-β-Gal: methyl 2,3,4,6-tetra-O-acetyl-β-D-galactopyranoside; Ac-Me-α-Man: methyl 2,3,4,6-tetra-O-acetyl-α-D-mannopyranoside; Ac-Me-β-Man: methyl 2,3,4,6-tetra-O-acetyl-β-D-mannopyranoside; GIPAW (Gauge Including Projector Augmented Waves) calculations: a DFT based method used for calculating nuclear magnetic resonance parameters; CP/MAS NMR: cross-polarisation (CP) magic angle spinning (MAS) NMR spectroscopy; δ_ss: chemical shift in ¹³C CP/MAS NMR spectrum; δ_t: theoretical chemical shift: as derived from GIPAW DFT; dis: distorted multiplet in ¹H NMR spectrum.     

Chem1D: a software package for electronic structure calculations on one-dimensional systems

We present a preliminary version of a software package, Chem1D, that performs molecular orbital calculations on one-dimensional atoms and molecules using the unadorned Coulomb operator 1/|x₁ ? x₂|. We describe methods for computing the necessary one- and two-electron integrals and outline the overall structure of the package. We use Chem1D to perform calculations on a set of small molecules and show that one-dimensional chemistry differs in a number of interesting ways from three-dimensional chemistry.     

Spectrophotometric Studies of the Energy Consumed During Oxidative Degradation of D-Fructose

ABSTRACT

Mechanistic investigation of the oxidative degradation of d-fructose (D-Fruc) has been studied by spectrophotometric technique. Molecular mechanics (MM +) calculations suggest that the potential energy (PE/kcal mol^?1) of the d-fruc (opening structure) is at least three (3.71) times more stable than the PE of the cycling structure of the same matrix. The oxidation constant (K _ox) of the anionic form of the d-Fruc (Fruc-NaOH) is about seven times greater than that of the protonated form (Fruc-H₂SO₄). Therefore, the anionic form is more highly oxidizable than is the cationic form of this matrix. The limit of detection can be as low as 18 ppm (mg L^?1) of d-Fruc. This is about 60 times lower than the blood sugar level (BSL) or 100 times lower than that reported previously. The proposed procedure was applied successfully for the oxidation of D-Fruc in uni-fructose powder. The anionic form of D-Fruc (Fruc-NaOH) has the ability to store energy about 744.72 kJ g^?1 h at 608 nm in a condensed lightweight form. Kinetic parameters of the oxidative degradation of the anionic form of D-Fruc at different concentration were deduced. A number of models were used to evaluate the kinetic parameters. The mechanism of the degradation of D-Fruc is explained on the basis of kinetic parameters.     

Synthesis of deuterium-labelled halogen derivatives of L-tryptophan catalysed by tryptophanase

The isotopomers of halogen derivatives of l-tryptophan (l-Trp) (4′-F-, 7′-F-, 5′-Cl- and 7′-Br-l-Trp), specifically labelled with deuterium in α-position of the side chain, were obtained by enzymatic coupling of the corresponding halogenated derivatives of indole with S-methyl-l-cysteine in ²H₂O, catalysed by enzyme tryptophanase (EC 4.1.99.1). The positional deuterium enrichment of the resulting tryptophan derivatives was controlled using ¹H NMR. In accordance with the mechanism of the lyase reaction, a 100% deuterium labelling was observed in the α-position; the chemical yields were between 23 and 51%. Furthermore, β-F-l-alanine, synthesized from β-F-pyruvic acid by the l-alanine dehydrogenase reaction, has been tested as a coupling agent to obtain the halogenated deuterium-labelled derivatives of l-Trp. The chemical yield (～30%) corresponded to that as observed with S-methyl-l-cysteine but the deuterium label was only 63%, probably due to the use of a not completely deuterated incubation medium.     

Real figure of two-dimensional spin-echo NMR spectra for a homonuclear two-spin system in rotating solids

Two-dimensional (2D) spin-echo NMR experiments have been carried out on polycrystalline [2,3-¹³C₂]-alanine under magic-angle sample spinning (MAS) conditions, so that two unusual resonance lines emerged along the F₁ axis (Kuwahara, D., Nakai, T., Ashida, J., and Miyajima, S., 1999, Chem. Phys. Lett., 305, 35). To examine the spectral structure observed in the F₁ direction more closely the 2D NMR experiment was undertaken using a sufficiently small t_l increment, yielding many more resonance lines on a spectrum sliced along the F₁ axis. The line distribution had a very unique and interesting structure. To elucidate the line positions theoretically, the signal for the 2D spin-echo experiment performed with any t₁ increment was calculated analytically for a homonuclear two-spin-1/2 system undergoing MAS. Virtually six resonance lines (exactly 12 resonance lines) occurred on a spectrum sliced along the F₁ axis. In addition, it was demonstrated that the intensities of some resonance lines were largely dependent on the dipolar interaction.     

Effect of lone-pair orientation on nuclear spin couplings

The ² J _nh and ¹ J _ch couplings involving ¹⁵N and ¹³C in oximes have been studied theoretically by the finite perturbation method employing CNDO/2 and INDO wave functions. The couplings are found to be significantly influenced by the orientation of the nitrogen lone-pair orbital. It has been shown that the dihedral-angle dependence of vicinal H-H coupling in methylamine is also influenced by the orientation of the lone-pair on nitrogen, leading to deviations in the couplings predicted by a Karplus-type equation. The localized molecular orbitals and the hybridization and orientation of the nitrogen lone-pair in these molecules have been obtained by the Edmiston-Ruedenberg transformation of the semi-empirical SCF molecular orbitals.     

Computational studies on non-succinimide-mediated stereoinversion mechanism of aspartic acid residues assisted by phosphate

ABSTRACT

Although nearly all of the amino acids that constitute proteins are l-amino acids, d-amino acid residues in human proteins have been recently reported. d-amino acid residues cause a change in the three-dimensional structure of proteins, and d-aspartic acid (Asp) residues are considered to be one of the causes of age-related diseases. The stereoinversion of Asp residues in peptides and proteins is thought to proceed via a succinimide intermediate; however, it has been reported that stereoinversion can occur even under conditions where a succinimide intermediate cannot be formed. In order to elucidate the non-succinimide-mediated stereoinversion pathway, we investigated the stereoinversion of l-Asp to d-Asp catalysed by phosphate and estimated the activation barrier using B3LYP/6?31+G(d,p) density functional theory (DFT) calculations. For the DFT calculations, a model compound in which the Asp residue is capped with acetyl and methyl-amino groups on the N- and C-termini, respectively, was used. The calculated activation barrier was not excessively high for the stereoinversion to occur in vivo. Therefore, this stereoinversion mechanism may compete with the succinimide-mediated mechanism.     

An attempt to find a connection between the atomic distribution in liquid and solid metals

The distance of nearest neighbours r ₁, as well as the ‘reduced’ densities extrapolated to 0°k of liquid and solid metals are compared. Some liquids are close-packed at 0°k. With increasing temperature the degree of atomic misfit increases while r ₁ stays constant or even decreases, contrary to the behaviour in the solid phase.     

Thermodynamic properties of clathrates: I. The heat capacity and entropy of argon in the argon quinol clathrates

Measurements have been made of the heat capacity C_p from ～ 13°k to ～ 273°k of five clathrates of argon and β-quinol. The argon content ranged from ～ 20 per cent to ～ 80 per cent of the maximum possible amount. Over much of the temperature range studied, C_p proved to be a linear function of the argon content, but from 13°k to 20°k, and from 50°k to 100°k the relation between C_p and argon content is obscure, and may, in fact, be non-linear. Estimates have been made of the contribution to C_p made by a mole of argon in the temperature region where C_p is a linear function of composition, and these experimental values have been compared with those calculated according to the theory of J. H. van der Waals, which is based on the cell model of Lennard-Jones and Devonshire. The agreement between theory and experiment is satisfactory.     

Line Positions and Intensities of the ν1+ ν2+ 3ν3, ν2+ 4ν3, and 3ν1+ 2ν2Bands of Ozone

Using a Fourier transform spectrometer, we have recorded the spectra of ozone in the region of 4600 cm⁻¹, with a resolution of 0.008 cm⁻¹. The strongest absorption in this region is due to the ν₁+ ν₂+ 3ν₃band which is in Coriolis interaction with the ν₂+ 4ν₃band. We have been able to assign more than 1700 transitions for these two bands. To correctly reproduce the calculation of energy levels, it has been necessary to introduce the (320) state which strongly perturbs the (113) and (014) states through Coriolis- and Fermi-type resonances. Seventy transitions of the 3ν₁+ 2ν₂band have also been observed. The final fit on 926 energy levels withJ_max= 50 andK_max= 16 gives rms = 3.1 × 10⁻³cm⁻¹and provides a satisfactory agreement of calculated and observed upper levels for most of the transitions. The following values for band centers are derived: ν₀(ν₁+ ν₂+ 3ν₃) = 4658.950 cm⁻¹, ν₀(3ν₁+ 2ν₂) = 4643.821 cm⁻¹, and ν₀(ν₂+ 4ν₃) = 4632.888 cm⁻¹. Line intensities have been measured and fitted, leading to the determination of transition moment parameters for the two bands ν₁+ ν₂+ 3ν₃and ν₂+ 4ν₃. Using these parameters we have obtained the following estimations for the integrated band intensities,S_V(ν₁+ ν₂+ 3ν₃) = 8.84 × 10⁻²²,S_V(ν₂+ 4ν₃) = 1.70 × 10⁻²², andS_V(3ν₁+ 2ν₂) = 0.49 × 10⁻²²cm⁻¹/molecule cm⁻²at 296 K, which correspond to a cutoff of 10⁻²⁶cm⁻¹/molecule cm⁻².     

Free radicals in pyrimidines: E.S.R. of a γ-irradiated single crystal of 5-nitrouracil

Free radicals are observed in γ-irradiated single crystals of 5-nitrouracil with the unpaired electron showing hyperfine interaction with one nitrogen atom. The principal values of hyperfine coupling are A_x = 22·5 g, A_y = 25·2 g, and A_z = 40·0 g, and the principal values of the spectroscopic splitting factor are g_u = 2·0117, g_v = 2·0064 and g_w = 2·0027. The relationship of the directions of the corresponding principal axes to the molecular orientations show that the unpaired electron must be located in an sp ² orbital on either N₍₁₎ or N₍₅₎. Considerations of the mechanism of radical formation and comparison to radiation damage in other molecules make the N₍₁₎ location seem more probable. The π interaction of the nitro group on C₍₅₎ evidently prevents the formulation of free radicals with the unpaired electron on C₍₅₎. That carbon atom is the most common location of unpaired electron density in other pyrimidine free radicals.