Electron paramagnetic resonance characterization of gamma irradiation damage centers in powder of L-(+)-tartaric acid,N-acetyl-L-alanine and 1-methyl-L-histidine

The electron paramagnetic resonance (EPR) of γ-irradiated powders of l-(+)-tartaric acid, N-acetyl-l-alanine and 1-methyl-l-histidine were investigated at room temperature. Radiation damage centers are attributed to HOOCCH(OH)?(OH)COOH, CH₃?HCOOH and ?CH₂?HCOOH radicals. The spectra were computer-simulated. Hyperfine structure constants and g-values were determined for these three radicals. The unirradiated samples showed no EPR signal. Some spectroscopic properties and suggestions concerning the possible structure of the radicals are discussed in this paper.     

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.     

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.     

The effect of gamma radiation of amino acid derivatives in the solid state: an EPR study

The spectroscopic features of free radicals produced in gamma irradiation of the N-methyl-dl – alanine, N,N – dimethyl glycine hydrochloride and d – (+) – galactosamine hydrochloride were investigated at room temperature at the dose 15?kGy using EPR technique. The paramagnetic species observed in these compounds were identified as CH₃?HCOOH, ?HOH(CHOH)₃NH₂(CH)₂O, and (CH₃)₂N?HCOOH.HCl, respectively. A comparison with a new paramagnetic species recently observed and characterized in irradiated amino acids indicates that the new radical presented here has a similar structure. In this paper, we have also studied the stability of these compounds at room temperature after irradiation.     

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.     

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.     

Structural studies on banana oil,isoamyl acetate,by means of microwave spectroscopy and quantum chemical calculations

The rotational spectrum of isoamyl acetate, H₃C–COO–(CH₂)₂–CH(CH₃)₂, has been recorded and assigned using a molecular beam Fourier transform microwave (MB-FTMW) spectrometer in the frequency range of 3–26.5?GHz. One conformer has been observed. By comparing the spectroscopic data with the quantum chemical data, it was found that the conformer observed does not have C_s symmetry. The rotational and centrifugal distortion constants were determined. The barrier to internal rotation of the acetate methyl group was found to be 93.98?cm^?1. Due to the high number of the conformers, a systematic nomenclature will be presented.     

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.     

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.     

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.     

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.     

Millimeter-wave spectrum and internal rotation of 1-silylpropyne,CH3CCSiH3

Rotational transitions of CH₃CCSiH₃ have been observed in the millimeter-wave region using a computer-controlled source-frequency modulation spectrometer with a 1.8-m-long free space absorption cell. The observed spectrum clearly showed the effect of internal rotation with a small potential barrier. It has been analyzed by calculating the torsion-rotation energies on the basis of torsional wave functions obtained by diagonalizing the torsional part of the Hamiltonian. The least-squares analysis has yielded the rotational constant B = 2068.2817(4) MHz and a few centrifugal distortion constants. The barrier height to internal rotation has been determined to be 3.77(70) cm^?1 from the contour map of the standard deviation. Also, the A rotational constant of the silyl group around the symmetry axis has been estimated by fixing the A constant of the methyl group to the value of CH₃CCH.     

Potential energy surfaces for the Walden inversion reaction

A semi-empirical valence bond calculation of potential surfaces for the gas phase reaction between methyl bromide and chloride ion is described. The system is treated in a four participant electron approximation with precautions to include the effects of orthogonalization to the core electrons not involved in bond formation during reaction. The core is taken to include the methyl group as a single fragment whose valence state energy is determined by hybridization at the carbon atom. The qualitative features of the surface are confirmed by a less extensive CNDO calculation.

The lowest potential surface is found to have a central dip, the minimum energy being 0·98 ev below the energy of the reaction products when the C-Cl distance is 3·60 a.u., the C-Br distance 4·11 a.u., and the H-C-Br angle 86°. Analogy with classical two-body scattering suggests that at incident energies of less than 2 ev, the reaction cross section is of the order of 10(1 + 1/E) å ², where E, the initial energy of relative motion, is in ev.     

Application of Brønsted's principle of congruence to n-alkane mixtures

The second virial coefficient of normal methane, ¹²CH₄, has been compared with that of the corresponding deutero compound ¹²CD₄, as well as with the other isotopic molecule, ¹³CH₄. These measurements were performed by means of a differential apparatus over a range of temperature extending from 110°k up to 300°k.     

Simulation of hydrogen adsorption in carbon nanotubes

Computer simulations are reported of hydrogen adsorption in multi-walled carbon nanotubes (MWNTs) and single-walled carbon nanotubes (SWNTs). The gas-solid interaction was modelled both as pure dispersion forces and also with a hypothetical model for chemisorption introduced in a previous paper (CRACKNELL, R., F., 2001, Phys. Chem. chem. Phys., 3, 2091). A two-centre model for hydrogen was employed and the grand canonical Monte Carlo methodology was used throughout. Uptake of hydrogen in the internal space of a carbon nanotube is predicted to be lower than in the optimal graphitic nanofibre with slitlike pores (provided the gas-solid potential is consistent). Part of the difference arises from the assumption of pore surface area used in converting the raw simulation data to gravimetric adsorption; however, the majority of the differences can be attributed to the curvature of the pore. This reduces the uptake of hydrogen (on a gravimetric basis) in spite of deepening the potential minimum inside the pore associated with dispersion forces. It is concluded that for the uptake of hydrogen in SWNTs of 5–10% reported by Heben (DILLON, A. C., JONES, K. M., BEKKEDAHL, T. A., KIANG, C. H., BETHUNE, D. S., AND HEBEN, M. J., 1997, Nature, 386, 377), gas-solid forces other than dispersion forces are required and most of the adsorption must occur in the interstices between SWNTs.     

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.     

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.     

Structural Assignments of 1‐(β‐d‐Glucopyranosyl)‐1,2,3‐triazoles by 1H‐ and 13C‐NMR Study

The ¹H‐ and ¹³C‐NMR spectra of 1‐β‐d‐glucopyranosyl‐1,2,3‐triazole‐4,5‐dimethyl carboxylate, 1‐β‐d‐glucopyranosyl‐1,2,3‐triazole‐4,5‐dicarboxamide, ‐dialkylcarboxamide‐N‐nucleosides 4–18, and 6‐amino‐4H‐1‐(1‐β‐d‐glucopyranosyl)‐8‐hydroxy‐1,2,3‐triazolo[4,5‐e][1,3]‐diazepin‐4‐one 19 had been studied. Resonance signals and anomeric configurations were assigned by homo‐ and heteronuclear two dimensional methods (DQF‐COSY, HSQC, HMBC, HMQC, ROESY).     

Charged hard dumbbell in the binding mean-spherical approximation

A simple model for charged hard dumbbell is proposed in the binding mean-spherical approximation (BIMSA). The thermodynamic properties are analytical solutions of the unique screening parameter Γ^B with full association. Critical point and vapour-liquid coexistence curve are identical to those of Kalyuzhnyi, Yu. V., 1998, Molec. Phys., 94, 735, where a site-site integral equation has to be solved. Substituting Γ without association for Γ^B, the BIMSA reduces to the simple interpolation scheme (SIS). A simple interpolation between the SIS and the BIMSA is proposed: this gives the critical point (T_c? = 0.0525, p?_c = 0.0640) which, for the time being, is the closest to the computer simulation results. Similarity between the charged hard dumbbell and the restricted primitive model of electrolyte is also addressed.     

Virial coefficients and equations of state for mixtures of hard discs,hard spheres and hard hyperspheres

The composition-independent virial coefficients of a d-dimensional binary mixture of (additive) hard hyperspheres following from a recent proposal for the equation of state of the mixture (Santos, A., Yuste, S. B., and López de Haro, M., 1999, Molec. Phys., 96, 1) are examined. Good agreement between theoretical estimates and available exact or numerical results is found for d = 2, 3, 4 and 5, except for mixtures whose components are very disparate in size. A slight modification that remedies this deficiency is introduced and the resummation of the associated virial series is carried out, leading to a new proposal for the equation of state. The case of binary hard sphere mixtures (d = 3) is analysed in some detail.