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.     

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.     

High pressure: a tool to improve the enzymatic production of glycosides

Naringinase, an enzyme complex that expresses α -l-rhamnosidase and β -d-glucosidase activities in native state, can be used to deglycosylate natural glycosides. The selective inactivation of one of these activities will allow the biosynthesis of different bioactive compounds in a simple, effective and cheap way. In this work, pressure and temperature were the tools used to selectively inactivate the activities expressed by naringinase. The main goal was the identification of pressure–temperature conditions to acquire conditions for the maximization of enzymatic hydrolysis of substrates with different numbers of glycosidic residues. α -l-Rhamnosidase was 32-fold more resistant against inactivation at 250 MPa than at atmospheric pressure. The best pressure condition to reduce β -d-glucosidase inactivation at 75°C was 173 MPa, while in the case of α -l-rhamnosidase inactivation at 85°C, it was above 250 MPa. Moreover, a selective inactivation of β -d-glucosidase activity of naringinase was attained, allowing an easy and cheap method with which to produce prunin and other expensive glycosides. The present work highlights the effect of high pressure on enzyme protection against thermal inactivation, demonstrating its potential as a powerful tool in biosynthesis.     

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.     

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.     

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.     

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).     

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.     

Enzymatic synthesis of some 15N-labelled l-amino acids

Our group has developed a stereospecific enzymatic method, which is very efficient for the in vitro synthesis of l-[¹⁵N]serine, l-[¹⁵N]methionine and l-[¹⁵N]glutamic acid. These amino acids were prepared from the corresponding α -ketoacids in the suitable enzymatic systems. The bacterial NAD-dependent amino acid dehydrogenases alanin dehydrogenase, leucin dehydrogenase and glutamate dehydrogenase were used as catalysts. Glucose dehydrogenase was used for the regeneration of NADH and ¹⁵NH₄Cl as isotopically labelled material at 99 at.% ¹⁵N. All reactions are inexpensive and easy to perform on a synthetically useful scale (1-10g) giving high yields of l-amino acids. The ¹⁵N isotope content was determined by mass spectrometry.     

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.     

Improved one-centre wave functions for the hydrogen and methane molecules

Corrections are made to the Joy-Parr hydrogen and the Saturno-Parr methane one-centre wave functions and the functions are accurately reminimized with respect to the energy. The electronic wave functions and total molecular energies are obtained for various internuclear distances and the equilibrium internuclear distance and the breathing force constant determined. Three methods for calculating the force constant are given and compared. The equilibrium bond length for hydrogen is found to be 1·38 a.u. (experimental, 1·40 a.u.) and the force constant 6·33 md/å (experimental, 5·75 md/å). For methane the equilibrium C-H distance is found to be 2·014 a.u. (experimental, 2·05 a.u. and the force constant 25·8 md/å (experimental, 23·5 md/å). The total computed molecular energies for the equilibrium configurations of hydrogen and methane are -1·1605 a.u. (experimental, -1·175 a.u.) and -39·8444 a.u. (experimental, -40·51 a.u.) respectively.     

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.     

Isotope effects in the tyrosinase catalysed hydroxylation of l-tyrosine methyl derivatives

To investigate isotope effects in the hydroxylation of [3′,5′-²H₂]-α-methyl- and [3′,5′-²H₂]-N-methyl-l-tyrosine, they were synthesised using acid catalysed isotope exchange at high temperature. The kinetic and solvent deuterium isotope effects on V_max and V_max/K_m parameters of tyrosinase in its action on methylated derivatives of l-tyrosine were determined using the non-competitive spectrophotometric method. Lineweaver–Burk plots were used to consider the inhibition type of O-methyl-l-tyrosine, revealing that it is an uncompetitive inhibitor of tyrosinase.     

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.     

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.     

50 years at the forefront of Physics

Mathemtical Techniques and Physical Applications. By J. Killingbeck and G. H. A. Cole. (Amdemic Press, 1971.) [Pp. xiv + 715.] £7£00. Scope: Textbook; reference. Level: Postgraduate; undergraduate.

Group Theory in Solid-state Physics. By H. W Streitwolf (Macdonald, 1971.) [Pp. 248.] £5·00. Scope: Textbook. Level: Postgraduate.

Statistical Physics. By Ya. P. Terletskii. (North-Holland, 1971.) [Pp xv+279.] $6·30. Scope: Textbook. Level: Postgraduate; undergraduate.

Ubsersichtsbeiträge zur Gasdynamik. Edited by E. Leiter and J. Zierep. (Springer-Verlag, 1971.) [Pp. 386.1 $40·70. Scope: Treatise. Level: Specialist/postgraduate.

Classical Theory of Particles and Melds. Vol. I and Vol. II. By K. H. Ruei. (University Press, Taiwan, Republic of China, 1971.) [Pp.: Vol. I, xxiii + 359; Vol. II, xxvi + 424.] Scope: Textbook. Level: Postgraduate; undergraduate.

Topics in Mathematical Physics. Vol. II: Spectral Theory and Wave Processes. By M. Sh. Birman. (Consultants Bureau, 1971.) [Pp. v + 121.] $14·00. Scope: Treatise. Level: For specialists only.

An Introduction to the Theory of Electromagnetic Waves. By A. C. Hewson. (Longman, 1971.) [Pp. viii+ 115.] £ 1·60. Scope: Textbook. Level: Undergraduate.

Modern Physics and Quantum Mechanics. By Elmer E. Anderson. (W. B. Saunders Co. Ltd., 1971.) [Pp. xi+430.] £6·20. Scope: Textbook. Level: Undergraduate.

Polarized Light and Optical Measurement. By Clarke and Grainqer. (Pergamon Press, 1971.) [Pp. viii+ 187.] £3·50 ($9·50.). Scope: Treatise. Level: Specialist/postgraduate.

Phenomena in Ionized Gases 1971. Edited by R. N. Franklin. (Donald Parsons, 1971.) [Pp. xl+450.] £12·00.

Technology Today. Edited by Edward de Bono. (Routledge &; Kegan Paul Press, 1971.) [Pp. xii+ 144.] Cloth edition £1·75; Paperback 50p. Scope: Survey. Level: General reader.

Diffusion Data. No. 1. Edited by DR. F. H. Wohlbier. (Trans Tech Publications, 1971.) [Pp. 289.] Scope: Library (reference). Level: Specialist/postgraduate.     

Semiempirical investigation of perturbations of the g factors of electronic-vibrational-rotational levels of hydrogen: III. The r 3Π g − and s 3Δ g − states of the H2 and D2 molecules

The g factors of rovibrational levels of the (4d)r ³Π _g ^? and (4d)s ³Δ _g ^? states of the H₂ and D₂ molecules have been obtained for the first time. These values were found within the nonadiabatic model taking into account the interaction of the 4dπ³Π_g and 4dδ³Δ_g states in the pure precession approximation using semiempirical values of the expansion coefficients of the wave function in an adiabatic basis, which was obtained for the first time for the states of the triplet 4d complex of terms of the hydrogen molecules, and the results of numerical calculation of the overlap integrals of the vibrational wave functions of these states. It is established that the interference effects of the interaction between the 4dπ³Π _g ^? and 4dδ³Δ _g ^? states lead to significant (up to 7 times for the r ³Π _g ^? state of the H₂ and D₂ molecules and 70 and 8 times for the s ³Δ _g ^? state of the H₂ and D₂ molecules, respectively) differences between the nonadiabatic values of the g factors and the corresponding adiabatic values. It is found that the perturbed values of the g factors are much closer to the values corresponding to the case of Hund’s d coupling of angular momenta than to the values corresponding to the b coupling. It is established that the perturbations of the g factors of rovibrational levels of the states of the 4d complex of terms are much greater (up to 2 times for the ³Π _g ^? states and 350 times for the ³Δ _g ^? states) than the perturbations of the same characteristics for the 3d complex of terms of the hydrogen molecule with the same vibrational and rotational quantum numbers.     

Cooperative binding of drugs on human serum albumin

In order to explain the adsorption isotherms of the amphiphilic penicillins nafcillin and cloxacillin onto human serum albumin (HSA), a cooperative multilayer adsorption model is introduced, combining the Brunauer–Emmet–Teller (BET) adsorption isotherm with an amphiphilic ionic adsorbate, whose chemical potential is derived from Guggenheim's theory. The non-cooperative model has been previously proved to qualitatively predict the measured adsorption maxima of these drugs [Varela, L. M., García, M., Pérez-Rodríguez, M., Taboada, P., Ruso, J. M., and Mosquera, V., 2001, J. chem. Phys., 114, 7682]. The surface interactions among adsorbed drug molecules are modelled in a mean-field fashion, so the chemical potential of the adsorbate is assumed to include a term proportional to the surface coverage, the constant of proportionality being the lateral interaction energy between bound molecules. The interaction energies obtained from the empirical binding isotherms are of the order of tenths of the thermal energy, therefore suggesting the principal role of van der Waals forces in the binding process.     

A re-examination of the I.R. spectrum of dinitrogen trioxide

Assuming a planar geometry of C _s symmetry and using a Urey-Bradley potential field, the force constants of dinitrogen trioxide have been re-determined within the formalism of Wilson's G-F matrix method. The outcome of the present investigation suggests a new set of force constants some of which are drastically (～ 50 per cent) different than those previously reported. Furthermore, since the i.r. frequencies used in the present investigation were obtained both in the solid state and at low temperatures, the mean amplitudes of thermal vibrations of both ¹⁴N₂O₃ and ¹⁵N₂O₃ are given at 77°k. Finally, it is suggested that more isotopic i.r. data is necessary to ascertain unequivocably the geometry of dinitrogen trioxide.