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.     

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.     

The kinetic and solvent deuterium isotope effects in the 4- and 5-positions of the indole ring on the enzymatic decomposition of L-tryptophan

The kinetic and solvent deuterium isotope effects in the 4- and 5-positions of the indole ring on the enzymatic decomposition of l-tryptophan catalysed by the enzyme TPase (EC. 4.1.99.1) were determined. The isotope effects were investigated by the non-competitive method using [4′-²H]-l-tryptophan, which was enriched in deuterium in 70% in the 4-position. The numerical values of isotope effects for 100% enrichment in deuterated label in that position were calculated by approximation. Those same isotope effects were determined for [5′-²H]-l-tryptophan fully deuteriated in the 5′ -position.     

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.     

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.     

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.     

Isotope effects in the enzymatic oxidation of tryptamine to 3-indolyl-acetaldehyde

The reaction mechanisms of the enzymatic deamination of tryptamine catalysed by the enzyme monoamine oxidase (MAO, EC 1.4.3.4) were investigated using the kinetic isotope effect and solvent isotope effect methods. The numerical values of these deuterium effects in the (1S) and (1R) positions of tryptamine were determined using the non-competitive spectrophotometry. The deuterium-labelled isotopologue [(1S)-²H]tryptamine was obtained in two steps by enzymatic coupling of indole with S-methyl-l-cysteine in a deuterated medium followed by enzymatic decarboxylation of the resulting [2-²H]-l-tryptophan. [(1R)-²H]tryptamine was obtained by enzymatic decarboxylation of l-tryptophan in the fully deuterated medium.     

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.     

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.     

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.     

Unexpected Reorganization Effects of Cold-Crystallized Polylactide Stereocomplex

Cold crystallization of poly (l-lactide)/poly (d-lactide) blends at low temperatures results in the formation of a stereocomplex with loose intermolecular packing. Upon heating, it undergoes significant reorganization into a compact one with an extremely high melting point via a solid–solid transition. In contrast, the stereocomplex crystallized at high temperatures exhibits little reorganization and thus a relatively low melting point.     

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.     

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.     

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.     

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.     

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.     

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.     

The anomalous temperature dependence of the sound velocity in water

The quantum yields of naphthalene vapour fluorescence at 225°c and of phenanthrene vapour fluorescence at 365°c excited by the Hg 313 μ line are independent of concentration up to 0·014 and 0·007 moles/l. respectively; this is attributed to fast dissociation relaxation of the excimer at these temperatures.

The fluorescence of naphthacene vapour excited at temperatures of 355–435°c by the group of Hg lines at 365 μ decreases with increasing pressure at pressures below that at which absorption of the incident radiation is virtually complete, and is attributed to a combination of self-quenching and reabsorption of fluorescence. An analysis of the data for the limiting cases of complete and negligible fluorescence reabsorption provides upper and lower limits for self-quenching constant which are consistent with unit collisional quenching efficiency and a lifetime of 5·3 ± 2·2 + 10^-9 sec at 355°c.     

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.     

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).