Molecular determinants in the bioactivation of the dopaminergic neurotoxin N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)

Summary Nineteen analogs of the dopaminergic neurotoxin N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) have been used as probes to study the structural parameters that influence MAO-catalyzed oxidation. In this study, the efficiency of enzyme-catalyzed substrate oxidation was found to be unrelated to parameters such as the ionization potential, dipole moment, net atomic charge at C5 and the dihedral angle between the phenyl ring and the tetrahydropyridine moiety. Conformational analysis revealed that substitution at the C2 position of MPTP yields atropisomers. It is suggested that one of these atropisomers would be either inactive or substantially less active than the other. Therefore, the relative oxidative efficiency and toxicity of these compounds reported earlier may have been significantly underestimated. Based on the conformational analysis and other data, a rudimentary model of the MAO substrate site has been developed which partially explains the substrate specificities of MAO A and MAO B.Each substrate binding site can be divided into two regions, (a) an amine-binding pocket (for the tetrahydropyridine moiety), and (b) a bulky substituent region (for the phenyl group and its substituents). The length of the substrate binding site (measured along the long axis of MPTP) is approximately 8.5 Å, and the width of the amine-binding pocket is approximately 2.5 Å (from C3 to C5). The bulky substituent region contains a central area for binding the phenyl group of MPTP. This central area is flanked by two hydrophobic pockets, P2 and P3. In MAO A, the pocket P2-A is oriented 45–135° relative to the plane of the tetrahydropyridine moiety, with a radius of 3.1 Å from C2 of the phenyl ring. The radius of a similar but smaller pocket, P2-B, in MAO B, is approximately 2.7 Å. In MAO B, the pocket P3-B (radius 2.36 Å from C3) is larger than a similar pocket P3-A (radius 1.70 Å from C3) in MAO A. The foregoing characterization suggests that differences in the size and topography of both of the substituent pockets play an important role in determining the substrate specificities of these two isozymes.     

Molecular potential-energy surfaces for chemical reaction dynamics

This paper reviews the construction of molecular potential-energy surfaces by an interpolation method which has been developed over the last several years. The method uses ab initio quantum chemistry calculations of the molecular electronic energy in an automated procedure to construct global potential- energy surfaces which can be used to simulate chemical reactions with either classical or quantum dynamics. The methodology is explained and several applications are presented to illustrate the approach. Received: 22 February 2002 / Accepted: 2 May 2002 / Published online: 6 November 2002 Correspondence to: M. A. Collins e-mail: collins@rsc.anu.edu.au Acknowledgements. The methods described in this overview are the result of collaborations with former members of my group, in particular with Josef Ischtwan, Meredith Jordon, Keiran Thompson and Ryan Bettens. I am also indebted for inspiration gained from many discussions with my colleagues Leo Radom and Donghui Zhang (National University of Singapore). This work has been supported by the Supercomputer Facility of the Australian National University and the Australian Partnership for Advanced Computing.     

Reagentless system for sulphite determination based on polyaniline

A new reagentless system for sulphite (or sulphur dioxide) determination is reported based on the use of an organic conducting polymer, polyaniline, and its absorbance variation at 550 nm, depending on the sulphite concentration. After chemical polymerisation of aniline a very thin film of polyaniline is obtained. Although the response is not fully reversible, each film can be used for at least 10 measurements for low analyte concentrations (up to 0.5 mg l⁻¹) and five measurements for higher sulphite concentrations. Moreover, the reproducibility, ease of preparation and low cost of the films, permit the use of a new disposable system for each measurement. When the change in absorbance at 550 nm was measured for 210 s (stabilisation time), the system showed a linear response, which ranged from 0.025 to 1.50 mg l⁻¹ of sulphite. A theory with regard to the reaction mechanism between the polyaniline films and sulphite is also proposed. The system was applied to sulphite determination in wine samples and the results were in agreement with those obtained by the Official Method of Analysis (iodometric titration).     

Functionality map analysis of the active site cleft of human thrombin

Summary The Multiple Copy Simultaneous Search methodology has been used to construct functionality maps for an extended region of human thrombin, including the active site. This method allows the determination of energetically favorable positions and orientations for functional groups defined by the user on the three-dimensional surface of a protein. The positions of 10 functional group sites are compared with those of corresponding groups of four thrombin-inhibitor complexes. Many, but not all features, of known thrombin inhibitors are reproduced by the method. The results indicate that certain aspects of the binding modes of these inhibitors are not optimal. In addition, suggestions are made for improving binding by interaction with functional group sites on the thrombin surface that are not used by the thrombin inhibitors. Abbreviations: MCSS, multiple copy simultaneous search; PPACK, d-phenylalanyl-l-propyl-l-arginine chloromethane; NAPAP, N -(2-naphthylsulfonylglycyl)-d-para-amidinophenylalanylpiperidine; argatroban, (2R,4R)-4-methyl-1-[N -(3-methyl-1,2,3,4-tetrahydro-8-quinolinylsulfonyl)-l-arginyl]-2-piperidine carboxylic acid; rms, root mean square. The thrombin residues are numbered according to the chymotrypsin-based numbering by Bode et al. [8]. P1, P2, P3, etc., denote the peptide inhibitor residues on the amino-terminal side of the scissile peptide bond, and S1, S2, S3, etc., the corresponding subsites of thrombin     

A computational study of the effect of an external electric field on the geometry of selected donor–acceptor complexes

To understand the effect of Au and thiol atoms in octane molecule, a structural and charge density analysis has been carried out by high level ab initio quantum chemical calculations using MP2 and B3PW91 methods with the basis sets 6-311G(d,p) and LANL2DZ. The optimized geometries, specifically, the geometry obtained from both levels reveal the effect of S- and Au-atoms in octane molecule. An introduction of sulfur atom in octane molecule lengthen its backbone C–C bond distances, and further adding of Au-atom at the terminals of octane dithiolate stabilizes these distances. The bond densities of the C–C bonds of octane are 1.6 eÅ⁻³, these values are decreased significantly and the charges are largely depleted, when thiol and Au-atoms added in the octane molecule. The presence of negative Laplacian ²ρ(r) at bond critical points of C–C and C–H bonds, indicate, the charges are concentrated in these bonds, confirm that these bonds exhibit an open shell type interaction. The moderate values of density and the negative Laplacian of S–C bonds confirm the covalent character. The positive ²ρ(r) value of Au–S bonds, characterize, the bonding interaction is a closed shell interaction. The combined observed low value of electron density and the positive Laplacian of Au–S bond comprises, the gold and S interaction is not a covalent interaction, but it is a very weak coordination bond interaction. The small positive value of total energy density in Au–S bond indicates, the charges in these bonds are highly depleted and this is further confirmed by the Laplacian of bond characterization.     

Electrophoretic mobility and molecular distribution studies of poly(amidoamine) dendrimers of defined charges

Generation 5 ethylenediamine (EDA)-cored poly(amidoamine) (PAMAM) dendrimers (E5, E denotes the EDA core and 5 the generation number) with different degrees of acetylation and carboxylation were synthesized and used as a model system to investigate the effect of charge and the influence of dendrimer surface modifications on electrophoretic mobility (EM) and molecular distribution. The surface-modified dendrimers were characterized by size-exclusion chromatography, 1H NMR, MALDI-TOF-MS, PAGE, and CE. The focus of our study was to determine how EM changes as a function of particle charge and molecular mass, and how the molecular distribution changes due to surface modifications. We demonstrate that partially modified dendrimers have much broader migration peaks than those of fully surface functionalized or unmodified E5 dendrimers due to variations in the substitution of individual dendrimer surfaces. EM decreased nonlinearly with increases in surface acetylation for both PAMAM acetamides and PAMAM succinamic acids, indicating a complex migration activity in CE separations that is not solely due to charge/mass ratio changes. These studies provide new insights into dendrimer properties under an electric field, as well as into the characterization of dendrimer-based materials being developed for medical applications.     

Molecular mechanics (MM2) calculations and cone angles of phosphine ligands

Molecular mechanics (MM2) calculations were performed on 54 conformations of 18 phosphines (PH₃; PH_3−nR_n, where n = 1,…3, and R = Me and Et, n = 1 or 2 and R =ⁱPr, and n = 1 and R =^tBu, PMe₂Et, PMeEt₂, and PPhMe₂, and PPh₂R where R = Me, Et, ⁱPr, ^tBu and Ph). The results are compared to those previously obtained from MINDO/3 and MNDO calculations, and to experimental data. Single conformer cone angles and weighted average cone angles were calculated from MM2 optimized geometries employing Tolman's general definition, and they are compared to Tolman's values, MINDO/3 results, and T.L. Brown's E_R values. Of the cone angle definitions used, the weighted average values are suggested as the best single representation of phosphine ligand sizes. The steric parameters (cone angle and E_R values) alone, and in conjunction with electronic parameters, are correlated with experimental data.     

Photoinduced electron transfer at liquid|liquid interfaces. Part VII. Correlation between self-organisation and structure of water-soluble photoactive species

The self-organisation of a variety of dyes at the water|1,2-dichloroethane interface was studied by admittance measurements, photocurrent–potential curves and light polarisation anisotropy of the photocurrent. The heterogeneous photo-oxidation of ferrocene was studied at interfaces sensitised by Sn(IV) meso-tetra-(4-carboxyphenyl) porphyrin dichloride (SnTPPC), chlorin e-6, protoporphyrin IX (protoIX) and Fe(III) protoporphyrin IX chloride (Fe-protoIX). Cyclic voltammograms and capacitance voltage curves exhibit different features associated with the self-assembly of the dye species at the liquid|liquid boundary. In the case of SnTPPC, the capacitance curves displayed the characteristic responses commonly associated with the specific adsorption of ionic species. On the other hand, chlorin e-6, protoIX and Fe-protoIX show rather complex behaviour suggesting not only changes in the excess charge but also in the dielectric permittivity of the interface. Differences in the photocurrent efficiency were also observed under the same experimental conditions. The relative magnitude of the photocurrent responses were rationalised in terms of the phenomenological electron transfer rate constant, the photon capture cross-sections and the lifetime of the triplet state as obtained from nanosecond flash photolysis. Finally, the average molecular orientation of the adsorbed photoactive species was estimated from the photocurrent dependence on the angle of light polarisation in total internal reflection. The results show a clear correlation between the orientation of the transition dipole and the distribution of the peripheral carboxyl groups responsible for the hydrophilic nature of the dyes.     

How to get access to long range states of highly excited molecules

Due to competition between ionic and covalent dissociation, the excited potential curves of the alkali dimers display long range structures, leading in some cases to secondary wells. We discuss the possibility of populating the well (with a depth of 1614.8 cm^-1, located at R _e = 30.5a ₀ ) that is present in the Na₂ potential curve and propose detection schemes. Received: 28 May 1998 / Revised: 5 August 1998 / Accepted: 24 September 1998     

Partial molal heat capacities of aqueous tetraalkylammonium bromides as functions of temperature

Enthalpies of solution have been measured from 5 to 85°C for aqueous tetraethyl- and tetrapropylammonium bromides, and the integral heat method is employed to evaluate for these electrolytes over a wide temperature range. Data taken from the literature have been used to evaluate for aqueous Bu₄NBr over a similar temperature range. These data, along with similar data for Me₄NBr, previously reported, have been used to evaluate absolute ionic heat capacities. While the absolute values agree only qualitatively with two other methods of division, the temperature dependences of the three methods essentially agree up to 65°C. Heat capacities due to structural effects on the solvent, obtained by subtracting the inherent heat capacities of the ions, are extraordinarily positive for all four tetraalkylammonium ions and have negative temperature coefficients, indicating that all four ions, including the tetramethylammonium ion, are structure-making ions.