Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

Summary Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.     

Newton polyhedra, unstable faces and the poles of Igusa's local zeta function

In this paper we examine when the order of a pole of Igusa's local zeta function associated to a polynomial is smaller than ``expected'. We carry out this study in the case that is sufficiently non-degenerate with respect to its Newton polyhedron , and the main result of this paper is a proof of one of the conjectures of Denef and Sargos. Our technique consists in reducing our question about the polynomial to the same question about polynomials , where are faces of depending on the examined pole and is obtained from by throwing away all monomials of whose exponents do not belong to . Secondly, we obtain a formula for Igusa's local zeta function associated to a polynomial , with unstable, which shows that, in this case, the upperbound for the order of the examined pole is obviously smaller than ``expected'.

     

Femtosecond laser fabrication of tubular waveguides in poly(methyl methacrylate)

Femtosecond laser direct writing is employed for the fabrication of buried tubular waveguides in bulk poly(methyl methacrylate). A novel technique using selective chemical etching is presented to resolve the two-dimensional refractive-index profile of the fabrication structures. End-to-end coupling in the waveguides reveals a near-field intensity distribution that results from the superimposition of several propagating modes with different azimuthal symmetries. Mode analysis of the tubular waveguides is performed using the finite-difference method, and the possible propagating mode profiles are compared with the experimental data.     

Treatment-related central nervous system toxicity: MR imaging evaluation with CT and clinical correlation

Thirteen patients with abnormal brain MR scans attributable to treatment-induced injury were retrospectively reviewed. All patients were treated with radiation therapy and 62% received chemotherapy. Five patients were graded as having severe white matter (WM) changes, four had moderate WM changes, and four had mild WM changes. CT was generally equivalent to MR in evaluation of severe and moderate WM abnormalities, whereas MR was superior to CT in detection of mild WM abnormalities. In general, the severity of changes depicted by MR/CT correlated with the extent of neurologic dysfunction. The most severe changes were seen in those patients treated with combination irradiation and chemotherapy.     

Measurement of total Zn and Zn isotope ratios by quadrupole ICP-MS for evaluation of Zn uptake in gills of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss)

This study evaluates the potential use of stable zinc isotopes in toxicity studies measuring zinc uptake by the gills of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss). The use of stable isotopes in such studies has several advantages over the use of radioisotopes, including cost, ease of handling, elimination of permit requirements, and waste disposal. A pilot study using brown trout was performed to evaluate sample preparation methods and the ability of a quadrupole inductively coupled plasma mass spectrometer (ICP-MS) system to successfully measure changes in the ⁶⁷Zn/⁶⁶Zn ratios for planned exposure levels and duration. After completion of the pilot study, a full-scale zinc exposure study using rainbow trout was performed. The results of these studies indicate that there are several factors that affect the precision of the measured ⁶⁷Zn/⁶⁶Zn ratios in the sample digests, including variations in sample size, endogenous zinc levels, and zinc uptake rates by individual fish. However, since these factors were incorporated in the calculation of the total zinc accumulated by the gills during the exposures, the data obtained were adequate for their intended use in calculating zinc binding and evaluating the influences of differences in water quality parameters.     

Practical preparation of benzyloxyacetic acids

An efficient and practical method for the preparation of benzyloxyacetic acids is described. The procedure involves the reaction of readily available chloroacetic acid with benzyl alcohol in the presence of powdered KOH providing a safer alternative to the known literature procedures, which completely eliminates the use of pyrophoric bases such as sodium hydride and sodium metal.     

Taking a little off the top: nanorod array morphology and growth studied by focused ion beam tomography

The high surface area, large aspect ratio, and porous nature of nanorod arrays make them excellent foundation materials for many devices. Of the many synthesis techniques for forming nanorods, glancing angle deposition (GLAD) offers one of the more straightforward and flexible methods for ensuring control of alignment, porosity, and architecture of the nanorods. Here we demonstrate the first use of a dual-beam (focused ion beam (FIB) combined with scanning electron microscopy (SEM)) instrument to section and image the internal morphology of a nanorod array fabricated using the GLAD technique. We have used the FIB-SEM to reconstruct the 3D composition of TiO(2) nanorods, allowing us to visualize for the first time the core structures of many potential devices. We have also been able to probe the relationship between critical parameters such as diameter (w(act)), internanorod spacing (ν(act)), center-to-center spacing (c(act)), and nanorod population density (d(act)) and the depth of the nanocolumn (t) for a single homogeneous structure. A continuous data set was obtained from a single 5-μm-thick GLAD film, avoiding the artifacts arising from the analysis of the top surfaces of multiple samples of varying thicknesses. An analysis of the acquired sectioned data has allowed us to determine that the critical nanocolumn parameters follow a power-law scaling trend with w(act) = 9.4t(0.35) nm, ν(act) = 15.2t(0.25) nm, c(act) = 24.8t(0.31) nm, and d(act) = 3402t(-0.65) columns μm(-2). Using the FIB/SEM images acquired for the TiO(2) nanorods, we have also investigated the evolution of individual nanocolumns and have observed that bifurcation and branching play a significant role in the extinction or survival of these nanorods. These findings will allow for the optimization of nanorod properties for device applications. Also, the FIB sectioning and reconstruction process developed here will permit for the investigation of nanorod arrays formed from a range of synthesis techniques and materials.     

Hydrogen bonding versus van der Waals interactions: competitive influence of noncovalent interactions on 2D self-assembly at the liquid-solid interface

The structures of the self-assembled monolayers of various 4-alkoxybenzoic acids physisorbed at the liquid-solid interface were established by employing scanning tunnelling microscopy (STM). This study has been essentially undertaken to explore the competitive influence of van der Waals and hydrogen-bonding interactions on the process of two-dimensional self-assembly. These acid derivatives form hydrogen-bonded dimers as expected; however, the dimers organise themselves in the form of relatively complex lamellae. The characteristic feature of these lamellae is the presence of regular discommensurations or kinks along the lamella propagation direction. The formation of kinked lamellae is discussed in light of the registry mechanism of the alkyl chains with the underlying graphite substrate. The location of the kinks along a lamella depends on the number (odd or even) of carbon atoms in the alkyl chain. This result indicates that concerted van der Waals interactions of the alkyl chain units introduce the odd/even chain-length effect on the surface-assembled supramolecular patterns. The odd/even effects are retained even upon complexation with a hydrogen-bond acceptor. However, as the solvent is changed from 1-phenyloctane to 1-octanoic acid, the kinked lamellae as well as the odd/even effects disappear. This solvent-induced convergence of supramolecular patterns is attained by means of co-crystallisation of octanoic acid molecules in the 2D crystal lattice, which is evident from high-resolution STM images. The solvent co-adsorption phenomenon is discussed in terms of competing van der Waals and hydrogen-bonding interactions.