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.     

Development of the force field parameters for phosphoimidazole and phosphohistidine

Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule--a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent.     

The parameterization and validation of generalized born models using the pairwise descreening approximation

Generalized Born Surface Area (GBSA) models for water using the Pairwise Descreening Approximation (PDA) have been parameterized by two different methods. The first method, similar to that used in previously reported parameterizations, optimizes all parameters against the experimental free energies of hydration of organic molecules. The second method optimizes the PDA parameters to compensate only for systematic errors of the PDA. The best models are compared to Poisson-Boltzmann calculations and applied to the computation of potentials of mean force (PMFs) for the association of various molecules. PMFs present a more rigorous test of the ability of a solvation model to correctly reproduce the screening of intermolecular interactions by the solvent, than its accuracy at predicting free energies of hydration of small molecules. Models derived with the first method are sometimes shown to fail to compute accurate potentials of mean force because of large errors in the computation of Born radii, while no such difficulties are observed with the second method. Furthermore, accurate computation of the Born radii appears to be more important than good agreement with experimental free energies of solvation. We discuss the source of errors in the potentials of mean force and suggest means to reduce them. Our findings suggest that Generalized Born models that use the Pairwise Descreening Approximation and that are derived solely by unconstrained optimization of parameters against free energies of hydration should be applied to the modeling of intermolecular interactions with caution.     

A low-temperature electron diffraction study of structural disorder and its relationship to the Kondo effect in ThAsSe

A low-temperature electron diffraction study has been carried out on ThAsSe to search for evidence of structural disorder associated with the low-temperature non-magnetic Kondo effect. A highly structured and extremely complex characteristic diffuse intensity distribution has been observed at low temperature and interpreted in terms of a gradual charge density wave type phase transition upon lowering of temperature involving disordered As-As dimerization within (001) planes. Plausible models of the proposed As-As dimerization have been obtained using a group theoretical approach.     

Riemann problem for kinematical conservation laws and geometrical features of nonlinear wavefronts

A pair of kinematical conservation laws (KCL) in a ray coordinatesystem (,t) are the basic equations governing the evolutionof a moving curve in two space dimensions. We first study elementarywave solutions and then the Riemann problem for KCL when themetric g, associated with the coordinate designating differentrays, is an arbitrary function of the velocity of propagationm of the moving curve. We assume that m>1 (m is appropriatelynormalized), for which the system of KCL becomes hyperbolic.We interpret the images of the elementary wave solutions inthe (,t)-plane to the (x,y)-plane as elementary shapes of themoving curve (or a nonlinear wavefront when interpreted in aphysical system) and then describe their geometrical properties.Solutions of the Riemann problem with different initial datagive the shapes of the nonlinear wavefront with different combinationsof elementary shapes. Finally, we study all possible interactionsof elementary shapes.     

Smooth Linearization for a Saddle on Banach Spaces

As a continuation of a previous work on linearization of class C¹ of diffeomorphisms and flows in infinite dimensions near a fixed point, in this work we deal with the case of a saddle point with some non-resonance restrictions for the linear part. Our result can be seen as an extension of results by Hartman [Boletin de la Sociedad Matematica Mexicana 5(2), 220–241 (1960)] and Aronson, Belitskii and Zhuzhoma [Introduction to the Qualitative Theory of Dynamical systems on surfaces, AMS Transl. Math. Monog. vol.153, pp. 268–277 (1996)] in dimension two. We also present an application to a system of nonlinear wave equations.AMS Subject Classifications: Primary: 35B05, 34G20. Secondary: 35B40, 34D05.Dedicated to Professor Shui-Nee Chow on the occasion of his 60th birthday     

Cycle Range Distributions for Gaussian Processes Exact and Approximative Results

Wave cycles, i.e. pairs of local maxima and minima, play an important role in many engineering fields. Many cycle definitions are used for specific purposes, such as crest–trough cycles in wave studies in ocean engineering and rainflow cycles for fatigue life predicition in mechanical engineering. The simplest cycle, that of a pair of local maximum and the following local minimum is also of interest as a basis for the study of more complicated cycles. This paper presents and illustrates modern computational tools for the analysis of different cycle distributions for stationary Gaussian processes with general spectrum. It is shown that numerically exact but slow methods will produce distributions in almost complete agreement with simulated data, but also that approximate and quick methods work well in most cases. Of special interest is the dependence relation between the cycle average and the cycle range for the simple maximum–minimum cycle and its implication for the range distribution. It is observed that for a Gaussian process with rectangular box spectrum, these quantities are almost independent and that the range is not far from a Rayleigh distribution. It will also be shown that had there been a Gaussian process where exact independence hold then the range would have had an exact Rayleigh distribution. Unfortunately no such Gaussian process exists.This revised version was published online in March 2005 with corrections to the cover date.     

Non-destructive testing of tubes using a time reverse numerical simulation (TRNS) method

A method for the detection of defects in cylindrical structures and the determination of their positions and orientations is presented in this paper. The scattered field, which is generated by the interaction of excited guided waves with a defect, is evaluated with an approach named time reverse numerical simulation method (TRNS). Since the excited waves and the scattered field propagate along the sample, the time-consuming scanning of the whole tube can be eliminated. The scattered displacement field is measured in three dimensions over time with a laser vibrometer at different locations distributed equally around the circumference at a fixed axial coordinate far away from the defect. Instead of analyzing the complicated time signals directly, they are played back in time. If the recorded displacement histories of the scattered field are reversed in time and played back in an identical structure, the waves travel back the same path and interfere to a maximum at their origin. The result is an amplitude increase at the position of the defect where the scattered field was generated. Instead of playing back the recorded time signals in an experiment, this step is replaced by a numerical simulation. Only this enables the visualization and detection of the amplitude increase. As long as the simulation is of high accuracy, the position of the maximum interference corresponds exactly to the location of the defect in the experiment, although no defect is implemented in the simulation.     

Surface morphology changes of poly(ethyleneterephthalate) fabrics induced by cold plasma treatments

Some selective cold plasma processing modify specific surface properties of textile polymeric materials such as their dyeability, wettability and hydrorepellence. To correlate the sample surface changes with the acquired surface properties allows one to obtain information on the chemical and physical processing involved in plasma treatment. In this work, atomic force microscopy (AFM) has been applied to investigate the morphological and topographical surface modifications induced by RF cold plasma processing of poly(ethyleneterephthalate) (PET) fabrics. Rms surface roughness and surface area of the samples are measured before and after the treatments. The morphology changes have been analysed as a function of the treatment time and air gas pressure. Measurements have been performed also using plasmas produced by different gases such as He, Ar, SF₆ and CF₄. The PET shows different behaviour with different gas plasmas. In the case of air, He and Ar gases the sample surface modifications seem to be mainly due to etching effects, while the fluorine atoms grafting probably is responsible for surface rearrangement process using SF₆ and CF₄ gases. As a consequence different surface properties are produced in the plasma treated samples. Article presented at the International Conference on the Frontiers of Plasma Physics and Technology, 9–14 December 2002, Bangalore, India.     

Elastic friction drive of surface acoustic wave motor

Importance of elastic deformation control to obtain large output force with a surface acoustic wave (SAW) motor is discussed in this paper. By adding pre-load to slider, stator and slider surfaces are deformed in a few tens nanometer. Appropriate deformation in normal direction against normal vibration displacement amplitude of SAW existed. By moderate deformation, the output force of the SAW motor was enlarged up to about 10 N and no-load speed was 0.7 m/s. To produce this performance, the transducer weight and slider size were only 4.2 g and 4 x 4 mm(2).By traveling wave propagation, surface particles of the SAW device move in elliptical motion. Due to the amplitude of the elliptical motion is 10 or 20 nm order, the contact condition of the slider is very critical. To control the contact condition, namely, the elastic deformation of the slider and stator surface in nanometer order, a lot of projections were fabricated on the slider surface. The projection diameter was 20 micro m. In static condition, the elastic deformation and stress were evaluated with the FEM analysis. From this calculation and the simulation result, it is consider that the wave crest is distorted, hence the elasticity has influence on the friction drive condition.Elastic deformation of the stator surface beneath the projection from the initial position were evaluated. In 4 x 4 mm(2) square area, the sliders had from 1089 to 23,409 projections. Depression was independent to the contact pressure. However, the output force depended on the depression although the projection density were different. From the view point of the output power of the motor, the proper depression was independent to the projection density. Around 25 nm depression, the output force and output power were maximized. This depression value was almost same as the vibration displacement amplitude of the stator transducer.