H3 potential surface in natural collision coordinates

Potential energy contour maps of the ground and electronically excited Porter-Karplus H₃ surfaces are presented. These maps are correlated with another set of figures showing molecular geometries. Particular attention is paid to the intersection of these electronic surfaces along the Jahn-Teller ridge. A difficulty with natural coordinates, “nonlinear schizophrenia”, is described and a simple procedure for avoiding the problem is presented.     

A method for finding the ridge between saddle points applied to rare event rate estimates

A method is presented for finding the ridge between first order saddle points on a multidimensional surface. For atomic scale systems, such saddle points on the energy surface correspond to atomic rearrangement mechanisms. Information about the ridge can be used to test the validity of the harmonic approximation to transition state theory, in particular to verify that second order saddle points--maxima along the ridge--are high enough compared to the first order saddle points. New minima along the ridge can also be identified during the path optimisation, thereby revealing additional transition mechanisms. The method is based on a string of discretisation points along a path between the first order saddle points and using an iterative optimisation which requires only the force acting on the atoms. At each iteration during the optimisation, the force is inverted along an unstable eigenmode perpendicular to the path. The method is applied to Al adatom diffusion on the Al(100) surface to find the ridge between 2-, 3- and 4-atom concerted displacements and hop mechanisms. A correction to the harmonic approximation of transition state theory was estimated by direct evaluation of the configuration integral along the ridge.     

Characterization of dynamic stick-and-break wetting behavior for various liquids on the surface of a highly viscoelastic polymer

A thermally stripped acrylic polymer was wet with a series of liquids possessing a broad range of properties. Previously, novel wetting behavior by water was reported for the polymer, which included the formation of a wetting ridge structure substantially larger than those reported elsewhere and the complete halting of the three-phase line. This allows metastable angles ranging from 0 degrees to greater than 150 degrees to be achieved through changes in the sessile drop volume. Greater advancing angles are prevented by the collapse of the drop, producing what has been described as stick-and-break propagation. In Wilhelmy plate experiments for metal plates coated with the polymer, this mechanism produces a quasi-periodic pattern of lines composed of ridge structures. Similar behavior was observed for all liquids tested. Differences were observed in the maximum force measured with a tensiometer (pinning force) and the average distance between ridges for the formed pattern (pinning distance). These quantities are shown to be related to the height of the ridge structures. The kinematic viscosity of the liquids appears to be an important variable for the wetting process. A comparison of pinning quantities at various rates with the master curve of the polymer indicate that its viscoelastic properties govern, to a great extent, the observed rate dependencies; i.e., higher rates produce greater elastic behavior and smaller ridge heights. Also important is the polymer's tendency for creep deformation. The ridge apex is shown to be displaced a significant distance through ridge deformation, which modifies its symmetry.     

Quantitative molecular similarity analysis (QMSA) methods for property estimation: a comparison of property-based,arbitrary, and tailored similarity spaces

Three classes of arbitrary quantitative molecular similarity analysis (QMSA) methods have been computed using atom pairs, topological indices, and physicochemical properties. Tailored QMSA models have been developed using a selected number of TIs chosen by ridge regression. The methods have been applied to the K-nearest neighbor based estimation of log P of two sets of chemicals. Results show that the property-based and tailored QMSA methods are superior to the arbitrary similarity methods in estimating log P of both sets of chemicals     

Quantitative molecular similarity analysis (QMSA) methods for property estimation: A comparison of property-based,arbitrary, and tailored similarity spaces

Three classes of arbitrary quantitative molecular similarity analysis (QMSA) methods have been computed using atom pairs, topological indices, and physicochemical properties. Tailored QMSA models have been developed using a selected number of TIs chosen by ridge regression. The methods have been applied to the K -nearest neighbor based estimation of log P of two sets of chemicals. Results show that the property-based and tailored QMSA methods are superior to the arbitrary similarity methods in estimating log P of both sets of chemicals     

Optimal neighbor selection in molecular similarity: comparison of arbitrary versus tailored prediction spaces

Three classes of arbitrary quantitative molecular similarity analysis (QMSA) methods have been computed using atom pairs (APs), topological indices (TIs), and principal components (PCs) derived from topological indices. Tailored QMSA models have been developed from TIs selected through ridge regression. K-nearest neighbor (kNN) based estimation has been applied to all of the methods to estimate normal vapor pressure (p(vap)) and water solubility (sol) for a set of 194 chemicals. Results show that the tailored QMSA methods are superior to arbitrary similarity methods in estimating both of these properties for the given set of chemicals.     

A novel matrix-assisted laser desorption/ionisation mass spectrometry imaging based methodology for the identification of sexual assault suspects

An increase in the use of condoms by sexual offenders has been observed. This is likely to be due both to the risk of sexually transmitted diseases and to prevent the transfer of DNA evidence. In this scenario the detection of condom lubricants at a crime scene could aid in proving corpus delicti. Here we show a novel application of Matrix-Assisted Laser Desorption/Ionisation Mass Spectrometry Imaging (MALDI MSI) for mapping the fingermark ridge pattern simultaneously to the detection of the condom lubricant within the fingermark itself. Two condom brands have been investigated to prove the concept. Condoms were handled producing lubricant-contaminated fingermarks. Images of the ridge pattern were obtained simultaneously to the detection of two lubricants, even several weeks after the fingermark deposition. The results therefore show the potential of MALDI MSI to link the suspect (identification through fingermark ridge pattern) to the crime (detection of condom lubricant) in one analysis. This would enable forensic scientists to provide evidence with stronger support in alleged cases of sexual assault.     

Application of ridge trace analysis in direct spectrophotometric calibration

The use of ridge trace analysis for multivariate calibration problems is described. Application is made to the simultaneous quantitative determination of components for several pharmaceutical systems with unknown sample UV spectra by the direct calibration technique. The results indicate that with the help of ridge trace analysis and ridge regression, the parameter k can be selected to obtain estimation of the colinearity of a system based on the stability of relative concentration as a function of k. Much information about the system to be analyzed can be obtained, such as whether there is colinearity among the variables, which measurement wavelength range is suitable for performing quantitative analysis, which components cannot be measured and which components can only be measured as a sum, and whether the quantitative model is correct.     

Lawsone: a novel reagent for the detection of latent fingermarks on paper surfaces

Lawsone (2-hydroxy-1,4-naphthoquinone) reacts with latent fingermark deposits on paper surfaces to yield purple-brown impressions of ridge details which are also photoluminescent; this compound represents the first in a completely new class of fingermark detection reagents.     

Multivariate calibration leverages and spectral F‐ratios via the filter factor representation

Diagnostics are fundamental to multivariate calibration (MC). Two common diagnostics are leverages and spectral F‐ratios and these have been formulated for many MC methods such as partial least square (PLS), principal component regression (PCR) and classical least squares (CLS). While these are some of the most common methods of calibration in analytical chemistry, ridge regression is also common place and yet spectral F‐ratios have not been developed for it. Noting that ridge regression is a form of Tikhonov regularization (TR) and using the unifying filter factor representation for MC, this paper develops the filter factor form of leverages and spectral F‐ratios. The approach is applied to a spectral data set to demonstrate computational speed‐up advantages and ease of implementation for the filter factor representation. Copyright © 2010 John Wiley & Sons, Ltd.     

A model study of vibrational excitation of carbon dioxide molecule by slow electrons: the role of wave packet sliding from the ridge

The method of an accurate calculation of vibrational excitation cross sections of a two-mode molecule by slow electrons within the framework of the local theory (the ‘boomerang’ model) is applied for a model study of the excitation of the symmetrical stretching vibrational modes of carbon dioxide in the two-mode approximation (i.e., only the symmetrical stretch and bending modes are included in the consideration). It is shown that the 'boomerang’ oscillations in the cross section are strongly suppressed due to the decay of the one-dimensional ‘boomerang' state caused by the anion wave packet sliding from the linear configuration ridge. Consequently, the bending motion in CO₂ molecule should to be taken into account even if only the processes without the final bending excitation are considered. A simple quasi one-dimensional model describing the system sliding from the ridge is put forward which treats this phenomenon as a decay of the initial wave packet via the series of diabatic resonant states related to unstable trajectory.     

Enhancement of ordinal CoMFA by ridge logistic partial least squares

Conventional comparative molecular field analysis (CoMFA) requires at least 3 orders of experimental data, such as IC 50 and K i, to obtain a good model, although practically there are many screening assays where biological activity is measured only by rating scale. To improve three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis, we developed in this study a modified ordinal classification-oriented CoMFA using partial-least-squares generalized linear regression and ridge estimation. The modified Logistic CoMFA was validated using a corticosteroid binding globulin receptor binding data set, a benchmark for 3D-QSAR, and an acetylcholine esterase inhibitor data set. Our results show that modification of Logistic CoMFA enhanced both prediction accuracy and 3D graphical analysis. In addition, the 3D graphical analysis of the modified Logistic CoMFA was much improved. This improvement resulted in more accurate information on the binding mode between proteins and ligands than in the case of conventional CoMFA.