Nonstationarity and related measures for time‐dependent hartree–fock and multiconfigurational models

Based on an earlier article (Eberly and Singh, Phys. Rev. D 1973 , 7, 359) and related works on short‐time evolution, this article proposes a many‐electron formulation for the nonstationarity degree which can be assigned to quantum system at each time point. The key measure introduced, , is a nonstationarity index that can be thought of as an inverse nominal lifetime at each instance of time. The index is directly computed from the time derivative of one‐electron density matrix and is a size‐consistent quantity. In this article, the approach is developed for the time‐dependent Hartree–Fock (TDHF), single‐excitation (TDCIS), and time‐dependent full configuration interaction (TDFCI) models. As a rule, nonstationarity effects are more pronounced in correlated electron systems, and a joint analysis of and the multiconfigurational character of wave functions apparently provide a deeper insight into dynamical molecular processes. The performed calculations on small molecules in laser fields show a preference for the TDCIS model when comparing TDCIS and TDHF with the “exact” TDFCI model. © 2013 Wiley Periodicals, Inc.     

A fast parallel clustering algorithm for molecular simulation trajectories

We implemented a GPU‐powered parallel k‐centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370‐residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k‐centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.     

Label free non-invasive imaging of topically applied actives in reconstructed human epidermis by confocal Raman spectroscopy

Raman spectroscopy has become a versatile tool for the in vivo characterization of skin. Here we describe use of Raman spectroscopy for high resolution optical cross sectioning to resolve skin constituents and administered drugs at the cellular level. Percutaneous penetration is typically studied using permeation cells with biopsies of animals or human skin. Although this technique provides valuable clinical data, little insight is gained in the microstructure of drug penetration (intercellular or transcellular) or in the mode of action of applied vehicles or penetration enhancers. Therefore, a Raman microspectroscopic method was combined with a confocal scanning setup to image the microstructure of commercially available skin models (SkinEthic^®) and the spatial distribution of penetrated actives. The models’ microstructure was scanned without any special treatment or environment such as cutting, staining, freezing, or application of vacuum. The non-invasive Raman images reveal the layered structure of stratum corneum. This in particular for lipids while water tends to be more evenly distributed. When penetration of the hydrophilic active glycerol and the lipophilic octyl methoxycinnamate, OMC, was studied, a strong correlation between the local distribution of skin constituents and the hydrophilic/lipophilic character of the active was observed.     

Structural and Dynamic Basis of Human Cytochrome P450 7B1: A Survey of Substrate Selectivity and Major Active Site Access Channels

Cytochrome P450 (CYP) 7B1 is a steroid cytochrome P450 7α‐hydroxylase that has been linked directly with bile salt synthesis and hereditary spastic paraplegia type 5 (SPG5). The enzyme provides the primary metabolic route for neurosteroids dehydroepiandrosterone (DHEA), cholesterol derivatives 25‐hydroxycholesterol (25‐HOChol), and other steroids such as 5α‐androstane‐3β,17β‐diol (anediol), and 5α‐androstene‐3β,17β‐diol (enediol). A series of investigations including homology modeling, molecular dynamics (MD), and automatic docking, combined with the results of previous experimental site‐directed mutagenesis studies and access channels analysis, have identified the structural features relevant to the substrate selectivity of CYP7B1. The results clearly identify the dominant access channels and critical residues responsible for ligand binding. Both binding free energy analysis and total interaction energy analysis are consistent with the experimental conclusion that 25‐HOChol is the best substrate. According to 20 ns MD simulations, the Phe cluster residues that lie above the active site, particularly Phe489, are proposed to merge the active site with the adjacent channel to the surface and accommodate substrate binding in a reasonable orientation. The investigation of CYP7B1–substrate binding modes provides detailed insights into the poorly understood structural features of human CYP7B1 at the atomic level, and will be valuable information for drug development and protein engineering.     

Sorptive elimination of fluoride from contaminated groundwater in a fixed bed column: A kinetic model validation based study

The current investigation involves a continuous adsorption experiment in a packed bed column for the sorptive elucidation of fluoride from contaminated groundwater using an activated soil-clay mixture. Through the combination of naturally accessible laterite soil with silica enriched clay (3:1 ratio), a low-cost Al–Si heterogeneous material has been developed. Following detailed characterization, the developed materials were employed in a long-time column process to achieve a high degree of fluoride separation from real-world groundwater. In a packed bed column investigation, the effect of bed height, initial fluoride concentration, and flow rate on the breakthrough properties of the adsorption system were investigated. By using a non-linear regression equation, three model kinetics, such as the Thomas Model, Adams-Bohart Model, and Yoon-Nelson Model, were fitted to validate the column-based experimental data, by analysing the breakthrough curves profiles, and distinct kinetic parameters. The Bed Depth Service Time Analysis (BDST) model was tested to express the effect of bed height on breakthrough curves, as well as to predict the time for breakthrough, and material depletion under optimal conditions. The Thomas and Yoon-Nelson models were identified to be the most appropriate ones for describing the entire breakthrough curve, whereas the Adams-Bohart model was only utilised to predict the first half of the dynamic process. With correlation coefficients (R²) 0.96, the experimental results were well suited to Thomas, Yoon-Nelson, and Adams-Bohart models. Finally, regeneration assessment was carried out where even after four cycles of operation, regenerated adsorbent showed a rejection efficacy of 78% to fluoride that proves the viability of the material and methodology.