Application of QM simulations and multivariate analysis in the study of alkene reactivity in the zeolite H‐ZSM5

Reported herein are the results of an investigation into the effect of the extended framework of the zeolite ZSM‐5 on the reaction energetics and structures of (a) the physisorbed complex formed between the zeolite and six alkenes, (b) the corresponding chemisorbed alkoxide intermediate and (c) the transition states (TS) connecting the two. For this, quantum mechanical (QM) simulations of ZSM‐5 in the presence and absence of the zeolite framework have been employed. A 46T density functional theory (DFT) cluster model and a 3T:46T DFT:UFF ONIOM model are used to represent the former scenario and a simple 3T DFT cluster model for the latter. The structural implications of neglecting the zeolite framework have been rigorously compared using the multivariate statistical method principal components analysis (PCA). This method allows one to assess the correlated nature of the changes in structure along the reaction coordinate, for multiple different alkenes, in a facile, reliable way. Copyright © 2008 John Wiley & Sons, Ltd.     

Theoretical analysis of peptidyl alpha-ketoheterocyclic inhibitors of human neutrophil elastase: Insight into the mechanism of inhibition and the application of QM/MM calculations in structure-based drug design

It has been suggested from QSAR data (P. D. Edwards, D. J. Wolanin, D.A. Andisik and M. W. Davis, J. Med. Chem., 1995, 38, 76) that the inhibition of elastase by peptidyl alpha-ketoheterocyclic inhibitors can occur in two ways, the less potent inhibitors forming a non-bonded Michaelis complex and the more potent set a covalently bonded enzyme-substrate intermediate. We report QM/MM studies of both binding and reactivity that confirm these findings, showing that the activity of the least potent set of inhibitors correlates with the calculated binding energy, and that of the more potent set correlates with the stability of the intermediate. These calculations show that QM/MM methods can be successfully employed to understand complicated structure-activity relationships and might be employed in the design and assessment of new inhibitors.     

Prediction of the potency of inhibitors of adenosine deaminase by QM/MM calculations

QM/MM calculations show that the potency of a range of inhibitors of adenosine deaminase correlates with the relative stability of the reaction intermediate at the active site, rather than with the inhibitor binding energy.     

Laser-induced concentric colour domains in a cholesteric liquid crystal mixture containing a nematic azobenzene dopant

The isothermal formation of concentric colour domains has been observed in a cholesteric mixture doped with 10 wt % of a photochromic nematic material. The host cholesteric mixture included the Merck materials BL131a and BL130, while the photochromic dopant was a mixture of 4-n-butyl-4'-n-alkoxyazobenzenes (BAAB). The helical pitch of the host cholesteric mixture was increased, as expected, on addition of the photochromic nematic material prior to irradiation with the molecules in the purely trans-configuration. On irradiation with low power (0.6 mW) argon ion laser light, cis-isomers formed within the interaction region and concentric colour domains appeared. Selective reflection from the colour domains occurred in the 400-560 nm spectral range. The coloured domains persisted in the time period following irradiation and extended beyond the interaction region because of diffusion of the cis-isomers. Using the diffusion equation, an expression has been obtained for the average concentration of cis-isomers in each of the coloured domains and the dependence of the reflection wavelength upon the concentration of cis-isomers has been determined.     

Material characterization for electroconvection

We report a set of material characterizations on the nematic mixture Mischung V . With these measurements, as well as previously known results, Mischung V becomes the second nematic liquid crystal possessing a complete set of known physical parameters relevant for electroconvection, enabling quantitative comparison with theoretical predictions to be made. Additionally, we have identified a stable dopant which induces in Mischung V the electrical conductivity necessary for observing the conduction regime of electroconvection. Mischung V is thus validated as a suitable substitute for materials that have traditionally been chosen for these types of experiments. However, Mischung V does not present the same experimental difficulties as traditional materials.     

Synthesis,Cytotoxicity and Antibacterial Studies of Novel Symmetrically and Nonsymmetrically 4‐(Methoxycarbonyl)benzyl‐Substituted N‐Heterocyclic Carbene–Silver Acetate Complexes

From the reaction of 1H‐imidazole ( 1a ), 4,5‐dichloro‐1H‐imidazole ( 1b ), 1H‐benzimidazole ( 1c ), 1‐methyl‐1H‐imidazole ( 1d ), and 1‐methyl‐1H‐benzimidazole ( 1f ) with methyl 4‐(bromomethyl)benzoate ( 2 ), symmetrically and nonsymmetrically 4‐(methoxycarbonyl)benzyl‐substituted N‐heterocyclic carbene (NHC) precursors, 3a – 3f , were synthesized. These NHC precursors were then reacted with silver(I) acetate (AgOAc) to yield the NHC–silver acetate complexes (acetato‐κO){1,3‐bis[4‐(methoxycarbonyl)benzyl]imidazol‐2‐ylidene}silver ( 4a ), (acetato‐κO){4,5‐dichloro‐1,3‐bis[4‐(methoxycarbonyl)benzyl]‐2,3‐dihydro‐1H‐imidazol‐2‐yl}silver ( 4b ), (acetato‐κO){1,3‐bis[4‐(methoxycarbonyl)benzyl]‐2,3‐dihydro‐1H‐benzimidazol‐2‐yl}silver ( 4c ), (acetato‐κO){1‐[4‐(methoxycarbonyl)benzyl]‐3‐methyl‐2,3‐dihydro‐1H‐imidazol‐2‐yl}silver ( 4d ), (acetato‐κO){4,5‐dichloro‐1‐[4‐(methoxycarbonyl)benzyl]‐3‐methyl‐2,3‐dihydro‐1H‐imidazol‐2‐yl}silver ( 4e ), and (acetato‐κO){1‐[4‐(methoxycarbonyl)benzyl]‐3‐methyl‐2,3‐dihydro‐1H‐benzimidazol‐2‐yl}silver ( 4f ), respectively. The three NHC–AgOAc complexes 4a, 4c , and 4d were characterized by single‐crystal X‐ray diffraction. All compounds studied in this work were preliminarily screened for their antimicrobial activities in vitro against Gram‐positive bacteria Staphylococcus aureus, and Gram‐negative bacteria Escherichia coli using the qualitative disk‐diffusion method. All NHC–AgOAc complexes exhibited weak‐to‐medium antibacterial activity with areas of clearance ranging from 4 to 7 mm at the highest amount used, while the NHC precursors showed significantly lower activity. In addition, NHC–AgOAc complexes 4a and 4b , and 4d – 4f exhibited in preliminary cytotoxicity tests on the human renal‐cancer cell line Caki‐1 medium‐to‐high cytotoxicities with IC₅₀ values ranging from 3.3±0.4 to 68.3±1 μM .     

Tricritical point in heterogeneous k-core percolation

k-core percolation is an extension of the concept of classical percolation and is particularly relevant to understanding the resilience of complex networks under random damage. A new analytical formalism has been recently proposed to deal with heterogeneous k-cores, where each vertex is assigned a local threshold k(i). In this Letter we identify a binary mixture of heterogeneous k-cores which exhibits a tricritical point. We investigate the new scaling scenario and calculate the relevant critical exponents, by analytical and computational methods, for Erd?s-Rényi networks and 2D square lattices.