Diffusion on a self-assembled monolayer: molecular modeling of a bound + mobile lubricant

The diffusion of tricresyl phosphate molecules on an octadecyltrichlorosilane self-assembled monolayer (SAM) was characterized using molecular dynamics simulations. The simulations predict that when placed on the top of a close-packed SAM, the molecules remain mobile on the surface with an isotropic diffusion activation energy of approximately 9 kJ/mol. In contrast, an anisotropic barrier that results from chain tilt within the SAM is predicted for diffusion into a defect created by reducing the alkane chain length within a cylinderical region of the surface. Once in the defect, the molecules become trapped by embedding part of the molecule into the side of the SAM.     

Isomerism due to the rotation of an alkyl side-chain attached to a heterocyclic ring: Crystal and molecular structure of two forms of 6-nitro-2,4-bis(1′,1′,2′-trichloropropyl)-1,3-benzdioxin

Compound I crystallizes in the space groupP2₁/c withZ=4,a=5.889(5),b=30.755(10),c=10.815(3) Å,=92.95(6)°. Compound II crystallizes in the space groupP2₁/n withZ=4,a=10.235(2),b=10.144(1),c=18.346(2) Å,=92.00(1)°. The structures were solved by direct methods and refined by full-matrix least squares, from room-temperature data obtained with an Enraf-Nonius CAD4 diffractometer, to conventionalR factors of 0.041 for I and 0.048 for II.In both isomers the dioxin ring has an approximate envelope conformation with a pseudoequatorial –CC1₂·CHCl·CH₃ group in the 2-position and a pseudoaxial –CCl₂·CHCl·CH₃ group in the 4-position. The molecular structures of I and II differ in that the group at the 2-position is rotated by about 120° in one isomer relative to its position in the other. Both compounds have packing patterns with a wave motif. In II there are interactions of the –NO₂ group with other atoms both between molecules in the same wave and also between molecules in adjacent waves. In I the interactions of the –NO₂ group with other atoms are in the same wave only with adjacent waves being packed together by van der Waals forces alone.     

The N,N-diacetylaminobenzene group in the structure of 6-methyl-8-N,N-diacetylamino-2,4-bis(trichloromethyl)-1,3-benzdioxin

Crystals of 6-methyl-8-N,N-diacetylamino-2,4-bis(trichloromethyl)-1,3-benzdioxin are triclinic, P¯1,Z=2,a=9.586(3),b=9.914(2),c=12.308(5) Å,=67.19(3),=71.95(3), =74.14(2)°. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 difFractometer, and refined by least squares to a finalR value of 0.039 using 3038 reflections. The heterocyclic ring has an envelope conformation. Of thecis-CCl₃ groups one CC1₃ group is pseudoequatorial while the –(C_Ar·C)CCl₃ group is pseudoaxial. (C_Ar)O-C 1.405(4); (C_Ar·O)C-O 1.387(4) Å; C_Ar-C(C_ax)-0 112.3(3); C(C_ax)-O-C(C_eq) 116.1(2)°; (C_Ar)O-C-O-C(C_Ar)58.2(3)°. The configuration of the diacetylamino group (DAA) issyn-anti. The -systems of the DAA and of the aromatic ring are approximately orthogonal, the deviations from orthogonality probably being caused by an intermolecular bifurcated hydrogen bond, each such interaction involving two molecules only, between thesyn O(=C) of the DAA and both hydrogen atoms bonded to the heterocyclic ring in a molecule of the enantiomer. The geometry of the DAA-benzene fragment is compared with those found in the other three published X-ray structures containing this group.     

Crystal and molecular structure of 6-nitro-1,3-benzdioxin: Comparison with the molecular structures of the 2,4-bis(dichloromethyl) and 2,4-bis(trichloromethyl) derivatives

6-Nitro-1,3-benzdioxin is orthorhombic,Pbca,a=7.278(4),b=19.292(3),c=10.978(1) Å,Z=8. The structure was solved by direct methods from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer and refined by least squares to a finalR value of 0.041 using 725 reflections. Some parameters associated with the heterocycle are torsion angle (C_Ar)O-C-O-C(C_Ar) 69.1(4)°; bond lengths C_Ar-O 1.362(3), (C_Ar)O-C 1.434(5), (C_Ar.O)C-O 1.377(5), O-C(C_Ar) 1.431(5), C-C_Ar 1.501(5) Å; bond angles C_Ar-O-C 113.5(3), O-C-O 111.5(3), C-O-C(C_Ar) 110.3(3), O-C-C_Ar 109.9(3)°;H_axH_ax 2.52(5) Å.     

Structure of the α-(allcis) form of 2,4,6-tris(trichloromethyl)-1-oxa-3,5-dithian

The higher-melting (mp 236°C)-isomer of dithioparachloral, i.e.,-2,4,6-tris(trichloromethyl)-1-oxa-3,5-dithian, is orthorhombic,Pnma,a=9.983(2),b=15.318(2),c=10.416(2) Å,V=1592.81 ų,Z=4. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least-squares to a finalR value of 0.040 using 1017 reflections. The molecule is in the chair conformation with all threecis-CCl₃ groups located pseudoequatorially. Endocyclic parameters are: torsion angles (deg) C-O-C-S 75.1(3), O-C-S-C –63.2(3), C-S-C-S 62.4(3); angles (deg) C-O-C 111.9(2), O-C-S 112.6(3), C-S-C 94.8(2), S-C-S 113.2(1); bond lengths (Å) O-C 1.426(5), C-S 1.824(4), S-C 1.818(3) (quoted in cyclic order).     

Structure and conformation of 6,8-dinitro-2,4-bis(trichloromethyl)-1,3-benzdioxin: X-ray crystallographic determination

6,8-dinitro-2,4-bis(trichloromethyl)-1,3-benzdioxin is monoclinic,P2₁/c,Z=4,a=12.348(2),b=11.575(3),c=12.183(4) Å,=107.48(2)°. The structure was solved by direct methods, from data collected at room temperature on an Enraf-Nonius CAD4 diffractometer, and refined by least-squares to a finalR value of 0.032 using 2192 reflections. The heterocyclic ring is an envelope structure, the dihedral angle between the plane of the aromatic ring and that containing five of the atoms of the heterocycle being 4.98(6)°. One -CCl₃ group is pseudoequatorial while the (Ar-C)CCl₃ group is pseudoaxial. C-C_eq 1.526(3) Å; C-C_ax 1.537(3) Å; C-C(C_ax)-O 112.4(2)°; C(C_ax)-O-C(C_eq) 115.2(2)°.     

Discontinuously propagating waves in the bathoferroin-catalyzed Belousov-Zhabotinsky reaction incorporated into a microemulsion

Three new types of discontinuously propagating waves are reported in the bathoferroin-catalyzed Belousov-Zhabotinsky (BZ) reaction dispersed in water-in-oil Aerosol OT microemulsion. Jumping waves (JWs) are typically observed at or above room temperature and develop from the familiar trigger waves. Bubble waves (BWs) typically emerge from trigger or JWs at similar temperatures, while rotating waves (RWs) evolve from JW at higher temperatures (>40 degrees C). All these waves propagate discontinuously in a saltatory fashion. Other characteristic features include a discontinuous front for BW consisting of small concentric waves (bubbles) and lateral rotation of annular RWs. All three types of waves, as well as segmented but continuously propagating waves, can coexist. A simple model that is able to describe both jumping and segmented waves is described.     

The development of an immobilized enzyme reactor containing glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi: the effect of species' specific differences on the immobilization

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in the life cycle of the Trypanosoma cruzi, and an immobilized enzyme reactor (IMER) has been developed for use in the on-line screening for GAPDH inhibitors. An IMER containing human GAPDH has been previously reported; however, these conditions produced a T. cruzi GAPDH-IMER with poor activity and stability. The factors affecting the stability of the human and T. cruzi GAPDHs in the immobilization process and the influence of pH and buffer type on the stability and activity of the IMERs have been investigated. The resulting T. cruzi GAPDH-IMER was coupled to an analytical octyl column, which was used to achieve chromatographic separation of NAD(+) from NADH. The production of NADH stimulated by d-glyceraldehyde-3-phosphate was used to investigate the activity and kinetic parameters of the immobilized T. cruzi GAPDH. The Michaelis-Menten constant (K(m)) values determined for d-glyceraldehyde-3-phosphate and NAD(+) were K(m) = 0.5 +/- 0.05 mM and 0.648 +/- 0.08 mM, respectively, which were consistent with the values obtained using the non-immobilized enzyme.     

Prediction and analysis of binding affinities for chemically diverse HIV-1 PR inhibitors by the modified SAFE_p approach

One of the biggest challenges in the "in silico" screening of enzyme ligands is to have a protocol that could predict the ligand binding free energies. In our group we have developed a very simple screening function (referred to as solvent accessibility free energy of binding predictor, SAFE_p) which we have applied previously to the study of peptidic HIV-1 protease (HIV-1 PR) inhibitors and later to cyclic urea type HIV-1 PR inhibitors. In this work, we have extended the SAFE_p protocol to a chemically diverse set of HIV-1 PR inhibitors with binding constants that differ by several orders of magnitude. The resulting function is able to reproduce the ranking and in many cases the value of the inhibitor binding affinities for the HIV-1 PR, with accuracy comparable with that of costlier protocols. We also demonstrate that the binding pocket SAFE_p analysis can contribute to the understanding of the physical forces that participate in ligand binding. The analysis tools afforded by our protocol have allowed us to identify an induced fit phenomena mediated by the inhibitor and have demonstrated that larger fragments do not necessarily contribute the most to the binding free energy, an outcome partially brought about by the substantial role the desolvation penalty plays in the energetics of binding. Finally, we have revisited the effect of the Asp dyad protonation state on the predicted binding affinities.     

Determination of free and protein-bound glutathione in HepG2 cells using capillary electrophoresis with laser-induced fluorescence detection

A rapid method using capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) was developed to determine free and protein-bound glutathione (GSH) in human HepG2 hepatocarcinoma cells. The samples were derivatized with 5-iodoacetamidofluorescein (5-IAF), and analyzed at 22 kV using sodium phosphate buffer (10mM, pH 11.4) and an uncoated 58 cm x 75 microm I.D. fused silica capillary. The analysis time was less than 10 min and N-acetylcysteine was used as internal standard. The derivatization conditions, such as reaction time, 5-IAF concentration, running buffer and cartridge temperature were optimized. Argon gas was used in the study to prevent the oxidization of GSH during sample preparation. The optimized method required only 30-40 nl sample per analysis and was fast and sensitive. The method was applied to the analyses of HepG2 cells treated with the small metal chelating agent, pyrrolidine dithiocarbamate (PDTC). The results demonstrate that the amount of protein-bound GSH, which reflects the amount of protein S-glutathionylation, increased in a time-dependent manner upon cell treatment with PDTC, reaching a maximum of over 50% increase 2h post-PDTC.