Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases

The successful application of high throughput molecular simulations to determine biochemical properties would be of great importance to the biomedical community if such simulations could be turned around in a clinically relevant timescale. An important example is the determination of antiretroviral inhibitor efficacy against varying strains of HIV through calculation of drug-protein binding affinities. We describe the Binding Affinity Calculator (BAC), a tool for the automated calculation of HIV-1 protease-ligand binding affinities. The tool employs fully atomistic molecular simulations alongside the well established molecular mechanics Poisson-Boltzmann solvent accessible surface area (MMPBSA) free energy methodology to enable the calculation of the binding free energy of several ligand-protease complexes, including all nine FDA approved inhibitors of HIV-1 protease and seven of the natural substrates cleaved by the protease. This enables the efficacy of these inhibitors to be ranked across several mutant strains of the protease relative to the wildtype. BAC is a tool that utilizes the power provided by a computational grid to automate all of the stages required to compute free energies of binding: model preparation, equilibration, simulation, postprocessing, and data-marshaling around the generally widely distributed compute resources utilized. Such automation enables the molecular dynamics methodology to be used in a high throughput manner not achievable by manual methods. This paper describes the architecture and workflow management of BAC and the function of each of its components. Given adequate compute resources, BAC can yield quantitative information regarding drug resistance at the molecular level within 96 h. Such a timescale is of direct clinical relevance and can assist in decision support for the assessment of patient-specific optimal drug treatment and the subsequent response to therapy for any given genotype.     

Fluorenes and styrenes by Au(I)-catalyzed annulation of enynes and alkynes

Intermolecular annulation of enynes and propargyl esters to selectively produce styrenes or fluorenes is reported. The divergent arene syntheses involve a Au-catalyzed, two-pot, multistep process proceeding by cis-diastereoselective cyclopropanation, cycloisomerization, and, finally, annulation or elimination.     

Synthesis, redox, and amphiphilic properties of responsive salycilaldimine-copper(II) soft materials

Hydrolysis of the asymmetric pyridine- and phenol-containing ligand HL (1) (2-hydroxy-4-6-di- tert-butylbenzyl-2-pyridylmethyl)imine) led to the use of bis-(3,5-di -tert-butyl-2-phenolato-benzaldehyde)copper(II), [Cu (II)(L (SAL)) 2] ( 1) as a precursor for bis-(2,4-di- tert-butyl-6-octadecyliminomethyl-phenolato)copper(II), [Cu (II)(L (2)) 2] ( 3), bis-(2,4-di- tert-butyl-6-octadecyl aminomethyl-phenolato)copper(II), [Cu (II)(L (2A)) 2] ( 3'), and bis-(2,4-di- tert-butyl-6-[(3,4,5-tris-dodecyloxy-phenylimino)-methyl]-phenolato)copper(II), [Cu (II)(L (3)) 2] ( 4). These complexes exhibit hydrophilic copper-containing head groups, hydrophobic alkyl and alkoxo tails, and present potential as precursors for redox-responsive Langmuir-Blodgett films. All systems were characterized by means of elemental, spectrometric, spectroscopic, and electrochemical techniques, and their amphiphilic properties were probed by means of compression isotherms and Brewster angle microscopy. Good redox activity was observed for 3 with two phenoxyl radical processes between 0.5 and 0.8 V vs Fc (+)/Fc, but this complex lacks amphiphilic behavior. To attain good balance between redox response and amphiphilicity, increased core flexibility in 3' and incorporation of alkoxy chains in 4 were attempted. Film formation with collapse at 14 mN.m (-1) was observed for the alkoxy-derivative but redox-response was seriously compromised. Core flexibility improved Langmuir film formation with a higher formal collapse and showed excellent cyclability of the ligand-based processes.     

Influence of the apical ligand in the thermotropic mesomorphism of cationic copper-based surfactants

A new pyridine-based bidentate ligand L (PyC18) was used to develop copper-containing surfactants that exhibit mesomorphism. Complexes [(L (PyC18)) 2Cu (II)Y]Y were synthesized, where Y is an anionic ligand bromo ( 1), nitrato ( 2), or perchlorato ( 3). The nature of these apical ligands determines the mesogenic behavior of 1- 3: The smallest bromo-substituted species 1 shows a metastable liquid crystalline phase at 110 degrees C, the nitrato-substituted 2 increases the transition temperature to 136 degrees C, and the bulky perchlorato-substituted 3 shows reversible mesophases at 153 degrees C. The behavior of these complexes shows similarities and suggests that at low temperatures the crystals of these compounds are bilayered structures with interdigitated alkyl tails. At higher temperatures the tails undergo rapid conformational changes that force these layers to swell until the opposing alkyl chains are separated from each other, and the mesophase is a monolayer smectic A. Small changes in the geometry of cationic mesogens can be imposed by the presence of apically coordinated anions, allowing for tuning in the properties of the resulting mesophases.     

Effects of excited state-excited state configurational mixing on emission bandshape variations in ruthenium-bipyridine complexes

The 77 K emission spectra of 21 [Ru(L) 4bpy] ( m+ ) complexes for which the Ru/bpy metal-to-ligand-charge-transfer ( (3)MLCT) excited-state energies vary from 12 500 to 18 500 cm (-1) have vibronic contributions to their bandshapes that implicate excited-state distortions in low frequency ( lf; hnu lf < 1000 cm (-1)), largely metal-ligand vibrational modes which most likely result from configurational mixing between the (3)MLCT and a higher energy metal centered ( (3)LF) excited state. The amplitudes of the lf vibronic contributions are often comparable to, or sometimes greater than those of medium frequency ( mf; hnu mf > 1000 cm (-1)), largely bipyridine (bpy) vibrational modes, and for the [Ru(bpy) 3] (2+) and [Ru(NH 3) 4bpy] (2+) complexes they are consistent with previously reported resonance-Raman (rR) parameters. However, far smaller lf vibronic amplitudes in the rR parameters have been reported for [Os(bpy) 3 ] (2+), and this leads to a group frequency approach for interpreting the 77 K emission bandshapes of [Ru(L) 4bpy] ( m+ ) complexes with the vibronic contributions from mf vibrational modes referenced to the [Os(bpy) 3] (2+) rR parameters (OB3 model) and the envelope of lf vibronic components represented by a "progression" in an "equivalent" single vibrational mode ( lf1 model). The lf1 model is referenced to rR parameters reported for [Ru(NH 3) 4bpy] (2+). The observation of lf vibronic components indicates that the MLCT excited-state potential energy surfaces of Ru-bpy complexes are distorted by LF/MLCT excited-state/excited-state configurational mixing, but the emission spectra only probe the region near the (3)MLCT potential energy minimum, and the mixing can lead to larger distortions elsewhere with potential photochemical implications: (a) such distortions may labilize the (3)MLCT excited state; and (b) the lf vibrational modes may contribute to a temperature dependent pathway for nonradiative relaxation.     

Analysis of carbohydrates in Lupinus albus stems on imposition of water deficit, using porous graphitic carbon liquid chromatography-electrospray ionization mass spectrometry

This work reports the development and application of a negative ion mode online LC-ESI-MS method for studying the effect of water deficit on the carbohydrate content of Lupinus albus stems, using a porous graphitic carbon (PGC) stationary phase and an ion trap mass spectrometer. Using this method, separation and detection of several water soluble carbohydrates, ranging from mono-, di-, and oligosaccharides (raffinose, stachyose, and verbascose) to sugar alcohols was achieved in approximately 10 min. This on-line PGC-LC-ESI-MS method shows good linearity with correlation coefficients R(2)>0.99, selectivity, short analysis time, and limits of detection (LOD) ranging from 0.4 to 9 pmol for sugars and 4-20 pmol for sugar alcohols. This PGC-LC-ESI-MS method is sensitive and allowed us to detect even small alterations in carbohydrate levels in L. albus stems that resulted from a mild/early water deficit (nmol g(-1)DW). This paper describes details of our method and its application to the quantitative analysis of water soluble underivatised carbohydrates extracted from L. albus stem tissues that have been subjected to early and severe water deficit conditions, followed by a rewatering period.     

Reaction of fluorogenic reagents with proteins III. Spectroscopic and electrophoretic behavior of proteins labeled with Chromeo P503

The spectroscopic and electrophoretic properties of proteins labeled with Chromeo P503 were investigated. Its photobleaching characteristics were determined by continually infusing Chromeo P503-labeled alpha-lactalbumin into a sheath-flow cuvette and monitored fluorescence as a function of laser power. The labeled protein is relatively photo-labile with an optimum excitation power of about 2 mW. The unreacted reagent is weakly fluorescent but present at much higher concentration than the labeled protein. The unreacted reagent undergoes photobleaching at a laser power more than an order of magnitude higher than the labeled protein. One-dimensional capillary electrophoresis analysis of Chromeo P503-labeled alpha-lactalbumin produced concentration detection limits (3sigma) of 12 pM and mass detection limits of 0.7 zmol, but with modest theoretical plate counts of 17,000. The reagent was employed for the two-dimensional capillary electrophoresis analysis of a homogenate prepared from a Barrett's esophagus cell line; the separation quality is similar to that produced by 3-(2-furoyl)quinoline-2-carboxaldehyde (FQ), a more commonly used reagent.     

G3 and density functional theory investigations of the structures and energies of SF(n)Cl (n=0-5) and their anions

Computations of structures and total energies have been carried out for neutral and anionic SF(n)Cl (n=0-5), using the composite G3 method and density functional theory (DFT) at the B3LYP6-311+G(3df) level. The total energies and zero-point energies have been used here to derive electron affinities, bond dissociation energies, and heats of formation. In addition, vibrational frequencies, polarizabilities, and dipole moments are reported. Results are compared with earlier work for SF(m) (m=1-6) and demonstrate how the relatively weak S-Cl bond and reduced symmetry influence the properties of these molecules and anions. Comparisons are also made between G3 and DFT results for SF(n)Cl. Of particular interest is the alternating pattern of agreement between calculated electron affinity values with n. These calculations also provide critical energetic data needed to understand experimental measurements of electron attachment to SF(5)Cl [Van Doren et al., J. Chem. Phys. 128, 094309 (2008)] for which numerous ion products have been reported in the literature at low electron energy.     

Perspectives on the crystal densities and packing coefficients of explosive compounds

We have investigated possible relationships between four crystal properties: experimental densities and computed intrinsic molecular volumes, packing coefficients and amounts of free space per molecule in the crystal lattices. Our focus was upon C-, H-, N-, O-containing explosive compounds. The objectives were to gain some insight into how densities might be increased, to improve detonation performance, and the amounts of free space per molecule decreased, to counter one of the factors promoting undesired sensitivity to accidental stimuli. The issue of molecular planarity was also examined. The best correlation found between the four properties is perhaps a surprising one: The free space per molecule increases as the molecules are bigger. On the other hand, some relationships that seem to be intuitively reasonable turn out to be quite weak. The principal positive conclusions are that it is desirable for explosive compounds to be composed of molecules that are small and preferably planar.

     

Fluorinated Azobenzenes for Shape‐Persistent Liquid Crystal Polymer Networks

Liquid crystal polymer networks respond with an anisotropic deformation to a range of external stimuli. When doped with molecular photoswitches, these materials undergo complex shape modifications under illumination. As the deformations are reversed when irradiation stops, applications where the activated shape is required to have thermal stability have been precluded. Previous attempts to incorporate molecular switches into thermally stable photoisomers were unsuccessful at photogenerating macroscopic shapes that are retained over time. Herein, we show that to preserve photoactivated molecular deformation on the macroscopic scale, it is important not only to engineer the thermal stability of the photoswitch but also to adjust the cross‐linking density in the polymer network and to optimize the molecular orientations in the material. Our strategy resulted in materials containing fluorinated azobenzenes that retain their photochemical shape for more than eight days, which constitutes the first demonstration of long‐lived photomechanical deformation in liquid‐crystal polymer networks.