Analysis of conformational polymorphism in pharmaceutical solids using solid-state NMR and electronic structure calculations

A detailed analysis of molecular structure in three polymorphic forms of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile is made using a combination of multidimensional solid-state NMR (SSNMR) experiments and molecular modeling via electronic structure calculations. These compounds, collectively referred to as ROY because of their red, orange, and yellow colors, share a similar molecular structure with the exception of the dihedral angle between the phenyl and thiophene rings. The ROY materials make it possible to study the influence of nearly a single degree of freedom on the associated NMR spectra. Using the 2D PASS (Antzutkin et al. J. Magn. Reson. A 1995, 115, 7) experiment, spectral editing techniques, and DFT-based calculations of the local fields, an analysis is made of the sensitivity of all carbon and nitrogen sites to changing molecular conformation. Chemical shift and dipolar coupling information obtained from these experiments vary noticeably between forms and are subsequently used to quantitatively determine aspects of molecular structure in these materials, including the coplanar angle between the phenyl and thiophene rings. The influence of motion on the methyl and nitro chemical shifts is also investigated. The accuracy of the information obtained from local field analysis and the model structure calculation demonstrates the capabilities of SSNMR as a quantitative structural method.     

New method to measure packing densities of self-assembled thiolipid monolayers

For a monolayer of 2,3-di-phytanyl-sn-glycerol-1-tetraethylene glycol-D,L-a-lipoic acid ester lipid (DPTL) self-assembled (SAM) at a gold electrode surface we propose a new method to determine the charge number per adsorbed molecule and the packing density (area per molecule) in the monolayer. The method relies on chronocoulometry to measure the charge density at the SAM covered gold electrode surface. Two series of measurements have to be performed. In the first series, charge densities are measured for a monolayer transferred from the air-solution to the metal-solution interface using the Langmuir-Blodgett (LB) technique. This series of measurements allows one to determine charge numbers per adsorbed DPTL molecule. The second series is performed using a gold electrode covered with a self-assembled monolayer. The charge densities obtained in this series are then used to calculate the packing density with the help of charge numbers per adsorbed DPTL determined in the first series. The area per adsorbed molecule determined by the new method was compared to the area per molecule determined by the popular reductive desorption method. The molecular area determined with the new method is about 20% larger than the area calculated from the van der Waals model, which is a physically reasonable result. In contrast, the popular reductive desorption method gives an area per molecule 20% lower than the minimum estimated based on a van der Waals model. This is a physically unreasonable result. It is also shown that the charge numbers per adsorbed molecule depend on the electrode potential and may assume values smaller than the number of electrons participating in the reductive desorption step. An explanation of the origin of the "partial charge numbers" is provided. We recommend the new method be used in future studies of thiol adsorption at metal surfaces.     

Products of the triplet excited state produced in the radiolysis of liquid benzene

The radiation chemical yields of the products derived from the triplet excited state produced in the radiolysis of liquid benzene with gamma-rays, 10 MeV 4He ions, and 10 MeV 12C ions have been determined. Iodine scavenging techniques have been used to examine the formation and role of radicals, especially the H atom and phenyl radical. For all irradiation types examined here, the increase in hydrogen iodide yields with increasing iodine concentration matches the increase in iodobenzene yields. This agreement suggests that the benzene triplet excited state is the common precursor for the H atom and the phenyl radical. Pulse radiolysis studies in liquid benzene have determined the rate coefficients for the reactions of phenyl radicals with iodine and with the solvent benzene to be 9.3 x 10(9) M(-1) s(-1) and 3.1 x 10(5) M(-1) s(-1), respectively. Direct measurements of polymer formation, which refers to trimers (C18) and higher order compounds (>C18), in liquid benzene radiolysis using gamma-rays, 4He ions, and 12C ions at relatively high doses have been performed using gel permeation chromatography. The yields of trimers increase from gamma-rays to 12C ions due to the increased importance of intratrack radical-radical reactions that can be scavenged by the radical scavenging reactions of iodine. On the other hand, the >C18 product yields decrease from gamma-rays to 12C ions. The structure of the polymer consists of a partly saturated ring as determined by infrared and gas chromatography/mass spectrometry studies. A schematic representation for the radiolytic decomposition of the benzene triplet excited state is presented.     

THE QUANTUM EFFICIENCY OF DYE-INDUCED PHOTOELECTRIC EFFECTS IN BILAYER MEMBRANES

Abstract— Voltage transients are generated across lipid bilayer membranes by light flashes as a result of photophysical processes in sorbed dyes which displace electrical charges. A theory is presented which indicates that: (i) the fraction of sorbed dye which displaces charge from one flash can be determined by the fractional reduction in the photovoltage amplitude resulting from a second and identical flash, providing the second flash occurs before dye excited by the first flash returns to its equilibrium condition. (ii) The photoeffect quantum efficiency can be determined from the fraction of dye displacing charge, the light intensity and the dyes' optical absorption cross section. Apparatus constraints required different experimental procedures for dyes with different excited state life times, which are discussed. Experimental results are presented for an azo dye, 3,3'-bis(α-(trimethyiammonium)methyl)azobenzenebromide (Bis-Q), three carbocyanine dyes in the series 3,3'-dimethyl-2,2'-oxacarbocyanine-iodide (diO-C₁-3), an amino-pyridinium dye, 4-( p -(dimethyl-amino)styryl)-1-rnethyl-pyridinium-iodide (di-1-ASP), and a xanthene dye, 2',4',5',7'-tetraiodofluorescein (erythrosin), the sodium salt of which is known as F, D and C red number 3. The dyes' optical absorption cross section values are uncertain owing to solvent and orientational effects in membranes. Photoeffect quantum efficiency values obtained by calculating optical absorption cross sections from the dyes' molar extinction coefficients in aqueous solutions are: Bis-Q (0.08), diO-C₁-3 (0.31), diO-C₂-3 (0.22), diO-C₅-3 (0.08), di-l-ASP (0.3) and erythrosin (0.39).     

Phase Behavior of a Designed Cyclopropyl Analogue of Monoolein: Implications for Low‐Temperature Membrane Protein Crystallization

Lipidic cubic phases (LCPs) are used in areas ranging from membrane biology to biodevices. Because some membrane proteins are notoriously unstable at room temperature, and available LCPs undergo transformation to lamellar phases at low temperatures, development of stable low‐temperature LCPs for biophysical studies of membrane proteins is called for. Monodihydrosterculin (MDS) is a designer lipid based on monoolein (MO) with a configurationally restricted cyclopropyl ring replacing the olefin. Small‐angle X‐ray scattering (SAXS) analyses revealed a phase diagram for MDS lacking the high‐temperature, highly curved reverse hexagonal phase typical for MO, and extending the cubic phase boundary to lower temperature, thereby establishing the relationship between lipid molecular structure and mesophase behavior. The use of MDS as a new material for LCP‐based membrane protein crystallization at low temperature was demonstrated by crystallizing bacteriorhodopsin at 20 °C as well as 4 °C.     

Inverse colloidal crystal membranes for hydrophobic interaction membrane chromatography

A collaborative study on the robustness and portability of a capillary electrophoresis‐mass spectrometry method for peptide mapping was performed by an international team, consisting of 13 independent laboratories from academia and industry. All participants used the same batch of samples, reagents and coated capillaries to run their assays, whereas they utilized the capillary electrophoresis‐mass spectrometry equipment available in their laboratories. The equipment used varied in model, type and instrument manufacturer. Furthermore, different types of sheath‐flow capillary electrophoresis–mass spectrometry interfaces were used. Migration time, peak height and peak area of ten representative target peptides of trypsin‐digested bovine serum albumin were determined by every laboratory on two consecutive days. The data were critically evaluated to identify outliers and final values for means, repeatability (precision within a laboratory) and reproducibility (precision between laboratories) were established. For relative migration time the repeatability was between 0.05 and 0.18% RSD and the reproducibility between 0.14 and 1.3% RSD. For relative peak area repeatability and reproducibility values obtained were 3–12 and 9–29% RSD, respectively. These results demonstrate that capillary electrophoresis‐mass spectrometry is robust enough to allow a method transfer across multiple laboratories and should promote a more widespread use of peptide mapping and other capillary electrophoresis‐mass spectrometry applications in biopharmaceutical analysis and related fields.     

Electron tunneling through sensitizer wires bound to proteins

We report a quantitative theoretical analysis of long-range electron transfer through sensitizer wires bound in the active-site channel of cytochrome P450cam. Each sensitizer wire consists of a substrate group with high binding affinity for the enzyme active site connected to a ruthenium-diimine through a bridging aliphatic or aromatic chain. Experiments have revealed a dramatic dependence of electron transfer rates on the chemical composition of both the bridging group and the substrate. Using combined molecular dynamics simulations and electronic coupling calculations, we show that electron tunneling through perfluorinated aromatic bridges is promoted by enhanced superexchange coupling through virtual reduced states. In contrast, electron flow through aliphatic bridges occurs by hole-mediated superexchange. We have found that a small number of wire conformations with strong donor–acceptor couplings can account for the observed electron tunneling rates for sensitizer wires terminated with either ethylbenzene or adamantane. In these instances, the rate is dependent not only on electronic coupling of the donor and acceptor but also on the nuclear motion of the sensitizer wire, necessitating the calculation of average rates over the course of a molecular dynamics simulation. These calculations along with related recent findings have made it possible to analyze the results of many other sensitizer-wire experiments that in turn point to new directions in our attempts to observe reactive intermediates in the catalytic cycles of P450 and other heme enzymes.     

The d'--d--d' vertical triad is less discriminating than the a'--a--a' vertical triad in the antiparallel coiled-coil dimer motif

Elucidating relationships between the amino-acid sequences of proteins and their three-dimensional structures, and uncovering non-covalent interactions that underlie polypeptide folding, are major goals in protein science. One approach toward these goals is to study interactions between selected residues, or among constellations of residues, in small folding motifs. The α-helical coiled coil has served as a platform for such studies because this folding unit is relatively simple in terms of both sequence and structure. Amino acid side chains at the helix-helix interface of a coiled coil participate in so-called "knobs-into-holes" (KIH) packing whereby a side chain (the knob) on one helix inserts into a space (the hole) generated by four side chains on a partner helix. The vast majority of sequence-stability studies on coiled-coil dimers have focused on lateral interactions within these KIH arrangements, for example, between an a position on one helix and an a' position of the partner in a parallel coiled-coil dimer, or between a--d' pairs in an antiparallel dimer. More recently, it has been shown that vertical triads (specifically, a'--a--a' triads) in antiparallel dimers exert a significant impact on pairing preferences. This observation provides impetus for analysis of other complex networks of side-chain interactions at the helix-helix interface. Here, we describe a combination of experimental and bioinformatics studies that show that d'--d--d' triads have much less impact on pairing preference than do a'--a--a' triads in a small, designed antiparallel coiled-coil dimer. However, the influence of the d'--d--d' triad depends on the lateral a'--d interaction. Taken together, these results strengthen the emerging understanding that simple pairwise interactions are not sufficient to describe side-chain interactions and overall stability in antiparallel coiled-coil dimers; higher-order interactions must be considered as well.     

Hybrid protein-lipid patterns from aluminum templates

An aqueous aluminum liftoff process suitable for fabrication of hybrid patterns of protein and supported lipid membrane on silica surfaces is described. Patterned aluminum thin films, which can be produced by conventional optical or electron beam lithography, are employed as sacrificial protecting layers to define the geometry of the protein-lipid patterns. The aluminum is lifted off in a mildly basic aqueous solution, which preserves the integrity of bound protein layers. The newly exposed substrate can then be filled with supported membrane by exposure to an aqueous vesicle suspension. The final substrate consists of patterned protein and lipid membranes with spatial resolution determined by aluminum patterns, down to 200 nm line widths in this case. Inorganic surfaces were characterized by atomic force microscopy and X-ray photoelectron spectroscopy while supported bilayers and protein patterns were characterized by epifluorescence microscopy.     

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

A general molecular mechanics (MM) model for treating aqueous Cu²⁺ and Zn²⁺ ions was developed based on valence bond (VB) theory and incorporated into the atomic multipole optimized energetics for biomolecular applications (AMOEBA) polarizable force field. Parameters were obtained by fitting MM energies to that computed by ab initio methods for gas‐phase tetra‐ and hexa‐aqua metal complexes. Molecular dynamics (MD) simulations using the proposed AMOEBA‐VB model were performed for each transition metal ion in aqueous solution, and solvent coordination was evaluated. Results show that the AMOEBA‐VB model generates the correct square‐planar geometry for gas‐phase tetra‐aqua Cu²⁺ complex and improves the accuracy of MM model energetics for a number of ligation geometries when compared to quantum mechanical (QM) computations. On the other hand, both AMOEBA and AMOEBA‐VB generate results for Zn²⁺–water complexes in good agreement with QM calculations. Analyses of the MD trajectories revealed a six‐coordination first solvation shell for both Cu²⁺ and Zn²⁺ ions in aqueous solution, with ligation geometries falling in the range reported by previous studies. © 2012 Wiley Periodicals, Inc.