Stepwise solvation of an amino acid: the appearance of zwitterionic structures

How many solvent molecules are required to solvate an amino acid? This apparently simple question, which relates to the number of solvent molecules necessary to change the amino acid from its gas-phase neutral structure to the zwitterionic solvated structure, remains unanswered to date. Here we present experimental and theoretical (density functional theory: B3LYP/6-31+G**) infrared spectra for tryptophan-watern complexes where n = 1-6, which suggest that the zwitterionic structure becomes competitive in energy at the high end of the series. Compelling evidence for a gradual transition to zwitterionic structures comes from tryptophan-methanol complexes up to n = 9. Starting from n = 5, the infrared spectra show increasing intensity in the diagnostic asymmetric COO- stretch and in the weaker NH3+ bending modes as the cluster size increases. Moreover, convergence toward the Fourier transform infrared spectrum of a solution of tryptophan in methanol is clearly observed. For small solvent complexes (n = 1-4), the microsolvation by methanol and water is shown to behave very similarly. A detailed comparison of the experimental and the theoretical spectra allows us to determine both the preferred solvent binding sites on the amino acid and the evolution of conformational structures of tryptophan as the number of attached solvent molecules increases.     

Nanoscale protein pores modified with PAMAM dendrimers

We describe nanoscale protein pores modified with a single hyperbranched dendrimer molecule inside the channel lumen. Sulfhydryl-reactive polyamido amine (PAMAM) dendrimers of generations 2, 3 and 5 were synthesized, chemically characterized, and reacted with engineered cysteine residues in the transmembrane pore alpha-hemolysin. Successful coupling was monitored using an electrophoretic mobility shift assay. The results indicate that G2 and G3 but not G5 dendrimers permeated through the 2.9 nm cis entrance to couple inside the pore. The defined molecular weight cutoff for the passage of hyperbranched PAMAM polymers is in contrast to the less restricted accessibility of flexible linear poly(ethylene glycol) polymers of comparable hydrodynamic volume. Their higher compactness makes sulfhydryl-reactive PAMAM dendrimers promising research reagents to probe the structure of porous membrane proteins with wide internal diameters. The conductance properties of PAMAM-modified proteins pores were characterized with single-channel current recordings. A G3 dendrimer molecule in the channel lumen reduced the ionic current by 45%, indicating that the hyperbranched and positively charged polymer blocked the passage of ions through the pore. In line with expectations, a smaller and less dense G2 dendrimer led to a less pronounced current reduction of 25%. Comparisons to recordings of PEG-modified pores revealed striking dissimilarities, suggesting that differences in the structural dynamics of flexible linear polymers vs compact dendrimers can be observed at the single-molecule level. Current recordings also revealed that dendrimers functioned as ion-selectivity filters and molecular sieves for the controlled passage of molecules. The alteration of pore properties with charged and hyperbranched dendrimers is a new approach and might be extended to inorganic nanopores with applications in sensing and separation technology.     

Reactivity studies on Fe(III)-(O2(2-))-Cu(II) compounds: influence of the ligand architecture and copper ligand denticity

Heme-Cu/O2 adducts are of interest in the elucidation of the fundamental metal-O2 chemistry occurring in heme-Cu enzymes which effect reductive O-O cleavage of dioxygen to water. In this report, the chemistry of four heme-peroxo-copper [FeIII-(O22-)-CuII]+ complexes (1-4), varying in their ligand architecture, copper-ligand denticity, or both and thus their structures and physical properties are compared in their reactivity toward CO, PPh3, acids, cobaltocene, and phenols. In 1 and 2, the copper(II) ligand is N4-tetradentate, and the peroxo unit is bound side-on to iron(III) and end-on to the copper(II). In contrast, 3 and 4 contain a N3-tridentate copper(II) ligand, and the peroxo unit is bound side-on to both metal ions. CO "displaces" the peroxo ligand from 2-4 to form reduced CO-FeII and CO-CuI species. PPh3 reacts with 3 and 4 displacing the peroxide ligand from copper, forming (porphyrinate)FeIII-superoxide plus CuI-PPh3 species. Complex 2 does not react with PPh3, and surprisingly, 1 reacts neither with PPh3 nor CO, exhibiting remarkable stability toward these reagents. The behavior of 1 and 2 compared to that of 3 and 4 correlates with the different denticity of the copper ligand (tetra vs tridentate). Complexes 1-4 react with HCl releasing H2O2, demonstrating the basic character of the peroxide ligand. Cobaltocene causes the two-electron reduction of 1-4 giving the corresponding micro-oxo [FeIII-(O2-)-CuII]+ complexes, in contrast to the findings for other heme-peroxo-copper species of different design. With t-butyl-substituted phenols, no reaction occurs with 1-4. The results described here emphasize how ligand design and variations influence and control not only the structure and physical properties but also the reactivity patterns for heme-Cu/O2 adducts. Implications for future investigations of protonated heme/Cu-peroxo complexes, low-spin analogues, and ultimately O-O cleavage chemistry are discussed.     

Synthesis and theoretical studies on rare three-coordinate lead complexes

A series of beta-diketiminate lead halide complexes has been synthesised LPbCl (2), LPbBr (3) and LPbI (4) (L = {N(2,6-(i)Pr(2)C(6)H(3))C(Me)}2CH]), which includes a rare example of a three-coordinate lead iodide (4). The chloride and bromide complexes, 2 and 3, are relatively stable in both the solid and solution states, only slowly decomposing to elemental lead over the course of a month in solution, the lead iodide 4 appears to be less stable and decomposes after 3 d in the solid state at ambient temperatures. The lead chloride complex 2 was treated with KN(SiMe3)2 to yield an unusual terminal lead amide complex LPbN(SiMe3)2 (5). Unlike three-coordinate beta-diketiminate transition metal-halide complexes, the ligands are present in a pyramidal arrangement around the lead centre, commonly attributed to the presence of a stereochemically active lone pair. We have investigated the influence of this lone pair on the geometry of the metal halide complexes 2-4, as well as the isostructural germanium and tin complexes (6 and 7, respectively) using DFT calculations. The lone pair in the lead complexes is significantly more diffuse than in the tin and germanium analogues and only a small amount of hybridisation between the 6s and 6p orbitals is observed.     

Reaction products in mass spectrometry elucidated with infrared spectroscopy

Determining the structure and dynamics of large biologically relevant molecules is one of the key challenges facing biology. Although X-ray crystallography (XRD) and nuclear magnetic resonance (NMR) yield accurate structural information, they are of limited use when sample quantities are low. Mass spectrometry (MS) on the other hand has been very successful in analyzing biological molecules down to atto-mole quantities and has hence begun to challenge XRD and NMR as the key technology in the life sciences. This trend has been further assisted by the development of MS techniques that yield structural information on biomolecules. Of these techniques, collision-induced dissociation (CID) and hydrogen/deuterium exchange (HDX) are among the most popular. Despite advances in applying these techniques, little direct experimental evidence had been available until recently to verify their proposed underlying reaction mechanisms. The possibility to record infrared spectra of mass-selected molecular ions has opened up a novel avenue in the structural characterization of ions and their reaction products. On account of its high pulse energies and wide wavelength tunability, the free electron laser for infrared experiments (FELIX) at FOM Rijnhuizen has been shown to be ideally suited to study trapped molecular ions with infrared photo-dissociation spectroscopy. In this paper, we review recent experiments in our laboratory on the infrared spectroscopic characterization of reaction products from CID and HDX, thereby corroborating some of the reaction mechanisms that have been proposed. In particular, it is shown that CID gives rise to linear fragment ion structures which have been proposed for some time, but also yields fully cyclical ring structures. These latter structures present a possible challenge for using tandem MS in the sequencing of peptides/proteins, as they can lead to a scrambling of the amino acid sequence information. In gas-phase HDX of an amino acid it is shown that the structure can be changed from a charge solvated to a zwitterionic structure, thereby demonstrating that HDX can be an invasive technique, in fact changing the structure of the analyte. These results emphasize that more fundamental work is required in order to understand the underlying mechanisms in two of the most important structural techniques in MS.     

On the position of the potential wall in DFT temporary anion calculations

A simple method was recently proposed [D. J. Tozer and F. De Proft, J. Chem. Phys., 2007, 127, 034108] for performing explicit density functional theory (DFT) calculations on temporary anions. The excess electron in the anion is bound by a potential wall, the position of which is determined by a single parameter lambda, chosen to reproduce an approximate, theoretical negative electron affinity in the corresponding neutral. In the present study, the system-dependence of lambda and the sensitivity of the negative affinities to this parameter are investigated for 34 organic molecules. The results demonstrate that the system-dependent lambda values can be replaced by a global, average value, with minimal effect on the affinities. It follows that the orbitals, electron density, and other properties of a temporary anion can be determined from a single DFT calculation on that anion, using a large, diffuse basis set. As an illustration, singly occupied molecular orbitals and spin densities are determined for the anions of guanine and adenine nucleobases. Despite the use of a diffuse basis set, the method yields quantities that are localised in the molecular framework, associated with vertical electron affinities of -1.2 eV and -0.8 eV, respectively.     

Active 3-D microscaffold system with fluid perfusion for culturing in vitro neuronal networks

This work demonstrated the design, fabrication, packaging, and characterization of an active microscaffold system with fluid perfusion/nutrient delivery functionalities for culturing in vitro neuronal networks from dissociated hippocampal rat pup neurons. The active microscaffold consisted of an 8 x 8 array of hollow, microfabricated, SU-8 towers (1.0 mm or 1.5 mm in height), with integrated, horizontal, SU-8 cross-members that connect adjacent towers, thus forming a 3-D grid that is conducive to branching, growth, and increased network formation of dissociated hippocampal neurons. Each microtower in the microscaffold system contained a hollow channel and multiple fluid ports for media delivery and perfusion of nutrients to the in vitro neuronal network growing within the microscaffold system. Additionally, there were two exposed Au electrodes on the outer wall of each microtower at varying heights (with insulated leads running within the microtower walls), which will later allow for integration of electrical stimulation/recording functionalities into the active microscaffold system. However, characterization of the stimulation/recording electrodes was not included in the scope of this paper. Design, fabrication, fluid packaging, and characterization of the active microscaffold system were performed. Furthermore, use of the active microscaffold system was demonstrated by culturing primary hippocampal embryonic rat pup neurons, and characterizing cell viability within the microscaffold system.     

Affinity‐Based Drug Delivery

Affinity‐based drug delivery systems utilize interactions between the therapeutic drug and the delivery system to manipulate drug loading and to control drug release. In this paper, affinity‐based drug delivery system syntheses, types of therapeutic factors delivered, and delivery system loading and release are discussed in detail. The paper is divided into three subsections, based on the type of delivery system: molecular imprinting systems, growth‐factor delivery, and cyclodextrin‐based delivery. The objective of this paper is to examine the current state of research, highlight the breakthroughs and challenges, point out potential impacts of this relatively new technology, and explore future developmental areas.

     

Liquid electrolytes for dye-sensitized solar cells

The present review offers a survey of liquid electrolytes used in dye-sensitized solar cells from the beginning of photoelectrochemical cell research. It handles both the solvents employed, and the prerequisites identified for an ideal liquid solvent, as well as the various effects of electrolyte solutes in terms of redox systems and additives. The conclusions of the present review call for more detailed molecular insight into the electrolyte-electrode interface reactions and structures.