Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

DNA intercalating studies of [Ru(bpy)<Subscript>2</Subscript>HPIP]<Superscript>2+</Superscript> with intramolecular hydrogen bond ligand based on introduction of copper ion

The effects of copper ion on the interaction of [Ru(bpy)₂HPIP]²⁺(bpy = 2,2′-bipyridine, HPIP = 2-(2-hydroxyphenyl) imidazo [4,5-f] [1, 10] phenanthroline) with DNA have been investigated by electronic absorption spectroscopy and fluorescence spectroscopy. HPIP ligand of the complex with an intramolecular hydrogen bond can bind Cu²⁺ in the absence of DNA, as revealed by the absorbance and fluorescence decrease for [Ru(bpy)₂HPIP]²⁺. The resultant heterometallic complex binds to DNA via intercalation of HPIP into the DNA base pairs and its DNA-binding ability is stronger than [Ru(bpy)₂HPIP]²⁺ itself. The DNA bound [Ru(bpy)₂HPIP]²⁺ cannot bind Cu²⁺ at low Cu²⁺ concentration and the intramolecular hydrogen bond in HPIP is located inside the DNA helix. While the Cu²⁺ concentration is relative high, Cu²⁺ can quench the fluorescence of DNA bound [Ru(bpy)₂HPIP]²⁺. The quenching reason is proposed.     

Extending the scope of enantiomer separation by capillary supercritical fluid chromatography on immobilized polysiloxane-anchored permethyl-β-cyclodextrin (Chirasil-Dex)

Immobilized polysiloxane-anchored permethyl-β-cyclodextrin (Chirasil-Dex) with a cyclodextrin content of approximately 30 % by weight, previously employed as a versatile chiral stationary phase for the separation of enantiomers by GC, has been used for the separation of enantiomers by capillary supercritical fluid chromatography (SFC). A considerable number of racemates could be resolved, e.g. aromatic alcohols, amino alcohols (TFA derivatives), and underivatized acids. Many pharmaceutical compounds were among those analyzed, including several NSAIDs (e.g. ibuprofen and ketoprofen), a steroidal drug (nor-gestrel), a barbiturate (hexobarbital), and others. Among the racemates resolved were many which cannot be analyzed by GC owing to low volatility or decomposition at elevated temperatures. For two racemates, analysis temperature and mobile phase density were systematically varied to give constant analysis times or capacity factors k. Low temperatures (ca 60 °C) yielded the best separation in term of separation factor, α, or resolution, R_s, even though higher densities had to be used. In comparison with GC, capillary SFC was able to furnish higher separation factors and similar resolution. The applicability of capillary SFC for the analysis of mixtures of cyclodextrin derivatives, e.g. those used in the synthesis of Chirasil-Dex, was, furthermore, demonstrated.     

Structural Study of Silica Xerogel Composites Containing Pd Aggregates

Composites containing Pd aggregates dispersed in amorphous silica are of interest from both a fundamental and applied point of view because of their attractive catalytic properties. The silica powders added with palladium, prepared by the sol-gel method, were studied using X-ray diffraction, and IR- and UV-Vis-spectrophotometry. Silica xerogel samples were prepared using a ethanol/H₂O/TEOS molar ratio of 4:11.6:1 and loaded with sodium tetrachloropalladate. The silica xerogel microstructure of the powders was studied as a function of annealing temperature. Attention was paid to the evolution of the glass matrix as well as the palladium aggregates in the SiO₂ matrix. We found in our samples partial crystallization of the glass matrix in form of quartz and cristobalite phases with palladium oxide and metallic palladium phase at 1000^∘C. The Rietveld refinement method was used in order to determine the percentage of the phase contents.     

Synthesis and in vivo study of metallofullerene based MRI contrast agent

Gd@C₈₂(OH)₄₀ has been developed as a new generation of MRI contrast agent. But recently, it was found that Gd@C₈₂(OH) _x with a larger number of OH (x>36) would lead to cage break and hence, release of highly toxic Gd ions. We synthesized the more stable Gd@C₈₂(OH) _x with less OH-number, Gd@C₈₂(OH)₁₆, and studied its proton relaxivity and MRI images. The results indicate that Gd@C₈₂(OH)₁₆ also gives high proton relaxivity, even higher than that of (NMG)₂-Gd-DTPA. The bio-distribution indicated that Gd@C₈₂(OH)₁₆ tends to be entrapped in the liver and kidney and remained in tissue for about 2 hours. The results suggest that the more stable metallofullerene derivative Gd@C₈₂(OH)₁₆ can be the potential candidate of the new MRI contrast agent.     

Macroporous poly(methyl methacrylate) produced by phase separation during polymerisation in solution

Polymethyl methacrylate (PMMA) sponges were obtained by polymerization in a solution with monomer/ethanol ratios up to 20:80. The material obtained after the elimination of the solvent present a homogeneous distribution of dispersed pores up to a monomer/ethanol ratio lower than 40:60. For higher ethanol contents in the reacting mixture, the morphology of the sponge corresponds to a network of PMMA microparticles, leaving large empty spaces leading to highly porous structure. The monomer/ethanol ratio during polymerization has a large influence on the porosity, thermal, and mechanical properties of the material and, for large solvent contents, on the size of the polymer microparticles.     

Synergies between micropreparative high-performance liquid chromatography and an instrumental optical biosensor

The recent development of an automated surface plasmon resonance technology for the measurement of biomolecular interactions (Pharmacia BIAcore) has provided new opportunities for the detection and analysis of protein-protein interactions. In the BIAcore, detection is based on changes in surface plasmon resonance which are monitored optically. Changes in surface plasmon resonance correspond to changes in surface concentration of macromolecules and can be monitored in real time.

We have found that the detection sensitivity obtainable with this technology (ng/ml concentrations of specific ligands are readily detectable for many applications) is complementary “in a bidirectional manner” to micropreparative HPLC. Thus micropreparative HPLC may be used to purify and characterise reagents for the biosensor, whilst the biosensor may be used to define chromatographic parameters such as elution conditions for affinity chromatography or serve as an affinity detector for fractions obtained during chromatographic purification.

Examples of such applications, including the potential of the biosensor to search for and monitor the purification of unknown ligands for which the target molecule has been identified, are shown. In particular, the use of the biosensor to monitor the purification of soluble epidermal growth factor receptor from A431 cell conditioned media is demonstrated.     

Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulations

A set of all-atom molecular dynamics simulations have been performed to better understand critical phenomena regarding a Hofmeister series of anions and lipid bilayers. The simulations isolate the effect of anion size and show clear differences in the interactions with the dipolar phoshpatidylcholine headgroup. Cl- anions penetrate into the headgroup region of the bilayer, but the simulations confirm theories which predict that larger anions penetrate more deeply, into a more heterogeneous and hydrophobic molecular region. That anion size leads to such differences in partitioning in the bilayer provides atomic-level support to hypotheses inspired by several experimental studies. The ability of larger anions to bury deep within the bilayer is correlated with a less well-structured hydration shell, shedding of which upon penetration incurs a smaller penalty for the larger anions than for Cl-.