Experimental studies of the dynamics of the bond-forming reactions of CF2(2+) with H2O using position-sensitive coincidence spectroscopy

The dynamics of the product channels forming OCF(+)+H(+)+HF and HCF(2) (+)+H(+)+O following the collisions of CF(2) (2+) with H(2)O have been investigated with a new position-sensitive coincidence experiment at a center-of-mass collision energy of 5.6 eV. The results show the formation of OCF(+) occurs via the formation of a doubly charged collision complex [H(2)O-CF(2)](2+) which subsequently undergoes a charge separating dissociation to form H(+) and HOCF(2) (+). The HOCF(2) (+) monocation subsequently fragments to form HF+OCF(+). The lifetimes of the collision complex and the HOCF(2) (+) ion are at least of the order of their rotational period. The kinetic energy release in this reaction indicates that it involves the ground state of CF(2) (2+) and forms the ground electronic states of OCF(+) and HF. The mechanism for forming HCF(2) (+) involves the direct and rapid abstraction of a hydride ion from H(2)O by CF(2) (2+). The resulting OH(+) ion subsequently fragments to H(+)+O, on a time scale at least comparable with its rotational period.     

Dynamic interaction of theory and experiment: total determination of the gas-phase molecular structure of tri-tert-butylphosphine oxide (OPBut3)

A new method to aid the determination of structures of sterically crowded molecules in the gas phase by dynamically linking the gas-phase electron diffraction (GED) refinement process with computational methods has been developed. The procedure involves refining the heavy-atom skeleton of the molecule using the GED data while continually updating the light-atom positions during the refinement using computational methods, in this case molecular mechanics. This removes errors associated with the assumption of local symmetry for the light-atom groups, which can affect the final values of the heavy-atom parameters. The refinement of the molecular structure of tri-tert-butyl phosphine oxide has been used to illustrate this new technique, which we call the DYNAMITE (DYNAMic Interaction of Theory and Experiment) method. Re-examination of the structure using this method has resulted in a shorter P-O distance than was found in a less sophisticated anaylsis, and is consistent with the molecule being regarded as O=PBut3, rather than O(-)-P+But3.     

Molecular cluster decay viewed as escape from a potential of mean force

We show that evaporation from a quasistable molecular cluster may be treated as a kinetic problem involving the stochastically driven escape of a molecule from a potential of mean force. We derive expressions for the decay rate, and a relationship between the depth of the potential and the change in system free energy upon loss of a molecule from the cluster. This establishes a connection between kinetic and thermodynamic treatments of evaporation, but also reveals differences in the prefactor in the rate expression. We perform constant energy molecular dynamics simulations of cluster dynamics to calculate potentials of mean force, friction coefficients and effective temperatures for use in the kinetic analysis, and to compare the results with the directly observed escape rates. We also use the simulations to estimate the escape rates by a probabilistic analysis. It is much more efficient to calculate the decay rate by the methods we have developed than it is to monitor escape directly, making these approaches potentially useful for the assessment of molecular cluster stability.     

Synthesis and photochemistry of a new class of photocleavable protein cross-linking reagents

A new series of photocleavable protein cross-linking reagents based on bis(maleimide) derivatives of diaryl disulfides have been synthesised. They have been functionalised with cysteine and transient absorption spectra for the photolysis reaction have been recorded by using the pump-probe technique with a time resolution of 100 femtoseconds. Photolysis of the disulfide bond yields the corresponding thiyl radicals in less than a picosecond. There is a significant amount of geminate recombination, but some of the radicals escape the solvent cage and the quantum yield for photocleavage is 30 % in water.     

Clustering files of chemical structures using the fuzzy k-means clustering method

This paper evaluates the use of the fuzzy k-means clustering method for the clustering of files of 2D chemical structures. Simulated property prediction experiments with the Starlist file of logP values demonstrate that use of the fuzzy k-means method can, in some cases, yield results that are superior to those obtained with the conventional k-means method and with Ward's clustering method. Clustering of several small sets of agrochemical compounds demonstrate the ability of the fuzzy k-means method to highlight multicluster membership and to identify outlier compounds, although the former can be difficult to interpret in some cases.     

Amperometric method for determining the degree of complexation of polyelectrolytes with cationic surfactants

The complexation of sodium polystyrene sulfonate with monovalent cationic surfactants at a microsized liquid/liquid interface has been studied using electrochemistry. The method is based on measurement of surfactant ion transfer across the interface between two immiscible electrolyte solutions (ITIES). The complexation of various cationic surfactants (alkylpyridinium- and trimethylammonium-) with oligosized polystyrene sulfonate was measured. Binding isotherms were used to determine the degree of binding as a function of the surfactant chain length and type of head group. It was found that the hydrophobicity of the surfactant was the predominant factor. The effect of the polyelectrolyte chain length on the binding mechanism was studied using cetylpyridinium chloride as a complexing agent. It was found that binding affinity, as well as cooperativity of the binding process, decreases with decreasing polyelectrolyte chain length. Thermodynamics of surfactant binding was measured using titration microcalorimetry. The thermodynamic data obtained show that the enthalpy of surfactant binding is not dependent on polymer chain length, but an increase in chain length makes the binding process entropically more favorable.     

Barrier-free intermolecular proton transfer induced by excess electron attachment to the complex of alanine with uracil

The photoelectron spectrum of the uracil-alanine anionic complex (UA)(-) has been recorded with 2.540 eV photons. This spectrum reveals a broad feature with a maximum between 1.6 and 2.1 eV. The vertical electron detachment energy is too large to be attributed to an (UA)(-) anionic complex in which an intact uracil anion is solvated by alanine, or vice versa. The neutral and anionic complexes of uracil and alanine were studied at the B3LYP and second-order M?ller-Plesset level of theory with 6-31++G(*) (*) basis sets. The neutral complexes form cyclic hydrogen bonds and the three most stable neutral complexes are bound by 0.72, 0.61, and 0.57 eV. The electron hole in complexes of uracil with alanine is localized on uracil, but the formation of a complex with alanine strongly modulates the vertical ionization energy of uracil. The theoretical results indicate that the excess electron in (UA)(-) occupies a pi(*) orbital localized on uracil. The excess electron attachment to the complex can induce a barrier-free proton transfer (BFPT) from the carboxylic group of alanine to the O8 atom of uracil. As a result, the four most stable structures of the uracil-alanine anionic complex can be characterized as a neutral radical of hydrogenated uracil solvated by a deprotonated alanine. Our current results for the anionic complex of uracil with alanine are similar to our previous results for the anion of uracil with glycine, and together they indicate that the BFPT process is not very sensitive to the nature of the amino acid's hydrophobic residual group. The BFPT to the O8 atom of uracil may be relevant to the damage suffered by nucleic acid bases due to exposure to low energy electrons.     

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulting model in reproducing various structural properties computed from atomistic trajectories of peptides in water. The addition of new dihedral angle potentials improves agreement with the contact maps computed from atomistic simulations significantly. We also address the question of which parameters derived from atomistic trajectories are transferable between different lengths of peptides. The modified coarse-grained model shows reasonable transferability of parameters for the amyloid- and elastin-like peptides. In addition, the improved coarse-grained model is also applied to investigate the self-assembly of β-sheet forming peptides on the microsecond time scale. The octapeptides SNNFGAIL and (GV)(4) are used to examine peptide aggregation in different environments, in water, and at the water-octane interface. At the interface, peptide adsorption occurs rapidly, and peptides spontaneously aggregate in favor of stretched conformers resembling β-strands.