Monte Carlo versus molecular dynamics simulations in heterogeneous systems: an application to the n-pentane liquid-vapor interface

The Monte Carlo (MC) and molecular dynamics (MD) methodologies are now well established for computing equilibrium properties in homogeneous fluids. This is not yet the case for the direct simulation of two-phase systems, which exhibit nonuniformity of the density distribution across the interface. We have performed direct MC and MD simulations of the liquid-gas interface of n-pentane using a standard force-field model. We obtained density and pressure components profiles along the direction normal to the interface that can be very different, depending on the truncation and long range correction strategies. We discuss the influence on predicted properties of different potential truncation schemes implemented in both MC and MD simulations. We show that the MD and MC profiles can be made in agreement by using a Lennard-Jones potential truncated via a polynomial function that makes the first and second derivatives of the potential continuous at the cutoff distance. In this case however, the predicted thermodynamic properties (phase envelope, surface tension) deviate from experiments, because of the changes made in the potential. A further readjustment of the potential parameters is needed if one wants to use this method. We conclude that a straightforward use of bulk phase force fields in MD simulations may lead to some physical inconsistencies when computing interfacial properties.     

First anhydrous gold perchlorato complex: ClO(2)Au(ClO(4))(4). Synthesis and molecular and crystal structure analysis

Chlorine trioxide, Cl(2)O(6), reacts with Au metal, AuCl(3), or HAuCl(4).nH(2)O to yield the well-defined chloryl salt, ClO(2)Au(ClO(4))(4). The crystal and molecular structure of ClO(2)Au(ClO(4))(4) was solved by a Rietveld analysis of powder X-ray diffraction data. The salt crystallizes in a monoclinic cell, space group C2/c, with cell parameters a = 15.074(5), b = 5.2944(2), and c = 22.2020(2) A and beta = 128.325(2) degrees. The structure displays discrete ClO(2)(+) ions lying in channels formed by Au(ClO(4))(4)(-) stacks. Au is located in a distorted square planar environment: Au-O = 1.87 and 2.06 A. [ClO(4)] groups are monodentate with ClO(b) = 1.53 and ClO(t) = 1.39 A (mean distances; O(b), oxygen bonded to Au; O(t), free terminal oxygen). A full vibrational study of the Au(ClO(4))(4)(-) anion is supported by DFT calculations.     

Synthesis, characterization and optical properties of pi-conjugated systems incorporating closo-dodecaborate clusters: new potential candidates for two-photon absorption processes

Non-centrosymmetric pi-conjugated systems incorporating closo-dodecaborate clusters, [NC-C6H4-C(H=N(H)-B12H11]-(2), [NC-C6H4-C(H)=C(H)-C(6)H(4)-C(H)=N(H)-B12H11]-(3), and [NC-C6H4-C(H)=C(H)-C6H4-C(H)=C(H)-C6H4-C(H)=N(H)-B12H11]-(4) have been synthesized by reaction of the monoamino derivative of B12, [B12H11NH3]-(1), with various arylaldehydes, R-C6H4-CHO. These Schiff base-like compounds were fully characterized by multinuclear NMR spectroscopy and mass spectrometry. In order to evaluate these boron rich pi-systems as potential materials for two-photon absorption (TPA) processes, UV linear absorption curves were recorded for 3 and 4, and comparatively studied with those of the boron-free pi-systems NC-C6H4-C(H)=N-CH3(5) and NC-C6H4-C(H)=C(H)-C6H4-C(H)=N-CH3(6). The donor effect of the boron cluster was evidenced by a shift to the lower energy of the absorption band in the spectra of systems incorporating B12. The two photon absorption (TPA) spectrum of compound , obtained by the up-conversion method, shows a resonance at 720 nm with a cross-section sigma(TPA) of 35 x 10(-50) cm(4) s photon(-1) molecule(-1). This value suggests the potential of B12 clusters to be used as new donor groups for the synthesis of non-linear materials.     

High accuracy analysis by isotope dilution mass spectrometry using an iterative exact matching technique

The selection of an appropriate isotope dilution mass spectrometry technique for the practical application of this potentially primary method of analysis is highly important. The NARL approach for the application of the exact matching double isotope dilution mass spectrometry technique developed by Henrion is presented. NARL's approach utilises exact matching to minimise the effect of measurement biases within the method but also includes the thorough examination of all other biasing factors. The approach has been successfully tested in international CCQM intercomparisons with other national metrology institutes.     

Theoretical study of the interaction of tetramethylammonium with double-stranded oligonucleotides

Computations are performed on the interaction specificities of tetramethylammonium (TMA) for double-stranded oligonucleotides held in the B conformation. The effects of base sequence and chain length are investigated. In the short oligomers (helices formed from dinucleoside monophosphates and trinucleoside diphosphates), the interaction energies of TMA are larger in the major groove of (dG)_n · (dC)_n than in the minor groove of either (dA)_n · (dT)_n or (dA—dT)_n. Upon lengthening the oligomers, and owing to the gradual shaping of the grooves of the helix and cumulative effect of the phosphates, TMA is shown to increasingly favor the minor groove of (dA)_n · (dT)_n with respect to the major groove of (dG)_n · (dC)_n, with a sizeable energy difference computed at the pentanucleoside hexaphosphate level. The binding of TMA in the minor groove of (dA)_n · (dT)_n involves stabilizing contacts with several sites, on the bases and on the deoxyriboses. Configurations locating the cation closer to the thymine strand are slightly preferred over configurations locating it closer to the adenine strand.     

2,4,6‐Trimethylphenyl isocyanide

The title compound, C₁₀H₁₁N, displays a crystallographic mirror plane that incorporates all the non‐H atoms, as well as the H atoms attached to the aromatic ring. The iso­cyano group is almost linear and shows an N[triple‐bond]C bond distance of 1.158 (3) Å.     

TRYPTOPHAN FLUORESCENCE LIFETIMES AS A FUNCTION OF EXCITATION WAVELENGTH*

Abstract— –Fluorescence decay times of aqueous dilute solutions (?20 µM) of L-tryptophan have been determined using the phase shift technique as well as single photon-counting coupled with synchrotron radiation (ACO at Orsay and SPEAR at Stanford). Decay times were obtained as a function of the excitation wavelength (in the spectral region 220–320 nm) monitoring emission of λ> 320 nm (in certain specified cases, λ> 360 nm). We have found that, at neutral pH and 20°C. fluorescence decays are single exponentials and independent of the excitation wavelength; under these conditions we find τ= 3.1 ± 0.1 ns.     

Oxidation of methionine residues in aqueous solutions: free methionine and methionine in granulocyte colony-stimulating factor

The free energy barriers and a mechanism of the oxidation of the amino acid methionine in water and in granulocyte colony-stimulating factor (G-CSF) are analyzed via combined quantum mechanical and molecular mechanical (QM/MM) methods, constrained molecular dynamics, and committor probability calculations. The computed free energy barrier of free methionine amino acid is very close to the measured value (14.7 +/- 1.2 versus 15.5 +/- 0.02 kcal/mol). The reaction coordinate was found to be the difference between the O-O bond of H2O2 and the S-O bond, where the S is the sulfur atom of the methionine residue. It was confirmed by computing the committor probability distribution and the distribution of constrained forces that this coordinate is not coupled to the activation of other degrees of freedom. The computed free energies of the oxidation of methionine residues in G-CSF indicate that the protein environment has insignificant effects on the reaction barriers of oxidation. This result further validates our proposal that the access of solvent to methionine sites, as measured by the two-shell water coordination number, governs the kinetics of the oxidation reaction of methionine groups in a protein molecule. We also found that the number of hydrogen bonds between the distal oxygen of H2O2 and the water molecules near the methionine increases along the reaction coordinate as oxidation progresses, indicating that the charge separation developed during the oxidation by H2O2 is stabilized by specific interactions with water molecules, such as hydrogen bonding.     

Silica particle-stabilized emulsions of silicone oil and water: aspects of emulsification

A study of the emulsification of silicone oil and water in the presence of partially hydrophobic, monodisperse silica nanoparticles is described. Emulsification involves the fragmentation of bulk liquids and the resulting large drops and the coalescence of some of those drops. The influence of particle concentration, oil/water ratio, and emulsification time on the relative extents of fragmentation and coalescence during the formation of emulsions, prepared using either batch or continuous methods, has been investigated. For batch emulsions, the average drop diameter decreases with increasing particle concentration as the extent of limited coalescence is reduced. Increasing the oil volume fraction in the emulsion at fixed aqueous particle concentration results in an increase in the average drop diameter together with a dramatic lowering of the uniformity of the drop size distribution as coalescence becomes increasingly significant until catastrophic phase inversion occurs. For low oil volume fractions (phi(o)), fragmentation dominates during emulsification since the mean drop size decreases with emulsification time. For higher phi(o) close to conditions of phase inversion, coalescence becomes more prevalent and the drop size increases with time with stable multiple emulsions forming as a result.     

Structural basis for the highly selective inhibition of MMP-13

Inhibitors for matrix metalloproteinases (MMPs) are under investigation for the treatment of cancer, arthritis, and cardiovascular disease. Here, we report a class of highly selective MMP-13 inhibitors (pyrimidine dicarboxamides) that exhibit no detectable activity against other MMPs. The high-resolution X-ray structures of three molecules of this series bound to MMP-13 reveal a novel binding mode characterized by the absence of interactions between the inhibitors and the catalytic zinc. The inhibitors bind in the S1' pocket and extend into an additional S1' side pocket, which is unique to MMP-13. We analyze the determinants for selectivity and describe the rational design of improved compounds with low nanomolar affinity.