Liquid dibromomethane under pressure: a computational study

Molecular dynamics simulations have been performed on liquid dibromomethane at thermodynamic states corresponding to temperature in the range 268-328 K and pressure varying from 1 bar to 3000 bar. The interaction model is a simple effective two-body pair potential with atom-atom Coulomb and Lennard-Jones interactions and molecules are rigid. Thermodynamic properties have been studied, including the isobaric thermal expansion coefficient, the isothermal compressibility, the heat capacities and the speed of sound. The simulation results exhibit a crossing of the isotherms of the isobaric thermal expansion coefficient at about 800 bar in very good agreement with the prediction of an isothermal fluctuation equation of state predicting such a crossing in the pressure range 650-900 bar, though experimental results up to 1000 bar do not find any crossing.

Translational and Rotational Diffusion in Liquid Water at Very High Pressure: A Simulation Study

Translational and rotational diffusion coefficients of liquid water have been computed from molecular dynamics simulation with a recent polarizable potential at 298, 400, and 550 K at very high pressure. At 298 K, the model reproduces the initial increase and the occurrence of a maximum for the translational and rotational diffusion coefficients when the pressure increases. At 400 and 550 K, translational and rotational diffusion coefficients are found to monotonically decrease when pressure increases in the gigapascal range, with the translational coefficient decreasing faster than the rotational one. At 400 K, such an evolution of the rotational diffusion coefficient contrasts with quasielastic neutron scattering results predicting a near independence of the rotational diffusion with a pressure increase above ≃0.5 GPa. An interpretation is proposed to explain this discrepancy. The pressure dependence of the translation-rotation coupling is analyzed. The anisotropy of rotational diffusion is investigated by computing the rotational diffusion tensor in a molecular system of axes and the reorientational correlation times of rank 1 and rank 2 of the inertia axes and of the OH bond vector. Deviation of the simulation data with respect to the predictions of the isotropic Debye model of rotational diffusion are quantified and can be used to estimate experimental rotational diffusion coefficients from experimental reorientational correlation times.

Geometry-dependent distributed polarizability models for the water molecule

Geometry-dependent distributed polarizability models have been constructed by fits to ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set for the water molecule in the field of a point charge. The investigated models include (i) charge-flow polarizabilities between chemically bonded atoms, (ii) isotropic or anisotropic dipolar polarizabilities on oxygen atom or on all atoms, and (iii) combinations of models (i) and (ii). For each model, the polarizability parameters have been optimized to reproduce the induction energy of a water molecule polarized by a point charge successively occupying a grid of points surrounding the molecule. The quality of the models is ascertained by examining their ability to reproduce these induction energies as well as the molecular dipolar and quadrupolar polarizabilities. The geometry dependence of the distributed polarizability models has been explored by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For each considered model, the distributed polarizability components have been fitted as a function of the geometry by a Taylor expansion in monomer coordinate displacements up to the sum of powers equal to 4.

Distributed polarizability models for imidazolium-based ionic liquids

Quantum chemical calculations are used to derive distributed polarizability models sufficiently accurate and compact to be used in classical molecular dynamics simulations of imidazolium-based room temperature ionic liquids. Two distributed polarizability models are fitted to reproduce the induction energy of three imidazolium cations (1,3-dimethyl-, 1-ethyl-3-methyl-, and 1-butyl-3-methylimidazolium) and four anions (tetrafluoroborate, hexafluorophosphate, nitrate, and thiocyanate) polarized by a point charge located successively on a grid of surrounding points. The first model includes charge-flow polarizabilities between first-neighbor atoms and isotropic dipolar polarizability on all atoms (except H), while the second model includes anisotropic dipolar polarizabilities on all atoms (except H). For the imidazolium cations, particular attention is given to the transferability of the distributed polarizability sets. The molecular polarizability and its anisotropy rebuilt by the distributed models are found to be in good agreement with the exact ab initio values for the three cations and 23 additional conformers of 1-ethyl-3-methyl-, 1-butyl-3-methyl-, 1-pentyl-3-methyl-, and 1-hexyl-3-methylimidazolium cations.

Cholesterol content drives distinct pharmacological behaviours of micro-opioid receptor in different microdomains of the CHO plasma membrane

Cholesterol in the plasma membrane of eukaryotic cells contributes to modulating the functions and signalling pathways of numerous transmembrane proteins, including G protein Coupled Receptors (GPCRs). We have previously shown that the function of the human micro-opioid receptor (hMOR) expressed in Saccharomyces cerevisiae is modulated by sterols including cholesterol. Here, we investigated the effects of cholesterol content on hMOR pharmacology and on hMOR partitioning in cholesterol-poor and -rich domains in eukaryotic mammalian cells (CHO). We show that cholesterol is required for the stabilization of a receptor conformation with high agonist affinity and for triggering G-protein activation after agonist binding to the receptor. Biochemical analysis of untreated and cholesterol-depleted membranes in cells expressing hMOR indicated that the receptor is only present in cholesterol poor domains, in the basal state. After agonist binding to untreated CHO membranes, two distinct populations of receptor were found in cholesterol-rich and -poor domains. Cholesterol depletion or treatment of CHO membranes with the G-protein-decoupling agent GppNHp prevented the redistribution, indicating that receptor activated states localized into cholesterol-rich domains. Pharmacological data and biochemical analysis indicate that distinct activated conformations of hMOR exist in CHO plasma membrane and correspond to microdomains differing by thickness and proportions of lipid components, including cholesterol.

Hit and miss of classical nucleation theory as revealed by a molecular simulation study of crystal nucleation in supercooled sulfur hexafluoride

Classical nucleation theory pictures the homogeneous nucleation of a crystal as the formation of a spherical crystalline embryo, possessing the properties of the macroscopic crystal, inside a parent supercooled liquid. In this work we study crystal nucleation in moderately supercooled sulfur hexafluoride by umbrella sampling simulations. The nucleation free energy evolves from 5.2kBT at T=170 K to 39.1kBT at T=195 K. The corresponding critical nucleus size ranges from 40 molecules at T=170 K to 266 molecules at T=195 K. Both nucleation free energy and critical nucleus size are shown to evolve with temperature according to the equations derived from the classical nucleation theory. Inspecting the obtained nuclei we show, however, that they present quite anisotropic shapes in opposition to the spherical assumption of the theory. Moreover, even though the critical nuclei possess the structure of the stable bcc plastic phase, the only mechanically stable crystal phase for SF6 in the temperature range investigated, they are shown to be less ordered than the corresponding macroscopic crystal. Their crystalline order is nevertheless shown to increase regularly with their size. This is confirmed by a study of a nucleus growth from a critical size to a size of the order of 10(4) molecules. Similarly to the fact that it does not affect the temperature dependence of the nucleation free energy and of the critical nucleus size, the ordering of the nucleus with size does not affect the growth rate of the nucleus.

Long-range electrostatic interactions in hybrid quantum and molecular mechanical dynamics using a lattice summation approach

A method based on a lattice summation technique for treating long-range electrostatic interactions in hybrid quantum mechanics/molecular mechanics simulations is presented in this article. The quantum subsystem is studied at the semiempirical level, whereas the solvent is described by a two-body potential of molecular mechanics. Molecular dynamics simulations of a (quantum) chloride ion in (classical) water have been performed to test this technique. It is observed that the application of the lattice summations to solvent-solvent interactions as well as on solute-solvent ones has a significant effect on solvation energy and diffusion coefficient. Moreover, two schemes for the computation of the long-range contribution to the electrostatic interaction energy are investigated. The first one replaces the exact charge distribution of the quantum solute by a Mulliken charge distribution. The long-range electrostatic interactions are then calculated for this charge distribution that interacts with the solvent molecule charges. The second one is more accurate and involves a modified Fock operator containing long-range electron-charge interactions. It is shown here that both schemes lead to similar results, the method using Mulliken charges for the evaluation of long-range interactions being, however, much more computationally efficient.

Molecular simulation of the homogeneous crystal nucleation of carbon dioxide

We report on a molecular simulation study of the homogeneous nucleation of CO2 in the supercooled liquid at low pressure (P = 5 MPa) and for degrees of supercooling ranging from 32% to 60%. In all cases, regardless of the degree of supercooling, the structure of the crystal nuclei is that of the Pa3 phase, the thermodynamically stable phase. For the more moderate degree of supercooling of 32%, the nucleation is an activated process and requires a method to sample states of high free energy. In this work, we apply a series of bias potentials, which promote the ordering of the centers of mass of the molecules and allow us to gradually grow crystal nuclei. The reliability of the results so obtained is assessed by studying the evolution of the nuclei in the absence of any bias potential, and by determining their probability of growth. We estimate that the size of the critical nucleus, for which the probability of growth is 0.5, is approximately 240 molecules. Throughout the nucleation process, the crystal nuclei clearly exhibit a Pa3 structure, in apparent contradiction with Ostwald's rule of stages. The other polymorphs have a much larger free energy. This makes their formation highly unlikely and accounts for the fact that the nucleation of CO2 proceeds directly in the stable Pa3 structure.

Atomistic simulation of the homogeneous nucleation and of the growth of N2 crystallites

We report on a computer simulation study of the early stages of the crystallization of molecular nitrogen. First, we study how homogeneous nucleation takes place in supercooled liquid N(2) for a moderate degree of supercooling. Using the umbrella sampling technique, we determine the free energy barrier of formation for a critical nucleus of N(2). We show that, in accord with Ostwald's rule of stages, the structure of the critical nucleus is predominantly that of a metastable polymorph (alpha-N(2) for the state point investigated). We then monitor the evolution of several critical nuclei through a series of unbiased molecular dynamics trajectories. The growth of N(2) crystallites is accompanied by a structural evolution toward the stable polymorph beta-N(2). The microscopic mechanism underlying this evolution qualitatively differs from that reported previously. We do not observe any dissolution or reorganization of the alpha-like core of the nucleus. On the contrary, we show that alpha-like and beta-like blocks coexist in postcritical nuclei. We relate the structural evolution to a greater adsorption rate of beta-like molecules on the surface and show that this transition actually starts well within the precritical regime. We also carefully investigate the effect of the system size on the height of the free energy barrier of nucleation and on the structure and size of the critical nucleus.

Reorganization and Growth of Metastable α-N2 Critical Nuclei into Stable β-N2 Crystals

We report on results on the crystal nucleation and growth of nitrogen. Using molecular dynamics simulations, we show that while nucleation proceeds into the metastable alpha-phase (i.e., the crystalline phase associated with the lowest free energy barrier of formation), growth of the crystallite proceeds through a reorganization of the nucleus into the thermodynamically stable beta-phase.

Interprotein interactions are responsible for the confined diffusion of a G-protein-coupled receptor at the cell surface

The monitoring of the movements of membrane proteins (or lipids) by single-particle tracking enables one to obtain reliable insights into the complex dynamic organization of the plasma membrane constituents. Using this technique, we investigated the diffusional behaviour of a G-protein-coupled receptor. The trajectories of the receptors revealed a diffusion mode combining a short-term rapid confined diffusion with a long-term slow diffusion. A detailed statistical analysis shows that the receptors have a diffusion confined to a domain which itself diffuses, the confinement being due to long-range attractive inter-protein interactions. The existing models of the dynamic organization of the cell membrane cannot explain our results. We propose a theoretical Brownian model of interacting proteins that is consistent with the experimental observations and accounts for the variations found as a function of the domain size of the short-term and long-term diffusion coefficients.

OPEP: a tool for the optimal partitioning of electric properties

OPEP is a suite of FORTRAN programs targeted at the optimal partitioning of molecular electric properties. It includes an interactive module for the construction of Cartesian grids of points, on which either the molecular electrostatic potential or the induction energy is mapped. The generation of distributed multipoles and polarizabilities is achieved using either the formalism of the normal equations of the least-squares problem, which restates the fitting procedure in terms of simple matrix operations, or a statistical approach, which provides a pictorial description of the distributed models of multipoles and polarizabilities, thereby allowing the pinpointing of pathological cases. Molecular symmetry is accounted for by means of local atomic frames, which are generated in an automated fashion. A Tcl/Tk graphical user interface wraps the suite of programs, thereby making OPEP a user-friendly package for building models of distributed multipoles and polarizabilities. OPEP is an open-source suite of programs distributed free of charge under the GNU general public license (GPL) at http://www.lctn.uhp-nancy.fr/Opep.

Autofluorescence spectroscopy of malpighian epithelial cells, as a new tool for analysis of cervical cancer precursors

A spectroscopic analysis of autofluorescence was investigated within the cell cytoplasm from cervical malpighian epithelia prepared on Thin-Prep smears. Autofluorescence emission spectra from 22 cervix were analyzed by microspectrofluorometry under a 363 nm laser excitation. Among the analyzed cervix, 6 were in normal limits, 6 in inflammatory limits, 5 were evocative of Low-Grade Squamous Intraepithelial Lesions (LGSILs) and 5 were evocative of High-Grade Squamous Intraepithelial Lesions (HGSILs). Cytoplasmic emission intensities at 450 nm of cells from inflammatory, LGSIL and HGSIL cervix were equivalent and were 3-fold higher than from normal cervix. All smears presented a two-fold lower autofluorescence emission in the cytoplasm than in the nucleus. The spectral profile analysis allows the discrimination of cells from inflammatory, LGSIL and HGSIL cervix. The 525/425 nm emission ratios were 0.75+/-0.1, 0.96+/-0.04 and 1.2+/-0.1 for inflammatory, LGSIL and HGSIL, respectively. We suggest that smears of normal, inflammatory, LGSIL and HGSIL cervix could be discriminated by the analysis of the 450 nm emission intensity and 525/425 nm emission ratios from cells of malpighian epithelia.

Microspectrofluorometry of autofluorescence emission from human leukemic living cells under oxidative stress

Image cytometry was applied to study the intracellular localization of autofluorescence and the influence of an oxidative stress on this emission. K562 erythroleukemia cancer cells were analyzed with a microspectrofluorometer, coupled with a Argon laser (Ar+) (363 nm). From each cell, 15 x 15 emission spectra were recorded in the 400-600 nm spectral range to generate a spectral image of autofluorescence. The intracellular locations of the autofluorescence emission and of the specific mitochondrial probe rhodamine 123 (R123) were matched. Under a 363 nm excitation, all spectra from K562 cells show equivalent profiles with a 455 nm maximum emission, near of reduced nicotinamide adenine dinucleotide-(Phosphate) solution (NAD(P)H) (465 nm maximum emission). The spatial distribution of autofluorescence is homogeneous and different from the one of R123. Hydrogen peroxide (H2O2) (200 microM) and menadione (Men) (5 microM) induce a weak spectral change and a decrease in autofluorescence intensity, down to 40% of the initial emission. Doxorubicin (Dox) induces a dose-dependent decrease in autofluorescence emission and a release of intracellular free radicals. When cells were pre-treated 1 h with 1 mM glutathione (GSH), Dox induces a lower free radicals release, no significant variation of autofluorescence intensity and a lower growth inhibitory effect. Images cytometry of autofluorescence suggest that the intracellular NAD(P)H would not be restricted to mitochondrial compartments. The release of free radicals was associated with a decrease in autofluorescence intensity, mainly attributed to NAD(P)H oxidation both inside and outside mitochondria.

Clinical applications of image cytometry to human tumour analysis

Image cytometry (ICM) is widely applied to the automated screening, the detection, the diagnosis, the classification, the prognosis and the therapeutic follow-up of different types of cancers (breast, bladder, cervix,...). This review describes the analysis methods and the applications of nuclear image analysis, the determination of DNA content and the analysis of morphometry and of nuclear texture. DNA content analysis can contribute to a prognostic information in addition to other prognostic factors for breast, renal and prostate cancers. For ovarian cancer, aneuploidy seems to be related to prognosis. Bladder tumours with DNA aneuploidy were frequently of high malignancy while ploidy was significantly correlated to relapse risk. For digestive cancers, patients presenting DNA diploid tumours show a better survival than patients with aneuploid ones. Morphometry seems to be a more important criterion than other conventional prognostic factors of invasive breast and digestive carcinomas. A differential diagnosis between normal and neoplastic thyroids is more precise when based on a quantitative evaluation of texture associated to morphometry. Textural parameters permit the discrimination of two populations of patients having a different prognosis and could thus be an aid for prognosis in prostatic cancers. Morphonuclear parameters contribute to separate low and high grade bladder carcinomas. Although ICM was frequently reported, results from the reported examples were not always obvious. In conclusion, the measurements obtained with ICM could be helpful for a decision in several cancers but could not be a substitute for the classical approach of the pathologist.

Plasma membrane coating with cationic silica particles and osmotic shock alters the morphology of bovine aortic endothelial cells

We have used a published method of membrane preparation based on the precoating of the apical membrane of aortic endothelial cells with cationic silica microbeads (with or without polyacrylic acid) in combination with an osmotic shock and mechanical shearing to isolate the apical from the basal plasma membranes of these cells, in vitro. After labeling of the plasma membrane of adherent endothelial cells with a fluorescent derivative of phosphatidylcholine and by using laser confocal fluorescence scanning microscopy, we found that this method of membrane isolation rapidly induced invaginations of the basal plasma membrane to an extent which makes this method unsuitable for further membrane lipid analysis. Morphological analysis of the cells and fluorescence recovery after photobleaching experiments on the plasma membranes were performed at each step of the purification procedure and showed that only hypotonic shock and mechanical shearing of the cells enabled the basal plasma membranes to be purified without significant morphological changes.

Characterization of acidic vesicles in multidrug-resistant and sensitive cancer cells by acridine orange staining and confocal microspectrofluorometry

To study the pH gradient status through membranes of acidic vesicles, either in sensitive or in multidrug-resistant living cancer cells, we monitored the fluorescence-emission spectra of acridine orange. Successive stainings with a pH-sensitive dye and AO showed that low-pH organelles were stained red by AO. In these compartments, high AO concentrations are driven by the pH gradient through membrane vesicles. The resulting rise in the dye's oligomeric/monomeric ratio induced an increase in the red/green (655-nm/530-nm) emission intensity ratio. Therefore, the accumulation of AO in acidic organelles was appraised by determination of the contribution of the red emission intensity (R%) in each emission spectrum, using laser scanning confocal microspectrofluorometry. In vesicles of multidrug-resistant K562-R cells, R% is significantly higher (72 +/- 10%) than the value (48 +/- 8%) from K562-sensitive cells (p < 0.001). This result is interpreted as a more important accumulation of AO in acidic cytoplasmic structures of resistant cells, which induces a shift from AO monomers (green emission) to self-associated structures (red emission). Equilibration of the pH gradient through acidic organelles was performed by addition of weak bases and carboxylic ionophores. Ammonium chloride (0.1 mM), methylamine (0.1 mM), monensine (10 microM), or nigericine (0.3 microM) all suppressed the initial difference of local AO accumulation between both cell lines. These agents decreased the red emission intensity for the resistant cell line but not for the sensitive one. The same effects were induced by 50 microM verapamil, a pleiotropic drug-resistance modulator. Our data allow the hypothesis of a higher pH gradient through membranes of acidic organelles, which would be a potential mechanism of multidrug resistance via the sequestration of weak bases inside these organelles.

12-O-tetradecanoylphorbol-13-acetate inhibits aminophospholipid translocase activity and modifies the lateral motions of fluorescent phospholipid analogs in the plasma membrane of bovine aortic endothelial cells

The tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) is a potent mitogenic factor which can replace the growth promoting activity of basic fibroblast growth factor (bFGF) on bovine aortic endothelial cells. However, TPA-treated cells lose their strict contact inhibition at confluence, which is a characteristic of cells grown in the presence of bFGF. We have examined whether these changes could be related to modifications of the transbilayer and lateral motions of fluorescent lipids, namely 1-acyl-2-[6-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]caproyl]-p hosphatidylcholine (C6-NBD-PC), -phosphatidylserine (C6-NBD-PS), and -phosphatidylethanolamine (C6-NBD-PE) inserted in the outer leaflet of the cell plasma membrane. In TPA-treated cells, the three fluorescent phospholipids remained located in the outer leaflet for at least 1 h at 20 degrees C after their insertion, indicating a blockade of the aminophospholipid translocase activity which is normally present in the plasma membrane of bFGF-treated cells. TPA also induced a large increase in the percentage of C6-NBD-PC and C6-NBD-PE probes which were free to diffuse laterally. The mobile fractions M reached values of approximately 100% for the two lipids, while for bFGF-treated cells they were found around 85 and 75%, respectively. For the C6-NBD-PS probe, M remained unchanged in bFGF and TPA-treated cells, at around 85%. TPA treatment also induced a twofold increase in the lateral diffusion coefficients of C6-NBD-PC and C6-NBD-PE, while that of C6-NBD-PS remained nearly unchanged. These effects of TPA may be related to the observed loss of differentiated properties of vascular endothelial cells and not to its mitogenic properties.