Molecular Ordering in Lipid Monolayers: An Atomistic Simulation

We report on atomistic simulations of DPPC lipid monolayers using the CHARMM36 lipid force field (and also the Slipid force field as a control case), combined with a four-point OPC water model. The entire two-phase region where domains of the "liquid-condensed" (LC) phase coexist with domains of the "liquid-expanded" (LE) phase has been explored. The simulations are long enough that the complete phase-transition stage, with two domains coexisting in the monolayer, is reached in all cases. Also, system sizes used are larger than those in previous works. As expected, domains of the minority phase are elongated, emphasizing the importance of anisotropic van der Waals and/or electrostatic dipolar interactions in the monolayer plane. The molecular structure is quantified in terms of distribution functions for the hydrocarbon chains and the PN dipoles. In contrast to previous work, where average distributions are calculated, distributions are here extracted for each of the coexisting phases by first identifying lipid molecules that belong to either LC or LE regions. In the case of the CHARMM36 force field, the three-dimensional distributions show that the average tilt angle of the chains with respect to the normal outward direction is (39.0 ± 0.1)° in the LC phase and (48.1 ± 0.5)° in the LC phase. In the case of the PN dipoles, the distributions indicate a tilt angle of (110.8 ± 0.5)° in the LC phase and (112.5 ± 0.5)° in the LE phase. These results are quantitatively different from those in previous works, which indicated a smaller normal component of the PN dipole. Also, the distributions of the monolayer-projected chains and PN dipoles have been calculated. Chain distributions peak along a particular direction in the LC domains, while they are uniform in the LE phase. Long-range ordering associated with the projected PN dipoles is absent in both phases. These results strongly suggest that LC domains do not exhibit dipolar ordering in the plane of the monolayer, the effect of these components being averaged out at short distances. Therefore, the only relevant component of the molecular dipoles, with regard to both intra- and long-range interdomain interactions, is normal to the monolayer. Also, the local orientation of chain projections is almost constant in LC domains and points in the direction along which domains are elongated, suggesting that the line tension driving the phase transition might be anisotropic with respect to the interfacial domain boundary.

Anisotropic line tension of domains in lipid monolayers

We formulate a simple effective model to describe molecular interactions in a lipid monolayer and calculate the line tension between coexisting domains. The model represents lipid molecules in terms of two-dimensional anisotropic particles on the plane of the monolayer. These particles interact through forces that are believed to be relevant for the understanding of fundamental properties of the monolayer: van der Waals interactions originating from lipid chains and dipolar forces between dipole groups in the molecular heads. The model stresses the liquid-crystalline nature of the ordered phase in lipid monolayers and explains coexistence properties between ordered and disordered phases in terms of molecular parameters. Thermodynamic and interfacial properties of the model are analyzed using density-functional theory. In particular, the line tension at the interface between ordered and disordered phases turns out to be highly anisotropic with respect to the angle between the nematic director and the interface separating the coexisting phases. This important feature mainly results from the tilt angle of lipid chains and, to a lesser extent, from dipolar interactions perpendicular to the monolayer. The role of the two dipolar components, parallel and perpendicular to the monolayer, is assessed by comparing with computer simulation results for lipid monolayers.

Solid-solid transitions induced by repulsive interactions revisited

We revisit a problem already studied 15 years ago by us in collaboration with Stell and Hemmer: the isostructural solid-solid transitions induced by repulsive particle interactions exhibited by classical systems interacting via the Stell-Hemmer potentials. The full phase diagram in the crystal region is obtained by applying a perturbation theory for classical solids used during our collaboration with Stell. Also, the performance of such a theory is now tested by comparing the perturbative phase diagram with that obtained from computer simulations. The latter was calculated using a recently refined method to obtain the free-energy of crystals by means of Monte Carlo simulations. The perturbation theory captures the correct topology and correctly identifies the stable, fcc and bcc, phases. In addition, the theory predicts the occurrence of special points: a point where the two stable structures coexist at the same density, and two critical points terminating the corresponding isostructural phase transitions for fcc and bcc phases. The location of some of these features in the phase diagram is predicted almost quantitatively. However, phase boundaries involving the non-compact bcc phase are much less accurate, a problem that can be traced to the poor representation used for the bcc phase of the reference, hard-sphere, system.

Robust Modeling and Scaffold Hopping: Case Study Based on HIV Reverse Transcriptase Inhibitors Type-1 Data

BACKGROUND

Human immunodeficiency virus type 1 (HIV-1) is the causative agent of AIDS occurs across mucosal surfaces or by direct inoculation.

OBJECTIVE

The objective of this study was to consider chemically diverse scaffold sets of HIV-1 Reverse Transcriptase Inhibitors (HIV-1 RTI) subjected to ideal oriented QSAR with large descriptor space.

METHOD

We generated a four-parameter QSAR model based on 111 data points, which provided an optimum prediction of HIV-1 RTI for overall 367 experimentally measured compounds.

RESULTS

The robustness of the model is demonstrated by its statistical validation (Ntraining = 111, R2 = 0.85, Q2lmo = 0.84) and by the prediction of HIV-1 inhibition activity for experimentally measured compounds.

CONCLUSION

Finally, 5 novel hit compounds were designed in silico by using a virtual screening approach. The new hits met all the pharmacophore constraints and predicted pIC50 values within the binding ability of HIV-1 RT protein targets.

Topological defects in a two-dimensional liquid crystal confined in a circular nanocavity

Using a microscopic theory based on excluded-volume interactions, we analyze the structure and thermodynamic stability of configurations in a two-dimensional liquid crystal confined into a (small) circular nanocavity. Weak homeotropic anchoring conditions are considered, and topological defects of total charge k=+1 are discussed. It is found that, for small cavity radii, the cavity is free of defects at the expense of surface free energy not being optimized. For larger cavities, a configuration with two repulsive k=+1/2-charge point defects is always stable. The two configurations are equally stable thermodynamically (structural or Frederiks transition) on a curve in the chemical potential-cavity radius plane. This curve ends for chemical potential and cavity radius below some critical values. Elastic-theory arguments are used to explain the stability of the defected structure compared with the one free of defects. Our results indicate that the two-defect structure is always more stable than the one with a single point defect of charge k=+1 at the cavity center, which, in agreement with computer simulation, is never found to be stable. Finally, the relation with the bulk behavior of the fluid is discussed.

New variants of polar glycopeptidolipids detected in Mycobacterium simiae, including 'habana' strains, as evidenced by electrospray ionization-ion trap-mass spectrometry

AIMS

To determine the composition of polar glycopeptidolipids (pGPLs) of Mycobacterium simiae and, particularly, those of 'habana' strains, in a search for specific markers given the immunogenic potential of 'habana' TMC 5135 in experimental tuberculosis.

METHODS AND RESULTS

pGPLs were determined in free lipid extracts using electrospray ionization-ion trap-mass spectrometry (ESI-IT-MS), working in both negative- and positive-ion mode. In the case of TMC 5135, the presence of the previously characterized GPL-II (containing 2,4-di-O-CH(3) glucuronic acid as distal sugar in the oligosaccharide antigenic moiety) and GPL-III (containing 4-O-CH(3) glucuronic acid as distal sugar) was confirmed using MS/MS and MS/MS/MS approaches. Interestingly, some 'habana' strains presented variants of GPL-II, designated GPL-II'-A and GPL-II'-B. A di-O-CH(3)-deoxy-hexose (tentatively, 2,3-di-O-CH(3)-fucose) was identified as the penultimate sugar in the oligosaccharide moiety of GPL-II'-A, whereas in GPL-II'-B the penultimate sugar was fucose (tentative identification). On the contrary, the distal sugar of the oligosaccharide chain of pGPLs of Myco. simiae ATCC 25275(T) was identified as tri-O-CH(3)-glucuronic acid (designated GPL-sim(T)-I, with two variants: GPL-sim(T)-I-A and GPL-sim(T)-I-B), O-CH(3)-glucuronic acid (designated GPL-sim(T)-II) and di-O-CH(3)-glucuronic acid (GPL-II'-A and GPL-II'-B). The penultimate sugar of the oligosaccharide chain of GPL-sim(T)-I-A and GPL-sim(T)-II was identified as di-O-CH(3)-deoxy-hexose (tentatively, 2,3-di-O-CH(3) fucose), and that of GPL-sim(T)-I-B as deoxy-hexose (tentatively, fucose). In all strains studied, each [M-H](-) and [M+Na](+) ion was revealed as a mixture of homologous compounds varying in the number of -O-CH(3) groups present in the oligosaccharide moiety and in the length of the fatty acyl linked to the peptide.

CONCLUSIONS

The present work indicates that, within a similar general pattern of pGPLs, different strains of Myco. simiae present some variations, so that new compounds (GPL-II'-A, GPL-II'-B, GPL-sim(T)-I-A, GPL-sim(T)-I-B and GPL-sim(T)-II) were defined. Noteworthy was the fact that the 'habana' strains clearly differed from the type strain of Myco. simiae.

SIGNIFICANCE AND IMPACT OF THE STUDY

The data obtained can be used in the delineation of the 'habana' group of Myco. simiae, including the quality control of the immunogenic strain 'habana' TMC 5135.

Depletion effects in smectic phases of hard-rod-hard-sphere mixtures

It is known that when hard spheres are added to a pure system of hard rods the stability of the smectic phase may be greatly enhanced, and that this effect can be rationalised in terms of depletion forces. In the present paper we first study the effect of orientational order on depletion forces in this particular binary system, comparing our results with those obtained adopting the usual approximation of considering the rods parallel and their orientations frozen. We consider mixtures with rods of different aspect ratios and spheres of different diameters, and we treat them within Onsager theory. Our results indicate that depletion effects, and consequently smectic stability, decrease significantly as a result of orientational disorder in the smectic phase when compared with corresponding data based on the frozen-orientation approximation. These results are discussed in terms of the tau parameter, which has been proposed as a convenient measure of depletion strength. We present closed expressions for tau, and show that it is intimately connected with the depletion potential. We then analyse the effect of particle geometry by comparing results pertaining to systems of parallel rods of different shapes (spherocylinders, cylinders and parallelepipeds). We finally provide results based on the Zwanzig approximation of a fundamental-measure density-functional theory applied to mixtures of parallelepipeds and cubes of different sizes. In this case, we show that the tau parameter exhibits a linear asymptotic behaviour in the limit of large values of the hard-rod aspect ratio, in conformity with Onsager theory, as well as in the limit of large values of the ratio of rod breadth to cube side length, d, in contrast to Onsager approximation, which predicts tau approximately d (3). Based on both this result and the Percus-Yevick approximation for the direct correlation function for a hard-sphere binary mixture in the same limit of infinite asymmetry, we speculate that, for spherocylinders and spheres, the tau parameter should be of order unity as d tends to infinity.

Capillary effects in a confined smectic phase of hard spherocylinders: influence of particle elongation

A system of hard rods confined into a pore with slit geometry (two parallel planar substrates) is studied theoretically in the regime of high packing fraction. In this regime the bulk system exhibits a nematic phase as well as a smectic-A (spatially layered) phase. When the system is confined, strong commensuration effects between the layer spacing and the pore width bring about a rich phenomenology, with a phase diagram showing layering and capillary transitions. The latter include capillary smectization transitions whereby a confined smectic phase occurs at conditions of saturation different from those of the corresponding bulk fluid. These transitions are seen to be intimately connected with layering transitions involving discontinuous changes in the number of layers inside the pore. This rich phenomenology is obtained by use of a sophisticated density-functional, Onsager-theory-based approach, especially suited to deal with strongly inhomogeneous fluids. The theory allows for a unified description of ordering and phase behavior of the fluid in confined geometry, and permits us to correlate the above behavior with the wetting properties of the fluid on a single substrate.

Capillary smectization and layering in a confined liquid crystal

Using density-functional theory, we have analyzed the phase behavior of a model liquid crystal confined between two parallel, planar surfaces (i.e., the so-called slit pore). As a result of confinement, a rich phase behavior arises. The complete liquid-crystal phase diagram of the confined fluid is mapped out as a function of wall separation and chemical potential. Strong commensuration effects in the film with respect to wall separation lead to enhanced smectic ordering, which gives capillary smectization (i.e., formation of a smectic phase in the pore), or frustrated smectic ordering, which suppresses capillary smectization. These effects also produce layering transitions. Our nonlocal density-functional-based analysis provides a unified picture of all the above phenomena.

Effects of wetting and anchoring on capillary phenomena in a confined liquid crystal

A fluid of hard spherocylinders of length-to-breadth ratio L/D=5 confined between two identical planar, parallel walls--forming a pore of slit geometry--has been studied using a version of the Onsager density-functional theory. The walls impose an exclusion boundary condition over the particle's centers of mass, while at the same time favoring a particular anchoring at the walls, either parallel or perpendicular to the substrate. We observe the occurrence of a capillary transition, i.e., a phase transition associated with the formation of a nematic film inside the pore at a chemical potential different from micro(b)-the chemical potential at the bulk isotropic-nematic transition. This transition terminates at an Ising-type surface critical point. In line with previous studies based on the macroscopic Kelvin equation and the mesoscopic Landau-de Gennes approach, our microscopic model indicates that the capillary transition is greatly affected by the wetting and anchoring properties of the semi-infinite system, i.e., when the fluid is in contact with a single wall or, equivalently, the walls are at a very large distance. Specifically, in a situation where the walls are preferentially wetted by the nematic phase in the semi-infinite system, one has the standard scenario with the capillary transition taking place at chemical potentials less than micro(b) (capillary nematization transition or capillary ordering transition). By contrast, if the walls tend to orientationally disorder the fluid, the capillary transition may occur at chemical potentials larger than micro(b), in what may be called a capillary isotropization transition or capillary disordering transition. Moreover, the anchoring transition that occurs in the semi-infinite system may affect very decisively the confinement properties of the liquid crystal and the capillary transitions may become considerably more complicated.

Wetting properties of a hard-spherocylinder fluid on a substrate

A density-functional theory is used to analyze the wetting properties of a fluid made up of hard spherocylinders of a length-to-breadth ratio L/D=5 on a model substrate. The substrate imposes an exclusion boundary condition over the molecular centres of mass, while at the same time favoring a definite molecular orientation, either parallel or perpendicular to the substrate, in a region next to the substrate. The wetting properties of this system are seen to depend on the strength with which the substrate orients the molecules: as the latter is increased, wetting by nematic phase is followed by a region of partial wetting which then leads to reentrant wetting by nematic. The two wetting transitions correspond to wetting films with nematic director perpendicular and parallel to the substrate, respectively. Also, in the region of partial wetting, an anchoring transition occurs in the substrate-nematic interface between two different director configurations (parallel and perpendicular to the substrate). Finally, a metastable wetting transition by isotropic is also obtained. This model considerably enriches the wetting phenomenology of the hard-spherocylinder fluid on substrates, of which only the pure hard wall, with no surface control parameter available, has been considered so far.

Density-functional study of the nematic-isotropic interface of hard spherocylinders

The Somoza-Tarazona density-functional theory is applied to the isotropic-nematic interface of hard spherocylinders with length (L)-to-diameter (D) ratios in the range L/D=5-20. Properties such as the density and orientational order-parameter profiles and the variation of interfacial tension with bulk nematic tilt angle agree qualitatively with results of previous studies at larger values of L/D using both computer simulation and the Onsager second-virial approximation. The minimum interfacial tension is obtained at a tilt angle of 90 degrees. For values of L/D approximately 5, it is found that the Onsager approximation predicts a spurious minimum in the interfacial tension at small tilt angles.

Self-consistent nonperturbative theory for classical systems

We construct a self-consistent nonperturbative theory for the structure and thermodynamics of a classical system of particles that goes beyond the usual approaches based on perturbation theory. Our theory, which gives accurate predictions for the phase diagram, is based on two ingredients: first, use is made of an exact expression for the free energy of a many-body system in terms of a reference system and a coupling integral connecting the latter to the final system; second, correlation functions may be very accurately approximated using a number of sum rules relating the radial distribution function with thermodynamic quantities. Consistency between the coupling integral expression and the sum rules may be achieved by means of a self-consistent process.

Density-functional theory of inhomogeneous systems of hard spherocylinders

The smectic-A phase boundaries of a hard-spherocylinder fluid are calculated using a density-functional theory based on one proposed earlier by Somoza and Tarazona [Phys. Rev. A 41, 965 (1990)]. Our calculations do not employ the translation-rotation decoupling approximation used in previous density-functional theories. The calculated phase boundaries agree well with computer simulation results up to aspect ratios L/D approximately 5 and are in better agreement with the simulations than are previous theories. We generalize the model fluid by including long-range interactions with quadrupolar orientational symmetry, which are taken into account by mean-field approximation. For sufficiently large strength, these interactions produce a smectic-C phase, which undergoes either a continuous or weakly first-order transition to the smectic-A phase. The theory and numerical methods discussed here can be applied to the analysis of interfacial phenomena.

Complex phase behavior induced by repulsive interactions

For a solid in which the interactions have a hard core plus a simple soft repulsive tail we show, using a perturbation theory, that the possible stable crystalline structures give rise to a rich phase behavior. We find two concomitant critical points each corresponding to phase transitions separating bcc and fcc structures, respectively, and the occurrence of a transition between fcc and bcc phases without change in density. This novel phenomenology may be relevant to the behavior of some metallic systems, colloids, and to water.

Phase behavior of binary hard-sphere mixtures from perturbation theory

Using a first-order perturbation theory, we have studied the phase diagram of a binary mixture of hard spheres for different values of the size ratio. Recent models for the two-body depletion potential between large spheres are used to take into account the role of the small spheres. The theory predicts a complex phase diagram including a fluid-solid transition at high packing fraction of small spheres, metastability of fluid-fluid demixing, an isostructural solid-solid transition at high packing fraction of the large spheres for sufficiently small values of the size ratio q of the spheres, and the tendency to sticky-sphere behavior in the limit q-->0. The agreement with recent simulation results is quite good. We also show that this phenomenology was already implicit in the pioneering work of Asakura and Oosawa.