Molecular dynamics investigation of bent-core molecules on a water surface

Molecular dynamics simulations are carried out for bent-core molecules at water surfaces. The water surface is shown to alter the equilibrium molecular structure significantly by causing a different class of torsional states to become more favorable. The equilibrium structure is also altered by the substitution of chlorine atoms for hydrogen atoms on the central phenyl ring in that this substitution forces the bent core to remain in a single torsional state rather than be delocalized among several torsional states. The consequences of these structural changes on the chirality and packing of these molecules on water surfaces are discussed.     

Synthesis,mesomorphic, photophysical and computational studies of new achiral four-ring unsymmetrical bent-core mesogens and their Copper(II) complexes

New achiral four-ring unsymmetrical bent-core mesogens derived from 2,5-dihydroxybenzaldehyde and their copper(II) complexes have been synthesised as a new design with an imine and ester linkage. These new bent-core molecules resemble hockey-stick shape, which possesses 4-n-alkyloxy chain (4-n-hexyloxy and 4-n-decyloxy) at one end and methyl or methoxy group at the other end of the molecule. The synthesis, spectroscopic characterisation, phase transition temperature and characterisation of phase behaviour are reported. The bent-core molecules exhibited monotropic nematic and smectic A phase depending on the terminal chain length. Interestingly, copper(II) complexes of bent-core molecules displayed monotropic nematic phase. This is the first report on copper(II) complexes of bent-core molecules that exhibited nematic phase. The four-ring bent-core molecule exhibited fluorescence with large stoke shift. The density functional theory calculations of bent-core molecules and their copper(II) complexes are carried out using Gaussian 09 program at B3LYP level to obtain the stable molecular conformation, dipole moment, highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO) energies and bending angle of the compounds. The natural atomic charges and electronic configurations of the atoms of free ligands as well as the complexes have been evaluated.     

Modeling the stability and the motion of DNA nucleobases on the gold surface

We simulate the structure and dynamics of the four DNA bases on the most stable gold surface. The experimental adsorption energies are reproduced to about 1 kcal mol(-1), and the existence of anchor points in the molecules is evidenced. The simulations also show that the bases drift on the gold surface with a degree of mobility that is not inversely proportional to the experimental (and calculated) desorption energies. When the same type of calculations is applied to pairs of bases it is seen that for at least two of them, namely GG and TT, there is a cooperative effect that increases their adsorption energy with respect to those of the single molecules. The molecular mobility on the surface is still present when a pair of interacting bases is considered.     

Topography of bent-core liquid crystals at the air/liquid crystal interface

Bent-core liquid crystals show a variety of novel structures involving the interplay of molecular bend, tilt and polarisation. Here we investigate the microstructures of the B4, B7 and the dark conglomerate (DC) phases at the air/liquid crystal interface. In these phases, bent-core molecules undergo complex self-assembly, forming helical nanofilaments (the B4 phase), layer undulations (the B7 phase) and disordered focal conics (the DC phase) in the bulk. However, due to the fluidity of the phases and the homeotropic alignment at the interface, several different topographies are observed at the air/liquid crystal interface. We will discuss the surface structures discovered so far in the B4, B7 and DC phases and show how they help us to understand the microstructure and the self-assembly of the liquid crystal phases of bent-core molecules.     

DFT and MD studies on the influence of the orientation of ester linkage groups in banana-shaped mesogens

The influence of the direction of ester linkage groups on the structural and electronic properties of five-ring banana-shaped molecules with a central 1,3-phenylene unit has been investigated including hexyloxy and dodecyloxy terminal chains. DFT studies on the B3LYP/6-31G(d) level were performed on the conformational behaviour of the ten isomers in a systematic way. The one- and two-fold potential energy scans show that the flexibility of the wings significantly depends on the orientation of the carboxyl linkage groups. Moreover, the different directions of the carboxyl groups between the aromatic rings cause remarkable changes on the dipole moment and its components of the molecules. These findings are supported by investigations on the global charge pattern of the molecules calculated from electrostatic potential group charges. The bending angle alpha obtained from a simple model for the five-ring bent-core molecules is a characteristic structural parameter which can be correlated with experimental findings. Calculations on the bent-core molecules in an external electric dipole field related to the direction of their polar axis show remarkable effects with respect to the flexibility and polarity of the isomers. First molecular dynamics simulations on the banana-shaped molecules were carried out within the AMBER 7 package. The trajectories of relevant structural parameters support the findings of the DFT studies. The results concerning the structure and polarity revealed from the DFT and MD calculations of the ten isomers can be correlated with data from dielectric measurements and mesophase properties.     

Structure, energetics, and dynamics of water adsorbed on the muscovite (001) surface: a molecular dynamics simulation

Molecular dynamics (MD) computer simulations of liquid water adsorbed on the muscovite (001) surface provide a greatly increased, atomistically detailed understanding of surface-related effects on the spatial variation in the structural and orientational ordering, hydrogen bond (H-bond) organization, and local density of H2O molecules at this important model phyllosilicate surface. MD simulations at constant temperature and volume (statistical NVT ensemble) were performed for a series of model systems consisting of a two-layer muscovite slab (representing 8 crystallographic surface unit cells of the substrate) and 0 to 319 adsorbed H2O molecules, probing the atomistic structure and dynamics of surface aqueous films up to 3 nm in thickness. The results do not demonstrate a completely liquid-like behavior, as otherwise suggested from the interpretation of X-ray reflectivity measurements and earlier Monte Carlo simulations. Instead, a more structurally and orientationally restricted behavior of surface H2O molecules is observed, and this structural ordering extends to larger distances from the surface than previously expected. Even at the largest surface water coverage studied, over 20% of H2O molecules are associated with specific adsorption sites, and another 50% maintain strongly preferred orientations relative to the surface. This partially ordered structure is also different from the well-ordered 2-dimensional ice-like structure predicted by ab initio MD simulations for a system with a complete monolayer water coverage. However, consistent with these ab initio results, our simulations do predict that a full molecular monolayer surface water coverage represents a relatively stable surface structure in terms of the lowest diffusional mobility of H2O molecules along the surface. Calculated energies of water adsorption are in good agreement with available experimental data.     

Langmuir monolayers of bent-core molecules

A systematic study of five different, symmetric bent-core liquid crystals in Langmuir thin films at the air/water interface is presented. Both the end chains (siloxane vs hydrocarbon) and the core (more or less amphiphilic) are varied, to allow an exploration of different possible layer structures at the interface. The characterization includes systematic surface pressure isotherms, Brewster angle microscopy, and surface potential measurements. The properties of these layers are strongly dependent on the individual type of molecule: the molecules with amphiphilic end chains lie quite flat on the surface, while the molecules with hydrophobic end chains construct multilayer structures. In both cases, the three-dimensional collapse structure is reversible.     

Specific Electrostatic Molecular Recognition in Water

The identification of pairs of small peptides that recognize each other in water exclusively through electrostatic interactions is reported. The target peptide and a structure‐biased combinatorial ligand library consisting of ≈78 125 compounds were synthesized on different sized beads. Peptide–peptide interactions could conveniently be observed by clustering of the small, fluorescently labeled target beads on the surface of larger ligand‐containing beads. Sequences of isolated hits were determined by MS/MS. The interactions of the complex showing the highest affinity were investigated by a novel single‐bead binding assay and by 2D NMR spectroscopy. Molecular dynamics (MD) studies revealed a putative mode of interaction for this unusual electrostatic binding event. High binding specificity occurred through a combination of topological matching and electrostatic and hydrogen‐bond complementarities. From MD simulations binding also seemed to involve three tightly bound water molecules in the interface between the binding partners. Binding constants in the submicromolar range, useful for biomolecular adhesion and in nanostructure design, were measured.     

Preference Prediction for the Stable Inclusion Complexes between Cyclodextrins and Monocyclic Insoluble Chemicals Based on Monte Carlo Docking Simulations

Cyclodextrins (CDs) are useful functional excipients, which are being used to camouflage undesirable pharmaceutical characteristics, especially poor aqueous solubility, through the inclusion complexation process with insoluble drugs. The selection of more efficient cyclodextrin is important to improve the bioavailability of drugs. In this study, the complexing and solubilizing abilities toward poorly water-soluble monocyclic molecules of natural CDs (α-CD, β-CD, and γ-CD) were investigated using Monte Carlo (MC) docking simulations studies. These theoretical results closely agree with the experimental observation of the complex stability in water of the various guests–CD complexes. Host preferences, based on the experimentally determined stability constants between host CDs and guest molecules, show excellent correlation with the calculated interaction energies of corresponding complexes. The inclusion complex with the lower MC docking interaction energy shows a higher value of stability constant than that of the other complex, and the prediction accuracy of the preferred complex for 21 host–guest pairs is 100%. This result indicates that the MC docking interaction energy could be employed as a useful parameter to select more efficient cyclodextrin as a host for the bioavailability of insoluble drugs. In this study, β-CD shows greater solubilizing efficacies toward guest molecules than those of α-CD and γ-CD, with the exception of one case due to the structure of a guest molecule containing one lipophilic cyclic moiety. The surface area change of CDs and hydrogen bonding between the host and guest also work as major factors for the formation of the stable complex.     

Effect of pH on the control of molecular orientation in monolayer of bent-core liquid crystal materials by Langmuir–Blodgett method

Control of molecular orientation at the substrate surface is significant to understand the surface science. Langmuir films of bent-core liquid crystals having alkyl chains at both ends were deposited on silicon substrate. Studies were carried out on air–water interface by changing pH of the subphase. On compression, molecules were arranged in stacks at high pH where as uniform monolayer was formed at lower pH. Limiting area increased at low pH, which resulted in the formation of monolayer after attaining a sustainable surface pressure. Langmuir films were transferred to silicon substrate, and atomic force microscopy images showed appropriate height profiles.     

Anisotropy in Langmuir layers of a bent-core liquid crystal

Langmuir layers of a symmetric bent-core molecule with hydrocarbon end chains and two chlorine atoms substituted on the central phenyl ring of the bent core were characterized by a combination of surface pressure isotherms, Brewster angle microscopy, and surface potential measurements. These layers were found to be optically anisotropic, in contrast to Langmuir layers of similar molecules with different substitutions on the core. After compression, the orientation of the optical axis was essentially uniform over the film. Upon decompression, the film broke into uniform islands or domains. Measuring domain reflectivity while changing the domain orientation allowed the determination of the tilt angle with respect to both domain features and the film normal, as well as the refractive index anisotropy. The tilt angle, near 90 degrees, suggests that the bent-core molecules lie quite flat on the surface.     

Multilayer adsorption of water at a rutile TiO2)(110) surface: towards a realistic modeling by molecular dynamics

We present a model combining ab initio concepts and molecular dynamics simulations for a more realistic treatment of complex adsorption processes. The energy, distance, and orientation of water molecules adsorbed on stoichiometric and reduced rutile TiO(2)(110) surfaces at 140 K are studied via constant temperature molecular dynamics simulations. From ab initio calculations relaxed atomic geometries for the surface and the most probable adsorption sites were derived. The study comprises (i) large two-dimensional surface supercells, providing a realistically low concentration of surface oxygen defects, and (ii) a water coverage sufficiently large to model the onset of the growth of a bulk phase of water on the surface. By our combined approach the influence of both, the metal oxide surface, below, and the bulk water phase, above, on the water molecules forming the interface between the TiO(2) surface and the water bulk layer is taken into account. The good agreement of calculated adsorption energies with experimental temperature programmed desorption spectra demonstrates the validity of our model.     

Dipolar interactions, molecular flexibility, and flexoelectricity in bent-core liquid crystals

The effects of dipolar interactions and molecular flexibility on the structure and phase behavior of bent-core molecular fluids are studied using Monte Carlo computer simulations. Some calculations of flexoelectric coefficients are also reported. The rigid cores of the model molecules consist of either five or seven soft spheres arranged in a "V" shape with external bend angle gamma. With purely repulsive sphere-sphere interactions and gamma = 0 degrees (linear molecules) the seven-sphere model exhibits isotropic, uniaxial nematic, and untilted and tilted smectic phases. With gamma > or = 20 degrees the untilted smectic phases disappear, while the system with gamma > or = 40 degrees shows a direct tilted smectic-isotropic fluid transition. The addition of electrostatic interactions between transverse dipole moments on the apical spheres is generally seen to reduce the degree of molecular inclination in tilted phases, and destabilizes the nematic and untilted smectic phases of linear molecules. The effects of adding three-segment flexible tails to the ends of five-sphere bent-core molecules are examined using configurational-bias Monte Carlo simulations. Only isotropic and smectic phases are observed. On the one hand, molecular flexibility gives rise to pronounced fluctuations in the smectic-layer structure, bringing the simulated system in better correspondence with real materials; on the other hand, the smectic phase shows almost no tilt. Lastly, the flexoelectric coefficients of various nematic phases--with and without attractive sphere-sphere interactions--are presented. The results are encouraging, but a large computational effort is required to evaluate the appropriate fluctuation relations reliably.     

Hydration and stability of nucleic acid bases and base pairs

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.     

Origin of repulsive force and structure/dynamics of interfacial water in OEG-protein interactions: a molecular simulation study

Molecular simulations were performed to investigate the origin of the strong repulsive force acting on a protein as the protein approaches an oligo (ethylene glycol) self-assembled monolayer (OEG-SAM) surface. Since the repulsive force is mainly generated from water molecules, the force from the water molecules near the surface was calculated layer by layer to further identify the molecular origin of the repulsive force. Results show that the strong repulsive force acting on the protein near the OEG-SAM surface is dominantly generated by the interfacial water molecules located between the OEG-SAM surface and lysozyme. A hydroxyl-terminated SAM (OH-SAM) surface was used for comparison. No significant repulsive force was observed from the water molecules between the protein and OH-SAM surface. Further studies show that the dipole distribution of the interfacial water molecules is significantly affected by the OEG-SAM surface, as opposed to the negligible impact from the OH-SAM surface. The interfacial water molecules above the OEG-SAM surface stay longer and reorient more slowly than those above the OH-SAM surface. These results from this work support the hypothesis that the OEG-SAM surface interacts strongly with interfacial water molecules and creates a stable hydration layer that prevents proteins from adsorbing to the surface.     

Structure of the B4 liquid crystal phase near a glass surface

The B4 liquid crystal phase of bent-core molecules, a smectic phase of helical nanofilaments, is one of the most complex hierarchical self-assemblies in soft materials. We describe the layer topology of the B4 phase of mesogens in the P-n-OPIMB homologous series near the liquid crystal/glass interface. Freeze-fracture transmission electron microscopy reveals that the twisted layer structure of the bulk is suppressed, the layers instead forming a structure with periodic layer undulations, with the topography depending on the distance from the glass. The surface layer structure is modeled as parabolic focal conic arrays generated by equidistant parabolas whose foci are defect lines along the glass surface. Nucleation and growth of toric focal conics near the glass substrate is also observed. Although the growth of twisted nanofilaments, the usual manifestation of structural chirality in the B4 phase, is suppressed near the surface, the smectic layers are intrinsically chiral, and the helical filaments that form on top of them grow with specific handedness.     

Anomalous dielectric relaxation of water molecules at the surface of an aqueous micelle

Dielectric relaxation of aqueous solutions of micelles, proteins, and many complex systems shows an anomalous dispersion at frequencies intermediate between those corresponding to the rotational motion of bulk water and that of the organized assembly or macromolecule. The precise origin of this anomalous dispersion is not well-understood. In this work we employ large scale atomistic molecular dynamics simulations to investigate the dielectric relaxation (DR) of water molecules in an aqueous micellar solution of cesium pentadecafluorooctanoate. The simulations clearly show the presence of a slow component in the moment-moment time correlation function [PhiMW(t)] of water molecules, with a time constant of about 40 ps, in contrast to only 9 ps for bulk water. Interestingly, the orientational time correlation function [Cmu(t)] of individual water molecules at the surface exhibits a component with a time constant of about 19 ps. We show that these two time constants can be related by the well-known micro-macrorelations of statistical mechanics. In addition, the reorientation of surface water molecules exhibits a very slow component that decays with a time constant of about 500 ps. An analysis of hydrogen bond lifetime and of the rotational relaxation in the coordinate frame fixed on the micellar body seems to suggest that the 500 ps component owes its origin to the existence of an extended hydrogen bond network of water molecules at the surface. However, this ultraslow component is not found in the total moment-moment time correlation function of water molecules in the solution. The slow DR of hydration water is found to be well correlated with the slow solvation dynamics of cesium ions at the water-micelle interface.     

Self-aggregation of the SDS surfactant at a solid-liquid interface

Molecular dynamics simulations of sodium dodecyl sulfate (SDS) molecules on a graphite surface are presented. The simulations were conducted at low and high surface coverage to study aggregation at the water/graphite interface. Results showed that at low surface coverage, the SDS molecules form hemicylindrical aggregates, in agreement with AFM experiments, whereas at high surface coverage, the surfactants form full cylinders. The latter aggregates have not been reported in systems of SDS on hydrophobic substrates, such as graphite. The unexpected results are explained in terms of a water layer adsorbed at the solid surface which was the responsible for the formation of these aggregates. Moreover, the SDS tails in the full cylindrical configuration became straighter than those of the hemicylindrical aggregate. Hydrogen bond formation between water and surfactant head groups was also studied, and it was found that they did not depend on the surfactant concentration.     

A theoretical study of the structure of the liquid Ga-diamond (111) interface

We present the results of a computer simulation study of the structure of the interface between liquid Ga and the (111) face of diamond, with which we reinterpret the findings from an x-ray reflectivity study of that interface [W. J. Huisman, J. F. Peters, M. J. Zwanenburg, S. A. de Vries, T. E. Derry, D. Abernathy, and J. F. van der Veen, Nature (London) 390, 379 (1997); Surf. Sci. 402-404, 866 (1998)]. That experimental study has been interpreted to show that the contact of Ga with the (111) face of diamond induces the formation of Ga(2) molecules for several layers into the bulk liquid, with the axes of the Ga(2) molecules in successive layers oriented perpendicular to the diamond surface. No driving force for the proposed formation of Ga(2) molecules is identified. The simulations reported in this paper are based on a model that permits chemical binding of Ga, as a dimer, to the C=C double bonds in the reconstructed (111) face of diamond, thereby identifying the driving force for dimerization. We show that an isolated pi complex with the Ga(2) axis perpendicular to the C=C double bond is stable. We then modify the pseudopotential-based self-consistent Monte Carlo simulation scheme for describing inhomogeneous liquid metals, using the calculated potential-energy surface of Ga(2)(C=C) in the region close to the diamond surface. In this model only the Ga adjacent to the diamond is composed of dimers. The interfacial density distribution obtained from the simulations predicts an x-ray reflectivity that is in good agreement with that observed.     

Stability of nucleic acid base pairs in organic solvents: molecular dynamics, molecular dynamics/quenching, and correlated ab initio study

The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations.