Properties of oxidized phospholipid monolayers: An atomistic molecular dynamics study

Non-saturated lipids in the lung surfactant are prone to oxidation by oxidative species present in air. In this Letter, oxidized monolayers of dioleoylphosphatidylcholine (DOPC) were studied by means of both molecular dynamics and potential of mean force calculations. Structural changes of the monolayer following oxidation were revealed, including orientational reversal of oxidized chains. Accumulation of oxidized lipids in the monolayer is observed for moderate oxidation ratios, whereas removal of the short-chain oxidation product is predicted at long timescales. Massive oxidation leads to the loss of the well-ordered monolayer structure and partial solubilization of the oxidized lipids in the aqueous subphase.     

Structure and diffusion of nanoparticle monolayers floating at liquid/vapor interfaces: a molecular dynamics study

Large-scale molecular dynamics simulations are used to simulate a layer of nanoparticles floating on the surface of a liquid. Both a low viscosity liquid, represented by Lennard-Jones monomers, and a high viscosity liquid, represented by linear homopolymers, are studied. The organization and diffusion of the nanoparticles are analyzed as the nanoparticle density and the contact angle between the nanoparticles and liquid are varied. When the interaction between the nanoparticles and liquid is reduced the contact angle increases and the nanoparticles ride higher on the liquid surface, which enables them to diffuse faster. In this case the short-range order is also reduced as seen in the pair correlation function. For the polymeric liquids, the out-of-layer fluctuation is suppressed and the short-range order is slightly enhanced. However, the diffusion becomes much slower and the mean square displacement even shows sub-linear time dependence at large times. The relation between diffusion coefficient and viscosity is found to deviate from that in bulk diffusion. Results are compared to simulations of the identical nanoparticles in 2-dimensions.     

Microscopic wetting of self-assembled monolayers with different surfaces: a combined molecular dynamics and quantum mechanics study

Molecular dynamics simulations are used to study the micronature of the organization of water molecules on the flat surface of well-ordered self-assembled monolayers (SAMs) of 18-carbon alkanethiolate chains bound to a silicon (111) substrate. Six different headgroups (-CH(3), -C═C, -OCH(3), -CN, -NH(2), -COOH) are used to tune the character of the surface from hydrophobic to hydrophilic, while the level of hydration is consistent on all six SAM surfaces. Quantum mechanics calculations are employed to optimize each alkyl chain of the different SAMs with one water molecule and to investigate changes in the configuration of each headgroup under hydration. We report the changes of the structure of the six SAMs with different surfaces in the presence of water, and the area of the wetted surface of each SAM, depending on the terminal group. Our results suggest that a corrugated and hydrophobic surface will be formed if the headgroups of SAM surface are not able to form H-bonds either with water molecules or between adjacent groups. In contrast, the formation of hydrogen bonds not only among polar heads but also between polar heads and water may enhance the SAM surface hydrophilicity and corrugation. We explicitly discuss the micromechanisms for the hydration of three hydrophilic SAM (CN-, NH(2)- and COOH-terminated) surfaces, which is helpful to superhydrophilic surface design of SAM in biomimetic materials.     

Large-scale molecular dynamics simulations of alkanethiol self-assembled monolayers

Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing, and molecular chain length. Our simulations show that the alkanethiol chains of 13-carbons tilt from the surface normal by a collective angle of 25 degrees along next-nearest-neighbor direction at 300 K. The tilt structure of 13-carbon alkanethiol system is found to depend strongly on temperature and exhibits hysteresis. At 350 K the 13-carbon alkanethiol system transforms to a disordered phase characterized by small collective tilt angle, flexible tilt direction, and random distribution of backbone planes. The tilt structure also depends on lattice spacing: With increasing lattice spacing a the tilt angle increases rapidly from a nearly zero value at a=4.7 A to as high as 34 degrees at a=5.3 A at 300 K for 13-carbon alkanethiol system. Finally, the effects of the molecular chain length on the tilt structure are significant at high temperatures.     

Odd-even variations in the wettability of n-alkanethiolate monolayers on gold by water and hexadecane: a molecular dynamics simulation study

Molecular dynamics (MD) simulations were performed to investigate odd-even chain length dependencies in the wetting properties of self-assembled monolayers (SAMs) of n-alkanethiols [CH3(CH2)n-1SH] on gold by water and hexadecane. Experimentally, the contact angle of hexadecane on the SAMs depends on whether n is odd or even, while contact angles for water show no odd-even dependence. Our MD simulations of this system included a microscopic droplet of either 256 water molecules or 60 hexadecane molecules localized on an n-alkanethiolate SAM on gold with either an even or odd chain length. Contact angles calculated for these nanoscopic droplets were consistent with experimentally observed macroscopic trends in wettability, namely, that hexadecane is sensitive to structural differences between odd- and even-chained SAMs while water is not. Structural properties for the SAMs (including features such as chain tilt, chain twist, and terminal methyl group tilt) were calculated during the MD simulations and used to generate IR spectra of these films that compared favorably with experimental spectra. MD simulations of SAMs in contact with slabs of water and hexadecane revealed that the effects of these solvents on the structure of the SAM was restricted to the chain terminus and had no effect on the inner structure of the SAM. The density profiles for water and hexadecane on the SAMs were different in that water displayed a significant depletion in its density at the liquid/SAM interface from its bulk value, while no such depletion occurred for hexadecane. This difference in contact may explain the lack of an odd-even variation in the wetting characteristics of water on these surfaces, because the water molecules are positioned further away from the surface and, therefore, are not sensitive to the structural differences in the average orientations for the terminal methyl groups in odd- and even-chained SAMs. In contrast, the differences in the wetting properties of hexadecane on the odd- and even-chained SAMs may reflect the closer proximity of these molecules to the SAM surface and a resulting greater sensitivity to the differences in the terminal methyl group orientations in the SAMs. SAM-solvent interaction energies were calculated during the MD simulations, yielding interaction energies that differed on the even- and odd-chained surfaces by approximately 10% for hexadecane and negligibly for water, in accord with estimates using experimental wetting results.     

H-Bond in methanol: a molecular dynamics study

A set of molecular dynamics (MD) simulations of methanol-d₄ at three temperatures in the liquid range (200, 250 and 300K) have been carried out. The equations of motion of 256 molecules interacting through a potential model due to Haughney et al. [J. Phys. Chem., 91 (1987) 4934] were solved using the velocity version of the Verlet algorithm. This rather large number of molecules was required for studying the behaviour of the system at momentum transfers as low as 0.25 Å⁻¹. It was found that the system experiences long period fluctuations, and therefore very long MD runs (of the order of 100 ps) are necessary in order to obtain accurate statistical averages. Computed static properties are in good agreement with those reported by Haughney et al. and the neutron weighted g(r) and the static structure factor compare favourably with available neutron diffraction data. The study of time-dependent properties through centre-of-mass autocorrelation functions (VACF, F_s(Q,t) and F(Q,t)) and their memory functions reveals features unknown in simple liquids and very similar to those found in liquid water. A close agreement between centre-of-mass single-particle autocorrelation functions and the translational part of QENS data is also observed. The dynamic structure factor for the centres of mass show distinctive side peaks in the same region of the (Q,ω) plane where recently collective excitations have been studied using coherent neutron scattering thus establishing the presence of propagating short wavelength modes. fa]Presented at the International Symposium on Hydrogen Bond Physics held at Il Ciocco, Barga, Italy, 11–14 September 1990.     

Microstructure of neat alcohols: a molecular dynamics study

Neat methanol and tert-butanol are studied by molecular dynamics with the focus on the microstructure of these two alcohols. The site-site radial distribution functions, the corresponding structure factors, and an effective local one-body density function are shown to be the appropriate statistical quantities that point in a complementary manner towards the same microstructure for any given liquid. Methanol is found to be a weakly associated liquid forming various chainlike patterns (open and closed) while tert-butanol is almost entirely associated and forms micellelike primary pattern. The presence of stable local microheterogeneity within homogeneous disordered phase appears as a striking feature of these liquids. The absence of any such apparent clustering in water--a stronger hydrogen bonding liquid--through the same two statistical quantities is analyzed.     

Photoinduced molecular reorientation dynamics in confined domains of Langmuir monolayers

In a photoresponsive Langmuir monolayer comprised of smectic-C-like domains of mesogenic trans-azobenzene derivative embedded within an isotropic matrix of its cis isomer counterpart, several structurally differing circular droplets were irradiated with linearly polarized light. This report describes the structural rearrangements that occurred in these droplets upon illumination followed by Brewster angle microscopy analysis. Starting from initial well-characterized and symmetric states, final photoaligned situations were reached in which the azimuth angles of the rod-shaped elongated molecules were found to be perpendicular to the electric component of the excitation light. The dynamical aspects of the photoalignments, including their transient patterns, are captured by a theoretical model that couples a relaxational principle incorporating long-range elastic forces with a kinetic formalism presenting an anisotropic rate law.     

Thermophoresis in liquids: a molecular dynamics simulation study

Thermophoresis in liquids is studied by molecular dynamics simulation (MD). A theory is developed that divides the problem in the way consistent with the characteristic scales. MD is then conducted to obtain the solution of each problem, which is to be all combined for macroscopic predictions. It is shown that when the temperature gradient is applied to the nonconducting liquid bath that contains neutral particles, there occurs a pressure gradient tangential to the particle surface at the particle-liquid interface. This may induce the flow in the interfacial region and eventually the particle to move. This applies to the material system that interacts through van der Waals forces and may be a general source of the thermophoresis phenomenon in liquids. The particle velocity is linearly proportional to the temperature gradient. And, in a large part of the given temperature range, the particle motion is in the direction toward the cold end and decreases with respect to the temperature. It is also shown that the particle velocity decreases or even reverses its sign in the lowest limit of the temperature range or with a particle of relatively weak molecular interactions with the liquid. The characteristics of the phenomenon are analyzed in molecular details.     

Force-induced insulin dimer dissociation: a molecular dynamics study

Understanding the forces and dynamics of insulin dissociation is critical for devising formulations for the treatment of insulin-dependent diabetes. In earlier work, we applied AFM-based force spectroscopy to covalently tethered and oriented insulin monomers to assess the effect of molecular orientation on insulin-insulin binding forces. We report here on steered molecular dynamics simulations of the insulin dissociation force spectroscopy experiment. Consistent with our experiments, our simulation results suggest that insulin dimer dissociation occurs near the limit of extensibility of the B-chain. We have also found that the forced dissociation of the insulin dimer is a rate-dependent process, involving significant conformational changes to the monomer(s). The insulin dimer dissociation pathway also depends on the relative strength of the inter-monomer interactions across the antiparallel beta-sheet interface and the intra-monomer interactions of residues A1 and A30 with the insulin B-chain. Our simulation results strongly support the design of bioactive insulin analogues that involves altering hydrogen bonding and hydrophobic interactions across the beta-sheet dimer interface.     

Polymer-nanoparticle interfacial behavior revisited: a molecular dynamics study

By tuning the polymer-filler interaction, filler size and filler loading, we use a coarse-grained model-based molecular dynamics simulation to study the polymer-filler interfacial structural (the orientations at the bond, segment and chain length scales, chain size and conformation), dynamic and stress-strain properties. Simulated results indicate that the interfacial region is composed of partial segments of different polymer chains, which is consistent with the experimental results presented by Chen et al. (Macromolecules, 2010, 43, 1076). Moreover, it is found that the interfacial region is within one single chain size (R(g)) range, irrespective of the polymer-filler interaction and the filler size, beyond which the bulk behavior appears. In the interfacial region, the orientation and dynamic behaviors are induced by the interfacial enthalpy, while the size and conformation of polymer chains near the filler are controlled by the configurational entropy. In the case of strong polymer-filler interaction (equivalent to the hydrogen bond), the innerest adsorbed polymer segments still undergo adsorption-desorption process, the transport of chain mass center in the interfacial region exhibits away from the glassy behavior, and no plastic-like yielding point appears in the stress-strain curve, which indicates that although the mobility of interfacial polymer chains is restricted, there exist no "polymer glassy layers" surrounding the filler. In addition, it is evidenced that the filler particle prefers selectively adsorbing the long polymer chains for attractive polymer-filler interaction, validating the experimental explanation of the change of the bound rubber (BR). In short, this work provides important information for further experimental and simulation studies of polymer-nanoparticle interfacial behavior.     

Liquid-vapor interface of methanol-water mixtures: a molecular dynamics study

Molecular dynamics simulations were carried out to investigate the structural and thermodynamic properties and variations in the dipole moments of the liquid-vapor interfaces of methanol-water mixtures. Various methanol-water compositions were simulated at room temperature. We found that methanol tends to concentrate at the interface, and the computed surface tension shows a composition dependence that is consistent with experimental measurements. The methanol molecule shows preferred orientation near the interface with the methyl group pointing into the vapor phase. The methanol in the mixture is found to have larger dipole moments than that of pure liquid methanol. The strong local field induced by the surrounding water molecules is partly the reason for this difference. The dependence of hydrogen-bonding patterns between methanol and water on the interface and the composition of the mixture is also discussed in the paper.     

Ligand-to-metal charge-transfer dynamics in a blue copper protein plastocyanin: a molecular dynamics study

Equilibrium and nonequilibrium dynamics of a blue copper protein plastocyanin in an oxidized state are studied by molecular dynamics (MD) simulation. Potential energy functions of the lowest seven electronic states, including ligand-to-metal charge-transfer (LMCT) and copper d --> d excited states, were taken from our previous work (Ando, K. J. Phys. Chem. B 2004, 108, 3940), which employed ab initio molecular orbital and density functional calculations on the active-site model. The equilibrium MD simulations in the ground state indicate that ligand motions coupled to transition from the ground state to the LMCT state are mostly represented by stretching and bending vibrations of the Cu-S(Cys) distance, Ndelta(His)-Cu-Ndelta(His) angle, and S(Cys)-Cu-[Ndelta(His)]2 trigonal pyramid structure. The nonequilibrium dynamics on the LMCT potential exhibit rapid decays in which surface crossings to the d --> d and the first excited states occur in 70-80 fs. The crossing dynamics mostly correlate with cleavage of the Cu-S(Cys) bond and the associated response in the Ndelta(His)-Cu-Ndelta(His) moiety. The average dynamics of the vertical energy gap coordinates exhibit an overdamped decay with a recurrence oscillation in 500 fs, which shows clear coherence surviving after the ensemble averaging. This oscillation stems mostly from the recoiling motion of the Ndelta(His)-Cu-Ndelta(His) part. The dynamics of the energy gaps after this coherent oscillation are randomized such that the ensemble average yields flat profiles along time, although each single trajectory exhibits fluctuations with amplitudes large enough to reach surface crossings. These indicate that the relaxation from the LMCT state first occurs via ballistic and coherent potential crossings in 70-80 and 500 fs, followed by thermally activated random transitions.     

Formation of protein molecular imprints within Langmuir monolayers: a quartz crystal microbalance study

Protein imprinting leading to enhanced rebinding of ferritin to ternary lipid monolayers is demonstrated using a quartz crystal microbalance. Monolayers consisting of cationic dioctadecyldimethylammonium bromide, non-ionic methyl stearate, and poly(ethylene glycol) bearing phospholipids were imprinted with ferritin at the air/water interface of a Langmuir-Blodgett trough and transferred hydrated to hydrophobic substrates for study. This immobilization was shown by fluorescence correlation spectroscopy to significantly hinder any further diffusion of lipids, while rebinding studies demonstrated up to a six-fold increase in ferritin adsorption to imprinted versus control monolayers. A diminished rebinding of ferritin to its imprint was observed through pH reduction to below the protein isoelectric point, demonstrating the electrostatic nature of the interaction. Rebinding to films where imprint pockets remained occupied by the template protein was also minimal. Studies with a smaller acidic protein revealed the importance of the steric influence of poly(ethylene glycol) in forming the protein binding pockets, as albumin-imprinted monolayers showed low binding of ferritin, while ferritin-imprinted monolayers readily accommodated albumin. The controllable structure-function relationship and limitations of this system are discussed with respect to the application of protein imprinting in sensor development as well as fundamental studies of proteins at dynamic interfaces.     

Adsorption of sulfite oxidase on self-assembled monolayers from molecular dynamics simulations

Sulfite oxidase (SO) is an enzyme catalyzing the terminal step of the metabolism of sulfur-containing amino acids that is essential for almost all living organisms. The catalytic activity of SO in vertebrates strongly depends on the efficiency of the intramolecular electron transfer (IET) between the catalytic Moco domain and the cytochrome b5 (cyt b5) domain. The IET process is assumed to be mediated by large domain motions of the cyt b5 domains within the enzyme. Thus, the interaction of SO with charged surfaces may affect the mobility of the cyt b5 domain required for IET and consequently hinder SO activation. In this study, we present a molecular dynamics approach to investigating the ionic strength dependence of the initial surface adsorption of SO in two different conformations-the crystallographic structure and the model structure for an activated SO-onto mixed amino- and hydroxyl-terminated SAMs. The results show for both conformations at low ionic strengths a strong adsorption of the cyt b5 units onto the SAM, which inhibits the domain motion event required for IET. Under higher ion concentrations, however, the interaction with the surface is weakened by the negatively charged ions acting as a buffer and competing in adsorption with the cathodic cyt b5 domains. This competition prevents the immobilization of the cytochrome b5 units onto the surface, allowing the intramolecular domain motions favoring IET. Our predictions support the interpretation of recent experimental spectroelectrochemical studies on SO.     

Silsesquioxane dendrimers as catalysts: a bite-sized molecular dynamics study

A method of calculating the bite (P-M-P) angle for dendritic ligands is reported. Diphenylphosphine terminated dendritic ligands were modified with either a single rhodium or a rhodium complex [HRh(CO)(2)] and molecular dynamics techniques used to run simulations to determine the dynamic bite angle (beta(d)) as a time averaged property. The effects of changing the composition of the dendritic branches is investigated and comparison with experimental hydroformylation data reveals that the dendrimer with the highest linear: branched ratio also has a dynamic bite angle closest to the theoretical ideal value of 120 degrees .     

Cooperativity in drug-DNA recognition: a molecular dynamics study.

NMR studies have shown that the minor groove-binding ligand Hoechst 33258 binds to the two T4/A4 tracts within the duplex d(CTTTTCGAAAAG)2 in a highly cooperative manner, such that in titration experiments no intermediate 1:1 complex can be detected. The NMR-derived structures of the free DNA and the 2:1 complex have been obtained, but can shed little light on what the origins of this cooperativity may be. Here we present the results of a series of molecular dynamics simulations on the free DNA, the 1:1 complex, and the 2:1 complex, which have been designed to enable us to calculate thermodynamic parameters associated with the molecular recognition events. The results of the molecular dynamics studies confirm that structural factors alone cannot explain the cooperativity observed, indeed when enthalpic and hydration factors are looked at in isolation, the recognition process is predicted to be slightly anticooperative. However, when changes in configurational entropy are taken into account as well, the overall free energy differences are such that the calculated cooperativity is in good agreement with that observed experimentally. The results indicate the power of molecular dynamics methods to provide reasonable explanations for phenomena that are difficult to explain on the basis of static models alone, and provide a nice example of the concept of "allostery without conformational change".     

Long-chain alkyl sulfonate micelle fission: a molecular dynamics study

In this study, we investigate micelle fission of long-chain alkyl sulfonate molecules using atomistic scale simulation. GROMACS software code with the united atom force field was applied. 0.5-μs parallel molecular dynamics simulation study was conducted for a surfactant/water system consisting of 192 sodium pentadecyl sulfonate and 40,553 water molecules. The large preassembled micelle was ruptured at Krafft above T?=?323-K temperature, and we track two ellipsoid-like micelles over the course of the production run. To estimate the micelle shape, we determined the principal moments of inertia and the eccentricity, which proved that the micelles have a pronounced prolate spheroid shape, which agrees well with our previous experimental data. The mechanism of micelle fission was explored in detail. The aggregation number, ionization degree, and other parameters obtained from simulation were consistent with existing experimental finding. The determined parameters in addition to simple visual inspection of trajectories revealed monomer-micelle exchange—with the estimated relaxation time τ ₁?=?10^??9s. We assume that the exchange process is conditioned by the unequal size of micelles leading to adjustment of aggregation number.     

Structure and ultrafast dynamics of liquid water: a quantum mechanics/molecular mechanics molecular dynamics simulations study

A quantum mechanics/molecular mechanics molecular dynamics simulation was performed for liquid water to investigate structural and dynamical properties of this peculiar liquid. The most important region containing a central reference molecule and all nearest surrounding molecules (first coordination shell) was treated by Hartree-Fock (HF), post-Hartree-Fock [second-order Moller-Plesset perturbation theory (MP2)], and hybrid density functional B3LYP [Becke's three parameter functional (B3) with the correlation functional of Lee, Yang, and Parr (LYP)] methods. In addition, another HF-level simulation (2HF) included the full second coordination shell. Site to site interactions between oxygen-oxygen, oxygen-hydrogen, and hydrogen-hydrogen atoms of all ab initio methods were compared to experimental data. The absence of a second peak and the appearance of a shoulder instead in the gO-O graph obtained from the 2HF simulation is notable, as this feature has been observed so far only for pressurized or heated water. Dynamical data show that the 2HF procedure compensates some of the deficiency of the HF one-shell simulation, reducing the difference between correlated (MP2) and HF results. B3LYP apparently leads to too rigid structures and thus to an artificial slow down of the dynamics.