Molecular dynamics simulations of water confined between matched pairs of hydrophobic and hydrophilic self-assembled monolayers

We have conducted a molecular dynamics (MD) simulation study of water confined between methyl-terminated and carboxyl-terminated alkylsilane self-assembled monolayers (SAMs) on amorphous silica substrates. In doing so, we have investigated the dynamic and structural behavior of the water molecules when compressed to loads ranging from 20 to 950 MPa for two different amounts of water (27 and 58 water molecules/nm2). Within the studied range of loads, we observe that no water molecules penetrate the hydrophobic region of the carboxyl-terminated SAMs. However, we observe that at loads larger than 150 MPa water molecules penetrate the methyl-terminated SAMs and form hydrogen-bonded chains that connect to the bulk water. The diffusion coefficient of the water molecules decreases as the water film becomes thinner and pressure increases. When compared to bulk diffusion coefficients of water molecules at the various loads, we found that the diffusion coefficients for the systems with 27 water molecules/nm2 are reduced by a factor of 20 at low loads and by a factor of 40 at high loads, while the diffusion coefficients for the systems with 58 water molecules/nm2 are reduced by a factor of 25 at all loads.

Water penetration of damaged self-assembled monolayers

The interaction of water with self-assembled monolayers (SAMs) on amorphous silica is investigated using classical molecular dynamics simulation. Damage is induced through shear simulations with model atomic force microscopy (AFM) tips and separately with controlled extraction. We find that SAM coatings that have been slightly damaged (by normal loads close to 10 nN from a 10-nm-diameter AFM tip) are susceptible to water penetration and migration to the underlying hydrophilic substrate. The controlled damage studies indicate that the presence of water tends to heal damage below a threshold radius and exploits and magnifies damage above this threshold. For the systems studied here, Si(OH)3(CH2)10CH3 alkylsilane chains on amorphous silica, this threshold radius is between 0.5 and 1.0 nm.

Water in nanoconfinement between hydrophilic self-assembled monolayers

Molecular dynamics (MD) simulations of water confined to subnanometer thicknesses between carboxyl-terminated alkanethiol self-assembled monolayers (SAMs) on gold were performed to address conflicts in the literature on the structure and response of water in confinement. The amount of water was varied to yield submonolayer to bilayer structures. The orientation of the water is affected by the confinement, especially in the submonolayer case. We find that the diffusion coefficient decreases as the film becomes thinner and at higher pressures. However, in all cases studied, liquid diffusion is always found. At maximal suppression, the diffusion constant is 2 orders of magnitude smaller than the bulk value.

Simulations of nanotribology with realistic probe tip models

We present the results of massively parallel molecular dynamics simulations aimed at understanding the nanotribological properties of alkylsilane self-assembled monolayers (SAMs) on amorphous silica. In contrast to studies with opposing flat plates, as found in the bulk of the simulation literature, we use a model system with a realistic AFM tip (radius of curvature ranging from 3 to 30 nm) in contact with a SAM-coated silica substrate. We compare the differences in response between systems in which chains are fully physisorbed, fully chemisorbed, and systems with a mixture of the two. Our results demonstrate that the ubiquitous JKR and DMT models do not accurately describe the contact mechanics of these systems. In shear simulations, we find that the chain length has minimal effects on both the friction force and coefficient. The tip radius affects the friction force only (i.e., the coefficient is unchanged) by a constant shift in magnitude due to the increase in pull-off force with increasing radius. We also find that at extremely low loads, on the order of 10 nN, shearing from the tip causes damage to the physisorbed monolayers by removal of molecules.

Structure and dynamics of water near the interface with oligo(ethylene oxide) self-assembled monolayers

We performed molecular dynamics simulations of the oligo(ethylene oxide) (OEO) self-assembled monolayers in water to determine the nature of the systems' interfacial structure and dynamics. The density profiles, hydrogen bonding, and water dynamics are calculated as a function of the area per molecule A of OEO. At the highest coverages, the interface is hydrophobic, and a density drop is found at the interface. The interfacial region becomes more like bulk water as A increases. The OEO and water become progressively more mixed, and hydrogen bonding increases within the interfacial region. Water mobility is slower within the interfacial region, but not substantially. The implications of our results on the resistance of OEO SAMs to protein adsorption are discussed. Our principal result is that as A increases the increasingly waterlike interfacial region provides a more protein-resistant surface. This finding supports recent experimental measurements that protein resistance is maximal for less than full coverage on Au.

Multiscale structure of the underwater adhesive of Phragmatopoma californica: a nanostructured latex with a steep microporosity gradient

Phragmatopoma Californica builds a tubular dwelling by gluing bits of sand and seashell together underwater with a proteinaceous adhesive. In the lab, the animals will build with 0.5 mm glass beads. Two spots of glue with a consistent volume of about 100 pL each are deposited on the glass beads before placement on the end of the tube. The animals wriggled the particles for 20-30 s before letting go, which suggested that the adhesive was sufficiently set within 30 s to support the glass beads. The structure of the adhesive joints was examined at the micro- and nanoscopic length scales using laser scanning confocal and atomic force microscopies. At the microscale, the adhesive was a cellular solid with cell diameters ranging from 0.5 to 6.0 mum, distributed to create a steep porosity gradient that ranged from near zero at the outside edges to about 50% at the center of the adhesive joint. At the nanoscale, the adhesive appeared to be an accretion of trillions of deformable nanospheres, reminiscent of a high-solids-content latex adhesive. The implications of the structure for the functionality of the adhesive is discussed.

How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations

Rhodopsin is the prototypical G-protein coupled receptor, coupling light activation with high efficiency to signaling molecules. The dark-state X-ray structures of the protein provide a starting point for consideration of the relaxation from initial light activation to conformational changes that may lead to signaling. In this study we create an energetically unstable retinal in the light activated state and then use molecular dynamics simulations to examine the types of compensation, relaxation, and conformational changes that occur following the cis-trans light activation. The results suggest that changes occur throughout the protein, with changes in the orientation of Helices 5 and 6, a closer interaction between Ala 169 on Helix 4 and retinal, and a shift in the Schiff base counterion that also reflects changes in sidechain interactions with the retinal. Taken together, the simulation is suggestive of the types of changes that lead from local conformational change to light-activated signaling in this prototypical system.

Nicotinamide Reverses Neurological and Neurovascular Deficits in Streptozotocin Diabetic Rats

In diabetes, activation of the nuclear enzyme poly(ADP-ribose) polymerase (PARP) is an important effector of oxidative-nitrosative injury, which contributes to the development of experimental diabetic peripheral neuropathy (DPN). However, the potential toxicity of complete PARP inhibition necessitates the utilization of weaker PARP inhibitors with additional therapeutic properties. Nicotinamide (vitamin B3) is a weak PARP inhibitor, antioxidant, and calcium modulator and can improve energy status and inhibit cell death in ischemic tissues. We report the dose-dependent effects of nicotinamide in an established model of early DPN. Control and streptozotocin-diabetic rats were treated with 200 to 400 mg/kg/day nicotinamide (i.p.) for 2 weeks after 2 weeks of untreated diabetes. Sciatic endoneurial nutritive blood flow was measured by microelectrode polarography and hydrogen clearance, and sciatic motor and hind-limb digital sensory nerve conduction velocities and thermal and mechanical algesia were measured by standard electrophysiological and behavioral tests. Malondialdehyde plus 4-hydroxyalkenal concentration in the sciatic nerve and amino acid-(4)-hydroxynonenal adduct and poly(ADP-ribosyl)ated protein expression in human Schwann cells were assessed by a colorimetric method with N-methyl-2-phenyl indole and Western blot analysis, respectively. Nicotinamide corrected increased sciatic nerve lipid peroxidation in concert with nerve perfusion deficits and dose-dependently attenuated nerve conduction slowing, as well as mechanical and thermal hyperalgesia. Nicotinamide (25 mM) prevented high (30 mM) glucose-induced overexpression of amino acid-(4)-hydroxynonenal adducts and poly(ADP-ribosyl)ated proteins in human Schwann cells. In conclusion, nicotinamide deserves consideration as an attractive, nontoxic therapy for the treatment of DPN.

Early diabetes-induced biochemical changes in the retina: comparison of rat and mouse models

AIMS/HYPOTHESIS

Recently, various transgenic and knock-out mouse models have become available for studying the pathogenesis of diabetic retinopathy. At the same time, diabetes-induced retinal changes in the wild-type mice remain poorly characterised. The present study compared retinal biochemical changes in rats and mice with similar (6-week) durations of streptozotocin-induced diabetes.

MATERIALS AND METHODS

The experiments were performed on Wistar rats and C57Bl6/J mice. Retinal glucose, sorbitol, fructose, lactate, pyruvate, glutamate, alpha-ketoglutarate and ammonia were measured spectrofluorometrically by enzymatic methods. Vascular endothelial growth factor (VEGF) protein was assessed by ELISA, and poly(ADP-ribosyl)ation by immunohistochemistry and western blot analysis. Free mitochondrial and cytosolic NAD(+)/NADH ratios were calculated from the glutamate and lactate dehydrogenase systems.

RESULTS

Retinal glucose concentrations were similarly increased in diabetic rats and mice, vs controls. Diabetic rats manifested approximately 26- and 5-fold accumulation of retinal sorbitol and fructose, respectively, whereas elevation of both metabolites in diabetic mice was quite modest. Correspondingly, diabetic rats had (1) increased retinal malondialdehyde plus 4-hydroxyalkenal concentrations, (2) reduced superoxide dismutase (SOD), glutathione peroxidase, glutathione reductase and glutathione transferase activities, (3) slightly increased poly(ADP-ribose) immunoreactivity and poly(ADP-ribosyl)ated protein abundance, and (4) VEGF protein overexpression. Diabetic mice lacked these changes. SOD activity was 21-fold higher in murine than in rat retinas (the difference increased to 54-fold under diabetic conditions), whereas other antioxidative enzyme activities were 3- to 10-fold lower. With the exception of catalase, the key antioxidant defence enzyme activities were increased, rather than reduced, in diabetic mice. Diabetic rats had decreased free mitochondrial and cytosolic NAD(+)/NADH ratios, consistent with retinal hypoxia, whereas both ratios remained in the normal range in diabetic mice.

CONCLUSIONS/INTERPRETATION

Mice with short-term streptozotocin-induced diabetes lack many biochemical changes that are clearly manifest in the retina of streptozotocin-diabetic rats. This should be considered when selecting animal models for studying early retinal pathology associated with diabetes.

Coarse-grained simulations of lipid bilayers

A minimal model of lipid molecules consisting of bead-spring representation is developed. The basic interactions are hydrophobic and polar interactions. Essential physical features of lipid bilayers are maintained using this model, and relatively long times can be simulated in comparison to atomistic models. Self-assembly from a random starting configuration to a bilayer can readily be followed using molecular dynamics simulations. The diffusion of lipid molecules well beyond their nearest neighbors is attained. As a basis for description of the model, the area per lipid, the bending modulus, and the area compressibility as a function of temperature and tail length are calculated. A liquid to gel transition is observed and quantitatively characterized. Both saturated and unsaturated lipids are treated.

Capillary waves at the liquid-vapor interface and the surface tension of water

Capillary waves occurring at the liquid-vapor interface of water are studied using molecular dynamics simulations. In addition, the surface tension, determined thermodynamically from the difference in the normal and tangential pressure at the liquid-vapor interface, is compared for a number of standard three- and four-point water models. We study four three-point models (SPC/E, TIP3P, TIP3P-CHARMM, and TIP3P-Ew) and two four-point models (TIP4P and TIP4P-Ew). All of the models examined underestimate the surface tension; the TIP4P-Ew model comes closest to reproducing the experimental data. The surface tension can also be determined from the amplitude of capillary waves at the liquid-vapor interface by varying the surface area of the interface. The surface tensions determined from the amplitude of the logarithmic divergence of the capillary interfacial width and from the traditional thermodynamic method agree only if the density profile is fitted to an error function instead of a hyperbolic tangent function.

Accelerated partial breast irradiation using interstitial high dose rate 192iridium brachytherapy: Early Australian experience and review of the literature

Summary Accelerated partial breast irradiation (APBI) is an evolving new technique of adjuvant irradiation in selected women with early-stage breast cancer. We developed a pilot programme of APBI in 2000 and report end results in seven patients followed for a mean of 42.7 months (range 29-55 months). Good to excellent cosmesis and no loco-regional relapse or systemic metastases have occurred. The literature related to APBI is reviewed.

Complementary matching in domain formation within lipid bilayers

Domain structure and formation in lipid bilayers are investigated by molecular dynamics simulations using a coarse-grained lipid model. The lipid bilayers consist of two lipid types that are identical except for tail length. At a temperature intermediate to the two melting temperatures of the constituent lipid types, gel domains spontaneously form from an initial random structure. The simulations reveal that the gel domains consist of both lipid types in a complementary match. If a long lipid is in the top monolayer, then a short lipid is underneath and vice versa. The gel domains have a larger thickness than the surrounding liquid phase. The thickness of the gel domains is close to that of the pure long lipid gel phase bilayers. However, since in the mixed gel domains the lipids are not tilted and in the pure gel phase the lipids are tilted, the two thicknesses are similar, and the underlying structure is therefore not distinguishable solely by thickness measurements.

Tribological properties of alkylsilane self-assembled monolayers

In this study, we perform molecular dynamics simulations of adhesive contact and friction between alkylsilane Si(OH)(3)(CX(2))(10)CX(3) and alkoxylsilane Si(OH)(2)(CX(2))(10)CX(3) (where X = H or F) self-assembled monolayers (SAMs) on an amorphous silica substrate. The alkylsilane SAMs are primarily hydrogen-bonded or physisorbed to the surface. The alkoxylsilane SAMs are covalently bonded or chemisorbed to the surface. Previously, we studied the chemisorbed systems. In this work, we study the physisorbed systems and compare the tribological properties with the chemisorbed systems. Furthermore, we examine how water at the interface of the SAMs and substrate affects the tribological properties of the physisorbed systems. When less than a third of a monolayer is present, very little difference in the microscopic friction coefficient mu or shear stresses is observed. For increasing amounts of water, the values of mu and the shear stresses decrease; this effect is somewhat more pronounced for fluorocarbon alkylsilane SAMs than for the hydrocarbon SAMs. The observed decrease in friction is a consequence of a slip plane that occurs in the water as the amount of water is increased. We studied the frictional behavior using relative shear velocities ranging from v = 2 cm/s to 2 m/s. Similar to previously reported results for alkoxylsilane SAMs, the values of the measured stress and mu for the alkylsilane SAM systems decrease monotonically with v.

Molecular dynamics simulations of grafted polyelectrolytes on two apposing walls

Molecular dynamics simulations of polyelectrolytes grafted to two apposing surfaces were performed. Bead-spring polymer models are used to treat flexible chains [e.g., sodium poly(styrene sulfonate)] and stiff chains (double-stranded DNA). The counterions are explicitly treated. The effect of the surface density of the grafted polymer, the chain length, and the gap width on the structure and the pressure were studied. Results are compared to experimental measurements and to simulations of polyelectrolyte brushes on a single surface. The density profiles exhibit a maximum not found in single surface data. The maximum is due to the brushes shrinking to avoid interpenetration.

How environment supports a state: molecular dynamics simulations of two states in bacteriorhodopsin suggest lipid and water compensation

The light-driven proton pump bacteriorhodopsin (bR) is a transmembrane protein that uses large conformational changes for proton transfer from the cytoplasmic to the extracellular regions. Crystal structures, due to their solvent conditions, do not resolve the effect of lipid molecules on these protein conformational changes. To begin to understand the molecular details behind such large conformational changes, we simulated two conformations of wild-type bacteriorhodopsin, one of the dark-adapted state and the second of an intermediate (M(O)) state, each within an explicit dimyristoyl-phosphatidylcholine (DMPC) lipid bilayer. The simulations included all-hydrogen and all-atom representations of protein, lipid, and water and were performed for 20 ns. We investigate the equilibrium properties and the dynamic motions of the two conformations in the lipid setting. We note that the conformational state of the M(O) intermediate bR remains markedly different from the dark-adapted bR state in that the M(O) intermediate shows rearrangement of the cytoplasmic portions of helices C, F, and G, and nearby loops. This difference in the states remained throughout the simulations, and the results are stable on the molecular dynamics timescale and provide an illustration of the changes in both lipid and water that help to stabilize a particular state. Our analysis focuses on how the environment adjusts to these two states and on how the dynamics of the helices, loops, and water molecules can be related to the pump mechanism of bacteriorhodopsin. For example, water generally behaves in the same manner on the extracellular sides of both simulations but is decreased in the cytoplasmic region of the M(O) intermediate. We suspect that the different water behavior is closely related to the fluctuations of microcavities volume in the protein interior, which is strongly coupled to the collective motion of the protein. Our simulation result suggests that experimental observation can be useful to verify a decreased number of waters in the cytoplasmic regions of the late-intermediate stages by measuring the rate of water exchange with the interior of the protein.

Frictional dynamics of fluorine-terminated alkanethiol self-assembled monolayers

The frictional dynamics of fluorine-terminated alkanethiol (S(CH2)8CF3) self-assembled monolayers (SAMs) on gold are studied using molecular dynamics simulations. The simulations treat the interactions between two SAMs on flat surfaces. The structure and frictional behavior are investigated as a function of applied pressure (200 MPa to 1 GPa) for a shear velocity of 2 m/s and compared to methyl-terminated alkanethiol SAMs. The maximum adhesive pressure between the SAMs is 220 MPa for both end groups. In agreement with experiments on the molecular scale, the shear stress and the coefficient of friction for CF3-terminated alkanethiols are larger than for CH3-terminated alkanethiols. The main source for the difference is primarily the tighter packing of the fluorinated terminal group resulting in a higher degree of order. The molecular scale coefficient of friction is correlated with the degree of order among all the systems.

Systematic study of the effect of disorder on nanotribology of self-assembled monolayers

The adhesion and friction between pairs of ordered and disordered self-assembled monolayers on SiO2 are studied using molecular dynamics. The disorder is introduced by randomly removing chains from a well ordered crystalline substrate and by attaching chains to an amorphous substrate. The adhesion force between monolayers at a given separation increases monotonically with chain length at full coverage and with coverage for fixed chain length. Friction simulations are performed at shear velocities between 0.02-2 m/s at constant applied pressures between 200 and 600 MPa. Stick-slip motion is observed at full coverage but disappears with disorder. With random defects, the friction becomes insensitive to chain length, defect density, and substrate.

Effect of mono- and multivalent salts on angle-dependent attractions between charged rods

Using molecular dynamics simulations we examine the effective interactions between two like-charged rods as a function of angle and separation. In particular, we determine how the competing electrostatic repulsions and multivalent-ion-induced attractions depend upon concentrations of simple and multivalent salts. We find that with increasing multivalent salt, the stable configuration of two rods evolves from isolated rods to aggregated perpendicular rods to aggregated parallel rods; at sufficiently high concentration, additional multivalent salt reduces the attraction. Monovalent salt enhances the attraction near the onset of aggregation and reduces it at a higher concentration of multivalent salt.

Evaluation of orally active poly(ADP-ribose) polymerase inhibitor in streptozotocin-diabetic rat model of early peripheral neuropathy

AIMS/HYPOTHESIS

Poly(ADP-ribose) polymerase activation depletes NAD+ and high-energy phosphates, activates protein kinase C, and affects gene expression in various tissues. This study was designed to characterise the effects of the potent, orally active poly(ADP-ribose) polymerase inhibitor PJ34 in the Wistar rat model of early diabetic neuropathy.

METHODS

Control and streptozotocin-diabetic rats were maintained with or without PJ34 treatment (30 mg x kg(-1) x day(-1)) for two weeks, after two weeks without treatment. Endoneurial blood flow was assessed by hydrogen clearance; metabolites and high-energy phosphates were assayed by enzymatic spectrofluorometric methods; and poly(ADP-ribose) was detected by immunohistochemistry.

RESULTS

Blood glucose concentrations were increased to a similar extent in untreated and PJ34-treated diabetic rats compared with controls. Intense poly(ADP-ribose) immunostaining was observed in the sciatic nerve of diabetic rats, but not in other groups. Final sciatic motor nerve conduction velocity and digital sensory nerve conduction velocity were reduced by 24% and 22% respectively in diabetic rats compared with controls (p<0.01 for both), and both were 98% corrected by PJ34 (p<0.01 vs diabetic group for both). In contrast, with PJ34 treatment, nerve blood flow showed a modest (17%) increase, and vascular conductance showed a tendency to increase. Free mitochondrial and cytosolic NAD+:NADH ratios, assessed from the glutamate and lactate dehydrogenase systems, phosphocreatine concentrations, and phosphocreatine:creatine ratios were decreased in diabetic rats and essentially normalised by PJ34. In both untreated and PJ34-treated diabetic rats, nerve glucose, sorbitol and fructose were increased to a similar extent. PJ34 did not affect any variables in control rats.

CONCLUSIONS/INTERPRETATION

Short-term poly(ADP-ribose) polymerase inhibitor treatment reverses functional and metabolic abnormalities of early diabetic neuropathy. Complete normalisation of nerve blood flow is not required for correction of motor or sensory nerve conduction velocities, provided that a therapeutic agent can restore nerve energy state via direct action on Schwann cells.