Mobility of Thermomyces lanuginosus lipase on a trimyristin substrate surface

We have studied the mobility of active and inactive Thermomyces lanuginosus lipase (TLL) on a spin-coated trimyristin substrate surface using fluorescence recovery after photobleaching (FRAP) in a confocal microscopy setup. By photobleaching a circular spot of fluorescently labeled TLL adsorbed on a smooth trimyristin surface, both the diffusion coefficient D and the mobile fraction f could be quantified. FRAP was performed on surfaces with different surface density of lipase and as a function of time after adsorption. The data showed that the mobility of TLL was significantly higher on the trimyristin substrate surfaces compared to our previous studies on hydrophobic model surfaces. For both lipase variants, the diffusion decreased to similar rates at high relative surface density of lipase, suggesting that crowding effects are dominant with higher adsorbed amount of lipase. However, the diffusion coefficient at extrapolated infinite surface dilution, D0, was higher for the active TLL compared to the inactive (D0 = 17.9 x 10(-11) cm2/s vs D0 = 4.1 x 10(-11) cm2/s, data for the first time interval after adsorption). Moreover, the diffusion decreased with time after adsorption, most evident for the active TLL. We explain the results by product inhibition, i.e., that the accumulation of negatively charged fatty acid products decreased the diffusion rate of active lipases with time. This was supported by sequential adsorption experiments, where the adsorbed amount under flow conditions was studied as a function of time after adsorption. A second injection of lipase led to a significantly lower increase in adsorbed amount when the trimyristin surface was pretreated with active TLL compared to pretreatment of inactive TLL.     

Lateral diffusion of molecules in two-component lipid bilayer: a Monte Carlo simulation study

Lateral diffusion of membrane components makes possible any in-plane membrane reaction and has a key role in signaling in cell membranes. In this report the equilibrium lateral diffusion of intrinsic molecules in an equimolar DMPC/DSPC mixture is simulated using a thoroughly tested two-state model of two-component phospholipid bilayers. The model has been successful in calculating the excess heat capacity function, the most frequent center-to-center distances between DSPC clusters, and the fractal dimensions of gel clusters (Sugar, I. P., Thompson, T. E., Biltonen, R. L. Biophys. J. 1999, 76, 2099-2110). In the gel/fluid mixed phase region, a diffusing intrinsic molecule may change its state from fluid to gel (or from gel to fluid) at any time. A common characterization of the diffusion of intrinsic molecules is given by the simulated average first-passage time curves. We find that these curves can be described as power functions containing two parameters, alpha and beta, except near the percolation threshold of gel/fluid or compositional clusters. We find also that the intrinsic molecules are involved in approximately normal diffusion, i.e., beta approximately 2 in the extreme gel and fluid phase regions, while in the gel/fluid and gel/gel mixed phase regions the diffusion is anomalous, i.e., beta not equal 2. In the mixed phase regions, when the initial local state of the diffusing molecule is not specified, each component is involved in sub-diffusion (beta > 2). In the gel/fluid mixed phase region molecules situated initially inside a fluid cluster are involved in sub-diffusion, but DMPC molecules situated initially inside a gel cluster are involved in super-diffusion (beta < 2). The possibility of anomalous diffusion in membranes apparently arises because the diffusing molecule visits a variety of different environments characterized by its relative proximity to various membrane components. The diffusion is actually anomalous when the components of the bilayer are nonrandomly distributed. The deviation from random distribution is strongly correlated with beta. Similar to the results of the NMR experiments, the calculated relative diffusion coefficient continuously decreases in the gel/fluid mixed phase region with decreasing temperature. In apparent contradiction, diffusion measured by fluorescence recovery after photobleaching (FRAP) demonstrates the existence of a threshold temperature, below which long-range diffusion of FRAP probe molecules is essentially blocked. This threshold temperature is highly correlated with the percolation temperature of gel clusters.     

Probing the interplay between chain diffusion and polymer crystal growth under nanoscale confinement: a study by single molecule fluorescence microscopy

Motions of single poly(ε-caprolactone) (PCL) molecules during the formation of the dendrite crystals in ultrathin films are captured by single molecule fluorescence microscopy. The relationship of single molecule diffusion coefficient with the crystal growth rate, together with radius curvature, side-branch spacing of dendrite crystal and morphology are examined. The results support Mullins-Sekerka (MS) instability as the origin of lamellar branching induced by a diffusion field generated by a gradient of polymer segment density ahead of the crystal. Further analysis of the molecular trajectories has recognized different types of motions, depending on the distance to the crystal front: Fickian diffusion in regions far away from the crystal, sub-diffusion in regions adjacent to the crystal, and directed motion between these two regions. Anti-correlation of successive steps is discovered accompanying the sub-diffusion, providing a clear signature of macromolecule crowding at the crystal growth front. This anomalous diffusion process in polymer ultrathin films presents a new insight into the understanding of the retarded dynamics of interfacial mass transport towards the crystal front. It is considered to play a decisive role in controlling the crystal growth and evolution of crystal morphology.     

Study of molecular behavior in a water nanocluster: size and temperature effect

Temperature and size effects on the behavior of nanoscale water molecule clusters are investigated by molecular dynamics simulations. The flexible three-centered (F3C) water potential is used to model the inter- and intramolecular interactions of the water molecule. The differences between the structural properties for the surface region and those for the interior region of the cluster are also investigated. It is found that as the temperature rises, the average number of hydrogen bonds per water molecule decreases, but the ratio of surface water molecules increases. After comparing the water densities in interior regions and the average number of hydrogen bonds in those regions, we find there is no apparent size effect on water molecules in the interior region, whereas the size of the water cluster has a significant influence on the behavior of water molecules at the surface region.     

Temperature and structural changes of water clusters in vacuum due to evaporation

This paper presents a study on evaporation of pure water clusters. Molecular dynamics simulations between 20 ns and 3 micros of clusters ranging from 125 to 4096 molecules in vacuum were performed. Three different models (SPC, TIP4P, and TIP5P) were used to simulate water, starting at temperatures of 250, 275, and 300 K. We monitored the temperature, the number of hydrogen bonds, the tetrahedral order, the evaporation, the radial distribution functions, and the diffusion coefficients. The three models behave very similarly as far as temperature and evaporation are concerned. Clusters starting at a higher temperature show a higher initial evaporation rate and therefore reach the point where evaporation stop (around 240 K) sooner. The radius of the clusters is decreased by 0.16-0.22 nm after 0.5 micros (larger clusters tend to decrease their radius slightly more), which corresponds to around one evaporated molecule per nm(2). The cluster temperature seems to converge towards 215 K independent of cluster size, when starting at 275 K. We observe only small structural changes, but the clusters modeled by TIP5P show a larger percentage of molecules with low diffusion coefficient as t-->infinity, than those using the two other water models. TIP4P seems to be more structured and more hydrogen bonds are formed than in the other models as the temperature falls. The cooling rates are in good agreement with experimental results, and evaporation rates agree well with a phenomenological expression based on experimental observations.     

Laws of thermal diffusion of individual molecules on the gold surface

By molecular dynamics simulations, we describe and discuss the mobility of single molecules on a metal surface. The calculated trajectories of 28 different molecules show that diffusion, subdiffusion and superdiffusion regimes exist. The trajectories also share some common features, which are expressed in the form of power laws that link the length of the path walked by the molecule, the molecular mass, and the surface-molecule interaction energy. The values of the exponents of the laws are easily rationalized and provide insight into the molecular behaviour on the surface. The calculations also show that the adsorption is governed by the combination of van der Waals and Coulomb molecule-surface interactions.     

隧道结电场辅助下叔丁胺分子在Cu(111)表面跳跃(英文)

采用扫描隧道显微镜(STM)于78 K研究了单个叔丁胺分子在Cu(111)表面的横向跃迁现象.研究发现叔丁胺分子的跳跃几率随隧道电流的增加而线性增加,这表明该过程是单电子激发过程;在不同极性的隧道结电场作用下,叔丁基胺分子跳跃行为发生的几率不同,这种现象可以用电场辅助的扩散过程解释.在不同极性电场作用下叔丁胺分子在Cu(111)表面的吸附能和扩散势垒不同,从而表现出不同的跳跃几率.     

Dynamics and Kinetics of Methanol-Graphite Interactions at Low Surface Coverage

The processes of molecular clustering, condensation, nucleation, and growth of bulk materials on surfaces, represent a spectrum of vapor-surface interactions that are important to a range of physical phenomena. Here, we describe studies of the initial stages of methanol condensation on graphite, which is a simple model system where gas–surface interactions can be described in detail using combined experimental and theoretical methods. Experimental molecular beam methods and computational molecular dynamics simulations are used to investigate collision dynamics and surface accommodation of methanol molecules and clusters at temperatures from 160 K to 240 K. Both single molecules and methanol clusters efficiently trap on graphite, and even in rarified systems methanol-methanol interactions quickly become important. A kinetic model is developed to simulate the observed behavior, including the residence time of trapped molecules and the quantified Arrhenius kinetics. Trapped molecules are concluded to rapidly diffuse on the surface to find and/or form clusters already at surface coverages below 10⁻⁶ monolayers. Conversely, clusters that undergo surface collisions fragment and subsequently lose more loosely bound molecules. Thus, the surface mediates molecular collisions in a manner that minimizes the importance of initial cluster size, but highlights a strong sensitivity to surface diffusion and intermolecular interactions between the hydrogen bonded molecules.     

Lipase surface diffusion studied by fluorescence recovery after photobleaching

We have analyzed surface diffusion properties of a variant of Thermomyces lanuginosa lipase (TLL) on hydrophilic silica and silica methylated with dichlorodimethylsilane (DDS) or octadecyltrichlorosilane (OTS). For this study a novel method for analysis of diffusion on solid surfaces was developed. The method is based on fluorescence recovery after photobleaching using confocal microscopy. When a rectangular area of the sample was photobleached, fluorescence recovery could be analyzed as one-dimensional diffusion, resulting in simplified mathematical expressions for fitting the data. The method was initially tested by measuring bovine serum albumin diffusion on glass, which led to a diffusion coefficient in good correspondence to earlier reports. For the analysis of TLL diffusion, ellipsometry data of TLL adsorption were used to calibrate fluorescence intensity to surface density of lipase, enabling measurements of the diffusion coefficient at different surface densities. The average diffusion coefficient was calculated in two time intervals after adsorption. Mobile fraction and diffusion coefficient were lowest on the OTS surface, when extrapolated to infinite surface dilution. Moreover, the diffusion rate decreased with time on the hydrophobic surfaces. Our observations can be explained by the surface dependence on the distribution of orientations and conformations of adsorbed TLL, where the transition from the closed to the catalytically active open and more hydrophobic structure is important.     

Diffusion of buffer layer assisted grown gold nanoclusters on Ru(100) and p(1 x 2)-O/Ru(100) surfaces

Patterning of metallic clusters on surfaces is demonstrated by utilizing a buffer layer assisted laser patterning technique (BLALP). This method has been employed in order to measure the diffusion of AFM and STM characterized size selected gold nanoclusters (5-10 nm diameter), over Ru(100) and p(1 x 2)-O/Ru(100) surfaces. Optical linear diffraction from gold cluster coverage gratings was utilized for the macroscopic diffusion measurements. The clusters were found to diffuse on the surface intact without significant coalescence or sintering. The barrier for metastable gold nanocluster diffusion on the surface is thought to be lower than the energy required for surface wetting. The apparent activation energy for diffusion was found to depend on the cluster size, increasing from 6.2 +/- 0.4 kcal/mol for 5 nm clusters to 10.6 +/- 0.5 kcal/mol for 9 nm clusters. The macroscopic diffusion of gold nanoclusters has been studied on the p(1 x 2)-O/Ru(100) surface as well, where surface diffusion was found to be rather insensitive to the clusters size with activation energy of 5.5 +/- 1 kcal/mol. The difference between the two surfaces is discussed in terms of a better commensurability (higher level of friction) of the gold facets at the contact area with the clean Ru(100) than in the case of the oxidized surface.     

Trajectory angle determination in one dimensional single molecule tracking data by orthogonal regression analysis

The quantitative assessment of single molecule diffusion trajectories by orthogonal regression analysis is reported. This analysis is broadly applicable to any single particle tracking experiments in which diffusion along one dimension (1D) is expected. It affords quantitative data on the (in plane) orientation of 1D trajectories, allowing for their absolute orientations to be determined. Histograms depicting the distribution of trajectory angles provide new physical insights into the degree of trajectory alignment, and by inference, materials order. Estimates of the errors in the trajectory angle and particle positioning along each trajectory are also obtained. The angle results are compared to those from single-step angle determinations. The advantages of the regression method include its simplicity and computational efficiency, and the ability to objectively differentiate between 1D and 2D/immobile trajectories. Its utility is demonstrated through analysis of single molecule diffusion trajectories in surfactant-templated mesoporous silica films as probed by wide-field fluorescence microscopy. The trajectory angle histograms obtained provide quantitative data on mean trajectory orientation and the degree of trajectory alignment in distinct populations and sample regions. Mesopore order was quantitatively assessed by implementation of an order parameter,

= 2-1, calculated from the individual trajectory angles in each of four representative sample regions. The results depict the presence of well-ordered domains (from microns to tens of microns in size), all having

≈ 0.9. The latter corresponds to an ≈14° average deviation of the individual trajectories from the mean trajectory (and mesopore) orientation in each domain.     

Molecules for organic electronics studied one by one

The electronic and geometrical structure of single difluoro-bora-1,3,5,7-tetraphenyl-aza-dipyrromethene (aza-BODIPY) molecules adsorbed on the Au(111) surface is investigated by low temperature scanning tunneling microscopy and spectroscopy in conjunction with ab initio density functional theory simulations of the density of states and of the interaction with the substrate. Our DFT calculations indicate that the aza-bodipy molecule forms a chemical bond with the Au(111) substrate, with distortion of the molecular geometry and significant charge transfer between the molecule and the substrate. Nevertheless, most likely due to the low corrugation of the Au(111) surface, diffusion of the molecule is observed for applied bias in excess of 1 V.     

Molecular dynamics simulations of a liquid crystalline molecule in the smectic A and E phases and in vacuum

Molecular dynamics simulations are performed in this work at 393 and 323 K for a mesogenic molecule ( R )-1-methylheptyl 4\[4-(2-allyloxyethoxy)biphenyl-4-carbonyloxy]benzoate in the simulated smectics A and E, respectively, and in a vacuum at 300 K, for a period of 1.0ns. The trajectories obtained from molecular dynamics simulations allow us to investigate the dynamical behaviour of this mesogenic molecule in the simulated smectic phases. This dynamical behaviour of a single molecule is presented using the distributions of dihedral angles and rotational diffusion around the C-axis defined by the simulated cells. Simulation results indicate that, except for the bonds near the end of the spacer segment, the dihedral angles all exhibit a single Gaussian-like distribution in the smectic A and E phases. Fluctuations of a dihedral angle about its mean value are more restricted in the smectics A and E than in those simulated in a vacuum. The average value of the fluctuations of the dihedral angles at the bonds in the spacer is found to be about 2 fold larger than that of fluctuations in the tail of the same molecule in the smectic A and E phases. In the smectic A phase, the distribution of orientations of a molecule about its long axis in a 36 molecule cell in which the outer molecules are fixed is found to have three distinct peaks. This result shows that the orientational fluctuations of single molecules are limited by confinement due to neighbouring molecules, i.e. that the layers have short-range structural correlations. The orientational distributions show larger fluctuations at the ends of the molecules.     

Reactions and clustering of water with silica surface

The interaction between silica surface and water is an important topic in geophysics and materials science, yet little is known about the reaction process. In this study we use first-principles molecular dynamics to simulate the hydrolysis process of silica surface using large cluster models. We find that a single water molecule is stable near the surface but can easily dissociate at three-coordinated silicon atom defect sites in the presence of other water molecules. These extra molecules provide a mechanism for hydrogen transfer from the original water molecule, hence catalyzing the reaction. The two-coordinated silicon atom is inert to the water molecule, and water clusters up to pentamer could be stably adsorbed at this site at room temperature.     

Structural rearrangement of c(70) monolayers induced by octanethiol adsorption

Mixed monolayers of C70 and octanethiol are prepared on Au(111) by a sequential adsorption method. A partial C70 monolayer is first formed and characterized, followed by the vapor deposition of octanethiol. This results in a well-ordered alkanethiol film where single C70 molecules and small molecular clusters are located at domain boundaries and in disordered regions. Substrate step defects have a large influence on the spatial distribution of C70; adjacent to a substrate defect, C70 binds preferentially on the upper terrace and is depleted on the lower terrace. We explain these observations as resulting from the kinetics of alkanethiol monolayer formation, and we present a simple model for the evolution of surface structure in the C70/octanethiol system.     

Chemical imaging of terrace-based active sites on gold

Scanning tunneling microscopy data of a mixed monolayer comprised of a 40:60 ratio of H8Si8O12 and C6H13-H7Si8O12 clusters on gold are presented. The images display a composite monolayer surface with well-defined domain regions of the individual components. Holes present at face-centered cubic (fcc) sites of the starting Au/H7Si8O12 adsorbate layer indicate the location of active sites for impinging C6H13-H7Si8O12 clusters. Adsorption of a C6H13-H7Si8O12 cluster likely yields a mobile hydrogen atom available to recombine with and desorb an adjacent H8Si8O12 cluster. Hydrogen atom diffusion along substrate [121] directions is the proposed pattern formation mechanism of the mixed monolayer. Imaging of the spherosiloxane cluster domains identifies a novel terrace-based active site located in the fcc regions of the Au(111) 23 x square root3 surface reconstruction.     

Redox activity and diffusion of hydrophilic, hydrophobic, and amphiphilic redox active molecules in a bicontinuous cubic phase

The objective was to examine how a bicontinuous cubic phase influences the diffusion and electrochemical activity of dissolved molecules. The cubic phase is a structure with three-dimensional continuous channels of water separated by an apolar membrane. A redox active molecule can dissolve in three different environments. A hydrophobic molecule will prefer the interior of the membrane, a hydrophilic molecule will prefer the water channels, and an amphiphilic molecule will be situated with its headgroup at the surface of the membrane and its tail in the interior. The electrochemical activity was measured with cyclic voltammetry and the transport behavior with chronocoulometry. All the molecules were redox active in the cubic phase; that is, all the molecules could reach the surface of the electrode and react. The cubic phase made the kinetics of the charge transfer slower, showing a quasi-reversible behavior. The reason may be that a layer of the membrane adheres to the hydrophobic electrode surface. The diffusion experiment showed that the diffusion was slower than in solution. The molecules that were restricted to diffuse within the membrane gave particularly low mass transport rates.     

Molecular Dynamics Studies of the Kinetics of Phase Changes in Clusters II: Crystal Nucleation from Molten (RbCl)256 and (RbCl)500 Clusters

Molecular dynamics computer simulations have been carried out to study the effects of cluster size and temperature on the nucleation rate of rubidium chloride clusters in the temperature range of 500-650 K. Clusters with 256 and 500 RbCl molecules have been studied and the results are compared with those obtained from 108 molecule clusters. The melting point (MP) of the clusters was observed to increase with the size of the clusters and can be described by a linear equation MP=997-405 N^−1/3, where N is the number of molecules in the cluster. The nucleation rate is found to decrease with increasing cluster size or increasing nucleation temperature. Both classical nucleation theory and diffuse interface theory are used to interpret our observed results.