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.     

Single molecule dynamics on hydrophobic self-assembled monolayers

The interactions between adsorbate molecules and hydrophobic surfaces are of significant interest due to their importance in a variety of biological and separation processes. However, it is challenging to extrapolate macroscopic ensemble-averaged force measurements to molecular-level phenomena. Using total internal reflection fluorescence microscopy to image individual molecules at hydrophobic solid-aqueous interfaces, we directly observed dynamic behavior associated with the interactions between fluorescently labeled dodecanoic acid (our probe molecules) and self-assembled monolayers (SAM) comprising n-alkyltriethoxysilanes with systematically increasing chain length (from n = 4-18). In all cases, we observed at least two characteristic surface residence times and two diffusive modes, suggesting the presence of multiple distinct adsorbed populations. In general, the mean surface residence time increased and the mobility decreased with increasing SAM chain length, consistent with stronger probe-surface interactions. However, these trends were not primarily due to changes in characteristic residence times or diffusion coefficients associated with the individual populations but rather to a dramatic increase in the fraction associated with the long-lived slow-moving population(s) on long-chain SAMs. In particular, on longer (16-18 carbon) alkylsilane monolayers, the probe molecule exhibited far fewer desorption-mediated "flights" than on short (4-6 carbon) monolayers. Additionally, probes on the longer chain surfaces were much more likely to exhibit extended surface residence times as opposed to short transient surface visits.     

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.     

Growth dynamics of self-assembled monolayers in dip-pen nanolithography

Using molecular dynamics simulations, we studied the growth mechanism of self-assembled monolayers in dip-pen nanolithography. A molecule dropping from the tip kicks out a molecule sitting on the substrate, and the displaced molecule in turn kicks out a molecule next to it. This kicking propagates and finally stops when it hits the periphery of the monolayer. This monolayer growth is faster than predicted from the previous diffusion theory. Increasing the molecule-substrate binding strength enhances the molecular deposition rate and makes the monolayer well-ordered.     

偶氮苯衍生物自组装单分子膜中的分子取响

利用反射红外光谱研究了金表面一系列具有不同碳链长度的偶氮苯巯基衍生物的自组装单分子膜.通过对比各向同性样品的透射谱和单分子膜的反射谱中各个吸收峰强度,定量地研究了分子中各部分的取向与分子结构的关系.我们分别提出了烷基链和偶氮基团取向计算的方法,利用该方法成功地求得了分子中各部分在膜的倾角.结果显示,当分子中烷基链长度增大时,碳链和偶氮苯基团相对于法线的倾斜逐渐加剧.这种倾角的变化归因于分子中碳链间范德华引力增大时,引起分子逐渐倾斜以达到最佳的范德华接触.同时研究发现,烷基链和偶氮基团受碳长度变化的影响并不相同.当分子中亚甲基数目增多时,烷基链的倾角迅速增大而偶氮苯倾角的增大则相对缓慢,这反映了它们在空间需求和本身刚性上的不同。     

Molecular chirality and charge transfer through self-assembled scaffold monolayers

The effect of molecular chirality on electron transmission is explored by photoelectrochemistry. Thiol-terminated chiral scaffold molecules containing a porphyrin chromophore were self-assembled on gold surfaces to form a monolayer. Incorporation of the SAM-coated gold into an electrochemical cell and illumination with visible light generated a cathodic photocurrent. When using circularly polarized light, the photocurrent displayed an asymmetry (different magnitude of photocurrent for right versus left polarization) that changed with the molecular chirality (left- or right-handedness of the scaffold). A symmetry constraint on the electronic coupling between the porphyrin and the organic scaffold is proposed as a possible mechanism for the photocurrent asymmetry.     

Molecular simulation studies of the structure of phosphorylcholine self-assembled monolayers

We report a study of the structure of phosphorylcholine self-assembled monolayers (PC-SAMs) on Au(111) surfaces using both molecular mechanics (MM) and molecular dynamics (MD) simulation techniques. The lattice structure (i.e., packing densities and patterns) of the PC chains was determined first, by examining the packing energies of different structures by MM simulations in an implicit solvent. The chain orientation (i.e., antiparallel and parallel arrangements of the PC head groups) was then evaluated. The initial azimuthal angles of the PC chains were also adjusted to ensure that the optimal lattice structure was found. Finally, the two most probable lattice structures were solvated with explicit water molecules and their energies were compared after 1.5 ns of MD simulations to verify the optimal structures obtained from MM. We found that the optimal lattice structure of the PC-SAM corresponds to a radical7 x radical7 R19degree lattice structure (i.e., surface coverage of 50.4 A(2)molecule) with a parallel arrangement of the head groups. The corresponding thickness of the optimal PC-SAM is 13.4 A which is in agreement with that from experiments. The head groups of the PC chains are aligned on the surface in such a way that their dipole components are minimized. The P-->N vector of the head groups forms an angle of 82 degrees with respect to the surface normal. The tilt direction of molecular chains was observed to be towards their next nearest neighbor.     

Maleimido-terminated self-assembled monolayers

Four approaches have been explored for the preparation of maleimido-functionalized self-assembled monolayers (SAMs) on silicon. SAMs prepared by self-assembly of maleimido-functionalized alkyltrichlorosilanes (11-maleimido-undecyl-trichlorosilane) on oxide-covered silicon yield higher signals from maleimido functionalities in ATR-IR (attenuated total reflection IR) spectroscopy and XPS (X-ray photoelectron spectroscopy) than the other three methods. The surface composition of maleimido groups was tailored further by the formation of mixed monolayers with nonfunctionalized alkyltrichlorosilanes (decyltrichlorosilane). The order of the alkyl chains within the monolayers only slightly depends on the composition of the mixed monolayers. We utilized the maleimido-terminated SAMs to bind various nucleophilic compounds, alkylamines, alkylthiols, and thiol-tagged DNA oligonucleotides by means of conjugate addition.     

Effect of concentration on the photo-orientation and relaxation dynamics of self-assembled monolayers of mixtures of an azobenzene-based triethoxysilane with octyltriethoxysilane

Self-assembled monolayers (SAMs) were prepared from solutions with different proportions of a photoactive, azobenzene-based, silanized derivative of disperse red one (dDR1), and octyltriethoxysilane (OTE), a shorter, nonphotoactive molecule. The in-plane photoinduced orientational ordering of the resulting two component monolayers was monitored via precision measurement of in-plane birefringence using a dedicated high-extinction polarimeter. Measurements of contact angle, absorption, and birefringence show that introduction of OTE into the dDR1 deposition solution produces a continuous reduction of the surface density of dDR1 in the SAM, enabling the study of photowriting and relaxation dynamics in monolayers ranging from 100% dDR1 to samples where the dDR1 coverage is about 35%. The orientational dynamics depend strongly on the areal density of dDR1. As the fractional area of dDR1 is reduced, the rates of photowriting, photoerasing, and thermal relaxation increase, and the local orientational confinement of the molecules becomes more heterogeneous.     

Molecular rectification in a metal-insulator-metal junction based on self-assembled monolayers

An electrical junction formed by mechanical contact between two self-assembled monolayers (SAMs)--a SAM formed from an dialkyl disulfide with a covalently linked tetracyanoquinodimethane group that is supported by silver (or gold) and a SAM formed from an alkanethiolate SAM that is supported by mercury-rectifies current. The precursor to the SAM on silver (or gold) was bis(20-(2-((2,5-cyclohexadiene-1,4-diylidene)dimalonitrile))decyl)) disulfide and that for the SAM on mercury was HS(CH(2))(n-1)CH(3) (n = 14, 16, 18). The electrical properties of the junctions were characterized by current-voltage measurements. The ratio of the conductivity of the junction in the forward bias (Hg cathodic) to that in the reverse bias (Hg anodic), at a potential of 1 V, was 9 +/- 2 when the SAM on mercury was derived from HS(CH(2))(15)CH(3). The ratio of the conductivity in the forward bias to that in the reverse bias increased with decreasing chain length of the alkanethiol used to form the SAM on mercury. These results demonstrate that a single redox center asymmetrically placed in a metal-insulator-metal junction can cause the rectification of current and indicate that a fixed dipole in the insulating region of a metal-insulator-metal junction is not required for rectification.     

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.     

Structures and dynamics of self-assembled surface monolayers observed by ultrafast electron crystallography

In this communication, we report our first study of self-assembled adsorbates on metal surfaces. Specifically, we studied single-crystal clean surfaces of Au(111) with and without a monolayer of reaction involving the assembly of 2-mercaptoacetic acid from 2,2'-dithiodiacetic acid. We also studied monolayers of iron hemes. With ultrafast electron crystallography, we are able to observe and isolate structural dynamics of the substrate (gold) and adsorbate(s) following an ultrafast temperature jump.     

Conformation and dynamics of arylthiol self-assembled monolayers on Au(111)

We report a computational investigation of the conformation and the dynamics of self-assembled monolayers (SAMs) of a set of aromatic thiols arranged in the ( radical3 x radical3)-R30 degrees packing ratio on a Au(111) surface using molecular dynamics (MD) simulations. It was found that the molecular conformations were better defined for the arylthiol with two phenyl groups as compared to those with a single phenyl group and that the chemical structure of the head and tail groups had a considerable influence on the system geometry. In line with the density functional theory (DFT) calculations of small thiol molecules, we found for the SAMs that the face-centered cubic (fcc) site on the Au(111) surface was the most preferred, followed by the hexagonal close-packed (hcp) site, while the bridge position showed the characteristics of a local energy maximum. The dynamics of thiol head groups on these three Au sites was found to govern the overall dynamics of SAMs as measured by the mean square displacement. We also report that both the conformation and the dynamics on the studied time scale were driven by the SAM formation energy.     

Molecular order and disorder in the frictional response of alkanethiol self-assembled monolayers

Molecular processes in the frictional response of an alkanethiol monolayer, self-assembled on a Au(111) surface, are studied by means of high-resolution friction force microscopy in ultrahigh vacuum. With increasing load, three regimes are observed on defect-free domains of the monolayer: smooth sliding with negligible friction, regular molecular stick-slip motion with increasing friction, and the onset of wear in the monolayer. Molecular contrast in the lateral force is found for inequivalent molecules within the unit cell of the c(4 × 2) superstructure. Significant differences in the frictional response are found between defect-free domains and areas including a domain boundary. Friction increases by an order of magnitude on domain boundaries in connection with irregular stick-slip motion. This increased friction at domain boundaries is observed at loads below the onset of wear.     

Molecular tilting and its impact on frictional properties of n-alkane self-assembled monolayers

Hydrophobic, methyl-terminated self-assembled monolayer (SAM) surfaces can be used to reduce friction. Among methyl-terminated SAMs, the frictional properties of alkanethiol SAMs and silane SAMs have been well-studied. In this research, we investigated friction of methyl-terminated n-hexatriacontane (C36) SAM and compared its friction properties with the alkanethiol and silane SAMs. Alkane SAM does not have an anchoring group. The alkane molecules stand on the surface by physical adsorption, which leads to a higher surface mobility of alkane molecules. We found that C36 SAM has a higher coefficient of friction than that of octadecyltrichlorosilane (OTS) silane. When an atomic force microscope (AFM) tip was swiped across the alkane SAM with a loading force, we found that the alkane SAM can withstand the tip loading pressure up to 0.48 GPa. Between 0.48 and 0.49Ga, the AFM tip partially penetrated the SAM. When the tip moved away, the deformed SAM healed and maintained the structural integrity. When the loading pressure was higher than 0.49 GPa, the alkane SAM was shaved into small pieces by the tip. In addition, we found that the molecular tilting of C36 molecules interacted with the tribological properties of the alkane SAM surface. On one hand, a higher loading force can push the rod-like alkane molecules to a higher tilting angle; on the other hand, a higher molecular tilting leads to a lower friction surface.     

Formation of gold-methanethiyl self-assembled monolayers

The energetics of formation of thiyl-gold self-assembled monolayers is investigated using density-functional theory simulations. It is found that the chemisorption of dimethyl disulfide on the reconstructed Au(111) (22 x radical3) surface is most favored at the fcc reconstruction stripe, with initial physisorption leading to disulfide dissociation, adatom/vacancy-pair formation, and then, at a coverage of 7.8% sulfur atoms per gold atom, surface reconstruction lifting. At higher coverages, monolayer formation proceeds similarly on the unreconstructed surface, leading to surface pitting. Formation of the analogous adatom/vacancy-pair bound dissociated adsorbate complex on exposure of the clean unreconstructed surface to methanethiol is shown to be endothermic, however.     

Electrochemistry of redox-active self-assembled monolayers

Redox-active self-assembled monolayers (SAMs) provide an excellent platform for investigating electron transfer kinetics. Using a well-defined bridge, a redox center can be positioned at a fixed distance from the electrode and electron transfer kinetics probed using a variety of electrochemical techniques. Cyclic voltammetry, AC voltammetry, electrochemical impedance spectroscopy, and chronoamperometry are most commonly used to determine the rate of electron transfer of redox-activated SAMs. A variety of redox species have been attached to SAMs, and include transition metal complexes (e.g., ferrocene, ruthenium pentaammine, osmium bisbipyridine, metal clusters) and organic molecules (e.g., galvinol, C₆₀). SAMs offer an ideal environment to study the outer-sphere interactions of redox species. The composition and integrity of the monolayer and the electrode material influence the electron transfer kinetics and can be investigated using electrochemical methods. Theoretical models have been developed for investigating SAM structure. This review discusses methods and monolayer compositions for electrochemical measurements of redox-active SAMs.     

Electron transfer dynamics of iridium oxide nanoparticles attached to electrodes by self-assembled monolayers

Self-assembled monolayers (SAMs) of carboxylated alkanethiolates (-S(CH(2))(n-1)CO(2)(-)) on flat gold electrode surfaces are used to tether small (ca. 2 nm d.) iridium(IV) oxide nanoparticles (Ir(IV)O(X) NPs) to the electrode. Peak potential separations in cyclic voltammetry (CV) of the nanoparticle Ir(IV/III) wave, in pH 13 aqueous base, increase with n, showing that the Ir(IV/III) apparent electron transfer kinetics of metal oxide sites in the nanoparticles respond to the imposed SAM electron transfer tunneling barrier. Estimated apparent electron transfer rate constants (k(app)(0)) for n = 12 and 16 are 9.8 and 0.12 s(-1). Owing to uncompensated solution resistance, k(app)(0) for n = 8 was too large to measure in the potential sweep experiment. For the cathodic scans, coulometric charges under the Ir(IV/III) voltammetric waves were independent of potential scan rate, suggesting participation of all of the iridium oxide redox sites (ca. 130 per NP) in the NPs. These experiments show that it is possible to control and study electron transfer dynamics of electroactive nanoparticles including, as shown by preliminary experiments, that of the electrocatalysis of water oxidation by iridium oxide nanoparticles.