Molecular simulation study of water interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled monolayers

Molecular simulations were performed to study a system consisting of protein (e.g., lysozyme) and self-assembled monolayers (SAMs) terminating with different chemical groups in the presence of explicit water molecules and ions. Mixed SAMs of oligo (ethylene glycol) [S(CH2)4(OCH2CH2)4OH, (OEG)] and hydroxyl-terminated SAMs [S(CH2)4OH] with a mole fraction of OEG at chiOEG = 0.2, 0.5, 0.8, and 1.0 were used in this study. In addition, methyl-terminated SAMs [S(CH2)11CH3] were also studied for comparison. The structural and dynamic behavior of hydration water, the flexibility and conformation state of SAMs, and the orientation and conformation of protein were examined. Simulation results were compared with those of experiments. It appears that there is a correlation between OEG surface resistance to protein adsorption and the surface density of OEG chains, which leads to a large number of tightly bound water molecules around OEG chains and the rapid mobility of hydrated SAM chains.     

Ice nucleation and phase behavior on oligo(ethylene glycol) and hydroxyl self-assembled monolayers: simulations and experiments

The nucleation and phase behavior of ultrathin D2O-ice overlayers have been studied on oligo(ethylene glycol) (OEG)-terminated and hydroxyl self-assembled monolayers (SAMs) at low temperatures in ultrahigh vacuum. Infrared reflection-absorption spectroscopy (IRAS) is used to characterize the ice overlayers, the SAMs, and the interactions occurring between the ice and the SAM surfaces. Spectral simulations, based on optical models in conjunction with Maxwell Garnett effective medium theory, point out the importance of including voids in the modeling of the ice structures, with void fractions reaching 60% in some overlayers. The kinetics of the phase transition from amorphous-like to crystalline-like ice upon isothermal annealing at 140 K is found to depend on the conformational state of the supporting OEG SAM surface. The rate is fast on the helical OEG SAMs and slow on the corresponding all-trans SAMs. This difference in kinetics is most likely due to a pronounced D2O interpenetration and binding to the all-trans segments of the ethylene glycol portion of the SAM. No such penetration and binding was observed on the helical OEG SAM.     

Understanding the nonfouling mechanism of surfaces through molecular simulations of sugar-based self-assembled monolayers

This paper presents a molecular simulation study of the interactions of a protein (lysozyme) with self-assembled monolayers (SAMs) of mannitol and sorbitol terminated alkanethiols in the presence of explicit water molecules and ions. The all-atom simulations were performed to calculate the force generated on the protein as a function of its distance above the SAM surfaces. The structural and dynamic properties of water molecules both above the SAM surfaces and around the SAM head groups were analyzed to provide a better understanding of the nonfouling behavior of the sugar-based SAM surfaces. Results from this work suggest that both mannitol and sorbitol SAMs generate a tightly bound, structured water layer around the SAM chains. This hydration layer creates a repulsive force on the protein when it approaches the surface, resulting in a nonfouling surface despite the presence of hydrogen-bond donor groups. This work demonstrates the importance of strong surface-water interactions for surface resistance to nonspecific protein adsorption.     

Protein-resistant self-assembled monolayers on gold with latent aldehyde functions

In the present study, oligo(ethylene glycol) (OEG)-linked alkanethiols were synthesized which carry a vicinal diol on one end of the OEG chain. After self-assembled monolayer (SAM) formation on gold, the vicinal diols were converted into aldehyde functions by exposure to aqueous NaIO4, as previously used for SAMs with OEG chains buried in the center of the SAM [Jang et al. Nano Lett. 2003, 3, 691-694]. Mixed SAMs with latent aldehydes on 5% of the OEG termini showed high protein resistance, which greatly slowed the kinetics of protein coupling on the time scale of minutes. Small bioligands (such as biocytin hydrazide) or small heterobifunctional crosslinkers (maleimidopropionyl hydrazide, pyridyldithiopropionyl hydrazide) with hydrazide functions were efficiently bound to the aldehyde functions on the SAM, providing for specific capture of streptavidin or for fast covalent binding of proteins with free thiols or maleimide functions, respectively. In conclusion, OEG-terminated SAMs with latent aldehydes serve as protein-resistant sensor surfaces which are easily functionalized with small ligands or with heterobifunctional crosslinkers to which the bait molecule is attached in a subsequent step.     

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.     

Reversible protein adsorption and bioadhesion on monolayers terminated with mixtures of oligo(ethylene glycol) and methyl groups

Surface-grafted, environmentally responsive polymers have shown great promise for controlling adsorption and desorption of macromolecules and cells on solid surfaces. In the paper, we demonstrate that certain mixed self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG) and methyl-terminated alkanethiolates on gold form surfaces with switchable hydrophobicity and tendency for protein adsorption and cellular attachment. At temperatures above 32 degrees C, SAMs with a surface density of approximately 50% OEG adsorbed significant amounts of pyruvate kinase and lysozyme, whereas below this temperature, these same SAMs were resistant to the adsorption of these proteins. Furthermore, protein layers adsorbed to these SAMs above 32 degrees C were removed upon rinsing with water below this temperature. Similar results were seen for attachment and release of the marine bacterium, Cobetia marina. The change from nonresistance to adsorptive state of the SAMs was concomitant with a change in advancing water contact angle. Vibrational sum frequency generation spectroscopy suggests that the temperature-induced changes coincide with a disorder-to-partial order transition of the hydrated methylene chains of the OEG moieties within the SAMs. Mixed OEG-methyl SAMs represent both a convenient means of controlling macromolecular and cellular adsorption within the laboratory and a useful tool for relating adsorption properties to molecular structures within the SAMs.     

Improved method for the preparation of carboxylic acid and amine terminated self-assembled monolayers of alkanethiolates

We present an improved method to prepare carboxylic acid (COOH) and amine (NH2) terminated self-assembled monolayers (SAMs) of alkanethiolates. In this method, a small amount of CF3COOH (for COOH-SAM) or N(CH2CH3)3 (for NH2-SAM) is added into the ethanolic solution of alkanethiols during SAM formation. The freshly formed COOH- and NH2-SAMs are then rinsed with an ethanolic solution of NH4OH or CH3COOH, respectively. Both SAMs prepared with the improved method show better quality in terms of surface chemical composition, roughness, and wettability as measured by X-ray photoelectron spectroscopy, atomic force microscopy, and contact angle, respectively. The formation of better SAMs can be attributed to the disruption of interplane hydrogen bonds.     

Soft-UV photolithography using self-assembled monolayers

We report thiol-on-gold self-assembled monolayers (SAMs) that can be photodeprotected using soft UV irradiation (lambda = 365 nm) to yield CO(2)H functionalized surfaces complementing those reported previously, which yielded NH(2) functionalized surfaces. The photolysis of these SAMs were monitored using a combination of surface sensitive techniques. In the SAM environment the photodeprotection yields are lower than those obtained for equivalent reactions in dilute solution. The protected carboxylic acids SAMs are shown to have a low yield approximately 50% due to competing photoreduction reactions of the nitro group. The results from infrared studies show that, as the photolysis progresses, the long chain protected residues reorganize and shield the functional COOH groups, thereby reducing the hydrophilic character of the surface.     

Functionalized self-assembled monolayers on ultraflat gold as platforms for single molecule force spectroscopy and imaging

Single molecule force spectroscopy is a valuable tool for studying unfolding and nanomechanical properties of proteins. The common practice is to stretch proteins from a surface that was dosed to give a reasonable hit rate and to analyze the curves that exhibit the expected characteristics of a single polymer. Whether the surface-bound proteins are indeed single and isolated remains unclear, and the undesirable protein/surface interactions that obscure informative features of the force curves are implicitly assumed to be absent. In this study, mixed self-assembled monolayers (SAMs) consisting of N-hydroxysuccinimide (NHS) and oligoethylene glycol (OEG) terminated thiols on an ultraflat gold surface were used to covalently immobilize proteins via lysine residues. By the optimization of attachment sites via lysine-NHS linkages amidst a protein-resistant layer of the OEG SAM, it was possible to isolate single proteins for study in a controlled fashion. The single protein distribution on the surface is clearly demonstrated by atomic force microscopy (AFM) imaging. The OEG also significantly reduces nonspecific tip-surface interactions between the cantilever and surface. Stretching covalently attached single proteins produces high-quality and reproducible force-extension curves. This experimental strategy is an attractive platform with which to study protein structure, interactions, and nanomechanical properties of single proteins.     

Immunosensor interface based on physical and chemical immunoglobulin G adsorption onto mixed self-assembled monolayers

An immunosensor interface based on mixed hydrophobic self-assembled monolayers (SAMs) of methyl and carboxylic acid terminated thiols with covalently attached human Immunoglobulin G (hIgG), is investigated. The densely packed and organised SAMs were characterised by contact angle measurements and cyclic voltammetry. The effect of the non-ionic surfactant, Tween 20, in preventing nonspecific adsorption is addressed by ellipsometry during physical and covalent hIgG immobilization on pure and mixed SAMs, respectively. It is clearly demonstrated that nonspecific adsorption due to hydrophobic interactions of hIgG on methyl ended groups is totally inhibited, whereas electrostatic/hydrogen bonding interactions with the exposed carboxylic groups prevail in the presence of surfactant. Results of ellipsometry and Atomic Force Microscopy, reveal that the surface concentration of covalently immobilized hIgG is determined by the ratio of COOH / CH(3)-terminated thiols in SAM forming solution. Moreover, the ellipsometric data demonstrates that the ratio of bound anti-hIgG / hIgG depends on the density of hIgG on the surface and that the highest ratio is close to three. We also report the selectivity and high sensitivity achieved by chronoamperometry in the detection of adsorbed hIgG and the reaction with its antibody.     

Nanoscale clustering of carbohydrate thiols in mixed self-assembled monolayers on gold

Self-assembled monolayers (SAMs) bearing pendant carbohydrate functionality are frequently employed to tailor glycan-specific bioactivity onto gold substrates. The resulting glycoSAMs are valuable for interrogating glycan-mediated biological interactions via surface analytical techniques, microarrays, and label-free biosensors. GlycoSAM composition can be readily modified during assembly by using mixed solutions containing thiolated species, including carbohydrates, oligo(ethylene glycol) (OEG), and other inert moieties. This intrinsic tunability of the self-assembled system is frequently used to optimize bioavailability and antibiofouling properties of the resulting SAM. However, until now, our nanoscale understanding of the behavior of these mixed glycoSAMs has lacked detail. In this study, we examined the time-dependent clustering of mixed sugar + OEG glycoSAMs on ultraflat gold substrates. Composition and surface morphologic changes in the monolayers were analyzed by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), respectively. We provide evidence that the observed clustering is consistent with a phase separation process in which surface-bound glycans self-associate to form dense glycoclusters within the monolayer. These observations have significant implications for the construction of mixed glycoSAMs for use in biosensing and glycomics applications.     

Atomic‐Level Elucidation of the Initial Stages of Self‐Assembled Monolayer Metallization and Nanoparticle Formation

The development of high‐performance molecular electronics and nanotech applications requires deep understanding of atomic level structural, electronic, and magnetic properties of electrode/molecular interfaces. Recent electrochemical experiments on self‐assembled monolayers (SAMs) have identified highly practical means to generate nanoparticles and metal monolayers suspended above substrate surfaces through SAM metallizations. A rational basis why this process is even possible is not yet well‐understood. To clarify the initial stages of interface formation during SAM metallization, we used first‐principles spin‐polarized density functional theory (DFT) calculations to study Pd diffusion on top of 4‐mercaptopyridine (4MP) SAMs on Au(111). After distinguishing potential‐energy surfaces (PESs) for different spin configurations for transition metal atoms on the SAM, we find adatom diffusion is not possible over the clean 4MP–SAM surface. Pre‐adsorption of transition‐metal atoms, however, facilitates atomic diffusion that appears to explain multiple reports on experimentally observed island and monolayer formation on top of SAMs. Furthermore, these diffusions most likely occur by moving across low‐lying and intersecting PESs of different spin states, opening the possibility of magnetic control over these systems. Vertical diffusion processes were also investigated, and the electrolyte was found to play a key role in preventing metal permeation through the SAM to the substrate.     

Controlled amine functionality in self-assembled monolayers via the hidden amine route: chemical and electronic tunability

A synthetic strategy for fabricating a dense amine functionalized self-assembled monolayer (SAM) on hydroxylated surfaces is presented. The assembly steps are monitored by X-ray photoelectron spectroscopy, Fourier transform infrared- attenuated total reflection, atomic force microscopy, variable angle spectroscopic ellipsometry, UV-vis surface spectroscopy, contact angle wettability, and contact potential difference measurements. The method applies alkylbromide-trichlorosilane for the fabrication of the SAM followed by surface transformation of the bromine moiety to amine by a two-step procedure: S(N)2 reaction that introduces the hidden amine, phthalimide, followed by the removal of the protecting group and exposing the free amine. The use of phthalimide moiety in the process enabled monitoring the substitution reaction rate on the surface (by absorption spectroscopy) and showed first-order kinetics. The simplicity of the process, nonharsh reagents, and short reaction time allow the use of such SAMs in molecular nanoelectronics applications, where complete control of the used SAM is needed. The different molecular dipole of each step of the process, which is verified by DFT calculations, supports the use of these SAMs as means to tune the electronic properties of semiconductors and for better synergism between SAMs and standard microelectronics processes and devices.     

Protein adsorption on oligo(ethylene glycol)-terminated alkanethiolate self-assembled monolayers: The molecular basis for nonfouling behavior

A study of protein resistance of oligo(ethylene glycol) (OEG), HS(CH2)11(OCH2CH2)nOH (n = 2, 4, and 6), self-assembled monolayers (SAMs) on Au(111) surfaces is presented here. Hydroxyl-terminated OEG-SAMs are chosen to avoid the hydrophobic effect observed with methyl-terminated OEG-SAMs, particularly at high packing densities. The structure of the OEG-SAM surfaces is controlled by adjusting the assembly solvent. These SAMs were characterized by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). Protein adsorption on these surfaces was investigated by surface plasmon resonance (SPR). OEG-SAMs assembled from mixed ethanol and water solutions show higher packing density on gold than those from pure ethanol solution. For EG2OH- and EG4OH-SAMs, proteins (i.e., fibrinogen and lysozyme) adsorb more on the densely packed SAMs prepared from mixed ethanol and water solutions, while EG6OH-SAMs generally resist protein adsorption regardless of the assembly solvent used.     

The Influence of Molecular Dipole Moment on the Redox-Induced Reorganization of α-Helical Peptide Self-Assembled Monolayers: An Electrochemical SPR Investigation

Self-assembled monolayers (SAMs) of ferrocene-labeled α-helical peptides were prepared on gold surfaces and studied using electrochemical surface plasmon resonance (EC-SPR). The leucine-rich peptides were synthesized with a cysteine sulfhydryl group either at the C- or N-terminus, enabling their immobilization onto gold surfaces with control of the direction of the molecular dipole moment. Two electroactive SAMs were studied, one in which all of the peptide dipole moments are oriented in the same direction (SAM1), and the other in which the peptide dipole moment of one peptide is aligned in the opposite direction to that of its surrounding peptide molecules (SAM2). Cyclic voltammetry combined with SPR measurements revealed that SAM reorientations concomitant with the oxidation of the ferrocene label were more significant in SAM2 than in SAM1. The substantially greater change in the peptide film thickness in the case of SAM2 is attributed to the electrostatic repulsion between the electrogenerated ferrocinium moiety and the positively charged gold surface. The greater permeability of SAM1 to electrolyte anions, on the other hand, appears to effectively neutralize this electrostatic repulsion. The film thickness change in SAM2 was estimated to be 0.25 ± 0.05 nm using numerical simulation. The timescale of the redox-induced SPR changes was established by chronoamperometry and time-resolved SPR measurements, followed by fitting of the SPR response to a stretched exponential function. The time constants measured for the anodic process were 16 and 6 ms for SAM1 and SAM2 respectively, indicating that the SAM thickness changes are notably fast.     

Controlling DNA orientation on mixed ssDNA/OEG SAMs

We present and characterize a mixed self-assembled monolayer (SAM) consisting of single-stranded oligonucleotide (ssDNA)- and oligo(ethylene glycol) (OEG)-terminated thiols. The ssDNA/OEG SAMs are prepared by simultaneous coadsorption from a common thiol solution over a broad range of compositions. Electron spectroscopy for chemical analysis (ESCA) is used to measure the surface coverage of ssDNA, whereas surface plasmon resonance (SPR) sensor is used to measure the hybridization of complementary ssDNA and protein resistance. Through the complementary use of these techniques, we find that the composition of OEG in the assembly solution controls a key parameter: the surface coverage of ssDNA on the surface. There is evidence that it influences the orientation of the immobilized ssDNA probes. Lower OEG concentrations yield a surface with higher ssDNA coverage and less favorable orientation, whereas higher OEG concentrations produce a surface with lower DNA coverage and more favorable orientation. Competition between these two effects controls the hybridization efficiency of the ssDNA surface. Compared to ssDNA surfaces prepared with other diluent thiols, the use of OEG improves the protein resistance of the surface, making it more broadly applicable.     

Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior

Fixed‐charge empirical force fields have been developed and widely used over the past three decades for all‐atom molecular simulations. Most simulation programs providing these methods enable only one set of force field parameters to be used for the entire system. Whereas this is generally suitable for single‐phase systems, the molecular environment at the interface between two phases may be sufficiently different from the individual phases to require a different set of parameters to be used to accurately represent the system. Recently published simulations of peptide adsorption to material surfaces using the CHARMM force field have clearly demonstrated this issue by revealing that calculated values of adsorption free energy substantially differ from experimental results. Whereas nonbonded parameters could be adjusted to correct this problem, this cannot be done without also altering the conformational behavior of the peptide in solution, for which CHARMM has been carefully tuned. We have developed a dual‐force‐field approach (Dual‐FF) to address this problem and implemented it in the CHARMM simulation package. This Dual‐FF method provides the capability to use two separate sets of nonbonded force field parameters within the same simulation: one set to represent intraphase interactions and a separate set to represent interphase interactions. Using this approach, we show that interfacial parameters can be adjusted to correct errors in peptide adsorption free energy without altering peptide conformational behavior in solution. This program thus provides the capability to enable both intraphase and interphase molecular behavior to be accurately and efficiently modeled in the same simulation. © 2012 Wiley Periodicals, Inc.     

Alternative method for fabricating chemically functionalized AFM tips: silane modification of HF-treated Si3N4 probes

An alternative method for fabricating functionalized, atomic force microscopy (AFM) tips is presented. This technique is simple and requires only minimal preparation and tip modification to generate chemically sensitive probes that have a robust organic monolayer of flexible terminal chemistry attached to the surface. Specifically, commercially microfabricated Si3N4 AFM tips were modified with self-assembled monolayers (SAMs) of octadecyltrichlorosilane and (11-bromoundecyl)trichlorosilane after removing the native silicon oxide surface layer with concentrated hydrofluoric acid. The structure of these SAM films on solid silicon nitride surfaces was studied using contact angle goniometry and Fourier transform infrared spectroscopy. Pull-off force measurements on various bare (mica, graphite, and silicon) and SAM-functionalized substrates confirm that mechanically robust, long-chain organic silane SAMs can be formed on HF-treated Si3N4 tips without the presence of an intervening oxide layer. Adhesion experiments show that the integrity of the organic film on the chemically modified tips is maintained over repeated measurements and that the functionalized tips can be used for chemical sensing experiments since strong discrimination between different surface chemistries is possible.     

Packing density of HS(CH2)(n)COOH self-assembled monolayers

Self-assembled monolayers (SAMs) of HS(CH(2))(n)COOH, n = 5, 10, 15 deposited from ethanol solution onto gold are prepared by five approaches, and their packing densities are evaluated by X-ray photoelectron spectroscopy (XPS) measurements. The five approaches are: (1) direct deposition; (2) acetic-acid-assisted deposition; (3) butyl-amine-assisted deposition; (4) displacement of a preformed HS(CH(2))(n)CH(3) (n = 5, 10, 15) SAMs; and (5) co-deposition with HS(CH(2))(n)CH(3) (n = 5, 10, 15). Packing density metrics are calculated from measurements of SAM and substrate photoemission intensities and their attenuations by two methods. In one case the attenuated photoemissions are expressed as a ratio relative to comparable measurements on an experimental HS(CH(2))(n)CH(3) model system. In the other case a new method is introduced where a calculated attenuation based on theoretical random coil and extended chain models is used as the reference to determine a packing density fraction. Packing densities are also correlated with the S2p(Au-bonded):Au4f peak area ratios and with shifts in the C1s binding energies. SAMs prepared by the direct deposition are a partial multilayer where a second molecular layer is physisorbed onto the SAM and not removable by solvent washing. The addition of acetic acid to the deposition solution disrupts dimer associations of HS(CH(2))(n)COOH in solution and at the surface of the monolayer and yields the most ordered monolayer with the highest density of -COOH groups. The addition of butyl amine results in a labile ammonium carbonate ion pair formation but results in a lower packing density in the SAM. The displacement of the preformed HS(CH(2))(n)CH(3) SAM and the co-deposition of HS(CH(2))(n)CH(3) with HS(CH(2))(n)COOH result in SAMs with little incorporation of the -COOH component.     

Preparation, characterization, resistance to protein adsorption, and specific avidin-biotin binding of poly(amidoamine) dendrimers functionalized with oligo(ethylene glycol) on gold

Protein-resistant films derived from the fifth-generation poly(amidoamine) dendrimers (PAMAM G5) functionalized with oligo(ethylene glycol) (OEG) derivatives consisting of various ethylene glycol units (EG(n), n = 3, 4, and 6) were prepared on the self-assembled monolayers (SAMs) of 11-mercaptoundecanoic acid (MUA) on gold substrates. The resulting films were characterized by ellipsometry, contact angle goniometry, and X-ray photoelectron spectroscopy (XPS). About 35% of the peripheral amines of the dendrimers were reacted with N-hydroxysuccinimide-terminated EG(n) derivatives (NHS-EG(n)). The dendrimer films showed improved stability over octadecanethiolate SAMs on gold in hot solvents, attributed to the formation of multiple amide bonds per PAMAM unit with underlying NHS-activated MUA monolayer. The EG(n)-attached PAMAM surfaces with n = 3 reduced the adsorption of fibrinogen to approximately 20% monolayer, whereas 2-3% for n = 4 or 6. The dendrimer films with various densities of EG(n) molecules on PAMAM surfaces were prepared by immersion of the NHS-terminated MUA-functionalized gold substrates in ethanolic solutions containing PAMAM and NHS-EG(n) of various mole ratios. The density (r) of the EG(n) molecules on the PAMAM surfaces is consistent with the mole ratio (r') of NHS-EG(n)/free amine of PAMAM in solutions. The resistance to protein adsorption of the resulting surfaces is correlated with the surface density and the length of the EG chains. At their respective r, the EG(n)-modified dendrimer films resisted approximately 95% adsorption of fibrinogen on gold surfaces. Finally, the specific binding of avidin to the approximately 5% and approximately 40% biotinylated EG3 dendrimers (surface density of biotin with respect to the total number of terminal amino groups on PAMAM G5) gave rise to about 50% and 100% surface coverage by avidin, respectively.