Covalent attachment of a transition metal coordination complex to functionalized oligo(phenylene-ethynylene) self-assembled monolayers

We have investigated the reaction of tetrakis(dimethylamido)titanium, Ti[N(CH(3))(2)](4), with N-isopropyl-N-[4-(thien-3-ylethynyl) phenyl] amine and N-isopropyl-N-(4-{[4-(thien-3-ylethynyl) phenyl]ethynyl}phenyl) amine self-assembled monolayers (SAMs), on polycrystalline Au substrates. The structure of the SAMs themselves has also been investigated. Both molecules form SAMs on polycrystalline Au bound by the thiophene group. The longer-molecular-backbone molecule forms a denser SAM, with molecules characterized by a smaller tilt angle. X-ray photoelectron spectroscopy (XPS) and angle-resolved XPS have been employed to examine the kinetics of adsorption, the spatial extent of reaction, and the stoichiometry of reaction. For both the SAMs, adsorption is described well by first-order Langmuirian kinetics, and adsorption is self-limiting from T(s) = -50 to 30 degrees C. The use of angle-resolved XPS clearly demonstrates that the Ti[N(CH(3))(2)](4) reacts exclusively with the isopropylamine end group via ligand exchange, and there is no penetration of the SAM, followed by reaction at the SAM-Au interface. Moreover, the SAM molecules remain bound to the Au surface via their thiopene functionalites. From XPS, we have found that, in both cases, approximately one Ti[N(CH(3))(2)](4) is adsorbed per two SAM molecules.     

The reaction of tetrakis(dimethylamido)titanium with self-assembled alkyltrichlorosilane monolayers possessing -OH, -NH2, and -CH3 terminal groups

The reactions of tetrakis(dimethylamido)titanium, Ti[N(CH(3))(2)](4), with alkyltrichlorosilane self-assembled monolayers (SAMs) terminated by -OH, -NH(2), and -CH(3) groups have been investigated with X-ray photoelectron spectroscopy (XPS). For comparison, a chemically oxidized Si surface, which serves as the starting point for formation of the SAMs, has also been investigated. In this work, we examined the kinetics of adsorption, the spatial extent, and stoichiometry of the reaction. Chemically oxidized Si has been found to be the most reactive surface examined here, followed by the -OH, -NH(2), and -CH(3) terminated SAMs, in that order. On all surfaces, the reaction of Ti[N(CH(3))(2)](4) was relatively facile, as evidenced by a rather weak dependence of the initial reaction probability on substrate temperature (T(s) = -50 to 110 degrees C), and adsorption could be described by first-order Langmuirian kinetics. The use of angle-resolved XPS demonstrated clearly that the anomalous reactivity of the -CH(3) terminated SAM could be attributed to reaction of Ti[N(CH(3))(2)](4) at the SAM/SiO(2) interface. Reaction on the -NH(2) terminated SAM proved to be the "cleanest", where essentially all of the reactivity could be associated with the terminal amine group. In this case, we found that approximately one Ti[N(CH(3))(2)](4) adsorbed per two SAM molecules. On all surfaces, there was significant loss of the N(CH(3))(2) ligand, particularly at high substrate temperatures, T(s) = 110 degrees C. These results show for the first time that it is possible to attach a transition metal coordination complex from the vapor phase to a surface with an appropriately functionalized self-assembled monolayer.     

Scanning tunneling microscopy, Fourier transform infrared spectroscopy, and electrochemical characterization of 2-naphthalenethiol self-assembled monolayers on the Au surface: a study of bridge-mediated electron transfer in Ru(NH3)6(2+)/Ru(NH3)6(3+) redox reactions

We have studied the structure, adsorption kinetics, and barrier properties of self-assembled monolayers of 2-naphthalenethiol on Au using electrochemical techniques, grazing-angle Fourier transform infrared (FTIR) spectroscopy, and scanning tunneling microscopy (STM). The results of cyclic voltammetric and impedance measurements using redox probes show that 2-naphthalenethiol on Au forms a stable and reproducible, but moderately blocking, monolayer. Annealing of the self-assembled monolayer (SAM)-modified surface at 72 +/- 2 degrees C remarkably improves the blocking property of the monolayer of 2-naphthalenethiol on Au. From the study of kinetics of SAM formation, we find that the self-assembly follows Langmuir adsorption isotherm. Our STM and FTIR results show that the molecules are adsorbed with the naphthalene ring tilted from the surface normal by forming a square root 3 x 3 R30 degrees overlayer structure. From our studies, we conclude that the electron-transfer reaction of ferro/ferricyanide in the freshly formed monolayer occurs predominantly through the pinholes and defects present in the monolayer. However, in the case of thermally annealed specimen, although the ferro/ferricyanide reaction is almost completely blocked, the electron-transfer reaction of hexaammineruthenium(III) chloride is not significantly inhibited. It is proposed that the electron-transfer reaction in the case of the ruthenium redox couple takes place by a tunneling mechanism through the high-electron-density aromatic naphthalene ring acting as a bridge between the monolayer-modified electrode and the ruthenium complex.     

Investigation of the Antifouling Properties of Phenyl Phosphorylcholine‐Based Modified Gold Surfaces

Low impedance, antifouling coatings on gold electrodes based on three new zwitterionic phenyl phosphorylcholine (PPC)‐based layers namely 1) reductively adsorbed PPC diazonium salt, 2) dithiocarbamate PPC SAM and 3) lipoamide PPC SAM (PPC coupled to α‐lipoic acid) were evaluated. The layers were assessed for their ability to limit nonspecific adsorption of proteins to electrode surface with some significant differences observed compared with previously studied PPC diazonium salts reductively adsorbed on glassy carbon. Fluorescence microscopy and electrochemical impedance spectroscopy results suggest that protein adsorption is sensitive to the difference in the structure of the PPC molecules and the charge neutrality of the layers. The lipoamide PPC SAM was shown to be the most effective at resisting nonspecific protein adsorption and this layer was as effective as the ‘gold standard’ of oligo(ethylene oxide) SAMs on gold and PPC diazonium salts reductively adsorbed on glassy carbon.     

In situ AFM studies on self-assembled monolayers of adsorbed surfactant molecules on well-defined H-terminated Si(111) surfaces in aqueous solutions

The formation of self-assembled monolayers (SAMs) of adsorbed cationic or anionic surfactant molecules on atomically flat H-terminated Si(111) surfaces in aqueous solutions was investigated by in situ AFM measurements, using octyl trimethylammonium chloride (C8TAC), dodecyl trimethylammonium chloride (C12TAC), octadecyl trimethylammonium chloride (C18TAC)) sodium dodecyl sulfate (STS), and sodium tetradecyl sulfate (SDS). The adsorbed surfactant layer with well-ordered molecular arrangement was formed when the Si(111) surface was in contact with 1.0x10(-4) M C18TAC, whereas a slightly roughened layer was formed for 1.0x10(-4) M C8TAC and C12TAC. On the other hand, the addition of alcohols to solutions of 1.0x10(-4) M C8TAC, C12TAC, or SDS improved the molecular arrangement in the adsorbed surfactant layer. Similarly, the addition of a salt, KCl, also improved the molecular arrangement for both the cationic and anionic surfactant layers. Moreover, the adsorbed surfactant layer with a well-ordered structure was formed in a solution of mixed cationic (C12TAC) and anionic (SDS) surfactants, though each surfactant alone did not form the well-ordered layer. These results were all explained by taking into account electrostatic repulsion between ionic head groups of adsorbed surfactant molecules as well as hydrophobic interaction between their alkyl chains, which increases with the increasing chain length, together with the increase in the hydrophobic interaction or the decrease in the electrostatic repulsion by incorporating alcohol molecules into the adsorbed surfactant layer, the decrease in the electrostatic repulsion by increasing the concentration of counterions, and the decrease in the electrostatic repulsion by alternate arrangement of cationic and anionic surfactant molecules. The present results have revealed various factors to form the well-ordered adsorbed surfactant layers on the H-Si(111) surface, which have a possibility of realizing the third generation surfaces with flexible structures and functions easily adaptable to circumstances.     

Concentration effects on adsorption of bacteriophage T4 lysozyme stability variants to silica

The adsorption kinetics and dodeceyltrimethylammonium bromide-mediated elution of the wild type and two structural stability mutants of bacteriophage T4 lysozyme were recorded in situ, at silica surfaces. Experiments were performed at different solution concentrations, ranging from 0.01 to 1.0 mg/ml. Plateau values of adsorbed mass generally increased with increasing solution concentration, with the adsorbed layer being only partially eluted by buffer. Treatment with surfactant removed more of the adsorbed protein in each case, with the remaining adsorbed mass varying little with concentration. Comparison of the data to an adsorption mechanism allowing for three adsorbed states, distinguished by binding strength, showed that the fraction of adsorbed molecules present in the most tightly bound state (state 3) decreased as adsorption occurred from solutions of increasing concentration. However, the absolute amounts of state 3 molecules present in each case were less dependent on solution concentration. Adsorption of T4 lysozyme into state 3 is suggested to occur early in the adsorption process and continue until some critical surface concentration is reached. Beyond this critical value of adsorbed mass, adsorption is suggested to progress with adoption of more loosely bound states.     

Probing adsorption sites of silica-supported platinum with (13)C(16)O + (12)C(16)O and (13)C(18)O + (12)C(16)O mixtures: a comparative fourier transform infrared investigation

A comparative investigation of the adsorption of (13)C(18)O + (12)C(16)O and (13)C(16)O + (12)C(16)O mixtures on silica-supported Pt has been conducted. It is advantageous to use (13)C(18)O + (12)C(16)O mixtures rather than (13)C(16)O + (12)C(16)O to probe the adsorption sites and electronic state of supported Group VIII metals because the vibrational bands of the adsorbed (13)C(18)O and (12)C(16)O isotopic molecules do not overlap. In addition, while an intensity redistribution suppresses the lower-frequency band with adsorbed (13)C(16)O and (12)C(16)O with vibrational frequencies differing by 50 cm(-1), the intensity redistribution is less pronounced with the adsorbed (13)C(18)O and (12)C(16)O in which the frequency difference is 100 cm(-1). Moreover, the small intensity redistribution that does occur between the bands of adsorbed (13)C(18)O and (12)C(16)O still allows the detection of the vibrational band of adsorbed (13)C(18)O at (13)C(18)O gas-phase concentrations as low as 3%. At such low concentrations, the dipole-dipole interaction between adsorbed (13)C(18)O molecules is negligible, and, hence, both the singleton frequency and the dipole-dipole shift for adsorbed CO may be obtained in a single experiment. Two types of strongly bound and one type of weakly bound linear CO-Pt adsorption complexes have been identified and characterized by their singleton frequencies and dipole-dipole coupling shifts. The origin of these CO adsorption modes is discussed.     

Irreversible thermal denaturation of beta-lactoglobulin retards adsorption of carrageenan onto beta-lactoglobulin-coated droplets

The influence of isothermal heat treatments on the adsorption of anionic carrageenan molecules to the surfaces of anionic beta-lactoglobulin-coated droplets has been investigated. The zeta-potential, mean particle diameter, microstructure, and creaming stability of emulsions containing beta-lactoglobulin-coated droplets and/or carrageenan molecules that had previously been heat treated at temperatures ranging from 30 to 90 degrees C for 20 min were measured (pH 6.0, 150 mM NaCl). Three different heat treatments were used to establish the physicochemical origin of the influence of thermal history on the adsorption of carrageenan molecules to the protein coated droplets: (i) droplets and carrageenan were mixed at room temperature, then heated together; (ii) droplets were heated, cooled to room temperature, then mixed with carrageenan; (iii) carrageenan was heated, cooled to room temperature, then mixed with droplets. For treatments i and ii appreciably more carrageenan adsorbed to the protein-coated droplet surfaces at temperatures < or = 60 degrees C than at higher temperatures. For treatment iii, carrageenan adsorbed to the droplet surfaces across the whole temperature range. These results suggest that an irreversible thermal denaturation of the adsorbed beta-lactoglobulin molecules inhibited the adsorption of carrageenan molecules to the droplet surfaces. We postulate that there is a patch of positive charge on the surface of the native globular protein molecules which becomes more diffuse upon thermal denaturation. We found that the carrageenan molecules were unable to protect the beta-lactoglobulin-coated droplets at high temperatures (T > 60 degrees C) because they desorbed from the droplet surfaces. Nevertheless, adsorption of iota-carrageenan was capable of protecting the droplets against flocculation caused by surface denaturation of the adsorbed proteins at lower temperatures (T < or = 50 degrees C).     

In-situ FTIR studies on self-assembled monolayers of surfactant molecules adsorbed on H-terminated Si(111) surfaces in aqueous solutions

The adsorption of a surfactant, sodium di-2-ethylhexyl sulfosuccinate (SDES), [C4H9CH(C2H5)CH2OCO][C4H9CH(C2H5)CH2OCOCH2]CHSO3- Na+, in an aqueous solution on an atomically flat H-terminated Si(111) [abbreviated as H-Si(111)] surface with a hydrophobic property was investigated by in-situ FTIR measurements. Immersion of the H-Si(111) surface in a solution of 1.0 x 10(-2) M SDES for more than 2 h led to formation of a self-assembled monolayer (SAM) with the alkyl chains having a tendency to be assembled perpendicular to the Si surface. The in-situ FTIR observation revealed that the adsorption was nearly complete about 60 min after the start of the immersion, and after that the adsorbed molecules changed their arrangement into an ordered mode. The Si-H peak in the FTIR spectrum remained unchanged with time in aqueous surfactant solution, in contrast to the case of immersion in pure water, indicating that the adsorbed surfactant protects the H-Si(111) surface from oxidation. No structural change in the SAM was observed when a negative potential of -700 mV vs Ag/AgCl was applied to the Si, whereas the adsorbed molecules changed their arrangement, accompanied by their substantial desorption and oxidation of the Si surface, when a positive potential of +700 mV was applied.     

"Sliding kinetics" of single-walled carbon nanotubes on self-assembled monolayer patterns: beyond random adsorption

We present the experimental results and theoretical model describing new adsorption kinetics of single-walled carbon nanotubes (swCNTs) onto self-assembled monolayer (SAM) including their sliding motion. The adsorption behavior of swCNTs on large-size SAM patterns is similar to the Langmuir isotherm, while that on nanoscale patterns shows a significant deviation which can be explained by the sliding motion of adsorbed nanotubes. The "sliding chamber" experiment confirms that swCNTs can align along the SAM patterns by sliding motion right above the SAM surfaces. This result provides new scientific insights regarding the adsorption kinetics of one-dimensional nanostructures, and, from a practical point of view, it can be an important guideline to design SAM patterns to assemble carbon nanotubes and nanowires into desired device structures.     

Enhanced stability of short- and long-chain diselenide self-assembled monolayers on gold probed by electrochemistry, spectroscopy, and microscopy

Well-ordered, compact, self-assembled monolayers (SAMs) of hexyl and dodecyl diselenides have been formed on oriented (111) gold surfaces. Monolayer formation has been effected by adsorption from neat diselenides as well as millimolar solutions of diselenides in alcohol. The monolayer formation is confirmed using electrochemical quartz crystal microbalance studies. The stability and permeability of the monolayers at various temperatures have been probed using reflection absorption infrared spectroscopy (RAIRS) and electrochemistry. The RAIRS studies in the dry state show the formation of highly ordered, compact structures when adsorbed from neat compounds compared to the monolayers adsorbed in the presence of alcohol. The monolayers adsorbed from neat diselenide are quite stable as a function of temperature irrespective of the chain length. The electrochemical studies based on the blocking behavior of the monolayers toward electron transfer between a diffusing species and the electrode surface reflect the stability and the compactness of the structure. The results point out that the presence of solvent molecules during the SAM formation hinders the organization of the monolayer structure, especially in the case of short-chain diselenide monolayers.     

Ab initio calculations of the reaction mechanisms for metal-nitride deposition from organo-metallic precursors onto functionalized self-assembled monolayers

An atomistic mechanism has been derived for the initial stages of the adsorption reaction for metal-nitride atomic layer deposition (ALD) from alkylamido organometallic precursors of Ti and Zr on alkyltrichorosilane-based self-assembled monolayers (SAMs). The effect of altering the terminal functional group on the SAM (including -OH, -NH2, -SH, and -NH(CH3)) has been investigated using the density functional theory and the MP2 perturbation theory. Reactions on amine-terminated SAMs proceed through the formation of a dative-bond complex with an activation barrier of 16-20 kcal/mol. In contrast, thiol-terminated SAMs form weak hydrogen-bonded intermediates with activation barriers between 7 and 10 kcal/mol. The deposition of Ti organometallic precursors on hydroxyl-terminated SAMs proceeds through the formation of stronger hydrogen-bonded complexes with barriers of 7 kcal/mol. Zr-based precursors form dative-bonded adducts with near barrierless transitions. This variety allows us to select a kinetically favorable substrate for a chosen precursor. The predicted order of reactivity of differently terminated SAMs and the temperature dependence of the initial reaction probability have been confirmed for Ti-based precursors by recent experimental results. We predict that the replacement of methyl groups by trifluoromethyl groups on the SAM backbone decreases the activation barrier for amine-terminated SAMs by 5 kcal/mol. This opens a route to alter the native reactivities of a given SAM termination, in this case making amine termination energetically viable. The surface distribution of SAM molecules has a strong effect on the adsorption kinetics of Ti-based precursors. Unimolecular side decomposition reactions were found to be kinetically competitive with adsorption at 400 K.     

Piezoelectric Sensor in Situ Monitoring Adsorption of Fibrinogen and Surfactant onto a Self-Assembled Monolayer of Alkanethiols

This report describes the use of a piezoelectric quartz crystal (PQC) sensor to investigate the nonspecific adsorption of fibrinogen (FN) and sodium dodecyl sulfate (SDS) onto a self-assembled monolayer (SAM) of alkanethiols on gold. The change in adsorption mass was monitored in situ by the PQC sensor. A kinetics model was proposed to describe the adsorption of the FN and SDS on the hydrophobic SAM surface. The adsorption kinetics parameters were determined from the responses of the PQC. The adsorption and desorption rate constants of the FN on the SAM surface were estimated to be (6.18 ± 0.53) × 10³ M⁻¹ s⁻¹ and (6.74 ± 0.72) × 10⁻³ s⁻¹, respectively. The rate constants for the adsorption and desorption of SDS on the SAM are (24.3 ± 1.4 M⁻¹ s⁻¹) and (1.52 ± 0.11) × 10⁻² s⁻¹, respectively. The adsorption of SDS on the SAM was reversible. The fractional coverage of the FN on the SAM surface was estimated from kinetics analyses to be 42–86% for the FN concentration range 25–400 μg/ml. Over 80% of the FN is irreversibly adsorbed on the SAM surface with respect to dilution of the bulk phase. The fraction of FN reversibly adsorbed increases with the bulk concentration of FN.     

Formation and dissolution processes of the 6-thioguanine (6TG) self-assembled monolayer. A kinetic study

This is a report on the kinetics of the destruction and formation processes of the 6-thioguanine self-assembled monolayer (6TG SAM) on a mercury electrode from acid solutions by chronoamperometry. The destruction of the 6TG SAM that has been previously formed under open circuit potential conditions is carried out by stepping the potential from an initial value where the chemisorbed layer is stable up to potentials where the molecules are no longer chemisorbed. The destruction of the SAM has been described by a model that involves three types of contributions: (i) a Langmuir-type adsorption process, (ii) a 2D nucleation mechanism followed by a growth controlled by surface diffusion, and (iii) a 2D nucleation mechanism followed by a growth at a constant rate. The nonlinear fit of the experimental transients by using this procedure allows the quantitative determination of the individual contributions to the overall process. The kinetics of the formation process is studied under electrochemical conditions. The chronoamperometric experiment allows us to monitor the early stages of 6TG SAM formation. The implications of the physisorbed state at low potentials in the type of monolayer formation and destruction processes as well as the influence of temperature are also discussed.     

Adsorption of cellulose triacetate on calcium silicate

Adsorption of cellulose triacetate from its chloroform solution on calcium silicate has been studied. The adsorption follows first order kinetics. The adsorption data are adequately described by the Langmuir isotherm indicating that the adsorbed polymer molecules behave as rigid molecules in the adsorbed state. An attempt has been made to fractionate cellulose triacetate employing the adsorption technique.     

Density functional theory investigation of benzenethiol adsorption on Au(111)

We have studied the adsorption of benzenethiol molecules on the Au(111) surface by using first principles total energy calculations. A single thiolate molecule is adsorbed at the bridge site slightly shifted toward the fcc-hollow site, and is tilted by 61 degrees from the surface normal. As for the self-assembled monolayer (SAM) structures, the (2 square root of 3 x square root of 3)R30 degrees herringbone structure is stabilized against the (square root 3 x square root 3)R30 degrees structure by large steric relaxation. In the most stable (2 square root 3 x square root 3)R30 degrees SAM structure, the molecule is adsorbed at the bridge site with the tilting angle of 21 degrees, which is much smaller compared with the single molecule adsorption. The van der Waals interaction plays an important role in forming the SAM structure. The adsorption of benzenethiolates induces the repulsive interaction between surface Au atoms, which facilitates the formation of surface Au vacancy.     

Probing enantiospecific interactions between proline and an l-glutathione self-assembled monolayer by modulation excitation ATR-IR spectroscopy

The interaction of proline with self-assembled monolayers (SAMs) of l-glutathione (gamma-glu-cys-gly) on gold was investigated by a combination of attenuated total reflection (ATR-IR) infrared and modulation excitation spectroscopy (MES). The latter technique makes use of phase-sensitive detection of periodically varying signals and allows discrimination between species with different kinetics such as dissolved proline and adsorbed molecules. By applying a convection-diffusion model coupled to adsorption and desorption, it was possible to extract relative adsorption and desorption rates from the experimental data for the two enantiomers of proline, fully accounting for mass transport within the flow-through cell. The results show that, in particular, the desorption kinetics is different for the two enantiomers. Therefore, the l-glutathione SAM can discriminate between enantiomers, d-proline being stronger bound. The IR spectra reveal that upon interaction with proline the adsorbed l-glutathione is protonated at the gly part of the molecule, which, in the absence of proline, is bound to the gold surface as carboxylate. The observed protonation of adsorbed l-glutathione upon interaction with proline goes along with a structural change of the former, which seems to play an important role for enantiodiscrimination.     

偶氮苯硫醇衍生物自组装成膜过程考察

The formation kinetics of the self-assembled monolayer (SAM) of an azobenzenealkanethiol, denoted as AzoC2SH on surface was studied using electrochemical techniques, and the monolayers prepared at different assembly times and concentration were also investigated. A two-step adsorption kinetics has been confirmed: the fast adsorption process and the following long-term reorganization. The equilibrium constant(K)for the adsorption and the interaction factor between adsorbate-adsorbate molecules (δ) were evaluated based on the Frumkin isotherm and determined to be (3. 17±0. 13)× 106 mol•L(-1) and -0.34±0.04, respectively. The Gibbs free energy (G)of SAM was determined to be -(37. 07±0. 13)kJ•mol(-1).     

Experimental studies on the adsorption of two surfactants on solid-aqueous interfaces: adsorption isotherms and kinetics

A quartz crystal microbalance with dissipation (QCM-D) was used to measure the adsorption from aqueous solutions of CTAB (cationic) and C(12)E(6) (nonionic) surfactants on gold and silica surfaces. QCM-D allows for the determination of adsorption isotherms and also the monitoring of the dynamics of adsorption in real time. By considering the atomic-scale roughness of the solid surfaces and the surface area per head group at the air/water interface, our experiments indicate that at bulk concentrations above the critical micelle concentration adsorbed C(12)E(6) forms a monolayer-like structure on both surfaces and CTAB yields a bilayer-like structure. Although our measurements do not allow us to discriminate between the morphology of the aggregates (i.e., between flat monolayers, hemicylinders, or hemispheres in the case of C(12)E(6) and between flat bilayers, cylinders, or spheres in the case of CTAB), these results are particularly significant when compared to recent QCM-D data reported by Macakova et al. (Macakova, L.; Blomberg, E.; Claesson, P. M. Langmuir 2007, 23, 12436). These authors reported that QCM-D overestimates the amount of CTAB adsorbed on silica by as much as 30-40% as a result of entrapped water. Our analysis suggests that the effect of entrapped solvent is not as important as previously assumed and, in fact, QCM-D may not overestimate the amount of CTAB adsorbed when roughness is considered. Results for the kinetics of adsorption suggest that the aggregate structure as well as whether micelles are present may influence the adsorption mechanism. We discuss our results in the perspective of molecular theories for both the equilibrium and kinetics of surfactant adsorption.     

Investigating detailed mechanism of hydrogen molecules adsorbing on single-wall carbon nanotubes using fitted force field parameters containing carbon–carbon interactions

The nonbonded and bonded force field parameters for carbon atoms in single-wall carbon nanotubes (SWNT) are fitted by means of quantum chemistry calculations with considering the periodic boundary conditions. The nonbonded parameters between carbon atoms and hydrogen atoms are fitted as well. All the fitted parameters are verified by comparing to quantum chemistry results and by calculating Young's modulus. Adsorption of Hydrogen molecules are then carried out on a bundle of self-assembled SWNTs. The adsorption isotherms are consistent to the Freundlich equation. Both hydrogen molecules adsorbed outside and inside the SWNTs are counted. According to our result, hydrogen molecules adsorbed inside the SWNTs are more stable at a relatively high temperature and are playing an important part in total amount of the adsorbed molecules. While C(10,10) have the highest adsorption capacities in most of the temperatures, hydrogen molecules inside C(5,5) are the most stable of all the four kinds of SWNTs. Thus, balancing adsorption capacities and strength of interaction can be important in choosing SWNT for gas adsorption. Besides, we deduct an equation that can describe the relation between hydrogen pressure and amount of SWNTs based on our simulation results. The hydrogen pressure may decrease by adding SWNTs in the system. The fitting method in our system is valid to SWNTs and can be tested in further studies of similar systems. © 2018 Wiley Periodicals, Inc.