Simulation of a monolayer of alkyl thiol chains

Abstract

Molecular dynamics simulations have been used to study the structure and dynamics of monolayers of long-chain molecules on a metallic substrate. The system consisted of 90 molecules held at a fixed surface density and periodically replicated in the plane of the surface. Two models have been studied as alternative representations of the admolecule–surface interactions in layers formed by the self-assembly of alkyl thiol [SH(CH2)15CH3] molecules onto a gold substrate. The principal difference between the two models is that in one, the S–C bond is required to lie nearly parallel to the substrate surface. After lengthy equilibration at room temperature, both models yield monolayers in which the chains are aligned and tilted with respect to the surface normal. Although the tilt angle is different for the two models, the thickness of the monolayers is the same and the influence of the ‘‘modified-headgroup’’ on the detailed structure of the film is confined to the region closest to the metal surface. There are striking differences in the chain rotational dynamics of the two models which are likely amenable to experimental verification.

Computer simulations of vapor–liquid phase equilibria of n-alkanes

“…One of the most popular models used in simulations of alkanes and monolayers 44 -46 is based on the OPLS model of Jorgensen et al 19 This model has been further refined by Hautman and Klein 44 to include bond bending. The OPLS model uses a united atom description in which CH 2 and CH 3 groups are considered as one united atom.…”

Observation of surface enhanced IR absorption coefficient in alkanethiol based self-assembled monolayers on GaAs(001)

“…Since the value of p is described classically as being proportional to the dipole moment derivative with respect to the normal coordinate of vibrational oscillation, 21,32 factors significant to a redistribution of electron density, such as molecular orbital intermixing and van der Waals forces, may result in increased oscillator strength, namely, ͉p SAM ͉ Ͼ ͉p liq ͉. The contribution of such factors stands to the reason given the important role of intermolecular forces driving the selfassembly mechanism, 17,33,34 and follows naturally from the discussion of phase related intensity variation outlined above. Note that in general, ⌬p may occur by virtue of a change in net permanent dipole or by induced dipole effects, i.e., a change in vibrational polarizability.…”

A sequential formula for electronic coupling in long range bridge-assisted electron transfer: Formulation of theory and application to alkanethiol monolayers

“…The We have also calculated the effect of additional parallel alkane thiol chains using the structure from Klein. 25 For one of the possible conformations of the ferrocenylcarboxyl group, 28 the effective coupling calculated from direct summation method for different numbers of additional chains is listed in Table I.…”

“…24 The coordinates of atoms in the alkane thiol portion of the system are those of Klein and coworkers, who employed a molecular dynamics calculation in conjunction with structural data. 25,26 The geometry of the ferrocenylcarboxyl group is obtained from the crystal structure of similar molecules. 27 In the supplemental material 28 we deposited the full Cartesian coordinates for the molecules being used in the present work.…”