We present Monte Carlo simulations of thermal, structural, and dynamic properties of a 27-segment lattice model protein adsorbed to a solid surface. The protein consists of a sequence of A and B segments whose order and topological contact energy values are chosen so that a unique (3x3x3 cubic) folded state occurs in the absence of an adsorbing surface [E. I. Shakhnovich and M. Gutin, Proc. Natl. Acad. Sci. USA 90, 7195 (1993)]. The surface consists of a plane of sites that interact either (i) equally with all contacting protein segments (an equal affinity surface) or (ii) more strongly with type A contacting segments (an A affinity surface). For both surfaces, we find the conformational change of an initially folded protein to begin with a continuous transition to a structure where all segments contact the surface. This is followed by a partial refolding to a low energy state; this step is continuous and results in full surface contact for the equal affinity surface and is activated and results in significant loss of surface contact for the A affinity surface. We also observe a lesser (greater) degree of average surface contact in the equal (A) affinity surface with an increase in temperature.

Using the ab initio potential of Shin et al. (to be published), we have calculated the bound states and infrared absorption spectrum of the van der Waals complex Ar...CO. The results show that Ar...CO cannot be treated as a quasirigid rotor, nor as a molecule with a free internal rotor. In particular, a transition to the first excited van der Waals bending level is predicted to be present in the spectrum, and its frequency varies with Ω (the projection quantum number of the total angular momentum onto the intermolecular axis going from the center of mass of CO to the Ar atom). It is also shown that, although the spectrum cannot be analyzed by the use of a rigid rotor model, rotational ‘‘constants’’ can still be defined for each value of Ω. This is consistent with the available experimental data and the predicted bending excitation can account for unassigned transitions in the infrared spectrum of this complex. Finally, a sensitivity analysis of the calculated spectrum with respect to the potential anisotropy has been performed.

Proteins often undergo changes in internal conformation upon interacting with a surface. We investigate the thermodynamics of surface induced conformational change in a lattice model protein using a multicanonical Monte Carlo method. The protein is a linear heteropolymer of 27 segments (of types A and B) confined to a cubic lattice. The segmental order and nearest neighbor contact energies are chosen to yield, in the absence of an adsorbing surface, a unique 3x3x3 folded structure. The surface is a plane of sites interacting either equally with A and B segments (equal affinity surface) or more strongly with the A segments (A affinity surface). We use a multicanonical Monte Carlo algorithm, with configuration bias and jump walking moves, featuring an iteratively updated sampling function that converges to the reciprocal of the density of states 1/Omega(E), E being the potential energy. We find inflection points in the configurational entropy, S(E)=k ln Omega(E), for all but a strongly adsorbing equal affinity surface, indicating the presence of free energy barriers to transition. When protein-surface interactions are weak, the free energy profiles F(E)=E-TS(E) qualitatively resemble those of a protein in the absence of a surface: a free energy barrier separates a folded, lowest energy state from globular, higher energy states. The surface acts in this case to stabilize the globular states relative to the folded state. When the protein surface interactions are stronger, the situation differs markedly: the folded state no longer occurs at the lowest energy and free energy barriers may be absent altogether.

Potential energy calculations have been performed for the system CO/n×Ar/Pt where the argon atoms play the role of spacer layers. A detailed analysis of the construction of this multidimensional potential energy surface is presented and discussed. The change of the nature of the adsorbate–substrate bond going from chemisorption to physisorption is studied within the frame of a stepwise approach. First we investigate an incommensurate model in which no coupling between the argon and the platinum atoms is considered. Several convergence tests have been done concerning the size and the binding sites of the metal surface, the rare gas network, and the combined system in order to ensure the stabilization of the calculations. A structural analysis of this potential energy surface is made considering the minima of the potential interaction, the bending angle of the CO with respect to the normal to the surface, and the distance between the CO center of mass and the surface. In a second stage of our study the lateral Ar–Ar and the Ar–Pt corrugation interactions are included in order to consider commensurate criteria. A new analysis of the behavior of the main physical observables of the system is given and the dependence of the calculations on the variation of the argon lattice parameter is shown as a function of the number of argon spacer layers. The results show that the equilibrium value of the argon lattice parameter changes when the number of spacer layers increases. It is found that the main contribution to the change in the strength of the force field between the molecule and the metal surface is given by the introduction of the first two argon spacer layers. Additional layers produce a smooth variation within the physisorption regime.