Probing the conformational energetics of alkyl thiols on gold surfaces by means of a morphing/steering non-equilibrium tool

Abstract

In this work we show that a non-equilibrium statistical tool based on Jarzynski's equality (JE) can be applied to achieve a sufficiently accurate mapping of the torsion free energy, bond-by-bond, for an alkyl thiol ligand tethered to a gold surface and sensing the presence of the surrounding cluster of similar chains. The strength of our approach is the employment of a strategy to let grow the internal energetics of the whole system (namely, the "energy morphing" stage recently presented by us in J. Comput. Chem., 2014, 35, 1865-1881) before initiating the rotational steering, which yields accurate results in terms of statistical uncertainties and bias on the free energy profiles. The work is mainly methodological and illustrates the feasibility of this kind of inspection on nanoscale molecular clusters with conformational flexibility. The outcomes for the archetype of self-assembled-monolayers considered here, a regular pattern of 10-carbon alkyl thiols on an ideal gold surface, give information on the conformational mobility of the ligands. Notably, such information is unlikely to be obtained by means of standard equilibrium techniques or by conventional molecular dynamics simulations.

Conformational Mobility in Monolayer-Protected Nanoparticles: From Torsional Free Energy Profiles to NMR Relaxation

“…Such an outcome is rather different from that obtained in our previous study on the coated planar surface. 28 In that case, the torsion potentials about the first two carbon−carbon bonds appeared to be quite different from that of n-butane, also in terms of qualitative features. Namely, we found that for the C1−C2 bond, the two gauche conformations appear to be much more stable (of about 20 k B T units at room temperature) with respect to the trans one, while for the C2− C3 bond the gauche conformations are less stable than the trans but they are separated by a large energy barrier of about 30 k B T. In passing from the planar situation to the nanoparticle arrangement, these peculiar features are lost.…”

“…A possibility would be to consider a more extended cluster around the probe chain, as done in ref 28 to check/search for convergence on the single-bond free energy profiles. However, the computational handling of the 15-chains cluster was very demanding, 41 hence such a cluster sets the actual treatable size for this kind of flexible NP coatings.…”

Multiscale modeling for interpreting nuclear magnetic resonance relaxation in flexible molecules

“…However, this is true also in standard MD simulations, where the diversity of the chemical environment of an atom is handled by defining the atom types. In the case discussed here of alkyl‐thiols tethered to a flat or curved (nanoparticle) Au surfaces, the coarse‐grained force fields indicated a certain degree of “portability,” that is, it is reasonable to expect that the free energy profile can fit also similar systems to those treated there. The results support the idea that it is possible to define a force field that can be written as sum of proper terms as is usually done in MD simulations, once the parallel concept of “atom types” is defined in the context of Brownian dynamics simulations.…”

“…Thus, under the DCM paradigm, the problem of the selection of the relevant coordinates is moved to the skimming of the set of the torsion angles of the molecule. While such a pre‐selection of the kind of degrees of freedom can be considered a limitation, the DCM model has been used with success in interpreting the magnetic spectroscopy of very different systems, and in all cases resorting to a fitting procedure was extremely limited if not necessary at all, making the whole approach predictive at least for small molecules.…”

“…Also, since the details of the internal energy grow smoothly, the morphing route allows the system to more efficiently sample the whole space of conformations, allowing a good estimation of POMF profiles even if the latter presents high (free) energy barriers. Such a strategy has been recently successfully applied in a study on clusters of 1‐decanethiol chains tethered to a planar gold surface, and on a gold nanoparticle . JEFREE is distributed within the GPL v2.0 license, and can be downloaded from our website (http://www.chimica.unipd.it/licc/software.html).…”