Molecular dynamics investigations of self-assembled monolayers

Hautman, Joseph; Bareman, James P.; Mar, Wen; Klein, Michael L.

doi:10.1039/ft9918702031

Cited by 116 publications

(127 citation statements)

References 37 publications

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“…In some cases, such as the interaction of water chains with OH-terminated alkanethiolate chains, given the complexity of the potential-energy surface, the use of a dynamical approach based on simulated annealing was essential for finding the lowest-energy configuration: Clearly the possibility of performing efficient ab initio molecular dynamics represents an important advantage of CPMD over other quantum chemistry methods. Previous MD calculations [11] on OH-terminated alkanethiolate chains have shown a tendency to form hydrogen bonds between the chain ends, however the surface is disordered, with a significant fraction of "free" OH groups: In particular, our clean, OH-terminated alkanethiolate chain system developed three H bonds [12] between surface OH groups (this particular value might be biased by our relatively small supercell).…”

Section: Model and Computational Methodsmentioning

confidence: 99%

Hydrophobic–Hydrophilic Interactions of Water with Alkanethiolate Chains from First‐Principles Calculations

et al. 2005

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The interaction of water with alkanethiolate chains is studied from first principles. A detailed analysis is performed by optimizing the structure of small water clusters, one-dimensional water chains, and ordered and disordered thin water layers adsorbed on hydroxyl(OH)- and methyl(CH3)-terminated alkanethiol monolayers. The hydrophilic/hydrophobic character of these two different substrates is investigated by means of an energetic analysis combined with hydrogen-bond counting. On the hydrophilic OH-terminated alkanethiol surface, zigzag, one-dimensional water chains and disordered thin water layers are the energetically favored structures. The ab initio results can be used to determine the optimal value of the empirical parameters characterizing a suitable force field to be used in classic molecular dynamics simulations.

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Section: Model and Computational Methodsmentioning

confidence: 99%

Hydrophobic–Hydrophilic Interactions of Water with Alkanethiolate Chains from First‐Principles Calculations

et al. 2005

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“…Hautman and Klein [20,21] performed molecular dynamics simulations of the thermal motions of these systems in the absence of any reliable knowledge of the force field parameters for the sulfur surface attachment.…”

Section: Cluster Models For Surface and Bulk Phenome1lqmentioning

confidence: 99%

Modeling Chemisorption Processes with Metal Cluster Systems: III. Model Thio-Alkyls on Gold Surfaces

Sellers

Ulman

Shnidman

et al. 1992

Cluster Models for Surface and Bulk Phenomena

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We have performed RECP Hartree-Fock + MBPT2 calculations of the equilibrium adsorbate structures and force constants of SH and SCH3 chemisorbed on the Au(lll) and Au(100) surfaces. We propose coverage schemes for thio-alkyl adsorbates for both surfaces. On both surfaces and for both adsorbates we find the surface -S-X angle to be linear in the hollow site. The on-top site is an energy maximum on both surfaces. The bonding scheme between the sulfur atom and the gold surface possesses sigrnaand pi character. A significant amount of backbonding is evident in these systems through the mixing of the (fully occupied) sulfur pi orbitals and the unoccupied pi orbitals of the cluster model of the surface. We attribute the straightening of the surface -s-x angle in going from the on-top site to the hollow site to the backbonding interaction. The force field parameters and structures we determine are necessary for molecular dynamics studies of self-assembling thio-alkyl mono layers on gold. We propose coverage schemes that are consistent with available observational data.

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“…18 In following studies of analogous systems, a periodic corrugation potential for S was added to force chemisorption in high-symmetry surface sites. 19,20 Pertsin and Grunze 21 modified this FF by using a harmonic corrugation term for S with parameters fitted on quantum-mechanical calculations. 22 The Hautman and Klein FF was also used in more recent studies of SAMs.…”

Section: Introductionmentioning

confidence: 99%

GolP: An atomistic force‐field to describe the interaction of proteins with Au(111) surfaces in water

Iori¹,

Felice²,

Molinari³

et al. 2008

J Comput Chem

250

417

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A classical atomistic force field to describe the interaction of proteins with gold (111) surfaces in explicit water has been devised. The force field is specifically designed to be easily usable in most common bio-oriented molecular dynamics codes, such as GROMACS and NAMD. Its parametrization is based on quantum mechanical (density functional theory [DFT] and second order Möller-Plesset perturbation theory [MP2]) calculations and experimental data on the adsorption of small molecules on gold. In particular, a systematic DFT survey of the interaction between Au(111) and the natural amino acid side chains has been performed to single out chemisorption effects. Van der Waals parameters have been instead fitted to experimental desorption energy data of linear alkanes and were also studied via MP2 calculations. Finally, gold polarization (image charge effects) is taken into account by a recently proposed procedure (Iori, F.; Corni, S. J Comp Chem 2008, 29, 1656). Preliminary validation results of GolP on an independent test set of small molecules show the good performances of the force field.

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Molecular dynamics investigations of self-assembled monolayers

Cited by 116 publications

References 37 publications

Hydrophobic–Hydrophilic Interactions of Water with Alkanethiolate Chains from First‐Principles Calculations

Hydrophobic–Hydrophilic Interactions of Water with Alkanethiolate Chains from First‐Principles Calculations

Modeling Chemisorption Processes with Metal Cluster Systems: III. Model Thio-Alkyls on Gold Surfaces

GolP: An atomistic force‐field to describe the interaction of proteins with Au(111) surfaces in water

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