B3LYP is the most widely used density-functional theory (DFT) approach because it is capable of accurately predicting molecular structures and other properties. However, B3LYP is not able to reliably model systems in which noncovalent interactions are important. Here we present a method that corrects this deficiency in B3LYP by using dispersion-correcting potentials (DCPs). DCPs are utilized by simple modifications to input files and can be used in any computational package that can read effective-core potentials. Therefore, the technique requires no programming. DCPs (developed for H, C, N, and O) produce the best results when used in conjunction with 6-31+G(2d,2p) basis sets. The B3LYP-DCP approach was tested on the S66, S22, and HSG-A benchmark sets of noncovalently interacting dimers and trimers and was found to, on average, significantly outperform almost all other DFT-based methods that were designed to treat van der Waals interactions. Users of B3LYP who wish to model systems in which noncovalent interactions (viz., steric repulsion, hydrogen bonding, π-stacking) are present, should consider B3LYP-DCP.

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The translational and orientational potential energy surfaces (PESs) of n-alkanethiols with up to four carbon atoms are studied for (√(3)×√(3))R30° self-assembled monolayers (SAMs). The PESs indicate that methanethiol may form SAM structures that are not accessible for long-chain thiols. The tilt of the thiol molecules is determined by a compromise between the preferred binding geometry at the sulfur atom and the steric requirements of the alkane chains. The Au-S bond lengths, offset from the bridge position (brg), and the Au-S-C bond angles result in tilt angles of the S-C bond in the range of 55-60°. As DFT/generalized gradient approximation systematically underestimates chain-chain interactions, the binding energies are corrected by comparison to MP2 interaction energies of alkane dimers in SAM-like configurations. The resulting thiol binding energies increase by approximately 1 kcal mol(-1) per CH(2) group, which results in a substantial stabilization of long-chain SAMs due to chain-chain interactions. Furthermore, as the chain length increases, the accessible range of backbone tilt angles is constrained due to steric effects. The combination of these two effects may explain why SAM structures with long-chain thiols exhibit higher order in experiments. For each thiol two favorable SAM structures are found with the sulfur head group at the fcc-brg and hcp-brg positions, respectively. These domains may coexist in thermal equilibrium. In combination with the symmetry of the gold (111) surface, this raises the possibility of up to six different domains on single-crystal terraces. Reconstructions by an adatom or vacancy of ethanethiol SAMs with (√(3)×√(3))R30° lattice are also studied using PES scans. The results indicate that adsorption of thiols next to a vacancy is favorable and may lead to point defects inside SAMs.

We recently showed that dispersion-correcting potentials (DCPs), atom-centered Gaussian-type functions developed for use with B3LYP (J. Phys. Chem. Lett. 2012, 3, 1738-1744 greatly improved the ability of the underlying functional to predict non-covalent interactions. However, the application of B3LYP-DCP for the β-scission of the cumyloxyl radical led a calculated barrier height that was over-estimated by ca. 8 kcal/mol. We show in the present work that the source of this error arises from the previously developed carbon atom DCPs, which erroneously alters the electron density in the C-C covalent-bonding region. In this work, we present a new C-DCP with a form that was expected to influence the electron density farther from the nucleus. Tests of the new C-DCP, with previously published H-, N-and O-DCPs, with B3LYP-DCP/6-31+G(2d,2p) on the S66, S22B, HSG-A, and HC12 databases of non-covalently interacting dimers showed that it is one of the most accurate methods available for treating intermolecular interactions, giving mean absolute errors (MAEs) of 0.19, 0.27, 0.16, and 0.18 kcal/mol, respectively. Additional testing on the S12L database of complexation systems gave an MAE of 2.6 kcal/mol, showing that the B3LYP-DCP/6-31+G(2d,2p) approach is one of the best-performing and feasible methods for treating large systems dominated by non-covalent interactions. Finally, we showed that C-C making/breaking chemistry is well-predicted using the newly developed DCPs. In addition to predicting a barrier height for the β-scission of the cumyloxyl radical that is within 1.7 kcal/mol of the high-level value, application of B3LYP-DCP/6-31+G(2d,2p) to 10 databases that include reaction barrier heights and energies, isomerization energies and relative conformation energies gives performance that is amongst the best of all available dispersion-corrected density-functional theory approaches.

ABSTRACT:The role of Au adatoms in high-density alkanethiol self-assembled monolayers (SAMs) has been investigated. Surface reconstructions in ethylthiol (ET) SAMs due to gold adatoms have been studied using DFT calculations. Relative energies are compared based on binding and surface energies calculated for different lattices using the same unit cell. We have found a structure with two ET-Au-ET adatom moieties binding on top of surface gold atoms as the most stable structure. Our model is consistent with the structural parameters obtained from experiments. In particular, the simulated STM image displays the characteristic zig-zag pattern.

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system.

Alkylsilane 3-mercaptopropyltrimethoxysilane (3MPT) monolayers with a functional end group -SH were used to immobilize Ag colloidal nanoparticles on photoinduced amphiphilic TiO(2) and hydroxylated SiO(2) surfaces. The differences in the adsorption of 3MPT and the immobilization of Ag colloids on both surfaces were studied. Under identical experimental conditions, 3MPT islands were formed on UV-exposed TiO(2) surfaces compared to continuous and flat monolayers formed on SiO(2). The significant structural differences found for monolayers of 3MPT on TiO(2) could be explained in terms of the different densities of hydroxyl groups and the microstructure of hydrophilic domains induced by UV irradiation. The surface properties were characterized using contact angle measurements and XPS. XPS showed an increase in the hydroxyl group's density and a decrease in the number of adsorbed hydrocarbon films on the TiO(2) surface as a function of the UV irradiation time. The density of the adsorbed 3MPT on TiO(2) surfaces as a function of the UV irradiation time was quantitatively related to the cosine of the water contact angles. Such a 3MPT distribution influenced the subsequent adsorption of Ag colloids and resulted in more isolated nanoparticles on the modified TiO(2) with a narrower size distribution.