Stefano Corni

Formation and relaxation of excited states in solution : A new time dependent polarizable continuum model based on time dependent density functional theory

In this paper a novel approach to study the formation and relaxation of excited states in solution is presented within the integral equation formalism version of the polarizable continuum model. Such an approach uses the excited state relaxed density matrix to correct the time dependent density functional theory excitation energies and it introduces a state-specific solvent response, which can be further generalized within a time dependent formalism. This generalization is based on the use of a complex dielectric permittivity as a function of the frequency, epsilonomega. The approach is here presented in its theoretical formulation and applied to the various steps involved in the formation and relaxation of electronic excited states in solvated molecules. In particular, vertical excitations (and emissions), as well as time dependent Stokes shift and complete relaxation from vertical excited states back to ground state, can be obtained as different applications of the same theory. Numerical results on two molecular systems are reported to better illustrate the features of the model.

Electronic excitation energies of molecules in solution: state specific and linear response methods for nonequilibrium continuum solvation models.

We present a formal comparison between the two different approaches to the calculation of electronic excitation energies of molecules in solution within the continuum solvation model framework, taking also into account nonequilibrium effects. These two approaches, one based on the explicit evaluation of the excited state wave function of the solute and the other based on the linear response theory, are here proven to give formally different expressions for the excitation energies even when exact eigenstates are considered. Calculations performed for some illustrative examples show that this formal difference has sensible effects on absolute solvatochromic shifts (i.e., with respect to gas phase) while it has small effects on relative (i.e., nonpolar to polar solvent) solvatochromic shifts.

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

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.

Electronic excitation energies of molecules in solution within continuum solvation models: investigating the discrepancy between state-specific and linear-response methods.

In a recent article [R. Cammi, S. Corni, B. Mennucci, and J. Tomasi, J. Chem. Phys. 122, 104513 (2005)], we demonstrated that the state-specific (SS) and the linear-response (LR) approaches, two different ways to calculate solute excitation energies in the framework of quantum-mechanical continuum models of solvation, give different excitation energy expressions. In particular, they differ in the terms related to the electronic response of the solvent. In the present work, we further investigate this difference by comparing the excitation energy expressions of SS and LR with those obtained through a simple model for solute-solvent systems that bypasses one of the basic assumptions of continuum solvation models, i.e., the use of a single Hartree product of a solute and a solvent wave function to describe the total solute-solvent wave function. In particular, we consider the total solute-solvent wave function as a linear combination of the four products of two solute states and two solvent electronic states. To maximize the comparability with quantum-mechanical continuum model the resulting excitation energy expression is recast in terms of response functions of the solvent and quantities proper for the solvated molecule. The comparison of the presented expressions with the LR and SS ones enlightens the physical meaning of the terms included or neglected by these approaches and shows that SS agrees with the results of the four-level model, while LR includes a term classified as dispersion in previous treatments and neglects another related to electrostatic. A discussion on the possible origin of the LR flaw is finally given.

Interaction of Amino Acids with the Au(111) Surface: Adsorption Free Energies from Molecular Dynamics Simulations

Interactions of proteins with inorganic surfaces are of high importance in biological events and in modern biotechnological applications. Therefore, peptides have been engineered to recognize inorganic surfaces with high specificity. However, the underlying interactions are still not well understood. Here, we investigated the adsorption of amino acids as protein building blocks onto a Au(111) surface. In particular, using molecular dynamics simulations, we calculated the potential of mean force between all the 20 amino acids and the gold surface. We found a strong dependence of the binding affinities on the chemical character of the amino acids. Additionally, the interaction free energy is correlated with the propensity of amino acids to form beta-sheets, hinting at design principles for gold binding peptides and induction of beta-sheet formation near surfaces.

GolP-CHARMM: First-principles based force fields for the interaction of proteins with Au(111) and Au(100)

Computational simulation of peptide adsorption at the aqueous gold interface is key to advancing the development of many applications based on gold nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, we present a force field, GolP-CHARMM, designed to capture peptide adsorption at both the aqueous Au(111) and Au(100) interfaces. The force field, compatible with the bio-organic force field CHARMM, is parametrized using a combination of experimental and first-principles data. Like its predecessor, GolP (Iori, F.; et al. J. Comput. Chem.2009, 30, 1465), this force field contains terms to describe the dynamic polarization of gold atoms, chemisorbing species, and the interaction between sp(2) hybridized carbon atoms and gold. A systematic study of small molecule adsorption at both surfaces using the vdW-DF functional (Dion, M.; et al. Phys. Rev. Lett.2004, 92, 246401-1. Thonhauser, T.; et al. Phys. Rev. B2007, 76, 125112) is carried out to fit and test force field parameters and also, for the first time, gives unique insights into facet selectivity of gold binding in vacuo. Energetic and spatial trends observed in our DFT calculations are reproduced by the force field under the same conditions. Finally, we use the new force field to calculate adsorption energies, under aqueous conditions, for a representative set of amino acids. These data are found to agree with experimental findings.

Docking of ubiquitin to gold nanoparticles.

Protein-nanoparticle associations have important applications in nanoscience and nanotechnology such as targeted drug delivery and theranostics. However, the mechanisms by which proteins recognize nanoparticles and the determinants of specificity are still poorly understood at the microscopic level. Gold is a promising material in nanoparticles for nanobiotechnology applications because of the ease of its functionalization and its tunable optical properties. Ubiquitin is a small, cysteine-free protein (ubiquitous in eukaryotes) whose binding to gold nanoparticles has been characterized recently by nuclear magnetic resonance (NMR). To reveal the molecular basis of these protein-nanoparticle interactions, we performed simulations at multiple levels (ab initio quantum mechanics, classical molecular dynamics and Brownian dynamics) and compared the results with experimental data (circular dichroism and NMR). The results provide a model of the ensemble of structures constituting the ubiquitin-gold surface complex, and insights into the driving forces for the binding of ubiquitin to gold nanoparticles, the role of nanoparticle surfactants (citrate) in the association process, and the origin of the perturbations in the NMR chemical shifts.

Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces

Combinatorial bio‐techniques have demonstrated that proteins can be good and even selective binders for several inorganic surfaces, including metals. However, the understanding of the basic physical mechanisms that govern such interactions did not keep up with the success in these experiments. The comprehension of such mechanisms would greatly benefit from the computational investigation of the problem. Because of the complexity of the system, classical molecular dynamics simulations based on an atomistic description appear to be the best compromise between reliability and feasibility. For proteins interacting with metal surfaces, however, methodological improvements with respect to standard Molecular Dynamics (MD) of proteins are needed, since the polarization of the metal induced by the protein (and the surrounding water) is not generally negligible. In this article, we present a simple approach to introduce metal polarization effects (often termed image effects) in MD simulations by exploiting standard features of bio‐oriented MD codes such as the widely used GROMACS and NAMD. Tests to show the reliability of the proposed methods are presented, and the results for a model application showing the importance of image effects are also discussed.

Surface enhanced Raman scattering from a single molecule adsorbed on a metal particle aggregate: A theoretical study

A methodology for the theoretical evaluation of Raman intensities for a molecule adsorbed on a metal particle aggregate, possibly in the presence of a solvent, is presented. The molecule is treated at the ab initio level, both in the evaluation of ground state electronic density and nuclear geometry, and in the evaluation of normal modes and Raman scattering factors. The whole metal aggregate, built by exploiting a Cluster–Cluster Aggregation (CCA) model, is described as an ensemble of polarizable dipoles. The metal particles nearest to the molecule are treated as a single complex shaped metal nanoparticle and the quasielectrostatic problem for the molecule–nanoparticle system is solved by using a Boundary Element Method (BEM). The solvent is modeled by using the Polarizable Continuum Model (PCM). Applications of the methodology to systems for which huge enhancements (1013–1014) of Raman intensities have been experimentally measured are given.

Enhanced response properties of a chromophore physisorbed on a metal particle

We present a theoretical methodology to study the electronic response properties of a chromophore physisorbed on a metal particle. In particular the chromophore is treated at ab initio level whereas the metal particle is described through its dielectric properties. The use of a boundary elements method for the resolution of the electrostatic problem allows the study of particles with complex shapes. The theoretical procedure is applied to the study of different quantities such as the chromophore effective polarizability, the UV-VIS absorption of the chromophore coated metal particle, and the surface enhanced Raman scattering (SERS) of the physisorbed molecule for two reliable chromophores (merocyanine dyes) physisorbed on copper and silver metal particles of various sizes and shapes.