Synthesis of corrugated C-based nanostructures by Br-corannulene oligomerization.

The structure and electronic properties of carbon-based nanostructures obtained by metal surface assisted synthesis is highly dependent on the nature of the precursor molecule. Here, we report on a combined scanning tunneling microscopy, soft X-ray spectroscopy and density functional theory investigation on the surface assisted polymerization of Br-corannulene at Ag(110) and on the possibility of building a mesh of π-conjugated polymers starting from buckyball shaped molecules. Indeed, the corannulene units form one-molecule-wide ribbons in which the natural concavity of the precursor molecule is maintained. These C-based nanostructures are corrugated and merge into a covalent network on the surface.

Water at the Interface Between Defective Graphene and Cu or Pt (111) Surfaces.

The presence of defects in the graphenic layers deposited on metal surfaces modifies the nature of the interaction. Unsaturated carbon atoms, due to vacancies in the lattice, form strong organometallic bonds with surface metal atoms that highly enhance the binding energy between the two materials. We investigate by means of a wide set of dispersion-corrected density functional theory calculations how such strong chemical bonds affect both the electronic properties of these hybrid interfaces and the chemical reactivity with water, which is commonly present in the working conditions. We compare different metal substrates (Cu vs Pt) that present a different type of interaction with graphene and with defective graphene. This comparative analysis allows us to unravel the controlling factors of water reactivity, the role played by the carbon vacancies and by the confinement or "graphene cover effect". Water is capable of breaking the C-Cu bond by dissociating at the undercoordinated carbon atom of the vacancy, restoring the weak van der Waals type of interaction between the two materials that allows for an easy detachment of graphene from the metal, but the same is not true in the case of Pt, where C-Pt bonds are much stronger. These conclusions can be used to rationalize water reactivity at other defective graphene/metal interfaces.

Synthesis of graphene nanoribbons with a defined mixed edge-site sequence by surface assisted polymerization of (1,6)-dibromopyrene on Ag(110).

By a combination of scanning tunneling microscopy, X-ray spectroscopic techniques and density functional theory calculations, we prove the formation of extended patterns of parallel, graphene nanoribbons with alternate zig-zag and armchair edges and selected width by surface-assisted Ullmann coupling polymerization and dehydrogenation of 1,6-dibromopyrene (C16H8Br2). Besides the relevance of these nanostructures for their possible application in nanodevices, we demonstrate the peculiarity of halogenated pyrene derivatives for the formation of nanoribbons, in particular on Ag(110). These results open the possibility of tuning the shape and dimension of nanoribbons (and hence the correlated electronic properties) by choosing suitably tailored or on-purpose designed molecular precursors.

Catalysis under Cover: Enhanced Reactivity at the Interface between (Doped) Graphene and Anatase TiO2.

The "catalysis under cover" involves chemical processes which take place in the confined zone between a 2D material, such as graphene, h-BN, or MoS2, and the surface of an underlying support, such as a metal or a semiconducting oxide. The hybrid interface between graphene and anatase TiO2 is extremely important for photocatalytic and catalytic applications because of the excellent and complementary properties of the two materials. We investigate and discuss the reactivity of O2 and H2O on top and at the interface of this hybrid system by means of a wide set of dispersion-corrected hybrid density functional calculations. Both pure and boron- or nitrogen-doped graphene are interfaced with the most stable (101) anatase surface of TiO2 in order to improve the chemical activity of the C-layer. Especially in the case of boron, an enhanced reactivity toward O2 dissociation is observed as a result of both the contribution of the dopant and of the confinement effect in the bidimensional area between the two surfaces. Extremely stable dissociation products are observed where the boron atom bridges the two systems by forming very stable B-O covalent bonds. Interestingly, the B defect in graphene could also act as the transfer channel of oxygen atoms from the top side across the C atomic layer into the G/TiO2 interface. On the contrary, the same conditions are not found to favor water dissociation, proving that the "catalysis under cover" is not a general effect, but rather highly depends on the interfacing material properties, on the presence of defects and impurities and on the specific reaction involved.

Theoretical Studies of Oxygen Reactivity of Free-Standing and Supported Boron-Doped Graphene.

Graphene inertness towards chemical reactivity can be considered as an accepted postulate by the research community. This limit has been recently overcome by chemically and physically modifying graphene through non-metal doping or interfacing with acceptor/donor materials (metals or semiconductors). As a result, outstanding performances as catalytic, electrocatalytic, and photocatalytic material have been observed. In this critical Review we report computational work performed, by our group, on the reactivity of free-standing, metal- and semiconductor-supported B-doped graphene towards oxygen, which is at the basis of extremely important energy-related chemical processes, such as the oxygen reduction reaction. It appears that a combination of doping and interfacing approaches for the activation of graphene can open unconventional and unprecedented reaction paths, thus boosting the potential of modified graphene in many chemical applications.

On-surface photo-dissociation of C-Br bonds: towards room temperature Ullmann coupling.

The surface-assisted synthesis of gold-organometallic hybrids on the Au(111) surface both by thermo- and light-initiated dehalogenation of bromo-substituted tetracene is reported. Combined X-ray photoemission (XPS) and scanning tunneling microscopy (STM) data reveal a significant increase of the surface order when mild reaction conditions are combined with 405 nm light irradiation.

Control of the intermolecular coupling of dibromotetracene on Cu(110) by the sequential activation of C-Br and C-H bonds.

Dibromotetracene molecules are deposited on the Cu(110) surface at room temperature. The complex evolution of this system has been monitored at different temperatures (i.e., 298, 523, 673, and 723 K) by means of a variety of complementary techniques that range from STM and temperature-programmed desorption (TPD) to high-resolution X-ray spectroscopy (XPS) and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). State-of-the-art density-functional calculations were used to determine the chemical processes that take place on the surface. After deposition at room temperature, the organic molecules are transformed into organometallic monomers through debromination and carbon-radical binding to copper adatoms. Organometallic dimers, trimers, or small oligomers, which present copper-bridged molecules, are formed by increasing the temperature. Surprisingly, further heating to 673 K causes the formation of elongated chains along the Cu(110) close-packed rows as a consequence of radical-site migration to the thermodynamically more stable molecule heads. Finally, massive dehydrogenation occurs at the highest temperature followed by ring condensation to nanographenic patches. This study is a paradigmatic example of how intermolecular coupling can be modulated by the stepwise control of a simple parameter, such as temperature, through a sequence of domino reactions.

The Dalton quantum chemistry program system.

Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, Møller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms.

Stereodirection of an α-ketoester at sub-molecular sites on chirally modified Pt(111): heterogeneous asymmetric catalysis.

Chirally modified Pt catalysts are used in the heterogeneous asymmetric hydrogenation of α-ketoesters. Stereoinduction is believed to occur through the formation of chemisorbed modifier-substrate complexes. In this study, the formation of diastereomeric complexes by coadsorbed methyl 3,3,3-trifluoropyruvate, MTFP, and (R)-(+)-1-(1-naphthyl)ethylamine, (R)-NEA, on Pt(111) was studied using scanning tunneling microscopy and density functional theory methods. Individual complexes were imaged with sub-molecular resolution at 260 K and at room temperature. The calculations find that the most stable complex isolated in room-temperature experiments is formed by the minority rotamer of (R)-NEA and pro-S MTFP. The stereodirecting forces in this complex are identified as a combination of site-specific chemisorption of MTFP and multiple non-covalent attractive interactions between the carbonyl groups of MTFP and the amine and aromatic groups of (R)-NEA.

Direct observation of molecular preorganization for chirality transfer on a catalyst surface.

The chemisorption of specific optically active compounds on metal surfaces can create catalytically active chirality transfer sites. However, the mechanism through which these sites bias the stereoselectivity of reactions (typically hydrogenations) is generally assumed to be so complex that continued progress in the area is uncertain. We show that the investigation of heterogeneous asymmetric induction with single-site resolution sufficient to distinguish stereochemical conformations at the submolecular level is finally accessible. A combination of scanning tunneling microscopy and density functional theory calculations reveals the stereodirecting forces governing preorganization into precise chiral modifier-substrate bimolecular surface complexes. The study shows that the chiral modifier induces prochiral switching on the surface and that different prochiral ratios prevail at different submolecular binding sites on the modifier at the reaction temperature.

Self-consistent meta-generalized gradient approximation study of adsorption of aromatic molecules on noble metal surfaces.

The adsorption of benzene, pyridine, and two nucleobases on the Au(111) surface has been investigated using a fully relaxed, self-consistent meta-generalized gradient approximation (meta-GGA) density functional theory setup with the M06-L functional. The meta-GGA based molecule-surface separations are shortened and the adsorption bond strengths of the molecules are greatly improved over the virtually non-interacting results obtained when using a plain GGA exchange-correlation functional. The nucleobases containing oxygen atoms show higher corrugation with adsorption site and orientation than the other aromatic molecules considered. The adsorption of pentacene is studied on Au, Ag, and Cu surfaces. In agreement with experiment, the adsorption energies are found to increase with decreasing nobleness, but the dependency is underestimated. We point out how the kinetic energy density can discriminate between covalent and non-covalent bonding regions of orbital overlap.

Excited-state polarizabilities of solvated molecules using cubic response theory and the polarizable continuum model.

The theory and an implementation of the solvent contribution to the cubic response function for the polarizable continuum model for multiconfigurational self-consistent field wave functions is presented. The excited-state polarizability of benzene, para-nitroaniline, and nitrobenzene has been obtained from the double residue of the cubic response function calculated in the presence of an acetonitrile and dioxane solvent. The calculated excited-state polarizabilities are compared to results obtained from the linear response function of the explicitly optimized excited states.

2D-3D transition for cationic and anionic gold clusters: a kinetic energy density functional study.

We present a density functional theory study of the energetics of isolated Au(n)+ (n = 5-10) and Au(n)- (n = 8-13) gold clusters. We compare our results to both theoretical and experimental values from the literature and find the use of meta-generalized gradient approximation (MGGA) functionals, in particular the M06-L functional, to be of importance in order to match experiment. The M06-L values suggest crossovers between 2D and 3D structures at n = 8 and 12 for cationic and anionic clusters, respectively. We suggest that the MGGA's stronger tendency toward 3D structures arises from their smaller gradient enhancement. Moreover, we show how MGGAs, in contrast to generalize gradient approximations with smaller gradient enhancements, avoid overestimating the bond energies by combining the information contained in the reduced gradient and the kinetic energy. This allows MGGAs to treat differently the exchange enhancement in the decaying density and bonding regions.

Analytic ab initio calculations of coherent anti-Stokes Raman scattering (CARS).

We present a theory for the analytic calculation of frequency-dependent polarizability gradients, and apply the methodology to the calculation of coherent anti-Stokes Raman scattering (CARS). The formalism used is based on an open-ended theory for the calculation of frequency-dependent molecular response properties of arbitrary order, also including contributions from perturbation-dependent basis sets. An important feature of our approach is the close connection between the formalism--which is fully matrix-based in an atomic orbital basis--and the implementation, allowing for the rapid implementation of higher-order molecular properties. Care is taken to allow the formalism to be utilized with linearly-scaling Hartree-Fock and density-functional theory codes. By avoiding the evaluation of responses due to geometry distortions, only 9 response equations need to be solved for the calculation of the CARS intensities, independent of the size of the molecular system. The theory is illustrated by calculations on a set of polyaromatic hydrocarbons using a DFT/B3LYP force field and Hartree-Fock polarizability gradients. Good agreement with the experimental CARS spectra of these compounds is obtained.

Second-harmonic generation in GFP-like proteins.

The second-order nonlinear optical properties of green fluorescent proteins (GFPs), such as the photoswitchable Dronpa and enhanced GFP (EGFP), have been studied at both the theoretical and experimental levels. In the case of Dronpa, both approaches are consistent in showing the rather counterintuitive result of a larger second-order nonlinear polarizability (or first hyperpolarizability, beta) for the protonated state, which has a higher transition energy, than for the deprotonated, fluorescent state with its absorption at lower energy. Moreover, the value of beta for the protonated form of Dronpa is among the highest reported for proteins. In addition to the pH dependence, we have found a wavelength dependence in the beta values. These properties are essential for the practical use of Dronpa or other GFP-like fluorescent proteins as second-order nonlinear fluorophores for symmetry-sensitive nonlinear microscopy imaging and as nonlinear optical sensors for electrophysiological processes. An accurate value of the first hyperpolarizability is also essential for any qualitative analysis of the nonlinear images.

Solvent effects on the three-photon absorption of a symmetric charge-transfer molecule.

We present a theoretical study of the solvent-induced three-photon absorption cross section of a highly conjugated fluorene derivative, performed using density functional (DFT) cubic response theory in combination with the polarizable continuum model. The applicability of the often used two-state model is examined by comparison against the full DFT response theory results. It is found that the simplified model performs poorly for the three-photon absorption properties of our symmetric charge-transfer molecule. The dielectric medium enhances the three-photon absorption cross section remarkably. The effects of solvent polarity and geometrical distortions have been carefully examined. A detailed comparison with experiment is presented.

Degenerate four-wave mixing in solution by cubic response theory and the polarizable continuum model.

We have derived and implemented the solvent contribution to the cubic response function for the polarizable continuum model in its integral equation formulation. The present formulation is valid both at the Hartree-Fock and at the Kohn-Sham density functional levels of theory, because both bear the same formal description of the solvent contribution through an additional additive term in the Hamiltonian operator. This new implementation is used to compute the solvent effect for the degenerate four-wave mixing process on three different classes of heteroaromatic chromophores: (I) triazine, benzoxazole, benzimidazole, and benzothiazole; (II) three benzothiazole derivatives; and (III) three tri-s-triazine derivatives. The results are first discussed in terms of the solvent effects on the calculated property and then compared to experimental data for the substrates of class (I) and (II).

Solvent effects on two-photon absorption of dialkylamino substituted distyrylbenzene chromophore.

Solvent effects on the two-photon absorption of a symmetrical diamino substituted distyrylbenzene chromophore have been studied using the density functional response theory in combination with the polarizable continuum model. It is shown that the dielectric medium has a rather small effect both on the bond length alternation and on the one-photon absorption spectrum, but it affects significantly the two-photon absorption cross section. It is found that both one- and two-photon absorptions are extremely sensitive to the planarity of the molecule, and the absorption intensity can be dramatically reduced by the conformation distortion. It has led to the conclusion that the experimentally observed anomalous solvent effect on the two-photon absorption of dialkylamino substituted distyrylbenzene chromophores cannot be attributed to the intrinsic properties of a single molecule and its interaction with solvents.

Two-photon absorption of [2.2]paracyclophane derivatives in solution: a theoretical investigation.

The two-photon absorption of a class of [2.2]paracyclophane derivatives has been studied using quadratic response and density functional theories. For the molecules investigated, several effects influencing the two-photon absorption spectra have been investigated, such as side-chain elongation, hydrogen bonding, the use of ionic species, and solvent effects, the latter described by the polarizable continuum model. The calculations have been carried out using a recent parallel implementation of the polarizable continuum model in the DALTON code. Special attention is given to those aspects that could explain the large solvent effect on the two-photon absorption cross sections observed experimentally for this class of compounds.

Parallelization of the integral equation formulation of the polarizable continuum model for higher-order response functions.

We present a parallel implementation of the integral equation formalism of the polarizable continuum model for Hartree-Fock and density functional theory calculations of energies and linear, quadratic, and cubic response functions. The contributions to the free energy of the solute due to the polarizable continuum have been implemented using a master-slave approach with load balancing to ensure good scalability also on parallel machines with a slow interconnect. We demonstrate the good scaling behavior of the code through calculations of Hartree-Fock energies and linear, quadratic, and cubic response function for a modest-sized sample molecule. We also explore the behavior of the parallelization of the integral equation formulation of the polarizable continuum model code when used in conjunction with a recent scheme for the storage of two-electron integrals in the memory of the different slaves in order to achieve superlinear scaling in the parallel calculations.