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We present an experimental study supported by molecular simulations of the influence of the shape of alkyl side groups on the interactions and self-organization of supramolecular assemblies, built from bis-urea-substituted toluene molecules deposited on Au(111) surfaces. In particular, we demonstrate the crucial importance of the presence of branched alkyl groups (i.e., ethylhexyl) that allow two adjacent supramolecular polymers to arrange closer to each other, leading to the formation of molecular “zippers”. Thus, steric constraints at the level of individual molecules can generate improved ordering between neighboring supramolecular polymers interacting with a planar substrate.

This Account presents recent advances in the design, synthesis, characterization, and potential applications of new hybrid materials based on carbon nanotube and electron donors. Fast charge separation and slow charge recombination are consistently observed in a variety of composites that contain porphyrin derivatives. The ultimate goal of using these systems to prepare practical photoelectrochemical devices is discussed, and a cell with a monochromatic efficiency of 8.5% conversion of light into current is illustrated.

We simulate the structure and dynamics of the four DNA bases on the most stable gold surface. The experimental adsorption energies are reproduced to about 1 kcal mol^-1, and the existence of anchor points in the molecules is evidenced. The simulations also show that the bases drift on the gold surface with a degree of mobility that is not inversely proportional to the experimental (and calculated) desorption energies. When the same type of calculations is applied to pairs of bases it is seen that for at least two of them, namely GG and TT, there is a cooperative effect that increases their adsorption energy with respect to those of the single molecules. The molecular mobility on the surface is still present when a pair of interacting bases is considered.

The combination of the hydrophobic fullerene core with hydrophilic functional groups of both ionic and nonionic nature produces organized structures with sizes that range from nanometer to micrometer length scales. The driving force toward this spontaneous organization is the amphiphilic character of the fullerene derivatives. To control both shape and size of the supramolecular assemblies and ultimately their function, important parameters that must be tuned are (i) the balance between the hydrophobic and the hydrophilic moieties, (ii) the effect of the environment, typically provided by simple solvents, (iii) the interface on which the aggregation occurs or, more precisely, surface templating effects, and (iv) the solvation process.

The adsorption of alkanes on a gold substrate is simulated by a simple computational scheme that combines the “glue model” for gold, a standard force field for alkanes, and a combination of the charge equilibration model and the Born−Mayer potential for their interaction. The adsorption energies of 10 short chains on the Au(111) surface are reproduced with an average error of less than 1 kcal mol^-1. The results allow extension of the use of the model to investigate the appeareance/disappeareance of ordered deposition on gold of longer alkanes. The unexpected transition to disorder occurs for chains between 18 and 26 carbon atoms and has been ascribed to the mismatch between the Au(111) lattice and the CH2 group periodicity, a feature that here is shown to hinder the formation of short, i.e., docking, C−Au distances.

Thin films of a benzylic amide macrocycle, the common component of a wide class of mechanically interlocked molecules, are prepared by vapor deposition on Au(111). The films are characterized by monochromated X-ray photoelectron spectroscopy (XPS) and high resolution electron energy loss spectroscopy (HREELS). The relative amounts of carbon, nitrogen, and oxygen are consistent with the formation of intact molecular species. At monolayer coverage, the relative intensity of out-of-plane to in-plane phenyl ring vibrational modes indicates that the macrocycle adopts a nearly flat-lying conformation. The formation of a chemisorption bond is evidenced by the presence of a Au−O stretching vibration and a low binding energy component in the O 1s core level region assigned to interfacial bonding. A decrease in film order and the absence of a preferred molecular orientation is observed at higher coverages. Computer modeling of the adsorption of the macrocycle on the surface rationalizes the experimental observations.

We show the spontaneous fabrication of organized structures with multiple lengthscales from a solution of rotaxanes cast onto a holey mesh in contact with a substrate. The mesh controls the spatial distribution of deposited material on a micrometer scale. The borders around a hole in the mesh pin the solution, and dewetting within the hole generates droplets of rotaxane with nanometer length scale. The droplet size is controlled by the radial concentration profile.

A thin film formed by an amphiphilic catenane is shown to exhibit bistable behavior. The film is grown by self-assembly from two different solutions onto a mica surface. Self-recognition of the solute molecules by the first monolayer of the adsorbed molecules drives the switch between two co-conformations, characterized by different polar character, which are nearly degenerate once deposited on the surface. The phenomenon takes the form of a wetting/dewetting transition and propagates the intramolecular change to the mesoscopic scale.

Calculated binding energies and spectroscopic properties of C70 dimers are presented. The two most stable isomers of the set of conceivable [2 + 2] cycloaddition products are isoenergetic, and both are compatible with NMR, infrared, and Raman data on the product recently synthesized by Lebedkin et al.

Application of the continuous symmetry measure to several hundred crystals that contain benzene, dichloromethane, chloroform, and acetone shows that the probability of finding the structures of these molecules distorted decreases exponentially with the amount of symmetry lowering. The implications of this trend are discussed in terms of B3LYP/6-31G* calculations and Boltzmann population.

Calculations of the relative stability of C118, C119, and C120, pure carbon species with both trivalent and tetravalent atoms, show the interplay between the various forms of molecular carbon and under which conditions they are thermodynamically accessible. The analysis is performed by quantum chemical screening of all the classical fullerenes with isolated pentagons (8148 isomers for C118 and 10774 isomers for C120) for comparison with the most stable structure of C119 and C60 dimer. While fullerenes show similar trends of stability over a range of temperatures, introduction of sp³ carbons profoundly affects them. It is concluded that very high synthetic temperatures may favor formation of clusters with tetravalent atoms.

¹³C NMR chemical shifts and relative energies of eight C119 isomers are calculated within the density-functional-based tight-binding (DFTB) and the IGLO-DFTB (individual gauge for local orbitals) models. The calculated ¹³C NMR pattern of one C2 isomer differs considerably from those of other candidates and has a close match with the spectrum of the experimental species. This isomer has also the lowest energy of those studied.

Optimisation of geometries of all 40 fullerene isomers of C40, using methods from molecular mechanics and tight-binding to full abinitio SCF and DFT approaches, confirms minimisation of pentagon adjacency as a major factor in relative stability. The consensus predictions of 11 out of 12 methods are that the isomer of lowest total energy is the D2 cage with the smallest possible adjacency count, and that energies rise linearly with the number of adjacencies. Quantum mechanical methods predict a slope of 80–100 kJ mol-1 per adjacency. Molecular mechanics methods are outliers, with the Tersoff potential giving a different minimum and its Brenner modification a poor correlation and much smaller penalty.

The DFTB (density-functional based tight-binding) method is used as a basis for simulating ¹³C NMR spectra of fullerenes and fullerene molecules. Magnetic shieldings are computed as sums of orbital contributions with the IGLO (individual gauge for local orbitals) method. This method is applied to the experimentally characterized fullerenes from C60 to C84. With one scaling parameter, qualitative agreement with experimental patterns and discrimination between alternative isomeric possibilities are achieved. A correlation between local geometry and calculated shift for atoms in pentagon sites is reported.

The effects of the introduction of a cis linkage in the simplest polyenic chain containing both a cis and a trans bond on its spectroscopy are studied by using extensive ab initio calculations of the vibronically induced transition moments to the lowest excited singlet state and the first- and second-order vibronic coupling matrix elements between the lowest electronic states. It is shown that the effect of lowering the symmetry from C2h to Cs is less important than that of vibronic coupling between the lower electronic states. As a result, the S1 ← S0 excitation spectrum is found to be dominated by bands arising from Herzberg−Teller borrowing. Support for this conclusion is found in the comparison of the theoretically predicted spectrum with excitation spectra in the solid state and by calculation of the first-order vibronic coupling matrix elements between S1 and S2. The well-known S0−S1 coupling, which leads to the frequency inversion of the completely in-phase C&dbd;C bond stretching vibration between the two states in all-trans polyenes, is shown to spread over several C&dbd;C bond stretching vibrations. Finally, it is found that the second-order S1−S2 couplings are not particularly affected in the isomerized molecule, in agreement with previous calculations that showed them in all-trans-octatetraene to be linked to stringlike behavior.

The electrochemistry of a benzylic amide [2]catenane was investigated and compared to that of its topologically trivial components. The redox behavior of both the catenane and the uninterlocked macrocycle can be largely understood in terms of the electrochemistry of smaller molecular fragments and simple molecular orbital considerations that show that the electroactivity of the C&dbd;O groups is split into two sets of quasi-degenerate potentials separated by a substantial gap. A fast intermolecular reaction follows the reduction of the macrocycle and smaller fragments, consistent with the corresponding dimers containing a new C−C bond linking two reduced carbonyls. The cyclic voltammetric behavior of the catenane differs significantly from that of the macrocycle&sbd;a feature that must therefore be directly attributable to the mechanically interlocked molecular architecture of the catenane. In particular, an intramolecular reaction (irreversible in the CV time scale) occurs in the catenane, which is shown to be a function of temperature and scan rate. Simulation of the cyclic voltammograms shows that the intramolecular reaction occurs on a time scale wider than that of circumrotation of the two rings in the neutral molecule, thus excluding that cyclic voltammetry (CV) is monitoring the latter process. Both the analysis of the electrochemical data and semiempirical quantum chemical (MNDO) calculations would suggest that the electrochemically induced reaction in the catenane is the soldering of the two interlocked macrocycles:  the formation of a C−C bond between two reduced carbonyl groups would thus prevent further rotation of the two interlocked rings.

The energetic costs of widening the classical fullerene definition to include carbon cages with octagonal as well as pentagonal and hexagonal faces are investigated theoretically. Relative energies of all 16 C40 and 620 C48 cages that can be assembled with one face octagonal, 14 pentagonal and all others hexagonal are calculated within two independent semi-empirical models and compared with the 295 C40 and 2664 C48 one-square, one-heptagon and classical-fullerene cages. All isomers are lo-cal minima on the potential surface, and many non-classical structures fall within the energy range spanned by the classical fullerenes. Penalties for introduction of a single non-classical face increase in the order heptagon < square < octagon, estimated for C48 as 58-123, 108-236, and 329-450 kJ mo-1, respectively, depending on model. The energy variation across the range of classical and non-classical structures is rationalised by extension of the isolated-pentagon rule: when 1

We report here the first results on the thin-film growth of benzylic amide catenanes. The films were deposited onto gold single crystals by two different methods: by sublimation under ultra-high vacuum and by dipping of the substrate into a solution of the catenane. Sublimation yielded well-ordered films (domain diameter ∼100 A˚) while dipping produced disordered films. The vibrational and electronic properties of these films were investigated by high-resolution electron energy loss spectroscopy (HREELS) as a function of film thickness. The vibrational spectra indicate that the first layer of catenanes is chemisorbed.

The 2:1 inclusion complex of p-tert-butylcalix[4]arene and p-xylene was investigated by a combination of inelastic neutron scattering, INS, experiments and MM3 molecular mechanics calculations. Since the INS spectrum depends only on the vibrational frequencies and the form of the normal modes, the reasonable agreement between experiments and calculations shows that they can be simulated by the MM3 model. Further it validates the use of MM3 to search for possible spectral signatures of a hypothetical 1:1 inclusion complex and for a partial study of the p-xylene dynamics within the cage. The latter is accomplished by locating the transition state of a complicated motion of the guest molecule inside the cavity. Transition-state theory is used to calculate the temperature-dependent rate constants, and subnanosecond time scales are obtained.

A combination of topological and quantum mechanical techniques is used to predict the energetically favored isomer set for the experimentally detected but as yet uncharacterized C116 fullerene. A systematic search and calculation at the QCFF/PI (quantum-consistent force field/π) semiempirical level of the energies of the 6063 isomers of C116 that satisfy the isolated-pentagon rule (IPR) find that the isomers in the most stable group have low degrees of eccentricity and are predicted by the highly discriminating hexagon-neighbor rule (HNR), for which a more generally applicable formulation is proposed.

Infrared and Raman spectroscopies along with molecular orbital calculations are used to study&sbd;for the first time&sbd;the vibrational motions of a topologically complicated chemical system, namely a [2]catenane of the benzylic amide type. Because of the intrinsic line width of the spectra, comparison of experiments and theory is only partially successful. The insight given by the simulations&sbd;which show that the C&dbd;O normal modes are delocalized while the N−H modes are localized&sbd;is, however, useful and makes us propose a simple model that explains both the larger line width of the spectra of the catenane with respect to those of the parent macrocycle and the great sensitivity of the infrared spectrum of the catenane to the environment. Examples of such sensitivity are the frequency shifts observed upon going from KBr to CsI, features not present in the case of the macrocycle.

Model semiempirical studies using quantum consistent force field/π (QCFF/PI) and density functional tight binding (DFTB) methods show the C20 dodecahedral fullerene to have the lowest energy of all 7595 mathematically possible 20-vertex trivalent polyhedral cages by a substantial margin (estimated at 521 (QCFF/PI) or 125 (DFTB) kJ mol^-1). A topological invariant based on the distribution of face sizes is used to correlate the energies and predict the best polyhedral structure for C22, which must be a nonfullerene cage. With 1 square, 10 pentagonal, and 2 hexagonal faces, this structure is verified to be more stable (by 259 (QCFF/PI), 60 (DFTB) kJ mol^-1) than its nearest trivalent polyhedral rival.

The accuracy of two density functional derived models&sbd;BLYP/6-31G* and B3LYP/6-31G*&sbd;is tested to calculate the molecular response to slow neutrons and infrared photons in a series of oligomers of thiophene. In the first type of experiment, the response is a function of the vibrational frequencies and the shapes of the normal modes; in the second, knowledge of the dipole moment surface is also necessary. The combination of the two simulations allows one to conclude that both models give fairly accurate vibrational frequencies and normal modes but may overestimate the infrared response in large systems. For this spectroscopy, BLYP/6-31G* and B3LYP/6-31G* find all the modes present in the experiment to be active. A few modes with modest activity are also calculated to appear strongly in the spectrum. Scaling of the force fields shows the complementary roles of the two methods. BLYP/6-31G* is very accurate&sbd;scaling factor of 1.00&sbd;in the calculation of the Cα−Cβ, Cα−Cα, and HCC force constants, and B3LYP/6-31G* does not require scaling of CS, SCC, CCC, and CSC force constants. On the basis of the combined use of the two models, a simple procedure is proposed that should give good agreement with experimental results of conjugated systems.

We predict that push−pull Buckminsterfullerenes have a high nonlinear optical response that makes pursuing their synthesis worthwhile. Three different semiempirical quantum chemical models concur to show that some isomers of push−pull C60 have a static first-order hyperpolarizability, β, comparable to or larger than that of all-trans 4-(dimethylamino)-4‘-nitrodiphenyloctatetraene. Because of the geometrical structure of push−pull Buckminsterfullerenes, standard models that explain the high response in planar conjugated systems cannot be used. Rather, it is found that conjugation and inductive effects contribute at the same time to β and the separation between the nitrogen-containing groups cannot fully simulate the results of the calculations. Although these complicated materials do not easily lend themselves to simple modeling, some of the correlations of β with electronic energies, dipole moments, bond orders, and other quantities of physical interest allow us to sift through the different contributions and partially simulate the relative ordering of the hyperpolarizabilities of the various isomers. A simple perturbation approach based on icosahedral C60 further confirms the results obtained by the correlations and warrants the search of a topological model able to account for the response. It is found that a linear relation exists between β and the shortest resonant paths between the grafting groups. Two types of resonant structures contribute. They are described in terms of single−double bond alternation. The first resonant structure starts and finishes with hexagon-hexagon alternation (i.e., double bonds) and contributes positively, the second starts and finishes with pentagon−hexagon (i.e., single bonds) and contributes negatively. The ratio of their contributions is roughly two to one.

Simulations of the solid-state structures of single-wall carbon nanotubes show that once a chiral twisting of a tube is included the interactions with the nearest tubes lock it in place. Comparison with experiments and implications for the catalytic activity of these new materials are discussed.

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