Accuracy of dispersion interactions in semiempirical and molecular mechanics models: the benzene dimer case.

The benzene dimer is arguably the simplest molecular analogue of graphitic materials. We present the systematic study of minima and transition states of the benzene dimer with semiempirical and molecular mechanics (MM) methods. Full minimizations on all conformations were performed and the results, geometries, and binding energies were compared with CCSD(T) and DFT-D results. MM yields the best results with three force fields MM3, OPLS, and AMOEBA, which reproduced nine out of the ten stationary points of the benzene dimer. We obtained new parameters for MM3 and OPLS that successfully reproduce all structures of the benzene dimer and showed improved accuracy over DFT-D in most dimer geometries. Semiempirical models were, unexpectedly, less accurate than MM methods. The most accurate semiempirical method for the benzene dimer is PM6-DH2. DFT-D was the only Hamiltonian that reproduced the variations of energy with geometry from CCSD(T) calculations accurately and is the method of choice for energies of periodic and molecular calculations of graphitic systems. In contrast, MM represents an accurate alternative to calculate geometries.

New parameterization scheme of DFT-D for graphitic materials.

A new parametrization scheme of DFT-D is proposed with the aim of devising a methodology for the study of graphitic material. The main feature of the new system is the geometry optimization within the fitting scheme. The DFT-D parameters are obtained for the benzene dimer, a good model molecule for graphitic systems. Very accurate CCSD(T) results are used as reference data for the benzene dimer, and the new method is shown to reproduce accurately its binding energies with small basis sets. After geometry optimization our new scheme performs better than the other methods. This approach generates proper geometries and accurate binding energies, even with small basis sets. We can expect this method to give similarly good results for larger graphitic systems.

A computational analysis of the insertion of carbon nanotubes into cellular membranes.

Carbon nanotubes have been proposed to serve as nano-vehicles to deliver genetic or therapeutic material into the interior of cells because of their capacity to cross the cell membrane. A detailed picture of the molecular mode of action of such a delivery is, however, difficult to obtain because of the concealing effects of the cell membrane. Here we report a systematic computational study of membrane insertion of individual carbon nanotubes and carbon nanotube bundles using two entirely different and unrelated techniques. First a static scan of the environmental free energy is carried out based on a membrane mimicry approach and different insertion geometries are assessed. Then the dynamics is investigated with a coarse-grained approach that was previously used in the study of the integration dynamics of nanoparticles into the bilayer. The results of both models point, for unfunctionalized carbon nanotubes, at a preference for the horizontal orientation inside the internal hydrophobic layer of the cell membrane. Finally, the energetics of the formation of bundles of carbon nanotubes is studied. The cellular membrane promotes aggregation of carbon nanotubes in its hydrophobic core and modifies the structural stability of the bundles.

Some Comments on Topological Approaches to the π-Electron Currents in Conjugated Systems.

Within the past two years, three sets of independent authors (Mandado, Ciesielski et al., and Randic) have proposed methods in which π-electron currents in conjugated systems are estimated by invoking the concept of circuits of conjugation. These methods are here compared with ostensibly similar approaches published more than 30 years ago by two of the present authors (Gomes and Mallion) and (likewise independently) by Gayoso. Patterns of bond currents and ring currents computed by these methods for the nonalternant isomer of coronene that was studied by Randic are also systematically compared with those calculated by the Hückel-London-Pople-McWeeny (HLPM) "topological" approach and with the ab initio, "ipso-centric" current-density maps of Balaban et al. These all agree that a substantial diamagnetic π-electron current flows around the periphery of the selected structure (which could be thought of as a "perturbed" [18]-annulene), and consideration is given to the differing trends predicted by these several methods for the π-electron currents around its central six-membered ring and in its internal bonds. It is observed that, for any method in which calculated π-electron currents respect Kirchhoff's Laws of current conservation at a junction, consideration of bond currents-as an alternative to the more-traditional ring currents-can give a different insight into the magnetic properties of conjugated systems. However, provided that charge/current conservation is guaranteed-or Kirchhoff's First Law holds for bond currents instead of the more-general current-densities-then ring currents represent a more efficient way of describing the molecular reaction to the external magnetic field: ring currents are independent quantities, while bond currents are not.

Molecular dynamics simulations of mouse ferrochelatase variants: what distorts and orientates the porphyrin?

Molecular dynamics simulations of the wild-type and variant forms of the mouse ferrochelatase in complex with the product (haem) have been performed using the GROMOS96 force field, in the NpT ensemble. Ferrochelatase, the last enzyme in the catalytic pathway of the haem biosynthesis, catalyses the reaction of insertion of a ferrous ion into protoporphyrin IX by distorting the planar geometry of the latter reactant. The simulations presented aim at understanding the role of active-site residues in this catalytic process. Analysis of the simulation trajectories explains the consequences of the mutations introduced and sheds more light on the role of the His209 residue in porphyrin macrocycle distortion. The function of residues coordinating propionate groups of the haem molecule is discussed in terms of stability of the substrate and product complexes.

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes.

A set of 44 Zinc-ligand bond-lengths and of 60 ligand-metal-ligand bond angles from 10 diverse transition-metal complexes, representative of the coordination spheres of typical biological Zn systems, were used to evaluate the performance of a total of 18 commonly available density functionals in geometry determination. Five different basis sets were considered for each density functional, namely two all-electron basis sets (a double-zeta and triple-zeta formulation) and three basis sets including popular types of effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden. The results show that there are presently several better alternatives to the popular B3LYP density functional for the determination of Zn-ligand bond-lengths and angles. BB1K, MPWB1K, MPW1K, B97-2 and TPSS are suggested as the strongest alternatives for this effect presently available in most computational chemistry software packages. In addition, the results show that the use of effective-core potentials (in particular Stuttgart-Dresden) has a very limited impact, in terms of accuracy, in the determination of metal-ligand bond-lengths and angles in Zinc-complexes, and is a good and safe alternative to the use of an all-electron basis set such as 6-31G(d) or 6-311G(d,p).

QM/QM study of the coverage effects on the adsorption of amino-cyclopentene at the Si(100) surface.

In this work, we have tested 30 different adsorption situations in several coverage scenarios for the 1-amino-3-cyclopentene (ACP) molecule on the Si(100) surface. We have used a five-spot testing zone inserted in the high-level part of a quantum-mechanical/quantum-mechanical study performed in a big cluster. By defining several different scenarios, each one with a typical adsorption energy, we were able to understand in detail the process of surface functionalization. We are able to justify why the functionalization of this silicon surface achieves only a coverage of approximately 0.5 ML (half monolayer) and why the completely covered surface should be thermodynamically impossible to obtain.

Molecular dynamics study of the calcium ion transfer across the water/nitrobenzene interface.

A study on the calcium ion transfer across the water/nitrobenzene interface is presented. The potential of mean force was calculated and a good agreement was found between the experimental and the calculated free energy of transfer. This is a monotonically increasing function of the distance to the interface, and the process was found to be non-activated. The evolution of the first and second hydration shells was analysed as a function of the distance to the interface; the first hydration shell remains intact whereas the second hydration shell suffers a severe water loss. Water finger formation was also found, with behaviour similar to that already described for other ions in different interfaces. As far as we know, a direct comparison between the calculated number of water molecules dragged with an ion into the organic phase and the experimental results is presented for the first time and a very good agreement was found.