The DFT-D method is shown to yield interaction energies between biologically important groups to an accuracy comparable to that obtained using state-of-the-art ab initio methods.

We have performed reference quantum-chemical calculations for about 130 structures of adenine dimers in stacked conformations, with special attention given to dimers that are either vertically compressed (parallel structures) or contain close interatomic contacts (non-parallel structures). Such geometries are sampled during thermal fluctuations of nucleic acids and contribute to the local conformational variability of these systems. Their theoretical characterization requires a good description of interaction energies in the short-range repulsion region. The reference calculations have been performed with the CBS(T) method, i.e., MP2/CBS computations corrected for higher-order electron-correlation effects using the CCSD(T) method. These benchmark data have been used to examine the performance of the DFT-D, SCS(MI)-MP2, MP2.5, M06-2X and CBS(SCS-D) quantum-mechanical methods, and of the AMBER Cornell et al. force field. The present results, as well as those of our previous study on stacked uracil dimers, confirm that the force field severely exaggerates the repulsion at short intermolecular distances. This behavior complicates the use of the force field in scans of the stacking-energy dependence on local conformational parameters in nucleic acids. Compared against the previous results obtained in the uracil dimer study, the performance of DFT-D to describe stacking at short intermolecular distances has worsened, showing for the adenine dimers a larger exaggeration of the repulsion, especially for structures where the monomers are parallel to each other. Despite these deviations, the performance of DFT-D is still reasonably good and this method provides, for example, a relatively inexpensive way to monitor stacking energies along molecular dynamics trajectories. The best performers are the MP2.5, SCS(MI)-MP2, and CBS(SCS-D) methods. In addition, the energy profiles given by the SCS(MI)-MP2 and CBS(SCS-D) methods are the ones that most closely resemble the CBS(T) data. Interestingly, the performance of the SCS(MI)-MP2 method for stacked adenine dimers is better than for stacked uracil dimers, indicating that the quality of the description may vary with the nucleobase composition. Even though the SCS(MI)-MP2 method cannot match the speed of DFT-D, the results so far render it a promising tool to study intrinsic interactions in systems of moderate size. In general, for most applications all the QM methods tested here are of sufficient accuracy.

We describe the use of density functional theory (DFT-D) and semiempirical (AM1-D and PM3-D) methods having an added empirical dispersion correction, to treat noncovalent interactions between molecules involving sulfur atoms. The DFT-D method, with the BLYP and B3LYP functionals, was judged against a small-molecule database involving sulfur-π, S-H···S, and C-H···S interactions for which high-level MP2 or CCSD(T) estimates of the structures and binding or interaction energies are available. This database was also used to develop appropriate AM1-D and PM3-D parameters for sulfur. The DFT-D, AM1-D, and PM3-D methods were further assessed by calculating the structures and binding energies for a set of eight sulfur-containing base pairs, for which high-level ab initio data are available. The mean absolute deviations (MAD) for both sets of structures shown by the DFT-D methods are 0.04 Å for the intermolecular distances and less than 0.7 kcal mol(-)(1) for the binding and interaction energies. The corresponding values are 0.3 Å and 1.5 kcal mol(-)(1) for the semiempirical methods. For the complexes studied, the dispersion contributions to the overall binding and interaction energies are shown to be important, particularly for the complexes involving sulfur-π interactions.

Abstract:We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantummechanics (QM) methods. Nonparallel stacking geometries often occur in nucleic acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the shortrange repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been carried out using the MP2 method extrapolated to the complete basis-set limit and corrected for higher-order electron-correlation contributions using CCSD(T) calculations with a medium-sized basis set. These reference calculations have been used as benchmark data to test the performance of the DFT-D, SCS(MI)-MP2, and DFT-SAPT QM methods and of the AMBER molecular-mechanics (MM) force field. The QM methods show close to quantitative agreement with the reference data, albeit the DFT-D method tends to modestly exaggerate the repulsion of steric clashes. The force field in general also provides a good description of base stacking for the systems studied here. However, for geometries with close interatomic contacts and clashes, the repulsion effects are rather severely exaggerated. The discrepancy reported here should not affect the overall stability of MD simulations and qualitative applications of the force field. However, it may affect the description of subtle quantitative effects such as the local conformational variations in B-DNA. Preliminary calculations for two H-bonded uracil base pairs, including one with a C-H · · · O H-bond, indicate excellent performance of the tested QM methods for all intermonomer distances. The force field, on the other hand, is less satisfactory, especially in the repulsive regions.

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The electronic structure of molecular systems containing transition metal atoms is traditionally studied using methods based on density functional theory (DFT). Although such an approach has been quite successful, the treatment of large systems, be they transition metal complexes, bioinorganic molecules or the solid state, is still extremely computationally demanding at this level, and may not be practical for many systems of interest. In this paper we describe how semi-empirical MO methods can be used to overcome these computational bottlenecks, yet still provide predictions of the necessary accuracy. We describe strategies to achieve this by focussing on: (i) obtaining appropriate parameters for transition metal atoms via a genetic algorithm, to be used within a parallelised implementation of neglect of differential diatomic overlap (NDDO) methods, and (ii) the use of multilevel treatments which involve DFT and semi-empirical methods to describe different regions of the molecule. Here we show by reference to histidine and porphyrin complexes, the importance of a correct partitioning of the organic substrate. We illustrate the potential of such a dual level approach by reporting preliminary results showing the catalytic role of the enzyme, dimethyl sulfoxide reductase.

We report the comparative study of the electrochemical and photoluminescent properties of two Ir(iii) complexes described as [Ir(F2ppy)2(N^N)][PF6], where the F2ppy ligand is 2-(2,4-difluorophenyl)pyridine and the N^N ligands are pyrazino[2,3-f][1,10]phenanthroline (ppl) and pyrazino[2,3-f][4,7]phenanthroline (ppz). The complexes were used for the fabrication of light-emitting electrochemical cells (LECs). The structures of the complexes have been corroborated by X-ray crystallography. Theoretical calculations were performed to understand the photophysical behavior of the complexes. Both in solution and solid state, the photoluminescence spectra shows that emission is significantly red-shifted in the [Ir(F2ppy)2(ppz)][PF6] complex compared with the [Ir(F2ppy)2(ppl)][PF6] complex. Besides, the [Ir(F2ppy)2(ppl)][PF6] complex exhibits a higher quantum yield and a longer excited state lifetime than the [Ir(F2ppy)2(ppz)][PF6] complex; therefore, in the last case non-radiative decay is predominant due to the stabilization of LUMO orbital (energy gap law). In the fabrication of LEC devices with the [Ir(F2ppy)2(ppl)][PF6] complex, light emission was obtained with a maximum value of luminance equal to 177 cd m(-2), while in the case of the [Ir(F2ppy)2(ppz)][PF6] complex, no luminance was observed. According to the photophysical data, the performance in LEC devices could be explained by the different position of the nitrogens in the ppl and ppz structural isomers, electronically affecting the complex, and therefore its properties. In addition, from the crystallographic analysis it is possible to note that the [Ir(F2ppy)2(ppz)][PF6] complex shows enhanced intermolecular and intramolecular interactions compared with [Ir(F2ppy)2(ppl)][PF6], and consequently a higher ordering of the molecules in the complex with ppz ligand can be expected. This higher order could favour the quenching processes, and consequently enhance the non-radiative deactivation.

Density functional theory (DFT-D) and semi-empirical (PM3-D) methods having an added dispersion correction have been used to study stabilising carbohydrate-aromatic and amino acid-aromatic interactions. The interaction energy for three simple sugars in different conformations with benzene, all give interaction energies close to 5 kcal mol(-1). Our original parameterization of PM3 (PM3-D) seriously overestimates this value, and has prompted a reparametrization which includes a modified core-core interaction term. With two additional parameters, the carbohydrate complexes, as well as the S22 data set, are well reproduced. The new PM3 scheme (PM3-D*) is found to describe the peptide bond-aromatic ring interactions accurately and, together with the DFT-D method, it is used to investigate the interaction of six amino acids with pyrene. Whilst the peptide backbone can adopt both stacked and T-shaped structures in the complexes with similar interaction energies, there is a preference for the unsaturated ring to adopt a stacked structure. Thus, peptides in which the latter interactions are maximised are likely to be the most effective for the functionalisation of carbon nanotubes.