Optical absorption in complexes of abasic DNA with noble-metal nanoclusters by first principles calculations.

Abasic sites (AP site) in a DNA duplex have been experimentally used to produce fluorescent Ag nanoclusters (NC) with a small number of atoms (n ≤ 6). These AP-DNA:NC complexes act as biological makers that help to locate genes associated with diseases related to single nucleotide polymorphisms (SNP), for example. Abasic sites are the most common SNP genetic variation, and their detection may help predict a host of genetically determined diseases. In this work, we report a theoretical study of the optical absorption spectra of AP-DNA:Ag4 and AP-DNA:Au4 complexes using a fully ab initio methodology. We consider several different base environments for the noble-metal nanocluster occupying the AP site, and compute the absorption spectra of sixteen AP-DNA:Ag4 and sixteen AP-DNA:Au4 complexes. We find that optical absorption in the AP-DNA:Ag4 complexes tends to concentrate in the green-to-violet range of frequencies (2.50 eV ≤ hω ≤ 3.2 eV) and that AP-DNA:Au4 complexes display absorption peaks in the violet-to-ultraviolet interval (hω ≥ 3.0 eV). An analysis of the optical absorption mechanisms in these complexes shows that they can be of local, charge-transfer, or hybrid nature, i.e., AP-DNA:NC complexes display the full variety of optical absorption processes in molecular systems. In particular, we identify both charge-transfer and hybrid processes involving several DNA bases surrounding the NC. Importantly, we find that even sequences where the Ag4 cluster is not in a guanine rich neighborhood display absorption peaks in the visible-light spectrum. Moreover, we obtain that the maximum intensities of the absorption peaks in complexes with pyrimidine vacancies are generally higher than those in complexes with purine vacancies. Regarding the selectivity of single-vacancy AP-DNA to specific noble-metal nanocluster sizes, our calculations show that the four-atom Ag4 (Au4) species fits naturally and binds into the AP-site in a single-vacancy AP-DNA.

Charge-transfer optical absorption mechanism of DNA:Ag-nanocluster complexes.

Optical properties of DNA:Ag-nanoclusters complexes have been successfully applied experimentally in Chemistry, Physics, and Biology. Nevertheless, the mechanisms behind their optical activity remain unresolved. In this work, we present a time-dependent density functional study of optical absorption in DNA:Ag_{4}. In all 23 different complexes investigated, we obtain new absorption peaks in the visible region that are not found in either the isolated Ag_{4} or isolated DNA base pairs. Absorption from red to green are predominantly of charge-transfer character, from the Ag_{4} to the DNA fragment, while absorption in the blue-violet range are mostly associated to electronic transitions of a mixed character, involving either DNA-Ag_{4} hybrid orbitals or intracluster orbitals. We also investigate the role of exchange-correlation functionals in the calculated optical spectra. Significant differences are observed between the calculations using the PBE functional (without exact exchange) and the CAM-B3LYP functional (which partly includes exact exchange). Specifically, we observe a tendency of charge-transfer excitations to involve purines bases, and the PBE spectra error is more pronounced in the complexes where the Ag cluster is bound to the purines. Finally, our results also highlight the importance of adding both the complementary base pair and the sugar-phosphate backbone in order to properly characterize the absorption spectrum of DNA:Ag complexes.

Room temperature compressibility and diffusivity of liquid water from first principles.

The isothermal compressibility of water is essential to understand its anomalous properties. We compute it by ab initio molecular dynamics simulations of 200 molecules at five densities, using two different van der Waals density functionals. While both functionals predict compressibilities within ~30% of experiment, only one of them accurately reproduces, within the uncertainty of the simulation, the density dependence of the self-diffusion coefficient in the anomalous region. The discrepancies between the two functionals are explained in terms of the low- and high-density structures of the liquid.