Search

Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag(+) is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg(2+). In contrast to prior studies of Ag(+) incorporation into double-stranded DNA, we remove the constraints of Watson-Crick pairing by focusing on homo-base DNA oligomers of the canonical bases. High resolution electro-spray ionization mass spectrometry reveals an unanticipated Ag(+)-mediated pairing of guanine homo-base strands, with higher stability than canonical guanine-cytosine pairing. By exploring unrestricted binding geometries, quantum chemical calculations find that Ag(+) bridges between non-canonical sites on guanine bases. Circular dichroism spectroscopy shows that the Ag(+)-mediated structuring of guanine homobase strands persists to at least 90 °C under conditions for which canonical guanine-cytosine duplexes melt below 20 °C. These findings are promising for DNA nanotechnology and metal-ion based biomedical science.

Electronic circular dichroism (ECD) is a powerful spectroscopy method for investigating chiral properties at the molecular level. ECD calculations with the commonly used linear-response time-dependent density functional theory (LR-TDDFT) framework can be prohibitively costly for large systems. To alleviate this problem, we present here an ECD implementation within the projector augmented-wave method in a real-time-propagation TDDFT framework in the open-source GPAW code. Our implementation supports both local atomic basis sets and real-space finite-difference representations of wave functions. We benchmark our implementation against an existing LR-TDDFT implementation in GPAW for small chiral molecules. We then demonstrate the efficiency of our local atomic basis set implementation for a large hybrid nanocluster and discuss the chiroptical properties of the cluster. [ABSTRACT FROM AUTHOR]

The interaction between metal atoms and nucleobases has been a topic of high interest due to the wide scientific and technological implications. Combining density functional theory simulations with a literature overview, we achieved an exhaustive study of the ground state electronic properties of DNA/RNA nucleobases interacting with gold and silver atoms at three charge states: neutral, cationic, and anionic. We describe the nature of the stability and electronic properties in each hybrid metallic structure. In addition to the metal interacting with the five isolated nucleobases, we included their respective DNA-WC base pairs and one case with the protonated sugar-phosphate backbone. As a general trend, we discerned that the energetic ordering of isomers follows simple electrostatic rules as expected from previous studies. Also, we found that although the metal localizes almost all of the extra charge in the anionic system, a donation of charge is shared almost equally in the cationic system. Furthermore, the frontier orbitals of the cationic system tend to have more effects from the pairing and inclusion of the backbone than the anionic system. Finally, the electronic gap varies greatly among all of the considered structures and could be further used as a fingerprint when searching DNA-metal hybrid structures.

We present density functional theory (DFT) calculations of atomic ionization potentials and lattice constants of simple solids from low atomic numbers Z to the large-Z limit. We compare different kinetic energy functional approximations [Kohn-Sham (KS) vs simple orbital-free functionals] and, in the case of orbital free, also different methods for including the nuclear potential (all-electron with the projector augmented wave method vs local pseudopotentials). For both ionization potentials and lattice constants, all-electron orbital-free DFT does yield the general trend of KS DFT for moderate values of the atomic number Z. For large values of Z, all-electron orbital-free DFT deviates from the KS DFT results. Local pseudopotentials give a better qualitative description by adding shell oscillations to the orbital-free DFT model. We show that both all-electron orbital-free DFT and KS DFT have a finite value for nonrelativistic lattice constants in the large-Z limit. [ABSTRACT FROM AUTHOR]

Our manuscript investigates a self-consistent solution of the statistical atom model proposed by Berthold-Georg Englert and Julian Schwinger (the ES model) and benchmarks it against atomicKohn- Sham and two orbital-free models of the Thomas-Fermi-Dirac (TFD)-1/5vW family. Results show that the ES model generally offers the same accuracy as the well-known TFD-λ vW model; however, the ES model corrects the failure in the Pauli potential near-nucleus region.We also point to the inability of describing low-Z atoms as the foremost concern in improving the present model. [ABSTRACT FROM AUTHOR]

In this paper, we obtain the energy band positions of amorphous carbon (a-C) surfaces in vacuum and in aqueous environment. The calculations are performed using a combination of (i) classical molecular dynamics (MD), (ii) Kohn-Sham density functional theory with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional, and (iii) the screened-exchange hybrid functional of Heyd, Scuseria, and Ernzerhof (HSE). PBE allows an accurate generation of a-C and the evaluation of the local electrostatic potential in the a-C/water system, HSE yields an improved description of energetic positions which is critical in this case, and classical MD enables a computationally affordable description of water. Our explicit calculation shows that, both in vacuo and in aqueous environment, the a-C electronic states available in the region comprised between the H2/H2O and O2/H2O levels of water correspond to both occupied and unoccupied states within the a-C pseudogap region. These are localized states associated to sp² sites in a-C. The band realignment induces a shift of approximately 300 meV of the a-C energy band positions with respect to the redox levels of water. [ABSTRACT FROM AUTHOR]

We present a computational scheme for orbital-free density functional theory (OFDFT) that simultaneously provides access to all-electron values and preserves the OFDFT linear scaling as a function of the system size. Using the projector augmented-wave method (PAW) in combination with real-space methods, we overcome some obstacles faced by other available implementation schemes. Specifically, the advantages of using the PAW method are twofold. First, PAW reproduces all-electron values offering freedom in adjusting the convergence parameters and the atomic setups allow tuning the numerical accuracy per element. Second, PAW can provide a solution to some of the convergence problems exhibited in other OFDFT implementations based on Kohn-Sham (KS) codes. Using PAW and real-space methods, our orbital-free results agree with the reference all-electron values with a mean absolute error of 10 meV and the number of iterations required by the self-consistent cycle is comparable to the KS method. The comparison of all-electron and pseudopotential bulk modulus and lattice constant reveal an enormous difference, demonstrating that in order to assess the performance of OFDFT functionals it is necessary to use implementations that obtain all-electron values. The proposed combination of methods is the most promising route currently available. We finally show that a parametrized kinetic energy functional can give lattice constants and bulk moduli comparable in accuracy to those obtained by the KS PBE method, exemplified with the case of diamond. [ABSTRACT FROM AUTHOR]

Ligand-stabilized aluminum clusters are investigated by density functional theory calculations. Analysis of Kohn-Sham molecular orbitals and projected density of states uncovers an electronic shell structure that adheres to the superatom complex model for ligand-stabilized aluminum clusters. In this current study, we explain how the superatom complex electron-counting rule is influenced by the electron-withdrawing ligand and a dopant atom in the metallic core. The results may guide the prediction of new stable ligand-stabilized (superatom) complexes, regardless of core and electron-withdrawing ligand composition. [ABSTRACT FROM AUTHOR]

The density-functional theory computations and powder X-ray crystallography are applied to study the structural, electronic, and optical properties of the thiolate-protected [Au.sub.38][(SR).sub.24] cluster. The study demonstrated a new mechanism for the strong chiral response of thiolate-protected gold clusters with achiral metal cores and ligands.

Near-infrared and Raman spectroscopy and time-dependent density functional calculations are used for characterizing gold clusters protected with iron-carbonyl ligands. The results have shown that these novel compounds bear many analogues to another class of gold clusters and this has added new dimension to the rich chemistry of gold-based clusters that is characterized as molecular metals.