Search results for "DFT"

Optimizing the SYBR green related cyanine dye structure to aim for brighter nucleic acid visualization

2022

In recent years, the studies of RNA and its use for the development of RNA based vaccines have increased drastically. Although cyanine dyes are commonly used probes for studying nucleic acids, in a wide range of applications, there is still a growing need for better and brighter dyes. To meet this demand, we have systematically studied the structure of SYBR green-related cyanine dyes to gain a deeper understanding of their interactions with biomolecules especially how they interact with nucleic acids and the structural components which makes them strongly fluorescent. Herein, five new dyes were synthesized, and their photophysical properties were evaluated. Observations of photophysical cha…

Identification of mixed bromidochloridotellurate anions in disordered crystal structures of (bdmim)2[TeX2Y4] (X, Y = Br, Cl; bdmim = 1-butyl-2,3-dime…

2014

The discrete mixed [TeBrxCl6−x]2− anions in their disordered crystal structures have been identified by using the phases prepared by the reaction of 1-butyl-2,3-dimethylimidazolium halogenides (bdmim)X with tellurium tetrahalogenides TeX4 (X = Cl, Br) as examples. Homoleptic (bdmim)2[TeX6] [X = Cl (1), Br (2)] and mixed (bdmim)2[TeBr2Cl4] (3), and (bdmim)2[TeBr4Cl2] (4) are formed depending on the choice of the reagents, and their crystal structures have been determined by single-crystal X-ray diffraction. The coordination environments of tellurium in all hexahalogenidotellurates are almost octahedral. Because of the crystallographic disorder, the mixed [TeBr2Cl4]2− and [TeBr4Cl2]2− anions …

Calculation of magnetic coupling constants with hybrid density functionals

2013

The currently available computational methods for the calculation of magnetic coupling constants with density functional theory have been reviewed. These methods include modern approximations to the exchangecorrelation functional, such as hybrid, range-separated and double-hybrid functionals, as well as approaches to treat the severe spin symmetry problems encountered in density functional calculations of magnetic interactions. In addition to the commonly used unrestricted Kohn–Sham formalism, density functional methods based on multireference wave functions and ensemble densities are also discussed. Performance of these models based on various studies has been summarized. The results indic…

Direct detection of 17O NMR in [Gd(DOTA)]- by NMR Spectroscopy

2015

The 17O NMR spectrum of the non-coordinated carboxyl oxygen in the GdIII-DOTA (DOTA = tetraazacyclododecanetetraacetic acid) complex has been observed experimentally. Its line width is essentially unaffected by paramagnetic relaxation due to gadolinium, and is only affected by the quadrupole pathway. The results are supported by the relevant parameters (hyperfine and quadrupole coupling constants) calculated by relativistic DFT methods. This finding opens up new avenues for investigating the structure and reactivity of paramagnetic GdIII complexes used as contrast agents in magnetic resonance imaging.

Structural and electronic properties of ion-exchangeable layered perovskites

2013

The modification of metal oxide surfaces with organic moieties has been widely studied as a method of preparing organic-inorganic hybrid materials for various applications. Among inorganic oxides, the ion-exchangeable layered perovskites, materials composed by perovskite-like slabs (ABO3, in which B is a small transition metal cation and A is a larger s-, d- or f-block cation) and intercalated cations, stimulated authors’ interest in reason of some encouraging electronic and reactive properties. In particular it is well known that the interlayer surface of layered-perovskites in their protonated form can be easily functionalized with organic groups, such as alcohols, organophosphonic acids,…

Stability, electronic structure, and optical properties of protected gold-doped silver Ag29-xAux (x = 0-5) nanoclusters

2017

In this work, we used density functional theory (DFT) and linear response time-dependent DFT (LR-TDDFT) to investigate the stability, electronic structure, and optical properties of Au-doped [Ag29−xAux(BDT)12(TPP)4]3− nanoclusters (BDT: 1,3-benzenedithiol; TPP triphenylphosphine) with x = 0–5. The aim of this work is to shed light on the most favorable doped structures by comparing our results with previously published experimental data. The calculated relative energies, ranging between 0.8 and 10 meV per atom, indicate that several doped Ag29−xAux nanoclusters are likely to co-exist at room temperature. However, only the Au-doped [Ag29−xAux(BDT)12(TPP)4]3− nanoclusters that have direct bon…

When the Grafting of Double Decker Phthalocyanines on Si(100)-2 × 1 Partly Affects the Molecular Electronic Structure

2016

International audience; A combined X-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), and density functional theory (DFT) study has been performed to characterize the adsorbate interaction of lutetium biphthalocyanine (LuPc2) molecules on the Si(100)-2 × 1 surface. Large molecule–substrate adsorption energies are computed and are found to compete with the molecule–molecule interactions of the double decker molecules. A particularly good matching between STM images and computed ones confirms the deformation of the molecule upon the absorption process. The comparison between DFT calculations and XP spectra reveals that the electronic distribution in the two plateaus …

Theoretical investigation of magnetic properties in Cu(II) complexes with bridging azide ions

2011

Noble Gases as Magnetic Probes in Fullerene Chemistry

2016

Since the early 1990s of the previous century, the use of magnetic active noble gas atom to indirectly probe the size and symmetry of fullerene cage has been reviewed. Molecular modeling of nuclear shielding (and chemical shift) using gauge-including atomic orbital (GIAO) approach at several levels of theory, including Hartree–Fock (HF), density functional theory (DFT), and coupled cluster (CC), is discussed. The advantage of using GIAO calculation to predict and closely reproduce experimental 3He and 129Xe NMR spectra is shown.

Stability, electronic structure, and optical properties of protected gold-doped silver Ag29−xAux (x = 0–5) nanoclusters

2017

In this work, we used density functional theory (DFT) and linear response time-dependent DFT (LR-TDDFT) to investigate the stability, electronic structure, and optical properties of Au-doped [Ag29-xAux(BDT)12(TPP)4]3- nanoclusters (BDT: 1,3-benzenedithiol; TPP triphenylphosphine) with x = 0-5. The aim of this work is to shed light on the most favorable doped structures by comparing our results with previously published experimental data. The calculated relative energies, ranging between 0.8 and 10 meV per atom, indicate that several doped Ag29-xAux nanoclusters are likely to co-exist at room temperature. However, only the Au-doped [Ag29-xAux(BDT)12(TPP)4]3- nanoclusters that have direct bon…