Elena Rykova

Towards relativistic ECP / DFT description of chemical bonding in E112 compounds: spin-orbit and correlation effects in E112X versus HgX (X=H, Au)

The relativistic effective core potential (RECP) approach combined with the spin-orbit DFT electron correlation treatment was applied to the study of the bonding of eka-mercury (E112) and mercury with hydrogen and gold atoms. Highly accurate small-core shape-consistent RECPs derived from Hartree-Fock-Dirac-Breit atomic calculations with Fermi nuclear model were employed. The accuracy of the DFT correlation treatment was checked by comparing the results in the scalar-relativistic (spin-orbit-free) limit with those of high level scalar-relativistic correlation calculations within the same RECP model. E112H was predicted to be slightly more stable than its lighter homologue (HgH). The E112-Au bond energy is expected to be ca. 25–30 % weaker than that of Hg-Au. The role of correlations and magnetic (spin-dependent) interactions in E112-X and Hg-X (X=H, Au) bonding is discussed. The present computational procedure can be readily applied to much larger systems and seems to be a promising tool for simulating E112 adsorption on metal surfaces.

Importance of spin-orbit effects on the isomerism profile of Au3: An ab initio study

Two-component relativistic density functional theory combined with high-level ab initio correlation techniques was applied to the study of the electronic structure and isomerism of Au(3). All calculations were performed with accurate small-core shape-consistent relativistic pseudopotentials. Density functional theory was used to determine the equilibrium structures of the Au(3) isomers and isomerization path and to estimate the contributions of spin-orbit effects to the ground state electronic energy along the path. The reliability of these estimates was verified through independent many-body multipartitioning perturbation theory calculations. Spin-orbit corrections were used to refine the isomerization energy profile computed by spin-orbit-free coupled cluster methods.

Relativistic effective core potential calculations of Hg and eka-Hg (E112) interactions with gold: Spin-orbit density functional theory modeling of Hg–Aun and E112–Aun systems

Interactions of eka-Hg (E112) and Hg atoms with small gold clusters were studied in the frame of the relativistic effective core potential model using the density functional theory (DFT) approach incorporating spin-dependent (magnetic) interactions. The choice of the exchange-correlation functional was based on a comparison of the results of DFT and large-scale coupled cluster calculations for E112Au and HgAu at the scalar relativistic level. A close similarity between the E112Aun and HgAun equilibrium structures was observed. The E112 binding energies on Aun are typically smaller than those for Hg by ca. 25%-32% and the equilibrium E112-Au separations are always slightly larger than their Hg-Au counterparts.

Ab initio study of Hg-Hg and E112-E112 van der Waals interactions

The ground electronic state of the eka-mercury dimer (E1122) was studied within the model of generalized relativistic effective core potentials. A combined procedure based on describing correlation effects by the scalar relativistic coupled-cluster method and on taking into account spin-dependent interactions by means of density-functional theory was used in the calculations. A high accuracy of this approach was confirmed by the results of similar calculations for the mercury dimer. It was found that the bond length is nearly 0.4 Å shorter in E1122 than in Hg2 and that the dissociation energy of the former is approximately twice as high as that of the latter dimer.

Prooligonucleotides exhibit less serum-protein binding than phosphodiester and phosphorothioate oligonucleotides.

Abstract The protein-binding properties of dodecathymidine derivatives (prooligos) bearing either methyl- or tert-butyl-S-acylthioethyl (Me- or tBuSATE) protecting groups were evaluated. The dissociation constants (Kd) were estimated for complexes of prooligos with serum blood proteins and lactoferrin using prooligos to compete the binding of the radiolabeled, alkylating probe oligonucleotide CIRp(T)12 with the proteins. tBuSATE and MeSATE prooligos have decreased affinity of binding with serum proteins and lactoferrin compared with their parent oligos. These data suggest that prooligos should cause less side effects which combined with their stability to nucleases and enhanced permeability into cells make them potentially useful for design of therapeutics.

Atomistic simulations of materials for optical chemical sensors: DFT-D calculations of molecular interactions between gas-phase analyte molecules and simple substrate models

The structures of complexes of some small molecules (formaldehyde, acetaldehyde, ammonia, methylamine, methanol, ethanol, acetone, benzene, acetonitrile, ethyl acetate, chloroform, and tetrahydrofuran, considered as possible analytes) with ethylbenzene and silanol (C6H5C2H5 and SiH3OH, considered as models of polystyrene and silica gel substrates) and with acridine (C13H9N, considered as a model of an indicator dye molecule of the acridine series) and the corresponding interaction energies have been calculated using the DFT-D approximation. The PBE exchange-correlation potential was used in the calculations. The structures of complexes between the analyte and the substrate were determined by optimizing their ground-state geometry using the SVP split-valence double-zeta plus polarization basis set. The complex formation energies were refined by single-point calculations at the calculated equilibrium geometries using the sufficiently large triple-zeta TZVPP basis set. The calculated interaction energies are used to assess the possibility of using dyes of the acridine series adsorbed on a polystyrene or silica substrate for detecting the small molecules listed above.

Roughness simulation for thin films prepared by atomic layer deposition

The kinetic lattice Monte Carlo method for film growth simulation without taking crystallization into account was applied to study the roughness of the HfO2 film grown by atomic layer deposition at 100–500°C from HfCl4 and H2O. The calculations were performed using a simplified kinetic mechanism of the growth of HfO2 films obtained by reducing the detailed kinetic mechanism developed earlier. Ab initio quantum-chemical calculations were performed to determine the kinetic parameters of diffusion processes on the surface of hafnium oxide that could influence film roughness. Because of the special features of atomic layer deposition, the rate of film growth and film roughness were finite even if surface relaxation was ignored. It was found that, irrespective of the temperature, the diffusion of hydrogen and adsorbed HfCl4 complexes did not change the profile of the growing film and only insignificantly increased the mean rate of growth. The results obtained were also qualitatively applicable to zirconium dioxide at fairly low (≤100°C) temperatures in the absence of crystallization.

Effect of analyte molecules on the electronic absorption and fluorescence spectra of a receptor center based on the 9-(diphenylamino)acridine dye adsorbed on silica clusters

The interaction of small analyte molecules, such as acetone, ammonia, methanol, ethanol, water, benzene, naphthalene, toluene, and dinitrotoluene with the 9-(diphenylamino)acridine (DPAA) dye adsorbed on a silica surface is studied theoretically within the DFT-D approximation. Electronic fluorescence and absorption spectra of analyte/DPAA/silica complexes are calculated within the TDDFT approximation. The procedure proposed for the calculation of electronic spectra provides reasonable estimates for the positions of fluorescence bands in good agreement with the experimental data and can be recommended for calculations of similar systems. The shifts of spectral bands due to interaction of the DPAA/silica system with the analytes are sufficient for the detection of most of the studied compounds. The DPAA/silica system can be successfully used as a material for fluorescent optical chemosensors.

First‐Principles‐Based Development of Kinetic Mechanisms in Chemically Active Light‐Emitting Nonthermal Plasmas and Gases

Recent progress in several related research areas such as first‐principles electronic‐structure calculations of atoms and diatomic molecules, theory of elementary processes, kinetics, and numerical engineering, and also continued exponential growth in computational resources enhanced by recent advances in massively parallel computing have opened the possibility of directly designing kinetics mechanisms to describe chemical processes and light emission in such complex media as nonequilibrium plasmas and reacting gases. It is important that plasma and combustion kinetics can be described in the framework of this direct approach to a sufficiently high accuracy, which makes it an independent predictive research tool complementary to experimental techniques. This paper demonstrates the capabilities of the first‐principles based approach to develop kinetic mechanisms. Two examples are discussed in detail: (1) the mechanism of hydrocarbon fuel combustion at high temperatures and (2) light emission in non‐thermal...

Molecular Interactions of Oligonucleotides in Organism – A Source of Broad Spectrum of Biological Activities

Abstract Oligodeoxynucleotides interact with a few proteins at the cell surface and in the bloodstream. These interactions determine cellular uptake, biodistribution and some nonspecific antiviral and immunomodulating effects of oligonucleotides.