E. Dushanov

Molecular dynamics studies of the interaction between water and oxide surfaces

The water-surface interaction is a research target of great importance for a broad spectrum of technological applications and fundamental scientific disciplines. In the present study, a comparative analysis is performed to clarify the structural and diffusion properties of water on a number of oxide surfaces. Based on the molecular dynamics (MD) simulation method, the water-surface interaction mechanism was investigated for the oxide materials TiO2 (anatase), Al2O3 (corundum), and Fe2O3 (hematite). A comparison of the water-TiO2 interaction with the water-Al2O3 and water-Fe2O3 systems demonstrates the specificity of the adsorption and layer formation on the atomic/molecular level scale. The obtained MD analysis data point to a considerable enhancement of water-TiO2 surface adsorption and a relatively high density distribution profile near the surface. The novel data on water structure and diffusion on oxide surfaces are discussed from the point of view of possible material innovation and design.

On Correlation Effect of the Van-der-Waals and Intramolecular Forces for the Nucleotide Chain - Metallic Nanoparticles - Carbon Nanotube Binding

Background: The tertiary system of nucleotide chain (NC) - gold nanoparticles (NPs) - carbon nanotube (CNT) represents a great interest in the modern research and application of the bio-nano-technologies. The application aspects include, for example, the development of electronic mobile diagnostic facilities, nanorobotic design for a drug delivery inside living cell, and so on. The small NC chain represents an important stage in the understanding of the interaction mechanism of a full DNA or RNA molecule with NP and CNT. In this regard, one has to mention the development of the DNA-CNT devices for the purposes of diagnostic applications in the chemical or drug delivery. Methods: For the NC-NP-CNT system, we have built up a series of the molecular dynamics (MD) models with different NC-NP configurations and performed their MD analysis. The entire system (the NC chain, gold NPs and CNT) was allowed to interact with each other by the only VdW forces. The Lennard-Jones short-ranged interaction was assumed between the NC, NP and CNT. For the CNT a many body Tersoff potential having a quantum-chemistry nature was used. So far, the so-called hybrid MD approach was realized, where the quantum-chemistry potential in combination with a classical trajectory calculation applied . Results: The peculiarities of the NC-NP interaction and bond formation inside of a CNT matrix were investigated along with the structural and dynamical behavior. The correlation effects between the weak Van der Waals (VdW) forces and intramolecular vibrations were enlighten for the molecular system consisting of a small nucleotide chain (NC), gold nanoparticles (NPs) and carbon nanotube (CNT) using molecular dynamics (MD) simulation method. Conclusion: The NC intermolecular motions were estimated from MD data thereby building the distance distributions, the angular and dihedral (torsional) bond energy graphs versus simulation time at different temperatures from T=100 K up to 300 K. The MD simulation results have shown that depending on the relative NC-NP position a different scenario of bonding between the NC-NP, within CNT matrix, is possible. We have observed the possibilities of formation of weak, strong and intermediate bonds between the NP-NC, which are overestimated by a presence of CNT matrix as confined environment. The NC chain can form with a particular gold atom a close contact, while with another under the same positional and temperature conditions the weak resultant bonding formation might be possible. We estimated the fluctuations in the NP-NC bonding processes for a single gold atomic case (models 1-3, NC-1NP-CNT), for the two (model 4-6, NC-2NP-CNT) and three (model 7, NC-3NP-CNT) gold particle ones. Thus, a concurrent effect between the NC intramolecular vibrations and a weak VdW interaction between the NC and gold NP were studied in detail.

Molecular dynamics simulations of formamide interaction with hydrocyanic acid on a catalytic surface TiO2

The behavior of water—formamide and hydrocyanic acid—formamide solutions on an anatase surface have been studied using molecular dynamics (MD) simulation method. The interaction activation energies have been estimated for the temperature range from 250 up to 400 K. The diffusion coefficients and structural radial distribution functions have been calculated for the formamide, water and hydrocyanic acid on an anatase surface. The calculated activation energies of the water—formamide—anatase and hydrocyanic acid—formamide—anatase systems were analyzed and compared. A comparative analysis of the systems under investigation was performed and a possible correlation between the obtained MD results and the molecular mechanism involving the formamide’s interaction with dioxide titan adsorbing surface were discussed.

Activation Energy Calculations for Formamide–TiO2 and Formamide–Pt Interactions in the Presence of Water

Formamide contains the four elements (C, H, O, and N) most required for life and it is attractive as a potential prebiotic starting material for nucleobase synthesis. In the presence of catalysts (for example, TiO2) and with moderate heating, formamide can pass surface energy barriers, yielding a complete set of nucleic bases and acyclonucleosides, and favoring both phosphorylations and transphosphorylations necessary for life. In the reaction mechanism, interaction with water seems to be an essential factor for the formamide molecule to function. In this paper, a formamide–water solution on a TiO

Structural and diffusion properties of formamide/water mixture interacting with TiO2 surface.

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[Simulation of Mutant P32T Homo- and Heterodimers of Human Inosine Triphosphate Pyrophosphatase hITPA].

(anatase) surface is simulated using the molecular dynamics method, and activation energy calculations are performed for the temperature range of T = 250 K to T = 400 K. A correlation is established between the diffusion and density profiles for the formamide and water molecules on an anatase surface. Also, the calculated activation energies of the formamide–water–anatase and formamide–water–platinum systems are compared. A comparative analysis is performed of the behavior of formamide–water and ethanol–water interaction on the same (anatase and platinum) surfaces.

A Novel Approach to Simulate a Charge Transfer in DNA Repair by an Anacystis nidulans Photolyase.

The photoreaction and adsorption properties on surfaces, thermal decomposition, chemical transformation, and other properties of the formamide molecule are widely used to understand the origins of the formation of biological molecules (nucleosides, amino acids, DNA, monolayers, etc.) needed for life. The titanium oxide (TiO2) surface can act both as a template on which the accumulation of adsorbed molecules like formamide occurs through the concentration effect, and as a catalytic material that lowers the activation energy needed for the formation of intermediate products. In this paper, a formamide-water solution interacting with TiO2 (anatase) surface is simulated using the molecular dynamics method. The structural, diffusion and density properties of formamide-water mixture on TiO2 are established for a wide temperature range from T=250 K up to T=400 K.

A molecular dynamic model for analyzing concentrations of electrolytes: Fractional molar dependences of microstructure properties

The structures of three forms of the dimeric enzyme human inosine triphosphate pyrophosphatase (hITPA) are considered for identifying conformation changes that determine the inactivation effect of the P32T mutation. Nanosecond molecular dynamics were analyzed and the values of mean-square deviations of atoms for the wild-type and mutant homodimers, as well as the heterodimer, were calculated. Simulation of an interval of 3 ns demonstrates stronger atom displacements in mutant protomers. During the simulated time interval, the strongest changes are observed in the loop between α2 and β2 (residues 28–33, the area of the P32T mutation), the loop between β5 and β6, and the C-terminal end. The loop between α2 and β2 has two conformations characterized by different position of Phe31 side group. The distance between Cys33(Cα) and Phe31(Cz) for wild-type and mutant protomers is ~ 9.0 and 5.5 Å, respectively. These conformations are stably maintained.

MD studies on conformational behavior of a DNA photolyase enzyme

An Anacystis nidulans photolyase enzyme containing two chromophore cofactors was simulated for a photoreaction DNA repairing process via molecular dynamics (MD) method. A novel approach has been introduced for the electron transfer between the FAD (flavin adenine dinucleotide; flavin) molecule and CPD (cyclobutane pyrimidine dimer). This approach involves four simulation stages with different charges for the FAD and CPD fragments and a role of a charged state of the active cofactor was qualified during the MD modeling. Observations show that flavin has actively participated in a charge transfer process, thereby involving the conformational changes of the DNA and CPD substrate fragment. The DNA conformation behavior has shown to correlate with the electron transfer from flavin to CPD. This is manifested on the similarities of the DNA repairing process by excision repair of the UV photoproducts.

JINR CICC in computational chemistry and nanotechnology problems: DL_POLY performance for different communication architectures

Aqueous electrolyte solutions play an important role in many electrophysical and chemical processes in aerospace technology and industrial applications. As noncovalent interactions, the interactions between ions are crucially important for biomolecular structures as well (protein structure folding, molecular level processes followed by ionic pair correlations, the formation of flexible hydrate shells, and so on). Specifically, ions (cations and anions with the same valence charges) can form stable pairs if their sizes match. The formation of ionic pairs can substantially affect the thermodynamic stabilities of proteins in the alkali salts physiologically present in the human body. Research aims and problems impose severe demands on readjustments of the ionic force fields and potential parameters developed to describe aqueous solutions and electrolytic systems. Ionic solutions and their interaction with biomolecules have been observed for over 100 years [1], but the behavior of such solutions remains poorly studied today. New data obtained in this work deals with parameterization strategies and adjustments for the ionic force fields of the alkali cations and halide anions that should be helpful in biomolecular research. Using molecular dynamics (MD) models, four electrolytic systems (HCl-H2O, LiCl-H2O, NaCl-H2O, and KCl-H2O) are investigated as binary mixtures of water and cations and anions, respectively. The intermolecular interaction parameters are varied for two of the four model electrolytes (HCl-H2O and NaCl-H2O) to simulate the possibility of different ionic shells forming during interaction with water. It is found that varying the potential parameters strongly affects the dynamic and structural characteristics of electrolyte systems. MD simulations are performed in the temperature range of 300 to 600 K with a step of 50 K. MD simulations for all electrolyte models (HCl-H2O, LiCl-H2O, NaCl-H2O, KCl-H2O) are also conducted for different molar fractions of electrolyte concentration: 16, 8, and 1 mol/kg. Energies of diffusion activation are calculated using the Arrhenius equation, thereby constructing temperature dependence graphs of diffusion coefficients for all four electrolyte systems. The observed diffusion properties of the electrolyte systems are found to correlate well with the energy and structural radial distribution data.