Unveiling the Intermolecular Interactions between Drug 5-Fluorouracil and Watson-Crick/Hoogsteen Base Pairs: A Computational Analysis.

The adsorption of 5-fluorouracil (5FU) on Watson-Crick (WC) base pairs and Hoogsteen (HT) base pairs has been studied using the dispersion-corrected density functional theory (DFT). The adsorption, binding energy, and thermochemistry for the drug 5FU on the WC and HT base pairs were determined. The most stable geometries were near planar geometry, and 5FU has a higher preference for WC than HT base pairs. The adsorption energies of 5FU on nucleobase pairs are consistently higher than pristine nucleobase pairs, indicating that nucleobase pair cleavage is less likely during the adsorption of the 5FU drug. The enthalpy change for the formation of 5FU-DNA base pairs is higher than that for the formation of 5FU-nucleobases and is enthalpy-driven. The E gap of AT base pairs is higher, suggesting that their chemical reactivity toward further reaction would be less than that of GC base pairs. The electron density difference (EDD) analysis shows a significant decrease in electron density in aromatic regions on the purine bases (adenine/guanine) compared to the pyrimidine bases. The MESP diagram of the stable 5FU-nucleobase pair complexes shows a directional interaction, with the positive regions in a molecule interacting with the negative region of other molecules. The atoms in molecule analysis show that the ρ(r) values of C=O···H-N are higher than those of N···H/N-H···O. The N···H intermolecular bonds between the base pair/drug and nucleobases are weak, closed shell interactions and are electrostatic in nature. The noncovalent interaction analysis shows that several new spikes are engendered along with an increase in their strength, which indicates that the H-bonding interactions are stronger and play a dominant role in stabilizing the complexes. Energy decomposition analysis shows that the drug-nucleobase pair complex has a marginal increase in the electrostatic contributions compared to nucleobase pair complexes.

Non-adiabatic excited-state time-dependent GW molecular dynamics (TDGW) satisfying extended Koopmans' theorem: An accurate description of methane photolysis.

There is a longstanding difficulty that time-dependent density functional theory relying on adiabatic local density approximation is not applicable to the electron dynamics, for example, for an initially excited state, such as in photochemical reactions. To overcome this, we develop non-adiabatic excited-state time-dependent GW molecular dynamics (TDGW) on the basis of the extended quasiparticle theory. Replacing Kohn-Sham orbitals/energies with correlated, interacting quasiparticle orbitals/energies allows the full correspondence to the excited-state surfaces and corresponding total energies, with satisfying extended Koopmans' theorem. We demonstrate the power of TDGW using methane photolysis, CH4→CH3•+H, an important initiation reaction for combustion/pyrolysis and hydrogen production of methane. We successfully explore several possible pathways and show how this reaction dynamics is captured accurately through simultaneously time-tracing all quasiparticle levels. TDGW scales as O(NB3-4), where NB is the number of basis functions, which is distinctly advantageous to performing dynamics using configuration interaction and coupled cluster methods.

All-proportional solid solution versus two-phase coexistence in the Ti-V alloy by first-principles phase field and SQS methods.

The microstructures of the Ti-V alloy are studied by purely first-principles calculations without relying on any empirical or experimental parameter. The special quasirandom structure model is employed to treat the all-proportional solid solution [Formula: see text] phase, while the first-principles phase field method or its variant is employed to treat the coexistence phases. The linearity of the calculated local free energy against the integer Ti[Formula: see text]V[Formula: see text] composition in the cluster expansion method manifests a clear evidence of the solid solution behavior. From a detailed energy comparison, our results are consistent with the experimental fact that the Ti-V alloy is an all-proportional solid solution of the [Formula: see text] phase at high temperatures and exhibits an [Formula: see text] coexistence at low temperatures. Moreover, it is found that mosaic-type microstructures may appear as a metastable phase, as observed by many experiments. The first-principles criterion for the all-proportional solid solution behavior presented in this paper is very general and can be applied to any other binary or multi-component alloys.

Electronegativity Difference as a Descriptor for the Oxidation-Inhibiting Effect of the Alloying Element during the Early Stages of Titanium Oxidation.

Degradation of the mechanical properties of α-titanium, which is used to manufacture parts of jet engines, due to high-temperature oxidation is detrimental for the engine components. Therefore, to overcome this problem there are ongoing endeavors to develop novel oxidation-resistant titanium alloys and improve the properties of the existing ones. In an effort to understand the effect of alloying on oxidation of the α-Ti(0001) surface and to identify descriptors for rational design of oxidation-resistant alloys, in this work, using density functional theory-based calculations, we studied oxygen sorption and surface to subsurface diffusion on pure and alloyed α-Ti(0001) surfaces. Zr, Hf, Nb, and Mo from the d block and Al, Ga, Si, and Ge from the p block were used as alloying elements. We find that the alloying elements prefer to segregate on the surface compared to the subsurface layers. Our calculations show that the diffusion barrier correlates with the difference in the electronegativity between the alloying element and Ti. Elements which are more electropositive than Ti are found to hinder the oxygen dissolution in Ti and vice versa. We propose that the electronegativity difference can act as a good descriptor for choosing alloying elements. Our results are in reasonably good agreement with experimental reports on the growth of oxide layers on these alloyed Ti surfaces.

Enhanced Selectivity in Volatile Organic Compound Gas Sensors Based on ReS2-FETs under Light-Assisted and Gate-Bias Tunable Operation.

Using a single-device two-dimensional (2D) rhenium disulfide (ReS2) field-effect transistor (FET) with enhanced gas species selectivity by light illumination, we reported a selective and sensitive detection of volatile organic compound (VOC) gases. 2D materials have the advantage of a high surface-area-to-volume ratio for high sensitivity to molecules attached to the surface and tunable carrier concentration through field-effect control from the back-gate of the channel, while keeping the top surface open to the air for chemical sensing. In addition to these advantages, ReS2 has a direct band gap also in multilayer cases, which sets it apart from other transition-metal dichalcogenides (TMDCs). We take advantage of the effective response of ReS2 to light illumination to improve the selectivity and gas-sensing efficiency of a ReS2-FET device. We found that light illumination modulates the drain current response in a ReS2-FET to adsorbed molecules, and the sensing activity differs depending on the gas species used, such as acetone, ethanol, and methanol. Furthermore, wavelength and carrier density rely on certain variations in light-modulated sensing behaviors for each chemical. The device will distinguish the gas concentration in a mixture of VOCs using the differences induced by light illumination, enhancing the selectivity of the sensor device. Our results shed new light on the sensing technologies for realizing a large-scale sensor network in the Internet-of-Things era.

A first-principles phase field method for quantitatively predicting multi-composition phase separation without thermodynamic empirical parameter.

To design tailored materials, it is highly desirable to predict microstructures of alloys without empirical parameter. Phase field models (PFMs) rely on parameters adjusted to match experimental information, while first-principles methods cannot directly treat the typical length scale of 10 µm. Combining density functional theory, cluster expansion theory and potential renormalization theory, we derive the free energy as a function of compositions and construct a parameter-free PFM, which can predict microstructures in high-temperature regions of alloy phase diagrams. Applying this method to Ni-Al alloys at 1027 °C, we succeed in reproducing evolution of microstructures as a function of only compositions without thermodynamic empirical parameter. The resulting patterns including cuboidal shaped precipitations are in excellent agreement with the experimental microstructures in each region of the Ni-Al phase diagram. Our method is in principle applicable to any kind of alloys as a reliable theoretical tool to predict microstructures of new materials.

Effect of mixed partial occupation of metal sites on the phase stability of γ-Cr23-xFe x C6 (x = 0-3) carbides.

The effect of mixed partial occupation of metal sites on the phase stability of the γ-Cr23-xFe x C6 (x = 0-3) carbides is explored as function of composition and temperature. Ab initio calculations combined with statistical thermodynamics approaches reveal that the site occupation of the carbides may be incorrectly predicted when only the commonly used approach of full sublattice occupation is considered. We found that the γ-M23C6 structure can be understood as a familiar sodium chloride structure with positively charged rhombic dodecahedron (M(4a) M12(48h)) and negatively charged cubo-octahedron (M8(32f) C6(24e)) super-ion clusters, together with interstitial metal atoms at the 8c sites. The stability of the partially occupied phase can be easily rationalized on the basis of a super-ion analysis of the carbide phase. This new understanding of γ-M23C6 carbides may facilitate further development of high-chromium heat-resistant steels.

Excellent room temperature deformability in high strain rate regimes of magnesium alloy.

Magnesium and its alloys have the lowest density among structural metallic materials; thus, this light-weight metal has great potential for reducing the weight, for example, of vehicles and trains. However, due to its crystal structure, deformability is poor; in particular, under compressive stress. In this study, we modified magnesium with bismuth as an alloying element, which has the characteristics of being likely to form precipitates instead of grain boundary segregation. The Mg-Bi binary alloy showed excellent deformability and high absorption of energy in high-strain rate regimes at room temperature via contribution of grain boundary sliding. These properties, which are closely comparable to those of conventional middle-strength aluminum alloys (Al-Mg and Al-Mg-Si series alloys), have never been observed before in magnesium alloys. The development of such properties opens the door for not only academic but also industrial research in magnesium.

Effect of Si on the oxidation reaction of α-Ti(0 0 0 1) surface: ab initio molecular dynamics study.

We present our ab initio molecular dynamics (MD) study of the effect of Si on the oxidation of α-Ti(0 0 0 1) surfaces. We varied the Si concentration in the first layer of the surface from 0 to 25 at.% and the oxygen coverage (θ) on the surface was varied up to 1 monolayer (ML). The MD was performed at 300, 600 and 973 K. For θ = 0.5 ML, oxygen penetration into the slab was not observed after 16 ps of MD at 973 K while for θ > 0.5 ML, oxygen penetration into the Ti slab was observed even at 300 K. From Bader charge analysis, we confirmed the formation of the oxide layer on the surface of the Ti slab. At higher temperatures, the Si atoms diffused from the first layer to the interior of the slab, while the Ti atoms moved from second layer to the first layer. The pair correlation function shows the formation of a disordered Ti-O network during the initial stage of oxidation. Si was found to have a strong influence on the penetration of oxygen in the Ti slab at high temperatures.

Theoretical and experimental investigation of the excellent p-n control in yttrium aluminoborides.

First-principles calculations were carried out to elucidate the excellent control of p-n characteristics recently reported for yttrium aluminoborides YxAlyB14 [Formula: see text] with different occupancies of Al sites [Formula: see text]. Such control of the occupancy of metal sites in borides is unusual. Calculations based on detailed x-ray diffraction data reveal a stable configuration of the atomic sites, indicating that such variation in occupancy is possible. A shift from positive through zero to negative values of the Seebeck coefficient is also clearly illustrated by determining the density of states for different configurations.

First-principles study of electronic structures and stability of body-centered cubic Ti-Mo alloys by special quasirandom structures.

The electronic structures and structural properties of body-centered cubic Ti-Mo alloys were studied by first-principles calculations. The special quasirandom structures (SQS) model was adopted to emulate the solid solution state of the alloys. The valence band electronic structures of Ti-Mo and Ti-Mo-Fe alloys were measured by hard x-ray photoelectron spectroscopy. The structural parameters and valence band photoelectron spectra were calculated using first-principles calculations. The results obtained with the SQS models showed better agreement with the experimental results than those obtained using the conventional ordered structure models. This indicates that the SQS model is effective for predicting the various properties of solid solution alloys by means of first-principles calculations.

Probing the structure, stability and hydrogen adsorption of lithium functionalized isoreticular MOF-5 (Fe, Cu, Co, Ni and Zn) by density functional theory.

Li adsorption on isoreticular MOFs with metal Fe, Cu, Co, Ni and Zn was studied using density function theory. Li functionalization shows a considerable structural change associated with a volume change in isoreticular MOF-5 except for the Zn metal center. Hydrogen binding energies on Li functionalized MOFs are seen to be in the range of 0.2 eV, which is the desired value for an ideal reversible storage system. This study has clearly shown that Li doping is possible only in Zn-based MOF-5, which would be better candidate to reversibly store hydrogen.

A lattice Monte Carlo simulation of the FePt alloy using a first-principles renormalized four-body interaction.

Although a lattice Monte Carlo method provides an effective, simple, and fast way to study thermodynamic properties of substitutional alloys, it cannot treat by itself the off-lattice effects, such as thermal vibrations and local distortions. Therefore, even if the interaction among atoms at lattice points is calculated accurately by means of first-principles calculations, the lattice Monte Carlo simulation overestimates the order-disorder phase transition temperature. In this paper, we treat this problem in the investigation of the FePt alloy, which has recently attracted considerable interest in its magnetic properties. We apply a simple version of the potential renormalization theory to determine the interaction among atoms, including partly the off-lattice effects by means of first-principles calculations. Then, we use the interaction to perform a lattice Monte Carlo simulation of the FePt alloy on a fcc lattice. From the results, we find that the transition temperature obtained after the present renormalization procedure becomes closer to the experimental value.

Thermodynamic properties of the Cu-Au system using a face-centered-cubic lattice model with a renormalized potential.

A Monte Carlo simulation is carried out to study thermodynamic properties of Cu-Au alloys using a face-centered-cubic (fcc) lattice-gas model. To obtain quantitatively accurate results, a Finnis-Sinclair-type potential, which has been widely used for molecular dynamics (MD) simulations, is employed. To overcome some shortcomings of lattice-gas models such as neglecting vibrational entropy, the potential is mapped onto the fcc lattice using the renormalization technique. The renormalized potential gives an improved Cu-Au phase diagram compared to the original MD potential applied directly on the lattice.