DFT and MD study of adsorption sensitivity of aluminium phosphide nanotube towards some air pollutant gas molecules

To investigate the adsorption behaviour of CS₂, CO₂, SO₂, H₂Se and H₂S gas molecules on the external surface of (6, 0) single-walled aluminium phosphide nanotube (AlPNT), the density functional theory (DFT) calculations at the B3LYP level of theory are performed. The partial densities of states (PDOS) for the SO₂ molecule, the S and O atoms of SO₂ molecule before and after adsorption on the surface of AlPNT have been plotted. The vibrational frequencies and physical properties such as chemical potential, chemical hardness, dipole moment and chemical electrophilicity of all studied complexes have been systematically investigated. The electron density and the Laplacian of the electron density for bond critical points have been examined by the AIM theory. Also the molecular dynamics (MD) simulations of two complexes with the minimum and maximum negative interaction energies that is: AlPNT/CO₂ and AlPNT/SO₂ complexes, respectively, have been considered.     

A Cellular Automata Model of Proton Hopping Down a Channel

Proton hopping is the process where a H‐atom on a hydronium ion forms a H‐bond with the O‐atom of a neighboring H₂O molecule. There is then an exchange of bonding forces when that covalent bond of the H‐atom in the hydronium ion changes to a H‐bond, and the previous H‐bond changes to a covalent bond with the neighboring O‐atom. The neighboring molecule now becomes a hydronium (H₃O⁺) ion. This process repeats itself very rapidly among neighboring hydronium and H₂O molecules. There is a flow of protonic character through bulk H₂O, referred to as proton hopping. This process carries information through living systems where H₂O is present. A cellular automata model of proton hopping down a channel has been created and studied. Variations in the rate of proton entry into the channel and the effects of the polar character of the channel walls was studied using the model. The behavior of the models corresponds to experimental results.     

Theoretical studies on the structures,intra- and inter-molecular hydrogen bonding interactions in HNF and HNF–H2O clusters in the gaseous,aqueous and solid phases

Hydrazimium nitroformate ([N₂H₅]⁺[C(NO₂)₃]^? , HNF) is an ionic oxidiser used in solid propellants. Its properties are easily affected by H₂O because of its hygroscopicity. In this article, density functional theory (DFT) and molecular dynamics (MD) were employed to study the isolated HNF molecule and the HNF–H₂O cluster in gas phase and in the aqueous solution. Three stable conformations were obtained for HNF in the gas phase and in the aqueous solution, respectively, and each conformation can form several different HNF–H₂O clusters. Irrespective of whether it is in gas phase or in solution, intramolecular hydrogen bond interactions and other interactions (e.g. the binding energy, the dispersion energy, the second-order perturbation energy and the energy gap between frontier orbitals) of HNF are weaker in the clusters than in the isolated state. The initial decomposition energy of the cluster is lower than that of the isolated HNF molecule in both gaseous and aqueous phases, while the dissociation processes are the same. Molecular dynamic simulations showed that the clustered H₂O elongates and weakens the C–NO₂ bond in the solid HNF–H₂O cluster compared with that in the solid HNF. H₂O reduces and weakens intramolecular N–HΛO bonds too, and O–HΛN is the dominant intermolecular hydrogen bond between HNF and H₂O.     

DFT study of CO<Subscript>2</Subscript> and H<Subscript>2</Subscript>O co-adsorption on carbon models of coal surface

The moisture content of coal affects the adsorption capacity of CO₂ on the coal surface. Since the hydrogen bonds are formed between H₂O and oxygen functional group, the H₂O cluster more easily adsorbs on the coal micropore than CO₂ molecule. The coal micropores are occupied by H₂O molecules that cannot provide extra space for CO₂ adsorption, which may leads to the reduction of CO₂ adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO₂ and adsorbed H₂O molecule are not clear. Density functional theory (DFT) calculations were performed to elucidate the effect of adsorbed H₂O to CO₂ adsorption. This study reports some typical coal-H₂O···CO₂ complexes, along with a detailed analysis of the geometry, energy, electrostatic potential (ESP), atoms in molecules (AIM), reduced density gradient (RDG), and energy decomposition analysis (EDA). The results show that H₂O molecule can more stably adsorb on the aromatic ring surface than CO₂ molecule, and the absolute values of local ESP maximum and minimum of H₂O cluster are greater than CO₂. AIM analysis shows a detailed interaction path and strength between atoms in CO₂ and H₂O, and RDG analysis shows that the interactions among CO₂, H₂O, and coal model belong to weak van der Waals force. EDA indicates that electrostatic and long-range dispersion terms play a primary role in the co-adsorption of CO₂ and H₂O. According to the DFT calculated results without considering micropore structure and functional group, it is shown that the adsorbed H₂O can promote CO₂ adsorption on the coal surface. These results demonstrate that the micropore factor plays a dominant role in affecting CO₂ adsorption capacity, the attractive interaction of adsorbed H₂O to CO₂ makes little contribution.     

Plasmachemical and heterogeneous processes in ozonizers with oxygen activation by a dielectric barrier discharge

Plasmachemical and heterogeneous processes of generation and loss of ozone in the atmosphericpressure dielectric barrier discharge in oxygen are studied theoretically. Plasmachemical and electronic kinetics in the stage of development and decay of a single plasma filament (microdischarge) are calculated numerically with and without allowance for the effects of ozone vibrational excitation and high initial ozone concentration. The developed analytical approach is applied to determine the output ozone concentration taking into account ozone heterogeneous losses on the Al₂O₃ dielectric surface. Using the results of quantummechanical calculations by the method of density functional theory, a multistage catalytic mechanism of heterogeneous ozone loss based on the initial passivation of a pure Al₂O₃ surface by ozone and the subsequent interaction of O₃ molecules with the passivated surface is proposed. It is shown that the conversion reaction 2O₃ → 3O₂ of a gas-phase ozone molecule with a physically adsorbed ozone molecule can result in the saturation of the maximum achievable ozone concentration at high specific energy depositions, the nonstationarity of the output ozone concentration, and its dependence on the prehistory of ozonizer operation.     

DFT studies of acrolein molecule adsorption on pristine and Al- doped graphenes

The ability of pristine graphene (PG) and Al-doped graphene (AlG) to detect toxic acrolein (C₃H₄O) was investigated by using density functional calculations. It was found that C₃H₄O molecule can be adsorbed on the PG and AlG with adsorption energies about ?50.43 and – v30.92 kcal mol^?1 corresponding to the most stable configurations, respectively. Despite the fact that interaction of C₃H₄O has no obvious effects on the of electronic properties of PG, the interaction between C₃H₄O and AlG can induce significant changes in the HOMO/LUMO energy gap of the sheet, altering its electrical conductivity which is beneficial to sensor designing. Thus, the AlG may be sensitive in the presence of C₃H₄O molecule and might be used in its sensor devices. Also, applying an external electric filed in an appropriate orientation (almost stronger than 0.01 a.u.) can energetically facilitate the adsorption of C₃H₄O molecule on the AlG.     

Water and Backbone Dynamics in a Hydrated Protein

Rotational immobilization of proteins permits characterization of the internal peptide and water molecule dynamics by magnetic relaxation dispersion spectroscopy. Using different experimental approaches, we have extended measurements of the magnetic field dependence of the proton-spin-lattice-relaxation rate by one decade from 0.01 to 300 MHz for ¹H and showed that the underlying dynamics driving the protein ¹H spin-lattice relaxation is preserved over 4.5 decades in frequency. This extension is critical to understanding the role of ¹H₂O in the total proton-spin-relaxation process. The fact that the protein-proton-relaxation-dispersion profile is a power law in frequency with constant coefficient and exponent over nearly 5 decades indicates that the characteristics of the native protein structural fluctuations that cause proton nuclear spin-lattice relaxation are remarkably constant over this wide frequency and length-scale interval. Comparison of protein-proton-spin-lattice-relaxation rate constants in protein gels equilibrated with ²H₂O rather than ¹H₂O shows that water protons make an important contribution to the total spin-lattice relaxation in the middle of this frequency range for hydrated proteins because of water molecule dynamics in the time range of tens of ns. This water contribution is with the motion of relatively rare, long-lived, and perhaps buried water molecules constrained by the confinement. The presence of water molecule reorientational dynamics in the tens of ns range that are sufficient to affect the spin-lattice relaxation driven by ¹H dipole-dipole fluctuations should make the local dielectric properties in the protein frequency dependent in a regime relevant to catalytically important kinetic barriers to conformational rearrangements.     

All-electron scalar relativistic calculation of water molecule adsorption onto small gold clusters

An all-electron scalar relativistic calculation was performed on Au _n H₂O (n = 1–13) clusters using density functional theory (DFT) with the generalized gradient approximation at PW91 level. The calculation results reveal that, after adsorption, the small gold cluster would like to bond with oxygen and the H₂O molecule prefers to occupy the single fold coordination site. Reflecting the strong scalar relativistic effect, Au _n geometries are distorted slightly but still maintain a planar structure. The Au–Au bond is strengthened and the H–O bond is weakened, as manifested by the shortening of the Au–Au bond-length and the lengthening of the H–O bond-length. The H–O–H bond angle becomes slightly larger. The enhancement of reactivity of the H₂O molecule is obvious. The Au–O bond-lengths, adsorption energies, VIPs, HLGs, HOMO (LUMO) energy levels, charge transfers and the highest vibrational frequencies of the Au–O mode for Au _n H₂O clusters exhibit an obvious odd-even oscillation. The most favorable adsorption between small gold clusters and the H₂O molecule takes place when the H₂O molecule is adsorbed onto an even-numbered Au _n cluster and becomes an Au _n H₂O cluster with an even number of valence electrons. The odd–even alteration of magnetic moments is observed in Au _n H₂O clusters and may serve as material with a tunable code capacity of “0” and “1” by adsorbing a H₂O molecule onto an odd or even-numbered small gold cluster.     

Molecular dynamics simulation on the decomposition of type SII hydrogen hydrate and the performance of tetrahydrofuran as a stabiliser

Molecular dynamics simulation is used to study the decomposition and stability of SII hydrogen and hydrogen/tetrahydrofuran (THF) hydrates at 150 K, 220 K and 100 bar. The modelling of the microscopic decomposition process of hydrogen hydrate indicates that the decomposition of hydrogen hydrate is led by the diffusive behaviour of H₂ molecules. The hydrogen/THF hydrate presents higher stability, by comparing the distributions of the tetrahedral angle of H₂O molecules, radial distribution functions of H₂O molecules and mean square displacements or diffusion coefficients of H₂O and H₂ molecules in hydrogen hydrate with those in hydrogen/THF hydrate. It is also found that the resistance of the diffusion behaviour of H₂O and H₂ molecules can be enhanced by encaging THF molecules in the (5¹²6⁴) cavities. Additionally, the motion of THF molecules is restricted due to its high interaction energy barrier. Accordingly, THF, as a stabiliser, is helpful in increasing the stability of hydrogen hydrate.     

Glow discharge with electrostatic confinement of electrons in a chamber bombarded by fast electrons

A metal substrate is immersed in plasma of glow discharge with electrostatic confinement of electrons inside the vacuum chamber volume V ≈ 0.12 m³ filled with argon or nitrogen at pressures 0.005–5 Pa, and dependence of discharge characteristics on negative substrate potential is studied. Emitted by the substrate secondary electrons bombard the chamber walls and it results in electron emission growth of the chamber walls and rise of gas ionization intensity inside the chamber. Increase of voltage U between the chamber and the substrate up to 10 kV at a constant discharge current I _d in the anode circuit results in a manifold rise of current I in the substrate circuit and decrease of discharge voltage U _d between the anode and the chamber from hundreds to tens of volts. At pressure p < 0.05 Pa nonuniformity of plasma density does not exceed ∼10%. Using the Child-Langmuir law, as well as measurement results of sheath width d between homogeneous plasma and a lengthy flat substrate dependent on voltage U ion current density j _i on the substrate surface and ion-electron emission coefficient γ _i are calculated. After the current in circuit of a substrate made of the same material is measured, the γ _i values may be used to evaluate the average dose of ion implantation. The rate of dose rise at a constant high voltage U is by an order of magnitude higher than in known systems equipped with generators of square-wave high-voltage pulses. Application to the substrate of 10-ms-wide sinusoidal high-voltage pulses, which follow each other with 100-Hz frequency, results in synchronous oscillations of voltage U and ion current I _i in the substrate circuit. In this case variation of the sheath width d due to oscillations of U and Ii is insignificant and d does not exceed several centimeters thus enabling substrate treatment in a comparatively small vacuum chamber.     

Oxidative degradation of quinazoline in supercritical water: a combined ReaxFF and DFT study

ABSTRACT

Quinazoline (Qu) is a representative heterocyclic compound in chemical wastewater. In this work, the supercritical water oxidation of Qu is investigated using molecular dynamics simulations based on the ReaxFF reactive force field combined with density functional theory (DFT) method. The detailed reaction pathways, transformation routes of nitrogen element, and kinetic behaviours are systematically analyzed at the atomistic level. Simulation results show that the increment of temperature and O₂ molecule accelerates the reaction rate and facilitates the complete destruction of Qu. The pyrimidine ring in Qu can be attacked by the OH radical, O₂ molecule, and H₂O molecule, thereby causing three main pathways for the pyrimidine ring-opening reaction. The aromatic ring undergoes a ring rearrangement process and opens under the attack of active O₂ molecules. DFT calculations demonstrate that the supercritical water cluster can decrease the cracking energy of chemical bonds and accelerate the degradation rate of Qu. In addition, the transformation routes of nitrogen element during reaction are described. NH₃ is found to be the primary N-containing product after ring-opening reactions and is an intermediate for the production of N₂. Finally, the value of activation energy is obtained as 123.0?kJ/mol, which is reasonably consistent with the experimental results.     

Magnesium spin state determines the energetics of an adenosinetriphosphate molecule

The molecular dynamics method (density functional theory) DFT:B3LYP (6-3IG** basis set, t = 310 K) was used to study interactions between a molecule of adenosinetriphosphate (ATP) (ATP subsystem) and the [Mg(H₂O)₆]²⁺ magnesium cofactor (Mg subsystem) in an aqueous medium simulated by 78 water molecules in the singlet (S) and triplet (T) states. Potential energy surfaces (PESs) for the S (lowest in energy) and T states (highest in energy) are significantly separated in space. Motion along them directs the Mg complex either to oxygen atoms of the γ-β-phosphate groups (O1–O2) (S state of PES) or to oxygen atoms of the β-α-phosphate groups (O2–O3) (T state of PES). Chelation of the γ-β- and β-α-phosphates leads to formation of a stable low-energy ([Mg(H₂O)₄-(OI-O2)ATP]^2?) complex or a metastable high-energy ([Mg(H₂O)₂-(O2–O3)ATP]^2?) complex, respectively, which differ in number of water molecules surrounding the Mg atom. Intersection of two T PESs is accompanied by formation of an unstable state characterized by redistribution of spins between the Mg and ATP subsystems. This state, being sensitive to interaction with the Mg nuclear spin (²⁵Mg), induces an unpaired electron spin, which initiates the ATP cleavage by the ion-radical mechanism, yielding a reactive ion radical of adenosinemonophosphate (·AMP^?), which was earlier found experimentally by the method of chemically induced dynamic nuclear polarization (CIDNP). Biological aspects of the results obtained are discussed.     

DFT studies of the adsorption and dissociation of H2O on the Al13 cluster: origins of this reactivity and the mechanism for H2 release

A theoretical study of the chemisorption and dissociation pathways of water on the Al₁₃ cluster was performed using the hybrid density functional B3LYP method with the 6-311+G(d, p) basis set. The activation energies, reaction enthalpies, and Gibbs free energy of activation for the reaction were determined. Calculations revealed that the H₂O molecule is easily adsorbed onto the Al₁₃ surface, forming adlayers. The dissociation of the first H₂O molecule from the bimolecular H₂O structure via the Grotthuss mechanism is the most kinetically favorable among the five potential pathways for O–H bond breaking. The elimination of H₂ in the reaction of an H₂O molecule with a hydrogen atom on the Al cluster via the Eley–Rideal mechanism has a lower activation barrier than the elimination of H₂ in the reaction of two adsorbed H atoms or the reaction of OH and H. Following the adsorption and dissociation of H₂O, the structure of Al₁₃ is distorted to varying degrees.

Simulation and optical spectroscopy of a DC discharge in a CH<Subscript>4</Subscript>/H<Subscript>2</Subscript>/N<Subscript>2</Subscript> mixture during deposition of nanostructured carbon films

Two-dimensional numerical simulations of a dc discharge in a CH₄/H₂/N₂ mixture in the regime of deposition of nanostructured carbon films are carried out with account of the cathode electron beam effects. The distributions of the gas temperature and species number densities are calculated, and the main plasmachemical kinetic processes governing the distribution of methyl radicals above the substrate are analyzed. It is shown that the number density of methyl radicals above the substrate is several orders of magnitude higher than the number densities of other hydrocarbon radicals, which indicates that the former play a dominant role in the growth of nanostructured carbon films. The model is verified by comparing the measured optical emission profiles of the H(n ≡ 3), C ₂ ^* , CH*, and CN* species and the calculated number densities of excited species, as well as the measured and calculated values of the discharge voltage and heat fluxes onto the electrodes and reactor walls. The key role of ion–electron recombination and dissociative excitation of H₂, C₂H₂, CH₄, and HCN molecules in the generation of emitting species (first of all, in the cold regions adjacent to the electrodes) is revealed.     

Hydration in purple membrane as a function of relative humidity

Neutron diffraction experiments on the purple membrane of Halobacterium halobium as a function of H₂OD₂O exchange in a wide relative humidity range, are described.Increasing relative humidity leads primarily to hydration of the lipid area in the membrane. The exchanged H density is higher in the centre of the protein than at the protein-lipid interface, in support of the hypothesis that the molecule has a hydrophilic interior. However, there is no aqueous pocket in the protein.     

The polythiophene molecular segment as a sensor model for H<Subscript>2</Subscript>O,HCN, NH<Subscript>3</Subscript>, SO<Subscript>3</Subscript>, and H<Subscript>2</Subscript>S: a density functional theory study

Studying the interaction of some atmospheric gases (H₂O, HCN, NH₃, SO₃ and H₂S) with 3PT oligomers is important in the development of polymeric sensors for gas detection. In the present study, we studied the relaxed geometries, interaction energies, charge analysis, HOMO–LUMO orbital analysis, and UV–vis spectra of all interacted systems using first-principles density functional theory (DFT). All these analyses indicated the potential of polythiophene as an inexpensive polymeric sensor for the analytes mentioned. Interaction energy values of ?19.90, ?19.66, ?14.01, ?8.70, and ?4.76 kJ mol^?1 were achieved for adsorption of SO₃, H₂O, NH₃, HCN, and H₂S on 3PT, respectively. Consequently, clarification of their physical parameters became the major focus of this study.     

Unveiling Amyloid-β<Subscript>1–42</Subscript> Interaction with Zinc in Water and Mixed Hexafluoroisopropanol Solution in Alzheimer’s Disease

Alzheimer’s disease (AD) is a neurodegenerative disorder caused by overproduction and accumulation of amyloid beta-peptide (Aβ). The hallmarks associated with this AD are the presence of Aβ plaques between the nerve cell in the brain which leading to synaptic loss in memory. The amyloid plaques contain of transition metals like zinc, copper and iron. In a healthy brain, the metal ions are present in balance concentration. High concentrations of Zn are normally released during neurotransmission process. The release of Zn might cause the aggregation of Aβ leading to AD. Amyloid-β_1–42 is the main type of Aβ in amyloid plaque. There still have limited explanation on how Aβ_1–42 interaction with Zn metal, as well as the effect of Zn metal on the Aβ structure in different solvents in atomic detail. Therefore, we investigated the structural changes of Aβ_1–42 in water (Aβ-H₂O) and the mixed hexafluoroisopropanol (HFIP) with water (Aβ-HFIP/H₂O). The mixed solvent consisted of hexafluoroisopropanol (HFIP) and water was used with the ratio of HFIP:H₂O (80:20). The effect of zinc ion was also examined for the interaction of Aβ peptide with zinc in water (Aβ-Zn-H₂O) and mixed solvent (Aβ-Zn-HFIP/H₂O) using all atom level molecular dynamics (MD) calculations for 1 μs. We found that Aβ-Zn-HFIP/H₂O contained more α-helix compared to Aβ-HFIP/H₂O while Aβ-H₂O and Aβ-Zn-H₂O produced well-dissolved structure and they contained more β-sheets. β-turns are possible to bind with the receptor proteins and may induce the aggregation process in AD. Thus, Aβ-H₂O and Aβ-Zn-H₂O have higher possibility leading to AD compared to Aβ-Zn-HFIP/H₂O and Aβ-HFIP/H₂O models.     

Simulation of ethylene conversion initiated by a streamer corona in an air flow

The conversion of ethylene (C₂H₄) at concentrations of 400 and 930 ppm in an air flow at a temperature of 295 K is simulated. Ethylene is added to air either upstream of the discharge chamber or in the reaction tube, downstream of a pulsed corona discharge. It is taken into account that the distribution of the gas components in the discharge zone is nonuniform due to the streamer nature of the discharge. In the reaction tube, all of the components are assumed to be uniform. Simulation results agree with the experiments carried out at voltage pulse amplitudes of 30 and 40 kV, a gas flow rate of 2–10 l/min, and a specific energy deposition of up to 0.15 J/cm³. It is shown that the ozone produced plays a governing role in the C₂H₄ conversion. It is found that it is possible to minimize the energy spent on conversion by choosing the optimum pulse repetition rate and the specific energy deposited per pulse. The presence of water vapor impedes the ethylene conversion and increases the concentration of formaldehyde and methane.     

Effect of Na+ and K+ Ions on the Initial Crystallization Process of Lysozyme in the Presence of D2O and H2O

In the initial stage of the crystallization of egg-white lysozyme, monomeric lysozyme aggregated rapidly to form a nucleus in the presence of high salt concentrations. In the present studies, we examined the initial aggregation process of lysozyme (initial crystallization process of lysozyme) in D₂O/H₂O with sodium ions or potassium ions, and investigated the relationship between the surface hydrophobicity and the aggregation rate of lysozyme. The effect of sodium ions or potassium ions on the initial aggregation process of lysozyme in D₂O was clearly different from H₂O. The initial aggregation rate of lysozyme in H₂O was slower than in D₂O. In the case of H₂O, the initial aggregation rate was about the same in both ions. But in the case of D₂O, the initial aggregation rate was affected by the ion species and the value was lower in potassium ions than in sodium ions. These results suggest that the interaction between lysozyme molecules is stronger in D₂O than in H₂O. Furthermore, sodium ions have a stronger effect on the interaction than potassium ions in the case of D₂O. There was a good correlation among the initial aggregation rate, surface hydrophobicity, and ζ-potential of lysozyme. The hydrophobic interaction may be an important active force in the initial aggregation process of lysozyme.     

Structures and excitation energies of ozone-water clusters O3(H2O)n (n = 1-4)

Hybrid density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations have been carried out for ozone-water clusters O₃(H₂O)_n (n = 1-4) in order to obtain hydration effects on the absorption spectrum of ozone. The first water molecule in n = 1 is bound to the ozone molecule by an oxygen orientation form in which the oxygen atom of H₂O orients the central oxygen atom of O₃. In n = 2, the water dimer is bound to O₃ and then the cyclic structure is formed as the most stable structure. For n = 3 (or n = 4), the cyclic water trimer (or tetramer) is bound by a hydrogen bond to the ozone molecule. The TD-DFT calculations of O₃(H₂O)_n (n = 0-4) show that the first and second excitation energies of O₃ are blue-shifted by the interaction with the water clusters. The magnitude of the spectral shift is largest in n = 2, and the shifts of the excitation energies are +0.07 eV for S₁ and +0.13 eV for S₂ states. In addition to the spectral shifts (S₁ and S₂ states), it is suggested that a charge-transfer band is appeared as a low-lying excited state above the S₁ and S₂ states. The origin of the spectrum shifts was discussed on the basis of theoretical results.