DFT study of the mechanism of the reaction of aminoguanidine with methylglyoxal

Density functional theory calculations were used in the theoretical investigation of the adsorption properties of sumanene towards molecules considered as common air pollutants: CO, CO₂ and NH₃. The insignificant perturbation of sumanene after adsorption and the adsorption energies obtained indicate a physisorption mechanism. It was shown that, contrary to carbon nanotubes, sumanene is able to adsorb CO molecules, and that adsorption of CO₂ by sumanene is stronger than adsorption of CO₂ by C₆₀. To better understand the adsorption characteristics of sumanene, density of states and natural bond order analyses were performed, which showed that chemical interactions exist and that these are more important mostly on the convex side. Better adsorption properties were obtained for the concave side as adsorption is dictated by physisorption mechanisms due to the specific bowl-shaped geometry of sumanene, because of which more negative charge is located precisely on the concave side. Molecular electrostatic potential surfaces were also used in order to better locate the adsorption sites and gain additional details about adsorption.

Theoretical Study of the TiO2 and MgO Surface Acidity and the Adsorption of Acids and Bases

We present ab-initio periodic Hartree–Fock calculations (crystal program) of small molecules on TiO₂ and MgO. The adsorption of the molecules may be molecular or dissociative. This depends on their acid and basic properties in the gas phase. For the molecular adsorption, the molecules are adsorbed as bases on Ti(+IV) sites, the adsorption energies correlate with the proton affinities. The dissociations on the surface correlate with the gas phase cleavages: thus, the dissociation of MeOH leads to a preferential basic cleavage (the fragment HO– is adsorbed on a Ti⁺⁴ ion and the fragment Me⁺ is adsorbed on a O²– ion of the oxide). The opposite result is obtained with MeSH. Another important factor is the adsorbate–adsorbate interaction: favorable cases are a sequence of H-bonds for the hydroxyl groups resulting from the water dissociation and the mode of adsorption for the ammonium ions. Lateral interactions also force the adsorbed CO₂ molecules to bend over the surface so that their mutual orientation resembles the geometry of the CO₂ dimer. With respect to water adsorption, MgO appears to be a basic oxide. As experimentally observed, NH₃ adsorbs preferentially on TiO₂ and CO₂ on MgO. However, this difference of reactivity should not be expressed in terms of acid vs. basic behaviour but in terms of hard and soft acidity. The MgO surface is a 'soft' acidic surface that reacts preferentially with the soft base, CO₂.     

Reverberation of excitation in neuronal networks interconnected through voltage-gated gap junction channels

We combined Hodgkin–Huxley equations and gating models of gap junction (GJ) channels to simulate the spread of excitation in two-dimensional networks composed of neurons interconnected by voltage-gated GJs. Each GJ channel contains two fast and slow gates, each exhibiting current–voltage (I-V) rectification and gating properties that depend on transjunctional voltage (V_j). The data obtained show how junctional conductance (g_j), which is necessary for synchronization of the neuronal network, depends on its size and the intrinsic firing rate of neurons. A phase shift between action potentials (APs) of neighboring neurons creates bipolar, short-lasting V_j spikes of approximately ±100 mV that induce V_j gating, leading to a small decay of g_j, which can accumulate into larger decays during bursting activity of neurons. We show that I-V rectification of GJs in local regions of the two-dimensional network of neurons can lead to unidirectional AP transfer and consequently to reverberation of excitation. This reverberation can be initiated by a single electrical pulse and terminated by a low-amplitude pulse applied in a specific window of reverberation cycle. Thus, the model accounts for the influence of dynamically modulatable electrical synapses in shaping the function of a neuronal network and the formation of reverberation, which, as proposed earlier, may be important for the development of short-term memory and its consolidation into long-term memory.     

Electrical and chemical properties of XeCl*(308 nm) exciplex lamp created by a dielectric barrier discharge

The aim of this work is to highlight, through numerical modeling, the chemical and the electrical characteristics of xenon chloride mixture in XeCl* (308 nm) excimer lamp created by a dielectric barrier discharge. A temporal model, based on the Xe/Cl₂ mixture chemistry, the circuit and the Boltzmann equations, is constructed. The effects of operating voltage, Cl₂ percentage in the Xe/Cl₂ gas mixture, dielectric capacitance, as well as gas pressure on the 308-nm photon generation, under typical experimental operating conditions, have been investigated and discussed. The importance of charged and excited species, including the major electronic and ionic processes, is also demonstrated. The present calculations show clearly that the model predicts the optimal operating conditions and describes the electrical and chemical properties of the XeCl* exciplex lamp.     

The electronic transport properties of B<Subscript>40</Subscript> fullerenes with chalcogens as anchor atoms

Fullerenes are the most popular molecules to use in applications related to molecular electronics because of their superconductive nature. These molecules show a diverse range of properties, including optical, electronic, and structural characteristics. In this work, we focused on the electronic transport properties of molecular devices consisting of the fullerene B₄₀ or B₄₀ with different anchor atoms between two gold electrodes in a two-probe configuration. The elements used as anchor atoms in the B₄₀ molecules were oxygen, selenium, and sulfur, i.e., chalcogens. The current characteristics of these fullerene-based molecular devices were calculated and analyzed. The analysis highlighted the superior electrical conductivity of the pure B₄₀ device compared to the devices based on its chalcogen-anchored variants. The conductivities of the molecular devices were ranked as follows: pure B₄₀?>?selenium-anchored > sulfur-anchored > oxygen-anchored B₄₀. It was also noted that the devices based on B₄₀ and its chalcogen-anchored variants gave nonzero conductance values at zero bias. These results pave the way for the application of these molecules in future nanodevices utilizing extremely small bias voltages.     

Reactivity of phosphorene with a 3d element trioxide (CrO<Subscript>3</Subscript>) considering van der Waals molecular interactions: a DFT-D2 study

First-principle calculations are performed to investigate the interaction between clean black phosphorene and the CrO₃ molecule which is known to be a powerful oxidizer and a suspected carcinogen. Van der Waals forces are included in all calculations through empirical corrections. Energetics studies are first done to determine the structural stability. Then charge density, Löwdin population analysis and electronic states are evaluated. Results show that the CrO₃ molecule, with an acceptor electron character, is chemisorbed on the phosphorene surface inducing minimal geometrical distortions, however, after adsorption, a partial charge gradient is produced between the P atoms located at the phosphorene upper and lower planes. Furthermore, variations on the CrO₃ concentration causes different interaction strengths. At high concentrations of adsorbed CrO₃ molecules, the interaction with the surface becomes stronger due to an increased steric effect between neighboring molecules. Nevertheless, this effect along with the geometrical distortions produced on the phosphorene structure, due to the large number of molecules adsorbed, leads to a decrement on the adsorption energy. It is expected that the reported results may render phosphorene as a promising material for application as a gas sensor.     

Selective detection of cyanogen halides by BN nanocluster: a DFT study

The electronic sensitivity and adsorption behavior toward cyanogen halides (X–CN; X?=?F, Cl, and Br) of a B₁₂N₁₂ nanocluster were investigated by means of density functional theory calculations. The X-head of these molecules was predicted to interact weakly with the BN cluster because of the positive σ-hole on the electronic potential surface of halogens. The X–CN molecules interact somewhat strongly with the boron atoms of the cluster via the N-head, which is accompanied by a large charge transfer from the X–CN to the cluster. The change in enthalpy upon the adsorption process (at room temperature and 1 atm) is about ?19.2, ?23.4, and ?30.5 kJ mol^?1 for X?=?F, Cl, and Br, respectively. The LUMO level of the BN cluster is largely stabilized after the adsorption process, and the HOMO–LUMO gap is significantly decreased. Thus, the electrical conductivity of the cluster is increased, and an electrical signal is generated that can help to detect these molecules. By increasing the atomic number of X, the signal will increase, which makes the sensor selective for cyanogen halides. Also, it was indicated that the B₁₂N₁₂ nanocluster benefits from a short recovery time as a sensor.     

Simultaneous Measurements of Cytoplasmic K Concentration and the Plasma Membrane Electrical Parameters in Single Membrane Samples of Chara corallina

The electrophysiological properties of cytoplasm-rich fragments (single membrane samples) prepared from internodal cells of Chara corallina were explored in conjunction with K⁺-sensitive microelectrode and current-voltage (I-V) measurements. This system eliminated the problem of the inaccessible cytoplasmic layer, while preserving many of the electrical characteristics of the intact cells. In 0.1 millimolar external K concentration (K_o⁺), the resting conductance (membrane conductance G_m, 0.85 ± 0.25 Siemens per square meter (±standard error)) of the single membrane samples, was dominated by the proton pump, as suggested by the response of the near-linear I-V characteristic to changes in external pH. Initial cytoplasmic K⁺ activities (a_K+), judged most reliable, gave values of 117 ± 67 millimolar; stable a_K+ values were 77 ± 31 millimolar. Equilibrium potentials for K⁺ (Nernst equilibrium potential) (E_K) calculated, using either of these data sets, were near the mean membrane potential (V_m). On a cell-to-cell basis, however, E_K was generally negative of the V_m, despite an electrogenic contribution from the Chara proton pump. When K_o⁺ was increased to 1.0 millimolar or above, G_m rose (by 8- to 10-fold in 10 millimolar K_o⁺), the steady state I-V characteristics showed a region of negative slope conductance, and V_m followed E_K. These results confirm previous studies which implicated a K_o⁺-induced and voltage-dependent permeability to K⁺ at the Chara plasma membrane. They provide an explanation for transitions between apparent K_o⁺-insensitive and K_o⁺-sensitive (`K⁺ electrode') behavior displayed by the membrane potential, as recorded in many algae and higher plant cells.     

Computational study of the NO,SO<Subscript>2</Subscript>, and NH<Subscript>3</Subscript> adsorptions on fragments of 3N-graphene and Al/3N graphene

The adsorption properties of common gas molecules (NO, NH₃, and SO₂) on the surface of 3N-graphene and Al/3N graphene fragments are investigated using density functional theory. The adsorption energies have been calculated for the most stable configurations of the molecules on the surface of 3N-graphene and Al/3N graphene fragments. The adsorption energies of Al/3N graphene-gas systems are ?220.5 kJ mol^?1 for Al/3NG-NO, ?111.9 kJ mol^?1 for Al/3NG-NH₃, and ?347.7 kJ mol^?1 for Al/3NG-SO₂, respectively. Compared with the 3N-graphene fragment, the Al/3N graphene fragment has significant adsorption energy. Furthermore, the molecular orbital, density of states, and electron densities distribution were used to explore the interaction between these molecules and the surface. We found that orbital hybridization exists between these molecules and the Al/3N graphene surface, which indicates that doping Al significantly increases the interaction between the gas molecules and Al/3N graphene. In addition, compared with Li, Al can more powerfully enhance adsorption of the 3N-graphene fragment. The results indicate that Al/3N graphene can be viewed as a new nanomaterial adsorbent for NO, NH₃, and SO₂.     

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.     

Nonlinearity in the I-V characteristics in thin lipid films: Effect of AC and DC fields

The current-voltage characteristics of bilayer lipid membranes of oxidized cholesterol separating two bathing solutions have already been extensively studied under a DC electric field. The observed deviation from linearity at high field has been explained by field-induced pore formation, which then act as ion channels in the membrane. Using thin films of oxidized cholesterol and of dipalmitoyl phosphatidylcholine, we have reported for the first time similar deviation from nonlinearity in the DC I-V characteristics when the applied field is above 40 V/cm. Upon application of an AC field, the conductivity increases as square of frequency, while the nonlinear nature of the I-V characteristic curve is still retained at all frequencies up to 5,000 Hz. Our results indicate that besides pore formation, the intrinsic electrical properties of the constituent lipid molecules are also responsible for the observed nonlinearity.     

Transition metal doped ZnO nanoclusters for carbon monoxide detection: DFT studies

Metal doped ZnO nanomaterials have attracted considerable attention as a chemical sensor for toxic gases. Here, the electronic sensitivity of pristine and Sc-, Ti-, V-, Cr-, Mn-, and Fe-doped Zn₁₂O₁₂ nanoclusters toward CO gas is investigated using density functional theory calculations. It is found that replacing a Zn atom by a Sc or Ti atom does not change the sensitivity of cluster but doping V and Cr atoms significantly increase the sensitivity. Also, Mn, or Fe doping slightly improves the sensitivity. It is predicted that among all, the Cr-doped ZnO cluster may be the most favorable sensor for CO detection because its electrical conductivity considerably changes after the CO adsorption, thereby, generating an electrical signal. The calculated Gibbs free energy change for the adsorption of CO molecule on the Cr-doped cluster is about -51.2 kcal mol^-1 at 298.15 K and 1 atm, and the HOMO-LUMO gap of the adsorbent is changed by about 117.8 %.     

Microhydration of caesium compounds: Cs,CsOH, CsI and Cs2I2 complexes with one to three H2O molecules of nuclear safety interest

The structure and properties of natural gas hydrates containing hydrocarbons, CO₂, and N₂ molecules were studied by using computational quantum chemistry methods via the density functional theory approach. All host cages involved in I, II, and H types structures where filled with hydrocarbons up to pentanes, CO₂ and N₂ molecules, depending on their size, and the structures of these host–guest systems optimized. Structural properties, vibrational spectra, and density of states were analyzed together with results from atoms-in-a-molecule and natural bond orbitals methods. The inclusion of dispersion terms in the used functional plays a vital role for obtaining reliable information, and thus, B97D functional was shown to be useful for these systems. Results showed remarkable interaction energies, not strongly affected by the type of host cage, with molecules tending to be placed at the center of the cavities when host cages and guest molecules cavities are of similar size, but with molecules approaching hexagonal faces for larger cages. Vibrational properties show remarkable features in certain regions, with shiftings rising from host-guest interactions, and useful patterns in the terahertz region rising from water surface vibrations strongly coupled with guest molecules. Likewise, calculations on crystal systems for the I and H types were carried out using a pseudopotential approach combined with Grimme’s method to take account of dispersion.

Carbon dioxide capture using covalent organic frameworks (COFs) type material—a theoretical investigation

The present work deals with a density functional theory (DFT) study of porous organic framework materials containing – groups for CO₂ capture. In this study, first principle calculations were performed for CO₂ adsorption using N-containing covalent organic framework (COFs) models. Ab initio and DFT-based methods were used to characterize the N-containing porous model system based on their interaction energies upon complexing with CO₂ and nitrogen gas. Binding energies (BEs) of CO₂ and N₂ molecules with the polymer framework were calculated with DFT methods. Hybrid B3LYP and second order MP2 methods combined with of Pople 6-31G(d,p) and correlation consistent basis sets cc-pVDZ, cc-pVTZ and aug-ccVDZ were used to calculate BEs. The effect of linker groups in the designed covalent organic framework model system on the CO₂ and N₂ interactions was studied using quantum calculations.     

Be<Superscript>2+ </Superscript>V<Superscript>-</Superscript> Dipole and Adsorptivity of Atomic H on LiH(001) Surface: ab initio Study

An attempt has been made to examine the properties of the title divalent cation impurity - cation vacancy dipole as well as the adsorptivity and diffusion of atomic hydrogen over the LiH (001) surface using ab initio methods of molecular electronic structure calculations. The LiH crystal surface was simulated and quantum clusters of variable size were surrounded by point charges to examine the I-V dipole orientation, cation vacancy migration and overlap effects. The effects of introducing an I-V dipole on the nature of adsorbate-substrate interactions and diffusion of an H atom over the surface were also examined. The results confirm that the (100) orientation of the I-V dipole is energetically more favorable than the (110) orientation and that the cation vacancy migrates without activation energy barriers. The I-V dipole enhances the adsorptivity of atomic hydrogen by ca. 4.96 eV, changes the nature of adsorption from physisorption to chemisorption and introduces an activation energy barrier to H diffusion over the surface. As the I-V dipole is introduced, the HOMO and LUMO levels of the substrate shift to higher energies, the band gap becomes narrower and the atomic charges on the adsorbed H increases. This change in the electronic structure makes the adsorptivity process, through the charge transfer from the H 1s singly occupied AO to the conduction band and from the valence band to the H 1s singly occupied AO more facile.     

Adsorption and dissociation of sulfur-based toxic gas molecules on silicene nanoribbons: a quest for high-performance gas sensors and catalysts

The adsorption behavior of sulfur-based toxic gases (H₂S and SO₂) on armchair silicene nanoribbons (ASiNRs) was investigated using first-principles density functional theory (DFT). Being a zero band gap material, application of bulk silicene is limited in nanoelectronics, despite its high carrier mobility. By restricting its dimensions into one dimension, construction of nanoribbons, and by introduction of a defect, its band gap can be tuned. Pristine armchair silicene nanoribbons (P-ASiNRs) have a very low sensitivity to gas molecules. Therefore, a defect was introduced by removal of one Si atom, leading to increased sensitivity. To deeply understand the impact of the aforementioned gases on silicene nanoribbons, electronic band structures, density of states, charge transfers, adsorption energies, electron densities, current-voltage characteristics and most stable adsorption configurations were calculated. H₂S is dissociated completely into HS and H species when adsorbed onto defective armchair silicene nanoribbons (D-ASiNRs). Thus, D-ASiNR is a likely catalyst for dissociation of the H₂S gas molecule. Conversely, upon SO₂ adsorption, P-ASiNR acts as a suitable sensor, whereas D-ASiNR provides enhanced sensitivity compared with P-ASiNR. On the basis of these results, D-ASiNR can be expected to be a disposable sensor for SO₂ detection as well as a catalyst for H₂S reduction.

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Graphical abstract Comparison of I-V characteristics of pristine and defective armchair silicene nanoribbons with H₂S and SO₂ adsorbed on them

     

A stomatal optimization theory to describe the effects of atmospheric CO2 on leaf photosynthesis and transpiration

Background and Aims

Global climate models predict decreases in leaf stomatal conductance and transpiration due to increases in atmospheric CO₂. The consequences of these reductions are increases in soil moisture availability and continental scale run-off at decadal time-scales. Thus, a theory explaining the differential sensitivity of stomata to changing atmospheric CO₂ and other environmental conditions must be identified. Here, these responses are investigated using optimality theory applied to stomatal conductance.

Methods

An analytical model for stomatal conductance is proposed based on: (a) Fickian mass transfer of CO₂ and H₂O through stomata; (b) a biochemical photosynthesis model that relates intercellular CO₂ to net photosynthesis; and (c) a stomatal model based on optimization for maximizing carbon gains when water losses represent a cost. Comparisons between the optimization-based model and empirical relationships widely used in climate models were made using an extensive gas exchange dataset collected in a maturing pine (Pinus taeda) forest under ambient and enriched atmospheric CO₂.

Key Results and Conclusion

In this interpretation, it is proposed that an individual leaf optimally and autonomously regulates stomatal opening on short-term (approx. 10-min time-scale) rather than on daily or longer time-scales. The derived equations are analytical with explicit expressions for conductance, photosynthesis and intercellular CO₂, thereby making the approach useful for climate models. Using a gas exchange dataset collected in a pine forest, it is shown that (a) the cost of unit water loss λ (a measure of marginal water-use efficiency) increases with atmospheric CO₂; (b) the new formulation correctly predicts the condition under which CO₂-enriched atmosphere will cause increasing assimilation and decreasing stomatal conductance.     

Molecular Simulation of Adsorption of Guest Molecules in Zeolitic Materials: A Comparative Study of Intermolecular Potentials

Abstract

Grand Canonical Monte Carlo simulation, together with an appropriate guest-host forcefield is shown to provide reasonably accurate predictions of adsorption properties of guest molecules in a variety of zeolitic materials. The use of a simple guest-host Kiselev-type potential permits the calculations to capture the essence of the behavior of simple guest-host systems such as rare gases or methane molecules in neutral AlPO₄-5. However, a full scale potential is needed in the more complex cases of large anisotropic molecules adsorbed in cationic zeolites (such as xylene isomers in faujasite). The guest-host potential model developed by Nicholson and coworkers is shown to allow an excellent transferability of the potential parameters from one guest/host system to another.     

Sensitivity Analysis of Gold Nanorod Biosensors for Single Molecule Detection

Single protein molecule detection is important for investigating molecular behavior and diagnosing diseases at an early stage. Gold nanorod (GNR) biosensors have shown promise for label-free detection of single protein molecules. However, for widespread applications of GNR biosensors with high sensitivity, detail studies are needed to understand the effects of the sensing environment and the molecular binding dynamics on the sensitivity. In this work, a comprehensive theoretical analysis with variable substrate, buffer, ligand, and binding position of the target molecules shows that GNR biosensors are highly sensitive for single molecule detection of biological samples including critical pathogens such as cancer marker thyroglobulin and human immunodeficiency virus (HIV) marker glycoprotein. We also propose and show that a GNR biosensor with a dielectric cladding layer on the body increases the sensitivity by orders of magnitude compared to other state-of-the-art biosensors.

     

The contributions of apoplastic,symplastic and gas phase pathways for water transport outside the bundle sheath in leaves

Water movement from the xylem to stomata is poorly understood. There is still no consensus about whether apoplastic or symplastic pathways are more important, and recent work suggests vapour diffusion may also play a role. The objective of this study was to estimate the proportions of hydraulic conductance outside the bundle sheath contributed by apoplastic, symplastic and gas phase pathways, using a novel analytical framework based on measurable anatomical and biophysical parameters. The calculations presented here suggest that apoplastic pathways provide the majority of conductance outside the bundle sheath under most conditions, whereas symplastic pathways contribute only a small proportion. The contributions of apoplastic and gas phase pathways vary depending on several critical but poorly known or highly variable parameters namely, the effective Poiseuille radius for apoplastic bulk flow, the thickness of cell walls and vertical temperature gradients within the leaf. The gas phase conductance should increase strongly as the leaf centre becomes warmer than the epidermis – providing up to 44% of vertical water transport for a temperature gradient of 0.2 K. These results may help to explain how leaf water transport is influenced by light absorption, temperature and differences in leaf anatomy among species.