Adsorption in slit pores and pore-size distribution: A molecular layer structure theory

A new approach is developed to analyze the thermodynamic properties of a sub-critical fluid adsorbed in a slit pore of activated carbon. The approach is based on a representation that an adsorbed fluid forms an ordered structure close to a smoothed solid surface. This ordered structure is modelled as a collection of parallel molecular layers. Such a structure allows us to express the Helmholtz free energy of a molecular layer as the sum of the intrinsic Helmholtz free energy specific to that layer and the potential energy of interaction of that layer with all other layers and the solid surface. The intrinsic Helmholtz free energy of a molecular layer is a function (at given temperature) of its two-dimensional density and it can be readily obtained from bulk-phase properties, while the interlayer potential energy interaction is determined by using the 10-4 Lennard-Jones potential. The positions of all layers close to the graphite surface or in a slit pore are considered to correspond to the minimum of the potential energy of the system. This model has led to accurate predictions of nitrogen and argon adsorption on carbon black at their normal boiling points. In the case of adsorption in slit pores, local isotherms are determined from the minimization of the grand potential. The model provides a reasonable description of the 0-1 monolayer transition, phase transition and packing effect. The adsorption of nitrogen at 77.35 K and argon at 87.29 K on activated carbons is analyzed to illustrate the potential of this theory, and the derived pore-size distribution is compared favourably with that obtained by the Density Functional Theory (DFT). The model is less time-consuming than methods such as the DFT and Monte-Carlo simulation, and most importantly it can be readily extended to the adsorption of mixtures and capillary condensation phenomena.

Ab initio studies of hydrogen desorption from low index magnesium hydride surface

The low index Magnesium hydride surfaces, MgH2(001) and MgH2(110), have been studied by ab intio Density Functional Theory (DFT) calculations. It was found that the MgH2(110) surface is more stable than MgH2(001) surface, which is in good agreement with the experimental observation. The H-2 desorption barriers vary depending on the crystalline surfaces that are exposed and also the specific H atom sites involved-they are found to be generally high, due to the thermodynamic stability of the MgH2, system, and are larger for the MgH2(001) surface. The pathway for recombinative desorption of one in-plane and one bridging H atom from the MgH2(110) surface was found to be the lowest energy barrier amongst those computed (172 KJ/mol) and is in good agreement with the experimental estimates. (c) 2006 Elsevier B.V. All rights reserved.

Catalytic effects of subsurface carbon in the chemisorption of hydrogen on a Mg(0001) surface: an ab-initio study

Ab initio density functional theory (DFT) calculations are performed to explore possible catalytic effects on the dissociative chemisorption of hydrogen on a Mg(0001) surface when carbon is incorporated into Mg materials. The computational results imply that a C atom located initially on a Mg(0001) surface can migrate into the subsurface and occupy an fcc interstitial site, with charge transfer to the C atom from neighboring Mg atoms. The effect of subsurface C on the dissociation of H-2 on the Mg(0001) surface is found to be relatively marginal: a perfect sublayer of interstitial C is calculated to lower the barrier by 0.16 eV compared with that on a pure Mg(0001) surface. Further calculations reveal, however, that sublayer C may have a significant effect in enhancing the diffusion of atomic hydrogen into the sublayers through fcc channels. This contributes new physical understanding toward rationalizing the experimentally observed improvement in absorption kinetics of H2 when graphite or single walled carbon nanotubes (SWCNT) are introduced into the Mg powder during ball milling.

New insights into the interaction of hydrogen atoms with boron-substituted carbon

Boron substitution in carbon materials has been comprehensively investigated using the density functional theory method. It was found that there is a correlation between the stability of the graphene sheet, the distribution of T electrons, the electrostatic potential, and the capability for hydrogen-atom adsorption. Boron substitution destabilizes the graphene structure, increases the density of the electron wave around the substitutional boron atoms, and lowers the electrostatic potential, thus improving the hydrogen adsorption energy on carbon. However, this improvement is only ca. 10-20% instead of a factor of 4 or 5. Our calculations also show that two substitutional boron atoms provide consistent and reliable results, but one substitutional boron results in contradictory conclusions. This is a warning to other computational chemists who work on boron substitution that the conclusion from one substitutional boron might not be reliable.

First-principle study of adsorption of hydrogen on Ti-doped Mg(0001) surface

Ab initio density functional theory (DFT) calculations are performed to study the adsorption of H-2 molecules on a Ti-doped Mg(0001) surface. We find that two hydrogen molecules are able to dissociate on top of the Ti atom with very small activation barriers (0.103 and 0.145 eV for the first and second H-2 molecules, respectively). Additionally, a molecular adsorption state of H-2 above the Ti atom is observed for the first time and is attributed to the polarization of the H-2 molecule by the Ti cation. Our results parallel recent findings for H-2 adsorption on Ti-doped carbon nanotubes or fullerenes. They provide new insight into the preliminary stages of hydrogen adsorption onto Ti-incorporated Mg surfaces.

Three-dimensional nitrogen-doped graphene supported molybdenum disulfide nanoparticles as an advanced catalyst for hydrogen evolution reaction

An efficient three-dimensional (3D) hybrid material of nitrogen-doped graphene sheets (N-RGO) supporting molybdenum disulfide (MoS2) nanoparticles with high-performance electrocatalytic activity for hydrogen evolution reaction (HER) is fabricated by using a facile hydrothermal route. Comprehensive microscopic and spectroscopic characterizations confirm the resulting hybrid material possesses a 3D crumpled few-layered graphene network structure decorated with MoS2 nanoparticles. Electrochemical characterization analysis reveals that the resulting hybrid material exhibits efficient electrocatalytic activity toward HER under acidic conditions with a low onset potential of 112 mV and a small Tafel slope of 44 mV per decade. The enhanced mechanism of electrocatalytic activity has been investigated in detail by controlling the elemental composition, electrical conductance and surface morphology of the 3D hybrid as well as Density Functional Theory (DFT) calculations. This demonstrates that the abundance of exposed active sulfur edge sites in the MoS2 and nitrogen active functional moieties in N-RGO are synergistically responsible for the catalytic activity, whilst the distinguished and coherent interface in MoS 2 /N-RGO facilitates the electron transfer during electrocatalysis. Our study gives insights into the physical/chemical mechanism of enhanced HER performance in MoS2/N-RGO hybrids and illustrates how to design and construct a 3D hybrid to maximize the catalytic efficiency.

In vitro protective effect and antioxidant mechanism of Resveratrol induced by Dapsone Hydroxylamine in human cells

Dapsone (DDS) hydroxylamine metabolites cause oxidative stress- linked adverse effects in patients, such as methemoglobin formation and DNA damage. This study evaluated the ameliorating effect of the antioxidant resveratrol (RSV) on DDS hydroxylamine (DDSNHOH) mediated toxicity in vitro using human erythrocytes and lymphocytes. The antioxidant mechanism was also studied using in-silico methods. In addition, RSV provided intracellular protection by inhibiting DNA damage in human lymphocytes induced by DDS-NHOH. However, whilst pretreatment with RSV (10-1000 μM significantly attenuated DDS-NHOH-induced methemoglobinemia, but it was not only significantly less effective than methylene blue (MET), but also post-treatment with RSV did not reverse methemoglobin formation, contrarily to that observed with MET. DDS-NHOH inhibited catalase (CAT) activity and reactive oxygen species (ROS) generation, but did not alter superoxide dismutase (SOD) activity in erythrocytes. Pretreatment with RSV did not alter these antioxidant enzymes activities in erythrocytes treated with DDS-NHOH. Theoretical calculations using density functional theory methods showed that DDS-NHOH has a pro-oxidant effect, whereas RSV and MET have antioxidant effect on ROS. The effect on methemoglobinemia reversion for MET was significantly higher than that of RSV. These data suggest that the pretreatment with resveratrol may decrease heme-iron oxidation and DNA damage through reduction of ROS generated in cells during DDS therapy.

Estudo in silico das interações da protease NS3-NS2B de DENV-2 com o inibidor peptídico Bz-nKRR-H com finalidades terapêuticas

Dengue virus is an important patogen that causes Dengue desease in all world, and belongs to Flavivirus gender. The virus consists of enveloped RNA with a single strand positive sense, 11Kb genome. The RNA is translated into a polyprotein precursor, wich is cleaved into 3 structural proteins (C, prM e E) and 7 non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B e NS5). The NS3 is a multifunctional protein, that besides to promote the polyprotein precursor cleavage, also have NTPase, helicase and RTPase activity. The NS3 needs a hydrophilic segment of 40 residues from the transmembrane NS2B protein (who acts like cofator) to realize this functions. Actually, there's no vacines available on the market, and the treatment are just symptomatic. The tetrapeptide inhibitor Bz-Nle-Lys-Arg-Arg-H (Ki de 5,8-7,0 M) was showed as a potent inhibitor μ for NS3prot in Dengue virus. That is a inteligent alternative to treat the dengue desease. The present work aimed analyse the interactions of the ligand bounded to the activity site to provid a clear and depth vision of that interaction. For this purpouse, it was conducted an in silico study, by using quantum mechanical calculations based on Density Functional Theory (DFT), with Generalized Gradient approximation (GGA) to describe the effects of exchange and correlation. The interaction energy of each amino acid belonging to the binding site to the ligand was calculated the using the method of molecular fragmentation with conjugated caps (MFCC). Besides energy, we calculated the distances, types of molecular interactions and atomic groups involved. The theoretical models used were satisfactory and show a more accurate description when the dielectric constant = 20 ε and 80 was used. The results demonstrate that the interaction energy of the system reached convergence at 13.5 A. Within a radius of 13,5A the most important residues were identified. Met49, Met84 and Asp81 perform interactions of hydrogen with the ligant. The Asp79 and Asp75 residues present high energy of attraction. Arg54, Arg85 and Lys 131 perform hydrogen interactions with the ligand, however, appear in BIRD graph having high repulsion energy with the inhibitor. The data also emphasizes the importance of residue Tyr161 and the involvement of the catalytic triad composed by Asp75, His51 and Ser135

Bioquímica quântica na diferenciação dos níveis de ativação de receptores AMPA por agonistas parciais Wilardina

In the central nervous system (CNS) of mammalian, fast synaptic transmission between nerve cells is performed primarily by α-amino-3-hydroxy-5-methyl-4- isoxazolepropionic acid (AMPA) receptors, an ionotropic glutamate receptor that is related with learning, memory and homeostasis of the nervous system. Impairments in their functions are correlated with development of many brain desorders, such as epilepsy, schizophrenia, autism, Parkinson and Alzheimer. The use of willardiine analogs has been shown a powerful tool to understanding of activation and desensitization mechanisms of this receptors, because the modification of a single ligand atom allows the observation of varying levels of efficacy. In this work, taking advantage of Fluorine Willardiine (1.35Å), Hydrogen Willardiine (1.65Å), Bromine Willardiine (1.8Å) and Iodine Willardiine (2.15Å) structures co-crystalized with GluA2 with codes 1MQI, 1MQJ, 1MQH and 1MQG, we attempted to energetically differentiate the four ligands efficacy. The complexes were submitted to energetic calculations based on density functional theory (DFT), under the optics of molecular fractionation with conjugate caps (MFCC) method. Obtained results show a relationship between the energetic values and willardiines efficacy order (FW> HW > BrW > IW), also show the importance of E705, R485, Y450, S654, T655, T480 e P478 as the amino acids that contribute most strongly with the interaction of four partial agonists. Furthermore, we outlined the M708 behaviour, attracted by FW and HW ligands, and repels by BrW and IW. With the datas reported on this work, it is possible for a better understanding of the AMPA receptor, which can serve as an aid in the development of new drugs for this system.

Estudo teórico das propriedades eletrônicas e termodinâmicas de nanofitas quasiperiódicas BCN

Nanoscale materials composed of boron, nitrogen, and carbon have unique properties and may be useful in new technologies. In this thesis, we investigate some properties of BCN nanoribbons constructed according to the Fibonacci quasiperiodic sequence. We analyze properties such as structural stability, electronic density of states, electronic specific heat, band structure, and energy band gap. We have performed first-principles calculations based on density functional theory implemented in the SIESTA code. The results showed that nanoribbons present a fixed value of the formation energy. The electronic density of states was used to calculate the specific heat. We found an oscillatory behavior of the electronic specific heat, in the low temperature regime. We analyze the electronic band structure to determine the energy band gap. The energy band gap oscillates as a function of the Fibonacci generation index n. Our work suggest that appropriate choice of the building block materials of the quasiperiodic sequence, may lead to a tuneable band gap of the quasiperiodic nanoribbons.

Magnetic properties of paramagnetic systems : density functional studies

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Effect of reaction mechanism on precursor exposure time in atomic layer deposition of silicon oxide and silicon nitride

Atomic layer deposition (ALD) of highly conformal, silicon-based dielectric thin films has become necessary because of the continuing decrease in feature size in microelectronic devices. The ALD of oxides and nitrides is usually thought to be mechanistically similar, but plasma-enhanced ALD of silicon nitride is found to be problematic, while that of silicon oxide is straightforward. To find why, the ALD of silicon nitride and silicon oxide dielectric films was studied by applying ab initio methods to theoretical models for proposed surface reaction mechanisms. The thermodynamic energies for the elimination of functional groups from different silicon precursors reacting with simple model molecules were calculated using density functional theory (DFT), explaining the lower reactivity of precursors toward the deposition of silicon nitride relative to silicon oxide seen in experiments, but not explaining the trends between precursors. Using more realistic cluster models of amine and hydroxyl covered surfaces, the structures and energies were calculated of reaction pathways for chemisorption of different silicon precursors via functional group elimination, with more success. DFT calculations identified the initial physisorption step as crucial toward deposition and this step was thus used to predict the ALD reactivity of a range of amino-silane precursors, yielding good agreement with experiment. The retention of hydrogen within silicon nitride films but not in silicon oxide observed in FTIR spectra was accounted for by the theoretical calculations and helped verify the application of the model.