Adsorption of Adenine and Thymine on Zeolites: FT-IR and EPR Spectroscopy and X-Ray Diffractometry and SEM Studies

The interactions of adenine and thymine with and adsorption on zeolites were studied using different techniques. There were two main findings. First, as shown by X-ray diffractometry, thymine increased the decomposition of the zeolites (Y, ZSM-5) while adenine prevented it. Second, zeolite Y adsorbed almost the same amount of adenine and thymine, thus both nucleic acid bases could be protected from hydrolysis and UV radiation and could be available for molecular evolution. The X-ray diffractometry and SEM showed that artificial seawater almost dissolved zeolite A. The adsorption of adenine on ZSM-5 zeolite was higher than that of thymine (Student-Newman-Keuls test-SNK p<0.05). Adenine was also more greatly adsorbed on ZSM-5 zeolite, when compared to other zeolites (SNK p<0.05). However the adsorption of thymine on different zeolites was not statistically different (SNK p>0.05). The adsorption of adenine and thymine on zeolites did not depend on pore size or Si/Al ratio and it was not explained only by electrostatic forces; rather van der Waals interactions should also be considered.     

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.     

The effects of structural parameters of zeolite on the adsorption of hydrogen: a molecular simulation study

The adsorption isotherm of hydrogen in zeolites FAU, LTA, KFI, RWY, RHO and TSC has been simulated employing grand canonical Monte Carlo procedure for a temperature range of 77 to 95 K and different pressures. The effects of structural composition, unit cell volume, framework density and specific surface area of zeolite on hydrogen adsorption in zeolites were investigated. The results clearly show that the adsorption of hydrogen in zeolites with the same silica density is a function of oxygen density at low pressures, and it is approximately the same at intermediate pressures. Nevertheless, at high pressures, the adsorption of hydrogen is a function of pore diameter for zeolites with same silica density. The effect of specific surface area on the adsorption isotherm of hydrogen on zeolites with approximately the same specific surface area is significant at low and high pressures. The results clearly indicate that the adsorption of hydrogen in RWY zeolite has maximum value at 77 K and at high pressures. The optimum condition of pressure for hydrogen adsorption isotherm in RWY zeolite is determined to be 600 bar. At a temperature of 77 K and a pressure of 600 bar, the adsorption of hydrogen in RWY zeolite is 6.93 wt %.     

Removal of free fatty acid in waste frying oil by esterification with methanol on zeolite catalysts

The removal of free fatty acid (FFA) in waste frying oil by esterification with methanol was conducted using various zeolite catalysts. The ZSM-5 (MFI), mordenite (MOR), faujasite (FAU), beta (BEA) zeolites, and silicalite were employed with different Si/Al molar ratio in the reaction. The effects of acidic properties and pore structure of the zeolite catalysts were discussed relating to the conversion of the FFA. The MFI zeolite induced an improvement of the removal efficiency of FFA by cracking to the FFA in its pore structure due to its narrow pore mouth. The catalytic activity for FFA removal was lowered with decreasing of acid strength of the zeolites. The strong acid sites of zeolites induced the high conversion of FFA comparatively. The acid strength and pore structure of acidic zeolites affected the catalytic activity in FFA removal.     

Theoretical Calculations on Zeolites: The Aluminium Substitution in Mordenite,Ferrierite and ZSM-5

Abstract

The experimental determination of Al siting in zeolites involves the use of multiple techniques. Great effort has been made on both, experimental and theoretical approaches. The present study presents a novel methodology for calculating Al/Si replacement energies. Simple semiempirical calculations were applied on Modenite, Ferrierite and ZSM-5 zeolites, resulting in good agreement with the experimetal evidences. We have found that the favored Al substitution sites are T3 and T4 in Mordenite, while T2 and T4 are in Ferrierite, and only the T9 site is favored in ZSM-5. The method presented is based on an average of partial Al/Si replacement energies, evaluated for all rings belonging to each T site, rather than in the calculation of a total replacement energy evaluated for only one representative aggregate.     

Differences in the adsorption and diffusion behaviour of water and non-polar gases in nanoporous carbon: role of cooperative effects of pore confinement and hydrogen bonding

We investigate the effect of pore confinement and molecular geometry on the adsorption and self-diffusion of H₂O, CO₂, Ar, CH₄, C₃H₆, SF₆ and C₅H₁₂, in a realistic model of nanoporous silicon carbide derived carbon (SiC-DC), constructed using hybrid reverse Monte Carlo simulation. Adsorption isotherms, adsorbate–adsorbate and adsorbate–adsorbent contributions to the isosteric heat of adsorption are determined to study the effect of pore confinement, microporosity and molecular geometry on adsorption of these gases. We describe the cooperative effect of pore confinement and hydrogen bonding on the formation of water clusters and anomalous adsorption behaviour of water compared with non-polar gases. We find that, in contrast to literature results based on the slit-pore model, pore-filling does not occur below the saturation pressure in hydrophobic amorphous carbon materials such as SiC-DC and activated carbon fibre. We also compare self-diffusivities and activation energy barriers of water and non-polar gases in the microporous structure of SiC-DC to identify underlying correlations with molecular properties. We demonstrate that the self-diffusivity of water deviates considerably from the correlation between diffusivity and molecular kinetic diameter observed for non-polar gases. This is attributed to the reduced diffusivity of water, and its relatively large energy barrier at high loadings despite its small kinetic diameter, which is due to the blocking effect of water clusters at pore entries.     

Diffusivity of CH4 In Model Silica Nanopores: Molecular Dynamics and Quasichemical Mean Field Theory

Equilibrium molecular dynamics and dual control volume grand canonical molecular dynamics experiments were carried out aiming at the investigation of the dependence of transport diffusivity upon the adsorbent pore size and sorbate concentration of CH₄ in cylindrical silica nanopores at 298?K, calibrated with respect to experimental data of zeolite VPI 5; the results of simulation were elaborated on the basis of the quasichemical mean field approximation via a theoretical model for surface diffusion. Our mapping procedure between simulation and quasichemical theory reveals that sorbate–sorbate energetics emerge as the physical reason for the variation of corrected (Darken) and hence transport diffusivity with respect to pore size and sorbed phase fractional occupancy.     

Semi-analytical mean-field model for predicting breathing in metal–organic frameworks

A new semi-analytical mean-field model is proposed to rationalise breathing of MIL-53 type materials. The model is applied on two case studies, the guest-induced breathing of MIL-53(Cr) with CO₂ and CH₄, and the phase transformations for MIL-53(Al) upon xenon adsorption. Experimentally, MIL-53(Cr) breathes upon CO₂ adsorption, which was not observed for CH₄. This result could be ascribed to the stronger interaction of carbon dioxide with the host matrix. For MIL-53(Al) a phase transition from the large pore phase could be enforced to an intermediate phase with volumes of about 1160–1300 Å³, which corresponds well to the phase observed experimentally upon xenon adsorption. Our thermodynamic model correlates nicely with the adsorption pressure model proposed by Coudert et al. Furthermore the model can predict breathing behaviour of other flexible materials, if the user can determine the free energy of the empty host, the interaction energy between a guest molecule and the host matrix and the pore volume accessible to the guest molecules. This will allow to generate the osmotic potential from which the equilibria can be deduced and the anticipated experimentally observed phase may be predicted.     

Entrapping Molecules in Zeolites Nanocavities: A Thermodynamic and Ab-Initio Study

Adsorption enthalpies of Ar, N₂, CO, H₂O, CH₃CN and NH₃ on H-BEA and H-MFI zeolites and on Silicalite, have been measured calorimetrically at 303K in order to assess the energetic features of dispersive forces interactions (confinement effects), H-bonding interactions with surface silanols and specific interactions with Lewis and Brønsted acidic sites. The adsorption of the molecular probes with model clusters mimicking surface silanols, Lewis and Bronsted sites has been simulated at ab-initio level. The combined use of the two different approaches allowed to discriminate among the different processes contributing to the measured (-Δ_adsH). Whereas CO and N₂ single out contributions from Lewis and Br{\o}nsted acidic sites, Ar is only sensitive to confinement effects. For H₂O, CH₃CN and NH₃ the adsorption on Brønsted sites is competitive with the adsorption on Lewis sites. The energy of interaction of H₂O with all considered zeolites is surprisingly higher than expected on the basis of -Δ_adsH vs PA correlation.     

Modeling of adsorption in nanopores

Adsorption in nonporous materials has been studied using Grand Canonical Monte Carlo simulations. We discuss three types of materials: (a) a model of cylindrical pores with smooth walls, representing MCM-41 like materials, (b) a model of cylindrical pores with regular structured walls (model of carbon nanotubes) and (c) a material with crystalline wall structure (zeolites). Typical problems related to the stability of adsorbed layers have been analyzed. We have shown that the mechanism of adsorption is strongly dependent on the structure of the pore walls. In the case of amorphous walls it may lead to metastable configurations. In nanotubes, the ordered corrugation structure of walls determines the low temperature structure of the adsorbed system. In 3D ordered porous system, such as zeolites, the mechanism of adsorption is mostly determined by characteristic sites of adsorption.Figure Adsorbed atoms and energy fluctuations at the pressure of the first layer formation of krypton atoms: (a) instantaneous numbers of adsorbed atoms (per nm² of the pore wall) as a function of the time of simulation (Monte Carlo steps) observed in a relatively long run, (b) the bimodal distribution of the energy fluctuations is a consequence of the behavior of the systems as shown in (a).     

Molecular simulations of adsorption and separation of acetylene and methane and their binary mixture on MOF-5, HKUST-1 and MOF-505 metal–organic frameworks

In this work, the adsorption of acetylene and its binary mixture with methane on MOF-5, HKUST-1 and MOF-505 was studied using Grand Canonical Monte Carlo molecular simulations. The preferred adsorption sites of acetylene and methane molecules into metal–organic frameworks (MOFs) were investigated. The simulated adsorption isotherms of acetylene on MOF-5 and MOF-505 agreed well with the experimental ones without any reparameterisation of the potential parameters but for HKUST-1 the interaction parameters of the acetylene and copper ion were reparameterised. Comparisons of the calculated adsorption isotherms of acetylene in the studied MOFs showed that the MOF-5 had the lowest adsorption capacity. Our results revealed that guest molecules were most adsorbed on the entrance windows of the octagon pore of HKUST-1, while the preferred adsorption sites were large pores and on the metal ion cluster of MOF-505 and MOF-5, respectively. Adsorption of binary mixtures of methane and acetylene on MOF-5, HKUST-1 and MOF-505 revealed that acetylene adsorption is higher than that of methane. Finally, the results showed that C₂H₂/CH₄ selectivity values on HKUST-1 are significantly higher than on MOF-505 and MOF-5. The preferred adsorption sites of acetylene and methane in an equimolar binary mixture were calculated and discussed.     

Methane and carbon dioxide adsorption and diffusion in amorphous,metal-decorated nanoporous silica

The adsorptive and diffusive behaviour of methane and carbon dioxide in amorphous nanoporous adsorbents composed of spherosilicate building blocks, in which isolated metal sites have been distributed, is examined. The adsorbent contains cubic silicate building blocks (spherosilicate units: Si₈O₂₀), which are cross linked by SiCl₂O₂ bridges and decorated with either –OTiCl₃ or –OSiMe₃ groups of the other cube corners. The model structures were generated to correspond to experimentally synthesised materials, matching physical properties including density, surface area and accessible volume. It is shown that both methane and carbon dioxide adsorb via physisorption only in the modelled materials. Adsorption isotherms and energies at 300 K for pressures up to 100 bar were generated via molecular simulation. The maximum gravimetric capacity of CH₄ is 16.9 wt%, occurring at 300 K and 97 bar. The maximum gravimetric capacity of CO₂ is 50.3 wt%, occurring at 300 K and 51.6 bar. The best performing adsorbent was a low-density (high accessible volume) material with no –OTiCl₃ groups. The presence of –OTiCl₃ did not enhance physisorption even on a volumetric basis, and the high molecular weight of –OTiCl₃ groups is a significant penalty on a gravimetric basis. Based on the pair correlation functions, the most favourable adsorption sites for both adsorbates are located in front of the faces of spherosilicate cubes. The self-diffusivity and activation energy for diffusion are also reported.     

ZSM-5(38)/Al-MCM-41复合分子筛对纤维素催化热解的影响

以纤维素为原料,以自制的不同硅铝比ZSM-5(38)/Al-MCM-41微-介孔复合分子筛为催化剂,在固定床反应器上进行了催化热解实验。采用XRD表征分子筛,采用GC-MS分析生物油成分,考查了催化剂的改变对生物质热解产物及生物油成分的影响。实验结果表明：添加催化剂后,生物油产率降低,且其含水率也有所增加。与未添加催化剂相比,生物油中D L-2,3-丁二醇有明显提高。其中,ZSM-5(38)/Al-MCM-41(20) 最有利于苯酚、愈创木酚 (2-甲氧基-苯酚) 的生成。此外,这几种催化剂均有利于小分子化合物的生成,其中,ZSM-5(38) 有利于C4~C5化合物的生成,微-介孔复合分子筛则有利于C6~C8化合物的生成。     

Chain versus Ring Structures of Selenium Confined in AlPO4-5 Zeolite

A tight binding grand canonical Monte Carlo simulation of the adsorption of selenium in AlPO₄-5 zeolite is presented. We show that the structure of confined Se varies from a stretched chain to a piling of Se₅ rings, with intermediate structures combining chains and rings. It depends on the thermodynamic conditions of the adsorption: the ring structures are favored at low temperatures and high pressures; chains are favored at higher temperatures and lower pressures. These results are in qualitative agreement with recent experimental results.     

N-octane diffusivity enhancement via carbon dioxide in silica slit-shaped nanopores – a molecular dynamics simulation

Equilibrium molecular dynamics simulations were conducted to study the competitive adsorption and diffusion of mixtures containing n-octane and carbon dioxide confined in slit-shaped silica pores of width 1.9 nm. Atomic density profiles substantiate strong interactions between CO₂ molecules and the protonated pore walls. Non-monotonic change in n-octane self-diffusion coefficients as a function of CO₂ loading was observed. CO₂ preferential adsorption to the pore surface is likely to attenuate the surface adsorption of n-octane, lower the activation energy for n-octane diffusivity, and consequently enhance n-octane mobility at low CO₂ loading. This observation was confirmed by conducting test simulations for pure n-octane confined in narrower pores. At high CO₂ loading, n-octane diffusivity is hindered by molecular crowding. Thus, n-octane diffusivity displays a maximum. In contrast, within the concentration range considered here, the self-diffusion coefficient predicted for CO₂ exhibits a monotonic increase with loading, which is attributed to a combination of effects including the saturation of the adsorption capacity of the silica surface. Test simulations suggest that the results are strongly dependent on the pore morphology, and in particular on the presence of edges that can preferentially adsorb CO₂ molecules and therefore affect the distribution of these molecules equally on the pore surface, which appears to be required to provide the effective enhancement of n-octane diffusivity.     

Towards optimal packing and diffusion of fullerene molecules in the Pc-PBBA covalent organic framework

We studied the adsorption and diffusion of the prototypical n-type semiconducting fullerene molecule, C₆₀, inside the pores of the p-type semiconductor, phthalocyanine phenylene-bis(boronic acid) (Pc-PBBA), a member of the class of two-dimensional covalent organic framework (COF) materials. This C₆₀/Pc-PBBA system is an example of an ordered p–n heterojunction suitable for photovoltaic solar cell applications. We found that the small 1.7 Å lateral offset present between COF layers leads to discrete adsorption sites inside the pore, forming essentially a periodic ‘lattice’ on which the fullerene diffuses. By categorising the location of such lattice sites, we found the maximum theoretical packing density of fullerene in representative helical, zigzag and staircase Pc-PBBA stacks, as well as an average packing density in randomly stacked Pc-PBBA layers. All these simulated packing densities (51% of bulk) closely matched related experimental results by Dogru et al. [M. Dogru, M. Handloser, F. Auras, T. Kunz, D. Medina, A. Hartschuh, P. Knochel, T. Bein. A photoconductive thienothiophene-based covalent organic framework showing charge transfer towards included fullerene. Angew Chem Int Ed. 2013;52:2920–2924]. (49% of bulk) for a similar fullerene–COF system, [6,6]-phenyl-C₆₁-butyric acid methyl ester/thienothiophene–COF, which produced a low power conversion efficiency. This shows that there is little improvement to be made to the electron transport in terms of fullerene packing density. We present values of the barriers for all diffusion pathways between neighbouring lattice sites categorised uniquely by a set of symmetry rules. Knowledge of these barriers allows us to generalise fullerene transport mechanisms within the Pc-PBBA pore. We observe that diffusion along the (vertical) pore axis is faster than (lateral) diffusion perpendicular to the pore axis; this will facilitate pore filling.     

Photostimulated formation of radicals on oxide surfaces

We present results ofin situ EPR investigations of the mechanism of photostimulated processes resulting in radical and ion-radical particle formation on the surfaces of oxide dielectrics (magnesium, calcium, aluminum oxides, zeolites). Three types of reactions are discussed:

1. Formation of oxygen anion-radicals on MgO and CaO surfaces.
2. Formation of benzene cation-radicals on ZSM-5 zeolites.
3. Formation of radical particles from aromatic nitrocompounds adsorbed on alumina.

On the basis of investigation of the spectral relationships and the properties of surface active centre, it is concluded that light is absorbed by coordinatively unsaturated surface sites in the first system, whereas in the other processes, electron donor-acceptor (EDA) complexes between adsorbed molecules and surface active sites are supposed to be key intermediates. These EDA complexes are shown to incorporate donor solvent molecules as well. In this case the energetic characteristics of the photoprocesses are substantially determined by the ionization potential of solvent molecules. Mechanisms of photo- and thermostimulated processes are compared and possible similarities are discussed for all the reactions studied.     

YUP.SCX: coaxing atomic models into medium resolution electron density maps

The structures of large macromolecular complexes in different functional states can be determined by cryo-electron microscopy, which yields electron density maps of low to intermediate resolutions. The maps can be combined with high-resolution atomic structures of components of the complex, to produce a model for the complex that is more accurate than the formal resolution of the map. To this end, methods have been developed to dock atomic models into density maps rigidly or flexibly, and to refine a docked model so as to optimize the fit of the atomic model into the map. We have developed a new refinement method called YUP.SCX. The electron density map is converted into a component of the potential energy function to which terms for stereochemical restraints and volume exclusion are added. The potential energy function is then minimized (using simulated annealing) to yield a stereochemically-restrained atomic structure that fits into the electron density map optimally. We used this procedure to construct an atomic model of the 70S ribosome in the pre-accommodation state. Although some atoms are displaced by as much as 33 Å, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments.     

Superior Performance of Microporous Aluminophosphate with LTA Topology in Solar‐Energy Storage and Heat Reallocation

Hydrophilic porous materials are recognized as very promising materials for water‐sorption‐based energy storage and transformation. In this study, a porous, zeolite‐like aluminophosphate with LTA (Linde Type A) topology is inspected as an energy‐storage material. The study is motivated by the material's high predicted pore volume. According to sorption and calorimetric tests, the aluminophosphate outperforms all other zeolite‐like and metal‐organic porous materials tested so far. It adsorbs water in an extremely narrow relative‐pressure interval (0.10 < p /p ₀ < 0.15) and exhibits superior water uptake (0.42 g g^?1) and energy‐storage capacity (527 kW h m^?3). It also shows remarkable cycling stability; after 40 cycles of adsorption/desorption its capacity drops by less than 2%. Desorption temperature for this material, which is one of crucial parameters in applications, is lower from desorption temperatures of other tested materials by 10–15 °C. Furthermore, its heat‐pump performance is very high, allowing efficient cooling in demanding conditions (with cooling power up to 350 kW h m^?3 even at 30 °C temperature difference between evaporator and environment). On the microscopic scale, sorption mechanism in AlPO₄‐LTA is elucidated by X‐ray diffraction, nuclear magnetic resonance measurements, and first‐principles calculations. In this aluminophosphate, energy is stored predominately in hydrogen‐bonded network of water molecules within the pores.