Time evolution of catalytic CO2 hydrogenation to methanol and dimethyl ether (DME) has been investigated in a high-temperature high-pressure reaction chamber where products accumulate over time. The employed catalysts are based on a nano-assembly composed of Cu nanoparticles infiltrated into a Zr doped SiOx mesoporous framework (SBA-15): Cu-Zr-SBA-15. The CO2 conversion was recorded as a function of time by gas chromatography-mass spectrometry (GC-MS) and the molecular activity on the catalyst’s surface was examined by diffuse reflectance in-situ Fourier transform infrared spectroscopy (DRIFTS). The experimental results showed that after 14 days a CO2 conversion of 25% to methanol and DME was reached when a DME selective catalyst was used which was also illustrated by thermodynamic equilibrium calculations. With higher Zr content in the catalyst, greater selectivity for methanol and a total 9.5% conversion to methanol and DME was observed, yielding also CO as an additional product. The time evolution profiles indicated that DME is formed directly from methoxy groups in this reaction system. Both DME and methanol selective systems show the thermodynamically highest possible conversion.

Chemical Vapor Deposition (CVD) is one of the technology platforms forming the backbone of the semiconductor industry and is vital in the production of electronic devices. To upscale a CVD process from the lab to the fab, large area uniformity and high run-to-run reproducibility are needed. We show by a combination of experiments and gas phase kinetics modeling that the combinations of Si and C precursors with the most well-matched gas phase chemistry kinetics gives the largest area of of homoepitaxial growth of SiC. Comparing CH4, C2H4 and C3H8 as carbon precursors to the SiF4 silicon precursor, CH4 with the slowest kinetics renders the most robust CVD chemistry with large area epitaxial growth and low temperature sensitivity. We further show by quantum chemical modeling how the surface chemistry is impeded by the presence of F in the system which limits the amount of available surface sites for the C to adsorb.

Ruthenium(IV)oxide (RuO₂) is a material used for various purposes. It acts as a catalytic agent in several reactions, for example oxidation of carbon monoxide. Furthermore, it is used as gate material in gas sensors. In this work theoretical and computational studies were made on adsorbed molecules on RuO₂ (110) surface, in order to follow the chemistry on the molecular level. Density functional theory calculations of the reactions on the surface have been performed. The calculated reaction and activation energies have been used as input for thermodynamic and kinetics calculations. A surface phase diagram was calculated, presenting the equilibrium composition of the surface at different temperature and gas compositions. The kinetics results are in line with the experimental studies of gas sensors, where water has been produced on the surface, and hydrogen is found at the surface which is responsible for the sensor response.

Monte Carlo and molecular dynamics simulations were performed to investigate the effect on the solubility, diffusion, and permeability of water and oxygen when adding graphene or single-walled carbon nanotubes (SWCNTs) to polyethylene (PE). When compared with pure PE, addition of graphene lowered the solubility of water, whereas at lower temperatures, the oxygen solubility increased because of the oxygen–graphene interaction. Addition of SWCNTs lowered the solubility of both water and oxygen when compared with pure PE. A detailed analysis showed that an ordered structure of PE is induced near the additive surface, which leads to a decrease in the diffusion coefficient of both penetrants in this region. The addition of graphene does not change the permeation coefficient of oxygen (in the direction parallel to the filler) and, in fact, may even increase this coefficient when compared with pure PE. In contrast, the water permeability is decreased when graphene is added to PE. The addition of SWCNTs decreases the permeability of both penetrants. Graphene can consequently be added to selectively increase the solubility and permeation of oxygen over water, at least at lower temperatures. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 589–602

The endogenous molecule 5-aminolevulinic acid (5ALA) and its methyl ester (Me-5ALA) have been used as prodrugs in photodynamic treatment of actinic keratosis and superficial non-melanoma skin cancers for over a decade. Recently, a novel set of 5ALA derivatives based on introducing a hydrolyzable oxime functionality was proposed and shown to generate considerably stronger onset of the photoactive molecule protoporphyrin IX (PpIX) in the cells. In the current work, we employ molecular dynamics simulation techniques to explore whether the higher intercellular concentration of PpIX caused by the oxime derivatives is related to enhanced membrane permeability, or whether other factors contribute to this. It is concluded that the oximes show overall similar accumulation at the membrane headgroup regions as the conventional derivatives and that the transmembrane permeabilities are in general close to that of 5ALA. The highest permeability of all compounds explored is found for Me-5ALA, which correlates with a considerably lower fee energy barrier at the hydrophobic bilayer center. The high PpIX concentration must hence be sought in other factors, where slow hydrolysis of the oxime functionality is a plausible reason, enabling stronger buildup of PpIX over time.

Monte Carlo and molecular dynamics simulations were performed to calculate solubility, S, and diffusion, D, coefficients of oxygen and water in polyethylene, and to obtain a molecular-level understanding of the diffusion mechanism. The permeation coefficient, P, was calculated from the product of S and D. The AMBER force field, which yields the correct polymer densities under the conditions studied, was used for the simulations, and it was observed that the results were not sensitive to the inclusion of atomic charges in the force field. The simulated S for oxygen and water are higher and lower than experimental data, respectively. The calculated diffusion coefficients are in good agreement with experimental data. Possible reasons for the discrepancy in the simulated and experimental solubilities, which results in discrepancies in the permeation coefficients, are discussed. The diffusion of both penetrants occurs mainly by large amplitude, infrequent jumps of the molecules through the polymer matrix.

Porphobilinogen synthase (PBGS) catalyzes the asymmetric condensation and cyclization of two 5-aminolevulinic acid (5-ALA) substrate molecules to give porphobilinogen (PBG). The chemical step of PBGS is herein revisited using QM/MM (ONIOM) calculations. Two different protonation states and several different mechanisms are considered. Previous mechanisms based on DFT-only calculations are shown unlikely to occur. According to these new calculations, the deprotonation step rather than ring closure is rate-limiting. Both the C–C bond formation first mechanism and the C–N bond formation first mechanism are possible, depending on how the A-site ALA binds to the enzyme. We furthermore propose that future work should focus on the substrate binding step rather than the enzymatic mechanism.

Molecular dynamics (MD) simulations have been used to study the melting of α- and β-poly (vinylidene fluoride) (α- and β-PVDF). It is seen that melting at the ends of the polymer chains precedes melting of the bulk crystal structure. Melting of α-PVDF initially occurs via transitions between the two gauche dihedral angles (G ↔ G′) followed by transitions between trans and gauche dihedral angles (T ↔ G/G′). Melting of β-PVDF initially occurs via T → G/G′ transitions and via transitions of complete β- (TTTT) to α- (TGTG') quartets. The melting point of β-PVDF is higher than that of α-PVDF, and the simulated melting points of both phases depend on the length of the polymer chains used in the simulations. Since melting starts at the chain ends, it is important to include these in the simulations, and simulations of infinitely long chains yield melting points far larger than the experimental values (at least for periodic cells of the size used in this work), especially for β-PVDF. The simulated heats of fusion are in agreement with available experimental data.

Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however,is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogensynthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for theformation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to14.0 kcal mol-1. We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.

In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.

Porphobilinogen synthase (PBGS) is a key enzyme in heme biosynthesis that catalyzes the formation of porphobilinogen (PBG) from two 5-aminolevulinic acid (5-ALA) molecules via formation of intersubstrateC-N and C-C bonds. The active site consists of several invariant residues, including two lysyl residues (Lys210 and Lys263; yeast numbering) that bind the two substrate moieties as Schiff bases. Based on experimental studies, various reaction mechanisms have been proposed for this enzyme that generally can be classified according to whether the intersubstrate C-C or C-N bond is formed first. However, the detailed catalytic mechanism of PBGS remains unclear. In the present study, we have employed density functional theory methods in combination with chemical models of the two key lysyl residues and two substrate moieties in order to investigate various proposed reaction steps and gain insight into the mechanism of PBGS. Importantly, it is found that mechanisms in which the intersubstrate C-N bond is formed first have a ratelimiting barrier (17.5 kcal/mol) that is lower than those in which the intersubstrate C-C bond is formed first (22.8 kcal/mol).

5-Aminolevulinic acid (5ALA) and ester derivates thereof are used as prodrugs in photodynamic therapy (PDT). The behavior of 5ALA and three esters of 5ALA in a DPPC lipid bilayer is investigated. In particular, the methyl ester displays a very different free energy profile, where the highest barrier is located in the region with highest lipid density, while the others have their peak in the middle of the membrane, and also displays a considerably lower permeability coefficient than neutral 5ALA and the ethyl ester. The zwitterion of 5ALA has the highest permeability constant, but a significant free energy minimum in the polar head-group region renders an accumulation in this region.

5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. In this study density functional theory calculations were performed on the tautomers of 5ALA and the tautomerization reaction mechanism from its enolic forms (5-amino-4-hydroxypent-3-enoic acid and 5-amino-4-hydroxypent-4-enoic acid) to the more stable 5ALA. The hydrated form 5-amino-4,4-dihydroxypentanoic acid was also studied. The lowest energy pathway of 5ALA tautomerization is by means of autocatalysis, in that an oxygen of the carboxylic group transfers the hydrogen atom as a "crane", with an activation energy of similar to 15 kcal/mol. This should be compared to the barriers of about 35 kcal/mol for water assisted tautomerization, and 60 kcal/mol for direct hydrogen transfer. For hydration of 5ALA, the water catalyzed activation barrier is found to be similar to 35 kcal/mol, approximately 5 kcal/mol lower than direct hydration.

5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. The addition of extracorporeal 5ALA and its alkyl ester derivatives are in current clinical use in photodynamical diagnostics and photodynamic therapy of tumors and skin disorders. In the current study density functional theory calculations are performed on 5ALA and its methyl, ethyl, and hexyl esters, in order to explore the basic chemical properties of these species. It is concluded that even in aqueous media the zwitterionic form of 5ALA is less stable than the non-zwitterionic one, that the local environment (lipid vs water) affects the energetics of reaction considerably, and that the hexyl species is most prone to hydrolysis of the three alkyl ester derivatives.