liu.seSearch for publications in DiVA
Change search
Link to record
Permanent link

Direct link
BETA
Publications (10 of 16) Show all publications
Atakan, A., Erdtman, E., Mäkie, P., Ojamäe, L. & Odén, M. (2018). Time evolution of the CO2 hydrogenation to fuels over Cu-Zr-SBA-15 catalysts. Journal of Catalysis, 362, 55-64
Open this publication in new window or tab >>Time evolution of the CO2 hydrogenation to fuels over Cu-Zr-SBA-15 catalysts
Show others...
2018 (English)In: Journal of Catalysis, ISSN 0021-9517, E-ISSN 1090-2694, Vol. 362, p. 55-64Article in journal (Refereed) Published
Abstract [en]

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.

Keywords
Cu-Zr-SBA-15, CO2 hydrogenation, Catalysis, Time evolution, Thermodynamics, Methanol, Dimethyl ether
National Category
Nano Technology Physical Chemistry
Identifiers
urn:nbn:se:liu:diva-147297 (URN)10.1016/j.jcat.2018.03.023 (DOI)000432770900007 ()
Note

Funding agencies: EUs Erasmus-Mundus program (The European School of Materials Doctoral Programme - DocMASE); Knut och Alice Wallenbergs Foundation [KAW 2012.0083]; Swedish Government Strategic Research Area (SFO Mat LiU) [2009 00971]; Swedish Energy Agency [42022-1]

Available from: 2018-04-16 Created: 2018-04-16 Last updated: 2018-06-14Bibliographically approved
Stenberg, P., Danielsson, Ö., Erdtman, E., Sukkaew, P., Ojamäe, L., Janzén, E. & Pedersen, H. (2017). Matching precursor kinetics to afford a more robust CVD chemistry: a case study of the C chemistry for silicon carbide using SiF4 as Si precursor. Journal of Materials Chemistry C, 5, 5818-5823
Open this publication in new window or tab >>Matching precursor kinetics to afford a more robust CVD chemistry: a case study of the C chemistry for silicon carbide using SiF4 as Si precursor
Show others...
2017 (English)In: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 5, p. 5818-5823Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2017
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-137446 (URN)10.1039/c7tc00138j (DOI)000403571200024 ()
Note

Funding agencies: Knut & Alice Wallenberg Foundation (KAW) project Isotopic Control for Ultimate Material Properties; Swedish Foundation for Strategic Research project SiC - the Material for Energy-Saving Power Electronics [EM11-0034]; Swedish Government Strategic Research

Available from: 2017-05-16 Created: 2017-05-16 Last updated: 2018-10-08Bibliographically approved
Erdtman, E., Andersson, M., Lloyd Spetz, A. & Ojamäe, L. (2017). Simulations of the thermodynamics and kinetics of NH3 at the RuO2 (110) surface. Surface Science, 656, 77-85
Open this publication in new window or tab >>Simulations of the thermodynamics and kinetics of NH3 at the RuO2 (110) surface
2017 (English)In: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 656, p. 9p. 77-85Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2017. p. 9
Keywords
Catalysis; Kinetics; Ruthenium dioxide; Sensor; Surface; Thermodynamics
National Category
Analytical Chemistry
Identifiers
urn:nbn:se:liu:diva-133425 (URN)10.1016/j.susc.2016.10.006 (DOI)000390969300012 ()
Available from: 2016-12-28 Created: 2016-12-28 Last updated: 2018-11-26
Erdtman, E., Bohlén, M., Ahlström, P., Gkourmpis, T., Berlin, M., Andersson, T. & Bolton, K. (2016). A molecular-level computational study of the diffusion and solubility of water and oxygen in carbonaceous polyethylene nanocomposites. Journal of Polymer Science Part B: Polymer Physics, 54(5), 589-602
Open this publication in new window or tab >>A molecular-level computational study of the diffusion and solubility of water and oxygen in carbonaceous polyethylene nanocomposites
Show others...
2016 (English)In: Journal of Polymer Science Part B: Polymer Physics, ISSN 0887-6266, E-ISSN 1099-0488, Vol. 54, no 5, p. 589-602Article in journal (Refereed) Published
Abstract [en]

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

Keywords
diffusion, molecular modeling, nanocomposites, polyethylene (PE), solubility
National Category
Polymer Chemistry Theoretical Chemistry Textile, Rubber and Polymeric Materials Polymer Technologies Nano Technology
Identifiers
urn:nbn:se:liu:diva-129607 (URN)10.1002/polb.23951 (DOI)
Funder
Knowledge Foundation
Available from: 2016-06-22 Created: 2016-06-22 Last updated: 2017-09-13
Eriksson, E. S. E., Erdtman, E. & Eriksson, L. A. (2016). Permeability of 5-aminolevulinic acid oxime derivatives in lipid membranes. Theoretical Chemistry accounts, 135(1), 1-9
Open this publication in new window or tab >>Permeability of 5-aminolevulinic acid oxime derivatives in lipid membranes
2016 (English)In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 135, no 1, p. 1-9Article in journal (Refereed) Published
Abstract [en]

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.

Keywords
5-ALA, 5-ALA derivatives, oximes, prodrugs, photodynamic therapy, permeability, membrane, molecular dynamics
National Category
Theoretical Chemistry Cancer and Oncology Cell Biology
Identifiers
urn:nbn:se:liu:diva-129615 (URN)10.1007/s00214-015-1798-0 (DOI)000401845300001 ()
Available from: 2016-06-22 Created: 2016-06-22 Last updated: 2018-10-15
Börjesson, A., Erdtman, E., Ahlström, P., Berlin, M., Andersson, T. & Bolton, K. (2013). Molecular modelling of oxygen and water permeation in polyethylene. Polymer, 54(12), 2988
Open this publication in new window or tab >>Molecular modelling of oxygen and water permeation in polyethylene
Show others...
2013 (English)In: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 54, no 12, p. 2988-Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2013
Keywords
Permeability, Polyethylene, Molecular simulation, Resursåtervinning, Computational modelling
National Category
Theoretical Chemistry Materials Chemistry Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:liu:diva-150079 (URN)10.1016/j.polymer.2013.03.065 (DOI)000319365900020 ()2320/12338 (Local ID)2320/12338 (Archive number)2320/12338 (OAI)
Funder
Knowledge Foundation
Available from: 2018-08-09 Created: 2018-08-09 Last updated: 2018-08-09
Tian, B.-X., Erdtman, E. & Eriksson, L. A. (2012). Catalytic Mechanism of Porphobilinogen Synthase: The Chemical Step Revisited by QM/MM Calculations. Journal of Physical Chemistry B, 116(40), 12105-12112
Open this publication in new window or tab >>Catalytic Mechanism of Porphobilinogen Synthase: The Chemical Step Revisited by QM/MM Calculations
2012 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 40, p. 12105-12112Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
American Chemical Society, 2012
Keywords
Enzymes, QM/MM, Simulation, Reaction mechanism, Porphobilinogen synthase, Resursåtervinning
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:liu:diva-150081 (URN)10.1021/jp304743c (DOI)000309648900005 ()22974111 (PubMedID)
Available from: 2015-11-13 Created: 2018-08-09 Last updated: 2018-10-29
Erdtman, E., Chelakara Satyanarayana, K. & Bolton, K. (2012). Simulation of α- and β-PVDF melting mechanisms. Polymer, 53(14), 2919-2926
Open this publication in new window or tab >>Simulation of α- and β-PVDF melting mechanisms
2012 (English)In: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 53, no 14, p. 2919-2926Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2012
Keywords
Poly(vinylidene fluoride), Melting mechanism, Molecular simulation, Resursåtervinning
National Category
Materials Chemistry
Identifiers
urn:nbn:se:liu:diva-150080 (URN)10.1016/j.polymer.2012.04.045 (DOI)000305590000014 ()
Available from: 2018-08-09 Created: 2018-08-09 Last updated: 2018-08-09
Erdtman, E., Bushnell, E. A. C., Gauld, J. W. & Eriksson, L. A. (2011). Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase. Computational and Theoretical Chemistry, 963(2-3), 479-489
Open this publication in new window or tab >>Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase
2011 (English)In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 963, no 2-3, p. 479-489Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Amsterdam: Elsevier, 2011
Keywords
Schiff base, 5-Aminolevulinic acid, Porphobilinogen synthase, Density functional theory, Catalysis
National Category
Natural Sciences Physical Chemistry Physical Chemistry Theoretical Chemistry
Identifiers
urn:nbn:se:liu:diva-150070 (URN)10.1016/j.comptc.2010.11.015 (DOI)000288834500036 ()2-s2.0-80054879916 (Scopus ID)
Available from: 2011-01-14 Created: 2018-08-09 Last updated: 2018-08-09
Bushnell, E. A. C., Erdtman, E., Llano, J., Eriksson, L. A. & Gauld, J. W. (2011). The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase. Journal of Computational Chemistry, 32(5), 822-834
Open this publication in new window or tab >>The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase
Show others...
2011 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 5, p. 822-834Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
New York: John Wiley & Sons, 2011
Keywords
uroporphyrinogen decarboxylase III, uroporphyrinogen III, porphyrin biosynthesis, quantum mechanics/molecular mechanics and density functional theory
National Category
Natural Sciences Physical Chemistry Physical Chemistry Theoretical Chemistry Theoretical Chemistry
Identifiers
urn:nbn:se:liu:diva-150066 (URN)10.1002/jcc.21661 (DOI)000288400600007 ()20941734 (PubMedID)2-s2.0-79951968121 (Scopus ID)
Available from: 2011-01-14 Created: 2018-08-09 Last updated: 2018-10-29
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-9455-9558