| 1. |
- Arhammar, C., et al.
(author)
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A theoretical study of possible point defects incorporated into alpha-alumina deposited by chemical vapor deposition
- 2013
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In: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 133:2, s. 1433-
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Journal article (peer-reviewed)abstract
- The energetics and electronic structure of carbon, chlorine, hydrogen, and sulfur in alpha-Al2O3 was investigated by first principles and thermodynamical calculations. These species are present in the gas phase during the synthesis of alpha-Al2O3 by chemical vapor deposition (CVD) but little is known of their solubility in this compound. The heat of formation from standard reference states of the elements varying the chemical potential of each element was calculated. An attempt to model the actual conditions in the CVD process was made, using the species and solid compounds present in a common CVD process as reference states. Our calculations suggest that sulfur from the catalyzing agent H2S will not solve in alpha-Al2O3 during deposition by CVD. It is found that the neutral chlorine and hydrogen interstitial defects display the lowest heat of formation, 281 and 280 kJ/mol, respectively, at the modeled CVD conditions. This energy is too high in order for neutral defects to form during CVD of alpha-Al2O3 at any significant amounts. The charged defects and their compensation were studied. Carbon substituting oxygen is found to be energetically favored under the modeled CVD conditions, considering carbon dioxide as competing species to solid solubility in alpha-Al2O3 at an energy of -128 kJ/mol. However, care needs to be taken when choosing the possible competing carbon-containing phases. Compensation of carbon substituting for oxygen by oxygen vacancies takes place at 110 kJ/mol from standard reference states, graphite, fcc-Al and O-2. The carbon solubility in Al2O3 is difficult to measure with standard analysis techniques such as X-ray diffraction and energy dispersive X-ray spectroscopy, but several stable compounds in the Al-C-O are available in the literature.
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| 2. |
- Baran, Jakub, 1980, et al.
(author)
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On the stability of single-walled carbon nanotubes and their binding strengths
- 2012
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In: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 131:9, s. 1-8
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Journal article (peer-reviewed)abstract
- We have studied the relative stability of hydrogen-terminated single-walled carbon nanotubes (SWNTs) segments, and open-ended SWNT fragments of varying diameter and chirality that are present at the interface of the catalytic metal particles during growth. We have found that hydrogen-terminated SWNTs differ by < 1 eV in stability among different chiralities, which presents a challenge for selective and property-controlled growth. In addition, both zigzag and armchair tubes can be the most stable chirality of hydrogen-terminated SWNTs, which is a fundamental obstacle for property-controlled growth utilizing thermodynamic stability. In contrast, the most armchair-like open-ended SWNTs segments are always the most stable ones, followed in sequence by chiral index up to the least stable zigzag segments. We explain the ordering by triple bond stabilization of the carbon dangling bonds at the open ends, which is a fragment stabilization effect that is only manifested when all bonds between two layers are broken. We show convincingly that the bond strength difference between zigzag and armchair tubes is not present when individual bonds are broken or formed. © Springer-Verlag 2012.
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| 3. |
- Barata-Morgado, Rute, et al.
(author)
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Theoretical study of the conformational equilibrium of 1,4-dioxane in gas phase, neat liquid, and dilute aqueous solutions
- 2013
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In: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 132:10, s. 1390-
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Journal article (peer-reviewed)abstract
- The conformational equilibrium of 1,4-dioxane in the gas phase, in the pure liquid, and in aqueous solution has been studied by means of the Average Solvent Electrostatic Potential from Molecular Dynamics (ASEP/MD) method and the Integral Equation Formalism for the Polarizable Continuum Model (IEF-PCM). The dioxane molecule was described at the DFT(B3LYP)/aug-cc-pVTZ level. In the three phases, the equilibrium is almost completely shifted toward the chair conformer, with populations of the twist-boat conformers lower than 0.01 %. The equilibrium is dominated by the internal energy of the molecule, as the solute-solvent interaction free energies are very similar in the three conformers considered (chair, 1,4 twist-boat, and 2,5 twist-boat). In the pure liquid, where the dioxane-dioxane interaction is dominated by the Lennard-Jones term, the structure is characteristic of a van der Waals liquid. However, the decrease in the C-H distance from gas phase to solution, the increase in the C-H vibrational frequencies, and the presence of a shoulder in the O-Haxial pair radial distribution function point to the presence of a weak C-H-O hydrogen bond. The analysis of the occupancy maps of water oxygen and hydrogen atoms around the 1,4-dioxane molecule confirms this conclusion. Contrary to what is found in small water-dioxane clusters, in the liquid, there is a preference for oxygen atoms to interact with axial hydrogen atoms to form C-H-O hydrogen bonds. Comparison of ASEP/MD and IEF-PCM results indicates that including specific interactions is very important for an adequate description of the solute-solvent interaction; however, the influence of these interactions does not translate in changes in the relative stability of the conformers because it cancels out when energy differences are calculated.
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| 4. |
- Danielsson, Örjan, 1973-, et al.
(author)
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Shortcomings of CVD modeling of SiC today
- 2013
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In: Theoretical Chemistry accounts. - : Springer Berlin/Heidelberg. - 1432-881X .- 1432-2234. ; 132:11, s. 1398-
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Journal article (peer-reviewed)abstract
- The active, epitaxial layers of silicon carbide (SiC) devices are grown by chemical vapor deposition (CVD), at temperatures above 1,600 °C, using silane and light hydrocarbons as precursors, diluted in hydrogen. A better understanding of the epitaxial growth process of SiC by CVD is crucial to improve CVD tools and optimize growth conditions. Through computational fluid dynamic (CFD) simulations, the process may be studied in great detail, giving insight to both flow characteristics, temperature gradients and distributions, and gas mixture composition and species concentrations throughout the whole CVD reactor. In this paper, some of the important parts where improvements are very much needed for accurate CFD simulations of the SiC CVD process to be accomplished are pointed out. First, the thermochemical properties of 30 species that are thought to be part of the gas-phase chemistry in the SiC CVD process are calculated by means of quantum-chemical computations based on ab initio theory and density functional theory. It is shown that completely different results are obtained in the CFD simulations, depending on which data are used for some molecules, and that this may lead to erroneous conclusions of the importance of certain species. Second, three different models for the gas-phase chemistry are compared, using three different hydrocarbon precursors. It is shown that the predicted gas-phase composition varies largely, depending on which model is used. Third, the surface reactions leading to the actual deposition are discussed. We suggest that hydrocarbon molecules in fact have a much higher surface reactivity with the SiC surface than previously accepted values.
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| 5. |
- Falklöf, Olle, et al.
(author)
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Toward ab initio refinement of protein X-ray crystal structures: Interpreting and correlating structural fluctuations
- 2012
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In: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 131
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Journal article (peer-reviewed)abstract
- © Springer-Verlag 2012. The refinement of protein crystal structures currently involves the use of empirical restraints and force fields that are known to work well in many situations but nevertheless yield structural models with some features that are inconsistent with detailed chemical analysis and therefore warrant further improvement. Ab initio electronic structure computational methods have now advanced to the point at which they can deliver reliable results for macromolecules in realistic times using linear-scaling algorithms. The replacement of empirical force fields with ab initio methods in a final refinement stage could allow new structural features to be identified in complex structures, reduce errors and remove computational bias from structural models. In contrast to empirical approaches, ab initio refinements can only be performed on models that obey basic qualitative chemical rules, imposing constraints on the parameter space of existing refinements, and this in turn inhibits the inclusion of unlikely structural features. Here, we focus on methods for determining an appropriate ensemble of initial structural models for an ab initio X-ray refinement, modeling as an example the high-resolution single-crystal X-ray diffraction data reported for the structure of lysozyme (PDB entry “2VB1”). The AMBER force field is used in a Monte Carlo calculation to determine an ensemble of 8 structures that together embody all of the partial atomic occupancies noted in the original refinement, correlating these variations into a set of feasible chemical structures while simultaneously retaining consistency with the X-ray diffraction data. Subsequent analysis of these results strongly suggests that the occupancies in the empirically refined model are inconsistent with protein energetic considerations, thus depicting the 2VB1 structure as a deep-lying minimum in its optimized parameter space that actually embodies chemically unreasonable features. Indeed, density-functional theory calculations for one specific nitrate ion with an occupancy of 62% indicate that water replaces this ion 38% of the time, a result confirmed by subsequent crystallographic analysis. It is foreseeable that any subsequent ab initio refinement of the whole structure would need to locate a globally improved structure involving significant changes to 2VB1 which correct these identified local structural inconsistencies.
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| 6. |
- Frecus, Bogdan, et al.
(author)
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Ab initio study of exchange coupling for the consistent understanding of the magnetic ordering at room temperature in V[TCNE] (x)
- 2014
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In: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 133:5, s. 1470-
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Journal article (peer-reviewed)abstract
- We report quantum chemical calculations providing the exchange coupling constants of the V[TCNE](2) model system, describing the amorphous room temperature molecular magnet V[TCNE] (x) (TCNE = tetracyanoethylene, x similar to 2). The geometry is optimized for the ideal lattice using density functional theory (DFT) calculations with periodic boundary conditions. Broken-symmetry DFT calculations indicate antiparallel spin alignment resulting in ferrimagnetic ordering, but heavily overestimate the value of the exchange coupling. Better estimates of the exchange coupling parameters between the V(II) ion and the [TCNE](-) anionic radical are obtained by means of multiconfigurational calculations performed on smaller molecular models cut from the optimized crystal lattice. Complete active space self-consistent field and multireference second-order perturbation theory calculations provide the sign and the strength of the nearest-neighbor as well as next-nearest-neighbor interactions along all three crystallographic directions. We are able to explain also intuitively the mechanism for antiferromagnetic spin coupling in terms of the superexchange pathways, discussing the role of the main four types of contributions to superexchange. Moreover, we clarify the influence of the transition metal ion on the strength of the exchange interaction and on the critical temperature for long-range ferrimagnetic ordering.
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| 7. |
- Gonzalez-Ramirez, Israel, et al.
(author)
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On the photoproduction of DNA/RNA cyclobutane pyrimidine dimers
- 2011
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In: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 128:4-6, s. 705-711
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Journal article (peer-reviewed)abstract
- The UV photoreactivity of different pyrimidine DNA/RNA nucleobases along the singlet manifold leading to the formation of cyclobutane pyrimidine dimers has been studied by using the CASPT2 level of theory. The initially irradiated singlet state promotes the formation of excimers between pairs of properly oriented nucleobases through the overlap between the pi structures of two stacked nucleobases. The system evolves then to the formation of cyclobutane pyrimidine dimers via a shearing-type conical intersection activating a [2 + 2] photocycloaddition mechanism. The relative location of stable excimer conformations or alternative decay channels with respect to the reactive degeneracy region explains the differences in the photoproduction efficiency observed in the experiments for different nucleobases sequences. A comparative analysis of the main structural parameters and energetic profiles in the singlet manifold is carried out for thymine, uracil, cytosine, and 5-methylcytosine homodimers. Thymine and uracil dimers display the most favorable paths, in contrast to cytosine. Methylation of the nucleobases seems to increase the probability for dimerization.
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| 8. |
- Grand, A., et al.
(author)
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Comparison of the Mechanism of Deamination of 5,6-dihydro-5-methylcytosine with other cytosine derivatives
- 2012
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In: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 131:4
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Journal article (peer-reviewed)abstract
- The mechanism of deamination of 5,6-dihydro-5-methylcytosine has been investigated theoretically and compared to those of other cytosine derivatives. The main goal is to understand the effect of C5-methylation and C5–C6 saturation upon the deamination rate. It is found that C5–C6 saturation tends to increase the local electrophilicity of the cytosine derivative on carbon C4. It is also concluded that C5-methylation displays an opposite effect on saturated versus unsaturated systems: on unsaturated systems, C5-methylation tends to increase the local electrophilicity on C4, while it reduces the local electrophilicity on C4 for saturated ones.
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| 9. |
- Indelicato, Paul, et al.
(author)
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Are MCDF calculations 101 % correct in the superheavy elements range?
- 2011
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In: Theoretical Chemistry accounts. - : Springer. - 1432-881X .- 1432-2234. ; 129:3-5, s. 495-505
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Journal article (peer-reviewed)abstract
- We explore QED and many-body effects in super-heavy elements up to Z = 173 using the multicon- figuration Dirac–Fock method. We study the effect of going beyond the average level approximation on the determination of the ground state of element 140 and compare with the recent work of Pekka Pyykko¨ on the periodic table for super-heavy elements (Pyykko¨, in Phys Chem Chem Phys, 13:161, 2011). We confirm that QED corrections are of the order of 1% on ionization energies. We show that the atomic number at which the 1s shell dives into the negative energy continuum is 173 and is not affected by the approximation employed to evaluate the electron–electron interaction.
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| 10. |
- Kalered, Emil, et al.
(author)
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Adsorption and surface diffusion of silicon growth species in silicon carbide chemical vapour deposition processes studied by quantum-chemical computations
- 2013
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In: Theoretical Chemistry accounts. - : Springer Verlag (Germany). - 1432-881X .- 1432-2234. ; 132:12
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Journal article (peer-reviewed)abstract
- The effect chlorine addition to the gas mixture has on the surface chemistry in the chemical vapour deposition (CVD) process for silicon carbide (SiC) epitaxial layers is studied by quantum-chemical calculations of the adsorption and diffusion of SiH2 and SiCl2 on the (000-1) 4H–SiC surface. SiH2 was found to bind more strongly to the surface than SiCl2 by approximately 100 kJ mol−1 and to have a 50 kJ mol−1 lower energy barrier for diffusion on the fully hydrogen-terminated surface. On a bare SiC surface, without hydrogen termination, the SiCl2 molecule has a somewhat lower energy barrier for diffusion. SiCl2 is found to require a higher activation energy for desorption once chemisorbed, compared to the SiH2 molecule. Gibbs free energy calculations also indicate that the SiC surface may not be fully hydrogen terminated at CVD conditions since missing neighbouring pair of surface hydrogens is found to be a likely type of defect on a hydrogen-terminated SiC surface.
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