| 1. |
- Al-Abdalla, A, et al.
(författare)
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Ab initio model potential embedded-cluster study of the ground and lowest excited states of Cr3+ defects in the elpasolites Cs2NaYCl6 and Cs2NaYBr6
- 1998
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Ingår i: Journal of Chemical Physics. - : Springer Science and Business Media LLC. - 0021-9606 .- 1089-7690. ; 108, s. 2005-2014
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we present the results of an ab initio model potential (AIMP) embedded-cluster study of the ground and lowest excited states of Cr3+ defects in the elpasolites Cs2NaYCl6 and Cs2NaYBr6; complete active space SCF (CASSCF) and averaged coupled-pair functional (ACPF) calculations are performed on CrCl63- and CrBr63- clusters embedded in ab initio model potential representations of the surrounding lattices Cs2NaYCl6 and Cs2NaYBr6. The experimental structural data are revisited and some new results are found which differ significantly from those available in the literature. The calculated local structure parameters and electronic transition energies which can be compared to experiments are found to be very good; new structural and spectroscopic results are produced which have been neither measured nor calculated, which are complementary to the available ones, and whose quality is expected to be high as well. In particular, the question of the competition of the excited-state absorptions with the potential vibronic laser emission has been adressed: A considerable overlap between the broad E-2(g) –> (2)A(1g) excited-state absorption and (4)A(2g) <– T-4(2g) emission bands is predicted in both materials, which must result in a reduction in the emission efficiency. Finally, it is shown that the quantum mechanical embedding effects due to the fact that the external Cs+, Na+, Y3+, Cl-, and Br- ions are not point charges, are non-negligible; lacking of these effects must be one of the reasons which make previous Density Functional Theory calculations show significantly larger discrepancies with the available experiments.
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| 2. |
- Alavi, Fatemeh Sadat, et al.
(författare)
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QM/MM study of the conversion of biliverdin into verdoheme by heme oxygenase
- 2019
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 138:5
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Tidskriftsartikel (refereegranskat)abstract
- It has been shown that after production of oxophlorin, the first step of intermediate, both production of biliverdin and production of verdoheme occur simultaneously (Alavi et al. in Dalton Trans 47:8283–8291, 2018). So the mechanism that converts biliverdin into verdoheme is the subject of some controversy. The detailed conversion of verdoheme to biliverdin was demonstrated before by the Jerusalem group, using combined quantum mechanical and molecular mechanical (QM/MM) calculations. Conversion of iron biliverdin to iron verdoheme in the presence of H + was investigated using the B3LYP method and the def2-QZVP basis set, considering dispersion effects with the DFT-D3 approach, obtaining accurate energies with large QM regions of almost 1000 atoms. Two spin states, singlet and triplet, were considered for the conversion of biliverdin to verdoheme. The reactant and product are triplet and singlet in their ground states, respectively. The potential energy surface suggests that a spin inversion takes place during the course of reaction after TS2. The ring closing process is exothermic by 5.8 kcal/mol with a kinetic barrier of 16.5 kcal/mol. The activation barrier for removing OH from the ring to produce iron verdoheme is estimated to be 23.2 kcal/mol.
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| 3. |
- Andersson, Kerstin, 1961-
(författare)
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Molecular properties of TCNQ and anions
- 2023
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Ingår i: Theoretical Chemistry accounts. - : Springer. - 1432-881X .- 1432-2234. ; 142:6
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Tidskriftsartikel (refereegranskat)abstract
- The purpose of the work is to calculate accurate values of molecular properties of tetracyanoquinodimethane (TCNQ) and anions using the complete active space self-consistent field and complete active space second-order perturbation theory methods. The accuracy has been evaluated using several basis sets and active spaces. The calculated properties have, in many cases, been confirmed by experimental data (within parentheses), e.g., 9.54 eV (9.61 eV) and 3.36 eV (3.38 eV) for the ionization potential and electron affinity, respectively, of TCNQ; 3.12 eV (3.01 eV) and 3.54 eV (3.42 or 3.60 eV) for transition energies to the two lowest-lying excited singlet states of TCNQ; − 0.03, 0.46 and 1.44 eV (0, 0.5 and 1.4 eV) for electronic energies in electron attachment of TCNQ forming $$\hbox {TCNQ}^-$$; and 3.88 eV (3.71 eV) for the transition energy to the second lowest-lying excited singlet state of $$\hbox {TCNQ}^{2-}$$. Further, the calculations have brought insight into some experimental observations, e.g., the shape of the fluorescence spectrum of TCNQ at 3–4 eV.
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| 4. |
- Andersson, Kerstin
(författare)
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The electronic spectrum of VCr
- 2003
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Ingår i: Theoretical Chemistry Accounts. - Heidelberg : Springer Science and Business Media LLC. - 1432-881X. ; 110:3, s. 218-223
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Tidskriftsartikel (refereegranskat)abstract
- The electronic spectrum of VCr has been studied using the complete-active-space self-consistent field complete-active-space second-order perturbation theory approach. Potential-energy curves for 12 electronic states have been computed. Transition energies, with respect to the X(2)Delta ground state, for some of the calculated electronic states are (with possible experimental values within parentheses) 0.53 eV (0.56) for A(2)Sigma(+), 1.03 eV (1. 14) for A(4)Delta, 1.20 eV (1.14) for B(2)Delta, 1.45 eV (1.51) for B(4)Delta, 1.60 eV (1.51, 1.78) for C(2)Delta, and 1.61 eV (1.63) for A(4)Sigma(-).
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| 5. |
- Arhammar, C., et al.
(författare)
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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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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 133:2, s. 1433-
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Tidskriftsartikel (refereegranskat)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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| 6. |
- Baran, Jakub, 1980, et al.
(författare)
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On the stability of single-walled carbon nanotubes and their binding strengths
- 2012
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 131:9, s. 1-8
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Tidskriftsartikel (refereegranskat)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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| 7. |
- Barata-Morgado, Rute, et al.
(författare)
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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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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 132:10, s. 1390-
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Tidskriftsartikel (refereegranskat)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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| 8. |
- Chen, Shilu, et al.
(författare)
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Technical aspects of quantum chemical modeling of enzymatic reactions : the case of phosphotriesterase
- 2008
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 120:4-6, s. 515-522
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Tidskriftsartikel (refereegranskat)abstract
- Quantum chemical methods are today a powerful tool in the study of enzymatic reaction mechanisms. In this paper we evaluate the adequacy of some of the technical approximations frequently used in the modeling of enzyme reactions with high level methods. These include the choice of basis set for geometry optimizations and energy evaluation, the choice of dielectric constant to model the enzyme surrounding, and the effects of locking the centers of truncation. As a test case, we choose the phosphotriesterase enzyme, which is a binuclear zinc enzyme that catalyzes the hydrolysis of organophosphate triesters.
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| 9. |
- Danielsson, Örjan, 1973-, et al.
(författare)
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Shortcomings of CVD modeling of SiC today
- 2013
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Ingår i: Theoretical Chemistry accounts. - : Springer Berlin/Heidelberg. - 1432-881X .- 1432-2234. ; 132:11, s. 1398-
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Tidskriftsartikel (refereegranskat)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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| 10. |
- Eek, William, 1976, et al.
(författare)
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Simple analysis of atomic reactivity: Thomas-Fermi theory with nonergodicity and gradient correction
- 2006
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 115:4, s. 266-273
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Tidskriftsartikel (refereegranskat)abstract
- Covalent bonding has been found to be related to the relaxation of dynamical constraints on electronic motion in atoms and molecules. The corresponding strain energy in an atom is therefore a measure of its inherent reactivity. Here, such reactivities of the atoms H through Ne are estimated by the use of the Thomas-Fermi density functional theory which can be simply implemented using parametrized exponential electron densities in two different forms-the traditional form assuming complete ergodicity and a modified form which accounts for nonergodicity and therefore strain. The Thomas-Fermi functional is amended by the incorporation of gradient correction of the kinetic energy according to the von Weizsacker prescription. This correction, implemented within the nonergodic form of the Thomas-Fermi theory, is scaled to yield total atomic energies in agreement with the Hartree-Fock results. The scaling factor shows a variation from around 0.07 for Be to 0.1 for Ne. The reactivity, measured by the stabilization brought by going to the ergodic form of quantization within the Thomas-Fermi theory, is zero for He and Ne and shows a broad peak around oxygen in apparent agreement with chemical intuition. Molecular bonding efficiencies are studied for some small molecules and are found to be relatively large for hydrides and smaller for diatomic molecules such as Be-2 and F-2.
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