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1.	Al-Abdalla, A, et al. (författare) Ab initio model potential embedded-cluster study of the ground and lowest excited states of Cr3+ defects in the elpasolites Cs2NaYCl6 and Cs2NaYBr6 1998 Ingår i: Journal of Chemical Physics. - : Springer Science and Business Media LLC. - 0021-9606 .- 1089-7690. ; 108, s. 2005-2014 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.
2.	Alavi, Fatemeh Sadat, et al. (författare) QM/MM study of the conversion of biliverdin into verdoheme by heme oxygenase 2019 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 138:5 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.
3.	Andersson, Kerstin, 1961- (författare) Molecular properties of TCNQ and anions 2023 Ingår i: Theoretical Chemistry accounts. - : Springer. - 1432-881X .- 1432-2234. ; 142:6 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.
4.	Andersson, Kerstin (författare) The electronic spectrum of VCr 2003 Ingår i: Theoretical Chemistry Accounts. - Heidelberg : Springer Science and Business Media LLC. - 1432-881X. ; 110:3, s. 218-223 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(-).
5.	Arhammar, C., et al. (författare) A theoretical study of possible point defects incorporated into alpha-alumina deposited by chemical vapor deposition 2013 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 133:2, s. 1433- 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.
6.	Baran, Jakub, 1980, et al. (författare) On the stability of single-walled carbon nanotubes and their binding strengths 2012 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 131:9, s. 1-8 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.
7.	Barata-Morgado, Rute, et al. (författare) Theoretical study of the conformational equilibrium of 1,4-dioxane in gas phase, neat liquid, and dilute aqueous solutions 2013 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 132:10, s. 1390- 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.
8.	Chen, Shilu, et al. (författare) Technical aspects of quantum chemical modeling of enzymatic reactions : the case of phosphotriesterase 2008 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 120:4-6, s. 515-522 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.
9.	Danielsson, Örjan, 1973-, et al. (författare) Shortcomings of CVD modeling of SiC today 2013 Ingår i: Theoretical Chemistry accounts. - : Springer Berlin/Heidelberg. - 1432-881X .- 1432-2234. ; 132:11, s. 1398- 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.
10.	Eek, William, 1976, et al. (författare) Simple analysis of atomic reactivity: Thomas-Fermi theory with nonergodicity and gradient correction 2006 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 115:4, s. 266-273 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.
11.	Eriksson, Emma S. E., et al. (författare) Permeability of 5-aminolevulinic acid oxime derivatives in lipid membranes 2016 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 135:1, s. 1-9 Tidskriftsartikel (refereegranskat)abstract 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.
12.	Falklöf, Olle, et al. (författare) Toward ab initio refinement of protein X-ray crystal structures: Interpreting and correlating structural fluctuations 2012 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 131 Tidskriftsartikel (refereegranskat)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.
13.	Feierberg, Isabella, et al. (författare) Computational modeling of enzymatic keto-enol isomerization reactions 2002 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 108:2, s. 71-84 Tidskriftsartikel (refereegranskat)abstract Catalysis of proton abstraction from nonacidic carbon atoms adjacent to a carbonyl or carboxylate group is a fundamental reaction in enzymology that has been extensively studied during the last few decades. Enzymes catalyzing these reactions, which normally involve labile enolic intermediates, need to overcome large pK a differences between the reacting groups as well as high intrinsic free-energy barriers. Here, we present an overview of results from recent computer simulation studies of keto-enol isomerization reactions catalyzed by the enzymes glyoxalase I, triosephopsphate isomerase and ketosteroid isomerase. For all three enzymes it is found that electrostatic stabilization of the transient enolate intermediates, either by charge–charge interactions or by hydrogen bonding, accounts for the main part of the activation free-energy barrier reduction. Another catalytic effect observed in all cases is the reduction of the reorganization energy by the enzyme active site. Some other factors that have been proposed to be important for these reactions are also discussed and evaluated.
14.	Finzel, Kati (författare) About the atomic shell structure in real space and the Pauli exclusion principle 2016 Ingår i: Theoretical Chemistry accounts. - : SPRINGER. - 1432-881X .- 1432-2234. ; 135:6, s. 148- Tidskriftsartikel (refereegranskat)abstract It is shown that any set of eigenfunctions (1s, 2s) of a bare Coulomb Hamiltonian exhibit the same atomic shell structure pattern for the real-space indicator a(1), which is defined as the ratio between the positive kinetic energy density and the electron density. Since this model Hamiltonian excludes all effects due to the electron-electron repulsion, the appearance of the atomic shell structure is attributed to the Pauli exclusion principle that arises from the requirements for a fermionic wavefunction. Since the derivation is independent of the nuclear charge and the energy of the system, reversely imposing proper atomic shell structure behavior in the design of kinetic energy functionals mimics the Pauli exclusion principle during a variational process.
15.	Finzel, Kati, et al. (författare) Functional constructions with specified functional derivatives 2016 Ingår i: Theoretical Chemistry accounts. - : SPRINGER. - 1432-881X .- 1432-2234. ; 135:12 Tidskriftsartikel (refereegranskat)abstract A bifunctional construction depending on a specified density-potential pair and an approximate guiding electron density functional is presented. The proposed bifunctional construction properly transforms under homogeneous coordinate scaling and yields the specified functional derivative, which determines the electron density. Whereas the method is general and applicable to all functional types, it will prove especially helpful in the context of orbital-free density functional theory, where most existing approximate density functionals predict inaccurate potentials.
16.	Finzel, Kati (författare) Reinvestigation of the ideal atomic shell structure and its application in orbital-free density functional theory 2016 Ingår i: Theoretical Chemistry accounts. - : SPRINGER. - 1432-881X .- 1432-2234. ; 135:4, s. 87- Tidskriftsartikel (refereegranskat)abstract It is shown how to determine the ideal shell radii solely as a function of the nuclear charge. With the help of those ideal shell radii, an approximation to the Pauli potential for atoms in their groundstate can be constructed. The so-called SSB-ideal potential (shell structure-based) yields self-consistent orbital-free electron densities with proper atomic shell structure from Hohenberg-Kohn variational principle.
17.	Francés-Monerris, Antonio, et al. (författare) Triplet versus singlet chemiexcitation mechanism in dioxetanone : a CASSCF/CASPT2 study 2017 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 136:6 Tidskriftsartikel (refereegranskat)abstract Chemiluminescence is a fundamental process of chemistry consisting in the conversion of chemical energy stored in chemical bonds into light. It is used by nature and by man-made technology, being especially relevant in chemical analysis. The understanding of the phenomenon strongly relies in the study of peroxide models such as 1,2-dioxetanones. In the present contribution, the singlet S2 and the triplet T2 potential energy surfaces of the unimolecular decomposition of 1,2-dioxetanone have been mapped along the O-O and C-C bond coordinates on the grounds of the multiconfigurational CASPT2//CASSCF approach. Results confirm the energy degeneracy between T2, T1, S1, and S0 at the TS region, whereas S2 is unambiguously predicted at higher energies. Triplet-state population is also supported by the spin-orbit couplings between the singlet and triplet states partaking in the process. In particular, the first-principle calculations show that decomposition along the T2 state is a competitive process, having a small (similar to 3 kcal/mol) energy barrier from the ground-state TS structure. The present findings can explain the higher quantum yield of triplet-state population with respect to the excited singlet states recorded experimentally for the uni-molecular decomposition of 1,2-dioxetanone models.
18.	Frecus, Bogdan, et al. (författare) Ab initio study of exchange coupling for the consistent understanding of the magnetic ordering at room temperature in V[TCNE] (x) 2014 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 133:5, s. 1470- Tidskriftsartikel (refereegranskat)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.
19.	Gaenko, Alexander V, et al. (författare) Ab initio DFT study of Z-E isomerization pathways of N-benzylideneaniline 2007 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 118:1, s. 271-279 Tidskriftsartikel (refereegranskat)abstract The ground state properties and absorption spectra of N-benzylideneaniline (NBA) have been studied at the density functional (DFT) and at the time-dependent density functional (TD-DFT) level of the theory. The equilibrium geometries of the E and Z isomers in the ground state and their vibrational frequencies have been computed. Furthermore, the excitation energies of the lowest excited singlet and triplet states and the potential energy curves along the torsion and the inversion isomerization coordinates were evaluated. The results are discussed in light of the available experimental data.
20.	Gonzalez-Luque, R, et al. (författare) Theoretical characterization of the absorption spectra of phenanthrene and its radical cation 2003 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X. ; 110:3, s. 224-232 Tidskriftsartikel (refereegranskat)abstract The vertical absorption spectra of phenanthrene and its radical cation have been studied theoretically by means of a multiconfigurational second-order perturbation approach. Singlet-singlet transition energies and oscillator strengths, and singlet-triplet excitation energies have been studied in the absorption spectrum of phenanthrene up to 6 eV. The absorption spectrum of the phenanthrene radical cation has been computed up to 3.4 eV. The results obtained confirm previous assignments and also lead to new interpretations of the main features of the spectra of these systems.
21.	Gonzalez-Ramirez, Israel, et al. (författare) On the photoproduction of DNA/RNA cyclobutane pyrimidine dimers 2011 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 128:4-6, s. 705-711 Tidskriftsartikel (refereegranskat)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.
22.	Grand, A., et al. (författare) Comparison of the Mechanism of Deamination of 5,6-dihydro-5-methylcytosine with other cytosine derivatives 2012 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 131:4 Tidskriftsartikel (refereegranskat)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.
23.	Gräfenstein, Jürgen, 1963, et al. (författare) The self-interaction error and the description of non-dynamic electron correlation in density functional theory 2009 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 123:3-4, s. 171-182 Tidskriftsartikel (refereegranskat)abstract The self-interaction error (SIE) plays a central role in density functional theory (DFT) when carried out with approximate exchange-correlation functionals. Its origin, properties, and consequences for the development of standard DFT to a method that can correctly describe multi-reference electron systems by treating dynamic and non-dynamic electron correlation on an equal footing, is discussed. In this connection, the seminal work of Colle and Salvetti on wave function-based correlation functionals that do no longer suffer from a SIE is essential. It is described how the Colle–Salvetti correlation functional is an anchor point for the derivation of a functional multi-reference DFT method.
24.	Gusarov, Sergey, et al. (författare) Correlation potentials for a multiconfigurational-based density functional theory with exact exchange 2004 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 112:2, s. 84-94 Tidskriftsartikel (refereegranskat)abstract A density functional theory based on a complete active space self consistent field (CASSCF) reference function with exact exchange is discussed. It is first shown that such a theory may be formulated with a correlation potential dependent on the density function and on the active space used. Auxiliary functions, such as the on-top two-particle density, are used to define uniquely the potential for different active spaces. The paper also analyses the correlation functional for some atomic and molecular cases. Large ab initio calculations are performed to obtain accurate density functions. A correlation potential is then fitted such that the reference CASSCF function gives the same density. The correlation potential values are saved in a data base for future analysis.
25.	Hermida-Ramón, Jose Manuel, et al. (författare) On the influence of the basis set superposition error on calculated vibrational frequencies 2003 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X. ; 110:3, s. 190-195 Tidskriftsartikel (refereegranskat)abstract The relation between the so called basis set superposition error and intramolecular vibrational frequencies calculated at the Hartree Fock SCF level of approximation was investigated. A linear conformation of HF dimer was chosen as test system for the investigation. It was found that the direct basis set superposition error for the studied system is rather small. It was further found that the shifts are mainly determined by the geometry parameters of the system
26.	Himo, Fahmi (författare) Quantum chemical modeling of enzyme active sites and reaction mechanisms 2006 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 116:03-jan, s. 232-240 Tidskriftsartikel (refereegranskat)abstract Density functional methods, in particular the B3LYP functional, together with the explosive enhancement of computational power, have in the last 5 years or so made it possible to model enzyme active sites and reaction mechanisms in a quite realistic way. Many mechanistic problems have indeed been addressed and solved. This review gives a brief account of the methods and models used to study enzyme active sites and their reaction mechanisms using quantum chemical methods. Examples are given from our recent work in this field. Future perspectives of the field are discussed.
27.	Illas, Francesc, et al. (författare) Spin symmetry requirements in density functional theory: The proper way to predict magnetic coupling constants in molecules and solids 2006 Ingår i: THEORETICAL CHEMISTRY ACCOUNTS. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 116:4-5, s. 587-597 Tidskriftsartikel (refereegranskat)
28.	Indelicato, Paul, et al. (författare) Are MCDF calculations 101 % correct in the superheavy elements range? 2011 Ingår i: Theoretical Chemistry accounts. - : Springer. - 1432-881X .- 1432-2234. ; 129:3-5, s. 495-505 Tidskriftsartikel (refereegranskat)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.
29.	Jonsson, D., et al. (författare) Magnetic hyperpolarizabilities in a cubic response formulation 1996 Ingår i: Theoretical Chemistry accounts. - 1432-881X .- 1432-2234. ; 93:4, s. 235-241 Tidskriftsartikel (refereegranskat)abstract We demonstrate the applicability of a recently derived cubic response function formalism for performing fully analytical calculations of hypermagnetizabilities, their anisotropy and their dispersion. The calculations involve the noble gas atoms, He, Ne, and Ar, and the corresponding isoelectronic halogen anions and alkali cations.
30.	Kalered, Emil, et al. (författare) Adsorption and surface diffusion of silicon growth species in silicon carbide chemical vapour deposition processes studied by quantum-chemical computations 2013 Ingår i: Theoretical Chemistry accounts. - : Springer Verlag (Germany). - 1432-881X .- 1432-2234. ; 132:12 Tidskriftsartikel (refereegranskat)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.
31.	Khan, MO, et al. (författare) Nonlinear electric response of polyampholytes 2003 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X. ; 110:3, s. 126-129 Tidskriftsartikel (refereegranskat)abstract The behavior of polyampholytes (PAs) in electric fields is investigated by Monte Carlo simulations. In bulk it is found that the response of the PA depends on the charge sequence. For small repeating units of positive and negative charges the response is linear, while bigger units results in a nonlinear response in both the induced dipole moment and the resulting polymer conformation. This is reflected in how PAs modify colloidal suspensions, and while PAs always decrease the repulsion between charged colloidal particles, some net-neutral PAs can even induce an effective attraction between the colloidal particles.
32.	Kleimark, Jonatan, et al. (författare) Ionization of ammonium dinitramide : decomposition pathways and ionization products 2013 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 132:12, s. UNSP 1412- Tidskriftsartikel (refereegranskat)abstract The decomposition pathways of ionized ammonium dinitramide (ADN) have been analyzed using the B3LYP and the M06-2X density functional theory methods, coupled cluster theory and the composite CBS-QB3 method. Ionization and subsequent decomposition of the major decomposition products have also been studied. The ADN(+) ion dissociates into the stable DN radical and NH4+ with a dissociation enthalpy of 50 kJ/mol. The subsequently formed DN+ ion has an activation enthalpy of 102 kJ/mol for decomposition into N2O, O-2 and NO+. A competing pathway for ionization and decomposition of ADN involves the HDN+ ion, which dissociates into NO2+ and HNNO2 with a barrier of only 17 kJ/mol. The ionization product HNNO2+ is stable toward further decomposition, and the barrier for isomerization to HONNO+ is 167 kJ/mol. The computed adibatic ionization potentials of ADN, HDN, DN and HNNO2 are 9.4, 11.5, 10.2 and 10.9 eV, respectively. The results of the study have implications for the future use of ADN in propellants for electromagnetic space propulsion.
33.	Labet, Vanessa, et al. (författare) Proton catalyzed hydrolytic deamination of cytosine : a computational study 2008 Ingår i: Theoretical Chemistry accounts. - Berlin Heidelberg : Springer. - 1432-881X .- 1432-2234. ; 120:4-6, s. 429-435 Tidskriftsartikel (refereegranskat)abstract Two pathways involving proton catalyzed hydrolytic deamination of cytosine (to uracil) are investigated at the PCM-corrected B3LYP/6-311G(d,p) level of theory, in the presence of an additional catalyzing water molecule. It is concluded that the pathway involving initial protonation at nitrogen in position 3 of the ring, followed by water addition at C4 and proton transfer to the amino group, is a likely route to hydrolytic deamination. The rate determining step is the addition of water to the cytosine, with a calculated free energy barrier in aqueous solution of G==140 kJ/mol. The current mechanism provides a lower barrier to deamination than previous work based on OH− catalyzed reactions, and lies closer to the experimental barrier derived from rate constants (Ea = 117 ± 4kJ/mol).
34.	Lahiri, A, et al. (författare) Molecular dynamics simulation of the preferred conformations of 2-thiouridine in aqueous solution 2007 Ingår i: THEORETICAL CHEMISTRY ACCOUNTS. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 117:2, s. 267-273 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
35.	Lin, Lili, et al. (författare) First-principles investigations on the anisotropic charge transport in 4,4 '-bis((E)-2-(naphthalen-2-yl)vinyl)-1,1 '-biphenyl single crystal 2014 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 133:9, s. 1551- Tidskriftsartikel (refereegranskat)abstract We applied the master equation method to investigate the anisotropic transport property of the 4,4'-bis((E)-2-(naphthalen-2-yl)vinyl)-1,1'-biphenyl molecular crystal based on first-principles calculation. It is found that the hole mobility has the largest value along the [100] direction, while electrons have the best transport property along the [010] direction. The anisotropic transport property was found to have close relationship with the charge transfer integral which is determined by the molecular stacking network in the crystals as well as the intermolecular frontier orbital overlap. In addition, the effect of the charge carrier density and the electronic field on the charge transport was also studied, and little effect was found except that the density is larger than 0.01 and the electronic field is increased to 1.0 x 106 V/cm. The kinetic Monte Carlo simulation method has also been used to study the anisotropic charge transport property, and consistent results were obtained as with the master equation method.
36.	Lindgren, Ingvar, 1931, et al. (författare) Combination of many-body perturbation theory and quantum electrodynamics 2015 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 134:11 Tidskriftsartikel (refereegranskat)abstract A procedure for energy-dependent perturbation expansion has been developed, based upon the covariant evolution operator method. This makes it possible to treat energy-dependent perturbations very much like the energy-independent ones in standard many-body perturbation theory. This has been applied to the non-radiative QED perturbations (retardation and virtual electron-positron pairs) as well as the radiative ones (electron self-energy, vacuum polarization and vertex correction). The combination of QED and electron correlation, beyond two-photon exchange, has been evaluated, using the Coulomb gauge. It turned out that in that gauge the extremely time-consuming model-space contributions of the self-energy and vertex corrections do not have to be evaluated in full. In the Feynman gauge no sensible results could be obtained in this way, as is demonstrated by the numerical results.
37.	Lindh, Roland, et al. (författare) Bjorn's top ten 2003 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 110:3, s. 115-117 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
38.	Lindh, Roland, 1958-, et al. (författare) Molecular integrals by numerical quadrature. I. Radial integration 2001 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 106:3, s. 178-187 Tidskriftsartikel (refereegranskat)abstract This article presents a numerical quadrature intended primarily for evaluating integrals in quantum chemistry programs based on molecular orbital theory, in particular density functional methods. Typically, many integrals must be computed. They are divided up into different classes, on the basis of the required accuracy and spatial extent. Ideally, each batch should be integrated using the minimal set of integration points that at the same time guarantees the required precision. Currently used quadrature schemes are far from optimal in this sense, and we are now developing new algorithms. They are designed to be flexible; such that given the range of functions to be integrated, and the required precision, the integration is performed as economically as possible with error bounds within specification. A standard approach is to partition space into a see of regions, where each region is integrated using a spherically polar grid. This article presents a radial quadrature which allows error control, uniform error distribution and uniform error reduction with increased number of radial grid points. A relative error less than 10(-14) for all s-type Gaussian integrands with an exponent range of 14 orders of magnitude is achieved with about 200 grid points. Higher angular I quantum numbers, lower precision or narrower exponent ranges require fewer points. The quadrature also allows controlled pruning of the angular grid in the vicinity of the nuclei.
39.	Lindh, Roland, et al. (författare) On the significance of the trigger reaction in the action of the calicheamicin γI 1 anti-cancer drug 1997 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 97:1, s. 203-210 Tidskriftsartikel (refereegranskat)abstract The significance of the so-called trigger reaction in the reaction mechanism of the calicheamicin γI 1 anti-cancer drug has been studied with ab initio quantum chemical methods. The structures of four fragments of calicheamicin γI 1, consisting of either 39 or 41 atoms, have been fully optimized using the Becke-Perdew86 density functional method and the 6-31G* basis sets. The four structures constitute members of an isodesmic reaction for which the reaction energy is a direct measure of the change in activation energy of the Bergman reaction, caused by the structural rearrangements of the preceding trigger reaction. This difference in activation energy has been calculated with density functional theory, using the exchange-correlation functional mentioned above, and with second-order Møller-Plesset perturbation theory (MP2), employing an ANO-type basis set. In both cases a value of 12 kcal/ mol is obtained. The study firmly supports the hypothesis that the significance of the trigger reaction is to saturate a double bond in the vicinity of the enediyne group, which counteracts the formation of the biradical state of the drug. The MP2 computations became feasible by a novel implementation of an integral-direct, distributed-data, parallel MP2 algorithm.
40.	Lindh, Roland, 1958-, et al. (författare) Semidirect parallel self-consistent field : the load balancing problem in the input/output intensive self-consistent field iterations 2003 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 110:3, s. 156-164 Tidskriftsartikel (refereegranskat)abstract The full capacity of contemporary parallel computers can, in the context of iterative ab initio procedures like, for example, self-consistent field (SCF) and multiconfigurational SCF, only be utilized if the disk and input/output (I/O) capacity are fully exploited before the implementation turns to an integral direct strategy. In a recent report on parallel semidirect SCF http://www.tc.cornell.edu/er/media/1996/collabrate.html, http://www.fp.mcs.anl.gd/grand-challenges/chem/non-direct/index.html it was demonstrated that super-linear speedups are achievable for algorithms that exploit scalable parallel I/O. In the I/O-intensive SCF iterations of this implementation a static load balancing, however, was employed, dictated by the initial iteration in which integral evaluation dominates the central processing unit activity and thus determines the load balancing. In the present paper we present the first implementation in which load balancing is achieved throughout the whole SCF procedure, i.e. also in subsequent iterations. The improved scalability of our new algorithm is demonstrated in some test calculations, for example, for 63-node calculation a speedup of 104 was observed in the computation of the two-electron integral contribution to the Fock matrix.
41.	Lundberg, Marcus, 1974-, et al. (författare) Modeling water exchange on monomeric and dimeric Mn centers 2003 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 110:3, s. 130-143 Tidskriftsartikel (refereegranskat)abstract Water exchange on Mn centers in proteins has been modeled with density functional theory using the B3LYP functional. The reaction barrier for dissociative water exchange on [Mn-IV(H2O)(2)(OH)(4)] is only 9.6 kcal mol(-1), corresponding to a rate of 6 x 10(5) s(-1). It has also been investigated how modifications of the model complex change the exchange rate. Three cases of water exchange on Mn dimers have been modeled. The reaction barrier for dissociative exchange of a terminal water ligand on [(H2O)(2)(OH)(2)Mn-IV(mu-O)(2)Mn-IV(H2O)(2) (OH)(2)] is 8.6 kcal mol(-1), while the bridging oxo group exchange with a ring-opening mechanism has a barrier of 19.2 kcal mol(-1). These results are intended for interpretations of measurements of water exchange for the oxygen evolving complex of photosystem II. Finally, a tautomerization mechanism for exchange of a terminal oxyl radical has been modeled for the synthetic 02 catalyst [(terpy)(H2O)Mn-IV(mu-O)(2)Mn-IV(O.)(terpy)](3+) (terpy=2,2':6,2"-terpyridine). The calculated reaction barrier is 14.7 kcal mol(-1).
42.	Merced Montero-Campillo, M., et al. (författare) Gas-phase reactivity tuned through the interaction with alkaline-earth derivatives 2019 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 138:5 Tidskriftsartikel (refereegranskat)abstract The cooperativity between MX2:XH alkaline-earth bonds and XH:NH3 hydrogen bonds (M=Mg, Ca; X=F, Cl) was investigated at the G4 level of theory. The cooperativity between these two non-covalent linkages is extremely large, to the point that the increase in their bond dissociation enthalpies may be as large as 240%. More importantly, the weaker the interaction, the larger the increase, so in some cases the linkage that stabilizes the most is the alkaline-earth bond, whereas in others is the hydrogen bond. In all cases, the formation of the MX2:XH:NH3 ternary complex is followed by a spontaneous proton transfer, very much as previously found for the Be-containing analogues. Similarly, MX2:FCl:NH3 complexes evolve from a chlorine-shared ternary complex (MX2FClNH3) or from an ion pair (MX2F-NH3Cl+) if M=Ca. Although F is the only halogen without sigma-hole, MgCl2 derivatives induce the appearance of a sigma-hole on it, though less deep than those induced by BeCl2. We have also studied whether Mg and Ca bond-containing complexes MR2:FY (R=H, F, Cl; Y=NH2, OH, F, Cl) may react to form radicals, as it has been found for the Be-containing analogues. These interactions provoke a drastic decrease in the F-Y bond dissociation enthalpy, very much as the one reported for the corresponding Be-analogues, to the point that in some cases the formation of the corresponding MR2F center dot+Y radicals becomes exothermic. Hence, the general conclusion of this study is that Mg or Ca derivatives give place to similar or even larger perturbations on the electron density than those induced by Be, a result not easily predictable.
43.	Minaev, Boris, et al. (författare) Solvent effects on optically detected magnetic resonance in triplet spin labels 2004 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 111:2-6, s. 168-175 Tidskriftsartikel (refereegranskat)abstract We have calculated solvent effects on the zero-field splitting (ZFS) constants induced by electron spin-spin coupling (SSC) in the low-lying triplet states of azaaromatic molecules in solutions using multiconfiguration self-consistent-field wave functions and the polarizable continuum model. The second-order spin-orbit coupling (SOC) contribution to the splitting of the (3)pipi(*) states is found to be almost negligible, and the calculations therefore provide a good estimate of the ZFS parameters and their solvent dependence based only on the electron spin-spin coupling expectation values. The correlation between the shift in the ZFS and the phosphorescence frequency that has been observed in optically detected magnetic resonance experiments in low-temperature glasses is supported by our direct SSC calculations without taking SOC into account. This makes it possible to distinguish between the two theories that earlier were proposed to explain the inhomogeneous broadening of triplet state spectra, and discard the one that is exclusively based on the SOC-induced mixing of the singlet and triplet states.
44.	Müller, Carsten, et al. (författare) Quantum Monte Carlo Calculation of Correlation Effects on Bond Orders 2007 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 117:1, s. 41-48 Tidskriftsartikel (refereegranskat)abstract We present a computational approach, using quantum Monte Carlo, that provides some insight into the effect of electron correlation on chemical bonding between individual pairs of atoms. Our approach rests upon a recently suggested relation between the bond order and charge fluctuations with respect to atomic domains. Within the present implementation we have taken a compromise between conceptual rigour and computational simplicity. In a first step atomic domains were obtained from Hartree-Fock (HF) densities, using Bader’s definition of atoms in molecules. These domains were used in a second step in quantum Monte Carlo calculations to determine bond orders for pairs of atoms. Correlation effects have been studied by comparison of HF bond orders with those obtained from pure diffusion quantum Monte Carlo calculations. We illustrate this concept for C–O and C–S bonds in different molecular environments. Our results suggest an approximate linear relation between bond order and bond length for these kinds of bonds.
45.	Olsen, Stine T., et al. (författare) A theoretical approach to molecular single-electron transistors 2011 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 130:4-6, s. 839-850 Tidskriftsartikel (refereegranskat)abstract We present theoretical methods and computational strategies of the effects of nanoparticles on linear optical properties of molecules. We present quantum mechanical-molecular mechanics response methods for calculating electromagnetic properties of molecules interacting with nanoparticles and we report strategies for calculating electronic and redox states of molecules sandwiched between gold nanoparticles.
46.	Oprea, Corneliu I., et al. (författare) DFT study of structure-properties correlations in [MnTPP][TCNE] quasi-one-dimensional molecular magnets 2011 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 129:6, s. 847-857 Tidskriftsartikel (refereegranskat)abstract We report the first band structure calculations of the quasi-one-dimensional [MnTPP][TCNE] compounds (TPP = meso-tetraphenylporphyrinato, TCNE = tetracyanoethylene), based on Density Functional Theory (DFT) methods, in order to interpret the magnetic ordering in these prototypic systems. We compare and contrast the results of broken-symmetry DFT calculations for extended systems, with periodic boundary conditions, and for finite systems, magnetic dimers modeling the actual molecular magnets. By varying systematically the main angles, we are able to determine the geometry dependence of the exchange interaction. Structure-properties correlations in these charge-transfer salts reveal the determinant role of the Mn-(N C) TCNE bond angle on the strength of the ferrimagnetic coupling between the S(1) = 2 spin located on the Mn(III)-porphyrin donor and the S(2) = 1/2 spin positioned on the cyanocarbon acceptor. When the Mn-(N C) TCNE angle is decreased, the intrachain magnetic coupling strengthens, correlated with the increase in the d(z)(2) - pi* orbital overlap. The exchange coupling constants resulting from DFT calculations of extended systems, with periodic boundary conditions, were found to be consistent with those obtained for the dimers, but systematically smaller. The exchange constants vary strongly with the functional used, hybrid functionals such as B3LYP leading to results that better correlate with the experimental mean-field critical temperatures. The coupling constant varies significantly with the type of broken-symmetry approach, depending on the overlap between magnetic orbitals, but weakly on the basis set once polarization effects are included. The electronic structure calculations for the extended systems provide a density of states consistent with the energy spectrum of the corresponding dimer, allowing for an intuitive explanation of the intrachain ferrimagnetic ordering.
47.	Pedersen, Henrik, et al. (författare) Studying chemical vapor deposition processes with theoretical chemistry 2014 Ingår i: Theoretical Chemistry accounts. - : Springer Verlag (Germany). - 1432-881X .- 1432-2234. ; 133:5, s. 1476- Tidskriftsartikel (refereegranskat)abstract In a chemical vapor deposition (CVD) process, a thin film of some material is deposited onto a surface via the chemical reactions of gaseous molecules that contain the atoms needed for the film material. These chemical reactions take place on the surface and in many cases also in the gas phase. To fully understand the chemistry in the process and thereby also have the best starting point for optimizing the process, theoretical chemical modeling is an invaluable tool for providing atomic-scale detail on surface and gas phase chemistry. This overview briefly introduces to the non-expert the main concepts, history and application of CVD, including the pulsed CVD variant known as atomic layer deposition, and put into perspective the use of theoretical chemistry in modeling these processes.
48.	Pedersen, Thomas Bondo, et al. (författare) Density fitting with auxiliary basis sets from Cholesky decompositions 2009 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 124:1-2, s. 1-10 Tidskriftsartikel (refereegranskat)abstract Recent progress in the use of Cholesky decomposition techniques within the density fitting approximation of two-electron integrals is reviewed with emphasis on the theoretical background. Special attention is paid to the fact that errors due to the density fitting approximation can be controlled by constructing auxiliary basis sets by means of Cholesky decomposition of either the entire or certain subblocks of the molecular two-electron integral matrix. Finally, the prospects of trivial linear-scaling calculation of fitting coefficients in the Cholesky decomposition-based density fitting scheme are outlined.
49.	Pettersson, Lars G. M., et al. (författare) X-ray emission spectroscopy : a genetic algorithm to disentangle core-hole-induced dynamics 2021 Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 140:12 Tidskriftsartikel (refereegranskat)abstract A genetic algorithm (GA) is developed and applied to make proper connections of final-state potential-energy surfaces and X-ray emission (XES) cross sections between steps in the time-propagation of H-bonded systems after a core–hole is created. We show that this modification results in significantly improved resolution of spectral features in XES with the semiclassical Kramers–Heisenberg approach which takes into account important interference effects. We demonstrate the effects on a water pentamer model as well as on two 17-molecules water clusters representing, respectively, tetrahedral (D2A2) and asymmetric (D1A1) H-bonding environments. For D2A2, the applied procedure improves significantly the obtained intensities, whereas for D1A1 the effects are smaller due to milder dynamics during the core–hole life-time as only one hydrogen is involved. We reinvestigate XES for liquid ethanol and, by properly disentangling the relevant states in the dense manifold of states using the GA, now resolve the important 3a′′ state as a peak rather than a shoulder. Furthermore, by applying the SpecSwap-RMC procedure, we reweigh the distribution of structures in the sampling of the liquid to fit to experiment and estimate the ratio between the main anti and gauche conformers in the liquid at room temperature. This combination of techniques will be generally applicable to challenging problems in liquid-phase spectroscopy.
50.	Polo, Victor, et al. (författare) Long-range and short-range Coulomb correlation effects as simulated by Hartree-Fock, local density approximation, and generalized gradient approximation exchange functionals 2003 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X. ; 109, s. 22-35 Tidskriftsartikel (refereegranskat)abstract Exchange functionals used in density functional theory (DFT) are generally considered to simulate long-range electron correlation effects. It is shown that these effects can be traced back to the self-interaction error (SIE) of approximate exchange functionals. An analysis of the SIE with the help of the exchange hole reveals that both short-range (dynamic) and long-range (nondynamic) electron correlation effects are simulated by DFT exchange where the local density approximation (LDA) accounts for stronger effects than the generalized gradient expansion (GGA). This is a result of the fact that the GGA exchange hole describes the exact exchange hole close to the reference electron more accurately than the LDA hole does. The LDA hole is more diffuse, thus leading to an underestimation of exchange and stronger SIE effects, where the magnitude of the SIE energy is primarily due to the contribution of the core orbitals. The GGA exchange hole is more compact, which leads to an exaggeration of exchange in the bond and the nonbonding region and negative SIE contributions. Partitioning of the SIE into intra-/interelectronic and individual orbital contributions makes it possible to test the performance of a given exchange functional in different regions of the molecule. It is shown that Hartree-Fock exchange always covers some long-range effects via interelectronic exchange while self-interaction-corrected DFT is lacking these effects.

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