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  • 1. Arhammar, C.
    et al.
    Silvearv, F.
    Bergman, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Norgren, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Materials Sciences.
    Pedersen, H.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    A theoretical study of possible point defects incorporated into alpha-alumina deposited by chemical vapor deposition2013In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 133, no 2, p. 1433-Article in journal (Refereed)
    Abstract [en]

    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.

  • 2. Baran, Jakub D.
    et al.
    Kolodziejczyk, Wojciech
    Larsson, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Larsson, Andreas J.
    On the stability of single-walled carbon nanotubes and their binding strengths2012In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 131, no 9, p. 1270-Article in journal (Refereed)
    Abstract [en]

    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.

  • 3. Barata-Morgado, Rute
    et al.
    Luz Sanchez, M.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Corchado, Jose C.
    Elena Martin, M.
    Munoz-Losa, Aurora
    Aguilar, Manuel A.
    Theoretical study of the conformational equilibrium of 1,4-dioxane in gas phase, neat liquid, and dilute aqueous solutions2013In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 132, no 10, p. 1390-Article in journal (Refereed)
    Abstract [en]

    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.

  • 4.
    Feierberg, Isabella
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Computational modeling of enzymatic keto-enol isomerization reactions2002In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 108, no 2, p. 71-84Article in journal (Refereed)
    Abstract [en]

    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.

  • 5.
    Francés-Monerris, Antonio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia 46071, Spain..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Roca-Sanjuan, Daniel
    Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia 46071, Spain..
    Triplet versus singlet chemiexcitation mechanism in dioxetanone: a CASSCF/CASPT2 study2017In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 136, no 6, article id 70Article in journal (Refereed)
    Abstract [en]

    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.

  • 6. Gaenko, Alexander V
    et al.
    Devarajan, Ajitha
    Gagliardi, Laura
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Orlandi, Giorgio
    Ab initio DFT study of Z-E isomerization pathways of N-benzylideneaniline2007In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 118, no 1, p. 271-279Article in journal (Refereed)
    Abstract [en]

    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.

  • 7. Gonzalez-Ramirez, Israel
    et al.
    Roca-Sanjuán, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Climent, Teresa
    Serrano-Perez, Juan Jose
    Merchan, Manuela
    Serrano-Andres, Luis
    On the photoproduction of DNA/RNA cyclobutane pyrimidine dimers2011In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 128, no 4-6, p. 705-711Article in journal (Refereed)
    Abstract [en]

    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.

  • 8. Gusarov, Sergey
    et al.
    Malmqvist, Per-Åke
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Roos, Björn O
    Correlation potentials for a multiconfigurational-based density functional theory with exact exchange2004In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 112, no 2, p. 84-94Article in journal (Refereed)
    Abstract [en]

    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.

  • 9.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Malmqvist, Per Åke
    Gagliardi, Laura
    Molecular integrals by numerical quadrature. I. Radial integration2001In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 106, no 3, p. 178-187Article in journal (Refereed)
    Abstract [en]

    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.

  • 10.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Malmqvist, Per-Åke
    Björn’s top ten2003In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 110, no 3, p. 115-117Article in journal (Other academic)
  • 11.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Ryde, Ulf
    Schütz, Martin
    On the significance of the trigger reaction in the action of the calicheamicin gamma(I)(1) anti-cancer drug1997In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 97, no 1-4, p. 203-210Article in journal (Refereed)
    Abstract [en]

    The significance of the so-called trigger reaction in the reaction mechanism of the calicheamicin gamma(1)(l) anti-cancer drug has been studied with ab initio quantum chemical methods. The structures of four fragments of calicheamicin gamma(1)(l), 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 for which the reaction energy is a direct 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 Moller-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.

  • 12.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Wisborg Krogh, Jesper
    Schütz, Martin
    Hirao, Kimihiko
    Semidirect parallel self-consistent field: the load balancing problem in the input/output intensive self-consistent field iterations2003In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 110, no 3, p. 156-164Article in journal (Refereed)
    Abstract [en]

    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.

  • 13.
    Lundberg, Marcus
    et al.
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University.
    Blomberg, M. R. A.
    Siegbahn, P. E. M.
    Modeling water exchange on monomeric and dimeric Mn centers2003In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 110, no 3, p. 130-143Article in journal (Refereed)
    Abstract [en]

    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).

  • 14.
    Müller, Carsten
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Flad, Heinz-Jürgen
    Kohout, Miroslav
    Reinhold, Joachim
    Quantum Monte Carlo Calculation of Correlation Effects on Bond Orders2007In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 117, no 1, p. 41-48Article in journal (Refereed)
    Abstract [en]

    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.

  • 15. Pedersen, Thomas Bondo
    et al.
    Aquilante, Francesco
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Density fitting with auxiliary basis sets from Cholesky decompositions2009In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 124, no 1-2, p. 1-10Article in journal (Refereed)
    Abstract [en]

    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.

  • 16. Prasad, B. Ram
    et al.
    Kamerlin, Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Florian, Jan
    Warshel, Arieh
    Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting2012In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 131, no 12, p. 1288-Article in journal (Refereed)
    Abstract [en]

    In the preceding article, "Perspective: Prechemistry conformational changes in DNA polymerase mechanisms" contributed by Schlick and coworkers as well as previous studies of these workers (Schlick et al. in Theor Chem Acc 131: 1287, 2012; Radhakrishnan and Schlick in J Am Chem Soc 127: 13245-13252, 2005; Radhakrishnan and Schlick in Biochem Biophys Res Commun 350: 521-529, 2006; Radhakrishnan et al. in Biochemistry 45: 15142-15156, 2006; Radhakrishnan and Schlick in Proc Natl Acad Sci USA 101: 5970-5975, 2004) have argued that the conformational changes preceding the chemical step contribute to DNA synthesis and to the fidelity of DNA polymerases. In one of our previous investigations (Ram Prasad and Warshel in Proteins 79:2900-2919, 2011), we argued and showed that as long as the free energy barriers associated with any of the prechemistry steps are not rate limiting, they could not contribute to the catalysis and then to the fidelity. Though all our arguments are based on exact and well-defined scientific logics, Schlick and coworkers seem to overlook some of the clear conditions in these arguments and in particular the requirement that the chemical step is rate limiting in their arguments that the prechemistry barriers contribute to the catalysis. In fact, as long as the prechemistry steps are not rate limiting, we have shown that the enzymes cannot carry the memory of the previous steps. We also address other potential misunderstandings about several key issues; First, we clarify that it is misleading to relate the prechemistry proposal to the clear fact that the substrate-induced conformational changes determine the final preorganization (the issue is the height of the barrier of the enzyme substrate system and not the trivial fact that the enzyme has to change its structure when the substrate binds). Second, we address the presumed role of dynamical effects in enzyme catalysis and the assumption that any observable should be explored in studies of biological function even if they are not relevant to the given effect. Third, we clarify that the fidelity cannot be explained or quantified by invoking the induced fit or conformational selection effects but by evaluating the free energy contributions to the rate-limiting steps from the structures of the corresponding systems (that of course can reflect the induce fit structural changes). Overall, we put a major emphasis on clarifying what is the prechemistry proposal and thus on trying to force the reader to focus on the only real controversy. We of course dismiss any implication that our studies cannot explore mutational effects as we actually pioneered such computational studies and we clarify that in studies of chemical rates, the focus must be placed on evaluating the chemical barriers, rather than on irrelevant factors, but that the calculations of the chemical barriers must consider all the factors that determine this barrier (including metal ions) and also examine if needed different problematic proposals such as dynamical effects, tunneling, and prechemistry.

  • 17. Rubio, Mercedes
    et al.
    Stålring, Jonna
    Bernhardsson, Anders
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Roos, Björn O
    Theoretical studies of isomers of C3H2 using a multiconfigurational approach2000In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 105, no 1, p. 15-30Article in journal (Refereed)
    Abstract [en]

    The C3H2 isomers are important molecules in interstellar space. An understanding of their electronic structure can contribute significantly to the interpretation of interstellar spectra. In a theoretical study of the C3H2 isomers a multiconfigurational treatment is of interest because many of the isomers are carbenes or diradicals. We present such an investigation of all possible C3H2 isomers. The most important features of their electronic and vibrational spectra are calculated. Earlier theoretical studies are reviewed and it is shown that the present study yields the same order of stability for the singlet and triplet states as most previous studies.

  • 18.
    Salhi-Benachenhou, Nessima
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Alvarez Idaboy, JR
    Lunell, Sten
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Eriksson, LA
    Formation of 2-hexene by cationic dimerization of propene: an ab initio and density functional theory study1997In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 97, no 1-4, p. 277-282Article in journal (Refereed)
    Abstract [en]

    The formation of a 2-hexene radical cation from a propene radical cation and a neutral propene molecule is investigated by means of ab initio UHF and spin projected MP2 calculations, as well as the SVWN and B3LYP levels of density functional theory. A stable addition complex, with loose CC bonds, is found. To proceed from the addition complex to the product. a locally planar transition state must be passed, with a migrating hydrogen located half-way between the donating and the accepting carbon atoms. At the highest computational levels considered, PMP2/6-31G(d,p)//MP2/3-21G and B3LYP/6-31G(d,p), this transition state lies approximately 11 and 13 kcal/mol, respectively above the addition complex. The high barrier is believed to be one reason why radical cation oligomerization of propene has not been detected experimentally, in contrast to the case of ethene, where the corresponding barrier is only a few kcal/mol.

  • 19.
    Zou, Yiming
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Larsson, F.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Larsson, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Effect of CVD diamond growth by doping with nitrogen2013In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 133, no 2, p. 1432-Article in journal (Refereed)
    Abstract [en]

    The purpose with the present investigation has been to support and explain the experimental observation made regarding the enhancing effect by N doping on especially the diamond (100)-2 x 1 growth rate. Within the present study, also the commonly observed diamond (111) and (110) surfaces were included, all assumed to be H-terminated. Density functional theory calculations were used, based on a plane wave approach under periodic boundary conditions. It was shown that the surface H abstraction reaction is most probably the rate-limiting step during diamond growth. In addition, the results showed that it is N, substitutionally positioned within the upper diamond surface, that will cause the growth rate improvement, and not nitrogen chemisorbed onto the growing surface in the form of either NH (or NH2). The here presented numerical value for the growth rate enhancement for the diamond (100)-2 x 1 surface is almost identical with the experimentally obtained one (3.7 vs. 3.6). In addition, the (111) and (110) surfaces were shown to undergo a different growth rate enhancement, with about half as much for the (111) and (110) surfaces as compared to the diamond (100)-2 x 1 surface (1.9, 1.7 vs. 3.7). Despite the rate improvement for all surface planes, this difference will bring about a preferred diamond (100) surface texture.

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