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  • 1.
    Ahlstrand, Emma
    et al.
    Linnæus University Centre for Biomaterials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Friedman, Ran
    Interaction Energies Between Metal Ions (Zn2+ and Cd2+) and Biologically Relevant Ligands2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 23, p. 2554-2562Article in journal (Refereed)
    Abstract [en]

    Interactions between the group XII metals Zn2+ and Cd2+ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn2+ or Cd2+ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion–ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE) = 1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE = 6.4 kcal/mol at 3.0 Å). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn2+ and Cd2+, in particular at ion–ligand separations that are longer than the equilibrium distances.

  • 2.
    Arteca, Gustavo A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Rank, Jean Pierre
    Tapia, Orlando
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Generalized electronic diabatic approach to structural similarity in two-dimensional potential energy surfaces of various topologies2008In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 108, no 4, p. 651-666Article in journal (Refereed)
    Abstract [en]

    Active site properties in some proteins can be affected by conformational fluctuations of neighbor residues, even when the latter are not involved directly in the binding process. A local environment thus appears to alter the relevant potential energy surface and its reaction paths. Here, some aspects of this phenomenon are simulated within a generalized electronic diabatic (GED) scheme to study the geometry and structural similarity for a class of two-dimensional (2D) energy surfaces. The electronic quantum state is a linear superposition of diabatic basis functions, each of which is taken to represent a single (pure) electronic state for the isolated material system. Here, we describe a model reaction of isomerization by shifts in amplitudes for three diabatic species (reactant, product, and an open-shell transition state) coupled in an external field. The "effective" 2D energy surface in the field is characterized in terms of critical points, and the amplitudes along the main reaction paths. A new feature is the introduction of a phase diagram where all possible potential-energy-surface topologies (consistent with three-state systems in two linear coordinates) are matched with actual model parameters. By varying the coupling strengths between diabatic states, we classify regions of this phase diagram in terms of electronic and structural similarities; some regions comprise models whose reaction paths have geometries that belong to the catchment region of the reactant, yet are electronically akin to the diabatic transition state or product.

  • 3.
    Arteca, Gustavo A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Tapia, Orlando
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Generalized electronic diabatic approach to structural similarity and the Hammond postulate2007In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 107, no 2, p. 382-395Article in journal (Refereed)
    Abstract [en]

    We revisit the notion of structural similarity along a reaction path within the context of a generalized electronic diabatic (GED) molecular model. In this approach, a reaction involving two closed-shell stable species is described as the evolution of a quantum state that superimposes at least three diabatic electronic species (reactant, product, and an open-shell transition state) coupled by an external electromagnetic field. Reactant and product amplitudes in this general state are also modulated by changing the geometry of a system of classical positive charges interacting with the electrons. By mapping these amplitudes over nuclear configurational space, we can follow the total quantum state along a reaction coordinate and establish its similarity to each of the diabatic species. As a result, chemical processes, and useful notions such as those of energy barriers and the Hammond postulate, emerge as consequence of Franck-Condon-like transitions between quantum states.

  • 4.
    Arteca, Gustavo
    et al.
    Département de Chimie et Biochimie and Biomolecular Sciences Programme, Laurentian University.
    Rank, Jean Pierre
    Département de Chimie et Biochimie and Biomolecular Sciences Programme, Laurentian University.
    Tapia, Orlando
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Simulating trends in reaction path geometry as a function of external fields: A generalized electronic diabatic model for two-dimensional energy surfaces2008In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 108, no 10, p. 1810-1820Article in journal (Refereed)
    Abstract [en]

    We introduce a protocol to represent quantum states as a linear superposition of model electronic diabatic basis states coupled in an external (static) elec. field. By considering an entire family of these models, we uncover trends in reaction-path geometry and the topol. of potential-energy surfaces, including all those that can be realized in a two-dimensional configurational space. Our approach can be used as a tool to model the key parameters (e.g., diabatic basis states, external field intensity) that yield desired geometrical characteristics in an actual potential energy surface. In this work, external agents such as laser fields, or a group of neighboring charges, are regarded as essential requirements to prompt, or trigger, the occurrence of a chem. process. In these cases, reaction path geometry can be modulated externally so as to yield processes that would appear to occur far from gas-phase geometries. This phenomenol. is intrinsically nonadiabatic. Our present approach accounts for the possibility of such features, i.e., the occurrence of quantum states whose electronic structures resemble products, while at geometries that are more similar to those of reactants.

  • 5. Bakker, Albert
    et al.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry.
    Lindgren, Jan
    Probst, Michael M
    Bopp, Philippe A
    Interaction of aluminum(III) with water. An ab initio study1999In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 75, no 4-5, p. 659-669Article in journal (Refereed)
    Abstract [en]

    Hydrated Al(3+) ions [Al(H(2)O)(n)](3+), n = 1-6, were examined with ab Initio self-consistent field (SCF) calculations. The relative contributions of two-, three-, and higher-body terms to the total interaction energy for an [Al(H(2)O)(6)](3+) complex were calculated The sum of all three-body contributions amounts to - 30% of the sum of all pair-additive contributions and is opposite in sign. The three-body energy contributions were also derived for two types of [Al(H(2)O)(2)](3+) complexes. in the first type, both water molecules reside in the first hydration shell of Al(3+) and in the second type there is one in the first shell and one in the second. Altogether 15,500 triplets were investigated and analytical two- and three-body potential energy functions were derived via a fitting procedure. (C) 1999 John Wiley & Sons, Inc.

  • 6.
    Bengtson, Charlotta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Stenrup, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Quantum nonlocality in the excitation energy transfer in the Fenna-Matthews-Olson complex2016In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 116, p. 1763-1771Article in journal (Refereed)
    Abstract [en]

    The Fenna-Matthews-Olson (FMO) complex - a pigment protein complex involved in photosynthesis in green sulfur bacteria - is remarkably efficient in transferring excitation energy from light harvesting antenna molecules to a reaction center. Recent experimental and theoretical studies suggest that quantum coherence and entanglement may play a role in this excitation energy transfer (EET). We examine whether bipartite quantum nonlocality, a property that expresses a stronger-than-entanglement form of correlation, exists between different pairs of chromophores in the FMO complex when modeling the EET by the hierarchically coupled equations of motion method. We compare the results for nonlocality with the amount of bipartite entanglement in the system. In particular, we analyze in what way these correlation properties are affected by different initial conditions. It is found that bipartite nonlocality only exists when the initial conditions are chosen in an unphysiological manner and probably is absent when considering the EET in the FMO complex in its natural habitat. It is also seen that nonlocality and entanglement behave quite differently in this system. In particular, for localized initial states, nonlocality only exists on a very short time scale and then drops to zero in an abrupt manner. As already known from previous studies, quantum entanglement between chromophore pairs on the other hand is oscillating and exponentially decaying and follow thereby a pattern more similar to the chromophore population dynamics. The abrupt disappearance of nonlocality in the presence of nonvanishing entanglement is a phenomenon we call nonlocality sudden death; a striking manifestation of the difference between these two types of correlations in quantum systems. 

  • 7. Bischof, Gerhard
    et al.
    Silbernagl, Alexander
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    Probst, Michael
    Quantum chemical study of the molecular dynamics of hydrated Li+ and Be2+ cations1997In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 65, no 5, p. 803-816Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations of clusters of Li+ and Be2(+) cations with up to 12 water molecules were performed calculating the particle trajectories using Hartree-Fock-derived forces. It was found that independent of the starting configuration tetrahedral clusters are obtained in less than 1 ps. Only for Li+ clusters, transition states with five and three water molecules are found. We discuss the structures of the clusters and the vibrational dynamics of the water molecules and compare them with other ab initio simulations, with simulations using analytical potential functions, and with static calculations. Water-dissociation (hydrogen transfer) reactions which take place at elevated temperatures were investigated. (C) 1997 John Wiley & Sons, Inc.

  • 8.
    Björkman, Torbjörn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Adaptive Smearing for Brillouin Zone Integration2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 5, p. 1025-1030Article in journal (Refereed)
    Abstract [en]

    We suggest a simple scheme for automatically determining the width parameter of smearing methods of the Brillouin zone integration in electronic structure calculation. The scheme retains one free parameter that at any time can be eliminated by choosing a denser k-space mesh until the desired accuracy is obtained. The tests are carried out in the context of Methfessel-Paxton smearing. This adaptive Gaussian smearing (AGS) is easily implemented, variational with respect to partial occupancies and free from spurious occupancies that are negative or larger than one. Its convergence properties are similar to those obtained with the modified tetrahedron method for energy resolution of >= 0.1 meV.

  • 9. Boström, Jonas
    et al.
    Veryazov, Valera
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Bondo Pedersen, Thomas
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical gradients of the second-order Møller–Plesset energy using Cholesky decompositions2014In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 114, no 5, p. 321-327Article in journal (Refereed)
    Abstract [en]

    An algorithm for computing analytical gradients of the second-order Møller–Plesset (MP2) energy using density fitting (DF) is presented. The algorithm assumes that the underlying canonical Hartree–Fock reference is obtained with the same auxiliary basis set, which we obtain by Cholesky decomposition (CD) of atomic electron repulsion integrals. CD is also used for the negative semidefinite MP2 amplitude matrix. Test calculations on the weakly interacting dimers of the S22 test set (Jurečka et al., Phys. Chem. Chem. Phys. 2006, 8, 1985) show that the geometry errors due to the auxiliary basis set are negligible. With double-zeta basis sets, the error due to the DF approximation in intermolecular bond lengths is better than 0.1 pm. The computational time is typically reduced by a factor of 6–7.

  • 10.
    Brändas, Erkki
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    The Statement of Goals of the International Society for Theoretical Chemical Physics2014In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 114, p. 961-962Article in journal (Refereed)
  • 11.
    Brändas, Erkki
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Faculty of Mathematics and Science.
    Goscinski, Osvaldo
    Uppsala University, Disciplinary Domain of Science and Technology, Faculty of Mathematics and Science.
    Darboux functions and power series expansions with examples from isoelectronic sequences1972In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 6, no S6, p. 59-72Article in journal (Refereed)
    Abstract [en]

    A procedure for summing a power series based on a Darboux function ansatz is developed. It involves computation of poles and residues of logarithmic derivatives using rational functions. Applications to the helium isoelectronic sequence condense the power series expansion (˜ 40 coefficients) to a few-parameter formula, which exhibits the singularity determining the radius of convergence. Accurate extrapolations of electron affinities and shielding factors are obtained.

  • 12.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    A theorem for complex symmetric matrices revisited.2009In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 109, no 13, p. 2860-2865Article in journal (Refereed)
    Abstract [en]

    In this contribution we will revisit the celebrated theorem that every   square matrix is similar to a (complex) symmetric matrix and that every   symmetric matrix is orthogonally similar to a given normal canonical   form. Specifically we will re-examine the proof as well as the   derivation of an explicit n-dimensional complex symmetric form. We will   extend the formula to incorporate the various powers of the original   normal form, a derivation not previously provided. Some examples of   these complex symmetric forms in chemical and physical applications are   indicated.

  • 13.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Arrows of Time and Fundamental Symmetries in Chemical Physics2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 3, p. 173-184Article in journal (Refereed)
    Abstract [en]

    The field of chemical and physical processes, using principal microscopic techniques, should today allegedly be identified as a fundamental branch of physics. The discipline, by tradition known as chemical physics, is undergoing rapid progress. This assessment, illustrated by the advances presented at this Congress, is characterized by modern developments and novel trends with a concrete bearing on original theoretical understanding, with the possibility to go beyond traditional interpretations and explanations. In this vein, we do not only consider nonrelativistic treatments of various types of molecules including interactions between these and polymers, theoretical examinations of chemical reactions, surface states and interface states, disordered phenomena etc., but also recent progress together with non-Hermitian extensions to quantum mechanics and statistical mechanics. The latter leads to a united edifice of theoretical constructions including the law of self-reference, which emerges in analogy with the illustrious Gödel theorem(s) of mathematical logic, that is, the assertion of the inherent limitations of all nontrivial axiomatic systems. The current development begets the foundation of temporal processes and associated invariance principles including the valuation of the various arrows of time. The present conjugate operator array formulation supports the possible gravitational origin of molecular chirality and other principal symmetry violations.

  • 14.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Arrows of time and fundamental symmetries in chemical physics2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 3, p. 173-184Article in journal (Refereed)
    Abstract [en]

    The field of chemical and physical processes, using principal microscopic techniques, should today allegedly be identified as a fundamental branch of physics. The discipline, by tradition known as chemical physics, is undergoing rapid progress. This assessment, illustrated by the advances presented at this Congress, is characterized by modern developments and novel trends with a concrete bearing on original theoretical understanding, with the possibility to go beyond traditional interpretations and explanations. In this vein, we do not only consider nonrelativistic treatments of various types of molecules including interactions between these and polymers, theoretical examinations of chemical reactions, surface states and interface states, disordered phenomena etc., but also recent progress together with non-Hermitean extensions to quantum mechanics and statistical mechanics. The latter leads to a united edifice of theoretical constructions including the law of self-reference, which emerges in analogy with the illustrious Godel theorem(s) of mathematical logic, that is, the assertion of the inherent limitations of all nontrivial axiomatic systems. The current development begets the foundation of temporal processes and associated invariance principles including the valuation of the various arrows of time. The present conjugate operator array formulation supports the possible gravitational origin of molecular chirality and other principal symmetry violations.

  • 15.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Godelian Structures and Self-Organization in Biological Systems2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 7-8, p. 1321-1332Article in journal (Refereed)
    Abstract [en]

    In 1986, Seel and Ladik asked, which role Godel's incompleteness theorem should have in a basic theory of biology. Recently, the author has tried to collect the conditions, which such a meta-theory must fulfill. A further argument concerned the deeper connection between classical canonical forms of so-called (triangular) Jordan blocks in the description of open quantal systems far from equilibrium and those of self-referential contradictions and paradoxes in philosophy and mathematical logic. Related examples were quoted from the emergence of self-organization in so-called dissipative structures with applications to both fundamental-and of higher order levels of organization. To bring this analogy closer together, we have developed a quantum logical formalism, describing such a Godelian situation, via the characterization of a well-defined "truth matrix." In this setting, the modus operandi of exploiting self-referential traits and paradoxical inconsistencies emphasize the possibility of a meta-code in complicated enough (biological) systems. In conclusion, we will revisit situations were the aforementioned self-referential property, together with the laws of physics and chemistry will guide our understanding of biology. We will finally consider subsequent implications on the various positions on artificial intelligence.

  • 16.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Microscopic self-organization and self-referential systems: a progress report.2009In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 109, no 14, p. 3500-3504Article in journal (Refereed)
    Abstract [en]

    It is contended that (the classical canonical form of) Jordan blocks, play a role analogous to those of paradoxes and self-referential contradictions in philosophy and mathematical logic. As examples we will briefly discuss the occurrence of such triangular units in appropriately generalized quantum theory of microscopic as well as open dissipative systems with structures appearing on both the fundamental as well as in higher order levels of organization. The mathematical structure centers on specific transformations within coherent-dissipative ensembles that exhibit certain factorization properties allowing prime number algorithms, cf. the Godel encoding system used to derive the celebrated incompleteness theorem. This prompts the suggestion that an additional meta-code, cf. the genetic code, might be a-scripted for the mapping between the genotype and phenotype spaces.

  • 17.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Non-hermitian quantum mechanics2012In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 112, no 15, p. 2764-2765Article, book review (Other academic)
  • 18.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Some Comments on the Problem of Decoherence2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 2, p. 215-224Article in journal (Refereed)
    Abstract [en]

    We consider a universally valid superposition principle derived from a general complex symmetric ansatz. The approach concerns open, dissipative systems and its significance for the examination and analysis of system-environment correlations. In particular, we discuss the concept of decoherence in the ensuing fundamental operator equations, incorporating simultaneously holistic and classical regimes. Despite its reductionist character, the theory applies to both micro-and macroscopic systems. Examples are drawn from general relativity, for example, the law of light deflection, the gravitational redshift, the time delay and the perihelion motion of Mercury, and from the macroscopic domain, for example, the emergence of selforganization in complicated enough systems. The preceding portrayal commends autonomicity and provides legitimate concepts of central importance in biological organization and artificial intelligence.

  • 19.
    Brändas, Erkki
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Szabados, Ágnes
    Eötvös Loránd University.
    Surján, Péter
    Eötvös Loránd University.
    Preface: Eighth Congress of the International Society for Theoretical ChemicalPhysics (ISTCP-VIII)2014In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 114, p. 959-960Article in journal (Refereed)
  • 20.
    Carlsen, Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Goscinski, Osvaldo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Quantal trajectories for adiabatic and nonadiabatic regimes of vibronic systems1999In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 75, no 4-5, p. 409-416Article in journal (Refereed)
    Abstract [en]

    Exact and averaged nuclear pseudorotational quantal trajectories are compared for Various adiabatic and vibronic states of the Longuet-Higgins E x epsilon Jahn-Teller model. It is argued that the usual averaging over the electronic motion could be understood as being a consequence of ergodicity. The failure of the Born-Oppenheimer factorization to obey the ergodic hypothesis was examined. A quantitative separation of the electronic and nuclear time-scales is, nevertheless, achieved for all regimes. It is shown that the short-time deviations from the global "drift" of the electronic and nuclear motions are perfectly correlated.

  • 21. Chen, Shu-Feng
    et al.
    Yue, Ling
    Liu, Ya-Jun
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Multireference theoretical studies on the solvent effect of firefly multicolor bioluminescence2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 13, p. 3371-3377Article in journal (Refereed)
    Abstract [en]

    In concert with the recent spectroscopic studies of the light-color modulation mechanism of firefly (Hirano et al., J Am Chem Soc 2009, 131, 2385), quantum chemical calculations using complete active space SCF (CASSCF), multistate complete active space second order perturbation (MS-CASPT2) theory as well as a time-dependent density functional theory (TD-DFT) approach with the Coulomb attenuated hybrid exchange-correlation functional (CAM-B3LYP) were performed on the excited state (S1) of the keto-form oxyluciferin (keto-OxyLH2). Benzene, DMSO, CH3CN, and H2O were chosen as polar solvents. The polarization effect of less polar solvent was considered by a simple model, complex of keto-OxyLH2, and NH3 with different covalent character. The calculated results supported the experimental conclusion: (1) the light emitter of bioluminescence is the S1 state of keto-OxyLH2 anion [(keto-1)*], and (2) light emission from (keto-1)* is modulated by the polarity of surrounding environment and the degree of covalent character of hydrogen bond between (keto-1)* and a protonated basic moiety. The mechanism of the multicolor bioluminescence was discussed from the theoretical viewpoint.

  • 22. Cicero, Giancarlo
    et al.
    Carbonera, Chiara
    Valegård, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Andersson, Inger
    Ranghino, Graziella
    Study of the oxidative half-reaction catalyzed by a non-heme ferrous catalytic center by means of structural and computational methodologies2007In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 107, no 6, p. 1514-1522Article in journal (Refereed)
    Abstract [en]

    Deacetoxycephalosporin C synthase (DAOCS) is a mononuclear ferrous enzyme that catalyzes the expansion of the five-membered thiazolidine ring of the penicillin nucleus into the six-membered dihydrothiazine ring of the cephalosporins. In the first half-reaction with dioxygen and 2-oxoglutarate, a reactive iron-oxygen species is produced that can subsequently react with the penicillin substrate to yield the cephalosporin. We describe quantum mechanical calculations of the first part of the reaction based on the high-resolution structures of the active site of DAOCS and its complexes with ligands. These studies are aimed at understanding how the reactive species can be produced and contained in the active site of the enzyme. The results demonstrate the priming of the active site by the co-substrate for oxygen binding and hint to the presence of a stable iron-peroxo intermediate in equilibrium with a more reactive ferryl species and the formation of CO2 as a leaving group by decarboxylation of 2-oxoglutarate. A conclusion from these studies is that substitution of CO2 by the penicillin substrate triggers the oxidation reaction in a booby-trap-like mechanism.

  • 23. Cicero, Giancarlo
    et al.
    Carbonera, Chiara
    Valegård, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Andersson, Inger
    Ranghino, Graziella
    Study of the oxidative half-reaction catalyzed by a non-heme ferrous catalytic center by means of structural and computational methodologies2007In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 107, no 6, p. 1514-1522Article in journal (Refereed)
    Abstract [en]

    Deacetoxycephalosporin C synthase (DAOCS) is a mononuclear ferrous enzyme that catalyzes the expansion of the five-membered thiazolidine ring of the penicillin nucleus into the six-membered dihydrothiazine ring of the cephalosporins. In the first half-reaction with dioxygen and 2-oxoglutarate, a reactive iron-oxygen species is produced that can subsequently react with the penicillin substrate to yield the cephalosporin. We describe quantum mechanical calculations of the first part of the reaction based on the high-resolution structures of the active site of DAOCS and its complexes with ligands. These studies are aimed at understanding how the reactive species can be produced and contained in the active site of the enzyme. The results demonstrate the priming of the active site by the co-substrate for oxygen binding and hint to the presence of a stable iron-peroxo intermediate in equilibrium with a more reactive ferryl species and the formation of CO2 as a leaving group by decarboxylation of 2-oxoglutarate. A conclusion from these studies is that substitution of CO2 by the penicillin substrate triggers the oxidation reaction in a booby-trap-like mechanism.

  • 24. Cicero, Giancarlo
    et al.
    Carbonera, Chiara
    Valegård, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Andersson, Inger
    Ranghino, Graziella
    Study of the oxidative half-reaction catalyzed by a non-heme ferrous catalytic center by means of structural and computational methodologies2007In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 107, no 6, p. 1514-1522Article in journal (Refereed)
    Abstract [en]

    Deacetoxycephalosporin C synthase (DAOCS) is a mononuclear ferrous enzyme that catalyzes the expansion of the five-membered thiazolidine ring of the penicillin nucleus into the six-membered dihydrothiazine ring of the cephalosporins. In the first half-reaction with dioxygen and 2-oxoglutarate, a reactive iron-oxygen species is produced that can subsequently react with the penicillin substrate to yield the cephalosporin. We describe quantum mechanical calculations of the first part of the reaction based on the high-resolution structures of the active site of DAOCS and its complexes with ligands. These studies are aimed at understanding how the reactive species can be produced and contained in the active site of the enzyme. The results demonstrate the priming of the active site by the co-substrate for oxygen binding and hint to the presence of a stable iron-peroxo intermediate in equilibrium with a more reactive ferryl species and the formation of CO2 as a leaving group by decarboxylation of 2-oxoglutarate. A conclusion from these studies is that substitution of CO2 by the penicillin substrate triggers the oxidation reaction in a booby-trap-like mechanism.

  • 25. Crespo, R.
    et al.
    Piqueras, M-C
    Aullo, J. M.
    Tapia, Orlando
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    A Theoretical Study of Semiclassic Models: Toward a Quantum Mechanical Representation of Chemical Processes2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 2, p. 263-271Article in journal (Refereed)
    Abstract [en]

    CASPT2 level of theory and aug-cc-pV6Z atomic basis set for hydrogen and 6 base states is sufficient to accurately reproduce the historical calculations of Kolos-Wolniewicz for H-2(1) Sigma(+)(g) potential energy curve. We found that for H + H process experimental and adiabatic theory results are contradictory. By analyzing different levels of semiclassic theory, we identify the nature of the failure. We propose an approximate scheme that may bridge semiclassic to QM model.

  • 26. Delgado-Barrio, Gerardo
    et al.
    Maruani, Jean
    Piecuch, Piotr
    Brändas, Erkki
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Special Issue: Proceedings from the Fourteenth European Workshop on Quantum Systems in Chemistry and Physics Preface2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 2, p. 203-204Article in journal (Other academic)
  • 27. Devarajan, Ajitha
    et al.
    Gaenko, Alexander
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Malmqvist, Per-Åke
    Role of Electronic Curve Crossing of Benzene S-1 State in the Photodissociation of Aryl Halides, Effect of Fluorination: RASSI-SO MS-CASPT2 Study2009In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 109, no 9, p. 1962-1974Article in journal (Refereed)
    Abstract [en]

    An ab initio study of the role of electronic curve crossing of benzene S-1 state in the photo dissociation dynamics of the iodobenzene and effect of fluorination is presented. Two dissociative life times observed in iodobenzene is attributed to the coupled repulsive potential energy curves of the low-lying n-sigma*, pi-sigma*, pi-pi* states. The direct channel is attributed to the alkyl like transition and the indirect channel is attributed to the mixing of the alkyl like transitions with the low lying benzene pi-pi* transitions. Fluorination of iodobenzene results in a substantial increase in the direct channel product. To analyze the possible role of electronic curve crossing of these transitions, potential energy curves of low-lying n-sigma*, pi-sigma*, pi-pi* states were studied including spin-orbit and relativistic effects using the Restricted Active Space state interaction multistate complete active space perturbation theory (RASSI-MS-CASPT2) method. Crossing behavior of spin-free and spin-orbit potential energy curves was analyzed for the role of the benzene S-1 state. Our results indicate the curve crossing region to be around 2.00-2.35 angstrom for both C6H5I and C6F5I. Analysis of effect of fluorination on the energies of states corresponding to benzene pi-pi* and n-sigma* transitions suggests an increase in the energy of benzene pi-pi* states and a decrease in the energy of the states corresponding to n-sigma* transitions. Increased spin-orbit gap, increased separation of the benzene S-1(pi-pi*) state and n-sigma* states in the region of curve crossing, lesser mixing of the pi-pi* and n-sigma* states, an order of magnitude decrease in the transition strength to the benzene singlet transition all contributed to the observed Substantial increase in the quantum yield of the direct channel product on fluorination of aryl halides.

  • 28.
    Dunne, Lawrence J.
    et al.
    Imperial College London.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Superconductivity from Repulsive Electronic Correlations on Alternant Cuprate and Iron-Based Lattices2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 17, p. 2053-2059Article in journal (Refereed)
    Abstract [en]

    A key question in the theory of high-temperature superconductivityis whether off-diagonal long-range order can beinduced wholly or in large part by repulsive electronic correlations. Electron pairs on cuprate and the iron-based pnictide and chalcogenide alternant lattices may interact with a strong shortrange Coulomb repulsion and much weaker longer range attractive tail. Here, we show that such interacting electrons can cooperate to produce a superconducting state in which time reversed electron pairs effectively avoid the repulsive part but reside predominantly in the attractive region of the potential. The alternant lattice structure is a key feature of such a stabilization mechanism leading to the occurrence of high-temperature superconductivity with dx2y2 or sign alternating s-wave or s-condensate symmetries

  • 29. Dunne, Lawrence J.
    et al.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Superconductivity from repulsive electronic correlations on alternant cuprate and iron-based lattices2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 17, p. 2053-2059Article in journal (Refereed)
    Abstract [en]

    A key question in the theory of high-temperature superconductivity is whether off-diagonal long-range order can be induced wholly or in large part by repulsive electronic correlations. Electron pairs on cuprate and the iron-based pnictide and chalcogenide alternant lattices may interact with a strong short-range Coulomb repulsion and much weaker longer range attractive tail. Here, we show that such interacting electrons can cooperate to produce a superconducting state in which time-reversed electron pairs effectively avoid the repulsive part but reside predominantly in the attractive region of the potential. The alternant lattice structure is a key feature of such a stabilization mechanism leading to the occurrence of high-temperature superconductivity with d(x2-y2) or sign alternating s-wave or s +/- condensate symmetries. 

  • 30.
    Fransson, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Theory of time-dependent transport in quantum dot systems2003In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 92, no 6, p. 471-477Article in journal (Refereed)
    Abstract [en]

    The formulation of the time-dependent tunnel current in quantum dot (QD) systems in the (generalized) transfer Hamiltonian formalism is reconsidered, taking into account the nonorthogonality between the subsystems. Exploiting the fact that only the total charge in the system is conserved, in general, gives rise to a new formulation of the transport theory. As a result, it is shown necessary to depart from the orthodox picture, in which the current is treated as a local property of the system. A general formula for the current is derived. By expressing properties of the quantum dot in the Hubbard I approximation with the loop correction, thereby including strong correlations of the QD states, numerical results are given for various time-dependent source-drain voltages

  • 31.
    Fängström, Torbjörn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Edvardsson, David
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Ericsson, Marie
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Lunell, Sten
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Enkvist, Christer
    Density functional study of chlorine-oxygen compounds related to the ClO self-reaction1998In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 66, no 3, p. 203-217Article in journal (Refereed)
    Abstract [en]

    Geometrical parameters, vibrational frequencies, relative stabilities, and dissociation energies of the three stable Cl2O2 isomers and the OClO and ClOO radicals were investigated by density functional theory (DFT). The present analysis shows that DFT using hybrid functionals is capable of describing these systems to at least the same degree of accuracy as ab initio methods. The average absolute bond-length deviation of ClClO2,, ClOOCl, and ClO2, from experimental results is 0.024/0.027 Angstrom, with a maximum deviation for the dichlorine peroxide O-O bond equal to 0.072/0.063 Angstrom, for the B3PW91 and B3LYP functionals, respectively. The average absolute bond-angle deviation for the hybrid functionals is 0.8 degrees. Harmonic vibrational frequencies calculated with DFT give for all Cl-O compounds good agreement with experiments. The dissociation energies of ClOOCl, OClO, and ClOO were found to be in good agreement with experiments, the average error being less than 1.2 kcal/mol. The two isomers chloryl chloride (ClClO2,) and dichlorine peroxide (ClOOCl) were found to be approximately 9 kcal/mol more stable than the chlorine chlorite (ClOClO) isomer. The ClOO isomer is predicted to be 3.0 kcal/mol more stable than OClO, in accordance with the experimental value of 4 kcal/mol.

  • 32. Gagliardi, Laura
    et al.
    Evangelisti, Stefano
    Bernhardsson, Anders
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Roos, Björn O
    Dissociation reaction of N-8 azapentalene to 4N(2): A theoretical study2000In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 77, no 1, p. 311-315Article in journal (Refereed)
    Abstract [en]

    We present a theoretical study on the dissociation reaction of Ng azapantalene to four N-2 molecules. The process proceeds via isomerization of Ns azapentalene to N-8 azidopentazole, which then dissociates directly into four nitrogen molecules. The calculations have determined the relative energies of the two isomers and the two transition states involved in the dissociation process. The results show azidopentazole to be 13 kcal/mol more stable than azapentalene. The barrier to dissociation into four N-2 molecules is computed to be 19 kcal/mol. It is concluded that Ns is not stable enough to be considered as a candidate for a high-energy density material. The calculations have been carried out using multiconfigurational self-consistent field and second-order perturbation theory.

  • 33.
    HERMANSSON, KERSTI
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    REDSHIFTS AND BLUESHIFTS OF OH VIBRATIONS1993In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 45, no 6, p. 747-758Article in journal (Refereed)
    Abstract [en]

    Ab initio calculations of potential energy, dipole moment, equilibrium OH distance, force constants, and anharmonic frequencies, and correlation between these quantities, are presented for a water molecule and an OH- ion in a uniform electric field of varying field strength. It is explained why a bound H2O molecule in nature always experiences a frequency downshift with respect to the free molecule, and a bound OH-1 ion, either a downshift or an upshift. The frequency-field variation is well accounted for by the expression DELTAnu(OH) is-proportional-to -E(parallel-to) . (dmu(parallel-to)free/dr(OH) + 1/2 . partial derivative mu(parallel-to)induced/partial derivative r(OH)). A frequency maximum occurs at the field strength where partial derivative mu(parallel-to)tot/partial derivative r(OH) is similar to 0. Two cases can be discerned: (1) the frequency maximum falls at a positive field strength when dmu(parallel-to)free/dr(OH) is positive (this is the situation for OH-), and (2) the maximum frequency falls at a negative field when dmu(parallel-to)free/dr(OH) is negative (this occurs for water). In general, for an OH bond in a bonding situation where the intermolecular interactions are dominated by electrostatic forces, the nonlinearity of the frequency shift with respect to an applied field is governed by how close to the frequency maximum one is, i.e., by both dmu(parallel-to)free/dr(OH) and partial derivative mu(parallel-to)induced/partial derivative r(OH). Correlation curves between the external linear force constant, k(ext), and r(OH,e) are closely linear over the whole field range studied here, whereas the frequency vs. r(OH,e) and force constants vs. r(OH,e) correlation curves form two approximately linear, parallel branches, corresponding to ''before'' and ''after'' the maximum in the frequency vs. field curves. Each branch of the nu vs. r(OH,e) curves has a slope of approximately -16,000 cm-1/angstrom.

  • 34.
    Hermansson, Kersti
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry.
    Ojamäe, Lars
    From Molecule to Cluster to Bulk - Water OH Vibrations in Different Surroundings1992In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 42, no 5, p. 1251-1270Article, review/survey (Refereed)
    Abstract [en]

    Vibrational spectra for the O-H stretching motion of HDO molecules in different surroundings have been calculated by quantum mechanical ab initio methods and compared with experimental spectra. The free water molecule, water chains, and ion-water clusters are discussed. Solvent effects on OH vibrations in liquid water have been calculated as well as "in-crystal" OH frequencies in some ice and ionic crystalline hydrate structures. The importance of nonadditivity effects, electron correlation (at the MP2 level), and long-range interactions for the total frequency downshift is demonstrated. It is shown that the inclusion of these effects, in conjunction with a variational quantum mechanical treatment of the anharmonic vibrational stretching motion (force constants up to the fourth order), yields vibrational frequencies in quantitative agreement with experiment for a wide range of aqueous systems.

  • 35.
    Karlsson, Erik B.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Entanglement creation in Compton scattering of neutrons on protons and its possible energetic consequences2015In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 115, no 19, p. 1412-1416Article in journal (Refereed)
    Abstract [en]

    It has been predicted that entanglement creation should be associated with a lowering of energy (as well as the well-known decrease of entropy) for certain types of interaction potentials. This is a principally important question and it is shown here that np-scattering has specific features that would make it suitable for experimental tests of this prediction using neutron scattering on hydrogen at high angles. For this purpose, the evolution of n-p entanglement in Compton scattering on protons at epithermal energies (20-200 eV) is calculated over the separation distance 0-1 angstrom, corresponding to times up to 10(-15) s after the collision. If an energy transfer is associated with the entanglement, it ought to be observable under these measurement conditions.

  • 36.
    Karlsson, Erik B.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Interpretation of the hydrogen anomaly in neutron and electron compton scattering2012In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 112, no 2, p. 587-602Article in journal (Refereed)
    Abstract [en]

    In Compton scattering with neutrons in the energy range 20-120 eV, it has been observed that the relative H/M cross sections in a variety of H-containing materials are 20-40% lower than expected from the composition ratio H/M (M being a heavier element in the same compound). The same phenomenon has also been observed in Compton scattering with electrons of 2 and 20 keV energy. There is, at present, no consensus about the reason for these anomalies. In this theory, they are explained as a result of interference when the scattering particle interacts with more than one hydrogen nucleus. The coherence volume of the actual setup, which limits the number of interfering particles, is therefore an important parameter. It is shown here that the large zero-point motion of the hydrogen nuclei leads to reductions in the scattering intensity from interfering pairs. Coherence is preserved over the sub-fs scattering times relevant for this process, even in the condensed systems studied. It is gradually lost when the scattering time is increased, which happens when the neutron energy is reduced (as reflected in lower anomalies for smaller scattering angles). Explicit expressions for the decoherence effect are presented and compared with experimental observation for a selection of observed H- and D-containing systems.

  • 37. Karlsson, H O
    et al.
    Bendazzoli, G L
    Goscinski, O
    Evangelisti, S
    Density of states of alternant cyclic polyenes (CH)(N) by a direct Lanczos method1997In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 63, no 3, p. 719-728Article in journal (Refereed)
    Abstract [en]

    A direct full configuration interaction approach, previously used for studying individual low-lying eigenvalues, is combined with iterative Lanczos calculations, in order to obtain global properties of large Hermitean Hamiltonian matrices. To this effect systematic generation of random start vectors is used to compute statistical approximations to the density of states (DOS). Applications for cyclic polyenes in order to illustrate the viability of the scheme modeled by correlated, tight-binding Pariser-Parr-Pople (PPP) Hamiltonians of increasing complexity are presented. The degree of correlation in the solutions is controlled by the parameter beta. Convergence properties of the DOS for N=10 and N=14 are studied varying the extent of correlation. (C) 1997 John Wiley & Sons, Inc.

  • 38.
    Karlsson, Hans O
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Bendazzoli, GL
    Goscinski, Osvaldo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Evangelisti, S
    Density of states of alternant cyclic polyenes (CH)(N) by a direct Lanczos method1997In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 63, no 3, p. 719-728Article in journal (Other academic)
    Abstract [en]

    A direct full configuration interaction approach, previously used for studying individual low-lying eigenvalues, is combined with iterative Lanczos calculations, in order to obtain global properties of large Hermitean Hamiltonian matrices. To this effect systematic generation of random start vectors is used to compute statistical approximations to the density of states (DOS). Applications for cyclic polyenes in order to illustrate the viability of the scheme modeled by correlated, tight-binding Pariser-Parr-Pople (PPP) Hamiltonians of increasing complexity are presented. The degree of correlation in the solutions is controlled by the parameter beta. Convergence properties of the DOS for N=10 and N=14 are studied varying the extent of correlation.

  • 39.
    Larsson, Sven
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Faculty of Mathematics and Science.
    Smith, Jr., Vedene H.
    Natural Spin Orbitals and Geminals for the Lithium 2S Ground State1972In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 6, no 6, p. 1019-1043Article in journal (Refereed)
  • 40.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Roos, Björn O
    A theoretical study of the diffuseness of the V(1B1u) state of planar ethylene1989In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 35, no 6, p. 813-825Article in journal (Refereed)
    Abstract [en]

    The ground (N) state and the 1B1u(V) excited state of planar ethylene have been studied at the CPF and MR-SDCI levels of theory, using an extended CGTO basis set of the ANO type. The investigation especially addresses the near-degeneracy problem in the ground state and the coupling between the diffuse character of the π* orbital and the amount of correlation included in the wave function of the V state. The MR-SDCI results yield a vertical excitation energy in the range 7.8–8.0 eV, whereas the CPF result is 7.9 eV. The best MR-SDCI result for 〈1π*‖z2‖1π*〉 is 7.8, whereas CPF calculations based on MR-SDCI INOS give the value 6.7. It is clear from the results that these numbers have not converged and that more extended calculations than was possible in the present work would yield an even more compact wave function.

  • 41.
    Lizárraga, R.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Nordström, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Sjöstedt, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Eriksson, Olle
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics.
    Non-collinear magnetization density in VAu42002In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 90, no 6, p. 1610-1613Article in journal (Refereed)
    Abstract [en]

    The spin and orbital magnetic moments of VAu4 have been calculated using a first principles method that allows for noncollinear magnetic ordering. The large spin–orbit coupling of the Au atom is argued to induce large noncollinear components of the magnetization density as well as a parallel coupling between spin and orbital moments of the V atom, in contrast to expectations from Hund's third rule.

  • 42.
    Lundberg, Marcus
    et al.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Nishimoto, Y.
    Nagoya Univ, Grad Sch Sci, Dept Chem, Chikusa Ku, Nagoya, Aichi 4648601, Japan.
    Irle, S.
    Nagoya Univ, Grad Sch Sci, Dept Chem, Chikusa Ku, Nagoya, Aichi 4648601, Japan.
    Delocalization errors in a hubbard-€like model: Consequences for density-€functional tight-€binding calculations of molecular systems2012In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 112, no 6, p. 1701-1711Article in journal (Refereed)
    Abstract [en]

    It has previously been shown that self-consistent-charge density-functional tight-binding (SCC-DFTB) suffers from a self-interaction error that leads to artificial stabilization of delocalized states. The effects of the error are similar to those appearing for many density functionals. In SCC-DFTB, the delocalization error is inherently related to the use of a Hubbard-like term to describe on-site charge interactions. The mathematical simplicity of this Hubbard-like term makes it easy to estimate if a complex system is subject to artificial stabilization of delocalized states and to quantitatively predict the delocalization error in the system energy at large fragment separation. The error is directly proportional to the on-site charge interaction term but decreases as the fragments become more asymmetric. The difference in orbital energies required to eliminate the delocalization error becomes equal to the Hubbard-like parameter of the fragment with the highest electron affinity. However, in most cases, the localized state will be favored by spin polarization, fragment repulsion, solvent effects, and large reorganization energies, in analogy to density functional theory, from which SCC-DFTB is derived. The presented analysis gives an early indication whether the standard approach is suitable, or if a different method is required to correct the delocalization error. In addition to cationic dimers, we discuss the effects of the delocalization error for asymmetric systems, bond dissociation of neutral molecules, and the description of mixed valence transition metal systems, exemplified by the enzyme cytochrome oxidase.

  • 43.
    Lundqvist, Maria J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Nilsing, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Persson, Petter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Lunell, Sten
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    DFT study of bare and dye-sensitized TiO2 clusters and nanocrystals2006In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 106, no 15, p. 3214-3234Article in journal (Refereed)
    Abstract [en]

    Structural and electronic properties of bare and dye-sensitized TiO2 clusters and nanoparticles with sizes of ?2 nm have been studied by density functional theory (DFT) calculations. Starting from truncated bulk lattice structures, the degree of structural reorganization, including the formation of Ti dbond O surface species, of bare TiO2 anatase nanocrystals, is found to be sensitive to the quality of the computational method. The electronic structures of optimized 1-2 nm nanoparticles show well-developed band structures with essentially no electronic bandgap defect states. Significant bandgap broadening due to quantum size effects is observed as the size of the nanocrystals is reduced from 2 nm to 1 nm in diameter, but further bandgap widening is limited by increasingly severe competing surface defect sites as the particles become smaller than ?1 nm in diameter. The applicability of the TiO2 nanocrystals in modeling the electronic structure and electronic coupling at dye-sensitized TiO2 nanocrystal interfaces has been investigated by attachment of pyridine to one of the nanoparticle models via phosphonic or carboxylic acid anchor groups.

  • 44. Melaccio, Federico
    et al.
    Olivucci, Massimo
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Ferré, Nicolas
    Unique QM/MM potential energy surface exploration using microiterations2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 13, p. 3339-3346Article in journal (Refereed)
    Abstract [en]

    The determination and the characterization of important points of a potential energy surface can be carried out routinely using any molecular modelling software based on either a quantum mechanical (QM) or a classical (molecular mechanics, MM) description of the particle interactions. However the coupling of the QM and MM descriptions (QM/MM) gives rise to severe efficiency limitations during a geometry optimization of the whole system, especially when both subsystems are coupled electrostatically. The present work introduces two simple improvements, mainly developed in the framework of the ElectroStatic Potential Fitted (ESPF) method to ensure the uniqueness of the QM/MM potential energy surface. The first one aims to improve the approximate Hessian matrix used in the QM optimization step. The second one tries to recouple electrostatically the QM and MM subsystems when microiterations are used. These methods are tested on a very simple system (a QM water molecule in a MM water box) before to be applied to the investigation of the light absorption in the rhodopsin protein at the multireference second-order perturbation level of theory (CASPT2). This work is dedicated to the memory of Prof. B. O. Roos. He was a great support for the implementation of the QM/MM method in the Molcas package.

  • 45. Moskalenko, SA
    et al.
    Liberman, M. A.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Dumanov, V
    Podlesny, V
    Collective Properties and Combined Quantum Transitions of Two-Dimensional Magnetoexcitons2010In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 110, no 1, p. 177-194Article in journal (Refereed)
    Abstract [en]

    The article consists of two parts describing two associated properties of two-dimensional magnetoexcitons. In the first part, the theory of combined exciton-cyclotron resonance in the quantum well structures is developed for a strong magnetic field. In the first part, we calculate the absorption band structure for optical quantum transitions with circularly polarized radiation creating a two-dimensional exciton and simultaneously exciting one of the resident electrons from the lowest to the first excited Landau level. In the second part, we discuss the collective elementary excitations of the system of two-dimensional magnetoexcitons in the ground state of Bose-Einstein condensation on the arbitrary wave vector (k) over bar not equal 0 in the Hartree-Fock approximation. The breaking of the gauge symmetry of the initial Hamiltonian was introduced following the idea proposed by Bogoliubov in his theory of quasi-averages. The energy spectrum of the collective elementary excitations is characterized by the interconnection of the exciton and plasmon branches. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 110: 177-194, 2010

  • 46.
    Nakai, Hiromi
    et al.
    Waseda University.
    Yoshizawa, Kazunari
    Kyusyu University.
    Ando, Koji
    Kyoto University.
    Nakajima, Takahito
    Riken.
    Brändas, Erkki
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Special Issue: Seventh Congress of the International Societyfor Theoretical Chemical Physics2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, p. 171-172Article, review/survey (Refereed)
    Abstract [en]

    This volume collects 58 selected papers from the scientific contributions presented at the Seventh Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII), organized by the team led by Professor Hiromi Nakai in Waseda, Tokyo, Japan, from September 2 to 8, 2011. The participants, 431 scientists from 32 countries/regions, presented novel concepts and methodologies in the fields of theoretical chemistry and physics, their application to physical/chemical phenomena, and discussed not only the insights obtained by the obtained by the presentations but also the new frontiers and future perspectives in the fields.

  • 47.
    Norberg, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Larsson, Per-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Dong, Xi-Cheng
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Salhi-Benachenhou, Nessima
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Lunell, Sten
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Bicyclopropylidene radical cation: A rehybridization ring opening to tetramethyleneethane2004In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 98, no 5, p. 473-483Article in journal (Refereed)
    Abstract [en]

    A computational study has been undertaken to elucidate the mechanism of the bicyclopropylidene radical cation (BCP•+) rearrangement into the tetramethyleneethane radical cation (TME•+). A stepwise mechanism is found for the first ring opening, with an activation energy of 7.3 kcal mol−1, while the second ring opening proceeds with no activation energy. Each ring opening is combined with a striking pyramidalization of one carbon atom in the central bond. In a natural bond orbital (NBO) analysis, the dominating reaction coordinate during the ring opening is found to be the olefinic carbon atom rehybridization, which also favors the continued bond breaking. Widely different ESR parameters are computed for the two sets of four protons in BCP•+, in excellent agreement with the observed spectrum, which are interpreted in the NBO analysis in terms of two hyperconjugative effects. Two minimum energy structures are located for TME•+, separated by a cusp on the internal rotation path of this cation, both of which show ESR parameters in good agreement with the observed spectrum for TME•+.

  • 48. Persson, Petter
    et al.
    Brinck, Tore
    Lindh, Roland
    Introduction2012In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 112, no 7, p. 1759-1759Article in journal (Refereed)
  • 49. Robb, Mike
    et al.
    Siegbahn, Per
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Foreword: Special Issue, A Celebration of the Scientific Achievements of Bjorn O. Roos2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 13, p. 3255-3255Article in journal (Refereed)
  • 50. Samanta, Sudipta
    et al.
    Kabir, Mukul
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science, Materials Theory.
    Bhattacharyya, Dhananjay
    Twist-dependent stacking energy of base-pair steps in B-DNA geometry: A density functional theory approach2008In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 108, no 6, p. 1173-1180Article in journal (Refereed)
    Abstract [en]

    Stacking energy of all the 10 unique DNA base-pair steps (bp step) are calculated using density functional theory within the ultrasoft pseudopotential plane wave method and local density approximation for the exchange-correlation functional. We have studied the dependence of stacking energy on twist angle, an aspect found difficult to explain using classical theory. We have found that the twist angle for different bp steps at stacking energy minimum matches extremely well with the values of average twist obtained from B-DNA crystal structure data. This indicates that the use of a proper quantum chemical method to calculate the pi-pi electronic interactions may explain stacking energy without incorporating hydrophobic interaction through solvent or effect of backbone through pseudobond. From the twist angle-dependent stacking energy profile, we have also generated the probability distributions of twist for all the bp steps and calculated the variance of the distribution. Our calculated variances show similar trend to that of the experimental data for which sufficient numbers of data are available. The TA, AT, and CG doublets show large variances among the 10 possible bp steps, indicating their maximum flexibility. This might be the case of unusual deformation observed at the TATA-box while binding to TBP protein.

12 1 - 50 of 60
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