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  • 1.
    Chen, Shilu
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fang, Wei-Hai
    Beijing Normal Univ, Coll Chem.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Technical aspects of quantum chemical modeling of enzymatic reactions: the case of phosphotriesterase2008In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 120, no 4-6, p. 515-522Article in journal (Refereed)
    Abstract [en]

    Quantum chemical methods are today a powerful tool in the study of enzymatic reaction mechanisms. In this paper we evaluate the adequacy of some of the technical approximations frequently used in the modeling of enzyme reactions with high level methods. These include the choice of basis set for geometry optimizations and energy evaluation, the choice of dielectric constant to model the enzyme surrounding, and the effects of locking the centers of truncation. As a test case, we choose the phosphotriesterase enzyme, which is a binuclear zinc enzyme that catalyzes the hydrolysis of organophosphate triesters.

  • 2.
    Frecus, Bogdan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Oprea, Corneliu I.
    Panait, Petre
    Ferbinteanu, Marilena
    Cimpoesu, Fanica
    Girtu, Mihai A.
    Ab initio study of exchange coupling for the consistent understanding of the magnetic ordering at room temperature in V[TCNE] (x)2014In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 133, no 5, p. 1470-Article in journal (Refereed)
    Abstract [en]

    We report quantum chemical calculations providing the exchange coupling constants of the V[TCNE](2) model system, describing the amorphous room temperature molecular magnet V[TCNE] (x) (TCNE = tetracyanoethylene, x similar to 2). The geometry is optimized for the ideal lattice using density functional theory (DFT) calculations with periodic boundary conditions. Broken-symmetry DFT calculations indicate antiparallel spin alignment resulting in ferrimagnetic ordering, but heavily overestimate the value of the exchange coupling. Better estimates of the exchange coupling parameters between the V(II) ion and the [TCNE](-) anionic radical are obtained by means of multiconfigurational calculations performed on smaller molecular models cut from the optimized crystal lattice. Complete active space self-consistent field and multireference second-order perturbation theory calculations provide the sign and the strength of the nearest-neighbor as well as next-nearest-neighbor interactions along all three crystallographic directions. We are able to explain also intuitively the mechanism for antiferromagnetic spin coupling in terms of the superexchange pathways, discussing the role of the main four types of contributions to superexchange. Moreover, we clarify the influence of the transition metal ion on the strength of the exchange interaction and on the critical temperature for long-range ferrimagnetic ordering.

  • 3.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Quantum chemical modeling of enzyme active sites and reaction mechanisms2006In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 116, no 03-jan, p. 232-240Article in journal (Refereed)
    Abstract [en]

    Density functional methods, in particular the B3LYP functional, together with the explosive enhancement of computational power, have in the last 5 years or so made it possible to model enzyme active sites and reaction mechanisms in a quite realistic way. Many mechanistic problems have indeed been addressed and solved. This review gives a brief account of the methods and models used to study enzyme active sites and their reaction mechanisms using quantum chemical methods. Examples are given from our recent work in this field. Future perspectives of the field are discussed.

  • 4. Jonsson, D.
    et al.
    Norman, P.
    Vahtras, O.
    Ågren, H.
    Magnetic hyperpolarizabilities in a cubic response formulation1996In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 93, no 4, p. 235-241Article in journal (Refereed)
    Abstract [en]

    We demonstrate the applicability of a recently derived cubic response function formalism for performing fully analytical calculations of hypermagnetizabilities, their anisotropy and their dispersion. The calculations involve the noble gas atoms, He, Ne, and Ar, and the corresponding isoelectronic halogen anions and alkali cations.

  • 5.
    Kleimark, Jonatan
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Delanoe, Romain
    Demaire, Alain
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Ionization of ammonium dinitramide: decomposition pathways and ionization products2013In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 132, no 12, p. UNSP 1412-Article in journal (Refereed)
    Abstract [en]

    The decomposition pathways of ionized ammonium dinitramide (ADN) have been analyzed using the B3LYP and the M06-2X density functional theory methods, coupled cluster theory and the composite CBS-QB3 method. Ionization and subsequent decomposition of the major decomposition products have also been studied. The ADN(+) ion dissociates into the stable DN radical and NH4+ with a dissociation enthalpy of 50 kJ/mol. The subsequently formed DN+ ion has an activation enthalpy of 102 kJ/mol for decomposition into N2O, O-2 and NO+. A competing pathway for ionization and decomposition of ADN involves the HDN+ ion, which dissociates into NO2+ and HNNO2 with a barrier of only 17 kJ/mol. The ionization product HNNO2+ is stable toward further decomposition, and the barrier for isomerization to HONNO+ is 167 kJ/mol. The computed adibatic ionization potentials of ADN, HDN, DN and HNNO2 are 9.4, 11.5, 10.2 and 10.9 eV, respectively. The results of the study have implications for the future use of ADN in propellants for electromagnetic space propulsion.

  • 6.
    Lin, Lili
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Shandong Normal Univ, Coll Phys & Elect, China.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Geng, Hua
    Shuai, Zhigang
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, China.
    First-principles investigations on the anisotropic charge transport in 4,4 '-bis((E)-2-(naphthalen-2-yl)vinyl)-1,1 '-biphenyl single crystal2014In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 133, no 9, p. 1551-Article in journal (Refereed)
    Abstract [en]

    We applied the master equation method to investigate the anisotropic transport property of the 4,4'-bis((E)-2-(naphthalen-2-yl)vinyl)-1,1'-biphenyl molecular crystal based on first-principles calculation. It is found that the hole mobility has the largest value along the [100] direction, while electrons have the best transport property along the [010] direction. The anisotropic transport property was found to have close relationship with the charge transfer integral which is determined by the molecular stacking network in the crystals as well as the intermolecular frontier orbital overlap. In addition, the effect of the charge carrier density and the electronic field on the charge transport was also studied, and little effect was found except that the density is larger than 0.01 and the electronic field is increased to 1.0 x 106 V/cm. The kinetic Monte Carlo simulation method has also been used to study the anisotropic charge transport property, and consistent results were obtained as with the master equation method.

  • 7.
    Minaev, Boris
    et al.
    KTH, Superseded Departments, Biotechnology.
    Loboda, Oleksandr
    KTH, Superseded Departments, Biotechnology.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ruud, K.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Solvent effects on optically detected magnetic resonance in triplet spin labels2004In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 111, no 2-6, p. 168-175Article in journal (Refereed)
    Abstract [en]

    We have calculated solvent effects on the zero-field splitting (ZFS) constants induced by electron spin-spin coupling (SSC) in the low-lying triplet states of azaaromatic molecules in solutions using multiconfiguration self-consistent-field wave functions and the polarizable continuum model. The second-order spin-orbit coupling (SOC) contribution to the splitting of the (3)pipi(*) states is found to be almost negligible, and the calculations therefore provide a good estimate of the ZFS parameters and their solvent dependence based only on the electron spin-spin coupling expectation values. The correlation between the shift in the ZFS and the phosphorescence frequency that has been observed in optically detected magnetic resonance experiments in low-temperature glasses is supported by our direct SSC calculations without taking SOC into account. This makes it possible to distinguish between the two theories that earlier were proposed to explain the inhomogeneous broadening of triplet state spectra, and discard the one that is exclusively based on the SOC-induced mixing of the singlet and triplet states.

  • 8. Oprea, Corneliu I.
    et al.
    Cimpoesu, Fanica
    Panait, Petre
    Frecus, Bogdan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ferbinteanu, Marilena
    Girtu, Mihai A.
    DFT study of structure-properties correlations in [MnTPP][TCNE] quasi-one-dimensional molecular magnets2011In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 129, no 6, p. 847-857Article in journal (Refereed)
    Abstract [en]

    We report the first band structure calculations of the quasi-one-dimensional [MnTPP][TCNE] compounds (TPP = meso-tetraphenylporphyrinato, TCNE = tetracyanoethylene), based on Density Functional Theory (DFT) methods, in order to interpret the magnetic ordering in these prototypic systems. We compare and contrast the results of broken-symmetry DFT calculations for extended systems, with periodic boundary conditions, and for finite systems, magnetic dimers modeling the actual molecular magnets. By varying systematically the main angles, we are able to determine the geometry dependence of the exchange interaction. Structure-properties correlations in these charge-transfer salts reveal the determinant role of the Mn-(N C) TCNE bond angle on the strength of the ferrimagnetic coupling between the S(1) = 2 spin located on the Mn(III)-porphyrin donor and the S(2) = 1/2 spin positioned on the cyanocarbon acceptor. When the Mn-(N C) TCNE angle is decreased, the intrachain magnetic coupling strengthens, correlated with the increase in the d(z)(2) - pi* orbital overlap. The exchange coupling constants resulting from DFT calculations of extended systems, with periodic boundary conditions, were found to be consistent with those obtained for the dimers, but systematically smaller. The exchange constants vary strongly with the functional used, hybrid functionals such as B3LYP leading to results that better correlate with the experimental mean-field critical temperatures. The coupling constant varies significantly with the type of broken-symmetry approach, depending on the overlap between magnetic orbitals, but weakly on the basis set once polarization effects are included. The electronic structure calculations for the extended systems provide a density of states consistent with the energy spectrum of the corresponding dimer, allowing for an intuitive explanation of the intrachain ferrimagnetic ordering.

  • 9.
    Rubio Pons, Oscar
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Minaev, Boris
    Loboda, Oleksandr
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ab initio calculations of vibronic activity in phosphorescence microwave double resonance spectra of para-dichlorobenzene2005In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 113, no 1, p. 15-27Article in journal (Refereed)
    Abstract [en]

    The phosphorescence spectrum of p-dichlorobenzene has been calculated using multiconfiguration self-consistent-field wave functions and the quadratic response technique. Attention has been paid to the intensity distribution of the singlet-triplet (B-3(1u)->(1)A(g)) transition through a number of vibronic subbands. The second order spin-orbit coupling (SOC) contribution to the spin splitting of the B-3(1u) ((3)pi pi*) state is found to be almost negligible, and the calculations therefore provide a good estimate for the zero-field splitting (ZFS) parameters based only on the electron spin-spin coupling expectation values. Nuclear quadrupole resonance constants for the different Cl isotopes are also calculated to accomplish the ZFS assignment. The electric dipole activity of the spin sublevels in the triplet singlet transitions to the ground-state vibrational levels is estimated by calculations of derivatives using distorted geometries which are shifted from the equilibrium position along different vibrational modes. A vibrational analysis of the phosphorescence spectrum, based on the SOC-induced mixing of the singlet and triplet states calculated along different vibrational modes, provides reasonable agreement with experimental data.

  • 10. Vallet, V.
    et al.
    Macak, Peter
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Wahlgren, U.
    Grenthe, Ingmar
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Inorganic Chemistry.
    Actinide chemistry in solution, quantum chemical methods and models2006In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 115, no 2-3, p. 145-160Article in journal (Refereed)
    Abstract [en]

    Theoretical modeling of actinide complexes requires access to structural parameters, information on electronic, vibration and rotation energy levels and thermodynamics properties. This article presents a critical review of theoretical studies of actinide chemistry in gas-phase and in solution and a comparison with experimental data in order to assess the applicability and accuracy by which various electronic structure theories can predict the required quantities. The quality of the basis set, the importance of electron correlation, the description of solute-solvent interactions is discussed in some detail.

  • 11. Wåhlin, Pernilla
    et al.
    Schimmelpfennig, Bernd
    Wahlgren, Ulf
    Grenthe, Ingmar
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Inorganic Chemistry.
    Vallet, Valerie
    On the combined use of discrete solvent models and continuum descriptions of solvent effects in ligand exchange reactions: a case study of the uranyl(VI) aquo ion2009In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 124, no 5-6, p. 377-384Article in journal (Refereed)
    Abstract [en]

    Modeling of the solvent is important when using quantum chemical methods for the assignment of mechanisms from experimental studies of the exchange of water between metal aquo ions and the bulk solvent. In the present study, we have investigated if and how the mechanisms for water exchange in the UO2(OH2)(5)(2+)-H2O system is affected by the choice of chemical models for the second coordination sphere and physical models for describing the cavity in conductor-like polarizable continuum (CPCM) models. In the first case, we have compared models with one and five waters in the second coordination sphere. For both models, we have compared cavities in which each atom is assigned one spherical cavity and one in which the water molecules are described by a single spherical cavity (the United Atom model). There are significant differences in the relative energy of dissociative and associative intermediates; however, they are not large enough to affect the conclusion that the water exchange proceeds through an associative/interchange mechanism.

  • 12.
    Zhang, Wenhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Carravetta, Vincenzo
    Monti, Susanna
    Interaction of biomolecular systems with titanium-based materials: computational investigations2009In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 123, no 3-4, p. 299-309Article in journal (Refereed)
    Abstract [en]

    Ab initio calculations and molecular dynamics simulations were performed to investigate the adsorption mode of various oligopeptides on titanium dioxide surfaces and to characterize their conformational behavior upon adsorption. The models were progressively improved obtaining a description compatible with the experimental observations.

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