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  • 301. Farahani, Pooria
    et al.
    Maeda, Satoshi
    Francisco, Joseph S.
    Lundberg, Marcus
    Mechanisms for the Breakdown of Halomethanes through Reactions with Ground-State Cyano Radicals2015In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 16, p. 181-190Article in journal (Refereed)
    Abstract [en]

    One route to break down halomethanes is through reactions with radical species. The capability of the artificial force-induced reaction algorithm to efficiently explore a large number of radical reaction pathways has been illustrated for reactions between haloalkanes (CX3Y; X=H, F; Y=Cl, Br) and ground-state ((2)sigma(+)) cyano radicals (CN). For CH3Cl+CN, 71 stationary points in eight different pathways have been located and, in agreement with experiment, the highest rate constant (10(8) s(-1)M(-1) at 298 K) is obtained for hydrogen abstraction. For CH3Br, the rate constants for hydrogen and halogen abstraction are similar (10(9) s(-1)M(-1)), whereas replacing hydrogen with fluorine eliminates the hydrogen-abstraction route and decreases the rate constants for halogen abstraction by 2-3 orders of magnitude. The detailed mapping of stationary points allows accurate calculations of product distributions, and the encouraging rate constants should motivate future studies with other radicals.

  • 302.
    Farahani, Pooria
    et al.
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, BR-05508000 Sao Paulo, SP, Brazil..
    Oliveira, Marcelo A.
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, BR-05508000 Sao Paulo, SP, Brazil..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Baader, Wilhelm J.
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, BR-05508000 Sao Paulo, SP, Brazil..
    A combined theoretical and experimental study on the mechanism of spiro-adamantyl-1,2-dioxetanone decomposition2017In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, no 28, p. 17462-17472Article in journal (Refereed)
    Abstract [en]

    1, 2-Dioxetanones have been considered as model compounds for bioluminescence processes. The unimolecular decomposition of these prototypes leads mainly to the formation of triplet excited states whereas in the catalysed decomposition of these peroxides singlet states are formed preferentially. Notwithstanding, these cyclic peroxides are important models to understand the general principles of chemiexcitation as they can be synthesised, purified and characterised. We report here results of experimental and theoretical approaches to investigating the decomposition mechanism of spiro-adamantyl- 1,2-dioxetanone. The activation parameters in the unimolecular decomposition of this derivative have been determined by isothermal kinetic measurements (30-70 degrees C) and the chemiluminescence activation energy calculated from the correlation of emission intensities. The activation energy for peroxide decomposition proved to be considerably lower than the chemiluminescence activation energy indicating the existence of different reaction pathways for ground and excited state formation. These experimental results are compared with the calculations at the complete active space second-order perturbation theory (CASPT2), which reveal a two-step biradical mechanism starting by weak peroxide bond breakage followed by carbon-carbon elongation. The theoretical findings also indicate different transition state energies on the excited and ground state surfaces during the C-C bond cleavage in agreement with the experimental activation parameters.

  • 303.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Roca-Sanjuan, Daniel
    Aquilante, Francesco
    A Two-Scale Approach to Electron Correlationin Multiconfigurational Perturbation Theory2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, p. 1609-1617Article in journal (Refereed)
    Abstract [en]

    We present a new approach for the calculation of dynamicelectron correlation effects in large molecular systems usingmulticonfigurational second-order perturbation theory(CASPT2). The method is restricted to cases where partitioningof the molecular system into an active site and an environmentis meaningful. Only dynamic correlation effects derivedfrom orbitals extending over the active site are included at theCASPT2 level of theory, whereas the correlation effects of theenvironment are retrieved at lower computational costs. Forsufficiently large systems, the small errors introduced by thisapproximation are contrasted by the substantial savings inboth storage and computational demands compared to thefull CASPT2 calculation. Provided that static correlation effectsare correctly taken into account for the whole system, the proposedscheme represent a hierarchical approach to the electroncorrelation problem, where two molecular scales aretreated each by means of the most suitable level of theory.

  • 304.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Roca-Sanjuan, Daniel
    Frances-Monerris, Antonio
    Fdez. Galvan, Ignacio
    Lindh, Roland
    Liu, Ya-Jun
    Advances in computationalphotochemistry and chemiluminescenceof biological and nanotechnologicalmolecules2017In: Photochemistry / [ed] Elisa Fasani and Angelo Albini, Royal Society of Chemistry, 2017, 44, p. 16-60Chapter in book (Refereed)
    Abstract [en]

    Recent advances (2014–2015) in computational photochemistry and chemiluminescencederive from the development of theory and from the application of state-of-the-art andnew methodology to challenging electronic-structure problems. Method developmentshave mainly focused, first, on the improvement of approximate and cheap methods toprovide a better description of non-adiabatic processes, second, on the modification ofaccurate methods in order to decrease the computation time and, finally, on dynamicsapproaches able to provide information that can be directly compared with experimentaldata, such as yields and lifetimes. Applications of the ab initio quantum-chemistry methodshave given rise to relevant findings in distinct fields of the excited-state chemistry.We brieflysummarise, in this chapter, the achievements on photochemical mechanisms andchemically-induced excited-state phenomena of interest in biology and nanotechnology.

  • 305.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Roca-Sanjuan, Daniel
    Zapata, Felipe
    Lindh, Roland
    Revisiting the Nonadiabatic Process in 1,2-Dioxetane2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, p. 5404-5411Article in journal (Refereed)
    Abstract [en]

    Determining the ground and excited-statedecomposition mechanisms of 1,2-dioxetane is essential tounderstand the chemiluminescence and bioluminescencephenomena. Several experimental and theoretical studies hasbeen performed in the past without reaching a converged description. The reason is in part associated with the complex nonadiabatic process taking place along the reaction. The present study is an extension of a previous work (De Vico, L.;Liu, Y.-J.; Krogh, J. W.; Lindh, R. J. Phys. Chem. A 2007, 111,8013−8019) in which a two-step mechanism was established for the chemiluminescence involving asynchronous O−O′ andC−C′ bond dissociations. New high-level multistate multiconfigurational reference second-order perturbation theory calculations and ab initio molecular dynamics simulations at constant temperature are performed in the present study, which provide further details on the mechanisms and allow to rationalize further experimental observations. In particular, the new results explain the high ratio of triplet to singlet dissociation products.

  • 306.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Roca-Sanjuán, Daniel
    Universitat de València, Spain.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Università di Bologna, Italy.
    A Two-Scale Approach to Electron Correlation in Multiconfigurational Perturbation Theory2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 22, p. 1609-1617Article, review/survey (Refereed)
    Abstract [en]

    We present a new approach for the calculation of dynamicelectron correlation effects in large molecular systems usingmulticonfigurational second-order perturbation theory(CASPT2). The method is restricted to cases where partitioningof the molecular system into an active site and an environment is meaningful. Only dynamic correlation effects derivedfrom orbitals extending over the active site are included at theCASPT2 level of theory, whereas the correlation effects of theenvironment are retrieved at lower computational costs. Forsufficiently large systems, the small errors introduced by thisapproximation are contrasted by the substantial savings inboth storage and computational demands compared to thefull CASPT2 calculation. Provided that static correlation effectsare correctly taken into account for the whole system, the proposed scheme represent a hierarchical approach to the electron correlation problem, where two molecular scales aretreated each by means of the most suitable level of theory.

  • 307.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vacher, Morgane
    Valentini, Alssio
    Frutos, Luis M.
    Fdez. Galvan, Ignacio
    Karlsson, Hans
    Lindh, Roland
    How Do Methyl Groups Enhance the Triplet Chemiexcitation Yield ofDioxetane?2017In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, p. 3790-3794Article in journal (Refereed)
    Abstract [en]

    Chemiluminescence is the emission of light as aresult of a nonadiabatic chemical reaction. The present work isconcerned with understanding the yield of chemiluminescence,in particular how it dramatically increases upon methylation of1,2-dioxetane. Both ground-state and nonadiabatic dynamics(including singlet excited states) of the decomposition reactionof various methyl-substituted dioxetanes have been simulated.Methyl-substitution leads to a significant increase in thedissociation time scale. The rotation around the O−C−C−Odihedral angle is slowed; thus, the molecular system stayslonger in the “entropic trap” region. A simple kinetic model isproposed to explain how this leads to a higher chemiluminescence yield. These results have important implications for the designof efficient chemiluminescent systems in medical, environmental, and industrial applications.

  • 308.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Yagoobi Nia, Narges
    Sabzyan, Hassan
    Zendehdel, Mahmoud
    Oftadeh, Mohsen
    A combined computational and experimental study of the [Co(bpy)3]2+/3+ complexesas one-electron outer-sphere redox couplesin dye-sensitized solar cell electrolyte media2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, p. 11481-11491Article in journal (Refereed)
    Abstract [en]

    A combined experimental and computational investigation conducted to understand the nature of theinteractions between cobalt II/III redox mediators ([Co(bpy)3]2+/3+) and their impact on the performanceof the corresponding dye-sensitized solar cells (DSCs) is reported. The fully optimized equilibriumstructures of cobalt(II/III)-tris-bipyridine complexes in the gas phase and acetonitrile solvent are obtainedby the density functional B3LYP method using LanL2DZ and 6-31G(d,p) basis sets. The harmonicvibrational frequencies, infrared intensities and Raman scattering activities of the complexes are alsocalculated. The scaled computational vibrational wavenumbers show very good agreement with theexperimental values. Calculations of the electronic properties of the complexes are also performed atthe TD-B3LYP/6-31G(p,d)[LanL2DZ] level of theory. Detailed interpretations of the infrared and Ramanspectra of the complexes in different phases are reported. Detailed atomic orbital coefficients of thefrontier molecular orbitals and their major contributions to electronic excitations of the complexes arealso reported. These results are in good agreement with the experimental electrochemical values.Marcus diagram is derived for the electron transfer reaction Co(II) + D35+ - Co(III) + D35 using theCo–N bond length as a reaction coordinate.

  • 309.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zendehdel, Mahmoud
    Yaghoobi Nia, Narges
    Nasr-Esfahani, Mojtaba
    Karbaschi, Mohamad Reza
    A combined computational and experimental study on the hydrogen bonding with chloride ion in a crab-claw like site of a new chromium Schiff base complex2016In: Inorganica Chimica Acta, ISSN 0020-1693, E-ISSN 1873-3255, Vol. 44, p. 150-161Article in journal (Refereed)
    Abstract [en]

    A combined experimental and computational study to understand the nature of the hydrogen bonding ina crab-claw site of a new synthesized chromium Schiff base complex is reported. The fully optimizedequilibrium structures of the Cr(III) complex in the presence and absence of chloride ion are obtainedat the B3LYP functional in conjunction with LanL2DZ basis set. The crystal structure of the chromiumSchiff base complex consists of [CrL2]+ cation, in which L is a tridentate Schiff base ligand with full nameof N-(2-(2-hydroxyethylamino)ethyl)5-methoxysalicylideneimine, and a chloride anion, in the asymmetricunit. The chromium(III) cation possesses a distorted octahedral geometry, coordinated with four nitrogenand two phenoxo oxygen atoms derived from two chelate Schiff base ligands. The harmonicvibrational frequencies, infrared intensities and Raman scattering activities of the complexes are alsoreported. The scaled computational geometry and vibrational wavenumbers are in very good agreementwith the experimental values of single crystal X-ray diffraction and FT-IR, respectively. The electronicproperties calculations of the complexes are also performed at the TD-B3LYP/LanL2DZ level of theory.The spectroscopic excitation parameters obtained for frontier molecular orbitals of the complexes arereported as well. These findings are in good agreement with the experimental UV–Vis diffuse-reflectancespectroscopy. Parabolic diagrams are derived for the chloride insertion and hydrogen bonding in thecrab-claw site with the average optimized H H distances of the effective hydrogen atoms in the crabclawsite as reaction coordinate.

  • 310. Fdez. Galván, Ignacio
    et al.
    Gustafsson, Hannes
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Chemiexcitation without the peroxide bond?: Replacing oxygen with other heteroatoms.2018In: ChemPhotoChem, p. 1-12Article in journal (Refereed)
    Abstract [en]

    Chemiexcitation is the population of electronic excited states from the electronic ground state via radiationless non-adiabatic transitions upon thermal activation. The subsequent emission of the excess of energy in the form of light is called chemiluminescence or bioluminescence when occurring in living organisms. Key intermediates in these reactions have been shown to contain a high-energy (often cyclic) peroxide which decomposes. The simplest molecules, 1,2-dioxetane and 1,2-dioxetanone, have thus been used extensively both theoretically and experimentally as model systems to understand the underlying mechanisms of chemiexcitation. An outstanding question remains whether the peroxide bond is a necessity and whether equivalent processes could happen in other simple molecules not containing an OO bond. In the present work, the decomposition reactions of four analogs of 1,2-dioxetane not containing a peroxide bond, the 1,2-oxazetidine anion, the 1,2-diazetidine anion, (neutral) 1,2-oxazetidine and 1,2-dithietane, have been studied theoretically using ab initio multicongurational methods. In particular, the reaction energy barriers and spin-orbit coupling strengths were calculated; the electronic degeneracy was studied and compared to the case of 1,2-dioxetane to assess the potentiality of chemiexcitation in the analog molecules.,

  • 311.
    Feierberg, Isabella
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Computational Studies of Enzymatic Enolization Reactions and Inhibitor Binding to a Malarial Protease2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Enolate formation by proton abstraction from an sp3-hybridized carbon atom situated next to a carbonyl or carboxylate group is an abundant process in nature. Since the corresponding nonenzymatic process in water is slow and unfavorable due to high intrinsic free energy barriers and high substrate pKa s, enzymes catalyzing such reaction steps must overcome both kinetic and thermodynamic obstacles.

    Computer simulations were used to study enolate formation catalyzed by glyoxalase I (GlxI) and 3-oxo-Δ5-steroid isomerase (KSI). The results, which reproduce experimental kinetic data, indicate that for both enzymes the free energy barrier reduction originates mainly from the balancing of substrate and catalytic base pKas. This was found to be accomplished primarily by electrostatic interactions. The results also suggest that the remaining barrier reduction can be explained by the lower reorganization energy in the preorganized enzyme compared to the solution reaction. Moreover, it seems that quantum effects, arising from zero-point vibrations and proton tunnelling, do not contribute significantly to the barrier reduction in GlxI. For KSI, the formation of a low-barrier hydrogen bond between the enzyme and the enolate, which is suggested to stabilize the enolate, was investigated and found unlikely. The low pKa of the catalytic base in the nonpolar active site of KSI may possibly be explained by the presence of a water molecule not detected by experiments.

    The hemoglobin-degrading aspartic proteases plasmepsinI and plasmepsin II from Plasmodium falciparum have emerged as putative drug targets against malaria. A series of C2- symmetric compounds with a 1,2-dihydroxyethylene scaffold were investigated for plasmepsin affinity, using computer simulations and enzyme inhibition assays. The calculations correctly predicted the stereochemical preferences of the scaffold and the effect of chemical modifications. Calculated absolute binding free energies reproduced experimental data well. As these inhibitors have down to subnanomolar inhibition constants of the plasmepsins and no measurable affinity to human cathepsin D, they constitute promising lead compounds for further drug development.

  • 312. Feifel, R.
    et al.
    Velkov, Yasen
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Carravetta, V.
    Angeli, C.
    Cimiraglia, R.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Sorensen, S. L.
    Piancastelli, M. N.
    De Fanis, A.
    Okada, K.
    Kitajima, M.
    Tanaka, T.
    Tanaka, H.
    Ueda, K.
    X-ray absorption and resonant Auger spectroscopy of O(2) in the vicinity of the O 1s ->sigma* resonance: Experiment and theory2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 6, article id 064304Article in journal (Refereed)
    Abstract [en]

    We report on an experimental and theoretical investigation of x-ray absorption and resonant Auger electron spectra of gas phase O(2) recorded in the vicinity of the O 1s ->sigma* excitation region. Our investigation shows that core excitation takes place in a region with multiple crossings of potential energy curves of the excited states. We find a complete breakdown of the diabatic picture for this part of the x-ray absorption spectrum, which allows us to assign an hitherto unexplained fine structure in this spectral region. The experimental Auger data reveal an extended vibrational progression, for the outermost singly ionized X (2)Pi(g) final state, which exhibits strong changes in spectral shape within a short range of photon energy detuning (0 eV>Omega>-0.7 eV). To explain the experimental resonant Auger electron spectra, we use a mixed adiabatic/diabatic picture selecting crossing points according to the strength of the electronic coupling. Reasonable agreement is found between experiment and theory even though the nonadiabatic couplings are neglected. The resonant Auger electron scattering, which is essentially due to decay from dissociative core-excited states, is accompanied by strong lifetime-vibrational and intermediate electronic state interferences as well as an interference with the direct photoionization channel. The overall agreement between the experimental Auger spectra and the calculated spectra supports the mixed diabatic/adiabatic picture.

  • 313.
    Feliciano, Gustavo T.
    et al.
    Univ Estadual Paulista UNESP, Inst Quim, Dept Fis Quim, Araraquara.
    Sanz-Navarro, Carlos
    CSIC, Catalan Inst Nanosci & Nanotechnol ICN2, Campus UAB, Barcelona; Barcelona Inst Sci & Technol, Campus UAB, Barcelona.
    Coutinho-Neto, Mauricio Domingues
    Univ Fed ABC, Ctr Ciencias Nat & Humanas, Santo Andre.
    Ordejon, Pablo
    CSIC, Catalan Inst Nanosci & Nanotechnol ICN2, Campus UAB, Barcelona; Barcelona Inst Sci & Technol, Campus UAB, Barcelona .
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Rocha, Alexandre Reily
    Univ Estadual Paulista UNESP, Inst Fis Teor, Sao Paulo; MIT, Dept Chem Engn, Cambridge.
    Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems: A QM/MM-NEGF Approach2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 2, p. 485-492Article in journal (Refereed)
    Abstract [en]

    The effects of the environment in nanoscopic materials can play a crucial role in device design. Particularly in biosensors, where the system is usually embedded in a solution, water and ions have to be taken into consideration in atomistic simulations of electronic transport for a realistic description of the system. In this work, we present a methodology that combines quantum mechanics/molecular mechanics methods (QM/MM) with the nonequilibrium Green’s function framework to simulate the electronic transport properties of nanoscopic devices in the presence of solvents. As a case in point, we present further results for DNA translocation through a graphene nanopore. In particular, we take a closer look into general assumptions in a previous work. For this sake, we consider larger QM regions that include the first two solvation shells and investigate the effects of adding extra k-points to the NEGF calculations. The transverse conductance is then calculated in a prototype sequencing device in order to highlight the effects of the solvent.

  • 314.
    Felicissimo, V.C.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). Universidade Federal de Minas Gerais, Brazil.
    Cesar, A.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Probing weak molecular orbital interactions in non-conjugated diene molecules by means of near-edge X-ray absorption spectroscopy2005In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, no 33, p. 7385-7395Article in journal (Refereed)
    Abstract [en]

    Carbon and oxygen near-edge X-ray absorption fine structure (NEXAFS) spectra of 1,4-cyclohexadiene, p-benzoquinone, norbornadiene, norbornadienone, and cis-cis-[4,4,2]propella-3,8-diene-11,12-dione were calculated by means of Hartree-Fock and hybrid density functional theory using the static-exchange (STEX) approximation. The NEXAFS spectra are used as a probe to identify weak molecular interactions between the two non-conjugated ethylenic pi* orbitals present in these molecules. We show that the X-ray absorption spectrum of 1,4-cyclohexadiene exhibits some particular spectral structures in the discrete energy region that evidence diene through-bond orbital interaction, whereas absorption peaks are identified in the norbornadiene and norbornadienone spectra that indicate effective through-space orbital interactions. The molecular structure of the cis-cis-[4,4,2]propella-3,8-diene-11,12-dione isomer is such that the indirect through-bond or through-space diene orbital interactions are too weak to be assigned by its C1s NEXAFS spectrum.

  • 315.
    Felicissimo, V.C.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). Universidade Federal de Minas Gerais, Brazil.
    Guimaraes, F.F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). Universidade Federal de Minas Gerais, Brazil.
    Cesar, A.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Proton transfer mediated by the vibronic coupling in oxygen core ionized states of glyoxalmonoxime studied by infrared-X-ray pump-probe spectroscopy.2006In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 110, no 47, p. 12805-12813Article in journal (Refereed)
    Abstract [en]

    The theory of IR-X-ray pump-probe spectroscopy beyond the Born-Oppenheimer approximation is developed and applied to the study of the dynamics of intramolecular proton transfer in glyoxalmonoxime leading to the formation of the tautomer 2-nitrosoethenol. Due to the IR pump pulses the molecule gains sufficient energy to promote a proton to a weakly bound well. A femtosecond X-ray pulse snapshots the wave packet route and, hence, the dynamics of the proton transfer. The glyoxalmonoxime molecule contains two chemically nonequivalent oxygen atoms that possess distinct roles in the hydrogen bond, a hydrogen donor and an acceptor. Core ionizations of these form two intersecting core-ionized states, the vibronic coupling between which along the OH stretching mode partially delocalizes the core hole, resulting in a hopping of the core hole from one site to another. This, in turn, affects the dynamics of the proton transfer in the core-ionized state. The quantum dynamical simulations of X-ray photoelectron spectra of glyoxalmonoxime driven by strong IR pulses demonstrate the general applicability of the technique for studies of intramolecular proton transfer in systems with vibronic coupling.

  • 316.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Karlsson, Hans
    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.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Quantum dynamics simulations of model chemiluminescence systems2014In: Luminescence (Chichester, England Print), ISSN 1522-7235, E-ISSN 1522-7243, Vol. 29, no S1, p. 67-67Article in journal (Other academic)
  • 317.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ugandi, Mihkel
    Uncontracted basis sets for ab initio calculations of muonic atoms and molecules2018In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, E-ISSN 1097-461X, Vol. 118, no 21, article id e25755Article in journal (Refereed)
    Abstract [en]

    n this work, we investigated muonic atoms and molecules from a quantum chemist's viewpoint by incorporating muons in the CASSCF model. With the aim of predicting muonic X‐ray energies, primitive muonic basis sets were developed for a selection of elements. The basis sets were then used in CASSCF calculations of various atoms and molecules to calculate muonic excited states. We described the influence of nuclear charge distribution in predicting muonic X‐ray energies. Effects of the electronic wave function on the muonic X‐ray energies were also examined. We have computationally demonstrated how the muon can act as a probe for the nuclear charge distribution or electronic wave function by considering lower or higher muonic excited states, respectively.

  • 318.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Xiao, Hong-Yan
    Navizet, Isabelle
    Liu, Ya-Jun
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    S0 → S3 transition in recombination products of photodissociated dihalomethanes2014In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 112, no 5-6, p. 575-582Article in journal (Refereed)
    Abstract [en]

    Species of the form CH2X–Y (X, Y = Br, I) have been proposed and identified as recombination products of the photodissociation of the parent dihalomethanes. Second-order complete active space perturbation theory (CASPT2) calculations of the vertical absorption energies considerably overestimate the experimental transient absorption band maxima, while the computationally cheaper time-dependent density functional theory (TD-DFT) method yields results with a reasonable agreement. In this work, we try to find the reason for this unexpected performance difference. In an initial study of the I2 molecule, we establish that CASPT2 is capable of providing quantitatively accurate results and that the TD-DFT values are only valid at first sight, but are qualitatively flawed. In the CASPT2 calculations for the CH2X–Y molecules, we include relativistic corrections, spin–orbit coupling, vibrational and thermal effects, and the solvent polarisation. Unfortunately, the results do not improve appreciably compared to the experimental measurements. We conclude that the good agreement of TD-DFT results is very likely fortuitous in this case as well, and that further theoretical and experimental investigations are probably needed to resolve the current discrepancy between CASPT2 and experiments.

  • 319. Fernández García-Prieto, F.
    et al.
    Aguilar, M. A.
    Fdez. Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Muñoz-Losa, A.
    Olivares del Valle, F. J.
    Sánchez, M. L.
    Martín, M. E.
    Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5504-5514Article in journal (Refereed)
    Abstract [en]

    Solvent effects on the UV–vis absorption spectra and molecular properties of four models of the photoactive yellow protein (PYP) chromophore have been studied with ASEP/MD, a sequential quantum mechanics/molecular mechanics method. The anionic trans-p-coumaric acid (pCA), thioacid (pCTA), methyl ester (pCMe), and methyl thioester (pCTMe) derivatives have been studied in gas phase and in water solution. We analyze the modifications introduced by the substitution of sulfur by oxygen atoms and hydrogen by methyl in the coumaryl tail. We have found some differences in the absorption spectra of oxy and thio derivatives that could shed light on the different photoisomerization paths followed by these compounds. In solution, the spectrum substantially changes with respect to that obtained in the gas phase. The n → π1* state is destabilized by a polar solvent like water, and it becomes the third excited state in solution displaying an important blue shift. Now, the π → π1* and π → π2* states mix, and we find contributions from both transitions in S1 and S2. The presence of the sulfur atom modulates the solvent effect and the first two excited states become practically degenerate for pCA and pCMe but moderately well-separated for pCTA and pCTMe.

  • 320. Ferrighi, L
    et al.
    Marchesan, D
    Ruud, K
    Frediani, Luca
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Coriani, S
    Gauge-origin-independent magnetizabilities of solvated molecules using the polarizable continuum model2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 123, no 20, p. 204104-Article in journal (Refereed)
    Abstract [en]

    We present an implementation of the polarizable continuum model in its integral equation formulation for the calculation of the magnetizabilities of solvated molecules. The gauge-origin independence of the calculated magnetizabilities and the fast basis set convergence are ensured through the use of London atomic orbitals. Our implementation can use Hartree-Fock and multiconfigurational self-consistent-field (MCSCF) wave functions as well as density-functional theory including hybrid functionals such as B3LYP. We present the results of dielectric continuum effects on water and pyridine using MCSCF wave functions, as well as dielectric medium effects on the magnetizability of the aromatic amino acids as a model for how a surrounding protein environment affects the magnetizability of these molecules. It is demonstrated that the dielectric medium effects on the magnetizability anisotropies of the aromatic amino acids may be substantial, being as large as 25% in the case of tyrosine.

  • 321.
    Finzel, Kati
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    About the atomic shell structure in real space and the Pauli exclusion principle2016In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 135, no 6, p. 148-Article in journal (Refereed)
    Abstract [en]

    It is shown that any set of eigenfunctions (1s, 2s) of a bare Coulomb Hamiltonian exhibit the same atomic shell structure pattern for the real-space indicator a(1), which is defined as the ratio between the positive kinetic energy density and the electron density. Since this model Hamiltonian excludes all effects due to the electron-electron repulsion, the appearance of the atomic shell structure is attributed to the Pauli exclusion principle that arises from the requirements for a fermionic wavefunction. Since the derivation is independent of the nuclear charge and the energy of the system, reversely imposing proper atomic shell structure behavior in the design of kinetic energy functionals mimics the Pauli exclusion principle during a variational process.

  • 322.
    Finzel, Kati
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    About the compatibility between ansatzes and constraints for a local formulation of orbital-free density functional theory2017In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 117, no 5, article id UNSP e25329Article in journal (Refereed)
    Abstract [en]

    Functional properties that are exact for the Hohenberg-Kohn functional may turn into mutually exclusive constraints at a given level of ansatz. This is exemplarily shown for the local density approximation. Nevertheless, it is possible to reach exactly the Kohn-Sham data from an orbital-free density functional framework based on simple one-point functionals by starting from the Levy-Perdew-Sahni formulation. The energy value is obtained from the density-potential pair, and therefore does not refer to the functional dependence of the potential expression. Consequently, the potential expression can be obtained from any suitable model and is not required to follow proper scaling behavior.

  • 323.
    Finzel, Kati
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    About the Difference Between Density Functionals Defined by Energy Criterion and Density Functionals Defined by Density Criterion: Exchange Functionals2016In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 116, no 15, p. 1187-1189Article in journal (Refereed)
    Abstract [en]

    The difference between density functionals defined by energy criterion and density functionals defined by density criterion is studied for the exchange functional. It is shown that Slater potentials are exact exchange potentials in the sense that they yield the Hartree-Fock electron density if all operators are given by local expressions. (C) 2016 Wiley Periodicals, Inc.

  • 324.
    Finzel, Kati
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Approximating the Pauli Potential in Bound Coulomb Systems2016In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 116, no 16, p. 1261-1266Article in journal (Refereed)
    Abstract [en]

    It is shown that the Pauli potential in bound Coulomb systems can in good approximation be composed from the corresponding atomic fragments. This provides a simple and fast procedure how to generate the Pauli potential in bound systems, which is needed to perform an orbital-free density functional calculation. The method is applicable to molecules and solids. (c) 2016 Wiley Periodicals, Inc.

  • 325.
    Finzel, Kati
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Ayers, Paul W.
    McMaster University, Canada.
    Functional constructions with specified functional derivatives2016In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 135, no 12, article id 255Article in journal (Refereed)
    Abstract [en]

    A bifunctional construction depending on a specified density-potential pair and an approximate guiding electron density functional is presented. The proposed bifunctional construction properly transforms under homogeneous coordinate scaling and yields the specified functional derivative, which determines the electron density. Whereas the method is general and applicable to all functional types, it will prove especially helpful in the context of orbital-free density functional theory, where most existing approximate density functionals predict inaccurate potentials.

  • 326.
    Finzel, Kati
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Baranov, Alexey I.
    Max Planck Institute Chemistry Phys Solids, Germany.
    A simple model for the Slater exchange potential and its performance for solids2017In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 117, no 1, p. 40-47Article in journal (Refereed)
    Abstract [en]

    A simple local model for the Slater exchange potential is determined by least square fit procedure from Hartree-Fock (HF) atomic data. Since the Slater potential is the exact exchange potential yielding HF electron density from Levy-Perdew-Sahni density functional formalism (Levy et al., Phys. Rev. A 1984, 30, 2745), the derived local potential is significantly more negative than the conventional local density approximation. On the set of 22 ionic, covalent and van der Waals solids including strongly correlated transition metal oxides, it has been demonstrated, that this simple model potential is capable of reproducing the band gaps nearly as good as popular meta GGA potentials in close agreement with experimental values.

  • 327.
    Finzel, Kati
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Davidsson, Joel
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Abrikosov, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Energy-Surfaces from the Upper Bound of the Pauli Kinetic Energy2016In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 116, no 18, p. 1337-1341Article in journal (Refereed)
    Abstract [en]

    Based on the Kohn-Sham Pauli potential and the Kohn-Sham electron density, the upper bound of the Pauli kinetic energy is tested as a suitable replacement for the exact Pauli kinetic energy for application in orbital-free density functional calculations. It is found that bond lengths for strong and moderately bound systems can be qualitatively predicted, but with a systematic shift toward larger bond distances with a relative error of 6% up to 30%. Angular dependence of the energy-surface cannot be modeled with the proposed functional. Therefore, the upper bound model is the first parameter-free functional expression for the kinetic energy that is able to qualitatively reproduce binding curves with respect to bond distortions. (C) 2016 Wiley Periodicals, Inc.

  • 328.
    Finzel, Kati
    et al.
    Linköping University, Department of Physics, Chemistry and Biology.
    Martin Pendas, Angel
    University of Oviedo, Spain.
    Francisco, Evelio
    University of Oviedo, Spain.
    Efficient algorithms for Hirshfeld-I charges2015In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 143, no 8, p. 084115-Article in journal (Refereed)
    Abstract [en]

    A new viewpoint on iterative Hirshfeld charges is presented, whereby the atomic populations obtained from such a scheme are interpreted as such populations which reproduce themselves. This viewpoint yields a self-consistent requirement for the Hirshfeld-I populations rather than being understood as the result of an iterative procedure. Based on this self-consistent requirement, much faster algorithms for Hirshfeld-I charges have been developed. In addition, new atomic reference densities for the Hirshfeld-I procedure are presented. The proposed reference densities are N-representable, display proper atomic shell structure and can be computed for any charged species.

  • 329.
    Firle, Sascha
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    Get a grip on chaos: Tailored measures for complex systems on surfaces1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Complex systems are ubiquitous in physics, biology and mathematics. This thesis is concerned with describing and understanding complex systems. Some new concepts about how large systems can be viewed in a lower dimensional framework are proposed. The systems presented are examples from ecology and chemistry. In both cases we have a large amount of interacting units that can be understood by focusing on more abstract featuresthat are the result of internal interactions.

    The predator-prey system investigated consists of ground beetles, Pterostichus cupreus L. (Coleoptera: Carabidae), that feeds on bird-cherry oat aphids. The beetles' movement can consistently be described by a combined model of surface diffusion and biased random walk. This allows conclusions about how fast and in which fashion the beetle covers its habitat.

    Movement is dependent on aphid densities and predation, in turn modifies aphid distributions locally. The presented generalized functional response theory describes predation rates in the presence of spatial heterogeneity. A single measure for fragmentation captures all essential features of the prey aggregation and allows the estimation of outbreak densities and distributions.

    The chemical example is the catalytic oxidation of CO on a Pt(110) single crystal surface. Unstable periodic orbits reconstructed from experimental data are used to reveal the topology of the attractor, underlying the time series dynamics. The found braid supports an orbit which implies that the time series is chaotic.

    The system is simulated numerically by a set of partial differential equations for surface coverage in one space dimension. The bifurcation diagram of the corresponding traveling wave ODE reveals the homoclinic and heteroclinic orbits that organize the phase space and mediate the transition to chaos. Studies in the PDE-framework relate this to the stability and to the interaction of pulse-like solutions.

  • 330.
    Fourre, Isabelle
    et al.
    University of Paris 06, France.
    Di Meo, Florent
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering. University of Limoges, France.
    Podloucka, Pavlina
    Palacky University, Czech Republic.
    Otyepka, Michal
    Palacky University, Czech Republic.
    Trouillas, Patrick
    University of Limoges, France; Palacky University, Czech Republic.
    Dimerization of quercetin, Diels-Alder vs. radical-coupling approach: a joint thermodynamics, kinetics, and topological study2016In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 22, no 8, p. 190-Article in journal (Refereed)
    Abstract [en]

    Quercetin is a prototypical antioxidant and prominent member of flavonoids, a large group of natural polyphenols. The oxidation of quercetin may lead to its dimerization, which is a paradigm of the more general polyphenol oligomerization. There exist two opposing mechanisms to describe the dimerization process, namely radical-coupling or Diels-Alder reactions. This work presents a comprehensive rationalization of this dimerization process, acquired from density functional theory (DFT) calculations. It is found that the two-step radical-coupling pathway is thermodynamically and kinetically preferred over the Diels-Alder reaction. This is in agreement with the experimental results showing the formation of only one isomer, whereas the Diels-Alder mechanism would yield two isomers. The evolution in bonding, occurring during these two processes, is investigated using the atoms in molecules (AIM) and electron localization function (ELF) topological approaches. It is shown that some electron density is accumulated between the fragments in the transition state of the radical-coupling reaction, but not in the transition state of the Diels-Alder process.

  • 331.
    Frances-Monerris, Antonio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Roca-Sanjuan, Daniel
    Fernandez Galvan, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Towards the Understanding of the Larger Phosphorescence Quantum Yield than Fluorescence in Dioxetanone2014In: Luminescence (Chichester, England Print), ISSN 1522-7235, E-ISSN 1522-7243, Vol. 29, p. 67-68Article in journal (Other academic)
  • 332.
    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.

  • 333. Fransson, T.
    et al.
    Burdakova, D.
    Norman, Patrick
    Linköping University, Sweden.
    K- and L-edge X-ray absorption spectrum calculations of closed-shell carbon, silicon, germanium, and sulfur compounds using damped four-component density functional response theory2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 19, p. 13591-13603Article in journal (Refereed)
    Abstract [en]

    X-ray absorption spectra of carbon, silicon, germanium, and sulfur compounds have been investigated by means of damped four-component density functional response theory. It is demonstrated that a reliable description of relativistic effects is obtained at both K- and L-edges. Notably, an excellent agreement with experimental results is obtained for L2,3-spectra - with spin-orbit effects well accounted for - also in cases when the experimental intensity ratio deviates from the statistical one of 2:1. The theoretical results are consistent with calculations using standard response theory as well as recently reported real-time propagation methods in time-dependent density functional theory, and the virtues of different approaches are discussed. As compared to silane and silicon tetrachloride, an anomalous error in the absolute energy is reported for the L2,3-spectrum of silicon tetrafluoride, amounting to an additional spectral shift of ∼1 eV. This anomaly is also observed for other exchange-correlation functionals, but it is seen neither at other silicon edges nor at the carbon K-edge of fluorine derivatives of ethene. Considering the series of molecules SiH4-XFX with X = 1, 2, 3, 4, a gradual divergence from interpolated experimental ionization potentials is observed at the level of Kohn-Sham density functional theory (DFT), and to a smaller extent with the use of Hartree-Fock. This anomalous error is thus attributed partly to difficulties in correctly emulating the electronic structure effects imposed by the very electronegative fluorines, and partly due to inconsistencies in the spurious electron self-repulsion in DFT. Substitution with one, or possibly two, fluorine atoms is estimated to yield small enough errors to allow for reliable interpretations and predictions of L2,3-spectra of more complex and extended silicon-based systems.

  • 334. Fransson, T.
    et al.
    Coriani, S.
    Christiansen, O.
    Norman, Patrick
    Linköping University, Sweden.
    Carbon X-ray absorption spectra of fluoroethenes and acetone: A study at the coupled cluster, density functional, and static-exchange levels of theory2013In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, no 12, article id 124311Article in journal (Refereed)
    Abstract [en]

    Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as the state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger π-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to π-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate π-peak separations due to spectral compressions, a characteristic which is inherent to this method.

  • 335. Fransson, T.
    et al.
    Saue, T.
    Norman, Patrick
    Linköping University, Sweden.
    Four-Component Damped Density Functional Response Theory Study of UV/Vis Absorption Spectra and Phosphorescence Parameters of Group 12 Metal-Substituted Porphyrins2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 5, p. 2324-2334Article in journal (Refereed)
    Abstract [en]

    The influences of group 12 (Zn, Cd, Hg) metal-substitution on the valence spectra and phosphorescence parameters of porphyrins (P) have been investigated in a relativistic setting. In order to obtain valence spectra, this study reports the first application of the damped linear response function, or complex polarization propagator, in the four-component density functional theory framework [as formulated in Villaume et al. J. Chem. Phys. 2010, 133, 064105 ]. It is shown that the steep increase in the density of states as due to the inclusion of spin-orbit coupling yields only minor changes in overall computational costs involved with the solution of the set of linear response equations. Comparing single-frequency to multifrequency spectral calculations, it is noted that the number of iterations in the iterative linear equation solver per frequency grid-point decreases monotonously from 30 to 0.74 as the number of frequency points goes from one to 19. The main heavy-atom effect on the UV/vis-absorption spectra is indirect and attributed to the change of point group symmetry due to metal-substitution, and it is noted that substitutions using heavier atoms yield small red-shifts of the intense Soret-band. Concerning phosphorescence parameters, the adoption of a four-component relativistic setting enables the calculation of such properties at a linear order of response theory, and any higher-order response functions do not need to be considered-a real, conventional, form of linear response theory has been used for the calculation of these parameters. For the substituted porphyrins, electronic coupling between the lowest triplet states is strong and results in theoretical estimates of lifetimes that are sensitive to the wave function and electron density parametrization. With this in mind, we report our best estimates of the phosphorescence lifetimes to be 460, 13.8, 11.2, and 0.00155 s for H2P, ZnP, CdP, and HgP, respectively, with the corresponding transition energies being equal to 1.46, 1.50, 1.38, and 0.89 eV.

  • 336. Fransson, T.
    et al.
    Zhovtobriukh, I.
    Coriani, S.
    Wikfeldt, K. T.
    Norman, Patrick
    Linköping University, Sweden.
    Pettersson, L. G. M.
    Requirements of first-principles calculations of X-ray absorption spectra of liquid water2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 1, p. 566-583Article in journal (Refereed)
    Abstract [en]

    A computational benchmark study on X-ray absorption spectra of water has been performed by means of transition-potential density functional theory (TP-DFT), damped time-dependent density functional theory (TDDFT), and damped coupled cluster (CC) linear response theory. For liquid water, using TDDFT with a tailored CAM-B3LYP functional and a polarizable embedding, we find that an embedding with over 2000 water molecules is required to fully converge spectral features for individual molecules, but a substantially smaller embedding can be used within averaging schemes. TP-DFT and TDDFT calculations on 100 MD structures demonstrate that TDDFT produces a spectrum with spectral features in good agreement with experiment, while it is more difficult to fully resolve the spectral features in the TP-DFT spectrum. Similar trends were also observed for calculations of bulk ice. In order to further establish the performance of these methods, small water clusters have been considered also at the CC2 and CCSD levels of theory. Issues regarding the basis set requirements for spectrum simulations of liquid water and the determination of gas-phase ionization potentials are also discussed.

  • 337.
    Fransson, Thomas
    Linköping University, Department of Physics, Chemistry and Biology.
    X-ray absorption spectroscopy by means of Lanczos-chain driven damped coupled cluster response theory2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A novel method by which to calculate the near edge X-rayabsorption fine structure region of the X-ray absorption spectrum has been derived and implemented. By means of damped coupled cluster theory at coupled cluster levels CCS, CC2, CCSD and CCSDR(3), the spectra of neon and methane have been investigated. Using methods incorprating double excitations, the important relaxation effects maybe taken into account by simultaneous excitation of the core electron and relaxation of other electrons. An asymmetric Lanczos-chain driven approach has been utilized as a means to partially resolve the excitation space given by the coupled cluster Jacobian. The K-edge of the systems have been considered, and relativistic effects are estimated with use of the Douglas--Kroll scalar relativistic Hamiltonian. Comparisons have been made to results obtained with the four-component static-exchange approach and ionization potentials obtained by the {Delta}SCF-method.

    The appropriate basis sets by which to describe the core and excited states have been been determined.  The addition of core-polarizing functions and diffuse or Rydberg functions is important for this description. Scalar relativistic effects accounts for an increase in excitation energies due to the contraction of the 1s-orbital, and this increase is seen to be 0.88 eV for neon. The coupled cluster hierachy shows a trend of convergence towards the experimental spectrum, with an 1s -> 3p excitation energy for neon of an accuracy of 0.40 eV at a relativistic CCSDR(3) level of theory. Results obtained at the damped coupled cluster and STEX levels of theory, respectively, are seen to be in agreement, with a mere relative energy shift.

  • 338. Fransson, Thomas
    et al.
    Rehn, Dirk Robert
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Norman, P.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Static polarizabilities and C-6 dispersion coefficients using the algebraic-diagrammatic construction scheme for the complex polarization propagator2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 146, no 9, article id 094301Article in journal (Refereed)
    Abstract [en]

    An implementation of the damped linear response function, or complex polarization propagator, using the algebraic-diagrammatic construction (ADC) scheme has been developed and utilized for the calculation of electric-dipole polarizabilities and C-6 dispersion coefficients. Four noble gases (He, Ne, Ar, and Kr), five n-alkanes (methane, ethane, propane, butane, and pentane), three carbonyls (formaldehyde, acetaldehyde, and acetone), and three unsaturated hydrocarbons (ethene, acetylene, and benzene) have been treated with the hierarchical set of models ADC(2), ADC(2)-x, and ADC(3/2), and comparison has been made to results obtained with damped linear response Hartree-Fock (HF) and coupled cluster singles and doubles (CCSD) theory as well as high-quality experimental estimates via the dipole oscillator strength distribution approach. This study marks the first ADC calculations of C-6 dispersion coefficients and the first ADC(3/2) calculations of static polarizabilities. Results at CCSD and ADC(3/2) levels of theory are shown to be of similar quality, with electron correlation effects increasing the molecular property values for all calculations except CCSD considerations of ethene and acetylene (attributed to an overestimation of bond electron density at HF level of theory). The discrepancies betweenCCSDand ADC(3/2) are partially due toADCoverestimating anisotropies, and discrepancies with respect to experimental values are partially due to the lack of zero-point vibrational effects in the present study.

  • 339.
    Fransson, Thomas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Zhovtobriukh, Iurii
    Fysikum, Stockholm University, Albanova, Stockholm, Sweden.
    Coriani, Sonia
    Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Trieste, Italy / Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark.
    Wikfeldt, Kjartan T.
    Fysikum, Stockholm University, Albanova, Stockholm, Sweden / Science Institute, University of Iceland, VR-III, Reykjavik, Iceland.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Pettersson, Lars G. M.
    Fysikum, Stockholm University, Albanova, Stockholm, Sweden.
    Requirements of first-principles calculations of X-ray absorption spectra of liquid water2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 1, p. 566-583Article in journal (Refereed)
    Abstract [en]

    A computational benchmark study on X-ray absorption spectra of water has been performed by means of transition-potential density functional theory (TP-DFT), damped time-dependent density functional theory (TDDFT), and damped coupled cluster (CC) linear response theory. For liquid water, using TDDFT with a tailored CAM-B3LYP functional and a polarizable embedding, we find that an embedding with over 2000 water molecules is required to fully converge spectral features for individual molecules, but a substantially smaller embedding can be used within averaging schemes. TP-DFT and TDDFT calculations on 100 MD structures demonstrate that TDDFT produces a spectrum with spectral features in good agreement with experiment, while it is more difficult to fully resolve the spectral features in the TP-DFT spectrum. Similar trends were also observed for calculations of bulk ice. In order to further establish the performance of these methods, small water clusters have been considered also at the CC2 and CCSD levels of theory. Issues regarding the basis set requirements for spectrum simulations of liquid water and the determination of gas-phase ionization potentials are also discussed.

  • 340.
    Frecus, Bogdan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical studies of EPR parameters of spin-labels incomplex environments2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis encloses quantum chemical calculations performed in the framework of density functional response theory for evaluating electron paramagnetic resonance (EPR) spin Hamiltonian parameters of various spin-labels in different environments. These parameters are the well known electronic g-tensor and the nitrogen hyperfine coupling constants, which are extensively explored in this work for various systems. A special attention was devoted to the relationships that form between the structural and spectroscopic properties that can be accounted for as an environmental inuence. Such environmental effects were addressed either within a fully quantum mechanical formalism, involving simplified model structures that still capture the physical properties of the extended system, or by employing a quantum mechanics/molecular mechanics (QM/MM) approach. The latter implies that the nitroxide spin label is treated quantum mechanically, while the environment is treated in a classical discrete manner, with appropriate force fields employed for its description. The state-of- the art techniques employed in this work allow for an optimum accounting of the environmental effects that play an important role for the behaviour of EPR properties of nitroxides spin labels. One achievement presented in this thesis includes the first theoretical con_rmation of an empirical assumption that is usually made for inter-molecular distance measurement experiments in deoxyribonucleic acid (DNA), involving pulsed electron-electron double resonance (PELDOR) and site-directed spin labeling (SDSL) techniques. This refers to the fact that the EPR parameters of the spin-labels are not affected by their interaction with the nucleobases from which DNA is constituted. Another important result presented deals with the inuence of a supramolecular complex on the EPR properties of an encapsulated nitroxide spin-label. The enclusion complex affects the hydrogen bonding topology that forms around the R2NO moiety of the nitroxide. This, on the other hand has a major impact on its structure which further on governs the magnitude of the spectroscopic properties. The projects and results presented in this thesis offer an example of successful usage of modern quantum chemistry techniques for the investigation of EPR parameters of spin-labels in complex systems.

     

  • 341.
    Frecus, Bogdan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    π –stacking effects on the EPR parameters of a prototypical DNA spin label2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 25, p. 10466-10471Article in journal (Refereed)
    Abstract [en]

    The character and value of spin labels for probing environments like double-stranded DNA depends on the degree of changeof the spin Hamiltonian parameters of the spin label induced by the environment. Herein we provide a systematic theoreticalinvestigation of this issue, based on a density functional theory method applied to a spin labeled DNA model system, focusingon the dependence of the EPR properties of the spin label on the π stacking and hydrogen bonding that occur upon incorporatingthe spin label into selected base pair inside DNA. It is found that the EPR spin Hamiltonian parameters of the spin label is onlynegligibly affected by its incorporation into DNA, when compared to the its free form. This result gives theoretical ground forthe common empirical assumption regarding the behaviour of spin Hamiltonian parameters made in EPR based measurementsof distance between spin labels incorporated into DNA.

  • 342. Freitag, Leon
    et al.
    Knecht, Stefan
    Keller, Sebastian F.
    Delcey, Mickaël G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pedersen, Thomas Bondo
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Reiher, Markus
    Gonzalez, Leticia
    Orbital entanglement and CASSCF analysis of the Ru-NO bond in a Ruthenium nitrosyl complex2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 22, p. 14383-14392Article in journal (Refereed)
    Abstract [en]

    Complete active space self-consistent field (CASSCF) wavefunctions and an orbital entanglement analysis obtained from a density-matrix renormalisation group (DMRG) calculation are used to understand the electronic structure, and, in particular, the Ru-NO bond of a Ru nitrosyl complex. Based on the configurations and orbital occupation numbers obtained for the CASSCF wavefunction and on the orbital entropy measurements evaluated for the DMRG wavefunction, we unravel electron correlation effects in the Ru coordination sphere of the complex. It is shown that Ru-NO pi bonds show static and dynamic correlation, while other Ru-ligand bonds feature predominantly dynamic correlation. The presence of static correlation requires the use of multiconfigurational methods to describe the Ru-NO bond. Subsequently, the CASSCF wavefunction is analysed in terms of configuration state functions based on localised orbitals. The analysis of the wavefunctions in the electronic singlet ground state and the first triplet state provides a picture of the Ru-NO moiety beyond the standard representation based on formal oxidation states. A distinct description of the Ru and NO fragments is advocated. The electron configuration of Ru is an equally weighted superposition of Ru-II and Ru-III configurations, with the Ru-III configuration originating from charge donation mostly from Cl ligands. However, and contrary to what is typically assumed, the electronic configuration of the NO ligand is best described as electroneutral.

  • 343.
    Friedman, Ran
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Ions and the protein surface revisited: extensive molecular dynamics simulations and analysis of protein structures in alkali-chloride solutions2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, p. 9213-9223Article in journal (Refereed)
    Abstract [en]

    Proteins interact with ions in various ways. The surface of proteins has an innate capability to bind ions, and it is also influenced by the screening of the electrostatic potential owing to the presence of salts in the bulk solution. Alkali metal ions and chlorides interact with the protein surface, but such interactions are relatively weak and often transient. In this paper, computer simulations and analysis of protein structures are used to characterize the interactions between ions and the protein surface. The results show that the ion-binding properties of protein residues are highly variable. For example, alkali metal ions are more often associated with aspartate residues than with glutamates, whereas chlorides are most likely to be located near arginines. When comparing NaCl and KCl solutions, it was found that certain surface residues attract the anion more strongly in NaCl. This study demonstrates that protein–salt interactions should be accounted for in the planning and execution of experiments and simulations involving proteins, particularly if subtle structural details are sought after.

  • 344.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Membrane-Ion Interactions2018In: Journal of Membrane Biology, ISSN 0022-2631, E-ISSN 1432-1424, Vol. 251, no 3, p. 453-460Article in journal (Refereed)
    Abstract [en]

    Biomembranes assemble and operate at the interface with electrolyte solutions. Interactions between ions in solutions and the lipid affect the membrane structure, dynamics and electrostatic potential. In this article, I review some of the experimental and computational methods that are used to study membrane-ions interactions. Experimental methods that account for membrane-ion interactions directly and indirectly are presented first. Then, studies in which molecular dynamics simulations were used to gain an understanding of membrane-ion interactions are surveyed. Finally, the current view on membrane-ion interactions and their significance is briefly discussed.

  • 345.
    Friedman, Ran
    University of Zürich, Switzerland.
    Proton Transfer on the Molecular Surface of Proteins and Model Systems2009In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 49, no 2, p. 149-153Article in journal (Refereed)
    Abstract [en]

    Proton transfer (PT) reactions take place oil the molecular Surface of proteins, membranes, ionic polymers, and other molecules. The rates of the reactions can be followed experimentally, while the atomistic details can be elucidated by molecular modeling. This manuscript gives a brief overview of the use of computer simulations and molecular modeling, in conjuction with experiments, to study PT reactions oil the surface of solvated molecules. An integrative approach is discussed, where molecular dynamics simulations are performed with a protein, and quantum-mechanics-based calculations are performed oil a small molecule. The simulation results allow the identification of the necessary conditions that yield PT reactions oil the molecular surface. The reactions are efficient when they involve a donor and acceptor located a few A apart and under the influence of a negative electrostatic field. In proton-pumping proteins, it is possible to identify such conditions a priori and locate proton-attracting antenna domains without the need to mutate each potential donor and acceptor. Based on density functional theory calculations, the arrangement of water molecules that interconnect the donor and acceptor moieties is suggested as the rate-limiting step for proton transfer on the molecular surface.

  • 346.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Simulations of Biomolecules in Electrolyte Solutions2019In: Advanced Theory and Simulations, E-ISSN 2513-0390, Vol. 2, no 4, p. 1-10, article id 1800163Article in journal (Refereed)
    Abstract [en]

    Biomolecules including proteins, lipid membranes, and nucleic acids operate at an aqueous milieu that includes solvated ions. The interactions with ions affect biomolecules in different ways depending on the nature of the solute and the type of the ions. The dynamic nature of small soluble ions makes it difficult to follow them by structural methods. Consequently, theories were developed to explain how biomolecules interact in an environment that includes electrolytes. Moreover, simulations studies are often used to study such systems at the molecular or atomistic level. The status of the field, and inparticular of simulation studies, is the subject of this progress report.

  • 347.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    The molecular mechanism behind resistance of the kinase FLT3 to the inhibitor quizartinib2017In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 85, no 11, p. 2143-2152Article in journal (Refereed)
    Abstract [en]

    Fms-like tyrosine kinase 3 (FLT3) is a receptor tyrosine kinase that is a drug target for leukemias. Several potent inhibitors of FLT3 exist, and bind to the inactive form of the enzyme. Unfortunately, resistance due to mutations in the kinase domain of FLT3 limits the therapeutic effects of these inhibitors. As in many other cases, it is not straightforward to explain why certain mutations lead to drug resistance. Extensive fully atomistic molecular dynamics (MD) simulations of FLT3 were carried out with an inhibited form (FLT-quizartinib complex), a free (apo) form, and an active conformation. In all cases, both the wild type (wt) proteins and two resistant mutants (D835F and Y842H) were studied. Analysis of the simulations revealed that impairment of protein-drug interactions cannot explain the resistance mutations in question. Rather, it appears that the active state of the mutant forms is perturbed by the mutations. It is therefore likely that perturbation of deactivation of the protein (which is necessary for drug binding) is responsible for the reduced affinity of the drug to the mutants. Importantly, this study suggests that it is possible to explain the source of resistance by mutations in FLT3 by an analysis of unbiased MD simulations.

  • 348.
    Friedman, Ran
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Boye, Kjetil
    Flatmark, Kjersti
    Molecular modelling and simulations in cancer research2013In: Biochimica et Biophysica Acta. CR. Reviews on Cancer, ISSN 0304-419X, E-ISSN 1879-2561, Vol. 1836, no 1, p. 1-14Article, review/survey (Refereed)
    Abstract [en]

    The complexity of cancer and the vast amount of experimental data available have made computer-aided approaches necessary. Biomolecular modelling techniques are becoming increasingly easier to use, whereas hardware and software are becoming better and cheaper. Cross-talk between theoretical and experimental scientists dealing with cancer-research from a molecular approach, however, is still uncommon. This is in contrast to other fields, such as amyloid-related diseases, where molecular modelling studies are widely acknowledged. The aim of this review paper is therefore to expose some of the more common approaches in molecular modelling to cancer scientists in simple terms, illustrating success stories while also revealing the limitations of computational studies at the molecular level.

  • 349.
    Friedman, Ran
    et al.
    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich .
    Caflisch, A
    Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring2009In: ChemMedChem, ISSN 1860-7179, E-ISSN 1860-7187, Vol. 4, no 8, p. 1317-1326Article in journal (Refereed)
    Abstract [en]

    Plasmepsins (PMs) are essential proteases of the plasmodia parasites and are therefore promising targets for developing drugs against malaria. We have discovered six inhibitors of PM II by high-throughput fragment-based docking of a diversity set of ∼40 000 molecules, and consensus scoring with force field energy functions. Using the common scaffold of the three most active inhibitors (IC50=2–5 μM), another seven inhibitors were identified by substructure search. Furthermore, these 13 inhibitors belong to at least three different classes of compounds. The in silico approach was very effective since a total of 13 active compounds were discovered by testing only 59 molecules in an enzymatic assay. This hit rate is about one to two orders of magnitude higher than those reported for medium- and high-throughput screening techniques in vitro. Interestingly, one of the inhibitors identified by docking was halofantrine, an antimalarial drug of unknown mechanism. Explicit water molecular dynamics simulations were used to discriminate between two putative binding modes of halofantrine in PM II.

  • 350.
    Friedman, Ran
    et al.
    University of Zürich, Switzerland.
    Caflisch, A
    On the orientation of the catalytic dyad in aspartic proteases2010In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 78, no 6, p. 1575-1582Article in journal (Refereed)
    Abstract [en]

    The recent re-refinement of the X-ray structure of apo plasmepsin II from Plasmodium falciparum suggests that the two carboxylate groups in the catalytic dyad are noncoplanar, (Robbins et al., Acta Crystallogr D Biol Crystallogr 2009;65: 294–296) in remarkable contrast with the vast majority of structures of aspartic proteases. Here, evidence for the noncoplanarity of the catalytic aspartates is provided by analysis of multiple explicit water molecular dynamics (MD) simulations of plasmepsin II, human β-secretase, and HIV-protease. In the MD runs of plasmepsin II, the angle between the planes of the two carboxylates of the catalytic dyad is almost always in the range 60°–120°, in agreement with the perpendicular orientation in the re-refined X-ray structure. The noncoplanar arrangement is prevalent also in the β-secretase simulations, as well as in the runs with the inhibitor-bound proteases. Quantum-mechanics calculations provide further evidence that before catalysis the noncoplanar arrangement is favored energetically in eukaryotic aspartic proteases. Remarkably, the coplanar orientation of the catalytic dyad is observed in MD simulations of HIV-protease at 100 K but not at 300 K, which indicates that the noncoplanar arrangement is favored by conformational entropy. This finding suggests that the coplanar orientation in the crystal structures of apo aspartic proteases is promoted by the very low temperature used for data collection (usually around 100 K).

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