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  • 1.
    Ali, Md Ehesan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Staemmler, Volker
    Illas, Francesc
    Oppeneer, Peter M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Designing the Redox-Driven Switching of Ferro- to Antiferromagnetic Couplings in Organic Diradicals2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 12, p. 5216-5220Article in journal (Refereed)
    Abstract [en]

    Switching of the magnetic exchange coupling from ferro- to antiferromagnetic or vice versa in a single molecule is an appealing but rarely occurring phenomenon in molecular magnetism. Here, we report this for an unprecedented pure organic system, computationally designed by tailoring a conformationally restricted, known nitroxide-diradical (Rajca et al. J. Am. Chem. Soc. 2007, 129, 10159). This ferro- to antiferromagnetic coupling switching of an "m-phenylene" based diradical is governed by a stereoelectronic effect and controlled by a redox-driven chemical reaction.

  • 2.
    Almlöf, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Carlsson, Jens
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Improving the accuracy of the linear interaction energy method for solvation free energies2007In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 3, no 6, p. 2162-2175Article in journal (Refereed)
    Abstract [en]

    A linear response method for estimating the free energy of solvation is presented and validated using explicit solvent molecular dynamics, thermodynamic perturbation calculations, and experimental data. The electrostatic contribution to the solvation free energy is calculated using a linear response estimate, which is obtained by comparison to the free energy calculated using thermodynamic perturbation. Systematic deviations from the value of 1/2 in the potential energy scaling factor are observed for some types of compounds, and these are taken into account by introducing specific coefficients for different chemical groups. The derived model reduces the rms error of the linear response estimate significantly from 1.6 to 0.3 kcal/mol on a training set of 221 molecules used to parametrize the model and from 3.7 to 1.3 kcal/mol on a test set of 355 molecules that were not used in the derivation of the model. The total solvation free energy is estimated by combining the derived model with an empirical size dependent term for predicting the nonpolar contribution. Using this model, the experimental hydration free energies for 192 molecules are reproduced with an rms error of 1.1 kcal/mol. The use of LIE in simplified binding free energy calculations to predict protein−ligand binding free energies is also discussed.

  • 3. Aquilante, Francesco
    et al.
    Malmqvist, Per-Åke
    Pedersen, Thomas Bondo
    Ghosh, Abhik
    Roos, Björn Olof
    Cholesky decomposition-based multiconfiguration second-order perturbation theory (CD-CASPT2): application to the spin-state energetics of Co-III(diiminato)(NPh).2008In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 5, p. 694-702Article in journal (Refereed)
    Abstract [en]

    The electronic structure and low-lying electronic states of a Co-III(diiminato)(NPh) complex have been studied using mulficonfigurational wave function theory (CASSCF/CASPT2) The results have been compared to those obtained with density functional theory. The best agreement with ab initio results is obtained with a modified B3LYP functional containing a reduced amount (15%) of Hartree-Fock exchange. A relativistic basis set with 869 functions has been employed in the most extensive ab initio calculations, where a Cholesky decomposition technique was used to overcome problems arising from the large size of the two-electron integral matrix. It is shown that this approximation reproduces results obtained with the full integral set to a high accuracy, thus opening the possibility to use this approach to perform multiconfigurational wave-function-based quantum chemistry on much larger systems relative to what has been possible until now.

  • 4. Bjorling, Alexander
    et al.
    Niebling, Stephan
    Marcellini, Moreno
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    van der Spoel, David
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Westenhoff, Sebastian
    Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 2, p. 780-787Article in journal (Refereed)
    Abstract [en]

    Time-resolved X-ray solution scattering is an increasingly popular method to measure conformational changes in proteins. Extracting structural information from the resulting difference X-ray scattering data is a daunting task. We present a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields. The molecule of interest is then refined toward experimental data using molecular dynamics simulation. Therefore, the energy landscape is biased toward conformations that agree with experimental data. We describe and verify the method, and we provide an implementation in GROMACS.

  • 5. Borstnar, Rok
    et al.
    Repic, Matej
    Kamerlin, Shina Caroline Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Vianello, Robert
    Mavri, Janez
    Computational Study of the pK(a) Values of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 10, p. 3864-3870Article in journal (Refereed)
    Abstract [en]

    Monoamine oxidase (MAO), which exists in two isozymic forms, MAO A and MAO B, is an important flavoenzyme responsible for the metabolism of amine neurotransmitters such as dopamine, serotonin, and norepinephrine. Despite extensive research effort, neither the catalytic nor the inhibition mechanisms of MAO have been completely understood. There has also been dispute with regard to the protonation state of the substrate upon entering the active site, as well as the identity of residues that are important for the initial deprotonation of irreversible acetylenic inhibitors, in accordance with the recently proposed mechanism. Therefore, in order to investigate features essential for the modes of action of MAO, we have calculated pK(a) values of three relevant tyrosine residues in the MAO B active site, with and without dopamine bound as the. substrate (as well as the pK(a) of the dopamine itself in the active site). The calculated pK(a) values for Tyr188, Tyr398, and Tyr435 in the complex are found to be shifted upward to 13.0, 13.7, and 14.7, respectively, relative to 10.1 in aqueous solution, ruling out the likelihood that they are viable proton acceptors. The altered tyrosine pK(a) values could be rationalized as an interplay of two opposing effects: insertion of positively charged bulky dopamine that lowers tyrosine pK(a) values, and subsequent removal of water molecules from the active site that elevates tyrosine pK(a) values, in which the latter prevails. Additionally, the pK(a) value of the bound dopamine (8.8) is practically unchanged compared to the corresponding value in aqueous solution (8.9), as would be expected from a charged amine placed in a hydrophobic active site consisting of aromatic moieties. We also observed potentially favorable cation-pi interactions between the -NH3+ group on dopamine and aromatic moieties, which provide a stabilizing effect to the charged fragment. Thus, we offer here theoretical evidence that the amine is most likely to be present in the active site in its protonated form, which is similar to the conclusion from experimental studies of MAO A (Jones et al. J. Neural Trans. 2007, 114, 707-712). However, the free energy cost of transferring the proton from the substrate to the bulk solvent is only 1.9 kcal mol(-1), leaving open the possibility that the amine enters the chemical step in its neutral form. In conjunction with additional experimental and computational work, the data presented here should lead toward a deeper understanding of mechanisms of the catalytic activity and irreversible inhibition of MAO B, which can allow for the design of novel and improved MAO B inhibitors.

  • 6. Bostrom, Jonas
    et al.
    Pitonak, Michal
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Neogrady, Pavel
    Pedersen, Thomas Bondo
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Coupled Cluster and Moller-Plesset Perturbation Theory Calculations of Noncovalent Intermolecular Interactions using Density Fitting with Auxiliary Basis Sets from Cholesky Decompositions2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 6, p. 1921-1928Article in journal (Refereed)
    Abstract [en]

    We compute noncovalent intermolecular interaction energies for the S22 test set [Phys. Chem. Chem. Phys. 2006, 8, 1985-1993] of molecules at the Moller-Plesset and coupled cluster levels of supermolecular theory using density fitting (DF) to approximate all two-electron integrals. The error due to the DF approximation is analyzed for a range of auxiliary basis sets derived from Cholesky decomposition (CD) in conjunction with correlation consistent and atomic natural orbital valence basis sets. A Cholesky decomposition threshold of 10(-4)E(h) for full molecular CD and its one-center approximation (1C-CD) generally yields errors below 0.03 kcal/mol, whereas 10(-3)E(h) is sufficient to obtain the same level of accuracy or better with the atomic CD (aCD) and atomic compact CD (acCD) auxiliary basis sets. Comparing to commonly used predefined auxiliary basis sets, we find that while the aCD and acCD sets are larger by a factor of 2-4 with triple-zeta AO basis sets, they provide results 1-2 orders of magnitude more accurate.

  • 7. Boström, Jonas
    et al.
    Aquilante, Francesco
    Pedersen, Thomas Bondo
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Ab Initio Density Fitting: Accuracy Assessment of Auxiliary Basis Sets from Cholesky Decompositions2009In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 5, no 6, p. 1545-1553Article in journal (Refereed)
    Abstract [en]

    The accuracy of auxiliary basis sets derived by Cholesky decompositions of the electron repulsion integrals is assessed in a series of benchmarks on total ground state energies and dipole moments of a large test set of molecules. The test set includes molecules composed of atoms from the first three rows of the periodic table as well as transition metals. The accuracy of the auxiliary basis sets are tested for the 6-31 G**, correlation consistent, and atomic natural orbital basis sets at the Hartree-Fock, density functional theory, and second-order Moller-Plesset levels of theory. By decreasing the decomposition threshold, a hierarchy of auxiliary basis sets is obtained with accuracies ranging from that of standard auxiliary basis sets to that of conventional integral treatments.

  • 8. Boström, Jonas
    et al.
    Aquilante, Francesco
    Pedersen, Thomas Bondo
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical gradients of Hartree-Fock exchange with density fitting approximations2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 1, p. 204-212Article in journal (Refereed)
    Abstract [en]

    We extend the local exchange (LK) algorithm [Aquilante, F.; Pedersen, T. B.; Lindh, R. J. Chem. Phys.2007, 126, 194106] to the calculation of analytical gradients with density fitting. We discuss the features of the screening procedure and demonstrate the possible advantages of using this formulation, which is easily interfaced to a standard integral-direct gradient code. With auxiliary basis sets obtained from Cholesky decomposition of atomic or molecular integral blocks with a decomposition threshold of 10-4Eh, typical errors due to the density fitting in bond lengths, bond angles, and dihedral angles are 0.1 pm, 0.1°, and 0.5°, respectively. The overall speedup of geometry optimizations is about 1 order of magnitude for atomic natural-orbital-type basis sets but much less pronounced for correlation-consistent basis sets.

  • 9. Boström, Jonas
    et al.
    Delcey, Mickael G
    Aquilante, Francesco
    Serrano-Andrés, Luis
    Bondo Pedersen, Tomas
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Calibration of Cholesky Auxiliary Basis Sets for Multiconfigurational Perturbation Theory Calculations of Excitation Energies2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 3, p. 747-754Article in journal (Refereed)
    Abstract [en]

    The accuracy of auxiliary basis sets derived from Cholesky decomposition of two-electron integrals is assessed for excitation energies calculated at the state-average complete active space self-consistent field (CASSCF) and multiconfigurational second order perturbation theory (CASPT2) levels of theory using segmented as well as generally contracted atomic orbital basis sets. Based on 196 valence excitations in 26 organic molecules and 72 Rydberg excitations in 3 organic molecules, the results show that Cholesky auxiliary basis sets can be used without compromising the accuracy of the multiconfigurational methods. Specifically, with a decomposition threshold of 10(-4) au, the mean error due to the Cholesky auxiliary basis set is 0.001 eV, or smaller, decreasing with increasing atomic orbital basis set quality.

  • 10. Caleman, Carl
    et al.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Hong, Minyan
    Hub, Jochen S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Costa, Luciano T.
    van der Spoer, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 1, p. 61-74Article in journal (Refereed)
    Abstract [en]

    The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys. 2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed expose of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem. 2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.

  • 11. Chaudret, Robin
    et al.
    Contreras-Garcia, Julia
    Delcey, Mickaël
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Parisel, Olivier
    Yang, Weitao
    Piquemal, Jean-Philip
    Revisiting H2O Nucleation around Au+ and Hg2+: The Peculiar "Pseudo-Soft" Character of the Gold Cation2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 5, p. 1900-1909Article in journal (Refereed)
    Abstract [en]

    In this contribution, we propose a deeper understanding of the electronic effects affecting the nucleation of water around the Au+ and Hg2+ metal cations using quantum chemistry. To do so, and in order to go beyond usual energetical studies, we make extensive use of state of the art quantum interpretative techniques combining ELF/NCI/QTAIM/EDA computations to capture all ranges of interactions stabilizing the well characterized microhydrated structures. The Electron Localization Function (ELF) topological analysis reveals the peculiar role of the Au+ outer-shell core electrons (subvalence) that appear already spatially preorganized once the addition of the first water molecule occurs. Thus, despite the addition of other water molecules, the electronic structure of Au(H2O)(+) appears frozen due to relativistic effects leading to a maximal acceptation of only two waters in gold's first hydration shell. As the values of the QTAIM (Quantum Theory of Atoms in Molecules) cations's charge is discussed, the Non Covalent Interactions (NCI) analysis showed that Au+ appears still able to interact through longer range van der Waals interaction with the third or fourth hydration shell water molecules. As these types of interaction are not characteristic of either a hard or soft metal cation, we introduced the concept of a "pseudo-soft" cation to define Au+ behavior. Then, extending the study, we performed the same computations replacing Au+ with Hg2+, an isoelectronic cation. If Hg2+ behaves like Au+ for small water clusters, a topological, geometrical, and energetical transition appears when the number of water molecules increases. Regarding the HSAB theory, this transition is characteristic of a shift of Hg2+ from a pseudosoft form to a soft ion and appears to be due to a competition between the relativistic and correlation effects. Indeed, if relativistic effects are predominant, then mercury will behave like gold and have a similar subvalence/geometry; otherwise when correlation effects are predominant, Hg2+ behaves like a soft cation.

  • 12. Chen, Shu-Feng
    et al.
    Liu, Ya-Jun
    Navizet, Isabelle
    Ferré, Nicolas
    Fang, Wei-Hai
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Systematic theoretical investigation on the light emitter of firefly2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 3, p. 798-803Article in journal (Refereed)
    Abstract [en]

    This is a systematic theoretical investigation on all the possible light emitters of firefly using multireference method. Six chemical forms of oxyluciferin (OxyLH2) molecules/anions were studied by a multi-state complete active space second order perturbation (MS-CASPT2) method in vacuum and DMSO. The calculated results and subsequent analysis excluded enol-OxyLH2, keto-OxyLH2 and enolate-OxyLH- as possible light emitters. The remaining three candidates, phenolate-enol-OxyLH-, phenolate-keto-OxyLH- and OxyL2-, were further investigated in protein by a MS-CASPT2/molecular mechanics (MM) study to explain the natural bioluminescence of firefly. By comparison of the MS-CASPT2/MM calculated results of phenolate-enol-OxyLH-, phenolate-keto-OxyLH- and OxyL2- with the experimental observation and detailed analysis, we concluded that the direct decomposition excited-state product of firefly dioxetanone in vivo and the only light emitter of firefly in natural bioluminescence is the first singlet exited state (S1) of phenolate-keto-OxyLH-.

  • 13. Chen, Shu-Feng
    et al.
    Navizet, Isabelle
    Roca-Sanjuán, Daniel
    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.
    Liu, Ya-Jun
    Ferre, Nicolas
    Chemiluminescence of Coelenterazine and Fluorescence of Coelenteramide: A Systematic Theoretical Study2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 8, p. 2796-2807Article in journal (Refereed)
    Abstract [en]

    A systematic investigation of the structural and spectroscopic properties of coelenteramide has been performed at the TD-CAM-B3LYP/6-31+G(d,p) level of theory, including various fluorescence and chemiluminescence states. The influence of geometric conformations, solvent polarity, protonation state, and the covalent character of the O-H bond of the hydroxyphenyl moiety were carefully studied. Striking differences in geometries and electronic structures among the states responsible for light emission were characterized. All fluorescence states can be described as a limited charge transfer process for a planar amide moiety. However, the chemiluminescence state is characterized by a much larger charge transfer that takes place over a longer distance. Moreover, the chemiluminescent coelenteramide structure exhibits an amide moiety that is no longer planar, in agreement with recent, more accurate ab initio results [Roca-Sanjuan et al J. Chem. Theory Comput. 2011, 7, 4060] Because the chemiluminescence state appears to be completely dark, a new mechanism is tentatively introduced for this process.

  • 14. Daku, Latevi Max Lawson
    et al.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Robinson, Timothy W.
    Hauser, Andreas
    Accurate Spin-State Energetics of Transition Metal Complexes. 1. CCSD(T), CASPT2, and DFT Study of [M(NCH)(6)](2+) (M = Fe, Co)2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 11, p. 4216-4231Article in journal (Refereed)
    Abstract [en]

    Highly accurate estimates of the high-spin/low-spin energy, difference Delta E-HL(el) in the high-spin complexes [Fe(NCH)(6)](2+) and [Co(NCH)(6)](2+) have been obtained from the results of CCSD(T) calculations extrapolated to the complete basis set limit. These estimates are shown to be strongly influenced by scalar relativistic effects. They have been used to assess the performances of the CASPT2 method and 30 density functionals of the GGA, meta-GGA, global hybrid, RSH, and double-hybrid types. For the CASPT2 method, the results of the assessment support the proposal [Kepenekian, M.; Robert, V.; Le Guennic, B. J. Chem. Phys. 2009, 131, 114702] that the ionization potential-electron affinity (IPEA) shift defining the zeroth-order Hamiltonian be raised from its standard value of 0.25 au to 0.50-0.70 au for the determination of Delta E-HL(el) in Fe(II) complexes with a [FeN6] core. At the DFT level, some of the assessed functionals proved to perform within chemical accuracy (+/- 350 cm(-1)) for the spin-state energetics of [Fe(NCH)(6)](2+), others for that of [Co(NCH)(6)](2+), but none of them simultaneously for both complexes. As demonstrated through a reparametrization of the CAM-PBEO range-separated hybrid, which led to a functional that performs within chemical accuracy for the spin-state energetics of both complexes, performing density functionals of broad applicability may be devised by including in their training sets highly accurate data like those reported here for [Fe(NCH)(6)](2+) and [Co(NCH)(6)](2+).

  • 15. De Vico, Luca
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Location of Two Seams in the Proximity of the C-2v pi pi Minimum Energy Path of Formaldehyde2009In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 5, no 1, p. 186-191Article in journal (Refereed)
    Abstract [en]

    Photochemical reactions rationalization is a key aspect for the understanding and setup of novel experiment and novel photoinitiated pathways. In this respect, the relationship between minimum energy paths over an excited-state and the intersection to lower potential energy surfaces is fundamental. In order to help the understanding of this relationship, in this study we present a novel kind of constraint for geometry optimizations, namely, an “orthogonality” constraint. Its possible applications are described. A complete example on how to retrieve the direct relationship between a minimum energy path over an excited-state potential energy surface and a conical intersection seam is given for C-2v symmetry constrained formaldehyde. The advantages of using the novel constraint when rationalizing a (photo)chemical reaction are presented.

  • 16. De Vico, Luca
    et al.
    Olivucci, Massimo
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    New general tools for constrained geometry optimizations2005In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 1, no 5, p. 1029-1037Article in journal (Refereed)
    Abstract [en]

    A modification of the constrained geometry optimization method by Anglada and Bofill (Anglada, J. M.; Bofill, J. M. J. Comput. Chem. 1997, 18, 992-1003) is designed and implemented. The changes include the choice of projection, quasi-line-search, and the use of a Rational Function optimization approach rather than a reduced-restricted-quasi-Newton-Raphson method in the optimization step. Furthermore, we show how geometrical constrains can be implemented in an approach based on nonreclunclant curvilinear coordinates avoiding the inclusion of the constraints in the set of redundant coordinates used to define the internal coordinates. The behavior of the new implementation is demonstrated in geometry optimizations featuring single or multiple geometrical constraints (bond lengths, angles, etc.), optimizations on hyperspherical cross sections (as in the computation of steepest descent paths), and location of energy minima on the intersection subspace of two potential energy surfaces (i.e. minimum energy crossing points). In addition, a novel scheme to determine the crossing point geometrically nearest to a given molecular structure is proposed.

  • 17. Dopieralski, Przemyslaw D.
    et al.
    Latajka, Zdzislaw
    Olovsson, Ivar
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Materials Chemistry, Structural Chemistry.
    Proton Transfer Dynamics in Crystalline Maleic Acid from Molecular Dynamics Calculations2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 5, p. 1455-1461Article in journal (Refereed)
    Abstract [en]

    The crystal structure of maleic acid, the cis conformer of HOOC-CH=CH-COOH has been investigated by Car-Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) simulations. The interesting feature of this compound, compared to the trans conformer, fumaric acid, is that both intra- and intermolecular hydrogen bonds are present. CPMD simulations at 100 K indicate that the energy barrier height for proton transfer is too high for thermal jumps over the barrier in both the intra- and intermolecular hydrogen bonds. Dynamics at 295 K reveal that the occupancy ratio of the proton distribution in both the intra- and intermolecular hydrogen bonds is 0.96/0.04. The time lag between the proton transfers in the intra- and intermolecular hydrogen bonds is in the range of 2-9 fs. This is slightly shorter than the time lag obtained previously for fumaric acid, where only intermolecular hydrogen bonds are present. It is also interesting to notice that in most cases the proton transfer process starts in the intramolecular hydrogen bond and subsequently follows in the intermolecular hydrogen bond. Vibrational spectra of the investigated system and its deuterated analogs HOOC-CH=CH-COOD and DOOC-CH=CH-COOD have been calculated and compared with experimental data.

  • 18.
    Elias-Wolff, Federico
    et al.
    Stockholm Univ, Dept Biochem & Biophys, Stockholm, Sweden; Stockholm Univ, Dept Mat & Environm Chem, Stockholm, Sweden.
    Lindén, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Lyubartsev, Alexander P.
    Stockholm Univ, Dept Mat & Environm Chem, Stockholm, Sweden.
    Brandt, Erik G.
    Stockholm Univ, Dept Mat & Environm Chem, Stockholm, Sweden.
    Computing Curvature Sensitivity of Biomolecules in Membranes by Simulated Buckling2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 3, p. 1643-1655Article in journal (Refereed)
    Abstract [en]

    Membrane curvature sensing, where the binding free energies of membrane-associated molecules depend on the local membrane curvature, is a key factor to modulate and maintain the shape and organization of cell membranes. However, the microscopic mechanisms are not well understood, partly due to absence of efficient simulation methods. Here, we describe a method to compute the curvature dependence of the binding free energy of a membrane associated probe molecule that interacts with a buckled membrane, which has been created by lateral compression of a flat bilayer patch. This buckling approach samples a wide range of curvatures in a single simulation, and anisotropic effects can be extracted from the orientation statistics. We develop an efficient and robust algorithm to extract the motion of the probe along the buckled membrane surface, and evaluate its numerical properties by extensive sampling of three coarse-grained model systems: local lipid density in a curved environment for single-component bilayers, curvature preferences of individual lipids in two-component membranes, and curvature sensing by a homotrimeric transmembrane protein. The method can be used to complement experimental data from curvature partition assays and provides additional insight into mesoscopic theories and molecular mechanisms for curvature sensing.

  • 19.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Roca-Sanjuan, Daniel
    Zapata, Felipe
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Revisiting the Nonadiabatic Process in 1,2-Dioxetane2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 12, p. 5404-5411Article in journal (Refereed)
    Abstract [en]

    Determining the ground and excited-state decomposition mechanisms of 1,2-dioxetane is essential to understand the chemiluminescence and bioluminescence phenomena. Several experimental and theoretical studies has been 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' and C-C' bond dissociations. New high-level multistate multi configurational 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.

  • 20.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Delcey, Mickael G.
    Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Chem, Kenneth S Pitzer Ctr Theoret Chem, Berkeley, CA 94720 USA..
    Pedersen, Thomas Bondo
    Univ Oslo, Dept Chem, Ctr Theoret & Computat Chem, POB 1033 Blindern, N-0315 Oslo, Norway..
    Aquilante, Francesco
    Univ Bologna, Dipartimento Chim G Ciamician, Via F Selmi 2, IT-40126 Bologna, Italy..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical State-Average Complete-Active-Space Self-Consistent Field Nonadiabatic Coupling Vectors: Implementation with Density-Fitted Two-Electron Integrals and Application to Conical Intersections2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 8, p. 3636-3653Article in journal (Refereed)
    Abstract [en]

    Analytical state-average complete-active-space self-consistent field derivative (nonadiabatic) coupling vectors are implemented. Existing formulations are modified such that the implementation is compatible with Cholesky-based density fitting of two-electron integrals, which results in efficient calculations especially with large basis sets. Using analytical nonadiabatic coupling vectors, the optimization of conical intersections is implemented within the projected constrained optimization method. The standard description and characterization of conical intersections is reviewed and clarified, and a practical and unambiguous system for their classification and interpretation is put forward. These new tools are subsequently tested and benchmarked for 19 different conical intersections. The accuracy of the derivative coupling vectors is validated, and the information that can be drawn from the proposed characterization is discussed, demonstrating its usefulness.

  • 21.
    Fischer, Nina M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ditz, Jonas C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Yildirim, Ahmet
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 7, p. 2938-2944Article in journal (Refereed)
    Abstract [en]

    In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Thew), Comput 2013, 9, 3527 3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of,::150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by approximate to 10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http://virtualchemistry.org, aimed at facilitating sharing and reuse of input files for molecular simulations.

  • 22. Garcia-Prieto, Francisco F.
    et al.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Munoz-Losa, Aurora
    Aguilar, Manuel A.
    Elena Martin, M.
    Solvent Effects on the Absorption Spectra of the para-Coumaric Acid Chromophore in Its Different Protonation Forms2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 10, p. 4481-4494Article in journal (Refereed)
    Abstract [en]

    The effects of the solvent and protonation state on the electronic absorption spectrum of the para-coumaric acid (pCA), a model of the photoactive yellow protein (PYP), have been studied using the ASEP/MD (averaged solvent electrostatic potential from molecular dynamics) method. Even though, in the protein, the chromophore is assumed to be in its phenolate monoanionic form, when it is found in water solution pH control can favor neutral, monoanionic, and dianionic species. As the pCA has two hydrogens susceptible of deprotonation, both carboxylate and phenolate monoanions are possible. Their relative stabilities are strongly dependent on the medium. In gas phase, the most stable isomer is the phenolate while in aqueous solution it is the carboxylate, although the population of the phenolate form is not negligible. The s-cis, s-trans, syn, and anti conformers have also been included in the study. Electronic excited states of the chromophore have been characterized by SA-CAS(14,12)-PT2/cc-pVDZ level of theory. The bright state corresponds, in all the cases, to a pi -> pi* transition involving a charge displacement in the system. The magnitude and direction of this displacement depends on the protonation state and on the environment (gas phase or solution). In the same way, the calculated solvatochromic shift of the absorption maximum depends on the studied form, being a red shift for the neutral, carboxylate monoanion, and dianionic chromophores and a blue shift for the phenolate monoanion. Finally, the contribution that the solvent electronic polarizability has on the solvent shift was analyzed. It represents a very important part of the total solvent shift in the neutral form, but its contribution is completly negligible in the mono- and dianionic forms.

  • 23.
    Garcia-Prieto, Francisco F.
    et al.
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Muñoz-Losa, Aurora
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Fdez. Galvan, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sanchez, M. Luz
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Aguilar, Manuel A.
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Martin, M. Elena
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore2017In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, no 2, p. 737-748Article in journal (Refereed)
    Abstract [en]

    Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methylated derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in the gas phase could not be located in aqueous solution. 2) Conical intersections (CIs) associated with the rotation of the single bond adjacent to the phenyl group are found for the four derivatives in water solution but only for thio derivatives in the gas phase. 3) The relative stability of minima and CIs is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the transcis photoisomerization through a CI that involves the rotation of the vinyl double bond, and the nonradiative, nonreactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with the lower energy, while in solution these are the conical intersections. In solution, the de-excitation prevalent path seems to be the photoisomerization for oxo compounds, while thio compounds return to the initial trans ground state without emission.

  • 24. Giussani, Angelo
    et al.
    Merchan, Manuela
    Roca-Sanjuan, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    Essential on the Photophysics and Photochemistry of the lndole Chromophore by Using a Totally Unconstrained Theoretical Approach2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 12, p. 4088-4096Article in journal (Refereed)
    Abstract [en]

    Indole is a chromophore present in many different molecules of biological interest, such as the essential amino acid tryptophan and the neurotransmitter serotonin. On the basis of CASPT2//CASSCF quantum chemical calculations, the photophysical properties of the system after UV irradiation have been studied through the exploration of the potential energy hypersurfaces of the singlet and triplet low-lying valence excited states. In contrast to previous studies, the present work has been carried out without imposing any restriction to the geometry of the molecule (C(1) symmetry) and by performing minimum energy path calculations, which is the only instrument able to provide the lowest-energy evolution of the system. Relevant findings to the photophysics of bare indole have been obtained, which compete with the currently accepted mechanism for the energy decay in the molecule. The results show the presence of a conical intersection (CI) between the initially populated (1)(L(a) pi pi*) and the (1)(L(b) pi pi*) state, easily accessible through a barrierless pathway from the Franck Condon region. At this CI region, part of the population is switched from the bright (1)(L(a) pi pi*) state to the (1)(L(b) pi pi*) state, and the system evolves toward a minimum structure from which the expected fluorescence takes place. The reported low values of the fluorescence quantum yield are explained by means of a new nonracliative mechanism specific for the (1)(L(b) pi pi*) state, in which the presence of an ethene-like CI between the (1)(L(b) pi pi*) and ground states is the main feature.

  • 25. Gonzalez-Ramirez, Israel
    et al.
    Segarra-Marti, Javier
    Serrano-Andres, Luis
    Merchan, Manuela
    Rubio, Mercedes
    Roca-Sanjuán, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    On the N-1-H and N-3-H Bond Dissociation in Uracil by Low Energy Electrons: A CASSCF/CASPT2 Study2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 8, p. 2769-2776Article in journal (Refereed)
    Abstract [en]

    The dissociative electron-attachment (DEA) phenomena at the N-1-H and N-3-H bonds observed experimentally at low energies (<3 eV) in uracil are studied with the CASSCF/CASPT2 methodology. Two valence bound pi(-) and two dissociative sigma(-) states of the uracil anionic species, together with the ground state of the neutral molecule, are proven to contribute to the shapes appearing in the experimental DEA cross sections. Conical intersections (CI) between the pi(-) and sigma(-) are established as the structures which activate the DEA processes. The N-1-H and N-3-H DEA mechanisms in uracil are described, and experimental observations are interpreted on the basis of two factors: (1) the relative energy of the (U-H)(-) + H fragments obtained after DEA with respect to the ground-state equilibrium structure (S-0) of the neutral molecule (threshold for DEA) and (2) the relative energy of the CIs also with respect to S-0 (band maxima). The pi(-)(1) state is found to be mainly responsible for the N-1-H bond breaking, whereas the pi(-)(2) state is proved to be involved in the cleavage of the N-3-H bond.

  • 26. Gozem, Samer
    et al.
    Huntress, Mark
    Schapiro, Igor
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Granovsky, Alexander A.
    Angeli, Celestino
    Olivucci, Massimo
    Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 11, p. 4069-4080Article in journal (Refereed)
    Abstract [en]

    The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge-transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed.

  • 27. Gozem, Samer
    et al.
    Melaccio, Federico
    Valentini, Alessio
    Filatov, Michael
    Huix-Rotllant, Miquel
    Ferre, Nicolas
    Manuel Frutos, Luis
    Angeli, Celestino
    Krylov, Anna I.
    Granovsky, Alexander A.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Olivucci, Massimo
    Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential Energy Surfaces at a Conical Intersection2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 8, p. 3074-3084Article in journal (Refereed)
    Abstract [en]

    We report and characterize ground-state and excited-state potential energy profiles using a variety of electronic structure methods along a loop lying on the branching plane associated with a conical intersection (Cl) of a reduced retinal model, the penta-2,4-dieniminium cation (PSB3). Whereas the performance of the equation-of-motion coupled-duster, density functional theory, and multireference methods had been tested along the excited- and ground-state paths of PSB3 in our earlier work, the ability of these methods to correctly describe the potential energy surface shape along a CI branching plane has not yet been investigated. This is the focus of the present contribution. We find, in agreement with earlier studies by others, that standard time-dependent DFT (TDDFT) does not yield the correct two-dimensional (i.e., conical) crossing along the branching plane but rather a one-dimensional (i.e., linear) crossing along the same plane. The same type of behavior is found for SS-CASPT2(IPEA=0), SS-CASPT2(IPEA=0.25), spin-projected SF-TDDFT, EOM-SF-CCSD, and, finally, for the reference MRCISD+Q method. In contrast, we found that MRCISD, CASSCF, MS-CASPT2(IPEA=0), MS-CASPT2(IPEA=0.25), XMCQDPT2, QD-NEVPT2, non-spin-projected SF-TDDFT, and SI-SA-REKS yield the expected conical crossing. To assess the effect of the different crossing topologies (i.e., linear or conical) on the PSB3 photoisomerization efficiency, we discuss the results of 100 semiclassical trajectories computed by CASSCF and SS-CASPT2(IPEA=0.25) for a PSB3 derivative. We show that for the same initial conditions, the two methods yield similar dynamics leading to isomerization quantum yields that differ by only a few percent.

  • 28.
    Grime, John M. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Khan, Malek O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry.
    Effects of discrete charge clustering in simulations of charged interfaces2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 10, p. 3205-3211Article in journal (Refereed)
    Abstract [en]

    A system of counterions between charged surfaces is investigated, with the surfaces represented by uniform charged planes and three different arrangements of discrete surface charges - an equispaced grid and two different clustered arrangements. The behaviors of a series of systems with identical net surface charge density are examined, with particular emphasis placed on the long ranged corrections via the method of “charged slabs” and the effects of the simulation cell size. Marked differences are observed in counterion distributions and the osmotic pressure dependent on the particular representation of the charged surfaces; the uniformly charged surfaces and equispaced grids of discrete charge behave in a broadly similar manner, but the clustered systems display a pronounced decrease in osmotic pressure as the simulation size is increased. The influence of the long ranged correction is shown to be minimal for all but the very smallest of system sizes.

  • 29.
    Hellström, Matti
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Band-Filling Correction Method for Accurate Adsorption Energy Calculations: A Cu/ZnO Case Study2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 11, p. 4673-4678Article in journal (Refereed)
    Abstract [en]

    We present a simple method, the “band-filling correction”, to calculate accurate adsorption energies (Eads) in the low coverage limit from finite-size supercell slab calculations using DFT. We show that it is necessary to use such a correction if charge transfer takes place between the adsorbate and the substrate, resulting in the substrate bands either filling up or becoming depleted. With this correction scheme, we calculate Eads of an isolated Cu atom adsorbed on the ZnO(101̅0) surface. Without the correction, the calculated Eads is highly coverage-dependent, even for surface supercells that would typically be considered very large (in the range from 1 nm × 1 nm to 2.5 nm × 2.5 nm). The correction scheme works very well for semilocal functionals, where the corrected Eads is converged within 0.01 eV for all coverages. The correction scheme also works well for hybrid functionals if a large supercell is used and the exact exchange interaction is screened.

  • 30. Hess, Berk
    et al.
    Kutzner, Carsten
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lindahl, Erik
    GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation2008In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 3, p. 435-447Article in journal (Refereed)
    Abstract [en]

    Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs; for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.

  • 31.
    Hub, Jochen S.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    de Groot, Bert L.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    g_wham-A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 12, p. 3713-3720Article in journal (Refereed)
    Abstract [en]

    The Weighted Histogram Analysis Method (WHAM) is a standard technique used to compute potentials of mean force (PMFs) from a set of umbrella sampling simulations. Here, we present a new WHAM implementation, termed g_wham, which is distributed freely with the GROMACS molecular simulation suite. g_wham estimates statistical errors using the technique of bootstrap analysis. Three bootstrap methods are supported: (i) bootstrapping new trajectories based on the umbrella histograms, (ii) bootstrapping of complete histograms, and (iii) Bayesian bootstrapping of complete histograms, that is, bootstrapping via the assignment of random weights to the histograms. Because methods ii and iii consider only complete histograms as independent data points, these methods do not require the accurate calculation of autocorrelation times. We demonstrate that, given sufficient sampling, bootstrapping new trajectories allows for an accurate error estimate. In the presence of long autocorrelations, however, (Bayesian) bootstrapping of complete histograms yields a more reliable error estimate, whereas bootstrapping of new trajectories may underestimate the error. In addition, we emphasize that the incorporation of autocorrelations into WHAM reduces the bias from limited sampling, in particular, when computing periodic PMFs in inhomogeneous systems such as solvated lipid membranes or protein channels.

  • 32. Huber, Stefan M.
    et al.
    Shahi, Abdul Rehaman Moughal
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Cramer, Christopher J.
    Gagliardi, Laura
    What Active Space Adequately Describes Oxygen Activation by a Late Transition Metal?: CASPT2 and RASPT2 Applied to Intermediates from the Reaction of O-2 with a Cu(I)-alpha-Ketocarboxylate2009In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 5, no 11, p. 2967-2976Article in journal (Refereed)
    Abstract [en]

    Multiconfigurational second-order perturbation theory calculations based on a complete active space reference wave function (CASPT2), employing active spaces of increasing size, are well converged at the level of 12 electrons in 12 orbitals for the singlet-triplet state-energy splittings of three supported copper-dioxygen and two supported copper-oxo complexes. Corresponding calculations using the restricted active space approach (RASPT2) offer similar accuracy with a significantly reduced computational overhead provided an inner (2,2) complete active space is included in the overall RAS space in order to account for strong biradical character in most of the compounds. The effects of the different active space choices and the outer RAS space excitations are examined, and conclusions are drawn with respect to the general applicability of the RASPT2 protocol.

  • 33.
    Kawatsu, Tsutomu
    et al.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Lundberg, Marcus
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Morokuma, Keiji
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan; Emory Univ, Cherry L Emerson Ctr Sci Computat, Atlanta, GA 30322 USA; Emory Univ, Dept Chem, Atlanta, GA 30322 USA.
    Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS)2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 2, p. 390-401Article in journal (Refereed)
    Abstract [en]

    The protein environment can have significant effects on the enzyme catalysis even though the reaction occurs locally at the reaction center. In this paper, we describe an efficient scheme that includes a classical molecular dynamics (MD) free-energy perturbation (FEP) correction to the reaction energy diagram, as a complement to the protein effect obtained from static ONIOM (QM:MM) calculations. The method is applied to eight different reaction steps, from the O2-bound reactant to formation of a high-valent ferryl-oxo intermediate, in the nonheme iron enzyme isopenicillin N synthase (IPNS), for which the QM:MM energy diagram has previously been computed [ Lundberg, M. et al. J. Chem. Theory Comput. 2009, 5, 220 ‚àí 234 ]. This large span of the reaction coordinate is covered by dividing each reaction step into microsteps using a virtual reaction coordinate, thus only requiring ONIOM information about the stationary points themselves. Protein effects are important for C‚àíH bond activation and heterolytic O‚àíO bond cleavage because both these two steps involve charge transfer, and compared to a static QM:MM energies, the dynamics of the protein environment changes the barrier for O‚àíO bond cleavage by several kcal/mol. The origin of the dynamical contribution is analyzed in two terms, the geometrical effect caused by the change in average protein geometry (compared to the optimized geometry) in the room temperature MD simulation with the solvent, and the statistical (entropic) effect resulting from fluctuations in the interactions between the active site and the protein environment. These two effects give significant contributions in different steps of the reaction.

  • 34.
    Kolesov, Grigory
    et al.
    Harvard Univ, John A Paulson Sch Engn & Appl Sci, Cambridge, MA 02138 USA..
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Harvard Univ, John A Paulson Sch Engn & Appl Sci, Cambridge, MA 02138 USA..
    Hoyt, Robert
    Harvard Univ, Dept Phys, Cambridge, MA 02138 USA..
    Vinichenko, Dmitry
    Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA..
    Kaxiras, Efthimios
    Harvard Univ, John A Paulson Sch Engn & Appl Sci, Cambridge, MA 02138 USA.;Harvard Univ, Dept Phys, Cambridge, MA 02138 USA..
    Real-Time TD-DFT with Classical Ion Dynamics: Methodology and Applications2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 2, p. 466-476Article in journal (Refereed)
    Abstract [en]

    We present a method for real-time propagation of electronic wave functions, within time-dependent density functional theory (RT-TDDFT), coupled to ionic motion through mean-field classical dynamics. The goal of our method is to treat large systems and complex processes, in particular photocatalytic reactions and electron transfer events on surfaces and thin films. Due to the complexity of these processes, computational approaches are needed to provide insight into the underlying physical mechanisms and are therefore crucial for the rational design of new materials. Because of the short time step required for electron propagation (of order similar to 10 attoseconds), these simulations are computationally very demanding. Our methodology is based on numerical atomic-orbital-basis sets for computational efficiency. In the computational package, to which we refer as TDAP-2.0 (Time-evolving Deterministic Atom Propagator), we have implemented a number of important features and analysis tools for more accurate and efficient treatment of large, complex systems and time scales that reach into a fraction of a picosecond. We showcase the capabilities of our method using four different examples: (i) photodissociation into radicals of opposite spin, (ii) hydrogen adsorption on aluminum surfaces, (iii) optical absorption of spin-polarized organic molecule containing a metal ion, and (iv) electron transfer in a prototypical dye sensitized solar cell.

  • 35.
    Kruchinina, Anastasia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    On-the-fly computation of frontal orbitals in density matrix expansions2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, p. 139-153Article in journal (Refereed)
  • 36.
    Kruchinina, Anastasia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Parameterless stopping criteria for recursive density matrix expansions2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, p. 5788-5802Article in journal (Refereed)
  • 37.
    Larsson, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Screening for the Location of RNA Using the Chloride Ion Distribution in Simulations of Virus Capsids2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 7, p. 2474-2483Article in journal (Refereed)
    Abstract [en]

    The complete structure of the genomic material inside a virus capsid remains elusive, although a limited amount of symmetric nucleic acid can be resolved in the crystal structure of 17 icosahedral viruses. The negatively charged sugar-phosphate backbone of RNA and DNA as well as the large positive charge of the interior surface of the virus capsids suggest that electrostatic complementarity is an important factor in the packaging of the genomes in these viruses. To test how much packing information is encoded by the electrostatic and steric envelope of the capsid interior, we performed extensive all-atom molecular dynamics (MD) simulations of virus capsids with explicit water molecules and solvent ions. The model systems were two small plant viruses in which significant amounts of RNA has been observed by X-ray crystallography: satellite tobacco mosaic virus (STMV, 62% RNA visible) and satellite tobacco necrosis virus (STNV, 34% RNA visible). Simulations of half-capsids of these viruses with no RNA present revealed that the binding sites of RNA correlated well with regions populated by chloride ions, suggesting that it is possible to screen for the binding sites of nucleic acids by determining the equilibrium distribution of negative ions. By including the crystallographically resolved RNA in addition to ions, we predicted the localization of the unresolved RNA in the viruses. Both viruses showed a hot-spot for RNA binding at the S-fold symmetry axis. The MD simulations were compared to predictions of the chloride density based on nonlinear Poisson-Boltzmann equation (PBE) calculations with mobile ions. Although the predictions are superficially similar, the PBE calculations overestimate the ion concentration close to the capsid surface and underestimate it far away, mainly because protein dynamics is not taken into account. Density maps from chloride screening can be used to aid in building atomic models of packaged virus genomes. Knowledge of the principles of genome packaging might be exploited for both antiviral therapy and technological applications.

  • 38.
    Lundberg, Marcus
    et al.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Kawatsu, T.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Vreven, T.
    Gaussian Inc, Wallingford, CT 06492 USA.
    Frisch, M. J.
    Gaussian Inc, Wallingford, CT 06492 USA.
    Morokuma, K.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Transition States in a Protein Environment: ONIOM QM:MM Modeling of Isopenicillin N Synthesis2009In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 5, no 1, p. 222-234Article in journal (Refereed)
    Abstract [en]

    To highlight the role of the protein in metal enzyme catalysis, we optimize ONIOM QM:MM transition states and intermediates for the full reaction of the nonheme iron enzyme isopenicillin N synthase (IPNS). Optimizations of transition states in large protein systems are possible using our new geometry optimizer with quadratic coupling between the QM and MM regions [Vreven, T. et al. MoL Phys. 2006, 104, 701-704]. To highlight the effect of the metal center, results from the protein model are compared to results from an active site model containing only the metal center and coordinating residues [Lundberg, M. et al. Biochemistry 2008, 47, 1031-10421. The analysis suggests that the main catalytic effect comes from the metal center, while the protein controls the reactivity to achieve high product specificity. As an example, hydrophobic residues align the valine substrate radical in a favorable conformation for thiazolicline ring closure and contribute to product selectivity and high stereospecificity. A low-barrier pathway for P-lactam formation is found where the proton required for heterolytic O-O bond cleavage comes directly from the valine N-H group of the substrate. The alternative mechanism, where the proton in 0-0 bond cleavage initially comes from an iron water ligand, can be disfavored by the electrostatic interactions with the surrounding protein. Explicit protein effects on transition states are typically 1-6 kcal/mol in the present enzyme and can be understood by considering whether the transition state involves large movements of the substrate as well as whether it involves electron transfer.

  • 39.
    Lundberg, Marcus
    et al.
    Fukui Institute for Fundamental Chemistry, Kyoto University.
    Sasakura, Y.
    Fukui Institute for Fundamental Chemistry, Kyoto University.
    Zheng, G. S.
    Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta..
    Morokuma, K.
    Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan; Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta. .
    Case Studies of ONIOM(DFT:DFTB) and ONIOM(DFT:DFTB:MM) for Enzymes and Enzyme Mimics2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 4, p. 1413-1427Article in journal (Refereed)
    Abstract [en]

    The replacement of standard molecular mechanics force fields by inexpensive molecular orbital (QM') methods in multiscale models has many advantages, e.g., a more straightforward description of mutual polarization and charge transfer between layers. The ONIOM(QM:QM') scheme with mechanical embedding can combine any two methods without prior parametrization or significant coding effort. In this scheme, the environmental effect is evaluated fully at the QM' level, and the accuracy therefore depends on how well the low-level QM' method describes the changes in electron density of the reacting region. To examine the applicability of the QM:QM' approach, we perform case studies with density-functional tight-binding (DFTB) as the low-level QM' method in two-layer ONIOM(B3LYP/6-31G(d):DFTB) models. The investigated systems include simple amino acid models one nonheme iron enzyme mimic, and the enzymatic reactions of Zn-beta-lactamase and trypsin. For the last example, we also illustrate the use of a three-layer ONIOM(B3LYP/6-31G(d):D::TB:Amber96) model. The ONIOM extension, compared to the QM calculation for the small model system, improves the relative energies, but high accuracy (deviations below 1 kcal/mol) is not achieved even with relatively large QM models. Polarization effects are fairly well described using DFTB, but in some cases QM and QM' methods converge to different electronk: states. We discuss when the QM:QM' approach is appropriate and the possibilities of estimating the quality of the ONIOM extension without having to make explicit benchmarks of the entire system.

  • 40.
    Mace, Amber
    et al.
    Stockholm Univ, Dept Mat & Environm Chem, SE-10691 Stockholm, Sweden.;Stockholm Univ, Berzelii Ctr EXSELENT Porous Mat, SE-10691 Stockholm, Sweden..
    Leetmaa, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Laaksonen, Aatto
    Stockholm Univ, Dept Mat & Environm Chem, SE-10691 Stockholm, Sweden.;Stockholm Univ, Berzelii Ctr EXSELENT Porous Mat, SE-10691 Stockholm, Sweden..
    Temporal Coarse Graining of CO2 and N-2 Diffusion in Zeolite NaKA: From the Quantum Scale to the Macroscopic2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 10, p. 4850-4860Article in journal (Refereed)
    Abstract [en]

    The kinetic CO2-over-N-2 sieving capabilities in narrow pore zeolites are dependent on the free-energy barriers of diffusion between the zeolite pores, which can be fine-tuned by altering the framework composition. An ab initio level of theory is necessary to accurately compute the energy barriers, whereas it is desirable to predict the macroscopic scale diffusion for industrial applications. Using ab initio molecular dynamics on the picosecond time scale, the free-energy barriers of diffusion can be predicted for different local pore properties in order to identify those that are rate-determining for the pore-to-pore diffusion. Specifically, we investigate the effects of the Na+-to-K+ exchange at the different cation sites and the CO, loading in Zeolite NaKA. These computed energy barriers are then used as input for the Kinetic Monte Carlo method, coarse graining the dynamic simulation steps to the pore-to-pore diffusion. With this approach, we simulate how the identified rate-determining properties as well as the application of skin-layer surface defects affect the diffusion driven uptake in a realistic Zeolite NaKA powder particle model on a macroscopic time scale. Lastly, we suggest a model by combining these effects, which provides an excellent agreement with the experimental CO2 and N-2 uptake behaviors presented by Liu et Commun. 2010, 46, 4502-4504).

  • 41. Manni, Giovanni Li
    et al.
    Ma, Dongxia
    Aquiliante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Olsen, Jeppe
    Gagliardi, Laura
    SplitGAS Method for Strong Correlation and the Challenging Case of Cr-22013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 8, p. 3375-3384Article in journal (Refereed)
    Abstract [en]

    A new multiconfigurational quantum chemical method, SplitGAS, is presented. The configuration interaction expansion, generated from a generalized active space, GAS, wave function is split in two parts, a principal part containing the most relevant configurations and an extended part containing less relevant, but not negligible, configurations. The partition is based on an orbital criterion. The SplitGAS method has been employed to study the HF, N-2, and Cr-2 molecules. The results on these systems, especially on the challenging, multiconfigurational Cr-2 molecule, are satisfactory. While SplitGAS is comparable with the GASSCF method in terms of memory requirements, it performs better than the complete active space method followed by second-order perturbation theory, CASPT2, in terms of equilibrium bond length, dissociation energy, and vibrational properties.

  • 42. Marazzi, Marco
    et al.
    Navizet, Isabelle
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    Frutos, Luis Manuel
    Photostability Mechanisms in Human gamma B-Crystallin: Role of the Tyrosine Corner Unveiled by Quantum Mechanics and Hybrid Quantum Mechanics/Molecular Mechanics Methodologies2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 4, p. 1351-1359Article in journal (Refereed)
    Abstract [en]

    The tyrosine corner is proposed as a featured element to enhance photostability in human gamma B-crystallin when exposed to UV irradiation. Different ultrafast processes were studied by multiconfigurational quantum chemistry coupled to molecular mechanics: photoinduced singlet singlet energy, electron and proton transfer, as well as population and evolution of triplet states. The minimum energy paths indicate two possible UV photoinduced events: forward backward proton-coupled electron transfer providing to the system a mechanism for ultrafast internal conversion, and energy transfer, leading to fluorescence or phosphorescence. The obtained results are in agreement with the available experimental data, being in line with the proposed photoinduced processes for the different tyrosine environments within gamma B-crystallin.

  • 43.
    Roca-Sanjuán, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    Delcey, Mickaël G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    Navizet, Isabelle
    Ferre, Nicolas
    Liu, Ya-Jun
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    Chemiluminescence and Fluorescence States of a Small Model for Coelenteramide and Cypridina Oxyluciferin: A CASSCF/CASPT2 Study2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 12, p. 4060-4069Article in journal (Refereed)
    Abstract [en]

    Fluorescence and chemiluminescence phenomena are often confused in experimental and theoretical studies on the luminescent properties of chemical systems. To establish the patterns that distinguish both processes, the fluorescent and chemiluminescent states of 2-acetamido-3-methylpyrazine, which is a small model of the coelenterazine/coelenteramide and Cypridina luciferin/oxyluciferin bioluminescent systems, were characterized by using the complete active space second-order perturbation (CASPT2) method. Differences in geometries and electronic structures among the states responsible for light emission were found. On the basis of the findings, some recommendations for experimental studies on chemiluminescence are suggested, and more appropriate theoretical approaches are proposed.

  • 44.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nonmonotonic recursive polynomial expansions for linear scaling calculation of the density matrix2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, p. 1233-1236Article in journal (Refereed)
  • 45. Rudberg, Elias
    et al.
    Rubensson, Emanuel H.
    Salek, Pawel
    Automatic Selection of Integral Thresholds by Extrapolation in Coulomb and Exchange Matrix Constructions2009In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 5, no 1, p. 80-85Article in journal (Refereed)
  • 46.
    Rudberg, Elias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Salek, Pawel
    Kohn–Sham density functional theory electronic structure calculations with linearly scaling computational time and memory usage2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, p. 340-350Article in journal (Refereed)
  • 47. Rudberg, Elias
    et al.
    Salek, Pawel
    Rinkevicius, Zilvinas
    Agren, Hans
    Heisenberg exchange in dinuclear manganese complexes: A density functional theory study2006In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 2, no 4, p. 981-989Article in journal (Refereed)
  • 48. Saethre, Bjorn Steen
    et al.
    Hoffmann, Alex C.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Order Parameters and Algorithmic Approaches for Detection and Demarcation of Interfaces in Hydrate-Fluid and Ice-Fluid Systems2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 12, p. 5606-5615Article in journal (Refereed)
    Abstract [en]

    Some aspects of the use of order parameter fields in molecular dynamics simulations to delimit solid phases containing water, namely ice and hydrate, in both hydrophilic and hydrophobic fluids are examined; this includes the influences of rectangular meshes and of filtering on the quality of these parameters. Three order parameters are studied: the mass density, rho; an angular tetrahedrality measure, Sg (Chau and Hardwick, Mol. Phys. 1998, 93, 511); and the water-dimer dihedral angle, F-4 (Rodger et al. Fluid Phase Equilib. 1996, 116, 326). The parameters are studied to find their ability to distinguish between bulk phases, their consistency in different environments, their noise susceptibility, and their ability to demarcate the interface region. Spatial sampling and filtering are covered in detail, and some temporal features are illustrated by using autocorrelation maps. The parameters are employed to determine the position of interfaces as functions of time and, with the capillary wave fluctuation method (Hoyt et al. Phys. Rev. Lett. 2001, 86, 5530; Math. Comput. Simul. 2010, 80, 1382), to estimate solid-fluid interfacial stiffnesses, with partial success for the hydrophilic/hydrophobic-type interfaces.

  • 49.
    Sand, Andrew M.
    et al.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Hoyer, Chad E.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Sharkas, Kamal
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Kidder, Katherine M.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Truhlar, Donald G.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Gagliard, Laura
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Analytic Gradients for Complete Active Space Pair-Density Functional Theory2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 1, p. 126-138Article in journal (Refereed)
    Abstract [en]

    Analytic gradient routines are a desirable feature for quantum mechanical methods, allowing for efficient determination of equilibrium and transition state structures and several other molecular properties. In this work, we present analytical gradients for multiconfiguration pair-density functional theory (MC-PDFT) when used with a state-specific complete active space self-consistent field reference wave function. Our approach constructs a Lagrangian that is variational in all wave function parameters. We find that MC-PDFT locates equilibrium geometries for several small- to medium-sized organic molecules that are similar to those located by complete active space second-order perturbation theory but that are obtained with decreased computational cost.

  • 50.
    Sauri, Vicenta
    et al.
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Gobbo, João P.
    Univ Sao Paulo, Inst Quim, BR-05508900 Sao Paulo, Brazil;USP Consortium Photochem Technol, NAPPhotoTech, BR-05508900 Sao Paulo, Brazil.
    Serrano-Pérez, Juan J.
    Univ London Imperial Coll Sci Technol & Med, Dept Chem, London SW7 2AZ, England.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Coto, Pedro B.
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain; Univ Erlangen Nurnberg, Inst Theoret Phys, D-91058 Erlangen, Germany; Univ Alcala de Henares, Dept Quim Fis, E-28871 Alcala De Henares, Spain.
    Serrano-Andrés, Luis
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Borin, Antonio C.
    Univ Sao Paulo, Inst Quim, BR-05508900 Sao Paulo, Brazil;USP Consortium Photochem Technol, NAPPhotoTech, BR-05508900 Sao Paulo, Brazil.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Merchán, Manuela
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Roca-Sanjuán, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Proton/Hydrogen Transfer Mechanisms in the Guanine-€“Cytosine Base Pair: Photostability and Tautomerism2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 1, p. 481-496Article in journal (Refereed)
    Abstract [en]

    Proton/hydrogen-transfer processes have been broadly studied in the past 50 years to explain the photostability and the spontaneous tautomerism in the DNA base pairs. In the present study, the CASSCF/CASPT2 methodology is used to map the two-dimensional potential energy surfaces along the stretched NH reaction coordinates of the guanine–cytosine (GC) base pair. Concerted and stepwise pathways are explored initially in vacuo, and three mechanisms are studied: the stepwise double proton transfer, the stepwise double hydrogen transfer, and the concerted double proton transfer. The results are consistent with previous findings related to the photostability of the GC base pair, and a new contribution to tautomerism is provided. The C-based imino-oxo and imino-enol GC tautomers, which can be generated during the UV irradiation of the Watson–Crick base pair, have analogous radiationless energy-decay channels to those of the canonical base pair. In addition, the C-based imino-enol GC tautomer is thermally less stable. A study of the GC base pair is carried out subsequently taking into account the DNA surroundings in the biological environment. The most important stationary points are computed using the quantum mechanics/molecular mechanics (QM/MM) approach, suggesting a similar scenario for the proton/hydrogen-transfer phenomena in vacuo and in DNA. Finally, the static model is complemented by ab initio dynamic simulations, which show that vibrations at the hydrogen bonds can indeed originate hydrogen-transfer processes in the GC base pair. The relevance of the present findings for the rationalization of the preservation of the genetic code and mutagenesis is discussed.

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