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  • 1.
    Abraham, Mark J
    et al.
    Australian National University, Australia.
    Gready, Jill E
    Australian National University.
    Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations2008In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 7Article in journal (Refereed)
    Abstract [en]

    We address the question of constructing a protocol for replica-exchange molecular dynamics (REMD) simulations that make efficient use of the replica space, assess whether published applications are achieving such "mixing" efficiency, and provide a how-to guide to assist users to plan efficient REMD simulations. To address our first question, we introduce and discuss three metrics for assessing the number of replica-exchange attempts required to justify the use of a replica scheme and define a "transit number" as the lower bound for the length of an efficient simulation. Our literature survey of applications of REMD simulations of peptides in explicit solvent indicated that authors are not routinely reporting sufficient details of their simulation protocols to allow readers to make independent assessments of the impact of the method on their results, particularly whether mixing efficiency has been achieved. Necessary details include the expected or observed replica-exchange probability, together with the total number of exchange attempts, the exchange period, and estimates of the autocorrelation time of the potential energy. Our analysis of cases where the necessary information was reported suggests that in many of these simulations there are insufficient exchanges attempted or an insufficiently long period between them to provide confidence that the simulation length justifies the size of the replica scheme. We suggest guidelines for designing REMD simulation protocols to ensure mixing efficiency. Two key recommendations are that the exchange period should in general be larger than 1 ps and the number of exchange attempts should be chosen to significantly exceed the transit number for the replica scheme.

  • 2.
    Aho, Noora
    et al.
    Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland.
    Buslaev, Pavel
    Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland.
    Jansen, Anton
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bauer, Paul
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Groenhof, Gerrit
    Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Scalable Constant pH Molecular Dynamics in GROMACS2022In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 18, no 10, p. 6148-6160Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the λ-coordinates, not only reduces the complexity associated with parametrizing the intramolecular interactions between the sites but also is easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.

  • 3. Badri, Zahra
    et al.
    Pathak, Shubhrodeep
    Fliegl, Heike
    Rashidi-Ranjbar, Parviz
    Bast, Radovan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Marek, Radek
    Foroutan-Nejad, Gina
    Ruud, Kenneth
    All-Metal Aromaticity: Revisiting the Ring Current Model among Transition Metal Clusters2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 11, p. 4789-4796Article in journal (Refereed)
    Abstract [en]

    We present new insight into the nature of aromaticity in metal clusters. We give computational arguments in favor of using the ring-current model over local indices, such as nucleus independent chemical shifts, for the determination of the magnetic aromaticity. Two approaches for estimating magnetically induced ring currents are employed for this purpose, one based on the quantum theory of atoms in molecules (QTAIM) and the other where magnetically induced current densities (MICD) are explicitly calculated. We show that the two-zone aromaticity/antiaromaticity of a number of 3d metallic clusters (Sc-3(-), Cu-3(+), and Cu-4(2-)) can be explained using the QTAIM-based magnetizabilities. The reliability of the calculated atomic and bond magnetizabilities of the metallic clusters are verified by comparison with MICD computed at the multiconfiguration self-consistent field (MCSCF) and density functional levels of theory. Integrated MCSCF current strength susceptibilities as well as a visual analysis of the calculated current densities confirm the interpretations based on the QTAIM magnetizabilities. In view of the new findings, we suggest a simple explanation based on classical electromagnetic theory to explain the anomalous magnetic shielding in different transition metal clusters. Our results suggest that the nature of magnetic aromaticity/antiaromaticity in transition-metal clusters should be assessed more carefully based on global indices.

  • 4.
    Bjelkmar, Pär
    et al.
    Stockholm University.
    Larsson, Per
    Cuendet, Michel
    EPFL Lausanne.
    Lindahl, Erik
    Stockholm University.
    Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 2, p. 459-466Article in journal (Refereed)
    Abstract [en]

    CHARMM27 is a widespread and popular force field for biomolecular simulation, and several recent algorithms such as implicit solvent models have been developed specifically for it. We have here implemented the CHARMM force field and all necessary extended functional forms in the GROMACS molecular simulation package, to make CHARMM-specific features available and to test them in combination with techniques for extended time steps, to make all major force fields available for comparison studies in GROMACS, and to test various solvent model optimizations, in particular the effect of Lennard-Jones interactions on hydrogens. The implementation has full support both for CHARMM-specific features such as multiple potentials over the same dihedral angle and the grid-based energy correction map on the phi, psi protein backbone dihedrals, as well as all GROMACS features such as virtual hydrogen interaction sites that enable 5 fs time steps. The medium-to-long time effects of both the correction maps and virtual sites have been tested by performing a series of 100 ns simulations using different models for water representation, including comparisons between CHARMM and traditional TIP3P. Including the correction maps improves sampling of near native-state conformations in our systems, and to some extent it is even able to refine distorted protein conformations. Finally, we show that this accuracy is largely maintained with a new implicit solvent implementation that works with virtual interaction sites, which enables performance in excess of 250 ns/day for a 900-atom protein on a quad-core desktop computer.

  • 5. 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.

  • 6.
    Brand, Manuel
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Ruprecht Karls Univ Heidelberg, Interdisciplinary Ctr Sci Comp, D-69120 Heidelberg, Germany..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Efficient and Parallel Implementation of Real and Complex Response Functions Employing the Second-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 20, no 1, p. 103-113Article in journal (Refereed)
    Abstract [en]

    We present the implementation of an efficient matrix-folded formalism for the evaluation of complex response functions and the calculation of transition properties at the level of the second-order algebraic-diagrammatic construction (ADC(2)) scheme. The underlying algorithms, in combination with the adopted hybrid MPI/OpenMP parallelization strategy, enabled calculations of the UV/vis spectra of a guanine oligomer series ranging up to 1032 contracted basis functions, thereby utilizing vast computational resources from up to 32,768 CPU cores. Further analysis of the convergence behavior of the involved iterative subspace algorithms revealed the superiority of a frequency-separated treatment of response equations even for a large spectral window, including 101 frequencies. We demonstrate the applicability to general quantum mechanical operators by the first reported electronic circular dichroism spectrum calculated with a complex polarization propagator approach at the ADC(2) level of theory.

  • 7.
    Brumboiu, Iulia Emilia
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Korea Adv Inst Sci & Technol, Dept Chem, Daejeon 34141, South Korea..
    Eriksson, Olle
    Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden.;Orebro Univ, Sch Sci & Technol, S-70182 Orebro, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Photoelectron Spectroscopy of Molecules Beyond the Electric Dipole Approximation2019In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 10, p. 5483-5494Article in journal (Refereed)
    Abstract [en]

    A methodology implemented to compute photoionization cross sections beyond the electric dipole approximation using Gaussian type orbitals for the initial state and plane waves for the final state is applied to molecules of various sizes. The molecular photoionization cross sections computed for valence molecular orbitals as a function of photon energy present oscillations due to the wave-like nature of both the outgoing photoelectron and of the incoming photon. These oscillations are damped by rotational and vibrational averaging or by performing a k-point summation for the solid state case. For core orbitals, the corrections introduced by going beyond the electric dipole approximation are comparable to the atomic case. For valence orbitals, nondipole corrections to the total photoinization cross sections can reach up to 20% at photon energies above 1 keV. The corrections to the differential cross sections calculated at the magic angle are larger, reaching values between 30% and 50% for all molecules included. Our findings demonstrate that photoelectron spectroscopy, especially angle-resolved, on, e.g., molecules and clusters on surfaces, using high photon energies, must be accompanied by theories that go beyond the electric dipole approximation.

  • 8.
    Buslaev, Pavel
    et al.
    Univ Jyvaskyla, Nanosci Ctr, Jyvaskyla 40014, Finland.;Univ Jyvaskyla, Dept Chem, Jyvaskyla 40014, Finland..
    Aho, Noora
    Univ Jyvaskyla, Nanosci Ctr, Jyvaskyla 40014, Finland.;Univ Jyvaskyla, Dept Chem, Jyvaskyla 40014, Finland..
    Jansen, Anton
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Bauer, Paul
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Groenhof, Gerrit
    Univ Jyvaskyla, Nanosci Ctr, Jyvaskyla 40014, Finland.;Univ Jyvaskyla, Dept Chem, Jyvaskyla 40014, Finland..
    Best Practices in Constant pH MD Simulations: Accuracy and Sampling2022In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 18, no 10, p. 6148-6160Article in journal (Refereed)
    Abstract [en]

    Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the A-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys. 1996, 105, 2414-2423] can be performed with little computational overhead and hfor each typeence be used to routinely perform MD simulations at microsecond time scales, as shown in the accompanying paper [Aho, N. et al. J. Chem. Theory Comput. 2022, DOI: 10.1021 /acs.jctc.2c00516]. At such time scales, however, the accuracy of the molecular mechanics force field and the parametrization becomes critical. Here, we address these issues and provide the community with guidelines on how to set up and perform long time scale constant pH MD simulations. We found that barriers associated with the torsions of side chains in the CHARMM36m force field are too high for reaching convergence in constant pH MD simulations on microsecond time scales. To avoid the high computational cost of extending the sampling, we propose small modifications to the force field to selectively reduce the torsional barriers. We demonstrate that with such modifications we obtain converged distributions of both protonation and torsional degrees of freedom and hence consistent pK(a) estimates, while the sampling of the overall configurational space accessible to proteins is unaffected as compared to normal MD simulations. We also show that the results of constant pH MD depend on the accuracy of the correction potentials. While these potentials are typically obtained by fitting a low-order polynomial to calculated free energy profiles, we find that higher order fits are essential to provide accurate and consistent results. By resolving problems in accuracy and sampling, the work described in this and the accompanying paper paves the way to the widespread application of constant pH MD beyond pK(a) prediction.

  • 9. Chaudret, Robin
    et al.
    Contreras-Garcia, Julia
    Delcey, Mickaël G.
    Uppsala universitet, Teoretisk kemi.
    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.

  • 10. Chen, Mo
    et al.
    Pendrill, Robert
    Widmalm, Göran
    Brady, John W.
    Wohlert, Jakob
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Molecular Dynamics Simulations of the Ionic Liquid 1-n-Butyl-3-Methylimidazolium Chloride and Its Binary Mixtures with Ethanol2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 10, p. 4465-4479Article in journal (Refereed)
    Abstract [en]

    Room temperature ionic liquids (ILs) of the imidazolium family have attracted much attention during the past decade for their capability to dissolve biomass. Besides experimental work, numerous compuational studies have been concerned with the physical properties of both neat ILs and their interactions with different solutes, in particular, carbohydrates. Many classical force fields designed specifically for ILs have been found to yield viscosities that are too high for the liquid state, which has been attributed to the fact that the effective charge densities are too high due to the lack of electronic polarizability. One solution to this problem has been uniform scaling of the partial charges by a scale factor in the range 0.6-0.9, depending on model. This procedure has been shown to improve the viscosity of the models, and also to positively affect other properties, such as diffusion constants and ionic conductivity. However, less attention has been paid to how this affects the overall thermodynamics of the system, and the problems it might create when the IL models are combined with other force fields (e.g., for solutes). In the present work, we employ three widely used IL force fields to simulate 1-n-buty1-3-methyl-imidazolium chloride in both the crystal and the liquid state, as well as its binary mixture with ethanol. Two approaches are used: one in which the ionic charge is retained at its full integer value and one in which the partial charges are uniformly reduced to 85%. We investigate and calculate crystal and liquid structures, molar heat capacities, heats of fusion, self-diffusion constants, ionic conductivity, and viscosity for the neat IL, and ethanol activity as a function of ethanol concentration for the binary mixture. We show that properties of the crystal are less affected by charge scaling compared to the liquid. In the liquid state, transport properties of the neat IL are generally improved by scaling, whereas values for the heat of fusion are unaffected, and results for the heat capacity are ambiguous. Neither full nor reduced charges could reproduce experimental ethanol activities for the whole range of compositions.

  • 11. Cordomi, Arnau
    et al.
    Edholm, Olle
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
    Perez, Juan J.
    Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers2009In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 5, no 8, p. 2125-2134Article in journal (Refereed)
    Abstract [en]

    The behavior of electrolytes in molecular dynamics simulations of zwitterionic phospholipid bilayers; is very sensitive to the force field parameters used. Here, several 200 ns molecular dynamics of simulations of dipalmitoyl phosphotidylcholine (PC) bilayers in 0.2 M sodium or potassium chloride using various common force field parameters for the cations are presented. All employed parameter sets give a larger number of Na+ ions than K+ ions that bind to the lipid heads, but depending on the parameter choice quite different results are seen. A wide range of coordination numbers for the Na+ and K+ ions is also observed. These findings have been analyzed and compared to published experimental data. Some simulations produce aggregates of potassium chloride, indicating (in accordance with published simulations) that these force fields do not reproduce the delicate balance between salt and solvated ions. The differences between the force fields can be characterized by one single parameter, the electrostatic radius of the ion, which is correlated to sigma(MO) (M represents Na+/K+), the Lennard-Jones radius. When this parameter exceeds a certain threshold, binding to the lipid heads is no longer observed. One would, however, need more accurate experimental data to judge or rank the different force fields precisely. Still, reasons for the poor performance of some of the parameter sets are clearly demonstrated, and a quality control. procedure is provided.

  • 12. Coriani, S.
    et al.
    Fransson, T.
    Christiansen, O.
    Norman, P.
    Asymmetric-lanczos-chain-driven implementation of electronic resonance convergent coupled-cluster linear response theory2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 5, p. 1616-1628Article in journal (Refereed)
    Abstract [en]

    We present an implementation of the damped coupled-cluster linear response function based on an asymmetric Lanczos chain algorithm for the hierarchy of coupled-cluster approximations CCS (coupled-cluster singles), CC2 (coupled-cluster singles and approximate doubles), and CCSD (coupled-cluster singles and doubles). Triple corrections to the excitation energies can be included via the CCSDR(3) (coupled-cluster singles and doubles with noniterative-triples-corrected excitation energies) approximation. The performance and some of the potentialities of the approach are investigated in calculations of the visible/ultraviolet absorption spectrum and the dispersion of the real polarizability in near-resonant regions of pyrimidine, the near-edge absorption fine structure (NEXAFS) of ammonia, and the direct determination of the C 6 dipole-dipole dispersion coefficient of the benzene dimer.

  • 13.
    De Gracia Triviño, Juan Angel
    et al.
    Department of Microtechnology and Nanoscience - MC2, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.
    Delcey, Mickael G
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE-223 62 Lund, Sweden.
    Wendin, Göran
    Department of Microtechnology and Nanoscience - MC2, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.
    Complete Active Space Methods for NISQ Devices: The Importance of Canonical Orbital Optimization for Accuracy and Noise Resilience2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 10, p. 2863-2872Article in journal (Refereed)
    Abstract [en]

    To avoid the scaling of the number of qubits with the size of the basis set, one can divide the molecular space into active and inactive regions, which is also known as complete active space methods. However, selecting the active space alone is not enough to accurately describe quantum mechanical effects such as correlation. This study emphasizes the importance of optimizing the active space orbitals to describe correlation and improve the basis-dependent Hartree-Fock energies. We will explore classical and quantum computation methods for orbital optimization and compare the chemically inspired ansatz, UCCSD, with the classical full CI approach for describing the active space in both weakly and strongly correlated molecules. Finally, we will investigate the practical implementation of a quantum CASSCF, where hardware-efficient circuits must be used and noise can interfere with accuracy and convergence. Additionally, we will examine the impact of using canonical and noncanonical active orbitals on the convergence of the quantum CASSCF routine in the presence of noise.

  • 14.
    Duan, Sai
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, G.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Univ Sci & Technol China, Peoples R China.
    Theory for Modeling of High Resolution Resonant and Nonresonant Raman Images2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 10, p. 4986-4995Article in journal (Refereed)
    Abstract [en]

    Tip-enhanced Raman imaging is capable of resolving the inner structure of a single molecule owing to the generation of highly localized nanocavity plasmon. Here we present a general theory and detailed computational methodology to fully describe resonant and nonresonant Raman scattering under the localized plasmonic field. We use an allylcarbinol molecule adsorbed on the gold surface as a model system to illustrate different effects on the Raman images. It is found that the ability of distinguishing an individual vibration mode is highly limited under the resonant condition due to the dominant contribution from the Franck-Condon term and the mode-independent component of the Herzberg-Teller term. The nonresonant Raman images of the single molecule are vibrationally distinguishable and present the vibrational motion of the corresponding vibrational modes in real space. Furthermore, the calculated results confirm that nonlinear optical effects can further improve the resolution of the images. The theoretical and computational methods presented here provide the basic tools to model high resolution Raman images at the single molecular level.

  • 15.
    Farahani, Pooria
    et al.
    Uppsala universitet.
    Roca-Sanjuan, Daniel
    Zapata, Felipe
    Lindh, Roland
    Revisiting the Nonadiabatic Process in 1,2-Dioxetane2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 12, p. 5404-5411Article in journal (Refereed)
    Abstract [en]

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

  • 16.
    Fernández Galván, Ignacio
    et al.
    Uppsala universitet, Teoretisk kemi.
    Vacher, Morgane
    Uppsala universitet, Teoretisk kemi.
    Alavi, Ali
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Angeli, Celestino
    Univ Ferrara, Dipartimento Sci Chim & Farmaceut, Via Luigi Borsari 46, I-44121 Ferrara, Italy.
    Aquilante, Francesco
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA.
    Bao, Jie J.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Bokarev, Sergey I.
    Univ Rostock, Inst Phys, Albert Einstein Str 23-24, D-18059 Rostock, Germany.
    Bogdanov, Nikolay A.
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Carlson, Rebecca K.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Chibotaru, Liviu F.
    Univ Leuven, Theory Nanomat Grp, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
    Creutzberg, Joel
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden;Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Dattani, Nike
    Harvard Smithsonian Ctr Astrophys, 60 Garden St, Cambridge, MA 02138 USA.
    Delcey, Mickael G
    Uppsala universitet, Teoretisk kemi.
    Dong, Sijia S.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Dreuw, Andreas
    Heidelberg Univ, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205 A, D-69120 Heidelberg, Germany.
    Freitag, Leon
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Manuel Frutos, Luis
    Univ Alcala De Henares, Dept Quim Analit Quim Fis & Ingn Quim, E-28871 Madrid, Spain;Univ Alcala De Henares, Inst Invest Quim Andres M del Rio, E-28871 Madrid, Spain.
    Gagliardi, Laura
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Gendron, Frederic
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA.
    Giussani, Angelo
    UCL, Dept Chem, 20 Gordon St, London WC1H 0AJ, England;Univ Valencia, Inst Ciencia Mol, Apartado 22085, ES-46071 Valencia, Spain.
    Gonzalez, Leticia
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Grell, Gilbert
    Univ Rostock, Inst Phys, Albert Einstein Str 23-24, D-18059 Rostock, Germany.
    Guo, Meiyuan
    Uppsala universitet, Teoretisk kemi.
    Hoyer, Chad E.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Johansson, Marcus
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Keller, Sebastian
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Knecht, Stefan
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Kovacevic, Goran
    Rudjer Boskovic Inst, Div Mat Phys, POB 180,Bijenicka 54, HR-10002 Zagreb, Croatia.
    Källman, Erik
    Uppsala universitet, Teoretisk kemi.
    Li Manni, Giovanni
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Lundberg, Marcus
    Uppsala universitet, Teoretisk kemi.
    Ma, Yingjin
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Mai, Sebastian
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Malhado, Joao Pedro
    Imperial Coll London, Dept Chem, London SW7 2AZ, England.
    Malmqvist, Per Ake
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Marquetand, Philipp
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Mewes, Stefanie A.
    Heidelberg Univ, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205 A, D-69120 Heidelberg, Germany;Massey Univ Albany, Ctr Theoret Chem & Phys, NZLAS, Private Bag 102904, Auckland 0632, New Zealand.
    Norell, Jesper
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden.
    Olivucci, Massimo
    Univ Siena, Dept Biotechnol Chem & Pharm, Via A Moro 2, I-53100 Siena, Italy;Bowling Green State Univ, Dept Chem, Bowling Green, OH 43403 USA;Univ Strasbourg, CNRS, USIAS, F-67034 Strasbourg, France;Univ Strasbourg, CNRS, Inst Phys & Chim Mat Strasbourg, F-67034 Strasbourg, France.
    Oppel, Markus
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Phung, Quan Manh
    Pierloot, Kristine
    Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
    Plasser, Felix
    Loughborough Univ, Dept Chem, Loughborough LE11 3TU, Leics, England.
    Reiher, Markus
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Sand, Andrew M.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Schapiro, Igor
    Hebrew Univ Jerusalem, Inst Chem, Jerusalem, Israel.
    Sharma, Prachi
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Stein, Christopher J.
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Sörensen, Lasse Kragh
    Uppsala universitet, Teoretisk kemi.
    Truhlar, Donald G.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Ugandi, Mihkel
    Uppsala universitet, Teoretisk kemi.
    Ungur, Liviu
    Natl Univ Singapore, Dept Chem, Singapore 117543, Singapore.
    Valentini, Alessio
    Res Unit MolSys, Theoret Phys Chem, Allee 6 Aout 11, B-4000 Liege, Belgium.
    Vancoillie, Steven
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Veryazov, Valera
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Weser, Oskar
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Wesolowski, Tomasz A.
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Widmark, Per-Olof
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Wouters, Sebastian
    Brantsandpatents, Pauline van Pottelsberghelaan 24, B-9051 Sint Denijs Westrem, Belgium.
    Zech, Alexander
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Zobel, J. Patrick
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Lindh, Roland
    Uppsala universitet, Organisk kemi.
    OpenMolcas: From Source Code to Insight2019In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 11, p. 5925-5964Article in journal (Refereed)
    Abstract [en]

    In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.

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

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

  • 18.
    Fransson, Thomas
    et al.
    Ruprecht Karls Univ Heidelberg, Interdisciplinary Ctr Sci Comp, D-69120 Heidelberg, Germany.;Stockholm Univ, Albanova, Fysikum, S-10691 Stockholm, Sweden..
    Brumboiu, Iulia E.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Vidal, Marta L.
    Tech Univ Denmark, DTU Chem, DK-2800 Lyngby, Denmark..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Coriani, Sonia
    Tech Univ Denmark, DTU Chem, DK-2800 Lyngby, Denmark.;NTNU Norwegian Univ Sci & Technol, Dept Chem, N-7991 Trondheim, Norway..
    Dreuw, Andreas
    Ruprecht Karls Univ Heidelberg, Interdisciplinary Ctr Sci Comp, D-69120 Heidelberg, Germany..
    XABOOM: An X-ray Absorption Benchmark of Organic Molecules Based on Carbon, Nitrogen, and Oxygen 1s -> pi* Transitions2021In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 17, no 3, p. 1618-1637Article in journal (Refereed)
    Abstract [en]

    The performance of several standard and popular approaches for calculating X-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges of 40 primarily organic molecules up to the size of guanine has been evaluated, focusing on the low-energy and intense 1s -> pi* transitions. Using results obtained with CVS-ADC(2)-x and fc-CVS-EOM-CCSD as benchmark references, we investigate the performance of CC2, ADC(2), ADC(3/2), and commonly adopted density functional theory (DFT)-based approaches. Here, focus is on precision rather than on accuracy of transition energies and intensities-in other words, we target relative energies and intensities and the spread thereof, rather than absolute values. The use of exchange-correlation functionals tailored for time-dependent DFT calculations of core excitations leads to error spreads similar to those seen for more standard functionals, despite yielding superior absolute energies. Long-range corrected functionals are shown to perform particularly well compared to our reference data, showing error spreads in energy and intensity of 0.2-0.3 eV and similar to 10%, respectively, as compared to 0.3-0.6 eV and similar to 20% for a typical pure hybrid. In comparing intensities, state mixing can complicate matters, and techniques to avoid this issue are discussed. Furthermore, the influence of basis sets in high-level ab initio calculations is investigated, showing that reasonably accurate results are obtained with the use of 6-311++G**. We name this benchmark suite as XABOOM (X-ray absorption benchmark of organic molecules) and provide molecular structures and ground-state self-consistent field energies and spectroscopic data. We believe that it provides a good assessment of electronic structure theory methods for calculating X-ray absorption spectra and will become useful for future developments in this field.

  • 19.
    Gong, Zuyong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Department of Chemical Physics, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, China.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Duan, Sai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Department of Chemical Physics, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, China.
    Significant Contributions of the Albrecht’s A Term to Nonresonant Raman Scattering Processes2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 11, p. 5385-5390Article in journal (Refereed)
    Abstract [en]

    The Raman intensity can be well described by the famous Albrecht’s Raman theory that consists of A and B terms. It is well-known that the contribution from Albrecht’s A term can be neglected without any loss of accuracy for far-off resonant Raman scattering processes. However, as demonstrated in this study, we have found that this widely accepted long-standing assumption fails drastically for totally symmetric vibration modes of molecules in general off-resonant Raman scattering. Perturbed first-principles calculations for water molecule show that strong constructive interference between the A and B terms occurs for the Raman intensity of the symmetric O-H stretching mode, which can account for ∼40% of the total intensity. Meanwhile, a minor destructive interference is found for the angle bending mode. The state-to-state mapping between Albrecht’s theory and perturbation theory allows us to verify the accuracy of the widely employed perturbation method for the dynamic/resonant Raman intensities. The model calculations rationalized from water molecule with the bending mode show that the perturbation method is a good approximation only when the absolute energy difference between the first excited state and the incident light is more than five times greater than the vibrational energy in the ground state.

  • 20.
    Harczuk, Ignat
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Agren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Studies of pH-Sensitive Optical Properties of the deGFP1 Green Fluorescent Protein Using a Unique Polarizable Force Field2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 8, p. 3492-3502Article in journal (Refereed)
    Abstract [en]

    The aim of this study is to identify the responsible molecular forms for the pH dependent optical properties of the deGFP1 green fluorescent protein mutant. We have carried out static and dynamic type calculations for all four protonation states of the chromophore to unravel the contributions due to finite temperature and the flexible protein backbone on the pH dependent optical properties. In particular, we have used a combined molecular dynamics and density functional molecular mechanics linear response approach by means of which the optical property calculations were carried out for the chromophore in the explicitly treated solvent and bioenvironment. Two different models were used to describe the environment electronic embedding and polarizable electronic embedding accounting for the polarization of the chromophore and the mutual polarization between the chromophore and the environment, respectively. For this purpose a polarizable force field was derived quantum mechanically for the protein environment by use of analytical response theory. While the gas-phase calculations for the chromophore predict that the induced red shift going from low to high pH is attributed to the change of molecular forms from neutral to zwitterionic, the two more advanced models that explicitly account for the protein backbone attribute the pH shift to a neutral to anionic conversion. Some ramifications of the results for the use of GFPs as pH sensors are discussed.

  • 21.
    Hess, Berk
    et al.
    Max-Planck Institut Mainz.
    Kutzner, Carsten
    Max-Planck Institut Göttingen.
    van der Spoel, David
    Uppsala University.
    Lindahl, Erik
    Stockholm University.
    GROMACS 4.0: 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 2, p. 435-Article 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.

  • 22.
    Hopmann, Kathrin H.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Quantum Chemical Modeling of the Dehalogenation Reaction of Haloalcohol Dehalogenase2008In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 7, p. 1129-1137Article in journal (Refereed)
    Abstract [en]

    The dehalogenation reaction of haloalcohol dehalogenase HheC from Agrobacterium radiobacter AD1 was investigated theoretically using hybrid density functional theory methods. HheC catalyzes the enantioselective conversion of halohydrins into their corresponding epoxides. The reaction is proposed to be mediated by a catalytic Ser132-Tyr145-Arg149 triad, and a distinct halide binding site is suggested to facilitate halide displacement by stabilizing the free ion. We investigated the HheC-mediated dehalogenation of (R)-2-chloro-1-phenylethanol using three quantum chemical models of various sizes. The calculated barriers and reaction energies give support to the suggested reaction mechanism. The dehalogenation occurs in a single concerted step, in which Tyr145 abstracts a proton from the halohydrin substrate and the substrate oxyanion displaces the chloride ion, forming the epoxide. Characterization of the involved stationary points is provided. Furthermore, by using three different models of the halide binding site, we are able to assess the adopted modeling methodology.

  • 23. Jansik, Branislav
    et al.
    Rizzo, Antonio
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Champagne, Benoit
    Strong two-photon circular dichroism in helicenes: A theoretical investigation2008In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 3, p. 457-467Article in journal (Refereed)
    Abstract [en]

    Using a recently derived origin-invariant quadratic response approach combined with time-dependent density functional theory, four representative helicenes are shown to present a very strong two-photon circular dichroism (TPCD) response, which makes them candidates for the first experimental observation of a TPCD effect. The large response is attributed to the unique combination of chirality and electron delocalization. Comparison with electronic circular dichroism and two-photon absorption (TPA) shows that the three effects exhibit complementary features for unravelling the molecular structures. In particular, for the four (M)-helicenes studied here, the first, i.e., low-energy, dominant Cotton band is always negative, whereas for TPCD it is positive. From an analysis of the frontier orbitals describing most of the one-electron excitation vectors, the largest TPCD response of tetramethoxy-bisquinone-dithia-[7]-helicene has been attributed to the charge-transfer character of the excited state, like for the parent TPA effect. Moreover, the TPCD intensities are found to be mostly governed by the electric and magnetic dipole contributions, while the electric quadrupole terms are, on a relative basis, less important.

  • 24. Kauczor, J.
    et al.
    Jørgensen, P.
    Norman, P.
    On the efficiency of algorithms for solving Hartree-Fock and Kohn-Sham response equations2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 6, p. 1610-1630Article in journal (Refereed)
    Abstract [en]

    The response equations as occurring in the Hartree-Fock, multiconfigurational self-consistent field, and Kohn-Sham density functional theory have identical matrix structures. The algorithms that are used for solving these equations are discussed, and new algorithms are proposed where trial vectors are split into symmetric and antisymmetric components. Numerical examples are given to compare the performance of the algorithms. The calculations show that the standard response equation for frequencies smaller than the highest occupied molecular orbital-lowest unoccupied molecular orbital gap is best solved using the preconditioned conjugate gradient or conjugate residual algorithms where trial vectors are split into symmetric and antisymmetric components. For larger frequencies in the standard response equation as well as in the damped response equation in general, the preconditioned iterative subspace approach with symmetrized trial vectors should be used. For the response eigenvalue equation, the Davidson algorithm with either paired or symmetrized trial vectors constitutes equally good options.

  • 25. Kauczor, J.
    et al.
    Norman, P.
    Efficient calculations of molecular linear response properties for spectral regions2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 6, p. 2449-2455Article in journal (Refereed)
    Abstract [en]

    Molecular spectra can be determined from molecular response functions, by solving the so-called damped response equations using the complex polarization propagator approach. The overall structure of response equations is identical for variational wave functions such as the Hartree-Fock, multiconfiguration self-consistent field, and Kohn-Sham density functional theory, and the key program module is the linear response equation solver. We present an implementation of the solver using the algorithm with symmetrized vectors, optimized for addressing spectral regions of a width of some 5-10 eV and a resolution below 0.1 eV. The work is illustrated by the consideration of UV-vis as well as near carbon K -edge absorption spectra of the C60 fullerene. We demonstrate that it is possible to converge tightly response equations for hundreds of optical frequencies in resonance regions of the spectrum at a cost not much exceeding the solution of a single response equation in the nonresonant region. Our work is implemented in the molecular orbital based module of the Dalton program and serves as a documentation of the code distributed in the Dalton2013 release version.

  • 26. Kimanius, Dari
    et al.
    Pettersson, Ingrid
    Schluckebier, Gerd
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm University, Sweden.
    Andersson, Magnus
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    SAXS-Guided Metadynamics2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 7, p. 3491-3498Article in journal (Refereed)
    Abstract [en]

    The small-angle X-ray scattering (SAXS) methodology enables structural characterization of biological macromolecules in solution. However, because SAXS provides low-dimensional information, several potential structural configurations can reproduce the experimental scattering profile, which severely complicates the structural refinement process. Here, we present a bias-exchange metadynamics refinement protocol that incorporates SAXS data as collective variables and therefore tags all possible configurations with their corresponding free energies, which allows identification of a unique structural solution. The method has been implemented in PLUMED and combined with the GROMACS simulation package, and as a proof of principle, we explore the Trp-cage protein folding landscape.

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  • 27. Kjaergaard, Thomas
    et al.
    Jorgensen, Poul
    Thorvaldsen, Andreas J.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Coriani, Sonia
    Gauge-Origin Independent Formulation and Implementation of Magneto-Optical Activity within Atomic-Orbital-Density Based Hartree-Fock and Kohn-Sham Response Theories2009In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 5, no 8, p. 1997-2020Article, review/survey (Refereed)
    Abstract [en]

    A Lagrangian approach has been used to derive gauge-origin independent expressions for two properties that rationalize magneto-optical activity, namely the Verdet constant V(omega) of the Faraday effect and the B term of magnetic circular dichroism. The approach is expressed in terms of an atomic-orbital density-matrix based formulation of response theory and use London atomic orbitals to parametrize the magnetic field dependence. It yields a computational procedure which is both gauge-origin independent and suitable for linear-scaling at the level of time-dependent Hartree-Fock and density functional theory. The formulation includes a modified preconditioned conjugated gradient algorithm, which projects out the excited state component from the solution to the linear response equation. This is required when solving one of the response equations for the determination of the B term and divergence is encountered if this component is not projected out. Illustrative results are reported for the Verdet constant of H-2, HF, CO, N2O, and CH3CH2CH3 and for the B term of pyrimidine, phosphabenzene, and pyridine. The results are benchmarked against gauge-origin independent CCSD values

  • 28.
    Knippenberg, Stefan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gieseking, Rebecca L.
    Rehn, Dirk R.
    Mukhopadhyay, Sukrit
    Dreuw, Andreas
    Bredas, Jean-Luc
    Benchmarking Post-Hartree-Fock Methods To Describe the Nonlinear Optical Properties of Polymethines: An Investigation of the Accuracy of Algebraic Diagrammatic Construction (ADC) Approaches2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 11, p. 5465-5476Article in journal (Refereed)
    Abstract [en]

    Third-order nonlinear optical (NLO) properties of polymethine dyes have been widely studied for applications such as all-optical switching. However, the limited accuracy of the current computational methodologies has prevented a comprehensive understanding of the nature of the lowest excited states and their influence on the molecular optical and NLO properties. Here, attention is paid to the lowest excited-state energies and their energetic ratio, as these characteristics impact the figure-of-merit for all-optical switching. For a series of model polymethines, we compare several algebraic diagrammatic construction (ADC) schemes for the polarization propagator with approximate second-order coupled cluster (CC2) theory, the widely used INDO/MRDCI approach and the symmetry adapted cluster configuration interaction (SAC-CI) algorithm incorporating singles and doubles linked excitation operators (SAC-CI SD-R). We focus in particular on the ground-to-excited state transition dipole moments and the corresponding state dipole moments, since these quantities are found to be of utmost importance for an effective description of the third-order polarizability gamma and two-photon absorption spectra. A sum-overstates expression has been used, which is, found to quickly converge. While ADC(3/2) has been found to be the most appropriate method to calculate these properties, CC2 performs poorly.

  • 29.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Carravetta, Vincenzo
    Li, Cui
    Monti, Susanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. CNR-ICCOM, Italy .
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Optical Properties of Gold Nanoclusters Functionalized with a Small Organic Compound: Modeling by an Integrated Quantum-Classical Approach2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 7, p. 3325-3339Article in journal (Refereed)
    Abstract [en]

    Motivated by the growing importance of organometallic nanostructured materials and nanoparticles as microscopic devices for diagnostic and sensing applications, and by the recent considerable development in the simulation of such materials, we here choose a prototype system para-nitroaniline (pNA) on gold nanoparticles to demonstrate effective strategies for designing metal nanoparticles with organic conjugates from fundamental principles. We investigated the motion, adsorption mode, and physical chemistry properties of gold-pNA particles, increasing in size, through classical molecular dynamics (MD) simulations in connection with quantum chemistry (QC) calculations. We apply the quantum mechanics-capacitance molecular mechanics method [Z. Rinkevicius et al. J. Chem. Theory Comput. 2014, 10, 989] for calculations of the properties of the conjugate nanoparticles, where time dependent density functional theory is used for the QM part and a capacitance-polarizability parametrization of the MM part, where induced dipoles and charges by metallic charge transfer are considered. Dispersion and short-range repulsion forces are included as well. The scheme is applied to one- and two-photon absorption of gold-pNA clusters increasing in size toward the nanometer scale. Charge imaging of the surface introduces red-shifts both because of altered excitation energy dependence and variation of the relative intensity of the inherent states making up for the total band profile. For the smaller nanoparticles the difference in the crystal facets are important for the spectral outcome which is also influenced by the surrounding MM environment.

  • 30.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Binding Mechanism and Magnetic Properties of a Multifunctional Spin Label for Targeted EPR Imaging of Amyloid Proteins: Insight from Atomistic Simulations and First-Principles Calculations2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 11, p. 4766-4774Article in journal (Refereed)
    Abstract [en]

    Electron paramagnetic resonance (EPR) imaging techniques provide a promising approach to detect amyloid structures which are of paramount importance in early-stage diagnosis of conformational diseases. Here, we report a combined molecular dynamics and density functional theory/molecular mechanics computational scheme for evaluation of the binding mechanism between a multifunctional spin label and the target amyloid protein. In addition, we consider evaluation of EPR spin Hamiltonian parameters with the aim of providing a better microscopic understanding and interpretation of EPR spectroscopy. The results from molecular dynamics simulations suggest that the oligothiophene conjugate part of the spin label interacts with hydrophobic residues of the amyloid protein through hydrophobic attraction and that both the N-O bond length and the N-O out-of-plane tilt angle in the nitroxide group are slightly diminished after, complexation with the protein. The translational and rotational motions of the protein bound spin label are considerably slowed compared to those of the free spin label in aqueous solution, but interestingly, hydrogen bonds formed between the nitroxide oxygen group and the surrounding water molecules are hardly affected by the presence Of the amyloid protein. First principles calculation's suggest that EPR spin Hamiltonian parameters including the nitroxide nitrogen hyperfine coupling tensor A(N) and electronic g tensor suffer noticeable changes upon complexation with the protein. The magnitude of the A(N) tensor is found,to:be. closely related to the nitroxide N-O out tilt angle, while the g tensor is affected by both the nitroxide N-O bond length as well as the interaction between the spin label and the amyloid protein With this work we show that state-of-the-art simulation techniques represent a promising way of providing a detailed understanding of the microscopic mechanisms responsible for the formation and stability of a spin label complexed with amyloid structures as well as the magnetic properties of the free and protein-bound spin label.

  • 31.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Two-Photon Absorption of Metal-Assisted Chromophores2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 12, p. 5630-5639Article in journal (Refereed)
    Abstract [en]

    Aiming to understand the effect of a metal surface on nonlinear optical properties and the combined effects of surface and solvent environments on such properties, we present a multiscale response theory study, integrated with dynamics of the two-photon absorption of 4-nitro-4'-amino-trans-stilbene physisorbed on noble metal surfaces, considering two such surfaces, Ag(111) and Au(111), and two solvents, cyclohexane and water, as cases for demonstration. A few conclusions of general character could be drawn: While the geometrical change of the chromophore induced by the environment was found to notably alter (diminish) the two-photon absorption cross section in the polar medium, the effects of the metal surface and solvent on the electronic structure of the chromophore surpasses the geometrical effects and leads to a considerably enhanced two-photon absorption cross section in the polar solvent. This enhancement of two-photon absorption arises essentially from the metal charge image induced enlargement of the difference between the dipole moment of the excited state and the ground state. The orientation-dependence of the two-photon absorption is found to connect with the lateral rotation of the chromophore, where the two-photon absorption reaches its maximum when the polarization of the incident light coincides with the long-axis of the chromophore. Our results demonstrate a distinct enhancement of the two-photon absorption by a metal surface and a polar medium and envisage the employment of metal-chromophore composite materials for future development of nonlinear optical materials with desirable properties.

  • 32.
    Linder, Mats
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Ranganathan, Anirudh
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    "Adapted Linear Interaction Energy": A Structure-Based LIE Parametrization for Fast Prediction of Protein-Ligand Affinities2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 2, p. 1230-1239Article in journal (Refereed)
    Abstract [en]

    We present a structure-based parametrization of the Linear Interaction Energy (LIE) method and show that it allows for the prediction of absolute protein-ligand binding energies. We call the new model "Adapted" LIE (ALIE) because the a and beta coefficients are defined by system-dependent descriptors and do therefore not require any empirical gamma term. The best formulation attains a mean average deviation of 1.8 kcal/mol for a diverse test set and depends on only one fitted parameter. It is robust with respect to additional fitting and cross-validation. We compare this new approach with standard LIE by Aqvist and co-workers and the LIE + gamma SASA model (initially suggested by Jorgensen and co-workers) against in-house and external data sets and discuss their applicabilities.

  • 33. List, Nanna Holmgaard
    et al.
    Zalesny, Robert
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Bartkowiak, Wojciech
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Relation between Nonlinear Optical Properties of Push-Pull Molecules and Metric of Charge Transfer Excitations2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 9, p. 4182-4188Article in journal (Refereed)
    Abstract [en]

    We establish the relationships between the metric of charge transfer excitation (Delta r) for the bright pi pi* state and the two-photon absorption probability as well as the first hyperpolarizability for two families of push pull pi-conjugated systems. As previously demonstrated by Guido et al. (J. Chem. Theory Comput. 2013, 9, 3118-3126), Delta r is a measure for the average hole electron distance upon excitation and can be used to discriminate between short- and long-range electronic excitations. We indicate two new benefits from using this metric for the analyses of nonlinear optical properties of push pull systems. First, the two-photon absorption probability and the first hyperpolarizability are found to be interrelated through Delta r; if, beta similar to (Delta r)(k), then roughly, delta(TPA) similar to (Delta r)(k+1). Second, a simple power relation between Delta r and the molecular hyperpolarizabilities of push pull systems offers the possibility of estimating properties for longer molecular chains without performing calculations of high-order response functions explicitly. We further demonstrate how to link the hyperpolarizabilities with the chain length of the push-pull pi-conjugated systems through the metric of charge transfer.

  • 34.
    Lundberg, Linnea
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
    Edholm, Olle
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
    Dispersion Corrections to the Surface Tension at Planar Surfaces2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 8, p. 4025-4032Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations are usually performed using cutoffs (r(c)) for the short-ranged dispersion interactions (r(-6)). For isotropic systems, long-range interactions are often added in a continuum approximation. This usually leads to excellent results that are independent of the cutoff length down to about 1 nm. For systems with interfaces or other anisotropic systems the situation is more complicated. We study here planar interfaces, focusing on the surface tension, which is sensitive to cutoffs. Previous analytic results giving the long-range correction to the surface tension of a liquid-vapor interface as a two- or three-dimensional integral are revisited. They are generalized by introducing a dispersion density profile which makes it possible to handle multicomponent systems. For the simple but common hyperbolic tangent profile the integral may be Taylor-expanded in the dimensionless parameter obtained by dividing the profile width with the cutoff length. This parameter is usually small, and excellent agreement with numerical calculations of the integral is obtained by keeping two terms in the expansion. The results are compared to simulations with different lengths of the cutoff for some simple systems. The surface tension in the simulations varies linearly in r(c)(-2), although a small r(c)(-4)-term may be added to improve the agreement. The slope of the r(c)(-2)-line could in several cases be predicted from the change in dispersion density at the interface. The disagreements observed in some cases when comparing to theory occur when the finite cutoff used in the simulations causes structural differences compared to long-range cutoffs or Ewald summation for the r(-6)-interactions.

  • 35.
    Manni, Giovanni Li
    et al.
    Max Planck Inst Solid State Res, Elect Struct Theory Dept, D-70569 Stuttgart, Germany..
    Galvan, Ignacio Fdez.
    Uppsala Univ, Dept Chem BMC, SE-75123 Uppsala, Sweden..
    Couto, Rafael Carvalho
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Delcey, Mickael G
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Lindh, Roland
    Uppsala Univ, Dept Chem BMC, SE-75123 Uppsala, Sweden.;Uppsala Univ, Uppsala Ctr Computat Chem UC3, SE-75123 Uppsala, Sweden..
    The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 20, p. 6933-6991Article in journal (Refereed)
    Abstract [en]

    The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.

  • 36. Matthews, James F.
    et al.
    Beckham, Gregg T.
    Bergenstråhle-Wohlert, Malin
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Biocomposites. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Brady, John W.
    Himmel, Michael E.
    Crowley, Michael F.
    Comparison of Cellulose I beta Simulations with Three Carbohydrate Force Fields2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 2, p. 735-748Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations of cellulose have recently become more prevalent due to increased interest in renewable energy applications, and many atomistic and coarse-grained force fields exist that can be applied to cellulose. However, to date no systematic comparison between carbohydrate force fields has been conducted for this important system. To that end, we present a molecular dynamics simulation study of hydrated, 36-chain cellulose I beta microfibrils at room temperature with three carbohydrate force fields (CHARMM35, GLYCAM06, and Gromos 45a4) up to the near-microsecond time scale. Our results indicate that each of these simulated microfibrils diverge from the cellulose 1 beta crystal structure to varying degrees under the conditions tested. The CHARMM35 and GLYCAM06 force fields eventually result in structures similar to those observed at 500 K with the same force fields, which are consistent with the experimentally observed high-temperature behavior of cellulose I. The third force field, Gromos 45a4, produces behavior significantly different from experiment, from the other two force fields, and from previously reported simulations with this force field using shorter simulation times and constrained periodic boundary conditions. For the GLYCAM06 force field, initial hydrogen-bond conformations and choice of electrostatic scaling factors significantly affect the rate of structural divergence. Our results suggest dramatically different time scales for convergence of properties of interest, which is important in the design of computational studies and comparisons to experimental data. This study highlights that further experimental and theoretical work is required to understand the structure of small diameter cellulose microfibrils typical of plant cellulose.

  • 37. Maurer, Patrick
    et al.
    Laio, Alessandro
    Hugosson, Håkan Wilhelm
    Colombo, Maria Carola
    Rothlisberger, Ursula
    Automated parametrization of biomolecular force fields from quantum mechanics/molecular mechanics (QM/MM) simulations through force matching2007In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 3, no 2, p. 628-639Article in journal (Refereed)
    Abstract [en]

    We introduce a novel procedure to parametrize biomolecular force fields. We perform finite-temperature quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, with the fragment or moiety that has to be parametrized being included in the QM region. By applying a force-matching algorithm, we derive a force field designed in order to reproduce the steric, electrostatic, and dynamic properties of the QM subsystem. The force field determined in this manner has an accuracy that is comparable to the one of the reference QM/MM calculation, but at a greatly reduced computational cost. This allows calculating quantities that would be prohibitive within a QM/MM approach, such as thermodynamic averages involving slow motions of a protein. The method is tested on three different systems in aqueous solution: dihydrogenphosphate, glycyl-alanine dipeptide, and a nitrosyl-dicarbonyl complex of technetium(I). Molecular dynamics simulations with the optimized force field show overall excellent performance in reproducing properties such as structures and dipole moments of the solutes as well as their solvation pattern.

  • 38.
    Murugan, N. Arul
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Schrader, Sigurd
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Role of Protonation State and Solvation on the pH Dependent Optical Properties of Bromocresol Green2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 9, p. 3958-3968Article in journal (Refereed)
    Abstract [en]

    pH sensors play a key role in many industrial and diagnostic applications. Mostly their usage is based on experience, and in many cases the working mechanisms of these sensors are not known in detail, thereby hindering a systematic improvement of such sensors for specific applications. In this report, we present results from combined quantum chemical and molecular mechanics calculations of molecular structures and optical absorption properties of bromocresol green (BRG) in aqueous solution with varying pH value. In the acidic pH range, this chromophore has an intense band with absorption maximum at 444 nm and in the basic pH regime the absorption spectra show a redshift toward 613 nm. In order to identify the molecular structures responsible for this pH dependent optical behavior the closed and open forms of BRG are studied using static approaches considering in each case the three possible protonated states namely, neutral, anionic, and dianionic. For the most significant forms, i.e. the open forms of BRG, extensive modeling based on the integrated approach has been carried out, where the structure and dynamics were studied using hybrid QM/MM molecular dynamics, while the excitation energy calculations were carried out using time dependent density functional theory wherein the surrounding solvent was described as polarizable continuum, semicontinuum, or via a molecular mechanics force-field. The anionic and dianionic forms of BRG have been recognized as molecular forms responsible for its acidic and basic pH behavior, respectively. In contrast to the case of solvatochromic probes, the different protonation states determine the optical behavior in different pH values for pH probes. Hence, the level of solvent description appears to be of minor importance. Independent of the level of theory used to describe the solvent, all models reproduce the spectral features of BRG in different pH and also the pH induced redshift in good agreement with experiment.

  • 39.
    Murugan, Natarajan Arul
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    pH-Induced Modulation of One- and Two-Photon Absorption Properties in a Naphthalene-Based Molecular Probe2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 8, p. 3660-3669Article in journal (Refereed)
    Abstract [en]

    Presently, there is a great demand for small probe molecules that can be used for two-photon excitation microscopy (TPM)-based monitoring of intracellular and intraorganelle activity and pH. The candidate molecules should ideally possess a large two-photon absorption cross section with optical properties sensitive to pH changes. In the present work, we investigate the potential of a methoxy napthalene (MONAP) derivative for its suitability to serve as a pH sensor using TPM. Using an integrated approach rooted in hybrid quantum mechanics/molecular mechanics, the structures, dynamics, and the one- and two-photon properties of the probe in dimethylformamide solvent are studied. It is found that the protonated form is responsible for the optical property of MONAP at moderately low pH, for which the calculated pH-induced red shift is in good agreement with experiments. A 2-fold increase in the two-photon absorption cross section in the IR region of the spectrum is predicted for the moderately low pH form of the probe, suggesting that this can be a potential probe for pH monitoring of living cells. We also propose some design principles aimed at obtaining control of the absorption spectral range of the probe by structural tuning. Our work indicates that the integrated approach employed is capable of capturing the pH-induced changes in structure and optical properties of organic molecular probes and that such in silico tools can be used to draw structure-property relationships to design novel molecular probes suitable for a specific application.

  • 40.
    Murugan, Natarajan Arul
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zalesny, Robert
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Chelation-Induced Quenching of Two-Photon Absorption of Azacrown Ether Substituted Distyryl Benzene for Metal Ion Sensing2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 2, p. 778-788Article in journal (Refereed)
    Abstract [en]

    Imaging of metal ion concentration, distribution, and dynamics can pave the way to diagnose a number of diseases and to identify the normal functioning of the human body. Recently, two-photon microscopy-based imaging of metal ions has become popular due to several favorable factors as compared to fluorescence-based imaging. However, much has to be investigated in order to design probes with large two-photon absorption cross sections and yet with selective binding affinity toward metal ions. In particular, it is crucial to recognize the mechanisms of metal ion-induced changes of the two-photon absorption intensity. The present paper contributes to this effort and reports on the results of extensive studies carried out to define a reliable computational protocol that can account for sampling, solvent, and finite temperature,effects for one- and two-photon properties of metal probes, using azacrown ether substituted distyrylbenzene embedded in solvents as a testbed. We employ a selection of theoretical approaches to model the structure of the probe alone and in the presence of Mg2+ ion in acetonitrile solvent, including static quantum-chemical calculations, rigid- and flexible-body molecular dynamics, and hybrid QM/MM molecular dynamics. For a set of solute-solvent configurations, the one- and the two-photon properties are computed using the recently developed polarizable embedding response approach. It is found that the hybrid QM/MM molecular dynamics based approach is the most successful one among other employed computational strategies, viz, reproduction of the metal ion-induced blue shift in the absorption wavelength and decrease in the two-photon absorption cross section, which actually is in excellent agreement with experimental data. The mechanism for such metal ion-induced changes in the optical properties is put forward using a few-state model. Possible design principles to tune the two-photon absorption properties of probes are also discussed.

  • 41. Nakagawa, Setsuko
    et al.
    Mark, Pekka
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Recipe of polarized one-electron potential optimization for development of polarizable force fields2007In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 3, no 6, p. 1947-1959Article in journal (Refereed)
    Abstract [en]

    Polarized one-electron potential (POP) optimization is a powerful and practical method to determine multicenter dipole polarizabilities that can be used for constructing polarizable force fields. The POP optimization is similar to the widely used electrostatic potential (ESP) optimization to determine the partial charges of molecules. However, while the ESP optimization targets the electrostatic potentials on a molecular surface, the POP optimization targets the change of electrostatic potentials on molecular surfaces which are induced by the field of a test charge on the molecular surface. Since only additional one-electron integrals for the test charge are required for the estimation of the surface potentials, the change of electrostatic potentials has been named polarized one-electron potentials. We show that in the POP optimization, both an explicitly interacting polarizability model and an implicitly interacting polarizability model can be used for the determination of the multicenter polarizabilities. In the explicitly interacting model, intramolecular induced dipole-induced dipole interaction is mutually included in the process of the POP optimization, but the interaction is not included in the implicitly interacting model. In the implicitly interacting polarizability model, a combined model of isotropic atom polarization and anisotropic bond polarization is shown to provide the best fitting results for nucleic acid bases which show large polarization anisotropy. A simple scaling model to the chemical bond has been newly proposed for the explicitly interacting polarizability model. We show that the simple model can be applied to molecular simulations without any damping of exponential type in the intramolecular induced dipole interaction. A detailed procedure for determination of the multicenter dipole polarizability by the POP optimization is also presented.

  • 42. Nåbo, L. J.
    et al.
    Holmgaard List, Nanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Steinmann, C.
    Kongsted, J.
    Computational Approach to Evaluation of Optical Properties of Membrane Probes2017In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, no 2, p. 719-726Article in journal (Refereed)
    Abstract [en]

    Computed optical properties of membrane probes are typically evaluated in the gas phase, i.e. neglecting the influence of the membrane. In this study, we examine how and to what extent a membrane influences the one- and two-photon absorption (1PA and 2PA, respectively) properties for a number of cholesterol analogs and thereby also evaluate the validity of the common gas phase approach. The membrane is modeled using the polarizable embedding scheme both with and without the effective external field extension of the polarizable embedding model. The shifts in excitation energies and 1PA oscillator strengths compared to the gas phase are relatively small, while the 2PA cross section is more affected. The electric field inside the membrane induces a larger change in the permanent electric dipole moment upon excitation of the analogs compared to the gas phase, which leads to an almost 2-fold increase in the 2PA cross section for one cholesterol analog. The relative trends observed in the membrane are the same as in the gas phase, and the use of gas phase calculations for qualitative comparison and design of cholesterol membrane probes is thus a useful and computationally efficient strategy.

  • 43.
    Oprea, Corneliu Ioan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ruud, K.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Restricted density functional quadratic response theory of electronic g-tensorsIn: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626Article in journal (Refereed)
  • 44. Orms, Natalie
    et al.
    Rehn, Dirk R.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Krylov, Anna I.
    Characterizing Bonding Patterns in Diradicals and Triradicals by Density-Based Wave Function Analysis: A Uniform Approach2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 2, p. 638-648Article in journal (Refereed)
    Abstract [en]

    Density-based wave function analysis enables unambiguous comparisons of the electronic structure computed by different methods and removes ambiguity of orbital choices. We use this tool to investigate the performance of different spin flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high- and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such as polyradicals. We show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of the bonding pattern.

  • 45.
    Osella, Silvio
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Univ Warsaw, Ctr New Technol, Banacha 2C, PL-02097 Warsaw, Poland.
    Di Meo, Florent
    Limoges Univ, Fac Pharm, INSERM, UMR 1248, 2 Rue Docteur Marcland, F-87025 Limoges, France..
    Natarajan Arul, Murugan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Fabre, Gabin
    Limoges Univ, LCSN EA1069, Fac Pharm, 2 Rue Dr Marcland, F-87025 Limoges, France..
    Ameloot, Marcel
    Hasselt Univ, Biomed Res Inst, B-3590 Diepenbeek, Belgium..
    Trouillas, Patrick
    Limoges Univ, Fac Pharm, INSERM, UMR 1248, 2 Rue Docteur Marcland, F-87025 Limoges, France.;Palacky Univ, Ctr Adv Technol & Mat, Fac Sci, Tr 17 Listopadu 12, Olomouc 77146, Czech Republic..
    Knippenberg, Stefan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Hasselt Univ, Biomed Res Inst, B-3590 Diepenbeek, Belgium..
    Combining (Non)linear Optical and Fluorescence Analysis of DiD To Enhance Lipid Phase Recognition2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 10, p. 5350-5359Article in journal (Refereed)
    Abstract [en]

    The widespread interest in phase recognition of lipid membranes has led to the use of different optical techniques to enable differentiation of healthy and not fully functional cells. In this work, we show how the combination of different (non)linear optical methods such as one-photon absorption (OPA), two-photon absorption (TPA), and second harmonic generation (SHG) as well as the study of the fluorescence decay time leads to an enhanced screening of membrane phases using a fluorescent 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine (DiD) probe. In the current study we consider the pure liquid disordered phases of DOPC (dioleoyl-sn-glycero-3-phosphocholine, room temperature) and DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 323 K), the solid gel phase of DPPC (298 K), and the liquid ordered phase of a 2:1 binary mixture of sphingomyelin and cholesterol. By means of extensive hybrid quantum mechanics molecular mechanics calculations and based upon the (non)linear absorption of the embedded probes, it is found that DiD can be used to identify the lipid bilayer phase. The joint TPA and SHG as well as fluorescence analyses qualifies DiD as a versatile probe for phase recognition. In particular, the SHG data obtained by means of hyper-Rayleigh scattering and by electric field induced second harmonic generation reveal differences in polarization of the probe in the different environments. The TPA results finally confirm the particular location of the probe in between the polar headgroup region of the 2:1 SM:Chol mixture in the liquid ordered phase.

  • 46.
    Osella, Silvio
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Jena, Naresh K.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Knippenberg, Stefan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Investigation into Biological Environments through (Non)linear Optics: A Multiscale Study of Laurdan Derivatives2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 12, p. 6169-6181Article in journal (Refereed)
    Abstract [en]

    The fluorescent marker Laurdan and its new derivative, C-Laurdan, have been investigated by means of theoretical calculations in a DOPC lipid bilayer membrane at room temperature, and a comparison is made with results from fluorescence experiments. Experimentally, the latter probe is known to have a higher sensitivity to the membrane polarity at the lipid headgroup region and has higher water solubility. Results from Molecular Dynamics (MD) simulations show that C-Laurdan is oriented with the carboxyl group toward the head of the membrane, with an angle of 50 degrees between the molecular backbone and the normal to the bilayer, in contrast to the orientation of the Laurdan headgroup whose carbonyl group is oriented toward the polar regions of the membrane and which describes an angle of ca. 70-80 degrees with the membrane normal. This contrast in orientation reflects the differences in transition dipole moment between the two probes and, in turn, the optical properties. QM/MM results of the probes show little differences for one- (OPA) and two-photon absorption (TPA) spectra, while the second harmonic generation (SHG) beta component is twice as large in Laurdan with respect to C-Laurdan probe. The fluorescence anisotropy decay analysis of the first excited state confirms that Laurdan has more rotational freedom in the DOPC membrane, while C-Laurdan experiences a higher hindrance, making it a better probe for lipid membrane phase recognition.

  • 47. Pedersen, M. N.
    et al.
    Hedegård, E. D.
    Olsen, J. M. H.
    Kauczor, J.
    Norman, Patrick
    Linköping University, Sweden.
    Kongsted, J.
    Damped response theory in combination with polarizable environments: The polarizable embedding complex polarization propagator method2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 3, p. 1164-1171Article in journal (Refereed)
    Abstract [en]

    We present a combination of the polarizable embedding (PE) scheme with the complex polarization propagator (CPP) method with the aim of calculating response properties including relaxation for large and complex systems. This new approach, termed PE-CPP, will benefit from the highly advanced description of the environmental electrostatic potential and polarization in the PE method as well as the treatment of near-resonant effects in the CPP approach. The PE-CPP model has been implemented in a Kohn-Sham density functional theory approach, and we present pilot calculations exemplifying the implementation for the UV/vis and carbon K-edge X-ray absorption spectra of the protein plastocyanin. Furthermore, technical details associated with a PE-CPP calculation are discussed.

  • 48.
    Pronk, Sander
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lundborg, Magnus
    Rotskoff, Grant
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Wesén, Björn
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Kasson, Peter M.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden.
    Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 6, p. 2600-2608Article in journal (Refereed)
    Abstract [en]

    Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide mote processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.

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  • 49.
    Rehn, Dirk Robert
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Resonant Inelastic X-ray Scattering Amplitudes and Cross Sections in the Algebraic Diagrammatic Construction/Intermediate State Representation (ADC/ISR) Approach2017In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, no 11, p. 5552-5559Article in journal (Refereed)
    Abstract [en]

    A scheme has been derived and implemented to gain computational access to the full electronic part of the Kramers-Heisenberg-Dirac (KHD) expression for resonant and nonresonant inelastic scattering amplitudes. Our implementation of this scheme is based on the complex polarization propagator in the algebraic diagrammatic construction (ADC) framework and within its intermediate state representation (ISR). The hierarchy of the second- and third-order ADC/ISR computational schemes known as ADC(2), ADC(2)-x, and ADC(3/2) is considered, and the calculated resonant inelastic X-ray scattering (RIXS) amplitudes and transition strengths for water are in excellent agreement with recent experimental data.

  • 50.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    de Almeida, Katia Júlia
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Oprea, Corneliu I.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ruud, Kenneth
    Univ Tromso, Dept Chem, Ctr Theoret & Computat Chem.
    Degenerate perturbation theory for electronic g tensors: leading-order relativistic effects2008In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 11, p. 1810-1828Article in journal (Refereed)
    Abstract [en]

    A new approach for the evaluation of the leading-order relativistic corrections to the electronic g tensors of molecules with a doublet ground state is presented. The methodology is based on degenerate perturbation theory and includes all relevant contributions to the g tensor shift up to order theta(alpha(4)) originating from the one-electron part of the Breit-Pauli Hamiltonian-that is, it allows for the treatment of scalar relativistic, spin-orbit, and mixed corrections to the spin and orbital Zeeman effects. This approach has been implemented in the framework of spin-restricted density functional theory and is in the present paper, as a first illustration of the theory, applied to study relativistic effects on electronic g tensors of dihalogen anion radicals X-2(-) (X = F, Cl, Br, I). The results indicate that the spin-orbit interaction is responsible for the large parallel component of the g tensor shift of Br-2(-) and I-2(-), and furthermore that both the leading-order scalar relativistic and spin-orbit corrections are of minor importance for the perpendicular component of the g tensor in these molecules since they effectively cancel each other. In addition to investigating the g tensors of dihalogen anion radicals, we also critically examine the importance of various relativistic corrections to the electronic g tensor of linear molecules with Sigma-type ground states and present a two-state model suitable for an approximate estimation of the g tensor in such molecules.

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