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  • 1.
    Bjelkmar, Pär
    et al.
    Theoretical and Computational Biophysics, Department of Theoretical Physics, Royal Institute of Technology.
    Larsson, Per
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Cuendet, Michel
    Swiss Institute of Bioinformatics.
    Hess, Berk
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Lindahl, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models2010Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, nr 2, s. 459-466Artikel i tidskrift (Refereegranskat)
    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 , ψ 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.

  • 2. Chaudhuri, Subhajyoti
    et al.
    Hedström, Svante
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Yale University, United States.
    Mendez-Hernandez, Dalvin D.
    Hendrickson, Heidi P.
    Jung, Kenneth A.
    Ho, Junming
    Batista, Victor S.
    Electron Transfer Assisted by Vibronic Coupling from Multiple Modes2017Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, nr 12, s. 6000-6009Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Understanding the effect of vibronic coupling on electron transfer (ET) rates is a challenge common to a wide range of applications, from electrochemical synthesis and catalysis to biochemical reactions and solar energy conversion. The Marcus-Jortner-Levich (MJL) theory offers a model of ET rates based on a simple analytic expression with a few adjustable parameters. However, the MJL equation in conjunction with density functional theory (DFT) has yet to be established as a predictive first-principles methodology. A framework is presented for calculating transfer rates modulated by molecular vibrations, that circumvents the steep computational cost which has previously necessitated approximations such as condensing the vibrational manifold into a single empirical frequency. Our DFT MJL approach provides robust and accurate predictions of ET rates spanning over 4 orders of magnitude in the 10(6)-10(10) s(-1) range. We evaluate the full MJL equation with a Monte Carlo sampling of the entire active space of thermally accessible vibrational modes, while using no empirical parameters. The contribution to the rate of individual modes is illustrated, providing insight into the interplay between vibrational degrees of freedom and changes in electronic state. The reported findings are valuable for understanding ET rates modulated by multiple vibrational modes, relevant to a broad range of systems within the chemical sciences.

  • 3. Chen, Mo
    et al.
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Brady, John W.
    Wohlert, Jakob
    Molecular Dynamics Simulations of the Ionic Liquid 1-n-Butyl-3-Methylimidazolium Chloride and Its Binary Mixtures with Ethanol2014Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, nr 10, s. 4465-4479Artikel i tidskrift (Refereegranskat)
    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.

  • 4.
    Dahlberg, Martin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Maliniak, Arnold
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Mechanical properties of coarse grained bilayers formed by cardiolipin and zwitterionic lipids2010Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, nr 5, s. 1638-1649Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Lipid shape and charge are connected with the physical properties and biological function of membranes. Cardiolipin, a double phospholipid with four chains and the potential of changing its charge with pH, is crucially connected with mitochondrial inner membrane shape, and recent experiments suggest that local pH changes allow highly curved local geometries. Here, we use a coarse grained molecular dynamics model to investigate the mechanical properties of cardiolipin bilayers, systematically varying the headgroup charge and composition in mixtures with zwitterionic DOPC or DOPE. Low cardiolipin charge, corresponding to low pH, was found to induce bending moduli on the order of kBT, and curved microdomains. On the length scale investigated, in contrast to continuum theoretical models, we found the area modulus and bending modulus to be inversely correlated for mixtures of cardiolipin and DOPC/DOPE, explainable by changes in the effective head group volume.

  • 5.
    Elías-Wolff, Federico
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Lindén, Martin
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Brandt, Erik G.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Computing Curvature Sensitivity of Biomolecules in Membranes by Simulated Buckling2018Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, nr 3, s. 1643-1655Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 6.
    Fransson, Thomas
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Ruprecht−Karls University, Germany.
    Dreuw, Andreas
    Simulating X-ray Emission Spectroscopy with Algebraic Diagrammatic Construction Schemes for the Polarization Propagator2019Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, nr 1, s. 546-556Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The calculation of X-ray emission spectra has been addressed with the algebraic diagrammatic construction (ADC) scheme, using a core-ionized wave function as the reference state. With this, the valence-to-core transitions are found as the first eigenstates with negative eigenvalues. The performance of the ADC hierarchical methods ADC(2), ADC(2)-x, and ADC(3/2) has been investigated on 17 transition of second row elements (C, N, O, F, and Ne), and 5 transitions of third-row elements (S and Cl). We report ADC(2) results within 0.20 +/- 0.36 eV of experimental values with an appropriate choice of basis set and when accounting for relativistic effects, with a slight tendency toward underestimating emission energies. By comparison, ADC(2)-x yields a similar spread in relative energies, but a consistent overestimation of approximately 1.5 eV. Going to ADC(3/2), we now observe an underestimation of emission energies and a larger error spread. By comparison, calculations of X-ray absorption spectra have been reported to favor the ADC(2)-x method, with ADC(2) showing the largest error when comparing to experimental values. The difference in ADC performance trends between these core spectroscopies are attributed to the different electron rearrangement effects in X-ray absorption and emission processes.

  • 7.
    Jämbeck, Joakim P. M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Eriksson, Emma S. E.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Eriksson, Leif A.
    Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model2014Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, nr 1, s. 5-13Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Liposomes are proposed as drug delivery systems and can in principle be designed so as to cohere with specific tissue types or local environments. However, little detail is known about the exact mechanisms for drug delivery and the distributions of drug molecules inside the lipid carrier. In the current work, a coarse-grained (CG) liposome model is developed, consisting of over 2500 lipids, with varying degrees of drug loading. For the drug molecule, we chose hypericin, a natural compound proposed for use in photodynamic therapy, for which a CG model was derived and benchmarked against corresponding atomistic membrane bilayer model simulations. Liposomes with 21-84 hypericin molecules were generated and subjected to 10 microsecond simulations. Distribution of the hypericins, their orientations within the lipid bilayer, and the potential of mean force for transferring a hypericin molecule from the interior aqueous droplet through the liposome bilayer are reported herein.

  • 8.
    Jämbeck, Joakim P. M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    An extension and further validation of an all atomistic force field for biological membranes2012Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, nr 8, s. 2938-2948Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Biological membranes are versatile in composition and host intriguing molecular processes. In order to be able to study these systems, an accurate model Hamiltonian or force field (FF) is a necessity. Here, we report the results of our extension of earlier developed all-atomistic FF parameters for fully saturated phospholipids that complements an earlier parameter set for saturated phosphatidylcholine lipids (J. Phys. Chem. B, 2012, 116, 3164-3179). The FF, coined Slipids (Stockholm lipids), now also includes parameters for unsaturated phosphatidylcholine and phosphatidylethanolamine lipids, e.g., POPC, DOPC, SOPC, POPE, and DOPE. As the extended set of parameters is derived with the same philosophy as previously applied, the resulting FF has been developed in a fully consistent manner. The capabilities of Slipids are demonstrated by performing long simulations without applying any surface tension and using the correct isothermal-isobaric (NPT) ensemble for a range of temperatures and carefully comparing a number of properties with experimental findings. Results show that several structural properties are very well reproduced, such as scattering form factors, NMR order parameters, thicknesses, and area per lipid. Thermal dependencies of different thicknesses and area per lipid are reproduced as well Lipid diffusion is systematically slightly underestimated, whereas the normalized lipid diffusion follows the experimental trends. This is believed to be due to the lack of collective movement in the relatively small bilayer patches used Furthermore, the compatibility with amino acid FFs from the AMBER family is tested in explicit transmembrane complexes of the WALP23 peptide with DLPC and DOPC bilayers, and this shows that Slipids can be used to study more complex and biologically relevant systems.

  • 9.
    Jämbeck, Joakim P. M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Another piece of the membrane puzzle: extending slipids further2013Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, nr 1, s. 774-784Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To be able to model complex biological membranes in a more realistic manner, the force field Slipids (Stockholm lipids) has been extended to include parameters for sphingomyelin (SM), phosphatidylglycerol (PG), phosphatidylserine (PS) lipids, and cholesterol. Since the parametrization scheme was faithful to the scheme used in previous editions of Slipids, all parameters are consistent and fully compatible. The results of careful validation of a number of key structural properties for one and two component lipid bilayers are in excellent agreement with experiments. Potentials of mean force for transferring water across binary mixtures of lipids and cholesterol were also computed in order to compare water permeability rates to experiments. In agreement with experimental and simulation studies, it was found that the permeability and partitioning of water is affected by cholesterol in lipid bilayers made of saturated lipids to the largest extent. With the extensions of Slipids presented here, it is now possible to study complex systems containing many different lipids and proteins in a fully atomistic resolution in the isothermic-isobaric (NPT) ensemble, which is the proper ensemble for membrane simulations.

  • 10.
    Kimanius, Dari
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Pettersson, Ingrid
    Schluckebier, Gerd
    Lindahl, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Andersson, Magnus
    SAXS-Guided Metadynamics2015Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, nr 7, s. 3491-3498Artikel i tidskrift (Refereegranskat)
    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.

  • 11. Lee, Jumin
    et al.
    Patel, Dhilon S.
    Ståhle, Jonas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Park, Sang-Jun
    Kern, Nathan R.
    Kim, Seonghoon
    Lee, Joonseong
    Cheng, Xi
    Valvano, Miguel A.
    Holst, Otto
    Knirel, Yuriy A.
    Qi, Yifei
    Jo, Sunhwan
    Klauda, Jeffery B.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Im, Wonpil
    CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans2019Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, nr 1, s. 775-786Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Glycolipids (such as glycoglycerolipids, glycosphingolipids, and glycosylphosphatidylinositol) and lipoglycans (such as lipopolysaccharides (LPS), lipooligosaccharides (LOS), mycobacterial lipoarabinomannan, and mycoplasma lipoglycans) are typically found on the surface of cell membranes and play crucial roles in various cellular functions. Characterizing their structure and dynamics at the molecular level is essential to understand their biological roles, but systematic generation of glycolipid and lipoglycan structures is challenging because of great variations in lipid structures and glycan sequences (i.e., carbohydrate types and their linkages). To facilitate the generation of all-atom glycolipid/LPS/LOS structures, we have developed Glycolipid Modeler and LPS Modeler in CHARMM-GUI (http://www.charmm-gui.org), a web-based interface that simplifies building of complex biological simulation systems. In addition, we have incorporated these modules into Membrane Builder so that users can readily build a complex symmetric or asymmetric biological membrane system with various glycolipids and LPS/LOS. These tools are expected to be useful in innovative and novel glycolipid/LPS/LOS modeling and simulation research by easing tedious and intricate steps in modeling complex biological systems and shall provide insight into structures, dynamics, and underlying mechanisms of complex glycolipid-/LPS-/LOS-containing biological membrane systems.

  • 12.
    Liao, Rong-Zhen
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Yu, Jian-Guo
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Quantum chemical modeling of enzymatic reactions: The case of decarboxylation2011Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 07, nr 05, s. 1494-1501Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a systematic study of the decarboxylation step of the enzyme aspartate decarboxylase with the purpose of assessing the quantum chemical cluster approach for modeling this important class of decarboxylase enzymes. Active site models ranging in size from 27 to 220 atoms are designed, and the barrier and reaction energy of this step are evaluated. To model the enzyme surrounding, homogeneous polarizable medium techniques are used with several dielectric constants. The main conclusion is that when the active site model reaches a certain size, the solvation effects from the surroundings saturate. Similar results have previously been obtained from systematic studies of other classes of enzymes, suggesting that they are of a quite general nature.

  • 13.
    Mace, Amber
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Ecole Polytechnique Fédéralede Lausanne (EPFL), Switzerland.
    Barthel, Senja
    Smit, Berend
    Automated Multiscale Approach To Predict Self-Diffusion from a Potential Energy Field2019Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, nr 4, s. 2127-2141Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    For large-scale screening studies there is a need to estimate the diffusion of gas molecules in nanoporous materials more efficiently than (brute force) molecular dynamics. In particular for systems with low diffusion coefficients molecular dynamics can be prohibitively expensive. An alternative is to compute the hopping rates between adsorption sites using transition state theory. For large-scale screening this requires the automatic detection of the transition states between the adsorption sites along the different diffusion paths. Here an algorithm is presented that analyzes energy grids for the moving particles. It detects the energies at which diffusion paths are formed, together with their directions. This allows for easy identification of nondiffusive systems. For diffusive systems, it partitions the grid coordinates assigned to energy basins and transitions states, permitting a transition state theory based analysis of the diffusion. We test our method on CH4 diffusion in zeolites, using a standard kinetic Monte Carlo simulation based on the output of our grid analysis. We find that it is accurate, fast, and rigorous without limitations to the geometries of the diffusion tunnels or transition states.

  • 14.
    Mace, Amber
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Leetmaa, Mikael
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Temporal Coarse Graining of CO2 and N-2 Diffusion in Zeolite NaKA: From the Quantum Scale to the Macroscopic2015Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, nr 10, s. 4850-4860Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 15.
    Mirzoev, Alexander
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    Lyubartsev, Alexander P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för fysikalisk kemi.
    MagiC: Software Package for Multiscale Modeling2013Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, nr 3, s. 1512-1520Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present software package MagiC, which is designed to perform systematic structure-based coarse graining of molecular models. The effective pairwise potentials between coarse-grained sites of low-resolution molecular models are constructed to reproduce structural distribution functions obtained from the modeling of the system in a high resolution (atomistic) description. The software supports coarse-grained tabulated intramolecular bond and angle interactions, as well as tabulated nonbonded interactions between different site types in the coarse-grained system, with the treatment of long-range electrostatic forces by the Ewald summation. Two methods of effective potential refinement are implemented: iterative Boltzmann inversion and inverse Monte Carlo, the latter accounting for cross-correlations between pair interactions. MagiC uses its own Metropolis Monte Carlo sampling engine, allowing parallel simulation of many copies of the system with subsequent averaging of the properties, which provides fast convergence of the method with nearly linear scaling at parallel execution.

  • 16. Mondal, Arobendo
    et al.
    Gaultois, Michael W.
    Pell, Andrew J.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Iannuzzi, Marcella
    Grey, Clare P.
    Hutter, Jürg
    Kaupp, Martin
    Large-Scale Computation of Nuclear Magnetic Resonance Shifts for Paramagnetic Solids Using CP2K2018Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, nr 1, s. 377-394Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Large-scale computations of nuclear magnetic resonance (NMR) shifts for extended paramagnetic solids (pNMR) are reported using the highly efficient Gaussian-augmented plane-wave implementation of the CP2K code. Combining hyperfine couplings obtained with hybrid functionals with g-tensors and orbital shieldings computed using gradient-corrected functionals, contact, pseudocontact, and orbital-shift contributions to pNMR shifts are accessible. Due to the efficient and highly parallel performance of CP2K, a wide variety of materials with large unit cells can be studied with extended Gaussian basis sets. Validation of various approaches for the different contributions to pNMR shifts is done first for molecules in a large supercell in comparison with typical quantum-chemical codes. This is then extended to a detailed study of g-tensors for extended solid transition-metal fluorides and for a series of complex lithium vanadium phosphates. Finally, lithium pNMR shifts are computed for Li3V2(PO4)(3), for which detailed experimental data are available. This has allowed an in-depth study of different approaches (e.g., full periodic versus incremental cluster computations of g-tensors and different functionals and basis sets for hyperfine computations) as well as a thorough analysis of the different contributions to the pNMR shifts. This study paves the way for a more-widespread computational treatment of NMR shifts for paramagnetic materials.

  • 17.
    Naome, Aymeric
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Stockholms universitet, Science for Life Laboratory (SciLifeLab). University of Namur, Belgium.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Stockholms universitet, Science for Life Laboratory (SciLifeLab). Stellenbosch University, South Africa.
    Vercauteren, Daniel P.
    A Coarse-Grained Simulation Study of the Structures, Energetics, and Dynamics of Linear and Circular DNA with Its Ions2015Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, nr 6, s. 2813-2826Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have studied the structural, energetics, and dynamical properties of a variety of linear and circular DNA fragments using a solvent-mediated coarse-grained (CG) model of DNA with explicit ions recently developed by us [Naome et al., J. Chem. Theory Comput., 2014, 10, 3541-3549]. We particularly examined the treatment of electrostatics and determined that a large cutoff is necessary to properly reproduce the DNA flexibility. Moreover, it is crucial to include long-ranged electrostatic interactions: a Particle Mesh Ewald scheme at low resolution is sufficient to avoid structural artifacts. We calculated the ring closure probabilities, as a j-factors, for DNA fragments of different lengths from equilibrium, as well. as restrained molecular dynamics (MD) simulations. The latter force integration method provided accurate results without model fitting. We generated topology and energy maps for DNA minicircles of various lengths and helical densities, at low and high ion concentrations. A general trend for structure compaction is observed, driven by an increase in writhing as the ionic concentration increases. Finally, we applied a reconstruction procedure to generate detailed molecular structures from the various superhelical conformations generated by the CG MD of the DNA minicircles. These pre-equilibrated reconstructed atomistic structures can serve as starting material for atomistic simulations.

  • 18.
    Naomé, Aymeric
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Stockholms universitet, Science for Life Laboratory (SciLifeLab). University of Namur, Belgium.
    Laaksonen, Aatto
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK). Stockholms universitet, Science for Life Laboratory (SciLifeLab). Stellenbosch University, South Africa.
    Vercauteren, Daniel P.
    A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method2014Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, nr 8, s. 3541-3549Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a new class of coarse-grained (CG) force fields (FFs) for B-DNA with explicit ions suited for large-scale mesoscale simulations at microsecond micrometer scale using a wide spectrum of particle simulation methods from molecular dynamics to dissipative particle dynamics. The effective solvent-mediated pairwise interactions making up the FFs are obtained by inverting radial distribution functions and other particle particle distributions obtained from all-atom simulations of numbers of octadecamer DNA fragments from the Ascona B-DNA library. The inverse Monte Carlo (IMC) method, later known as Newton inversion (NI) (Lyubartsev, A. P.; Laaksonen, A. Phys. Rev. E, 1995, 52, 3730-3737), was used together with the iterative Boltzmann inversion (IBI) scheme to compute the effective CG potentials. We show that this systematic structure-based approach is capable of providing converged potentials that accurately reproduce the structural features of the underlying atomistic system within a few percents of relative difference. We also show that a simple one-site-per-nucleotide model with 10 intramolecular pair interaction potentials is able to reproduce key features of DNA, for example, the persistence length and its dependence on the ionic concentration, experimentally determined around 50 nm at physiological salt concentration.

  • 19. Pronk, Sander
    et al.
    Pouya, Iman
    Lundborg, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Rotskoff, Grant
    Wesén, Björn
    Kasson, Peter M.
    Lindahl, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
    Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform2015Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, nr 6, s. 2600-2608Artikel i tidskrift (Refereegranskat)
    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.

  • 20.
    Siegbahn, Per E. M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Blomberg, Margareta R. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Energy Diagrams for Water Oxidation in Photosystem II Using Different Density Functionals2014Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, nr 1, s. 268-272Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The full sequence of intermediates in the water oxidation process in photosystem II has recently been characterized by model calculations, in good agreement with experiments. In the present paper, the energy diagram obtained is used as a benchmark test for several density functionals. Only the results using B3LYP with 15% or 20% show good agreement with experiments. The other functionals tried show errors for some energy levels as large as 20-30 kcal/mol. The reason for these large errors is that the error for three consecutive oxidations of Mn(III) to Mn(IV) accumulates as the cluster is oxidized.

  • 21.
    Siegbahn, Per E. M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Blomberg, Margareta R. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Chen, Shi-Lu
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Significant van der Weals Effects in Transition Metal Complexes2010Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, nr 7, s. 2040-2044Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    There is, in general, very good experience using hybrid DFT to study mechanisms of enzyme reactions containing transition metals. For redox reactions, the B3LYP* functional, which has 15% exact exchange, has been shown to be particularly accurate. Still, there are some cases which have turned out to be quite difficult with large errors. In the present study, the effects of van der Waals interaction have been investigated for these cases, using the empirical formula of Grimme. The results are encouraging.

  • 22. Wennberg, Christian L.
    et al.
    Murtola, Teemu
    Hess, Berk
    Lindahl, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties2013Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, nr 8, s. 3527-3537Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The accuracy of electrostatic interactions in molecular dynamics advanced tremendously with the introduction of particle-mesh Ewald (PME) summation almost 20 years ago. Lattice summation electrostatics is now the de facto standard for most types of biomolecular simulations, and in particular, for lipid bilayers, it has been a critical improvement due to the large charges typically present in zwitterionic lipid headgroups. In contrast, Lennard-Jones interactions have continued to be handled with increasingly longer cutoffs, partly because few alternatives have been available despite significant difficulties in tuning cutoffs and parameters to reproduce lipid properties. Here, we present a new Lennard-Jones PME implementation applied to lipid bilayers. We confirm that long-range contributions are well approximated by dispersion corrections in simple systems such as pentadecane (which makes parameters transferable), but for inhomogeneous and anisotropic systems such as lipid bilayers there are large effects on surface tension, resulting in up to 5.5% deviations in area per lipid and order parameters-far larger than many differences for which reparameterization has been attempted. We further propose an approximation for combination rules in reciprocal space that significantly reduces the computational cost of Lennard-Jones PME and makes accurate treatment of all nonbonded interactions competitive with simulations employing long cutoffs. These results could potentially have broad impact on important applications such as membrane proteins and free energy calculations.

  • 23. Wennberg, Christian L.
    et al.
    Murtola, Teemu
    Pall, Szilard
    Abraham, Mark J.
    Hess, Berk
    Lindahl, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation2015Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, nr 12, s. 5737-5746Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Long-range lattice summation techniques such as the particle-mesh Ewald (PME) algorithm for electrostatics have been revolutionary to the precision and accuracy of molecular simulations in general. Despite the performance penalty associated with lattice summation electrostatics, few biomolecular simulations today are performed without it. There are increasingly strong arguments for moving in the same direction for Lennard-Jones (LJ) interactions, and by using geometric approximations of the combination rules in reciprocal space, we have been able to make a very high-performance implementation available in GROMACS. Here, we present a new way to correct for these approximations to achieve exact treatment of Lorentz-Berthelot combination rules within the cutoff, and only a very small approximation error remains outside the cutoff (a part that would be completely ignored without LJ-PME). This not only improves accuracy by almost an order of magnitude but also achieves absolute biomolecular simulation performance that is an order of magnitude faster than any other available lattice summation technique for LJ interactions. The implementation includes both CPU and GPU acceleration, and its combination with improved scaling LJ-PME simulations now provides performance close to the truncated potential methods in GROMACS but with much higher accuracy.

  • 24. Westerlund, Annie M.
    et al.
    Harpole, Tyler J.
    Blau, Christian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Delemotte, Lucie
    Inference of Calmodulin's Ca2+-Dependent Free Energy Landscapes via Gaussian Mixture Model Validation2018Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, nr 1, s. 63-71Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A free energy landscape estimation method based on the well-known Gaussian mixture model (GMM) is used to compare the efficiencies of thermally enhanced sampling methods with respect to regular molecular dynamics. The simulations are carried out on two binding states of calmodulin, and the free energy estimation method is compared with other estimators using a toy model. We show that GMM with cross-validation provides a robust estimate that is not subject to overfitting. The continuous nature of Gaussians provides better estimates on sparse data than canonical histogramming. We find that diffusion properties determine the sampling method effectiveness, such that diffusion-dominated apo calmodulin is most efficiently sampled by regular molecular dynamics, while holo calmodulin, with its rugged free energy landscape, is better sampled by enhanced sampling methods.

  • 25.
    Wåhlin, Pernilla
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Danilo, Cécile
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Université des Sciences et Technologies de Lille 1, France.
    Vallet, Valérie
    Réal, Florent
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Flament, Jean-Pierre
    Wahlgren, Ulf
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita).
    An Investigation of the Accuracy of Different DFT Functionals on the Water Exchange Reaction in Hydrated Uranyl(VI) in the Ground State and the First Excited State2008Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, nr 4, s. 569-577Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We discuss the accuracy of density functional theory (DFT) in the gas phase for the water-exchange reactions in the uranyl(VI) aqua ion taking place both in the electronic ground state and in the first excited state (the luminescent 3Δg state). The geometries of the reactant and intermediates have been optimized using DFT and the B3LYP functional, with a restricted closed-shell formalism for the electronic ground state and either an unrestricted open-shell formalism or the time-dependent DFT method for the 3Δg state. The relative energies have been computed with wave-function-based methods such as Møller–Plesset second-order perturbation theory, or a minimal multireference perturbative calculation (minimal CASPT2); coupled-cluster method (CCSD(T)); DFT with B3LYP, BLYP, and BHLYP correlation and exchange functionals; and the hybrid DFT−multireference configuration interaction method. The results obtained with second-order perturbative methods are in excellent agreement with those obtained with the CCSD(T) method. However, DFT methods overestimate the energies of low coordination numbers, yielding to too high and too low reaction energies for the associative and dissociative reactions, respectively. Part of the errors appears to be associated with the amount of Hartree–Fock exchange used in the functional; for the dissociative intermediate in the ground state, the pure DFT functionals underestimate the reaction energy by 20 kJ/mol relative to wave-function-based methods, and when the amount of HF exchange is increased to 20% (B3LYP) and to 50% (BHLYP), the error is decreased to 13 and 4 kJ/mol, respectively.

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